Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adja...

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Published in	The ISME Journal Vol. 14; no. 1; pp. 202 - 216
Main Authors	Jiao, Shuo, Yang, Yunfeng, Xu, Yiqin, Zhang, Jie, Lu, Yahai
Format	Journal Article
Language	English
Published	London Nature Publishing Group UK 01.01.2020 Oxford University Press
Subjects	38/23 631/326/2565/855 704/158/852 Agricultural land Agriculture Archaea - genetics Archaea - isolation & purification Assembly Bacteria - genetics Bacteria - isolation & purification Biomedical and Life Sciences China Coexistence Corn Dispersal Dispersion Ecological monitoring Ecology Ecosystem Evolutionary Biology Fungi - genetics Fungi - isolation & purification High-Throughput Nucleotide Sequencing Life Sciences Microbial Ecology Microbial Genetics and Genomics Microbiology Microbiomes Microbiota Microorganisms Oryza Rice fields Soil Microbiology Soils Zea mays China
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Abstract	Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.
AbstractList	Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems. Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.
Author	Lu, Yahai Jiao, Shuo Xu, Yiqin Yang, Yunfeng Zhang, Jie
Author_xml	– sequence: 1 givenname: Shuo surname: Jiao fullname: Jiao, Shuo organization: College of Urban and Environmental Sciences, Peking University – sequence: 2 givenname: Yunfeng orcidid: 0000-0001-8274-6196 surname: Yang fullname: Yang, Yunfeng organization: State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University – sequence: 3 givenname: Yiqin surname: Xu fullname: Xu, Yiqin organization: College of Urban and Environmental Sciences, Peking University – sequence: 4 givenname: Jie surname: Zhang fullname: Zhang, Jie organization: College of Urban and Environmental Sciences, Peking University – sequence: 5 givenname: Yahai orcidid: 0000-0002-1702-9868 surname: Lu fullname: Lu, Yahai email: luyh@pku.edu.cn organization: College of Urban and Environmental Sciences, Peking University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/31611655$$D View this record in MEDLINE/PubMed
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Snippet	Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a...
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SubjectTerms	38/23 631/326/2565/855 704/158/852 Agricultural land Agriculture Archaea - genetics Archaea - isolation & purification Assembly Bacteria - genetics Bacteria - isolation & purification Biomedical and Life Sciences China Coexistence Corn Dispersal Dispersion Ecological monitoring Ecology Ecosystem Evolutionary Biology Fungi - genetics Fungi - isolation & purification High-Throughput Nucleotide Sequencing Life Sciences Microbial Ecology Microbial Genetics and Genomics Microbiology Microbiomes Microbiota Microorganisms Oryza Rice fields Soil Microbiology Soils Zea mays
Title	Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China
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