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1

Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7  

SciTech Connect

Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.

Suen, Garret [University of Wisconsin, Madison; Stevenson, David M [USDA-ARS, Madison WI; Bruce, David [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Boyum, Julie [University of Wisconsin, Madison; Mead, David [University of Wisconsin, Madison; Weimer, Paul J [USDA-ARS, Madison WI

2011-01-01T23:59:59.000Z

2

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations  

Science Conference Proceedings (OSTI)

We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus lIB, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudogenes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.

Xie, Gary [Los Alamos National Laboratory; Detter, Chris [Los Alamos National Laboratory; Bruce, David [Los Alamos National Laboratory; Challacome, Jean F [Los Alamos National Laboratory; Brettin, Thomas S [Los Alamos National Laboratory; Barabote, Ravi D [UC DAVIS; Leu, David [UC DAVIS; Normand, Philippe [CNRS, UNIV LYON; Necsula, Anamaria [CNRS, UNIV LYON; Daubin, Vincent [CNRS, UNIV LYON; Medigue, Claudine [CNRS/GENOSCOPE; Adney, William S [NREL; Xu, Xin C [UC DAVIS; Lapidus, Alla [DOE JOINT GENOME INST.; Pujic, Pierre [CNRS, UNIV LYON; Richardson, Paul [DOE JOINT GENOME INST; Berry, Alison M [UC DAVIS

2008-01-01T23:59:59.000Z

3

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations  

Science Conference Proceedings (OSTI)

We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus 11B, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudo genes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.

Xie, Gary [Los Alamos National Laboratory; Detter, John C [Los Alamos National Laboratory; Bruce, David C [Los Alamos National Laboratory; Challacombe, Jean F [Los Alamos National Laboratory; Brettin, Thomas S [Los Alamos National Laboratory; Necsulea, Anamaria [UNIV LYON; Daubin, Vincent [UNIV LYON; Medigue, Claudine [GENOSCOPE; Adney, William S [NREL; Xu, Xin C [UC DAVIS; Lapidus, Alla [JGI; Pujic, Pierre [UNIV LYON; Berry, Alison M [UC DAVIS; Barabote, Ravi D [UC DAVIS; Leu, David [UC DAVIS; Normand, Phillipe [UNIV LYON

2009-01-01T23:59:59.000Z

4

Complete Genome Sequence of the Thermophilic, Piezophilic, Heterotrophic Bacterium Marinitoga piezophila KA3  

Science Conference Proceedings (OSTI)

Marinitoga piezophila KA3 is a thermophilic, anaerobic, chemoorganotrophic, sulfur-reducing bacterium isolated from the Grandbonum deep-sea hydrothermal vent site at the East Pacific Rise (13 degrees N, 2,630-m depth). The genome of M. piezophila KA3 comprises a 2,231,407-bp circular chromosome and a 13,386-bp circular plasmid. This genome was sequenced within Department of Energy Joint Genome Institute CSP 2010.

Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Vannier, Pauline [Ifremer, Plouzane, France; Oger, Phil [University of Lyon, France; Bartlett, Douglas [University of California, San Diego & La Jolla; Noll, Kenneth M [University of Connecticut, Storrs; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Jebbar, Mohamed [Ifremer, Plouzane, France

2012-01-01T23:59:59.000Z

5

Thermostable purified endoglucanase from thermophilic bacterium acidothermus cellulolyticus  

DOE Patents (OSTI)

A substantially purified high molecular weight cellulase enzyme having a molecular weight of between about 156,000 to about 203,400 daltons isolated from the bacterium Acidothermus cellulolyticus (ATCC 43068) and a method of producing it are disclosed. The enzyme is water soluble, possesses both C.sub.1 and C.sub.x types of enzymatic activity, has a high degree of stability toward heat and exhibits both a high optimum temperature activity and high inactivation characteristics.

Tucker, Melvin P. (Lakewood, CO); Grohmann, Karel (Littleton, CO); Himmel, Michael E. (Littleton, CO); Mohagheghi, Ali (Golden, CO)

1992-01-01T23:59:59.000Z

6

Glycoside hydrolase inventory drives plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus  

NLE Websites -- All DOE Office Websites (Extended Search)

Glycoside Glycoside Hydrolase Inventory Drives Plant Polysaccharide Deconstruction by the Extremely Thermophilic Bacterium Caldicellulosiruptor saccharolyticus Amy L. VanFossen, Inci Ozdemir, Samantha L. Zelin, Robert M. Kelly Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905; telephone: 919-515-6396; fax: 919-515-3465; e-mail: rmkelly@eos.ncsu.edu Received 15 November 2010; revision received 22 January 2011; accepted 1 February 2011 Published online in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/bit.23093 ABSTRACT: The genome of Caldicellulosiruptor saccharoly- ticus encodes a range of glycoside hydrolases (GHs) that mediate plant biomass deconstruction by this bacterium. Two GH-based genomic loci that appear to be central to the hydrolysis of hemicellulosic and cellulosic substrates

7

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus  

SciTech Connect

Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life. We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres. Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.

Saw, Jimmy H [Los Alamos National Laboratory; Mountain, Bruce W [NEW ZEALAND; Feng, Lu [NANKAI UNIV; Omelchenko, Marina V [NCBI/NLM/NIH; Hou, Shaobin [UNIV OF HAWAII; Saito, Jennifer A [UNIV OF HAWAII; Stott, Matthew B [NEW ZEALAND; Li, Dan [NANKAI UNIV; Zhao, Guang [NANKAI UNIV; Wu, Junli [NANKAI UNIV; Galperin, Michael Y [NCBI/NLM/NIH; Koonin, Eugene V [NCBI/NLM/NIH; Makarova, Kira S [NCBI/NLM/NIH; Wolf, Yuri I [NCBI/NLM/NIH; Rigden, Daniel J [UNIV OF LIVERPOOL; Dunfield, Peter F [UNIV OF CALGARY; Wang, Lei [NANKAI UNIV; Alam, Maqsudul [UNIV OF HAWAII

2008-01-01T23:59:59.000Z

8

Cellulolytic Microorganisms from Thermal Environments  

Science Conference Proceedings (OSTI)

Thermal, anaerobic environments rich in decaying plant material are a potential source of novel cellulolytic bacteria. Samples collected from geothermal aquifers in the Yellowstone National Park (YNP) were used to select for cellulolytic thermophiles. Laboratory enrichments on dilute-acid pretreated plant biomass (switchgrass, Populus), and crystalline cellulose (Avicel) resulted in the isolation of 247 environmental clones. The majority of individual clones were affiliated with the cellulolytic bacteria of phylum Firmicutes, followed by xylanolytic and saccharolytic members of the phylum Dictyoglomi. Among the Firmicutes, the clones were affiliated with the genera Caldicellulosiruptor (54.4%), Caloramator (11.5%), Thermoanaerobacter (8.8%), Thermovenabulum (4.1%), and Clostridium (2.0%). From established anaerobic thermophilic enrichments a total of 81 single strains of the genera Caldicellulosiruptor (57%) and Thermoanaerobacter (43%) were isolated. With continuous flow enrichment on Avicel, increases in the relative abundance of Caloramator sp. was observed over clones detected from the Caldicellulosiruptor. Complex communities of interacting microorganisms bring about cellulose decomposition in nature, therefore using up-to-date approaches may yield novel cellulolytic microorganisms with high activity and a rapid rate of biomass conversion to biofuels.

Vishnivetskaya, Tatiana A [ORNL; Raman, Babu [ORNL; Phelps, Tommy Joe [ORNL; Podar, Mircea [ORNL; Elkins, James G [ORNL

2012-01-01T23:59:59.000Z

9

Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b  

Science Conference Proceedings (OSTI)

Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physicochemical gradient. This genome was sequenced to be a comparative resource for the study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy s (DOE s) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).

Vishnivetskaya, T. [University of Tennessee, Knoxville (UTK); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L [ORNL; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Brettin, Tom [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Kathariou, Sophia [North Carolina State University; Ramaley, Robert F. [University of Nebraska Medical Center; Rodrigues, Debora F. [University of Houston, Houston; Hendrix, Christie [Yellowstone National Park; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; Tiedje, James M. [Michigan State University, East Lansing

2011-01-01T23:59:59.000Z

10

Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b  

Science Conference Proceedings (OSTI)

Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physico-chemical gradient. This genome was sequenced to be a comparative resource for study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy's (DOE) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).

Vishnivetskaya, T. [University of Tennessee, Knoxville (UTK); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Kathariou, Sophia [North Carolina State University; Ramaley, Robert F. [University of Nebraska Medical Center; Rodrigues, Debora F. [University of Houston, Houston; Hendrix, Christie [Yellowstone National Park; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; Tiedje, James M. [Michigan State University, East Lansing

2011-01-01T23:59:59.000Z

11

Genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T)  

Science Conference Proceedings (OSTI)

Thermodesulfatator indicus Moussard et al. 2004 is a member of the genomically so far poorly characterized family Thermodesulfobacteriaceae in the phylum Thermodesulfobacteria. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Chang, Yun-Juan [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2012-01-01T23:59:59.000Z

12

Thermosyntropha lipolytica gen. nov., sp. nov., a lipolytic, anaerobic, alkalitolerant, thermophilic bacterium utilizing short- and long-chain fatty acids in syntrophic coculture with a methanogenic archaeum  

Science Conference Proceedings (OSTI)

Three strains of an anaerobic thermophilic organoheterotrophic lipolytic alkalitolerant bacterium, Thermosyntropha lipolytica gen. nov., sp. nov. (type strain JW/VS-264{sup T}; DSM 11003) were isolated from alkaline hot springs of Lake Bogoria (Kenya). The cells were nonmotile, non-spore forming, straight or slightly curved rods. At 60{degrees}C, the pH range for growth determined at 25{degrees}C [pH{sup 25{degrees}C}] was 7.15 to 9.5, with an optimum between 8.1 and 8.9 (pH{sup 60{degrees}C} of 7.6 and 8.1). At a pH{sup 25{degrees}C} of 8.5 temperature range for growth was from 52 to 70{degrees}C, with an optimum between 60 and 66{degrees}C. The shortest doubling time was around 1 h. In pure culture the bacterium grew in a mineral base medium supplemented with yeast extract, tryptone, Casamino Acids, betaine, and crotonate as carbon sources, producing acetate as a major product and constitutively a lipase. During growth in the presence of olive oil, free long-chain fatty acids were accumulated in the medium but the pure culture syntrophic coculture (Methanobacterium strain JW/VS-M29) the lipolytic bacteria grew on triacylglycerols and linear saturated and unsaturated fatty acids with 4 to 18 carbon atoms, but glycerol was not utilized. Fatty acids with even numbers of carbon atoms were degraded to acetate and methane, while from odd-numbered fatty acids 1 mol of propionate per mol of fatty acid was additionally formed. 16S rDNA sequence analysis identified Syntrophospora and Syntrophomonas spp. as closest phylogenetic neighbors.

Svetlitshnyi, V.; Wiegel, J. [Univ. of Georgia, Athens, GA (United States); Rainey, F. [German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)

1996-10-01T23:59:59.000Z

13

Targeted Mutagenesis Tool in Mesophilic Cellulolytic ...  

Biomass and Biofuels Targeted Mutagenesis Tool in Mesophilic Cellulolytic Clostridia Species Oak Ridge National Laboratory. Contact ORNL About This ...

14

Thermostable purified endoglucanase from thermophilic bacterium ...  

National Renewable Energy Laboratory - Visit the NREL Commercialization and Technology Transfer ... possesses both C.sub.1 and C.sub.x types of enzymatic activity, ...

15

Hemicellulases from anaerobic thermophiles. Progress report  

DOE Green Energy (OSTI)

The longterm goal of this research effort is to obtain an anaerobic thermophilic bacterium that efficiently converts various hemicellulose-containing biomass to ethanol over a broad pH range. The strategy is to modify the outfit and regulation of the rate-limiting xylanases, glycosidases and xylan esterases in the ethanologenic, anaerobic thermophile Thermoanaerobacter ethanolicus, which grows between pH 4.5 and 9.5. Although it utilizes xylans, the xylanase, acetyl(xylan) esterase and O-methylglucuronidase activities in T. ethanolicus are barely measurable and regarded as the rate limiting steps in its xylan utilization. Thus, and also due to the presently limited knowledge of hemicellulases in anaerobic thermophiles, we characterize the hemicellulolytic enzymes from this and other anaerobic thermophiles as enzyme donors. Beside the active xylosidase/arabinosidase from T. ethanolicus, exhibiting the two different activities, we characterized 2 xylosidases, two acetyl(xylan) esterases, and an O-methylglucuronidase from Thermoanaerobacterium spec. We will continue with the characterization of xylanases from novel isolated slightly acidophilic, neutrophilic and slightly alkalophilic thermophiles. We have cloned, subcloned and partially sequenced the 165,000 Da (2 x 85,000) xylosidase/arabinosidase from T. ethanolicus and started with the cloning of the esterases from Thermoanaerobacterium spec. Consequently, we will develop a shuttle vector and continue to apply electroporation of autoplasts as a method for cloning into T. ethanolicus.

Wiegel, J.

1994-05-01T23:59:59.000Z

16

Anaerobic thermophilic culture  

DOE Patents (OSTI)

A newly discovered thermophilic anaerobe is described that was isolated in a biologically pure culture and designated Thermoanaerobacter ethanolicus ATCC 3/550. T. Ethanolicus is cultured in aqueous nutrient medium under anaerobic, thermophilic conditions and is used in a novel process for producing ethanol by subjecting carbohydrates, particularly the saccharides, to fermentation action of the new microorganism in a biologically pure culture.

Ljungdahl, Lars G. (Athens, GA); Wiegel, Jurgen K. W. (Gottingen, DE)

1981-01-01T23:59:59.000Z

17

Complete Genome Sequence of the Cellulose-Degrading Bacterium Cellulosilyticum lentocellum  

SciTech Connect

Cellulosilyticum lentocellum DSM 5427 is an anaerobic, endospore-forming member of the Firmicutes. We describe the complete genome sequence of this cellulose-degrading bacterium; originally isolated from estuarine sediment of a river that received both domestic and paper mill waste. Comparative genomics of cellulolytic clostridia will provide insight into factors that influence degradation rates.

Miller, David A [Cornell University; Suen, Garret [University of Wisconsin, Madison; Bruce, David [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Meincke, Linda [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Teshima, Hazuki [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Fox, Brian G. [University of Wisconsin, Madison; Angert, Esther R. [Cornell University; Currie, Cameron [University of Wisconsin, Madison

2011-01-01T23:59:59.000Z

18

Anaerobic thermophilic culture system  

DOE Patents (OSTI)

A mixed culture system of the newly discovered microorganism Thermoanaerobacter ethanolicus ATCC31550 and the microorganism Clostridium thermocellum ATCC31549 is described. In a mixed nutrient culture medium that contains cellulose, these microorganisms have been coupled and cultivated to efficiently ferment cellulose to produce recoverable quantities of ethanol under anaerobic, thermophilic conditions.

Ljungdahl, Lars G. (Athens, GA); Wiegel, Jurgen K. W. (Gottingen, DE)

1981-01-01T23:59:59.000Z

19

Anaerobic High-Throughput Cultivation Method for Isolation of Thermophiles Using Biomass-Derived Substrates  

Science Conference Proceedings (OSTI)

Flow cytometry (FCM) techniques have been developed for sorting mesophilic organisms, but the difficulty increases if the target microbes are thermophilic anaerobes. We demonstrate a reliable, high-throughput method of screening thermophilic anaerobic organisms using FCM and 96-well plates for growth on biomass-relevant substrates. The method was tested using the cellulolytic thermophiles Clostridium ther- mocellum (Topt = 55 C), Caldicellulosiruptor obsidiansis (Topt = 78 C) and the fermentative hyperthermo- philes, Pyrococcus furiosus (Topt = 100 C) and Thermotoga maritima (Topt = 80 C). Multi-well plates were incubated at various temperatures for approximately 72 120 h and then tested for growth. Positive growth resulting from single cells sorted into individual wells containing an anaerobic medium was verified by OD600. Depending on the growth substrate, up to 80 % of the wells contained viable cultures, which could be transferred to fresh media. This method was used to isolate thermophilic microbes from Rabbit Creek, Yellowstone National Park (YNP), Wyoming. Substrates for enrichment cultures including crystalline cellulose (Avicel), xylan (from Birchwood), pretreated switchgrass and Populus were used to cultivate organisms that may be of interest to lignocellulosic biofuel production.

Hamilton-Brehm, Scott [ORNL; Vishnivetskaya, Tatiana A [ORNL; Allman, Steve L [ORNL; Mielenz, Jonathan R [ORNL; Elkins, James G [ORNL

2012-01-01T23:59:59.000Z

20

Why Sequence Thermophilic Methanoarchaea?  

NLE Websites -- All DOE Office Websites (Extended Search)

Thermophilic Methanoarchaea? Thermophilic Methanoarchaea? Microbes that reduce carbon dioxide to methane catalyze a significant component of the carbon cycle on Earth and are responsible for most of the methane in the atmospere. Since methane contributes significantly to the greenhouse effect, understanding the biological controls on emissions of methane may provide the opportunity to compensate for the emission of other important trace gases, such as CO2. In addition, methane is a common fuel, and the biological production of methane catalyzed by these bacteria has great potential as an alternative fuel source. This application is of special significance because it is "CO2 neutral", ie., it does not result in the net emissions of greenhouse gases to the earth's atmosphere.

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Complete genome of the cellyloytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evloutionary adaptations  

SciTech Connect

We present here the complete 2.4 Mb genome of the cellulolytic actinobacterial thermophile, Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized, and significantly elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. A novel feature of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes is that they are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. Interestingly, CBM3 was found to be always N-terminal to CBM2, suggesting a functional constraint driving this organization. While the catalytic domains of these modular enzymes are either diverse or unrelated, the CBMs were found to be highly conserved in sequence and may suggest selective substrate-binding interactions. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and non-coding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles, and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and presence of three laterally-acquired genomic islands of likely ecophysiological value.

Barabote, Ravi D.; Xie, Gary; Leu, David H.; Normand, Philippe; Necsulea, Anamaria; Daubin, Vincent; Medigue, Claudine; Adney, William S.; Xu,Xin Clare; Lapidus, Alla; Detter, Chris; Pujic, Petar; Bruce, David; Lavire, Celine; Challacombe, Jean F.; Brettin, Thomas S.; Berry, Alison M.

2009-01-01T23:59:59.000Z

22

Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same  

DOE Patents (OSTI)

The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Duan, Junxin; Tang, Lan; Liu, Ye; Wu, Wenping; Quinlan, Jason; Kramer, Randall

2013-06-18T23:59:59.000Z

23

Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same  

SciTech Connect

The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Lopez de Leon, Alfredo (Davis, CA); Ding, Hanshu (Davis, CA); Brown, Kimberly (Elk Grove, CA)

2012-06-26T23:59:59.000Z

24

Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same  

DOE Patents (OSTI)

The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated nucleic acids encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the nucleic acids as well as methods for producing and using the polypeptides.

Dotson, William D. (Plainsboro, NJ); Greenier, Jennifer (Vacaville, CA); Ding, Hanshu (Davis, CA)

2007-09-18T23:59:59.000Z

25

Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same  

DOE Patents (OSTI)

The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

Lopez de Leon, Alfredo (Davis, CA); Ding, Hanshu (Davis, CA); Brown, Kimberly (Elk Grove, CA)

2011-10-25T23:59:59.000Z

26

Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same  

DOE Patents (OSTI)

The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

2012-10-16T23:59:59.000Z

27

Hemicellulases from the ethanologenic thermophile, Thermoanaerobacter ethanolicus and related anaerobic thermophiles. Final report, September 1992--June 1996  

DOE Green Energy (OSTI)

The short term goals of this application were to characterize hemicellulases from anaerobic thermophiles on the biochemical and molecular level to extend the presently limited knowledge of hemicellulases in anaerobic thermophilic bacteria. This objective includes the following tasks: (1) Traditional purification and biochemical/biophysical characterization of xylanases from the newly isolated, slightly alkalitolerant strain NDF190, and the slightly acid-tolerant strain YS485, both with high xylanolytic activities, and of the 4-O-methyl glucuronidase and arabinosidase from strain NDF190 and the acetyl (xylan) esterase from T. ethanolicus. This also includes determining the N-terminal sequences and obtaining gene probes. (2) Elucidation of the regulation of hemicellulolytic enzymes in anaerobic thermophiles. (3) To clone into E. coli and identify the multiplicity of the enzymes involved in hemicellulose degradation by T. ethanolicus and other suitable organisms. (4) To purify and characterize the recombinant enzymes with the goal of identifying the best enzymes for cloning into the ethanologenic T. ethanolicus to obtain an optimized hemicellulose utilization by this bacterium.

Wiegel, J.

1998-09-01T23:59:59.000Z

28

Complete genome sequences for the anaerobic, extremely thermophilic plant biomass-degrading bacteria Caldicellulosiruptor hydrothermalis, Caldicellulosiruptor kristjanssonii, Caldicellulosiruptor kronotskyensis, Caldicellulosiruptor owensenis, and Caldicellulosiruptor lactoaceticus  

Science Conference Proceedings (OSTI)

The genus Caldicellulosiruptor contains the most thermophilic, plant biomass-degrading bacteria isolated to date. Previously, genome sequences from three cellulolytic members of this genus were reported (C. saccharolyticus, C. bescii, and C. obsidiansis). To further explore the physiological and biochemical basis for polysaccharide degradation within this genus, five additional genomes were sequenced: C. hydrothermalis, C. kristjanssonii, C. kronotskyensis, C. lactoaceticus, and C. owensensis. Taken together, the seven completed and one draft-phase Caldicellulosiruptor genomes suggest that, while central metabolism is highly conserved, significant differences in glycoside hydrolase inventories and numbers of carbohydrate transporters exist, a finding which likely relates to variability observed in plant biomass degradation capacity.

Blumer-Schuette, Sara E. [North Carolina State University; Ozdemir, Inci [North Carolina State University; Mistry, Dhaval [North Carolina State University; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Walston Davenport, Karen [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Adams, Michael W. W. [University of Georgia, Athens, GA; Kelly, Robert M [North Carolina State University

2011-01-01T23:59:59.000Z

29

Why sequence carbon monoxide oxidizing thermophiles?  

NLE Websites -- All DOE Office Websites (Extended Search)

carbon monoxide oxidizing thermophiles? carbon monoxide oxidizing thermophiles? Many microbes that use carbon monoxide as an energy source are found in high temperature environments such as geothermal areas. Researchers think that these carboxydotrophs may be involved in reducing potentially toxic carbon monoxide hotspots by combine with water to form hydrogen, carbon dioxide and acetate, which are in turn used for thermophilic energy conservation and carbon sequestration mechanisms. The project focuses on sequencing two closely related microbes, one of which is Carboxydothermus hydrogenformans. A strain of C. hydrogenformans has been grown in hydrogen-enriched synthesis gas (syngas), which contains a mix of hydrogen and carbon monoxide. Researchers are interested in sequencing both microbial strains to track the genome's evolution and

30

Complete Genome Sequence of the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aurantiacus  

Science Conference Proceedings (OSTI)

Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria.

Tang, Kuo-Hsiang [Washington University, St. Louis; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Honchak, Barbara M [Washington University, St. Louis; Karbach, Lauren E [Washington University, St. Louis; Land, Miriam L [ORNL; Lapidus, Alla L. [Joint Genome Institute, Walnut Creek, California; Larimer, Frank W [ORNL; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [Joint Genome Institute, Walnut Creek, California; Pierson, Beverly K [University of Puget Sound, Tacoma, WA

2011-01-01T23:59:59.000Z

31

Fructose-1,6-bisphosphatase from a hyper-thermophilic bacterium...  

NLE Websites -- All DOE Office Websites (Extended Search)

theory may be applied to explain why hyperthermophilic microorganisms need stabilize heat-sensitive metabolites, such as F16P. It has been suggested that labile NADPH 30,31...

32

Biochemical Characterization of ?-Xylan Acting Glycoside Hydrolases from the Thermophilic Bacterium Caldicellulosiruptor Saccharolyticus.  

E-Print Network (OSTI)

??Fossil fuels have been the dominant source for energy around the world since the industrial revolution, however, with the increasing demand for energy and decreasing… (more)

Cao, Jin

2012-01-01T23:59:59.000Z

33

Impact of Cell Wall Acetylation on Corn Stover Hydrolysis by Cellulolytic and Xylanolytic Enzymes  

SciTech Connect

Analysis of variously pretreated corn stover samples showed neutral to mildly acidic pretreatments were more effective at removing xylan from corn stover and more likely to maintain the acetyl to xylopyranosyl ratios present in untreated material than were alkaline treatments. Retention of acetyl groups in the residual solids resulted in greater resistance to hydrolysis by endoxylanase alone, although the synergistic combination of endoxylanase and acetyl xylan esterase enzymes permitted higher xylan conversions to be observed. Acetyl xylan esterase alone did little to improve hydrolysis by cellulolytic enzymes, although a direct relationship was observed between the enzymatic removal of acetyl groups and improvements in the enzymatic conversion of xylan present in substrates. In all cases, effective xylan conversions were found to significantly improve glucan conversions achievable by cellulolytic enzymes. Additionally, acetyl and xylan removal not only enhanced the respective initial rates of xylan and glucan conversion, but also the overall extents of conversion. This work emphasizes the necessity for xylanolytic enzymes during saccharification processes and specifically for the optimization of acetyl esterase and xylanase synergies when biomass processes include milder pretreatments, such as hot water or sulfite steam explosion.

Selig, M. J.; Adney, W. S.; Himmel, M. E.; Decker, S. R.

2009-01-01T23:59:59.000Z

34

Extreme thermophiles: moving beyond single-enzyme biocatalysis  

NLE Websites -- All DOE Office Websites (Extended Search)

COCHE-51; NO. OF PAGES 10 COCHE-51; NO. OF PAGES 10 Please cite this article in press as: Frock AD, Kelly RM. Extreme thermophiles: moving beyond single-enzyme biocatalysis, Curr Opin Chem Eng (2012), http://dx.doi.org/10.1016/ j.coche.2012.07.003 Available online at www.sciencedirect.com Extreme thermophiles: moving beyond single-enzyme biocatalysis Andrew D Frock and Robert M Kelly Extremely thermophilic microorganisms have been sources of thermostable and thermoactive enzymes for over 30 years. However, information and insights gained from genome sequences, in conjunction with new tools for molecular genetics, have opened up exciting new possibilities for biotechnological opportunities based on extreme thermophiles that go beyond single-step biotransformations. Although the pace for discovering novel microorganisms has slowed over

35

Onestep production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: Opportunities and challenges  

NLE Websites -- All DOE Office Websites (Extended Search)

One-step One-step production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: Opportunities and challenges One-step consolidated bioprocessing that integrates cellulase production, cellulose hydrolysis, and product fermentation into a single step for decreasing costly cellulase use, increasing volumetric productivity, and reducing capital investment is widely accepted for low-cost production of biofuels or other value-added biochemicals. Considering the narrow margins between biomass and low-value biocommodities, good physiological performance of industrial microbes is crucial for economically viable production. Bacillus subtilis, the best-characterized Gram-positive microorganism, is a major industrial microorganism with numerous valuable features such as hexose and pentose utilization, low-nutrient needs,

36

Development and Evaluation of Methods to Infer Biosynthesis and Substrate Consumption in Cultures of Cellulolytic Microorganisms  

NLE Websites -- All DOE Office Websites (Extended Search)

and and Evaluation of Methods to Infer Biosynthesis and Substrate Consumption in Cultures of Cellulolytic Microorganisms Evert K. Holwerda, Lucas D. Ellis, Lee R. Lynd Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire, 03755; telephone: 1-6036462231; fax: 1-6036462277; e-mail: lee.r.lynd@dartmouth.edu ABSTRACT: Concentrations of biosynthate (microbial bio- mass plus extracellular proteins) and residual substrate were inferred using elemental analysis for batch cultures of Clostridium thermocellum. Inferring residual substrate based on elemental analysis for a cellulose (Avicel)-grown culture shows similar results to residual substrate determined by quantitative saccharification using acid hydrolysis. Inference based on elemental analysis is also compared to different on- line measurements: base addition, CO

37

Why sequence thermophiles in Great Basin hot springs?  

NLE Websites -- All DOE Office Websites (Extended Search)

thermophiles in Great Basin hot springs? thermophiles in Great Basin hot springs? A thermophile is an organism that thrives in extremely hot temperature conditions. These conditions are found in the Great Basin hot springs, where the organisms have been exposed to unique conditions which guide their lifecycle. High temperature environments often support large and diverse populations of microorganisms, which appear to be hot spots of biological innovation of carbon fixation. Sequencing these microbes that make their home in deadly heat could provide various insights into understanding energy production and carbon cycling. Converting cellulosic biomass to ethanol is one of the most promising strategies to reduce petroleum consumption in the near future. This can only be achieved by enhancing recovery of fermentable sugars from complex

38

[Conversion of acetic acid to methane by thermophiles: Progress report  

DOE Green Energy (OSTI)

The objective of this project is to provide an understanding of thermophilic anaerobic microorganisms capable of breaking down acetic acid, the precursor of two-thirds of the methane produced by anaerobic bioreactors. Recent results include: (1) the isolation of Methanothrix strain CALLS-1, which grows much more rapidly than mesophilic strains; (2) the demonstration that thermophilic cultures of Methanosarcina and Methanothrix show minimum thresholds for acetate utilization of 1--2.5 mM and 10--20{mu}m respectively, in agreement with ecological data indicating that Methanothrix is favored by low acetate concentration; (3) the demonstration of high levels of thermostable acetyl-coA synthetase and carbon monoxide dehydrogenase in cell-free extracts of Methanothrix strains CALS-1; (4) the demonstration of methanogenesis from acetate and ATP in cell free extracts of strain CALS-1. (5) the demonstration that methanogenesis from acetate required 2 ATP/methane, and, in contrast to Methanosarcina, was independent of hydrogen and other electron donors; (6) the finding that entropy effects must be considered when predicting the level of hydrogen in thermophilic syntrophic cultures. (7) the isolation and characterization of the Desulfotomaculum thermoacetoxidans. Current research is centered on factors which allow thermophilic Methanothrix to compete with Methanosarcina.

Zinder, S.

1991-12-31T23:59:59.000Z

39

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Feb.  

NLE Websites -- All DOE Office Websites (Extended Search)

Feb. Feb. 2010, p. 1014-1020 Vol. 76, No. 4 0099-2240/10/$12.00 doi:10.1128/AEM.01903-09 Copyright © 2010, American Society for Microbiology. All Rights Reserved. Caldicellulosiruptor obsidiansis sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park ᰔ Scott D. Hamilton-Brehm, Jennifer J. Mosher, Tatiana Vishnivetskaya, Mircea Podar, Sue Carroll, Steve Allman, Tommy J. Phelps, Martin Keller, and James G. Elkins* BioEnergy Science Center, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 Received 7 August 2009/Accepted 2 December 2009 A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47 T , was isolated from Obsidian Pool, Yellowstone National Park, WY. The isolate was a nonmotile, non-spore-forming, Gram- positive

40

Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSAT) from a deep-sea hydrothermal vent  

SciTech Connect

Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 is the type species of the ge- nus Desulfurobacterium which belongs to the family Desulfurobacteriaceae. The species is of interest because it represents the first thermophilic bacterium that can act as a primary pro- ducer in the temperature range of 45-75 C (optimum 70 C) and is incapable of growing un- der microaerophilic conditions. Strain BSAT preferentially synthesizes high-melting-point fatty acids (C18 and C20) which is hypothesized to be a strategy to ensure the functionality of the membrane at high growth temperatures. This is the second completed genome sequence of a member of the family Desulfurobacteriaceae and the first sequence from the genus Desulfu- robacterium. The 1,541,968 bp long genome harbors 1,543 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Daligault, Hajnalka E. [Los Alamos National Laboratory (LANL); Mwirichia, Romano [Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Pan, Chongle [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Wirth, Reinhard [Universitat Regensburg, Regensburg, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain  

SciTech Connect

A recently discovered thermophilic bacterium, Geobacillus thermoglucosidasius M10EXG, ferments a range of C5 (e.g., xylose) and C6 sugars (e.g., glucose) and istolerant to high ethanol concentrations (10percent, v/v). We have investigated the central metabolism of this bacterium using both in vitro enzyme assays and 13C-based flux analysis to provide insights into the physiological properties of this extremophile and explore its metabolism for bio-ethanol or other bioprocess applications. Our findings show that glucose metabolism in G. thermoglucosidasius M10EXG proceeds via glycolysis, the pentose phosphate pathway, and the TCA cycle; the Entner?Doudoroff pathway and transhydrogenase activity were not detected. Anaplerotic reactions (including the glyoxylate shunt, pyruvate carboxylase, and phosphoenolpyruvate carboxykinase) were active, but fluxes through those pathways could not be accuratelydetermined using amino acid labeling. When growth conditions were switched from aerobic to micro-aerobic conditions, fluxes (based on a normalized glucose uptake rate of 100 units (g DCW)-1 h-1) through the TCA cycle and oxidative pentose phosphate pathway were reduced from 64+-3 to 25+-2 and from 30+-2 to 19+-2, respectively. The carbon flux under micro-aerobic growth was directed formate. Under fully anerobic conditions, G. thermoglucosidasius M10EXG used a mixed acid fermentation process and exhibited a maximum ethanol yield of 0.38+-0.07 mol mol-1 glucose. In silico flux balance modeling demonstrates that lactate and acetate production from G. thermoglucosidasius M10EXG reduces the maximum ethanol yieldby approximately threefold, thus indicating that both pathways should be modified to maximize ethanol production.

Tang, Yinjie J.; Sapra, Rajat; Joyner, Dominique; Hazen, Terry C.; Myers, Samuel; Reichmuth, David; Blanch, Harvey; Keasling, Jay D.

2009-01-20T23:59:59.000Z

42

Difference between Life and Death of Bacterium against Microwave ...  

Science Conference Proceedings (OSTI)

... Electric and Magnetic Fields, Ultrasound, Lasers, and Mechanical Work. ... of Bacterium against Microwave Power under Microwave Irradiated Cultivation.

43

First Knot Discovered in Ancient Bacterium Protein  

NLE Websites -- All DOE Office Websites (Extended Search)

First Knot Discovered in Ancient Bacterium Protein First Knot Discovered in Ancient Bacterium Protein The first knotted protein from the most ancient type of single-celled organism, an archaebacterium, has been discovered by researchers from Argonne National Laboratory and the University of Toronto using the Advanced Photon Source (APS) at Argonne. It is one of the few times that a knot has been seen in any protein structure. Protein folding theory previously held that forming a knot was beyond the ability of a protein. Image of knotted protein. The newly discovered knotted protein comes from a microorganism called Methanobacterium thermoautotrophicum. This organism is of interest to industry for its ability to break down waste products and produce methane gas. Scientists know which gene codes for the 268-amino acid protein, but

44

Solubilization, Solution Equilibria, and Biodegradation of PAH's under Thermophilic Conditions  

Science Conference Proceedings (OSTI)

Biodegradation rates of PAHs are typically low at mesophilic conditions and it is believed that the kinetics of degradation is controlled by PAH solubility and mass transfer rates. Solubility tests were performed on phenanthrene, fluorene and fluoranthene at 20 C, 40 C and 60 C and, as expected, a significant increase in the equilibrium solubility concentration and of the rate of dissolution of these polycyclic aromatic hydrocarbons (PAHs) was observed with increasing temperature. A first-order model was used to describe the PAH dissolution kinetics and the thermodynamic property changes associated with the dissolution process (enthalpy, entropy and Gibb's free energy of solution) were evaluated. Further, other relevant thermodynamic properties for these PAHs, including the activity coefficients at infinite dilution, Henry's law constants and octanol-water partition coefficients, were calculated in the temperature range 20-60 C. In parallel with the dissolution studies, three thermophilic Geobacilli were isolated from compost that grew on phenanthrene at 60 C and degraded the PAH more rapidly than other reported mesophiles. Our results show that while solubilization rates of PAHs are significantly enhanced at elevated temperatures, the biodegradation of PAHs under thermophilic conditions is likely mass transfer limited due to enhanced degradation rates.

Viamajala, S.; Peyton, B. M.; Richards, L. A.; Petersen, J. N.

2007-01-01T23:59:59.000Z

45

One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtilis  

NLE Websites -- All DOE Office Websites (Extended Search)

step step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtilis Xiao-Zhou Zhang a , Noppadon Sathitsuksanoh a,b , Zhiguang Zhu a , Y.-H. Percival Zhang a,b,c,n a Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA b Institute for Critical Technology and Applied Science, Virginia Tech, Blacksburg, VA 24061, USA c BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA a r t i c l e i n f o Article history: Received 28 December 2010 Received in revised form 9 April 2011 Accepted 25 April 2011 Keywords: Bacillus subtilis Cellulase engineering Consolidated bioprocessing Endoglucanase Lactate Metabolic engineering Directed evolution a b s t r a c t Although intensive efforts have been made to create recombinant cellulolytic microorganisms,

46

Cassava Stillage Treatment by Thermophilic Anaerobic Continuously Stirred Tank Reactor (CSTR)  

Science Conference Proceedings (OSTI)

This paper assesses the performance of a thermophilic anaerobic Continuously Stirred Tank Reactor (CSTR) in the treatment of cassava stillage under various organic loading rates (OLRs) without suspended solids (SS) separation. The reactor was seeded with mesophilic anaerobic granular sludge

Gang Luo; Li Xie; Zhonghai Zou; Qi Zhou

2010-01-01T23:59:59.000Z

47

Conversion of sugarcane bagasse to carboxylic acids under thermophilic conditions  

E-Print Network (OSTI)

With the inevitable depletion of the petroleum supply and increasing energy demands in the world, interest has been growing in bioconversion of lignocellulosic biomass (e.g., sugarcane bagasse). Lignocellulosic biomass is an abundant, inexpensive, and renewable resource. Most of current conversion technologies require expensive enzymes and sterility. In contrast, the patented MixAlco process requires no enzymes or sterility, making it attractive to convert lignocellulosic biomass to transportation fuels and valuable chemicals. This study focuses on pretreatment and thermophilic fermentation in the MixAlco process. Ammonium bicarbonate (NH4HCO3) was discovered to be a better pH buffer than previously widely used calcium carbonate (CaCO3) in anaerobic fermentations under thermophilic conditions (55°C). The desired pH should be controlled within 6.5 to 7.5. Over 85% acetate content in the product was found in paper fermentations and bagasse fermentations. Hot-lime-water-treated bagasse countercurrent fermentations buffered by ammonium bicarbonate achieved 50–60% higher total product concentrations than those using calcium carbonate. It was nearly double in paper batch fermentations if the pH was controlled around 7.0. Ammonium bicarbonate is a “weak” methane inhibitor, so a strong methane inhibitor (e.g., iodoform) is still required in ammonium bicarbonate buffered fermentations. Residual calcium salts did not show significant effects on ammonium bicarbonate buffered fermentations. Lake inocula from the Great Salt Lake, Utah, proved to be feasible in ammonium bicarbonate buffered fermentations. Under mesophilic conditions (40°C), the inoculum from the Great Salt Lake increased the total product concentration about 30%, compared to the marine inoculum. No significant fermentation performance difference, however, was found under thermophilic conditions. The Continuum Particle Distribution Model (CPDM) is a powerful tool to predict product concentrations and conversions for long-term countercurrent fermentations, based on batch fermentation data. The experimental acid concentrations and conversions agree well with the CPDM predictions (average absolute error < 15%). Aqueous ammonia treatment proved feasible for bagasse. Air-lime-treated bagasse had the highest acid concentration among the three treated bagasse. Air-lime treatment coupled with ammonium bicarbonate buffered fermentations is preferred for a “crop-tofuel” process. Aqueous ammonia treatment combined with ammonium bicarbonate buffered fermentations is a viable modification of the MixAlco process, if “ammonia recycle” is deployed.

Fu, Zhihong

2007-05-01T23:59:59.000Z

48

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

DOE Green Energy (OSTI)

Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfatereducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptideand amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely injected into reservoirs for oil recovery purposes, are biodegraded and provide biocorrosive microbial communities with an important source of nutrients.

Duncan, Kathleen E.; Gieg, Lisa M.; Parisi, Victoria A.; Tanner, Ralph S.; Green Tringe, Susannah; Bristow, Jim; Suflita, Joseph M.

2009-09-16T23:59:59.000Z

49

Pathway engineering to improve ethanol production by thermophilic bacteria  

DOE Green Energy (OSTI)

Continuation of a research project jointly funded by the NSF and DOE is proposed. The primary project goal is to develop and characterize strains of C. thermocellum and C. thermosaccharolyticum having ethanol selectivity similar to more convenient ethanol-producing organisms. An additional goal is to document the maximum concentration of ethanol that can be produced by thermophiles. These goals build on results from the previous project, including development of most of the genetic tools required for pathway engineering in the target organisms. As well, we demonstrated that the tolerance of C. thermosaccharolyticum to added ethanol is sufficiently high to allow practical utilization should similar tolerance to produced ethanol be demonstrated, and that inhibition by neutralizing agents may explain the limited concentrations of ethanol produced in studies to date. Task 1 involves optimization of electrotransformation, using either modified conditions or alternative plasmids to improve upon the low but reproducible transformation, frequencies we have obtained thus far.

Lynd, L.R.

1998-12-31T23:59:59.000Z

50

Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass  

DOE Green Energy (OSTI)

Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60 C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80 C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

Gladden, J.M.; Allgaier, M.; Miller, C.S.; Hazen, T.C.; VanderGheynst, J.S.; Hugenholtz, P.; Simmons, B.A.; Singer, S.W.

2011-05-01T23:59:59.000Z

51

Computational design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles  

NLE Websites -- All DOE Office Websites (Extended Search)

design design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles Olson and Lynd Olson and Lynd Journal of Biological Engineering 2012, 6:5 http://www.jbioleng.org/content/6/1/5 R E S E A R C H Open Access Computational design and characterization of a temperature-sensitive plasmid replicon for gram positive thermophiles Daniel G Olson 1,3 and Lee R Lynd 1,2,3* Abstract Background: Temperature-sensitive (Ts) plasmids are useful tools for genetic engineering, but there are currently none compatible with the gram positive, thermophilic, obligate anaerobe, Clostridium thermocellum. Traditional mutagenesis techniques yield Ts mutants at a low frequency, and therefore requires the development of high-throughput screening protocols, which are also not available for this organism. Recently there has been progress in the development

52

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass  

SciTech Connect

Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the littlestudied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify .3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.

D'haeseleer, Patrik; Gladden, John M.; Allgaier, Martin; Chain, Patrick; Tringe, Susannah G.; Malfatti, Stephanie; Aldrich, Joshua T.; Nicora, Carrie D.; Robinson, Errol W.; Pasa-Tolic, Ljiljana; Hugenholtz, Philip; Simmons, Blake A.; Singer, Steven W.

2013-07-19T23:59:59.000Z

53

Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314T)  

SciTech Connect

Thermovirga lienii Dahle and Birkeland 2006 is a member to the genomically so far uncharacterized genus Thermovirga in the phylum 'Synergistetes'. Members of the only recently (2007) proposed phylum 'Synergistetes' are of interest because of their isolated phylogenetic position and their diverse habitats, e.g. from man to oil well. The genome of T. lienii Cas60314T is only the 5th genome sequence (3rd completed) from this phylum to be published. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,999,646 bp long genome (including one plasmid) with its 1,914 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2012-01-01T23:59:59.000Z

54

Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30  

Science Conference Proceedings (OSTI)

Development of alternative, non-petroleum based sources of bioenergy that can be applied in the short-term find great promise in the use of highly abundant and renewable lignocellulosic plant biomass.1 This material obtained from different feedstocks, such as forest litter or agricultural residues, can yield liquid fuels and other chemical products through biorefinery processes.2 Biofuels are obtained from lignocellulosic materials by chemical pretreatment of the biomass, followed by enzymatic decomposition of cellulosic and hemicellulosic compounds into soluble sugars that are converted to desired chemical products via microbial metabolism and fermentation.3, 4 To release soluble sugars from polymeric cellulose multiple enzymes are required, including endoglucanase, exoglucanase, and ?-glucosidase.5, 6 However, the enzymatic hydrolysis of cellulose into soluble sugars remains a significant limiting factor to the efficient and economically viable utilization of lignocellulosic biomass for transport fuels.7, 8 The primary industrial source of cellulose and hemicellulases is the mesophilic soft-rot fungus Trichoderma reesei,9 having widespread applications in food, feed, textile, pulp, and paper industries.10 The genome encodes 200 glycoside hydrolases, including 10 cellulolytic and 16 hemicellulolytic enzymes.11 The hypercellulolytic catabolite derepressed strain RUT-C30 was obtained through a three-step UV and chemical mutagenesis of the original T. reesei strain QM6a,12, 13 in which strains M7 and NG14 were intermediate, having higher cellulolytic activity than the parent strain but less activity and higher catabolite repression than RUT-C30.14 Numerous methods have been employed to optimize the secreted enzyme cocktail of T. reesei including cultivation conditions, operational parameters, and mutagenesis.3 However, creating an optimal and economical enzyme mixture for production-scale biofuels synthesis may take thousands of experiments to identify.

Anderson, Lindsey N.; Culley, David E.; Hofstad, Beth A.; Chauvigne-Hines, Lacie M.; Zink, Erika M.; Purvine, Samuel O.; Smith, Richard D.; Callister, Stephen J.; Magnuson, Jon M.; Wright, Aaron T.

2013-12-01T23:59:59.000Z

55

[Conversion of acetic acid to methane by thermophiles]. Annual progress report  

DOE Green Energy (OSTI)

Acetate is the precursor of approximately two-thirds of the methane produced by anaerobic bioreactors and many other methanogenic habitats. Besides their intrinsic interest, thermophilic acetotrophic methanogenic cultures usually grow at least twice as fast as their mesophilic counterparts, making them more amenable to study. In recent years, attention has been mainly focused on the thermophilic acetate utilizing methanogen Methanothrix strain CALS-1. Methanothrix, also called Methanosaeta, is one of only two methanogenic genera known to convert acetate to methane, the other being Methanosarcina. The faster-growing more versatile Methanosarcina has been better studied. However, when one examines anaerobic digestor contents, Methanothrix is often the dominant acetate-utilizing methanogen. As described in previous progress reports, the authors have achieved methanogenesis from acetate in cell-free extracts of Methanothrix strain CALS-1 grown in a pH auxostat. Using these cell extracts, specific activities for methanogenesis from acetate and ATP of 100--300 nmol/min were routinely obtained, levels comparable to the rate in whole cells, which is not usually the case in methanogenic extracts. Recently obtained results are given and discussed for the following: Methanogenesis in crude extracts; Role of the cell membrane in methanogenesis from acetate; Carbon monoxide dehydrogenase; Novel thermophilic cultures converting acetate to methane; and Methanol-utilizing methanogen.

Zinder, S.H.

1994-02-01T23:59:59.000Z

56

High-solids enrichment of thermophilic microbial communities and their enzymes on bioenergy feedstocks  

SciTech Connect

Thermophilic microbial communities that are active in a high-solids environment offer great potential for the discovery of industrially relevant enzymes that efficiently deconstruct bioenergy feedstocks. In this study, finished green waste compost was used as an inoculum source to enrich microbial communities and associated enzymes that hydrolyze cellulose and hemicellulose during thermophilic high-solids fermentation of the bioenergy feedstocks switchgrass and corn stover. Methods involving the disruption of enzyme and plant cell wall polysaccharide interactions were developed to recover xylanase and endoglucanase activity from deconstructed solids. Xylanase and endoglucanase activity increased by more than a factor of 5, upon four successive enrichments on switchgrass. Overall, the changes for switchgrass were more pronounced than for corn stover; solids reduction between the first and second enrichments increased by a factor of four for switchgrass while solids reduction remained relatively constant for corn stover. Amplicon pyrosequencing analysis of small-subunit ribosomal RNA genes recovered from enriched samples indicated rapid changes in the microbial communities between the first and second enrichment with the simplified communities achieved by the third enrichment. The results demonstrate a successful approach for enrichment of unique microbial communities and enzymes active in a thermophilic high-solids environment.

Reddy, A. P.; Allgaier, M.; Singer, S.W.; Hazen, T.C.; Simmons, B.A.; Hugenholtz, P.; VanderGheynst, J.S.

2011-04-01T23:59:59.000Z

57

A Streamlined Strategy for Biohydrogen Production with an Alkaliphilic Bacterium  

Science Conference Proceedings (OSTI)

Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, biohydrogen production remains inefficient and heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium strain sapolanicus, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. sapolanicus ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen and acetate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

Elias, Dwayne A [ORNL; Wall, Judy D. [University of Missouri; Mormile, Dr. Melanie R. [Missouri University of Science and Technology; Begemann, Matthew B [University of Wisconsin, Madison

2012-01-01T23:59:59.000Z

58

The photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis  

Science Conference Proceedings (OSTI)

The history and methods of membrane protein crystallization are described. The solution of the structure of the photosynthetic reaction center from the bacterium Rhodopseudomonas viridis is described, and the structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Conclusions about the structure of the photosystem II reaction center from plants are drawn, and aspects of membrane protein structure are discussed. 68 refs., 15 figs., 2 tabs.

Deisenhofer, J. (Univ. of Texas Southwestern Medical Center, Dallas (USA)); Michel, H. (Max-Planck-Institute for Biophysics, Frankfurt (West Germany))

1989-09-29T23:59:59.000Z

59

Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens  

SciTech Connect

The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

Daniel P. Molloy

2004-02-24T23:59:59.000Z

60

Ultrastable phosphoglucose isomerase through immobilization of cellulosebinding moduletagged thermophilic enzyme on lowcost highcapacity cellulosic adsorbent  

NLE Websites -- All DOE Office Websites (Extended Search)

Ultra-stable phosphoglucose isomerase through immobilization of cellulose- Ultra-stable phosphoglucose isomerase through immobilization of cellulose- binding module-tagged thermophilic enzyme on low-cost high-capacity cellulosic adsorbent Suwan Myung 1,2 , Xiao-Zhou Zhang 1 , Y.-H. Percival Zhang 1,2,3* Running title: One-step protein purification and immobilization 1 Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, 210-A Seitz Hall, Blacksburg, VA 24061, USA 2 Institute for Critical Technology and Applied Science (ICTAS), Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA 3 DOE BioEnergy Science Center (BESC), Oak Ridge, TN 37831, USA *Corresponding author. Tel: 540-231-7414; Fax: 540-231-7414; Email: ypzhang@vt.edu Biocatalysts and Bioreactor Design

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61

Bacterium Helps in the Formation of Gold | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

Creating a Precise Atomic-Scale Map of Quantum Dots Creating a Precise Atomic-Scale Map of Quantum Dots Getting to the Roots of Lethal Hairs Stressing Out the Twins in Magnesium Size-Related Behavior of Anatase Nanocrystals under Extreme Pressure Boron-Based Compounds Trick a Biomedical Protein Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed Bacterium Helps in the Formation of Gold OCTOBER 13, 2009 Bookmark and Share Top: An ultra-thin section of C. metallidurans containing a gold nanoparticle. Bottom: This image shows maps of pure gold with other elements. By determining what elements there are, scientists can see where the gold is located in relation to the cells. These maps are quantitative

62

Why sequence radiation-resistant bacterium Deinococcus grandis?  

NLE Websites -- All DOE Office Websites (Extended Search)

radiation-resistant radiation-resistant bacterium Deinococcus grandis? A fifth of the United States' electricity is generated from nuclear power, which can also be used for medical procedures and other applications. The radioactive waste generated by nuclear reactors, hospitals and universities need to be disposed of in specially selected sites. Deinococcus bacteria have the capacity to add electrons to a variety of metals, including uranium, chromium, mercury, technetium, iron and manganese. Due to this unique characteristic, this group of extremely radiation-resistant bacteria has been considered as a prospective candidate to help clean up radioactive waste sites. However, many Deinococcus bacteria require oxygen, which is a problem considering most waste environments are anaerobic.

63

Effects of selected thermophilic microorganisms on crude oils at elevated temperatures and pressures. Final report  

Science Conference Proceedings (OSTI)

During the past several years, a considerable amount of work has been carried out showing that microbially enhanced oil recovery (MEOR) is promising and the resulting biotechnology may be deliverable. At the Brookhaven National Laboratory (BNL), systematic studies have been conducted which dealt with the effects of thermophilic and thermoadapted bacteria on the chemical and physical properties of selected types of crude oils at elevated temperatures and pressures. Particular attention was paid to heavy crude oils from Venezuela, California, Alabama, Arkansas, Wyoming, Alaska, and other oil producing areas. Current studies indicate that during the biotreatment several chemical and physical properties of crude oils are affected. The oils are (1) emulsified; (2) acidified; (3) there is a qualitative and quantitative change in light and heavy fractions of the crudes; (4) there are chemical changes in fractions containing sulfur compounds; (5) there is an apparent reduction in the concentration of trace metals; (6) the qualitative and quantitative changes appear to be microbial species dependent; and (7) there is a distinction between {open_quotes}biodegraded{close_quotes} and {open_quotes}biotreated{close_quotes} oils. Preliminary results indicate the introduced microorganisms may become the dominant species in the bioconversion of oils. These studies also indicate the biochemical interactions between crude oils and microorganisms follow distinct trends, characterized by a group of chemical markers. Core-flooding experiments have shown significant additional crude oil recoveries are achievable with thermophilic microorganisms at elevated temperatures similar to those found in oil reservoirs. In addition, the biochemical treatment of crude oils has technological applications in downstream processing of crude oils such as in upgrading of low grade oils and the production of hydrocarbon based detergents.

Premuzic, E.T.; Lin, M.S.

1995-07-01T23:59:59.000Z

64

Thermophilic Thermotoga maritima ribose-5-phosphate isomerase RpiB: Optimized heat treatment purification and basic characterization  

NLE Websites -- All DOE Office Websites (Extended Search)

Thermophilic Thermophilic Thermotoga maritima ribose-5-phosphate isomerase RpiB: Optimized heat treatment purification and basic characterization Fangfang Sun a , Xiao-Zhou Zhang a,b , Suwan Myung a,c , Y.-H. Percival Zhang a,b,c,d,⇑ a Biological Systems Engineering Department, 304 Seitz Hall, Virginia Tech, Blacksburg, VA 24061, USA b Gate Fuels Inc., 3107 Alice Drive, Blacksburg, VA 24060, USA c Institute for Critical Technology and Applied Science (ICTAS), Virginia Tech, Blacksburg, VA 24061, USA d DOE BioEnergy Science Center (BESC), Oak Ridge, TN 37831, USA a r t i c l e i n f o Article history: Received 27 December 2011 and in revised form 26 January 2012 Available online 8 February 2012 Keywords: Biofuel Cascade enzyme factories Heat treatment purification Pentose phosphate isomerase Ribose-5-phosphate isomerase Thermoenzyme a b s t r a c t The open reading frame TM1080 from Thermotoga

65

High rate mesophilic, thermophilic, and temperature phased anaerobic digestion of waste activated sludge: A pilot scale study  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer High temperatures were tested in single and two-stage anaerobic digestion of waste activated sludge. Black-Right-Pointing-Pointer The increased temperature demonstrated the possibility of improving typical yields of the conventional mesophilic process. Black-Right-Pointing-Pointer The temperature phased anaerobic digestion process (65 + 55 Degree-Sign C) showed the best performances with yields of 0.49 m{sup 3}/kgVS{sub fed}. Black-Right-Pointing-Pointer Ammonia and phosphate released from solids destruction determined the precipitation of struvite in the reactor. - Abstract: The paper reports the findings of a two-year pilot scale experimental trial for the mesophilic (35 Degree-Sign C), thermophilic (55 Degree-Sign C) and temperature phased (65 + 55 Degree-Sign C) anaerobic digestion of waste activated sludge. During the mesophilic and thermophilic runs, the reactor operated at an organic loading rate of 2.2 kgVS/m{sup 3}d and a hydraulic retention time of 20 days. In the temperature phased run, the first reactor operated at an organic loading rate of 15 kgVS/m{sup 3}d and a hydraulic retention time of 2 days while the second reactor operated at an organic loading rate of 2.2 kgVS/m{sup 3}d and a hydraulic retention time of 18 days (20 days for the whole temperature phased system). The performance of the reactor improved with increases in temperature. The COD removal increased from 35% in mesophilic conditions, to 45% in thermophilic conditions, and 55% in the two stage temperature phased system. As a consequence, the specific biogas production increased from 0.33 to 0.45 and to 0.49 m{sup 3}/kgVS{sub fed} at 35, 55, and 65 + 55 Degree-Sign C, respectively. The extreme thermophilic reactor working at 65 Degree-Sign C showed a high hydrolytic capability and a specific yield of 0.33 gCOD (soluble) per gVS{sub fed}. The effluent of the extreme thermophilic reactor showed an average concentration of soluble COD and volatile fatty acids of 20 and 9 g/l, respectively. Acetic and propionic acids were the main compounds found in the acids mixture. Because of the improved digestion efficiency, organic nitrogen and phosphorus were solubilised in the bulk. Their concentration, however, did not increase as expected because of the formation of salts of hydroxyapatite and struvite inside the reactor.

Bolzonella, David, E-mail: david.bolzonella@univr.it [University of Verona, Department of Biotechnology, Strada Le Grazie, 15, 37134 Verona (Italy); Cavinato, Cristina, E-mail: cavinato@unive.it [University of Venice, Department of Environmental Sciences, Computer Science and Statistics, Dorsoduro 2137, 30123 Venice (Italy); Fatone, Francesco, E-mail: francesco.fatone@univr.it [University of Verona, Department of Biotechnology, Strada Le Grazie, 15, 37134 Verona (Italy); Pavan, Paolo, E-mail: pavan@unive.it [University of Venice, Department of Environmental Sciences, Computer Science and Statistics, Dorsoduro 2137, 30123 Venice (Italy); Cecchi, Franco, E-mail: franco.cecchi@univr.it [University of Verona, Department of Biotechnology, Strada Le Grazie, 15, 37134 Verona (Italy)

2012-06-15T23:59:59.000Z

66

Thermophilic α-glucan phosphorylase from Clostridium thermocellum: Cloning, characterization and enhanced thermostability  

NLE Websites -- All DOE Office Websites (Extended Search)

Molecular Molecular Catalysis B: Enzymatic 65 (2010) 110-116 Contents lists available at ScienceDirect Journal of Molecular Catalysis B: Enzymatic j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / m o l c a t b Thermophilic ␣-glucan phosphorylase from Clostridium thermocellum: Cloning, characterization and enhanced thermostability Xinhao Ye a , Joe Rollin a , Yi-Heng Percival Zhang a,b,c,∗ a Biological Systems Engineering Department, Virginia Polytechnic Institute and State University, 210-A Seitz Hall, Blacksburg, VA 24061, USA b Institute for Critical Technology and Applied Science (ICTAS), Virginia Polytechnic Institute and State University, 210-A Seitz Hall, Blacksburg, VA 24061, USA c DOE Bioenergy Science Center, Oak Ridge, TN 37831, USA a r t i c l e i n f o Article history: Available online 25 January 2010 Keywords: ␣-Glucan phosphorylase Biocatalysis Building

67

A plant growth-promoting bacterium that decreases nickel toxicity in seedlings  

SciTech Connect

A plant growth-promoting bacterium, Kluyvera ascorbata SUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni{sup 2+}, Pb{sup 2+}, Zn{sup 2+}, and CrO{sub 4}{sup {minus}}, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity. In addition, protection by the bacterium against nickel toxicity was evident in pot experiments with canola and tomato seeds. The presence of K. ascorbata SUD165 had no measurable influence on the amount of nickel accumulated per milligram (dry weight) of either roots or shoots of canola plants. Therefore, the bacterial plant growth-promoting effect in the presence of nickel was probably not attributable to the reduction of nickel uptake by seedlings. Rather, it may reflect the ability of the bacterium to lower the level of stress ethylene induced by the nickel.

Burd, G.I.; Dixon, D.G.; Glick, B.R. [Univ. of Waterloo, Ontario (Canada). Dept. of Biology

1998-10-01T23:59:59.000Z

68

Microsoft Word - _FINAL_JB246-09_AT_032609.doc  

NLE Websites -- All DOE Office Websites (Extended Search)

J. Bacteriol. J. Bacteriol. (Revised 03/26/09: JB256-09) Genome Announcement Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725 Irina A. Kataeva 1,4 , Sung-Jae Yang 1,4 , Phuongan Dam 1,3,4 , Farris L Poole II 1 , Yanbin Yin 1,3,4 , Fengfeng Zhou 1,3,4 , Wen-chi Chou 1,3,4 , Ying Xu 1,3,4 , Lynne Goodwin 6 , David R. Sims 6 , John C. Detter 6 , Loren J. Hauser 5 , Janet Westpheling 2,4 and Michael W. W. Adams 1,4 * 1 Department of Biochemistry and Molecular Biology, 2 Department of Genetics and 3 Institute of Bioinformatics, University of Georgia, GA 30602; 4 BioEnergy Science Center and 5 Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831;

69

Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGAT)  

SciTech Connect

Anaerobaculum mobile Menes and Muxi 2002 is one of three described species of the genus Anaerobaculum, family Synergistaceae, phylum Synergistetes. This anaerobic and motile bac- terium ferments a range of carbohydrates and mono- and dicarboxylic acids with acetate, hy- drogen and CO2 as end products. A. mobile NGAT is the first member of the genus Anaerobaculum and the sixth member of the phylum Synergistetes with a completely se- quenced genome. Here we describe the features of this bacterium, together with the com- plete genome sequence, and annotation. The 2,160,700 bp long single replicon genome with its 2,053 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Stackebrandt, Erko [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Held, Brittany [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

2013-01-01T23:59:59.000Z

70

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1  

Science Conference Proceedings (OSTI)

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

2011-01-01T23:59:59.000Z

71

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1  

SciTech Connect

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

Xie, Gary [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL

2011-01-01T23:59:59.000Z

72

In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)  

Science Conference Proceedings (OSTI)

Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, Calif

Mosier, Annika [Stanford University

2012-03-22T23:59:59.000Z

73

Dry-thermophilic anaerobic digestion of organic fraction of municipal solid waste: Methane production modeling  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer Methane generation may be modeled by means of modified product generation model of Romero Garcia (1991). Black-Right-Pointing-Pointer Organic matter content and particle size influence the kinetic parameters. Black-Right-Pointing-Pointer Higher organic matter content and lower particle size enhance the biomethanization. - Abstract: The influence of particle size and organic matter content of organic fraction of municipal solid waste (OFMSW) in the overall kinetics of dry (30% total solids) thermophilic (55 Degree-Sign C) anaerobic digestion have been studied in a semi-continuous stirred tank reactor (SSTR). Two types of wastes were used: synthetic OFMSW (average particle size of 1 mm; 0.71 g Volatile Solids/g waste), and OFMSW coming from a composting full scale plant (average particle size of 30 mm; 0.16 g Volatile Solids/g waste). A modification of a widely-validated product-generation kinetic model has been proposed. Results obtained from the modified-model parameterization at steady-state (that include new kinetic parameters as K, Y{sub pMAX} and {theta}{sub MIN}) indicate that the features of the feedstock strongly influence the kinetics of the process. The overall specific growth rate of microorganisms ({mu}{sub max}) with synthetic OFMSW is 43% higher compared to OFMSW coming from a composting full scale plant: 0.238 d{sup -1} (K = 1.391 d{sup -1}; Y{sub pMAX} = 1.167 L CH{sub 4}/gDOC{sub c}; {theta}{sub MIN} = 7.924 days) vs. 0.135 d{sup -1} (K = 1.282 d{sup -1}; Y{sub pMAX} = 1.150 L CH{sub 4}/gDOC{sub c}; {theta}{sub MIN} = 9.997 days) respectively. Finally, it could be emphasized that the validation of proposed modified-model has been performed successfully by means of the simulation of non-steady state data for the different SRTs tested with each waste.

Fdez-Gueelfo, L.A., E-mail: alberto.fdezguelfo@uca.es [Department of Chemical Engineering and Food Technology, Faculty of Science, University of Cadiz, 11510 Puerto Real, Cadiz (Spain); Alvarez-Gallego, C. [Department of Chemical Engineering and Food Technology, Faculty of Science, University of Cadiz, 11510 Puerto Real, Cadiz (Spain); Sales, D. [Department of Environmental Technologies, Faculty of Marine and Environmental Sciences, University of Cadiz, 11510 Puerto Real, Cadiz (Spain); Romero Garcia, L.I. [Department of Chemical Engineering and Food Technology, Faculty of Science, University of Cadiz, 11510 Puerto Real, Cadiz (Spain)

2012-03-15T23:59:59.000Z

74

The Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132 as a Model for Understanding Bacterial Mercury  

E-Print Network (OSTI)

Bacterial Mercury Methylation Contact: Cynthia Gilmour (gilmourc@si.edu, 443-482-2498) DOE/Office of Science Contact: Cynthia Gilmour (gilmourc@si.edu, 443-482-2498) DOE/Office of Science/Biological & Environmental/Biological & Environmental Research ·The ORNL Mercury Science Focus Area is developing the Hg-methylating bacterium

75

The primary structure of cytochrome c-554 from the green photosynthetic bacterium Chloroflexus aurantiacus  

Science Conference Proceedings (OSTI)

The complete nucleotide sequence of the cytochrome c-554 gene from the green photosynthetic bacterium Chloroflexus aurantiacus has been determined. The derived amino acid sequence showed that the cytochrome precursor protein consists of 414 residues and contains 4-Cys-X-X-Cys-His- heme binding motifs. The only regions of the cytochrome c-554 sequence that were found to be significantly similar to the sequences of cytochromes from other organisms were the heme binding sites. The highest similarity was found with the heme binding segments in the four-heme reaction center cytochrome subunit from the purple photosynthetic bacterium Rhodopseudomonas viridis. The importance of this similarity for the evolutionary relationship between Chloroflexus and the purple bacteria is discussed.

Dracheva, S.; Williams, J.C.; Blankenship, R.E. (Arizona State Univ., Tempe (United States)); Van Driessche, G.; Van Beeumen, J.J. (State Univ., Ghent (Belgium))

1991-12-03T23:59:59.000Z

76

Response to Comments on "A Bacterium That Can Grow Using Arsenic Instead of Phosphorus"  

SciTech Connect

Concerns have been raised about our recent study describing a bacterium that can grow using arsenic (As) instead of phosphorus (P). Our data suggested that As could act as a substitute for P in major biomolecules in this organism. Although the issues raised are of investigative interest, we contend that they do not invalidate our conclusions. We argue that while no single line of evidence we presented was sufficient to support our interpretation of the data, taken as an entire dataset we find no plausible alternative to our conclusions. Here we reply to the critiques and provide additional arguments supporting the assessment of the data we reported.

Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

2011-03-07T23:59:59.000Z

77

A bacterium that can grow by using arsenic instead of phosphorus  

DOE Green Energy (OSTI)

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

2010-11-01T23:59:59.000Z

78

Tumor Necrosis Factor Receptor p55 Is Essential for Intrahepatic Granuloma Formation and Hepatocellular Apoptosis in a Murine Model of Bacterium-Induced Fulminant Hepatitis  

E-Print Network (OSTI)

Tumor necrosis factor receptor p55 is essential for intrahepatic granuloma formation and hepatocellular apoptosis in a murine model of bacterium-induced fulminant hepatitis.

H Tsuji; A Harada; N Mukaida; Y Nakanuma; H Bluethmann; K Yamakawa; S I Nakamura; K I Kobayashi; Hirokazu Tsuji; Akihisa Harada; Naofumi Mukaida; Yasuni Nakanuma; Horst Bluethmann; Shuichi Kaneko; Kiyotaka Yamakawa; Shin-ichi Nakamura

1996-01-01T23:59:59.000Z

79

Microbial who-done-it for biofuels  

NLE Websites -- All DOE Office Websites (Extended Search)

with both JBEI and Lawrence Livermore National Laboratory (LLNL). Working with a compost-derived consortium of thermophillic bacterium adapted to grow on switchgrass, a...

80

Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638  

SciTech Connect

Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa x deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar as an energy feedstock on marginal, non-agricultural soils using endophytic bacteria as growth promoting agents. Poplar is considered as the model tree species for the production of lignocellulosic biomass destined for biofuel production. The plant growth promoting endophytic bacterium Enterobacter sp. 638 can improve the growth of poplar on marginal soils by as much as 40%. This prompted us to sequence the genome of this strain and, via comparative genomics, identify functions essential for the successful colonization and endophytic association with its poplar host. Analysis of the genome sequence, combined with metabolite analysis and quantitative PCR, pointed to a remarkable interaction between Enterobacter sp. 638 and its poplar host with the endophyte responsible for the production of a phytohormone, and a precursor for another that poplar is unable to synthesize, and where the production of the plant growth promoting compounds depended on the presence of plant synthesized compounds, such as sucrose, in the growth medium. Our results provide the basis to better understanding the synergistic interactions between poplar and Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar on marginal, non-agricultural soils using endophytic bacteria such as Enterobacter sp. 638 as growth promoting agents.

Taghavi, S.; van der Lelie, D.; Hoffman, A.; Zhang, Y.-B.; Walla, M. D.; Vangronsveld, J.; Newman, L.; Monchy, S.

2010-05-13T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
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81

Enzyme inactivation by ethanol and development of a kinetic model for thermophilic simultaneous saccharification and fermentation at 50C with Thermoanaerobacterium saccharolyticum ALK2  

NLE Websites -- All DOE Office Websites (Extended Search)

Enzyme Enzyme Inactivation by Ethanol and Development of a Kinetic Model for Thermophilic Simultaneous Saccharification and Fermentation at 50 -C with Thermoanaerobacterium saccharolyticum ALK2 Kara K. Podkaminer, 1 Xiongjun Shao, 1 David A. Hogsett, 2 Lee R. Lynd 1 1 Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; telephone: 603-646-2231; fax: 603-646-2277; e-mail: lee.lynd@dartmouth.edu 2 Mascoma Corporation, Lebanon, New Hampshire Received 6 August 2010; revision received 16 November 2010; accepted 14 December 2010 Published online 29 December 2010 in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/bit.23050 ABSTRACT: Studies were undertaken to understand phe- nomena operative during simultaneous saccharification and fermentation (SSF) of a model cellulosic substrate (Avicel) at 508C with enzymatic hydrolysis mediated

82

Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T)  

SciTech Connect

Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262 T forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na + ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na + ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Mwirichia, Romano [Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

2011-01-01T23:59:59.000Z

83

Photocatabolism of aromatic compounds by the phototrophic purple bacterium Rhodomicrobium vannielii  

Science Conference Proceedings (OSTI)

The phototrophic purple non-sulfur bacterium Thodomicrobium vannielii grew phototrophically (illuminated anaerobic conditions) on a variety of aromatic compounds (in the presence of CO{sub 2}). Benzoate was universally photocatabolized by all five strains of R. vannielii examined, and benzyl alcohol was photocatabolized by four of the five strains. Catabolism of benzyl alcohol by phototrophic bacteria has not been previously reported. Other aromatic substrates supporting reasonably good growth of R. vannielii strains were the methozylated benzoate derivatives vanillate (4-hydroxy-3-methoxybenzoate) and syringate (4-hydroxy-3,5-dimethoxybenzoate). However, catabolism of vanillate and syringate led to significant inhibition of bacteriochlorophyll synthesis in R. vannielii cells, eventually causing cultures to cease growing. No such effect on photopigment synthesis in cells grown on benzoate or benzyl alcohol was observed. Along with a handful of other species of anoxygenic phototrophic bacteria, the ability of the species R. vannielii to photocatabolize aromatic compounds indicates that this organism may also be ecologically significant as a consumer of aromatic derivatives in illuminated anaerobic habitats in nature.

Wright, G.E.; Madigan, M.T. (Southern Illinois Univ., Carbondale (USA))

1991-07-01T23:59:59.000Z

84

Efficient degradation of lignocellulosic plant biomass without pretreatment by the 9 thermophilic anaerobe, Anaerocellum thermophilum DSM 6725  

SciTech Connect

Very few cultivated microorganisms can degrade lignocellulosic biomass without chemical pretreatment. We show here that 'Anaerocellum thermophilum' DSM 6725, an anaerobic bacterium that grows optimally at 75 C, efficiently utilizes various types of untreated plant biomass, as well as crystalline cellulose and xylan. These include hardwoods such as poplar, low-lignin grasses such as napier and Bermuda grasses, and high-lignin grasses such as switchgrass. The organism did not utilize only the soluble fraction of the untreated biomass, since insoluble plant biomass (as well as cellulose and xylan) obtained after washing at 75 C for 18 h also served as a growth substrate. The predominant end products from all growth substrates were hydrogen, acetate, and lactate. Glucose and cellobiose (on crystalline cellulose) and xylose and xylobiose (on xylan) also accumulated in the growth media during growth on the defined substrates but not during growth on the plant biomass. A. thermophilum DSM 6725 grew well on first- and second-spent biomass derived from poplar and switchgrass, where spent biomass is defined as the insoluble growth substrate recovered after the organism has reached late stationary phase. No evidence was found for the direct attachment of A. thermophilum DSM 6725 to the plant biomass. This organism differs from the closely related strain A. thermophilum Z-1320 in its ability to grow on xylose and pectin. Caldicellulosiruptor saccharolyticus DSM 8903 (optimum growth temperature, 70 C), a close relative of A. thermophilum DSM 6725, grew well on switchgrass but not on poplar, indicating a significant difference in the biomass-degrading abilities of these two otherwise very similar organisms.

Yang, Sung-Jae [University of Georgia, Athens, GA; Kataeva, Irina [University of Georgia, Athens, GA; Hamilton-Brehm, Scott [ORNL; Engle, Nancy L [ORNL; Tschaplinski, Timothy J [ORNL; Doeppke, Crissa [National Renewable Energy Laboratory (NREL); Davis, Dr. Mark F. [National Renewable Energy Laboratory (NREL); Westpheling, Janet [University of Georgia, Athens, GA; Adams, Michael W. W. [University of Georgia, Athens, GA

2009-01-01T23:59:59.000Z

85

Thermophilic Methanol Utilization by  

E-Print Network (OSTI)

: acetate ADH: alcohol dehydrogenase Bio-FGD: biological flue-gas desulfurization COD: chemical oxygen desulfurization In sub-section 1.1.1, sulfur dioxide emission and general aspects of the flue gas desulfurization heaters, metallurgical operations, roasting and sintering, coke oven plants, processing of titanium

Groningen, Rijksuniversiteit

86

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations  

Science Conference Proceedings (OSTI)

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

Bollmann, Annette [Miami University, Oxford, OH; Sedlacek, Christopher J [Miami University, Oxford, OH; Laanbroek, Hendrikus J [Netherlands Institute of Ecology (NIOO-KNAW); Suwa, Yuichi [Chuo University, Tokyo, Japan; Stein, Lisa Y [University of California, Riverside; Klotz, Martin G [University of Louisville, Louisville; Arp, D J [Oregon State University; Sayavedra-Soto, LA [Oregon State University; Lu, Megan [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL)

2013-01-01T23:59:59.000Z

87

Thermoanaerobacterium aotearoense sp. nov., a slightly acidophilic, anaerobic thermophile isolated from various hot springs in New Zealand, and emendation of the genus Thermoanaerobacterium  

Science Conference Proceedings (OSTI)

Six moderately acidophilic, thermophilic bacterial strains with similar properties were isolated from geothermally heated water and sediment samples collected in New Zealand. These Gram stain-negative but Gram type-positive, rod-shaped bacteria formed oval terminal endospores. The cells were peritrichously flagellated and exhibited tumbling motility. At 60{degrees}C the pH range for growth was 3.8 to 6.8, and the optimum pH was 5.2 when the organisms were grown with xylose. At pH 5.2 the temperature range for growth was 35 to 66{degrees}C, and the optimum temperature was 60 to 63{degrees}C. The fermentation products from flucose or xylose were ethanol, acetate, lactate, CO{sub 2}, and H{sub 2}. The DNA G+C content was 34.5 to 35 mol%. On the basis of properties such as formation of elemental sulfur from thiosulfate, growth at acidic pH values at elevated temperatures, and the results of a 16S rRNA sequence comparison performed with previously validly published species belonging to the genus Thermoanaerobacterium, we propose that strain JW/SL-NZ613{sup T} (T = type strain) and five similar strains isolated from samples collected in New Zealand represent a new species, Thermoanaerobacterium aotearoense. Strain JW/SL-NZ613{sup T} (= DSM 10170) is the type strain of this species.

Shu-Ying Liu; Wiegel, J. [Univ. of Georiga, Athens, GA (United States); Rainey, F.A. [Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig (Germany)] [and others

1996-04-01T23:59:59.000Z

88

Deletion of the Cel48S cellulase from Clostridium thermocellum  

Science Conference Proceedings (OSTI)

Clostridium thermocellum is a thermophilic anaerobic bacterium that rapidly solubilizes cellulose with the aid of a multienzyme cellulosome complex. Creation of knockout mutants for Cel48S (also known as CelS, SS, and S8), the most abundant cellulosome subunit, was undertaken to gain insight into its role in enzymatic and microbial cellulose solubilization. Cultures of the Cel48S deletion mutant (S mutant) were able to completely solubilize 10 g/L crystalline cellulose. The cellulose hydrolysis rate of the S mutant strain was 60% lower than the parent strain, with the S mutant strain also exhibiting a 40% reduction in cell yield. The cellulosome produced by the S mutant strain was purified by affinity digestion, characterized enzymatically, and found to have a 35% lower specific activity on Avicel. The composition of the purified cellulosome was analyzed by tandem mass spectrometry with APEX quantification and no significant changes in abundance were observed in any of the major (>1% of cellulosomal protein) enzymatic subunits. Although most cellulolytic bacteria have one family 48 cellulase, C. thermocellum has two, Cel48S and Cel48Y. Cellulose solubilization by a Cel48S and Cel48Y double knockout was essentially the same as that of the Cel48S single knockout. Our results indicate that solubilization of crystalline cellulose by C. thermocellum can proceed to completion without expression of a family 48 cellulase.

Olson, Daniel G [Mascoma Corporation; Tripathi, Shital A. [Mascoma Corporation; Giannone, Richard J [ORNL; Lo, Jonathan [Dartmouth College; Caiazza, Nicky [ORNL; Hogsett, David A [ORNL; Hettich, Robert {Bob} L [ORNL; Guss, Adam M [ORNL; Dubrovsky, Genia [Dartmouth College; Lynd, Lee R [ORNL

2010-01-01T23:59:59.000Z

89

High-Quality Draft Genome Sequence of the Opitutaceae Bacterium Strain TAV1, a Symbiont of the Wood-Feeding Termite Reticulitermes flavipes  

Science Conference Proceedings (OSTI)

Microbial communities in the termite hindgut are essential for degrading plant material. We present the high-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, the first member of the phylum Verrucomicrobia to be isolated from wood-feeding termites. The genomic analysis reveals genes coding for lignocellulosic degradation and nitrogen fixation.

Isanapong, Jantiya [University of Texas, Arlington; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, James [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Rodrigues, Jorge L.M. [University of Texas, Arlington

2012-01-01T23:59:59.000Z

90

Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1T), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Treponema stenostrepta comb. nov., and Treponema zuelzerae comb. nov., and emendation of the genus Tr  

SciTech Connect

Spirochaeta caldaria Pohlschroeder et al. 1995 is an obligately anaerobic, spiral-shaped bac- terium that is motile via periplasmic flagella. The type strain, H1T, was isolated in 1990 from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA, and is of in- terest because it enhances the degradation of cellulose when grown in co-culture with Clos- tridium thermocellum. Here we provide a taxonomic re-evaluation for S. caldaria based on phylogenetic analyses of 16S rRNA sequences and whole genomes, and propose the reclassi- fication of S. caldaria and two other Spirochaeta species as members of the emended genus Treponema. Whereas genera such as Borrelia and Sphaerochaeta possess well-distinguished genomic features related to their divergent lifestyles, the physiological and functional ge- nomic characteristics of Spirochaeta and Treponema appear to be intermixed and are of little taxonomic value. The 3,239,340 bp long genome of strain H1T with its 2,869 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Scheuner, Carmen [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Han, Cliff [Los Alamos National Laboratory (LANL); Lu, Megan [Los Alamos National Laboratory (LANL); Misra, Monica [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2013-01-01T23:59:59.000Z

91

NlST Technical Note 1353 Trapped Ions and Laser Cooling 111  

E-Print Network (OSTI)

. Alicyclobacillus vulcanalis sp. nov., a new thermophilic, acidophilic bacterium isolated from Coso Hot Springs evapotranspiration captured by seasonally pumping wells in river valleys. Journal of Hydrology 318: 334-347. · Wen, F

92

Available Technologies: Thermophilic Endoglucanase Enzymes ...  

... reaction that combines cellulose hydrolysis by the Thermotoga maritima enzyme with pretreatment conditions such as steam expansion or ionic ...

93

Novel Thermophilic Cellobiohydrolase - Energy Innovation ...  

Therefore, the JBEI technology opens the possibility of one pot saccharification of lignocellulosic biomass. In addition, the JBEI technology is ...

94

Thermophilic Endoglucanase Enzymes Engineered for ...  

Hydrolysis of pretreated biomass for biofuels production; Paper recycling and pulp processing for paper manufacturing;

95

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June  

NLE Websites -- All DOE Office Websites (Extended Search)

0, 0, p. 3545-3553 Vol. 76, No. 11 0099-2240/10/$12.00 doi:10.1128/AEM.02689-09 Copyright © 2010, American Society for Microbiology. All Rights Reserved. Diversity of Bacteria and Glycosyl Hydrolase Family 48 Genes in Cellulolytic Consortia Enriched from Thermophilic Biocompost ᰔ Javier A. Izquierdo, 1,2 Maria V. Sizova, 1,2 † and Lee R. Lynd 1,2 * Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 Received 4 November 2009/Accepted 30 March 2010 The enrichment from nature of novel microbial communities with high cellulolytic activity is useful in the identification of novel organisms and novel functions that enhance the fundamental understanding of micro- bial cellulose degradation. In this work we identify predominant organisms in three cellulolytic

96

MICROBIAL FERMENTATION OF ABUNDANT BIOPOLYMERS: CELLULOSE AND CHITIN  

DOE Green Energy (OSTI)

Our research has dealt with seven major areas of investigation: i) characterization of cellulolytic members of microbial consortia, with special attention recently given to Clostridium phytofermentans, a bacterium that decomposes cellulose and produces uncommonly large amounts of ethanol, ii) investigations of the chitinase system of Cellulomonas uda; including the purification and characterization of ChiA, the major component of this enzyme system, iii) molecular cloning, sequence and structural analysis of the gene that encodes ChiA in C. uda, iv) biofilm formation by C. uda on nutritive surfaces, v) investigations of the effects of humic substances on cellulose degradation by anaerobic cellulolytic microbes, vi) studies of nitrogen metabolism in cellulolytic anaerobes, and vii) understanding the molecular architecture of the multicomplex cellulase-xylanase system of Clostridium papyrosolvens. Also, progress toward completing the research of more recent projects is briefly summarized. Major accomplishments include: 1. Characterization of Clostridium phytofermentans, a cellulose-fermenting, ethanol-producing bacterium from forest soil. The characterization of a new cellulolytic species isolated from a cellulose-decomposing microbial consortium from forest soil was completed. This bacterium is remarkable for the high concentrations of ethanol produced during cellulose fermentation, typically more than twice the concentration produced by other species of cellulolytic clostridia. 2. Examination of the use of chitin as a source of carbon and nitrogen by cellulolytic microbes. We discovered that many cellulolytic anaerobes and facultative aerobes are able to use chitin as a source of both carbon and nitrogen. This major discovery expands our understanding of the biology of cellulose-fermenting bacteria and may lead to new applications for these microbes. 3. Comparative studies of the cellulase and chitinase systems of Cellulomonas uda. Results of these studies indicate that the chitinase and cellulase systems of this bacterium are distinct in terms of the proteins involved and the regulation of their production. 4. Characterization of the chitinase system of C. uda. A 70,000-Mr endochitinase, designated ChiA, was purified from C. uda culture supernatant fluids and characterized. 5. Analysis of chiA, which codes for the major enzymatic component of the chitinase system of C. uda. The gene encoding the endochitinase ChiA in C. uda was cloned, its complete nucleotide sequence was determined and its implications were investigated. 6. Formation of biofilms by C. uda on cellulose and chitin. Microscopic observations indicated that, under conditions of nitrogen limitation, C. uda cells grew as a biofilm attached tightly to the surface of cellulose or chitin. 7. Development of tools for a genetic approach to studies of cellulose fermentation by cellulolytic clostridia. We have explored the potential of various techniques, and obtained evidence indicating that Tn916 mutagenesis may be particularly effective in this regard. As part of this research, we identified the presence of a plasmid in one strain, which was cloned, sequenced, and analyzed for its utility in the development of vectors for genetic studies. 8. Effects of humic substances on cellulose degradation by anaerobic cellulolytic microbes. We determined that humic substances play an important role in the anaerobic cellulose decomposition and in the physiology of cellulose-fermenting soil bacteria. 9. Nitrogenases of cellulolytic clostridia. We described a nitrogenase gene from a cellulolytic clostridium and presented evidence, based on sequence analyses and conserved gene order, for lateral gene transfer between this bacterium and a methanogenic archaeon. 10. Characterization of Clostridium hungatei, a new N2-fixing cellulolytic species isolated from a methanogenic consortium from soil. 11. Understanding the molecular architecture of the multicomplex cellulase-xylanase system of Clostridium papyrosolvens. We discovered that C. papyrosolvens produces a multiprotein, multicom

Leschine, Susan

2009-10-31T23:59:59.000Z

97

The Genome Sequence of Psychrobacter arcticus 273-4, a Psychroactive Siberian Permafrost Bacterium, Reveals Mechanisms for Adaptation to Low-Temperature Growth  

Science Conference Proceedings (OSTI)

Psychrobacter arcticus strain 273-4, which grows at temperatures as low as -10 degrees C, is the first cold-adapted bacterium from a terrestrial environment whose genome was sequenced. Analysis of the 2.65-Mb genome suggested that some of the strategies employed by P. arcticus 273-4 for survival under cold and stress conditions are changes in membrane composition, synthesis of cold shock proteins, and the use of acetate as an energy source. Comparative genome analysis indicated that in a significant portion of the P. arcticus proteome there is reduced use of the acidic amino acids and proline and arginine, which is consistent with increased protein flexibility at low temperatures. Differential amino acid usage occurred in all gene categories, but it was more common in gene categories essential for cell growth and reproduction, suggesting that P. arcticus evolved to grow at low temperatures. Amino acid adaptations and the gene content likely evolved in response to the long-term freezing temperatures (-10 degrees C to -12 degrees C) of the Kolyma (Siberia) permafrost soil from which this strain was isolated. Intracellular water likely does not freeze at these in situ temperatures, which allows P. arcticus to live at subzero temperatures.

Ayala-del-Rio, Hector L. [Michigan State University, East Lansing; Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Grzymski, Joseph J. [Desert Research Institute, Reno, NV; Ponder, Monica [Michigan State University, East Lansing; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Bergholz, Peter [Michigan State University, East Lansing; Bartolo, Genevive [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Bakermans, Corien [Michigan State University, East Lansing; Rodrigues, Debora [Michigan State University, East Lansing; Klappenbach, Joel [Michigan State University, East Lansing; Zarka, Dan [Michigan State University, East Lansing; Larimer, Frank W [ORNL; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Murray, Alison [Desert Research Institute, Reno, NV; Thomashow, Michael [Michigan State University, East Lansing; Tiedje, James M. [Michigan State University, East Lansing

2010-01-01T23:59:59.000Z

98

IMPACTS OF BIOFILM FORMATION ON CELLULOSE FERMENTATION  

Science Conference Proceedings (OSTI)

This project addressed four major areas of investigation: i) characterization of formation of Cellulomonas uda biofilms on cellulose; ii) characterization of Clostridium phytofermentans biofilm development; colonization of cellulose and its regulation; iii) characterization of Thermobifida fusca biofilm development; colonization of cellulose and its regulation; and iii) description of the architecture of mature C. uda, C. phytofermentans, and T. fusca biofilms. This research is aimed at advancing understanding of biofilm formation and other complex processes involved in the degradation of the abundant cellulosic biomass, and the biology of the microbes involved. Information obtained from these studies is invaluable in the development of practical applications, such as the single-step bioconversion of cellulose-containing residues to fuels and other bioproducts. Our results have clearly shown that cellulose-decomposing microbes rapidly colonize cellulose and form complex structures typical of biofilms. Furthermore, our observations suggest that, as cells multiply on nutritive surfaces during biofilms formation, dramatic cell morphological changes occur. We speculated that morphological changes, which involve a transition from rod-shaped cells to more rounded forms, might be more apparent in a filamentous microbe. In order to test this hypothesis, we included in our research a study of biofilm formation by T. fusca, a thermophilic cellulolytic actinomycete commonly found in compost. The cellulase system of T. fusca has been extensively detailed through the work of David Wilson and colleagues at Cornell, and also, genome sequence of a T. fusca strain has been determine by the DOE Joint Genome Institute. Thus, T. fusca is an excellent subject for studies of biofilm development and its potential impacts on cellulose degradation. We also completed a study of the chitinase system of C. uda. This work provided essential background information for understanding how C. uda colonizes and degrades insoluble substrates. Major accomplishments of the project include: • Development of media containing dialysis tubing (described by the manufacturer as “regenerated cellulose”) as sole carbon and energy source and a nutritive surface for the growth of cellulolytic bacteria, and development of various microscopic methods to image biofilms on dialysis tubing. • Demonstration that cultures of C. phytofermentans, an obligate anaerobe, C. uda, a facultative aerobe, and T. fusca, a filamentous aerobe, formed microbial communities on the surface of dialysis tubing, which possessed architectural features and functional characteristics typical of biofilms. • Demonstration that biofilm formation on the nutritive surface, cellulose, involves a complex developmental processes, including colonization of dialysis tubing, formation of cell clusters attached to the nutritive surface, cell morphological changes, formation of complex structures embedded in extracellular polymeric matrices, and dispersal of biofilm communities as the nutritive surface is degraded. • Determination of surface specificity and regulatory aspects of biofilm formation by C. phytofermentans, C. uda, and T. fusca. • Demonstration that biofilm formation by T. fusca forms an integral part of the life cycle of this filamentous cellulolytic bacterium, including studies on the role of mycelial pellet formation in the T. fusca life cycle and a comparison of mycelial pellets to surface-attached T. fusca biofilms. • Characterization of T. fusca biofilm EPS, including demonstration of a functional role for EPS constituents. • Correlation of T. fusca developmental life cycle and cellulase gene expression.

Leschine, Susan

2009-10-31T23:59:59.000Z

99

Thermophilic Biotrickling Filtration of Ethanol Vapors  

E-Print Network (OSTI)

helps control erosion, conserve moisture and reduce weed growth. It can be organic (compost, leaf mold

100

Thermophilic Cellulases Compatible with Ionic Liquid ...  

Potential for consolidated pretreatment and saccharification of lignocellulosic biomass; Applications and Industries. Deconstruction of biomass for ...

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101

Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1 T ), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta  

SciTech Connect

Spirochaeta coccoides Droege et al. 2006 is a member of the genus Spirochaeta Ehrenberg 1835, one of the oldest named genera within the Bacteria. S. coccoides is an obligately anaerobic, Gram-negative, non-motile, spherical bacterium that was isolated from the hindgut contents of the termite Neotermes castaneus. The species is of interest because it may play an important role in the digestion of breakdown products from cellulose and hemicellulose in the termite gut. Here we provide a taxonomic re-evaluation for strain SPN1{sup T}, and based on physiological and genomic characteristics, we propose its reclassification as a novel species in the genus Sphaerochaeta, a recently published sister group of the Spirochaeta. The 2,227,296 bp long genome of strain SPN1{sup T} with its 1,866 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Han, Cliff [Los Alamos National Laboratory (LANL); Scheuner, Carmen [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lu, Megan [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Gronow, Sabine [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

102

deb_pone.0062881 1..10  

NLE Websites -- All DOE Office Websites (Extended Search)

Construction Construction of a Stable Replicating Shuttle Vector for Caldicellulosiruptor Species: Use for Extending Genetic Methodologies to Other Members of This Genus Daehwan Chung 1,2 , Minseok Cha 1,2 , Joel Farkas 1,2¤ , Janet Westpheling 1,2 * 1 Department of Genetics, University of Georgia, Athens, Georgia, United States of America, 2 The BioEnergy Science Center, Department of Energy, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America Abstract The recalcitrance of plant biomass is the most important barrier to its economic conversion by microbes to products of interest. Thermophiles have special advantages for biomass conversion and members of the genus Caldicellulosiruptor are the most thermophilic cellulolytic microbes known. In this study, we report the construction of a replicating shuttle vector for Caldicellulosiruptor species based on

103

Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement  

NLE Websites -- All DOE Office Websites (Extended Search)

Overcoming Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement Daehwan Chung 1,2 , Joel Farkas 1,2 and Janet Westpheling 1,2* Abstract Background: Thermophilic microorganisms have special advantages for the conversion of plant biomass to fuels and chemicals. Members of the genus Caldicellulosiruptor are the most thermophilic cellulolytic bacteria known. They have the ability to grow on a variety of non-pretreated biomass substrates at or near ~80°C and hold promise for converting biomass to bioproducts in a single step. As for all such relatively uncharacterized organisms with desirable traits, the ability to genetically manipulate them is a prerequisite for making them useful. Metabolic engineering of pathways for product synthesis is relatively simple compared to engineering the ability to utilize

104

Available Technologies: Engineered Bacterium with Resistance ...  

Khudyakov, J.I., D’haeseleer, P.D., Borglin, S.E., DeAngelis, K.M., Woo, H., Lindquist, E.A., Hazen, T.C., Simmons, B.A., Thelan, M.P., ...

105

Enzyme stabilization by domain insertion into a thermophilic protein  

E-Print Network (OSTI)

as fermentation of inulin into bioethanol. The conventional method for enzyme stabilization involves mutagenesis and oligofructan, as well as fermentation into bioethanol (Pandey et al., 1999; Chi et al., 2009). The operating

Ostermeier, Marc

106

Identification and characterisation of hemicellulases from thermophilic Actinomycetes.  

E-Print Network (OSTI)

?? To ensure the sustainability of bioethanol production, major attention has been directed to develop feedstocks which provide an alternative to food-crop biomass. Lignocellulosic (LC)… (more)

Matthews, Lesley-Ann A

2010-01-01T23:59:59.000Z

107

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

E-Print Network (OSTI)

in Alaskan North Slope Oil Facilities Kathleen E. Duncan,in Alaskan North Slope oil production facilities. Title:in Alaskan North Slope Oil Facilities Authors: Kathleen E.

Duncan, Kathleen E.

2010-01-01T23:59:59.000Z

108

Thermophilic Gram-Positive Biocatalysts for Biomass Conversion to Ethanol  

DOE Green Energy (OSTI)

These new second generation biocatalysts have the potential to reduce the cost of SSF by minimizing the amount of fungal cellulases, a significant cost component in the use of biomass as a renewable resource for production of fuels and chemicals.

Shanmugam, K.T.; Ingram, L.O.; Maupin-Furlow, J.A.; Preston, J.F.; Aldrich, H.C.

2003-12-01T23:59:59.000Z

109

Microbial Ecology of Thermophilic Anaerobic Digestion. Final Report  

DOE R&D Accomplishments (OSTI)

This grant supported research on methanogenic archaea. The two major areas that were supported were conversion of acetic acid to methane and nitrogen fixation by Methanosarcina. Among the achievements of this research were the isolation of novel methanogenic cultures, elucidation of the pathways from acetate to methane, description of a specific DNA-binding complex in nitrogen fixing methanogens, and demonstration of an alternative nitrogenase in Methanosarcina.

Zinder, Stephen H.

2000-04-15T23:59:59.000Z

110

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

E-Print Network (OSTI)

ethane, propane or butane. Concentrations of metabolitesacid COO - CH 3 O H 3 C Butane (C 4 H 10 ) H 3 C CH 3 O - O

Duncan, Kathleen E.

2010-01-01T23:59:59.000Z

111

Kinetics of inactivation of indicator pathogens during thermophilic anaerobic digestion  

E-Print Network (OSTI)

in large amounts in coal and natural gas processing, petroleum industries, biogas production, and sewage

112

Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities  

E-Print Network (OSTI)

Synergistetes North Sea oil well sp. clone TCB169x (isolated from a North Sea oil well and described as a memberlienii Synergistes North Sea oil well Cas60314 (DQ071273)

Duncan, Kathleen E.

2010-01-01T23:59:59.000Z

113

Fermentation method producing ethanol  

DOE Patents (OSTI)

Ethanol is the major end product of an anaerobic, thermophilic fermentation process using a mutant strain of bacterium Clostridium thermosaccharolyticum. This organism is capable of converting hexose and pentose carbohydrates to ethanol, acetic and lactic acids. Mutants of Clostridium thermosaccharolyticum are capable of converting these substrates to ethanol in exceptionally high yield and with increased productivity. Both the mutant organism and the technique for its isolation are provided.

Wang, Daniel I. C. (Belmont, MA); Dalal, Rajen (Chicago, IL)

1986-01-01T23:59:59.000Z

114

Effect of Lignin Removal by Alkaline Peroxide Pretreatment on the Susceptibility of Corn Stover to Purified Cellulolytic and Xylanolytic Enzymes  

Science Conference Proceedings (OSTI)

Pretreatment of corn stover with alkaline peroxide (AP) at pH 11.5 resulted in reduction of lignin content in the residual solids as a function of increasing batch temperature. Scanning electron microscopy of these materials revealed notably more textured surfaces on the plant cell walls as a result of the delignifying pretreatment. As expected, digestion of the delignified samples with commercial cellulase preparations showed an inverse relationship between the content of lignin present in the residual solids after pretreatment and the extent of both glucan and xylan conversion achievable. Digestions with purified enzymes revealed that decreased lignin content in the pretreated solids did not significantly impact the extent of glucan conversion achievable by cellulases alone. Not until purified xylanolytic activities were included with the cellulases were significant improvements in glucan conversion realized. In addition, an inverse relationship was observed between lignin content after pretreatment and the extent of xylan conversion achievable in a 24-h period with the xylanolytic enzymes in the absence of the cellulases. This observation, coupled with the direct relationship between enzymatic xylan and glucan conversion observed in a number of cases, suggests that the presence of lignins may not directly occlude cellulose present in lignocelluloses but rather impact cellulase action indirectly by its association with xylan.

Selig, M. J.; Vinzant, T. B.; Himmel, M. E.; Decker, S. R.

2009-01-01T23:59:59.000Z

115

Bioconversion of plant biomass to ethanol. Final report, 15 December 1976-31 December 1978  

DOE Green Energy (OSTI)

Two approaches to ethanol production via thermophilic mixed culture fermentation of pretreated wood were investigated. The initial studies of wood biodelignification by Chrysosporium pruinosum and subsequent mixed culture fermentation to ethanol using a cellulolytic strain of sporocytophaga and a strain of Bacillus stearothermophilus proved to be premature for a development effort. Studies of the fermentation of SO/sub 2//steam-treated poplar by a mixed culture of C. thermocellum and C. thermosaccharolyticum were, however, technically and economically promising. Wood pretreatment to enhance microbial utilization, the microbiology and biochemistry of pure and mixed culture fermentation of cellulose by C. thermocellum and C. thermocellum and C. thermosaccharolyticum, and techniques for improving ethanol tolerance and yield were investigated. Considerable progress in overcoming the technical barriers to efficient ethanol production from wood have been demonstrated; however, additional studies and development work are required before technical feasibility can be established.

Brooks, R.E.; Su, T.M.; Brennan, M.J. Jr.; Frick, J.; Lynch, M.

1979-07-01T23:59:59.000Z

116

Caldicellulosiruptor Core and Pangenomes Reveal Determinants for  

Science Conference Proceedings (OSTI)

Extremely thermophilic bacteria of the genus Caldicellulosiruptor utilize carbohydrate components of plant cell walls, including cellulose and hemicellulose, facilitated by a diverse set of glycoside hydrolases (GHs). From a biofuel perspective, this capability is crucial for deconstruction of plant biomass into fermentable sugars. While all species from the genus grow on xylan and acidpretreated switchgrass, growth on crystalline cellulose is variable. The basis for this variability was examined using microbiological, genomic, and proteomic analyses of eight globally diverse Caldicellulosiruptor species. The open Caldicellulosiruptor pangenome (4,009 open reading frames [ORFs]) encodes 106 GHs, representing 43 GH families, but only 26 GHs from 17 families are included in the core (noncellulosic) genome (1,543 ORFs). Differentiating the strongly cellulolytic Caldicellulosiruptor species from the others is a specific genomic locus that encodes multidomain cellulases from GH families 9 and 48, which are associated with cellulose-binding modules. This locus also encodes a novel adhesin associated with type IV pili, which was identified in the exoproteome bound to crystalline cellulose. Taking into account the core genomes, pangenomes, and individual genomes, the ancestral Caldicellulosiruptor was likely cellulolytic and evolved, in some cases, into species that lost the ability to degrade crystalline cellulose while maintaining the capacity to hydrolyze amorphous cellulose and hemicellulose.

Blumer-Schuette, Sara E. [North Carolina State University; Giannone, Richard J [ORNL; Zurawski, Jeffrey V [North Carolina State University; Ozdemir, Inci [North Carolina State University; Ma, Qin [University of Georgia, Athens, GA; Yin, Yanbin [University of Georgia, Athens, GA; Xu, Ying [University of Georgia, Athens, GA; Kataeva, Irena [University of Georgia, Athens, GA; Poole, Farris [University of Georgia, Athens, GA; Adams, Michael W. W. [University of Georgia, Athens, GA; Hamilton-Brehm, Scott [ORNL; Elkins, James G [ORNL; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Cottingham, Robert W [ORNL; Hettich, Robert {Bob} L [ORNL; Kelly, Robert M [North Carolina State University

2012-01-01T23:59:59.000Z

117

November 19, 2011 1  

NLE Websites -- All DOE Office Websites (Extended Search)

9, 2011 1 9, 2011 1 2 S-layer homology (SLH) domain proteins Csac_0678 and Csac_2722 implicated in 3 plant polysaccharide deconstruction by the extremely thermophilic bacterium 4 Caldicellulosiruptor saccharolyticus 5 6 Inci Ozdemir, Sara E. Blumer-Schuette, and Robert M. Kelly* 7 8 Department of Chemical and Biomolecular Engineering, 9 North Carolina State University, Raleigh, NC 27695-7905 10 11 12 Submitted to: Applied and Environmental Microbiology (November, 2011) 13 AEM07031-11 (Revised Version of AEM05791-1) 14 15 Running title: S-layer homology domain proteins in C. saccharolyticus 16 17 Keywords: Caldicellulosiruptor saccharolyticus, extreme thermophile, plant biomass, 18 glycoside hydrolases, S-layer homology domains 19 20 21 *Address correspondence to: Robert M. Kelly 22

118

Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans  

Science Conference Proceedings (OSTI)

Chemolithoautotrophic bacteria can be of industrial and environmental importance, but they present a challenge for systems biology studies, as their central metabolism deviates from that of model organisms and there is a much less extensive experimental basis for their gene annotation than for typical organoheterotrophs. For microbes with sequenced genomes but unconventional metabolism, the ability to create knockout mutations can be a powerful tool for functional genomics and thereby render an organism more amenable to systems biology approaches. In this chapter, we describe a genetic system for Thiobacillus denitrificans, with which insertion mutations can be introduced by homologous recombination and complemented in trans. Insertion mutations are generated by in vitro transposition, the mutated genes are amplified by the PCR, and the amplicons are introduced into T. denitrificans by electroporation. Use of a complementation vector, pTL2, based on the IncP plasmid pRR10 is also addressed.

Beller, H.R.; Legler, T.C.; Kane, S.R.

2011-07-15T23:59:59.000Z

119

Inoculation of hybrid poplar with the endophytic bacterium Enterobacte...  

NLE Websites -- All DOE Office Websites (Extended Search)

II (F v 'F m ', panel d), the operating efficiency of photosystem II (F q 'F m ', panel e) and the efficiency factor of photosystem II (F q 'F v ', panel f) in the plants...

120

Fermentation and Electrohydrogenic Approaches to Hydrogen Production - DOE Hydrogen and Fuel Cells Program FY 2012 Annual Progress Report  

NLE Websites -- All DOE Office Websites (Extended Search)

8 8 DOE Hydrogen and Fuel Cells Program FY 2012 Annual Progress Report Pin-Ching Maness (Primary Contact), Katherine Chou, and Lauren Magnusson National Renewable Energy Laboratory (NREL) 15013 Denver West Parkway Golden, CO 80401 Phone: (303) 384-6114 Email: pinching.maness@nrel.gov DOE Manager HQ: Eric Miller Phone: (202) 287-5829 Email: Eric.Miller@hq.doe.gov Subcontractor: Bruce Logan, Pennsylvania State University, State College, PA Start Date: October 1, 2004 Projected End Date: Project continuation and direction determined annually by DOE Fiscal Year (FY) 2012 Objectives Optimize sequencing fed-batch parameters in converting * cellulose to hydrogen by the cellulolytic bacterium Clostridium thermocellum; aimed at lowering feedstock cost. Improve plasmid stability in * C. thermocellum; aimed

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

High-solids enrichment of thermophilic microbial communities and their enzymes on bioenergy feedstocks  

E-Print Network (OSTI)

and their enzymes on bioenergy feedstocks Amitha P. ReddyVanderGheynst 1,2* Joint BioEnergy Institute, Emeryville, CA2009. The water footprint of bioenergy. Proceedings of the

Reddy, A. P.

2012-01-01T23:59:59.000Z

122

Scalable economic extracellular synthesis of CdS nanostructured particles by a non-pathogenic thermophile  

SciTech Connect

We report microbially facilitated synthesis of cadmium sulfide (CdS) nanostructured particles (NP) using anaerobic, metal-reducing Thermoanaerobacter sp. The extracellular CdS crystallites were <10 nm in size with yields of ~3 g/L of growth medium/month with demonstrated reproducibility and scalability up to 24 L. During synthesis, Thermoanaerobacter cultures reduced thiosulfate and sulfite salts to H2S, which reacted with Cd2+ cations to produce thermodynamically favored NP in a single step at 65oC with catalytic nucleation on the cell surfaces. Photoluminescence (PL) analysis of dry CdS NP revealed an exciton-dominated PL peak at 440 nm, having a narrow full width at half maximum of 10 nm. A PL spectrum of CdS NP produced by dissimilatory sulfur reducing bacteria was dominated by features associated with radiative exciton relaxation at the surface. High reproducibility of CdS NP PL features important for scale-up conditions was confirmed from test tubes to 24L batches at a small fraction of the manufacturing cost associated with conventional inorganic NP production processes.

Moon, Ji Won [ORNL] [ORNL; Ivanov, Ilia N [ORNL] [ORNL; Duty, Chad E [ORNL] [ORNL; Love, Lonnie J [ORNL] [ORNL; Rondinone, Adam Justin [ORNL; Wang, Wei [ORNL] [ORNL; Li, Dr. Yi-Liang [University of Tennessee, Knoxville (UTK)] [University of Tennessee, Knoxville (UTK); Madden, Andrew [ORNL] [ORNL; Mosher, Jennifer J [ORNL] [ORNL; Hu, Michael Z. [ORNL] [ORNL; Suresh, Anil K [ORNL] [ORNL; Rawn, Claudia J [ORNL] [ORNL; Jung, Hyunsung [ORNL] [ORNL; Lauf, Robert J [ORNL] [ORNL; Phelps, Tommy Joe [ORNL] [ORNL

2013-01-01T23:59:59.000Z

123

Process for Generation of Hydrogen Gas from Various Feedstocks Using Thermophilic Bacteria  

DOE Green Energy (OSTI)

A method for producing hydrogen gas is provided comprising selecting a bacteria from the Order Thermotogales, subjecting the bacteria to a feedstock and to a suitable growth environment having an oxygen concentration below the oxygen concentration of water in equilibrium with air; and maintaining the environment at a predetermined pH and at a temperature of at least approximately 45 degrees C. for a time sufficient to allow the bacteria to metabolize the feedstock.

Ooteghem Van, Suellen

2005-09-13T23:59:59.000Z

124

High-solids enrichment of thermophilic microbial communities and their enzymes on bioenergy feedstocks  

E-Print Network (OSTI)

incubated samples. Carbon dioxide concentration was measuredAalborg, Orangeburg, NY). Carbon dioxide and flow data weredata acquisition system; carbon dioxide evolution rate (CER)

Reddy, A. P.

2012-01-01T23:59:59.000Z

125

Process for generation of hydrogen gas from various feedstocks using thermophilic bacteria  

SciTech Connect

A method for producing hydrogen gas is provided comprising selecting a bacteria from the Order Thermotogales, subjecting the bacteria to a feedstock and to a suitable growth environment having an oxygen concentration below the oxygen concentration of water in equilibrium with air; and maintaining the environment at a predetermined pH and at a temperature of at least approximately 45.degree. C. for a time sufficient to allow the bacteria to metabolize the feedstock.

Ooteghem, Suellen Van (Morgantown, WV)

2005-09-13T23:59:59.000Z

126

Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods  

DOE Patents (OSTI)

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

Thompson, David N. (Idaho Falls, ID); Apel, William A. (Jackson, WY); Thompson, Vicki S. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID); Lacey, Jeffrey A. (Idaho Falls, ID)

2011-12-06T23:59:59.000Z

127

Thermophilic and thermoacidophilic sugar transporter genes and enzymes from alicyclobacillus acidocaldarius and related organisms, methods  

DOE Patents (OSTI)

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

Thompson, David N. (Idaho Falls, ID); Apel, William A. (Jackson, WY); Thompson, Vicki S. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID); Lacey, Jeffrey A. (Idaho Falls, ID)

2011-06-14T23:59:59.000Z

128

Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods  

SciTech Connect

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

Thompson, David N; Apel, William A; Thompson, Vicki S; Reed, David W; Lacey, Jeffrey A

2013-11-05T23:59:59.000Z

129

Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from alicyclobacillus acidocaldarius and related organisms, methods  

DOE Patents (OSTI)

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

Thompson, David N. (Idaho Falls, ID); Apel, William A. (Jackson, WY); Thompson, Vicki S. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID); Lacey, Jeffrey A. (Idaho Falls, ID); Henriksen, Emily D. (Idaho Falls, ID)

2010-12-28T23:59:59.000Z

130

Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from alicyclobacillus acidocaldarius and related organisms, methods  

Science Conference Proceedings (OSTI)

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

Thompson, David N. (Idaho Falls, ID); Apel, William A. (Jackson, WY); Thompson, Vicki S. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID); Lacey, Jeffrey A. (Idaho Falls, ID); Henriksen, Emily D. (Idaho Falls, ID)

2012-06-19T23:59:59.000Z

131

Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods  

SciTech Connect

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Reed, David W.; Lacey, Jeffrey A.

2013-01-15T23:59:59.000Z

132

Thermophilic and thermoacidophilic biopolymer-degrading genes and enzymes from alicyclobacillus acidocaldarius and related organisms, methods  

SciTech Connect

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of at least partially degrading, cleaving, or removing polysaccharides, lignocellulose, cellulose, hemicellulose, lignin, starch, chitin, polyhydroxybutyrate, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius.

Thompson, David N; Apel, William A; Thompson, Vicki S; Reed, David W; Lacey, Jeffrey A; Henriksen, Emily D

2013-07-30T23:59:59.000Z

133

Thermophilic and thermoacidophilic sugar transporter genes and enzymes from Alicyclobacillus acidocaldarius and related organisms, methods  

SciTech Connect

Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods for transporting sugars across cell membranes using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Reed, David W.; Lacey, Jeffrey A.

2013-01-29T23:59:59.000Z

134

Oxygen Effects on Thermophilic Microbial Populations in Biofilters Treating Nitric Oxide Containing Off-Gas Streams  

SciTech Connect

Electricity generation from coal has increased by an average of 51 billion kWh per year over the past 3 years. For this reason cost-effective strategies to control nitrogen oxides (NOx) from coal-fired power plant combustion gases must be developed. Compost biofilters operated at 55°C at an empty bed contact time (EBCT) of 13 seconds were shown to be feasible for removal of nitric oxide (NO) from synthetic flue gas. Denitrifying microbial populations in these biofilters were shown to reduce influent NO feeds by 90 to 95% at inlet NO concentrations of 500 ppmv. Oxygen was shown to have a significant effect on the NO removal efficiency demonstrated by these biofilters. Two biofilters were set up under identical conditions for the purpose of monitoring NO removal as well as changes in the microbial population in the bed medium under anaerobic and aerobic conditions. Changes in the microbial population were monitored to determine the maximum oxygen tolerance of a denitrifying biofilter as well as methods of optimizing microbial populations capable of denitrification in the presence of low oxygen concentrations. Nitric oxide removal dropped to between 10 and 20% when oxygen was present in the influent stream. The inactive compost used to pack the biofilters may have also caused the decreased NO removal efficiency compared to previous biofiltration experiments. Analysis of the bed medium microbial population using environmental scanning electron microscopy indicated significant increases in biomass populating the surface of the compost when compared to unacclimated compost.

Lee, Brady Douglas; Apel, William Arnold; Smith, William Aaron

2004-04-01T23:59:59.000Z

135

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum  

E-Print Network (OSTI)

Complementation in Geothermal Microbial Mats'' Grant No. MCB0605301 awarded to Frank Robb and Albert Colman- tional complex could provide synergies such as the presentation of a large protein surface area

Badger, Jonathan

136

Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways  

Science Conference Proceedings (OSTI)

Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of L-lactate (Dldh) and/or acetate (Dpta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end-products. Cellobiose-grown cultures of the Dldh strain had identical biomass accumulation, fermentation end-products, transcription profile, and intracellular metabolite concentrations compared to its parent strain (DSM1313 Dhpt Dspo0A). The Dpta-deficient strain grew slower and had 30 % lower final biomass concentration compared to the parent strain, yet produced 75% more ethanol. A Dldh Dpta double-mutant strain evolved for faster growth had a growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to Dpta. Free amino acids were secreted by all examined strains, with both Dpta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for Dldh Dpta reached 5 mM by the end of growth, or 2.7 % of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to sixfold in the Dpta and 16-fold in the Dldh Dpta strain. We hypothesize that the deletions in fermentation end-product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP* through increased production of amino acids.

Van Der Veen, Douwe [ORNL; Lo, Jonathan [Dartmouth College; Brown, Steven D [ORNL; Johnson, Courtney M [ORNL; Tschaplinski, Timothy J [ORNL; Martin, Madhavi Z [ORNL; Engle, Nancy L [ORNL; Van den Berg, Robert A [Katholieke University Leuven, Belgium; Argyros, Aaron [Mascoma Corporation; Caiazza, Nicky [Mascoma Corporation; Guss, Adam M [ORNL; Lynd, Lee R [Thayer School of Engineering at Dartmouth

2013-01-01T23:59:59.000Z

137

Characterization of Clostridium thermocellum strains with disrupted fermentation end product pathways  

SciTech Connect

Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of Llactate ( ldh) and/or acetate ( pta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end products. Cellobiose-grown cultures of the ldh strain had identical biomass accumulation, fermentation end products, transcription profile and intracellular metabolite concentrations compared to its parent strain (DSM1313 hpt spo0A). The pta-deficient strain grew slower and had 30% lower final biomass concentration compared to the parent strain, yet produced 75% more ethanol. A ldh pta double mutant strain evolved for faster growth had growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to pta. Free amino acids were secreted by all examined strains, with both pta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for ldh pta reached 5 mM by the end of growth, or 2.7% of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to 6-fold in the pta and 16-fold in the ldh pta strain. We hypothesize that the deletions in fermentation end product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP+ through increased production of amino acids.

Van Der Veen, Douwe [ORNL; Lo, Jonathan [Dartmouth College; Brown, Steven D [ORNL; Johnson, Courtney M [ORNL; Tschaplinski, Timothy J [ORNL; Martin, Madhavi Z [ORNL; Engle, Nancy L [ORNL; Argyros, Aaron [Mascoma Corporation; Van den Berg, Robert A [Katholieke University Leuven, Belgium; Caiazza, Nicky [Mascoma Corporation; Guss, Adam M [ORNL; Lynd, Lee R [Thayer School of Engineering at Dartmouth

2013-01-01T23:59:59.000Z

138

6099.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

Nov. Nov. 2010, p. 6099-6100 Vol. 192, No. 22 0021-9193/10/$12.00 doi:10.1128/JB.00950-10 Copyright © 2010, American Society for Microbiology. All Rights Reserved. GENOME ANNOUNCEMENTS Complete Genome Sequence of the Cellulolytic Thermophile Caldicellulosiruptor obsidiansis OB47 Tᰔ James G. Elkins, 1,2 * Adriane Lochner, 1,2 Scott D. Hamilton-Brehm, 1,2 Karen Walston Davenport, 3 Mircea Podar, 1,2 Steven D. Brown, 1,2 Miriam L. Land, 2 Loren J. Hauser, 1,2 Dawn M. Klingeman, 1,2 Babu Raman, 1,2 Lynne A. Goodwin, 3 Roxanne Tapia, 3 Linda J. Meincke, 3 J. Chris Detter, 4 David C. Bruce, 3 Cliff S. Han, 3 Anthony V. Palumbo, 1,2 Robert W. Cottingham, 1,2 Martin Keller, 1,2 and David E. Graham 2 BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 1 ; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 2 ; Los Alamos National

139

Suite of Activity-Based Probes for Cellulose-Degrading Enzymes  

Science Conference Proceedings (OSTI)

Microbial glycoside hydrolases play a dominant role in the biochemical conversion of cellulosic biomass to high-value biofuels. Anaerobic cellulolytic bacteria are capable of producing multicomplex catalytic subunits containing cell-adherent cellulases, hemicellulases, xylanases, and other glycoside hydrolases to facilitate the degradation of highly recalcitrant cellulose and other related plant cell wall polysaccharides. Clostridium thermocellum is a cellulosome producing bacterium that couples rapid reproduction rates to highly efficient degradation of crystalline cellulose. Herein, we have developed and applied a suite of difluoromethylphenyl aglycone, N-halogenated glycosylamine, and 2-deoxy-2-fluoroglycoside activity-based protein profiling (ABPP) probes to the direct labeling of the C. thermocellum cellulosomal secretome. These activity-based probes (ABPs) were synthesized with alkynes to harness the utility and multimodal possibilities of click chemistry, and to increase enzyme active site inclusion for LC-MS analysis. We directly analyzed ABP-labeled and unlabeled global MS data, revealing ABP selectivity for glycoside hydrolase (GH) enzymes in addition to a large collection of integral cellulosome-containing proteins. By identifying reactivity and selectivity profiles for each ABP, we demonstrate our ability to widely profile the functional cellulose degrading machinery of the bacterium. Derivatization of the ABPs, including reactive groups, acetylation of the glycoside binding groups, and mono- and disaccharide binding groups, resulted in considerable variability in protein labeling. Our probe suite is applicable to aerobic and anaerobic cellulose degrading systems, and facilitates a greater understanding of the organismal role associated within biofuel development.

Chauvigne-Hines, Lacie M.; Anderson, Lindsey N.; Weaver, Holly M.; Brown, Joseph N.; Koech, Phillip K.; Nicora, Carrie D.; Hofstad, Beth A.; Smith, Richard D.; Wilkins, Michael J.; Callister, Stephen J.; Wright, Aaron T.

2012-12-19T23:59:59.000Z

140

Multiple Syntrophic Interactions in a Terephthalate-Degrading Methanogenic Consortium  

E-Print Network (OSTI)

lipids on thermophilic anaerobic-digestion and reduction ofrecently isolated from anaerobic digestion processes (Imachilipids on thermophilic anaerobic-digestion and reduction of

Lykidis, Athanasios

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


141

Trichloroethene Removal From Waste Gases in Anaerobic Biotrickling Filters Through Reductive Dechlorination  

E-Print Network (OSTI)

1) during thermophilic anaerobic digestion for production ofa keen interest in anaerobic digestion as well, and it wasfor thermophilic anaerobic digestion, and should stimulate

Popat, Sudeep Chandrakant

2010-01-01T23:59:59.000Z

142

acs_PR_pr-2011-00536j 1..13  

NLE Websites -- All DOE Office Websites (Extended Search)

1, 1, 2011 r 2011 American Chemical Society 5302 dx.doi.org/10.1021/pr200536j | J. Proteome Res. 2011, 10, 5302-5314 ARTICLE pubs.acs.org/jpr Label-free Quantitative Proteomics for the Extremely Thermophilic Bacterium Caldicellulosiruptor obsidiansis Reveal Distinct Abundance Patterns upon Growth on Cellobiose, Crystalline Cellulose, and Switchgrass Adriane Lochner, †,‡,§,|| Richard J. Giannone, ‡,||,^ Martin Keller, †,‡ Garabed Antranikian, § David E. Graham,* ,†,# and Robert L. Hettich* ,‡,^ † Biosciences Division; ^ Chemical Sciences Division; ‡ BioEnergy Science Center at Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States § Technical Microbiology, Hamburg University of Technology, Kasernenstrasse 12, D-21073 Hamburg, Germany # Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996,

143

Why Sequence Bacillus coagulans?  

NLE Websites -- All DOE Office Websites (Extended Search)

Bacillus coagulans? Bacillus coagulans? Bacilus coagulans strain 36D1 and its close relatives are ideal biocatalysts for fermentation of lignocellulosic biomass to fuels and chemicals. This bacterium is an acidophile and a moderate thermophile (grows at pH 5.0 and at 55°C). These characteristics are similar to the optimal conditions for the activity of fungal cellulases, which have been developed with significant support from DOE for simultaneous saccharification and fermentation (SSF) of cellulose to useful products (fuel ethanol, lactic acid, etc.). The optimal growth conditions for the biocatalysts currently used by industry for production of ethanol or lactic acid significantly differ from the optimal conditions for cellulase activity. This mismatch leads to higher usage of expensive cellulases than

144

NREL: Energy Sciences - Kara Podkaminer  

NLE Websites -- All DOE Office Websites (Extended Search)

Kara Podkaminer Kara Podkaminer Postdoctoral Researcher Photo of Kara Podkaminer Phone: (303) 384-7970 Email: Kara.Podkaminer@nrel.gov At NREL Since: 2011 Kara Podkaminer received her Ph.D. in Engineering Sciences from the Thayer School of Engineering at Dartmouth College in 2011. For her dissertation work, she studied the thermophilic, anaerobic bacterium Thermoanaerobacterium saccharolyticum ALK2 and its application in a thermophliic SSF process. At NREL, Dr. Podkaminer is working on heterologous protein expression in T. reesei, looking to better understand the bottlenecks and increase protein production. This work will serve as the foundation for future expression of NREL's chimera proteins. Printable Version NREL is a national laboratory of the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, operated by the Alliance for Sustainable Energy, LLC.

145

Exchange of Type II Dockerin-Containing Subunits of the C. thermocellum Cellulosome as Revealed by SNAP-tags  

Science Conference Proceedings (OSTI)

Clostridium thermocellum is a thermophilic anaerobic bacterium which efficiently hydrolyzes and metabolizes cellulose to ethanol through the action of its cellulosome, a multiprotein enzymatic complex. A fluorescent protein probe, consisting of a type II dockerin module fused to a SNAP-tag, was developed in order to gain insight into the quaternary configuration of the cellulosome and to investigate the effect of deleting cipA, the protein scaffold on which the cellulosome is built. Fluorescence microscopy suggested that the probe had localized to polycellulosomal protuberances on the cell surface. Surprisingly, fluorescence intensity did not substantially change in the cipA deletion mutants. Sequential labeling experiments suggested that this was a result of bound type II dockerins from CipA being replaced by unbound type II dockerins from the fluorophore-SNAP-XDocII probe. This mechanism of dockerin exchange could represent an efficient means for modifying cellulosome composition.

Waller, Benjamin [Dartmouth College; Olson, Daniel G. [Thayer School of Engineering at Dartmouth; Currie, Devin [Dartmouth College; Guss, Adam M [ORNL; Lynd, Lee R [Thayer School of Engineering at Dartmouth

2013-01-01T23:59:59.000Z

146

Environmental genomics reveals a single species ecosystem deep within the Earth  

Science Conference Proceedings (OSTI)

DNA from low biodiversity fracture water collected at 2.8 km depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, comprises>99.9percent of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent lifestyle well suited to long-term isolation from the photosphere deep within Earth?s crust, and offers the first example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

Chivian, Dylan; Brodie, Eoin L.; Alm, Eric J.; Culley, David E.; Dehal, Paramvir S.; DeSantis, Todd Z.; Gihring, Thomas M.; Lapidus, Alla; Lin, Li-Hung; Lowry, Stephen R.; Moser, Duane P.; Richardson, Paul; Southam, Gordon; Wanger, Greg; Pratt, Lisa M.; Andersen, Gary L.; Hazen, Terry C.; Brockman, Fred J.; Arkin, Adam P.; Onstott, Tullis C.

2008-09-17T23:59:59.000Z

147

Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum  

Science Conference Proceedings (OSTI)

Clostridium thermocellum is a thermophilic, obligately anaerobic, Gram-positive bacterium that is a candidate microorganism for converting cellulosic biomass into ethanol through consolidated bioprocessing. Ethanol intolerance is an important metric in terms of process economics, and tolerance has often been described as a complex and likely multigenic trait for which complex gene interactions come into play. Here, we resequence the genome of an ethanol-tolerant mutant, show that the tolerant phenotype is primarily due to a mutated bifunctional acetaldehyde-CoA/alcohol dehydrogenase gene (adhE), hypothesize based on structural analysis that cofactor specificity may be affected, and confirm this hypothesis using enzyme assays. Biochemical assays confirm a complete loss of NADH-dependent activity with concomitant acquisition of NADPH-dependent activity, which likely affects electron flow in the mutant. The simplicity of the genetic basis for the ethanol-tolerant phenotype observed here informs rational engineering of mutant microbial strains for cellulosic ethanol production.

Brown, Steven D [ORNL; Guss, Adam M [ORNL; Karpinets, Tatiana V [ORNL; Parks, Jerry M [ORNL; Smolin, Nikolai [ORNL; Yang, Shihui [ORNL; Land, Miriam L [ORNL; Klingeman, Dawn Marie [ORNL; Bhandiwad, Ashwini [Thayer School of Engineering at Dartmouth; Rodriguez, Jr., Miguel [ORNL; Raman, Babu [Dow Chemical Company, The; Shao, Xiongjun [Thayer School of Engineering at Dartmouth; Mielenz, Jonathan R [ORNL; Smith, Jeremy C [ORNL; Keller, Martin [ORNL; Lynd, Lee R [Thayer School of Engineering at Dartmouth

2011-01-01T23:59:59.000Z

148

Novel Thermo-Acidophilic Bacteria Isolated from Geothermal Sites in Yellowstone National Park: Physiological and Phylogenetic Characteristics  

Science Conference Proceedings (OSTI)

Moderately thermophilic acidophilic bacteria were isolated from geothermal (30–83 °C) acidic (pH 2.7– 3.7) sites in Yellowstone National Park. The temperature maxima and pH minima of the isolates ranged from 50 to 65 °C, and pH 1.0–1.9. Eight of the bacteria were able to catalyze the dissimilatory oxidation of ferrous iron, and eleven could reduce ferric iron to ferrous iron in anaerobic cultures. Several of the isolates could also oxidize tetrathionate. Six of the iron-oxidizing isolates, and one obligate heterotroph, were low G+C gram-positive bacteria (Firmicutes). The former included three Sulfobacillus-like isolates (two closely related to a previously isolated Yellowstone strain, and the third to a mesophilic bacterium isolated from Montserrat), while the other three appeared to belong to a different genus. The other two iron-oxidizers were an Actinobacterium (related to Acidimicrobium ferrooxidans) and a Methylobacterium-like isolate (a genus within the a-Proteobacteria that has not previously been found to contain either iron-oxidizers or acidophiles). The other three (heterotrophic) isolates were also a-Proteobacteria and appeared be a novel thermophilic Acidisphaera sp. An ARDREA protocol was developed to discriminate between the iron-oxidizing isolates. Digestion of amplified rRNA genes with two restriction enzymes (SnaBI and BsaAI) separated these bacteria into five distinct groups; this result was confirmed by analysis of sequenced rRNA genes.

D. B. Johnson; N. Okibe; F. F. Roberto

2003-07-01T23:59:59.000Z

149

Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT)  

Science Conference Proceedings (OSTI)

Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which comprises five species of the order Clostridiales. Sulfobacillus species are of interest for comparison to other sulfur and iron oxidizers and also have biomining applications. This is the first completed genome sequence of a type strain of the genus Sulfobacillus, and the second published genome of a member of the species S. acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp, harbors 3,626 protein-coding and 69 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Pan, Chongle [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

150

Complete genome of the cellyloytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evloutionary adaptations  

E-Print Network (OSTI)

Holliday junction DNA helicase B hypothetical proteinprotein, and the fourth has a helicase domain and could be ahypothetical protein helicase domain protein conserved

Barabote, Ravi D.

2009-01-01T23:59:59.000Z

151

Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain  

E-Print Network (OSTI)

explore its metabolism for bioethanol or other bioprocessthe metabolic pathways for bioethanol production as well as

Tang, Yinjie J.

2009-01-01T23:59:59.000Z

152

Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain  

E-Print Network (OSTI)

Lab, Berkeley, 94720, (4) Sandia National Laboratories, POresearch was provided by the Sandia National LaboratoriesDevelopment Program. Sandia is a multi-program laboratory

Tang, Yinjie J.

2009-01-01T23:59:59.000Z

153

Analysis of Metabolic Pathways and Fluxes in a Newly Discovered Thermophilic and Ethanol-Tolerant Geobacillus Strain  

E-Print Network (OSTI)

assumed a glucose uptake rate equal to 5 mM hr -1 DCW -1 .uptake rate of 100 units (gm DCW) -1 ·hr -1 ) through theto a value of 100 units (gm DCW) -1 hr -1 , the model

Tang, Yinjie J.

2009-01-01T23:59:59.000Z

154

Biofabrication of discrete spherical gold nanoparticles using the metal-reducing bacterium, Shewanella oneidensis  

Science Conference Proceedings (OSTI)

Nanocrystallites have garnered substantial interest due to their varying applications including catalysis. Consequently important aspects related to control of shape/size and syntheses through economical and non-hazardous means are desirable. Highly efficient bioreduction based natural fabrication approaches that utilize microbes and or -plant extracts are poised to meet these needs. Here we show that the gamma- proteobacterium, Shewanella oneidensis MR-1, can reduce tetrachloro aurate (III) ions, producing discrete extracellular spherical gold nanocrystallites. The particles were homogeneous with multiple size distributions and produced under ambient conditions at high yield, 88% of theoretical maximum. Further characterization revealed that the particles consist of spheres in the size range of 2-50 nm, with an average of 12 5 nm. The nanoparticles were hydrophilic, biocompatible, and resisted aggregation even after several months. The particles are likely capped by a detachable protein/peptide coat. UV-vis and Fourier transform infrared spectroscopy, X-ray diffraction, energy dispersive X-ray spectra and transmission electron microscopy measurements confirmed the formation as well the crystalline nature of the nanoparticles. The antibacterial activity of these gold nanoparticles was assessed using Gram-negative (E. coli and S. oneidensis) and Gram-positive (B. subtilis) bacteria. Toxicity assessments divulged that the particles were neither toxic nor inhibitory to any of these bacteria.

Suresh, Anil K [ORNL; Pelletier, Dale A [ORNL; Wang, Wei [ORNL; Broich, Michael L [ORNL; Moon, Ji Won [ORNL; Gu, Baohua [ORNL; Allison, David P [ORNL; Joy, David Charles [ORNL; Phelps, Tommy Joe [ORNL; Doktycz, Mitchel John [ORNL

2011-01-01T23:59:59.000Z

155

Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4T)  

SciTech Connect

Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella, which belongs to the family Cytophagaceae. The species is of interest because it is able to grow at temperatures as low as 4 C. This is the first completed genome sequence of a member of the genus Runella and the sixth sequence from the family Cytophagaceae. The 6,919,729 bp long genome consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0 kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Copeland, A [U.S. Department of Energy, Joint Genome Institute; Zhang, Xiaojing [Los Alamos National Laboratory (LANL); Misra, Monica [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Pan, Chongle [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J C [U.S. Department of Energy, Joint Genome Institute; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Ngatchou, Olivier Duplex [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

156

Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1T)  

SciTech Connect

Muricauda ruestringensis Bruns et al. 2001 is the type species of the genus Muricauda, which belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. The species is of interest because of its isolated position in the genomically unexplored genus Muricauda, which is located in a part of the tree of life containing not many organisms with sequenced genomes. The genome, which consists of a circular chromosome of 3,842,422 bp length with a total of 3,478 protein-coding and 47 RNA genes, is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Pan, Chongle [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

157

Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T)  

SciTech Connect

Holophaga foetida Liesack et al. 1994 is a member to the genomically so far poorly characterized family Holophagaceae in the class Holophagae within the phylum Acidibacteria. H. foetida is of interest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4T is the first sequenced genome of a member of the class Holophagae. Here we describe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Held, Brittany [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

158

Aptamer from whole-bacterium SELEX as new therapeutic reagent against virulent Mycobacterium tuberculosis  

SciTech Connect

Worldwide, tuberculosis (TB) remains the most frequent and important infectious disease causing morbidity and death. One-third of the world's population is infected with Mycobacterium tuberculosis (MTB), the etiologic agent of TB. Because of the global health problems of TB, the development of potent new anti-TB drugs without cross-resistance with known antimycobacterial agents is urgently needed. In this study, we have applied a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process to identify a single aptamer (NK2) that binds to virulent strain M. tuberculosis (H37Rv) with high affinity and specificity. We have found that this aptamer improves CD4{sup +}T cells to produce IFN-{gamma} after binding to H37Rv. The different component between H37Rv and BCG was identified as some membrane protein. Moreover, the survival rates of mice challenged with i.v. H37Rv have been prolonged after treatment with single injection of aptamer NK2. The bacterial numbers were significantly lower in the spleen of mice treated with aptamer NK2. The histopathological examination of lung biopsy specimens showed lesser pulmonary alveolar fusion and swelling in the presence of the aptamer. These results suggest that aptamer NK2 has inhibitory effects on M. tuberculosis and can be used as antimycobacterial agent.

Chen, Fan [Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, State Key Laboratory of Virology, Wuhan University School of Medicine, Donghu Road 165, Wuhan 430071, Hubei Province (China); Zhou, Jing [Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, State Key Laboratory of Virology, Wuhan University School of Medicine, Donghu Road 165, Wuhan 430071, Hubei Province (China); Luo, Fengling [Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, State Key Laboratory of Virology, Wuhan University School of Medicine, Donghu Road 165, Wuhan 430071, Hubei Province (China); Mohammed, Al-Bayati [Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, State Key Laboratory of Virology, Wuhan University School of Medicine, Donghu Road 165, Wuhan 430071, Hubei Province (China); Zhang, Xiao-Lian [Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, State Key Laboratory of Virology, Wuhan University School of Medicine, Donghu Road 165, Wuhan 430071, Hubei Province (China)]. E-mail: zxl_65@163.com

2007-06-08T23:59:59.000Z

159

Genome Sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium  

Science Conference Proceedings (OSTI)

Chthoniobacter flavusis Ellin428 is the first isolate from subdivision 2 of the bacterial phylum Verrucomicrobia. C. flavusis Ellin428 can metabolize many of the saccharide components of plant biomass but does not grow with amino acids or organic acids other than pyruvate.

Kant, Ravi [University of Helsinki; Van Passel, Mark W.J. [Wageningen University and Research Centre, The Netherlands; Palva, Airi [University of Helsinki; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; De Vos, Willem M. [Wageningen University and Research Centre, The Netherlands; Janssen, Peter H. [AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand; Smidt, Hauke [Wageningen University and Research Centre, The Netherlands

2011-01-01T23:59:59.000Z

160

Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)  

Science Conference Proceedings (OSTI)

Saccharomonospora azurea Runmao et al. 1987 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonosoras are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist and over-heated grain, where they might play a role in the primary degradation of plant material by attacking hemicellulose. They are Gram-negative staining organisms classified among the usually Gram-positive actinomycetes. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for with a completely sequenced type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence with project status 'permanent draft', and annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Held, Brittany [Los Alamos National Laboratory (LANL); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Potter, Gabriele [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
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We encourage you to perform a real-time search of NLEBeta
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161

Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15T)  

SciTech Connect

Saccharomonospora marina Liu et al. 2010 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Next to S. viridis and S. azurea, S. marina is the third member in the genus Saccharomonospora for with a completely sequenced (permanent draft status) type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lu, Megan [Los Alamos National Laboratory (LANL); Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Potter, Gabriele [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Li, Wen-Jun [Yunnan University, Kunming, China; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

162

Interactions of Fe(II) with the iron oxidizing bacterium Rhodopseudomonas palustris TIE-1  

E-Print Network (OSTI)

Microbial anaerobic iron oxidation has long been of interest to biologists and geologists, both as a possible mechanism for the creation of banded iron formations before the rise of oxygen, and as a model system for organisms ...

Bird, Lina J. (Lina Joana)

2013-01-01T23:59:59.000Z

163

Making a Better Hydrogen Producing Bacterium | U.S. DOE Office...  

Office of Science (SC) Website

Contact Information Biological & Environmental Research (BER) U.S. Department of Energy SC-23Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301)...

164

Quantitative Tools for Dissection of Hydrogen-Producing Metabolic Networks-Final Report  

DOE Green Energy (OSTI)

During this project we have pioneered the development of integrated experimental-computational technologies for the quantitative dissection of metabolism in hydrogen and biofuel producing microorganisms (i.e. C. acetobutylicum and various cyanobacteria species). The application of these new methodologies resulted in many significant advances in the understanding of the metabolic networks and metabolism of these organisms, and has provided new strategies to enhance their hydrogen or biofuel producing capabilities. As an example, using mass spectrometry, isotope tracers, and quantitative flux-modeling we mapped the metabolic network structure in C. acetobutylicum. This resulted in a comprehensive and quantitative understanding of central carbon metabolism that could not have been obtained using genomic data alone. We discovered that biofuel production in this bacterium, which only occurs during stationary phase, requires a global remodeling of central metabolism (involving large changes in metabolite concentrations and fluxes) that has the effect of redirecting resources (carbon and reducing power) from biomass production into solvent production. This new holistic, quantitative understanding of metabolism is now being used as the basis for metabolic engineering strategies to improve solvent production in this bacterium. In another example, making use of newly developed technologies for monitoring hydrogen and NAD(P)H levels in vivo, we dissected the metabolic pathways for photobiological hydrogen production by cyanobacteria Cyanothece sp. This investigation led to the identification of multiple targets for improving hydrogen production. Importantly, the quantitative tools and approaches that we have developed are broadly applicable and we are now using them to investigate other important biofuel producers, such as cellulolytic bacteria.

Rabinowitz, Joshua D.; Dismukes, G.Charles.; Rabitz, Herschel A.; Amador-Noguez, Daniel

2012-10-19T23:59:59.000Z

165

Laboratory Directed Research & Development program. Annual report to the Department of Energy  

Science Conference Proceedings (OSTI)

This report briefly discusses the following projects coordinated at Brookhaven National Laboratory: investigation of the utility of max-entropy methods for the analysis of powder diffraction data; analysis of structures and interactions of nucleic acids and proteins by small angle x-ray diffraction; relaxographic MRI and functional MRI; very low temperature infra-red laser absorption as a potential analytical tool; state-resolved measurements of H{sub 2} photodesorption: development of laser probes of H{sub 2} for in-situ accelerator measurements; Siberian snake prototype development for RHIC; synthesis and characterization of novel microporous solids; ozone depletion, chemistry and physics of stratospheric aerosols; understanding the molecular basis for the synthesis of plant fatty acids possessing unusual double bond positions; structure determination of outer surface proteins of the Lyme disease spirochete; low mass, low-cost multi-wire proportional chambers for muon systems of collider experiments; theory of self-organized criticality; development of the PCR-SSCP technique for the detection, at the single cell level, of specific genetic changes; feasibility of SPECT in imaging of F-18 FDG accumulation in tumors; visible free electron laser oscillator experiment; study of possible 2 + 2 TeV muon-muon collider; ultraviolet FEL R & D; precision machining using hard x-rays; new directions in in-vivo enzyme mapping: catechol-O-methyltransferase; proposal to develop a high rate muon polarimeter; development of intense, tunable 20-femtosecond laser systems; use of extreme thermophilic bacterium thermatoga maritima as a source of ribosomal components and translation factors for structural studies; and biochemical and structural studies of Chaperon proteins from thermophilic bacteria and other experiments.

Ogeka, G.J.; Romano, A.J.

1995-12-01T23:59:59.000Z

166

Life and hydrothermal vents  

NLE Websites -- All DOE Office Websites (Extended Search)

Life and hydrothermal vents Life and hydrothermal vents Name: williamh Status: N/A Age: N/A Location: N/A Country: N/A Date: Around 1993 Question: Are there biological communities near hydrothermal vents in the ocean? Is there any life inside the hydrothermal vent? Replies: If the presence of microorganisms in hot springs and geysers are any indication, I am certain there is life inside hydrothermal vents. These heat loving organisms are termed "thermophiles" and thrive where other life dies. They are able to survive in extreme heat due to the unique way their proteins are synthesized. The May 1993 Discover has a special article on thermophiles. wizkid Life at high temperature became very interesting to molecular biologists recently. The enormously useful technique known as PCR, (polymerase chain reaction), by which very small amounts of rare DNA can be amplified to large concentrations (Jurassic Park!), depends on having a DNA polymerase (the enzyme that synthesizes complementary DNA strands during replication of chromosomes), that can work at high temperatures, or at least can survive repeated high temperature cycles. PCR depends on synthesis of DNA followed by forced separation of the daughter strands at high temperature, followed by new synthesis, to amplify DNA exponentially. At any rate, normal bacterial polymerase will not work because the high temperature cycles kill it. Enter the now infamous, patented Taq polymerase, isolated from Thermus aquaticus, a hot spring bacterium, which works after heating to up to 94 C! So knowledge of life at high temperature allowed molecular biologists to get PCR to work, with all its benefits in cloning very rare genes and amplifying small amounts of DNA for forensic work etc.

167

Neptunium (V) Adsorption to a Halophilic Bacterium Under High Ionic Strength Conditions: A Surface Complexation Modeling Approach  

Science Conference Proceedings (OSTI)

Rationale for experimental design: Np(V) -- important as analog for Pu(V) and for HLW scenarios; High ionic strength -- relevant to salt-based repositories such as the WIPP; Halophilic microorganisms -- representative of high ionic strength environments. For the first time showed: Significant adsorbant to halophilic microorganisms over entire pH range under high ionic strength conditions; Strong influence of ionic strength with increasing adsorption with increasing ionic strength (in contrast to trends of previous low ionic strength studies); Effect of aqueous Np(V) and bacterial surface site speciation on adsorption; and Developed thermodynamic models that can be incorporated into geochemical speciation models to aid in the prediction of the fate and transport of Np(V) in more complex systems.

Ams, David A [Los Alamos National Laboratory

2012-06-11T23:59:59.000Z

168

Inoculation of hybrid poplar with the endophytic bacterium Enterobacter sp. 638 increases biomass but does not impact leaf level physiology  

SciTech Connect

Endophytic bacteria have been shown to provide several advantages to their host, including enhanced growth. Inoculating biofuel species with endophytic bacteria is therefore an attractive option to increase the productivity of biofuel feedstocks. Here, we investigated the effect of inoculating hard wood cuttings of Populus deltoides Bartr. x Populus. nigra L. clone OP367 with Enterobacter sp. 638. After 17 weeks, plants inoculated with Enterobacter sp. 638 had 55% greater total biomass than un-inoculated control plants. Study of gas exchange and fluorescence in developing and mature leaves over a diurnal cycle and over a 5 week measurement campaign revealed no effects of inoculation on photosynthesis, stomatal conductance, photosynthetic water use efficiency or the maximum and operating efficiency of photosystem II. However, plants inoculated with Enterobacter sp. 638 had a canopy that was 39% larger than control plants indicating that the enhanced growth was fueled by increased leaf area, not by improved physiology. Leaf nitrogen content was determined at two stages over the 5 week measurement period. No effect of Enterobacter sp. 638 on leaf nitrogen content was found indicating that the larger plants were acquiring sufficient nitrogen. Enterobacter sp. 638 lacks the genes for N{sub 2} fixation, therefore the increased availability of nitrogen likely resulted from enhanced nitrogen acquisition by the 84% larger root system. These data show that Enterobacter sp. 638 has the potential to dramatically increase productivity in poplar. If fully realized in the production environment, these results indicate that an increase in the environmental and economic viability of poplar as a biofuel feedstock is possible when inoculated with endophytic bacteria like Enterobacter sp. 638.

Rogers, A.; McDonald, K.; Muehlbauer, M. F.; Hoffman, A.; Koenig, K.; Newman, L.; Taghavi, S.; Van Der Lelie, D.

2011-01-01T23:59:59.000Z

169

Complete genome sequence of the marine, cellulose and xylan degrading bacterium Glaciecola sp. 4H-3-7+YE-5  

DOE Green Energy (OSTI)

Glaciecola sp. 4H-3-7+YE-5 was isolated from deep sea sediments at Suruga Bay in Japan and is capable of efficiently hydrolyzing cellulose and xylan. The complete genome sequence of Glaciecola sp. 4H-3-7+YE-5 revealed several genes encoding putatively novel glycoside hydrolases associated with plant biomass degradation.

Klippel, Dr Barbara [Technische Universitat Hamburg-Harburg (Hamburg University of Technology); Bruce, David [Los Alamos National Laboratory (LANL); Davenport, Karen W. [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Han, Shunsheng [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Wiebusch, Sigrid [Technische Universitat Hamburg-Harburg (Hamburg University of Technology); Basner, Alexander [Technische Universitat Hamburg-Harburg (Hamburg University of Technology); Abe, Fumiyoshi [Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Horikoshi, Koki [Japan Agency for Marine-Earth Science and Technology (JAMSTEC); Antranikian, Garabed [Technische Universitat Hamburg-Harburg (Hamburg University of Technology)

2011-01-01T23:59:59.000Z

170

Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8T)  

SciTech Connect

Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N. soli strain JS13-8T is of interest for its ability to produce a variety of glycosyl hydrolases. The ge- nome of N. soli strain JS13-8T is only the second genome sequence of a type strain from the family Chitinophagaceae to be published, and the first one from the genus Niabella. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Munk, Christine [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Ivanova, N [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

171

The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon  

E-Print Network (OSTI)

A biochemically active MCM-like helicase in Bacillus cereus.of archaea. The main helicase in bacteria is DnaB, whiletein was a functional helicase but had no primase activ-

Valas, Ruben E; Bourne, Philip E

2011-01-01T23:59:59.000Z

172

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)  

Science Conference Proceedings (OSTI)

Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpe- tosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative pre- dation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic en- zymes. The genome of H. aurantiacus strain 114-95T is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.

Kiss, Hajnalka [Los Alamos National Laboratory (LANL); Nett, Markus [Hans Knöll Institute, Jena, Germany; Domin, Nicole [Hans Knöll Institute, Jena, Germany; Martin, Karin [Hans Knöll Institute, Jena, Germany; Maresca, Julia A. [Pennsylvania State University, University Park, PA; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Berry, Kerrie W. [United States Department of Energy Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Schmutz, Jeremy [Stanford University; Brettin, Thomas S [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bryant, Donald A. [Pennsylvania State University, University Park, PA

2011-01-01T23:59:59.000Z

173

Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans  

SciTech Connect

Despite intense interest in the response to radiation in D. radiodurans, little is known about how the organism responds to other stress factors. Our previous studies indicated that D. radiodurans mounts a regulated protective response to heat shock, and that expression of the groESL and dnaKJ operons are induced in response to elevated temperature. In order to gain greater insight into the heat shock response of D. radiodurans on a more global scale, we undertook the study reported here. Using whole-cell semiquantitative mass spectrometric proteomics integrated with global transcriptome microarray analyses, we have determined a core set of highly induced heat shock genes whose expression correlates well at the transcriptional and translational levels. In addition, we observed that the higher the absolute expression of a given gene at physiological conditions, the better the quantitative correlation between RNA and protein expression levels.

Schmid, Amy K.; Lipton, Mary S.; Mottaz, Heather M.; Monroe, Matthew E.; Smith, Richard D.; Lidstrom, Mary E.

2005-05-01T23:59:59.000Z

174

Targeted Enhancement of H2 and CO2 Uptake for Autotrophic Production of Biodiesel in the Lithoautotrophic Bacterium Ralsonia Eutropha  

SciTech Connect

CO2 and H2 are promising feedstocks for production of valuable biocompounds. Ralstonia eutropha utilizes these feedstocks to generate energy (ATP) and reductant (NAD(P)H) via oxidation of H2 by a membrane-bound (MBH) and a soluble hydrogenase (SH) for CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle. Increased expression of the enzyme that fixes CO2 (RubisCO) resulted in 6-fold activity improvement in vitro, while increased expression of the MBH operon or the SH operon plus MBH operon maturation factors necessary for activity resulted in a 10-fold enhancement. Current research involves genetic manipulation of two endogenous cbb operons for increased expression, analysis of expression and activity of CBB/MBH/SH, cofactor ratios, and downstream products during autotrophic growth in control versus enhanced strains, and development of strategies for long-term, optimal overexpression. These studies will improve our understanding of autotrophic metabolism and provide a chassis strain for autotrophic production of biodiesel and other valuable carbon biocompounds.

Eckert, C. A.; Sullivan, R.; Johnson, C.; Yu, J.; Maness, P. C.

2013-01-01T23:59:59.000Z

175

Liquid Fuel from Heat-Loving Microorganisms: H2-Dependent Conversion of CO2 to Liquid Electrofuels by Extremely Thermophilic Archaea  

SciTech Connect

Electrofuels Project: NC State is working with the University of Georgia to create Electrofuels from primitive organisms called extremophiles that evolved before photosynthetic organisms and live in extreme, hot water environments with temperatures ranging from 167-212 degrees Fahrenheit The team is genetically engineering these microorganisms so they can use hydrogen to turn carbon dioxide directly into alcohol-based fuels. High temperatures are required to distill the biofuels from the water where the organisms live, but the heat-tolerant organisms will continue to thrive even as the biofuels are being distilled—making the fuel-production process more efficient. The microorganisms don’t require light, so they can be grown anywhere—inside a dark reactor or even in an underground facility.

2010-07-01T23:59:59.000Z

176

Comparison of different procedures to stabilize biogas formation after process failure in a thermophilic waste digestion system: Influence of aggregate formation on process stability  

Science Conference Proceedings (OSTI)

Highlights: Black-Right-Pointing-Pointer Mechanism of process recovery with calcium oxide. Black-Right-Pointing-Pointer Formation of insoluble calcium salts with long chain fatty acids and phosphate. Black-Right-Pointing-Pointer Adsorption of VFAs by the precipitates resulting in the formation of aggregates. Black-Right-Pointing-Pointer Acid uptake and phosphate release by the phosphate-accumulating organisms. Black-Right-Pointing-Pointer Microbial degradation of volatile fatty acids in the aggregates. - Abstract: Following a process failure in a full-scale biogas reactor, different counter measures were undertaken to stabilize the process of biogas formation, including the reduction of the organic loading rate, the addition of sodium hydroxide (NaOH), and the introduction of calcium oxide (CaO). Corresponding to the results of the process recovery in the full-scale digester, laboratory experiments showed that CaO was more capable of stabilizing the process than NaOH. While both additives were able to raise the pH to a neutral milieu (pH > 7.0), the formation of aggregates was observed particularly when CaO was used as the additive. Scanning electron microscopy investigations revealed calcium phosphate compounds in the core of the aggregates. Phosphate seemed to be released by phosphorus-accumulating organisms, when volatile fatty acids accumulated. The calcium, which was charged by the CaO addition, formed insoluble salts with long chain fatty acids, and caused the precipitation of calcium phosphate compounds. These aggregates were surrounded by a white layer of carbon rich organic matter, probably consisting of volatile fatty acids. Thus, during the process recovery with CaO, the decrease in the amount of accumulated acids in the liquid phase was likely enabled by (1) the formation of insoluble calcium salts with long chain fatty acids, (2) the adsorption of volatile fatty acids by the precipitates, (3) the acid uptake by phosphorus-accumulating organisms and (4) the degradation of volatile fatty acids in the aggregates. Furthermore, this mechanism enabled a stable process performance after re-activation of biogas production. In contrast, during the counter measure with NaOH aggregate formation was only minor resulting in a rapid process failure subsequent the increase of the organic loading rate.

Kleyboecker, A.; Liebrich, M.; Kasina, M. [Microbial GeoEngineering, Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany); Kraume, M. [Chemical and Process Engineering, Technical University Berlin, 10623 Berlin (Germany); Wittmaier, M. [Institute for Recycling and Environmental Protection, Bremen University of Applied Sciences, 28199 Bremen (Germany); Wuerdemann, H., E-mail: wuerdemann@gfz-potsdam.de [Microbial GeoEngineering, Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany)

2012-06-15T23:59:59.000Z

177

2006 ANNUAL POULTRY ACTIVITIES  

E-Print Network (OSTI)

. Shih designed and patented a thermophilic anaerobic digestion system that converts poultry waste the thermophilic anaerobic digester developed in his lab. The enzyme was purified and characterized. Later his

178

Energies 2010, 3, 899-919; doi:10.3390/en3050899 ISSN 1996-1073  

E-Print Network (OSTI)

of a thermophilic beta-glucosidase for cellulosic bioethanol production. Appl. Biochem. Biotechnol. 161, 301-312. (5

Lovley, Derek

179

Final Report on Development of Thermoanaerobacterium saccharolyticum for the conversion of lignocellulose to ethanol  

DOE Green Energy (OSTI)

This project addressed the need for economical technology for the conversion of lignocellulosic biomass to fuels, specifically the conversion of pretreated hardwood to ethanol. The technology developed is a set of strains of the bacterium Thermoanaerobacterium saccharolyticum and an associated fermentation process for pretreated hardwood. Tools for genetic engineering and analysis of the organism were developed, including a markerless mutation method, a complete genome sequence and a set of gene expression profiles that show the activity of its genes under a variety of conditions relevant to lignocellulose conversion. Improved strains were generated by selection and genetic engineering to be able to produce higher amounts of ethanol (up to 70 g/L) and to be able to better tolerate inhibitory compounds from pretreated hardwood. Analysis of these strains has generated useful insight into the genetic basis for desired properties of biofuel producing organisms. Fermentation conditions were tested and optimized to achieve ethanol production targets established in the original project proposal. The approach proposed was to add cellulase enzymes to the fermentation, a method called Simultaneous Saccharification and Fermentation (SSF). We had reason to think SSF would be an efficient approach because the optimal temperature and pH for the enzymes and bacterium are very close. Unfortunately, we discovered that commercially available cellulases are inactivated in thermophilic SSF by a combination of low redox potential and ethanol. Despite this, progress was made against the fermentation targets using bacterial cellulases. Thermoanaerobacterium saccharolyticum may still prove to be a commercially viable technology should cellulase enzyme issues be addressed. Moreover, the organism was demonstrated to produce ethanol at approximately theoretical yield from oligomeric hemicellulose extracts, an ability that may prove to be uniquely valuable in pretreatment configurations in which cellulose and hemicellulose are separated.

Herring, Christopher D.; Kenealy, William R.; Shaw, A. Joe; Raman, Babu; Tschaplinski, Timothy J.; Brown, Steven D.; Davison, Brian H.; Covalla, Sean F.; Sillers, W. Ryan; Xu, Haowen; Tsakraklides, Vasiliki; Hogsett, David A.

2012-01-24T23:59:59.000Z

180

Embargoed Deletion  

NLE Websites -- All DOE Office Websites (Extended Search)

PNAS proof PNAS proof Embargoed Deletion of Cel48S Q:1 from Clostridium thermocellum ; 2 Daniel G. Olson a,b,c , Shital A. Tripathi a,c , Richard J. Giannone c,d , Jonathan Lo b,c , Nicky C. Caiazza a,c , David A. Hogsett a,c , Robert Hettich c,d , Adam M. Guss b,c , Genia Dubrovsky b,c , and Lee R. Lynd a,b,c,e,1 a Mascoma Corporation, NH 03766; b Thayer School of Engineering and e Department of Biological Sciences, Dartmouth College, NH 03755; and c BioEnergy Science Center, d Oak Ridge National Laboratory, TN 37830 Q:3 Edited* by Lonnie O'Neal Ingram, University of Florida, Gainesville, FL, and approved August 16, 2010 (received for review April 9, 2010) Clostridium thermocellum is a thermophilic anaerobic bacterium that rapidly solubilizes cellulose with the aid of a multienzyme cel- lulosome complex. Creation of knockout mutants for Cel48S (also known as CelS, S S , and S8), the most abundant cellulosome

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181

Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum  

NLE Websites -- All DOE Office Websites (Extended Search)

Redirecting Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum Yu Deng a,c , Daniel G. Olson a,c , Jilai Zhou a,c , Christopher D. Herring a,b,c , A. Joe Shaw d , Lee R. Lynd a,b,c,n a Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA b Mascoma Corporation, Lebanon, NH 03766, USA c BioEnergy Science Center, Oak Ridge, TN 37830, USA d Novogy, Inc. Cambridge, MA 02138, USA a r t i c l e i n f o Article history: Received 24 August 2012 Received in revised form 6 November 2012 Accepted 16 November 2012 Available online 29 November 2012 Keywords: Clostridium thermocellum Ethanol yield Pyruvate kinase Malate shunt a b s t r a c t In Clostridium thermocellum, a thermophilic anaerobic bacterium able to rapidly ferment cellulose to ethanol, pyruvate kinase (EC 2.7.1.40) is absent based on both the genome sequence and enzymatic

182

gkq1281 1..15  

NLE Websites -- All DOE Office Websites (Extended Search)

Insights Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725 Phuongan Dam 1,2,3 , Irina Kataeva 2,3 , Sung-Jae Yang 2,3 , Fengfeng Zhou 1,2,3 , Yanbin Yin 1,2,3 , Wenchi Chou 1,3 , Farris L. Poole II 2,3 , Janet Westpheling 3,4 , Robert Hettich 3 , Richard Giannone 3 , Derrick L. Lewis 3,5 , Robert Kelly 3,5 , Harry J. Gilbert 2,6 , Bernard Henrissat 7 , Ying Xu 1,2,3, * and Michael W. W. Adams 2,3, * 1 Institute of Bioinformatics, 2 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, 3 BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, 4 Department of Genetics, University of Georgia, Athens, GA 30602, 5 Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, 6 Complex Carbohydrate Research Center, University

183

Transgenic Plants Lower the Costs of Cellulosic Biofuels (Fact Sheet)  

DOE Green Energy (OSTI)

A new transgenic maize was observed to be less recalcitrant than wild-type biomass, as manifested through lower severity requirements to achieve comparable levels of conversion. Expression of a single gene derived from bacteria in plants has resulted in transgenic plants that are easier and cheaper to convert into biofuels. Part of the high production cost of cellulosic biofuels is the relatively poor accessibility of substrates to enzymes due to the strong associations between plant cell wall components. This biomass recalcitrance makes costly thermochemical pretreatment necessary. Scientists at the National Renewable Energy Laboratory (NREL) have created transgenic maize expressing an active glycosyl hydrolase enzyme, E1 endoglucanase, originally isolated from a thermophilic bacterium, Acidothermus cellulolyticus. This engineered feedstock was observed to be less recalcitrant than wild-type biomass when subjected to reduced severity pretreatments and post-pretreatment enzymatic hydrolysis. This reduction in recalcitrance was manifested through lower severity requirements to achieve comparable levels of conversion of wild-type biomass. The improvements observed are significant enough to positively affect the economics of the conversion process through decreased capital construction costs and decreased degradation products and inhibitor formation.

Not Available

2011-11-01T23:59:59.000Z

184

Interactions of Endoglucanases with Amorphous Cellulose Films Resolved by Neutron Reflectometry and Quartz Crystal Microbalance with Dissipation Monitoring  

Science Conference Proceedings (OSTI)

A study of the interaction of four endoglucanases with amorphous cellulose films by neutron reflectometry (NR) and quartz crystal microbalance with dissipation monitoring (QCM-D) is reported. The endoglucanases include a mesophilic fungal endoglucanase (Cel45A from H. insolens), a processive endoglucanase from a marine bacterium (Cel5H from S. degradans), and two from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima). The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. The endoglucanases displayed highly diverse behavior. Cel45A and Cel5H, which possess carbohydrate-binding modules (CBMs), penetrated and digested within the bulk of the films to a far greater extent than Cel9A and Cel5A, which lack CBMs. While both Cel45A and Cel5H were active within the bulk of the films, striking differences were observed. With Cel45A, substantial film expansion and interfacial broadening were observed, whereas for Cel5H the film thickness decreased with little interfacial broadening. These results are consistent with Cel45A digesting within the interior of cellulose chains as a classic endoglucanase, and Cel5H digesting predominantly at chain ends consistent with its designation as a processive endoglucanase.

Cheng, Gang [Joint Bioenergy Institute; Liu, Zelin [Virginia Polytechnic Institute and State University (Virginia Tech); Kent, Michael S [Sandia National Laboratories (SNL); Majewski, Jaroslaw [Los Alamos National Laboratory (LANL); Michael, Jablin [Los Alamos National Laboratory (LANL); Jaclyn, Murton K [Sandia National Laboratories (SNL); Halbert, Candice E [ORNL; Datta, Supratim [Joint Bioenergy Institute; Chao, Wang [Virginia Polytechnic Institute and State University (Virginia Tech); Brown, Page [Sandia National Laboratories (SNL)

2012-01-01T23:59:59.000Z

185

Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically  

SciTech Connect

Chloroflexus aurantiacus J-10-fl is a thermophilic green bacterium, a filamentous anoxygenic phototroph, and the model organism of the phylum Chloroflexi. We applied high-throughput, liquid chromatography-mass spectrometry in a global quantitative proteomics investigation of C. aurantiacus cells grown under oxic (chemoorganoheterotrophically) and anoxic (photoorganoheterotrophically) redox states. Our global analysis identified 13,524 high-confidence peptides that matched to 1,286 annotated proteins, 242 of which were either uniquely identified or significantly increased in abundance under anoxic culture conditions. Fifty-three of the 242 proteins are previously characterized photosynthesis-related proteins, including chlorosome proteins, proteins involved in the bacteriochlorophyll biosynthesis, 3-hydroxypropionate (3-OHP) CO2 fixation pathway, and components of electron transport chains. The remaining 190 proteins have not previously been reported. Of these, five proteins were found to be encoded by genes from a novel operon and observed only in photoheterotrophically grown cells. These proteins candidates may prove useful in further deciphering the phototrophic physiology of C. aurantiacus and other filamentous anoxygenic phototrophs.

Cao, Li; Bryant, Donald A.; Schepmoes, Athena A.; Vogl, Kajetan; Smith, Richard D.; Lipton, Mary S.; Callister, Stephen J.

2012-01-17T23:59:59.000Z

186

Inside the guts of wood-eating catfishes: can they digest wood?  

E-Print Network (OSTI)

the cellulolytic system of the wood-boring marine mollusk2008), how diVerent are the wood-eating catWshes from otherendosymbionts and digest wood, or are these wood- eating

German, Donovan P.

2009-01-01T23:59:59.000Z

187

Complete Genome Sequence of the Marine Cellulose-and Xylan-Degrading Bacterium Glaciecola sp. Strain 4H-3-7+YE-5  

E-Print Network (OSTI)

was funded in part by the BioEnergy Science Center, a U.S.Department of Energy Bioenergy Research Center supported bywas funded in part by the BioEnergy Science Center, a U.S.

Klippel, Barbara

2013-01-01T23:59:59.000Z

188

The ultimate ethanol: Technoeconomic evaluation of ethanol manufacture, comparing yeast vs Zymomonas bacterium fermentations. [Zymomonas mobilis:a5; Saccharomyces cerevisiae:a6  

SciTech Connect

If ethanol could be produced at a low enough price to serve as the precursor to ethylene and butadiene, it and its derivatives could account for 159 billion lb, or 50% of the US production of 316 billion lb of synthetic organic chemicals, presently valued at $113 billion. This use would consume 3.4 billion bu of corn, or {approximately}40% of the corn crop. This study evaluates advance process engineering and genetic engineering techniques that could generate savings and reduce production costs. The most rewarding development strategy appears to be to demonstrate at pilot scale the use of immobilized Zymomonas mobilis bacteria in a fluidized-bed bioreactor operating in a continuous mode over an extended period of time. Throughput should be adjusted to control product concentration at {approximately}100 g/L (i.e., as close to the threshold of inhibition as possible). There appears to be no inherent design limitation to effect the engineering improvements required in the advanced process operation. The above scenario assumes that the presently available, product-inhibited organisms would be used. In a longer-term, more difficult research effort, it might be possible to reduce or eliminate product inhibition. As a result, price would be reduced further to $1.75 for the Zymomonas system or $1.85 for the yeast fermentation. It is recommended that the engineering proveout of the advanced process be continued at a pilot scale and that a laboratory program aimed at reducing product inhibition and/or increasing specific productivity be initiated. 49 refs., 11 figs., 19 tabs.

Busche, R.M. (Bio En-Gene-Er Associates, Inc., Wilmington, DE (United States)); Scott, C.D.; Davison, B.H. (Oak Ridge National Lab., TN (United States)); Lynd, L.R. (Dartmouth Coll., Hanover, NH (United States))

1991-08-01T23:59:59.000Z

189

Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastro-intestinal tract  

Science Conference Proceedings (OSTI)

Victivallis vadensis ATCC BAA-548 represents the first cultured representative from the novel phylum Lentisphaerae, a deep-branching bacterial lineage. Few cultured bacteria from this phylum are known, and V. vadensis therefore represents an important organism for evolutionary studies. V. vadensis is a strictly anaerobic sugar-fermenting isolate from the human gastro-intestinal tract.

Van Passel, Mark W.J. [Wageningen University and Research Centre, The Netherlands; Kant, Ravi [University of Helsinki; Palva, Airi [University of Helsinki; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Davenport, Karen W. [Los Alamos National Laboratory (LANL); Sims, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; De Vos, Willem M. [Wageningen University and Research Centre, The Netherlands; Smidt, Hauke [Wageningen University and Research Centre, The Netherlands; Zoetendal, Erwin G. [Wageningen University and Research Centre, The Netherlands

2011-01-01T23:59:59.000Z

190

Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692T) from the alkaline Lake Magadi in the East African Rift  

SciTech Connect

Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacte- rium that is motile via periplasmic flagella. The type strain of the species, Z-7692T, was iso- lated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second 'true' member of the genus Spirochaeta with a genome-sequenced type strain to be pub- lished. The 3,285,855 bp long genome of strain Z-7692T with its 2,817 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Scheuner, Carmen [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Teshima, Hazuki [Los Alamos National Laboratory (LANL); Held, Brittany [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute

2013-01-01T23:59:59.000Z

191

Binding and Direct Electrochemistry of OmcA, an Outer-Membrane Cytochrome from an Iron Reducing Bacterium, with Oxide Electrodes: A Candidate Biofuel Cell System  

SciTech Connect

Dissimilatory iron-reducing bacteria transfer electrons to solid ferric respiratory electron acceptors. Outer-membrane cytochromes expressed by these organisms are of interest in both microbial fuel cells and biofuel cells. We use optical waveguide lightmode spectroscopy (OWLS) to show that OmcA, an 85 kDa decaheme outer-membrane c-type cytochrome from Shewanella oneidensis MR-1, adsorbs to isostructural Al2O3 and Fe2O3 in similar amounts. Adsorption is ionic-strength and pH dependent (peak adsorption at pH 6.5–7.0). The thickness of the OmcA layer on Al2O3 at pH 7.0 [5.8 ± 1.1 (2r) nm] from OWLS is similar, within error, to that observed using atomic force microscopy (4.8 ± 2 nm). The highest adsorption density observed was 334 ng cm 2 (2.4 · 1012 molecules cm 2), corresponding to a monolayer or 9.9 nm diameter spheres or submonolayer coverage by smaller molecules. Direct electrochemistry of OmcA on Fe2O3 electrodes was observed using cyclic voltammetry, with cathodic peak potentials of 380 to 320 mV versus Ag/AgCl. Variations in the cathodic peak positions are speculatively attributed to redox-linked conformation change or changes in molecular orientation. OmcA can exchange electrons with ITO electrodes at higher current densities than with Fe2O3. Overall, OmcA can bind to and exchange electrons with several oxides, and thus its utility in fuel cells is not restricted to Fe2O3.

Eggleston, Carrick M.; Voros, Janos; Shi, Liang; Lower, Brian H.; Droubay, Timothy; Colberg, Patricia J.

2008-02-15T23:59:59.000Z

192

Complete genome sequence of Saccharomonospora viridis type strain (P101T)  

E-Print Network (OSTI)

diversity in hot synthetic compost as revealed by PCR-isolated from mushroom compost. Soil Biol Biochem 2001, 33:thermophile, hot compost, Gram-negative actinomycete,

Pati, Amrita

2010-01-01T23:59:59.000Z

193

Focus Area 2 - Biomass Deconstruction and Conversion : BioEnergy...  

NLE Websites -- All DOE Office Websites (Extended Search)

Deconstruction and Conversion BESC research in biomass deconstruction and conversion targets CBP by studying model organisms and thermophilic anaerobes to understand novel...

194

Computational Methods for Evaluating Microbial Diversity  

E-Print Network (OSTI)

I Methods for environmental diversity surveys using the 16Sassessment of thermophile diversity. Biochem Soc Trans, 32(G. G. Lødeng. Microbial diversity during biodegradation of

Soergel, David Alexander Wolfgang

2010-01-01T23:59:59.000Z

195

High level expression of Acidothermus cellulolyticus ?-1, 4-endoglucanase in transgenic rice enhances the hydrolysis of its straw by cultured cow gastric fluid  

Science Conference Proceedings (OSTI)

Large-scale production of effective cellulose hydrolytic enzymes is the key to the bioconversion of agricultural residues to ethanol. The goal of this study was to develop a rice plant as a bioreactor for the large-scale production of cellulose hydrolytic enzymes via genetic transformation, and to simultaneously improve rice straw as an efficient biomass feedstock for conversion of cellulose to glucose. In this study, the cellulose hydrolytic enzyme {beta}-1, 4-endoglucanase (E1) from the thermophilic bacterium Acidothermus cellulolyticus was overexpressed in rice through Agrobacterium-mediated transformation. The expression of the bacterial gene in rice was driven by the constitutive Mac promoter, a hybrid promoter of Ti plasmid mannopine synthetase promoter and cauliflower mosaic virus 35S promoter enhancer with the signal peptide of tobacco pathogenesis-related protein for targeting the protein to the apoplastic compartment for storage. A total of 52 transgenic rice plants from six independent lines expressing the bacterial enzyme were obtained, which expressed the gene at high levels with a normal phenotype. The specific activities of E1 in the leaves of the highest expressing transgenic rice lines were about 20 fold higher than those of various transgenic plants obtained in previous studies and the protein amounts accounted for up to 6.1% of the total leaf soluble protein. Zymogram and temperature-dependent activity analyses demonstrated the thermostability of the enzyme and its substrate specificity against cellulose, and a simple heat treatment can be used to purify the protein. In addition, hydrolysis of transgenic rice straw with cultured cow gastric fluid yielded almost twice more reducing sugars than wild type straw. Taken together, these data suggest that transgenic rice can effectively serve as a bioreactor for large-scale production of active, thermostable cellulose hydrolytic enzymes. As a feedstock, direct expression of large amount of cellulases in transgenic rice may also facilitate saccharification of cellulose in rice straw and significantly reduce the costs for hydrolytic enzymes.

Chou, Hong L.; Dai, Ziyu; Hsieh, Chia W.; Ku, Maurice S.

2011-12-10T23:59:59.000Z

196

Complete Genome Sequence of the Anaerobic Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LFT  

Science Conference Proceedings (OSTI)

The genome of the anaerobic halophilic alkalithermophile Natranaerobius thermophiles consists of one chromosome and two plasmids.The present study is the first to report the completely sequenced genome of polyextremophile and the harboring genes harboring genes associated with roles in regulation of intracellular osmotic pressure, pH homeostasis, and thermophilic stability.

Mesbah, Noha [University of Georgia, Athens, GA; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Wiegel, Juergen [University of Georgia, Athens, GA

2011-01-01T23:59:59.000Z

197

POPULATION ECOLOGY Comparative Predation on Naturally Occurring Gypsy Moth  

E-Print Network (OSTI)

bacterium.16 Another health worry is horizontal gene transfer. Because diseases like Ebola, AIDS, Lyme

Berkowitz, Alan R.

198

Rangeland Ecol Manage 59:330333 | May 2006 Grass Repellency to the Red Imported Fire Ant  

E-Print Network (OSTI)

in homeostasis so that another organism, with disparate genetic interests, might also benefit? This question has of cellulolytic fungi, which reaches its pinnacle in the mound-building genera Macrotermes and Odontotermes soil at rates exceeding that of other mound- building termites in the environment (Table 5.3). The Nest

Perry, Gad

199

This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research  

E-Print Network (OSTI)

due to the fact that large amounts of cellulases are required to breakdown cellulose to fermentable. Directed evolution of a thermophilic beta-glucosidase for cellulosic bioethanol production. Appl. Biochem

Zhao, Huimin

200

Structure of the Soluble Domain of Cytochrome f from the Cyanobacterium Phormidium laminosum,  

E-Print Network (OSTI)

Spirulina maxima (22). Properties of cytochrome f from the moderately thermophilic cyanobacterium Phormidium to the high entropic cost of ordering a water molecule. The conservation and rarity of the buried water chain

Cramer, William A.

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

doi:10.1016/j.copbio.2008.04.007  

NLE Websites -- All DOE Office Websites (Extended Search)

Extremely thermophilic microorganisms for biomass conversion: status and prospects Sara E Blumer-Schuette 1,4 , Irina Kataeva 2,4 , Janet Westpheling 3,4 , Michael WW Adams 2,4 and...

202

This Provisional PDF  

NLE Websites -- All DOE Office Websites (Extended Search)

thermophilic simultaneous saccharification and fermentation (tSSF) Biotechnology for Biofuels 2012, 5:43 doi:10.11861754-6834-5-43 Kara K Podkaminer (kara.podkaminer@nrel.gov)...

203

The winds of (evolutionary) change: Breathing new life into microbiology  

DOE Green Energy (OSTI)

To date, over 1500 prokaryotes have been characterized by small subunit rRNA sequencing and molecular phylogeny has had an equally profound effect on our understanding of relationship among eukaryotic microorganisms. The universal phylogenetic tree readily shows however how artificial the strong distinction between the eukaryote and prokaryotes has become. The split between the Archaea and the Bacteria is now recognized as the primary phylogenetic division and that the Eucarya have branched from the same side of the tree as the Archaea. Both prokaryotic domains would seem to be of thermophilic origin suggesting that life arose in a very warm environment. Among the Archaea, all of the Crenarchaeota cultured to date are thermophiles, and the deepest euryarchaeal branchings are represented exclusively by thermophiles. Among the Bacteria, the deepest known branchings are again represented exclusively by thermophiles, and thermophilia is widely scattered throughout the domain. The Archaea comprise a small number of quite disparate phenotypes that grow in unusual niches. All are obligate or facultative anaerobes. All cultured crenarchaeotes are thermophilic, some even growing optimally above the normal boiling temperature of water. The Archaeoglobales are sulfate reducers growing at high temperatures. The extreme halophiles grow only in highly saline environments. The methanogens are confined to a variety of anaerobic niches, often thermophilic. The Bacteria, on the other hand, are notable as being the source of life`s photosynthetic capacity. Five kingdoms of bacteria contain photosynthetic species; and each of the five manifests a distinct type of (chlorophyll-based) photosynthesis.

Olsen, G.J.; Woese, C.R. [Univ. of Illinois, Urbana, IL (United States). Dept. of Microbiology; Overbeek, R.A. [Argonne National Lab., IL (United States)

1996-03-01T23:59:59.000Z

204

Dispersant solutions for dispersing hydrocarbons  

DOE Patents (OSTI)

A dispersant solution includes a hydrocarbon dispersing solution derived from a bacterium from ATCC 75527, ATCC 75529, or ATCC 55638.

Tyndall, Richard L. (Clinton, TN)

1997-01-01T23:59:59.000Z

205

Doctor blading artificial nacre and bone  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

206

Bird Bones in Bending and Torsion  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

207

Effect of aging on the microstructure, hardness and chemical ...  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

208

Molecular and ultrastructural changes in human bone with ...  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

209

Bioinspired Grippers Based on the Seahorse Tail  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

210

Multi-Scale Study of Deformation and Fracture in Diseased Bone  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

211

Protective Role of Arapaima Scales: Structure and Mechanical ...  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

212

Dentin Hard Tissue Stabilization Using Functionalized Chitosan ...  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

213

Roles of collagen fibrils on the mechanical properties of skin  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

214

Bio-inspired mechanical strengthening of single crystals of calcite  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

215

Probing the interaction of cells-nanoparticles using Force-Distance  

Science Conference Proceedings (OSTI)

Microbial synthesis and fabrication of palladium nanoparticle catalysts by using the metal ion-reducing bacterium Shewanella algae · Micromechanical ...

216

Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010  

Science Conference Proceedings (OSTI)

Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S se- quence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2T as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analy- sis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2T (= DSM 2912 = NBRC 15312) and propose its reclassi- fication as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da Costa and Rainey, 2010 is emended. The 3,384,766 bp genome with its 3,323 protein-coding and 78 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Chen, Feng [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Daum, Chris [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Chang, Yun-Juan [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute

2011-01-01T23:59:59.000Z

217

Cellulases: ambiguous nonhomologous enzymes in a genomic perspective  

Science Conference Proceedings (OSTI)

The key material for bioethanol production is cellulose, which is one of the main components of the plant cell wall. Enzymatic depolymerization of cellulose is an essential step in bioethanol production, and can be accomplished by fungal and bacterial cellulases. Most of the biochemically characterized bacterial cellulases come from only a few cellulose-degrading bacteria, thus limiting our knowledge of a range of cellulolytic activities that exist in nature. The recent explosion of genomic data offers a unique opportunity to search for novel cellulolytic activities; however, the absence of clear understanding of structural and functional features that are important for reliable computational identification of cellulases precludes their exploration in the genomic datasets. Here, we explore the diversity of cellulases and propose a genomic approach to overcome this bottleneck.

Sukharnikov, Leonid O [ORNL; Cantwell, Brian J [ORNL; Podar, Mircea [ORNL; Zhulin, Igor B [University of Tennessee (UTK) and Oak Ridge National Laboratory (ORNL)

2011-01-01T23:59:59.000Z

218

Exo-endo cellulase fusion protein  

DOE Patents (OSTI)

The present invention relates to a heterologous exo-endo cellulase fusion construct, which encodes a fusion protein having cellulolytic activity comprising a catalytic domain derived from a fungal exo-cellobiohydrolase and a catalytic domain derived from an endoglucanase. The invention also relates to vectors and fungal host cells comprising the heterologous exo-endo cellulase fusion construct as well as methods for producing a cellulase fusion protein and enzymatic cellulase compositions.

Bower, Benjamin S. (Palo Alto, CA); Larenas, Edmund A. (Palo Alto, CA); Mitchinson, Colin (Palo Alto, CA)

2012-01-17T23:59:59.000Z

219

A study of over-production and enhanced secretion of enzymes. Quarterly report 2  

DOE Green Energy (OSTI)

This project is concerned with the over-production of ligno-cellulolytic enzymes which are relevant to the paper-pulp industry and agricultural community. Since ligno-cellulosics are components of wood, the project involves the forest, a renewable energy resource. Attention is focused on the following: over-production of polyphenol oxidase; establishment of the route of polyphenol oxidase secretion; regulation of polyphenol oxidase secretion; purification of extracellular oxidase.

Dashek, W.V.

1993-04-08T23:59:59.000Z

220

fulltext.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

I: I: characterization of the extracellular proteome of the extreme thermophile Caldicellulosiruptor saccharolyticus by GeLC-MS 2 David Muddiman & Genna Andrews & Derrick Lewis & Jaspreet Notey & Robert Kelly Received: 3 May 2010 / Revised: 13 June 2010 / Accepted: 20 June 2010 / Published online: 10 July 2010 # Springer-Verlag 2010 Abstract The proteome of extremely thermophilic micro- organisms affords a glimpse into the dynamics of microbial ecology of high temperature environments. The secretome, or extracellular proteome of these microorganisms, no doubt harbors technologically important enzymes and other ther- mostable biomolecules that, to date, have been characterized only to a limited extent. In the first of a two-part study on selected thermophiles, defining the secretome requires a sample preparation method that has no negative impact on all downstream

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
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to obtain the most current and comprehensive results.


221

Why Sequence Thermovibrio ammonificans?  

NLE Websites -- All DOE Office Websites (Extended Search)

Thermovibrio ammonificans? Thermovibrio ammonificans? Thermophilic and hyperthermophilic microorganisms are an important component of geothermal ecosystems, which include continental hot springs, solfataras, and both shallow and deep-sea hydrothermal vents. These organisms play a critical role in our understanding of several fundamental biological processes, such as microbial adaptations to elevated temperatures and prokaryotic evolution, and they represent a natural source for the discovery of thermostable enzymes. T. ammonificans in the process of dividing. Photo courtesy Valentin Starovoytov and Costantino Vetriani, Rutgers University The isolation and characterization of microorganisms that are thermophilic, anaerobic, and chemolithoautotrophic (getting energy by oxidizing inorganic

222

AEM.01400-10v1.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

Oct 8, 2010 rmk Oct 8, 2010 rmk Phylogenetic, microbiological and glycoside hydrolase diversity within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor 5 Sara E. Blumer-Schuette, Derrick L. Lewis # , and Robert M. Kelly * Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905 # Present address: Novozymes Biologicals, Salem, VA 10 Submitted to: Applied and Environmental Microbiology (June, 2010) Running title: Plant biomass deconstruction by Caldicellulosiruptor species 15 Keywords: Caldicellulosiruptor, extreme thermophile, plant biomass, glycoside hydrolases *Address correspondence to: Robert M. Kelly 20 Department of Chemical and Biomolecular Engineering

223

Licensing : BioEnergy Science Center  

NLE Websites -- All DOE Office Websites (Extended Search)

Inventions Inventions 32 records A Broad Environmental Stress-Inducible Promoter and its Application in Crops A Novel Monolignol that reduces recalcitrance of plant cell walls Caloramator sp. Tolerance of Pretreatment Inhibitors from LIgnocellulosics Cellulose and xylan fermentation by novel anaerobic thermophilic clostridia isolated from self-heated biocompost Compositions and Methods for Improved Plant Feedstock Consolidated Bioprocessing Method using Thermophilic Microorganisms Engineering male sterility or non-transgenic pollen by pollen-specific expression of a restriction enzyme Flow-through Pretreatment of Lignocellulosic Biomass with Inorganic Nanoporous Membranes Gene and Gene Clusters that Enable Degradation of Recalcitrant Biological Materials Genes to Increase Growth in Monocots

224

Available Technologies: Engineering Bacteria for Wastewater ...  

Offers carbon sequestration ... The bacterium uses the metabolic energy derived from sulfide oxidation and the carbon derived from CO2 to generate desired products.

225

Alistair Rogers | BNL  

NLE Websites -- All DOE Office Websites (Extended Search)

A., Koenig, K., Newman, L., Taghavi, S., and Van Der Lelie, D. Inoculation of hybrid poplar with the endophytic bacterium Enterobacter sp. 638 increases biomass but does not...

226

Poster Session - Programmaster.org  

Science Conference Proceedings (OSTI)

The metal ion-reducing bacterium, Shewanella algae, was able to reduced metal ... Developed here is a micro-scale-based flow stress model of cortical bone.

227

E13: An Experimentally-based Flow Stress Model for Cortical Bone  

Science Conference Proceedings (OSTI)

Developed here is a micro-scale-based flow stress model of cortical bone. In order to ... Catalysts by Using the Metal Ion-reducing Bacterium Shewanella Algae.

228

Overcoming the Brittleness of Glass through Bio-inspiration and ...  

Science Conference Proceedings (OSTI)

The micro-cracks, positioned along specific surfaces within the material, coalesce ... Catalysts by Using the Metal Ion-reducing Bacterium Shewanella Algae.

229

The Influence of Nb on the Rare Earth Heavy Rail Steel Mechanical ...  

Science Conference Proceedings (OSTI)

Micro-alloying through the additions of Nb or rare earth (RE) elements has been proved ... Group Metals by the Metal-ion Reducing Bacterium Shewanella Algae.

230

The Mechanical Property and Potential Biomedical Applications of ...  

Science Conference Proceedings (OSTI)

Based on the micro-CT and SEM observation, we confirmed that the cuttlebone could ... Catalysts by Using the Metal Ion-reducing Bacterium Shewanella Algae.

231

The Molecular Foundry  

NLE Websites -- All DOE Office Websites (Extended Search)

of the respiratory capability of the dissimilatory metal reducing bacterium Shewanella oneidensis MR-1. Shewanella uses a network of multiheme cytochromes to transfer...

232

2013 | U.S. DOE Office of Science (SC)  

Office of Science (SC) Website

& Innovation The Other Route to Biofuels Scientists identify key genes for increasing oil in plant leaves. Read More An image of the bacterium Caldicellulosiruptor bescii,...

233

untitled  

NLE Websites -- All DOE Office Websites (Extended Search)

anaerobic bacterium 'Anaerocellum thermophilum' strain Z-1320 was isolated from a hot spring almost two decades ago and deposited in the German Collection of Microorganisms...

234

Impact of Laser-sustained Plasma on Titanium Substrates without ...  

Science Conference Proceedings (OSTI)

Difference between Life and Death of Bacterium against Microwave Power under ... Sintering and Plastic Deformation of Ceramics under Pulsed Electric Current.

235

Understanding Non-thermal Microwave Effects in Materials Processing  

Science Conference Proceedings (OSTI)

Difference between Life and Death of Bacterium against Microwave Power under ... Sintering and Plastic Deformation of Ceramics under Pulsed Electric Current.

236

Sintering and Plastic Deformation of Ceramics under Pulsed Electric ...  

Science Conference Proceedings (OSTI)

Furthermore, an overview is given of the microscopic pulsed electric current ... Difference between Life and Death of Bacterium against Microwave Power under

237

Microwave Application to Environmental Problems : Model ...  

Science Conference Proceedings (OSTI)

Difference between Life and Death of Bacterium against Microwave Power under ... Sintering and Plastic Deformation of Ceramics under Pulsed Electric Current.

238

In Situ Dilatometry and Electrical Resistivity Measurements of ...  

Science Conference Proceedings (OSTI)

Difference between Life and Death of Bacterium against Microwave Power under ... Sintering and Plastic Deformation of Ceramics under Pulsed Electric Current.

239

Exchange of Cs Ion in Clay Minerals by Microwave Application  

Science Conference Proceedings (OSTI)

Difference between Life and Death of Bacterium against Microwave Power under ... Sintering and Plastic Deformation of Ceramics under Pulsed Electric Current.

240

Application of Microwave Heating for Reduction of ...  

Science Conference Proceedings (OSTI)

Difference between Life and Death of Bacterium against Microwave Power under ... Sintering and Plastic Deformation of Ceramics under Pulsed Electric Current.

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


241

Experimental Studies on Biological Responses to the Applications ...  

Science Conference Proceedings (OSTI)

Difference between Life and Death of Bacterium against Microwave Power under ... Sintering and Plastic Deformation of Ceramics under Pulsed Electric Current.

242

Rapid Baking of Friction Material with Microwaves  

Science Conference Proceedings (OSTI)

The curing is followed by baking in electrical oven with multistage heating for ... Difference between Life and Death of Bacterium against Microwave Power under

243

The Bulletin - BNL's Weekly Newspaper  

NLE Websites -- All DOE Office Websites (Extended Search)

that infect bacteria, might be used as a weapon against the bacterium that causes Lyme disease. This idea went nowhere but got John interested in producing surface proteins...

244

Bioenergy - Super microbe | ornl.gov  

NLE Websites -- All DOE Office Websites (Extended Search)

microbe A newly discovered microbe may offer a cost-effective solution that makes biofuel production more efficient. Researchers have found an anaerobic bacterium called...

245

Directed enzyme evolution: beyond the low-hanging fruit Moshe Goldsmith and Dan S Tawfik  

E-Print Network (OSTI)

to the ratio of conversion rates at all substrate concentrations, and therefore comprises the stan- dard the nucleotide and sugar 1-phosphate promiscuity of nucleotidyltransferase RmlA via directed evolution. J Biol: Directed evolution of a thermophilic beta-glucosidase for cellulosic bioethanol production. Appl Biochem

Tawfik, Dan S.

246

Long term biosustainability in a high energy, low diversity crustal biome  

DOE Green Energy (OSTI)

Geochemical, microbiological, and molecular analyses of alkaline saline groundwater at 2.8 kilometers depth in Archaean metabasalt revealed a microbial biome dominated by a single phylotype affiliated with thermophilic sulfate reducers belonging to Firmicutes. These sulfate reducers were sustained by geologically produced sulfate and hydrogen at concentrations sufficient to maintain activities for millions of years with no apparent reliance on photosynthetically derived substrates.

Lin, L-H.; Wang, P-L.; Rumble, D.; Lippmann-Pipke, J.; SherwoodLollar, B.; Boice, E.; Pratt, L.; Brodie, E.; Hazen, T.C.; Andersen,G.L.; DeSantis, T.; Moser, D.P.; Kershaw, D.; Onstott, T.

2006-10-01T23:59:59.000Z

247

Anaerobic methane oxidation in metalliferous hydrothermal sediments: influence on carbon flux and  

E-Print Network (OSTI)

Biology, 2 Department of Earth and Planetary Sciences, Harvard University, 3 School of Engineering and Applied Science, Harvard University, Cambridge, MA 01238, USA. 4 Department of Marine Sciences, University mesophilic to thermophilic AOM in hydro- thermal sediments recovered from the Middle Valley vent field

Girguis, Peter R.

248

Invention and International Diffusion of Climate Change Mitigation Technologies: An Empirical Approach  

E-Print Network (OSTI)

acquisition system of on-line sensors, which provided measurements of pH, temperature, rH, and biogas ¯ow rate model only the biogas production rate Q is meas- urable, and we suppose that the initial values of Bioinstrumentation and Automation, BAS, So®a. References Ahring BK. 1995. Methanogenesis in thermophilic biogas

Paris-Sud XI, Université de

249

Recycle of enzymes and substrate following enzymatic hydrolysis of steam-pretreated aspenwood  

SciTech Connect

The commercial production of chemicals and fuels from lignocellulosic residues by enzymatic means still requires considerable research on both the technical and economic aspects. Two technical problems that have been identified as requiring further research are the recycle of the enzymes used in hydrolysis and the reuse of the recalcitrant cellulose remaining after incomplete hydrolysis. Enzyme recycle is required to lower the cost of the enzymes, while the reuse of the spent cellulose will lower the feedstock cost. The conversion process studied was a combined enzymatic hydrolysis and fermentation (CHF) procedure that utilized the cellulolytic enzymes derived from the fungus Trichoderma harzianum E58 and the yeast Saccharomyces cerevisiae. The rate and extent of hydrolysis and ethanol production was monitored as was the activity and hydrolytic potential of the enzymes remaining in the filtrate after the hydrolysis period. When a commercial cellulose was used as the substrate for a routine 2-day CHF process, 60% of the original filter paper activity could be recovered. When steam-treated, water-extracted aspenwood was used as the substrate, only 13% of the original filter paper activity was detected after a similar procedure. The combination of 60% spent enzymes with 40% fresh enzymes resulted in the production of 30% less reducing sugars than the original enzyme mixture. Since 100% hydrolysis of the cellulose portion is seldom accomplished in an enzymatic hydrolysis process, the residual cellulose was used as a substrate for the growth of T. harzianum E58 and production of cellulolytic enzymes. The residue remaining after the CHF process was used as a substrate for the production of the cellulolytic enzymes. The production of enzymes from the residue of the Solka Floc hydrolysis was greater than the production of enzymes from the original Solka Floc. (Refs. 14).

Mes-Hartree, M.; Hogan, C.M.; Saddler, J.N.

1987-09-01T23:59:59.000Z

250

Nucleotide sequences specific to Francisella tularensis and methods for the detection of Francisella tularensis  

DOE Patents (OSTI)

Described herein is the identification of nucleotide sequences specific to Francisella tularensis that serves as a marker or signature for identification of this bacterium. In addition, forward and reverse primers and hybridization probes derived from these nucleotide sequences that are used in nucleotide detection methods to detect the presence of the bacterium are disclosed.

McCready, Paula M. (Tracy, CA); Radnedge, Lyndsay (San Mateo, CA); Andersen, Gary L. (Berkeley, CA); Ott, Linda L. (Livermore, CA); Slezak, Thomas R. (Livermore, CA); Kuczmarski, Thomas A. (Livermore, CA); Vitalis, Elizabeth A (Livermore, CA)

2007-02-06T23:59:59.000Z

251

Processing of cellulosic material by a cellulase-containing cell-free fermentate produced from cellulase-producing bacteria, ATCC 55702  

DOE Patents (OSTI)

Bacteria which produce large amounts of a cellulase-containing cell-free fermentate, have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase degrading bacterium ATCC 55702, which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic materials.

Dees, H. Craig (Lenoir City, TN)

1998-01-01T23:59:59.000Z

252

Synergistic Enhancement of Cellobiohydrolase Performance on Pretreated Corn Stover by Addition of Xylanase and Esterase Activities  

Science Conference Proceedings (OSTI)

Significant increases in the depolymerization of corn stover cellulose by cellobiohydrolase I (Cel7A) from Trichoderma reesei were observed using small quantities of non-cellulolytic cell wall-degrading enzymes. Purified endoxylanase (XynA), ferulic acid esterase (FaeA), and acetyl xylan esterase (Axe1) all enhanced Cel7A performance on corn stover subjected to hot water pretreatment. In all cases, the addition of these activities improved the effectiveness of the enzymatic hydrolysis in terms of the quantity of cellulose converted per milligram of total protein. Improvement in cellobiose release by the addition of the non-cellulolytic enzymes ranged from a 13-84% increase over Cel7A alone. The most effective combinations included the addition of both XynA and Axe1, which synergistically enhance xylan conversions resulting in additional synergistic improvements in glucan conversion. Additionally, we note a direct relationship between enzymatic xylan removal in the presence of XynA and the enhancement of cellulose hydrolysis by Cel7A.

Selig, M. J.; Knoshaug E. P.; Adney, W. S.; Himmel, M. E.; Decker, S. R.

2007-11-01T23:59:59.000Z

253

JGI - Why Sequence Alvinella pompejana?  

NLE Websites -- All DOE Office Websites (Extended Search)

Pompeii Worm? Pompeii Worm? Alvinella pompeiiana One of the most thermophilic eukaryotes, Alvinella pompejana, the Pompeii worm, is a resident of the Pacific deep-sea hydrothermal vent area. These worms reside on black smoker chimneys 2500 meters under the ocean surface where they experience (1) the highest temperatures and temperature gradients known for any eukaryote (20-80°C), (2) a toxic soup of heavy metals, and (3) very low pH. Thus their environment is perhaps the most extreme known for any eukaryote. This project unites cDNA sequencing, which is crucial for genetic and protein analysis, with macromolecular structure determination by x-ray crystallography, solution small-angle x-ray scattering, and electron microscopy. Proteins from thermophilic sources, currently limited to unicellular bacteria and archaea, have proven to be

254

Methanogenic Population Dynamics during Start-Up of Anaerobic Digesters Treating Municipal Solid Waste  

E-Print Network (OSTI)

Abstract: An aggressive start-up strategy was used to initiate codigestion in two anaerobic, continuously mixed bench-top reactors at mesophilic (37°C) and thermophilic (55°C) conditions. The digesters were inoculated with mesophilic anaerobic sewage sludge and cattle manure and were fed a mixture of simulated municipal solid waste and biosolids in proportions that reflect U.S. production rates. The design organic loading rate was 3.1 kg volatile solids/m 3 /day and the retention time was 20 days. Ribosomal RNA-targeted oligonucleotide probes were used to determine the methanogenic community structure in the inocula and the digesters. Chemical analyses were performed to evaluate digester performance. The aggressive start-up strategy was successful for the thermophilic reactor, despite the use of a

Biosolids; Matt E. Griffin; Katherine D. Mcmahon; Roderick I. Mackie; Lutgarde Raskin

1997-01-01T23:59:59.000Z

255

Improvements of biomass deconstruction enzymes  

DOE Green Energy (OSTI)

Sandia National Laboratories and DSM Innovation, Inc. collaborated on the investigation of the structure and function of cellulases from thermophilic fungi. Sandia's role was to use its expertise in protein structure determination and X-ray crystallography to solve the structure of these enzymes in their native state and in their substrate and product bound states. Sandia was also tasked to work with DSM to use the newly solved structure to, using computational approaches, analyze enzyme interactions with both bound substrate and bound product; the goal being to develop approaches for rationally designing improved cellulases for biomass deconstruction. We solved the structures of five cellulases from thermophilic fungi. Several of these were also solved with bound substrate/product, which allowed us to predict mutations that might enhance activity and stability.

Sale, K. L.

2012-03-01T23:59:59.000Z

256

JGI - Why Sequence Terephthalate-Degrading Microbial Community?  

NLE Websites -- All DOE Office Websites (Extended Search)

a Terephthalate-Degrading Microbial Community? a Terephthalate-Degrading Microbial Community? Every year, enormous amounts of high-strength terephthalate-containing wastewater are produced as a byproduct of the plastics industry. The wastewater is currently treated by using anaerobic biological treatment processes that involve mesophilic (moderate-temperature-loving) microbes growing at 35-37°C. Recently, a thermophilic (heating-loving) terephthalate-degrading community growing at around 55°C has been developed in a lab-scale bioreactor as a more efficient alternative to the mesophilic process. Metagenomic characterization of the thermophilic bioreactor community, followed by perturbation studies, may lead to an optimized process, which will have significant impact on the plastic production industry in terms of wastewater treatment costs and operational

257

Mixed oxide nanoparticles and method of making  

DOE Green Energy (OSTI)

Methods and apparatus for producing mixed oxide nanoparticulates are disclosed. Selected thermophilic bacteria cultured with suitable reducible metals in the presence of an electron donor may be cultured under conditions that reduce at least one metal to form a doped crystal or mixed oxide composition. The bacteria will form nanoparticles outside the cell, allowing easy recovery. Selection of metals depends on the redox potentials of the reducing agents added to the culture. Typically hydrogen or glucose are used as electron donors.

Lauf, Robert J. (Oak Ridge, TN); Phelps, Tommy J. (Knoxville, TN); Zhang, Chuanlun (Columbia, MO); Roh, Yul (Oak Ridge, TN)

2002-09-03T23:59:59.000Z

258

Biogas from waste in Belgium  

SciTech Connect

This article describes plans for a dry anaerobic composting plant in Brecht, Belgium. The new plant will utilize dry conditions and thermophilic temperatures to produce an average of 6 to 8 volumes of biogas per volume of reactor per day could be produced from vegetable, fruit, garden and paper waste, and a soil amendment from the organic fraction of municipal solid waste according to researchers.

Not Available

1991-08-01T23:59:59.000Z

259

Bioconversion of plant biomass to ethanol. Annual report and revised research plan, January 1977--January 1978  

DOE Green Energy (OSTI)

The objective of this research is to demonstrate on a laboratory scale the technical feasibility of the direct microbial conversion of pretreated wood to ethanol. During the first year of this contract, we investigated the feasibility of biologically delignifying wood with C. pruinosum and directly fermenting the pretreated wood to ethanol with a mixed culture. Bench-top fermentations of a thermophilic bacillus growing on glucose and of a mixed culture of thermophilic sporocytophaga (US) and a thermophilic bacillus growing on microcrystalline and amorphous cellulose were evaluated for growth and ethanol production. In the mixed culture fermentation of amorphous and microcrystalline cellulose, the specific rate of substrate depletion was calculated to be 0.087 hr/sup -1/ and 0.0346 hr/sup -1/, respectively. However, defining the growth requirements of C. pruinosum and sporocytophaga (US) proved more difficult than originally anticipated. In order to achieve the program objectives within the contract period, a revised research plan was developed based upon chemical pretreatment and the direct fermentation of pretreated hardwood to ethanol. In place of the biological delignification pretreatment step, we have substituted a chemically supplemented steam pretreatment step to partially delignify wood and to enhance its accessibility to microbial utilization. Clostridium thermocellum, which ferments cellulose directly to ethanol and acetic acid, has replaced the mixed culture fermentation stage for ethanol production. Research on the production of ethanol from xylose by the thermophilic bacillus ZB-B2 is retained as one means of utilizing the hemicellulose fraction of hardwood. Work on the genetic improvement of the ethanol yields of both cultures by suppressing acetic acid production is also retained. The rationale, experimental approach, and economic considerations of this revised research plan are also presented.

Brooks, R.E.; Bellamy, W.D.; Su, T.M.

1978-03-23T23:59:59.000Z

260

The elusive middle domain of Hsp104 and ClpB: Location and function Morgan E. DeSantis a,b  

E-Print Network (OSTI)

domains was largely resolved in 2003 when a 3.0 Ã? crystal structure of ClpB (TClpB) from the thermophilic of this review, we have provided a unified nomenclature to describe regions of the MD in ClpB, TClpB, and Hsp104% identity. Unfortunately, full-length TClpB did not crystallize in its functional hexameric structure

Shorter, James

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Thermostabilization of desulfurization enzymes from Rhodococcos sp. IGTS8. Final technical report  

SciTech Connect

The objective of this project was to develop thermophilic cultures capable of expressing the desulfurization (dsz) operon of Rhodococcus sp. IGTS8. The approaches taken in this project included the development of plasmid and integrative expression vectors that function well in Thermus thermophilus, the cloning of Rhodococcus dsz genes in Thermus expression vectors, and the isolation of bacterial cultures that express the dsz operon at thermophilic temperatures. This project has resulted in the development of plasmid and integrative expression vectors for use in T. thermophilus. The dsz genes have been expressed at moderately thermophilic temperatures (52 C) in Mycobacterium phlei and at temperatures as high as 72 C in T. thermophilus. The tools and methods developed in this project will be generally useful for the expression of heterologous genes in Thermus. Key developments in the project have been the isolation of a Mycobacterium phlei culture capable of expressing the desulfurization operon at 52 C, development of plasmid and integrative expression vectors for Thermus thermophilus, and the development of a host-vector system based on the malate dehydrogenase gene that allows plasmids to be stably maintained in T. thermophilus and provides a convenient reporter gene for the accurate quantification of gene expression. Publications have been prepared regarding each of these topics; these preprints are included.

John J. Kilbane II

2000-12-15T23:59:59.000Z

262

Copyright ? 1996, American Society for Microbiology Isolation of Thermus Strains from Hot Composts (60 to 80?C)  

E-Print Network (OSTI)

aerobic, thermophilic bacteria related to the genus Thermus were isolated from thermogenic composts at temperatures between 65 and 82?C. These bacteria were present in different types of wastes (garden and kitchen wastes and sewage sludge) and in all the industrial composting systems studied (open-air windrows, boxes with automated turning and aeration, and closed bioreactors with aeration). Isolates grew fast on a rich complex medium at temperatures between 40 and 80?C, with optimum growth between 65 and 75?C. Nutritional characteristics, total protein profiles, DNA-DNA hybridization (except strain JT4), and restriction fragment length polymorphism profiles of the DNAs coding for the 16S rRNAs (16S rDNAs) showed that Thermus strains isolated from hot composts were closely related to Thermus thermophilus HB8. These newly isolated T. thermophilus strains have probably adapted to the conditions in the hot-compost ecosystem. Heterotrophic, ovalspore-forming, thermophilic bacilli were also isolated from hot composts, but none of the isolates was able to grow at temperatures above 70?C. This is the first report of hot composts as habitats for a high number of thermophilic bacteria related to the genus Thermus. Our study suggests that Thermus strains play an important role in organic-matter degradation during the thermogenic phase (65 to 80?C) of the composting process. Composting is a self-heating, aerobic, solid-phase, biodegradative process of organic-waste materials (7, 8). During the

Trello Beffa; Michel Blanc; Pierre-françois Lyon; Gudrun Vogt; Marcello Marchiani; Johanna Lott Fischer

1995-01-01T23:59:59.000Z

263

PETROLEUM BIOREFINING FOR POLLUTION PREVENTION  

DOE Green Energy (OSTI)

The objective of this project was to isolate and characterize thermophilic bacterial cultures that can be used for the selective removal of nitrogen, sulfur, and/or metals in the biorefining of petroleum. The project was completed on schedule and no major difficulties were encountered. Significant progress was made on multiple topics relevant to the development of a petroleum biorefining process capable of operating at thermophilic temperatures. New cultures capable of selectively cleaving C-N or C-S bonds in molecules relevant to petroleum were obtained, and the genes encoding the enzymes for these unique biochemical reactions were cloned and sequenced. Genetic tools were developed that enable the use of Thermus thermophilus as a host to express any gene of interest, and information was obtained regarding the optimum conditions for the growth of T. thermophilus. The development of a practical biorefining process still requires further research and the future research needs identified in this project include the development of new enzymes and pathways for the selective cleavage of C-N or C-S bonds that have higher specific activities, increased substrate range, and are capable of functioning at thermophilic temperatures. Additionally, there is a need for process engineering research to determine the maximum yield of biomass and cloned gene products that can be obtained in fed-batch cultures using T. thermophilus, and to determine the best configuration for a process employing biocatalysts to treat petroleum.

John J. Kilbane II

2002-03-01T23:59:59.000Z

264

A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq  

E-Print Network (OSTI)

The SMc01113/YbeY protein, belonging to the UPF0054 family, is highly conserved in nearly every bacterium. However, the function of these proteins still remains elusive. Our results show that SMc01113/YbeY proteins share ...

Pandey, Shree P.

265

Alistair Rogers  

NLE Websites -- All DOE Office Websites (Extended Search)

Hoffman A, Koenig K, Newman L, Taghavi S, van der Lelie D (2012) Inoculation of hybrid poplar with the endophytic bacterium Enterobacter sp. 638 increases biomass but does not...

266

Bioreductive recovery of platinum group metals by the metal-ion ...  

Science Conference Proceedings (OSTI)

The metal ion-reducing bacterium, Shewanella algae, was found to exhibit the ability to reduce and deposit the PGM ions (Pd(II), Pt(IV), Rh(III)) into metal ...

267

Scientific Innovation Through Integration Capabilities Series  

NLE Websites -- All DOE Office Websites (Extended Search)

that the outer- membrane cytochromes, MtrC and OmcA, of the metal-reducing bacterium Shewanella oneidensis MR-1 are key to reducing and transforming ferrihydrite. Moreover, both...

268

Microsoft Word - RPSEA Final Report RPSEA Format ns.docx  

NLE Websites -- All DOE Office Websites (Extended Search)

halotolerant, sulfate---reducing bacterium isolated from exhaust water of a Tunisian oil refinery. Int J Syst Evol Microbiol 59: 1 059---63 12. Blum JS, Han S, Lanoil B,...

269

The effect of temperature on bacterial degradation of EDTA in pH ...  

Science Conference Proceedings (OSTI)

1990), Gram-negative isolates BNC1and ANP 11. (No¨rtemann 1992, 2005; Kluener et al. 1998), and. Gram-negative bacterium DSM 9103 belonging to a.

270

Production of Clostridium difficile toxin in a medium totally free of both animal and dairy proteins or digests  

E-Print Network (OSTI)

In the hope of developing a vaccine against Clostridium difficile based on its toxin(s), we have developed a fermentation medium for the bacterium that results in the formation of Toxin A and contains no meat or dairy ...

Demain, Arnold L.

271

Biometrics, Surveys and For Britain's woodlands to contribute effectively  

E-Print Network (OSTI)

and sociologists. The project focuses on Lyme disease, caused by a bacterium Borrelia burgdorferi sensu lato (Bb hope to help those involved in the countryside to understand how to deal with diseases such as Lyme

272

Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria  

E-Print Network (OSTI)

Strain HIMB100 is a planktonic marine bacterium in the class Alphaproteobacteria. This strain is of interest because it is one of the first known isolates from a globally ubiquitous clade of marine bacteria known as SAR116 ...

Grote, Jana

2011-01-01T23:59:59.000Z

273

Elucidation of Beta-Oxidation Pathways in Ralstonia Eutropha H16 by Examination of Global Gene Expression  

E-Print Network (OSTI)

Ralstonia eutropha H16 is capable of growth and polyhydroxyalkanoate production on plant oils and fatty acids. However, little is known about the triacylglycerol and fatty acid degradation pathways of this bacterium. We ...

Zeng, Qiandong

274

Microsoft Word - 2007_jgi_final.doc  

NLE Websites -- All DOE Office Websites (Extended Search)

M.O., K. Heguri, K. Hirata, and K. Miyamoto. 2005. Production of alternatives to fuel oil from organic waste by the alkane-producing bacterium, Vibrio furnissii M1. J. Appl....

275

Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing  

E-Print Network (OSTI)

The UPF0054 protein family is highly conserved with homologues present in nearly every sequenced bacterium. In some bacteria, the respective gene is essential, while in others its loss results in a highly pleiotropic ...

Davies, Bryan W.

276

Nocardioides basaltis sp. nov., isolated from black Kyoung-Ho Kim,1  

E-Print Network (OSTI)

Tidal flat Saline lake (Antarctica) Groundwater Oil shale Soil Soil *Different results were reported pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column. Int J

Bae, Jin-Woo

277

Selection and optimization of gene targets for the metabolic engineering of E. coli  

E-Print Network (OSTI)

This thesis is about identifying genetic interventions that improve the performance of targeted pathways in the metabolism of the bacterium Escherichia coli. Three case studies illustrate three disparate approaches to ...

Fischer, Curt R., Ph. D. Massachusetts Institute of Technology

2009-01-01T23:59:59.000Z

278

Antimicrobial product and process  

DOE Patents (OSTI)

A composition for controlling a plant disease caused by a plant pathogenic bacterium is disclosed. The composition comprises an activity for inhibiting the growth of the plant pathogenic bacterium and is extracted in an aqueous solvent from particles of malted cereal grain. The composition is used either in dry or wet form by application to plant parts, such as potato seed pieces, that are to be protected from the pathogenic bacteria.

Barrett, Karen B. (Idaho Falls, ID)

1997-01-01T23:59:59.000Z

279

Antimicrobial product and process  

DOE Patents (OSTI)

A composition for controlling a plant disease caused by a plant pathogenic bacterium is disclosed. The composition comprises an activity for inhibiting the growth of the plant pathogenic bacterium and is extracted in an aqueous solvent from particles of malted cereal grain. The composition is used either in dry or wet form by application to plant parts, such as potato seed pieces, that are to be protected from the pathogenic bacteria. 6 figs.

Barrett, K.B.

1997-12-16T23:59:59.000Z

280

Microbial diversity of cellulose hydrolysis  

NLE Websites -- All DOE Office Websites (Extended Search)

871; 871; NO. OF PAGES 5 Please cite this article in press as: Wilson DB. Microbial diversity of cellulose hydrolysis, Curr Opin Microbiol (2011), doi:10.1016/j.mib.2011.04.004 Available online at www.sciencedirect.com Microbial diversity of cellulose hydrolysis David B Wilson Enzymatic hydrolysis of cellulose by microorganisms is a key step in the global carbon cycle. Despite its abundance only a small percentage of microorganisms can degrade cellulose, probably because it is present in recalcitrant cell walls. There are at least five distinct mechanisms used by different microorganisms to degrade cellulose all of which involve cellulases. Cellulolytic organisms and cellulases are extremely diverse possibly because their natural substrates, plant cell walls, are very diverse. At this time the microbial ecology of cellulose degradation in any environment is still

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June  

NLE Websites -- All DOE Office Websites (Extended Search)

1, 1, p. 4042-4054 Vol. 77, No. 12 0099-2240/11/$12.00 doi:10.1128/AEM.02811-10 Copyright © 2011, American Society for Microbiology. All Rights Reserved. Use of Label-Free Quantitative Proteomics To Distinguish the Secreted Cellulolytic Systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis ᰔ † Adriane Lochner, 1,3,4 Richard J. Giannone, 2,3 Miguel Rodriguez, Jr., 1,3 Manesh B. Shah, 2 Jonathan R. Mielenz, 1,3 Martin Keller, 1,3 Garabed Antranikian, 4 David E. Graham, 1,5 * and Robert L. Hettich 2,3 * Biosciences Division, 1 Chemical Sciences Division, 2 and BioEnergy Science Center, 3 Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831; Technical Microbiology, Hamburg University of Technology, Kasernenstrasse 12, D-21073 Hamburg, Germany 4 ; and Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996 5 Received

282

BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS The  

NLE Websites -- All DOE Office Websites (Extended Search)

The The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity Xiao-Zhou Zhang & Zuoming Zhang & Zhiguang Zhu & Noppadon Sathitsuksanoh & Yunfeng Yang & Y.-H. Percival Zhang Received: 21 July 2009 / Revised: 29 August 2009 / Accepted: 31 August 2009 / Published online: 15 October 2009 # Springer-Verlag 2009 Abstract Family 48 glycoside hydrolases (cellobiohydro- lases) are among the most important cellulase components for crystalline cellulose hydrolysis mediated by cellulolytic bacteria. Open reading frame (Cphy_3368) of Clostridium phytofermentans ISDg encodes a putative family 48 glycoside hydrolase (CpCel48) with a family 3 cellulose- binding module. CpCel48 was successfully expressed as two soluble intracellular forms with or without a C-terminal

283

AEM.01219-10v1.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

KHUPRSKLOLF $QDHURELF %DFWHULD IURP %LRFRPSRVW $EOH WR 'HJUDGH KHUPRSKLOLF $QDHURELF %DFWHULD IURP %LRFRPSRVW $EOH WR 'HJUDGH 1 &HOOXORVH DQG ;\ODQ 2 Cellulolytic and Xylanolytic Bacteria 3 0 9 6L]RYD   -$ ,]TXLHUGR   16 3DQLNRY  DQG / 5 /\QG̅  4 1 Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755 5 2 BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 6 3 Department of Biology, Northeastern University, Boston, Massachusetts 02115 7 ̅Corresponding author: Lee R. Lynd 8 E-mail: Lee.R.Lynd@Dartmouth.EDU 9 Phone: 603-646-2231 10 Fax: 603-646-2277 11 Copyright © 2011, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

284

A minimal set of bacterial cellulases for consolidated bioprocessing of lignocellulose  

NLE Websites -- All DOE Office Websites (Extended Search)

11 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 11 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 1 Biotechnol. J. 2011, 6 DOI 10.1002/biot.201100157 www.biotechnology-journal.com 1 Introduction Cellulosic material is the most abundant renew- able bioresource. Cellulose biodegradation medi- ated by cellulases and/or cellulolytic microorgan- isms represents one of the largest flows in the global carbon cycle [1]. The utilization of a small fraction of cellulosic materials (e.g., 5-10%) for the production of biofuels and value-added chemicals would greatly decrease reliance on crude oil, pro- mote rural economy, decrease net greenhouse emissions, and increase national energy security [1-3]. Cost-effective release of fermentable sugars from non-food biomass through biomass pretreat- ment/enzymatic hydrolysis is still the largest ob-

285

Nitrogen and Sulfur Requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on Cellulosic Substrates in Minimal Nutrient Media  

Science Conference Proceedings (OSTI)

Growth media for cellulolytic Clostridium thermocellum and Caldicellulosiruptor bescii bacteria usually contain excess nutrients that would increase costs for consolidated bioprocessing for biofuel production and create a waste stream with nitrogen, sulfur and phosphate. C. thermocellum was grown on crystalline cellulose with varying concentrations of nitrogen and sulfur compounds, and growth rate and alcohol production response curves were determined. Both bacteria assimilated sulfate in the presence of ascorbate reductant, increasing the ratio of oxidized to reduced fermentation products. From these results, a low ionic strength, defined minimal nutrient medium with decreased nitrogen, sulfur, phosphate and vitamin supplements was developed for the fermentation of cellobiose, cellulose and acid-pretreated Populus. Carbon and electron balance calculations indicate the unidentified residual fermentation products must include highly reduced molecules. Both bacterial populations were maintained in co-cultures with substrates containing xylan or hemicellulose in defined medium with sulfate and basal vitamin supplements.

Kridelbaugh, Donna M [ORNL; Nelson, Josh C [ORNL; Engle, Nancy L [ORNL; Tschaplinski, Timothy J [ORNL; Graham, David E [ORNL

2013-01-01T23:59:59.000Z

286

A study of overproduction and enhanced secretion of enzymes. Quarterly report  

DOE Green Energy (OSTI)

Wood decay within forests, a significant renewable photosynthetic energy resource, is caused primarily by Basidiomycetous fungi, e.g., white rot fungi. These organisms possess the ability to degrade lignin, cellulose and hemicellulose, the main organic polymers of wood. In the case of the white rot fungi, e.g., Coriolus versicolor, the capacity results from the fungus` ability to elaborate extracellular cellulolytic and ligninolytic enzymes. With regard to the latter, at least one of the enzymes, polyphenol oxidase (PPO) appears within a defined growth medium. This proposal focuses on the over-production and enhanced secretion of PPO, cellulase and lignin peroxidase. There are two major sections to the proposal: (1) overproduction of lignocellulolytic enzymes by genetic engineering methodologies and hyper-production and enhanced secretion of these enzymes by biochemical/electro microscopical techniques and (2) the biochemical/electron microscopical method involves substrate induction and the time-dependent addition of respiration and PPO enzymes.

Dashek, W.V.

1993-09-01T23:59:59.000Z

287

Saccharification of bamboo carbohydrates for the production of ethanol  

SciTech Connect

Bamboo carbohydrates were hydrolyzed with commercial amylases and a mixture of fungal culture broths containing cellulolytic and hemicellulolytic enzymes. The effects of cooking temperature and the size of fiber particles were also investigated. It was found that the higher the cooking temperature, the higher the rate of sugar formation and the lower the viscosity of the slurry. Additions of cellulose and hemicellulose digesting enzymes increased the sugar yield and decreased the viscosity of both the cooked and noncooked slurries. A smaller size of particle appeared to favor the average saccharification rate. Although glucose, xylose, and cellobiose were present in the hydrolysates, only 50% of the total carbohydrate was digested, and 78.9% of this was converted to reducing sugars. The alcohol efficiency for the fermentation of cooked and noncooked mashes by Saccharomyces was about 85%.

De Menezes, T.J.B.; Azzini, A.; Dos Santos, C.L.M.

1983-04-01T23:59:59.000Z

288

doi:10.1016/j.copbio.2008.04.008  

NLE Websites -- All DOE Office Websites (Extended Search)

A A biophysical perspective on the cellulosome: new opportunities for biomass conversion Shi-You Ding 1 , Qi Xu 1 , Michael Crowley 1 , Yining Zeng 1 , Mark Nimlos 2 , Raphael Lamed 3 , Edward A Bayer 4 and Michael E Himmel 1 The cellulosome is a multiprotein complex, produced primarily by anaerobic microorganisms, which functions to degrade lignocellulosic materials. An important topic of current debate is whether cellulosomal systems display greater ability to deconstruct complex biomass materials (e.g. plant cell walls) than nonaggregated enzymes, and in so doing would be appropriate for improved, commercial bioconversion processes. To sufficiently understand the complex macromolecular processes between plant cell wall polymers, cellulolytic microbes, and their secreted enzymes, a highly concerted research approach is required. Adaptation of existing biophysical techniques

289

Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance  

DOE Green Energy (OSTI)

Some ionic liquids (ILs) have been shown to be very effective solvents for biomass pretreatment. It is known that some ILs can have a strong inhibitory effect on fungal cellulases, making the digestion of cellulose inefficient in the presence of ILs. The identification of IL-tolerant enzymes that could be produced as a cellulase cocktail would reduce the costs and water use requirements of the IL pretreatment process. Due to their adaptation to high salinity environments, halophilic enzymes are hypothesized to be good candidates for screening and identifying IL-resistant cellulases. Using a genome-based approach, we have identified and characterized a halophilic cellulase (Hu-CBH1) from the halophilic archaeon, Halorhabdus utahensis. Hu-CBH1 is present in a gene cluster containing multiple putative cellulolytic enzymes. Sequence and theoretical structure analysis indicate that Hu-CBH1 is highly enriched with negatively charged acidic amino acids on the surface, which may form a solvation shell that may stabilize the enzyme, through interaction with salt ions and/or water molecules. Hu-CBH1 is a heat tolerant haloalkaliphilic cellulase and is active in salt concentrations up to 5 M NaCl. In high salt buffer, Hu-CBH1 can tolerate alkali (pH 11.5) conditions and, more importantly, is tolerant to high levels (20percent w/w) of ILs, including 1-allyl-3-methylimidazolium chloride ([Amim]Cl). Interestingly, the tolerances to heat, alkali and ILs are found to be salt-dependent, suggesting that the enzyme is stabilized by the presence of salt. Our results indicate that halophilic enzymes are good candidates for the screening of IL-tolerant cellulolytic enzymes.

Zhang, Tao; Datta, Supratim; Eichler, Jerry; Ivanova, Natalia; Axen, Seth D.; Kerfeld, Cheryl A.; Chen, Feng; Kyrpides, Nikos; Hugenholtz, Philip; Cheng, Jan-Fang; Sale, Kenneth L.; Simmons, Blake; Rubin, Eddy

2011-02-17T23:59:59.000Z

290

Comparison of different liquid anaerobic digestion effluents as inocula and nitrogen sources for solid-state batch anaerobic digestion of corn stover  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer Compared methane production of solid AD inoculated with different effluents. Black-Right-Pointing-Pointer Food waste effluent (FWE) had the largest population of acetoclastic methanogens. Black-Right-Pointing-Pointer Solid AD inoculated with FWE produced the highest methane yield at F/E ratio of 4. Black-Right-Pointing-Pointer Dairy waste effluent (DWE) was rich of cellulolytic and xylanolytic bacteria. Black-Right-Pointing-Pointer Solid AD inoculated with DWE produced the highest methane yield at F/E ratio of 2. - Abstract: Effluents from three liquid anaerobic digesters, fed with municipal sewage sludge, food waste, or dairy waste, were evaluated as inocula and nitrogen sources for solid-state batch anaerobic digestion of corn stover in mesophilic reactors. Three feedstock-to-effluent (F/E) ratios (i.e., 2, 4, and 6) were tested for each effluent. At an F/E ratio of 2, the reactor inoculated by dairy waste effluent achieved the highest methane yield of 238.5 L/kgVS{sub feed}, while at an F/E ratio of 4, the reactor inoculated by food waste effluent achieved the highest methane yield of 199.6 L/kgVS{sub feed}. The microbial population and chemical composition of the three effluents were substantially different. Food waste effluent had the largest population of acetoclastic methanogens, while dairy waste effluent had the largest populations of cellulolytic and xylanolytic bacteria. Dairy waste also had the highest C/N ratio of 8.5 and the highest alkalinity of 19.3 g CaCO{sub 3}/kg. The performance of solid-state batch anaerobic digestion reactors was closely related to the microbial status in the liquid anaerobic digestion effluents.

Xu Fuqing; Shi Jian [Department of Food, Agricultural and Biological Engineering, Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691 (United States); Lv Wen; Yu Zhongtang [Department of Animal Sciences, Ohio State University, Columbus, OH 43210 (United States); Li Yebo, E-mail: li.851@osu.edu [Department of Food, Agricultural and Biological Engineering, Ohio State University, Ohio Agricultural Research and Development Center, 1680 Madison Ave., Wooster, OH 44691 (United States)

2013-01-15T23:59:59.000Z

291

Microbial dissolution of silicate materials. Final report  

DOE Green Energy (OSTI)

The objective of this research was to better understand the role of selected thermophilic bacteria in the colonization and dissolution of silicate minerals, with potential applications to the HDR Project. The demonstration of enhanced dissolution from microbial effects is critically dependent on providing a mineral bait within a media deficient in the critical nutrient found in the mineral (e.g., Fe). Reproducible experimental conditions in batch experiments require agitation to expose mineral powders, as well as nearly similar initial conditions for both inoculated cultures and controls. It is difficult, but not impossible to ensure reproducible conditions with microbes favoring filamentous growth habits.

Schwartzman, D. [Howard Univ., Washington, DC (United States). Dept. of Biology

1996-03-26T23:59:59.000Z

292

Biological conversion of biomass to methane. Quarterly progress report, September 1--November 30, 1978  

DOE Green Energy (OSTI)

The viability of wheat straw as a feedstock for methane production by anaerobic digestion was investigated and the results obtained compared with that obtained with corn stover. Poor conversion was obtained with the wheat straw under thermophilic conditions, but better than that obtained with corn. In addition the residue has no value as an animal feed. A mild thermochemical pretreatment of the corn prior to anaerobic digestion improved the conversion efficiency and the value of the residue as an animal feed. It is assumed that similar pretreatment of wheat straw would improve its conversion efficiency. Slurry and pumping characteristics of wheat straw particles were reported. (JSR)

Pfeffer, J T

1978-12-01T23:59:59.000Z

293

High ethanol producing derivatives of Thermoanaerobacter ethanolicus  

DOE Patents (OSTI)

Derivatives of the newly discovered microorganism Thermoanaerobacter ethanolicus which under anaerobic and thermophilic conditions continuously ferment substrates such as starch, cellobiose, glucose, xylose and other sugars to produce recoverable amounts of ethanol solving the problem of fermentations yielding low concentrations of ethanol using the parent strain of the microorganism Thermoanaerobacter ethanolicus are disclosed. These new derivatives are ethanol tolerant up to 10% (v/v) ethanol during fermentation. The process includes the use of an aqueous fermentation medium, containing the substrate at a substrate concentration greater than 1% (w/v).

Ljungdahl, Lars G. (Athens, GA); Carriera, Laura H. (Athens, GA)

1983-01-01T23:59:59.000Z

294

High ethanol producing derivatives of Thermoanaerobacter ethanolicus  

DOE Patents (OSTI)

Derivatives of the newly discovered microorganism Thermoanaerobacter ethanolicus which under anaerobic and thermophilic conditions continuously ferment substrates such as starch, cellobiose, glucose, xylose and other sugars to produce recoverable amounts of ethanol solving the problem of fermentations yielding low concentrations of ethanol using the parent strain of the microorganism Thermoanaerobacter ethanolicus are disclosed. These new derivatives are ethanol tolerant up to 10% (v/v) ethanol during fermentation. The process includes the use of an aqueous fermentation medium, containing the substrate at a substrate concentration greater than 1% (w/v).

Ljungdahl, L.G.; Carriera, L.H.

1983-05-24T23:59:59.000Z

295

Combination biological and microwave treatments of used rubber products  

DOE Patents (OSTI)

A process and resulting product is provided in which a vulcanized solid particulate, such as vulcanized crumb rubber, has select chemical bonds altered by biotreatment with thermophillic microorganisms selected from natural isolates from hot sulfur springs. Following the biotreatment, microwave radiation is used to further treat the surface and to treat the bulk interior of the crumb rubber. The resulting combined treatments render the treated crumb rubber more suitable for use in new rubber formulations. As a result, larger loading levels and sizes of the treated crumb rubber can be used in new rubber mixtures and good properties obtained from the new recycled products.

Fliermans, Carl B. (Augusta, GA); Wicks, George G. (Aiken, SC)

2002-01-01T23:59:59.000Z

296

Production of extremophilic bacterial cellulase enzymes in aspergillus niger.  

SciTech Connect

Enzymes can be used to catalyze a myriad of chemical reactions and are a cornerstone in the biotechnology industry. Enzymes have a wide range of uses, ranging from medicine with the production of pharmaceuticals to energy were they are applied to biofuel production. However, it is difficult to produce large quantities of enzymes, especially if they are non-native to the production host. Fortunately, filamentous fungi, such as Aspergillus niger, are broadly used in industry and show great potential for use a heterologous enzyme production hosts. Here, we present work outlining an effort to engineer A. niger to produce thermophilic bacterial cellulases relevant to lignocellulosic biofuel production.

Gladden, John Michael

2013-09-01T23:59:59.000Z

297

Controlled production of cellulases in plants for biomass conversion. Progress report, June 15, 1996--March 10, 1997  

DOE Green Energy (OSTI)

The goal of this project is to facilitate conversion of plant biomass to usable energy by developing transgenic plants that express genes for microbial cellulases, which can be activated after harvest of the plants. In particular, we want to determine the feasibility of targeting an endoglucanase and a cellobiohydrolase to the plant apoplast (cell wall milieu). The apoplast not only contains cellulose, the substrate for the enzymes, but also can tolerate large amounts of foreign protein. To avoid detrimental effects of cellulase expression in plants, we have chosen enzymes with high temperature optima; the genes for these enzymes are from thermophilic organisms that can use cellulose as a sole energy source.

Danna, K.J.

1997-06-01T23:59:59.000Z

298

Cellulase producing microorganism ATCC 55702  

DOE Patents (OSTI)

Bacteria which produce large amounts of cellulase--containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualifies for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

Dees, H. Craig (Lenoir City, TN)

1997-01-01T23:59:59.000Z

299

Detergent composition comprising a cellulase containing cell-free fermentate produced from microorganism ATCC 55702 or mutant thereof  

DOE Patents (OSTI)

Bacteria which produce large amounts of a cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

Dees, H. Craig (Lenoir City, TN)

1998-01-01T23:59:59.000Z

300

Method of producing a cellulase-containing cell-free fermentate produced from microorganism ATCC 55702  

DOE Patents (OSTI)

Bacteria which produce large amounts of cellulose-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

Dees, H. Craig (Lenoir City, TN)

1998-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

Cellulase-containing cell-free fermentate produced from microorganism ATCC 55702  

DOE Patents (OSTI)

Bacteria which produce large amounts of cellulase-containing cell-free fermentate have been identified. The original bacterium (ATCC 55703) was genetically altered using nitrosoguanidine (MNNG) treatment to produce the enhanced cellulase producing bacterium (ATCC 55702), which was identified through replicate plating. ATCC 55702 has improved characteristics and qualities for the degradation of cellulosic waste materials for fuel production, food processing, textile processing, and other industrial applications. ATCC 55702 is an improved bacterial host for genetic manipulations using recombinant DNA techniques, and is less likely to destroy genetic manipulations using standard mutagenesis techniques.

Dees, H. Craig (Lenoir City, TN)

1997-12-16T23:59:59.000Z

302

Anaerobic fermentation of beef cattle manure. Final report  

DOE Green Energy (OSTI)

The research to convert livestock manure and crop residues into methane and a high protein feed ingredient by thermophilic anaerobic fermentation are summarized. The major biological and operational factors involved in methanogenesis were discussed, and a kinetic model that describes the fermentation process was presented. Substrate biodegradability, fermentation temperature, and influent substrate concentration were shown to have significant effects on CH/sub 4/ production rate. The kinetic model predicted methane production rates of existing pilot and full-scale fermentation systems to within 15%. The highest methane production rate achieved by the fermenter was 4.7 L CH/sub 4//L fermenter day. This is the highest rate reported in the literature and about 4 times higher than other pilot or full-scale systems fermenting livestock manures. Assessment of the energy requirements for anaerobic fermentation systems showed that the major energy requirement for a thermophilic system was for maintaining the fermenter temperature. The next major energy consumption was due to the mixing of the influent slurry and fermenter liquor. An approach to optimizing anaerobic fermenter designs by selecting design criteria that maximize the net energy production per unit cost was presented. Based on the results, we believe that the economics of anaerobic fermentation is sufficiently favorable for farm-scale demonstration of this technology.

Hashimoto, A.G.; Chen, Y.R.; Varel, V.H.

1981-01-01T23:59:59.000Z

303

Anaerobic fermentation of agricultural residue: potential for improvement and implementation. Final report  

DOE Green Energy (OSTI)

The results of studies designed to evaluate the potential of rapidly improving the technology of anaerobic fermentation of agricultural residues and methods of implementing it in existing agricultural operations are reported. The main objectives of this study were to: identify simple and low cost anaerobic fermentor design criteria that would be appropriate in small agricultural operations, develop high rate fermentor concepts that would enable multiple product recovery from the reactor, expand the information base particularly in the area of temperature influence on the process, and to review sociological and economic issues relating to implementation of fermentation technology. This study has identified several major anaerobic fermentation concepts which illustrate that the technology may be rapidly improved. A simple reactor design utilizing an unmixed plug flow concept was shown to be comparable to the more complex completely mixed reactor when using dairy cow residue. A high rate thermophilic reactor designed to encourage flotation of particulate solids illustrated that liquid, solid, and gaseous products can be generated within the anaerobic fermentor thus eliminating an additional dewatering unit process. A third reactor concept involved extension of the anaerobic attached microbial film expanded bed to the treatment of cow manure slurries. A high rate of methane generation was recorded. Comprehensive thermophilic fermentation studies (60/sup 0/C) indicated that the increased temperature resulted in little improvement in total quantity or the rate of yield of gas over that obtained with mesophilic fermentation with reactor retention periods greater than 10 days. Finally, other areas where preliminary date were obtained are noted.

Jewell, W. J.; Capener, H. R.; Dell'orto, S.

1978-02-01T23:59:59.000Z

304

53 (2008) APPLICATIONS OF MATHEMATICS No. 5, 409432 MODELLING BIOREMEDIATION OF POLLUTED SOILS IN  

E-Print Network (OSTI)

a porous medium contaminated with some pollutant. The biomass grows feeding on the pollutant and affecting species in presence of a growing biomass feeding on the pollutant. In turn, the growing bacterial with a well-known bacterium. The biomass may distribute in water as suspension (free biomass) or attached

Primicerio, Mario

305

Bioremediation of nanomaterials  

DOE Patents (OSTI)

The present invention provides a method comprising the use of microorganisms for nanotoxicity study and bioremediation. In some embodiment, the microorganisms are bacterial organisms such as Gram negative bacteria, which are used as model organisms to study the nanotoxicity of the fullerene compounds: E. coli W3110, a human related enterobacterium and Shewanella oneidensis MR-1, an environmentally important bacterium with versatile metabolism.

Chen, Frank Fanqing; Keasling, Jay D; Tang, Yinjie J

2013-05-14T23:59:59.000Z

306

Genome Sequence of Streptomyces viridosporus Strain T7A ATCC 39115, a Lignin-Degrading Actinomycete  

Science Conference Proceedings (OSTI)

We announce the availability of the genome sequence of Streptomyces viridosporus strain T7A ATCC 39115, a plant biomass- degrading actinomycete. This bacterium is of special interest because of its capacity to degrade lignin, an underutilized compo- nent of plants in the context of bioenergy. It has a full complement of genes for plant biomass catabolism.

Davis, Jennifer R. [Brown University; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Teshima, Hazuki [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Wei, Chia-Lin [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Sello, Jason K. [Brown University

2013-01-01T23:59:59.000Z

307

Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis  

E-Print Network (OSTI)

Rhodococcus sp. 124 is a Gram-positive soil bacterium being developed for the manufacture of (-)cis-(1S,2R)-1-aminoindan-2-ol, a key precursor in the production of the HIV-1 protease inhibitor CrixivanTM, from the aromatic ...

Parker, Jefferson A. (Jefferson Alexander), 1974-

2004-01-01T23:59:59.000Z

308

Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata: Progress report for the period June 5, 1986-June 4, 1987  

DOE Green Energy (OSTI)

This document describes research conducted between June 1986 and June 1987. Results dealing with the organization and regulation of genes in the photosynthetic bacterium Rhodobacter capsulatus includes cloning, sequencing, and demonstrating characterizing the products of genes that regulate expression of nitrogen fixation genes; the connection between DNA supercoiling mediated by DNA gyrase and nif gene expression; and mapping the entire chromosome of R. capsulatus.

Haselkorn, R.

1987-03-01T23:59:59.000Z

309

Assessing and communicating animal  

E-Print Network (OSTI)

framework of risk communication. The initial focus will be on Lyme disease (also known as Lyme borreliosis), an infectious disease caused by the bacterium Borrelia burgdorferi s.l. Lyme disease is found in a number Protection Agency (Lyme Borreliosis Unit) and a number of other RELU projects. Further information

310

Interactions of uranium with bacteria and kaolinite clay Toshihiko Ohnukia,*, Takahiro Yoshidaa  

E-Print Network (OSTI)

Interactions of uranium with bacteria and kaolinite clay Toshihiko Ohnukia,*, Takahiro Yoshidaa of uranium (VI) by a bacterium, Bacillus subtilis, suspended in a slurry of kaolinite clay, to elucidate, removed approximately 80% of the associated uranium. However, in the presence of B. subtilis the amount

Kasama, Takeshi

311

THE GREENTECH MEDIA WEEKLY NEWSLETTER  

E-Print Network (OSTI)

:56 PM Electricity-Generating Geobacter Bacteria Made Stronger Geobacter. It's a bacterium that turns in a microbial fuel cell. So far, the currents generated have been too weak for practical purposes, however. Also like ocean floors, or generating electricity from the same bioremediation bacteria that clean up

Lovley, Derek

312

Available online at www.sciencedirect.com Colloids and Surfaces B: Biointerfaces 62 (2008) 232237  

E-Print Network (OSTI)

, it is also essential that these coatings have a highly uniform surface chemistry. © 2007 Elsevier B.V. All facilities [5,6], cooling towers [7], marine surfaces [8,9], medical device surfaces [10], to name a few, is essential for taking appropri- ate measures to reduce biofouling. Once a bacterium reaches the vicinity

313

Detecting Cellulase Penetration Into Corn Stover Cell Walls by Immuno-Electron Microscopy  

Science Conference Proceedings (OSTI)

In general, pretreatments are designed to enhance the accessibility of cellulose to enzymes, allowing for more efficient conversion. In this study, we have detected the penetration of major cellulases present in a commercial enzyme preparation (Spezyme CP) into corn stem cell walls following mild-, moderate- and high-severity dilute sulfuric acid pretreatments. The Trichoderma reesei enzymes, Cel7A (CBH I) and Cel7B (EG I), as well as the cell wall matrix components xylan and lignin were visualized within digested corn stover cell walls by immuno transmission electron microscopy (TEM) using enzyme- and polymer-specific antibodies. Low severity dilute-acid pretreatment (20 min at 100 C) enabled <1% of the thickness of secondary cell walls to be penetrated by enzyme, moderate severity pretreatment at (20 min at 120 C) allowed the enzymes to penetrate {approx}20% of the cell wall, and the high severity (20 min pretreatment at 150 C) allowed 100% penetration of even the thickest cell walls. These data allow direct visualization of the dramatic effect dilute-acid pretreatment has on altering the condensed ultrastructure of biomass cell walls. Loosening of plant cell wall structure due to pretreatment and the subsequently improved access by cellulases has been hypothesized by the biomass conversion community for over two decades, and for the first time, this study provides direct visual evidence to verify this hypothesis. Further, the high-resolution enzyme penetration studies presented here provide insight into the mechanisms of cell wall deconstruction by cellulolytic enzymes.

Donohoe, B. S.; Selig, M. J.; Viamajala, S.; Vinzant, T. B.; Adney, W. S.; Himmel, M. E.

2009-06-15T23:59:59.000Z

314

Microbiology and physiology of anaerobic fermentation of cellulose. Progress report (4/30/91--4/30/92) and outline of work for the period 9/1/92--9/1/93  

DOE Green Energy (OSTI)

The authors are continuing their efforts to partly dissociate the cellulolytic enzyme complex of C. thermocellum. This complex named cellulosome (also existing as polycellulosome) consists of perhaps as many as 26 different subunits. It is extremely resistant to dissociation and denaturation. Treatments with urea and SDS have little effect unless the latter treatment is at high temperature. Significantly, some of the subunits after SDS dissociation have CMCase (endoglucanase) activity but no activity toward crystalline cellulose. The only reported success of hydrolysis of crystalline cellulose by cellulosomal subunits is by Wu et al. who isolated two protein fractions labeled SL and SS which when combined exhibit a low (about 1% of the original cellulosome) activity toward crystalline cellulose. The long standing goal is still to determine the activities of the individual subunits, to characterize them, to find out how they are associated in the cellulosome, and to establish the minimum number of subunits needed for efficient hydrolysis of crystalline cellulose. This report also presents the results of experiments on cellulose hydrolysis in aerobic fungi, as well as other anaerobic bacteria.

Ljungdahl, L.G.

1992-12-31T23:59:59.000Z

315

Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity  

DOE Green Energy (OSTI)

Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

Wei, H.; Tucker, M. P.; Baker, J. O.; Harris, M.; Luo, Y. H.; Xu, Q.; Himmel, M. E.; Ding, S. Y.

2012-04-01T23:59:59.000Z

316

Hemicellulolytic organisms in the particle-associated microbiota of the hoatzin crop  

DOE Green Energy (OSTI)

The hoatzin (Opisthocomus hoazin) is a South American herbivorous bird, that has an enlarged crop analogous to the rumen, where foregut microbes degrade the otherwise indigestible plant materials, providing energy to the host. The crop harbors an impressive array of microorganisms with potentially novel cellulolytic enzymes. Thie study describes the composition ofthe particle-associated microbiota in the hoatzin crop, combining a survey of 16S rRNA genes in 7 adult birds and metagenome sequencing of two animals. The pyrotag survey demonstrates that Prevotellaceae, are the most abundant and ubiquitous taxa, suggesting that the degradation of hemicellulose is an important activity in the crop. Nonetheless, preliminary results from the metagnome of the particle-associated microbiota of two adult birds show that the crop microbiome contains a high number of genes encoding cellulases (such as GH5) more abundant than those of the termite gut, as well as genes encoding hemicellulases. These preliminary results show that the carbohydate-active enzyme genes in the cropmetagenome could be a source of biochemical catalysts able to deconstruct plant biomass.

Godoy-Vitorino, Filipa; Malfatti, Stephanie; Garcia-Amado, Maria A.; Dominguez-Bello, Maria Gloria; Hugenholtz, Phillip; Tringe, Susannah

2011-05-31T23:59:59.000Z

317

Neutron Reflectometry and QCM-D Study of the Interaction of Cellulase Enzymes with Films of Amorphous Cellulose  

Science Conference Proceedings (OSTI)

Improving the efficiency of enzymatic hydrolysis of cellulose is one of the key technological hurdles to reduce the cost of producing ethanol and other transportation fuels from lignocellulosic material. A better understanding of how soluble enzymes interact with insoluble cellulose will aid in the design of more efficient enzyme systems. We report a study involving neutron reflectometry (NR) and quartz crystal microbalance with dissipation (QCM-D) of the interaction of a commercial fungal enzyme extract (T. viride), two purified endoglucanses from thermophilic bacteria (Cel9A from A. acidocaldarius and Cel5A from T. maritima), and a mesophilic fungal endoglucanase (Cel45A from H. insolens) with amorphous cellulose films. The use of amorphous cellulose is motivated by the promise of ionic liquid pretreatment as a second generation technology that disrupts the native crystalline structure of cellulose. NR reveals the profile of water through the film at nm resolution, while QCM-D provides changes in mass and film stiffness. At 20 oC and 0.3 mg/ml, the T. viride cocktail rapidly digested the entire film, beginning from the surface followed by activity throughout the bulk of the film. For similar conditions, Cel9A and Cel5A were active for only a short period of time and only at the surface of the film, with Cel9A releasing 40 from the ~ 700 film and Cel5A resulting in only a slight roughening/swelling effect at the surface. Subsequent elevation of the temperature to the Topt in each case resulted in a very limited increase in activity, corresponding to the loss of an additional 60 from the film for Cel9A and 20 from the film for Cel5A, and very weak penetration into and digestion within the bulk of the film, before the activity again ceased. The results for Cel9A and Cel5A contrast sharply with results for Cel45A where very rapid and extensive penetration and digestion within the bulk of the film was observed at 20 C. We speculate that the large differences are due to the use of the thermophilic enzymes far below their optimal temperatures and also the presence of a cellulose binding module (CBM) on Cel45A while the thermophilic enzymes lack a CBM.

Halbert, Candice E [ORNL; Ankner, John Francis [ORNL; Kent, Michael S [Sandia National Laboratories (SNL); Jaclyn, Murton K [Sandia National Laboratories (SNL); Browning, Jim [ORNL; Cheng, Gang [Joint Bioenergy Institute; Liu, Zelin [Virginia Polytechnic Institute and State University (Virginia Tech); Majewski, Jaroslaw [Los Alamos National Laboratory (LANL); Supratim, Datta [Joint Bioenergy Institute; Michael, Jablin [Los Alamos National Laboratory (LANL); Bulent, Akgun [NIST Center for Neutron Research (NCRN), Gaithersburg, MD; Alan, Esker [Virginia Polytechnic Institute and State University (Virginia Tech); Simmons, Blake [Sandia National Laboratories (SNL)

2011-01-01T23:59:59.000Z

318

Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass  

NLE Websites -- All DOE Office Websites (Extended Search)

Metabolic Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass Minseok Cha 1,3 , Daehwan Chung 1,3 , James G Elkins 2,3 , Adam M Guss 2,3 and Janet Westpheling 1,3* Abstract Background: Members of the anaerobic thermophilic bacterial genus Caldicellulosiruptor are emerging candidates for consolidated bioprocessing (CBP) because they are capable of efficiently growing on biomass without conventional pretreatment. C. bescii produces primarily lactate, acetate and hydrogen as fermentation products, and while some Caldicellulosiruptor strains produce small amounts of ethanol C. bescii does not, making it an attractive background to examine the effects of metabolic engineering. The recent development of methods for genetic manipulation has set the stage for rational engineering of this genus for improved biofuel

319

Blog Feed: Vehicles | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

December 9, 2010 December 9, 2010 Country-Fried Biofuels Instead of tossing your grease and used cooking oil, let a clean cities coordinator in your area help recycle it into biodiesel. December 7, 2010 Country-Fried Biofuels Some Clean Cities coalitions, supported by the Vehicle Technologies Program in EERE, have worked with their local governments to make holiday drippings into clean fuel. December 3, 2010 Innovations: Making Biofuels More Efficient A new project is using thermophilic extremophiles -- microorganisms that grow optimally in temperatures above 160 deg F -- to produce a new highly efficient fuel. Learn more. December 2, 2010 Civil War Icon Becomes National Clean Energy Model Nearly a century and a half after the first shots of the Civil War, Fort Sumter National Monument is poised to become a national model for clean

320

Innovations: Making Biofuels More Efficient | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Innovations: Making Biofuels More Efficient Innovations: Making Biofuels More Efficient Innovations: Making Biofuels More Efficient December 3, 2010 - 11:40am Addthis Ginny Simmons Ginny Simmons Former Managing Editor for Energy.gov, Office of Public Affairs What are the key facts? Currently all biofuels rely on photosynthetic plants to convert energy from sunlight into usable fuel, but the overall efficiency of this is low. A new ARPA-E project is using thermophilic extremophiles -- microorganisms that grow optimally in temperatures above 160 deg F -- to produce a new highly efficient fuel. On Tuesday, Secretary Chu spoke of the need for new innovations to lead the U.S. into a new green economy. This project out of Energy's Advanced Research Projects Agency is an example of just that. Currently all biofuels rely on photosynthetic plants to convert energy from

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

Biocaldol | Open Energy Information  

Open Energy Info (EERE)

Biocaldol Biocaldol Jump to: navigation, search Name Biocaldol Place London, England, United Kingdom Zip NW1 0NH Sector Biomass Product Biocaldol uses thermophilic microorganisms to ferment inaccessible biomass sugars into ethanol. Coordinates 51.506325°, -0.127144° Loading map... {"minzoom":false,"mappingservice":"googlemaps3","type":"ROADMAP","zoom":14,"types":["ROADMAP","SATELLITE","HYBRID","TERRAIN"],"geoservice":"google","maxzoom":false,"width":"600px","height":"350px","centre":false,"title":"","label":"","icon":"","visitedicon":"","lines":[],"polygons":[],"circles":[],"rectangles":[],"copycoords":false,"static":false,"wmsoverlay":"","layers":[],"controls":["pan","zoom","type","scale","streetview"],"zoomstyle":"DEFAULT","typestyle":"DEFAULT","autoinfowindows":false,"kml":[],"gkml":[],"fusiontables":[],"resizable":false,"tilt":0,"kmlrezoom":false,"poi":true,"imageoverlays":[],"markercluster":false,"searchmarkers":"","locations":[{"text":"","title":"","link":null,"lat":51.506325,"lon":-0.127144,"alt":0,"address":"","icon":"","group":"","inlineLabel":"","visitedicon":""}]}

322

4762.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

July July 2009, p. 4762-4769 Vol. 75, No. 14 0099-2240/09/$08.00ϩ0 doi:10.1128/AEM.00236-09 Copyright © 2009, American Society for Microbiology. All Rights Reserved. Efficient Degradation of Lignocellulosic Plant Biomass, without Pretreatment, by the Thermophilic Anaerobe "Anaerocellum thermophilum" DSM 6725 ᰔ Sung-Jae Yang, 1,2 # Irina Kataeva, 1,2 # Scott D. Hamilton-Brehm, 2 Nancy L. Engle, 2 Timothy J. Tschaplinski, 2 Crissa Doeppke, 2,3 Mark Davis, 2,3 Janet Westpheling, 2,4 and Michael W. W. Adams 1,2 * Departments of Biochemistry & Molecular Biology 1 and Genetics, 4 University of Georgia, Athens, Georgia 30602; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 2 ; and National Renewable Energy Laboratory, Golden, Colorado 80401 3 Received 31 January 2009/Accepted 15 May 2009 Very few cultivated microorganisms

323

CX-002564: Categorical Exclusion Determination | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

64: Categorical Exclusion Determination 64: Categorical Exclusion Determination CX-002564: Categorical Exclusion Determination FPE Renewables, LLC CX(s) Applied: B5.1 Date: 05/26/2010 Location(s): Lynden, Washington Office(s): Energy Efficiency and Renewable Energy, Golden Field Office The Washington Department of Commerce will provide $320,000 of Recovery Act funds to FPE Renewables, LLC to upgrade an existing anaerobic digester at Vander Haak Dairy in Lynden, Washington. This upgrade project will convert the digester from mesophillic operation to thermophillic operation. This conversion will require additional heat recovery capacity in a new generator set, a collection pit to provide a more consistent feedstock mixture, and some mechanical and utility upgrades to accommodate the additional heat and electricity. This project will allow FPE Renewables to

324

1475-2859-8-30.fm  

NLE Websites -- All DOE Office Websites (Extended Search)

Microbial Cell Factories Microbial Cell Factories Open Access Research Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration Yiran Wang 1 and Y-H Percival Zhang* 1,2,3 Address: 1 Biological Systems Engineering Department, 210-A Seitz Hall, Virginia Polytechnic Institute and State University, Blacksburg, Virgina 24061, USA, 2 Institute for Critical Technology and Applied Sciences (ICTAS) Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA and 3 DOE BioEnergy Science Center (BESC), Oak Ridge, Tennessee 37831, USA Email: Yiran Wang - yiran@vt.edu; Y-H Percival Zhang* - ypzhang@vt.edu * Corresponding author Abstract Background: Thermostable enzymes from thermophilic microorganisms are playing more and

325

fulltext.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

RELEV RELEV ANT ENZYMES AND PROTEINS One-step purification and immobilization of thermophilic polyphosphate glucokinase from Thermobifida fusca YX: glucose-6-phosphate generation without ATP Hehuan Liao & Suwan Myung & Y.-H. Percival Zhang Received: 25 May 2011 / Revised: 17 June 2011 / Accepted: 19 June 2011 # Springer-V erlag 2011 Abstract The discovery of stable and active polyphosphate glucokinase (PPGK, EC 2.7.1.63) would be vital to cascade enzyme biocatalysis that does not require a costly A TP input. An open reading frame Tfu_1811 from Thermobifida fusca YX encoding a putative PPGK was cloned and the recombinant protein fused with a family 3 cellulose-binding module (CBM-PPGK) was overexpressed in Escherichia coli. Mg 2+ was an indispensible activator. This enzyme exhibited the highest activity in the presence of 4 mM Mg 2+ at 55°C and pH 9.0. Under its suboptimal

326

1483.full.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

7 January 2011. 7 January 2011. 2011, 193(6):1483. DOI: 10.1128/JB.01515-10. J. Bacteriol. and Robert M. Kelly Walston-Davenport, Shunsheng Han, Michael W. W. Adams Kyrpides, Natalia Ivanova, John C. Detter, Karen Tanja Woyke, Natalia Mikhailova, Amrita Pati, Nikos C. Goodwin, Samuel Pitluck, Miriam L. Land, Loren J. Hauser, Susan Lucas, Alla Lapidus, Jan-Fang Cheng, Lynne A. Sara E. Blumer-Schuette, Inci Ozdemir, Dhaval Mistry, Caldicellulosiruptor lactoaceticus , and Caldicellulosiruptor owensensis , Caldicellulosiruptor kronotskyensis , Caldicellulosiruptor kristjanssonii , Caldicellulosiruptor hydrothermalis Biomass-Degrading Bacteria Anaerobic, Extremely Thermophilic Plant Complete Genome Sequences for the http://jb.asm.org/content/193/6/1483 Updated information and services can be found at:

327

Degradation of cellulosic biomass and its subsequent utilization for the production of chemical feedstocks. Progress report, September 1-November 30, 1978  

DOE Green Energy (OSTI)

Studies on the accumulation of glucose during the fermentation of cellulose by Clostridium thermocellum are discussed. Production of ethanol and its relationship to growth rate in C. thermocellum is reported. Different biomasses were tested for ethanol yields. These included exploded poplar, sugar cane, bagasse, corn cobs, sweet gum, rice straw, and wheat straw. Thermophilic bacteria were tested to determine relationship of temperature to yield of ethanol. A preliminary report on isolating plaque forming emits derived from C. thermocellum is presented as well as the utilization of carbohydrates in nutrition. A cellulose enzyme is being purified from C. thermocellum. The production of chemical feedstocks by fermentation is reported. Acrylic acid, acetone/butanol, and acetic acid, produced by C. propionicum, C. acetobutylicum, and C. thermoaceticum, are discussed. (DC)

Wang, D.I.; Cooney, C.L.; Demain, A.L.; Gomez, R.F.; Sinskey, A.J.

1978-11-01T23:59:59.000Z

328

Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney  

Science Conference Proceedings (OSTI)

Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1 T was the first isolate within the phylum ThermusDeinococcus to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1 T is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Copeland, A [U.S. Department of Energy, Joint Genome Institute; Gu, Wei [U.S. Department of Energy, Joint Genome Institute; Yasawong, Montri [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Pan, Chongle [ORNL; Brambilla, Evelyne-Marie [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Tindall, Brian [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Sikorski, Johannes [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

2012-01-01T23:59:59.000Z

329

Application of bacterial leaching technology to deep solution-mining conditions for uranium extraction. Final report, September 1, 1978-September 30, 1981  

SciTech Connect

Microorganisms were evaluated for use in recovery of uranium under conditions of in-situ solution mining. The cultures tested were Thiobacillus ferrooxidans, the faculative-thermophilic TH3 strain, and two Sulfolobus species. Growth of the organisms occurred in the presence of 0.34 to 5.0 mM uranyl ion with higher concentrations being inhibitory. Uranium ore from the Anaconda Minerals Co. Jackpile mine was not readily leachable by microorganisms. To support bacterial activity the ore was supplemented with pyrite or ferrous iron. The ore possessed some toxic properties. T. ferrooxidans was able to assist in leaching of uranium from the ore at a hydrostatic pressure of 10.3 MPa.

Brierley, J.A.; Brierley, C.L.; Torma, A.E.

1982-03-01T23:59:59.000Z

330

Comparison of biochemical microbial effects in enhanced oil recovery (MEOR)  

Science Conference Proceedings (OSTI)

Experimental data dealing with the interactions between certain microbial species and crude oils indicates that these interactions are selective and occur via biochemical pathways which can be characterized by the chemical composition of the initial crude oil and that of the end products. In the studies discussed in this paper, the microbial species used were thermophilic and/or thermoadapted microorganisms which thrive in harsh environments (e.g., pH, temperature, pressure, salinity). Crude oils chosen for biotreatment represented a wide range of oils, which varied from relatively light oils to heavy, high sulfur content oils. The crude oils used have also been distinguished in terms of their geological history, i.e., heavy, because they are immature or heavy, because they have been biodegraded. The significance of biodegraded'' vs. biotreated'' crude oil in MEOR also discussed.

Premuzic, E.T.; Lin, M.S.; Manowitz, B.

1992-11-01T23:59:59.000Z

331

Comparison of biochemical microbial effects in enhanced oil recovery (MEOR)  

Science Conference Proceedings (OSTI)

Experimental data dealing with the interactions between certain microbial species and crude oils indicates that these interactions are selective and occur via biochemical pathways which can be characterized by the chemical composition of the initial crude oil and that of the end products. In the studies discussed in this paper, the microbial species used were thermophilic and/or thermoadapted microorganisms which thrive in harsh environments (e.g., pH, temperature, pressure, salinity). Crude oils chosen for biotreatment represented a wide range of oils, which varied from relatively light oils to heavy, high sulfur content oils. The crude oils used have also been distinguished in terms of their geological history, i.e., heavy, because they are immature or heavy, because they have been biodegraded. The significance of ``biodegraded`` vs. ``biotreated`` crude oil in MEOR also discussed.

Premuzic, E.T.; Lin, M.S.; Manowitz, B.

1992-11-01T23:59:59.000Z

332

In situ thermally enhanced biodegradation of petroleum fuel hydrocarbons and halogenated organic solvents  

DOE Patents (OSTI)

An in situ thermally enhanced microbial remediation strategy and a method for the biodegradation of toxic petroleum fuel hydrocarbon and halogenated organic solvent contaminants. The method utilizes nonpathogenic, thermophilic bacteria for the thermal biodegradation of toxic and carcinogenic contaminants, such as benzene, toluene, ethylbenzene and xylenes, from fuel leaks and the chlorinated ethenes, such as trichloroethylene, chlorinated ethanes, such as 1,1,1-trichloroethane, and chlorinated methanes, such as chloroform, from past solvent cleaning practices. The method relies on and takes advantage of the pre-existing heated conditions and the array of delivery/recovery wells that are created and in place following primary subsurface contaminant volatilization efforts via thermal approaches, such as dynamic underground steam-electrical heating.

Taylor, Robert T. (Livermore, CA); Jackson, Kenneth J. (San Leandro, CA); Duba, Alfred G. (Livermore, CA); Chen, Ching-I (Danville, CA)

1998-01-01T23:59:59.000Z

333

In situ thermally enhanced biodegradation of petroleum fuel hydrocarbons and halogenated organic solvents  

DOE Patents (OSTI)

An in situ thermally enhanced microbial remediation strategy and a method for the biodegradation of toxic petroleum fuel hydrocarbon and halogenated organic solvent contaminants are described. The method utilizes nonpathogenic, thermophilic bacteria for the thermal biodegradation of toxic and carcinogenic contaminants, such as benzene, toluene, ethylbenzene and xylenes, from fuel leaks and the chlorinated ethenes, such as trichloroethylene, chlorinated ethanes, such as 1,1,1-trichloroethane, and chlorinated methanes, such as chloroform, from past solvent cleaning practices. The method relies on and takes advantage of the pre-existing heated conditions and the array of delivery/recovery wells that are created and in place following primary subsurface contaminant volatilization efforts via thermal approaches, such as dynamic underground steam-electrical heating. 21 figs.

Taylor, R.T.; Jackson, K.J.; Duba, A.G.; Chen, C.I.

1998-05-19T23:59:59.000Z

334

Monitoring Acidophilic Microbes with Real-Time Polymerase Chain Reaction (PCR) Assays  

Science Conference Proceedings (OSTI)

Many techniques that are used to characterize and monitor microbial populations associated with sulfide mineral bioleaching require the cultivation of the organisms on solid or liquid media. Chemolithotrophic species, such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, or thermophilic chemolithotrophs, such as Acidianus brierleyi and Sulfolobus solfataricus can grow quite slowly, requiring weeks to complete efforts to identify and quantify these microbes associated with bioleach samples. Real-time PCR (polymerase chain reaction) assays in which DNA targets are amplified in the presence of fluorescent oligonucleotide primers, allowing the monitoring and quantification of the amplification reactions as they progress, provide a means of rapidly detecting the presence of microbial species of interest, and their relative abundance in a sample. This presentation will describe the design and use of such assays to monitor acidophilic microbes in the environment and in bioleaching operations. These assays provide results within 2-3 hours, and can detect less than 100 individual microbial cells.

Frank F. Roberto

2008-08-01T23:59:59.000Z

335

DOE Joint Genome Institute: Advancing Next Gen Biofuels by Turning Up the  

NLE Websites -- All DOE Office Websites (Extended Search)

October 2, 2011 October 2, 2011 Advancing Next Gen Biofuels by Turning Up the Heat on Biomass Pretreatment Processes WALNUT CREEK, Calif.-The nation's Renewable Fuels Standard calls for annual production of 36 billion gallons of biofuel by 2022. One of the biggest hurdles to achieving this goal lies in optimizing the multistep process involved in breaking down plant biomass and then converting it into fermentable sugars that can be refined into fuel for our transportation needs. To overcome this challenge, the U.S. Department of Energy supports several projects focused on identifying enzymes from fungi and microbes such as cellulases-that breakdown plant cell walls-and heat-tolerant industrial-strength host cell systems to drive these reactions. Photo: The thermophilic fungus M. thermophila

336

ENHANCED PRACTICAL PHOTOSYNTHETIC CO2 MITIGATION  

DOE Green Energy (OSTI)

This quarterly report documents significant achievements in the Enhanced Practical Photosynthetic CO{sub 2} Mitigation project during the period from 1/03/2001 through 4/02/2001. Many of the activities and accomplishments are continuations of work initiated and reported in last quarter's status report. Major activities and accomplishments for this quarter include: Three sites in Yellowstone National Park have been identified that may contain suitable organisms for use in a bioreactor; Full-scale culturing of one thermophilic organism from Yellowstone has progressed to the point that there is a sufficient quantity to test this organism in the model-scale bioreactor; The effects of the additive monoethanolamine on the growth of one thermophilic organism from Yellowstone has been tested; Testing of growth surface adhesion and properties is continuing; Construction of a larger model-scale bioreactor to improve and expand testing capabilities is completed and the facility is undergoing proof tests; Model-scale bioreactor tests examining the effects of CO{sub 2} concentration levels and lighting levels on organism growth rates are continuing; Alternative fiber optic based deep-penetration light delivery systems for use in the pilot-scale bioreactor have been designed, constructed and tested; An existing slug flow reactor system has been modified for use in this project, and a proof-of-concept test plan has been developed for the slug flow reactor; Research and testing of water-jet harvesting techniques is continuing, and a harvesting system has been designed for use in the model-scale bioreactor; and The investigation of comparative digital image analysis as a means for determining the ''density'' of algae on a growth surface is continuing Plans for next quarter's work and an update on the project's web page are included in the conclusions.

Dr. David J. Bayless; Dr. Morgan Vis; Dr. Gregory Kremer; Dr. Michael Prudich; Dr. Keith Cooksey; Dr. Jeff Muhs

2001-04-16T23:59:59.000Z

337

Co-digestion of cattle manure with food waste and sludge to increase biogas production  

Science Conference Proceedings (OSTI)

Highlights: Black-Right-Pointing-Pointer Small increase in methane production was observed applying sonication pretreatment. Black-Right-Pointing-Pointer Biogas productions between 720 and 1100 mL/Lreactor day were achieved. Black-Right-Pointing-Pointer Volatile solids removal efficiencies ranged between 53% and 60%. Black-Right-Pointing-Pointer Lower methane yields were obtained when operating under thermophilic conditions. Black-Right-Pointing-Pointer Optimum OLR in lab-scale CSTR was 1.2-1.3 g VS/L day (HRT: 20 days). - Abstract: Anaerobic co-digestion strategies are needed to enhance biogas production, especially when treating certain residues such as cattle/pig manure. This paper presents a study of co-digestion of cattle manure with food waste and sewage sludge. With the aim of maximising biogas yields, a series of experiments were carried out under mesophilic and thermophilic conditions using continuously stirred-tank reactors, operating at different hydraulic residence times. Pretreatment with ultrasound was also applied to compare the results with those obtained with non-pretreated waste. Specific methane production decreases when increasing the OLR and decreasing HRT. The maximum value obtained was 603 LCH{sub 4}/kg VS{sub feed} for the co-digestion of a mixture of 70% manure, 20% food waste and 10% sewage sludge (total solid concentration around 4%) at 36 Degree-Sign C, for an OLR of 1.2 g VS/L day. Increasing the OLR to 1.5 g VS/L day led to a decrease of around 20-28% in SMP. Lower methane yields were obtained when operating at 55 Degree-Sign C. The increase in methane production when applying ultrasound to the feed mixtures does not compensate for the energy spent in this pretreatment.

Maranon, E., E-mail: emara@uniovi.es [Department of Chemical Engineering and Environmental Technology, University Institute of Technology of Asturias, Campus of Gijon, University of Oviedo, 33203 Gijon (Spain); Castrillon, L.; Quiroga, G.; Fernandez-Nava, Y. [Department of Chemical Engineering and Environmental Technology, University Institute of Technology of Asturias, Campus of Gijon, University of Oviedo, 33203 Gijon (Spain); Gomez, L.; Garcia, M.M. [Zero Emissions Technology, 41018 Seville (Spain)

2012-10-15T23:59:59.000Z

338

O R I G I N A L P A P E R Thermodesulfobacterium  

NLE Websites -- All DOE Office Websites (Extended Search)

Thermodesulfobacterium Thermodesulfobacterium geofontis sp. nov., a hyperthermophilic, sulfate-reducing bacterium isolated from Obsidian Pool, Yellowstone National Park Scott D. Hamilton-Brehm * Robert A. Gibson * Stefan J. Green * Ellen C. Hopmans * Stefan Schouten * Marcel T. J. van der Meer * John P. Shields * Jaap S. S. Damste ´ * James G. Elkins Received: 20 July 2012 / Accepted: 4 January 2013 Ó Springer Japan (outside the USA) 2013 Abstract A novel sulfate-reducing bacterium designated OPF15 T was isolated from Obsidian Pool, Yellowstone National Park, Wyoming. The phylogeny of 16S rRNA and functional genes (dsrAB) placed the organism within the family Thermodesulfobacteriaceae. The organism dis- played hyperthermophilic temperature requirements for growth with a range of 70-90 °C and an optimum of 83 °C. Optimal pH was around 6.5-7.0 and the organism required the presence of H 2 or formate

339

Made Famous By Erin Brockovich: A Potent Pollutant and its Nemesis  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Made Famous By Erin Brockovich: A Potent Pollutant and its Nemesis Made Famous By Erin Brockovich: A Potent Pollutant and its Nemesis Bacterium Made Famous By Erin Brockovich: A Potent Pollutant and its Nemesis Bacterium July 2, 2012 - 4:49pm Addthis Brookhaven’s National Synchrotron Light Source x-ray beamline was used to reveal the atomic structure of the bioremediation enzyme. The liquid nitrogen in the foreground keeps the crystallized enzyme cool, protecting it from the heat of the x-rays that would otherwise damage the crystal. | Photo by Brookhaven National Laboratory Brookhaven's National Synchrotron Light Source x-ray beamline was used to reveal the atomic structure of the bioremediation enzyme. The liquid nitrogen in the foreground keeps the crystallized enzyme cool, protecting it from the heat of the x-rays that would otherwise damage the crystal. |

340

Why sequence for reverse metabolic engineering of Escherichia coli?  

NLE Websites -- All DOE Office Websites (Extended Search)

for reverse metabolic for reverse metabolic engineering of Escherichia coli? Bioenergy researchers are interested in harnessing microbes to produce alcohols for fuel use because these cells are relatively easy to grow and study. The bacteria Escherichia coli and Corynebacterium glutamucum, both of which have been used to produce alcohols, have already been sequenced and had their genomes annotated. For this project, mutants of E. coli and C. glutamucum will be sequenced to find out how to boost alcohol production in these bacteria for bioenergy use. E. coli Photo: CDC/Evangeline Sowers, Janice Carr Previous work with E. coli has shown that the bacterium can produce alcohols with five-carbon atoms. Further study of the bacterium's mutants could lead to the production of even more complex, longer-chain alcohols

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

Why sequence Actinotalea fermentans?  

NLE Websites -- All DOE Office Websites (Extended Search)

Actinotalea fermentans? Actinotalea fermentans? Actinotalea fermentans is a bacterium isolated from a landfill and grows best in moderate temperature, where it ferments cellulose to acetate and ethanol aerobically. This organism was previously considered as a potential way to convert cellulose to ethanol for use as a fuel, but the fermentation reaction always led to reduced yields, reducing the bacterium's usefulness. Recently, scientists have engineered synthetic co-cultures of A. fermentans with yeast to produce useful chemicals and fuels directly from cellulose or agricultural feedstocks such as corn stover, switchgrass, poplar and sugarcane bagasse. This technique will allow A. fermentans to be used to convert cellulose to ethanol while allowing researchers to avoid the same

342

News Room | Argonne National Laboratory  

NLE Websites -- All DOE Office Websites (Extended Search)

News Room News Room In a 3D structure of the protein, the binding site is shown in pink, representing a potential drug target. The green molecule shows binding of an antibiotic to the protein. Click to enlarge. Image courtesy of Wladek Minor. Newly ID'd protein provides target for antibiotic-resistant hospital bacterium Full Story » Researchers have made inroads into tackling a bacterium that plagues hospitals and is highly resistant to most antibiotics. Andrey Elagin (left), postdoctoral scholar at the Enrico Fermi Institute at the University of Chicago, and Matthew Wetstein, the Grainger Postdoctoral Fellow at the Enrico Fermi Institute at the University of Chicago, adjust the optics in the Large Area Picosecond Photodetector testing facility. The facility uses extremely short laser pulses to precisely measure the time resolution of the photodetectors. Click to enlarge.

343

Membrane protein kit may lead to better targeted drugs | Argonne National  

NLE Websites -- All DOE Office Websites (Extended Search)

Argonne biologists Deborah Hanson and Phil Laible developed a kit that enables its users to easily generate large amounts of membrane proteins. To view a larger version of the image, click on it. Argonne biologists Deborah Hanson and Phil Laible developed a kit that enables its users to easily generate large amounts of membrane proteins. To view a larger version of the image, click on it. Argonne biologists Deborah Hanson and Phil Laible developed a kit that enables its users to easily generate large amounts of membrane proteins. To view a larger version of the image, click on it. Filamentous cells of the bacterium Rhodobacter sphaeroides. Argonne scientists received an R&D100 Award for using Rhodobacter to develop a new system for growing membrane proteins used in drug discovery research. Image by Sheng-Wen Chui, University of Oxford. To view a larger version of the image, click on it. Filamentous cells of the bacterium Rhodobacter sphaeroides. Argonne

344

Discovery through Teamwork | U.S. DOE Office of Science (SC)  

NLE Websites -- All DOE Office Websites (Extended Search)

Discovery through Teamwork Discovery through Teamwork Discovery & Innovation Stories of Discovery & Innovation Brief Science Highlights SBIR/STTR Highlights Contact Information Office of Science U.S. Department of Energy 1000 Independence Ave., SW Washington, DC 20585 P: (202) 586-5430 07.29.13 Discovery through Teamwork By coordinating capabilities across institutions, DOE Bioenergy Research Center scientists identify a powerful new microbe for biofuel processing. Print Text Size: A A A Subscribe FeedbackShare Page Click to enlarge photo. Enlarge Photo An image of the bacterium Caldicellulosiruptor bescii, named for the DOE BioEnergy Science Center (BESC). Photo courtesy of Michael W. W. Adams The bacterium Caldicellulosiruptor bescii, named for the DOE BioEnergy Science Center (BESC).

345

Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4. 1 and its use for whole-genome shotgun sequence assembly  

Science Conference Proceedings (OSTI)

Rhodobacter sphaeroides 2.4.1 is a facultative photoheterotrophic bacterium with tremendous metabolic diversity, which has significantly contributed to our understanding of the molecular genetics of photosynthesis, photoheterotrophy, nitrogen fixation, hydrogen metabolism, carbon dioxide fixation, taxis, and tetrapyrrole biosynthesis. To further understand this remarkable bacterium, and to accelerate an ongoing sequencing project, two whole-genome restriction maps (EcoRI and HindIII) of R. sphaeroides strain 2.4.1 were constructed using shotgun optical mapping. The approach directly mapped genomic DNA by the random mapping of single molecules. The two maps were used to facilitate sequence assembly by providing an optical scaffold for high-resolution alignment and verification of sequence contigs. Our results show that such maps facilitated the closure of sequence gaps by the early detection of nascent sequence contigs during the course of the whole-genome shotgun sequencing process.

Shou, S. [Univ. Wisc.-Madison; Kvikstad, E. [Univ. Wisc.-Madison; Kile, A. [Univ. Wisc.-Madison; Severin, J. [Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4. 1 and its use for whole-genome shotgun sequence assembly; Forrest, D. [Univ. Wisc.-Madison; Runnheim, R. [Univ. Wisc.-Madison; Churas, C. [Univ. Wisc.-Madison; Hickman, J. W. [Univ. Wisc.-Madison; Mackenzie, C. [University of Texas–Houston Medical School; Choudhary, M. [University of Texas–Houston Medical School; Donohue, T. [Univ. Wisc.-Madison; Kaplan, S. [University of Texas–Houston Medical School; Schwartz, D. C. [Univ. Wisc.-Madison

2003-09-01T23:59:59.000Z

346

Diffusion in active magnetic colloids  

E-Print Network (OSTI)

Properties of active colloids of circle swimmers are reviewed. As an particular example of active magnetic colloids the magnetotactic bacteria under the action of a rotating magnetic field is considered. The relation for a diffusion coefficient due to the random switching of the direction of rotation of their rotary motors is derived on the basis of the master equation. The obtained relation is confirmed by the direct numerical simulation of random trajectory of a magnetotactic bacterium under the action of the Poisson type internal noise due to the random switching of rotary motors. The results obtained are in qualitative and quantitative agreement with the available experimental results and allows one to determine the characteristic time between the switching events of a rotary motor of the bacterium.

Reinis Taukulis; Andrejs Cebers

2013-10-04T23:59:59.000Z

347

Development of a Proteoliposome Model to Probe Transmembrane Electron-Transfer Reactions  

Science Conference Proceedings (OSTI)

The mineral respiring bacterium Shewanella oneidensis uses a protein complex, MtrCAB, composed of two decaheme cytochromes brought together inside a transmembrane porin to transport electrons across the outer membrane to a variety of mineral-based electron acceptors. A proteoliposome system has been developed that contains methyl viologen (MV) as an internalised electron acceptor and valinomycin (V) as a membrane associated cation exchanger. These proteoliposomes can be used as a model system to investigate MtrCAB function.

White, Gaye F.; Shi, Zhi; Shi, Liang; Dohnalkova, Alice; Fredrickson, Jim K.; Zachara, John M.; Butt, Julea N.; Richardson, David J.; Clarke, Thomas

2012-12-01T23:59:59.000Z

348

Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases  

DOE Green Energy (OSTI)

To efficiently deconstruct recalcitrant plant biomass to fermentable sugars in industrial processes, biocatalysts of higher performance and lower cost are required. The genetic diversity found in the metagenomes of natural microbial biomass decay communities may harbor such enzymes. Our goal was to discover and characterize new glycoside hydrolases (GHases) from microbial biomass decay communities, especially those from unknown or never previously cultivated microorganisms. From the metagenome sequences of an anaerobic microbial community actively decaying poplar biomass, we identified approximately 4,000 GHase homologs. Based on homology to GHase families/activities of interest and the quality of the sequences, candidates were selected for full-length cloning and subsequent expression. As an alternative strategy, a metagenome expression library was constructed and screened for GHase activities. These combined efforts resulted in the cloning of four novel GHases that could be successfully expressed in Escherichia coli. Further characterization showed that two enzymes showed significant activity on p-nitrophenyl-{alpha}-L-arabinofuranoside, one enzyme had significant activity against p-nitrophenyl-{beta}-D-glucopyranoside, and one enzyme showed significant activity against p-nitrophenyl-{beta}-D-xylopyranoside. Enzymes were also tested in the presence of ionic liquids. Metagenomics provides a good resource for mining novel biomass degrading enzymes and for screening of cellulolytic enzyme activities. The four GHases that were cloned may have potential application for deconstruction of biomass pretreated with ionic liquids, as they remain active in the presence of up to 20% ionic liquid (except for 1-ethyl-3-methylimidazolium diethyl phosphate). Alternatively, ionic liquids might be used to immobilize or stabilize these enzymes for minimal solvent processing of biomass.

Li L. L.; van der Lelie D.; Taghavi, S.; McCorkle, S. M.; Zhang, Y.-B.; Blewitt, M. G.; Brunecky, R.; Adney, W. S.; Himmel, M. E.; Brumm, P.; Drinkwater, C.; Mead, D. A.; Tringe, S. G.

2011-08-01T23:59:59.000Z

349

Genome, transcriptome, and secretome analysis of wood decay fungus postia placenta supports unique mechanisms of lignocellulose conversion  

SciTech Connect

Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative {beta}-1-4 endoglucanase were expressed at high levels relative to glucose grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC{center_dot}MSIMS). Also upregulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H202. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H202 react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons to the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.

Martinez, Diego [Los Alamos National Laboratory; Challacombe, Jean F [Los Alamos National Laboratory; Misra, Monica [Los Alamos National Laboratory; Xie, Gary [Los Alamos National Laboratory; Brettin, Thomas [Los Alamos National Laboratory; Morgenstern, Ingo [CLARK UNIV; Hibbett, David [CLARK UNIV.; Schmoll, Monika [UNIV WIEN; Kubicek, Christian P [UNIV WIEN; Ferreira, Patricia [CIB, CSIC, MADRID; Ruiz - Duenase, Francisco J [CIB, CSIC, MADRID; Martinez, Angel T [CIB, CSIC, MADRID; Kersten, Phil [FOREST PRODUCTS LAB; Hammel, Kenneth E [FOREST PRODUCTS LAB; Vanden Wymelenberg, Amber [U. WISCONSIN; Gaskell, Jill [FOREST PRODUCTS LAB; Lindquist, Erika [DOE JGI; Sabati, Grzegorz [U. WISCONSIN; Bondurant, Sandra S [U. WISCONSIN; Larrondo, Luis F [U. CATHOLICA DE CHILE; Canessa, Paulo [U. CATHOLICA DE CHILE; Vicunna, Rafael [U. CATHOLICA DE CHILE; Yadavk, Jagiit [U. CINCINATTI; Doddapaneni, Harshavardhan [U. CINCINATTI; Subramaniank, Venkataramanan [U. CINCINATTI; Pisabarro, Antonio G [PUBLIC U. NAVARRE; Lavin, Jose L [PUBLIC U. NAVARRE; Oguiza, Jose A [PUBLIC U. NAVARRE; Master, Emma [U. TORONTO; Henrissat, Bernard [CNRS, MARSEILLE; Coutinho, Pedro M [CNRS, MARSEILLE; Harris, Paul [NOVOZYMES, INC.; Magnuson, Jon K [PNNL; Baker, Scott [PNNL; Bruno, Kenneth [PNNL; Kenealy, William [MASCOMA, INC.; Hoegger, Patrik J [GEORG-AUGUST-U.; Kues, Ursula [GEORG-AUGUST-U; Ramaiva, Preethi [NOVOZYMES, INC.; Lucas, Susan [DOE JGI; Salamov, Asaf [DOE JGI; Shapiro, Harris [DOE JGI; Tuh, Hank [DOE JGI; Chee, Christine L [UNM; Teter, Sarah [NOVOZYMES, INC.; Yaver, Debbie [NOVOZYMES, INC.; James, Tim [MCMASTER U.; Mokrejs, Martin [CHARLES U.; Pospisek, Martin [CHARLES U.; Grigoriev, Igor [DOE JGI; Rokhsar, Dan [DOE JGI; Berka, Randy [NOVOZYMES; Cullen, Dan [FOREST PRODUCTS LAB

2008-01-01T23:59:59.000Z

350

Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil  

DOE Green Energy (OSTI)

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.

DeAngelis, Kristen; Allgaier, Martin; Chavarria, Yaucin; Fortney, Julian; Hugenholtz, Phillip; Simmons, Blake; Sublette, Kerry; Silver, Whendee; Hazen, Terry

2011-07-14T23:59:59.000Z

351

Efficient breakdown of lignocellulose using mixed-microbe populations for bioethanol production.  

DOE Green Energy (OSTI)

This report documents progress in discovering new catalytic technologies that will support the development of advanced biofuels. The global shift from petroleum-based fuels to advanced biofuels will require transformational breakthroughs in biomass deconstruction technologies, because current methods are neither cost effective nor sufficiently efficient or robust for scaleable production. Discovery and characterization of lignocellulolytic enzyme systems adapted to extreme environments will accelerate progress. Obvious extreme environments to mine for novel lignocellulolytic deconstruction technologies include aridland ecosystems (ALEs), such as those of the Sevilleta Long Term Ecological Research (LTER) site in central New Mexico (NM). ALEs represent at least 40% of the terrestrial biosphere and are classic extreme environments, with low nutrient availability, high ultraviolet radiation flux, limited and erratic precipitation, and extreme variation in temperatures. ALEs are functionally distinct from temperate environments in many respects; one salient distinction is that ALEs do not accumulate soil organic carbon (SOC), in marked contrast to temperate settings, which typically have large pools of SOC. Low productivity ALEs do not accumulate carbon (C) primarily because of extraordinarily efficient extracellular enzyme activities (EEAs) that are derived from underlying communities of diverse, largely uncharacterized microbes. Such efficient enzyme activities presumably reflect adaptation to this low productivity ecosystem, with the result that all available organic nutrients are assimilated rapidly. These communities are dominated by ascomycetous fungi, both in terms of abundance and contribution to ecosystem-scale metabolic processes, such as nitrogen and C cycling. To deliver novel, robust, efficient lignocellulolytic enzyme systems that will drive transformational advances in biomass deconstruction, we have: (1) secured an award through the Department of Energy (DoE) Joint Genome Institute (JGI) to perform metatranscriptomic functional profiling of eukaryotic microbial communities of blue grama grass (Bouteloua gracilis) rhizosphere (RHZ) soils and (2) isolated and provided initial genotypic and phenotypic characterization data for thermophilic fungi. Our preliminary results show that many strains in our collection of thermophilic fungi frequently outperform industry standards in key assays; we also demonstrated that this collection is taxonomically diverse and phenotypically compelling. The studies summarized here are being performed in collaboration with University of New Mexico and are based at the Sevilleta LTER research site.

Murton, Jaclyn K.; Ricken, James Bryce; Powell, Amy Jo

2009-11-01T23:59:59.000Z

352

Simple technologies for on-farm composting of cattle slurry solid fraction  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer Simple management techniques were examined for composting slurry solid fraction. Black-Right-Pointing-Pointer Composting slurry solids was effective without bulking agents, turning or rewetting. Black-Right-Pointing-Pointer Maximum rates of organic matter destruction were observed in short piles. Black-Right-Pointing-Pointer Thermophilic temperatures in tall piles maximised sanitation and moisture reduction. Black-Right-Pointing-Pointer The simple compost management approach maximised N retention and agronomic value. - Abstract: Composting technologies and control systems have reached an advanced stage of development, but these are too complex and expensive for most agricultural practitioners for treating livestock slurries. The development of simple, but robust and cost-effective techniques for composting animal slurries is therefore required to realise the potential benefits of waste sanitation and soil improvement associated with composted livestock manures. Cattle slurry solid fraction (SF) was collected at the rates of 4 m{sup 3} h{sup -1} and 1 m{sup 3} h{sup -1} and composted in tall (1.7 m) and short (1.2 m) static piles, to evaluate the physicochemical characteristics and nutrient dynamics of SF during composting without addition of bulking agent materials, and without turning or water addition. Highest maximum temperatures (62-64 Degree-Sign C) were measured in tall piles compared to short piles (52 Degree-Sign C). However, maximum rates of organic matter (OM) destruction were observed at mesophilic temperature ranges in short piles, compared to tall piles, whereas thermophilic temperatures in tall piles maximised sanitation and enhanced moisture reduction. Final OM losses were within the range of 520-660 g kg{sup -1} dry solids and the net loss of OM significantly (P < 0.001) increased nutrient concentrations during the composting period. An advanced degree of stabilization of the SF was indicated by low final pile temperatures and C/N ratio, low concentrations of NH{sub 4}{sup +} and increased concentrations of NO{sub 3}{sup -} in SF composts. The results indicated that minimum intervention composting of SF in static piles over 168 days can produce agronomically effective organic soil amendments containing significant amounts of OM (772-856 g kg{sup -1}) and plant nutrients. The implications of a minimal intervention management approach to composting SF on compost pathogen reduction are discussed and possible measures to improve sanitation are suggested.

Brito, L.M., E-mail: miguelbrito@esa.ipvc.pt [Escola Superior Agraria, Instituto Politecnico de Viana do Castelo, Refoios, 4990-706 Ponte de Lima (Portugal) and Mountain Research Centre (CIMO), IPB, Campus de St Apolonia, Apartado 1172, 5301-855 Braganca (Portugal); Mourao, I. [Escola Superior Agraria, Instituto Politecnico de Viana do Castelo, Refoios, 4990-706 Ponte de Lima (Portugal) and Mountain Research Centre (CIMO), IPB, Campus de St Apolonia, Apartado 1172, 5301-855 Braganca (Portugal); Coutinho, J., E-mail: j_coutin@utad.pt [C. Quimica, DeBA, EC Vida e Ambiente, Universidade de Tras-os-Montes e Alto Douro, ap 1013, 5001-911 Vila Real (Portugal); Smith, S.R., E-mail: s.r.smith@imperial.ac.uk [Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London, SW7 2AZ (United Kingdom)

2012-07-15T23:59:59.000Z

353

Composting in small laboratory pilots: Performance and reproducibility  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer We design an innovative small-scale composting device including six 4-l reactors. Black-Right-Pointing-Pointer We investigate the performance and reproducibility of composting on a small scale. Black-Right-Pointing-Pointer Thermophilic conditions are established by self-heating in all replicates. Black-Right-Pointing-Pointer Biochemical transformations, organic matter losses and stabilisation are realistic. Black-Right-Pointing-Pointer The organic matter evolution exhibits good reproducibility for all six replicates. - Abstract: Small-scale reactors (<10 l) have been employed in composting research, but few attempts have assessed the performance of composting considering the transformations of organic matter. Moreover, composting at small scales is often performed by imposing a fixed temperature, thus creating artificial conditions, and the reproducibility of composting has rarely been reported. The objectives of this study are to design an innovative small-scale composting device safeguarding self-heating to drive the composting process and to assess the performance and reproducibility of composting in small-scale pilots. The experimental setup included six 4-l reactors used for composting a mixture of sewage sludge and green wastes. The performance of the process was assessed by monitoring the temperature, O{sub 2} consumption and CO{sub 2} emissions, and characterising the biochemical evolution of organic matter. A good reproducibility was found for the six replicates with coefficients of variation for all parameters generally lower than 19%. An intense self-heating ensured the existence of a spontaneous thermophilic phase in all reactors. The average loss of total organic matter (TOM) was 46% of the initial content. Compared to the initial mixture, the hot water soluble fraction decreased by 62%, the hemicellulose-like fraction by 68%, the cellulose-like fraction by 50% and the lignin-like fractions by 12% in the final compost. The TOM losses, compost stabilisation and evolution of the biochemical fractions were similar to observed in large reactors or on-site experiments, excluding the lignin degradation, which was less important than in full-scale systems. The reproducibility of the process and the quality of the final compost make it possible to propose the use of this experimental device for research requiring a mass reduction of the initial composted waste mixtures.

Lashermes, G.; Barriuso, E. [INRA, UMR1091 Environment and Arable Crops (INRA, AgroParisTech), F-78850 Thiverval-Grignon (France); Le Villio-Poitrenaud, M. [VEOLIA Environment - Research and Innovation, F-78520 Limay (France); Houot, S., E-mail: sabine.houot@grignon.inra.fr [INRA, UMR1091 Environment and Arable Crops (INRA, AgroParisTech), F-78850 Thiverval-Grignon (France)

2012-02-15T23:59:59.000Z

354

Dosage-Dependent Proteome Response of Shewanella oneidensis MR-1 to Acute Chromate Challenge  

Science Conference Proceedings (OSTI)

Proteome alterations in the metal-reducing bacterium Shewanella oneidensis MR-1 in response to different acute dose challenges (0.3, 0.5, or 1 mM) of the toxic metal chromate [Cr(VI)] were characterized with multidimensional HPLC-MS/MS on a linear trapping quadrupole MS. A total of 2,406 functionally diverse proteins were identified, with a subset demonstrating dosage-dependent up- and down-regulated expression, such as proteins involved in detoxification and iron binding and transport.

Thompson, Melissa R [ORNL; Verberkmoes, Nathan C [ORNL; Chourey, Karuna [ORNL; Shah, Manesh B [ORNL; Thompson, Dorothea K [ORNL; Hettich, Robert {Bob} L [ORNL

2007-01-01T23:59:59.000Z

355

Comparison of the response of bacterial luminescence and mitochondrial respiration to the effluent of an oil refinery  

Science Conference Proceedings (OSTI)

The effects of oil refinery effluents on rat mitochondrial respiration and on the luminescence of the bacterium Photobacterium phosphoreum were compared. Mitochondria from male Wistar rat livers were exposed to different concentrations of refinery effluents in a semiclosed 3-ml reaction vessel. Respiration was measured polarographically with an oxygen electrode. Effects on P. phosphoreum were measured by the standard test developed by Microbics. The mitochondrial method showed EC50s in the range from 1 to 7.5%, while Microtox gave EC50 in the range from 30 to 42%. The higher sensitivity of mitochondria may be exploited in the development of a sensitive biosensor for toxicity of oil refinery effluents.

Riisberg, M.; Bratlie, E.; Stenersen, J. [Univ. of Oslo (Norway)

1996-04-01T23:59:59.000Z

356

Genome Sequence of the Ethene- and Vinyl Chloride-Oxidizing Actinomycete Nocardioides sp Strain JS614  

Science Conference Proceedings (OSTI)

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

Coleman, Nicholas V [University of Sydney, Australia; Wilson, Neil L [University of Sydney, Australia; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Han, Shunsheng [Los Alamos National Laboratory (LANL); Hauser, Loren John [ORNL; Israni, Sanjay [U.S. Department of Energy, Joint Genome Institute; Kim, Edwin [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Larimer, Frank W [ORNL; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, Paul [U.S. Department of Energy, Joint Genome Institute; Schmutz, Jeremy [Stanford University; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Thompson, Sue [Los Alamos National Laboratory (LANL); Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Spain, Jim C [Georgia Institute of Technology; Gossett, James G [Cornell University; Mattes, Timothy E [University of Iowa

2011-01-01T23:59:59.000Z

357

Final report for DOE grant FG02-06ER15805  

Science Conference Proceedings (OSTI)

DOE funding was used to investigate the role of the phosphotransferase system (PTS) in the symbiotic, nodulating bacterium Sinorhizobium meliloti. This system is well studied in several bacterial species. However, itâ??s organization and function in S. meliloti is substantially different than in the those other, well-studied bacteria. The S. meliloti PTS, through our DOE-funded work, has become a model for how this important signal transduction system works in the a-proteobacteria. We have found that the PTS is relatively simple, used for only signal transduction and not transport, and is involved in regulation of carbon metabolism in response to carbon availability and nitrogen availability.

Daniel Gage

2012-05-31T23:59:59.000Z

358

Environmentally Safe Control of Zebra Mussel Fouling  

Science Conference Proceedings (OSTI)

The two primary objectives of this USDOE-NETL contract were successfully achieved during the project: (1) to accelerate research on the development of the bacterium Pseudomonas fluorescens strain CL145A (Pf-CL145A) as a biocontrol agent for zebra mussels (Dreissena polymorpha) and quagga mussels (Dreissena rostriformis bugensis)--two invasive freshwater bivalve species that are infesting water pipes in power plants; and (2) to identify a private-sector company that would move forward to commercialize Pf-CL145A as a substitute for the current polluting use of biocide chemicals for control of these dreissenid mussels in power plant pipes.

Daniel Molloy

2008-02-29T23:59:59.000Z

359

Klebsiella pneumoniae inoculants for enhancing plant growth  

DOE Patents (OSTI)

A biological inoculant for enhancing the growth of plants is disclosed. The inoculant includes the bacterial strains Herbaspirillum seropedicae 2A, Pantoea agglomerans P101, Pantoea agglomerans P102, Klebsiella pneumoniae 342, Klebsiella pneumoniae zmvsy, Herbaspirillum seropedicae Z152, Gluconacetobacter diazotrophicus PA15, with or without a carrier. The inoculant also includes strains of the bacterium Pantoea agglomerans and K. pneumoniae which are able to enhance the growth of cereal grasses. Also disclosed are the novel bacterial strains Herbaspirillum seropedicae 2A, Pantoea agglomerans P101 and P102, and Klebsiella pneumoniae 342 and zmvsy.

Triplett, Eric W. (Middleton, WI); Kaeppler, Shawn M. (Oregon, WI); Chelius, Marisa K. (Greeley, CO)

2008-07-01T23:59:59.000Z

360

Sensing Applications of Fluctuations and Noise  

E-Print Network (OSTI)

Noise and time-dependent fluctuations are usually undesirable signals. However, they have many applications. This dissertation deals with two kinds of sensing applications of fluctuation and noise: soil bulk density assessment and bacterium sensing. The measurement of Vibration-Induced Conductivity Fluctuations (VICOF) provides information about the bulk density and other parameters of soils. Bulk density is the physical property of soils that is important to both the agriculture and construction industries. The traditional measurements of soil bulk density are often time-consuming, expensive or destructive. To determine the soil bulk density without the above drawbacks, the VICOF measurement scheme was proposed. The research of VICOF in this dissertation includes two parts: the initial phase of study and the new methods and their theory. In the initial phase of study, the simple experiments, theory, and simulations of VICOF were tested for relations between the soil bulk density, wetness, salinity, and the VICOF data. Then, new measurement arrangements and their theoretical models were proposed to improve the weaknesses of the initial approach (such as large scattering of data due to loose and heavy contacts) and to calculate the relationship between the measured signals and the electromechanical transport parameters of the soils. The bacterium sensing study in this dissertation was proposed to explore simple, practical, rapid, sensitive, specific, portable, and inexpensive ways to detect and recognize bacteria by Fluctuation-Enhanced Sensing (FES). One such potential way of bacterium sensing is to analyze their odor. The research of bacterium sensing also includes two parts: the initial phase of study and the new methods and their theory. The initial phase study was proposed to explore the possibility of detecting and identifying bacteria by sensing their odor via FES with commercial Taguchi sensors. Then the subsequently developed new methods and their theory provide a simple way to generate binary patterns with perfect reproducibility based on the spectral slopes in different frequency ranges at FES. This new type of signal processing and pattern recognition is implemented at the block diagram level using the building elements of analog circuitries and a few logic gates with total power consumption in the microWatts range.

Chang, Hung-Chih

2010-12-01T23:59:59.000Z

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
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361

Effectiveness of different Frankia cell types as inocula for the actinorhizal plant Casuarina  

Science Conference Proceedings (OSTI)

The soil bacterium Frankia of the Actinomycetales, capable of forming N{sub 2}-fixing symbiotic root nodules on a diverse array of actinorhizal plants, has several morphological forms when grown in pure culture. Fresh hydrated preparations of whole cells, hyphae, and spores were all infective on seedlings of Casuarina at different dilutions. Desiccated hyphae showed no infection capacity, while desiccated spores remained infective, although at a reduced level. On the basis of most-probably-number statistics, spore suspensions were 3 orders of magnitude more infective than hyphae.

Burleigh, S.; Torrey, J.G. (Harvard Univ., Petersham, MA (USA))

1990-08-01T23:59:59.000Z

362

Factors controlling pathogen destruction during anaerobic digestion of biowastes  

SciTech Connect

Anaerobic digestion is the principal method of stabilising biosolids from urban wastewater treatment in the UK, and it also has application for the treatment of other types of biowaste. Increasing awareness of the potential risks to human and animal health from environmental sources of pathogens has focused attention on the efficacy of waste treatment processes at destroying pathogenic microorganisms in biowastes recycled to agricultural land. The degree of disinfection achieved by a particular anaerobic digester is influenced by a variety of interacting operational variables and conditions, which can often deviate from the ideal. Experimental investigations demonstrate that Escherichia coli and Salmonella spp. are not damaged by mesophilic temperatures, whereas rapid inactivation occurs by thermophilic digestion. A hydraulic, biokinetic and thermodynamic model of pathogen inactivation during anaerobic digestion showed that a 2 log{sub 10} reduction in E. coli (the minimum removal required for agricultural use of conventionally treated biosolids) is likely to challenge most conventional mesophilic digesters, unless strict maintenance and management practices are adopted to minimise dead zones and by-pass flow. Efficient mixing and organic matter stabilisation are the main factors controlling the rate of inactivation under mesophilic conditions and not a direct effect of temperature per se on pathogenic organisms.

Smith, S.R. [Centre for Environmental Control and Waste Management, Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom)]. E-mail: s.r.smith@imperial.ac.uk; Lang, N.L. [Centre for Environmental Control and Waste Management, Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Cheung, K.H.M. [Centre for Environmental Control and Waste Management, Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Spanoudaki, K. [Centre for Environmental Control and Waste Management, Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom)

2005-07-01T23:59:59.000Z

363

Biotechnological research and development for biomass conversion to chemicals and fuels  

DOE Green Energy (OSTI)

It is likely that a growing need to produce chemicals and fuels from renewable resources will stimulate the development of biotechnology as a commerical enterprise of considerable potential. The purpose of the analysis and the development structure that could lead to establishing this new technology are presented. Two general goals are recommended: (i) in the near term, to revive the older fermentation industry and, by the addition of sophisticated technology, to make it competitive; (ii) in the longer term, to develop a new biotechnology largely based on lignocellulose. Specific research projects are outlined in these two areas and also for the following: microbial formation of hydrocarbons; methane from anaerobic digestion; lignin; methanol. For cellulose conversion to ethanol the relative merits of using added cellulases or, alternatively, direct fermentation with anaerobic thermophiles, are discussed. In selecting suitable feedstocks for biotechnological processes there is a need to use a production-extraction-conversion system as a basis for evaluation. An effective research workforce for developing biotechnology must be pluridisciplinary. The strategy adopted at the Solar Energy Research Institute is to design the Biotechnology Branch as an integrated set of three Groups: Biochemistry and Molecular Genetics; Microbiology; Chemical and Biochemical Engineering.

Villet, R.

1980-08-01T23:59:59.000Z

364

Multiple Syntrophic Interactions in a Terephthalate-Degrading Methanogenic Consortium  

SciTech Connect

Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium tinside a hyper-mesophilic (i.e., between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified ?-oxidation to H{sub 2}/CO{sub 2} and acetate. These intermediates are converted to CH{sub 4}/CO{sub 2} by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1 populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to COsub 2}/H{sub 2} and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H{sub 2}-producing syntroph ? methanogen partnership that may serve to improve community stability.

Lykidis, Athanasios; Chen, Chia-Lung; Tringe, Susannah G.; McHardy, Alice C.; Copeland, Alex 5; Kyrpides, Nikos C.; Hugenholtz, Philip; Liu, Wen-Tso

2010-08-05T23:59:59.000Z

365

Monfort dirt lot experiments. Status report  

DOE Green Energy (OSTI)

A mobile processing unit is being used to investigate the feasibility of producing fuel gas and an energy-intensive refeed product from dirt feedlot residues by anaerobic fermentation. Results to date have shown that: a stable fermentation can be achieved utilizing aged feedlot pen residue if a sufficient adaptation period is provided. Methane yields of 2.75 ft/sup 3//pound volatile solids fed can be attained at a loading rate of 0.25 pounds volatile solids/ft/sup 3/, 10 day retention time and thermophilic temperature of 57/sup 0/C. The fermentor liquid effluent is acceptable to cattle as a feed ingredient and was used to provide one-half the daily supplemental protein for twenty steers. Residual pharmaceuticals and low levels of heavy metals as well as various anions and cations may possibly impose some additional stress upon the system but do not present a significant detriment to successful operation. Feedlot residue is highly variable in both dry matter and inert content with typical particle size in the micron range.

Not Available

1978-03-31T23:59:59.000Z

366

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community  

Science Conference Proceedings (OSTI)

Development of cellulosic biofuels from non-food crops is currently an area of intense research interest. Tailoring depolymerizing enzymes to particular feedstocks and pretreatment conditions is one promising avenue of research in this area. Here we added a green-waste compost inoculum to switchgrass (Panicum virgatum) and simulated thermophilic composting in a bioreactor to select for a switchgrass-adapted community and to facilitate targeted discovery of glycoside hydrolases. Smallsubunit (SSU) rRNA-based community profiles revealed that the microbial community changed dramatically between the initial and switchgrass-adapted compost (SAC) with some bacterial populations being enriched over 20-fold. We obtained 225 Mbp of 454-titanium pyrosequence data from the SAC community and conservatively identified 800 genes encoding glycoside hydrolase domains that were biased toward depolymerizing grass cell wall components. Of these, ,10percent were putative cellulasesmostly belonging to families GH5 and GH9. We synthesized two SAC GH9 genes with codon optimization for heterologous expression in Escherichia coli and observed activity for one on carboxymethyl cellulose. The active GH9 enzyme has a temperature optimum of 50uC and pH range of 5.5 to 8 consistent with the composting conditions applied. We demonstrate that microbial communities adapt to switchgrass decomposition using simulated composting condition and that full-length genes can be identified from complex metagenomic sequence data, synthesized and expressed resulting in active enzyme.

Reddy, Amitha; Allgaier, Martin; Park, Joshua I.; Ivanoval, Natalia; Dhaeseleer, Patrik; Lowry, Steve; Sapra, Rajat; Hazen, Terry C.; Simmons, Blake A.; VanderGheynst, Jean S.; Hugenholtz, Philip

2011-05-11T23:59:59.000Z

367

Economic feasibility of biochemical processes for the upgrading of crudes and the removal of sulfur, nitrogen, and trace metals from crude oil -- Benchmark cost establishment of biochemical processes on the basis of conventional downstream technologies. Final report FY95  

Science Conference Proceedings (OSTI)

During the past several years, a considerable amount of work has been carried out showing that microbially enhanced oil recovery (MEOR) is promising and the resulting biotechnology may be deliverable. At Brookhaven National Laboratory (BNL), systematic studies have been conducted which dealt with the effects of thermophilic and thermoadapted bacteria on the chemical and physical properties of selected types of crude oils at elevated temperatures and pressures. Current studies indicate that during the biotreatment several chemical and physical properties of crude oils are affected. The oils are (1) emulsified; (2) acidified; (3) there is a qualitative and quantitative change in light and heavy fractions of the crudes; (4) there are chemical changes in fractions containing sulfur compounds; (5) there is an apparent reduction in the concentration of trace metals; and (6) the qualitative and quantitative changes appear to be microbial species dependent; and (7) there is a distinction between biodegraded and biotreated oils. The downstream biotechnological crude oil processing research performed thus far is of laboratory scale and has focused on demonstrating the technical feasibility of downstream processing with different types of biocatalysts under a variety of processing conditions. Quantitative economic analysis is the topic of the present project which investigates the economic feasibility of the various biochemical downstream processes which hold promise in upgrading of heavy crudes, such as those found in California, e.g., Monterey-type, Midway Sunset, Honda crudes, and others.

Premuzic, E.T.

1996-08-01T23:59:59.000Z

368

Comparison of Three Bed Packings for the Biological Removal of Nitric Oxide from Gas Streams  

Science Conference Proceedings (OSTI)

Environmental and health issues coupled with increasingly stringent nitrogen oxide (NOx) emission standards indicates a need for the development of alternative low-cost technologies for the removal of NOx from gas streams. Biological NOx conversion offers promise as a novel treatment method. Thermophilic denitrifying bacteria indigenous to composts and soils are capable of converting NOx to environmentally benign nitrogen via a dissimilatory reductive pathway. The present study compares the performance of three bioreactor packing materials (compost, perlite, and biofoam) for the removal of nitric oxide (NO) from a simulated wet-scrubbed combustion gas. Although all three materials performed well (>85% NO removal) at residence times of 70-80 seconds, the compost performed better than the other materials at shorter residence times (13-44 seconds). The perlite and biofoam materials, however, both offer long-term thermal stability and lower pressure drop compared with compost. The feasibility of biological NOx conversion processes will depend on the combined factors of NOx removal ability and pressure drop. The results presented here suggest that the compost, perlite and biofoam systems, subject to further optimization, offer potential for the biological removal of NOx from gas streams.

Lee, Brady Douglas; Flanagan, W. P.; Barnes, Charles Marshall; Barrett, Karen B.; Zaccardi, Larry Bryan; Apel, William Arnold

2000-10-01T23:59:59.000Z

369

Prediction of temperature and thermal inertia effect in the maturation stage and stockpiling of a large composting mass  

SciTech Connect

A macroscopic non-steady state energy balance was developed and solved for a composting pile of source-selected organic fraction of municipal solid waste during the maturation stage (13,500 kg of compost). Simulated temperature profiles correlated well with temperature experimental data (ranging from 50 to 70 deg. C) obtained during the maturation process for more than 50 days at full scale. Thermal inertia effect usually found in composting plants and associated to the stockpiling of large composting masses could be predicted by means of this simplified energy balance, which takes into account terms of convective, conductive and radiation heat dissipation. Heat losses in a large composting mass are not significant due to the similar temperatures found at the surroundings and at the surface of the pile (ranging from 15 to 40 deg. C). In contrast, thermophilic temperature in the core of the pile was maintained during the whole maturation process. Heat generation was estimated with the static respiration index, a parameter that is typically used to monitor the biological activity and stability of composting processes. In this study, the static respiration index is presented as a parameter to estimate the metabolic heat that can be generated according to the biodegradable organic matter content of a compost sample, which can be useful in predicting the temperature of the composting process.

Barrena, R. [Escola Universitaria Politecnica del Medi Ambient, Universitat Autonoma de Barcelona, Rbla Pompeu Fabra 1, 08100-Mollet del Valles, Barcelona (Spain); Canovas, C. [Escola Universitaria Politecnica del Medi Ambient, Universitat Autonoma de Barcelona, Rbla Pompeu Fabra 1, 08100-Mollet del Valles, Barcelona (Spain); Sanchez, A. [Escola Universitaria Politecnica del Medi Ambient, Universitat Autonoma de Barcelona, Rbla Pompeu Fabra 1, 08100-Mollet del Valles, Barcelona (Spain)]. E-mail: asanchez@eupma.uab.es

2006-07-01T23:59:59.000Z

370

Biological conversion of biomass to methane. Final report, June 1, 1976-January 31, 1980  

DOE Green Energy (OSTI)

An experimental methane fermentation system was constructed for the purpose of evaluating the processng requirements and conversion efficiencies associated with production of methane from various organic feed stocks. The fermentation reactors had an operating volume 0.775 m/sup 3/. This permitted operation with an approximate continuous feed of milled organics including beef feedlot manure, corn stover, wheat straw and alfalfa hay. A thermochemical pretreatment was applied to the corn stover and wheat straw in order to increase the biodegradability of these substrates. Working with these large units provided sufficient volumes of fermented slurry for evaluation of the dewatering properties of these slurries. Kinetic data were obtained by operating four reactors at different retention times. These data were used to calculate a first order rate constant and the percent of substrate volatile solids that were biodegradable. These data were obtained on beef feed lot manure at 40/sup 0/C and 60/sup 0/C nominal fermentation temperatures. Data from the fermentation of corn stover showed that the biodegradability of the stover volatile solids was only 36 percent at the thermophilic fermentation temperature. The first order rate constant was found to be 0.25 day/sup -1/. Thermochemical pretreatment increased the biodegradability of stover volatile solids to 71 percent. The final substrate tested was a green crop that was field dried - alfalfa. Significant foaming problems were encountered with this material. The volatile solids were found to be 74 percent biodegradable at a fermentation temperature of 60/sup 0/C. (MHR)

Pfeffer, J T

1980-02-01T23:59:59.000Z

371

ENHANCED PRACTICAL PHOTOSYNTHETIC CO2 MITIGATION  

DOE Green Energy (OSTI)

This is the first quarterly report of the project Enhanced Practical Photosynthetic CO{sub 2} Mitigation. The official project start date, 10/02/2000, was delayed until 10/31/2000 due to an intellectual property dispute that was resolved. However, the delay forced a subsequent delay in subcontracting with Montana State University, which then delayed obtaining a sampling permit from Yellowstone National Park. However, even with these delays, the project moved forward with some success. Accomplishments for this quarter include: Culturing of thermophilic organisms from Yellowstone; Testing of mesophilic organisms in extreme CO{sub 2} conditions; Construction of a second test bed for additional testing; Purchase of a total carbon analyzer dedicated to the project; Construction of a lighting container for Oak Ridge National Laboratory optical fiber testing; Modified lighting of existing test box to provide more uniform distribution; Testing of growth surface adhesion and properties; Experimentation on water-jet harvesting techniques; and Literature review underway regarding uses of biomass after harvesting. Plans for next quarter's work and an update on the project's web page are included in the conclusions.

Dr. David J. Bayless; Dr. Morgan Vis; Dr. Gregory Kremer; Dr. Michael Prudich; Dr. Keith Cooksey; Dr. Jeff Muhs

2001-01-16T23:59:59.000Z

372

Degradation of cellulosic biomass and its subsequent utilization for the production of chemical feedstocks. Progress report, December 1, 1976--February 28, 1977  

DOE Green Energy (OSTI)

The microbial degradation of cellulosic biomass has focused on the use of a thermophilic (55 to 60/sup 0/C), anaerobic microorganism, Clostridium thermocellum. When this organism is grown with a crystalline cellulose, the cellulases produced are mainly extracellular. This same organism when grown on solka floc, high specific growth rates are exhibited as well as the ability to produce high concentrations of soluble reducing sugars. The rate of soluble sugar production appears to be growth associated. Studies on acrylic acid production are focused on two organisms: Peptostreptococcus elsdenii and Clostridium propionicum. An economic analysis on the acetone/butanol fermentation has been completed. The results show that continuous operation can reduce significantly the production cost compared to batch operation with the cost of raw material being major fractions for both processes. An increase in solvent concentration will effect substantial cost reduction. The production of acetic acid by Clostridium thermoaceticum has been shown to occur rapidly by this organism. Acetic acid concentration between 15 to 20 gm/liter have been achieved, corresponding to 86 percent of the theoretical maximum yield.

Wang, D.I.C.; Cooney, C.L.; Demain, A.L.; Gomez, R.F.; Sinskey, A.J.

1977-05-01T23:59:59.000Z

373

Extremozymes for bioprocessing  

DOE Green Energy (OSTI)

For many years, people have been seeking to employ enzymes, proteins that act as biocatalysts, as environmentally friendly replacements for many currently used industrial processes, as well as for the production of fuels and chemicals from biomass sources such as waste paper and agricultural residues. Current applications of enzymes include enzyme-assisted bleaching of wood pulp, preparation of textiles, design of biosensors, enzyme diagnostic kits, and bioremediation of toxic metals and chlorinated chemicals. However, until fairly recently, most of these enzymes came from mesophilic sources--organisms that grow at moderate temperatures (20--50 C) and pH 5 to 8. Frequently, these enzymes are not robust enough to perform well in industrial processes, have little tolerance for organic solvents or toxic chemicals, lose activity rapidly during catalysis, and cannot be used at high temperatures and alkaline or acidic conditions. But there are microorganisms that are known to grow under extreme conditions such as high temperature (thermophiles), low temperature (psychrophiles), acidic pH (acidophiles), and alkaline pH (alkalinophiles). The enzymes, extremozymes, from such microorganisms are active under the extreme conditions of temperature and pH at which the extremophiles grow. Use of extremozymes extends the potential temperature range for efficient enzymatic reactions to between 40 C and 100 C.

Evans, B.R.; Zhou, J.; Poole, T.L.; Bunick, G.J.; Palumbo, A.V.; Woodward, J.

1998-11-01T23:59:59.000Z

374

Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge  

Science Conference Proceedings (OSTI)

To evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted Lucky Strike (37 17'N, 32 16.3'W, depth 1600-1750 m) and the ultramafic-hosted Rainbow (36 13'N, 33 54.1'W, depth 2270-2330 m) vent fields along the Mid-Atlantic Ridge (MAR). Using multiplexed barcoded pyrosequencing of the variable region 4 (V4) of the 16S rRNA genes, we show statistically significant differences between the archaeal and bacterial communities associated with the different vent fields. Quantitative polymerase chain reaction (qPCR) assays of the functional gene diagnostic for methanogenesis (mcrA), as well as geochemical modelling to predict pore fluid chemistries within the deposits, support the pyrosequencing observations. Collectively, these results show that the less reduced, hydrogen-poor fluids at Lucky Strike limit colonization by strict anaerobes such as methanogens, and allow for hyperthermophilic microaerophiles, like Aeropyrum. In contrast, the hydrogen-rich reducing vent fluids at the ultramafic-influenced Rainbow vent field support the prevalence of methanogens and other hydrogen-oxidizing thermophiles at this site. These results demonstrate that biogeographical patterns of hydrothermal vent microorganisms are shaped in part by large scale geological and geochemical processes.

Flores, Gilberto E [Portland State University; Campbell, James H [ORNL; Kirshtein, Julie D [United States Geological Survey, Reston, VA; Meneghin, Jennifer [Portland State University; Podar, Mircea [ORNL; Steinberg, Joshua [Oregon Episcopal School, Portland, OR; Seewald, Jeffrey S [Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA; Tivey, Margaret Kingston [Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA; Voytek, Mary A [United States Geological Survey & National Aeronautics and Space Administration; Reysenbach, Anna-Louise [Portland State University; Yang, Zamin Koo [ORNL

2011-01-01T23:59:59.000Z

375

JB.00266-12.full.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

May 9, 2012 sbs May 9, 2012 sbs 1 Caldicellulosiruptor core and pan genomes reveal determinants for 2 non-cellulosomal thermophilic deconstruction of plant biomass 3 Sara E. Blumer-Schuette (seblumer@ncsu.edu) 1, 4 , Richard J. Giannone 4 (giannonerj@ornl.gov) 2, 4 , Jeffrey V. Zurawski (jvzuraws@ncsu.edu) 1, 4 , Inci Ozdemir 5 (iozdemi@ncsu.edu) 1, 4 , Qin Ma (maqin2001@gmail.com) 3, 4 , Yanbin Yin 6 (yanbin.yin@gmail.com) 3, 4 , Ying Xu (xyn@bmb.uga.edu) 3, 4 , Irina Kataeva 7 (kataeva@bmb.uga.edu) 3, 4 , Farris L. Poole II (fpoole@bmb.uga.edu) 3, 4 , Michael W. W. Adams 8 (adams@bmb.uga.edu) 3, 4 , Scott D. Hamilton-Brehm (hamiltonbres@ornl.gov) 2, 4 , James G. 9 Elkins (elkinsjg@ornl.gov) 2, 4 , Frank W. Larimer (larimerfw@ornl.gov) 2 , Miriam L. Land 10 (landml@ornl.gov) 2 , Loren Hauser (hauserlj@ornl.gov)

376

Oxidation and methylation of dissolved elemental mercury by anaerobic bacteria  

Science Conference Proceedings (OSTI)

Methylmercury is a neurotoxin that poses significant health risks to humans. Some anaerobic sulphate- and iron-reducing bacteria can methylate oxidized forms of mercury, generating methylmercury1-4. One strain of sulphate-reducing bacteria (Desulfovibrio desulfuricans ND132) can also methylate elemental mercury5. The prevalence of this trait among different bacterial strains and species remains unclear, however. Here, we compare the ability of two strains of the sulphate-reducing bacterium Desulfovibrio and one strain of the iron-reducing bacterium Geobacter to oxidise and methylate elemental mercury in a series of laboratory incubations. Experiments were carried out under dark, anaerobic conditions, in the presence of environmentally-relevant concentrations of elemental mercury. We report differences in the ability of these organisms to oxidise and methylate elemental mercury. In line with recent findings5, we show that Desulfovibrio desulfuricans ND132 can both oxidise and methylate elemental mercury. However, the rate of methylation of elemental mercury is only about one third the rate of methylation of oxidized mercury. We also show that Desulfovibrio alaskensis G20 can oxidise, but not methylate, elemental mercury. Geobacter sulfurreducens PCA is able to oxidise and methylate elemental mercury in the presence of cysteine. We suggest that the activity of methylating and non-methylating bacteria may together enhance the formation of methylmercury in anaerobic environments.

Hu, Haiyan [ORNL] [ORNL; Lin, Hui [ORNL] [ORNL; Zheng, Wang [ORNL] [ORNL; Tomanicek, Stephen J [ORNL] [ORNL; Johs, Alexander [ORNL] [ORNL; Feng, Xinbin [ORNL] [ORNL; Elias, Dwayne A [ORNL] [ORNL; Liang, Liyuan [ORNL] [ORNL; Liang, Liyuan [ORNL] [ORNL; Gu, Baohua [ORNL] [ORNL

2013-01-01T23:59:59.000Z

377

Substrate Recognition Strategy for Botulinum Neurotoxin  

NLE Websites -- All DOE Office Websites (Extended Search)

Substrate Recognition Strategy for Botulinum Neurotoxin Print Substrate Recognition Strategy for Botulinum Neurotoxin Print Clostridal neurotoxins (CNTs) are the causative agents of the neuroparalytic diseases botulism and tetanus. By inhibiting release of the neurotransmitter acetylcholine, for example, the neurotoxin produced by the bacterium Clostridium botulinum interferes with nerve impulses and causes a paralysis of respiratory and skeletal muscles that can cause death. Researchers from Stanford University have now determined the first structure of a CNT in complex with its target. The structure at a resolution of 2.1 Å, together with enzyme kinetic data, reveals an array of active sites (exosites) that give the CNT its deadly specificity. Botulism Toxin The best thing one can say about botulism is that it is relatively rare. At worst, botulism can ultimately result in death due to respiratory failure resulting from paralysis of the muscles used in breathing. The muscle paralysis is caused by the neurotoxin produced by the bacterium Clostridium botulinum, which can be ingested with contaminated food, enter the body through wounds, or (in the case of infants where there is little competition from other microbes) germinate in the intestine from spores. Given early after onset of symptoms, an antitoxin exists that can prevent further damage, but a more effective treatment for this and other neurotoxin-caused illnesses, such as tetanus, await a more detailed understanding of how the toxin works at the molecular level.

378

Substrate Recognition Strategy for Botulinum Neurotoxin  

NLE Websites -- All DOE Office Websites (Extended Search)

Substrate Recognition Strategy for Botulinum Neurotoxin Print Substrate Recognition Strategy for Botulinum Neurotoxin Print Clostridal neurotoxins (CNTs) are the causative agents of the neuroparalytic diseases botulism and tetanus. By inhibiting release of the neurotransmitter acetylcholine, for example, the neurotoxin produced by the bacterium Clostridium botulinum interferes with nerve impulses and causes a paralysis of respiratory and skeletal muscles that can cause death. Researchers from Stanford University have now determined the first structure of a CNT in complex with its target. The structure at a resolution of 2.1 Å, together with enzyme kinetic data, reveals an array of active sites (exosites) that give the CNT its deadly specificity. Botulism Toxin The best thing one can say about botulism is that it is relatively rare. At worst, botulism can ultimately result in death due to respiratory failure resulting from paralysis of the muscles used in breathing. The muscle paralysis is caused by the neurotoxin produced by the bacterium Clostridium botulinum, which can be ingested with contaminated food, enter the body through wounds, or (in the case of infants where there is little competition from other microbes) germinate in the intestine from spores. Given early after onset of symptoms, an antitoxin exists that can prevent further damage, but a more effective treatment for this and other neurotoxin-caused illnesses, such as tetanus, await a more detailed understanding of how the toxin works at the molecular level.

379

Structure and function of Frankia vesicles in denitrogen fixation by actinorhizal plants: Annual technical progress report for period January 1, 1987-November 15, 1987  

Science Conference Proceedings (OSTI)

Frankia is a filamentous soil bacterium of the Actinomycetales that is capable of fixation of atmospheric dinitrogen both in the free-living state and within root modules of a number of woody dicotyledonous plants in a symbiotic process. The bacterium is of special interest because of its genetic capacity to differentiate terminal swellings of the hyphal filaments called vesicles. Vesicles form in the free-living organism when deprived of combined nitrogen substrates under aerobic conditions. A multilaminate envelope surrounds the vesicle providing a barrier to direct exposure of the oxygen-labile nitrogenase enzyme that forms within the vesicle. In root nodules, vesicles may or may not form, depending upon the structural configuration of the host plant cells, the ambient oxygen concentration surrounding the root nodule and the expression of host-microbial interactions under the control of the two genomes. Under varying stresses of nutrient availability and the changing gaseous environment, remarkable adaptations may occur in either or both partners of the symbiosis to optimize dinitrogen fixation. 9 refs.

Torrey, J.G.

1987-11-20T23:59:59.000Z

380

Biological conversion of synthesis gas. Project status report, October 1, 1992--December 31, 1992  

DOE Green Energy (OSTI)

Syngas is known to contain approximately 1 percent H{sub 2}S, along with CO{sub 2}, C0{sub 2}, H{sub 2} and CH{sub 4}. Similarly, the syngas may become contaminated with oxygen, particularly during reactor start-up and during maintenance. Previous studies with the water-gas shift bacterium Rhodospirillum rubrum have shown that the bacterium is tolerant of small quantities of oxygen, but the effects of oxygen on CO-consumption are unknown. Similarly, R. rubrum is known to be tolerant of H{sub 2}S, with high concentrations of H{sub 2}S negatively affecting CO-uptake. Batch experiments were thus carried out to determine the effects of H{sub 2}S and O{sub 2} on CO-uptake by R. rubrum. The results of these experiments were quantified by using Monod equations modified by adding terms for CO, H{sub 2}S and O{sub 2} inhibition. The techniques used in determining kinetic expressions previously shown for other gas-phase substrate bacterial systems including R. rubrum were utilized.

Ackerson, M.D.; Clausen, E.C.; Gaddy, J.L.

1993-01-05T23:59:59.000Z

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381

Biological conversion of synthesis gas  

DOE Green Energy (OSTI)

Syngas is known to contain approximately 1 percent H[sub 2]S, along with CO[sub 2], C0[sub 2], H[sub 2] and CH[sub 4]. Similarly, the syngas may become contaminated with oxygen, particularly during reactor start-up and during maintenance. Previous studies with the water-gas shift bacterium Rhodospirillum rubrum have shown that the bacterium is tolerant of small quantities of oxygen, but the effects of oxygen on CO-consumption are unknown. Similarly, R. rubrum is known to be tolerant of H[sub 2]S, with high concentrations of H[sub 2]S negatively affecting CO-uptake. Batch experiments were thus carried out to determine the effects of H[sub 2]S and O[sub 2] on CO-uptake by R. rubrum. The results of these experiments were quantified by using Monod equations modified by adding terms for CO, H[sub 2]S and O[sub 2] inhibition. The techniques used in determining kinetic expressions previously shown for other gas-phase substrate bacterial systems including R. rubrum were utilized.

Ackerson, M.D.; Clausen, E.C.; Gaddy, J.L.

1993-01-05T23:59:59.000Z

382

Final Report - "CO2 Sequestration in Cell Biomass of Chlorobium Thiosulfatophilum"  

SciTech Connect

World carbon dioxide emissions from the combustion of fossil fuels have increased at a rate of about 3 percent per year during the last 40 years to over 24 billion tons today. While a number of methods have been proposed and are under study for dealing with the carbon dioxide problem, all have advantages as well as disadvantages which limit their application. The anaerobic bacterium Chlorobium thiosulfatophilum uses hydrogen sulfide and carbon dioxide to produce elemental sulfur and cell biomass. The overall objective of this project is to develop a commercial process for the biological sequestration of carbon dioxide and simultaneous conversion of hydrogen sulfide to elemental sulfur. The Phase I study successfully demonstrated the technical feasibility of utilizing this bacterium for carbon dioxide sequestration and hydrogen sulfide conversion to elemental sulfur by utilizing the bacterium in continuous reactor studies. Phase II studies involved an advanced research and development to develop the engineering and scale-up parameters for commercialization of the technology. Tasks include culture isolation and optimization studies, further continuous reactor studies, light delivery systems, high pressure studies, process scale-up, a market analysis and economic projections. A number of anaerobic and aerobic microorgansims, both non-photosynthetic and photosynthetic, were examined to find those with the fastest rates for detailed study to continuous culture experiments. C. thiosulfatophilum was selected for study to anaerobically produce sulfur and Thiomicrospira crunogena waws selected for study to produce sulfate non-photosynthetically. Optimal conditions for growth, H2S and CO2 comparison, supplying light and separating sulfur were defined. The design and economic projections show that light supply for photosynthetic reactions is far too expensive, even when solar systems are considered. However, the aerobic non-photosynthetic reaction to produce sulfate with T. crunogena produces a reasonable return when treating a sour gas stream of 120 million SCFD containing 2.5 percent H2S. In this case, the primary source of revenue is from desulfurization of the gas stream. While the technology has significant application in sequestering carbon dioxide in cell biomass or single cell proten (SCP), perhaps the most immediate application is in desulfurizing LGNG or other gas streams. This biological approach is a viable economical alternative to existing hydrogen sulfide removal technology, and is not sensitive to the presence of hydrocarbons which act as catalyst poisons.

James L. Gaddy, PhD; Ching-Whan Ko, PhD

2009-05-04T23:59:59.000Z

383

Biological conversion of biomass to methane beef lot manure studies. Semiannual progress report, June 1, 1976--November 30, 1977  

DOE Green Energy (OSTI)

A series of experiments was conducted to determine the performance characteristics of the methane fermentation process using beef feed lot manure as a substrate. Manure was obtained from the University of Illinois beef farm. This manure was processed through four parallel fermentors each having a capacity of 775 liters. A continuous feed system was employed to determine the conversion efficiency. The effluent from the fermentation units was evaluated to determine its dewatering characteristics and the quality of the liquid and solid residues. A simple simulation model was developed to evaluate the effect of various operating conditions on processing costs and the net income. These studies clearly show that thermophilic fermentation (58 to 60/sup 0/C) substantially increase the gas yield and the rate of gas production over that obtained at the mesophilic fermentation temperature. System stability is very good. Substantial decreases in temperature or significant increases in loadings did not disrupt the process. Solids recovery from the fermented slurry was accomplished with screens, vacuum drum filters and centrifuge. Solids capture was poor unless massive dosags of conditioning chemicals were added. In terms of investment and operating costs, simple screens (20 mesh size) would capture 75 to 80 percent of the recoverable suspended solids. Manure that is obtained from open lots, especially when it has been exposed to the environment for extended periods, offers little potential for methane production. The biodegradability of this material is so low that the cost of producing the gas far exceeds its value. Fresh manure such as that obtained from environmental lots produced significant quantities of gas. It is probable that an economic system can be developed using this material as a substrate.

Pfeffer, J T; Quindry, G E

1978-05-01T23:59:59.000Z

384

The Genome Sequence of the psychrophilic archaeon, Methanococcoides burtonii: the Role of Genome Evolution in Cold-adaptation  

SciTech Connect

Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five tiered Evidence Rating system that ranked annotations from Evidence Rating (ER) 1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall/membrane/envelope biogenesis COG genes are over-represented. Likewise, signal transduction (COG category T) genes are over-represented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two over-represented COG categories appear to have been acquired from {var_epsilon}- and {delta}-proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they play an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it adapted from a marine, to an Antarctic lake environment.

Allen, Michelle A.; Lauro, Federico M.; Williams, Timothy J.; Burg, Dominic; Siddiqui, Khawar S.; De Francisci, David; Chong, Kevin W.Y.; Pilak, Oliver; Chew, Hwee H.; De Maere, Matthew Z.; Ting, Lily; Katrib, Marilyn; Ng, Charmaine; Sowers, Kevin R.; Galperin, Michael Y.; Anderson, Iain J.; Ivanova, Natalia; Dalin, Eileen; Martinez, Michelle; Lapidus, Alla; Hauser, Loren; Land, Miriam; Thomas, Torsten; Cavicchioli, Ricardo

2009-04-01T23:59:59.000Z

385

The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation  

Science Conference Proceedings (OSTI)

Psychrophilic archaea are abundant and perform critical roles throughout the Earth's expansive cold biosphere. Here we report the first complete genome sequence for a psychrophilic methanogenic archaeon, Methanococcoides burtonii. The genome sequence was manually annotated including the use of a five-tiered evidence rating (ER) system that ranked annotations from ER1 (gene product experimentally characterized from the parent organism) to ER5 (hypothetical gene product) to provide a rapid means of assessing the certainty of gene function predictions. The genome is characterized by a higher level of aberrant sequence composition (51%) than any other archaeon. In comparison to hyper/thermophilic archaea, which are subject to selection of synonymous codon usage, M. burtonii has evolved cold adaptation through a genomic capacity to accommodate highly skewed amino-acid content, while retaining codon usage in common with its mesophilic Methanosarcina cousins. Polysaccharide biosynthesis genes comprise at least 3.3% of protein coding genes in the genome, and Cell wall, membrane, envelope biogenesis COG genes are overrepresented. Likewise, signal transduction (COG category T) genes are overrepresented and M. burtonii has a high 'IQ' (a measure of adaptive potential) compared to many methanogens. Numerous genes in these two overrepresented COG categories appear to have been acquired from - and -Proteobacteria, as do specific genes involved in central metabolism such as a novel B form of aconitase. Transposases also distinguish M. burtonii from other archaea, and their genomic characteristics indicate they have an important role in evolving the M. burtonii genome. Our study reveals a capacity for this model psychrophile to evolve through genome plasticity (including nucleotide skew, horizontal gene transfer and transposase activity) that enables adaptation to the cold, and to the biological and physical changes that have occurred over the last several thousand years as it adapted from a marine to an Antarctic lake environment.

Allen, Michele A [University of New South Wales; Lauro, Federico M [University of New South Wales; Williams, Timothy J [University of New South Wales; Burg, Dominic [University of New South Wales; Siddiqui, Khawar S [University of New South Wales; DeFrancisci, Davide [University of New South Wales; Chong, Kevin WY [University of New South Wales; Pilak, Oliver [University of New South Wales; Chew, Hwee H [University of New South Wales; DeMaere, Matthew Z [University of New South Wales; Ting, Lily [University of New South Wales; Katrib, Marilyn [University of New South Wales; Ng, Charmaine [University of New South Wales; Sowers, Kevin R [University of Maryland; Galperin, Michael Y. [National Center for Biotechnology Information; Anderson, Iain [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Martinez, Michele [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Thomas, Torsten [University of New South Wales; Cavicchioli, Ricardo [University of New South Wales

2009-01-01T23:59:59.000Z

386

Fair Oaks Dairy Farms Cellulosic Ethanol Technology Review Summary  

SciTech Connect

At Fair Oaks Dairy, dried manure solids (''DMS'') are currently used as a low value compost. United Power was engaged to evaluate the feasibility of processing these DMS into ethanol utilizing commercially available cellulosic biofuels conversion platforms. The Fair Oaks Dairy group is transitioning their traditional ''manure to methane'' mesophilic anaerobic digester platform to an integrated bio-refinery centered upon thermophilic digestion. Presently, the Digested Manure Solids (DMS) are used as a low value soil amendment (compost). United Power evaluated the feasibility of processing DMS into higher value ethanol utilizing commercially available cellulosic biofuels conversion platforms. DMS was analyzed and over 100 potential technology providers were reviewed and evaluated. DMS contains enough carbon to be suitable as a biomass feedstock for conversion into ethanol by gasification technology, or as part of a conversion process that would include combined heat and power. In the first process, 100% of the feedstock is converted into ethanol. In the second process, the feedstock is combusted to provide heat to generate electrical power supporting other processes. Of the 100 technology vendors evaluated, a short list of nine technology providers was developed. From this, two vendors were selected as finalists (one was an enzymatic platform and one was a gasification platform). Their selection was based upon the technical feasibility of their systems, engineering expertise, experience in commercial or pilot scale operations, the ability or willingness to integrate the system into the Fair Oaks Biorefinery, the know-how or experience in producing bio-ethanol, and a clear path to commercial development.

Andrew Wold; Robert Divers

2011-06-23T23:59:59.000Z

387

Effectiveness of three bulking agents for food waste composting  

Science Conference Proceedings (OSTI)

Rather than landfilling, composting the organic fraction of municipal solid wastes recycles the waste as a safe and nutrient enriched soil amendment, reduces emissions of greenhouse gases and generates less leachate. The objective of this project was to investigate the composting effectiveness of three bulking agents, namely chopped wheat (Triticum) straw, chopped mature hay consisting of 80% timothy (milium) and 20% clover (triphullum) and pine (pinus) wood shavings. These bulking agents were each mixed in duplicates at three different ratios with food waste (FW) and composted for 10 days using prototype in-vessel composters to observe their temperature and pH trends. Then, each mixture was matured in vertical barrels for 56 days to measure their mass loss and final nutrient content and to visually evaluate their level of decomposition. Chopped wheat straw (CWS) and chopped hay (CH) were the only two formulas that reached thermophilic temperatures during the 10 days of active composting when mixed with FW at a wet mass ratio of 8.9 and 8.6:1 (FW:CWS and FW:CH), respectively. After 56 days of maturation, these two formulas were well decomposed with no or very few recognizable substrate particles, and offered a final TN exceeding the original. Wood shavings (WS) produced the least decomposed compost at maturation, with wood particles still visible in the final product, and with a TN lower than the initial. Nevertheless, all bulking agents produced compost with an organic matter, TN, TP and TK content suitable for use as soil amendment.

Adhikari, Bijaya K. [Department of Bioresource Engineering, Macdonald Campus of McGill University, 21 111 Lakeshore, Ste Anne de Bellevue (Quebec), H9X 3V9 (Canada); Barrington, Suzelle [Department of Bioresource Engineering, Macdonald Campus of McGill University, 21 111 Lakeshore, Ste Anne de Bellevue (Quebec), H9X 3V9 (Canada)], E-mail: suzelle.barrington@mcgill.ca; Martinez, Jose [Cemagref, Rennes Regional Centre, 7 avenue du Cucille, CS 64427, F-35044 Rennes (France); King, Susan [Department of Bioresource Engineering, Macdonald Campus of McGill University, 21 111 Lakeshore, Ste Anne de Bellevue (Quebec), H9X 3V9 (Canada)

2009-01-15T23:59:59.000Z

388

Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload  

Science Conference Proceedings (OSTI)

Highlights: Black-Right-Pointing-Pointer Two types of methanogens are necessary to respond successfully to perturbation. Black-Right-Pointing-Pointer Diversity of methanogens correlates with the VFA concentration and methane yield. Black-Right-Pointing-Pointer Aggregates indicate tight spatial relationship between minerals and microorganisms. - Abstract: Microbial community diversity in two thermophilic laboratory-scale and three full-scale anaerobic co-digesters was analysed by genetic profiling based on PCR-amplified partial 16S rRNA genes. In parallel operated laboratory reactors a stepwise increase of the organic loading rate (OLR) resulted in a decrease of methane production and an accumulation of volatile fatty acids (VFAs). However, almost threefold different OLRs were necessary to inhibit the gas production in the reactors. During stable reactor performance, no significant differences in the bacterial community structures were detected, except for in the archaeal communities. Sequencing of archaeal PCR products revealed a dominance of the acetoclastic methanogen Methanosarcina thermophila, while hydrogenotrophic methanogens were of minor importance and differed additionally in their abundance between reactors. As a consequence of the perturbation, changes in bacterial and archaeal populations were observed. After organic overload, hydrogenotrophic methanogens (Methanospirillum hungatei and Methanoculleus receptaculi) became more dominant, especially in the reactor attributed by a higher OLR capacity. In addition, aggregates composed of mineral and organic layers formed during organic overload and indicated tight spatial relationships between minerals and microbial processes that may support de-acidification processes in over-acidified sludge. Comparative analyses of mesophilic stationary phase full-scale reactors additionally indicated a correlation between the diversity of methanogens and the VFA concentration combined with the methane yield. This study demonstrates that the coexistence of two types of methanogens, i.e. hydrogenotrophic and acetoclastic methanogens is necessary to respond successfully to perturbation and leads to stable process performance.

Lerm, S.; Kleyboecker, A. [International Centre for Geothermal Research (ICGR), GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany); Miethling-Graff, R. [International Centre for Geothermal Research (ICGR), GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany); Johann Heinrich von Thuenen Institut, Bundesforschungsinstitut fuer Laendliche Raeume, Wald und Fischerei Institut fuer Biodiversitaet, 38116 Braunschweig (Germany); Alawi, M.; Kasina, M.; Liebrich, M. [International Centre for Geothermal Research (ICGR), GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany); Wuerdemann, H., E-mail: wuerdemann@gfz-potsdam.de [International Centre for Geothermal Research (ICGR), GFZ German Research Centre for Geosciences, 14473 Potsdam (Germany)

2012-03-15T23:59:59.000Z

389

Degradation of cellulosic biomass and its subsequent utilization for the production of chemical feedstocks. Progress report, March 1, 1977--May 31, 1977  

DOE Green Energy (OSTI)

The degradation of cellulosic biomass continues to focus on the anaerobic thermophile Clostridium thermocellum. When grown on crystalline cellulose (MN300) in batch culture, there is an initial rapid accumulation of reducing sugars but the sugars are rapidly metabolized in later times during the fermentation. When grown on Solka floc with periodic addition of the substrate, there is a continual accumulation of reducing sugars (xylose, glucose, and cellobiose) as well as ethanol and acetic acid during the entire course of the fermentation. In the presence of surfactant in the growth medium, there is an increased appearance of extracellular cellulases. A chemically defined medium is being developed for growth Cl. thermocellum in order to study the enzyme regulations. Lastly, a trinitrophenyl-carboxylmethyl cellulose substrate for determining cellulose activity appears to be a promising and rapid assay. Progress in the genetic manipulations has been cautious but promising. Preliminary evidence leads to optimistic projection on the presence of plasmids and bacteriophage in Cl. thermocellum. The production of chemical feedstocks continues to focus on acrylic acid, acetone/butanol and acetic acid. Studies with cell free extracts of Clostridium propionicum have shown the production and accumulation of acrylic acid from lactic acid. The use of electron acceptor in cell-free systems has shown effective prevention on the reduction of acrylic acid to propionic acid. Medium development and strain selection using available acetone/butanol producing Cl. acetobutylicum have been initiated. There is every indication that these strains are capable to produce mixed solvents close to the theoretical maximum yield. An accurate and rapid method for quantifying acetic acid was developed. This technique is being used to examine the pertinent parameters on the production of acetic acid by Clostridium thermoaceticum.

Wang, D.I.C.; Cooney, C.L.; Demain, A.L.; Gomez, R.F.; Sinskey, A.J.

1977-06-01T23:59:59.000Z

390

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks  

SciTech Connect

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at itsoptimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.

Makarova, Kira S.; Omelchenko, Marina V.; Gaidamakova, Elena K.; Matrosova, Vera Y.; Vasilenko, Alexander; Zhai, Min; Lapidus, Alla; Copeland, Alex; Kim, Edwin; Land, Miriam; Mavrommatis, Konstantinos; Pitluck, Samuel; Richardson, Paul M.; Detter, Chris; Brettin, Thomas; Saunders, Elizabeth; Lai, Barry; Ravel, Bruce; Kemner, Kenneth M.; Wolf, Yuri I.; Sorokin, Alexander; Gerasimova, Anna V.; Gelfand, Mikhail S.; Fredrickson, James K.; Koonin, Eugene V.; Daly, Michael J.

2007-07-24T23:59:59.000Z

391

Metabolic engineering of Caldicellulosiruptor bescii yields increased hydrogen production from lignocellulosic biomass  

Science Conference Proceedings (OSTI)

Background: Members of the anaerobic thermophilic bacterial genus Caldicellulosiruptor are emerging candidates for consolidated bioprocessing (CBP) because they are capable of efficiently growing on biomass without conventional pretreatment. C. bescii produces primarily lactate, acetate and hydrogen as fermentation products, and while some Caldicellulosiruptor strains produce small amounts of ethanol C. bescii does not, making it an attractive background to examine the effects of metabolic engineering. The recent development of methods for genetic manipulation has set the stage for rational engineering of this genus for improved biofuel production. Here, we report the first targeted gene deletion, the gene encoding lactate dehydrogenase (ldh), for metabolic engineering of a member of this genus. Results: A deletion of the C. bescii L-lactate dehydrogenase gene (ldh) was constructed on a non-replicating plasmid and introduced into the C. bescii chromosome by marker replacement. The resulting strain failed to produce detectable levels of lactate from cellobiose and maltose, instead increasing production of acetate and H2 by 21-34% relative to the wild type and pyrFA parent strains. The same phenotype was observed on a real-world substrate switchgrass (Panicum virgatum). Furthermore, the ldh deletion strain grew to a higher maximum optical density than the wild type on maltose and cellobiose, consistent with the prediction that the mutant would gain additional ATP with increased acetate production. Conclusions: Deletion of ldh in C. bescii is the first use of recently developed genetic methods for metabolic engineering of these bacteria. This deletion resulted in a redirection of electron flow from production of lactate to acetate and hydrogen. New capabilities in metabolic engineering combined with intrinsic utilization of lignocellulosic materials position these organisms to provide a new paradigm for consolidated bioprocessing of fuels and other products from biomass.

Cha, Minseok [University of Georgia, Athens, GA; Chung, Daehwan [University of Georgia, Athens, GA; Elkins, James G [ORNL; Guss, Adam M [ORNL; Westpheling, Janet [University of Georgia, Athens, GA

2013-01-01T23:59:59.000Z

392

Controlled production of cellulases in plants for biomass conversion. Annual report, March 11, 1997--March 14, 1998  

DOE Green Energy (OSTI)

The goal of this project is to facilitate conversion of plant biomass to usable energy by developing transgenic plants that express genes for microbial cellulases, which can be activated after harvest of the plants. In particular, the feasibility of targeting an endoglucanase and a cellobiohydrolase to the plant apoplast (cell wall milieu) is to be determined. To avoid detrimental effects of cellulose expression in plants, enzymes with high temperature optima were chosen; the genes for these enzymes are from thermophilic organisms that can use cellulose as a sole energy source. During the past year (year 2 of the grant), efforts have been focused on testing expression of endoglucanase E{sub 1}, from Acidothermus cellulolyticus, in the apoplast of both tobacco suspension cells and Arabidopsis thaliana plants. Using the plasmids constructed during the first year, transgenic cells and plants that contain the gene for the E{sub 1} catalytic domain fused to a signal peptide sequence were obtained. This gene was constructed so that the fusion protein will be secreted into the apoplast. The enzyme is made in large quantities and is secreted into the apoplast. More importantly, it is enzymatically active when placed under optimal reaction conditions (high temperature). Moreover, the plant cells and intact plants exhibit no obvious problems with growth and development under laboratory conditions. Work has also continued to improve binary vectors for Agrobacterium-mediated transformation, to determine activity of E{sub 1} at various temperatures, and to investigate the activity of the 35S Cauliflower Mosaic Virus promoter in E. coli. 9 figs.

Danna, K.J.

1998-06-01T23:59:59.000Z

393

APS User News, Issue 58  

NLE Websites -- All DOE Office Websites (Extended Search)

8, November 11, 2009 8, November 11, 2009 CONTENTS MESSAGE FROM MURRAY SCIENCE NEWS 1. Fast CCD Detector Collaboration 2. Science & Research Highlights The Power of Proteins: Prion Diseases Demystified Bacterium Helps in the Formation of Gold Getting to the Roots of Lethal Hairs Creating a Precise Atomic-Scale Map of Quantum Dots USER MATTERS 3. Users and the Flu Season 4. Workshop on the Role of Synchrotron Radiation in Solving Scientific Challenges in Advanced Nuclear Energy Systems 5. First Experiment at the Linac Coherent Light Source 6. New Postings Available on Employment Bulletin Board FACILITY NEWS 7. Recent SAC Meeting Focuses on APS Upgrade 8. The Life Sciences Council at the APS 9. Fitness Center Now Open in New Location AWARDS AND HONORS 10. APS Users Awarded 2009 Nobel Prize in Chemistry

394

Why Sequence Allochromatium vinosum?  

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Allochromatium vinosum? Allochromatium vinosum? Anoxygenic purple sulfur bacteria flourish in globally occurring habitats, wherever light reaches sulfidic water layers or sediments, and often grow as dense accumulations in conspicuous blooms in freshwater as well as marine aquatic ecosystems. Here they are not only major players in the reoxidation of sulfide produced by sulfate-reducing bacteria in deeper anoxic layers but also important primary producers of fixed carbon (up to 83% of primary production in lakes can be anoxygenic). The overall goal of this project is to obtain a comprehensive understanding of the metabolic network present in a globally occurring anoxygenic purple sulfur bacterium, to thereby better understand its contribution to global carbon, sulfur, and nitrogen fluxes and to obtain a solid basis for its use in the removal of

395

Nobel Prize | 2009 Chemistry Prize, Steitz and Ramakrishnan  

NLE Websites -- All DOE Office Websites (Extended Search)

Steitz and Ramakrishnan Steitz and Ramakrishnan Thomas A. Steitz and Venkatraman Ramakrishnan. Diagram of a ribosome An x-ray structure of a bacterium ribosome. Credit: the Royal Swedish Academy of Sciences Taking Atomic-Level "Pictures" of Protein Factories Two of the three recipients of the 2009 Nobel Prize in Chemistry conducted a substantial part of their award-winning research at Brookhaven's National Synchrotron Light Source (NSLS). They used the NSLS and other synchrotron sources to produce atomic-level images that helped reveal the inner-workings of the ribosome, a cellular complex responsible for producing the thousands of proteins that are required for living cells. Venkatraman Ramakrishnan, of the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, a former employee in Brookhaven's

396

Why Sequence Zymomonas mobilis strains?  

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Zymomonas mobilis strains? Zymomonas mobilis strains? Z. mobilis industrial strain CP4, originating from Brazil, vigorously fermenting glucose to ethanol and CO2 (gas bubbles in the culture tube). Photo courtesy Katherine M. Pappas. A primary goal for the U.S., the E.U., and other nations is to find cleaner, safer and renewable alternatives to fossil fuels, and to that end 4 billion gallons of corn-derived ethanol was used as fuel additive in 2006, in the U.S. alone. The bacterium Zymomonas mobilis is a highly potent ethanol producer already used in industrial-scale fermentations. Zymomonas converts sugars to ethanol and carbon dioxide, exhibiting up to 98% yields, minimal by-products, simple fermentation requirements, and several-fold the production rates of yeast. Beside its robust capability for biofuel

397

Advancing the art of tuberculosis detection  

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Advancing art of tuberculosis detection Advancing art of tuberculosis detection Advancing the art of tuberculosis detection New approach to finding a TB biomarker could provide earlier diagnosis. April 19, 2013 Los Alamos National Laboratory researcher Harshini Mukundan is exploring new ways to detect and diagnose tuberculosis. Los Alamos National Laboratory researcher Harshini Mukundan is exploring new ways to detect and diagnose tuberculosis. Contact Nancy Ambrosiano Communications Office (505) 667-0471 Email This observation has far-reaching applications to the understanding of the interaction of the human host with many pathogens, not just TB. LOS ALAMOS, N.M., April 19, 2013-New work from Los Alamos National Laboratory shows promise for stemming the advance of tuberculosis (TB) by revealing how the bacterium interacts with its human hosts and thus

398

NREL: Energy Sciences - Larry Taylor  

NLE Websites -- All DOE Office Websites (Extended Search)

Larry Taylor Larry Taylor Research Scientist Phone: (303) 384-7784 Email: larry.taylor@nrel.gov At NREL Since: 2007 Larry Taylor received his Ph.D. in Environmental Molecular Biology and Biotechnology from the Marine and Estuarine Environmental Sciences department at the University of Maryland, College Park. His dissertation work focused on the functional genomics of the plant cell wall degrading enzyme systems of the marine bacterium Saccharophagus degradans 2-40, which was isolated from decaying salt marsh grass the Chesapeake Bay watershed in 1988. Preliminary genomic analyses revealed that the S. degradans encodes more than 180 predicted carbohydrases. Under the direction of Prof. Ronald M. Weiner, and in collaboration with Dr. Bernard Henrisaat, Dr. Taylor identified the predicted cellulase system of S. degradans through sequence

399

Secrets of the Lacewing's Silk | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

Structure of the Cell Nucleus "Gatekeeper" Structure of the Cell Nucleus "Gatekeeper" The Power of Proteins: Prion Diseases Demystified Bacterium Helps in the Formation of Gold Creating a Precise Atomic-Scale Map of Quantum Dots Getting to the Roots of Lethal Hairs Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed Secrets of the Lacewing's Silk NOVEMBER 2, 2009 Bookmark and Share Top: In laying her eggs, the female green lacewing first secretes a drop of liquid silk onto a stem or leaf, then stretches the silk out into a fine strand as she lifts her abdomen from the substrate. A few seconds later, she deposits an egg on the tip of the stalk. Then she repositions herself

400

FY 2005 funded projects  

NLE Websites -- All DOE Office Websites (Extended Search)

5 LDRD PROJECTS 5 LDRD PROJECTS LDRD Project Project Title P.I. Dept/Bldg. 03-004 High-Brightness, High-Power Electron Beams I. Ben-Zvi CAD/817 03-056 Structural Properties of Methane Hydrates D. Mahajan ES&T/815 03-064 Investigation of Neutron and Gamma Probes to Detect Explosives in Sealed Containers M. Todosow ES&T/475B 03-094 Structural Studies on the Integral Membrane Protein AlkB J. Shanklin BIO/463 03-099 The microPET Study of Gene Expression in Rodents P. Thanos MED/490 03-104 Hydrogen Atom Transfer from Carbon to Metal - Relevance of a Novel Reaction to Catalyzed Hydrocarbon Conversions M. Bullock CHEM/555A 03-105 Radioprotection in D. Radiodurans, a Radiation Resistant Bacterium D. Cabelli CHEM/555A 03-107 New Development of Norepinephrine Transporter

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

EMSL: Environmental Molecular Sciences Laboratory  

NLE Websites -- All DOE Office Websites (Extended Search)

Back Pause Slideshow Slide 1 Next Back Pause Slideshow Slide 1 Next Step at a Time An international team of scientists has isolated and characterized a key protein related to sulfate respiration. Understanding how microbes respire sulfate is important for understanding global sulfur and carbon cycles and for quantifying carbon dioxide emissions. Research Highlights Watch a virtual tour of EMSL Biofuel breakdown A collaborative study shows that Enterobacter lignolyticus SCF1 can multitask quite successfully: degrade lignin as both a food source and for breathing - the first soil bacterium to demonstrate this dual capability. Research Highlights Watch a virtual tour of EMSL The hidden ties that bind EMSL scientists took advantage of advanced instrumental capabilities, a specially designed experimental cell and theoretical modeling to

402

A Key Enzyme to the Potency of an Anticancer Agent  

NLE Websites -- All DOE Office Websites (Extended Search)

A Key Enzyme to the Potency of A Key Enzyme to the Potency of an Anticancer Agent A Key Enzyme to the Potency of an Anticancer Agent Print Wednesday, 28 May 2008 00:00 Incorporation of halogen atoms into drug molecules often increases biological activity. This is the case with salinosporamide A (sal A), a natural product from the marine bacterium Salinispora tropica that is 500 times more active than sal B, its nonchlorinated analog. Sal A is in phase I human clinical trials for the treatment of multiple myeloma and solid tumors. A group of researchers, using diffraction data collected at ALS Beamline 8.2.2, discovered and characterized the chlorinating SalL enzyme, a crucial component in sal A biosynthesis that uses a unique chlorine-activating mechanism. Chlorine-Loving Enzyme Speeds Things Up

403

Regulation of extracellular polygalacturonase production in Pseudomonas solanacearum. Progress report, [May 1, 1992--April 30, 1994  

DOE Green Energy (OSTI)

Pseudomonas solanacearum is an economically important plant pathogen that causes bacterial wilt disease of diverse crops. The bacterium produces at least three isozymes of polygalacturonase, which degrade plant cell walls and contribute substantially to bacterial wilt disease development. The central objective of this research project is to determine how expression of these enzymes is regulated. To this end, we isolated a positive trans-acting regulator of polygalacturonase production (pehR). We have focused on further characterization of the pehR mutant pheonotype, and studies of pehR expression. Preliminary results suggest pehR also regulates bacterial motility. An investigation of two unusual tyrosine phosphoproteins in P. solanacearum is also described.

Allen, C.

1994-06-01T23:59:59.000Z

404

Life Redefined: Microbes Built with Arsenic  

DOE Green Energy (OSTI)

Life can survive in many harsh environments, from extreme heat to the presence of deadly chemicals. However, life as we know it has always been based on the same six elements -- carbon, oxygen, nitrogen, hydrogen, sulfur and phosphorus. Now it appears that even this rule has an exception. In the saline and poisonous environment of Mono Lake, researchers have found a bacterium that can grow by incorporating arsenic into its structure in place of phosphorus. X-ray images taken at SLAC's synchrotron light source reveal that this microbe may even use arsenic as a building block for DNA. Please join us as we describe this discovery, which rewrites the textbook description of how living cells work.

Webb, Sam (SLAC and Felisa Wolfe-Simon, NASA and U.S. Geological Survey)

2011-03-22T23:59:59.000Z

405

1  

NLE Websites -- All DOE Office Websites (Extended Search)

Counting small RNA in disease-causing Counting small RNA in disease-causing organisms June 17, 2013 Small molecules of RNA (tens to hundreds of nucleotides in length) play a key regulatory role in bacteria. Due to their small size, directly measuring the number of small RNA (sRNA) present in a single bacterium has proven so far to be an impossible task. Standard methods of measuring the number of specific nucleic acid molecules present in a single cell suffer from too much background and false positives when scientists attempt to image short targets. In research featured on the cover of the journal Analytical Chemistry, Los Alamos researchers demonstrated improved technical methods capable of directly counting small RNA molecules in pathogenic (disease- causing) bacteria. Significance of the research

406

Purple Bacteria Develops Its Own Form of Sunscreen | U.S. DOE Office of  

Office of Science (SC) Website

Purple Bacteria Develops Its Own Form Purple Bacteria Develops Its Own Form of "Sunscreen" Energy Frontier Research Centers (EFRCs) EFRCs Home Centers Research Science Highlights Highlight Archives News & Events Publications Contact BES Home 05.03.12 Purple Bacteria Develops Its Own Form of "Sunscreen" Print Text Size: A A A RSS Feeds FeedbackShare Page Scientific Achievement Found that specific pigments in the light harvesting complex of a photosynthetic bacterium act primarily to protect the cell from damage by excess sunlight Significance and Impact May aid the design of both natural and artificial light harvesting systems to minimize deleterious effects of exposure to too much light energy Research Details In photosynthetic organisms, carotenoids typically act as supplementary

407

NREL: Energy Sciences - Lauren Magnusson  

NLE Websites -- All DOE Office Websites (Extended Search)

Lauren Magnusson Lauren Magnusson Research Associate Photo of Lauren Magnusson Phone: (303) 384-7725 Email: lauren.magnusson@nrel.gov At NREL Since: 2008 Lauren Magnusson received her M.Sc. in Biosystems Engineering from the University of Manitoba in 2008, where she worked under the supervision of Dr. Nazim Cicek. During her time at the U of M, she focused on cellulosic hydrogen production using the bacterium Clostridium thermocellum. Her research showed that long-term, stable H2 production can be achieved during direct fermentation of an insoluble cellulosic substrate under continuous culture conditions, and that C. thermocellum is capable of fermenting complex lignocellulosic materials without pretreament. At NREL, she is currently working with Dr. Pin-Ching Maness on hydrogen production from

408

Mobile RNA is Poised and Ready | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

Glass Does a Double-Take Glass Does a Double-Take Welcoming a New Family of Superconductors A Lensless X-ray Camera for Nanoscale Materials and Biological Specimens The Collagen Protein Viewed at Unprecedented Detail Assembling Nanoparticles the Easy DNA-Way Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed Mobile RNA is Poised and Ready APRIL 10, 2008 Bookmark and Share Ribbon representation of the group II splicing intron. To see a 360° rotation of the recently solved O. iheyensis IIC intron crystal structure, click here (credit: Kevin Keating). A new picture of a genetic parasite isolated from a deep-sea bacterium is helping researchers see how certain specialized segments of RNA escape from

409

Xu Y. Computational  

NLE Websites -- All DOE Office Websites (Extended Search)

Xu Xu Y. Computational challenges in deciphering genomic structures of bacteria. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY 25(1): 53-70 Jan. 2010 Computational Challenges in Deciphering Genomic Structures of Bacteria Ying Xu (Å ) Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, The University of Georgia, Athens, GA 30602, U.S.A. BESC BioEnergy Science Center, U.S.A. College of Computer Science and Technology, Jilin University, Changchun 130012, China E-mail: xyn@bmb.uga.edu Received October 1, 2009; revised November 16, 2009. Abstract This article addresses how the functionalities of the cellular machinery of a bacterium might have constrained the genomic arrangement of its genes during evolution and how we can study such problems using computational approaches, taking full advantage

410

JGI - Why Sequence Rhodobacter sphaeroides?  

NLE Websites -- All DOE Office Websites (Extended Search)

Rhodobacter sphaeroides? Rhodobacter sphaeroides? How can a photosynthetic bacterium help us understand a fundamental question in evolutionary biology? The acquisition and loss of genetic information permits the adaptation of an organism to an ever-changing environment. However, this genetic flux is a double-edged sword. On the one hand, it permits the acquisition of new adaptive traits, but this process may result in the damage or loss of functioning genetic systems, with possibly dire consequences for the individual or species. How can such genomic plasticity occur without being severely disruptive to the ongoing lifestyle of an organism? One possible solution to this dilemma is the presence of genomic "safe zones," where the insertion or deletion of DNA is not disruptive to the genome at large. Such safe zones may also

411

e00605-13.full.pdf  

NLE Websites -- All DOE Office Websites (Extended Search)

Clostridium Clostridium sp. Strain DL-VIII, a Novel Solventogenic Clostridium Species Isolated from Anaerobic Sludge Safiyh Taghavi, a,b Javier A. Izquierdo, a Daniel van der Lelie a,b Center for Agricultural and Environmental Biosolutions, RTI International, Research Triangle Park, North Carolina, USA a ; Biosciences Department, Brookhaven National Laboratory, Upton, New York, USA b We report the genome sequence of Clostridium sp. strain DL-VIII, a novel Gram-positive, endospore-forming, solventogenic bacterium isolated from activated anaerobic sludge of a wastewater treatment plant. Aside from a complete sol operon, the 6,477,357-bp genome of DL-VIII reveals genes for several unique enzymes with applications in lignocellulose degradation, in- cluding two phenolic acid decarboxylases. Received 5 July 2013 Accepted 11 July 2013 Published 8 August 2013 Citation Taghavi S,

412

Stanford Synchrotron Radiation Lightsource  

NLE Websites -- All DOE Office Websites (Extended Search)

Botulinum Neurotoxin is Bio-shielded by NTNHA in a Handshake Complex Botulinum Neurotoxin is Bio-shielded by NTNHA in a Handshake Complex SSRL Science Summary - October 2012 Figure A single reconstructed slice and a volume rendering of the tomography sequence. Botulinum neurotoxins (BoNTs) invade motor neurons at their junctions with muscular tissue, where the toxins disable the release of the neurotransmitter acetylcholine and subsequently paralyze the affected muscles. Accidental BoNT poisoning primarily occurs through ingestion of food products contaminated by Clostridium botulinum, the bacterium that produces BoNTs. However, BoNTs by themselves are fragile and sensitive to low pH environments and digestive proteases. So how do they survive the harsh environment of the host's gastrointestinal tract? Researchers at Sanford-Burnham Research Institute and the Medical School of

413

Why Sequence Pedomicrobium manganicum?  

NLE Websites -- All DOE Office Websites (Extended Search)

Pedomicrobium manganicum? Pedomicrobium manganicum? Pedomicrobium manganicum lives in one of the most hostile environments on the planet, the surface of desert rocks. This ecological niche can expose it within minutes or hours to massive fluctuations in temperature, ultraviolet irradiation, and desiccation. Consequently, its genome must have evolved to encode the diverse physiological capabilities required for survival in this inhospitable environment. This bacterium is also found in aquatic and marine environments, within sediments extracted from deep boreholes and soils. Of particular relevance to the Department of Energy is that it forms a significant part of the bacterial soil population of Uranium Mill Tailing Remedial Action Sites (UMTRAs). It is the only member of that population that has not been examined by genome sequencing.

414

Why sequence freshwater manganese depositing β-proteobacterium  

NLE Websites -- All DOE Office Websites (Extended Search)

freshwater manganese depositing β-proteobacterium freshwater manganese depositing β-proteobacterium (Siderocapsaceae)? Stream biofilms are key component of stream food webs and contain bacteria that contribute to the carbon and nitrogen cycles. A slow-growing bacterium isolated from a freshwater stream biofilm has potential bioenergy and bioremediation applications. JOSHI_001 is part of a class of bacteria that deposit iron and manganese precipitates externally to the colony early in its life cycle and could be used for fuel cells and to help clean up manganese contaminated water. Members of the Siderocapsaceae family to which JOSHI_001 belongs have been observed in biofilms for the past century, but have never before been isolated and cultivated in a laboratory environment. As a result, researchers have not been able to learn about the

415

EMSL: Environmental Molecular Sciences Laboratory  

NLE Websites -- All DOE Office Websites

Science Science FAQ Search EMSL Home About EMSL Science Capabilities User Access Publications News Contacts Back Pause Slideshow Slide 1 Next Biofuel breakdown A collaborative study shows that Enterobacter lignolyticus SCF1 can multitask quite successfully: degrade lignin as both a food source and for breathing - the first soil bacterium to demonstrate this dual capability. Research Highlights Watch a virtual tour of EMSL The hidden ties that bind EMSL scientists took advantage of advanced instrumental capabilities, a specially designed experimental cell and theoretical modeling to successfully deduce the how molecules of carboxylic acid- a common organic acid found in nature - bind to ceria nanoparticle surfaces. Research Highlights Watch a virtual tour of EMSL Ditch the dirt

416

"Temple of the Mind" Unlocked | Advanced Photon Source  

NLE Websites -- All DOE Office Websites (Extended Search)

A Key to Drought Resistant Crops A Key to Drought Resistant Crops Secrets of the Lacewing's Silk The Structure of the Cell Nucleus "Gatekeeper" The Power of Proteins: Prion Diseases Demystified Bacterium Helps in the Formation of Gold Science Highlights Archives: 2013 | 2012 | 2011 | 2010 2009 | 2008 | 2007 | 2006 2005 | 2004 | 2003 | 2002 2001 | 2000 | 1998 | Subscribe to APS Science Highlights rss feed "Temple of the Mind" Unlocked DECEMBER 4, 2009 Bookmark and Share This glutamate receptor may play a crucial role memory and learning. (E. Gouaux et al../Nature) The full structure of a fiendishly complicated and important brain protein has been determined by researchers using two U.S. Department of Energy (DOE) light sources, potentially enabling the development of new treatments

417

Publications of the Life Sciences Division, ORNL  

NLE Websites -- All DOE Office Websites (Extended Search)

LSD logo Life Sciences Division LSD logo Life Sciences Division Oak Ridge National Laboratory Programs Partners Organization Highlights In the News --- Home Internal (Restricted Access) Contacts Publications 2003 Publications/Presentations Akabani, G., S. J. Kennel, and M. R. Zalutsky, "Microdosimetric analysis of alpha-particle-emitting targeted radiotherapeutics using histological images," J. Nucl. Med. 44(5):792-805 (May 2003). Allain, L. R., D. N. Stratis, C. M. Cullum, J. Mobley, M. R. Hajaligol, and T. Vo-Dinh, "Real-time detection of PAH mixtures in the vapor phase at high temperatures," J. Anal. Appl. Pyrolysis 66(1-2):145-154 (January 2003). Chain, P., J. Lamerdin, F. Larimer, W. Regala, V. Lao, M. Land, L. Hauser, A. Hooper, M. Klotz, J. Norton, L. Sayavedra- Soto, D. Arciero, N. Hommes, M. Whittaker, and D. Arp, "Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph NitrosomonaseEuropaea," J. Bacteriology 185(9):2759-2773 (May 2003).

418

Identification  

NLE Websites -- All DOE Office Websites (Extended Search)

a a Bifunctional UDP-4-keto-pentose/UDP-xylose Synthase in the Plant Pathogenic Bacterium Ralstonia solanacearum Strain GMI1000, a Distinct Member of the 4,6-Dehydratase and Decarboxylase Family * □ S Received for publication, September 16, 2009, and in revised form, January 15, 2010 Published, JBC Papers in Press, January 29, 2010, DOI 10.1074/jbc.M109.066803 Xiaogang Gu ‡ , John Glushka ‡ , Yanbin Yin § , Ying Xu § , Timothy Denny ¶ , James Smith ‡ , Yingnan Jiang ‡ , and Maor Bar-Peled ‡ʈ1 From the ‡ Complex Carbohydrate Research Center, the § Computational System Biology Laboratory, Department of Biochemistry and Molecular Biology, and the Institute of Bioinformatics, and the Departments of ¶ Plant Pathogen and ʈ Plant Biology, University of Georgia, Athens, Georgia 30602 The UDP-sugar interconverting enzymes involved in UDP- GlcA metabolism are well

419

Draft Genome Sequence  

NLE Websites -- All DOE Office Websites (Extended Search)

Draft Draft Genome Sequence of Serratia sp. Strain ATCC 39006, a Model Bacterium for Analysis of the Biosynthesis and Regulation of Prodigiosin, a Carbapenem, and Gas Vesicles Peter C. Fineran, a Marina C. Iglesias Cans, a Joshua P. Ramsay, b Nabil M. Wilf, b Desiree Cossyleon, a Matthew B. McNeil, a Neil R. Williamson, b Rita E. Monson, b S. Anette Becher, c Jo-Ann L. Stanton, d Kim Brügger, e Steven D. Brown, f George P. C. Salmond b Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand a ; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom b ; AgResearch Ltd., Invermay Agricultural Centre, Mosgiel, New Zealand c ; Department of Anatomy, University of Otago, Dunedin, New Zealand d ; EASIH, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom e ; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,

420

Why sequence Acetobacter aceti ATCC 23746?  

NLE Websites -- All DOE Office Websites (Extended Search)

Acetobacter aceti ATCC 23746? Acetobacter aceti ATCC 23746? Acetobacter are most commonly known as the bacteria responsible for the production of vinegar. They are frequently found in grain-based fermentations such as wine and beer production, and can reduce product yields by increasing the acidity of the batch. Because these Gram-negative bacteria are strictly aerobic, they are often limited in ethanol plants to areas like the propagation tank where they have access to oxygen. Bacteria such as these are a serious concern to bioenergy researchers working on scaling up production of cellulosic ethanol. The genome sequence of A. aceti, a key member of the Acetobacteraceae family, could help control contamination as well as provide a more comprehensive understanding of ethanol and acid tolerance in this bacterium, leading to a better

Note: This page contains sample records for the topic "thermophilic cellulolytic bacterium" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


421

Chlorinated Hydrocarbon Degradation in Plants: Mechanisms and Enhancement of Phytoremediation of Groundwater Contamination  

SciTech Connect

Several varieties of transgenic poplar containing cytochrome P-450 2E1 have been constructed and are undergoing tests. Strategies for improving public acceptance and safety of transgenic poplar for chlorinated hydrocarbon phytoremediation are being developed. We have discovered a unique rhizobium species that lives within the stems of poplar and we are investigating whether this bacterium contributes nitrogen fixed from the air to the plant and whether this endophyte could be used to introduce genes into poplar. Studies of the production of chloride ion from TCE have shown that our present P-450 constructs did not produce chloride more rapidly than wild type plants. Follow-up studies will determine if there are other rate limiting downstream steps in TCE metabolism in plants. Studies of the metabolism of carbon tetrachloride in poplar cells have provided evidence that the native plant metabolism is due to the activity of oxidative enzymes similar to the mammalian cytochrome P-450 2E1.

Strand, Stuart E.

2002-06-01T23:59:59.000Z

422

Crystallization and preliminary X-ray crystallographic studies of the outer membrane cytochrome OmcA from Shewanella oneidensis MR-1  

Science Conference Proceedings (OSTI)

The outer membrane cytochrome OmcA functions as a terminal metal reductase in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. The ten-heme centers shuttle electrons from the transmembrane donor complex to extracellular electron acceptors. Here, the crystallization and preliminary crystallographic analysis of OmcA are reported. Crystals of OmcA were grown by the sitting-drop vapor-diffusion method using PEG 20 000 as a precipitant. The OmcA crystals belonged to space group P21, with unit-cell parameters a = 93.0, b = 246.0, c = 136.6 A ° , * = 90, * = 97.8, * = 90*. X-ray diffraction data were collected to a maximum resolution of 3.25 A ° .

Tomanicek, S. J.; Johs, Alexander; Sawhney, M. S.; Shi, Liang; Liang, L.

2012-01-01T23:59:59.000Z

423

Crystallization and preliminary X-ray crystallographic studies of the outer membrane cytochrome OmcA from Shewanella oneidensis MR-1  

SciTech Connect

The outer membrane cytochrome OmcA functions as a terminal metal reductase in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1. The ten-heme centers shuttle electrons from the transmembrane donor complex to extracellular electron acceptors. Here, the crystallization and preliminary crystallographic analysis of OmcA are reported. Crystals of OmcA were grown by the sitting-drop vapor-diffusion method using PEG 20 000 as a precipitant. The OmcA crystals belonged to space group P2{sub 1}, with unit-cell parameters a = 93.0, b = 246.0, c = 136.6 {angstrom}, = 90, {beta} = 97.8, {gamma} = 90{sup o}. X-ray diffraction data were collected to a maximum resolution of 3.25 {angstrom}.

Tomanicek, S.J.; Johs, A.; Sawhney, M.S.; Shi, L.; Liang, L. (PNNL); (ORNL)

2012-05-24T23:59:59.000Z

424

Biogenic formation of photoactive arsenic-sulfide nanotubes by Shewanella sp. strain HN-41  

SciTech Connect

Microorganisms facilitate the formation of a wide range of minerals that have unique physical and chemical properties as well as morphologies that are not produced by abiotic processes. Here, we report the production of an extensive extracellular network of filamentous, arsenic-sulfide (As-S) nanotubes (20–100 nm in diameter by 30 µm in length) by the dissimilatory metal-reducing bacterium Shewanella sp. HN-41. The As-S nanotubes, formed via the reduction of As(V) and S2O, were initially amorphous As2S3 but evolved with increasing incubation time toward polycrystalline phases of the chalcogenide minerals realgar (AsS) and duranusite (As4S). Upon maturation, the As-S nanotubes behaved as metals and semiconductors in terms of their electrical and photoconductive properties, respectively. The As-S nanotubes produced by Shewanella may provide useful materials for novel nano- and opto-electronic devices.

Lee, Ji-Hoon; Kim, Min-Gyu; Yoo, Bongyoung; Myung, Nosang V.; Maeng, Jongsun; Lee, Takhe; Dohnalkova, Alice; Fredrickson, Jim K.; Sadowsky, Michael J.; Hur, Hor-Gil

2007-12-18T23:59:59.000Z