Dissimilatory reduction of nitrate in seawater by a Methylophaga strain containing two highly divergent narG sequences
Methylophaga spp. are methylotrophs commonly associated with marine environments and have been defined as strict aerobic methylotrophs. They have been shown previously to represent 50–70% of the bacterial population in the biofilm of the methanol-fed denitrification reactor treating a large seawater...
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description | Methylophaga
spp. are methylotrophs commonly associated with marine environments and have been defined as strict aerobic methylotrophs. They have been shown previously to represent 50–70% of the bacterial population in the biofilm of the methanol-fed denitrification reactor treating a large seawater aquarium at the Montreal Biodome. It was therefore surprising to find such a high concentration of
Methylophaga
spp. in anoxic conditions. In this study, we showed by cultivation-independent and -dependent approaches that one
Methylophaga
strain present in the anoxic biofilm is involved in the denitrification process. DNA stable-isotope probing (SIP) experiments in which the biofilm was cultured under denitrifying conditions with
13
C-methanol have revealed the enrichment of one particular taxon. By screening a 16S ribosomal RNA gene library derived from a
13
C-DNA fraction of the SIP gradients, 62% of the library was composed of one sequence affiliated with the genus
Methylophaga
. One strain, named JAM1, representing this
Methylophaga
species was isolated. It grows aerobically but also under denitrifying conditions by reducing nitrate into nitrite. The nitrate-reducing activity was correlated with the presence and the expression of two highly divergent
narG
genes (
narG
1 and
narG
2).
narG
1 showed a high percentage of identity with the corresponding part of
narG
found in
Thiobacillus denitrificans,
which suggests a recent acquisition of
narG
in strain JAM1 by horizontal gene transfer. This study provides the first direct evidence of the adaptation of a
Methylophaga
species to an oxygen-limited environment. |
doi_str_mv | 10.1038/ismej.2010.47 |
format | Article |
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spp. are methylotrophs commonly associated with marine environments and have been defined as strict aerobic methylotrophs. They have been shown previously to represent 50–70% of the bacterial population in the biofilm of the methanol-fed denitrification reactor treating a large seawater aquarium at the Montreal Biodome. It was therefore surprising to find such a high concentration of
Methylophaga
spp. in anoxic conditions. In this study, we showed by cultivation-independent and -dependent approaches that one
Methylophaga
strain present in the anoxic biofilm is involved in the denitrification process. DNA stable-isotope probing (SIP) experiments in which the biofilm was cultured under denitrifying conditions with
13
C-methanol have revealed the enrichment of one particular taxon. By screening a 16S ribosomal RNA gene library derived from a
13
C-DNA fraction of the SIP gradients, 62% of the library was composed of one sequence affiliated with the genus
Methylophaga
. One strain, named JAM1, representing this
Methylophaga
species was isolated. It grows aerobically but also under denitrifying conditions by reducing nitrate into nitrite. The nitrate-reducing activity was correlated with the presence and the expression of two highly divergent
narG
genes (
narG
1 and
narG
2).
narG
1 showed a high percentage of identity with the corresponding part of
narG
found in
Thiobacillus denitrificans,
which suggests a recent acquisition of
narG
in strain JAM1 by horizontal gene transfer. This study provides the first direct evidence of the adaptation of a
Methylophaga
species to an oxygen-limited environment.</description><identifier>ISSN: 1751-7362</identifier><identifier>EISSN: 1751-7370</identifier><identifier>DOI: 10.1038/ismej.2010.47</identifier><identifier>PMID: 20393572</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/208/325/2482 ; 631/326/41 ; 631/326/47 ; Anoxic conditions ; Aquariums ; Bacterial Proteins ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Biofilms ; Biofilms - growth & development ; Biomedical and Life Sciences ; Biotechnology ; Carbon Isotopes ; Carbon Isotopes - metabolism ; Cluster Analysis ; Computer Science ; Cultivation ; Denitrification ; Deoxyribonucleic acid ; DNA ; DNA, Bacterial ; DNA, Bacterial - chemistry ; DNA, Bacterial - genetics ; DNA, Ribosomal ; DNA, Ribosomal - chemistry ; DNA, Ribosomal - genetics ; Ecology ; Evolutionary Biology ; Life Sciences ; Marine environment ; Methanol ; Methanol - metabolism ; Methylophaga ; Microbial Ecology ; Microbial Genetics and Genomics ; Microbiology ; Molecular Sequence Data ; Nitrate Reductase ; Nitrate Reductase - genetics ; Nitrate Reductase - metabolism ; Nitrates ; Nitrates - metabolism ; Nitrites ; Nitrites - metabolism ; original-article ; Oxidation-Reduction ; Oxygen ; Oxygen - analysis ; Phylogeny ; Piscirickettsiaceae ; Piscirickettsiaceae - classification ; Piscirickettsiaceae - genetics ; Piscirickettsiaceae - isolation & purification ; Piscirickettsiaceae - metabolism ; Reactors ; RNA, Ribosomal, 16S ; RNA, Ribosomal, 16S - genetics ; Seawater ; Seawater - chemistry ; Seawater - microbiology ; Sequence Analysis, DNA ; Staining and Labeling ; Staining and Labeling - methods ; Taxa ; Thiobacillus denitrificans</subject><ispartof>The ISME Journal, 2010-10, Vol.4 (10), p.1302-1313</ispartof><rights>International Society for Microbial Ecology 2010</rights><rights>Copyright Nature Publishing Group Oct 2010</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c469t-1d365b5016eeeab2eafd50e25b40dc21b4fe026e00640b7d4aadf2313c93a3eb3</citedby><cites>FETCH-LOGICAL-c469t-1d365b5016eeeab2eafd50e25b40dc21b4fe026e00640b7d4aadf2313c93a3eb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,315,781,785,886,27929,27930</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20393572$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://riip.hal.science/pasteur-00819611$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Auclair, Julie</creatorcontrib><creatorcontrib>Lépine, François</creatorcontrib><creatorcontrib>Parent, Serge</creatorcontrib><creatorcontrib>Villemur, Richard</creatorcontrib><title>Dissimilatory reduction of nitrate in seawater by a Methylophaga strain containing two highly divergent narG sequences</title><title>The ISME Journal</title><addtitle>ISME J</addtitle><addtitle>ISME J</addtitle><description>Methylophaga
spp. are methylotrophs commonly associated with marine environments and have been defined as strict aerobic methylotrophs. They have been shown previously to represent 50–70% of the bacterial population in the biofilm of the methanol-fed denitrification reactor treating a large seawater aquarium at the Montreal Biodome. It was therefore surprising to find such a high concentration of
Methylophaga
spp. in anoxic conditions. In this study, we showed by cultivation-independent and -dependent approaches that one
Methylophaga
strain present in the anoxic biofilm is involved in the denitrification process. DNA stable-isotope probing (SIP) experiments in which the biofilm was cultured under denitrifying conditions with
13
C-methanol have revealed the enrichment of one particular taxon. By screening a 16S ribosomal RNA gene library derived from a
13
C-DNA fraction of the SIP gradients, 62% of the library was composed of one sequence affiliated with the genus
Methylophaga
. One strain, named JAM1, representing this
Methylophaga
species was isolated. It grows aerobically but also under denitrifying conditions by reducing nitrate into nitrite. The nitrate-reducing activity was correlated with the presence and the expression of two highly divergent
narG
genes (
narG
1 and
narG
2).
narG
1 showed a high percentage of identity with the corresponding part of
narG
found in
Thiobacillus denitrificans,
which suggests a recent acquisition of
narG
in strain JAM1 by horizontal gene transfer. This study provides the first direct evidence of the adaptation of a
Methylophaga
species to an oxygen-limited environment.</description><subject>631/208/325/2482</subject><subject>631/326/41</subject><subject>631/326/47</subject><subject>Anoxic conditions</subject><subject>Aquariums</subject><subject>Bacterial Proteins</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biofilms</subject><subject>Biofilms - growth & development</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Carbon Isotopes</subject><subject>Carbon Isotopes - metabolism</subject><subject>Cluster Analysis</subject><subject>Computer Science</subject><subject>Cultivation</subject><subject>Denitrification</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA, Bacterial</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Ribosomal</subject><subject>DNA, Ribosomal - chemistry</subject><subject>DNA, Ribosomal - genetics</subject><subject>Ecology</subject><subject>Evolutionary Biology</subject><subject>Life Sciences</subject><subject>Marine environment</subject><subject>Methanol</subject><subject>Methanol - metabolism</subject><subject>Methylophaga</subject><subject>Microbial Ecology</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Nitrate Reductase</subject><subject>Nitrate Reductase - genetics</subject><subject>Nitrate Reductase - metabolism</subject><subject>Nitrates</subject><subject>Nitrates - metabolism</subject><subject>Nitrites</subject><subject>Nitrites - metabolism</subject><subject>original-article</subject><subject>Oxidation-Reduction</subject><subject>Oxygen</subject><subject>Oxygen - analysis</subject><subject>Phylogeny</subject><subject>Piscirickettsiaceae</subject><subject>Piscirickettsiaceae - classification</subject><subject>Piscirickettsiaceae - genetics</subject><subject>Piscirickettsiaceae - isolation & purification</subject><subject>Piscirickettsiaceae - metabolism</subject><subject>Reactors</subject><subject>RNA, Ribosomal, 16S</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Seawater</subject><subject>Seawater - chemistry</subject><subject>Seawater - microbiology</subject><subject>Sequence Analysis, DNA</subject><subject>Staining and Labeling</subject><subject>Staining and Labeling - methods</subject><subject>Taxa</subject><subject>Thiobacillus denitrificans</subject><issn>1751-7362</issn><issn>1751-7370</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</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>eNp9kUFv1DAQRiMEoqVw5IoscaCXLGM7sZNjVWiLtIgLnC0nmSReJfZiO1vl3-OyZUEIcZqx_PT5s16WvaawocCr9ybMuNswSOdCPsnOqSxpLrmEp6ddsLPsRQg7gFIKIZ9nZwx4zUvJzrPDBxOCmc2ko_Mr8dgtbTTOEtcTa6LXEYmxJKC-T6snzUo0-YxxXCe3H_WgSUhQIlpnY5rGDiTeOzKaYZxW0pkD-gFtJFb72xTzfUHbYniZPev1FPDV47zIvt18_Hp9l2-_3H66vtrmbSHqmNOOi7IpgQpE1A1D3XclICubArqW0aboEZhAAFFAI7tC665nnPK25ppjwy-y_Jg76kntvZm1X5XTRt1dbdVeh4iLVwAVrQWlB5r4d0d-712qGqKaTWhxmrRFtwQly5IKLipI5OV_SSopk6KSVZ3Qt3-hO7d4m_6tKLC6qkQy-btq610IHvtTXwrqQbX6qVo9qFaFTPybx9SlmbE70b_cJmBzBEK6sgP6P5_9V-IPsjm2LA</recordid><startdate>20101001</startdate><enddate>20101001</enddate><creator>Auclair, Julie</creator><creator>Lépine, François</creator><creator>Parent, Serge</creator><creator>Villemur, Richard</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</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>3V.</scope><scope>7QL</scope><scope>7SN</scope><scope>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</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>ATCPS</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>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>SOI</scope><scope>7TN</scope><scope>F1W</scope><scope>H95</scope><scope>L.G</scope><scope>7X8</scope><scope>1XC</scope></search><sort><creationdate>20101001</creationdate><title>Dissimilatory reduction of nitrate in seawater by a Methylophaga strain containing two highly divergent narG sequences</title><author>Auclair, Julie ; Lépine, François ; Parent, Serge ; Villemur, Richard</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c469t-1d365b5016eeeab2eafd50e25b40dc21b4fe026e00640b7d4aadf2313c93a3eb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>631/208/325/2482</topic><topic>631/326/41</topic><topic>631/326/47</topic><topic>Anoxic conditions</topic><topic>Aquariums</topic><topic>Bacterial Proteins</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>Biofilms</topic><topic>Biofilms - growth & development</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Carbon Isotopes</topic><topic>Carbon Isotopes - metabolism</topic><topic>Cluster Analysis</topic><topic>Computer Science</topic><topic>Cultivation</topic><topic>Denitrification</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA, Bacterial</topic><topic>DNA, Bacterial - chemistry</topic><topic>DNA, Bacterial - genetics</topic><topic>DNA, Ribosomal</topic><topic>DNA, Ribosomal - chemistry</topic><topic>DNA, Ribosomal - genetics</topic><topic>Ecology</topic><topic>Evolutionary Biology</topic><topic>Life Sciences</topic><topic>Marine environment</topic><topic>Methanol</topic><topic>Methanol - metabolism</topic><topic>Methylophaga</topic><topic>Microbial Ecology</topic><topic>Microbial Genetics and Genomics</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Nitrate Reductase</topic><topic>Nitrate Reductase - genetics</topic><topic>Nitrate Reductase - metabolism</topic><topic>Nitrates</topic><topic>Nitrates - metabolism</topic><topic>Nitrites</topic><topic>Nitrites - metabolism</topic><topic>original-article</topic><topic>Oxidation-Reduction</topic><topic>Oxygen</topic><topic>Oxygen - analysis</topic><topic>Phylogeny</topic><topic>Piscirickettsiaceae</topic><topic>Piscirickettsiaceae - classification</topic><topic>Piscirickettsiaceae - genetics</topic><topic>Piscirickettsiaceae - isolation & purification</topic><topic>Piscirickettsiaceae - metabolism</topic><topic>Reactors</topic><topic>RNA, Ribosomal, 16S</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Seawater</topic><topic>Seawater - chemistry</topic><topic>Seawater - microbiology</topic><topic>Sequence Analysis, DNA</topic><topic>Staining and Labeling</topic><topic>Staining and Labeling - methods</topic><topic>Taxa</topic><topic>Thiobacillus denitrificans</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Auclair, Julie</creatorcontrib><creatorcontrib>Lépine, François</creatorcontrib><creatorcontrib>Parent, Serge</creatorcontrib><creatorcontrib>Villemur, Richard</creatorcontrib><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>Ecology Abstracts</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>ProQuest Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</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)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</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>SciTech Premium Collection (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Environmental Science Collection</collection><collection>Environment Abstracts</collection><collection>Oceanic 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) Professional</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>The ISME Journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Auclair, Julie</au><au>Lépine, François</au><au>Parent, Serge</au><au>Villemur, Richard</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Dissimilatory reduction of nitrate in seawater by a Methylophaga strain containing two highly divergent narG sequences</atitle><jtitle>The ISME Journal</jtitle><stitle>ISME J</stitle><addtitle>ISME J</addtitle><date>2010-10-01</date><risdate>2010</risdate><volume>4</volume><issue>10</issue><spage>1302</spage><epage>1313</epage><pages>1302-1313</pages><issn>1751-7362</issn><eissn>1751-7370</eissn><abstract>Methylophaga
spp. are methylotrophs commonly associated with marine environments and have been defined as strict aerobic methylotrophs. They have been shown previously to represent 50–70% of the bacterial population in the biofilm of the methanol-fed denitrification reactor treating a large seawater aquarium at the Montreal Biodome. It was therefore surprising to find such a high concentration of
Methylophaga
spp. in anoxic conditions. In this study, we showed by cultivation-independent and -dependent approaches that one
Methylophaga
strain present in the anoxic biofilm is involved in the denitrification process. DNA stable-isotope probing (SIP) experiments in which the biofilm was cultured under denitrifying conditions with
13
C-methanol have revealed the enrichment of one particular taxon. By screening a 16S ribosomal RNA gene library derived from a
13
C-DNA fraction of the SIP gradients, 62% of the library was composed of one sequence affiliated with the genus
Methylophaga
. One strain, named JAM1, representing this
Methylophaga
species was isolated. It grows aerobically but also under denitrifying conditions by reducing nitrate into nitrite. The nitrate-reducing activity was correlated with the presence and the expression of two highly divergent
narG
genes (
narG
1 and
narG
2).
narG
1 showed a high percentage of identity with the corresponding part of
narG
found in
Thiobacillus denitrificans,
which suggests a recent acquisition of
narG
in strain JAM1 by horizontal gene transfer. This study provides the first direct evidence of the adaptation of a
Methylophaga
species to an oxygen-limited environment.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>20393572</pmid><doi>10.1038/ismej.2010.47</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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subjects | 631/208/325/2482 631/326/41 631/326/47 Anoxic conditions Aquariums Bacterial Proteins Bacterial Proteins - genetics Bacterial Proteins - metabolism Biofilms Biofilms - growth & development Biomedical and Life Sciences Biotechnology Carbon Isotopes Carbon Isotopes - metabolism Cluster Analysis Computer Science Cultivation Denitrification Deoxyribonucleic acid DNA DNA, Bacterial DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Ribosomal DNA, Ribosomal - chemistry DNA, Ribosomal - genetics Ecology Evolutionary Biology Life Sciences Marine environment Methanol Methanol - metabolism Methylophaga Microbial Ecology Microbial Genetics and Genomics Microbiology Molecular Sequence Data Nitrate Reductase Nitrate Reductase - genetics Nitrate Reductase - metabolism Nitrates Nitrates - metabolism Nitrites Nitrites - metabolism original-article Oxidation-Reduction Oxygen Oxygen - analysis Phylogeny Piscirickettsiaceae Piscirickettsiaceae - classification Piscirickettsiaceae - genetics Piscirickettsiaceae - isolation & purification Piscirickettsiaceae - metabolism Reactors RNA, Ribosomal, 16S RNA, Ribosomal, 16S - genetics Seawater Seawater - chemistry Seawater - microbiology Sequence Analysis, DNA Staining and Labeling Staining and Labeling - methods Taxa Thiobacillus denitrificans |
title | Dissimilatory reduction of nitrate in seawater by a Methylophaga strain containing two highly divergent narG sequences |
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