Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane-Degrading Bacterium

Chen, Gao; Murdoch, Robert W.; Mack, E. Erin; Seger, Edward S.; Loeffler, Frank E.

doi:10.1128/genomeA.00897-17

Title: Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane-Degrading Bacterium

Journal Article · Thu Sep 14 00:00:00 EDT 2017 · Genome Announcements

DOI:https://doi.org/10.1128/genomeA.00897-17· OSTI ID:1399397

Chen, Gao ^[1]; Murdoch, Robert W. ^[2]; Mack, E. Erin ^[3]; Seger, Edward S. ^[4];

^[5]

Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering
Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology
E. I. DuPont de Nemours and Company, Newark, DE (United States). Corporate Remediation Group
Chemours Company, Wilmington, DE (United States)
Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Biosystems Engineering and Soil Science; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division

ABSTRACT Dehalobacterium formicoaceticumutilizes dichloromethane as the sole energy source in defined anoxic bicarbonate-buffered mineral salt medium. The products are formate, acetate, inorganic chloride, and biomass. The bacterium’s genome was sequenced using PacBio, assembled, and annotated. The complete genome consists of one 3.77-Mb circular chromosome harboring 3,935 predicted protein-encoding genes.

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

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1399397

Alternate ID(s):: OSTI ID: 1470849

Journal Information:: Genome Announcements, Vol. 5, Issue 37; ISSN 2169-8287

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (22)

Versatile and open software for comparing large genomes Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L. Genome Biology, Vol. 5, Issue 2, R12 https://doi.org/10.1186/gb-2004-5-2-r12	journal	January 2004
Bacterial growth with chlorinated methanes. Leisinger, T.; Braus-Stromeyer, S. A. Environmental Health Perspectives, Vol. 103, Issue suppl 5 https://doi.org/10.1289/ehp.95103s433	journal	June 1995
Identifying bacterial genes and endosymbiont DNA with Glimmer Delcher, Arthur L.; Bratke, Kirsten A.; Powers, Edwin C. Bioinformatics, Vol. 23, Issue 6 https://doi.org/10.1093/bioinformatics/btm009	journal	January 2007
The IGS Standard Operating Procedure for Automated Prokaryotic Annotation Galens, Kevin; Orvis, Joshua; Daugherty, Sean Standards in Genomic Sciences, Vol. 4, Issue 2 https://doi.org/10.4056/sigs.1223234	journal	April 2011
Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina Genome Announcements, Vol. 4, Issue 2 https://doi.org/10.1128/genomeA.00037-16	journal	March 2016
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
Biodegradation of dichloromethane and its utilization as a growth substrate under methanogenic conditions. Freedman, D. L.; Gossett, J. M. Applied and Environmental Microbiology, Vol. 57, Issue 10 https://doi.org/10.1128/AEM.57.10.2847-2857.1991	journal	January 1991
Initial Characterization of a Reductive Dehalogenase from Desulfitobacterium chlororespirans Co23. Loffler, F. E.; Sanford, R. A.; Tiedje, J. M. Applied and environmental microbiology, Vol. 62, Issue 10 https://doi.org/10.1128/AEM.62.10.3809-3813.1996	journal	January 1996
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation Koren, Sergey; Walenz, Brian P.; Berlin, Konstantin Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.215087.116	journal	March 2017
Acetogenesis from dichloromethane by a two-component mixed culture comprising a novel bacterium. Magli, A.; Rainey, F. A.; Leisinger, T. Applied and environmental microbiology, Vol. 61, Issue 8 https://doi.org/10.1128/AEM.61.8.2943-2949.1995	journal	January 1995
Dichloromethane Fermentation by a Dehalobacter sp. in an Enrichment Culture Derived from Pristine River Sediment Justicia-Leon, Shandra D.; Ritalahti, Kirsti M.; Mack, E. Erin Applied and Environmental Microbiology, Vol. 78, Issue 4 https://doi.org/10.1128/AEM.07325-11	journal	December 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/25.5.955	journal	March 1997
Bacterial Degradation of Dichloromethane Brunner, Walter; Staub, Doris; Leisinger, Thomas Applied and Environmental Microbiology, Vol. 40, Issue 5 https://doi.org/10.1128/AEM.40.5.950-958.1980	journal	January 1980
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
Isolation and characterization of Dehalobacterium formicoaceticum gen. nov. sp. nov., a strictly anaerobic bacterium utilizing dichloromethane as source of carbon and energy Mägli, Andreas; Wendt, Matthias; Leisinger, T. Archives of Microbiology, Vol. 166, Issue 2 https://doi.org/10.1007/s002030050362	journal	August 1996
Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG Crabtree, Jonathan; Agrawal, Sonia; Mahurkar, Anup Bioinformatics, Vol. 30, Issue 21 https://doi.org/10.1093/bioinformatics/btu505	journal	July 2014
Dichloromethane utilized by an anaerobic mixed culture: acetogenesis and methanogenesis Stromeyer, Susanna A.; Winkelbauer, Wolfgang; Kohler, Herbert Biodegradation, Vol. 2, Issue 2 https://doi.org/10.1007/BF00114603	journal	January 1991
Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2. Kohler-Staub, D.; Leisinger, T. Journal of Bacteriology, Vol. 162, Issue 2 https://doi.org/10.1128/JB.162.2.676-681.1985	journal	January 1985
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum) Pierce, Elizabeth; Xie, Gary; Barabote, Ravi D. Environmental Microbiology, Vol. 10, Issue 10, p. 2550-2573 https://doi.org/10.1111/j.1462-2920.2008.01679.x	journal	July 2008
‘ Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina Systematic and Applied Microbiology, Vol. 40, Issue 3 https://doi.org/10.1016/j.syapm.2016.12.001	journal	April 2017
Metabolism of Dichloromethane by the Strict Anaerobe Dehalobacterium formicoaceticum Mägli, Andreas; Messmer, Michael; Leisinger, Thomas Applied and Environmental Microbiology, Vol. 64, Issue 2 https://doi.org/10.1128/AEM.64.2.646-650.1998	journal	January 1998
Draft Genome Sequence of Medusavirus Stheno, Isolated from the Tatakai River of Uji, Japan Yoshida, Koki; Zhang, Ruixuan; Garcia, Kimberly G. Microbiology Resource Announcements, Vol. 10, Issue 1 https://doi.org/10.1128/mra.01323-20	journal	January 2021

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‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets Kuntal, Bhusan K.; Chandrakar, Pranjal; Sadhu, Sudipta The ISME Journal, Vol. 13, Issue 2 https://doi.org/10.1038/s41396-018-0291-x	journal	October 2018

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