Grazing and soil moisture transitions reorganize cross-library co-abundance modules of resistance and virulence genes in alpine wetland soils.

Antibiotic resistance genes (ARGs), heavy-metal resistance genes (HMRGs) and virulence factor genes (VFGs) can coexist in soils, yet their joint responses to hydrological and grazing pressures remain unclear. We combined shotgun metagenomics, a unified co-abundance network, fixed-module environmental-stratum deletion, threshold modelling, and contig, metagenome-assembled genome (MAG) and mobile genetic element (MGE) annotations across 32 alpine wetland plots spanning continuous soil water content and two grazing intensities. The unified network identified 14 representative cross-library hubs and four candidate modules whose coordinated states explained peripheral coactivation better than individual hubs, with M01-M03 showing more consistent support across sensitivity analyses than M04. All modules retained all three gene libraries after grazing- or moisture-stratum deletion, but connectivity, occupancy and cross-edge activity changed in module-specific ways. Within this dataset, a candidate soil-water-content transition near 89.4% separated contrasting responses and revealed partial decoupling between sample-level activation and cross-sample topology. Carrier support was heterogeneous, with M03 showing the strongest partial MAG- and MGE-associated support, whereas mobility-related responses varied among modules and environments. Overall, grazing and moisture reorganized rather than uniformly intensified these gene assemblages. Co-abundance and carrier association indicate genomic organization and mobility-related potential, not realized pollution risk or horizontal transfer.