Evolutionary Strategies for Heavy Metal Resistance: Genomic Plasticity in <i>Pseudomonas</i> Versus Stability in <i>Aeromonas</i> and <i>Bacillus</i>

Heavy metal resistance represents a critical microbial trait shaped by lineage-specific evolutionary pressures, yet its genomic foundations and diversification across major bacterial taxa remain poorly resolved. This study presented a comparative pangenomic analysis of <i>Aeromonas</i> (n = 32), <i>Bacillus</i> (n = 123), and <i>Pseudomonas</i> (n = 350)-three phylogenetically and ecologically distinct genera frequently enriched in metal-contaminated environments and exhibiting notable differences in resistance architectures. All three genera exhibited open pangenomes, with fitted expansion indices of 0.003 (<i>Aeromonas</i>), 0.03 (<i>Bacillus</i>), and 0.04 (<i>Pseudomonas</i>), each showing strong model fit (R² > 0.98). <i>Pseudomonas</i> harbored a significantly greater number of resistance genes, with copper and zinc resistance genes exceeding 25 per strain in some cases. Most heavy metal resistance genes across the three genera were subject to purifying selection (dN/dS < 1), and no significant expansion or contraction of these gene families was observed (<i>p</i> > 0.05). The presence of these genera and their lineage-specific resistance determinants may serve as bioindicators of heavy metal exposure, offering valuable references for assessing contamination levels through environmental metagenomics.