title: Predicting taxonomic and functional structure of microbial communities in acid mine drainage.
abstract: Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities.
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.|Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Jialiang
authors.initials: J
authors.lastname: Kuang
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Linan
authors.initials: L
authors.lastname: Huang
authors.affiliation: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Linxing
authors.initials: L
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Zhengshuang
authors.initials: Z
authors.lastname: Hua
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Pu
authors.initials: P
authors.lastname: Jia
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Shengjin
authors.initials: S
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Jintian
authors.initials: J
authors.lastname: Li
authors.affiliation: Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.|Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.|State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, People's Republic of China.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Shu
mesh_terms: D000143:Acids; D001419:Bacteria / Q000145:classification* / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D044822:Biodiversity; D002681:China; D016000:Cluster Analysis; D004463:Ecology; D000071251:Extreme Environments; D060587:Groundwater / Q000382:microbiology*; D006863:Hydrogen-Ion Concentration; D059013:Microbial Consortia; D008906:Mining; D009584:Nitrogen / Q000378:metabolism; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D062065:Wastewater / Q000737:chemistry / Q000382:microbiology
chemical_list: D000143:Acids; D009584:Nitrogen; D012336:RNA, Ribosomal, 16S; D062065:Wastewater