Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))
Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing b...
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| creator | Spring, Stefan Nolan, Matt Lapidus, Alla Glavina Del Rio, Tijana Copeland, Alex Tice, Hope Cheng, Jan-Fang Lucas, Susan Land, Miriam Chen, Feng Bruce, David Goodwin, Lynne Pitluck, Sam Ivanova, Natalia Mavromatis, Konstantinos Mikhailova, Natalia Pati, Amrita Chen, Amy Palaniappan, Krishna Hauser, Loren Chang, Yun-Juan Jeffries, Cynthia D Munk, Christine Kiss, Hajnalka Chain, Patrick Han, Cliff Brettin, Thomas Detter, John C Schüler, Esther Göker, Markus Rohde, Manfred Bristow, Jim Eisen, Jonathan A Markowitz, Victor Hugenholtz, Philip Kyrpides, Nikos C Klenk, Hans-Peter |
| description | Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. |
| doi_str_mv | 10.4056/sigs.581048 |
| format | Article |
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(ORNL), Oak Ridge, TN (United States)</creatorcontrib><description>Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.</description><identifier>ISSN: 1944-3277</identifier><identifier>EISSN: 1944-3277</identifier><identifier>DOI: 10.4056/sigs.581048</identifier><identifier>PMID: 21304676</identifier><language>eng</language><publisher>England: Michigan State University</publisher><subject>ACETATES ; BACTERIA ; BASIC BIOLOGICAL SCIENCES ; CHROMOSOMES ; Deltaproteobacteria ; Desulfohalobiaceae ; GEBA ; GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE ; GENES ; Gram-negative ; hydrogen utilization ; hypersaline lake ; LAKES ; mesophile ; moderately halophilic ; Proteobacteria ; RNA ; SEDIMENTS ; SENEGAL ; Short Genome Reports ; STRAINS ; strictly anaerobic ; SUBSTRATES ; sulfate-reducer</subject><ispartof>Standards in genomic sciences, 2010-01, Vol.2 (1), p.38-48</ispartof><rights>2009 Spring et al.</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c406t-a11e867dd353b35e265cf6e3887ce56e465909ac4b0775c71d7cce2362c957543</citedby><cites>FETCH-LOGICAL-c406t-a11e867dd353b35e265cf6e3887ce56e465909ac4b0775c71d7cce2362c957543</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035252/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035252/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21304676$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/981794$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Spring, Stefan</creatorcontrib><creatorcontrib>Nolan, Matt</creatorcontrib><creatorcontrib>Lapidus, Alla</creatorcontrib><creatorcontrib>Glavina Del Rio, Tijana</creatorcontrib><creatorcontrib>Copeland, Alex</creatorcontrib><creatorcontrib>Tice, Hope</creatorcontrib><creatorcontrib>Cheng, Jan-Fang</creatorcontrib><creatorcontrib>Lucas, Susan</creatorcontrib><creatorcontrib>Land, Miriam</creatorcontrib><creatorcontrib>Chen, Feng</creatorcontrib><creatorcontrib>Bruce, David</creatorcontrib><creatorcontrib>Goodwin, Lynne</creatorcontrib><creatorcontrib>Pitluck, Sam</creatorcontrib><creatorcontrib>Ivanova, Natalia</creatorcontrib><creatorcontrib>Mavromatis, Konstantinos</creatorcontrib><creatorcontrib>Mikhailova, Natalia</creatorcontrib><creatorcontrib>Pati, Amrita</creatorcontrib><creatorcontrib>Chen, Amy</creatorcontrib><creatorcontrib>Palaniappan, Krishna</creatorcontrib><creatorcontrib>Hauser, Loren</creatorcontrib><creatorcontrib>Chang, Yun-Juan</creatorcontrib><creatorcontrib>Jeffries, Cynthia D</creatorcontrib><creatorcontrib>Munk, Christine</creatorcontrib><creatorcontrib>Kiss, Hajnalka</creatorcontrib><creatorcontrib>Chain, Patrick</creatorcontrib><creatorcontrib>Han, Cliff</creatorcontrib><creatorcontrib>Brettin, Thomas</creatorcontrib><creatorcontrib>Detter, John C</creatorcontrib><creatorcontrib>Schüler, Esther</creatorcontrib><creatorcontrib>Göker, Markus</creatorcontrib><creatorcontrib>Rohde, Manfred</creatorcontrib><creatorcontrib>Bristow, Jim</creatorcontrib><creatorcontrib>Eisen, Jonathan A</creatorcontrib><creatorcontrib>Markowitz, Victor</creatorcontrib><creatorcontrib>Hugenholtz, Philip</creatorcontrib><creatorcontrib>Kyrpides, Nikos C</creatorcontrib><creatorcontrib>Klenk, Hans-Peter</creatorcontrib><creatorcontrib>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</creatorcontrib><title>Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))</title><title>Standards in genomic sciences</title><addtitle>Stand Genomic Sci</addtitle><description>Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.</description><subject>ACETATES</subject><subject>BACTERIA</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>CHROMOSOMES</subject><subject>Deltaproteobacteria</subject><subject>Desulfohalobiaceae</subject><subject>GEBA</subject><subject>GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE</subject><subject>GENES</subject><subject>Gram-negative</subject><subject>hydrogen utilization</subject><subject>hypersaline lake</subject><subject>LAKES</subject><subject>mesophile</subject><subject>moderately halophilic</subject><subject>Proteobacteria</subject><subject>RNA</subject><subject>SEDIMENTS</subject><subject>SENEGAL</subject><subject>Short Genome Reports</subject><subject>STRAINS</subject><subject>strictly anaerobic</subject><subject>SUBSTRATES</subject><subject>sulfate-reducer</subject><issn>1944-3277</issn><issn>1944-3277</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><recordid>eNpVkc1LJDEQxYOsqIxz8i7taZVl3HyncxGWWV3FAWHRc0hnqmci3cnYSS_Mf7-RUdG6VEH9ePWoh9AJwZccC_kz-VW6FDXBvN5DR0RzPmNUqW-f5kM0TekZl2Jaaa4P0CElDHOp5BG6n8d-00GGagUh9lAleBkhOKhiW_2GNHZtXNsuNn7sqwFyYyEkqPJ2U9A8WB-q89u_5wTji4tjtN_aLsH0rU_Q08314_x2tnj4czf_tZg5jmWeWUKglmq5ZII1TACVwrUSWF0rB0ICl0JjbR1vsFLCKbJUzgFlkjotlOBsgq52upux6WHpIBQjndkMvrfD1kTrzddN8Guziv8Mw0xQQYvA2U4gpuxNcj6DW7sYArhsdE3Klwrz_e3IEMtHUja9Tw66zgaIYzK1IJTWVOlC_tiRbogpDdB-OCHYvIZkXkMyu5AKffrZ_Af7Hgn7Dy27jIw</recordid><startdate>20100128</startdate><enddate>20100128</enddate><creator>Spring, Stefan</creator><creator>Nolan, Matt</creator><creator>Lapidus, Alla</creator><creator>Glavina Del Rio, Tijana</creator><creator>Copeland, Alex</creator><creator>Tice, Hope</creator><creator>Cheng, Jan-Fang</creator><creator>Lucas, Susan</creator><creator>Land, Miriam</creator><creator>Chen, Feng</creator><creator>Bruce, David</creator><creator>Goodwin, Lynne</creator><creator>Pitluck, Sam</creator><creator>Ivanova, Natalia</creator><creator>Mavromatis, Konstantinos</creator><creator>Mikhailova, Natalia</creator><creator>Pati, Amrita</creator><creator>Chen, Amy</creator><creator>Palaniappan, Krishna</creator><creator>Hauser, Loren</creator><creator>Chang, Yun-Juan</creator><creator>Jeffries, Cynthia D</creator><creator>Munk, Christine</creator><creator>Kiss, Hajnalka</creator><creator>Chain, Patrick</creator><creator>Han, Cliff</creator><creator>Brettin, Thomas</creator><creator>Detter, John C</creator><creator>Schüler, Esther</creator><creator>Göker, Markus</creator><creator>Rohde, Manfred</creator><creator>Bristow, Jim</creator><creator>Eisen, Jonathan A</creator><creator>Markowitz, Victor</creator><creator>Hugenholtz, Philip</creator><creator>Kyrpides, Nikos C</creator><creator>Klenk, Hans-Peter</creator><general>Michigan State University</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20100128</creationdate><title>Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))</title><author>Spring, Stefan ; Nolan, Matt ; Lapidus, Alla ; Glavina Del Rio, Tijana ; Copeland, Alex ; Tice, Hope ; Cheng, Jan-Fang ; Lucas, Susan ; Land, Miriam ; Chen, Feng ; Bruce, David ; Goodwin, Lynne ; Pitluck, Sam ; Ivanova, Natalia ; Mavromatis, Konstantinos ; Mikhailova, Natalia ; Pati, Amrita ; Chen, Amy ; Palaniappan, Krishna ; Hauser, Loren ; Chang, Yun-Juan ; Jeffries, Cynthia D ; Munk, Christine ; Kiss, Hajnalka ; Chain, Patrick ; Han, Cliff ; Brettin, Thomas ; Detter, John C ; Schüler, Esther ; Göker, Markus ; Rohde, Manfred ; Bristow, Jim ; Eisen, Jonathan A ; Markowitz, Victor ; Hugenholtz, Philip ; Kyrpides, Nikos C ; Klenk, Hans-Peter</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c406t-a11e867dd353b35e265cf6e3887ce56e465909ac4b0775c71d7cce2362c957543</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>ACETATES</topic><topic>BACTERIA</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>CHROMOSOMES</topic><topic>Deltaproteobacteria</topic><topic>Desulfohalobiaceae</topic><topic>GEBA</topic><topic>GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE</topic><topic>GENES</topic><topic>Gram-negative</topic><topic>hydrogen utilization</topic><topic>hypersaline lake</topic><topic>LAKES</topic><topic>mesophile</topic><topic>moderately halophilic</topic><topic>Proteobacteria</topic><topic>RNA</topic><topic>SEDIMENTS</topic><topic>SENEGAL</topic><topic>Short Genome Reports</topic><topic>STRAINS</topic><topic>strictly anaerobic</topic><topic>SUBSTRATES</topic><topic>sulfate-reducer</topic><toplevel>online_resources</toplevel><creatorcontrib>Spring, Stefan</creatorcontrib><creatorcontrib>Nolan, Matt</creatorcontrib><creatorcontrib>Lapidus, Alla</creatorcontrib><creatorcontrib>Glavina Del Rio, Tijana</creatorcontrib><creatorcontrib>Copeland, Alex</creatorcontrib><creatorcontrib>Tice, Hope</creatorcontrib><creatorcontrib>Cheng, Jan-Fang</creatorcontrib><creatorcontrib>Lucas, Susan</creatorcontrib><creatorcontrib>Land, Miriam</creatorcontrib><creatorcontrib>Chen, Feng</creatorcontrib><creatorcontrib>Bruce, David</creatorcontrib><creatorcontrib>Goodwin, Lynne</creatorcontrib><creatorcontrib>Pitluck, Sam</creatorcontrib><creatorcontrib>Ivanova, Natalia</creatorcontrib><creatorcontrib>Mavromatis, Konstantinos</creatorcontrib><creatorcontrib>Mikhailova, Natalia</creatorcontrib><creatorcontrib>Pati, Amrita</creatorcontrib><creatorcontrib>Chen, Amy</creatorcontrib><creatorcontrib>Palaniappan, Krishna</creatorcontrib><creatorcontrib>Hauser, Loren</creatorcontrib><creatorcontrib>Chang, Yun-Juan</creatorcontrib><creatorcontrib>Jeffries, Cynthia D</creatorcontrib><creatorcontrib>Munk, Christine</creatorcontrib><creatorcontrib>Kiss, Hajnalka</creatorcontrib><creatorcontrib>Chain, Patrick</creatorcontrib><creatorcontrib>Han, Cliff</creatorcontrib><creatorcontrib>Brettin, Thomas</creatorcontrib><creatorcontrib>Detter, John C</creatorcontrib><creatorcontrib>Schüler, Esther</creatorcontrib><creatorcontrib>Göker, Markus</creatorcontrib><creatorcontrib>Rohde, Manfred</creatorcontrib><creatorcontrib>Bristow, Jim</creatorcontrib><creatorcontrib>Eisen, Jonathan A</creatorcontrib><creatorcontrib>Markowitz, Victor</creatorcontrib><creatorcontrib>Hugenholtz, Philip</creatorcontrib><creatorcontrib>Kyrpides, Nikos C</creatorcontrib><creatorcontrib>Klenk, Hans-Peter</creatorcontrib><creatorcontrib>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Standards in genomic sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Spring, Stefan</au><au>Nolan, Matt</au><au>Lapidus, Alla</au><au>Glavina Del Rio, Tijana</au><au>Copeland, Alex</au><au>Tice, Hope</au><au>Cheng, Jan-Fang</au><au>Lucas, Susan</au><au>Land, Miriam</au><au>Chen, Feng</au><au>Bruce, David</au><au>Goodwin, Lynne</au><au>Pitluck, Sam</au><au>Ivanova, Natalia</au><au>Mavromatis, Konstantinos</au><au>Mikhailova, Natalia</au><au>Pati, Amrita</au><au>Chen, Amy</au><au>Palaniappan, Krishna</au><au>Hauser, Loren</au><au>Chang, Yun-Juan</au><au>Jeffries, Cynthia D</au><au>Munk, Christine</au><au>Kiss, Hajnalka</au><au>Chain, Patrick</au><au>Han, Cliff</au><au>Brettin, Thomas</au><au>Detter, John C</au><au>Schüler, Esther</au><au>Göker, Markus</au><au>Rohde, Manfred</au><au>Bristow, Jim</au><au>Eisen, Jonathan A</au><au>Markowitz, Victor</au><au>Hugenholtz, Philip</au><au>Kyrpides, Nikos C</au><au>Klenk, Hans-Peter</au><aucorp>Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Complete genome sequence of Desulfohalobium retbaense type strain (HR(100))</atitle><jtitle>Standards in genomic sciences</jtitle><addtitle>Stand Genomic Sci</addtitle><date>2010-01-28</date><risdate>2010</risdate><volume>2</volume><issue>1</issue><spage>38</spage><epage>48</epage><pages>38-48</pages><issn>1944-3277</issn><eissn>1944-3277</eissn><abstract>Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.</abstract><cop>England</cop><pub>Michigan State University</pub><pmid>21304676</pmid><doi>10.4056/sigs.581048</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | Standards in genomic sciences, 2010-01, Vol.2 (1), p.38-48 |
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| subjects | ACETATES BACTERIA BASIC BIOLOGICAL SCIENCES CHROMOSOMES Deltaproteobacteria Desulfohalobiaceae GEBA GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE GENES Gram-negative hydrogen utilization hypersaline lake LAKES mesophile moderately halophilic Proteobacteria RNA SEDIMENTS SENEGAL Short Genome Reports STRAINS strictly anaerobic SUBSTRATES sulfate-reducer |
| title | Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)) |
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