Variation of bacterial and fungal community structures in the rhizosphere of hybrid and standard rice cultivars and linkage to CO2 flux
Abstract A field experiment was conducted with cultivation of hybrid and conventional cultivars in a rice paddy from China. Rhizosphere soil was sampled and CO2 flux was measured at tillering (S1), grain filling (S2) and ripening (S3) across the growth stages. Microbial community structure, abundanc...
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| Veröffentlicht in: | FEMS microbiology ecology 2011-10, Vol.78 (1), p.116-128 |
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| creator | Hussain, Qaiser Liu, Yongzhuo Zhang, Afeng Pan, Genxing Li, Lianqing Zhang, Xuhui Song, Xiangyun Cui, Liqiang Jin, Zhenjiang |
| description | Abstract
A field experiment was conducted with cultivation of hybrid and conventional cultivars in a rice paddy from China. Rhizosphere soil was sampled and CO2 flux was measured at tillering (S1), grain filling (S2) and ripening (S3) across the growth stages. Microbial community structure, abundance and activity were analyzed using a combination of functional (enzymes) and denaturing gradient gel electrophoresis (DGGE) and real-time PCR molecular approaches. Invertase and urease activities, total microbial biomass carbon, bacterial 16S rRNA and fungal internal transcribed spacer rRNA gene copies were found to be the highest at S2 under both cultivars, being greater under the hybrid cultivar than under the conventional cultivar across the stages. Moreover, the CO2 flux was 11%, 16% and 25% higher under the hybrid cultivar than under the conventional cultivar at S1, S2 and S3, respectively. Principal component analyses of the PCR-DGGE profile revealed a significant difference between conventional and hybrid cultivars across growth stages. Sequencing DGGE bands of the bacterial 16S rRNA gene showed that a particular bacterial group ofAlphaproteobacteria was enhanced and several distinct operational taxonomic units markedly resembledAscomycota under the hybrid cultivar. These illustrate a significant selection of a particular group of bacteria and fungi of the hybrid cultivar. However, the potential impacts of these cultivar effects in soil C and N cycling deserve further field studies. |
| doi_str_mv | 10.1111/j.1574-6941.2011.01128.x |
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A field experiment was conducted with cultivation of hybrid and conventional cultivars in a rice paddy from China. Rhizosphere soil was sampled and CO2 flux was measured at tillering (S1), grain filling (S2) and ripening (S3) across the growth stages. Microbial community structure, abundance and activity were analyzed using a combination of functional (enzymes) and denaturing gradient gel electrophoresis (DGGE) and real-time PCR molecular approaches. Invertase and urease activities, total microbial biomass carbon, bacterial 16S rRNA and fungal internal transcribed spacer rRNA gene copies were found to be the highest at S2 under both cultivars, being greater under the hybrid cultivar than under the conventional cultivar across the stages. Moreover, the CO2 flux was 11%, 16% and 25% higher under the hybrid cultivar than under the conventional cultivar at S1, S2 and S3, respectively. Principal component analyses of the PCR-DGGE profile revealed a significant difference between conventional and hybrid cultivars across growth stages. Sequencing DGGE bands of the bacterial 16S rRNA gene showed that a particular bacterial group ofAlphaproteobacteria was enhanced and several distinct operational taxonomic units markedly resembledAscomycota under the hybrid cultivar. These illustrate a significant selection of a particular group of bacteria and fungi of the hybrid cultivar. However, the potential impacts of these cultivar effects in soil C and N cycling deserve further field studies.</description><identifier>ISSN: 0168-6496</identifier><identifier>EISSN: 1574-6941</identifier><identifier>DOI: 10.1111/j.1574-6941.2011.01128.x</identifier><identifier>PMID: 21569061</identifier><identifier>CODEN: FMECEZ</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Alphaproteobacteria - classification ; Alphaproteobacteria - genetics ; Alphaproteobacteria - growth & development ; Ascomycota ; Bacteria ; Bacteria - classification ; Bacteria - genetics ; Bacteria - metabolism ; Base Sequence ; Biomass ; Carbon - analysis ; Carbon - metabolism ; Carbon Cycle ; Carbon dioxide ; Carbon Dioxide - analysis ; Carbon Dioxide - metabolism ; China ; CO2 flux ; Community structure ; Cultivars ; Ecology ; enzyme activities ; Fluctuations ; Fungi - classification ; Fungi - genetics ; Fungi - metabolism ; Genes, rRNA ; microbial community dynamics ; Microbiology ; molecular fingerprints ; Molecular Sequence Data ; Oryza - microbiology ; Oryza sativa ; Rhizosphere ; rice cultivars ; rice rhizosphere ; RNA, Ribosomal, 16S - genetics ; Soil - chemistry ; Soil Microbiology ; Soil Pollutants - analysis</subject><ispartof>FEMS microbiology ecology, 2011-10, Vol.78 (1), p.116-128</ispartof><rights>2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved 2011</rights><rights>2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved</rights><rights>2011 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-c4038-2eb4459afe170817bde55422b474dd5770cbf27e287b6b802112832aaed7c0b03</citedby></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.1574-6941.2011.01128.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6941.2011.01128.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21569061$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Hussain, Qaiser</creatorcontrib><creatorcontrib>Liu, Yongzhuo</creatorcontrib><creatorcontrib>Zhang, Afeng</creatorcontrib><creatorcontrib>Pan, Genxing</creatorcontrib><creatorcontrib>Li, Lianqing</creatorcontrib><creatorcontrib>Zhang, Xuhui</creatorcontrib><creatorcontrib>Song, Xiangyun</creatorcontrib><creatorcontrib>Cui, Liqiang</creatorcontrib><creatorcontrib>Jin, Zhenjiang</creatorcontrib><title>Variation of bacterial and fungal community structures in the rhizosphere of hybrid and standard rice cultivars and linkage to CO2 flux</title><title>FEMS microbiology ecology</title><addtitle>FEMS Microbiol Ecol</addtitle><description>Abstract
A field experiment was conducted with cultivation of hybrid and conventional cultivars in a rice paddy from China. Rhizosphere soil was sampled and CO2 flux was measured at tillering (S1), grain filling (S2) and ripening (S3) across the growth stages. Microbial community structure, abundance and activity were analyzed using a combination of functional (enzymes) and denaturing gradient gel electrophoresis (DGGE) and real-time PCR molecular approaches. Invertase and urease activities, total microbial biomass carbon, bacterial 16S rRNA and fungal internal transcribed spacer rRNA gene copies were found to be the highest at S2 under both cultivars, being greater under the hybrid cultivar than under the conventional cultivar across the stages. Moreover, the CO2 flux was 11%, 16% and 25% higher under the hybrid cultivar than under the conventional cultivar at S1, S2 and S3, respectively. Principal component analyses of the PCR-DGGE profile revealed a significant difference between conventional and hybrid cultivars across growth stages. Sequencing DGGE bands of the bacterial 16S rRNA gene showed that a particular bacterial group ofAlphaproteobacteria was enhanced and several distinct operational taxonomic units markedly resembledAscomycota under the hybrid cultivar. These illustrate a significant selection of a particular group of bacteria and fungi of the hybrid cultivar. However, the potential impacts of these cultivar effects in soil C and N cycling deserve further field studies.</description><subject>Alphaproteobacteria - classification</subject><subject>Alphaproteobacteria - genetics</subject><subject>Alphaproteobacteria - growth & development</subject><subject>Ascomycota</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - genetics</subject><subject>Bacteria - metabolism</subject><subject>Base Sequence</subject><subject>Biomass</subject><subject>Carbon - analysis</subject><subject>Carbon - metabolism</subject><subject>Carbon Cycle</subject><subject>Carbon dioxide</subject><subject>Carbon Dioxide - analysis</subject><subject>Carbon Dioxide - metabolism</subject><subject>China</subject><subject>CO2 flux</subject><subject>Community structure</subject><subject>Cultivars</subject><subject>Ecology</subject><subject>enzyme activities</subject><subject>Fluctuations</subject><subject>Fungi - classification</subject><subject>Fungi - genetics</subject><subject>Fungi - metabolism</subject><subject>Genes, rRNA</subject><subject>microbial community dynamics</subject><subject>Microbiology</subject><subject>molecular fingerprints</subject><subject>Molecular Sequence Data</subject><subject>Oryza - microbiology</subject><subject>Oryza sativa</subject><subject>Rhizosphere</subject><subject>rice cultivars</subject><subject>rice rhizosphere</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Soil - chemistry</subject><subject>Soil Microbiology</subject><subject>Soil Pollutants - analysis</subject><issn>0168-6496</issn><issn>1574-6941</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUcuO0zAUtRCIKYVfQJZYsEqwHT-SBQtUzQDSoNkAW8t2nKlLEhc_oOUH-G2cdpgFCGHJL52HdM8BAGJU47Je7WrMBK14R3FNEMZ12aStDw_A6h54CFYI87bitOMX4EmMO4Qwayh6DC4IZrxDHK_Az88qOJWcn6EfoFYm2fIfoZp7OOT5tjyNn6Y8u3SEMYVsUg42QjfDtLUwbN0PH_dbG-yi3x51cP1JHFM5VehhcMZCk8fkvqkQT9jo5i_q1sLk4eaGwGHMh6fg0aDGaJ_d3Wvw6ery4-ZddX3z9v3mzXVlKGrailhNKevUYLFALRa6t4xRQjQVtO-ZEMjogQhLWqG5bhFZcmmIUrYXBmnUrMHLs-8--K_ZxiQnF40dRzVbn6PsSry8pEP_z0SMC0zJ4vniD-bO5zCXMSRmWFDCi2dhPb9jZT3ZXu6Dm1Q4yt9dFMLrM-G7G-3xHsdILp3LnVyqlUu1culcnjqXB3l1-eE05Ro0Z73P-3-oq7_UzS_1KK5o</recordid><startdate>20111001</startdate><enddate>20111001</enddate><creator>Hussain, Qaiser</creator><creator>Liu, Yongzhuo</creator><creator>Zhang, Afeng</creator><creator>Pan, Genxing</creator><creator>Li, Lianqing</creator><creator>Zhang, Xuhui</creator><creator>Song, Xiangyun</creator><creator>Cui, Liqiang</creator><creator>Jin, Zhenjiang</creator><general>Blackwell Publishing Ltd</general><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</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></search><sort><creationdate>20111001</creationdate><title>Variation of bacterial and fungal community structures in the rhizosphere of hybrid and standard rice cultivars and linkage to CO2 flux</title><author>Hussain, Qaiser ; Liu, Yongzhuo ; Zhang, Afeng ; Pan, Genxing ; Li, Lianqing ; Zhang, Xuhui ; Song, Xiangyun ; Cui, Liqiang ; Jin, Zhenjiang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4038-2eb4459afe170817bde55422b474dd5770cbf27e287b6b802112832aaed7c0b03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Alphaproteobacteria - classification</topic><topic>Alphaproteobacteria - genetics</topic><topic>Alphaproteobacteria - growth & development</topic><topic>Ascomycota</topic><topic>Bacteria</topic><topic>Bacteria - classification</topic><topic>Bacteria - genetics</topic><topic>Bacteria - metabolism</topic><topic>Base Sequence</topic><topic>Biomass</topic><topic>Carbon - analysis</topic><topic>Carbon - metabolism</topic><topic>Carbon Cycle</topic><topic>Carbon dioxide</topic><topic>Carbon Dioxide - analysis</topic><topic>Carbon Dioxide - metabolism</topic><topic>China</topic><topic>CO2 flux</topic><topic>Community structure</topic><topic>Cultivars</topic><topic>Ecology</topic><topic>enzyme activities</topic><topic>Fluctuations</topic><topic>Fungi - classification</topic><topic>Fungi - genetics</topic><topic>Fungi - metabolism</topic><topic>Genes, rRNA</topic><topic>microbial community dynamics</topic><topic>Microbiology</topic><topic>molecular fingerprints</topic><topic>Molecular Sequence Data</topic><topic>Oryza - microbiology</topic><topic>Oryza sativa</topic><topic>Rhizosphere</topic><topic>rice cultivars</topic><topic>rice rhizosphere</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Soil - chemistry</topic><topic>Soil Microbiology</topic><topic>Soil Pollutants - analysis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Hussain, Qaiser</creatorcontrib><creatorcontrib>Liu, Yongzhuo</creatorcontrib><creatorcontrib>Zhang, Afeng</creatorcontrib><creatorcontrib>Pan, Genxing</creatorcontrib><creatorcontrib>Li, Lianqing</creatorcontrib><creatorcontrib>Zhang, Xuhui</creatorcontrib><creatorcontrib>Song, Xiangyun</creatorcontrib><creatorcontrib>Cui, Liqiang</creatorcontrib><creatorcontrib>Jin, Zhenjiang</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</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><jtitle>FEMS microbiology ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Hussain, Qaiser</au><au>Liu, Yongzhuo</au><au>Zhang, Afeng</au><au>Pan, Genxing</au><au>Li, Lianqing</au><au>Zhang, Xuhui</au><au>Song, Xiangyun</au><au>Cui, Liqiang</au><au>Jin, Zhenjiang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Variation of bacterial and fungal community structures in the rhizosphere of hybrid and standard rice cultivars and linkage to CO2 flux</atitle><jtitle>FEMS microbiology ecology</jtitle><addtitle>FEMS Microbiol Ecol</addtitle><date>2011-10-01</date><risdate>2011</risdate><volume>78</volume><issue>1</issue><spage>116</spage><epage>128</epage><pages>116-128</pages><issn>0168-6496</issn><eissn>1574-6941</eissn><coden>FMECEZ</coden><abstract>Abstract
A field experiment was conducted with cultivation of hybrid and conventional cultivars in a rice paddy from China. Rhizosphere soil was sampled and CO2 flux was measured at tillering (S1), grain filling (S2) and ripening (S3) across the growth stages. Microbial community structure, abundance and activity were analyzed using a combination of functional (enzymes) and denaturing gradient gel electrophoresis (DGGE) and real-time PCR molecular approaches. Invertase and urease activities, total microbial biomass carbon, bacterial 16S rRNA and fungal internal transcribed spacer rRNA gene copies were found to be the highest at S2 under both cultivars, being greater under the hybrid cultivar than under the conventional cultivar across the stages. Moreover, the CO2 flux was 11%, 16% and 25% higher under the hybrid cultivar than under the conventional cultivar at S1, S2 and S3, respectively. Principal component analyses of the PCR-DGGE profile revealed a significant difference between conventional and hybrid cultivars across growth stages. Sequencing DGGE bands of the bacterial 16S rRNA gene showed that a particular bacterial group ofAlphaproteobacteria was enhanced and several distinct operational taxonomic units markedly resembledAscomycota under the hybrid cultivar. These illustrate a significant selection of a particular group of bacteria and fungi of the hybrid cultivar. However, the potential impacts of these cultivar effects in soil C and N cycling deserve further field studies.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>21569061</pmid><doi>10.1111/j.1574-6941.2011.01128.x</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Alphaproteobacteria - classification Alphaproteobacteria - genetics Alphaproteobacteria - growth & development Ascomycota Bacteria Bacteria - classification Bacteria - genetics Bacteria - metabolism Base Sequence Biomass Carbon - analysis Carbon - metabolism Carbon Cycle Carbon dioxide Carbon Dioxide - analysis Carbon Dioxide - metabolism China CO2 flux Community structure Cultivars Ecology enzyme activities Fluctuations Fungi - classification Fungi - genetics Fungi - metabolism Genes, rRNA microbial community dynamics Microbiology molecular fingerprints Molecular Sequence Data Oryza - microbiology Oryza sativa Rhizosphere rice cultivars rice rhizosphere RNA, Ribosomal, 16S - genetics Soil - chemistry Soil Microbiology Soil Pollutants - analysis |
| title | Variation of bacterial and fungal community structures in the rhizosphere of hybrid and standard rice cultivars and linkage to CO2 flux |
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