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Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene  copA . In this study, a local BLASTN method using a  copA  database built in this study was developed to recover full-length putative  copA  sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative  copA  sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected  copA  sequences detected in the tailings metagenome showed that topology of the  copA  phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of  copA  diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore  copA  (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses.

Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes