Microbial community dynamics across salinity gradients in coastal aquifers: Linking hydrogeochemical variability to prokaryotic diversity in a seawater-intruded aquifer of the Pearl River Delta, China.

Coastal groundwater salinization driven by seawater intrusion creates dynamic salt-freshwater interfaces with steep biogeochemical gradients. While hydrological changes during seawater intrusion are well characterized, the linkage between hydrogeochemical variability and microbial community structure remains poorly resolved. Here, an integrated approach coupling V4-region 16S rRNA amplicon sequencing (Illumina) with geochemical profiling was employed to decipher prokaryotic diversity dynamics and environmental determinants in a Quaternary aquifer undergoing salinization, Pearl River Delta, China. Proteobacteria dominated bacterial communities across salinity gradients, whereas archaeal assemblages shifted from Thaumarchaeota-dominated freshwater zones to Methanobacteriota-enriched brackish/saline groundwater. High-salinity zones harbored anaerobic functional taxa, including sulfate-reducing Desulfovibrio and methanogenic Methanococcus, confirming active sulfate reduction and methanogenesis in the aquifer-processes critical to carbon and sulfur cycling in coastal groundwater systems. Microbial α-diversity correlated positively with salinity (total dissolved solids, TDS >1 g/L), despite non-linear community shifts along the intrusion path. Vector-based redundancy analysis identified TDS and total nitrogen (TN) as primary drivers of microbial assemblage restructuring (p < 0.01). Our results established salinity as a master regulator of groundwater microbiome composition and function, with direct implications for predicting biogeochemical feedbacks (e.g., methane emissions, sulfide mobilization) in coastal aquifers under climate-driven seawater intrusion. This mechanistic understanding of microbe-environment interactions supports optimized management of contaminated coastal groundwater resources facing salinization threats.