Diversity of methanogenic archaea in a mangrove sediment and isolation of a new Methanococcoides strain
Mangrove forest sediments produce significant amounts of methane, but the diversity of methanogenic archaea is not well known at present. Therefore, 16S rRNA gene libraries were made using archaea-specific primers and DNA extracted directly from Tanzanian mangrove sediment samples as a template. Ana...
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| Veröffentlicht in: | FEMS microbiology letters 2009-02, Vol.291 (2), p.247-253 |
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| creator | Lyimo, Thomas J Pol, Arjan Jetten, Mike S.M Op den Camp, Huub J.M |
| description | Mangrove forest sediments produce significant amounts of methane, but the diversity of methanogenic archaea is not well known at present. Therefore, 16S rRNA gene libraries were made using archaea-specific primers and DNA extracted directly from Tanzanian mangrove sediment samples as a template. Analysis of sequence data showed phylotypes closely related to cultivated methylotrophic methanogenic archaea from the marine environment, or distantly related to acetoclastic and hydrogenotrophic methanogenic archaea. In an attempt to isolate relevant methanogenic archaea, we succeeded in obtaining a new mesophilic methylotrophic methanogenic archaeon (strain MM1) capable of utilizing methanol and methylated amines as the only substrates. Under optimum conditions, the cells of strain MM1 exhibited a high specific growth rate (μ) of 0.21±0.03 (i.e. doubling time of 3.2 h) on both methanol and trimethylamine. The 16S rRNA gene sequence of strain MM1 clustered with five environmental clones, indicating that MM1 is an important methanogenic methylotroph in mangrove sediments. Based on physiological and phylogenetic analyses, strain MM1 is proposed to be included in the species of Methanococcoides methylutens. |
| doi_str_mv | 10.1111/j.1574-6968.2008.01464.x |
| format | Article |
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Therefore, 16S rRNA gene libraries were made using archaea-specific primers and DNA extracted directly from Tanzanian mangrove sediment samples as a template. Analysis of sequence data showed phylotypes closely related to cultivated methylotrophic methanogenic archaea from the marine environment, or distantly related to acetoclastic and hydrogenotrophic methanogenic archaea. In an attempt to isolate relevant methanogenic archaea, we succeeded in obtaining a new mesophilic methylotrophic methanogenic archaeon (strain MM1) capable of utilizing methanol and methylated amines as the only substrates. Under optimum conditions, the cells of strain MM1 exhibited a high specific growth rate (μ) of 0.21±0.03 (i.e. doubling time of 3.2 h) on both methanol and trimethylamine. The 16S rRNA gene sequence of strain MM1 clustered with five environmental clones, indicating that MM1 is an important methanogenic methylotroph in mangrove sediments. Based on physiological and phylogenetic analyses, strain MM1 is proposed to be included in the species of Methanococcoides methylutens.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1111/j.1574-6968.2008.01464.x</identifier><identifier>PMID: 19146579</identifier><identifier>CODEN: FMLED7</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>Amines ; Archaea ; Archaea - classification ; Archaea - genetics ; Archaea - isolation & purification ; Archaea - metabolism ; Bacteriology ; Biodiversity ; Biological and medical sciences ; Brackish ; Deoxyribonucleic acid ; DNA ; DNA, Archaeal - genetics ; DNA, Ribosomal - genetics ; Fundamental and applied biological sciences. Psychology ; Gene libraries ; Geologic Sediments - microbiology ; Growth rate ; mangrove sediment ; Mangrove swamps ; Marine environment ; Methanococcoides ; Methanococcoides methylutens ; Methanogenic archaea ; methanogens ; Methanol ; Methanol - metabolism ; Methanosarcinaceae - classification ; Methanosarcinaceae - genetics ; Methanosarcinaceae - isolation & purification ; Methanosarcinaceae - metabolism ; Methylamines - metabolism ; Microbiology ; Molecular Sequence Data ; Phylogeny ; Primers ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Sediment samplers ; Sediments ; Substrates ; Systematics ; Termites ; Trimethylamine</subject><ispartof>FEMS microbiology letters, 2009-02, Vol.291 (2), p.247-253</ispartof><rights>2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved 2008</rights><rights>2008 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><rights>2009 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4544-f26da6c2fbd20a8208b52b0a2ba170291cab150c6afd15723d7c44b0b7cfea793</citedby><cites>FETCH-LOGICAL-c4544-f26da6c2fbd20a8208b52b0a2ba170291cab150c6afd15723d7c44b0b7cfea793</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1574-6968.2008.01464.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6968.2008.01464.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>315,781,785,1418,27929,27930,45579,45580</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21030735$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19146579$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lyimo, Thomas J</creatorcontrib><creatorcontrib>Pol, Arjan</creatorcontrib><creatorcontrib>Jetten, Mike S.M</creatorcontrib><creatorcontrib>Op den Camp, Huub J.M</creatorcontrib><title>Diversity of methanogenic archaea in a mangrove sediment and isolation of a new Methanococcoides strain</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>Mangrove forest sediments produce significant amounts of methane, but the diversity of methanogenic archaea is not well known at present. Therefore, 16S rRNA gene libraries were made using archaea-specific primers and DNA extracted directly from Tanzanian mangrove sediment samples as a template. Analysis of sequence data showed phylotypes closely related to cultivated methylotrophic methanogenic archaea from the marine environment, or distantly related to acetoclastic and hydrogenotrophic methanogenic archaea. In an attempt to isolate relevant methanogenic archaea, we succeeded in obtaining a new mesophilic methylotrophic methanogenic archaeon (strain MM1) capable of utilizing methanol and methylated amines as the only substrates. Under optimum conditions, the cells of strain MM1 exhibited a high specific growth rate (μ) of 0.21±0.03 (i.e. doubling time of 3.2 h) on both methanol and trimethylamine. The 16S rRNA gene sequence of strain MM1 clustered with five environmental clones, indicating that MM1 is an important methanogenic methylotroph in mangrove sediments. Based on physiological and phylogenetic analyses, strain MM1 is proposed to be included in the species of Methanococcoides methylutens.</description><subject>Amines</subject><subject>Archaea</subject><subject>Archaea - classification</subject><subject>Archaea - genetics</subject><subject>Archaea - isolation & purification</subject><subject>Archaea - metabolism</subject><subject>Bacteriology</subject><subject>Biodiversity</subject><subject>Biological and medical sciences</subject><subject>Brackish</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Archaeal - genetics</subject><subject>DNA, Ribosomal - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene libraries</subject><subject>Geologic Sediments - microbiology</subject><subject>Growth rate</subject><subject>mangrove sediment</subject><subject>Mangrove swamps</subject><subject>Marine environment</subject><subject>Methanococcoides</subject><subject>Methanococcoides methylutens</subject><subject>Methanogenic archaea</subject><subject>methanogens</subject><subject>Methanol</subject><subject>Methanol - metabolism</subject><subject>Methanosarcinaceae - classification</subject><subject>Methanosarcinaceae - genetics</subject><subject>Methanosarcinaceae - isolation & purification</subject><subject>Methanosarcinaceae - metabolism</subject><subject>Methylamines - metabolism</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Phylogeny</subject><subject>Primers</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Sediment samplers</subject><subject>Sediments</subject><subject>Substrates</subject><subject>Systematics</subject><subject>Termites</subject><subject>Trimethylamine</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkc1u1DAURiMEotPCK4AlBLsM1z9xkgULVCggTcUCurZuHGfqUWIPdtJ23h6nGRUJgcAbW_I59md_WUYorGkab3drWpQil7Ws1gygWgMVUqzvHmWrh43H2Qp4WeUU6vIkO41xBwCCgXyandA68UVZr7LtB3tjQrTjgfiODGa8Rue3xllNMOhrNEisI0gGdNvgbwyJprWDcSNB1xIbfY-j9W6WkThzSy6XI7TX2tvWRBLHgNY9y5502Efz_DifZVcXH7-ff843Xz99OX-_ybUohMg7JluUmnVNywArBlVTsAaQNUhLYDXV2NACtMSuTS9lvC21EA00pe4MljU_y94s5-6D_zGZOKrBRm36Hp3xU1RSVowXjP8TZFAKKDkk8NVv4M5PwaVHKMZBMlFzWSSqWigdfIzBdGof7IDhoCiouTO1U3M1aq5GzZ2p-87UXVJfHC-YmsG0v8RjSQl4fQQwauy7gE7b-MAxCjwlnTO8W7hb25vDfwdQF5ebeZV8vvh-2v_Fzv8U_-VidegVbkNKdvWNAeVAi0qw9N0_AVNXymY</recordid><startdate>200902</startdate><enddate>200902</enddate><creator>Lyimo, Thomas J</creator><creator>Pol, Arjan</creator><creator>Jetten, Mike S.M</creator><creator>Op den Camp, Huub J.M</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Wiley-Blackwell</general><general>Oxford University Press</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>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>F1W</scope><scope>H95</scope><scope>H96</scope><scope>L.G</scope><scope>7X8</scope></search><sort><creationdate>200902</creationdate><title>Diversity of methanogenic archaea in a mangrove sediment and isolation of a new Methanococcoides strain</title><author>Lyimo, Thomas J ; Pol, Arjan ; Jetten, Mike S.M ; Op den Camp, Huub J.M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4544-f26da6c2fbd20a8208b52b0a2ba170291cab150c6afd15723d7c44b0b7cfea793</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Amines</topic><topic>Archaea</topic><topic>Archaea - classification</topic><topic>Archaea - genetics</topic><topic>Archaea - isolation & purification</topic><topic>Archaea - metabolism</topic><topic>Bacteriology</topic><topic>Biodiversity</topic><topic>Biological and medical sciences</topic><topic>Brackish</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Archaeal - genetics</topic><topic>DNA, Ribosomal - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene libraries</topic><topic>Geologic Sediments - microbiology</topic><topic>Growth rate</topic><topic>mangrove sediment</topic><topic>Mangrove swamps</topic><topic>Marine environment</topic><topic>Methanococcoides</topic><topic>Methanococcoides methylutens</topic><topic>Methanogenic archaea</topic><topic>methanogens</topic><topic>Methanol</topic><topic>Methanol - metabolism</topic><topic>Methanosarcinaceae - classification</topic><topic>Methanosarcinaceae - genetics</topic><topic>Methanosarcinaceae - isolation & purification</topic><topic>Methanosarcinaceae - metabolism</topic><topic>Methylamines - metabolism</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Phylogeny</topic><topic>Primers</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Sediment samplers</topic><topic>Sediments</topic><topic>Substrates</topic><topic>Systematics</topic><topic>Termites</topic><topic>Trimethylamine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lyimo, Thomas J</creatorcontrib><creatorcontrib>Pol, Arjan</creatorcontrib><creatorcontrib>Jetten, Mike S.M</creatorcontrib><creatorcontrib>Op den Camp, Huub J.M</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>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 2: Ocean Technology, Policy & Non-Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lyimo, Thomas J</au><au>Pol, Arjan</au><au>Jetten, Mike S.M</au><au>Op den Camp, Huub J.M</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Diversity of methanogenic archaea in a mangrove sediment and isolation of a new Methanococcoides strain</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2009-02</date><risdate>2009</risdate><volume>291</volume><issue>2</issue><spage>247</spage><epage>253</epage><pages>247-253</pages><issn>0378-1097</issn><eissn>1574-6968</eissn><coden>FMLED7</coden><abstract>Mangrove forest sediments produce significant amounts of methane, but the diversity of methanogenic archaea is not well known at present. Therefore, 16S rRNA gene libraries were made using archaea-specific primers and DNA extracted directly from Tanzanian mangrove sediment samples as a template. Analysis of sequence data showed phylotypes closely related to cultivated methylotrophic methanogenic archaea from the marine environment, or distantly related to acetoclastic and hydrogenotrophic methanogenic archaea. In an attempt to isolate relevant methanogenic archaea, we succeeded in obtaining a new mesophilic methylotrophic methanogenic archaeon (strain MM1) capable of utilizing methanol and methylated amines as the only substrates. Under optimum conditions, the cells of strain MM1 exhibited a high specific growth rate (μ) of 0.21±0.03 (i.e. doubling time of 3.2 h) on both methanol and trimethylamine. The 16S rRNA gene sequence of strain MM1 clustered with five environmental clones, indicating that MM1 is an important methanogenic methylotroph in mangrove sediments. Based on physiological and phylogenetic analyses, strain MM1 is proposed to be included in the species of Methanococcoides methylutens.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>19146579</pmid><doi>10.1111/j.1574-6968.2008.01464.x</doi><tpages>7</tpages></addata></record> |
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| ispartof | FEMS microbiology letters, 2009-02, Vol.291 (2), p.247-253 |
| issn | 0378-1097 1574-6968 |
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| source | MEDLINE; Access via Wiley Online Library; Oxford University Press Journals All Titles (1996-Current) |
| subjects | Amines Archaea Archaea - classification Archaea - genetics Archaea - isolation & purification Archaea - metabolism Bacteriology Biodiversity Biological and medical sciences Brackish Deoxyribonucleic acid DNA DNA, Archaeal - genetics DNA, Ribosomal - genetics Fundamental and applied biological sciences. Psychology Gene libraries Geologic Sediments - microbiology Growth rate mangrove sediment Mangrove swamps Marine environment Methanococcoides Methanococcoides methylutens Methanogenic archaea methanogens Methanol Methanol - metabolism Methanosarcinaceae - classification Methanosarcinaceae - genetics Methanosarcinaceae - isolation & purification Methanosarcinaceae - metabolism Methylamines - metabolism Microbiology Molecular Sequence Data Phylogeny Primers RNA, Ribosomal, 16S - genetics rRNA 16S Sediment samplers Sediments Substrates Systematics Termites Trimethylamine |
| title | Diversity of methanogenic archaea in a mangrove sediment and isolation of a new Methanococcoides strain |
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