Functional Molecular Ecological Networks
Abstract
Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2more »
- Authors:
-
- Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Tsinghua Univ., Beijing (China). Dept. of Environmental Science and Engineering
- Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology; Glomics Inc., Norman, OK (United States)
- Clemson Univ., SC (United States). School of Computing
- Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Oklahoma, Norman, OK (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division
- OSTI Identifier:
- 1626091
- Grant/Contract Number:
- AC02-05CH11231; SC0004601
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mBio (Online)
- Additional Journal Information:
- Journal Name: mBio (Online); Journal Volume: 1; Journal Issue: 4; Journal ID: ISSN 2150-7511
- Publisher:
- American Society for Microbiology (ASM)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Microbiology
Citation Formats
Zhou, Jizhong, Deng, Ye, Luo, Feng, He, Zhili, Tu, Qichao, and Zhi, Xiaoyang. Functional Molecular Ecological Networks. United States: N. p., 2010.
Web. doi:10.1128/mbio.00169-10.
Zhou, Jizhong, Deng, Ye, Luo, Feng, He, Zhili, Tu, Qichao, & Zhi, Xiaoyang. Functional Molecular Ecological Networks. United States. https://doi.org/10.1128/mbio.00169-10
Zhou, Jizhong, Deng, Ye, Luo, Feng, He, Zhili, Tu, Qichao, and Zhi, Xiaoyang. Tue .
"Functional Molecular Ecological Networks". United States. https://doi.org/10.1128/mbio.00169-10. https://www.osti.gov/servlets/purl/1626091.
@article{osti_1626091,
title = {Functional Molecular Ecological Networks},
author = {Zhou, Jizhong and Deng, Ye and Luo, Feng and He, Zhili and Tu, Qichao and Zhi, Xiaoyang},
abstractNote = {Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change.},
doi = {10.1128/mbio.00169-10},
journal = {mBio (Online)},
number = 4,
volume = 1,
place = {United States},
year = {Tue Oct 05 00:00:00 EDT 2010},
month = {Tue Oct 05 00:00:00 EDT 2010}
}
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