Functional Molecular Ecological Networks

作者：Jizhong Zhou, Ye Deng, Feng Luo, Zhili He, Qichao Tu, Xiaoyang Zhi · 发表于：mBio · 年份：2010 · DOI：10.1128/mbio.00169-10 · 被引用次数：1061 · 研究领域：Bioinformatics and Genomic Networks、Complex Network Analysis Techniques、Gut microbiota and health

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 CO 2 (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, CO 2 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 CO 2 (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...