Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum 'Verrucomicrobia', isolated from seawater by in situ cultivation
1 Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan 2 Marine Biotechnology Institute Co. Ltd, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan Correspondence Jaewoo Yoon aa57058{at}mail.ecc.u-tokyo.ac.jp Five Gram-negative, white-pig...
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creator | Yoon, Jaewoo Yasumoto-Hirose, Mina Matsuo, Yoshihide Nozawa, Midori Matsuda, Satoru Kasai, Hiroaki Yokota, Akira |
description | 1 Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
2 Marine Biotechnology Institute Co. Ltd, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
Correspondence Jaewoo Yoon aa57058{at}mail.ecc.u-tokyo.ac.jp
Five Gram-negative, white-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater from Japan and the Republic of Palau by use of an in situ cultivation technique. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the five novel isolates, 02PA-Ca-133 T , YM14-201 T , H-MN57 T , H-MN48 and MN1-156, were closely affiliated to members of subdivision 4 within the phylum Verrucomicrobia . The novel isolates shared 96100 % sequence similarity with each other and showed less than 90 % similarity with the cultivated strains of subdivision 4. DNADNA relatedness values between strains 02PA-Ca-133 T , YM14-201 T and H-MN57 T were less than 70 %; the value commonly accepted as the threshold for the phylogenetic definition of a species. Antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the five strains were 5157 mol%. The major menaquinone was MK-7 and C 16 : 0 , C 16 : 1 7 c and anteiso-C 15 : 0 were the major fatty acids. On the basis of polyphasic taxonomic evidence, it is concluded that these strains should be classified as representing a new genus and three novel species in subdivision 4 of the phylum Verrucomicrobia , for which the names Pelagicoccus mobilis gen. nov., sp. nov. [type strain 02PA-Ca-133 T (=MBIC08004 T =IAM 15422 T =KCTC 13126 T )], Pelagicoccus albus sp. nov. [type strain YM14-201 T (=MBIC08272 T =IAM 15421 T =KCTC 13124 T )] and Pelagicoccus litoralis sp. nov. [type strain H-MN57 T (=MBIC08273 T =IAM 15423 T =KCTC 13125 T )] are proposed.
Abbreviations: ONPG, o-nitrophenol - D -galactosidase; PUF, polyurethane foam; TEM, transmission electron microscopy
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains 02PA-Ca-133 T , YM14-201 T and H-MN57 T are AB286015 , AB286016 and AB286017 , respectively.
Details of the composition of the P medium used in the paper are available as supplementary material with the online version of this paper.
Present address: Okinawa Prefecture Collaboration of Regi |
doi_str_mv | 10.1099/ijs.0.64970-0 |
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2 Marine Biotechnology Institute Co. Ltd, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
Correspondence Jaewoo Yoon aa57058{at}mail.ecc.u-tokyo.ac.jp
Five Gram-negative, white-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater from Japan and the Republic of Palau by use of an in situ cultivation technique. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the five novel isolates, 02PA-Ca-133 T , YM14-201 T , H-MN57 T , H-MN48 and MN1-156, were closely affiliated to members of subdivision 4 within the phylum Verrucomicrobia . The novel isolates shared 96100 % sequence similarity with each other and showed less than 90 % similarity with the cultivated strains of subdivision 4. DNADNA relatedness values between strains 02PA-Ca-133 T , YM14-201 T and H-MN57 T were less than 70 %; the value commonly accepted as the threshold for the phylogenetic definition of a species. Antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the five strains were 5157 mol%. The major menaquinone was MK-7 and C 16 : 0 , C 16 : 1 7 c and anteiso-C 15 : 0 were the major fatty acids. On the basis of polyphasic taxonomic evidence, it is concluded that these strains should be classified as representing a new genus and three novel species in subdivision 4 of the phylum Verrucomicrobia , for which the names Pelagicoccus mobilis gen. nov., sp. nov. [type strain 02PA-Ca-133 T (=MBIC08004 T =IAM 15422 T =KCTC 13126 T )], Pelagicoccus albus sp. nov. [type strain YM14-201 T (=MBIC08272 T =IAM 15421 T =KCTC 13124 T )] and Pelagicoccus litoralis sp. nov. [type strain H-MN57 T (=MBIC08273 T =IAM 15423 T =KCTC 13125 T )] are proposed.
Abbreviations: ONPG, o-nitrophenol - D -galactosidase; PUF, polyurethane foam; TEM, transmission electron microscopy
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains 02PA-Ca-133 T , YM14-201 T and H-MN57 T are AB286015 , AB286016 and AB286017 , respectively.
Details of the composition of the P medium used in the paper are available as supplementary material with the online version of this paper.
Present address: Okinawa Prefecture Collaboration of Regional Entities for the Advancement of Technological Excellence, JST Okinawa Health Biotechnology Research Development Center, 12-75 Suzaki, Uruma Okinawa 904-2234, Japan.</description><identifier>ISSN: 1466-5026</identifier><identifier>EISSN: 1466-5034</identifier><identifier>DOI: 10.1099/ijs.0.64970-0</identifier><identifier>PMID: 17625161</identifier><language>eng</language><publisher>Reading: Soc General Microbiol</publisher><subject>Anti-Bacterial Agents - pharmacology ; Bacteria - chemistry ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacteriology ; Base Composition ; Biological and medical sciences ; Cell Wall - chemistry ; Diaminopimelic Acid - analysis ; DNA, Bacterial - chemistry ; DNA, Bacterial - genetics ; DNA, Ribosomal - chemistry ; DNA, Ribosomal - genetics ; Fatty Acids - analysis ; Fundamental and applied biological sciences. Psychology ; Genes, rRNA ; Japan ; Microbial Sensitivity Tests ; Microbiology ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Muramic Acids - analysis ; Nucleic Acid Hybridization ; Palau ; Phylogeny ; RNA, Bacterial - genetics ; RNA, Ribosomal, 16S - genetics ; Seawater - microbiology ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Systematics ; Vitamin K 2 - analysis</subject><ispartof>International journal of systematic and evolutionary microbiology, 2007-07, Vol.57 (7), p.1377-1385</ispartof><rights>2008 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c459t-97fd957909065d0fb4fe904b4304ee5315fa3902d432d53958525a6701f90e5e3</citedby><cites>FETCH-LOGICAL-c459t-97fd957909065d0fb4fe904b4304ee5315fa3902d432d53958525a6701f90e5e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,3746,3747,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=18950563$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17625161$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yoon, Jaewoo</creatorcontrib><creatorcontrib>Yasumoto-Hirose, Mina</creatorcontrib><creatorcontrib>Matsuo, Yoshihide</creatorcontrib><creatorcontrib>Nozawa, Midori</creatorcontrib><creatorcontrib>Matsuda, Satoru</creatorcontrib><creatorcontrib>Kasai, Hiroaki</creatorcontrib><creatorcontrib>Yokota, Akira</creatorcontrib><title>Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum 'Verrucomicrobia', isolated from seawater by in situ cultivation</title><title>International journal of systematic and evolutionary microbiology</title><addtitle>Int J Syst Evol Microbiol</addtitle><description>1 Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
2 Marine Biotechnology Institute Co. Ltd, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
Correspondence Jaewoo Yoon aa57058{at}mail.ecc.u-tokyo.ac.jp
Five Gram-negative, white-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater from Japan and the Republic of Palau by use of an in situ cultivation technique. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the five novel isolates, 02PA-Ca-133 T , YM14-201 T , H-MN57 T , H-MN48 and MN1-156, were closely affiliated to members of subdivision 4 within the phylum Verrucomicrobia . The novel isolates shared 96100 % sequence similarity with each other and showed less than 90 % similarity with the cultivated strains of subdivision 4. DNADNA relatedness values between strains 02PA-Ca-133 T , YM14-201 T and H-MN57 T were less than 70 %; the value commonly accepted as the threshold for the phylogenetic definition of a species. Antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the five strains were 5157 mol%. The major menaquinone was MK-7 and C 16 : 0 , C 16 : 1 7 c and anteiso-C 15 : 0 were the major fatty acids. On the basis of polyphasic taxonomic evidence, it is concluded that these strains should be classified as representing a new genus and three novel species in subdivision 4 of the phylum Verrucomicrobia , for which the names Pelagicoccus mobilis gen. nov., sp. nov. [type strain 02PA-Ca-133 T (=MBIC08004 T =IAM 15422 T =KCTC 13126 T )], Pelagicoccus albus sp. nov. [type strain YM14-201 T (=MBIC08272 T =IAM 15421 T =KCTC 13124 T )] and Pelagicoccus litoralis sp. nov. [type strain H-MN57 T (=MBIC08273 T =IAM 15423 T =KCTC 13125 T )] are proposed.
Abbreviations: ONPG, o-nitrophenol - D -galactosidase; PUF, polyurethane foam; TEM, transmission electron microscopy
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains 02PA-Ca-133 T , YM14-201 T and H-MN57 T are AB286015 , AB286016 and AB286017 , respectively.
Details of the composition of the P medium used in the paper are available as supplementary material with the online version of this paper.
Present address: Okinawa Prefecture Collaboration of Regional Entities for the Advancement of Technological Excellence, JST Okinawa Health Biotechnology Research Development Center, 12-75 Suzaki, Uruma Okinawa 904-2234, Japan.</description><subject>Anti-Bacterial Agents - pharmacology</subject><subject>Bacteria - chemistry</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteriology</subject><subject>Base Composition</subject><subject>Biological and medical sciences</subject><subject>Cell Wall - chemistry</subject><subject>Diaminopimelic Acid - analysis</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>DNA, Ribosomal - chemistry</subject><subject>DNA, Ribosomal - genetics</subject><subject>Fatty Acids - analysis</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes, rRNA</subject><subject>Japan</subject><subject>Microbial Sensitivity Tests</subject><subject>Microbiology</subject><subject>Microscopy, Electron, Transmission</subject><subject>Molecular Sequence Data</subject><subject>Muramic Acids - analysis</subject><subject>Nucleic Acid Hybridization</subject><subject>Palau</subject><subject>Phylogeny</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Seawater - microbiology</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Systematics</subject><subject>Vitamin K 2 - analysis</subject><issn>1466-5026</issn><issn>1466-5034</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkUtv1DAUhSMEoqWwZIu8gbJownVsx_WyqnhJlWABbC0nuZ5x5cSDncxo_i6_BA-TMurGPvb97vHjFMVrChUFpT64-1RB1XAloYQnxTnlTVMKYPzpf103Z8WLlO4B8gbA8-KMyqYWtKHnxZ_v6M3KdaHr5kSG0DrvElnhWJExbKsrkjYP6hFpfJvHhyIxY_-47t0Uojl4nQymdUQ8aPRkwKHFmEiwJM1t77YuuTASTnZuWrsxs0g2672fB3L5C2OcuzC4Lub7mcsr4lLwZsKe2BgGktDs8iqSdk9ya3LTTLrZT25rpmz6snhmjU_4apkvip-fPv64_VLeffv89fbmruy4UFOppO2VkAoUNKIH23KLCnjLGXBEwaiwhimoe87qXjAlrkUtTCOBWgUokF0U746-mxh-z5gmPbjUofdmxDAnLUFSQSXNYHkE83tSimj1JrrBxL2moA-h6hyqBv0vVA2Zf7MYz-2A_YleUszA2wUwqTPeRjN2Lp24ayVANCxz74_c2q3WOxdR56CXbw2HQ4XUUlMmJfsLsKe7bQ</recordid><startdate>20070701</startdate><enddate>20070701</enddate><creator>Yoon, Jaewoo</creator><creator>Yasumoto-Hirose, Mina</creator><creator>Matsuo, Yoshihide</creator><creator>Nozawa, Midori</creator><creator>Matsuda, Satoru</creator><creator>Kasai, Hiroaki</creator><creator>Yokota, Akira</creator><general>Soc General Microbiol</general><general>Society for General Microbiology</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>7X8</scope></search><sort><creationdate>20070701</creationdate><title>Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum 'Verrucomicrobia', isolated from seawater by in situ cultivation</title><author>Yoon, Jaewoo ; Yasumoto-Hirose, Mina ; Matsuo, Yoshihide ; Nozawa, Midori ; Matsuda, Satoru ; Kasai, Hiroaki ; Yokota, Akira</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c459t-97fd957909065d0fb4fe904b4304ee5315fa3902d432d53958525a6701f90e5e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Anti-Bacterial Agents - pharmacology</topic><topic>Bacteria - chemistry</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacteriology</topic><topic>Base Composition</topic><topic>Biological and medical sciences</topic><topic>Cell Wall - chemistry</topic><topic>Diaminopimelic Acid - analysis</topic><topic>DNA, Bacterial - chemistry</topic><topic>DNA, Bacterial - genetics</topic><topic>DNA, Ribosomal - chemistry</topic><topic>DNA, Ribosomal - genetics</topic><topic>Fatty Acids - analysis</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes, rRNA</topic><topic>Japan</topic><topic>Microbial Sensitivity Tests</topic><topic>Microbiology</topic><topic>Microscopy, Electron, Transmission</topic><topic>Molecular Sequence Data</topic><topic>Muramic Acids - analysis</topic><topic>Nucleic Acid Hybridization</topic><topic>Palau</topic><topic>Phylogeny</topic><topic>RNA, Bacterial - genetics</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Seawater - microbiology</topic><topic>Sequence Analysis, DNA</topic><topic>Sequence Homology, Nucleic Acid</topic><topic>Systematics</topic><topic>Vitamin K 2 - analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yoon, Jaewoo</creatorcontrib><creatorcontrib>Yasumoto-Hirose, Mina</creatorcontrib><creatorcontrib>Matsuo, Yoshihide</creatorcontrib><creatorcontrib>Nozawa, Midori</creatorcontrib><creatorcontrib>Matsuda, Satoru</creatorcontrib><creatorcontrib>Kasai, Hiroaki</creatorcontrib><creatorcontrib>Yokota, Akira</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>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>Yoon, Jaewoo</au><au>Yasumoto-Hirose, Mina</au><au>Matsuo, Yoshihide</au><au>Nozawa, Midori</au><au>Matsuda, Satoru</au><au>Kasai, Hiroaki</au><au>Yokota, Akira</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum 'Verrucomicrobia', isolated from seawater by in situ cultivation</atitle><jtitle>International journal of systematic and evolutionary microbiology</jtitle><addtitle>Int J Syst Evol Microbiol</addtitle><date>2007-07-01</date><risdate>2007</risdate><volume>57</volume><issue>7</issue><spage>1377</spage><epage>1385</epage><pages>1377-1385</pages><issn>1466-5026</issn><eissn>1466-5034</eissn><abstract>1 Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
2 Marine Biotechnology Institute Co. Ltd, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
Correspondence Jaewoo Yoon aa57058{at}mail.ecc.u-tokyo.ac.jp
Five Gram-negative, white-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater from Japan and the Republic of Palau by use of an in situ cultivation technique. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the five novel isolates, 02PA-Ca-133 T , YM14-201 T , H-MN57 T , H-MN48 and MN1-156, were closely affiliated to members of subdivision 4 within the phylum Verrucomicrobia . The novel isolates shared 96100 % sequence similarity with each other and showed less than 90 % similarity with the cultivated strains of subdivision 4. DNADNA relatedness values between strains 02PA-Ca-133 T , YM14-201 T and H-MN57 T were less than 70 %; the value commonly accepted as the threshold for the phylogenetic definition of a species. Antibiotic susceptibility tests and amino acid analysis of cell-wall hydrolysates indicated that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the five strains were 5157 mol%. The major menaquinone was MK-7 and C 16 : 0 , C 16 : 1 7 c and anteiso-C 15 : 0 were the major fatty acids. On the basis of polyphasic taxonomic evidence, it is concluded that these strains should be classified as representing a new genus and three novel species in subdivision 4 of the phylum Verrucomicrobia , for which the names Pelagicoccus mobilis gen. nov., sp. nov. [type strain 02PA-Ca-133 T (=MBIC08004 T =IAM 15422 T =KCTC 13126 T )], Pelagicoccus albus sp. nov. [type strain YM14-201 T (=MBIC08272 T =IAM 15421 T =KCTC 13124 T )] and Pelagicoccus litoralis sp. nov. [type strain H-MN57 T (=MBIC08273 T =IAM 15423 T =KCTC 13125 T )] are proposed.
Abbreviations: ONPG, o-nitrophenol - D -galactosidase; PUF, polyurethane foam; TEM, transmission electron microscopy
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains 02PA-Ca-133 T , YM14-201 T and H-MN57 T are AB286015 , AB286016 and AB286017 , respectively.
Details of the composition of the P medium used in the paper are available as supplementary material with the online version of this paper.
Present address: Okinawa Prefecture Collaboration of Regional Entities for the Advancement of Technological Excellence, JST Okinawa Health Biotechnology Research Development Center, 12-75 Suzaki, Uruma Okinawa 904-2234, Japan.</abstract><cop>Reading</cop><pub>Soc General Microbiol</pub><pmid>17625161</pmid><doi>10.1099/ijs.0.64970-0</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Anti-Bacterial Agents - pharmacology Bacteria - chemistry Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Bacteriology Base Composition Biological and medical sciences Cell Wall - chemistry Diaminopimelic Acid - analysis DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Ribosomal - chemistry DNA, Ribosomal - genetics Fatty Acids - analysis Fundamental and applied biological sciences. Psychology Genes, rRNA Japan Microbial Sensitivity Tests Microbiology Microscopy, Electron, Transmission Molecular Sequence Data Muramic Acids - analysis Nucleic Acid Hybridization Palau Phylogeny RNA, Bacterial - genetics RNA, Ribosomal, 16S - genetics Seawater - microbiology Sequence Analysis, DNA Sequence Homology, Nucleic Acid Systematics Vitamin K 2 - analysis |
title | Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum 'Verrucomicrobia', isolated from seawater by in situ cultivation |
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