Comparative genomics of the metal tolerant soil bacterium Achromobacter strain H380

Abstract Background Metal-tolerant environmental bacteria provide a tractable system for examining how genomic diversity relates to persistence under chemical stress. Achromobacter sp. H380, isolated from mining-affected soil, displays tolerance to several metals. Its genomic relationship to other Achromobacter strains and the distribution of its associated gene repertoire remain to be resolved. Results We combined the phenotypic profile of H380 with whole-genome sequencing and comparative analysis of 35 Achromobacter genomes. The H380 assembly comprised a 5,675,223-bp circular chromosome with a GC content of 67.94% and 5,278 predicted genes. A phylogeny based on 2,082 single-copy orthologous groups placed H380 in a seven-genome subclade. Within this subclade, H380 and ANB-1 shared 99.26% average nucleotide identity, whereas H380 showed substantially lower identity to the remaining strains. The seven-genome subclade contained 3,275 core and 6,979 pan-genome gene families, and H380 carried 461 strain-specific gene families within the 35-genome comparison. Seven subclade-associated candidates encoded predicted transport, regulatory and metabolic functions. Searches of environmental protein sequences recovered more distant homologues rather than close matches suitable for tracking the H380 subclade. Conclusions H380 combines a metal-tolerant phenotype with a distinct accessory gene repertoire within a genomically heterogeneous Achromobacter subclade. The analysis defines its comparative genomic context and identifies candidate functions for investigating environmental persistence and metal tolerance.