From the micro-scale to the habitat: Assessment of soil bacterial community structure as shown by soil structure directed sampling
Natural structural units of a luvisol under maize crop were studied to assess if soil structure directed sampling could improve the understanding of arrangements of bacteria in spatially constraint location. Three habitats were defined: (i) soil around fine lateral roots (rhizo-aggregates), (ii) soi...
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| Veröffentlicht in: | Soil biology & biochemistry 2009, Vol.41 (1), p.29-36 |
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| creator | Remenant, Benoît Grundmann, Geneviève L. Jocteur-Monrozier, Lucile |
| description | Natural structural units of a luvisol under maize crop were studied to assess if soil structure directed sampling could improve the understanding of arrangements of bacteria in spatially constraint location. Three habitats were defined: (i) soil around fine lateral roots (rhizo-aggregates), (ii) soil close to basal roots (core clods) and (iii) unplanted soil between rows (bare soil clods). These habitats were also investigated with maize plants resulting from
Azospirillum lipoferum CRT1 inoculated seeds as a model of enhanced fine root system. Rhizo-aggregates were clearly separated from each other (disconnected habitat) in contrast to micro-samples (fragments) from clods, which belong to cohesive macro-structures. Genetic fingerprints on metagenomic extracts were used to characterize the structure of bacterial communities on 95 micro-samples from the three habitats. For eubacteria, automated RISA (Ribosomal Intergenic Spacer Analysis) of ITS (Internal Transcribed Spacer) profiles were performed. PCR–RFLP on
nifH gene were used to describe the N-fixer guilds. Exploratory multivariate analyses (PCA and MDS) revealed bacterial community patterns in the sampled habitats. On the basis of ITS profiles, rhizo-aggregates harboured closely related communities, distant from those of the unplanted soil, and each sampled rhizo-aggregate could therefore be considered as a sub-unit of the whole macro-habitat, comprising all the fine roots. The observed low dissimilarity of disconnected rhizo-aggregates is likely to result from the direct influence of maize root tips on the recruitment of rhizosphere bacteria. Molecular fingerprints of
nifH from basal root clods (core) were more similar to bare soil than to rhizo-aggregates, indicating similar ecological conditions without, or with, at least, poor maize exudating root influence. Although our study was performed on a limited number of situations, the distribution of bacteria was revealed to be patterned by soil structure units, which is a first step to improve the modelling of microbial ecology in soils. |
| doi_str_mv | 10.1016/j.soilbio.2008.09.005 |
| format | Article |
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Azospirillum lipoferum CRT1 inoculated seeds as a model of enhanced fine root system. Rhizo-aggregates were clearly separated from each other (disconnected habitat) in contrast to micro-samples (fragments) from clods, which belong to cohesive macro-structures. Genetic fingerprints on metagenomic extracts were used to characterize the structure of bacterial communities on 95 micro-samples from the three habitats. For eubacteria, automated RISA (Ribosomal Intergenic Spacer Analysis) of ITS (Internal Transcribed Spacer) profiles were performed. PCR–RFLP on
nifH gene were used to describe the N-fixer guilds. Exploratory multivariate analyses (PCA and MDS) revealed bacterial community patterns in the sampled habitats. On the basis of ITS profiles, rhizo-aggregates harboured closely related communities, distant from those of the unplanted soil, and each sampled rhizo-aggregate could therefore be considered as a sub-unit of the whole macro-habitat, comprising all the fine roots. The observed low dissimilarity of disconnected rhizo-aggregates is likely to result from the direct influence of maize root tips on the recruitment of rhizosphere bacteria. Molecular fingerprints of
nifH from basal root clods (core) were more similar to bare soil than to rhizo-aggregates, indicating similar ecological conditions without, or with, at least, poor maize exudating root influence. Although our study was performed on a limited number of situations, the distribution of bacteria was revealed to be patterned by soil structure units, which is a first step to improve the modelling of microbial ecology in soils.</description><identifier>ISSN: 0038-0717</identifier><identifier>EISSN: 1879-3428</identifier><identifier>DOI: 10.1016/j.soilbio.2008.09.005</identifier><identifier>CODEN: SBIOAH</identifier><language>eng</language><publisher>Amsterdam: Elsevier Ltd</publisher><subject>Agricultural sciences ; agricultural soils ; Agronomy. Soil science and plant productions ; Azospirillum lipoferum ; Biochemistry and biology ; Biological and medical sciences ; Chemical, physicochemical, biochemical and biological properties ; Clods ; community structure ; corn ; DNA ; Eubacteria ; Fundamental and applied biological sciences. Psychology ; genes ; habitats ; internal transcribed spacers ; ITS ; Life Sciences ; Micro-aggregates ; microbial genetics ; Molecular fingerprint ; Multivariate analyses ; multivariate analysis ; nifH ; nitrogen-fixing bacteria ; Physical properties ; Physics, chemistry, biochemistry and biology of agricultural and forest soils ; restriction fragment length polymorphism ; Rhizosphere ; root nodules ; seed inoculation ; soil bacteria ; soil ecology ; Soil science ; Soil structure ; Soil study ; Structure, texture, density, mechanical behavior. Heat and gas exchanges ; Zea mays</subject><ispartof>Soil biology & biochemistry, 2009, Vol.41 (1), p.29-36</ispartof><rights>2008</rights><rights>2009 INIST-CNRS</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c459t-2e5e51863b377016d2e8a95753556b3ee12749737de5c3feffb4d4ead72a33513</citedby><cites>FETCH-LOGICAL-c459t-2e5e51863b377016d2e8a95753556b3ee12749737de5c3feffb4d4ead72a33513</cites><orcidid>0000-0003-1223-005X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.soilbio.2008.09.005$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,780,784,885,3548,4022,27922,27923,27924,45994</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21030371$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://univ-lyon1.hal.science/hal-02545063$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Remenant, Benoît</creatorcontrib><creatorcontrib>Grundmann, Geneviève L.</creatorcontrib><creatorcontrib>Jocteur-Monrozier, Lucile</creatorcontrib><title>From the micro-scale to the habitat: Assessment of soil bacterial community structure as shown by soil structure directed sampling</title><title>Soil biology & biochemistry</title><description>Natural structural units of a luvisol under maize crop were studied to assess if soil structure directed sampling could improve the understanding of arrangements of bacteria in spatially constraint location. Three habitats were defined: (i) soil around fine lateral roots (rhizo-aggregates), (ii) soil close to basal roots (core clods) and (iii) unplanted soil between rows (bare soil clods). These habitats were also investigated with maize plants resulting from
Azospirillum lipoferum CRT1 inoculated seeds as a model of enhanced fine root system. Rhizo-aggregates were clearly separated from each other (disconnected habitat) in contrast to micro-samples (fragments) from clods, which belong to cohesive macro-structures. Genetic fingerprints on metagenomic extracts were used to characterize the structure of bacterial communities on 95 micro-samples from the three habitats. For eubacteria, automated RISA (Ribosomal Intergenic Spacer Analysis) of ITS (Internal Transcribed Spacer) profiles were performed. PCR–RFLP on
nifH gene were used to describe the N-fixer guilds. Exploratory multivariate analyses (PCA and MDS) revealed bacterial community patterns in the sampled habitats. On the basis of ITS profiles, rhizo-aggregates harboured closely related communities, distant from those of the unplanted soil, and each sampled rhizo-aggregate could therefore be considered as a sub-unit of the whole macro-habitat, comprising all the fine roots. The observed low dissimilarity of disconnected rhizo-aggregates is likely to result from the direct influence of maize root tips on the recruitment of rhizosphere bacteria. Molecular fingerprints of
nifH from basal root clods (core) were more similar to bare soil than to rhizo-aggregates, indicating similar ecological conditions without, or with, at least, poor maize exudating root influence. Although our study was performed on a limited number of situations, the distribution of bacteria was revealed to be patterned by soil structure units, which is a first step to improve the modelling of microbial ecology in soils.</description><subject>Agricultural sciences</subject><subject>agricultural soils</subject><subject>Agronomy. Soil science and plant productions</subject><subject>Azospirillum lipoferum</subject><subject>Biochemistry and biology</subject><subject>Biological and medical sciences</subject><subject>Chemical, physicochemical, biochemical and biological properties</subject><subject>Clods</subject><subject>community structure</subject><subject>corn</subject><subject>DNA</subject><subject>Eubacteria</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>genes</subject><subject>habitats</subject><subject>internal transcribed spacers</subject><subject>ITS</subject><subject>Life Sciences</subject><subject>Micro-aggregates</subject><subject>microbial genetics</subject><subject>Molecular fingerprint</subject><subject>Multivariate analyses</subject><subject>multivariate analysis</subject><subject>nifH</subject><subject>nitrogen-fixing bacteria</subject><subject>Physical properties</subject><subject>Physics, chemistry, biochemistry and biology of agricultural and forest soils</subject><subject>restriction fragment length polymorphism</subject><subject>Rhizosphere</subject><subject>root nodules</subject><subject>seed inoculation</subject><subject>soil bacteria</subject><subject>soil ecology</subject><subject>Soil science</subject><subject>Soil structure</subject><subject>Soil study</subject><subject>Structure, texture, density, mechanical behavior. Heat and gas exchanges</subject><subject>Zea mays</subject><issn>0038-0717</issn><issn>1879-3428</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><recordid>eNqFkU9v1DAQxSMEEkvhIyB8AYlDgv_EccIFrSraIq3EAXq2HGfS9SqJF4_Taq98cpxmVY49WRr_ZubNe1n2ntGCUVZ9ORTo3dA6X3BK64I2BaXyRbZhtWpyUfL6ZbahVNQ5VUy9zt4gHiilXDKxyf5eBT-SuAcyOht8jtYMQKJ_LO1N66KJX8kWERBHmCLxPVm2kdbYCMGZgVg_jvPk4olgDLONcwBikODeP0ykPa34_6_OBUitHUEzHgc33b3NXvVmQHh3fi-y26vvvy9v8t3P6x-X211uS9nEnIMEyepKtEKpdHbHoTaNVFJIWbUCgHFVNkqoDqQVPfR9W3YlmE5xI0Q69iL7vM7dm0EfgxtNOGlvnL7Z7vRSS5aUklbifmE_rewx-D8zYNSjQwvDYCbwM-pkdCV4LZ4FWdOwKslNoFzB5DJigP5JAqN6iVEf9DnGZXqtaaNTjKnv43mBWbLpg5msw6dmzqigQi3zP6xcb7w2dyExt794WkyZXHxpEvFtJSCZfO8gaLQOJgtrIrrz7hkt_wB0nMAg</recordid><startdate>2009</startdate><enddate>2009</enddate><creator>Remenant, Benoît</creator><creator>Grundmann, Geneviève L.</creator><creator>Jocteur-Monrozier, Lucile</creator><general>Elsevier Ltd</general><general>Elsevier</general><scope>FBQ</scope><scope>IQODW</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7SN</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>1XC</scope><orcidid>https://orcid.org/0000-0003-1223-005X</orcidid></search><sort><creationdate>2009</creationdate><title>From the micro-scale to the habitat: Assessment of soil bacterial community structure as shown by soil structure directed sampling</title><author>Remenant, Benoît ; Grundmann, Geneviève L. ; Jocteur-Monrozier, Lucile</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c459t-2e5e51863b377016d2e8a95753556b3ee12749737de5c3feffb4d4ead72a33513</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Agricultural sciences</topic><topic>agricultural soils</topic><topic>Agronomy. Soil science and plant productions</topic><topic>Azospirillum lipoferum</topic><topic>Biochemistry and biology</topic><topic>Biological and medical sciences</topic><topic>Chemical, physicochemical, biochemical and biological properties</topic><topic>Clods</topic><topic>community structure</topic><topic>corn</topic><topic>DNA</topic><topic>Eubacteria</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>genes</topic><topic>habitats</topic><topic>internal transcribed spacers</topic><topic>ITS</topic><topic>Life Sciences</topic><topic>Micro-aggregates</topic><topic>microbial genetics</topic><topic>Molecular fingerprint</topic><topic>Multivariate analyses</topic><topic>multivariate analysis</topic><topic>nifH</topic><topic>nitrogen-fixing bacteria</topic><topic>Physical properties</topic><topic>Physics, chemistry, biochemistry and biology of agricultural and forest soils</topic><topic>restriction fragment length polymorphism</topic><topic>Rhizosphere</topic><topic>root nodules</topic><topic>seed inoculation</topic><topic>soil bacteria</topic><topic>soil ecology</topic><topic>Soil science</topic><topic>Soil structure</topic><topic>Soil study</topic><topic>Structure, texture, density, mechanical behavior. Heat and gas exchanges</topic><topic>Zea mays</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Remenant, Benoît</creatorcontrib><creatorcontrib>Grundmann, Geneviève L.</creatorcontrib><creatorcontrib>Jocteur-Monrozier, Lucile</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Ecology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Soil biology & biochemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Remenant, Benoît</au><au>Grundmann, Geneviève L.</au><au>Jocteur-Monrozier, Lucile</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>From the micro-scale to the habitat: Assessment of soil bacterial community structure as shown by soil structure directed sampling</atitle><jtitle>Soil biology & biochemistry</jtitle><date>2009</date><risdate>2009</risdate><volume>41</volume><issue>1</issue><spage>29</spage><epage>36</epage><pages>29-36</pages><issn>0038-0717</issn><eissn>1879-3428</eissn><coden>SBIOAH</coden><abstract>Natural structural units of a luvisol under maize crop were studied to assess if soil structure directed sampling could improve the understanding of arrangements of bacteria in spatially constraint location. Three habitats were defined: (i) soil around fine lateral roots (rhizo-aggregates), (ii) soil close to basal roots (core clods) and (iii) unplanted soil between rows (bare soil clods). These habitats were also investigated with maize plants resulting from
Azospirillum lipoferum CRT1 inoculated seeds as a model of enhanced fine root system. Rhizo-aggregates were clearly separated from each other (disconnected habitat) in contrast to micro-samples (fragments) from clods, which belong to cohesive macro-structures. Genetic fingerprints on metagenomic extracts were used to characterize the structure of bacterial communities on 95 micro-samples from the three habitats. For eubacteria, automated RISA (Ribosomal Intergenic Spacer Analysis) of ITS (Internal Transcribed Spacer) profiles were performed. PCR–RFLP on
nifH gene were used to describe the N-fixer guilds. Exploratory multivariate analyses (PCA and MDS) revealed bacterial community patterns in the sampled habitats. On the basis of ITS profiles, rhizo-aggregates harboured closely related communities, distant from those of the unplanted soil, and each sampled rhizo-aggregate could therefore be considered as a sub-unit of the whole macro-habitat, comprising all the fine roots. The observed low dissimilarity of disconnected rhizo-aggregates is likely to result from the direct influence of maize root tips on the recruitment of rhizosphere bacteria. Molecular fingerprints of
nifH from basal root clods (core) were more similar to bare soil than to rhizo-aggregates, indicating similar ecological conditions without, or with, at least, poor maize exudating root influence. Although our study was performed on a limited number of situations, the distribution of bacteria was revealed to be patterned by soil structure units, which is a first step to improve the modelling of microbial ecology in soils.</abstract><cop>Amsterdam</cop><pub>Elsevier Ltd</pub><doi>10.1016/j.soilbio.2008.09.005</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0003-1223-005X</orcidid></addata></record> |
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| subjects | Agricultural sciences agricultural soils Agronomy. Soil science and plant productions Azospirillum lipoferum Biochemistry and biology Biological and medical sciences Chemical, physicochemical, biochemical and biological properties Clods community structure corn DNA Eubacteria Fundamental and applied biological sciences. Psychology genes habitats internal transcribed spacers ITS Life Sciences Micro-aggregates microbial genetics Molecular fingerprint Multivariate analyses multivariate analysis nifH nitrogen-fixing bacteria Physical properties Physics, chemistry, biochemistry and biology of agricultural and forest soils restriction fragment length polymorphism Rhizosphere root nodules seed inoculation soil bacteria soil ecology Soil science Soil structure Soil study Structure, texture, density, mechanical behavior. Heat and gas exchanges Zea mays |
| title | From the micro-scale to the habitat: Assessment of soil bacterial community structure as shown by soil structure directed sampling |
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