Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park

Brumm, Phillip J.; Land, Miriam L.; Mead, David A.

doi:10.1186/s40793-015-0031-z

Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park

Journal Article · Mon Oct 05 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0031-z· OSTI ID:1260598

Brumm, Phillip J. ^[1]; Land, Miriam L. ^[2]; Mead, David A. ^[1]

Lucigen Corp., Middleton, WI (United States); Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Geobacillus thermoglucosidasius C56-YS93 was one of several thermophilic organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. Comparison of 16 S rRNA sequences confirmed the classification of the strain as a G. thermoglucosidasius species. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). The genome of G. thermoglucosidasius C56-YS93 consists of one circular chromosome of 3,893,306 bp and two circular plasmids of 80,849 and 19,638 bp and an average G + C content of 43.93 %. G. thermoglucosidasius C56-YS93 possesses a xylan degradation cluster not found in the other G. thermoglucosidasius sequenced strains. This cluster appears to be related to the xylan degradation cluster found in G. stearothermophilus. G. thermoglucosidasius C56-YS93 possesses two plasmids not found in the other two strains. Ultimately, one plasmid contains a novel gene cluster coding for proteins involved in proline degradation and metabolism, the other contains a collection of mostly hypothetical proteins.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: FC02-07ER64494; AC02-05CH11231; AC52-07NA27344

OSTI ID:: 1260598

Alternate ID(s):: OSTI ID: 1265819

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 10; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (60)

Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies Zerbino, Daniel R. Current Protocols in Bioinformatics, Vol. 31, Issue 1 https://doi.org/10.1002/0471250953.bi1105s31	journal	September 2010
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen Krogh, Anders; Larsson, Björn; von Heijne, Gunnar Journal of Molecular Biology, Vol. 305, Issue 3 https://doi.org/10.1006/jmbi.2000.4315	journal	January 2001
Thermophilic Protease-Producing Geobacillus from Buranga Hot Springs in Western Uganda Hawumba, Joseph F.; Theron, Jacques; Brözel, Volker S. Current Microbiology, Vol. 45, Issue 2 https://doi.org/10.1007/s00284-001-0116-3	journal	August 2002
Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench Takami, Hideto; Nishi, Shinro; Lu, Jei Extremophiles, Vol. 8, Issue 5 https://doi.org/10.1007/s00792-004-0394-3	journal	May 2004
Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin Costa, Kyle C.; Navarro, Jason B.; Shock, Everett L. Extremophiles, Vol. 13, Issue 3 https://doi.org/10.1007/s00792-009-0230-x	journal	February 2009
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass Xu, Xiaoheng; Feng, Guangyan; Huang, Linkai Molecular Biology Reports, Vol. 47, Issue 3 https://doi.org/10.1007/s11033-020-05279-9	journal	February 2020
New xylanases to obtain modified eucalypt fibres with high-cellulose content Valls, Cristina; Gallardo, Oscar; Vidal, Teresa Bioresource Technology, Vol. 101, Issue 19 https://doi.org/10.1016/j.biortech.2010.04.085	journal	October 2010
Genome sequencing in microfabricated high-density picolitre reactors Margulies, Marcel; Egholm, Michael; Altman, William E. Nature, Vol. 437, Issue 7057, p. 376-380 https://doi.org/10.1038/nature03959	journal	July 2005
Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing Brofelth, Mattias; Ekstrand, Anna Isinger; Gour, Shashank Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-1068-0	journal	July 2020
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
Three novel halotolerant and thermophilic Geobacillus strains from shallow marine vents Maugeri, Teresa L.; Gugliandolo, Concetta; Caccamo, Daniela Systematic and Applied Microbiology, Vol. 25, Issue 3 https://doi.org/10.1078/0723-2020-00119	journal	January 2002
Influence of supplemental endoglucanase or xylanase on volatile fatty acid production from ruminant feed by ruminal in vitro cultures Tricarico, Juan M.; Dawson, Karl A. Archives of Animal Nutrition, Vol. 59, Issue 5 https://doi.org/10.1080/17450390500247865	journal	October 2005
The Value of Basic Research: Discovery of Thermus aquaticus and Other Extreme Thermophiles Brock, Thomas D. Genetics, Vol. 146, Issue 4 https://doi.org/10.1093/genetics/146.4.1207	journal	August 1997
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
Rfam: an RNA family database Griffiths-Jones, S. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg006	journal	January 2003
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes Overbeek, R. Nucleic Acids Research, Vol. 33, Issue 17 https://doi.org/10.1093/nar/gki866	journal	September 2005
The integrated microbial genomes (IMG) system Markowitz, V. M. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj024	journal	January 2006
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide Liolios, K. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj145	journal	January 2006
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp848	journal	November 2009
IMG 4 version of the integrated microbial genomes comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt963	journal	October 2013
Isolation and Characterization of Acidothermus cellulolyticus gen. nov., sp. nov., a New Genus of Thermophilic, Acidophilic, Cellulolytic Bacteria MOHAGHEGHI, A.; GROHMANN, K.; HIMMEL, M. International Journal of Systematic Bacteriology, Vol. 36, Issue 3, p. 435-443 https://doi.org/10.1099/00207713-36-3-435	journal	July 1986
DNA Relatedness of Thermus Strains, Description of Thermus brockianus sp. nov., and Proposal To Reestablish Thermus thermophilus (Oshima and Imahori) Williams, R. A. D.; Smith, K. E.; Welch, S. G. International Journal of Systematic Bacteriology, Vol. 45, Issue 3 https://doi.org/10.1099/00207713-45-3-495	journal	July 1995
Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost. Sung, M. H.; Kim, H.; Bae, J. W. International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 6 https://doi.org/10.1099/00207713-52-6-2251	journal	November 2002
Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov. Nazina, T. N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 6 https://doi.org/10.1099/ijs.0.02932-0	journal	November 2004
Geobacillus lituanicus sp. nov. Kuisiene, N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 6 https://doi.org/10.1099/ijs.0.02976-0	journal	November 2004
The Geobacillus paradox: why is a thermophilic bacterial genus so prevalent on a mesophilic planet? Zeigler, D. R. Microbiology, Vol. 160, Issue Pt_1 https://doi.org/10.1099/mic.0.071696-0	journal	October 2013
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities Ewing, Brent; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.186	journal	March 1998
Consed: A Graphical Tool for Sequence Finishing Gordon, David; Abajian, Chris; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.195	journal	March 1998
Assembly of Viral Metagenomes from Yellowstone Hot Springs Schoenfeld, T.; Patterson, M.; Richardson, P. M. Applied and Environmental Microbiology, Vol. 74, Issue 13 https://doi.org/10.1128/aem.02598-07	journal	April 2008
Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium Wiegand, S.; Rabausch, U.; Chow, J. Genome Announcements, Vol. 1, Issue 2 https://doi.org/10.1128/genomea.00092-13	journal	February 2013
The L-Arabinan Utilization System of Geobacillus stearothermophilus Shulami, S.; Raz-Pasteur, A.; Tabachnikov, O. Journal of Bacteriology, Vol. 193, Issue 11 https://doi.org/10.1128/jb.00222-11	journal	April 2011
Complete Genome Sequence of Geobacillus thermoglucosidans TNO-09.020, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment Zhao, Y.; Caspers, M. P.; Abee, T. Journal of Bacteriology, Vol. 194, Issue 15 https://doi.org/10.1128/jb.00318-12	journal	July 2012
Fine Structure of Thermus aquaticus, an Extreme Thermophile Brock, Thomas D.; Edwards, Mercedes R. Journal of Bacteriology, Vol. 104, Issue 1 https://doi.org/10.1128/jb.104.1.509-517.1970	journal	January 1970
Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile Brock, Thomas D.; Freeze, Hudson Journal of Bacteriology, Vol. 98, Issue 1 https://doi.org/10.1128/jb.98.1.289-297.1969	journal	January 1969
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures Pride, David T.; Schoenfeld, Thomas BMC Genomics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2164-9-420	journal	January 2008
The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
Community Analysis of Plant Biomass-Degrading Microorganisms from Obsidian Pool, Yellowstone National Park Vishnivetskaya, Tatiana A.; Hamilton-Brehm, Scott D.; Podar, Mircea Microbial Ecology, Vol. 69, Issue 2 https://doi.org/10.1007/s00248-014-0500-8	journal	October 2014
Bacillus thermoglucosidasius sp. nov., a New Species of Obligately Thermophilic Bacilli Suzuki, Yuzuru; Kishigami, Takashi; Inoue, Kiyoshi Systematic and Applied Microbiology, Vol. 4, Issue 4 https://doi.org/10.1016/S0723-2020(83)80006-X	journal	December 1983
Using both xylanase and laccase enzymes for pulp bleaching Valls, Cristina; Roncero, M. Blanca Bioresource Technology, Vol. 100, Issue 6 https://doi.org/10.1016/j.biortech.2008.10.009	journal	March 2009
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Tamura, K.; Peterson, D.; Peterson, N. Molecular Biology and Evolution, Vol. 28, Issue 10 https://doi.org/10.1093/molbev/msr121	journal	May 2011
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
RNAmmer: consistent and rapid annotation of ribosomal RNA genes Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas Nucleic Acids Research, Vol. 35, Issue 9 https://doi.org/10.1093/nar/gkm160	journal	April 2007
PHAST: A Fast Phage Search Tool Zhou, Y.; Liang, Y.; Lynch, K. H. Nucleic Acids Research, Vol. 39, Issue suppl https://doi.org/10.1093/nar/gkr485	journal	June 2011
DNA Relatedness of Thermus Strains, Description of Thermus brockianus sp. nov., and Proposal To Reestablish Thermus thermophilus (Oshima and Imahori) Williams, R. A. D.; Smith, K. E.; Welch, S. G. International Journal of Systematic Bacteriology, Vol. 46, Issue 2 https://doi.org/10.1099/00207713-46-2-629	journal	April 1996
Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Ivanov, M. V.; Lysenko, A. M.; Petrunyaka, V. V. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 2 https://doi.org/10.1099/00207713-51-2-433	journal	March 2001
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment Ewing, Brent; Hillier, LaDeana; Wendl, Michael C. Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.175	journal	March 1998
Assembly of Viral Metagenomes from Yellowstone Hot Springs Schoenfeld, T.; Patterson, M.; Richardson, P. M. Applied and Environmental Microbiology, Vol. 74, Issue 13 https://doi.org/10.1128/AEM.02598-07	journal	April 2008
The L-Arabinan Utilization System of Geobacillus stearothermophilus Shulami, S.; Raz-Pasteur, A.; Tabachnikov, O. Journal of Bacteriology, Vol. 193, Issue 11 https://doi.org/10.1128/JB.00222-11	journal	April 2011
Complete Genome Sequence of Geobacillus thermoglucosidans TNO-09.020, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment Zhao, Y.; Caspers, M. P.; Abee, T. Journal of Bacteriology, Vol. 194, Issue 15 https://doi.org/10.1128/JB.00318-12	journal	July 2012
Fine Structure of Thermus aquaticus, an Extreme Thermophile Brock, Thomas D.; Edwards, Mercedes R. Journal of Bacteriology, Vol. 104, Issue 1 https://doi.org/10.1128/JB.104.1.509-517.1970	journal	January 1970
Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring Hugenholtz, Philip; Pitulle, Christian; Hershberger, Karen L. Journal of Bacteriology, Vol. 180, Issue 2 https://doi.org/10.1128/JB.180.2.366-376.1998	journal	January 1998
The Glucuronic Acid Utilization Gene Cluster from Bacillus stearothermophilus T-6 Shulami, Smadar; Gat, Orit; Sonenshein, Abraham L. Journal of Bacteriology, Vol. 181, Issue 12 https://doi.org/10.1128/JB.181.12.3695-3704.1999	journal	June 1999
Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile Brock, Thomas D.; Freeze, Hudson Journal of Bacteriology, Vol. 98, Issue 1 https://doi.org/10.1128/JB.98.1.289-297.1969	journal	January 1969
Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium Wiegand, S.; Rabausch, U.; Chow, J. Genome Announcements, Vol. 1, Issue 2 https://doi.org/10.1128/genomeA.00092-13	journal	February 2013
Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile Brock, Thomas D.; Freeze, Hudson Plazi.org taxonomic treatments database https://doi.org/10.15468/s2apce	dataset	January 1969

Cited By (6)

Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting Lemos, Leandro N.; Pereira, Roberta V.; Quaggio, Ronaldo B. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00644	journal	April 2017
Microbial diversity of thermophiles with biomass deconstruction potential in a foliage‐rich hot spring Lee, Li Sin; Goh, Kian Mau; Chan, Chia Sing MicrobiologyOpen, Vol. 7, Issue 6 https://doi.org/10.1002/mbo3.615	journal	March 2018
Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species Suzuki, Hirokazu Applied Microbiology and Biotechnology, Vol. 102, Issue 24 https://doi.org/10.1007/s00253-018-9422-6	journal	October 2018
Origin and phylogenetic relationships of [4Fe–4S]‐containing O ₂ sensors of bacteria Barth, C.; Weiss, M. C.; Roettger, M. Environmental Microbiology, Vol. 20, Issue 12 https://doi.org/10.1111/1462-2920.14411	journal	October 2018
Draft Genome Sequence of Parageobacillus thermoglucosidasius Strain TG4, a Hydrogenogenic Carboxydotrophic Bacterium Isolated from a Marine Sediment Inoue, Masao; Tanimura, Ayumi; Ogami, Yusuke Microbiology Resource Announcements, Vol. 8, Issue 5 https://doi.org/10.1128/mra.01666-18	journal	January 2019
Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. Pogrebnyakov, Ivan; Jendresen, Christian Bille; Nielsen, Alex Toftgaard PLOS ONE, Vol. 12, Issue 2 https://doi.org/10.1371/journal.pone.0171313	journal	February 2017

Figures / Tables (11)

Similar Records

Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park

Journal Article · Mon Oct 19 00:00:00 EDT 2015 · Standards in Genomic Sciences · OSTI ID:1259497

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biomass
Geobacillus thermoglucosidasius C56-YS93
Hot springs
Prophage
Xylan

Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park [Supplemental Data] Brumm, Phillip; Land, Miriam; Mead, David https://doi.org/10.6084/m9.figshare.c.3606449 The current record is supplemented by this dataset	dataset	October 2015
Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park Brumm, Phillip; Land, Miriam; Mead, David https://doi.org/10.6084/m9.figshare.c.3606449.v1 The current record is supplemented by this dataset	dataset	October 2015
Additional file 1: Table S1. of Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park Brumm, Phillip; Land, Miriam; Mead, David https://doi.org/10.6084/m9.figshare.c.3606449_d1 The current record is supplemented by this text	text	January 2015
Additional file 1: Table S1. of Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park Brumm, Phillip; Land, Miriam; Mead, David https://doi.org/10.6084/m9.figshare.c.3606449_d1.v1 The current record is supplemented by this figure	figure	October 2015

Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park

Citation Formats

References (60)

Cited By (6)

Linked Research (4)

Figures / Tables (11)

Similar Records

Related Subjects