Abstract
BackgroundMetagenomics 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.ResultsTaxonomic 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.ConclusionOur study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0330-4) contains supplementary material, which is available to authorized users.
Highlights
Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment
Sequencing, de novo assembly, gene prediction and functional annotation Metagenomic DNA was subjected to Illumina MiSeq sequencing, and approximately 3.4 million short DNA sequences were used for bioinformatics analysis
A large proportion of sequences were assigned to COG category [S] (80,561 coding sequences (CDS); 16.19 %) and COG category [R] (General function prediction only) (39,507 CDSs; 7.94 %), indicating large pools of potential unknown functional genes in copper bioleaching operations
Summary
Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. 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. Copper mine tailings with low-grade was used for bioleaching heaps in the field of industrial applications, representing a type of acidic environments of anthropogenic origin [11]. Issues associated with life in the oligotrophic, extremely acidic environments have been discussed in a number of reviews and papers, including the occurrence and composition of microbial communities [13,14,15], their strategies to tolerate the metal and low pH [16, 17], as well as their metabolisms and functions [18, 19]
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