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Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO(2)
Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO(2), is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society of Microbiology
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143843/ https://www.ncbi.nlm.nih.gov/pubmed/21791581 http://dx.doi.org/10.1128/mBio.00122-11 |
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author | Zhou, Jizhong Deng, Ye Luo, Feng He, Zhili Yang, Yunfeng |
author_facet | Zhou, Jizhong Deng, Ye Luo, Feng He, Zhili Yang, Yunfeng |
author_sort | Zhou, Jizhong |
collection | PubMed |
description | Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO(2), is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO(2) enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO(2) levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management. |
format | Online Article Text |
id | pubmed-3143843 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | American Society of Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-31438432011-07-28 Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO(2) Zhou, Jizhong Deng, Ye Luo, Feng He, Zhili Yang, Yunfeng mBio Research Article Understanding the interactions among different species and their responses to environmental changes, such as elevated atmospheric concentrations of CO(2), is a central goal in ecology but is poorly understood in microbial ecology. Here we describe a novel random matrix theory (RMT)-based conceptual framework to discern phylogenetic molecular ecological networks using metagenomic sequencing data of 16S rRNA genes from grassland soil microbial communities, which were sampled from a long-term free-air CO(2) enrichment experimental facility at the Cedar Creek Ecosystem Science Reserve in Minnesota. Our experimental results demonstrated that an RMT-based network approach is very useful in delineating phylogenetic molecular ecological networks of microbial communities based on high-throughput metagenomic sequencing data. The structure of the identified networks under ambient and elevated CO(2) levels was substantially different in terms of overall network topology, network composition, node overlap, module preservation, module-based higher-order organization, topological roles of individual nodes, and network hubs, suggesting that the network interactions among different phylogenetic groups/populations were markedly changed. Also, the changes in network structure were significantly correlated with soil carbon and nitrogen contents, indicating the potential importance of network interactions in ecosystem functioning. In addition, based on network topology, microbial populations potentially most important to community structure and ecosystem functioning can be discerned. The novel approach described in this study is important not only for research on biodiversity, microbial ecology, and systems microbiology but also for microbial community studies in human health, global change, and environmental management. American Society of Microbiology 2011-07-26 /pmc/articles/PMC3143843/ /pubmed/21791581 http://dx.doi.org/10.1128/mBio.00122-11 Text en Copyright © 2011 Zhou et al. http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License (http://creativecommons.org/licenses/by-nc-sa/3.0/) , which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Zhou, Jizhong Deng, Ye Luo, Feng He, Zhili Yang, Yunfeng Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO(2) |
title | Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO(2) |
title_full | Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO(2) |
title_fullStr | Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO(2) |
title_full_unstemmed | Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO(2) |
title_short | Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO(2) |
title_sort | phylogenetic molecular ecological network of soil microbial communities in response to elevated co(2) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143843/ https://www.ncbi.nlm.nih.gov/pubmed/21791581 http://dx.doi.org/10.1128/mBio.00122-11 |
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