Complete genome sequence of Methanospirillum hungatei type strain JF1

Gunsalus, Robert; Cook, Lauren E.; Crable, Bryan R.; Rohlin, Lars; McDonald, Erin; Mouttaki, Housna; Sieber, Jessica R.; Poweleit, Nicole; Zhou, Hong; Lapidus, Alla; Daligault, Hajnalka E.; Land, Miriam L.; Gilna, Paul; Ivanova, Natalia; Kyripides, Nikos; Culley, David E.; McInerney, Michael J.

doi:10.1186/s40793-015-0124-8

Complete genome sequence of Methanospirillum hungatei type strain JF1

Journal Article · Wed Jan 06 00:00:00 EST 2016 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0124-8· OSTI ID:1243176

Gunsalus, Robert ^[1]; Cook, Lauren E. ^[2]; Crable, Bryan R. ^[3]; Rohlin, Lars ^[2]; McDonald, Erin ^[2]; Mouttaki, Housna ^[4]; Sieber, Jessica R. ^[3]; Poweleit, Nicole ^[2]; Zhou, Hong ^[2]; Lapidus, Alla ^[5]; Daligault, Hajnalka E. ^[6]; Land, Miriam L. ^[7]; Gilna, Paul ^[7]; Ivanova, Natalia ^[8]; Kyripides, Nikos ^[9]; Culley, David E. ^[10]; McInerney, Michael J. ^[3]

Univ. of California, Los Angeles, CA (United States). Dept. of Microbiology, Immunology, and Molecular Genetics; Univ. of California, Los Angeles, CA (United States). UCLA-DOE Institute for Genomics and Proteomics
Univ. of California, Los Angeles, CA (United States). Dept. of Microbiology, Immunology, and Molecular Genetics
Univ. of Oklahoma, Norman, OK (United States)
Univ. of California, Los Angeles, CA (United States). Dept. of Microbiology, Immunology, and Molecular Genetics; Univ. of Oklahoma, Norman, OK (United States)
St. Petersburg State University, St. Petersburg (Russia); St. Petersburg Academic University, St. Petersburg (Russia)
St. Petersburg State University, St. Petersburg (Russia)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
DOE Joint Genome Institute, Walnut Creek, CA (United States)
DOE Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Methanospirillum hungatei strain JF1 is a hydrogenotrophic methanogen that belongs to the order Methanomicrobiales. Members of the genus Methanospirillum are commonly encountered in syntrophic association with fermenting microorganisms. M. hungatei serves as the model partner organism in laboratory cocultures that syntrophically oxidize fatty and aromatic acids. Furthermore, when grown syntrophically, M. hungatei rapidly uses the hydrogen or formate produced by its syntrophic partner and maintains the concentration of these metabolites at very low levels so that the degradation of the syntrophic substrate is thermodynamically favorable.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Univ. of Oklahoma, Norman, OK (United States)

Sponsoring Organization:: ORNL work for others; USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Chemical Sciences, Geosciences & Biosciences Division; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC05-00OR22725; AC05-76RL01830; FC02-02ER63421; FG02-96ER20214; FG03-86ER13498

OSTI ID:: 1243176

Alternate ID(s):: OSTI ID: 1604953
OSTI ID: 1265977

Report Number(s):: PNNL-SA--100776; BM0101020

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 11; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (55)

Anaerobic degradation of benzoate to methane by a microbial consortium Ferry, J. G.; Wolfe, R. S. Archives of Microbiology, Vol. 107, Issue 1 https://doi.org/10.1007/bf00427864	journal	January 1976
Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms Jackson, Bradley E.; Bhupathiraju, V. K.; Tanner, Ralph S. Archives of Microbiology, Vol. 171, Issue 2 https://doi.org/10.1007/s002030050685	journal	January 1999
Novel polar lipids from the methanogen Methanospirillum hungatei GP1 Kushwaha, S. C.; Kates, M.; Sprott, G. D. Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism, Vol. 664, Issue 1 https://doi.org/10.1016/0005-2760(81)90038-2	journal	April 1981
Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens Welte, Cornelia; Deppenmeier, Uwe Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1837, Issue 7 https://doi.org/10.1016/j.bbabio.2013.12.002	journal	July 2014
Syntrophy in anaerobic global carbon cycles McInerney, Michael J.; Sieber, Jessica R.; Gunsalus, Robert P. Current Opinion in Biotechnology, Vol. 20, Issue 6 https://doi.org/10.1016/j.copbio.2009.10.001	journal	December 2009
The archaellum: an old motility structure with a new name Jarrell, Ken F.; Albers, Sonja-Verena Trends in Microbiology, Vol. 20, Issue 7 https://doi.org/10.1016/j.tim.2012.04.007	journal	July 2012
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
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
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
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
IMG ER: a system for microbial genome annotation expert review and curation Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N. Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp393	journal	June 2009
Methanospirillum, a New Genus of Methanogenic Bacteria, and Characterization of Methanospirillum hungatii sp.nov. Ferry, J. G.; Smith, P. H.; Wolfe, R. S. International Journal of Systematic Bacteriology, Vol. 24, Issue 4 https://doi.org/10.1099/00207713-24-4-465	journal	October 1974
Syntrophus buswellii gen. nov., sp. nov.: a Benzoate Catabolizer from Methanogenic Ecosystems Mountfort, D. O.; Brulla, W. J.; Krumholz, L. R. International Journal of Systematic Bacteriology, Vol. 34, Issue 2 https://doi.org/10.1099/00207713-34-2-216	journal	April 1984
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
Structural, mass and elemental analyses of storage granules in methanogenic archaeal cells: Storage granules in methanogenic archaeal cells Toso, Daniel B.; Henstra, Anne M.; Gunsalus, Robert P. Environmental Microbiology, Vol. 13, Issue 9 https://doi.org/10.1111/j.1462-2920.2011.02531.x	journal	August 2011
The archaeal flagellum: a different kind of prokaryotic motility structure Thomas, Nikhil A.; Bardy, Sonia L.; Jarrell, Ken F. FEMS Microbiology Reviews, Vol. 25, Issue 2 https://doi.org/10.1111/j.1574-6976.2001.tb00575.x	journal	April 2001
Nutritional and biochemical characterization of Methanospirillum hungatii. Ferry, J. G.; Wolfe, R. S. Applied and Environmental Microbiology, Vol. 34, Issue 4 https://doi.org/10.1128/aem.34.4.371-376.1977	journal	January 1977
Propionate-Degrading Bacterium, Syntrophobacter wolinii sp. nov. gen. nov., from Methanogenic Ecosystems Boone, David R.; Bryant, Marvin P. Applied and Environmental Microbiology, Vol. 40, Issue 3 https://doi.org/10.1128/aem.40.3.626-632.1980	journal	January 1980
Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium McInerney, M. J.; Bryant, M. P.; Hespell, R. B. Applied and Environmental Microbiology, Vol. 41, Issue 4 https://doi.org/10.1128/aem.41.4.1029-1039.1981	journal	January 1981
Chemotaxis in Methanospirillum hungatei Migas, John; Anderson, Karen L.; Cruden, D. L. Applied and Environmental Microbiology, Vol. 55, Issue 1 https://doi.org/10.1128/aem.55.1.264-265.1989	journal	January 1989
Identification and Isolation of Anaerobic, Syntrophic Phthalate Isomer-Degrading Microbes from Methanogenic Sludges Treating Wastewater from Terephthalate Manufacturing Qiu, Y. -L.; Sekiguchi, Y.; Imachi, H. Applied and Environmental Microbiology, Vol. 70, Issue 3 https://doi.org/10.1128/aem.70.3.1617-1626.2004	journal	March 2004
The Anaerobic Mesophilic Cellulolytic Bacteria 1 Hungate, R. E. Bacteriological Reviews, Vol. 14, Issue 1 https://doi.org/10.1128/br.14.1.1-49.1950	journal	January 1950
Novel Archaeal Adhesion Pilins with a Conserved N Terminus Esquivel, R. N.; Xu, R.; Pohlschroder, M. Journal of Bacteriology, Vol. 195, Issue 17 https://doi.org/10.1128/jb.00572-13	journal	June 2013
Fine structure of Methanospirillum hungatii. Zeikus, J. G.; Bowen, V. G. Journal of Bacteriology, Vol. 121, Issue 1 https://doi.org/10.1128/jb.121.1.373-380.1975	journal	January 1975
Energetics of syntrophic cooperation in methanogenic degradation Schink, B. Microbiology and Molecular Biology Reviews, Vol. 61, Issue 2 https://doi.org/10.1128/mmbr.61.2.262-280.1997	journal	June 1997
Methanogens: reevaluation of a unique biological group. Balch, W. E.; Fox, G. E.; Magrum, L. J. Microbiological Reviews, Vol. 43, Issue 2 https://doi.org/10.1128/mr.43.2.260-296.1979	journal	January 1979
Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation Sieber, Jessica R.; McInerney, Michael J.; Gunsalus, Robert P. Annual Review of Microbiology, Vol. 66, Issue 1 https://doi.org/10.1146/annurev-micro-090110-102844	journal	October 2012
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
Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A Rohlin, Lars; Gunsalus, Robert P. BMC Microbiology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2180-10-62	journal	January 2010
Physiology, Ecology, Phylogeny, and Genomics of Microorganisms Capable of Syntrophic Metabolism McInerney, Michael J.; Struchtemeyer, Christopher G.; Sieber, Jessica Annals of the New York Academy of Sciences, Vol. 1125, Issue 1 https://doi.org/10.1196/annals.1419.005	journal	March 2008
The Genomic Standards Consortium Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy PLoS Biology, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pbio.1001088	journal	June 2011
Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOBT) Plugge, Caroline M.; Henstra, Anne M.; Worm, Petra Standards in Genomic Sciences, Vol. 7, Issue 1 https://doi.org/10.4056/sigs.2996379	journal	September 2012
The Revised Road Map to the Manual Garrity, George M.; Bell, Julia A.; Lilburn, Timothy Bergey's Manual of Systematics of Archaea and Bacteria https://doi.org/10.1002/9781118960608.bm00023	book	January 2015
The Revised Road Map to the Manual Garrity, George M.; Bell, Julia A.; Lilburn, Timothy Bergey’s Manual® of Systematic Bacteriology https://doi.org/10.1007/0-387-28021-9_21	book	January 2005
Bergey’s Manual® of Systematic Bacteriology Brenner, Don J.; Krieg, Noel R.; Staley, James T. Springer New York, NY https://doi.org/10.1007/0-387-28022-7	book	January 2005
Bergey’s Manual® of Systematic Bacteriology Boone, David R.; Castenholz, Richard W.; Garrity, George M. Springer New York, NY https://doi.org/10.1007/978-0-387-21609-6	book	January 2001
Phylum All. Euryarchaeota phy. nov. Garrity, George M.; Holt, John G.; Whitman, William B. Bergey’s Manual® of Systematic Bacteriology https://doi.org/10.1007/978-0-387-21609-6_17	book	January 2001
Anaerobic degradation of benzoate to methane by a microbial consortium Ferry, J. G.; Wolfe, R. S. Archives of Microbiology, Vol. 107, Issue 1 https://doi.org/10.1007/BF00427864	journal	January 1976
Techniques for Cultivating Methanogens Wolfe, Ralph S. Methods in Methane Metabolism, Part A https://doi.org/10.1016/B978-0-12-385112-3.00001-9	book	March 2011
Improved strategy for presumptive identification of methanogens using 16S riboprinting Wright, André-Denis G.; Pimm, Carolyn Journal of Microbiological Methods, Vol. 55, Issue 2 https://doi.org/10.1016/S0167-7012(03)00169-6	journal	November 2003
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
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata Pagani, I.; Liolios, K.; Jansson, J. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1100	journal	December 2011
Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and emended descriptions of the genus Methanospirillum and Methanospirillum hungatei Iino, T.; Mori, K.; Suzuki, K. -i. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 11 https://doi.org/10.1099/ijs.0.020131-0	journal	December 2009
Energetics of syntrophic cooperation in methanogenic degradation. Schink, B. Microbiology and molecular biology reviews : MMBR, Vol. 61, Issue 2 https://doi.org/10.1128/.61.2.262-280.1997	journal	January 1997
Nutritional and biochemical characterization of Methanospirillum hungatii. Ferry, J. G.; Wolfe, R. S. Applied and Environmental Microbiology, Vol. 34, Issue 4 https://doi.org/10.1128/AEM.34.4.371-376.1977	journal	January 1977
Propionate-Degrading Bacterium, Syntrophobacter wolinii sp. nov. gen. nov., from Methanogenic Ecosystems Boone, David R.; Bryant, Marvin P. Applied and Environmental Microbiology, Vol. 40, Issue 3 https://doi.org/10.1128/AEM.40.3.626-632.1980	journal	January 1980
Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium McInerney, M. J.; Bryant, M. P.; Hespell, R. B. Applied and Environmental Microbiology, Vol. 41, Issue 4 https://doi.org/10.1128/AEM.41.4.1029-1039.1981	journal	January 1981
Chemotaxis in Methanospirillum hungatei Migas, John; Anderson, Karen L.; Cruden, D. L. Applied and Environmental Microbiology, Vol. 55, Issue 1 https://doi.org/10.1128/AEM.55.1.264-265.1989	journal	January 1989
Identification and Isolation of Anaerobic, Syntrophic Phthalate Isomer-Degrading Microbes from Methanogenic Sludges Treating Wastewater from Terephthalate Manufacturing Qiu, Y. -L.; Sekiguchi, Y.; Imachi, H. Applied and Environmental Microbiology, Vol. 70, Issue 3 https://doi.org/10.1128/AEM.70.3.1617-1626.2004	journal	March 2004
Novel Archaeal Adhesion Pilins with a Conserved N Terminus Esquivel, R. N.; Xu, R.; Pohlschroder, M. Journal of Bacteriology, Vol. 195, Issue 17 https://doi.org/10.1128/JB.00572-13	journal	June 2013
Fine structure of Methanospirillum hungatii. Zeikus, J. G.; Bowen, V. G. Journal of Bacteriology, Vol. 121, Issue 1 https://doi.org/10.1128/JB.121.1.373-380.1975	journal	January 1975
The Anaerobic Mesophilic Cellulolytic Bacteria 1 Hungate, R. E. Bacteriological Reviews, Vol. 14, Issue 1 https://doi.org/10.1128/MMBR.14.1.1-49.1950	journal	January 1950
Methanogens: reevaluation of a unique biological group. Balch, W. E.; Fox, G. E.; Magrum, L. J. Microbiological Reviews, Vol. 43, Issue 2 https://doi.org/10.1128/MMBR.43.2.260-296.1979	journal	January 1979

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Complete genome sequence of Methanospirillum hungatei type strain JF1 [Supplemental Data] Gunsalus, Robert; Cook, Lauren; Crable, Bryan https://doi.org/10.6084/m9.figshare.c.3631223 The current record is supplemented by this dataset	dataset	January 2016
Complete genome sequence of Methanospirillum hungatei type strain JF1 [Supplemental Data] Gunsalus, Robert; Cook, Lauren; Crable, Bryan https://doi.org/10.6084/m9.figshare.c.3631223.v1 The current record is supplemented by this figure	figure	January 2016
Additional file 2: Figure S2. of Complete genome sequence of Methanospirillum hungatei type strain JF1 Gunsalus, Robert; Cook, Lauren; Crable, Bryan https://doi.org/10.6084/m9.figshare.c.3631223_d1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 2: Figure S2. of Complete genome sequence of Methanospirillum hungatei type strain JF1 Gunsalus, Robert; Cook, Lauren; Crable, Bryan https://doi.org/10.6084/m9.figshare.c.3631223_d1.v1 The current record is supplemented by this figure	figure	January 2016
Additional file 1: Figure S1. of Complete genome sequence of Methanospirillum hungatei type strain JF1 Gunsalus, Robert; Cook, Lauren; Crable, Bryan https://doi.org/10.6084/m9.figshare.c.3631223_d2 The current record is supplemented by this dataset	dataset	January 2016
Additional file 1: Figure S1. of Complete genome sequence of Methanospirillum hungatei type strain JF1 Gunsalus, Robert; Cook, Lauren; Crable, Bryan https://doi.org/10.6084/m9.figshare.c.3631223_d2.v1 The current record is supplemented by this figure	figure	January 2016

Complete genome sequence of Methanospirillum hungatei type strain JF1

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