Multi-omics integration reveals how coordinated microbial mechanisms maintain biogeochemical stability in water-limited soils

Microbial communities maintain biogeochemical function despite environmental stress, yet whether functional redundancy, metabolic complementarity, and temporal partitioning operate in coordination across environmental transitions remains unclear. We integrated genome-resolved metatranscriptomics with metabolomics collected from Saguaro National Park, Arizona in 2021, to link taxon-specific gene expression to metabolite shifts during monsoon-driven transitions. Multi-omics analyses supported three coordinated stability mechanisms. Overlapping carbon and nitrogen pathways indicated functional redundancy, while nitrification and cross-taxon cooperation suggested metabolic complementarity. Distinct transcriptional signatures revealed temporal partitioning: dry-adapted taxa expressed stress tolerance, carbon storage turnover, and NADPH-generating pathways, whereas wet-adapted taxa activated glycolysis, tricarboxylic acid cycle, and carbohydrate-processing enzymes after rainfall. Metabolite profiles mirrored these shifts, with osmoprotectants accumulating during drought and amino acids and oxidative stress metabolites increasing after rewetting. Multi-omics integration explained transcriptional (69%) and metabolite variance (14%). These findings improve predictions of ecosystem responses to altered precipitation and inform the design of stress-resilient microbial consortia. Multi-omics integration linked taxon-specific gene expression to metabolite shifts, explaining 69% of transcriptional and 14% of metabolite variance. Coordinated redundancy, complementarity, and temporal partitioning underpin soil stability across monsoon transitions.