Groundwater microbiomes balance resilience and vulnerability to hydroclimatic extremes

Abstract Groundwater health is increasingly threatened by climate change, which alters precipitation patterns, leading to groundwater recharge shifts. These shifts impact subsurface microbial communities, crucial for maintaining ecosystem functions. In this decade-long study of carbonate aquifers, we analyzed 815 bacterial 16S rRNA gene datasets, 226 dissolved organic matter (DOM) profiles, 387 metabolomic datasets, and 174 seepage microbiomes. Our findings reveal distinct short- and long-term temporal patterns of groundwater microbiomes driven by environmental fluctuations. Microbiomes of hydrologically connected aquifers exhibit lower temporal stability due to stochastic processes and greater susceptibility to surface disturbances, yet demonstrate remarkable resilience. Conversely, more isolated aquifer microbiomes resist short-term changes, governed by deterministic processes, but exhibit reduced stability under prolonged stress. Variability in seepage-associated microorganisms, DOM, and metabolic diversity further drives microbiome dynamics. These findings highlight the dual vulnerability of groundwater systems to acute or chronic pressures and the need for sustainable management to mitigate hydroclimatic extremes.