Aquifer geochemistry shapes microbial diversity and carbon and nitrogen cycling potential

Despite the importance of groundwater and its ecosystem functions, including nitrogen cycling, subsurface microbial biodiversity and ecology remain poorly understood globally. We investigated how aquifer geochemistry shapes microbial diversity and metabolic potential across Aotearoa New Zealand using shotgun metagenomics of 39 groundwater samples from 11 regions. We recovered 494 high- and medium-quality metagenome-assembled genomes (MAGs), which clustered into four groups (A, B, C1 and C2), based on hydrochemistry, and differed significantly in taxonomy and metabolic pathways. Cluster A had the highest microbial diversity and was dominated by uncultured taxa, particularly Patescibacteria . Carbon fixation pathways, predominantly the Calvin-Benson-Bassham and reductive tricarboxylic acid cycles, varied among clusters and were associated with different redox metabolisms. Aerobic respiration pathways also differed, particularly the microaerophilic cbb ₃ cytochrome c oxidase. Differences were also observed in nitrogen, sulfur, carbohydrate and organic acid metabolism, with several MAGs strongly correlated with nitrate, sulfate and potassium. Our findings demonstrate that aquifer geochemistry is a major determinant of microbial community structure and metabolic potential across Aotearoa New Zealand groundwater ecosystems.