Balancing Act: Groundwater microbiomes' resilience and vulnerability to hydroclimatic extremes

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 microbiome sequences. 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 they demonstrate remarkable resilience. Conversely, isolated aquifer microbiomes show resistance to short-term changes, governed by deterministic processes, but exhibit reduced stability under prolonged stress. Variability in seepage-associated microorganisms, DOM, and metabolic diversity further drive microbiome dynamics. While shifts in DOM influence the potential functions of the microbiome, its overall functional potential demonstrates high temporal stability and resilience over time, largely due to functional redundancy. These findings highlight the dual vulnerability of groundwater systems to acute and chronic pressures, emphasizing the critical need for sustainable management strategies to mitigate the impacts of hydroclimatic extremes.