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Abstract Sandy sediment beaches covering 70% of non‐ice‐covered coastlines are important ecosystems for nutrient cycling along the land‐ocean continuum. Subterranean estuaries (STEs), where groundwater and seawater meet, are hotspots for biogeochemical cycling within sandy beaches. The STE microbial community facilitates biogeochemical reactions, determining the fate of nutrients, including nitrogen (N), supplied by groundwater. Nitrification influences the fate of N, oxidising reduced dissolved inorganic nitrogen (DIN), making it available for N removal. We used metabarcoding of 16S rRNA genes and quantitative PCR (qPCR) of ammonia monooxygenase (amoA) genes to characterise spatial and temporal variation in STE microbial community structure and nitrifying organisms. We examined nitrifier diversity, distribution and abundance to determine how geochemical measurements influenced their distribution in STEs. Sediment microbial communities varied with depth (p‐value = 0.001) and followed geochemical gradients in dissolved oxygen (DO), salinity, pH, dissolved inorganic carbon and DIN. Genetic potential for nitrification in the STE was evidenced by qPCR quantification ofamoAgenes. Ammonia oxidiser abundance was best explained by DIN, DO and pH. Our results suggest that geochemical gradients are tightly linked to STE community composition and nitrifier abundance, which are important to determine the fate and transport of groundwater‐derived nutrients to coastal waters. 

Abstract Subterranean estuaries (STEs) form at the land‐sea boundary where groundwater and seawater mix. These biogeochemically reactive zones influence groundwater‐borne nutrient concentrations and speciation prior to export via submarine groundwater discharge (SGD). We examined a STE located along the York River Estuary (YRE) to determine if SGD delivers dissolved inorganic nitrogen (DIN) and phosphorus (DIP) to the overlying water. We assessed variations in STE geochemical profiles with depth across locations, times, and tidal stages, estimated N removal along the STE flow path, measured hydraulic gradients to estimate SGD, and calculated potential nutrient fluxes. Salinity, dissolved oxygen (DO), DIN, and DIP varied significantly with depth and season (p < 0.05), but not location or tidal stage. Ammonium dominated the DIN pool deep in the STE. Moving toward the sediment surface, ammonium concentrations decreased as nitrate and DO concentrations increased, suggesting nitrification. Potential sediment N removal rates mediated by denitrification were <8 mmoles N m⁻² d⁻¹. The total groundwater discharge rate was 38 ± 11 L m⁻² d⁻¹; discharge followed tidal and seasonal patterns. Net SGD nutrient fluxes were 0.065–3.2 and 0.019–0.093 mmoles m⁻² d⁻¹for DIN and DIP, respectively. However, microbial N removal in the STE may attenuate 0.58% to >100% of groundwater DIN. SGD fluxes were on the same order of magnitude as diffusive benthic fluxes but accounted for <10% of the nutrients delivered by fluvial advection in the YRE. Our results indicate the importance of STE biogeochemical transformations to SGD flux estimations and their role in coastal eutrophication and nutrient dynamics. 

The nitrogen (N) loss processes have not been well examined in subterranean estuaries (STEs) between land and sea. We utilized a 15N isotope tracer method, q-PCR, and high-throughput sequencing to reveal the activities, abundances, and community compositions of N loss communities in a STE in Gloucester Point, Virginia, US. The highest activities, abundances and diversity of denitrifiers and anammox bacteria were detected at 50–60 cm depth in the aerobic-anaerobic transition zone (AATZ) characterized by sharp redox gradients. nirS-denitrifiers and anammox bacteria were affiliated to 10 different clusters and three genera, respectively. Denitrification and anammox played equal roles with an estimated N loss of 13.15 mmol N m−3 day−1. A positive correlation between ammonia oxidizing prokaryote abundances and DO as well as NOx− suggested that nitrification produces NOx− which supports the hotspot of denitrification and anammox within the AATZ. Overall, these results highlight the roles of N loss communities in STEs 

Codenitrification is a reactive nitrogen (N) removal pathway producing hybrid dinitrogen (N2) by combining nitrite (NO2–) and a partner-N substrate. Abiotic codenitrification also produces hybrid N2 through nitrosation of organic N by NO2–, but it is poorly constrained in soil N cycles. We determined the importance of abiotic codenitrification in soils and examined factors controlling abiotic codenitrification using live soils, sterile soils, and sterile solutions. Abiotic codenitrification in sterile soils ranged from 0.12 ± 0.001 to 0.60 ± 0.08 nmoles 29N2-N g–1 day–1, which accounts for 2.3 to 8.2% of total N2 production measured in live soils. Increased abiotic N2 production was observed in soils with the addition of an organic N partner (glutamine). Consistent with previous work, higher rates were observed in lower-pH soils, but the highest rate was found in the soil with the highest carbon:nitrogen (C:N) ratio. We further investigated a range of organic N partners and the influence of concentration and pH on abiotic codenitrification in solution. Similar to sterile soil incubations, abiotic 29N2 production was negatively correlated with increasing pH in solution. Greater rates of abiotic 29N2 production were measured as the substrate concentration increased and pH decreased. Solution experiments also showed that addition of organic N partners increased abiotic codenitrification rates, which are positively correlated with the C:N ratios of organic N partners. This is the first study demonstrating the importance of N removal through abiotic codenitrification in acidic soils and the C:N ratio of organic N partners as a controlling factor in abiotic codenitrification.