Climate and land use change variables affect microbial assemblage and denitrification capability in organic-rich subterranean estuaries

Microbial communities in subterranean estuaries (STE) mediate biogeochemical reactions of coastal groundwater discharging to the oceans; however, studies on their response to abrupt environmental changes caused by climate and land use changes 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 different nitrate (NO3-) inputs, saline solution, and incubation times, which were used as proxies of land use, salinization of the shallow aquifer, and climate changes. We found a highly reducing habitat and amplification of genes related to denitrification, sulfate reduction, and methanogenesis processes. Core communities consisted of Clostridia, Bacilli, Alphaproteobacteria, Gammaproteobacteria, and Desulfobaccia were observed. The qualitative degradation of terrestrial, plant-derived organic matter (i.e., tannin and lignin) was predicted to not being affected by environmental changes because of it being implemented by core communities and the abundance of electron donor and acceptors. We observed that the assemblages of less prevalent taxa were influenced by seasonal sampling and incubation times, while denitrification was affected by groundwater and seawater inputs. Long-term incubation gave sufficient time for microbes to degrade less labile DOM, promoted the re-release of buried solid phase organic matter into the active carbon cycle, and increased the relative abundance of biofilm or spore-forming taxa while decreasing that of rare taxa such as methanogenic archaea. Our results illustrate the sensitivity of microbial assemblages to environmental change and their capacity to mediate C and N cycles in coastal areas, further affecting coastal water quality and ecosystem-scale biogeochemistry. Plain Language SummaryThis study investigated how microbial communities in subterranean estuaries (STE) respond to climate and land use changes. Understanding microbial responses is essential, considering they control the degradation of terrestrial solutes transported to the ocean. STE sediments collected from different seasons were incubated with different nitrate inputs, saline solution, and incubation times to represent changing groundwater quality, sea level rise, and groundwater residence time, respectively. The relative proportions of core microbial groups (Clostridia, Bacilli, Alphaproteobacteria, Gammaproteobacteria, and Desulfobaccia) were stable across all treatments; however, less adaptable groups did not survive long incubation times. Seawater addition negatively affected nitrate removal, while plant-derived organic matter degradation was not significantly influenced by changing environmental parameters. The study highlights how microbial communities and metabolic processes related tothe carbon and nitrogen cycles are susceptible to environmental change. Ultimately, these changes in the microbial community can affect water quality and ecosystem health in coastal areas. This study investigated how microbial communities in subterranean estuaries (STE) relative proportions of core microbial groups (Clostridia, Bacilli, Alphaproteobacteria, Gammaproteobacteria, and Desulfobaccia) were stable across all treatments; health in coastal areas. Key points- Core communities proportions were stable across different treatments and contributed to plant-derived DOM degradation alongside fermenters and methanogens. - Sediment denitrification capability was associated with groundwater and seawater input. - Long-term groundwater residence time negatively influenced rare biosphere.