Multi-omics reveals the systematical influence of composite heavy metal(loid)s on soil microbial function: Elemental...

As the core of soil material cycling, soil microecosystems contaminated by combined heavy metal(loid)s have attracted widespread concern. Previous studies mostly focused on community-level ecological functions, neglecting genomic-level investigations and comprehensive microbial adaptation mechanisms. Here, we integrated multi-omics (metagenomics, genome assemblies, comparative genomics) with field and lab studies to explore responses from community to genomic scales. We found that metal(loid)s altered the assembly of microbial functional genes and weakened functional networks linking carbon, nitrogen, phosphorus, and sulfur cycling. They reduced the potential of carbohydrate metabolism, carbon fixation, and sulfur metabolism involved in protein synthesis and disrupted normal organic matter decomposition (via certain CAZymes). Conversely, they increased the potential of methanogenesis, denitrification, and organic phosphorus mineralization, as well as stimulating dissimilatory sulfate reduction and sulfur disproportionation. Microbes employed multi-level strategies to combat persistent heavy metal(loid)s stress, including reducing metal ion uptake, facilitating intracellular detoxification, and activating efflux pathways. They underwent adaptive evolution through mechanisms such as enhancing the synthesis and transportation of siderophores, strengthening DNA damage repair, and promoting genome streamlining. Notably, our analysis revealed that horizontal gene transfer, mediated by mobile genetic elements, drives the acquisition of resistance genes. This study provides systematic genomic evidence for such adaptive mechanisms in functional microbes, greatly advancing our understanding of their bioremediation potential.