title: Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.
abstract: The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.
authors.affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Lin-xing
authors.initials: LX
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Min
authors.initials: M
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Li-nan
authors.initials: LN
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Zheng-shuang
authors.initials: ZS
authors.lastname: Hua
authors.affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Jia-liang
authors.initials: JL
authors.lastname: Kuang
authors.affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Sheng-jin
authors.initials: SJ
authors.lastname: Li
authors.affiliation: State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen University, Guangzhou, People's Republic of China.
authors.forename: Wen-sheng
authors.initials: WS
authors.lastname: Shu
mesh_terms: D042763:Acidithiobacillus; D000143:Acids / Q000378:metabolism; D001419:Bacteria / Q000235:genetics*; D044822:Biodiversity; D004783:Environmental Microbiology; D006863:Hydrogen-Ion Concentration; D056186:Metagenomics / Q000379:methods*; D008906:Mining
chemical_list: D000143:Acids