Microbial Networks in Subsurface Sediment Porewater: Key Drivers for Organic Matter Degradation and Groundwater Chemistry Evolution

Subsurface microbial communities are essential drivers in biogeochemical cycles, yet their sampling and characterization remain challenging. Specifically, microbial assemblages in sedimentary porewater have been largely overlooked in existing research. In this study, we collected sufficient aquifer sediments for porewater extraction and biogeochemical analyses from four drilling sites in an aquifer characterized by active microbial activity, organic-rich deposits, and elevated levels of geogenic ammonium. Distinct microbial communities were identified in bound porewater, free porewater, and groundwater, with lactate/acetate, nitrite, and Fe(II), respectively, emerging as the dominant intermediates. Nitrogen metabolism pathways evolved from fermentation in bound porewater to denitrification in free porewater, culminating in various ammonium-producing processes in groundwater. Network analysis highlighted three metabolic modules: bound porewater as an energy supply center delivering organic acids, free porewater as a chemolithotrophic hub consuming nitrate, and groundwater as a resource convergence center. In groundwater, iron reduction and ammonium production were mediated by nodes Geobacteraceae and Erysipelothrix, which exhibited the highest network stress (2082) and shortest average path length (1.32). These findings emphasize the critical role of porewater microbiomes in organic matter degradation and groundwater environment evolution, calling for further studies on this essential sediment–groundwater interface across diverse aquatic ecosystems.