Microbial Assemblages and Metabolic Activity in Organic‐Rich Subterranean Estuaries: Impact of Climate and Land Use Changes

Abstract Microbial communities in subterranean estuaries mediate biogeochemical reactions of coastal groundwater discharging into the oceans; however, studies on their response to abrupt environmental changes caused by climate and land use alterations are still limited. In this study, we conducted a controlled laboratory study using combined geochemical and metagenomic approaches to investigate microbial structures and their metabolic pathways under a wide range of nitrate () inputs, saline solutions, and incubation times. These factors served as proxies for land use, salinization of the shallow aquifer, and climate changes. We found a highly reducing habitat and an amplification of genes related to denitrification, sulfate reduction, and methanogenesis processes. Core communities consisting of Clostridia, Bacilli, Alphaproteobacteria, Gammaproteobacteria, and Desulfobaccia were observed across all treatments. The metabolic prediction of plant‐derived organic matter (i.e., tannin and lignin) degradation was not affected by inputs or salinity because of it being implemented by core communities and the abundance of electron donors and acceptors. Quantification of denitrification genes shows that they are susceptible to inputs and seawater ions. Long‐term incubation allowed sufficient time for microbes to degrade less labile DOM, promoting the re‐release of buried solid phase organic matter into the active carbon cycle and increasing the relative abundance of biofilm or spore‐forming taxa while decreasing that of rare taxa. Our results illustrate the sensitivity of microbial assemblages to environmental changes and their capacity to altering the C and N cycles in coastal areas, further affecting coastal water quality and ecosystem‐scale biogeochemistry.