Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens
Abstract Molecular diversity of rumen archaea was analyzed by PCR amplification and sequencing of two 16S rRNA clone libraries prepared from the bovine rumen fluid using two different archaea-specific primer sets. The first library of 19 clones which was generated with primers D30 and D33, produced...
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| Veröffentlicht in: | FEMS microbiology letters 2001-06, Vol.200 (1), p.67-72 |
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| creator | Tajima, Kiyoshi Nagamine, Takafumi Matsui, Hiroki Nakamura, Mutsumi Aminov, Rustam I. |
| description | Abstract
Molecular diversity of rumen archaea was analyzed by PCR amplification and sequencing of two 16S rRNA clone libraries prepared from the bovine rumen fluid using two different archaea-specific primer sets. The first library of 19 clones which was generated with primers D30 and D33, produced essentially two groups of sequences, one affiliated with Methanomicrobium mobile (21% of clones) and the other – with the uncultured archaeal sequences from anaerobic digester, which are distantly associated with Thermoplasma (79% of clones). The second library of 25 clones, which was generated with primers 0025e Forward and 1492 Reverse, produced a higher degree of diversity: in addition to the previous two groups, with the M. mobile- (56%) and Thermoplasma-associated sequences (20%), four clones (16%) were identified as Methanobrevibacter spp. The remaining two sequences were associated with unidentified archaeal sequences from the rumen and swine waste. Phylogenetic placement of eight almost complete 16S rRNA sequences revealed the existence of a novel cluster of the rumen Euryarchaeota, which is not affiliated with the known methanogenic archaea. |
| doi_str_mv | 10.1111/j.1574-6968.2001.tb10694.x |
| format | Article |
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Molecular diversity of rumen archaea was analyzed by PCR amplification and sequencing of two 16S rRNA clone libraries prepared from the bovine rumen fluid using two different archaea-specific primer sets. The first library of 19 clones which was generated with primers D30 and D33, produced essentially two groups of sequences, one affiliated with Methanomicrobium mobile (21% of clones) and the other – with the uncultured archaeal sequences from anaerobic digester, which are distantly associated with Thermoplasma (79% of clones). The second library of 25 clones, which was generated with primers 0025e Forward and 1492 Reverse, produced a higher degree of diversity: in addition to the previous two groups, with the M. mobile- (56%) and Thermoplasma-associated sequences (20%), four clones (16%) were identified as Methanobrevibacter spp. The remaining two sequences were associated with unidentified archaeal sequences from the rumen and swine waste. Phylogenetic placement of eight almost complete 16S rRNA sequences revealed the existence of a novel cluster of the rumen Euryarchaeota, which is not affiliated with the known methanogenic archaea.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1111/j.1574-6968.2001.tb10694.x</identifier><identifier>PMID: 11410351</identifier><identifier>CODEN: FMLED7</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Animals ; Archaea ; Archaea - classification ; Archaea - genetics ; Archaea - isolation & purification ; Bacteria - genetics ; Bacteriology ; Biological and medical sciences ; Cattle ; Eukaryotic Cells ; Euryarchaeota ; Euryarchaeota - classification ; Euryarchaeota - genetics ; Evolution, Molecular ; Fundamental and applied biological sciences. Psychology ; Gene Library ; Genetics ; Methanogenic archaea ; Methanogenic bacteria ; Methanomicrobium mobile ; Microbiology ; Molecular diversity ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogenetics ; Phylogeny ; RNA, Archaeal - genetics ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Rumen ; Rumen - microbiology ; Sequence Analysis, DNA ; Swine ; Systematics ; Thermoplasma</subject><ispartof>FEMS microbiology letters, 2001-06, Vol.200 (1), p.67-72</ispartof><rights>2001 Federation of European Microbiological Societies 2001</rights><rights>2002 INIST-CNRS</rights><rights>2001 Federation of European Microbiological Societies</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4887-a406580fae02d9cd618b30d666657bb6b45bbbff904e563f53b7889819dc432f3</citedby><cites>FETCH-LOGICAL-c4887-a406580fae02d9cd618b30d666657bb6b45bbbff904e563f53b7889819dc432f3</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.1574-6968.2001.tb10694.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6968.2001.tb10694.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=14162636$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11410351$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tajima, Kiyoshi</creatorcontrib><creatorcontrib>Nagamine, Takafumi</creatorcontrib><creatorcontrib>Matsui, Hiroki</creatorcontrib><creatorcontrib>Nakamura, Mutsumi</creatorcontrib><creatorcontrib>Aminov, Rustam I.</creatorcontrib><title>Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>Abstract
Molecular diversity of rumen archaea was analyzed by PCR amplification and sequencing of two 16S rRNA clone libraries prepared from the bovine rumen fluid using two different archaea-specific primer sets. The first library of 19 clones which was generated with primers D30 and D33, produced essentially two groups of sequences, one affiliated with Methanomicrobium mobile (21% of clones) and the other – with the uncultured archaeal sequences from anaerobic digester, which are distantly associated with Thermoplasma (79% of clones). The second library of 25 clones, which was generated with primers 0025e Forward and 1492 Reverse, produced a higher degree of diversity: in addition to the previous two groups, with the M. mobile- (56%) and Thermoplasma-associated sequences (20%), four clones (16%) were identified as Methanobrevibacter spp. The remaining two sequences were associated with unidentified archaeal sequences from the rumen and swine waste. Phylogenetic placement of eight almost complete 16S rRNA sequences revealed the existence of a novel cluster of the rumen Euryarchaeota, which is not affiliated with the known methanogenic archaea.</description><subject>Animals</subject><subject>Archaea</subject><subject>Archaea - classification</subject><subject>Archaea - genetics</subject><subject>Archaea - isolation & purification</subject><subject>Bacteria - genetics</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Cattle</subject><subject>Eukaryotic Cells</subject><subject>Euryarchaeota</subject><subject>Euryarchaeota - classification</subject><subject>Euryarchaeota - genetics</subject><subject>Evolution, Molecular</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Library</subject><subject>Genetics</subject><subject>Methanogenic archaea</subject><subject>Methanogenic bacteria</subject><subject>Methanomicrobium mobile</subject><subject>Microbiology</subject><subject>Molecular diversity</subject><subject>Molecular Sequence Data</subject><subject>Nucleic Acid Conformation</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>RNA, Archaeal - genetics</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Rumen</subject><subject>Rumen - microbiology</subject><subject>Sequence Analysis, DNA</subject><subject>Swine</subject><subject>Systematics</subject><subject>Thermoplasma</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2001</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqVkd1u1DAQhSMEotvCKyALRO8S7NhxHKReVBUFpOVH_FxbtjPZ9ZLEi52wu-_Cw-J0I4oQCDE3lsbfOZ7xSZLHBGck1rNNRoqSpbziIssxJtmgCeYVy_Z3ksXPq7vJAtNSpARX5UlyGsIGY8xyzO8nJ4QwgmlBFsn39-tD61bQw2ANUr1qD8EG5BqkvFkrUC0i_CPyH95eotZqr7yFgBrvOjSsAfmxgx6FcbWCMISbFuxtGKA3cGOCevcNWrTybtz-4hrbA1IhOGPVADXa2WGNvvRu16MOhrXqp5HCg-Reo9oAD-fzLPl8_eLT1at0-e7l66vLZWqYEGWqGOaFwI0CnNeVqTkRmuKaxypKrblmhda6aSrMoOC0KaguhagEqWrDaN7Qs-T86Lv17usYN5GdDQbaVvXgxiBLXLG8EPSfIIm-OaZ5BJ_8Bm7c6OPvBplTQnAcg1SRen6kjHcheGjk1ttO-YMkWE5Ry42c8pRTnnKKWs5Ry30UP5qfGHUH9a10zjYCT2dABaPaxqve2HDLMcJzTnnkLo7czrZw-I8R5PWbJS-jvjjqY8R_Uad_WuAHh93W1A</recordid><startdate>20010612</startdate><enddate>20010612</enddate><creator>Tajima, Kiyoshi</creator><creator>Nagamine, Takafumi</creator><creator>Matsui, Hiroki</creator><creator>Nakamura, Mutsumi</creator><creator>Aminov, Rustam I.</creator><general>Blackwell Publishing Ltd</general><general>Blackwell</general><general>Oxford University Press</general><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>AEUYN</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>7X8</scope></search><sort><creationdate>20010612</creationdate><title>Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens</title><author>Tajima, Kiyoshi ; Nagamine, Takafumi ; Matsui, Hiroki ; Nakamura, Mutsumi ; Aminov, Rustam I.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4887-a406580fae02d9cd618b30d666657bb6b45bbbff904e563f53b7889819dc432f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2001</creationdate><topic>Animals</topic><topic>Archaea</topic><topic>Archaea - classification</topic><topic>Archaea - genetics</topic><topic>Archaea - isolation & purification</topic><topic>Bacteria - genetics</topic><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Cattle</topic><topic>Eukaryotic Cells</topic><topic>Euryarchaeota</topic><topic>Euryarchaeota - classification</topic><topic>Euryarchaeota - genetics</topic><topic>Evolution, Molecular</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Library</topic><topic>Genetics</topic><topic>Methanogenic archaea</topic><topic>Methanogenic bacteria</topic><topic>Methanomicrobium mobile</topic><topic>Microbiology</topic><topic>Molecular diversity</topic><topic>Molecular Sequence Data</topic><topic>Nucleic Acid Conformation</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>RNA, Archaeal - genetics</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>rRNA 16S</topic><topic>Rumen</topic><topic>Rumen - microbiology</topic><topic>Sequence Analysis, DNA</topic><topic>Swine</topic><topic>Systematics</topic><topic>Thermoplasma</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tajima, Kiyoshi</creatorcontrib><creatorcontrib>Nagamine, Takafumi</creatorcontrib><creatorcontrib>Matsui, Hiroki</creatorcontrib><creatorcontrib>Nakamura, Mutsumi</creatorcontrib><creatorcontrib>Aminov, Rustam I.</creatorcontrib><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 One Sustainability</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>MEDLINE - Academic</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tajima, Kiyoshi</au><au>Nagamine, Takafumi</au><au>Matsui, Hiroki</au><au>Nakamura, Mutsumi</au><au>Aminov, Rustam I.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2001-06-12</date><risdate>2001</risdate><volume>200</volume><issue>1</issue><spage>67</spage><epage>72</epage><pages>67-72</pages><issn>0378-1097</issn><eissn>1574-6968</eissn><coden>FMLED7</coden><abstract>Abstract
Molecular diversity of rumen archaea was analyzed by PCR amplification and sequencing of two 16S rRNA clone libraries prepared from the bovine rumen fluid using two different archaea-specific primer sets. The first library of 19 clones which was generated with primers D30 and D33, produced essentially two groups of sequences, one affiliated with Methanomicrobium mobile (21% of clones) and the other – with the uncultured archaeal sequences from anaerobic digester, which are distantly associated with Thermoplasma (79% of clones). The second library of 25 clones, which was generated with primers 0025e Forward and 1492 Reverse, produced a higher degree of diversity: in addition to the previous two groups, with the M. mobile- (56%) and Thermoplasma-associated sequences (20%), four clones (16%) were identified as Methanobrevibacter spp. The remaining two sequences were associated with unidentified archaeal sequences from the rumen and swine waste. Phylogenetic placement of eight almost complete 16S rRNA sequences revealed the existence of a novel cluster of the rumen Euryarchaeota, which is not affiliated with the known methanogenic archaea.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>11410351</pmid><doi>10.1111/j.1574-6968.2001.tb10694.x</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| source | Oxford University Press Journals All Titles (1996-Current); MEDLINE; Wiley Online Library Journals Frontfile Complete; Alma/SFX Local Collection |
| subjects | Animals Archaea Archaea - classification Archaea - genetics Archaea - isolation & purification Bacteria - genetics Bacteriology Biological and medical sciences Cattle Eukaryotic Cells Euryarchaeota Euryarchaeota - classification Euryarchaeota - genetics Evolution, Molecular Fundamental and applied biological sciences. Psychology Gene Library Genetics Methanogenic archaea Methanogenic bacteria Methanomicrobium mobile Microbiology Molecular diversity Molecular Sequence Data Nucleic Acid Conformation Phylogenetics Phylogeny RNA, Archaeal - genetics RNA, Ribosomal, 16S - genetics rRNA 16S Rumen Rumen - microbiology Sequence Analysis, DNA Swine Systematics Thermoplasma |
| title | Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens |
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