Acidobacterial community responses to agricultural management of soybean in Amazon forest soils
Abstract This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidob...
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| Veröffentlicht in: | FEMS microbiology ecology 2013-03, Vol.83 (3), p.607-621 |
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| creator | Navarrete, Acácio A. Kuramae, Eiko E. de Hollander, Mattias Pijl, Agata S. van Veen, Johannes A. Tsai, Siu M. |
| description | Abstract
This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1–8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area. |
| doi_str_mv | 10.1111/1574-6941.12018 |
| format | Article |
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This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1–8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.</description><identifier>ISSN: 0168-6496</identifier><identifier>EISSN: 1574-6941</identifier><identifier>DOI: 10.1111/1574-6941.12018</identifier><identifier>PMID: 23013447</identifier><identifier>CODEN: FMECEZ</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>16S rRNA gene ; Acidobacteria - genetics ; Acidobacteria - growth & development ; Agricultural land ; Agricultural management ; Agriculture - methods ; Agronomy. Soil science and plant productions ; Aluminum ; Animal, plant and microbial ecology ; Biological and medical sciences ; Brazil ; DNA, Bacterial - isolation & purification ; Ecology ; Forest soils ; Fundamental and applied biological sciences. Psychology ; General agroecology ; General agroecology. Agricultural and farming systems. Agricultural development. Rural area planning. Landscaping ; General agronomy. Plant production ; Generalities. Agricultural and farming systems. Agricultural development ; Glycine max - microbiology ; Land use ; land‐use changes ; Microbial ecology ; Microbiology ; Phylogeny ; Rhizosphere ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA ; Soil - analysis ; soil factors ; Soil management ; Soil Microbiology ; Soybeans ; Trees - microbiology ; tropical rainforest ; Various environments (extraatmospheric space, air, water) ; Warning systems</subject><ispartof>FEMS microbiology ecology, 2013-03, Vol.83 (3), p.607-621</ispartof><rights>2012 Federation of European Microbiological Societies 2012</rights><rights>2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><rights>2014 INIST-CNRS</rights><rights>2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.</rights><rights>Copyright © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5768-4c6a63a8edd954fc7d90035285f088649b4ee7300ff2c9ce71f3867a1eebf1753</citedby><cites>FETCH-LOGICAL-c5768-4c6a63a8edd954fc7d90035285f088649b4ee7300ff2c9ce71f3867a1eebf1753</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%2F1574-6941.12018$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1574-6941.12018$$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=26852021$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23013447$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Navarrete, Acácio A.</creatorcontrib><creatorcontrib>Kuramae, Eiko E.</creatorcontrib><creatorcontrib>de Hollander, Mattias</creatorcontrib><creatorcontrib>Pijl, Agata S.</creatorcontrib><creatorcontrib>van Veen, Johannes A.</creatorcontrib><creatorcontrib>Tsai, Siu M.</creatorcontrib><title>Acidobacterial community responses to agricultural management of soybean in Amazon forest soils</title><title>FEMS microbiology ecology</title><addtitle>FEMS Microbiol Ecol</addtitle><description>Abstract
This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1–8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.</description><subject>16S rRNA gene</subject><subject>Acidobacteria - genetics</subject><subject>Acidobacteria - growth & development</subject><subject>Agricultural land</subject><subject>Agricultural management</subject><subject>Agriculture - methods</subject><subject>Agronomy. Soil science and plant productions</subject><subject>Aluminum</subject><subject>Animal, plant and microbial ecology</subject><subject>Biological and medical sciences</subject><subject>Brazil</subject><subject>DNA, Bacterial - isolation & purification</subject><subject>Ecology</subject><subject>Forest soils</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General agroecology</subject><subject>General agroecology. Agricultural and farming systems. Agricultural development. Rural area planning. Landscaping</subject><subject>General agronomy. Plant production</subject><subject>Generalities. Agricultural and farming systems. Agricultural development</subject><subject>Glycine max - microbiology</subject><subject>Land use</subject><subject>land‐use changes</subject><subject>Microbial ecology</subject><subject>Microbiology</subject><subject>Phylogeny</subject><subject>Rhizosphere</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Soil - analysis</subject><subject>soil factors</subject><subject>Soil management</subject><subject>Soil Microbiology</subject><subject>Soybeans</subject><subject>Trees - microbiology</subject><subject>tropical rainforest</subject><subject>Various environments (extraatmospheric space, air, water)</subject><subject>Warning systems</subject><issn>0168-6496</issn><issn>1574-6941</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc1rFTEUxYMo9lldu5MBEUSYNt_JLB-lVaHiRtchk7kpKTPJM5mhPP96M77XKiI0m0Du79x7bg5Crwk-I_WcE6F4KztOzgjFRD9Bm4eXp2iDidSt5J08QS9KucWYCMbxc3RCGSaMc7VBZuvCkHrrZsjBjo1L07TEMO-bDGWXYoHSzKmxNzm4ZZyXXJnJRnsDE8S5Sb4pad-DjU2IzXayP1NsfKrauRbCWF6iZ96OBV4d71P0_ery28Wn9vrrx88X2-vWCVVNcietZFbDMHSCe6eGDmMmqBYea11X6DmAYhh7T13nQBHPtFSWAPSeKMFO0ftD311OP5Y63kyhOBhHGyEtxRBGhKRCKP04SjVT9Xc6UtG3_6C3acmxLrJSazuiaaXOD5TLqZQM3uxymGzeG4LNGpNZQzFrKOZ3TFXx5th36ScYHvj7XCrw7gjY4uzos40ulD-c1IJiuhoUB-4ujLB_bK65uvxyb-DDQZeW3X9V7V9ufwFlI7TW</recordid><startdate>201303</startdate><enddate>201303</enddate><creator>Navarrete, Acácio A.</creator><creator>Kuramae, Eiko E.</creator><creator>de Hollander, Mattias</creator><creator>Pijl, Agata S.</creator><creator>van Veen, Johannes A.</creator><creator>Tsai, Siu M.</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>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7ST</scope><scope>SOI</scope></search><sort><creationdate>201303</creationdate><title>Acidobacterial community responses to agricultural management of soybean in Amazon forest soils</title><author>Navarrete, Acácio A. ; Kuramae, Eiko E. ; de Hollander, Mattias ; Pijl, Agata S. ; van Veen, Johannes A. ; Tsai, Siu M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5768-4c6a63a8edd954fc7d90035285f088649b4ee7300ff2c9ce71f3867a1eebf1753</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>16S rRNA gene</topic><topic>Acidobacteria - genetics</topic><topic>Acidobacteria - growth & development</topic><topic>Agricultural land</topic><topic>Agricultural management</topic><topic>Agriculture - methods</topic><topic>Agronomy. Soil science and plant productions</topic><topic>Aluminum</topic><topic>Animal, plant and microbial ecology</topic><topic>Biological and medical sciences</topic><topic>Brazil</topic><topic>DNA, Bacterial - isolation & purification</topic><topic>Ecology</topic><topic>Forest soils</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General agroecology</topic><topic>General agroecology. Agricultural and farming systems. Agricultural development. Rural area planning. Landscaping</topic><topic>General agronomy. Plant production</topic><topic>Generalities. Agricultural and farming systems. Agricultural development</topic><topic>Glycine max - microbiology</topic><topic>Land use</topic><topic>land‐use changes</topic><topic>Microbial ecology</topic><topic>Microbiology</topic><topic>Phylogeny</topic><topic>Rhizosphere</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Soil - analysis</topic><topic>soil factors</topic><topic>Soil management</topic><topic>Soil Microbiology</topic><topic>Soybeans</topic><topic>Trees - microbiology</topic><topic>tropical rainforest</topic><topic>Various environments (extraatmospheric space, air, water)</topic><topic>Warning systems</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Navarrete, Acácio A.</creatorcontrib><creatorcontrib>Kuramae, Eiko E.</creatorcontrib><creatorcontrib>de Hollander, Mattias</creatorcontrib><creatorcontrib>Pijl, Agata S.</creatorcontrib><creatorcontrib>van Veen, Johannes A.</creatorcontrib><creatorcontrib>Tsai, Siu M.</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>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Ecology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Environment Abstracts</collection><collection>Environment Abstracts</collection><jtitle>FEMS microbiology ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Navarrete, Acácio A.</au><au>Kuramae, Eiko E.</au><au>de Hollander, Mattias</au><au>Pijl, Agata S.</au><au>van Veen, Johannes A.</au><au>Tsai, Siu M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Acidobacterial community responses to agricultural management of soybean in Amazon forest soils</atitle><jtitle>FEMS microbiology ecology</jtitle><addtitle>FEMS Microbiol Ecol</addtitle><date>2013-03</date><risdate>2013</risdate><volume>83</volume><issue>3</issue><spage>607</spage><epage>621</epage><pages>607-621</pages><issn>0168-6496</issn><eissn>1574-6941</eissn><coden>FMECEZ</coden><abstract>Abstract
This study focused on the impact of land-use changes and agricultural management of soybean in Amazon forest soils on the abundance and composition of the acidobacterial community. Quantitative real-time PCR (q-PCR) assays and pyrosequencing of 16S rRNA gene were applied to study the acidobacterial community in bulk soil samples from soybean croplands and adjacent native forests, and mesocosm soil samples from soybean rhizosphere. Based on qPCR measurements, Acidobacteria accounted for 23% in forest soils, 18% in cropland soils, and 14% in soybean rhizosphere of the total bacterial signals. From the 16S rRNA gene sequences of Bacteria domain, the phylum Acidobacteria represented 28% of the sequences from forest soils, 16% from cropland soils, and 17% from soybean rhizosphere. Acidobacteria subgroups 1–8, 10, 11, 13, 17, 18, 22, and 25 were detected with subgroup 1 as dominant among them. Subgroups 4, 6, and 7 were significantly higher in cropland soils than in forest soils, which subgroups responded to decrease in soil aluminum. Subgroups 6 and 7 responded to high content of soil Ca, Mg, Mn, and B. These results showed a differential response of the Acidobacteria subgroups to abiotic soil factors, and open the possibilities to explore acidobacterial subgroups as early-warning bioindicators of agricultural soil management effects in the Amazon area.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>23013447</pmid><doi>10.1111/1574-6941.12018</doi><tpages>15</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 16S rRNA gene Acidobacteria - genetics Acidobacteria - growth & development Agricultural land Agricultural management Agriculture - methods Agronomy. Soil science and plant productions Aluminum Animal, plant and microbial ecology Biological and medical sciences Brazil DNA, Bacterial - isolation & purification Ecology Forest soils Fundamental and applied biological sciences. Psychology General agroecology General agroecology. Agricultural and farming systems. Agricultural development. Rural area planning. Landscaping General agronomy. Plant production Generalities. Agricultural and farming systems. Agricultural development Glycine max - microbiology Land use land‐use changes Microbial ecology Microbiology Phylogeny Rhizosphere RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA Soil - analysis soil factors Soil management Soil Microbiology Soybeans Trees - microbiology tropical rainforest Various environments (extraatmospheric space, air, water) Warning systems |
| title | Acidobacterial community responses to agricultural management of soybean in Amazon forest soils |
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