Microbial Community Structure and Predicted Functional Potential Across Environmental Gradients Influenced by Submarine Groundwater Discharge in Tropical Coral Reef Intertidal Sediments

Submarine groundwater discharge (SGD) delivers land-derived nutrients to coastal waters, but its effects on benthic microbial communities in tropical coral reef intertidal sediments are largely unknown. We studied the Duzaiping Marine Protected Area on Liuqiu Island, Taiwan, where groundwater seeps through a coral reef limestone platform. Surface sediments and bottom water from 19 sites were analyzed for dissolved nutrients, 16S rRNA amplicon diversity, and predicted functional potential (FAPROTAX). Groundwater discharge points had salinities of 2–3 and NO2− + NO3−, PO43−, and SiO2 concentrations up to 623.94, 7.07, and 245.83 µM, respectively. Principal component analysis resolved three geochemically distinct groups: Groundwater (GW), Mixed, and Seawater (SW). Microbial communities were significantly differentiated between GW and SW groups. Nitrospiraceae, Nitrosomonadaceae, Burkholderiaceae, and Pseudomonadaceae were enriched at the discharge points, consistent with nitrification and putative denitrification. Halieaceae and Xenococcaceae were most abundant in the marine-dominated zone. Predicted aerobic ammonia and nitrite oxidation were enriched in GW sediments, whereas predicted fermentation was enriched in SW sediments. Woeseiaceae abundance correlated positively with phosphate and predicted nitrification. SGD thus alters nutrient stoichiometry and sorts benthic microbial communities, with predicted functional profiles shifting from nitrogen transformation near discharge points to heterotrophic decomposition in marine-dominated sediments.