Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex; Lapidus, Alla L.; Pillay, Manoj; Ivanova, Natalia; del Rio, Tijana Glavina; Kyrpides, Nikos C.; Woyke, Tanja; Muyzer, Gerard

doi:10.1186/s40793-017-0268-9

Title: Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

Journal Article · Thu Sep 21 00:00:00 EDT 2017 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-017-0268-9· OSTI ID:1618978

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex; Lapidus, Alla L.; Pillay, Manoj; Ivanova, Natalia; del Rio, Tijana Glavina; Kyrpides, Nikos C.; Woyke, Tanja;

Dethiobacter alkaliphilus strain AHT1 T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is thus a Gram-positive bacterium with low GC content, within the phylum Firmicutes. We report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1 T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.

View Journal Article

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618978

Alternate ID(s):: OSTI ID: 1416924

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Vol. 12 Journal Issue: 1; ISSN 1944-3277

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

Citation Metrics:

Cited by: 14 works

Citation information provided by
Web of Science

References (50)

The Microbial Sulfur Cycle at Extremely Haloalkaline Conditions of Soda Lakes Sorokin, Dimitry Y.; Kuenen, J. Gijs; Muyzer, Gerard Frontiers in Microbiology, Vol. 2 https://doi.org/10.3389/fmicb.2011.00044	journal	January 2011
The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.632	journal	July 2009
A high cell wall negative charge is necessary for the growth of the alkaliphile Bacillus lentus C-125 at elevated pH Aono, R.; Ito, M.; Joblin, K. N. Microbiology, Vol. 141, Issue 11 https://doi.org/10.1099/13500872-141-11-2955	journal	November 1995
Microbial diversity and biogeochemical cycling in soda lakes Sorokin, Dimitry Y.; Berben, Tom; Melton, Emily Denise Extremophiles, Vol. 18, Issue 5 https://doi.org/10.1007/s00792-014-0670-9	journal	August 2014
The hypBFCDE operon from Rhizobium leguminosarum biovar viciae is expressed from an Fnr-type promoter that escapes mutagenesis of the fnrN gene. Hernando, Y.; Palacios, J. M.; Imperial, J. Journal of Bacteriology, Vol. 177, Issue 19 https://doi.org/10.1128/jb.177.19.5661-5669.1995	journal	October 1995
Proposals Concerning the Higher Taxa of Bacteria Gibbons, N. E.; Murray, R. G. E. International Journal of Systematic Bacteriology, Vol. 28, Issue 1 https://doi.org/10.1099/00207713-28-1-1	journal	January 1978
Dethiobacter alkaliphilus gen. nov. sp. nov., and Desulfurivibrio alkaliphilus gen. nov. sp. nov.: two novel representatives of reductive sulfur cycle from soda lakes Sorokin, D. Yu.; Tourova, T. P.; Mußmann, Marc Extremophiles, Vol. 12, Issue 3 https://doi.org/10.1007/s00792-008-0148-8	journal	March 2008
Complete Genome Sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T Pester, M.; Brambilla, E.; Alazard, D. Journal of Bacteriology, Vol. 194, Issue 22 https://doi.org/10.1128/JB.01392-12	journal	October 2012
Biosynthesis of isoprenoids via the non-mevalonate pathway Eisenreich, W.; Bacher, A.; Arigoni, D. Cellular and Molecular Life Sciences, Vol. 61, Issue 12, p. 1401-1426 https://doi.org/10.1007/s00018-004-3381-z	journal	June 2004
Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization: Microbial and functional diversity of subsurface aquifer Tiago, Igor; Veríssimo, António Environmental Microbiology, Vol. 15, Issue 6 https://doi.org/10.1111/1462-2920.12034	journal	November 2012
Approved Lists of Bacterial Names Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D. International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1 https://doi.org/10.1099/00207713-30-1-225	journal	January 1980
Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes Poser, Alexander; Lohmayer, Regina; Vogt, Carsten Extremophiles, Vol. 17, Issue 6 https://doi.org/10.1007/s00792-013-0582-0	journal	September 2013
A procedure for the isolation of deoxyribonucleic acid from micro-organisms Marmur, J. Journal of Molecular Biology, Vol. 3, Issue 2 https://doi.org/10.1016/S0022-2836(61)80047-8	journal	April 1961
Solexa Ltd Bennett, Simon Pharmacogenomics, Vol. 5, Issue 4 https://doi.org/10.1517/14622416.5.4.433	journal	June 2004
Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120 Agervald, Åsa; Stensjö, Karin; Holmqvist, Marie BMC Microbiology, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2180-8-69	journal	January 2008
Biosynthesis of Squalene from Farnesyl Diphosphate in Bacteria: Three Steps Catalyzed by Three Enzymes Pan, Jian-Jung; Solbiati, Jose O.; Ramamoorthy, Gurusankar ACS Central Science, Vol. 1, Issue 2 https://doi.org/10.1021/acscentsci.5b00115	journal	April 2015
Complete genome sequence of Kytococcus sedentarius type strain (541T) Sims, David; Brettin, Thomas; Detter, John C. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.761	journal	July 2009
Massively parallel sequencing Rogers, Yu-Hui; Venter, J. Craig Nature, Vol. 437, Issue 7057 https://doi.org/10.1038/437326a	journal	September 2005
Prokaryotic communities of the north-eastern Mongolian soda lakes Sorokin, Dimitry Yu.; Gorlenko, Vladimir M.; Namsaraev, Bair B. Hydrobiologia, Vol. 522, Issue 1-3 https://doi.org/10.1023/B:HYDR.0000029989.73279.e4	journal	July 2004
�ber das Vitamin B12-Bed�rfnis phototropher Schwefelbakterien Pfennig, Norbert; Lippert, Klaus Dieter Archiv f�r Mikrobiologie, Vol. 55, Issue 3 https://doi.org/10.1007/BF00410246	journal	January 1966
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
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
IMG: the integrated microbial genomes database and comparative analysis system Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1044	journal	December 2011
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
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans Visser, Michael; Parshina, Sofiya N.; Alves, Joana I. Standards in Genomic Sciences, Vol. 9, Issue 3 https://doi.org/10.4056/sigs.4718645	journal	March 2014
Microbial diversity in The Cedars, an ultrabasic, ultrareducing, and low salinity serpentinizing ecosystem Suzuki, S.; Ishii, S.; Wu, A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 38 https://doi.org/10.1073/pnas.1302426110	journal	September 2013
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
V-Type H ⁺ -ATPase/Synthase from a Thermophilic Eubacterium, Thermus Thermophilus : SUBUNIT STRUCTURE AND OPERON Yokoyama, Ken; Ohkuma, Shoji; Taguchi, Hideki Journal of Biological Chemistry, Vol. 275, Issue 18 https://doi.org/10.1074/jbc.275.18.13955	journal	April 2000
Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes' Jumas-Bilak, E.; Roudiere, L.; Marchandin, H. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 5 https://doi.org/10.1099/ijs.0.006718-0	journal	April 2009
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1219	journal	November 2012
The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1: The genome of Desulfotomaculum reducens Junier, Pilar; Junier, Thomas; Podell, Sheila Environmental Microbiology https://doi.org/10.1111/j.1462-2920.2010.02242.x	journal	June 2010
ARB: a software environment for sequence data Ludwig, W. Nucleic Acids Research, Vol. 32, Issue 4 https://doi.org/10.1093/nar/gkh293	journal	February 2004
Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments Aüllo, Thomas; Ranchou-Peyruse, Anthony; Ollivier, Bernard Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00362	journal	January 2013
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku950	journal	October 2014
F1F0-ATP synthases of alkaliphilic bacteria: Lessons from their adaptations Hicks, David B.; Liu, Jun; Fujisawa, Makoto Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1797, Issue 8 https://doi.org/10.1016/j.bbabio.2010.02.028	journal	August 2010
Evolutionary primacy of sodium bioenergetics Mulkidjanian, Armen Y.; Galperin, Michael Y.; Makarova, Kira S. Biology Direct, Vol. 3, Issue 1 https://doi.org/10.1186/1745-6150-3-13	journal	January 2008
Complete Genome Sequence of the Anaerobic, Halophilic Alkalithermophile Natranaerobius thermophilus JW/NM-WN-LF Zhao, B.; Mesbah, N. M.; Dalin, E. Journal of Bacteriology, Vol. 193, Issue 15 https://doi.org/10.1128/JB.05157-11	journal	June 2011
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
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Molecular aspects of bacterial pH sensing and homeostasis Krulwich, Terry A.; Sachs, George; Padan, Etana Nature Reviews Microbiology, Vol. 9, Issue 5 https://doi.org/10.1038/nrmicro2549	journal	April 2011
Sequence logos: a new way to display consensus sequences Schneider, Thomas D.; Stephens, R. Michael Nucleic Acids Research, Vol. 18, Issue 20 https://doi.org/10.1093/nar/18.20.6097	journal	January 1990
The EMBL-EBI bioinformatics web and programmatic tools framework Li, Weizhong; Cowley, Andrew; Uludag, Mahmut Nucleic Acids Research, Vol. 43, Issue W1 https://doi.org/10.1093/nar/gkv279	journal	April 2015
A new pheromone trail-based genetic algorithm for comparative genome assembly Zhao, Fangqing; Zhao, Fanggeng; Li, Tao Nucleic Acids Research, Vol. 36, Issue 10 https://doi.org/10.1093/nar/gkn168	journal	April 2008
The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation Mavromatis, Konstantinos; Land, Miriam L.; Brettin, Thomas S. PLoS ONE, Vol. 7, Issue 12 https://doi.org/10.1371/journal.pone.0048837	journal	December 2012
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
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
MGcV: the microbial genomic context viewer for comparative genome analysis Overmars, Lex; Kerkhoven, Robert; Siezen, Roland J. BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-209	journal	January 2013

Similar Records

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2^T, a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes

Journal Article · Thu Sep 08 00:00:00 EDT 2016 · Standards in Genomic Sciences · OSTI ID:1618978

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex; +9 more

Complete Genome Sequence of Alkaliphilus metalliredigens QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-contaminated Leachate Ponds

Journal Article · Thu Nov 03 00:00:00 EDT 2016 · Genome Announcements · OSTI ID:1618978

Hwang, C.; Copeland, A.; Lucas, Susan; +23 more

Alkaliphilus transvaalensis gen. nov., sp. nov., an extremely alkaliphilic bacterium isolated from a deep South African gold mine

Journal Article · Sun Jul 01 00:00:00 EDT 2001 · International Journal of Systematic and Evolutionary Microbiology · OSTI ID:1618978

Takai, Ken; Moser, Duane P; Onstott, Tullis C; +4 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
extreme environment
soda lake
sediment
haloalkaliphilic
gram-positive
firmicutes

Title: Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

Citation Formats

References (50)

Similar Records

Related Subjects