Bacterial Community Diversity in the Brazilian Atlantic Forest Soils
The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra...
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| Veröffentlicht in: | Microbial ecology 2010-11, Vol.60 (4), p.840-849 |
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| creator | Bruce, Thiago Martinez, Ivana B Maia Neto, Oswaldo Vicente, Ana Carolina P Kruger, Ricardo H Thompson, Fabiano L |
| description | The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29-54%), Proteobacteria (16-38%), and Verrucomicrobia (0.6-14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41-152) and species (263-446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria. |
| doi_str_mv | 10.1007/s00248-010-9750-2 |
| format | Article |
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A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29-54%), Proteobacteria (16-38%), and Verrucomicrobia (0.6-14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41-152) and species (263-446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria.</description><identifier>ISSN: 0095-3628</identifier><identifier>EISSN: 1432-184X</identifier><identifier>DOI: 10.1007/s00248-010-9750-2</identifier><identifier>PMID: 20886336</identifier><identifier>CODEN: MCBEBU</identifier><language>eng</language><publisher>New York: New York : Springer-Verlag</publisher><subject>Acid soils ; Acidobacteria ; Agricultural soils ; Agrology ; Arthrobacter ; Bacillus ; Bacteria ; Bacteria - classification ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacteria - metabolism ; Biodiversity ; Biological and medical sciences ; Biomedical and Life Sciences ; Brazil ; Burkholderia ; Cellulose ; Cultivation ; DNA, Bacterial - genetics ; Ecology ; Forest soils ; Fundamental and applied biological sciences. Psychology ; Geoecology/Natural Processes ; Libraries ; Life Sciences ; Microbial Ecology ; Microbiology ; Molecular Sequence Data ; National parks ; Nature Conservation ; Paenibacillus ; Phylogeny ; Proteobacteria ; Pseudomonas ; Ralstonia ; RNA, Ribosomal, 16S - genetics ; Sedimentary soils ; Serratia ; Soil - analysis ; Soil bacteria ; SOIL MICROBIOLOGY ; Soil microorganisms ; Streptomyces ; Trees - microbiology ; Verrucomicrobia ; Water Quality/Water Pollution</subject><ispartof>Microbial ecology, 2010-11, Vol.60 (4), p.840-849</ispartof><rights>2010 Springer Science+Business Media, Inc.</rights><rights>Springer Science+Business Media, LLC 2010</rights><rights>2015 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c544t-a90b9e510b30694b68c60a487ff6dfa14bf9094eb8262a026e2a5a73d84d47ab3</citedby><cites>FETCH-LOGICAL-c544t-a90b9e510b30694b68c60a487ff6dfa14bf9094eb8262a026e2a5a73d84d47ab3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/40926486$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/40926486$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,776,780,799,27901,27902,41464,42533,51294,57992,58225</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23730018$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20886336$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bruce, Thiago</creatorcontrib><creatorcontrib>Martinez, Ivana B</creatorcontrib><creatorcontrib>Maia Neto, Oswaldo</creatorcontrib><creatorcontrib>Vicente, Ana Carolina P</creatorcontrib><creatorcontrib>Kruger, Ricardo H</creatorcontrib><creatorcontrib>Thompson, Fabiano L</creatorcontrib><title>Bacterial Community Diversity in the Brazilian Atlantic Forest Soils</title><title>Microbial ecology</title><addtitle>Microb Ecol</addtitle><addtitle>Microb Ecol</addtitle><description>The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29-54%), Proteobacteria (16-38%), and Verrucomicrobia (0.6-14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41-152) and species (263-446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria.</description><subject>Acid soils</subject><subject>Acidobacteria</subject><subject>Agricultural soils</subject><subject>Agrology</subject><subject>Arthrobacter</subject><subject>Bacillus</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacteria - metabolism</subject><subject>Biodiversity</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Brazil</subject><subject>Burkholderia</subject><subject>Cellulose</subject><subject>Cultivation</subject><subject>DNA, Bacterial - genetics</subject><subject>Ecology</subject><subject>Forest soils</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Geoecology/Natural Processes</subject><subject>Libraries</subject><subject>Life Sciences</subject><subject>Microbial Ecology</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>National parks</subject><subject>Nature Conservation</subject><subject>Paenibacillus</subject><subject>Phylogeny</subject><subject>Proteobacteria</subject><subject>Pseudomonas</subject><subject>Ralstonia</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sedimentary soils</subject><subject>Serratia</subject><subject>Soil - analysis</subject><subject>Soil bacteria</subject><subject>SOIL MICROBIOLOGY</subject><subject>Soil microorganisms</subject><subject>Streptomyces</subject><subject>Trees - microbiology</subject><subject>Verrucomicrobia</subject><subject>Water Quality/Water Pollution</subject><issn>0095-3628</issn><issn>1432-184X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqFkUtv1TAQhS0EopfCD2ABREiIVWBsT_xYtrcUkCqxKJXYWZNcp_gqj2InSOXX4yiXVmIBK1uab86ZmcPYcw7vOIB-nwAEmhI4lFZXUIoHbMNRipIb_PaQbQBsVUolzBF7ktIegGsl5GN2JMAYJaXasLNTaiYfA3XFduz7eQjTbXEWfvqYll8Yium7L04j_QpdoKE4mToaptAU52P0aSoux9Clp-xRS13yzw7vMbs6__B1-6m8-PLx8_bkomwqxKkkC7X1FYdagrJYK9MoIDS6bdWuJY51a8Gir41QgkAoL6giLXcGd6iplsfs7ap7E8cfc7Z3fUiN7_JIfpyTs4CYN9Tqv2SmlEHFRSZf_0XuxzkOeQ1nQKOpLFYZ4ivUxDGl6Ft3E0NP8dZxcEsUbo3C5SjcEoVbhF8ehOe697u7jj-3z8CbA0Cpoa6NNDQh3XNSy5yYyZxYuZRLw7WP9xP-y_3F2rRP0xjvRBGsUGgW81drvaXR0XXMxleXArgEbkFXUsrfOy6xhA</recordid><startdate>20101101</startdate><enddate>20101101</enddate><creator>Bruce, Thiago</creator><creator>Martinez, Ivana B</creator><creator>Maia Neto, Oswaldo</creator><creator>Vicente, Ana Carolina P</creator><creator>Kruger, Ricardo H</creator><creator>Thompson, Fabiano L</creator><general>New York : Springer-Verlag</general><general>Springer Science + Business Media, Inc</general><general>Springer-Verlag</general><general>Springer</general><general>Springer Nature B.V</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>7SN</scope><scope>7T7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</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>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>F1W</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>H95</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>L.G</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20101101</creationdate><title>Bacterial Community Diversity in the Brazilian Atlantic Forest Soils</title><author>Bruce, Thiago ; Martinez, Ivana B ; Maia Neto, Oswaldo ; Vicente, Ana Carolina P ; Kruger, Ricardo H ; Thompson, Fabiano L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c544t-a90b9e510b30694b68c60a487ff6dfa14bf9094eb8262a026e2a5a73d84d47ab3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Acid soils</topic><topic>Acidobacteria</topic><topic>Agricultural soils</topic><topic>Agrology</topic><topic>Arthrobacter</topic><topic>Bacillus</topic><topic>Bacteria</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacteria - metabolism</topic><topic>Biodiversity</topic><topic>Biological and medical sciences</topic><topic>Biomedical and Life Sciences</topic><topic>Brazil</topic><topic>Burkholderia</topic><topic>Cellulose</topic><topic>Cultivation</topic><topic>DNA, Bacterial - genetics</topic><topic>Ecology</topic><topic>Forest soils</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Geoecology/Natural Processes</topic><topic>Libraries</topic><topic>Life Sciences</topic><topic>Microbial Ecology</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>National parks</topic><topic>Nature Conservation</topic><topic>Paenibacillus</topic><topic>Phylogeny</topic><topic>Proteobacteria</topic><topic>Pseudomonas</topic><topic>Ralstonia</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sedimentary soils</topic><topic>Serratia</topic><topic>Soil - analysis</topic><topic>Soil bacteria</topic><topic>SOIL MICROBIOLOGY</topic><topic>Soil microorganisms</topic><topic>Streptomyces</topic><topic>Trees - microbiology</topic><topic>Verrucomicrobia</topic><topic>Water Quality/Water Pollution</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bruce, Thiago</creatorcontrib><creatorcontrib>Martinez, Ivana B</creatorcontrib><creatorcontrib>Maia Neto, Oswaldo</creatorcontrib><creatorcontrib>Vicente, Ana Carolina P</creatorcontrib><creatorcontrib>Kruger, Ricardo H</creatorcontrib><creatorcontrib>Thompson, Fabiano L</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>Ecology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</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>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</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>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</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>Earth, Atmospheric & Aquatic 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>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Microbial ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bruce, Thiago</au><au>Martinez, Ivana B</au><au>Maia Neto, Oswaldo</au><au>Vicente, Ana Carolina P</au><au>Kruger, Ricardo H</au><au>Thompson, Fabiano L</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Bacterial Community Diversity in the Brazilian Atlantic Forest Soils</atitle><jtitle>Microbial ecology</jtitle><stitle>Microb Ecol</stitle><addtitle>Microb Ecol</addtitle><date>2010-11-01</date><risdate>2010</risdate><volume>60</volume><issue>4</issue><spage>840</spage><epage>849</epage><pages>840-849</pages><issn>0095-3628</issn><eissn>1432-184X</eissn><coden>MCBEBU</coden><abstract>The aim of this study was to characterize the bacterial community diversity of the Brazilian Atlantic forest soil by means of both cultivation and 16S rRNA clone libraries. A collection of 86 representative isolates, obtained from six samples of Atlantic forest soils from the National Park of Serra dos Órgãos (PARNASO), belonged to the genera Arthrobacter, Bacillus, Burkholderia, Leifsonia, Paenibacillus, Pseudomonas, Ralstonia, Serratia, and Streptomyces according to the 16S rRNA sequences. Representative isolates from the different genera degraded cellulose and lignin. The culture-independent analysis based on 894 partial 16S rRNA gene sequences revealed that the most frequently retrieved groups belonged to the phyla Acidobacteria (29-54%), Proteobacteria (16-38%), and Verrucomicrobia (0.6-14%). The majority of the sequences (82.6%) were unidentified singletons and doubletons, indicating a high diversity of rare unique sequences. Chao1 estimator disclosed a high number of phyla (41-152) and species (263-446). This is the first survey on the Atlantic Forest soils using a combination of cultivation and culture-independent approaches. We conclude that the Brazilian Atlantic Forest soil represents a vast source of novel bacteria.</abstract><cop>New York</cop><pub>New York : Springer-Verlag</pub><pmid>20886336</pmid><doi>10.1007/s00248-010-9750-2</doi><tpages>10</tpages></addata></record> |
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| subjects | Acid soils Acidobacteria Agricultural soils Agrology Arthrobacter Bacillus Bacteria Bacteria - classification Bacteria - genetics Bacteria - isolation & purification Bacteria - metabolism Biodiversity Biological and medical sciences Biomedical and Life Sciences Brazil Burkholderia Cellulose Cultivation DNA, Bacterial - genetics Ecology Forest soils Fundamental and applied biological sciences. Psychology Geoecology/Natural Processes Libraries Life Sciences Microbial Ecology Microbiology Molecular Sequence Data National parks Nature Conservation Paenibacillus Phylogeny Proteobacteria Pseudomonas Ralstonia RNA, Ribosomal, 16S - genetics Sedimentary soils Serratia Soil - analysis Soil bacteria SOIL MICROBIOLOGY Soil microorganisms Streptomyces Trees - microbiology Verrucomicrobia Water Quality/Water Pollution |
| title | Bacterial Community Diversity in the Brazilian Atlantic Forest Soils |
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