Mining a bioremediation genetic toolbox in the novel environmental bacteria Enterobacter cloacae strain amazonensis

The rise of environmental pollution is a threat to planetary and human health. Microbes encode a wide range of enzymes with sophisticated catalytic properties to mitigate toxic chemicals from nature. Bioprospecting environmental bacteria can be a powerful resource for improved enzymes to optimize bioremediation processes. Here, we present a promising genetic toolbox sequenced from a novel multi-resistant bacterial strain isolated from industrial wastewater and sewage-contaminated stream in the city of Manaus, Amazonas, Brazil. We report Enterobacter cloacae amazonensis as a highly heavy-metal resistant and antibiotic multi-resistant strain. Functional and comparative genomics of the E. cloacae strain amazonensis draft genome revealed the annotation of 104 genes encoding proteins involved in the metabolism of copper, cobalt, zinc, cadmium, chromium, mercury and arsenic, as well as a plethora of broad-spectrum resistant genes. As a proof of concept, we characterized a plasmid mobile element from the amazonensis strain, pEN_Amazonensis, in the model biotechnological workhorse E. coli, leading to the robust acquisition of mercury and antibiotic resistance. Here, we highlighted the potential of bioprospecting genetic novelty from environmental bacteria through comparative genomics, paving the way for a genetic toolbox for bioremediation processes.