Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation
A methanogenic organism, designated strain HB-1T, from the domain Archaea was isolated from groundwater sampled from a subsurface Miocene formation located in Horonobe, Hokkaido, Japan. The strain grew on methanol, dimethylamine, trimethylamine, dimethylsulfide and acetate but not on monomethylamine...
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| Veröffentlicht in: | International journal of systematic and evolutionary microbiology 2011-10, Vol.61 (Pt 10), p.2503-2507 |
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| container_title | International journal of systematic and evolutionary microbiology |
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| creator | Shimizu, Satoru Upadhye, Rahul Ishijima, Yoji Naganuma, Takeshi |
| description | A methanogenic organism, designated strain HB-1T, from the domain Archaea was isolated from groundwater sampled from a subsurface Miocene formation located in Horonobe, Hokkaido, Japan. The strain grew on methanol, dimethylamine, trimethylamine, dimethylsulfide and acetate but not on monomethylamine, H2/CO2, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-reaction-negative, non-motile, irregular cocci that were 1.4–2.9 µm in diameter and occurred singly or in pairs. The strain grew at 20–42 °C (optimum 37 °C), at pH 6.0–7.75 (optimum pH 7.0–7.25) and in 0–0.35 M NaCl (optimum 0.1 M). The G+C content of the genomic DNA was 41.4 mol%. 16S rRNA gene sequencing revealed that the strain was a member of the genus Methanosarcina but that it clearly differed from all recognized species of this genus (93.1–97.9 % sequence similarity). The phenotypic and phylogenetic features of strain HB-1T indicate that it represents a novel species of the genus Methanosarcina, for which the name Methanosarcina horonobensis sp. nov. is proposed. The type strain is HB-1T ( = DSM 21571T = JCM 15518T = NBRC 102577T). |
| doi_str_mv | 10.1099/ijs.0.028548-0 |
| format | Article |
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The strain grew on methanol, dimethylamine, trimethylamine, dimethylsulfide and acetate but not on monomethylamine, H2/CO2, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-reaction-negative, non-motile, irregular cocci that were 1.4–2.9 µm in diameter and occurred singly or in pairs. The strain grew at 20–42 °C (optimum 37 °C), at pH 6.0–7.75 (optimum pH 7.0–7.25) and in 0–0.35 M NaCl (optimum 0.1 M). The G+C content of the genomic DNA was 41.4 mol%. 16S rRNA gene sequencing revealed that the strain was a member of the genus Methanosarcina but that it clearly differed from all recognized species of this genus (93.1–97.9 % sequence similarity). The phenotypic and phylogenetic features of strain HB-1T indicate that it represents a novel species of the genus Methanosarcina, for which the name Methanosarcina horonobensis sp. nov. is proposed. The type strain is HB-1T ( = DSM 21571T = JCM 15518T = NBRC 102577T).</description><identifier>ISSN: 1466-5034</identifier><identifier>ISSN: 1466-5026</identifier><identifier>EISSN: 1466-5034</identifier><identifier>DOI: 10.1099/ijs.0.028548-0</identifier><identifier>PMID: 21112985</identifier><language>eng</language><publisher>Reading: International Union of Microbiological Societies</publisher><subject>acetates ; Bacteriology ; Base Composition ; Biological and medical sciences ; Carbon - metabolism ; Cluster Analysis ; dimethyl sulfide ; dimethylamine ; DNA ; DNA, Archaeal - chemistry ; DNA, Archaeal - genetics ; DNA, Ribosomal - chemistry ; DNA, Ribosomal - genetics ; Fundamental and applied biological sciences. Psychology ; genes ; Genes, rRNA ; groundwater ; Groundwater - microbiology ; Hydrogen-Ion Concentration ; isopropyl alcohol ; Japan ; methanogens ; methanol ; Methanosarcina ; Methanosarcina - classification ; Methanosarcina - genetics ; Methanosarcina - isolation & purification ; Methanosarcina - physiology ; Microbiology ; Molecular Sequence Data ; new species ; phenotype ; Phylogeny ; ribosomal RNA ; RNA, Archaeal - genetics ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA ; sequence homology ; Sequence Homology, Nucleic Acid ; sodium chloride ; Systematics ; Temperature ; trimethylamine</subject><ispartof>International journal of systematic and evolutionary microbiology, 2011-10, Vol.61 (Pt 10), p.2503-2507</ispartof><rights>2015 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c454t-2caf168a41fea3500453ce2686d22ebe32ed77da0d23f8c0f9326607985d858c3</citedby><cites>FETCH-LOGICAL-c454t-2caf168a41fea3500453ce2686d22ebe32ed77da0d23f8c0f9326607985d858c3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,3733,27901,27902</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24628299$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21112985$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shimizu, Satoru</creatorcontrib><creatorcontrib>Upadhye, Rahul</creatorcontrib><creatorcontrib>Ishijima, Yoji</creatorcontrib><creatorcontrib>Naganuma, Takeshi</creatorcontrib><title>Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation</title><title>International journal of systematic and evolutionary microbiology</title><addtitle>Int J Syst Evol Microbiol</addtitle><description>A methanogenic organism, designated strain HB-1T, from the domain Archaea was isolated from groundwater sampled from a subsurface Miocene formation located in Horonobe, Hokkaido, Japan. The strain grew on methanol, dimethylamine, trimethylamine, dimethylsulfide and acetate but not on monomethylamine, H2/CO2, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-reaction-negative, non-motile, irregular cocci that were 1.4–2.9 µm in diameter and occurred singly or in pairs. The strain grew at 20–42 °C (optimum 37 °C), at pH 6.0–7.75 (optimum pH 7.0–7.25) and in 0–0.35 M NaCl (optimum 0.1 M). The G+C content of the genomic DNA was 41.4 mol%. 16S rRNA gene sequencing revealed that the strain was a member of the genus Methanosarcina but that it clearly differed from all recognized species of this genus (93.1–97.9 % sequence similarity). The phenotypic and phylogenetic features of strain HB-1T indicate that it represents a novel species of the genus Methanosarcina, for which the name Methanosarcina horonobensis sp. nov. is proposed. The type strain is HB-1T ( = DSM 21571T = JCM 15518T = NBRC 102577T).</description><subject>acetates</subject><subject>Bacteriology</subject><subject>Base Composition</subject><subject>Biological and medical sciences</subject><subject>Carbon - metabolism</subject><subject>Cluster Analysis</subject><subject>dimethyl sulfide</subject><subject>dimethylamine</subject><subject>DNA</subject><subject>DNA, Archaeal - chemistry</subject><subject>DNA, Archaeal - genetics</subject><subject>DNA, Ribosomal - chemistry</subject><subject>DNA, Ribosomal - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>genes</subject><subject>Genes, rRNA</subject><subject>groundwater</subject><subject>Groundwater - microbiology</subject><subject>Hydrogen-Ion Concentration</subject><subject>isopropyl alcohol</subject><subject>Japan</subject><subject>methanogens</subject><subject>methanol</subject><subject>Methanosarcina</subject><subject>Methanosarcina - classification</subject><subject>Methanosarcina - genetics</subject><subject>Methanosarcina - isolation & purification</subject><subject>Methanosarcina - physiology</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>new species</subject><subject>phenotype</subject><subject>Phylogeny</subject><subject>ribosomal RNA</subject><subject>RNA, Archaeal - genetics</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>sequence homology</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>sodium chloride</subject><subject>Systematics</subject><subject>Temperature</subject><subject>trimethylamine</subject><issn>1466-5034</issn><issn>1466-5026</issn><issn>1466-5034</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpN0M9v1TAMB_AIgdgPuHKEXBAXWpy0TdMjmmAgbeKw7Rz5pc5epjZ5JO0k_nuC-oCdbFkfW_KXsTcCagHD8Mk_5BpqkLprdQXP2Klolao6aNrnT_oTdpbzA0AZALxkJ1IIIQfdnbJ4TcseQ8yYrA_I9zHFEHcUss88H2oe4mP9kSOfN3dPwVte8B4pBu5znHChkbsU56JGogPP6y6vyaElfu2jpUDcxTTj4mN4xV44nDK9PtZzdvf1y-3Ft-rqx-X3i89XlW27dqmkRSeUxlY4wqYDaLvGklRajVLSjhpJY9-PCKNsnLbghkYqBX35adSdts05-7DdPaT4c6W8mNlnS9OEgeKajR6UlhqkKrLepE0x50TOHJKfMf0yAsyfjE3J2IDZMjZQFt4eT6-7mcZ__G-oBbw_AswWJ5cwWJ__u1ZJLYehuHebcxgN3qdi7m4kiPIuKNX3qvkNBS2O7w</recordid><startdate>20111001</startdate><enddate>20111001</enddate><creator>Shimizu, Satoru</creator><creator>Upadhye, Rahul</creator><creator>Ishijima, Yoji</creator><creator>Naganuma, Takeshi</creator><general>International Union of Microbiological Societies</general><general>Society for General Microbiology</general><scope>FBQ</scope><scope>IQODW</scope><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>7X8</scope></search><sort><creationdate>20111001</creationdate><title>Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation</title><author>Shimizu, Satoru ; Upadhye, Rahul ; Ishijima, Yoji ; Naganuma, Takeshi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c454t-2caf168a41fea3500453ce2686d22ebe32ed77da0d23f8c0f9326607985d858c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>acetates</topic><topic>Bacteriology</topic><topic>Base Composition</topic><topic>Biological and medical sciences</topic><topic>Carbon - metabolism</topic><topic>Cluster Analysis</topic><topic>dimethyl sulfide</topic><topic>dimethylamine</topic><topic>DNA</topic><topic>DNA, Archaeal - chemistry</topic><topic>DNA, Archaeal - genetics</topic><topic>DNA, Ribosomal - chemistry</topic><topic>DNA, Ribosomal - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>genes</topic><topic>Genes, rRNA</topic><topic>groundwater</topic><topic>Groundwater - microbiology</topic><topic>Hydrogen-Ion Concentration</topic><topic>isopropyl alcohol</topic><topic>Japan</topic><topic>methanogens</topic><topic>methanol</topic><topic>Methanosarcina</topic><topic>Methanosarcina - classification</topic><topic>Methanosarcina - genetics</topic><topic>Methanosarcina - isolation & purification</topic><topic>Methanosarcina - physiology</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>new species</topic><topic>phenotype</topic><topic>Phylogeny</topic><topic>ribosomal RNA</topic><topic>RNA, Archaeal - genetics</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>sequence homology</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>sodium chloride</topic><topic>Systematics</topic><topic>Temperature</topic><topic>trimethylamine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shimizu, Satoru</creatorcontrib><creatorcontrib>Upadhye, Rahul</creatorcontrib><creatorcontrib>Ishijima, Yoji</creatorcontrib><creatorcontrib>Naganuma, Takeshi</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</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>Shimizu, Satoru</au><au>Upadhye, Rahul</au><au>Ishijima, Yoji</au><au>Naganuma, Takeshi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation</atitle><jtitle>International journal of systematic and evolutionary microbiology</jtitle><addtitle>Int J Syst Evol Microbiol</addtitle><date>2011-10-01</date><risdate>2011</risdate><volume>61</volume><issue>Pt 10</issue><spage>2503</spage><epage>2507</epage><pages>2503-2507</pages><issn>1466-5034</issn><issn>1466-5026</issn><eissn>1466-5034</eissn><abstract>A methanogenic organism, designated strain HB-1T, from the domain Archaea was isolated from groundwater sampled from a subsurface Miocene formation located in Horonobe, Hokkaido, Japan. The strain grew on methanol, dimethylamine, trimethylamine, dimethylsulfide and acetate but not on monomethylamine, H2/CO2, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-reaction-negative, non-motile, irregular cocci that were 1.4–2.9 µm in diameter and occurred singly or in pairs. The strain grew at 20–42 °C (optimum 37 °C), at pH 6.0–7.75 (optimum pH 7.0–7.25) and in 0–0.35 M NaCl (optimum 0.1 M). The G+C content of the genomic DNA was 41.4 mol%. 16S rRNA gene sequencing revealed that the strain was a member of the genus Methanosarcina but that it clearly differed from all recognized species of this genus (93.1–97.9 % sequence similarity). The phenotypic and phylogenetic features of strain HB-1T indicate that it represents a novel species of the genus Methanosarcina, for which the name Methanosarcina horonobensis sp. nov. is proposed. The type strain is HB-1T ( = DSM 21571T = JCM 15518T = NBRC 102577T).</abstract><cop>Reading</cop><pub>International Union of Microbiological Societies</pub><pmid>21112985</pmid><doi>10.1099/ijs.0.028548-0</doi><tpages>5</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | acetates Bacteriology Base Composition Biological and medical sciences Carbon - metabolism Cluster Analysis dimethyl sulfide dimethylamine DNA DNA, Archaeal - chemistry DNA, Archaeal - genetics DNA, Ribosomal - chemistry DNA, Ribosomal - genetics Fundamental and applied biological sciences. Psychology genes Genes, rRNA groundwater Groundwater - microbiology Hydrogen-Ion Concentration isopropyl alcohol Japan methanogens methanol Methanosarcina Methanosarcina - classification Methanosarcina - genetics Methanosarcina - isolation & purification Methanosarcina - physiology Microbiology Molecular Sequence Data new species phenotype Phylogeny ribosomal RNA RNA, Archaeal - genetics RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA sequence homology Sequence Homology, Nucleic Acid sodium chloride Systematics Temperature trimethylamine |
| title | Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation |
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