Copper removal capability and genomic insight into the lifestyle of copper mine inhabiting Micrococcus yunnanensis GKSM13.

Heavy metal pollution in mining areas is a serious environmental concern. The exploration of mine-inhabiting microbes, especially bacteria may use as an effective alternative for the remediation of mining hazards. A highly copper-tolerant strain GKSM13 was isolated from the soil of the Singhbhum copper mining area and characterized for significant copper (Cu) removal potential and tolerance to other heavy metals. The punctate, yellow-colored, coccoid strain GKSM13 was able to tolerate 500 mg L Cu. Whole-genome sequencing identified strain GKSM13 as Micrococcus yunnanensis, which has a 2.44 Mb genome with 2176 protein-coding genes. The presence of putative Cu homeostasis genes and other heavy metal transporters/response regulators or transcription factors may responsible for multi-metal resistance. The maximum Cu removal of 89.2% was achieved at a pH of 7.5, a temperature of 35.5 °C, and an initial Cu ion concentration of 31.5 mg L. Alteration of the cell surface, deposition of Cu in the bacterial cell, and the involvement of hydroxyl, carboxyl amide, and amine groups in Cu removal were observed using microscopic and spectroscopic analysis. This study is the first to reveal a molecular-based approach for the multi-metal tolerance and copper homeostasis mechanism of M. yunnanensis GKSM13.