Genome-based insights into metal co-resistance in Amazonian mercury-resistant bacteria: ecological lifestyle and biosafety implications for bioremediation.

UNLABELLED: Mercury (Hg) pollution from artisanal gold mining represents a serious environmental and public health problem, especially in the Amazon Basin. Although mercury-resistant bacteria provide significant detoxification potential, their deployment needs genomic screening to assess both ecological lifestyle and biosafety. In this study, we analyzed the genomes of two highly mercury-resistant strains, Pseudomonas paracarnis TP30 and Burkholderia contaminans TR100, isolated from Hg-contaminated sediments in the Colombian Amazon. Both genomes contain broad-spectrum mer operons flanked by mobile genetic elements but differ in structure: TP30 encodes phage-associated mobility genes within a chromosomal mer locus, while TR100 has multiple metal resistance genes (MRGs) and a plasmid-borne mer operon embedded in a transposon. Despite the widespread presence of MRGs, both genomes show remarkably low levels of antibiotic resistance genes (ARGs), which contrasts with typical ARG-MRG co-selection patterns. Lifestyle prediction and gene-content analysis show that TP30 is a soil-adapted, environmentally persistent strain. At the same time, TR100, despite exhibiting a mixed ecological signal typical of the Burkholderia cepacia complex, lacks key virulence factors and displays features consistent with a non-pathogenic lifestyle. Our genomic analyses indicate that TP30 and TR100 harbor desirable traits for mercury bioremediation, including broad-spectrum Hg resistance, low antibiotic resistance gene content, and the absence of major pathogenicity markers, making them promising candidates for further evaluation under controlled conditions.

IMPORTANCE: Mercury pollution from artisanal gold mining poses a significant threat to ecosystems and human health worldwide, particularly in vulnerable regions like the Amazon. Robust mercury-resistant bacteria offer a sustainable solution for detoxifying contaminated environments, but their potential application requires careful genomic assessment to minimize biosafety risks. This study integrates comparative genomics, resistance profiling, and lifestyle prediction to evaluate two highly mercury-resistant bacterial isolates from mining sediments. We show that these strains harbor broad-spectrum mercury resistance genes with low antibiotic resistance burdens and lack key virulence markers, supporting their suitability as environmentally adapted candidates. By coupling metal detoxification potential with genomic screening, our work highlights a framework for identifying promising, high-performance candidates for bioremediation, advancing microbiological solutions to address metal pollution in impacted ecosystems.