Ancient Roman saltworks drive the present-day microbial community profiles in a coastal aquifer

Historical salinization from ancient saltworks can leave a long-lasting imprint on coastal aquifers, but its impacts on subsurface microbial communities and ecosystem functioning remain poorly understood. This study examined how legacy salt inputs from Roman saltworks in the Tiber River delta (Fiumicino, Italy) continue to shape present-day groundwater chemistry, microbial community structure, and metabolic potential of the coastal aquifer. We analyzed groundwater samples from non-salinized and salinized units of the same aquifer using integrated hydrogeochemical characterization, flow cytometry, 16S rRNA gene amplicon sequencing, and functional metabolic assays. Salinized samples exhibited elevated chloride, bromide, sodium, and sulfate concentrations, with distinctive ionic ratios (Br/Sr, Cl/K, SO/Ca) indicating dissolution of salt deposits rather than contemporary seawater intrusion. Salinization reduced the microbial diversity and shifted communities from diverse freshwater-adapted families toward an abundant halotolerant assemblage dominated by Campylobacterota (families Sulfurimonadaceae and Sulfurovaceae). Functional annotation suggested broadly conserved potentials for carbon, nitrogen, and sulfur cycling. However, the Biolog assays revealed higher heterotrophic respiration and carbon substrate use but lower functional diversity in salinized samples, with particularly enhanced polymer degradation. Ordination analyses showed a clear separation of aquifer units along the salinization gradient, with coordinated chemical and microbial vectors indicating alternative ecosystem states sustained by millennia-old anthropogenic salt inputs. Our findings showed that ancient saltworks can drive persistent hydrogeochemical alteration, select specialized halotolerant microbiomes, and reconfigure carbon and nutrient processing while maintaining core biogeochemical functions, with critical implications for coastal groundwater management strategies.