Physiology, Heavy Metal Resistance, and Genome Analysis of Two Cupriavidus gilardii Strains Isolated from the Naica Mine (Mexico)

Here, we report the characterization of two <i>Cupriavidus</i> strains, NOV2-1 and OV2-1, isolated from an iron-oxide deposit in an underground tunnel of the Naica mine in Mexico. This unique biotope, characterized by its high temperature (≈50 °C) and the presence of heavy metals, is no longer available for sampling at this time. The genomes of NOV2-1 and OV2-1 comprised two replicons: a chromosome of 3.58 and 3.53 Mb, respectively, and a chromid of 2.1 Mb in both strains. No plasmids were found. The average nucleotide identity and the core genome phylogeny showed that NOV2-1 and OV2-1 belonged to the <i>Cupriavidus gilardii</i> species. NOV2-1 and OV2-1 grew up to 48 °C, with an optimal temperature of 42 °C. Discrete differences were observed between <i>C. gilardii</i> CCUG38401^T, NOV2-1, and OV2-1 in the biochemical tests. NOV2-1 and OV2-1 presented resistance to zinc, lead, copper, cadmium, nickel, and cobalt. Several complete and incomplete gene clusters related to the resistance to these heavy metals (<i>ars</i>, <i>czc</i>, <i>cop</i> 1, <i>sil</i>-<i>cop</i> 2, <i>cup</i>, <i>mmf</i>, and <i>mer</i>) were detected in the genome of these strains. Although further studies are needed to determine the origin and role of the detected gene clusters, it is suggested that the <i>czc</i> system may have been mobilized by horizontal gene transfer. This study expands the extreme biotopes where <i>Cupriavidus</i> strains can be retrieved.