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 inter...

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Autores principales:	Jizhong Zhou, Ye Deng, Feng Luo, Zhili He, Qichao Tu, Xiaoyang Zhi
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2010
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7cbfa0deebaf499ead20df00cc3de5be
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spelling	oai:doaj.org-article:7cbfa0deebaf499ead20df00cc3de5be2021-11-15T15:38:15ZFunctional Molecular Ecological Networks10.1128/mBio.00169-102150-7511https://doaj.org/article/7cbfa0deebaf499ead20df00cc3de5be2010-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00169-10https://doaj.org/toc/2150-7511ABSTRACT 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. IMPORTANCE Microorganisms are the foundation of the Earth's biosphere and play integral and unique roles in various ecosystem processes and functions. In an ecosystem, various microorganisms interact with each other to form complicated networks. Elucidating network interactions and their responses to environmental changes is difficult due to the lack of appropriate experimental data and an appropriate theoretical framework. This study provides a conceptual framework to construct interaction networks in microbial communities based on high-throughput functional gene array hybridization data. It also first documents that elevated carbon dioxide in the atmosphere dramatically alters the network interactions in soil microbial communities, which could have important implications in assessing the responses of ecosystems to climate change. The conceptual framework developed allows microbiologists to address research questions unapproachable previously by focusing on network interactions beyond the listing of, e.g., the number and abundance of species. Thus, this study could represent transformative research and a paradigm shift in microbial ecology.Jizhong ZhouYe DengFeng LuoZhili HeQichao TuXiaoyang ZhiAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 1, Iss 4 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Jizhong Zhou Ye Deng Feng Luo Zhili He Qichao Tu Xiaoyang Zhi Functional Molecular Ecological Networks
description	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 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. IMPORTANCE Microorganisms are the foundation of the Earth's biosphere and play integral and unique roles in various ecosystem processes and functions. In an ecosystem, various microorganisms interact with each other to form complicated networks. Elucidating network interactions and their responses to environmental changes is difficult due to the lack of appropriate experimental data and an appropriate theoretical framework. This study provides a conceptual framework to construct interaction networks in microbial communities based on high-throughput functional gene array hybridization data. It also first documents that elevated carbon dioxide in the atmosphere dramatically alters the network interactions in soil microbial communities, which could have important implications in assessing the responses of ecosystems to climate change. The conceptual framework developed allows microbiologists to address research questions unapproachable previously by focusing on network interactions beyond the listing of, e.g., the number and abundance of species. Thus, this study could represent transformative research and a paradigm shift in microbial ecology.
format	article
author	Jizhong Zhou Ye Deng Feng Luo Zhili He Qichao Tu Xiaoyang Zhi
author_facet	Jizhong Zhou Ye Deng Feng Luo Zhili He Qichao Tu Xiaoyang Zhi
author_sort	Jizhong Zhou
title	Functional Molecular Ecological Networks
title_short	Functional Molecular Ecological Networks
title_full	Functional Molecular Ecological Networks
title_fullStr	Functional Molecular Ecological Networks
title_full_unstemmed	Functional Molecular Ecological Networks
title_sort	functional molecular ecological networks
publisher	American Society for Microbiology
publishDate	2010
url	https://doaj.org/article/7cbfa0deebaf499ead20df00cc3de5be
work_keys_str_mv	AT jizhongzhou functionalmolecularecologicalnetworks AT yedeng functionalmolecularecologicalnetworks AT fengluo functionalmolecularecologicalnetworks AT zhilihe functionalmolecularecologicalnetworks AT qichaotu functionalmolecularecologicalnetworks AT xiaoyangzhi functionalmolecularecologicalnetworks
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Functional Molecular Ecological Networks

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