title: GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage.
abstract: Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems.
authors.affiliation: School of Mineral Processing and Bioengineering, Central South University, Changsha, Hunan 410083, China.
authors.forename: Jianping
authors.initials: J
authors.lastname: Xie
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.forename: Xinxing
authors.initials: X
authors.lastname: Liu
authors.forename: Xueduan
authors.initials: X
authors.lastname: Liu
authors.forename: Joy D
authors.initials: JD
authors.lastname: Van Nostrand
authors.forename: Ye
authors.initials: Y
authors.lastname: Deng
authors.forename: Liyou
authors.initials: L
authors.lastname: Wu
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.forename: Guanzhou
authors.initials: G
authors.lastname: Qiu
mesh_terms: D001419:Bacteria / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism; D002681:China; D003300:Copper; D024881:Drug Resistance, Bacterial; D017753:Ecosystem; D005798:Genes, Bacterial; D014644:Genetic Variation; D019216:Metals, Heavy / Q000494:pharmacology; D008697:Methane / Q000378:metabolism; D008906:Mining; D009584:Nitrogen / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013447:Sulfites / Q000378:metabolism; D014871:Water Microbiology
chemical_list: D019216:Metals, Heavy; D013447:Sulfites; D002244:Carbon; D003300:Copper; D009584:Nitrogen; D008697:Methane