title: Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap.
abstract: BACKGROUND
  Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap.
  
  
  RESULTS
  Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system.
  
  
  CONCLUSIONS
  Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap.
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China. zixuange2010@126.com.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China. zixuange2010@126.com.
authors.forename: Xian
authors.initials: X
authors.lastname: Zhang
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China. 135611006@csu.edu.cn.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China. 135611006@csu.edu.cn.
authors.forename: Jiaojiao
authors.initials: J
authors.lastname: Niu
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China. liangyili@hotmail.com.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China. liangyili@hotmail.com.
authors.forename: Yili
authors.initials: Y
authors.lastname: Liang
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China. xueduanliu@yahoo.com.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China. xueduanliu@yahoo.com.
authors.forename: Xueduan
authors.initials: X
authors.lastname: Liu
authors.affiliation: School of Minerals Processing and Bioengineering, Central South University, Changsha, China. yinhuaqun@gmail.com.|Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China. yinhuaqun@gmail.com.
authors.forename: Huaqun
authors.initials: H
authors.lastname: Yin
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D044822:Biodiversity; D057486:Carbon Cycle; D002681:China; D003300:Copper; D004783:Environmental Microbiology; D005296:Ferrous Compounds / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D017665:Hydroxyl Radical / Q000378:metabolism; D007218:Industrial Microbiology / Q000379:methods; D054892:Metagenome; D064307:Microbiota; D008906:Mining; D009584:Nitrogen / Q000378:metabolism; D012997:Solvents; D013455:Sulfur / Q000378:metabolism
chemical_list: D005296:Ferrous Compounds; D012997:Solvents; D017665:Hydroxyl Radical; D013455:Sulfur; D003300:Copper; D009584:Nitrogen