Beyond the Dominant Geological Metal(loid): Co-Occurring Metal(loid)s Are Linked to Microbial Assembly and Resistomes in Mercury-Enriched Soils

Abstract High geological background regions are naturally enriched with multiple, typically low bioavailability metal(loid)s. Superimposed mining, smelting, and agricultural inputs create complex yet poorly studied environments. Using metagenomics, we profiled bacterial community assembly and life history strategies in a mercury (Hg)-enriched geological area with elevated co-occurring metal(loid)s. Bacterial composition, structure, and community assembly, as well as the abundances of metal resistance genes (MRGs) and antibiotic resistance genes (ARGs), were independent of Hg concentration. Instead, cadmium (Cd), ammonium nitrogen (NH4+-N), soil organic matter (SOM), and available potassium (AK) were significantly associated with ARG/MRG variation (p < 0.05). Moreover, elevated Cd intensified heterogeneous selection (HeS) while suppressing homogeneous selection (HoS) (p < 0.05). This shift also led communities enriched in “nutrient recycling” traits adopted a resource acquisition strategy together with competitor traits (MRGs and ARGs), and nitrogen metabolism. These traits likely reflect a strategy prioritizing resource use efficiency and nutrient competitiveness. Moreover, elevated Cd exacerbated the codissemination risks of resistance genes and pathogenicity (p < 0.001). Thus, Cd was more strongly associated than Hg with bacterial community and resistome variation in Hg-enriched geological soils, underscoring the need to consider co-occurring metal(loid)s when assessing ecological responses in high-background regions.