Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene
1 S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia 2 Netherlands Institute of Ecology, Centre for Terrestrial Ecology, 6666 ZG Heteren, The Netherlands 3 Netherlands Institute of Ecology, Centre for Limnology, 3631 AC Nieuwersluis, The Netherlands 4 G....
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| Veröffentlicht in: | International journal of systematic and evolutionary microbiology 2009-10, Vol.59 (10), p.2538-2545 |
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| creator | Vorob'ev, Alexey V de Boer, Wietse Folman, Larissa B Bodelier, Paul L. E Doronina, Nina V Suzina, Natalia E Trotsenko, Yuri A Dedysh, Svetlana N |
| description | 1 S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
2 Netherlands Institute of Ecology, Centre for Terrestrial Ecology, 6666 ZG Heteren, The Netherlands
3 Netherlands Institute of Ecology, Centre for Limnology, 3631 AC Nieuwersluis, The Netherlands
4 G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
Correspondence Svetlana N. Dedysh dedysh{at}mail.ru
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beechwood blocks during decay by the white-rot fungus Hypholoma fasciculare and were designated strains BW863 T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863 T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH 3.1–6.5 (with an optimum at pH 4.5–5.0) and at 4–30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually large amounts (about 90 %) of C 18 : 1 7 c , thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of the novel isolates is 61.8–62.8 mol%. On the basis of 16S rRNA gene sequence similarity, strains BW863 T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2 T (96.5–97 %). Comparative sequence analysis of mxaF , the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of the two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity between the MxaF sequences of the acidophilic isolates and those from known alpha-, beta- and gammaproteobacterial methylotrophs was respectively 69–75, 61–63 and 64–67 %. The data therefore suggest that strains BW863 T and BW872 represent a novel genus and species of methylotrophic bacteria, for which the name Methylovirgula ligni gen. nov., sp. nov. is proposed. Strain BW863 T (=DSM 19998 T =NCIMB 14408 T ) is the type strain of Methylovirgula ligni .
Abbreviations: ICM, intracytoplasmic membrane; PLFA, phospholipid fatty acid; PMS, phenazine methosulfate; RuBisCO, ribulose-1,5-bisphosphate carboxylase/oxygenase; RuBP, ribulose bisphosphate; SIP, stable-isotope probing
The GenBank/EMBL/DDBJ accession numbers f |
| doi_str_mv | 10.1099/ijs.0.010074-0 |
| format | Article |
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2 Netherlands Institute of Ecology, Centre for Terrestrial Ecology, 6666 ZG Heteren, The Netherlands
3 Netherlands Institute of Ecology, Centre for Limnology, 3631 AC Nieuwersluis, The Netherlands
4 G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
Correspondence Svetlana N. Dedysh dedysh{at}mail.ru
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beechwood blocks during decay by the white-rot fungus Hypholoma fasciculare and were designated strains BW863 T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863 T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH 3.1–6.5 (with an optimum at pH 4.5–5.0) and at 4–30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually large amounts (about 90 %) of C 18 : 1 7 c , thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of the novel isolates is 61.8–62.8 mol%. On the basis of 16S rRNA gene sequence similarity, strains BW863 T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2 T (96.5–97 %). Comparative sequence analysis of mxaF , the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of the two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity between the MxaF sequences of the acidophilic isolates and those from known alpha-, beta- and gammaproteobacterial methylotrophs was respectively 69–75, 61–63 and 64–67 %. The data therefore suggest that strains BW863 T and BW872 represent a novel genus and species of methylotrophic bacteria, for which the name Methylovirgula ligni gen. nov., sp. nov. is proposed. Strain BW863 T (=DSM 19998 T =NCIMB 14408 T ) is the type strain of Methylovirgula ligni .
Abbreviations: ICM, intracytoplasmic membrane; PLFA, phospholipid fatty acid; PMS, phenazine methosulfate; RuBisCO, ribulose-1,5-bisphosphate carboxylase/oxygenase; RuBP, ribulose bisphosphate; SIP, stable-isotope probing
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences and partial mxaF gene sequences of strains BW863 T and BW872 are respectively FM252034 and FM252035 (16S rRNA gene) and FM252036 and FM252037 ( mxaF ), and those for the partial nifH and cbbL gene sequences of strain BW863 T are respectively FM252038 and FM252039 .
EMs contrasting the morphology of strain BW863 T and Methylocapsa acidiphila B2 T , a graph showing the growth response of strain BW863 T to pH and an extended 16S rRNA gene-sequence based neighbour-joining tree are available as supplementary material with the online version of this paper.</description><identifier>ISSN: 1466-5026</identifier><identifier>EISSN: 1466-5034</identifier><identifier>DOI: 10.1099/ijs.0.010074-0</identifier><identifier>PMID: 19622650</identifier><language>eng</language><publisher>England: Soc General Microbiol</publisher><subject>Acids - metabolism ; Alcohol Oxidoreductases - genetics ; Autotrophic Processes ; Bacteria ; Bacterial Proteins - genetics ; Beijerinckiaceae - classification ; Beijerinckiaceae - genetics ; Beijerinckiaceae - isolation & purification ; Beijerinckiaceae - metabolism ; DNA, Bacterial - genetics ; DNA, Ribosomal - genetics ; Evolution, Molecular ; Hypholoma fasciculare ; Methanol - metabolism ; Methylobacterium ; Methylocapsa acidiphila ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S - genetics</subject><ispartof>International journal of systematic and evolutionary microbiology, 2009-10, Vol.59 (10), p.2538-2545</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c329t-bcdbb38b584e16c35671c8e8ca6c1d5a2261cf53593b9cff99f5e641d59279ea3</citedby><cites>FETCH-LOGICAL-c329t-bcdbb38b584e16c35671c8e8ca6c1d5a2261cf53593b9cff99f5e641d59279ea3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,3746,3747,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19622650$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Vorob'ev, Alexey V</creatorcontrib><creatorcontrib>de Boer, Wietse</creatorcontrib><creatorcontrib>Folman, Larissa B</creatorcontrib><creatorcontrib>Bodelier, Paul L. E</creatorcontrib><creatorcontrib>Doronina, Nina V</creatorcontrib><creatorcontrib>Suzina, Natalia E</creatorcontrib><creatorcontrib>Trotsenko, Yuri A</creatorcontrib><creatorcontrib>Dedysh, Svetlana N</creatorcontrib><title>Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene</title><title>International journal of systematic and evolutionary microbiology</title><addtitle>Int J Syst Evol Microbiol</addtitle><description>1 S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
2 Netherlands Institute of Ecology, Centre for Terrestrial Ecology, 6666 ZG Heteren, The Netherlands
3 Netherlands Institute of Ecology, Centre for Limnology, 3631 AC Nieuwersluis, The Netherlands
4 G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
Correspondence Svetlana N. Dedysh dedysh{at}mail.ru
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beechwood blocks during decay by the white-rot fungus Hypholoma fasciculare and were designated strains BW863 T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863 T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH 3.1–6.5 (with an optimum at pH 4.5–5.0) and at 4–30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually large amounts (about 90 %) of C 18 : 1 7 c , thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of the novel isolates is 61.8–62.8 mol%. On the basis of 16S rRNA gene sequence similarity, strains BW863 T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2 T (96.5–97 %). Comparative sequence analysis of mxaF , the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of the two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity between the MxaF sequences of the acidophilic isolates and those from known alpha-, beta- and gammaproteobacterial methylotrophs was respectively 69–75, 61–63 and 64–67 %. The data therefore suggest that strains BW863 T and BW872 represent a novel genus and species of methylotrophic bacteria, for which the name Methylovirgula ligni gen. nov., sp. nov. is proposed. Strain BW863 T (=DSM 19998 T =NCIMB 14408 T ) is the type strain of Methylovirgula ligni .
Abbreviations: ICM, intracytoplasmic membrane; PLFA, phospholipid fatty acid; PMS, phenazine methosulfate; RuBisCO, ribulose-1,5-bisphosphate carboxylase/oxygenase; RuBP, ribulose bisphosphate; SIP, stable-isotope probing
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences and partial mxaF gene sequences of strains BW863 T and BW872 are respectively FM252034 and FM252035 (16S rRNA gene) and FM252036 and FM252037 ( mxaF ), and those for the partial nifH and cbbL gene sequences of strain BW863 T are respectively FM252038 and FM252039 .
EMs contrasting the morphology of strain BW863 T and Methylocapsa acidiphila B2 T , a graph showing the growth response of strain BW863 T to pH and an extended 16S rRNA gene-sequence based neighbour-joining tree are available as supplementary material with the online version of this paper.</description><subject>Acids - metabolism</subject><subject>Alcohol Oxidoreductases - genetics</subject><subject>Autotrophic Processes</subject><subject>Bacteria</subject><subject>Bacterial Proteins - genetics</subject><subject>Beijerinckiaceae - classification</subject><subject>Beijerinckiaceae - genetics</subject><subject>Beijerinckiaceae - isolation & purification</subject><subject>Beijerinckiaceae - metabolism</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Ribosomal - genetics</subject><subject>Evolution, Molecular</subject><subject>Hypholoma fasciculare</subject><subject>Methanol - metabolism</subject><subject>Methylobacterium</subject><subject>Methylocapsa acidiphila</subject><subject>Molecular Sequence Data</subject><subject>Phylogeny</subject><subject>RNA, Ribosomal, 16S - genetics</subject><issn>1466-5026</issn><issn>1466-5034</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kUFv1DAUhC1ERUvhyhH5RIXUhOc4duIjqlpAasUFzpbtOBtXTrLYzpb9EfxnHGWBGyc_eT7Pk2cQekOgJCDEB_cYSyiBADR1Ac_QBak5LxjQ-vnfueLn6GWMjwD5AuAFOieCVxVncIF-Pdg0HP18cGG3eIW9200O7-xU4mk-lNc47v9MasKzzrpK1h-xMq6b94PzzlzjXpnFJ5XcYZXGzTKFVTdYK5NscMuIn1wasMKD2w0Z6zId8qaEx5_qbt1pX6GzXvloX5_OS_T97vbbzefi_uunLzcf7wtDK5EKbTqtaatZW1vCDWW8Iaa1rVHckI6p_DdiekaZoFqYvheiZ5bXWRJVI6yil-hq892H-cdiY5Kji8Z6ryY7L1E2tIaGNy3J5Lv_khWpRA51BcsNNGGOMdhe7oMbVThKAnKtSuaqJMitKgn5wduT86JH2_3DT91k4P0GrHk9uWBljmh02V-7eXVjYvWuGG3pb46poCA</recordid><startdate>20091001</startdate><enddate>20091001</enddate><creator>Vorob'ev, Alexey V</creator><creator>de Boer, Wietse</creator><creator>Folman, Larissa B</creator><creator>Bodelier, Paul L. E</creator><creator>Doronina, Nina V</creator><creator>Suzina, Natalia E</creator><creator>Trotsenko, Yuri A</creator><creator>Dedysh, Svetlana N</creator><general>Soc General Microbiol</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20091001</creationdate><title>Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene</title><author>Vorob'ev, Alexey V ; de Boer, Wietse ; Folman, Larissa B ; Bodelier, Paul L. 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E</creatorcontrib><creatorcontrib>Doronina, Nina V</creatorcontrib><creatorcontrib>Suzina, Natalia E</creatorcontrib><creatorcontrib>Trotsenko, Yuri A</creatorcontrib><creatorcontrib>Dedysh, Svetlana N</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of systematic and evolutionary microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Vorob'ev, Alexey V</au><au>de Boer, Wietse</au><au>Folman, Larissa B</au><au>Bodelier, Paul L. E</au><au>Doronina, Nina V</au><au>Suzina, Natalia E</au><au>Trotsenko, Yuri A</au><au>Dedysh, Svetlana N</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene</atitle><jtitle>International journal of systematic and evolutionary microbiology</jtitle><addtitle>Int J Syst Evol Microbiol</addtitle><date>2009-10-01</date><risdate>2009</risdate><volume>59</volume><issue>10</issue><spage>2538</spage><epage>2545</epage><pages>2538-2545</pages><issn>1466-5026</issn><eissn>1466-5034</eissn><abstract>1 S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
2 Netherlands Institute of Ecology, Centre for Terrestrial Ecology, 6666 ZG Heteren, The Netherlands
3 Netherlands Institute of Ecology, Centre for Limnology, 3631 AC Nieuwersluis, The Netherlands
4 G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
Correspondence Svetlana N. Dedysh dedysh{at}mail.ru
Two strains of Gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria were isolated from beechwood blocks during decay by the white-rot fungus Hypholoma fasciculare and were designated strains BW863 T and BW872. They are capable of methylotrophic growth and assimilate carbon via the ribulose-bisphosphate pathway. In addition to methanol, the novel isolates utilized ethanol, pyruvate and malate. Strains BW863 T and BW872 are obligately acidophilic, mesophilic organisms capable of growth at pH 3.1–6.5 (with an optimum at pH 4.5–5.0) and at 4–30 °C. Phospholipid fatty acid profiles of these bacteria contain unusually large amounts (about 90 %) of C 18 : 1 7 c , thereby resembling the profiles of Methylobacterium strains. The predominant quinone is Q-10. The DNA G+C content of the novel isolates is 61.8–62.8 mol%. On the basis of 16S rRNA gene sequence similarity, strains BW863 T and BW872 are most closely related to the acidophilic methanotroph Methylocapsa acidiphila B2 T (96.5–97 %). Comparative sequence analysis of mxaF , the gene encoding the large subunit of methanol dehydrogenase, placed the MxaF sequences of the two novel strains in a cluster that is distinct from all previously described MxaF sequences of cultivated methylotrophs. The identity between the MxaF sequences of the acidophilic isolates and those from known alpha-, beta- and gammaproteobacterial methylotrophs was respectively 69–75, 61–63 and 64–67 %. The data therefore suggest that strains BW863 T and BW872 represent a novel genus and species of methylotrophic bacteria, for which the name Methylovirgula ligni gen. nov., sp. nov. is proposed. Strain BW863 T (=DSM 19998 T =NCIMB 14408 T ) is the type strain of Methylovirgula ligni .
Abbreviations: ICM, intracytoplasmic membrane; PLFA, phospholipid fatty acid; PMS, phenazine methosulfate; RuBisCO, ribulose-1,5-bisphosphate carboxylase/oxygenase; RuBP, ribulose bisphosphate; SIP, stable-isotope probing
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences and partial mxaF gene sequences of strains BW863 T and BW872 are respectively FM252034 and FM252035 (16S rRNA gene) and FM252036 and FM252037 ( mxaF ), and those for the partial nifH and cbbL gene sequences of strain BW863 T are respectively FM252038 and FM252039 .
EMs contrasting the morphology of strain BW863 T and Methylocapsa acidiphila B2 T , a graph showing the growth response of strain BW863 T to pH and an extended 16S rRNA gene-sequence based neighbour-joining tree are available as supplementary material with the online version of this paper.</abstract><cop>England</cop><pub>Soc General Microbiol</pub><pmid>19622650</pmid><doi>10.1099/ijs.0.010074-0</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | International journal of systematic and evolutionary microbiology, 2009-10, Vol.59 (10), p.2538-2545 |
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| source | Electronic Journals Library; MEDLINE; Microbiology Society; Alma/SFX Local Collection |
| subjects | Acids - metabolism Alcohol Oxidoreductases - genetics Autotrophic Processes Bacteria Bacterial Proteins - genetics Beijerinckiaceae - classification Beijerinckiaceae - genetics Beijerinckiaceae - isolation & purification Beijerinckiaceae - metabolism DNA, Bacterial - genetics DNA, Ribosomal - genetics Evolution, Molecular Hypholoma fasciculare Methanol - metabolism Methylobacterium Methylocapsa acidiphila Molecular Sequence Data Phylogeny RNA, Ribosomal, 16S - genetics |
| title | Methylovirgula ligni gen. nov., sp. nov., an obligately acidophilic, facultatively methylotrophic bacterium with a highly divergent mxaF gene |
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