National Library of Energy BETA

Sample records for bacterial biofilm development

  1. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Real-Time Chemical Imaging of Bacterial Biofilm Development Print Wednesday, 25 August 2010 00:00 Scientists have ...

  2. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial ...

  3. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Real-Time Chemical Imaging of Bacterial Biofilm Development Print Wednesday, 25 August 2010 00:00 Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively,

  4. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have ... The ability to image the chemical reactions in living cells in real time, especially in ...

  5. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce

  6. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce

  7. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce

  8. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce

  9. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce

  10. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce

  11. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce

  12. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Real-Time Chemical Imaging of Bacterial Biofilm Development Print Scientists have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial biofilms. Almost all bacteria can form biofilms-dynamic communities of cells enclosed in self-produced matrices of polymers that stick to other bacteria or surfaces in water-containing environments. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce

  13. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    researchers studied why the antimicrobial agent mitomycin-C (MMC) does not kill some E. coli in biofilms, focusing on the entrance of MMC into bacterial cells and the subsequent...

  14. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    microwell edge. To evaluate this technique's potential, researchers studied why the antimicrobial agent mitomycin-C (MMC) does not kill some E. coli in biofilms, focusing on the...

  15. Spatially resolved characterization of biogenic manganese oxideproduction within a bacterial biofilm

    SciTech Connect (OSTI)

    Toner, Brandy; Fakra, Sirine; Villalobos, Mario; Warwick, Tony; Sposito, Garrison

    2004-10-01

    Pseudomonas putida strain MnB1, a biofilm forming bacteria, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of Mn{sub (aq)}{sup +2} by P. putida was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm using scanning transmission x-ray microscopy (STXM) combined with near edge x-ray absorption fine structure (NEXAFS) spectroscopy at the Mn-L{sub 2,3} absorption edges. Subsamples were collected from growth flasks containing 0.1 mM and 1 mM total Mn at 16, 24, 36 and 48 hours after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at 40 nm resolution. Manganese NEXAFS spectra were extracted from x-ray energy sequences of STXM images (stacks) and fit with linear combinations of well characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III) and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn{sub (aq)}{sup +2} was removed from solution by P. putida and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission x-ray microscopy is a promising tool to advance the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.

  16. Laser Desorption Postionization Mass Spectrometry of Antibiotic-Treated Bacterial Biofilms using Tunable Vacuum Ultraviolet Radiation

    SciTech Connect (OSTI)

    Gasper, Gerald L.; Takahashi, Lynelle K.; Zhou, Jia; Ahmed, Musahid; Moore, Jerry F.; Hanley, Luke

    2010-08-04

    Laser desorption postionization mass spectrometry (LDPI-MS) with 8.0 ? 12.5 eV vacuum ultraviolet synchrotron radiation is used to single photon ionize antibiotics andextracellular neutrals that are laser desorbed both neat and from intact bacterial biofilms. Neat antibiotics are optimally detected using 10.5 eV LDPI-MS, but can be ionized using 8.0 eV radiation, in agreement with prior work using 7.87 eV LDPI-MS. Tunable vacuum ultraviolet radiation also postionizes laser desorbed neutrals of antibiotics and extracellular material from within intact bacterial biofilms. Different extracellular material is observed by LDPI-MS in response to rifampicin or trimethoprim antibiotic treatment. Once again, 10.5 eV LDPI-MS displays the optimum trade-off between improved sensitivity and minimum fragmentation. Higher energy photons at 12.5 eV produce significant parent ion signal, but fragment intensity and other low mass ions are also enhanced. No matrix is added to enhance desorption, which is performed at peak power densities insufficient to directly produce ions, thus allowing observation of true VUV postionization mass spectra of antibiotic treated biofilms.

  17. APPLICATIONS OF BIOTECHNOLOGY IN DEVELOPMENT OF BIOMATERIALS: NANOTECHNOLOGY AND BIOFILMS

    SciTech Connect (OSTI)

    Brigmon, R.; Berry, T.; Narayan, R.

    2010-11-29

    Biotechnology is the application of biological techniques to develop new tools and products for medicine and industry. Due to various properties including chemical stability, biocompatibility, and specific activity, e.g. antimicrobial properties, many new and novel materials are being investigated for use in biosensing, drug delivery, hemodialysis, and other medical applications. Many of these materials are less than 100 nanometers in size. Nanotechnology is the engineering discipline encompassing designing, producing, testing, and using structures and devices less than 100 nanometers. One of the challenges associated with biomaterials is microbial contamination that can lead to infections. In recent work we have examined the functionalization of nanoporous biomaterials and antimicrobial activities of nanocrystalline diamond materials. In vitro testing has revealed little antimicrobial activity against Pseudomonas fluorescens bacteria and associated biofilm formation that enhances recalcitrance to antimicrobial agents including disinfectants and antibiotics. Laser scanning confocal microscopy studies further demonstrated properties and characteristics of the material with regard to biofilm formation.

  18. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    1-cm-diameter silicon chip (light green) that has been subjected to deep reactive ion etching to form a hydrophilic microchannel or microwell (measuring 1 mm 20-40 m 10-15...

  19. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley coupled infrared (IR) rays from ALS Beamline 1.4.3 to the first open-channel microfluidic platform to...

  20. Real-Time Chemical Imaging of Bacterial Biofilm Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    provides enough water to sustain the living cells without producing interference on mid-IR spectroscopy. The mid-IR light (2.5-15.5 mm wavelength, or 4000-650 cm-1 wavenumber)...

  1. New information about bacterial enzymes to help scientists develop...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    about bacterial enzymes to help scientists develop more effective antibiotics, cancer drugs By Jo Napolitano * November 5, 2015 Tweet EmailPrint Scientists studying the...

  2. Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community

    SciTech Connect (OSTI)

    Mueller, Ryan; Dill, Brian; Pan, Chongle; Belnap, Christopher P.; Thomas, Brian; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2011-01-01

    Proteomes of acid mine drainage biofilms at different stages of ecological succession were examined to understand microbial responses to changing community membership. We evaluated the degree of reproducibility of the community proteomes between samples of the same growth stage and found stable and predictable protein abundance patterns across time and sampling space, allowing for a set of 50 classifier proteins to be identified for use in predicting growth stages of undefined communities. Additionally, physiological changes in the dominant species, Leptospirillum Group II, were analysed as biofilms mature. During early growth stages, this population responds to abiotic stresses related to growth on the acid mine drainage solution. Enzymes involved in protein synthesis, cell division and utilization of 1- and 2-carbon compounds were more abundant in early growth stages, suggesting rapid growth and a reorganization of metabolism during biofilm initiation. As biofilms thicken and diversify, external stresses arise from competition for dwindling resources, which may inhibit cell division of Leptospirillum Group II through the SOS response. This population also represses translation and synthesizes more complex carbohydrates and amino acids in mature biofilms. These findings provide unprecedented insight into the physiological changes that may result from competitive interactions within communities in natural environments.

  3. Dynamic Metabolism Studies of Live Bacterial Films

    SciTech Connect (OSTI)

    Majors, Paul D.; Mclean, Jeffrey S.

    2008-11-01

    Bacterial film (biofilm) microbes exist within spatial (nutrient, electron-acceptor, pH, etc.) gradients of their own making. Correspondingly, biofilm bacteria are physiologically and functionally distinct from free-floating bacteria and from their own species at differing biofilm depths. This article describes our efforts to develop noninvasive nuclear magnetic resonance (NMR) technologies for biofilm-metabolism studies. This involves integrating NMR with controlled-cultivation methods to interrogate microbial physiology live and under known growth conditions. NMR is uniquely capable of providing depth-resolved metabolic and transport information in a non-invasive, non-sample-consuming fashion, providing information required for experimental reactive transport studies. We have studied mono-species biofilms relevant to environment remediation and human health. We describe these technologies, discuss their advantages and limitations, and give examples of their application.

  4. The effect of glutaraldehyde on the development of marine biofilms formed on surfaces of AISI 304 stainless steel

    SciTech Connect (OSTI)

    Tapper, R.C.; Smith, J.R.; Beech, I.B.; Viera, M.R.; Guiamet, P.S.; Videla, H.; Swords, C.L.; Edyvean, R.G.J.

    1997-08-01

    The effect of pre-conditioning polished and unpolished AISI 304 stainless steel surfaces with glutaraldehyde on the attachment, growth and morphology of an aerobic consortium of marine bacteria was investigated using total cell number counts, epifluorescence microscopy, Atomic Force Microscopy (AFM), Environmental Scanning Electron Microscopy (ESEM) and grazing-angle Fourier Transform Infrared (FTIR) spectroscopy. Both fully hydrated and dehydrated biofilms were studied using AFM and ESEM. Formation of the conditioning layer on steel surfaces from the culture medium, in the presence and absence of glutaraldehyde was monitored in-situ employing AFM and Grazing Angle FTIR spectroscopy. The influence of both surface area and surface energy upon the numbers of bacteria attached to polished and unpolished coupons was determined. This study has shown the influence of pretreatment of AISI 304 stainless steel with glutaraldehyde upon biofilm formation and has demonstrated the ability of AFM, ESEM and FTIR to be used as valuable tools for the in-situ investigation of the effect of biocides on bacterial biofilms.

  5. New information about bacterial enzymes to help scientists develop more

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    effective antibiotics, cancer drugs | Argonne National Laboratory information about bacterial enzymes to help scientists develop more effective antibiotics, cancer drugs By Jo Napolitano * November 5, 2015 Tweet EmailPrint Scientists studying the biosynthesis and production of microbial natural products now have a greater insight into the process thanks to research conducted at the U.S. Department of Energy's Argonne National Laboratory in collaboration with scientists from the Scripps

  6. Heterotrophic Archaea Contribute to Carbon Cycling in Low-pH, Suboxic Biofilm Communities

    SciTech Connect (OSTI)

    Justice, Nicholas B; Pan, Chongle; Mueller, Ryan; Spaulding, Susan E.; Shah, Vega; Sun, Christine; Yelton, Alexis P; Miller, CS; Thomas, BC; Shah, Manesh B; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2012-01-01

    Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from Bacteria- to Archaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (pH 1.0,38 C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescent in situ hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected 2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of Ferroplasma and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.

  7. Permeabilizing biofilms

    DOE Patents [OSTI]

    Soukos, Nikolaos S.; Lee, Shun; Doukas,; Apostolos G.

    2008-02-19

    Methods for permeabilizing biofilms using stress waves are described. The methods involve applying one or more stress waves to a biofilm, e.g., on a surface of a device or food item, or on a tissue surface in a patient, and then inducing stress waves to create transient increases in the permeability of the biofilm. The increased permeability facilitates delivery of compounds, such as antimicrobial or therapeutic agents into and through the biofilm.

  8. Microscale Confinement features in microfluidic devices can affect biofilm

    SciTech Connect (OSTI)

    Kumar, Aloke; Karig, David K; Neethirajan, Suresh; Acharya, Rajesh K; Mukherjee, Partha P; Retterer, Scott T; Doktycz, Mitchel John

    2013-01-01

    Biofilms are aggregations of microbes that are encased by extra-cellular polymeric substances (EPS) and adhere to surfaces and interfaces. Biofilm development on abiotic surfaces is a dynamic process, which typically proceeds through an initial phase of adhesion of plankntonic microbes to the substrate, followed by events such as growth, maturation and EPS secretion. However, the coupling of hydrodynamics, microbial adhesion and biofilm growth remain poorly understood. Here, we investigate the effect of semiconfined features on biofilm formation. Using a microfluidic device and fluorescent time-lapse microscopy, we establish that confinement features can significantly affect biofilm formation. Biofilm dynamics change not only as a function of confinement features, but also of the total fluid flow rate, and our combination of experimental results and numerical simulations reveal insights into the link between hydrodynamics and biofilm formation.

  9. IMPACTS OF BIOFILM FORMATION ON CELLULOSE FERMENTATION

    SciTech Connect (OSTI)

    Leschine, Susan

    2009-10-31

    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

  10. Thiol reductive stress induces cellulose-anchored biofilm formation in Mycobacterium tuberculosis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Trivedi, Abhishek; Mavi, Parminder Singh; Bhatt, Deepak; Kumar, Ashwani

    2016-04-25

    Mycobacterium tuberculosis (Mtb) forms biofilms harbouring antibiotic-tolerant bacilli in vitro, but the factors that induce biofilm formation and the nature of the extracellular material that holds the cells together are poorly understood. Here we show that intracellular thiol reductive stress (TRS) induces formation of Mtb biofilms in vitro, which harbour drug-tolerant but metabolically active bacteria with unchanged levels of ATP/ADP, NAD+/NADH and NADP+/NADPH. The development of these biofilms requires DNA, RNA and protein synthesis. Transcriptional analysis suggests that Mtb modulates only similar to 7% of its genes for survival in biofilms. In addition to proteins, lipids and DNA, the extracellularmore » material in these biofilms is primarily composed of polysaccharides, with cellulose being a key component. Lastly, our results contribute to a better understanding of the mechanisms underlying Mtb biofilm formation, although the clinical relevance of Mtb biofilms in human tuberculosis remains unclear.« less

  11. Development of a Low Input and sustainable Switchgrass Feedstock Production System Utilizing Beneficial Bacterial Endophytes

    SciTech Connect (OSTI)

    Mei, Chuansheng; Nowak, Jerzy; Seiler, John

    2014-10-24

    Switchgrass represents a promising feedstock crop for US energy sustainability. However, its broad utilization for bioenergy requires improvements of biomass yields and stress tolerance. In this DOE funded project, we have been working on harnessing beneficial bacterial endophytes to enhance switchgrass performance and to develop a low input feedstock production system for marginal lands that do not compete with the production of food crops. We have demonstrated that one of most promising plant growth-promoting bacterial endophytes, Burkholderia phytofirmans strain PsJN, is able to colonize roots and significantly promote growth of switchgrass cv. Alamo under in vitro, growth chamber, greenhouse, as well as field conditions. Furthermore, PsJN bacterization improved growth and development of switchgrass seedlings, significantly stimulated plant root and shoot growth, and tiller number in the field, and enhanced biomass accumulation on both poor (p<0.001) and rich (p<0.05) soils, with more effective stimulation of plant growth in low fertility soil. Plant physiology measurements showed that PsJN inoculated Alamo had consistently lower transpiration, lower stomatal conductance, and higher water use efficiency in greenhouse conditions. These physiological changes may significantly contribute to the recorded growth enhancement. PsJN inoculation rapidly results in an increase in photosynthetic rates which contributes to the advanced growth and development. Some evidence suggests that this initial growth advantage decreases with time when resources are not limited such as in greenhouse studies. Additionally, better drought resistance and drought hardening were observed in PsJN inoculated switchgrass. Using the DOE-funded switchgrass EST microarray, in a collaboration with the Genomics Core Facility at the Noble Foundation, we have determined gene expression profile changes in both responsive switchgrass cv. Alamo and non-responsive cv. Cave-in-Rock (CR) following Ps

  12. Biofilm treatment of soil for waste containment and remediation

    SciTech Connect (OSTI)

    Turner, J.P.; Dennis, M.L.; Osman, Y.A.; Chase, J.; Bulla, L.A.

    1997-12-31

    This paper examines the potential for creating low-permeability reactive barriers for waste treatment and containment by treating soils with Beijerinckia indica, a bacterium which produces an exopolysaccharide film. The biofilm adheres to soil particles and causes a decrease in soil hydraulic conductivity. In addition, B. Indica biodegrades a variety of polycyclic aromatic hydrocarbons and chemical carcinogens. The combination of low soil hydraulic conductivity and biodegradation capabilities creates the potential for constructing reactive biofilm barriers from soil and bacteria. A laboratory study was conducted to evaluate the effects of B. Indica on the hydraulic conductivity of a silty sand. Soil specimens were molded with a bacterial and nutrient solution, compacted at optimum moisture content, permeated with a nutrient solution, and tested for k{sub sat} using a flexible-wall permeameter. Saturated hydraulic conductivity (k{sub sat}) was reduced from 1 x 10{sup -5} cm/sec to 2 x 10{sup -8} cm/sec: by biofilm treatment. Permeation with saline, acidic, and basic solutions following formation of a biofilm was found to have negligible effect on the reduced k{sub sat}, for up to three pore volumes of flow. Applications of biofilm treatment for creating low-permeability reactive barriers are discussed, including compacted liners for bottom barriers and caps and creation of vertical barriers by in situ treatment.

  13. In situ biofilm coupon device

    DOE Patents [OSTI]

    Peyton, Brent M.; Truex, Michael J.

    1997-01-01

    An apparatus for characterization of in-situ microbial biofilm populations in subsurface groundwater. The device permits biofilm-forming microorganisms to adhere to packing material while emplaced in a groundwater strata, so that the packing material can be later analyzed for quantity and type of microorganisms, growth rate, and nutrient requirements.

  14. In situ biofilm coupon device

    DOE Patents [OSTI]

    Peyton, B.M.; Truex, M.J.

    1997-06-24

    An apparatus is disclosed for characterization of in-situ microbial biofilm populations in subsurface groundwater. The device permits biofilm-forming microorganisms to adhere to packing material while emplaced in a groundwater strata, so that the packing material can be later analyzed for quantity and type of microorganisms, growth rate, and nutrient requirements. 3 figs.

  15. Adhesion and formation of microbial biofilms in complex microfluidic devices

    SciTech Connect (OSTI)

    Kumar, Aloke [ORNL; Karig, David K [ORNL; Neethirajan, Suresh [University of Guelph; Suresh, Anil K [ORNL; Srijanto, Bernadeta R [ORNL; Mukherjee, Partha P [ORNL; Retterer, Scott T [ORNL; Doktycz, Mitchel John [ORNL

    2012-01-01

    Shewanella oneidensis is a metal reducing bacterium, which is of interest for bioremediation and clean energy applications. S. oneidensis biofilms play a critical role in several situations such as in microbial energy harvesting devices. Here, we use a microfluidic device to quantify the effects of hydrodynamics on the biofilm morphology of S. oneidensis. For different rates of fluid flow through a complex microfluidic device, we studied the spatiotemporal dynamics of biofilms, and we quantified several morphological features such as spatial distribution, cluster formation and surface coverage. We found that hydrodynamics resulted in significant differences in biofilm dynamics. The baffles in the device created regions of low and high flow in the same device. At higher flow rates, a nonuniform biofilm develops, due to unequal advection in different regions of the microchannel. However, at lower flow rates, a more uniform biofilm evolved. This depicts competition between adhesion events, growth and fluid advection. Atomic force microscopy (AFM) revealed that higher production of extra-cellular polymeric substances (EPS) occurred at higher flow velocities.

  16. From Nanowires to Biofilms: An Exploration of Novel Mechanisms of Uranium Transformation Mediated by Geobacter Bacteria

    SciTech Connect (OSTI)

    REGUERA, GEMMA

    2014-01-16

    One promising strategy for the in situ bioremediation of radioactive groundwater contaminants that has been identified by the SBR Program is to stimulate the activity of dissimilatory metal-reducing microorganisms to reductively precipitate uranium and other soluble toxic metals. The reduction of U(VI) and other soluble contaminants by Geobacteraceae is directly dependent on the reduction of Fe(III) oxides, their natural electron acceptor, a process that requires the expression of Geobacter’s conductive pili (pilus nanowires). Expression of conductive pili by Geobacter cells leads to biofilm development on surfaces and to the formation of suspended biogranules, which may be physiological closer to biofilms than to planktonic cells. Biofilm development is often assumed in the subsurface, particularly at the matrix-well screen interface, but evidence of biofilms in the bulk aquifer matrix is scarce. Our preliminary results suggest, however, that biofilms develop in the subsurface and contribute to uranium transformations via sorption and reductive mechanisms. In this project we elucidated the mechanism(s) for uranium immobilization mediated by Geobacter biofilms and identified molecular markers to investigate if biofilm development is happening in the contaminated subsurface. The results provided novel insights needed in order to understand the metabolic potential and physiology of microorganisms with a known role in contaminant transformation in situ, thus having a significant positive impact in the SBR Program and providing novel concept to monitor, model, and predict biological behavior during in situ treatments.

  17. Three-Dimensional Imaging and Quantification of Biomass and Biofilms in Porous Media

    SciTech Connect (OSTI)

    Dorthe Wildenschild

    2012-10-10

    A new method to resolve biofilms in three dimensions in porous media using high-resolution synchrotron-based x-ray computed microtomography (CMT) has been developed. Imaging biofilms in porous media without disturbing the natural spatial arrangement of the porous media and associated biofilm has been a challenging task, primarily because porous media generally precludes conventional imaging via optical microscopy; x-ray tomography offers a potential alternative. One challenge for using this method is that most conventional x-ray contrast agents are water-soluble and easily diffuse into biofilms. To overcome this problem, silver-coated microspheres were added to the fluid phase to create an x-ray contrast that does not diffuse into the biofilm mass. Using this approach, biofilm imaging in porous media was accomplished with sufficient contrast to differentiate between the biomass- and fluid-filled pore spaces. The method was validated by using a two-dimensional micro-model flow cell where both light microscopy and CMT imaging were used to im age the biofilm. The results of this work has been published in Water Resources Research (Iltis et al., 2010). Additional work needs to be done to optimize this imaging approach, specifically, we find that the quality of the images are highly dependent on the coverage of the biofilm with Ag particles, - which means that we may have issues in dead-end pore space and for very low density (fluffy) biofilms. What we can image for certain with this technique is the biofilm surface that is well-connected to flow paths and thus well-supplied with nutrients etc.

  18. Diffusion in biofilms respiring on electrodes

    SciTech Connect (OSTI)

    Renslow, Ryan S.; Babauta, Jerome T.; Majors, Paul D.; Beyenal, Haluk

    2012-11-15

    The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (De) in biofilms respiring on electrodes. Two model electrochemically active biofilms, Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1, were investigated. A novel nuclear magnetic resonance microimaging perfusion probe capable of simultaneous electrochemical and pulsed-field gradient nuclear magnetic resonance (PFG-NMR) techniques was used. PFG-NMR allowed for noninvasive, nondestructive, high spatial resolution in situ De measurements in living biofilms respiring on electrodes. The electrodes were polarized so that they would act as the sole terminal electron acceptor for microbial metabolism. We present our results as both two-dimensional De heat maps and surface-averaged relative effective diffusion coefficient (Drs) depth profiles. We found that (1) Drs decreases with depth in G. sulfurreducens biofilms, following a sigmoid shape; (2) Drs at a given location decreases with G. sulfurreducens biofilm age; (3) average De and Drs profiles in G. sulfurreducens biofilms are lower than those in S. oneidensis biofilms—the G. sulfurreducens biofilms studied here were on average 10 times denser than the S. oneidensis biofilms; and (4) halting the respiration of a G. sulfurreducens biofilm decreases the De values. Density, reflected by De, plays a major role in the extracellular electron transfer strategies of electrochemically active biofilms.

  19. Nanoparticles to Mitigate Biofilm Growth. (Conference) | SciTech...

    Office of Scientific and Technical Information (OSTI)

    Nanoparticles to Mitigate Biofilm Growth. Citation Details In-Document Search Title: Nanoparticles to Mitigate Biofilm Growth. Abstract not provided. Authors: Altman, Susan Jeanne ...

  20. Spatial and temporal dynamics of cellulose degradation and biofilm formation by Caldicellulosiruptor obsidiansis and Clostridium thermocellum Caldicellulosiruptor obsidiansis

    SciTech Connect (OSTI)

    Wang, Zhiwu; Lee, Sueng-Hwan; Elkins, James G; Morrell-Falvey, Jennifer L

    2011-01-01

    Cellulose degradation is one of the major bottlenecks of a consolidated bioprocess that employs cellulolytic bacterial cells as catalysts to produce biofuels from cellulosic biomass. In this study, we investigated the spatial and temporal dynamics of cellulose degradation by Caldicellulosiruptor obsidiansis, which does not produce cellulosomes, and Clostridium thermocellum, which does produce cellulosomes. Results showed that the degradation of either regenerated or natural cellulose was synchronized with biofilm formation, a process characterized by the formation and fusion of numerous crater-like depressions on the cellulose surface. In addition, the dynamics of biofilm formation were similar in both bacteria, regardless of cellulosome production. Only the areas of cellulose surface colonized by microbes were significantly degraded, highlighting the essential role of the cellulolytic biofilm in cellulose utilization. After initial attachment, the microbial biofilm structure remained thin, uniform and dense throughout the experiment. A cellular automaton model, constructed under the assumption that the attached cells divide and produce daughter cells that contribute to the hydrolysis of the adjacent cellulose, can largely simulate the observed process of biofilm formation and cellulose degradation. This study presents a model, based on direct observation, correlating cellulolytic biofilm formation with cellulose degradation.

  1. Modeling for Anaerobic Fixed-Bed Biofilm Reactors

    SciTech Connect (OSTI)

    Liu, B. Y. M.; Pfeffer, J. T.

    1989-06-01

    The specific objectives of this research were: 1. to develop an equilibrium model for chemical aspects of anaerobic reactors; 2. to modify the equilibrium model for non-equilibrium conditions; 3. to incorporate the existing biofilm models into the models above to study the biological and chemical behavior of the fixed-film anaerobic reactors; 4. to experimentally verify the validity of these models; 5. to investigate the biomass-holding ability of difference packing materials for establishing reactor design criteria.

  2. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.; Prowant, Matthew S.; Nettleship, Ian; Addleman, Raymond S.; Bonheyo, George T.

    2015-12-07

    Here, the accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. Herein, a novel photographic method is described that uses biomolecular staining and image analysis to enhance contrast of early stage biofouling. A robust algorithm was developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs and results weremore » compared to independent measurements of cell density. Results from image analysis quantified biofilm growth intensity accurately and with approximately the same precision of the more laborious cell counting method. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field. Broad spectrum staining highlights fouling biomass, photography quickly captures a large area of interest, and image analysis rapidly quantifies fouling in the image.« less

  3. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

    SciTech Connect (OSTI)

    Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.; Prowant, Matthew S.; Nettleship, Ian; Addleman, Raymond S.; Bonheyo, George T.

    2015-12-07

    Here, the accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. Herein, a novel photographic method is described that uses biomolecular staining and image analysis to enhance contrast of early stage biofouling. A robust algorithm was developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs and results were compared to independent measurements of cell density. Results from image analysis quantified biofilm growth intensity accurately and with approximately the same precision of the more laborious cell counting method. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field. Broad spectrum staining highlights fouling biomass, photography quickly captures a large area of interest, and image analysis rapidly quantifies fouling in the image.

  4. DEVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

    SciTech Connect (OSTI)

    Bill W. Bogan; Brigid M. Lamb; Gemma Husmillo; Kristine Lowe; J. Robert Paterek; John J. Kilbane II

    2004-12-01

    The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Various chemicals that inhibit the growth and/or the metabolism of corrosion-associated microbes such as sulfate reducing bacteria, denitrifying bacteria, and methanogenic bacteria were evaluated to determine their ability to inhibit corrosion in experiments utilizing pure and mixed bacterial cultures, and planktonic cultures as well as mature biofilms. Planktonic cultures are easier to inhibit than mature biofilms but several compounds were shown to be effective in decreasing the amount of metal corrosion. Of the compounds tested hexane extracts of Capsicum pepper plants and molybdate were the most effective inhibitors of sulfate reducing bacteria, bismuth nitrate was the most effective inhibitor of nitrate reducing bacteria, and 4-((pyridine-2-yl)methylamino)benzoic acid (PMBA) was the most effective inhibitor of methanogenic bacteria. All of these compounds were demonstrated to minimize corrosion due to MIC, at least in some circumstances. The results obtained in this project are consistent with the hypothesis that any compound that disrupts the metabolism of any of the major microbial groups present in corrosion-associated biofilms shows promise in limiting the amount/rate of corrosion. This approach of controlling MIC by controlling the metabolism of biofilms is more environmentally benign than the current approach involving the use of potent biocides, and warrants further investigation.

  5. Resisting Bacterial Resistance

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Resisting Bacterial Resistance 1663 Los Alamos science and technology magazine Latest Issue:July 2016 past issues All Issues » submit Resisting Bacterial Resistance Los Alamos scientists are taking an in-depth look at how bacteria defeat death-by-antibiotics. March 8, 2016 Artist rendering of green bacteria Gram-negative bacteria have evolved multiple strategies for self-defense-including mechanisms to pump out any molecules that could kill them, such as antibiotics. "We want to ensure

  6. Annual progress Report on research related to our research project Stabilization of Plutonium in Subsurface Environments via Microbial Reduction and Biofilm Formation funded by the Environmental Remediation Sciences Division (ERSD)

    SciTech Connect (OSTI)

    New, Mary

    2006-06-01

    The overarching goal of this research project is to investigate and optimize the mechanisms for in situ immobilization of Pu species by naturally-occurring bacteria. Specific research objectives are: (a) investigate the mechanism of bacterial accumulation and immobilization of plutonium species by biofilm formation under aerobic conditions and (b) to demonstrate the direct and indirect stabilization of Pu via dissimilatory reduction by Geobacter metallireducens.

  7. Bacterial extracellular lignin peroxidase

    DOE Patents [OSTI]

    Crawford, Donald L. (Moscow, ID); Ramachandra, Muralidhara (Moscow, ID)

    1993-01-01

    A newly discovered lignin peroxidase enzyme is provided. The enzyme is obtained from a bacterial source and is capable of degrading the lignin portion of lignocellulose in the presence of hydrogen peroxide. The enzyme is extracellular, oxidative, inducible by lignin, larch wood xylan, or related substrates and capable of attacking certain lignin substructure chemical bonds that are not degradable by fungal lignin peroxidases.

  8. Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; Regan, John M.; Mench, Matthew M.

    2016-08-15

    This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions inmore » a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Lastly, simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.« less

  9. Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

    SciTech Connect (OSTI)

    Wang, Jianjun; Shen, Jianhaua; Wu, Yucheng; Tu, Chen; Soininen , Janne; Stegen, James C.; He, Jizheng; Liu, Xingqi; Zhang, Lu; Zhang, Enlou

    2013-02-28

    Increasing evidence emerged for non-random spatial distributions for microbes, but the underlying processes resulting in microbial assemblage variation among and within Earths ecosystems is still lacking. For instance, some studies showed that the deterministic processes by habitat specialization are important, while other studies hold that bacterial communities are assembled by neutral forces. Here we examine the relative importance of deterministic and stochastic processes for bacterial communities from subsurface environments, as well as stream biofilm, lake water, lake sediment and soil using pyrosequencing of 16S rRNA gene. We show that there is a general pattern in phylogenetic signal in species niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups, and for three sample groups, that spatial distance reflects unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight

  10. A biofilm microreactor system for simultaneous electrochemical and nuclear magnetic resonance techniques

    SciTech Connect (OSTI)

    Renslow, Ryan S.; Babauta, Jerome T.; Majors, Paul D.; Mehta, Hardeep S.; Ewing, R. James; Ewing, Thomas; Mueller, Karl T.; Beyenal, Haluk

    2014-03-01

    In order to fully understand electrochemically active biofilms and the limitations to their scale-up in industrial biofilm reactors, a complete picture of the microenvironments inside the biofilm is needed. Nuclear magnetic resonance (NMR) techniques are ideally suited for the study of biofilms and for probing their microenvironments because these techniques allow for non-invasive interrogation and in situ monitoring with high resolution. By combining NMR with simultaneous electrochemical techniques, it is possible to sustain and study live electrochemically active biofilms. Here, we introduce a novel biofilm microreactor system that allows for simultaneous electrochemical and NMR techniques (EC-NMR) at the microscale. Microreactors were designed with custom radiofrequency resonator coils, which allowed for NMR measurements of biofilms growing on polarized gold electrodes. For an example application of this system, we grew Geobacter sulfurreducens biofilms. NMR was used to investigate growth media flow velocities, which were compared to simulated laminar flow, and electron donor concentrations inside the biofilms. We use Monte Carlo error analysis to estimate standard deviations of the electron donor concentration measurements within the biofilm. The EC-NMR biofilm microreactor system can ultimately be used to correlate extracellular electron transfer rates with metabolic reactions and explore extracellular electron transfer mechanisms.

  11. LATERAL GENE TRANSFER AND THE HISTORY OF BACTERIAL GENOMES

    SciTech Connect (OSTI)

    Howard Ochman

    2006-02-22

    The aims of this research were to elucidate the role and extent of lateral transfer in the differentiation of bacterial strains and species, and to assess the impact of gene transfer on the evolution of bacterial genomes. The ultimate goal of the project is to examine the dynamics of a core set of protein-coding genes (i.e., those that are distributed universally among Bacteria) by developing conserved primers that would allow their amplification and sequencing in any bacterial taxa. In addition, we adopted a bioinformatic approach to elucidate the extent of lateral gene transfer in sequenced genome.

  12. In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS

    SciTech Connect (OSTI)

    Hua, Xin; Yu, Xiao-Ying; Wang, Zhaoying; Yang, Li; Liu, Bingwen; Zhu, Zihua; Tucker, Abigail E.; Chrisler, William B.; Hill, Eric A.; Thevuthasan, Suntharampillai; Lin, Yuehe; Liu, Songqin; Marshall, Matthew J.

    2014-02-26

    The first results of using a novel single channel microfluidic reactor to enable Shewanella biofilm growth and in situ characterization using time-of-flight secondary ion mass spectrometry (ToF-SIMS) in the hydrated environment are presented. The new microfluidic interface allows direct probing of the liquid surface using ToF-SIMS, a vacuum surface technique. The detection window is an aperture of 2 m in diameter on a thin silicon nitride (SiN) membrane and it allows direct detection of the liquid surface. Surface tension of the liquid flowing inside the microchannel holds the liquid within the aperture. ToF-SIMS depth profiling was used to drill through the SiN membrane and the biofilm grown on the substrate. In situ 2D imaging of the biofilm in hydrated state was acquired, providing spatial distribution of the chemical compounds in the biofilm system. This data was compared with a medium filled microfluidic reactor devoid of biofilm and dried biofilm samples deposited on clean silicon wafers. Principle Component Analysis (PCA) was used to investigate these observations. Our results show that imaging biofilms in the hydrated environment using ToF-SIMS is possible using the unique microfluidic reactor. Moreover, characteristic biofilm fatty acids fragments were observed in the hydrated biofilm grown in the microfluidic channel, illustrating the advantage of imaging biofilm in its native environment.

  13. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known...

  14. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the...

  15. Visualization of Bacterial Microcompartment Facet Assembly Using...

    Office of Scientific and Technical Information (OSTI)

    Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy Prev Next Title: Visualization of Bacterial Microcompartment Facet ...

  16. Direct measurement and characterization of active photosynthesis zones inside biofuel producing and wastewater remediating microalgal biofilms

    SciTech Connect (OSTI)

    Bernstein, Hans C.; Kesaano, Maureen; Moll, Karen; Smith, Terence; Gerlach, Robin; Carlson, Ross; Miller, Charles D.; Peyton, Brent; Cooksey, Keith; Gardner, Robert D.; Sims, Ronald C.

    2014-03-01

    Abstract: Microalgal biofilm based technologies are of keen interest due to their high biomass concentrations and ability to utilize renewable resources, such as light and CO2. While photoautotrophic biofilms have long been used for wastewater remediation applications, biofuel production represents a relatively new and under-represented focus area. However, the direct measurement and characterization of fundamental parameters required for physiological analyses are challenging due to biofilm heterogeneity. This study evaluated oxygenic photosynthesis and biofuel precursor molecule production using a novel rotating algal biofilm reactor (RABR) operated at field- and laboratory-scales for wastewater remediation and biofuel production, respectively. Clear differences in oxygenic-photosynthesis, respiration and biofuel-precursor capacities were observed between the two systems and different conditions based on light and nitrogen availability. Nitrogen depletion was not found to have the same effect on lipid accumulation compared to prior planktonic studies. Physiological characterizations of these microalgal biofilms identify potential areas for future process optimization.

  17. Activated ClpP kills persisters and eradicates a chronic biofilm infection.

    SciTech Connect (OSTI)

    Conlon, Brian P.; Nakayasu, Ernesto S.; Fleck, Laura E.; LaFleur, Michael D.; Isabella, Vincent M.; Coleman, K.; Leonard, Steve N.; Smith, Richard D.; Adkins, Joshua N.; Lewis, Kim

    2013-11-21

    The current antibiotic crisis stems from two distinct phenomena-drug resistance, and drug tolerance. Resistance mechanisms such as drug efflux or modification prevent antibiotics from binding to their targets 1, allowing pathogens to grow. Antibiotic tolerance is the property of persister cells, phenotypic variants of regular bacteria 2. Antibiotics kill by corrupting targets, but these are inactive in dormant persisters, leading to tolerance. Persisters were first identified by Joseph Bigger in 1944, when he discovered a surviving sub-population of Staphylococcus following treatment with penicillin3. Persisters are largely responsible for recalcitrance of chronic diseases such as tuberculosis, and various infections associated with biofilms - endocarditis, osteomyelitis, infections of catheters and indwelling devices, and deep-seated infections of soft tissues 4. There are a number of redundant pathways involved in persister formation5,6 precluding development of drugs inhibiting their formation. The acyldepsipeptide antibiotic (ADEP 4) has been shown to activate the ClpP protease resulting in death of growing cells 7. Here we show that ADEP4 activated ClpP becomes a fairly non-specific protease and kills persister cells by degradation of over 400 intracellular targets. clpP mutants are resistant to ADEP4 7, but we find that they display increased susceptibility to killing by a range of conventional antibiotics. Combining ADEP4 with rifampicin leads to eradication of persisters, stationary and biofilm populations of Staphylococcus aureus in vitro and in a deep-seated murine infection. Target corruption/activation provides an approach to killing persisters and eradicating chronic infections.

  18. Molecular Characterization of Bacterial Respiration on Minerals

    SciTech Connect (OSTI)

    Blake, Robert C.

    2013-04-26

    The overall aim of this project was to contribute to our fundamental understanding of proteins and biological processes under extreme environmental conditions. We sought to define the biochemical and physiological mechanisms that underlie biodegradative and other cellular processes in normal, extreme, and engineered environments. Toward that end, we sought to understand the substrate oxidation pathways, the electron transport mechanisms, and the modes of energy conservation employed during respiration by bacteria on soluble iron and insoluble sulfide minerals. In accordance with these general aims, the specific aims were two-fold: To identify, separate, and characterize the extracellular biomolecules necessary for aerobic respiration on iron under strongly acidic conditions; and to elucidate the molecular principles whereby these bacteria recognize and adhere to their insoluble mineral substrates under harsh environmental conditions. The results of these studies were described in a total of nineteen manuscripts. Highlights include the following: 1. The complete genome of Acidithiobacillus ferrooxidans ATCC 23270 (type strain) was sequenced in collaboration with the DOE Joint Genome Institute; 2. Genomic and mass spectrometry-based proteomic methods were used to evaluate gene expression and in situ microbial activity in a low-complexity natural acid mine drainage microbial biofilm community. This was the first effort to successfully analyze a natural community using these techniques; 3. Detailed functional and structural studies were conducted on rusticyanin, an acid-stable electron transfer protein purified from cell-free extracts of At. ferrooxidans. The three-dimensional structure of reduced rusticyanin was determined from a combination of homonuclear proton and heteronuclear 15N- and 13C-edited NMR spectra. Concomitantly, the three-dimensional structure of oxidized rusticyanin was determined by X-ray crystallography to a resolution of 1.9 A by multiwavelength

  19. Magnetic microbes: Bacterial magnetite biomineralization

    SciTech Connect (OSTI)

    Prozorov, Tanya

    2015-09-14

    Magnetotactic bacteria are a diverse group of prokaryotes with the ability to orient and migrate along the magnetic field lines in search for a preferred oxygen concentration in chemically stratified water columns and sediments. These microorganisms produce magnetosomes, the intracellular nanometer-sized magnetic crystals surrounded by a phospholipid bilayer membrane, typically organized in chains. Magnetosomes have nearly perfect crystal structures with narrow size distribution and species-specific morphologies, leading to well-defined magnetic properties. As a result, the magnetite biomineralization in these organisms is of fundamental interest to diverse disciplines, from biotechnology to astrobiology. As a result, this article highlights recent advances in the understanding of the bacterial magnetite biomineralization.

  20. Biosynthesis and structural characterization of silver nanoparticles from bacterial isolates

    SciTech Connect (OSTI)

    Zaki, Sahar; El Kady, M.F.; Abd-El-Haleem, Desouky

    2011-10-15

    Graphical abstract: In this study five bacterial isolates belong to different genera were found to be able to biosynthesize silver nanoparticles. Biosynthesis and spectral characterization are reported here. Highlights: {yields} About 300 bacterial isolates were screened for their ability to produce nanosilvers {yields} Five of them were potential candidates for synthesis of silver nanoparticles {yields} Production of silver nanoparticles was examined using UV-Vis, XRD, SEM and EDS. {yields} The presence of nanoparticles with all five bacterial isolates was confirmed. -- Abstract: This study aimed to develop a green process for biosynthesis of silver nanomaterials by some Egyptian bacterial isolates. This target was achieved by screening an in-house culture collection consists of 300 bacterial isolates for silver nanoparticle formation. Through screening process, it was observed that strains belonging to Escherichia coli (S30, S78), Bacillus megaterium (S52), Acinetobacter sp. (S7) and Stenotrophomonas maltophilia (S54) were potential candidates for synthesis of silver nanoparticles. The extracellular production of silver nanoparticles by positive isolates was investigated by UV-Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results demonstrated that UV-visible spectrum of the aqueous medium containing silver ion showed a peak at 420 nm corresponding to the plasmon absorbance of silver nanoparticles. Scanning electron microscopy micrograph showed formation of silver nanoparticles in the range of 15-50 nm. XRD-spectrum of the silver nanoparticles exhibited 2{theta} values corresponding to the silver nanocrystal that produce in hexagonal and cubic crystal configurations with different plane of orientation. In addition, the signals of the silver atoms were observed by EDS-spectrum analysis that confirms the presence of silver nanoparticles (Ag

  1. Bacterial Population Genetics in a Forensic Context

    SciTech Connect (OSTI)

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations augmented by phylogenetic representations

  2. Natural bacterial communities serve as quantitative geochemical...

    Office of Scientific and Technical Information (OSTI)

    approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior...

  3. Magnetic microbes: Bacterial magnetite biomineralization

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Prozorov, Tanya

    2015-09-14

    Magnetotactic bacteria are a diverse group of prokaryotes with the ability to orient and migrate along the magnetic field lines in search for a preferred oxygen concentration in chemically stratified water columns and sediments. These microorganisms produce magnetosomes, the intracellular nanometer-sized magnetic crystals surrounded by a phospholipid bilayer membrane, typically organized in chains. Magnetosomes have nearly perfect crystal structures with narrow size distribution and species-specific morphologies, leading to well-defined magnetic properties. As a result, the magnetite biomineralization in these organisms is of fundamental interest to diverse disciplines, from biotechnology to astrobiology. As a result, this article highlights recent advances inmore » the understanding of the bacterial magnetite biomineralization.« less

  4. 3D Reconstruction of Biological Organization and Mineralization in Sediment Attached Biofilms During Uranium Bioremediation

    SciTech Connect (OSTI)

    Banfield, Jillian; Comolli, Luis R.; Singer, Steve

    2014-11-17

    development of a platform for routine correlative cryogenic microscopy and spectroscopy with samples prepared on-site. 2) The determination of which organisms dominate planktonic and biofilm communities in the subsurface. 3) Identification of microorganism-mineral associations and discovery of a novel mechanism that sustains activity of iron-reducing bacteria. 4) The detection of bacteria from the OP11-OD1-WWE3 (etc.) radiation and elucidation of their remarkable structural organization by cryog-TEM cryo-electron tomograhpy (cryo-ET). 5) Extensive analysis of biofilms and documentation of the association of cells and Se minerals. 6) The comparison of expressed c-type cytochromes between pure cultures of G. bemidjiensis and related field populations, provided insight into possible molecular mechanisms for U(VI) reduction in the aquifer. At least sixteen publications will result from this project (partial support), which provide both graduate student and post doctoral training.

  5. Characterization of Biofilm in 200W Fluidized Bed Reactors

    SciTech Connect (OSTI)

    Lee, Michelle H.; Saurey, Sabrina D.; Lee, Brady D.; Parker, Kent E.; Eisenhauer, Emalee ER; Cordova, Elsa A.; Golovich, Elizabeth C.

    2014-09-29

    Contaminated groundwater beneath the 200 West Area at the Hanford Site in Southeast Washington is currently being treated using a pump and treat system to remove organics, inorganics, radionuclides, and metals. A granular activated carbon-based fluidized bed reactor (FBR) has been added to remove nitrate, hexavalent chromium and carbon tetrachloride. Initial analytical results indicated the microorganisms effectively reduced many of the contaminants to less than cleanup levels. However shortly thereafter operational upsets of the FBR include carbon carry over, over production of microbial extracellular polymeric substance (biofilm) materials, and over production of hydrogen sulfide. As a result detailed investigations were undertaken to understand the functional diversity and activity of the microbial community present in the FBR over time. Molecular analyses including terminal restriction fragment length polymorphism analysis, quantitative polymerase chain reaction and fluorescent in situ hybridization analyses were performed on the microbial community extracted from the biofilm within the bed and from the inoculum, to determine functional dynamics of the FBR bed over time and following operational changes. Findings from these analyses indicated: 1) the microbial community within the bed was completely different than community used for inoculation, and was likely from the groundwater; 2) analyses early in the testing showed an FBR community dominated by a few Curvibacter and Flavobacterium species; 3) the final sample taken indicated that the microbial community in the FBR bed had become more diverse; and 4) qPCR analyses indicated that bacteria involved in nitrogen cycling, including denitrifiers and anaerobic ammonia oxidizing bacteria, were dominant in the bed. These results indicate that molecular tools can be powerful for determining functional diversity within FBR type reactors. Coupled with micronutrient, influent and effluent chemistry evaluations, a more

  6. Mechanisms of bacterially catalyzed reductive dehalogenation

    SciTech Connect (OSTI)

    Picardal, F.W.

    1992-12-31

    Nine bacteria were tested for the ability to dehalogenate tetrachloromethane (CT), tetrachloroethene (PCE), and 1, 1, 1-trichloroethane (TCA) under anaerobic conditions. Three bacteria were able to reductively dehalogenate CT. Dehalogenation ability was not readily linked to a common metabolism or changes in culture redox potential. None of the bacteria tested were able to dehalogenate PCE or TCA. One of the bacteria capable of dehalogenating CT, Shewanella putrefaciens, was chosen as a model organism to study mechanisms of bacterially catalyzed reductive dehalogenation. The effect of a variety of alternate electron acceptors on CT dehalogenation ability by S. putrefaciens was determined. oxygen and nitrogen oxides were inhibitory but Fe (III), trimethylamine oxide, and fumarate were not. A model of the electron transport chain of S. putrefaciens was developed to explain inhibition patterns. A period of microaerobic growth prior to CT exposure increased the ability of S. putrefaciens to dehalogenate CT. A microaerobic growth period also increased cytochrome concentrations. A relationship between cytochrome content and dehalogenation ability was developed from studies in which cytochrome concentrations in S. putrefaciens were manipulated by changing growth conditions. Stoichiometry studies using {sup 14}C-CT suggested that CT was first reduced to form a trichloromethyl radical. Reduction of the radical to produce chloroform and reaction of the radical with cellular biochemicals explained observed product distributions. Carbon dioxide or other fully dehalogenated products were not found.

  7. Radionuclide scintigraphy of bacterial nephritis

    SciTech Connect (OSTI)

    Conway, J.J.; Weiss, S.C.; Shkolnik, A.; Yogev, R.; Firlit, C.; Traisman, E.S.

    1984-01-01

    Pyelonephritis is a leading cause of renal failure and is expected to cost as much as three billion dollars in 1984. The diagnosis of urinary tract infection is usually not difficult. However, localization of the infection within the renal parenchyma as opposed to the collecting system is much more difficult. Flank pain, fever, bacteiuria and evidence of parenchymal involvement by intravenous urography may be absent or unrecognized particularly in the infant. Ultrasound and Nuclear Medicine are advocated as better methods to define parenchymal involvement. Such definition is important in the consideration of treatment since parenchymal involvement of the kidney carries a much more ominous potential outcome than infection restricted to within the collecting system. 38 children with a clinical diagnosis of urinary tract infection were studied. 26 of the patients demonstrated abnormal renal parenchymal findings with Gallium-67 Citrate or Tc-99m Glucoheptonate scintigraphy. Intravenous urography was notably ineffective with only 5 of the 20 interpreted as abnormal due to parenchymal disease or decreased function. 11 were entirely normal while only 5 demonstrated scars or hydronephrosis. Only 10 of 17 patients demonstrated intranvesicoureteral reflux on x-ray or nuclear cystography. Ultrasound depicted 6 of 20 patients as having parenchymal abnormalities. Seven were normal. Nonspecific findings such as dilitation of the renal pelvis or renal enlargement was noted in 11 of the 20 patients. Radionuclide Scintigraphy is the most efficacious modality to detect since acute bacterial nephritis.

  8. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA

  9. Bacterial Cellulose Composites Opportunities and Challenges

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    x 10 -7 K -1 ), High Aspect Ratio (50) Nano-sized: Interesting Optical & Barrier ... June 26, 2012 3 Leonard.Fifield@PNNL.gov Bacterial Cellulose in Polymer Composites Nano ...

  10. Harnessing the Bacterial Power of Nanomagnets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Harnessing the Bacterial Power of Nanomagnets Harnessing the Bacterial Power of Nanomagnets Print Wednesday, 30 September 2009 00:00 Nanometer-size magnets have wide-ranging uses, from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of nanoparticles with well-controlled size and tunable magnetic properties. The synthesis of such nanomagnets, however, often requires elevated temperatures and toxic solvents,

  11. 3D Imaging of Microbial Biofilms: Integration of Synchrotron Imaging and an Interactive Visualization Interface

    SciTech Connect (OSTI)

    Thomas, Mathew; Marshall, Matthew J.; Miller, Erin A.; Kuprat, Andrew P.; Kleese van Dam, Kerstin; Carson, James P.

    2014-08-26

    Understanding the interactions of structured communities known as “biofilms” and other complex matrixes is possible through the X-ray micro tomography imaging of the biofilms. Feature detection and image processing for this type of data focuses on efficiently identifying and segmenting biofilms and bacteria in the datasets. The datasets are very large and often require manual interventions due to low contrast between objects and high noise levels. Thus new software is required for the effectual interpretation and analysis of the data. This work specifies the evolution and application of the ability to analyze and visualize high resolution X-ray micro tomography datasets.

  12. Lessons Learned from Bacterial Transport Experiments at the South Oyster Site

    SciTech Connect (OSTI)

    Scheibe, Timothy D; Hubbard, Susan S; Onstott, Tullis C; Deflaun, Mary F

    2011-09-27

    This paper provides a high-level review of bacterial transport experiments conducted by a multi-investigator, multi-institution, multi-disciplinary team of researchers under the auspices of the U. S. Department of Energy. The experiments considered were conducted during the time period 1999-2001 at a field site near the town of Oyster, Virginia known as the South Oyster Site, and included four major experimental campaigns aimed at understanding and quantifying bacterial transport in the subsurface environment. Several key elements of the research are discussed here: 1) Quantification of bacterial transport in physically and biogeochemically heterogeneous aquifers, 2) evaluation of the efficacy of conventional colloid filtration theory, 3) scale effects in bacterial transport, 4) development of new methods for microbial enumeration and screening for low adhesion strains, 5) application of novel hydrogeophysical techniques for aquifer characterization, and 6) experiences regarding management of a large field research effort.

  13. PEROXOTITANATE- AND MONOSODIUM METAL-TITANATE COMPOUNDS AS INHIBITORS OF BACTERIAL GROWTH

    SciTech Connect (OSTI)

    Hobbs, D.

    2011-01-19

    Sodium titanates are ion-exchange materials that effectively bind a variety of metal ions over a wide pH range. Sodium titanates alone have no known adverse biological effects but metal-exchanged titanates (or metal titanates) can deliver metal ions to mammalian cells to alter cell processes in vitro. In this work, we test a hypothesis that metal-titanate compounds inhibit bacterial growth; demonstration of this principle is one prerequisite to developing metal-based, titanate-delivered antibacterial agents. Focusing initially on oral diseases, we exposed five species of oral bacteria to titanates for 24 h, with or without loading of Au(III), Pd(II), Pt(II), and Pt(IV), and measuring bacterial growth in planktonic assays through increases in optical density. In each experiment, bacterial growth was compared with control cultures of titanates or bacteria alone. We observed no suppression of bacterial growth by the sodium titanates alone, but significant (p < 0.05, two-sided t-tests) suppression was observed with metal-titanate compounds, particularly Au(III)-titanates, but with other metal titanates as well. Growth inhibition ranged from 15 to 100% depending on the metal ion and bacterial species involved. Furthermore, in specific cases, the titanates inhibited bacterial growth 5- to 375-fold versus metal ions alone, suggesting that titanates enhanced metal-bacteria interactions. This work supports further development of metal titanates as a novel class of antibacterials.

  14. Investigations of Structure and Metabolism within Shewanella oneidensis MR-1 Biofilms

    SciTech Connect (OSTI)

    Mclean, Jeffrey S.; Majors, Paul D.; Reardon, Catherine L.; Bilskis, Christina L.; Reed, Samantha B.; Romine, Margaret F.; Fredrickson, Jim K.

    2008-07-01

    Biofilms are known to possess spatially and temporally varying metabolite concentration profiles at the macroscopic and microscopic scales. This results in varying growth environments within that may ultimately drive species diversity, determine biofilm structure and also the spatial arrangement of the community members. Using noninvasive nuclear magnetic resonance (NMR) microscopic imaging/spectroscopy and confocal imaging, we investigated anaerobic reduction kinetics, structural variation, and the stratification of metabolism within live biofilms of the facultative anaerobic dissimilatory metal-reducing Shewanella oneidensis strain MR-1. Biofilms were pregrown using a defined minimal media in a homebuilt constant depth film fermenter and subsequently transferred to an in-magnet sample chamber under laminar flow for NMR measurements. The sample was subjected to various, rapidly switched substrate/ anaerobic electron acceptor combinations (fumarate, dimethyl sulfoxide, and nitrate electron acceptors). Localized NMR spectroscopy was used to non-invasively monitored the spectra of hydrogen-containing metabolites at high temporal resolution (4.5 min) under oxygen-limited conditions. Anaerobic reduction was immediately observed upon switching feed solutions indicate that no gene induction (transcriptional response) was needed for MR-1 to switch between fumarate, dimethyl sulfoxide (DMSO) and nitrate electron acceptors. In parallel experiments, confocal microscopy was used with constitutively expressed fluorescent reporters to independently investigate structural changes in response to the availability of electron acceptor and also the outcome of metabolic competition under oxygen-limited conditions. A clearer understanding of the metabolic diversity and plasticity of the biofilm mode of growth as well as how this possibly translates to the environmental fitness is made possible through the use of non-invasive and non-destructive techniques such as described here.

  15. Synthetic analogs of bacterial quorum sensors

    DOE Patents [OSTI]

    Iyer, Rashi S.; Ganguly, Kumkum; Silks, Louis A.

    2013-01-08

    Bacterial quorum-sensing molecule analogs having the following structures: ##STR00001## and methods of reducing bacterial pathogenicity, comprising providing a biological system comprising pathogenic bacteria which produce natural quorum-sensing molecule; providing a synthetic bacterial quorum-sensing molecule having the above structures and introducing the synthetic quorum-sensing molecule into the biological system comprising pathogenic bacteria. Further is provided a method of targeted delivery of an antibiotic, comprising providing a synthetic quorum-sensing molecule; chemically linking the synthetic quorum-sensing molecule to an antibiotic to produce a quorum-sensing molecule-antibiotic conjugate; and introducing the conjugate into a biological system comprising pathogenic bacteria susceptible to the antibiotic.

  16. Synthetic analogs of bacterial quorum sensors

    DOE Patents [OSTI]

    Iyer, Rashi; Ganguly, Kumkum; Silks, Louis A.

    2011-12-06

    Bacterial quorum-sensing molecule analogs having the following structures: ##STR00001## and methods of reducing bacterial pathogenicity, comprising providing a biological system comprising pathogenic bacteria which produce natural quorum-sensing molecule; providing a synthetic bacterial quorum-sensing molecule having the above structures and introducing the synthetic quorum-sensing molecule into the biological system comprising pathogenic bacteria. Further is provided a method of targeted delivery of an antibiotic, comprising providing a synthetic quorum-sensing molecule; chemically linking the synthetic quorum-sensing molecule to an antibiotic to produce a quorum-sensing molecule-antibiotic conjugate; and introducing the conjugate into a biological system comprising pathogenic bacteria susceptible to the antibiotic.

  17. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  18. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  19. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  20. Developing a low input and sustainable switchgrass feedstock production

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    system utilizing beneficial bacterial endophytes | Department of Energy Developing a low input and sustainable switchgrass feedstock production system utilizing beneficial bacterial endophytes Developing a low input and sustainable switchgrass feedstock production system utilizing beneficial bacterial endophytes Dr. Chuansheng Mei gave this presentation at the Symbiosis Conference. symbiosis_conference_mei.pdf (2.47 MB) More Documents & Publications Symbiosis Biofeedstock Conference:

  1. Gamma-irradiated bacterial preparation having anti-tumor activity

    DOE Patents [OSTI]

    Vass, Arpad A.; Tyndall, Richard L.; Terzaghi-Howe, Peggy

    1999-01-01

    A bacterial preparation from Pseudomonas species isolated #15 ATCC 55638 that has been exposed to gamma radiation exhibits cytotoxicity that is specific for neoplastic carcinoma cells. A method for obtaining a bacterial preparation having antitumor activity consists of suspending a bacterial isolate in media and exposing the suspension to gamma radiation. A bacterial preparation of an aged culture of an amoeba-associated bacteria exhibits anti-reverse transcriptase activity. A method for obtaining a bacterial preparation having anti-reverse transcriptase activity from an amoeba-associated bacterial isolate grown to stationary phase is disclosed.

  2. A New Link Between Human and Bacterial Signaling Machinery

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A New Link Between Human and Bacterial Signaling Machinery A New Link Between Human and Bacterial Signaling Machinery Print Tuesday, 19 August 2014 10:34 The human immune system...

  3. Selenium Speciation in Biofilms from Granular Sludge Bed Reactors Used for Wastewater Treatment

    SciTech Connect (OSTI)

    van Hullenbusch, Eric; Farges, Francois; Lenz, Markus; Lens, Piet; Brown, Gordon E., Jr.; /Stanford U., Geo. Environ. Sci. /SLAC, SSRL

    2006-12-13

    Se K-edge XAFS spectra were collected for various model compounds of Se as well as for 3 biofilm samples from bioreactors used for Se-contaminated wastewater treatment. In the biofilm samples, Se is dominantly as Se(0) despite Se K-edge XANES spectroscopy cannot easily distinguish between elemental Se and Se(-I)-bearing selenides. EXAFS spectra indicate that Se is located within aperiodic domains, markedly different to these known in monoclinic red selenium. However, Se can well occur within nanodivided domains related to monoclinic red Se, as this form was optically observed at the rim of some sludges. Aqueous selenate is then efficiently bioreduced, under sulfate reducing and methanogenic conditions.

  4. Selenium Speciation in Biofilms from Granular Sludge Bed Reactors Used for Wastewater Treatment

    SciTech Connect (OSTI)

    Hullenbusch, Eric van; Farges, Francois; Lenz, Markus; Lens, Piet; Brown, Gordon E. Jr.

    2007-02-02

    Se K-edge XAFS spectra were collected for various model compounds of Se as well as for 3 biofilm samples from bioreactors used for Se-contaminated wastewater treatment. In the biofilm samples, Se is dominantly as Se(0) despite Se K-edge XANES spectroscopy cannot easily distinguish between elemental Se and Se(-I)-bearing selenides. EXAFS spectra indicate that Se is located within aperiodic domains, markedly different to these known in monoclinc red selenium. However, Se can well occur within nanodivided domains related to monoclinic red Se, as this form was optically observed at the rim of some sludges. Aqueous selenate is then efficiently bioreduced, under sulfate reducing and methanogenic conditions.

  5. Developing a low input and sustainable switchgrass feedstock...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Developing a low input and sustainable switchgrass feedstock production system utilizing beneficial bacterial endophytes Developing a low input and sustainable switchgrass ...

  6. Harnessing the Bacterial Power of Nanomagnets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Harnessing the Bacterial Power of Nanomagnets Print Nanometer-size magnets have wide-ranging uses, from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of nanoparticles with well-controlled size and tunable magnetic properties. The synthesis of such nanomagnets, however, often requires elevated temperatures and toxic solvents, resulting in high environmental and energy costs. Metal-reducing microorganisms

  7. Harnessing the Bacterial Power of Nanomagnets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Harnessing the Bacterial Power of Nanomagnets Print Nanometer-size magnets have wide-ranging uses, from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of nanoparticles with well-controlled size and tunable magnetic properties. The synthesis of such nanomagnets, however, often requires elevated temperatures and toxic solvents, resulting in high environmental and energy costs. Metal-reducing microorganisms

  8. Harnessing the Bacterial Power of Nanomagnets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Harnessing the Bacterial Power of Nanomagnets Print Nanometer-size magnets have wide-ranging uses, from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of nanoparticles with well-controlled size and tunable magnetic properties. The synthesis of such nanomagnets, however, often requires elevated temperatures and toxic solvents, resulting in high environmental and energy costs. Metal-reducing microorganisms

  9. Harnessing the Bacterial Power of Nanomagnets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Harnessing the Bacterial Power of Nanomagnets Print Nanometer-size magnets have wide-ranging uses, from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of nanoparticles with well-controlled size and tunable magnetic properties. The synthesis of such nanomagnets, however, often requires elevated temperatures and toxic solvents, resulting in high environmental and energy costs. Metal-reducing microorganisms

  10. Harnessing the Bacterial Power of Nanomagnets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Harnessing the Bacterial Power of Nanomagnets Print Nanometer-size magnets have wide-ranging uses, from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of nanoparticles with well-controlled size and tunable magnetic properties. The synthesis of such nanomagnets, however, often requires elevated temperatures and toxic solvents, resulting in high environmental and energy costs. Metal-reducing microorganisms

  11. Harnessing the Bacterial Power of Nanomagnets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Harnessing the Bacterial Power of Nanomagnets Print Nanometer-size magnets have wide-ranging uses, from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of nanoparticles with well-controlled size and tunable magnetic properties. The synthesis of such nanomagnets, however, often requires elevated temperatures and toxic solvents, resulting in high environmental and energy costs. Metal-reducing microorganisms

  12. Harnessing the Bacterial Power of Nanomagnets

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Harnessing the Bacterial Power of Nanomagnets Print Nanometer-size magnets have wide-ranging uses, from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of nanoparticles with well-controlled size and tunable magnetic properties. The synthesis of such nanomagnets, however, often requires elevated temperatures and toxic solvents, resulting in high environmental and energy costs. Metal-reducing microorganisms

  13. Real time viability detection of bacterial spores

    DOE Patents [OSTI]

    Vanderberg, Laura A.; Herdendorf, Timothy J.; Obiso, Richard J.

    2003-07-29

    This invention relates to a process for detecting the presence of viable bacterial spores in a sample and to a spore detection system, the process including placing a sample in a germination medium for a period of time sufficient for commitment of any present viable bacterial spores to occur, mixing the sample with a solution of a lanthanide capable of forming a fluorescent complex with dipicolinic acid, and, measuring the sample for the presence of dipicolinic acid, and the system including a germination chamber having inlets from a sample chamber, a germinant chamber and a bleach chamber, the germination chamber further including an outlet through a filtering means, the outlet connected to a detection chamber, the detection chamber having an inlet from a fluorescence promoting metal chamber and the detection chamber including a spectral excitation source and a means of measuring emission spectra from a sample, the detection chamber further connected to a waste chamber. A germination reaction mixture useful for promoting commitment of any viable bacterial spores in a sample including a combination of L-alanine, L-asparagine and D-glucose is also described.

  14. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial

  15. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial

  16. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial

  17. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial

  18. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial

  19. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial

  20. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 Print Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the chemical underpinnings of developing bacterial

  1. Time-Resolved

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Ultrafast Spectroscopy of Warm Dense Matter Real-Time Chemical Imaging of Bacterial Biofilm Development Using Light to Control How X Rays Interact with Matter X-Ray Imaging of...

  2. The Carboxysome and Other Bacterial Microcompartments

    SciTech Connect (OSTI)

    Kerfeld, Cheryl A.; Greenleaf, William B.; Kinney, James N.

    2010-06-23

    - Carboxysomes are part of the carbon concentrating mechanism in cyanobacteria and chemoautotrophs. - Carboxysomes are a subclass of bacterial microcompartments (BMCs); BMCs can encapsulate a range of metabolic processes. - Like some viral particles, the carboxysome can be modeled as an icosahedron-in its case, having 4,000-5,000 hexameric shell subunits and 12 surface pentamers to generate curvature. - The threefold axis of symmetry of the CsoS1D protein in carboxysomes forms a pore that can open and close, allowing for selective diffusion. - Genetic modules encoding BMC shell proteins and the enzymes that they encapsulate are horizontally transferable, suggesting they enable bacteria to adapt to diverse environments.

  3. Detoxification of organophosphate nerve agents by bacterial phosphotriesterase

    SciTech Connect (OSTI)

    Ghanem, Eman; Raushel, Frank M. . E-mail: raushel@tamu.edu

    2005-09-01

    Organophosphates have been widely used as insecticides and chemical warfare agents. The health risks associated with these agents have necessitated the need for better detoxification and bioremediation tools. Bacterial enzymes capable of hydrolyzing the lethal organophosphate nerve agents are of special interest. Phosphotriesterase (PTE) isolated from the soil bacteria Pseudomonas diminuta displays a significant rate enhancement and substrate promiscuity for the hydrolysis of organophosphate triesters. Directed evolution and rational redesign of the active site of PTE have led to the identification of new variants with enhanced catalytic efficiency and stereoselectivity toward the hydrolysis of organophosphate neurotoxins. PTE has been utilized to protect against organophosphate poisoning in vivo. Biotechnological applications of PTE for detection and decontamination of insecticides and chemical warfare agents are developing into useful tools. In this review, the catalytic properties and potential applications of this remarkable enzyme are discussed.

  4. Metallization of bacterial cellulose for electrical and electronic device manufacture

    DOE Patents [OSTI]

    Evans, Barbara R.; O'Neill, Hugh M.; Jansen, Valerie Malyvanh; Woodward, Jonathan

    2011-06-07

    A method for the deposition of metals in bacterial cellulose and for the employment of the metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The method for impregnating bacterial cellulose with a metal comprises placing a bacterial cellulose matrix in a solution of a metal salt such that the metal salt is reduced to metallic form and the metal precipitates in or on the matrix. The method for the construction of a fuel cell comprises placing a hydrated bacterial cellulose support structure in a solution of a metal salt such that the metal precipitates in or on the support structure, inserting contact wires into two pieces of the metal impregnated support structure, placing the two pieces of metal impregnated support structure on opposite sides of a layer of hydrated bacterial cellulose, and dehydrating the three layer structure to create a fuel cell.

  5. Metallization of bacterial cellulose for electrical and electronic device manufacture

    DOE Patents [OSTI]

    Evans, Barbara R [Oak Ridge, TN; O'Neill, Hugh M [Knoxville, TN; Jansen, Valerie Malyvanh [Memphis, TN; Woodward, Jonathan [Knoxville, TN

    2010-09-28

    A method for the deposition of metals in bacterial cellulose and for the employment of the metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The method for impregnating bacterial cellulose with a metal comprises placing a bacterial cellulose matrix in a solution of a metal salt such that the metal salt is reduced to metallic form and the metal precipitates in or on the matrix. The method for the construction of a fuel cell comprises placing a hydrated bacterial cellulose support structure in a solution of a metal salt such that the metal precipitates in or on the support structure, inserting contact wires into two pieces of the metal impregnated support structure, placing the two pieces of metal impregnated support structure on opposite sides of a layer of hydrated bacterial cellulose, and dehydrating the three layer structure to create a fuel cell.

  6. Metallization of bacterial cellulose for electrical and electronic device manufacture

    SciTech Connect (OSTI)

    Evans, Barbara R.; O'Neill, Hugh M.; Jansen, Valerie Malyvanh; Woodward, Jonathan

    2006-01-17

    The employment of metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The fuel cell includes an electrolyte membrane comprising a membrane support structure comprising bacterial cellulose, an anode disposed on one side of the electrolyte membrane, and a cathode disposed on an opposite side of the electrolyte membrane. At least one of the anode and the cathode comprises an electrode support structure comprising bacterial cellulose, and a catalyst disposed in or on the electrode support structure.

  7. Bacterial Enzymes and Antibiotic Resistance- Oral Presentation

    SciTech Connect (OSTI)

    Maltz, Lauren

    2015-08-25

    By using protein crystallography and X-ray diffraction, structures of bacterial enzymes were solved to gain a better understanding of how enzymatic modification acts as an antibacterial resistance mechanism. Aminoglycoside phosphotransferases (APHs) are one of three aminoglycoside modifying enzymes that confer resistance to the aminoglycoside antibiotics via enzymatic modification, rendering many drugs obsolete. Specifically, the APH(2”) family vary in their substrate specificities and also in their preference for the phosphate donor (ADP versus GDP). By solving the structures of members of the APH(2”) family of enzymes, we can see how domain movements are important to their substrate specificity. Our structure of the ternary complex of APH(2”)-IIIa with GDP and kanamycin, when compared to the known structures of APH(2”)-IVa, reveals that there are real physical differences between these two enzymes, a structural finding that explains why the two enzymes differ in their preferences for certain aminoglycosides. Another important group of bacterial resistance enzymes are the Class D β-lactamases. Oxacillinase carbapenemases (OXAs) are part of this enzyme class and have begun to confer resistance to ‘last resort’ drugs, most notably carbapenems. Our structure of OXA-143 shows that the conformational flexibility of a conserved hydrophobic residue in the active site (Val130) serves to control the entry of a transient water molecule responsible for a key step in the enzyme’s mechanism. Our results provide insight into the structural mechanisms of these two different enzymes.

  8. The Fate of Marine Bacterial Exopolysaccharide in Natural Marine...

    Office of Scientific and Technical Information (OSTI)

    Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that ...

  9. Genomic Sequencing of Single Bacterial Cells (2010 JGI User Meeting)

    SciTech Connect (OSTI)

    Woyke, Tanje

    2010-03-26

    Tanja Woyke from the DOE JGI on the "Genomic Sequencing of Single Bacterial Cells" on March 26, 2010 at the 5th Annual DOE JGI User Meeting

  10. Two poplar-associated bacterial isolates induce additive favorable...

    Office of Scientific and Technical Information (OSTI)

    in a constructed plant-microbiome system Prev Next Title: Two poplar-associated bacterial isolates induce additive favorable responses in a constructed plant-microbiome ...

  11. Coal desulfurization by bacterial treatment and column flotation. Final report

    SciTech Connect (OSTI)

    Kawatra, S.K.

    1994-06-01

    A review of the literature showed that bacterial leaching, using the microorganism Thiobacillus ferrooxidans, was a very effective technique for removing pyrite from coal, as it could dissolve even the finest pyrite particles without the need for expensive reagents or extreme processing conditions. Unfortunately, bacterial leaching is also rather slow, and so the initial goal of this research was to decrease the leaching time as much as possible. However, this still left the bacteria needing approximately a week to remove half of the pyritic sulfur, and so a faster technique was sought. Since it had been reported in the literature that T. ferrooxidans could be used to depress the flotation of pyrite during froth flotation of coal, this was investigated further. By studying the recovery mechanisms of coal-pyrite in froth flotation, it was found that pyrite was being recovered by entrainment and by locking to coal particles, not by true flotation of hydrophobic pyrite. Therefore, no pyrite depressant could be of any significant benefit for keeping pyrite out of the coal froth product, and it was much more important to prevent entrainment from occurring. Countercurrent flotation columns were invented to essentially eliminate entrainment effects, by washing the froth and reducing mixing of the froth and tailings products. Existing flotation columns tend to be quite simple, and in order to give reasonable product quality they must be very tall (typically 30--45 feet). As a result, they have difficulty in handling the high froth volumes which occur in coal flotation, and are awkward to install in existing plants. The bulk of this project therefore concentrated on developing an improved coal flotation column, and testing it under actual plant conditions.

  12. Lessons learned from bacterial transport research at the South Oyster Site

    SciTech Connect (OSTI)

    Scheibe, T.; Hubbard, S.S.; Onstott, T.C.; DeFlaun, M.F.

    2011-04-01

    This paper provides a review of bacterial transport experiments conducted by a multi-investigator, multi-institution, multi-disciplinary team of researchers under the auspices of the U. S. Department of Energy (DOE). The experiments were conducted during the time period 1999-2001 at a field site near the town of Oyster, Virginia known as the South Oyster Site, and included four major experimental campaigns aimed at understanding and quantifying bacterial transport in the subsurface environment. Several key elements of the research are discussed here: (1) quantification of bacterial transport in physically, chemically and biologically heterogeneous aquifers, (2) evaluation of the efficacy of conventional colloid filtration theory, (3) scale effects in bacterial transport, (4) development of new methods for microbial enumeration and screening for low adhesion strains, (5) application of novel hydrogeophysical techniques for aquifer characterization, and (6) experiences regarding management of a large field research effort. Lessons learned are summarized in each of these areas. The body of literature resulting from South Oyster Site research has been widely cited and continues to influence research into the controls exerted by aquifer heterogeneity on reactive transport (including microbial transport). It also served as a model (and provided valuable experience) for subsequent and ongoing highly-instrumented field research efforts conducted by DOE-sponsored investigators.

  13. Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

    SciTech Connect (OSTI)

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-04-07

    Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retained in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.

  14. Reconstruction of a Bacterial Genome from DNA Cassettes

    SciTech Connect (OSTI)

    Christopher Dupont; John Glass; Laura Sheahan; Shibu Yooseph; Lisa Zeigler Allen; Mathangi Thiagarajan; Andrew Allen; Robert Friedman; J. Craig Venter

    2011-12-31

    This basic research program comprised two major areas: (1) acquisition and analysis of marine microbial metagenomic data and development of genomic analysis tools for broad, external community use; (2) development of a minimal bacterial genome. Our Marine Metagenomic Diversity effort generated and analyzed shotgun sequencing data from microbial communities sampled from over 250 sites around the world. About 40% of the 26 Gbp of sequence data has been made publicly available to date with a complete release anticipated in six months. Our results and those mining the deposited data have revealed a vast diversity of genes coding for critical metabolic processes whose phylogenetic and geographic distributions will enable a deeper understanding of carbon and nutrient cycling, microbial ecology, and rapid rate evolutionary processes such as horizontal gene transfer by viruses and plasmids. A global assembly of the generated dataset resulted in a massive set (5Gbp) of genome fragments that provide context to the majority of the generated data that originated from uncultivated organisms. Our Synthetic Biology team has made significant progress towards the goal of synthesizing a minimal mycoplasma genome that will have all of the machinery for independent life. This project, once completed, will provide fundamentally new knowledge about requirements for microbial life and help to lay a basic research foundation for developing microbiological approaches to bioenergy.

  15. Associations between bacterial communities of house dust and infant gut

    SciTech Connect (OSTI)

    Konya, T.; Koster, B.; Maughan, H.; Escobar, M.; Azad, M.B.; Guttman, D.S.; Sears, M.R.; Becker, A.B.; Brook, J.R.; Takaro, T.K.; Kozyrskyj, A.L.; Scott, J.A.

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  16. Allelic variation contributes to bacterial host specificity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; et al

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population andmore » functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.« less

  17. Allelic variation contributes to bacterial host specificity

    SciTech Connect (OSTI)

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

  18. One Bacterial Cell, One Complete Genome

    SciTech Connect (OSTI)

    Woyke, Tanja; Tighe, Damon; Mavrommatis, Konstantinos; Clum, Alicia; Copeland, Alex; Schackwitz, Wendy; Lapidus, Alla; Wu, Dongying; McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A.; Bristow, James; Cheng, Jan-Fang

    2010-04-26

    While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200?900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

  19. Insights from twenty years of bacterial genome sequencing

    SciTech Connect (OSTI)

    Land, Miriam L; Hauser, Loren John; Jun, Se Ran; Nookaew, Intawat; Leuze, Michael Rex; Ahn, Tae-Hyuk; Karpinets, Tatiana V; Lund, Ole; Kora, Guruprasad H; Wassenaar, Trudy; Poudel, Suresh; Ussery, David W

    2015-01-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome

  20. DEVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

    SciTech Connect (OSTI)

    Bill W. Bogan; Brigid M. Lamb; John J. Kilbane II

    2004-10-30

    The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Previous testing indicated that the growth, and the metal corrosion caused by pure cultures of sulfate reducing bacteria were inhibited by hexane extracts of some pepper plants. This quarter tests were performed to determine if chemical compounds other than pepper extracts could inhibit the growth of corrosion-associated microbes and to determine if pepper extracts and other compounds can inhibit corrosion when mature biofilms are present. Several chemical compounds were shown to be capable of inhibiting the growth of corrosion-associated microorganisms, and all of these compounds limited the amount of corrosion caused by mature biofilms to a similar extent. It is difficult to control corrosion caused by mature biofilms, but any compound that disrupts the metabolism of any of the major microbial groups present in corrosion-associated biofilms shows promise in limiting the amount/rate of corrosion.

  1. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ALSNews Vol. 312 Print Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the chemical underpinnings of developing

  2. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

    SciTech Connect (OSTI)

    Hodkinson, Brendan P; Gottel, Neil R; Schadt, Christopher Warren; Lutzoni, Francois

    2011-01-01

    Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.

  3. Electroporation of Functional Bacterial Effectors into Mammalian Cells

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Sontag, Ryan L.; Mihai, Cosmin; Orr, Galya; Savchenko, Alexei; Skarina, Tatiana; Cui, Hong; Cort, John R.; Adkins, Joshua N.; Brown, Roslyn N.

    2015-01-19

    Electroporation was used to insert purified bacterial virulence effector proteins directly into living eukaryotic cells. Protein localization was monitored by confocal immunofluorescence microscopy. This method allows for studies on trafficking, function, and protein-protein interactions using active exogenous proteins, avoiding the need for heterologous expression in eukaryotic cells.

  4. Successional trajectories of rhizosphere bacterial communities over consecutive seasons

    SciTech Connect (OSTI)

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Brodie, Eoin L.; Zhou, Jizhong; Firestone, Mary

    2015-08-04

    It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal

  5. Successional trajectories of rhizosphere bacterial communities over consecutive seasons

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Shi, Shengjing; Nuccio, Erin; Herman, Donald J.; Rijkers, Ruud; Estera, Katerina; Li, Jiabao; da Rocha, Ulisses Nunes; He, Zhili; Pett-Ridge, Jennifer; Brodie, Eoin L.; et al

    2015-08-04

    It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative tomore » background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. We document the successional patterns of rhizosphere bacterial communities associated with a “wild” annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address “domesticated” plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable

  6. Differentiation of Microbial Species and Strains in Coculture Biofilms by Multivariate Analysis of Laser Desorption Postionization Mass Spectra

    SciTech Connect (OSTI)

    University of Illinois at Chicago; Montana State University; Bhardwaj, Chhavi; Cui, Yang; Hofstetter, Theresa; Liu, Suet Yi; Bernstein, Hans C.; Carlson, Ross P.; Ahmed, Musahid; Hanley, Luke

    2013-04-01

    7.87 to 10.5 eV vacuum ultraviolet (VUV) photon energies were used in laser desorption postionization mass spectrometry (LDPI-MS) to analyze biofilms comprised of binary cultures of interacting microorganisms. The effect of photon energy was examined using both tunable synchrotron and laser sources of VUV radiation. Principal components analysis (PCA) was applied to the MS data to differentiate species in Escherichia coli-Saccharomyces cerevisiae coculture biofilms. PCA of LDPI-MS also differentiated individual E. coli strains in a biofilm comprised of two interacting gene deletion strains, even though these strains differed from the wild type K-12 strain by no more than four gene deletions each out of approximately 2000 genes. PCA treatment of 7.87 eV LDPI-MS data separated the E. coli strains into three distinct groups two ?pure? groups and a mixed region. Furthermore, the ?pure? regions of the E. coli cocultures showed greater variance by PCA when analyzed by 7.87 eV photon energies than by 10.5 eV radiation. Comparison of the 7.87 and 10.5 eV data is consistent with the expectation that the lower photon energy selects a subset of low ionization energy analytes while 10.5 eV is more inclusive, detecting a wider range of analytes. These two VUV photon energies therefore give different spreads via PCA and their respective use in LDPI-MS constitute an additional experimental parameter to differentiate strains and species.

  7. Natural bacterial communities serve as quantitative geochemical biosensors

    SciTech Connect (OSTI)

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; Earles, Jennifer E.; Phillips, Jana; Techtmann, Steve M.; Joyner, Dominique C.; Elias, Dwayne A.; Bailey, Kathryn L.; Hurt, Richard A.; Preheim, Sarah P.; Sanders, Matthew C.; Yang, Joy; Mueller, Marcella A.; Brooks, Scott; Watson, David B.; Zhang, Ping; He, Zhili; Dubinsky, Eric A.; Adams, Paul D.; Arkin, Adam P.; Fields, Matthew W.; Zhou, Jizhong; Alm, Eric J.; Hazen, Terry C.

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.

  8. Natural bacterial communities serve as quantitative geochemical biosensors

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; Olesen, Scott W.; Paradis, Charles; Wu, Liyou; Campbell, James H.; Fortney, Julian L.; Mehlhorn, Tonia L.; Lowe, Kenneth A.; et al

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination,more » even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.« less

  9. DOE-Funded Research on Bacterial Enzyme Could Lead to Cheaper...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    DOE-Funded Research on Bacterial Enzyme Could Lead to Cheaper Biofuel DOE-Funded Research on Bacterial Enzyme Could Lead to Cheaper Biofuel May 28, 2014 - 12:24pm Addthis A ...

  10. ALSNews Vol. 312

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    2 ALSNews Vol. 312 Print Wednesday, 25 August 2010 00:00 Real-Time Chemical Imaging of Bacterial Biofilm Development Almost all bacteria can form biofilms--dynamic communities of cells enclosed in self-produced matrices of polymers. Coordinated collectively, these bacteria defend against antagonists, break down recalcitrant materials, and produce biofuels. Researchers from Berkeley Lab, Lawrence Livermore National Lab, and UC Berkeley have developed a robust and label-free method to probe the

  11. Argonne OutLoud: Invisible Influence: A Bacterial Guide to Your...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Invisible Influence: A Bacterial Guide to Your Health (Dec. 11, 2014) Share Topic Community Outreach Environment Biology Environmental biology Metagenomics...

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

    SciTech Connect (OSTI)

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

    2011-05-01

    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.

  13. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Axen, Seth D.; Erbilgin, Onur; Kerfeld, Cheryl A.; Tanaka, Mark M.

    2014-10-23

    Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found inmore » seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should

  14. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method

    SciTech Connect (OSTI)

    Axen, Seth D.; Erbilgin, Onur; Kerfeld, Cheryl A.; Tanaka, Mark M.

    2014-10-23

    Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful

  15. Development and Integration of Genome-Enabled Techniques to Track and Predict the Cycling of Carbon in Model Microbial Communities

    SciTech Connect (OSTI)

    Banfield, Jillian

    2014-11-26

    The primary objective of this project was to establish widely applicable, high-throughput omics methods for tracking carbon flow in microbial communities at a strain-resolved molecular level. We developed and applied these methods to study a well-established microbial community model system with a long history of omics innovation: chemoautotrophic biofilms grown in an acid mine drainage (AMD) environment. The methods are now being transitioned (in a new project) to study soil. Using metagenomics, stable-isotope proteomics, stable-isotope metabolomics, transcriptomics, and microscopy, we tracked carbon flow during initial biofilm growth involving CO2 fixation, through the maturing biofilm community consisting of multiple trophic levels, and during an anaerobic degradative phase after biofilms sink. This work included explicit consideration of the often overlooked roles of archaea and microbial eukaryotes (fungi) in carbon turnover. We also analyzed where the eosystem begins to fail in response to thermal perturbation, and how perturbation propagates through a carbon cycle. We investigated the form of strain variation in microbial communities, the importance of strain variants, and the rate and form of strain evolution. Overall, the project generated an array of new, integrated omics approaches and provided unprecedented insight into the functioning of a natural ecosystem. This project supported graduate training for five Ph.D. students and three post doctoral fellows and contributed directly to at least 26 publications (two in Science).

  16. Method for construction of bacterial strains with increased succinic acid production

    DOE Patents [OSTI]

    Donnelly, Mark I.; Sanville-Millard, Cynthia; Chatterjee, Ranjini

    2000-01-01

    A fermentation process for producing succinic acid is provided comprising selecting a bacterial strain that does not produce succinic acid in high yield, disrupting the normal regulation of sugar metabolism of said bacterial strain, and combining the mutant bacterial strain and selected sugar in anaerobic conditions to facilitate production of succinic acid. Also provided is a method for changing low yield succinic acid producing bacteria to high yield succinic acid producing bacteria comprising selecting a bacterial strain having a phosphotransferase system and altering the phosphotransferase system so as to allow the bacterial strain to simultaneously metabolize different sugars.

  17. Convergent bacterial microbiotas in the fungal agricultural systems of insects

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; et al

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associatedmore » with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.« less

  18. Convergent bacterial microbiotas in the fungal agricultural systems of insects

    SciTech Connect (OSTI)

    Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; Klepzig, Kier D.; Currie, Cameron R.

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.

  19. Ex Situ Formation of Metal Selenide Quantum Dots Using Bacterially Derived Selenide Precursors

    SciTech Connect (OSTI)

    Fellowes, Jonathan W.; Pattrick, Richard; Lloyd, Jon; Charnock, John M.; Coker, Victoria S.; Mosselmans, JFW; Weng, Tsu-Chien; Pearce, Carolyn I.

    2013-04-12

    Luminescent quantum dots were synthesized using bacterially derived selenide (SeII-) as the precursor. Biogenic SeII- was produced by the reduction of Se-IV by Veillonella atypica and compared directly against borohydride-reduced Se-IV for the production of glutathione-stabilized CdSe and beta-mercaptoethanol-stabilized ZnSe nanoparticles by aqueous synthesis. Biological SeII- formed smaller, narrower size distributed QDs under the same conditions. The growth kinetics of biologically sourced CdSe phases were slower. The proteins isolated from filter sterilized biogenic SeII- included a methylmalonyl-CoA decarboxylase previously characterized in the closely related Veillonella parvula. XAS analysis of the glutathione-capped CdSe at the S K-edge suggested that sulfur from the glutathione was structurally incorporated within the CdSe. A novel synchrotron based XAS technique was also developed to follow the nucleation of biological and inorganic selenide phases, and showed that biogenic SeII- is more stable and more resistant to beam-induced oxidative damage than its inorganic counterpart. The bacterial production of quantum dot precursors offers an alternative, 'green' synthesis technique that negates the requirement of expensive, toxic chemicals and suggests a possible link to the exploitation of selenium contaminated waste streams.

  20. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; et al

    2015-01-09

    The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes withmore » different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.« less

  1. Progressive structural changes of Avicel, bleached softwood, and bacterial cellulose during enzymatic hydrolysis

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kafle, Kabindra; Shin, Heenae; Lee, Christopher M.; Park, Sunkyu; Kim, Seong H.

    2015-10-14

    A comprehensive picture of structural changes of cellulosic biomass during enzymatic hydrolysis is essential for a better understanding of enzymatic actions and development of more efficient enzymes. In this study, a suite of analytical techniques including sum frequency generation (SFG) spectroscopy, infrared (IR) spectroscopy, x-ray diffraction (XRD), and x-ray photoelectron spectroscopy (XPS) were employed for lignin-free model biomass samples—Avicel, bleached softwood, and bacterial cellulose—to find correlations between the decrease in hydrolysis rate over time and the structural or chemical changes of biomass during the hydrolysis reaction. The results showed that the decrease in hydrolysis rate over time appears to correlatemore » with the irreversible deposition of non-cellulosic species (either reaction side products or denatured enzymes, or both) on the cellulosic substrate surface. The crystallinity, degree of polymerization, and meso-scale packing of cellulose do not seem to positively correlate with the decrease in hydrolysis rate observed for all three substrates tested in this study. Moreover, it was also found that the cellulose Iα component of the bacterial cellulose is preferentially hydrolyzed by the enzyme than the cellulose Iβ component.« less

  2. Progressive structural changes of Avicel, bleached softwood, and bacterial cellulose during enzymatic hydrolysis

    SciTech Connect (OSTI)

    Kafle, Kabindra; Shin, Heenae; Lee, Christopher M.; Park, Sunkyu; Kim, Seong H.

    2015-10-14

    A comprehensive picture of structural changes of cellulosic biomass during enzymatic hydrolysis is essential for a better understanding of enzymatic actions and development of more efficient enzymes. In this study, a suite of analytical techniques including sum frequency generation (SFG) spectroscopy, infrared (IR) spectroscopy, x-ray diffraction (XRD), and x-ray photoelectron spectroscopy (XPS) were employed for lignin-free model biomass samples—Avicel, bleached softwood, and bacterial cellulose—to find correlations between the decrease in hydrolysis rate over time and the structural or chemical changes of biomass during the hydrolysis reaction. The results showed that the decrease in hydrolysis rate over time appears to correlate with the irreversible deposition of non-cellulosic species (either reaction side products or denatured enzymes, or both) on the cellulosic substrate surface. The crystallinity, degree of polymerization, and meso-scale packing of cellulose do not seem to positively correlate with the decrease in hydrolysis rate observed for all three substrates tested in this study. Moreover, it was also found that the cellulose Iα component of the bacterial cellulose is preferentially hydrolyzed by the enzyme than the cellulose Iβ component.

  3. Virus and Bacterial Cell Chemical Analysis by NanoSIMS

    SciTech Connect (OSTI)

    Weber, P; Holt, J

    2008-07-28

    In past work for the Department of Homeland Security, the LLNL NanoSIMS team has succeeded in extracting quantitative elemental composition at sub-micron resolution from bacterial spores using nanometer-scale secondary ion mass spectrometry (NanoSIMS). The purpose of this task is to test our NanoSIMS capabilities on viruses and bacterial cells. This initial work has proven successful. We imaged Tobacco Mosaic Virus (TMV) and Bacillus anthracis Sterne cells using scanning electron microscopy (SEM) and then analyzed those samples by NanoSIMS. We were able resolve individual viral particles ({approx}18 nm by 300 nm) in the SEM and extract correlated elemental composition in the NanoSIMS. The phosphorous/carbon ratio observed in TMV is comparable to that seen in bacterial spores (0.033), as was the chlorine/carbon ratio (0.11). TMV elemental composition is consistent from spot to spot, and TMV is readily distinguished from debris by NanoSIMS analysis. Bacterial cells were readily identified in the SEM and relocated in the NanoSIMS for elemental analysis. The Ba Sterne cells were observed to have a measurably lower phosphorous/carbon ratio (0.005), as compared to the spores produced in the same run (0.02). The chlorine/carbon ratio was approximately 2.5X larger in the cells (0.2) versus the spores (0.08), while the fluorine/carbon ratio was approximately 10X lower in the cells (0.008) than the spores (0.08). Silicon/carbon ratios for both cells and spores encompassed a comparable range. The initial data in this study suggest that high resolution analysis is useful because it allows the target agent to be analyzed separate from particulates and other debris. High resolution analysis would also be useful for trace sample analysis. The next step in this work is to determine the potential utility of elemental signatures in these kinds of samples. We recommend bulk analyses of media and agent samples to determine the range of media compositions in use, and to determine how

  4. Production of extremophilic bacterial cellulase enzymes in aspergillus niger.

    SciTech Connect (OSTI)

    Gladden, John Michael

    2013-09-01

    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.

  5. One-pot refolding of core histones from bacterial inclusion bodies...

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Search Results Journal Article: One-pot refolding of core histones from bacterial inclusion bodies allows rapid reconstitution of histone octamer Citation Details ...

  6. Argonne OutLoud: Invisible Influence: A Bacterial Guide to Your Health

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    (Dec. 11, 2014) | Argonne National Laboratory Invisible Influence: A Bacterial Guide to Your Health (Dec. 11, 2014) Share Topic Community Outreach Environment Biology Environmental biology Metagenomics

  7. Effect of Divalent Cation Removal on the Structure of Gram-Negative Bacterial Outer Membrane Models

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Clifton, Luke A.; Skoda, Maximilian W. A.; Le Brun, Anton P.; Ciesielski, Filip; Kuzmenko, Ivan; Holt, Stephen A.; Lakey, Jeremy H.

    2014-12-09

    The Gram-negative bacterial outer membrane (GNB-OM) is asymmetric in its lipid composition with a phospholipid-rich inner leaflet and an outer leaflet predominantly composed of lipopolysaccharides (LPS). LPS are polyanionic molecules, with numerous phosphate groups present in the lipid A and core oligosaccharide regions. The repulsive forces due to accumulation of the negative charges are screened and bridged by the divalent cations (Mg2+ and Ca2+) that are known to be crucial for the integrity of the bacterial OM. Indeed, chelation of divalent cations is a well-established method to permeabilize Gram-negative bacteria such as Escherichia coli. Here, we use X-ray and neutronmore » reflectivity (XRR and NR, respectively) techniques to examine the role of calcium ions in the stability of a model GNB-OM. Using XRR we show that Ca2+ binds to the core region of the rough mutant LPS (RaLPS) films, producing more ordered structures in comparison to divalent cation free monolayers. Using recently developed solid-supported models of the GNB-OM, we study the effect of calcium removal on the asymmetry of DPPC:RaLPS bilayers. We show that without the charge screening effect of divalent cations, the LPS is forced to overcome the thermodynamically unfavorable energy barrier and flip across the hydrophobic bilayer to minimize the repulsive electrostatic forces, resulting in about 20% mixing of LPS and DPPC between the inner and outer bilayer leaflets. These results reveal for the first time the molecular details behind the well-known mechanism of outer membrane stabilization by divalent cations. This confirms the relevance of the asymmetric models for future studies of outer membrane stability and antibiotic penetration.« less

  8. Effect of Divalent Cation Removal on the Structure of Gram-Negative Bacterial Outer Membrane Models

    SciTech Connect (OSTI)

    Clifton, Luke A.; Skoda, Maximilian W. A.; Le Brun, Anton P.; Ciesielski, Filip; Kuzmenko, Ivan; Holt, Stephen A.; Lakey, Jeremy H.

    2014-12-09

    The Gram-negative bacterial outer membrane (GNB-OM) is asymmetric in its lipid composition with a phospholipid-rich inner leaflet and an outer leaflet predominantly composed of lipopolysaccharides (LPS). LPS are polyanionic molecules, with numerous phosphate groups present in the lipid A and core oligosaccharide regions. The repulsive forces due to accumulation of the negative charges are screened and bridged by the divalent cations (Mg2+ and Ca2+) that are known to be crucial for the integrity of the bacterial OM. Indeed, chelation of divalent cations is a well-established method to permeabilize Gram-negative bacteria such as Escherichia coli. Here, we use X-ray and neutron reflectivity (XRR and NR, respectively) techniques to examine the role of calcium ions in the stability of a model GNB-OM. Using XRR we show that Ca2+ binds to the core region of the rough mutant LPS (RaLPS) films, producing more ordered structures in comparison to divalent cation free monolayers. Using recently developed solid-supported models of the GNB-OM, we study the effect of calcium removal on the asymmetry of DPPC:RaLPS bilayers. We show that without the charge screening effect of divalent cations, the LPS is forced to overcome the thermodynamically unfavorable energy barrier and flip across the hydrophobic bilayer to minimize the repulsive electrostatic forces, resulting in about 20% mixing of LPS and DPPC between the inner and outer bilayer leaflets. These results reveal for the first time the molecular details behind the well-known mechanism of outer membrane stabilization by divalent cations. This confirms the relevance of the asymmetric models for future studies of outer membrane stability and antibiotic penetration.

  9. A novel cofactor-binding mode in bacterial IMP dehydrogenases explains inhibitor selectivity

    SciTech Connect (OSTI)

    Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; Joachimiak, Andrzej

    2015-01-09

    The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5'-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. As a result, these findings offer a potential strategy for further ligand optimization.

  10. Structure-based receptor MIMICS targeted against bacterial superantigen toxins

    DOE Patents [OSTI]

    Gupta, Goutam; Hong-Geller, Elizabeth; Shiflett, Patrick R.; Lehnert, Nancy M.

    2009-08-18

    The invention provides therapeutic compositions useful in the treatment of bacterial superantigen mediated conditions, such as Toxic Shock Syndrome. The compositions comprise genetically engineered bifunctional polypeptides containing a specific T-cell receptor binding domain and a specific MHC class II receptor binding domain, each targeting non-overlapping epitopes on a superantigen molecule against which they are designed. The anti-superantigen "receptor mimetics" or "chimeras" are rationally designed to recreate the modality of superantigen binding directly to both the TCR and the MHC-II receptor, and are capable of acting as decoys for superantigen binding, effectively out-competing the host T-cell and MHC-II receptors, the natural host receptors.

  11. ASSESSMENT OF MARKER PROTEINS IDENTIFIED IN WHOLE CELL EXTRACTS FOR BACTERIAL SPECIATION USING LIQUID CHROMATOGRAPHY ELECTROSPRAY IONIZATION TANDEM MASS SPECTROMETRY

    SciTech Connect (OSTI)

    Kooken, Jennifer M.; Fox, Karen F.; Fox, Alvin; Wunschel, David S.

    2014-02-02

    ASSESSMENT OF MARKER PROTEINS IDENTIFIED IN WHOLE CELL EXTRACTS FOR BACTERIAL SPECIATION USING LIQUID CHROMATOGRAPHY ELECTROSPRAY IONIZATION TANDEM MASS SPECTROMETRY

  12. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    SciTech Connect (OSTI)

    Kingsley, Mark T

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, an d analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: (1) to assess the potential terrorist threat to U.S. agricultural crops, (2) to determine whether suitable assays exist to monitor that threat, and (3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  13. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    SciTech Connect (OSTI)

    Kingsley, Mark T.

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, and analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: 1) to assess the potential terrorist threat to U.S. agricultural crops, 2) to determine whether suitable assays exist to monitor that threat, and 3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  14. Model Studies of the Dynamics of Bacterial Flagellar Motors

    SciTech Connect (OSTI)

    Bai, F; Lo, C; Berry, R; Xing, J

    2009-03-19

    The Bacterial Flagellar Motor is a rotary molecular machine that rotates the helical filaments which propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation and switching mechanism of the motor. In our previous paper, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here we further analyze this model. In this paper we show (1) the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with the latest experiment by Lo et al.; (2) with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, recently observed by Yuan and Berg; (3) the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwelling time distribution. Predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental verification.

  15. Bacterial microcompartment assembly: The key role of encapsulation peptides

    SciTech Connect (OSTI)

    Aussignargues, Clément; Paasch, Bradley C.; Gonzalez-Esquer, Raul; Erbilgin, Onur; Kerfeld, Cheryl A.

    2015-06-23

    Bacterial microcompartments (BMCs) are proteinaceous organelles used by a broad range of bacteria to segregate and optimize metabolic reactions. Their functions are diverse, and can be divided into anabolic (carboxysome) and catabolic (metabolosomes) processes, depending on their cargo enzymes. The assembly pathway for the β-carboxysome has been characterized, revealing that biogenesis proceeds from the inside out. The enzymes coalesce into a procarboxysome, followed by encapsulation in a protein shell that is recruited to the procarboxysome by a short (~17 amino acids) extension on the C-terminus of one of the encapsulated proteins. A similar extension is also found on the N- or C-termini of a subset of metabolosome core enzymes. These encapsulation peptides (EPs) are characterized by a primary structure predicted to form an amphipathic α-helix that interacts with shell proteins. In this study, we review the features, function and widespread occurrence of EPs among metabolosomes, and propose an expanded role for EPs in the assembly of diverse BMCs.

  16. Bacterial microcompartment assembly: The key role of encapsulation peptides

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Aussignargues, Clément; Paasch, Bradley C.; Gonzalez-Esquer, Raul; Erbilgin, Onur; Kerfeld, Cheryl A.

    2015-06-23

    Bacterial microcompartments (BMCs) are proteinaceous organelles used by a broad range of bacteria to segregate and optimize metabolic reactions. Their functions are diverse, and can be divided into anabolic (carboxysome) and catabolic (metabolosomes) processes, depending on their cargo enzymes. The assembly pathway for the β-carboxysome has been characterized, revealing that biogenesis proceeds from the inside out. The enzymes coalesce into a procarboxysome, followed by encapsulation in a protein shell that is recruited to the procarboxysome by a short (~17 amino acids) extension on the C-terminus of one of the encapsulated proteins. A similar extension is also found on the N-more » or C-termini of a subset of metabolosome core enzymes. These encapsulation peptides (EPs) are characterized by a primary structure predicted to form an amphipathic α-helix that interacts with shell proteins. In this study, we review the features, function and widespread occurrence of EPs among metabolosomes, and propose an expanded role for EPs in the assembly of diverse BMCs.« less

  17. Structures of Arg- and Gln-type bacterial cysteine dioxygenase homologs: Arg- and Gln-type Bacterial CDO Homologs

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Driggers, Camden M.; Hartman, Steven J.; Karplus, P. Andrew

    2015-01-01

    In some bacteria, cysteine is converted to cysteine sulfinic acid by cysteine dioxygenases (CDO) that are only ~15–30% identical in sequence to mammalian CDOs. Among bacterial proteins having this range of sequence similarity to mammalian CDO are some that conserve an active site Arg residue (“Arg-type” enzymes) and some having a Gln substituted for this Arg (“Gln-type” enzymes). Here, we describe a structure from each of these enzyme types by analyzing structures originally solved by structural genomics groups but not published: a Bacillus subtilis “Arg-type” enzyme that has cysteine dioxygenase activity (BsCDO), and a Ralstonia eutropha “Gln-type” CDO homolog ofmore » uncharacterized activity (ReCDOhom). The BsCDO active site is well conserved with mammalian CDO, and a cysteine complex captured in the active site confirms that the cysteine binding mode is also similar. The ReCDOhom structure reveals a new active site Arg residue that is hydrogen bonding to an iron-bound diatomic molecule we have interpreted as dioxygen. Notably, the Arg position is not compatible with the mode of Cys binding seen in both rat CDO and BsCDO. As sequence alignments show that this newly discovered active site Arg is well conserved among “Gln-type” CDO enzymes, we conclude that the “Gln-type” CDO homologs are not authentic CDOs but will have substrate specificity more similar to 3-mercaptopropionate dioxygenases.« less

  18. Facile method to stain the bacterial cell surface for super-resolution fluorescence microscopy

    SciTech Connect (OSTI)

    Gunsolus, Ian L.; Hu, Dehong; Mihai, Cosmin; Lohse, Samuel E.; Lee, Chang-Soo; Torelli, Marco; Hamers, Robert J.; Murphy, Catherine; Orr, Galya; Haynes, Christy L.

    2014-01-01

    A method to fluorescently stain the surfaces of both Gram-negative and Gram-positive bacterial cells compatible with super-resolution fluorescence microscopy is presented. This method utilizes a commercially-available fluorescent probe to label primary amines at the surface of the cell. We demonstrate efficient staining of two bacterial strains, the Gram-negative Shewanella oneidensis MR-1 and the Gram-positive Bacillus subtilis 168. Using structured illumination microscopy and stochastic optical reconstruction microscopy, which require high quantum yield or specialized dyes, we show that this staining method may be used to resolve the bacterial cell surface with sub-diffraction-limited resolution. We further use this method to identify localization patterns of nanomaterials, specifically cadmium selenide quantum dots, following interaction with bacterial cells.

  19. Towards an informative mutant phenotype for every bacterial gene

    SciTech Connect (OSTI)

    Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.; Tarjan, Daniel R.; Xu, Zhuchen; Shao, Wenjen; Leon, Dacia; Arkin, Adam P.; Skerker, Jeffrey M.

    2014-08-11

    Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, in Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness.

  20. Compensation for L212GLU in bacterial reaction centers

    SciTech Connect (OSTI)

    Hanson, D.K.; Deng, Y.L.; Schiffer, M.; Sebban, P.

    1995-12-31

    In wild-type bacterial reaction centers (RC), residue L212Glu, which is located about 5 {Angstrom} away from Q{sub B}, is involved in the delivery of the second proton to Q{sub B{sup 2}{minus}} [1-4]. We previously constructed the L212Glu-L213Asp {yields} Ala-Ala double mutant of Rhodobacter capsulatus, and it is incapable of photosynthetic growth (PS{sup {minus}}) due to interruption of the proton transfer pathway to Q{sub B}[3,4]. We have isolated several photocompetent (PS{sup +}) phenotypic revertants of this L212-L213AA double mutant [3-7]. The compensatory mutations that restore function in these strains are diverse and show that neither L212Glu nor L213Asp is absolutely required for efficient light-induced electron or proton transfer. Genotypic revertant and second-site mutations, located within the Q{sub B} binding picket or at more distant sites, can compensate for mutations at L212 and L213 to restore photocompetence. One of the phenotypic revertants of the L212Ala-L213Ala double mutant carries a genotypic reversion of L213Ala to Asp; the Ala substitution at L212 remains. We were intrigued that this L212Glu {yields} Ala mutant R. capsulatus is photocompetent, while the L212Glu {yields} Gln mutant of R. sphaeroides is not, particularly since the sequence identity in the Q{sub B} site of these two strains is 90{percent} [8]. To this end, we constructed the L212Glu {yields} Gln mutant in R. capsulatus, and it is also PS{sup {minus}}. To determine the function that is lost in the L212Gln mutant but restored by Ala at that site, we selected four PS{sup +} revertants from the L212Gln strain.

  1. Towards an informative mutant phenotype for every bacterial gene

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Deutschbauer, Adam; Price, Morgan N.; Wetmore, Kelly M.; Tarjan, Daniel R.; Xu, Zhuchen; Shao, Wenjen; Leon, Dacia; Arkin, Adam P.; Skerker, Jeffrey M.

    2014-08-11

    Mutant phenotypes provide strong clues to the functions of the underlying genes and could allow annotation of the millions of sequenced yet uncharacterized bacterial genes. However, it is not known how many genes have a phenotype under laboratory conditions, how many phenotypes are biologically interpretable for predicting gene function, and what experimental conditions are optimal to maximize the number of genes with a phenotype. To address these issues, we measured the mutant fitness of 1,586 genes of the ethanol-producing bacterium Zymomonas mobilis ZM4 across 492 diverse experiments and found statistically significant phenotypes for 89% of all assayed genes. Thus, inmore » Z. mobilis, most genes have a functional consequence under laboratory conditions. We demonstrate that 41% of Z. mobilis genes have both a strong phenotype and a similar fitness pattern (cofitness) to another gene, and are therefore good candidates for functional annotation using mutant fitness. Among 502 poorly characterized Z. mobilis genes, we identified a significant cofitness relationship for 174. For 57 of these genes without a specific functional annotation, we found additional evidence to support the biological significance of these gene-gene associations, and in 33 instances, we were able to predict specific physiological or biochemical roles for the poorly characterized genes. Last, we identified a set of 79 diverse mutant fitness experiments in Z. mobilis that are nearly as biologically informative as the entire set of 492 experiments. Therefore, our work provides a blueprint for the functional annotation of diverse bacteria using mutant fitness.« less

  2. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

    SciTech Connect (OSTI)

    Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.; Santee, C.A.; Bradford, M.A.; Treseder, K.K.; Wallenstein, M.D.; Brodie, E.L.

    2011-04-18

    Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.

  3. The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhang, Zilian; Chen, Yi; Wang, Rui; Cai, Ruanhong; Fu, Yingnan; Jiao, Nianzhi; Quigg, Antonietta

    2015-11-16

    Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not bemore » completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. Finally, the fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.« less

  4. Lubricating bacteria model for the growth of bacterial colonies exposed to ultraviolet radiation

    SciTech Connect (OSTI)

    Zhang Shengli; Zhang Lei; Liang Run; Zhang Erhu; Liu Yachao; Zhao Shumin

    2005-11-01

    In this paper, we study the morphological transition of bacterial colonies exposed to ultraviolet radiation by modifying the bacteria model proposed by Delprato et al. Our model considers four factors: the lubricant fluid generated by bacterial colonies, a chemotaxis initiated by the ultraviolet radiation, the intensity of the ultraviolet radiation, and the bacteria's two-stage destruction rate with given radiation intensities. Using this modified model, we simulate the ringlike pattern formation of the bacterial colony exposed to uniform ultraviolet radiation. The following is shown. (1) Without the UV radiation the colony forms a disklike pattern and reaches a constant front velocity. (2) After the radiation is switched on, the bacterial population migrates to the edge of the colony and forms a ringlike pattern. As the intensity of the UV radiation is increased the ring forms faster and the outer velocity of the colony decreases. (3) For higher radiation intensities the total population decreases, while for lower intensities the total population increases initially at a small rate and then decreases. (4) After the UV radiation is switched off, the bacterial population grows both outward as well as into the inner region, and the colony's outer front velocity recovers to a constant value. All these results agree well with the experimental observations [Phys. Rev. Lett. 87, 158102 (2001)]. Along with the chemotaxis, we find that lubricant fluid and the two-stage destruction rate are critical to the dynamics of the growth of the bacterial colony when exposed to UV radiation, and these were not previously considered.

  5. The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities

    SciTech Connect (OSTI)

    Zhang, Zilian; Chen, Yi; Wang, Rui; Cai, Ruanhong; Fu, Yingnan; Jiao, Nianzhi; Quigg, Antonietta

    2015-11-16

    Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not be completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. Finally, the fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.

  6. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

    SciTech Connect (OSTI)

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D.; Zak, Donald R.; Kuske, Cheryl R.

    2015-04-23

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes) in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.

  7. Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Hesse, Cedar N.; Mueller, Rebecca C.; Vuyisich, Momchilo; Gallegos-Graves, La Verne; Gleasner, Cheryl D.; Zak, Donald R.; Kuske, Cheryl R.

    2015-04-23

    Anthropogenic N deposition alters patterns of C and N cycling in temperate forests, where forest floor litter decomposition is a key process mediated by a diverse community of bacteria and fungi. To track forest floor decomposer activity we generated metatranscriptomes that simultaneously surveyed the actively expressed bacterial and eukaryote genes in the forest floor, to compare the impact of N deposition on the decomposers in two natural maple forests in Michigan, USA, where replicate field plots had been amended with N for 16 years. Site and N amendment responses were compared using about 74,000 carbohydrate active enzyme transcript sequences (CAZymes)more » in each metatranscriptome. Parallel ribosomal RNA (rRNA) surveys of bacterial and fungal biomass and taxonomic composition showed no significant differences in either biomass or OTU richness between the two sites or in response to N. Site and N amendment were not significant variables defining bacterial taxonomic composition, but they were significant for fungal community composition, explaining 17 and 14% of the variability, respectively. The relative abundance of expressed bacterial and fungal CAZymes changed significantly with N amendment in one of the forests, and N-response trends were also identified in the second forest. Although the two ambient forests were similar in community biomass, taxonomic structure and active CAZyme profile, the shifts in active CAZyme profiles in response to N-amendment differed between the sites. One site responded with an over-expression of bacterial CAZymes, and the other site responded with an over-expression of both fungal and different bacterial CAZymes. Both sites showed reduced representation of fungal lignocellulose degrading enzymes in N-amendment plots. The metatranscriptome approach provided a holistic assessment of eukaryote and bacterial gene expression and is applicable to other systems where eukaryotes and bacteria interact.« less

  8. LLNL Genomic Assessment: Viral and Bacterial Sequencing Needs for TMTI, Tier 1 Report

    SciTech Connect (OSTI)

    Slezak, T; Borucki, M; Lenhoff, R; Vitalis, E

    2009-09-29

    virulence or host range genes. This approach will provide information that can be used by structural biologists to help develop therapeutics and vaccines. We have pointed out such high priority strains of which we are aware, and note that if any such isolates should be discovered, they will rise to the top priority. We anticipate difficulty locating samples with unusual resistance phenotypes, in particular. Sequencing strategies for isolates in queue 1 should aim for as complete finishing status as possible, since high-quality initial annotation (gene-calling) will be necessary for the follow-on protein structure analyses contributing to countermeasure development. Queue 2 for sequencing determination will be more dynamic than queue 1, and samples will be added to it as they become available to the TMTI program. 2. Selection of isolates that will provide broader information about diversity and phylogenetics and aid in specific detection as well as forensics. This approach focuses on sequencing of isolates that will provide better resolution of variants that are (or were) circulating in nature. The finishing strategy for queue 2 does not require complete closing with annotation. This queue is more static, as there is considerable phylogenetic data, and in this report we have sought to reveal gaps and make suggestions to fill them given existing sequence data and strain information. In this report we identify current sequencing gaps in both priority queue categories. Note that this is most applicable to the bacterial pathogens, as most viruses are by default in queue 1. The Phase I focus of this project is on viral hemorrhagic fever viruses and Category A bacterial agents as defined to us by TMTI. We have carried out individual analyses on each species of interest, and these are included as chapters in this report. Viruses and bacteria are biologically very distinct from each other and require different methods of analysis and criteria for sequencing prioritization. Therefore

  9. Bacterial inosine 5'-monophosphate dehydrogenase ("IMPDH") DNA as a dominant selectable marker in mammals and other eukaryotes

    DOE Patents [OSTI]

    Huberman, Eliezer; Baccam, Mekhine J.

    2007-02-27

    The present invention relates to a nucleic acid sequence and its corresponding protein sequence useful as a dominant selectable marker in eukaryotes. More specifically the invention relates to a nucleic acid encoding a bacterial IMPDH gene that has been engineered into a eukaryotic expression vectors, thereby permitting bacterial IMPDH expression in mammalian cells. Bacterial IMPDH expression confers resistance to MPA which can be used as dominant selectable marker in eukaryotes including mammals. The invention also relates to expression vectors and cells that express the bacterial IMPDH gene as well as gene therapies and protein synthesis.

  10. Reactive hydroxyl radical-driven oral bacterial inactivation by radio frequency atmospheric plasma

    SciTech Connect (OSTI)

    Kang, Sung Kil; Lee, Jae Koo; Choi, Myeong Yeol; Koo, Il Gyo; Kim, Paul Y.; Kim, Yoonsun; Kim, Gon Jun; Collins, George J.; Mohamed, Abdel-Aleam H.

    2011-04-04

    We demonstrated bacterial (Streptococcus mutans) inactivation by a radio frequency power driven atmospheric pressure plasma torch with H{sub 2}O{sub 2} entrained in the feedstock gas. Optical emission spectroscopy identified substantial excited state OH generation inside the plasma and relative OH formation was verified by optical absorption. The bacterial inactivation rate increased with increasing OH generation and reached a maximum 5-log{sub 10} reduction with 0.6%H{sub 2}O{sub 2} vapor. Generation of large amounts of toxic ozone is drawback of plasma bacterial inactivation, thus it is significant that the ozone concentration falls within recommended safe allowable levels with addition of H{sub 2}O{sub 2} vapor to the plasma.

  11. LLNL Genomic Assessment: Viral and Bacterial Sequencing Needs for TMTI, Task 1.4.2 Report

    SciTech Connect (OSTI)

    Slezak, T; Borucki, M; Lam, M; Lenhoff, R; Vitalis, E

    2010-01-26

    Good progress has been made on both bacterial and viral sequencing by the TMTI centers. While access to appropriate samples is a limiting factor to throughput, excellent progress has been made with respect to getting agreements in place with key sources of relevant materials. Sharing of sequenced genomes funded by TMTI has been extremely limited to date. The April 2010 exercise should force a resolution to this, but additional managerial pressures may be needed to ensure that rapid sharing of TMTI-funded sequencing occurs, regardless of collaborator constraints concerning ultimate publication(s). Policies to permit TMTI-internal rapid sharing of sequenced genomes should be written into all TMTI agreements with collaborators now being negotiated. TMTI needs to establish a Web-based system for tracking samples destined for sequencing. This includes metadata on sample origins and contributor, information on sample shipment/receipt, prioritization by TMTI, assignment to one or more sequencing centers (including possible TMTI-sponsored sequencing at a contributor site), and status history of the sample sequencing effort. While this system could be a component of the AFRL system, it is not part of any current development effort. Policy and standardized procedures are needed to ensure appropriate verification of all TMTI samples prior to the investment in sequencing. PCR, arrays, and classical biochemical tests are examples of potential verification methods. Verification is needed to detect miss-labeled, degraded, mixed or contaminated samples. Regular QC exercises are needed to ensure that the TMTI-funded centers are meeting all standards for producing quality genomic sequence data.

  12. Bacterially induced precipitation of CaCO sub 3 : An example from studies of cyanobacterial mats

    SciTech Connect (OSTI)

    Chafetz, H.S.

    1990-04-30

    Bacteria induce the precipitation of calcium carbonate in the laboratory and in nature by altering their chemical environment. Geologists are recognizing the possibility that bacterially induced precipitates may form significant mineral deposits, unfortunately, there are currently no sound criteria by which they can be recognized in recent sediments, or in the rock record. Cultures of aerobic and facultative bacteria from cyanobacterial mats on Andros Island, Bahamas, and Baffin Bay, Texas, induced the precipitation of calcium carbonate under controlled conditions. Crusts, the largest features formed, are composed of 5--200{mu}m diameter bundles which are, in turn, composed of numerous individual crystals. The smallest observed features are 0.1--0.4{mu}m spheres and rods which comprise some individual crystals and crystal bundles. Crystal bundles resembling rhombohedra, tetragonal disphenoids, tetragonal dipyramids, and calcite dumbbells appear to be uniquely bacterial in origin, and they have all been observed in recent sediments. Swollen rods, discs, curved dumbbells, and 50--200{mu}m optically continuous crystals resembling brushes may be uniquely bacterial in origin, however, they have not been reported by other laboratories nor observed in natural settings. Presence of any of these forms in recent sediments should be taken as strong evidence for bacterial influence. Spheres and aragonite dumbbells have also been observed in natural environments, however, they are not always bacterial in origin. Precipitation of calcium carbonate occurs preferentially on dead cyanobacteria in the presence of bacteria. Lithification of algal mats to form stromatolites may take place in the zone of decaying organic matter due to bacterial activity.

  13. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

    SciTech Connect (OSTI)

    Wu, C.H.; Sercu, B.; Van De Werhorst, L.C.; Wong, J.; DeSantis, T.Z.; Brodie, E.L.; Hazen, T.C.; Holden, P.A.; Andersen, G.L.

    2010-03-01

    Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. Using a high-density microarray (PhyloChip), we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs) common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and a-proteobacteria) found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A) from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  14. Bacterial CRISPR/Cas DNA endonucleases: A revolutionary technology that could dramatically impact viral research and treatment

    SciTech Connect (OSTI)

    Kennedy, Edward M.; Cullen, Bryan R.

    2015-05-15

    CRISPR/Cas systems mediate bacterial adaptive immune responses that evolved to protect bacteria from bacteriophage and other horizontally transmitted genetic elements. Several CRISPR/Cas systems exist but the simplest variant, referred to as Type II, has a single effector DNA endonuclease, called Cas9, which is guided to its viral DNA target by two small RNAs, the crRNA and the tracrRNA. Initial efforts to adapt the CRISPR/Cas system for DNA editing in mammalian cells, which focused on the Cas9 protein from Streptococcus pyogenes (Spy), demonstrated that Spy Cas9 can be directed to DNA targets in mammalian cells by tracrRNA:crRNA fusion transcripts called single guide RNAs (sgRNA). Upon binding, Cas9 induces DNA cleavage leading to mutagenesis as a result of error prone non-homologous end joining (NHEJ). Recently, the Spy Cas9 system has been adapted for high throughput screening of genes in human cells for their relevance to a particular phenotype and, more generally, for the targeted inactivation of specific genes, in cell lines and in vivo in a number of model organisms. The latter aim seems likely to be greatly enhanced by the recent development of Cas9 proteins from bacterial species such as Neisseria meningitidis and Staphyloccus aureus that are small enough to be expressed using adeno-associated (AAV)-based vectors that can be readily prepared at very high titers. The evolving Cas9-based DNA editing systems therefore appear likely to not only impact virology by allowing researchers to screen for human genes that affect the replication of pathogenic human viruses of all types but also to derive clonal human cell lines that lack individual gene products that either facilitate or restrict viral replication. Moreover, high titer AAV-based vectors offer the possibility of directly targeting DNA viruses that infect discrete sites in the human body, such as herpes simplex virus and hepatitis B virus, with the hope that the entire population of viral DNA genomes

  15. EERE Success Story-DOE-Funded Research on Bacterial Enzyme Could Lead to

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Cheaper Biofuel | Department of Energy Research on Bacterial Enzyme Could Lead to Cheaper Biofuel EERE Success Story-DOE-Funded Research on Bacterial Enzyme Could Lead to Cheaper Biofuel May 28, 2014 - 12:24pm Addthis A microorganism found in heated freshwater pools may hold the key to more efficient, cost-effective biofuel production. Researchers at the Department of Energy's National Renewable Energy Laboratory found that an enzyme known as CelA can digest cellulose almost twice as fast as

  16. MICROFLUIDIC MODULES FOR ISOLATION OF RECOMBINANT CYTOKINE FROM BACTERIAL LYSATES

    SciTech Connect (OSTI)

    Retterer, Scott T; Doktycz, Mitchel John

    2014-01-01

    The portability and personalization of health-care diagnostics and treatments benefits from advancements and applications of micro and nanotechnology. Modularization and miniaturization of standardized biochemical processes and tests facilitates the advancement and customization of analyte detection and diagnosis on-chip. The goal of our work here is to develop modular platforms for on-chip biochemical processing of synthesized biologics for a range of on-demand applications. Our report focuses on the initial development, characterization and application of microfluidic size exclusion/gel filtration and ion exchange protein concentration modules for cytokine isolation from spiked cell extracts.

  17. Engineered enzymatically active bacteriophages and methods of uses thereof

    DOE Patents [OSTI]

    Collins, James J; Kobayashi, Hideki; Kearn, Mads; Araki, Michihiro; Friedland, Ari; Lu, Timothy Kuan-Ta

    2012-05-22

    The present invention provides engineered bacteriophages that express at least one biofilm degrading enzyme on their surface and uses thereof for degrading bacterial biofilms. The invention also provides genetically engineered bacteriophages expressing the biofilm degrading enzymes and proteins necessary for the phage to replicate in different naturally occurring biofilm producing bacteria. The phages of the invention allow a method of biofilm degradation by the use of one or only a few administration of the phage because the system using these phages is self perpetuating, and capable of degrading biofilm even when the concentration of bacteria within the biofilm is low.

  18. Quadrature conductivity: A quantitative indicator of bacterial abundance in porous media

    SciTech Connect (OSTI)

    Chi Zhang; Andre Revil; Yoshiko Fujita; Junko Munakata-Marr; George Redden

    2014-09-01

    ABSTRACT The abundance and growth stages of bacteria in subsurface porous media affect the concentrations and distributions of charged species within the solid-solution interfaces. Therefore, spectral induced polarization (SIP) measurements can be used to monitor changes in bacterial biomass and growth stage. Our goal was to gain a better understanding of the SIP response of bacteria present in a porous material. Bacterial cell surfaces possess an electric double layer and therefore become polarized in an electric field. We performed SIP measurements over the frequency range of 0.11 kHz on cell suspensions alone and cell suspensions mixed with sand at four pore water conductivities. We used Zymomonas mobilis at four different cell densities (in- cluding the background). The quadrature conductivity spectra exhibited two peaks, one around 0.050.10 Hz and the other around 110 Hz. Because SIP measurements on bacterial suspensions are typically made at frequencies greater than 1 Hz, these peaks have not been previously reported. In the bac-terial suspensions in growth medium, the quadrature conduc-tivity at peak I was linearly proportional to the density of the bacteria. For the case of the suspensions mixed with sands, we observed that peak II presented a smaller increase in the quadrature conductivity with the cell density. A comparison of the experiments with and without sand grains illustrated the effect of the porous medium on the overall quadrature con- ductivity response (decrease in the amplitude and shift of the peaks to the lower frequencies). Our results indicate that for a given porous medium, time-lapse SIP has potential for mon- itoring changes in bacterial abundance within porous media.

  19. K+ block is the mechanism of functional asymmetry in bacterial Nav channels

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ngo, Van; Wang, Yibo; Haas, Stephan; Noskov, Sergei Y.; Farley, Robert A.; Weinstein, Harel

    2016-01-04

    Crystal structures of several bacterial Nav channels have been recently published and molecular dynamics simulations of ion permeation through these channels are consistent with many electrophysiological properties of eukaryotic channels. Bacterial Nav channels have been characterized as functionally asymmetric, and the mechanism of this asymmetry has not been clearly understood. To address this question, we combined non-equilibrium simulation data with two-dimensional equilibrium unperturbed landscapes generated by umbrella sampling and Weighted Histogram Analysis Methods for multiple ions traversing the selectivity filter of bacterial NavAb channel. This approach provided new insight into the mechanism of selective ion permeation in bacterial Nav channels.more » The non-equilibrium simulations indicate that two or three extracellular K+ ions can block the entrance to the selectivity filter of NavAb in the presence of applied forces in the inward direction, but not in the outward direction. The block state occurs in an unstable local minimum of the equilibrium unperturbed free-energy landscape of two K+ ions that can be ‘locked’ in place bymodest applied forces. In contrast to K+, three Na+ ions move favorably through the selectivity filter together as a unit in a loose “knock-on” mechanism of permeation in both inward and outward directions, and there is no similar local minimum in the two-dimensional free-energy landscape of two Na+ ions for a block state. The useful work predicted by the non-equilibrium simulations that is required to break the K+ block is equivalent to large applied potentials experimentally measured for two bacterial Nav channels to induce inward currents of K+ ions. Here, these results illustrate how inclusion of non-equilibrium factors in the simulations can provide detailed information about mechanisms of ion selectivity that is missing from mechanisms derived from either crystal structures or equilibrium unperturbed free

  20. A functional gene array for detection of bacterial virulence elements

    SciTech Connect (OSTI)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  1. Oxygen-­dependent regulation of bacterial lipid production

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lemmer, Kimberly C.; Dohnalkova, Alice C.; Noguera, Daniel R.; Donohue, Timothy J.

    2015-05-02

    Understanding the mechanisms of lipid accumulation in microorganisms is important for several reasons. In addition to providing insight into assembly of biological membranes, lipid accumulation has important applications in the production of renewable fuels and chemicals. The photosynthetic bacterium Rhodobacter sphaeroides is an attractive organism to study lipid accumulation, as it has the somewhat unique ability to increase membrane production at low O₂ tensions. Under these conditions, R. sphaeroides develops invaginations of the cytoplasmic membrane to increase its membrane surface area for housing of the membrane-bound components of its photosynthetic apparatus. Here we use fatty acid levels as a reportermore » of membrane lipid content. We show that, under low-O₂ and anaerobic conditions, the total fatty acid content per cell increases 3-fold. We also find that the increases in the amount of fatty acid and photosynthetic pigment per cell are correlated as O₂ tensions or light intensity are changed. To ask if lipid and pigment accumulation were genetically separable, we analyzed strains with mutations in known photosynthetic regulatory pathways. While a strain lacking AppA failed to induce photosynthetic pigment-protein complex accumulation, it increased fatty acid content under low O2 conditions. We also found that an intact PrrBA pathway is required for low O2-induced fatty acid accumulation. In conclusion, our findings suggest a previously unknown role of R. sphaeroides transcriptional regulators in increasing fatty acid and phospholipid accumulation in response to decreased O₂ tension.« less

  2. Oxygen-­dependent regulation of bacterial lipid production

    SciTech Connect (OSTI)

    Lemmer, Kimberly C.; Dohnalkova, Alice C.; Noguera, Daniel R.; Donohue, Timothy J.

    2015-05-02

    Understanding the mechanisms of lipid accumulation in microorganisms is important for several reasons. In addition to providing insight into assembly of biological membranes, lipid accumulation has important applications in the production of renewable fuels and chemicals. The photosynthetic bacterium Rhodobacter sphaeroides is an attractive organism to study lipid accumulation, as it has the somewhat unique ability to increase membrane production at low O₂ tensions. Under these conditions, R. sphaeroides develops invaginations of the cytoplasmic membrane to increase its membrane surface area for housing of the membrane-bound components of its photosynthetic apparatus. Here we use fatty acid levels as a reporter of membrane lipid content. We show that, under low-O₂ and anaerobic conditions, the total fatty acid content per cell increases 3-fold. We also find that the increases in the amount of fatty acid and photosynthetic pigment per cell are correlated as O₂ tensions or light intensity are changed. To ask if lipid and pigment accumulation were genetically separable, we analyzed strains with mutations in known photosynthetic regulatory pathways. While a strain lacking AppA failed to induce photosynthetic pigment-protein complex accumulation, it increased fatty acid content under low O2 conditions. We also found that an intact PrrBA pathway is required for low O2-induced fatty acid accumulation. In conclusion, our findings suggest a previously unknown role of R. sphaeroides transcriptional regulators in increasing fatty acid and phospholipid accumulation in response to decreased O₂ tension.

  3. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

    SciTech Connect (OSTI)

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; Trimble, William; Meyer, Folker; Guglielmini, Julien; Rocha, Eduardo P. C.; Polz, Martin F.

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells. Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.

  4. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; Trimble, William; Meyer, Folker; Guglielmini, Julien; Rocha, Eduardo P. C.; Polz, Martin F.

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells.more » Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.« less

  5. Clone Bacterial Thermal Stable Enzymes in T. Reesei: Cooperative Research and Development Final Report, CRADA Number CRD-01-00105

    SciTech Connect (OSTI)

    Himmel, M. E.

    2010-08-01

    The focus of this CRADA was on improving the efficacy of GCI's primary host for commercial cellulase production, Trichoderma reesei.

  6. Improved Bacterial and Viral Recoveries from 'Complex' Samples using Electrophoretically Assisted Acoustic Focusing

    SciTech Connect (OSTI)

    Ness, K; Rose, K; Jung, B; Fisher, K; Mariella, Jr., R P

    2008-03-27

    Automated front-end sample preparation technologies can significantly enhance the sensitivity and reliability of biodetection assays [1]. We are developing advanced sample preparation technologies for biowarfare detection and medical point-of-care diagnostics using microfluidic systems with continuous sample processing capabilities. Here we report an electrophoretically assisted acoustic focusing technique to rapidly extract and enrich viral and bacterial loads from 'complex samples', applied in this case to human nasopharyngeal samples as well as simplified surrogates. The acoustic forces capture and remove large particles (> 2 {micro}m) such as host cells, debris, dust, and pollen from the sample. We simultaneously apply an electric field transverse to the flow direction to transport small ({le} 2 {micro}m), negatively-charged analytes into a separate purified recovery fluid using a modified H-filter configuration [Micronics US Patent 5,716,852]. Hunter and O'Brien combined transverse electrophoresis and acoustic focusing to measure the surface charge on large particles, [2] but to our knowledge, our work is the first demonstration combining these two techniques in a continuous flow device. Marina et al. demonstrated superimposed dielectrophoresis (DEP) and acoustic focusing for enhanced separations [3], but these devices have limited throughput due to the rapid decay of DEP forces. Both acoustic standing waves and electric fields exert significant forces over the entire fluid volume in microchannels, thus allowing channels with larger dimensions (> 100 {micro}m) and high throughputs (10-100 {micro}L/min) necessary to process real-world volumes (1 mL). Previous work demonstrated acoustic focusing of microbeads [4] and biological species [5] in various geometries. We experimentally characterized our device by determining the biological size-cutoff where acoustic radiation pressure forces no longer transport biological particles. Figure 1 shows images of E

  7. Characterization of the bacterial metagenome in an industrial algae bioenergy production system

    SciTech Connect (OSTI)

    Huang, Shi; Fulbright, Scott P; Zeng, Xiaowei; Yates, Tracy; Wardle, Greg; Chisholm, Stephen T; Xu, Jian; Lammers, Peter

    2011-03-16

    Cultivation of oleaginous microalgae for fuel generally requires growth of the intended species to the maximum extent supported by available light. The presence of undesired competitors, pathogens and grazers in cultivation systems will create competition for nitrate, phosphate, sulfate, iron and other micronutrients in the growth medium and potentially decrease microalgal triglyceride production by limiting microalgal health or cell density. Pathogenic bacteria may also directly impact the metabolism or survival of individual microalgal cells. Conversely, symbiotic bacteria that enhance microalgal growth may also be present in the system. Finally, the use of agricultural and municipal wastes as nutrient inputs for microalgal production systems may lead to the introduction and proliferation of human pathogens or interfere with the growth of bacteria with beneficial effects on system performance. These considerations underscore the need to understand bacterial community dynamics in microalgal production systems in order to assess microbiome effects on microalgal productivity and pathogen risks. Here we focus on the bacterial component of microalgal production systems and describe a pipeline for metagenomic characterization of bacterial diversity in industrial cultures of an oleaginous alga, Nannochloropsis salina. Environmental DNA was isolated from 12 marine algal cultures grown at Solix Biofuels, a region of the 16S rRNA gene was amplified by PCR, and 16S amplicons were sequenced using a 454 automated pyrosequencer. The approximately 70,000 sequences that passed quality control clustered into 53,950 unique sequences. The majority of sequences belonged to thirteen phyla. At the genus level, sequences from all samples represented 169 different genera. About 52.94% of all sequences could not be identified at the genus level and were classified at the next highest possible resolution level. Of all sequences, 79.92% corresponded to 169 genera and 70 other taxa. We

  8. Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Bond-Lamberty, Benjamin; Bolton, Harvey; Fansler, Sarah J.; Heredia-Langner, Alejandro; Liu, Chongxuan; McCue, Lee Ann; Smith, Jeff L.; Bailey, Vanessa L.

    2016-03-02

    The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampledmore » the original 1994 soil transplants and controls, measuring CO2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5 °C monthly maximum air temperature, +50 mm yr-1precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. Lastly, these results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even

  9. Sterilization of bacterial endospores by an atmospheric-pressure argon plasma jet

    SciTech Connect (OSTI)

    Uhm, Han S.; Lim, Jin P.; Li, Shou Z.

    2007-06-25

    Argon plasma jets penetrate deep into ambient air and create a path for oxygen radicals to sterilize microbes. A sterilization experiment with bacterial endospores indicates that an argon-oxygen plasma jet very effectively kills endospores of Bacillus atrophaeus (ATCC 9372), thereby demonstrating its capability to clean surfaces and its usefulness for reinstating contaminated equipment as free from toxic biological warfare agents. However, the spore-killing efficiency of the atmospheric-pressure argon-oxygen jet depends very sensitively on the oxygen concentration in the argon gas.

  10. Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens

    SciTech Connect (OSTI)

    Aylward, Frank O.; Burnum, Kristin E.; Scott, Jarrod J.; Suen, Garret; Tringe, Susannah G.; Adams, Sandra M.; Barry, Kerrie W.; Nicora, Carrie D.; Piehowski, Paul D.; Purvine, Samuel O.; Starrett, Gabriel J.; Goodwin, Lynne A.; Smith, Richard D.; Lipton, Mary S.; Currie, Cameron R.

    2012-09-01

    Herbivores gain access to nutrients stored in plant biomass largely by harnessing the metabolic activities of microbes. Leaf-cutter ants of the genus Atta are a hallmark example; these dominant Neotropical herbivores cultivate symbiotic fungus gardens on massive quantities of fresh plant forage. As the external digestive system of the ants, fungus gardens facilitate the production and sustenance of millions of workers in mature Atta colonies. Here we use metagenomic, and metaproteomic techniques to characterize the bacterial diversity and overall physiological potential of fungus gardens from two species of Atta. Our analysis of over 1.2 Gbp of community metagenomic sequence and three 16S pyrotag libraries reveals that, in addition to harboring the dominant fungal crop, these ecosystems contain abundant populations of Enterobacteriaceae, including the genera Enterobacter, Pantoea, Klebsiella, Citrobacter, and Escherichia. We show that these bacterial communities possess genes commonly associated with lignocellulose degradation, and likely participate in the processing of plant biomass. Additionally, we demonstrate that bacteria in these environments encode a diverse suite of biosynthetic pathways, and that they may enrich the nitrogen-poor forage of the ants with B-vitamins, amino acids, and proteins. These results are consistent with the hypothesis that fungus gardens are highly-specialized fungus-bacteria communities that efficiently convert plant material into usable energy for their ant hosts. Together with recent investigations into the microbial symbionts of vertebrates, our work underscores the importance of microbial communities to the ecology and evolution of herbivorous metazoans.

  11. Bacterial Community Succession During in situ Uranium Bioremediation: Spatial Similarities Along Controlled Flow Paths

    SciTech Connect (OSTI)

    Hwang, Chiachi; Wu, Weimin; Gentry, Terry J.; Carley, Jack; Corbin, Gail A.; Carroll, Sue L.; Watson, David B.; Jardine, Phil M.; Zhou, Jizhong; Criddle, Craig S.; Fields, Matthew W.

    2009-05-22

    Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction, and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5 y period. Analyses showed that the communities changed in a manner consistent with geochemical variations that occurred along temporal and spatial scales. Canonical correspondence analysis revealed that the levels of nitrate, uranium, sulfide, sulfate, and ethanol strongly correlated with particular bacterial populations. As sulfate and U(VI) levels declined, sequences representative of sulfate-reducers and metal-reducers were detected at high levels. Ultimately, sequences associated with sulfate-reducing populations predominated, and sulfate levels declined as U(VI) remained at low levels. When engineering controls were compared to the population variation via canonical ordination, changes could be related to dissolved oxygen control and ethanol addition. The data also indicated that the indigenous populations responded differently to stimulation for bio-reduction; however, the two bio-stimulated communities became more similar after different transitions in an idiosyncratic manner. The strong associations between particular environmental variables and certain populations provide insight into the establishment of practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls and microbial ecology.

  12. Structural Studies of Bacterial Enzymes and their Relation to Antibiotic Resistance Mechanisms - Final Paper

    SciTech Connect (OSTI)

    Maltz, Lauren

    2015-08-27

    By using protein crystallography and X-ray diffraction, structures of bacterial enzymes were solved to gain a better understanding of how enzymatic modification acts as an antibacterial resistance mechanism. Aminoglycoside phosphotransferases (APHs) are one of three aminoglycoside modifying enzymes that confer resistance to the aminoglycoside antibiotics via enzymatic modification, rendering many drugs obsolete. Specifically, the APH(2) family vary in their substrate specificities and also in their preference for the phosphate donor (ADP versus GDP). By solving the structures of members of the APH(2) family of enzymes, we can see how domain movements are important to their substrate specificity. Our structure of the ternary complex of APH(2)-IIIa with GDP and kanamycin, when compared to the known structures of APH(2)-IVa, reveals that there are real physical differences between these two enzymes, a structural finding that explains why the two enzymes differ in their preferences for certain aminoglycosides. Another important group of bacterial resistance enzymes are the Class D ?- lactamases. Oxacillinase carbapenemases (OXAs) are part of this enzyme class and have begun to confer resistance to last resort drugs, most notably carbapenems. Our structure of OXA-143 shows that the conformational flexibility of a conserved hydrophobic residue in the active site (Val130) serves to control the entry of a transient water molecule responsible for a key step in the enzymes mechanism. Our results provide insight into the structural mechanisms of these two different enzymes

  13. 1

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Breakthrough antibacterial approach could resolve serious skin infections August 26, 2014 Los Alamos and partners test ionic liquids to break bacterial biofilm layer and save lives LOS ALAMOS, N.M., Aug. 26, 2014-Like a protective tent over a colony of harmful bacteria, biofilms make the treatment of skin infections especially difficult. Microorganisms protected in a biofilm pose a significant health risk due to their antibiotic resistance and recalcitrance to treatment, and biofilm-protected

  14. sustainable development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sustainable development - Sandia Energy Energy Search Icon Sandia Home Locations Contact Us ... Hydrogen Infrastructure Hydrogen Production Market Transformation Fuel Cells ...

  15. Bacterially induced precipitation of CaCO{sub 3}: An example from studies of cyanobacterial mats. Final report

    SciTech Connect (OSTI)

    Chafetz, H.S.

    1990-04-30

    Bacteria induce the precipitation of calcium carbonate in the laboratory and in nature by altering their chemical environment. Geologists are recognizing the possibility that bacterially induced precipitates may form significant mineral deposits, unfortunately, there are currently no sound criteria by which they can be recognized in recent sediments, or in the rock record. Cultures of aerobic and facultative bacteria from cyanobacterial mats on Andros Island, Bahamas, and Baffin Bay, Texas, induced the precipitation of calcium carbonate under controlled conditions. Crusts, the largest features formed, are composed of 5--200{mu}m diameter bundles which are, in turn, composed of numerous individual crystals. The smallest observed features are 0.1--0.4{mu}m spheres and rods which comprise some individual crystals and crystal bundles. Crystal bundles resembling rhombohedra, tetragonal disphenoids, tetragonal dipyramids, and calcite dumbbells appear to be uniquely bacterial in origin, and they have all been observed in recent sediments. Swollen rods, discs, curved dumbbells, and 50--200{mu}m optically continuous crystals resembling brushes may be uniquely bacterial in origin, however, they have not been reported by other laboratories nor observed in natural settings. Presence of any of these forms in recent sediments should be taken as strong evidence for bacterial influence. Spheres and aragonite dumbbells have also been observed in natural environments, however, they are not always bacterial in origin. Precipitation of calcium carbonate occurs preferentially on dead cyanobacteria in the presence of bacteria. Lithification of algal mats to form stromatolites may take place in the zone of decaying organic matter due to bacterial activity.

  16. Program Development

    SciTech Connect (OSTI)

    Atencio, Julian J.

    2014-05-01

    This presentation covers how to go about developing a human reliability program. In particular, it touches on conceptual thinking, raising awareness in an organization, the actions that go into developing a plan. It emphasizes evaluating all positions, eliminating positions from the pool due to mitigating factors, and keeping the process transparent. It lists components of the process and objectives in process development. It also touches on the role of leadership and the necessity for audit.

  17. Economic Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Economic Development Economic Development Los Alamos is committed to investing and partnering in economic development initiatives and programs that have a positive impact to stimulate business growth that creates jobs and strengthens communities in Northern New Mexico. September 20, 2013 R&M Construction from Santa Clara Pueblo is a 2015 Native American Venture Acceleration Fund recipient. R&M Construction from Santa Clara Pueblo is a 2015 Native American Venture Acceleration Fund

  18. Technology Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    ... Developing advanced materials such as novel coatings and composites. Defining and validating control strategies for wave energy converters (WECs) to improve power performance. ...

  19. Structure of the Transmembrane Regions of a Bacterial Cyclic Nucleotide-Regulated Channel

    SciTech Connect (OSTI)

    Clayton,G.; Latieri, S.; Heginbotham, L.; Unger, V.; Morais-Cabral, J.

    2008-01-01

    The six-transmembrane helix (6 TM) tetrameric cation channels form the largest ion channel family, some members of which are voltage-gated and others are not. There are no reported channel structures to match the wealth of functional data on the non-voltage-gated members. We determined the structure of the transmembrane regions of the bacterial cyclic nucleotide-regulated channel MlotiK1, a non-voltage-gated 6 TM channel. The structure showed how the S1-S4 domain and its associated linker can serve as a clamp to constrain the gate of the pore and possibly function in concert with ligand-binding domains to regulate the opening of the pore. The structure also led us to hypothesize a new mechanism by which motions of the S6 inner helices can gate the ion conduction pathway at a position along the pore closer to the selectivity filter than the canonical helix bundle crossing.

  20. Conservation of Modules but not Phenotype in Bacterial Response to Environmental Stress

    SciTech Connect (OSTI)

    Timberlake, Sonia; Joachimiak, Marcin; Joyner, Dominique; Chakraborty, Romy; Baumohl, Jason; Dehal, Paramvir; Arkin, Adam; Hazen, Terry; Alm, Eric

    2010-05-17

    Microbes live in changing environments and change their phenotype via gene regulation in response. Although this transcriptional response is important for fitness, very little is known about how it evolves in microbes. We started by asking a number of high-level questions about the evolution of transcriptional phenotype: (1) To what extent is transcriptional response conserved, i.e. do conserved genes respond similarly to the same condition; (2) To what extent are transcriptional modules conserved; and (3) Does there exist a general stress response to a variety of stressors? To illuminate these questions, we analyzed more than 500 microarray experiments across the bacterial domain. We looked for conservation of transcriptional regulation both in close sister species and vastly divergent clades. In addition, we produced and analyzed an extensive in-house compendium of environmental stress data in three metal-reducing bacteria.

  1. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Payne, Samuel H.; Monroe, Matthew E.; Overall, Christopher C.; Kiebel, Gary R.; Degan, Michael G.; Gibbons, Bryson C.; Fujimoto, Grant M.; Purvine, Samuel O.; Adkins, Joshua N.; Lipton, Mary S.; et al

    2015-08-18

    This dataset deposition announces the submission to public repositories of the PNNL Biodiversity Library, a large collection of global proteomics data for 112 bacterial and archaeal organisms. The data comprises 35,162 tandem mass spectrometry (MS/MS) datasets from ~10 years of research. All data has been searched, annotated and organized in a consistent manner to promote reuse by the community. Protein identifications were cross-referenced with KEGG functional annotations which allows for pathway oriented investigation. We present the data as a freely available community resource. A variety of data re-use options are described for computational modeling, proteomics assay design and bioengineering. Instrumentmore » data and analysis files are available at ProteomeXchange via the MassIVE partner repository under the identifiers PXD001860 and MSV000079053.« less

  2. The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

    SciTech Connect (OSTI)

    Payne, Samuel H.; Monroe, Matthew E.; Overall, Christopher C.; Kiebel, Gary R.; Degan, Michael G.; Gibbons, Bryson C.; Fujimoto, Grant M.; Purvine, Samuel O.; Adkins, Joshua N.; Lipton, Mary S.; Smith, Richard D.

    2015-08-18

    This dataset deposition announces the submission to public repositories of the PNNL Biodiversity Library, a large collection of global proteomics data for 112 bacterial and archaeal organisms. The data comprises 35,162 tandem mass spectrometry (MS/MS) datasets from ~10 years of research. All data has been searched, annotated and organized in a consistent manner to promote reuse by the community. Protein identifications were cross-referenced with KEGG functional annotations which allows for pathway oriented investigation. We present the data as a freely available community resource. A variety of data re-use options are described for computational modeling, proteomics assay design and bioengineering. Instrument data and analysis files are available at ProteomeXchange via the MassIVE partner repository under the identifiers PXD001860 and MSV000079053.

  3. Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Burstein, David; Sun, Christine L.; Brown, Christopher T.; Sharon, Itai; Anantharaman, Karthik; Probst, Alexander J.; Thomas, Brian C.; Banfield, Jillian F.

    2016-02-03

    Here, current understanding of microorganism–virus interactions, which shape the evolution and functioning of Earth’s ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. Wemore » correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides.« less

  4. High Bacterial Diversity of Biological Soil Crusts in Water Tracks over Permafrost in the High Arctic Polar Desert

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Steven, Blaire; Lionard, Marie; Kuske, Cheryl R.; Vincent, Warwick F.

    2013-08-13

    In this paper we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relativemore » abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Finally, taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.« less

  5. Software Developers

    Broader source: Energy.gov [DOE]

    Because SEED will provide a common, open-source data framework, software developers will be able to write applications that access the data in a consistent way (with proper permissions), or build functionalities onto the SEED platform in a replicable way.

  6. Leadership Development

    Broader source: Energy.gov [DOE]

    DOE's Leadership & Development Programs are designed to strengthen the participant’s capacity to lead by deepening their understanding of the DOE’s core values and key leadership characteristics and behaviors, which is the foundation of our model for success.

  7. Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kao-Kniffin, J.; Woodcroft, B. J.; Carver, S. M.; Bockheim, J. G.; Handelsman, J.; Tyson, G. W.; Hinkel, K. M.; Mueller, C. W.

    2015-12-18

    We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the activemore » layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.« less

  8. Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska

    SciTech Connect (OSTI)

    Kao-Kniffin, J.; Woodcroft, B. J.; Carver, S. M.; Bockheim, J. G.; Handelsman, J.; Tyson, G. W.; Hinkel, K. M.; Mueller, C. W.

    2015-12-18

    We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the active layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.

  9. Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Eloe-Fadrosh, Emiley A.; Paez-Espino, David; Jarett, Jessica; Dunfield, Peter F.; Hedlund, Brian P.; Dekas, Anne E.; Grasby, Stephen E.; Brady, Allyson L.; Dong, Hailiang; Briggs, Brandon R.; et al

    2016-01-27

    We analyse the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle withmore » conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.« less

  10. Guanidino groups greatly enhance the action of antimicrobial peptidomimetics against bacterial cytoplasmic membranes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Andreev, Konstantin; Bianchi, Christopher; Laursen, Jonas S.; Citterio, Linda; Hein-Kristensen, Line; Gram, Lone; Kuzmenko, Ivan; Olsen, Christian A.; Gidalevitz, David

    2014-05-28

    In this study, antimicrobial peptides or their synthetic mimics are a promising class of potential new antibiotics. Herein we assess the effect of the type of cationic side chain (i.e., guanidino vs. amino groups) on the membrane perturbing mechanism of antimicrobial ?-peptide?-peptoid chimeras. Langmuir monolayers composed of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylglycerol (DPPG) were used to model cytoplasmic membranes of both Gram-positive and Gram-negative bacteria, while lipopolysaccharide Kdo2-lipid A monolayers were mimicking the outer membrane of Gram-negative species. We report the results of the measurements using an array of techniques, including high-resolution synchrotron surface X-ray scattering, epifluorescence microscopy, and in vitro antimicrobial activity tomorestudy the molecular mechanisms of peptidomimetic interaction with bacterial membranes. We found guanidino group-containing chimeras to exhibit greater disruptive activity on DPPG monolayers than the amino group-containing analogues. However, this effect was not observed for lipopolysaccharide monolayers where the difference was negligible. Furthermore, the addition of the nitrobenzoxadiazole fluorophore did not reduce the insertion activity of these antimicrobials into both model membrane systems examined, which may be useful for future cellular localization studies.less

  11. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Berni Canani, Roberto; Sangwan, Naseer; Stefka, Andrew T.; Nocerino, Rita; Paparo, Lorella; Aitoro, Rosita; Calignano, Antonio; Khan, Aly A.; Gilbert, Jack A.; Nagler, Cathryn R.

    2015-09-22

    Dietary intervention with extensively hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG (EHCF+LGG) accelerates tolerance acquisition in infants with cow’s milk allergy (CMA). We examined whether this effect is attributable, at least in part, to an influence on the gut microbiota. Fecal samples from healthy controls (n=20) and from CMA infants (n=19) before and after treatment with EHCF with (n=12) and without (n=7) supplementation with LGG were compared by 16S rRNA-based operational taxonomic unit clustering and oligotyping. Differential feature selection and generalized linear model fitting revealed that the CMA infants have a diverse gut microbial community structure dominated by Lachnospiraceaemore » (20.5±9.7%) and Ruminococcaceae (16.2±9.1%). Blautia, Roseburia and Coprococcus were significantly enriched following treatment with EHCF and LGG, but only one genus, Oscillospira, was significantly different between infants that became tolerant and those that remained allergic. However, most tolerant infants showed a significant increase in fecal butyrate levels, and those taxa that were significantly enriched in these samples, Blautia and Roseburia, exhibited specific strain-level demarcations between tolerant and allergic infants. As a result, our data suggest that EHCF+LGG promotes tolerance in infants with CMA, in part, by influencing the strain-level bacterial community structure of the infant gut.« less

  12. Real-time Bacterial Detection by Single Cell Based Sensors UsingSynchrotron FTIR Spectromicroscopy

    SciTech Connect (OSTI)

    Veiseh, Mandana; Veiseh, Omid; Martin, Michael C.; Bertozzi,Carolyn; Zhang, Miqin

    2005-08-10

    Microarrays of single macrophage cell based sensors weredeveloped and demonstrated for real time bacterium detection bysynchrotron FTIR microscopy. The cells were patterned on gold-SiO2substrates via a surface engineering technique by which the goldelectrodes were immobilized with fibronectin to mediate cell adhesion andthe silicon oxide background were passivated with PEG to resist proteinadsorption and cell adhesion. Cellular morphology and IR spectra ofsingle, double, and triple cells on gold electrodes exposed tolipopolysaccharide (LPS) of different concentrations were compared toreveal the detection capabilities of these biosensors. The single-cellbased sensors were found to generate the most significant IR wave numbervariation and thus provide the highest detection sensitivity. Changes inmorphology and IR spectrum for single cells exposed to LPS were found tobe time- and concentration-dependent and correlated with each other verywell. FTIR spectra from single cell arrays of gold electrodes withsurface area of 25 mu-m2, 100 mu-m2, and 400 mu-m2 were acquired usingboth synchrotron and conventional FTIR spectromicroscopes to study thesensitivity of detection. The results indicated that the developedsingle-cell platform can be used with conventional FTIRspectromicroscopy. This technique provides real-time, label-free, andrapid bacterial detection, and may allow for statistic and highthroughput analyses, and portability.

  13. Thermodynamics of Electron Flow in the Bacterial Deca-heme Cytochrome MtrF

    SciTech Connect (OSTI)

    Breuer, Marian; Zarzycki, Piotr P.; Blumberger, Jochen; Rosso, Kevin M.

    2012-07-01

    Electron transporting multiheme cytochromes are essential to the metabolism of microbes that inhabit soils and carry out important biogeochemical processes. Recently the first crystal structure of a prototype bacterial deca-heme cytochrome (MtrF) has been resolved and its electrochemistry characterized. However, the molecular details of electron conductance along heme chains in the cytochrome are difficult to access via experiment due to the nearly identical chemical nature of the heme cofactors. Here we employ large-scale molecular dynamics simulations to compute the reduction potentials of the ten hemes of MtrF in aqueous solution. We find that as a whole they fall within a range of about 0.3 V in agreement with experiment. Individual reduction potentials give rise to a free energy profile for electron conduction that is approximately symmetric with respect to the center of the protein. Our calculations indicate that there is no significant potential bias along the orthogonal octa- and tetra-heme chains suggesting that under aqueous conditions MtrF is a nearly reversible two-dimensional conductor.

  14. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    SciTech Connect (OSTI)

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  15. Instrument Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Cloud and Aerosol Characterization for the ARM Central Facility: Multiple Remote Sensor Techniques Development K. Sassen Department of Meteorology University of Utah Salt lake City, UT 84112 overcome the poor data-handling capabilities that handi- capped multiple-channellidar studies in the past. The true diversity of transmitted and received polarization states of our system is illustrated at the bottom of Table 1. Note that the first full POL field tests will be made at the upcoming 1991

  16. Two poplar-associated bacterial isolates induce additive favorable responses in a constructed plant-microbiome system

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Jawdy, Sara S.; Gunter, Lee E.; Engle, Nancy L.; Yang, Zamin Koo; Lu, Tse-Yuan S.; Tschaplinski, Timothy J.; Tuskan, Gerald A.; Doktycz, Mitchel John; Pelletier, Dale A.; Weston, David J.; et al

    2016-04-26

    Here, the biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. In this work we study the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Inoculation individually with either bacterial isolate increased root growth relative to uninoculated controls. Root area, photosynthetic efficiency, gene expression and metabolite expression data in individual and dual inoculated treatments indicate that the effects of these bacteria are unique and additive, suggesting that the function of a microbiome communitymore » may be predicted from the additive functions of the individual members.« less

  17. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc{sub 1} complex

    SciTech Connect (OSTI)

    Martin, Daniel R.; Matyushov, Dmitry V.

    2015-04-28

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 ?s of atomistic molecular dynamics simulations of the membrane-bound bc{sub 1} bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ?0.1-1.6 ?s contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

  18. Impact of bacteria and bacterial components on osteogenic and adipogenic differentiation of adipose-derived mesenchymal stem cells

    SciTech Connect (OSTI)

    Fiedler, Tomas; Salamon, Achim; Adam, Stefanie; Herzmann, Nicole; Taubenheim, Jan; Peters, Kirsten

    2013-11-01

    Adult mesenchymal stem cells (MSC) are present in several tissues, e.g. bone marrow, heart muscle, brain and subcutaneous adipose tissue. In invasive infections MSC get in contact with bacteria and bacterial components. Not much is known about how bacterial pathogens interact with MSC and how contact to bacteria influences MSC viability and differentiation potential. In this study we investigated the impact of three different wound infection relevant bacteria, Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes, and the cell wall components lipopolysaccharide (LPS; Gram-negative bacteria) and lipoteichoic acid (LTA; Gram-positive bacteria) on viability, proliferation, and osteogenic as well as adipogenic differentiation of human adipose tissue-derived mesenchymal stem cells (adMSC). We show that all three tested species were able to attach to and internalize into adMSC. The heat-inactivated Gram-negative E. coli as well as LPS were able to induce proliferation and osteogenic differentiation but reduce adipogenic differentiation of adMSC. Conspicuously, the heat-inactivated Gram-positive species showed the same effects on proliferation and adipogenic differentiation, while its cell wall component LTA exhibited no significant impact on adMSC. Therefore, our data demonstrate that osteogenic and adipogenic differentiation of adMSC is influenced in an oppositional fashion by bacterial antigens and that MSC-governed regeneration is not necessarily reduced under infectious conditions. - Highlights: Staphylococcus aureus, Streptococcus pyogenes and Escherichia coli bind to and internalize into adMSC. Heat-inactivated cells of these bacterial species trigger proliferation of adMSC. Heat-inactivated E. coli and LPS induce osteogenic differentiation of adMSC. Heat-inactivated E. coli and LPS reduce adipogenic differentiation of adMSC. LTA does not influence adipogenic or osteogenic differentiation of adMSC.

  19. A multifactor analysis of fungal and bacterial community structure of the root microbiome of mature Populus deltoides trees

    SciTech Connect (OSTI)

    Shakya, Migun; Gottel, Neil R; Castro Gonzalez, Hector F; Yang, Zamin; Gunter, Lee E; Labbe, Jessy L; Muchero, Wellington; Bonito, Gregory; Vilgalys, Rytas; Tuskan, Gerald A; Podar, Mircea; Schadt, Christopher Warren

    2013-01-01

    Bacterial and fungal communities associated with plant roots are central to the host- health, survival and growth. However, a robust understanding of root-microbiome and the factors that drive host associated microbial community structure have remained elusive, especially in mature perennial plants from natural settings. Here, we investigated relationships of bacterial and fungal communities in the rhizosphere and root endosphere of the riparian tree species Populus deltoides, and the influence of soil parameters, environmental properties (host phenotype and aboveground environmental settings), host plant genotype (Simple Sequence Repeat (SSR) markers), season (Spring vs. Fall) and geographic setting (at scales from regional watersheds to local riparian zones) on microbial community structure. Each of the trees sampled displayed unique aspects to it s associated community structure with high numbers of Operational Taxonomic Units (OTUs) specific to an individual trees (bacteria >90%, fungi >60%). Over the diverse conditions surveyed only a small number of OTUs were common to all samples within rhizosphere (35 bacterial and 4 fungal) and endosphere (1 bacterial and 1 fungal) microbiomes. As expected, Proteobacteria and Ascomycota were dominant in root communities (>50%) while other higher-level phylogenetic groups (Chytridiomycota, Acidobacteria) displayed greatly reduced abundance in endosphere compared to the rhizosphere. Variance partitioning partially explained differences in microbiome composition between all sampled roots on the basis of seasonal and soil properties (4% to 23%). While most variation remains unattributed, we observed significant differences in the microbiota between watersheds (Tennessee vs. North Carolina) and seasons (Spring vs. Fall). SSR markers clearly delineated two host populations associated with the samples taken in TN vs. NC, but overall genotypic distances did not have a significant effect on corresponding communities that could be

  20. Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Andersen, Gary L.; Mormile, Melanie R.

    2014-10-07

    Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean ismore » the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.« less

  1. Structurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses

    SciTech Connect (OSTI)

    Dong, Na; Zhu, Yongqun; Lu, Qiuhe; Hu, Liyan; Zheng, Yuqing; Shao, Feng

    2012-10-10

    Rab GTPases are frequent targets of vacuole-living bacterial pathogens for appropriate trafficking of the vacuole. Here we discover that bacterial effectors including VirA from nonvacuole Shigella flexneri and EspG from extracellular Enteropathogenic Escherichia coli (EPEC) harbor TBC-like dual-finger motifs and exhibits potent RabGAP activities. Specific inactivation of Rab1 by VirA/EspG disrupts ER-to-Golgi trafficking. S. flexneri intracellular persistence requires VirA TBC-like GAP activity that mediates bacterial escape from autophagy-mediated host defense. Rab1 inactivation by EspG severely blocks host secretory pathway, resulting in inhibited interleukin-8 secretion from infected cells. Crystal structures of VirA/EspG-Rab1-GDP-aluminum fluoride complexes highlight TBC-like catalytic role for the arginine and glutamine finger residues and reveal a 3D architecture distinct from that of the TBC domain. Structure of Arf6-EspG-Rab1 ternary complex illustrates a pathogenic signaling complex that rewires host Arf signaling to Rab1 inactivation. Structural distinctions of VirA/EspG further predict a possible extensive presence of TBC-like RabGAP effectors in counteracting various host defenses.

  2. Mechanism of Bacterial Cell-Surface Attachment Revealed by the Structure of Cellulosomal Type II Cohesin-dockerin Complex

    SciTech Connect (OSTI)

    Adams,J.; Pal, G.; Jia, Z.; Smith, S.

    2006-01-01

    Bacterial cell-surface attachment of macromolecular complexes maintains the microorganism in close proximity to extracellular substrates and allows for optimal uptake of hydrolytic byproducts. The cellulosome is a large multienzyme complex used by many anaerobic bacteria for the efficient degradation of plant cell-wall polysaccharides. The mechanism of cellulosome retention to the bacterial cell surface involves a calcium-mediated protein-protein interaction between the dockerin (Doc) module from the cellulosomal scaffold and a cohesin (Coh) module of cell-surface proteins located within the proteoglycan layer. Here, we report the structure of an ultra-high-affinity (K{sub a} = 1.44 x 10{sup 10} M{sup 1-}) complex between type II Doc, together with its neighboring X module from the cellulosome scaffold of Clostridium thermocellum, and a type II Coh module associated with the bacterial cell surface. Identification of X module-Doc and X module-Coh contacts reveal roles for the X module in Doc stability and enhanced Coh recognition. This extremely tight interaction involves one face of the Coh and both helices of the Doc and comprises significant hydrophobic character and a complementary extensive hydrogen-bond network. This structure represents a unique mechanism for cell-surface attachment in anaerobic bacteria and provides a rationale for discriminating between type I and type II Coh modules.

  3. Selection for Unequal Densities of Sigma70 Promoter-like Signalsin Different Regions of Large Bacterial Genomes

    SciTech Connect (OSTI)

    Huerta, Araceli M.; Francino, M. Pilar; Morett, Enrique; Collado-Vides, Julio

    2006-03-01

    The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that are recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently-transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to investigate the generality of this pattern, we have used position weight matrices describing the -35 and -10 promoter boxes of E. coli to search for these motifs in 43 additional genomes belonging to most established bacterial phyla, after specific calibration of the matrices according to the base composition of the noncoding regions of each genome. We have found that all bacterial species analyzed contain similar promoter-like motifs, and that, in most cases, these motifs follow the same genomic distribution observed in E. coli. Differential densities between regulatory and nonregulatory regions are detectable in most bacterial genomes, with the exception of those that have experienced evolutionary extreme genome reduction. Thus, the phylogenetic distribution of this pattern mirrors that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is the outcome of a process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential

  4. Nozzle development

    SciTech Connect (OSTI)

    Dodge, F.T.; Dodge, L.G.; Johnson, J.E.

    1989-06-01

    The objective of this program has been the development of experimental techniques and data processing procedures to allow for the characterization of multi-phase fuel nozzles using laboratory tests. Test results were to be used to produce a single value coefficient-of-performance that would predict the performance of the fuel nozzles independent of system application. Several different types of fuel nozzles capable of handling multi-phase fuels have been characterized for: (a) fuel flow rate versus delivery pressure, (b) fuel-air ratio throughout the fuel spray or plume and the effective cone angle of the injector, and (c) fuel drop- or particle-size distribution as a function of fluid properties. Fuel nozzles which have been characterized on both single-phase liquids and multi-phase liquid-solid slurries include a variable-film-thickness nozzle, a commercial coal-water slurry (CWS) nozzle, and four diesel injectors of different geometries (tested on single-phase fluids only). Multi-phase mixtures includes CWS with various coal loadings, surfactant concentrations, and stabilizer concentrations, as well as glass-bead water slurries with stabilizing additives. Single-phase fluids included glycerol-water mixtures to vary the viscosity over a range of 1 to 1500 cP, and alcohol-water mixtures to vary the surface tension from about 22 to 73 dyne/cm. In addition, tests were performed to characterize straight-tube gas-solid nozzles using two differences size distributions of glass beads in air. Standardized procedures have been developed for processing measurements of spray drop-size characteristics and the overall cross-section average drop or particle size. 43 refs., 60 figs., 7 tabs.

  5. The Siderocalin/Enterobactin Interaction: A Link between Mammalian Immunity and Bacterial Iron Transport

    SciTech Connect (OSTI)

    Meux, Susan C.

    2008-05-12

    The siderophore enterobactin (Ent) is produced by enteric bacteria to mediate iron uptake. Ent scavenges iron and is taken up by the bacteria as the highly stable ferric complex [Fe{sup III}(Ent)]{sup 3-}. This complex is also a specific target of the mammalian innate immune system protein, Siderocalin (Scn), which acts as an anti-bacterial agent by specifically sequestering siderophores and their ferric complexes during infection. Recent literature suggesting that Scn may also be involved in cellular iron transport has increased the importance of understanding the mechanism of siderophore interception and clearance by Scn; Scn is observed to release iron in acidic endosomes and [Fe{sup III}(Ent)]{sup 3-} is known to undergo a change from catecholate to salicylate coordination in acidic conditions, which is predicted to be sterically incompatible with the Scn binding pocket (also referred to as the calyx). To investigate the interactions between the ferric Ent complex and Scn at different pH values, two recombinant forms of Scn with mutations in three residues lining the calyx were prepared: Scn-W79A/R81A and Scn-Y106F. Binding studies and crystal structures of the Scn-W79A/R81A:[Fe{sup III}(Ent)]{sup 3-} and Scn-Y106F:[Fe{sup III}(Ent)]{sup 3-} complexes confirm that such mutations do not affect the overall conformation of the protein but do weaken significantly its affinity for [Fe{sup III}(Ent)]{sup 3-}. Fluorescence, UV-Vis and EXAFS spectroscopies were used to determine Scn/siderophore dissociation constants and to characterize the coordination mode of iron over a wide pH range, in the presence of both mutant proteins and synthetic salicylate analogs of Ent. While Scn binding hinders salicylate coordination transformation, strong acidification results in the release of iron and degraded siderophore. Iron release may therefore result from a combination of Ent degradation and coordination change.

  6. Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

    SciTech Connect (OSTI)

    Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.

    2015-09-04

    Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha–1 yr–1). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Provided the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.

  7. Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.

    2015-09-04

    Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing ofmore » ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha–1 yr–1). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Provided the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.« less

  8. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; MacKichan, Joanna; Kato-Maeda, Midori; Miller, Steve; Nadarajan, Rohan; Brodie, Eoin L.; Lynch, Susan V.; Heimesaat, Markus M.

    2015-02-06

    According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n =more » 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.« less

  9. Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

    SciTech Connect (OSTI)

    Hollister, Emily B; Schadt, Christopher Warren; Palumbo, Anthony Vito; Ansley, R J; Boutton, Thomas W

    2010-01-01

    In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.

  10. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens

    SciTech Connect (OSTI)

    Srinivasan, Ramya; Karaoz, Ulas; Volegova, Marina; MacKichan, Joanna; Kato-Maeda, Midori; Miller, Steve; Nadarajan, Rohan; Brodie, Eoin L.; Lynch, Susan V.; Heimesaat, Markus M.

    2015-02-06

    According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.

  11. An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

    SciTech Connect (OSTI)

    Song, Zhen; Kenney, Janice P.L.; Fein, Jeremy B.; Bunker, Bruce A.

    2015-02-09

    Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

  12. Lipopolysaccharide density and structure govern the extent and distance of nanoparticle interaction with actual and model bacterial outer membranes

    SciTech Connect (OSTI)

    Jacobson, Kurt H.; Gunsolus, Ian L.; Kuech, Thomas R.; Troiano, Julianne M.; Melby, Eric S.; Lohse, Samuel E.; Hu, Dehong; Chrisler, William B.; Murphy, Catherine; Orr, Galya; Geiger, Franz M.; Haynes, Christy L.; Pedersen, Joel A.

    2015-07-24

    Design of nanomedicines and nanoparticle-based antimicrobial and antifouling formulations, and assessment of the potential implications of nanoparticle release into the environment require understanding nanoparticle interaction with bacterial surfaces. Here we demonstrate electrostatically driven association of functionalized nanoparticles with lipopolysaccharides of Gram-negative bacterial outer membranes and find that lipopolysaccharide structure influences the extent and location of binding relative to the lipid-solution interface. By manipulating the lipopolysaccharide content in Shewanella oneidensis outer membranes, we observed electrostatically driven interaction of cationic gold nanoparticles with the lipopolysaccharide-containing leaflet. We probed this interaction by quartz crystal microbalance with dissipation monitoring (QCM-D) and second harmonic generation (SHG) using solid-supported lipopolysaccharide-containing bilayers. Association of cationic nanoparticles increased with lipopolysaccharide content, while no association of anionic nanoparticles was observed. The harmonic-dependence of QCM-D measurements suggested that a population of the cationic nanoparticles was held at a distance from the outer leaflet-solution interface of bilayers containing smooth lipopolysaccharides (those bearing a long O-polysaccharide). Additionally, smooth lipopolysaccharides held the bulk of the associated cationic particles outside of the interfacial zone probed by SHG. Our results demonstrate that positively charged nanoparticles are more likely to interact with Gram-negative bacteria than are negatively charged particles, and this interaction occurs primarily through lipopolysaccharides.

  13. Lipopolysaccharide Density and Structure Govern the Extent and Distance of Nanoparticle Interaction with Actual and Model Bacterial Outer Membranes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Jacobson, Kurt H.; Gunsolus, Ian L.; Kuech, Thomas R.; Troiano, Julianne M.; Melby, Eric S.; Lohse, Samuel E.; Hu, Dehong; Chrisler, William B.; Murphy, Catherine J.; Orr, Galya; et al

    2015-07-24

    We report that design of nanomedicines and nanoparticle-based antimicrobial and antifouling formulations, and assessment of the potential implications of nanoparticle release into the environment require understanding nanoparticle interaction with bacterial surfaces. Here we demonstrate electrostatically driven association of functionalized nanoparticles with lipopolysaccharides of Gram-negative bacterial outer membranes and find that lipopolysaccharide structure influences the extent and location of binding relative to the lipid-solution interface. By manipulating the lipopolysaccharide content in Shewanella oneidensis outer membranes, we observed electrostatically driven interaction of cationic gold nanoparticles with the lipopolysaccharide-containing leaflet. We probed this interaction by quartz crystal microbalance with dissipation monitoring (QCM-D) andmore » second harmonic generation (SHG) using solid-supported lipopolysaccharide-containing bilayers. Association of cationic nanoparticles increased with lipopolysaccharide content, while no association of anionic nanoparticles was observed. The harmonic-dependence of QCM-D measurements suggested that a population of the cationic nanoparticles was held at a distance from the outer leaflet-solution interface of bilayers containing smooth lipopolysaccharides (those bearing a long O-polysaccharide). Additionally, smooth lipopolysaccharides held the bulk of the associated cationic particles outside of the interfacial zone probed by SHG. Lastly, our results demonstrate that positively charged nanoparticles are more likely to interact with Gram-negative bacteria than are negatively charged particles, and this interaction occurs primarily through lipopolysaccharides.« less

  14. The development and application of engineered proteins for bioremediation

    SciTech Connect (OSTI)

    Trewhella, J.

    1995-09-26

    Clean up of the toxic legacy of the Cold War is projected to be the most expensive domestic project the nation has yet undertaken. Remediation of the Department of Energy and Department of Defense toxic waste sites alone are projected to cost {approximately}$1 trillion over a 20-30 year period. New, cost effective technologies are needed to attack this enormous problem. Los Alamos has put together a cross-divisional team of scientist to develop science based bioremediation technology to work toward this goal. In the team we have expertise in: (1) molecular, ecosystem and transport modeling; (2) genetic and protein engineering; (3) microbiology and microbial ecology; (4) structural biology; and (5) bioinorganic chemistry. This document summarizes talks at a workshop of different aspects of bioremediation technology including the following: Introducing novel function into a Heme enzyme: engineering by excavation; cytochrome P-450: ideal systems for bioremediation?; selection and development of bacterial strains for in situ remediation of cholorinated solvents; genetic analysis and preparation of toluene ortho-monooxygenase for field application in remediation of trichloroethylene; microbial ecology and diversity important to bioremediation; engineering haloalkane dehalogenase for bioremediation; enzymes for oxidative biodegradation; indigenous bacteria as hosts for engineered proteins; performance of indigenous bacterial, hosting engineered proteins in microbial communities.

  15. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    SciTech Connect (OSTI)

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Baelum, Jacob; Tas, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Phillip; Prieme, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.

  16. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    SciTech Connect (OSTI)

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Blum, Jacob; Ta?, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priem, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.

  17. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore » of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

  18. Framework for a physical map of the human 22q13 region using bacterial artificial chromosomes (BACs)

    SciTech Connect (OSTI)

    Schmitt, H.; Kim, Ung-Jin; Slepak, T.

    1996-04-01

    Detailed physical maps of entire chromosomes based on combined genetic, cytogenetic, and structural information are essential components for positional cloning and genomic sequencing. Despite the wealth of genetic information of the known diseases in the chromosome 22q13 region, the construction of a detailed physical map of the terminal region is difficult due to the sparsity of the genetic markers. We present here a map of bacterial artificial chromosome (BAC) contigs that cover a number of genetic loci in the 22q13 region. One hundred thirty-six BACs with an average insert size of 140 kb are assembled into 35 contigs defined by 64 markers in 22q13-qter. Twenty-three anonymous markers are now linked to the previously mapped genetic anchor points. 55 refs., 4 figs., 3 tabs.

  19. Uncovering the transmembrane metal binding site of the novel bacterial major facilitator superfamily-type copper importer CcoA

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Khalfaoui-Hassani, Bahia; Verissimo, Andreia F.; Koch, Hans -Georg; Daldal, Fevzi

    2016-01-19

    In this study, uptake and trafficking of metals and their delivery to their respective metalloproteins are important processes. Cells need precise control of each step to avoid exposure to excessive metal concentrations and their harmful consequences. Copper (Cu) is a required micronutrient used as a cofactor in proteins. However, in large amounts, it can induce oxidative damage; hence, Cu homeostasis is indispensable for cell survival. Biogenesis of respiratory heme-Cu oxygen (HCO) reductases includes insertion of Cu into their catalytic subunits to form heme-Cu binuclear centers. Previously, we had shown that CcoA is a major facilitator superfamily (MFS)-type bacterial Cu importermore » required for biogenesis of cbb3-type cytochromecoxidase (cbb3-Cox). Here, using Rhodobacter capsulatus, we focused on the import and delivery of Cu to cbb3-Cox. By comparing the CcoA amino acid sequence with its homologues from other bacterial species, we located several well-conserved Met, His, and Tyr residues that might be important for Cu transport. We determined the topology of the transmembrane helices that carry these residues to establish that they are membrane embedded, and substituted for them amino acids that do not ligand metal atoms. Characterization of these mutants for their uptake of radioactive64Cu and cbb3-Cox activities demonstrated that Met233 and His261 of CcoA are essential and Met237 and Met265 are important, whereas Tyr230 has no role for Cu uptake or cbb3-Cox biogenesis. These findings show for the first time that CcoA-mediated Cu import relies on conserved Met and His residues that could act as metal ligands at the membrane-embedded Cu binding domain of this transporter.« less

  20. Energy Frontier Research Centers

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    a pore, the impact of mineral surfaces on bacterial survival, and the influence of biofilm formation on the movement of CO 2 . In addition, they collected field data that...

  1. Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

    SciTech Connect (OSTI)

    Xu, Qingping; Mengin-Lecreulx, Dominique; Liu, Xueqian W.; Patin, Delphine; Farr, Carol L.; Grant, Joanna C.; Chiu, Hsiu-Ju; Jaroszewski, Lukasz; Knuth, Mark W.; Godzik, Adam; Lesley, Scott A.; Elsliger, Marc-André; Deacon, Ashley M.; Wilson, Ian A.

    2015-09-15

    ABSTRACT

    Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (ordl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminall-Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation.

    IMPORTANCEPeptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural

  2. Insights into substrate specificity of NlpC/P60 cell wall hydrolases containing bacterial SH3 domains

    SciTech Connect (OSTI)

    Xu, Qingping; Mengin-Lecreulx, Dominique; Liu, Xueqian W.; Patin, Delphine; Farr, Carol L.; Grant, Joanna C.; Chiu, Hsiu -Ju; Jaroszewski, Lukasz; Knuth, Mark W.; Godzik, Adam; Lesley, Scott A.; Elsliger, Marc -André; Deacon, Ashley M.; Wilson, Ian A.

    2015-09-15

    Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. In addition, these enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (ordl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminall-Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation.

    Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60

  3. Insights into substrate specificity of NlpC/P60 cell wall hydrolases containing bacterial SH3 domains

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Xu, Qingping; Mengin-Lecreulx, Dominique; Liu, Xueqian W.; Patin, Delphine; Farr, Carol L.; Grant, Joanna C.; Chiu, Hsiu -Ju; Jaroszewski, Lukasz; Knuth, Mark W.; Godzik, Adam; et al

    2015-09-15

    Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. In addition, these enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (ordl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminall-Ala. Their crystal structures revealed a highly conserved structure consisting ofmore » two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation.Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show

  4. Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Price, Morgan N.; Arkin, Adam P.

    2015-12-15

    Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 1012 individuals and a typical level of homologous recombination (r/m= 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that Ne is<107. An argument for high Ne values for bacteria has been the high genetic diversity within many bacterial “species,” but thismore » diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate Ne correctly. Given an estimate ofNe, standard population genetics models imply that selection should be sufficient to drive evolution if Ne ×s is >1, where s is the selection coefficient. We found that this remains approximately correct if background selection is occurring or when population structure is present. Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force ifs is above 10-7 or so. Because bacteria form huge populations with trillions of individuals, the simplest theoretical prediction is that the better allele at a site would predominate even if its advantage was just 10-9 per generation. In other words, virtually every nucleotide would be at the local optimum in most individuals. A more sophisticated theory considers that bacterial genomes have millions of sites each and selection events on these many sites could interfere with each other, so that only larger effects would be important. However, bacteria can exchange genetic material, and in principle, this exchange could eliminate the interference between the evolution of

  5. Fuel Fabrication Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Fuel Cycle Research & Development Fuel Cycle Research & Development Fuel Cycle Research & Development The mission of the Fuel Cycle Research and Development (FCRD) program is to conduct research and development to help develop sustainable fuel cycles, as described in the Nuclear Energy Research and Development Roadmap. Sustainable fuel cycle options are those that improve uranium resource utilization, maximize energy generation, minimize waste generation, improve safety, and limit

  6. Synthesis and anti-bacterial activity of Cu, Ag and Cu-Ag alloy nanoparticles: A green approach

    SciTech Connect (OSTI)

    Valodkar, Mayur; Modi, Shefaly; Pal, Angshuman; Thakore, Sonal

    2011-03-15

    Research highlights: {yields} Synthesis of novel nanosized copper-silver alloys of different compositions. {yields} Completely green approach for synthesis of water soluble bimetallic nanoparticle. {yields} Interesting anti-bacterial activity of as synthesized metal and alloy nanoparticle. -- Abstract: Metallic and bimetallic nanoparticles of copper and silver in various proportions were prepared by microwave assisted chemical reduction in aqueous medium using the biopolymer, starch as a stabilizing agent. Ascorbic acid was used as the reducing agent. The silver and copper nanoparticles exhibited surface plasmon absorption resonance maxima (SPR) at 416 and 584 nm, respectively; while SPR for the Cu-Ag alloys appeared in between depending on the alloy composition. The SPR maxima for bimetallic nanoparticles changes linearly with increasing copper content in the alloy. Transmission electron micrograph (TEM) showed monodispersed particles in the range of 20 {+-} 5 nm size. Both silver and copper nanoparticles exhibited emission band at 485 and 645 nm, respectively. The starch-stabilized nanoparticles exhibited interesting antibacterial activity with both gram positive and gram negative bacteria at micromolar concentrations.

  7. Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Anantharaman, Karthik; Brown, Christopher T.; Burstein, David; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Williams, Kenneth H.; Banfield, Jillian F.

    2016-01-28

    Five closely related populations of bacteria from the Candidate Phylum (CP) Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR), were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugarsmore » including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Furthermore, phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. In conclusion, we propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.« less

  8. Teacher Development Programs

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    teachers Teacher Development Programs LLNL Teacher Development LLNL's Science Education Program provides professional development instruction to in-service and pre-service middle school, high school, and community college science teachers

  9. ORISE: Web Development

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Web Development As computer-based applications become increasingly popular for the delivery of health care training and information, the need for Web development in support of ...

  10. SES CANDIDATE DEVELOPMENT PROGRAM

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Development Plan (EDP) NAME OF SES CANDIDATE: DATE: EXECUTIVE CORE QUALIFICATION 1: LEADING CHANGE This core qualification encompasses the ability to develop and implement an ...