Functional Metagenomics to Mine Soil Microbiome for Novel Cadmium Resistance Genetic Determinants

Metal resistance genes are valuable resources for genetic engineering of bioremediation tools. In this study, novel genetic determinants involved in cadmium (Cd) resistance were identified using a small-insert metagenomic DNA library constructed from an arable soil microbiome. A total of 16 recombinant plasmids harboring 49 putative open reading frames (ORFs) were found to be associated with enhanced Cd tolerance. In addition to several ORFs for ion transport/chelation and stress response, most ORFs were assumed to be associated with non-direct metal resistance mechanisms such as energy metabolism, protein/amino acid metabolism, carbohydrate/fatty acid metabolism, and signal transduction. Furthermore, 13 ORFs from five clones selected at random were cloned and subject to Cd resistance assay. Eight of these ORFs were positive for Cd resistance when expressed in Escherichia coli, among which four ORFs significantly reduced Cd accumulation and one increased Cd enrichment of the host cells. Notably, C1-ORF1, potentially encoding a histidine kinase-like adenosine triphosphatase, was the most effective Cd resistance determinant and reduced host Cd accumulation by 33.9%. These findings highlight the vast capacity of soil microbiome as a source of gene pool for bioengineering. The novel genetic determinants for Cd resistance identified in this study merit further systematic explorations into their molecular mechanisms.