Functional Molecular Ecological Networks
Functional Molecular Ecological Networks
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DOI：
10.1128/mbio.00169-10
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发表时间：
2010-09-01
期刊：
影响因子：
6.4
通讯作者：
Zhi, Xiaoyang
中科院分区：
文献类型：
--
作者：
Zhou, Jizhong;Deng, Ye;Zhi, Xiaoyang
生物多样性及其对环境变化的反应是生态学和社会的中心问题。几乎所有微生物生物多样性研究的重点都是“物种”的丰富性和丰富性，而不是它们之间的相互作用。虽然网络方法在描述物种之间的生态相互作用方面是强大的，但定义微生物群落中的网络结构是一个巨大的挑战。此外，尽管高二氧化碳(ECO(2))对植物生长和初级生产力的刺激作用已经得到了很好的证实，但它对地下微生物群落的影响，特别是微生物之间的相互作用，却知之甚少。在此，基于随机矩阵理论(RMT)的概念框架，利用长期的草原FACE(自由空气，CO2增加)实验中土壤微生物群落的高通量功能基因芯片杂交数据，建立了识别功能分子生态网络的概念框架。我们的结果表明，RMT在识别微生物群落中的功能分子生态网络方面是强大的。ECO(2)和环境CO2(ACO(2))下的功能分子生态网络都具有无标度、小世界、模块化、层次化等复杂系统的一般特征。然而，ECO(2)和ACO(2)的功能分子生态网络的拓扑结构在整个群落、单个功能基因类别/组和功能基因/序列的水平上明显不同，这表明ECO(2)显著改变了不同微生物功能基因/种群之间的网络相互作用。这种网络结构的变化也与土壤地球化学变量密切相关。总之，阐明微生物群落中的网络相互作用及其对环境变化的响应对于微生物生态学、系统微生物学和全球变化的研究具有重要意义。重要微生物是地球生物圈的基础，在各种生态系统过程和功能中发挥着不可或缺的独特作用。在生态系统中，各种微生物相互作用，形成复杂的网络。由于缺乏适当的实验数据和适当的理论框架，很难阐明网络相互作用及其对环境变化的响应。本研究提供了一个基于高通量功能基因阵列杂交数据构建微生物群落中相互作用网络的概念框架。它还首次证明，大气中二氧化碳的增加极大地改变了土壤微生物群落中的网络相互作用，这可能对评估生态系统对气候变化的反应具有重要意义。开发的概念框架使微生物学家能够通过关注网络相互作用而解决以前无法触及的研究问题，而不仅仅是列出物种的数量和丰度。因此，这项研究可能代表着微生物生态学的变革性研究和范式转变。
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 (eCO(2)) 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 eCO(2) and ambient CO2 (aCO(2)) 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 eCO(2) and aCO(2), at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO(2) 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.