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Abstract The tidal tributaries of the lower Chesapeake Bay experience seasonally recurring harmful algal blooms and the significance of submarine groundwater discharge (SGD) as a nutrient vector is largely unknown. Here, we determined seasonal SGD nutrient loads in two tributaries with contrasting hydrodynamic conditions, river‐fed (York River) vs. tidally dominated (Lafayette River). Radon surveys were performed in each river to quantify SGD at the embayment‐scale during spring and fall 2021. Total SGD was determined from a²²²Rn mass balance and Monte Carlo simulations. Submarine groundwater discharge rates differed by a factor of two during spring (Lafayette = 11 ± 17 cm d⁻¹; York = 6 ± 10 cm d⁻¹) and a factor of six during fall (Lafayette = 19 ± 27 cm d⁻¹; York = 3 ± 7 cm d⁻¹). Groundwater N concentrations and fluxes varied seasonally in the York (4–7 mmol N m⁻²d⁻¹). In the Lafayette River, seasonal N fluxes (22–37 mmol N m⁻²d⁻¹) were driven by seasonal water exchange rates, likely due to recurrent saltwater intrusion. Submarine groundwater discharge–derived nutrient fluxes were orders of magnitude greater than riverine inputs and runoff in each system. Additionally, sediment N removal by denitrification and anaerobic ammonium oxidation would only remove ~ 1–11% of dissolved inorganic nitrogen supplied through SGD. The continued recurrence of harmful algal blooms in the Bay's tidal tributaries may be indicative of an under‐accounting of submarine groundwater‐borne nutrient sources. This study highlights the importance of including SGD in water quality models used to advise restoration efforts in the Chesapeake Bay region and beyond. 

Abstract Dissolved organic matter (DOM) is the foundation of the microbial loop and plays an important role in estuarine water quality and ecosystem metabolism. Because estuaries are influenced by DOM with different sources and composition, changing hydrologic regimes, and diverse microbial community assemblages, the biological fate of DOM (i.e., microbial degradation) differs across spatiotemporal scales and between DOM pools. To better understand controls on DOM degradation, we characterized the biogeochemical and physical conditions of the York River Estuary (YRE), a sub-estuary of the Chesapeake Bay in southeast Virginia (USA), during October 2018 and February, April, and July 2019. We then evaluated how these conditions influenced the degradation of dissolved organic carbon (DOC) and nitrogen (DON) and chromophoric dissolved organic matter (CDOM) by conducting parallel dark incubations of surface water collected along the YRE. Compared to other sampling dates, DOC reactivity (ΔDOC (%)) was over two-fold higher in October when freshwater discharge was lower, temperatures were warmer, and autochthonous, aquatic sources of DOC dominated. ΔDOC (%) was near zero when allochthonous, terrestrial sources of DOC were more abundant and when temperatures were cooler during higher discharge periods in February when precipitation in the Chesapeake Bay region was anomalously high. DON was up to six times less reactive than DOC and was sometimes produced during the incubations whereas ΔCDOM (%) was highly variable between sampling periods. Like ΔDOC (%), spatiotemporal patterns in ΔDON (%) were controlled primarily by hydrology and DOM source and composition. Our results show that higher freshwater discharge associated with prolonged wet periods decreased estuarine flushing time and increased the delivery of allochthonous DOM derived from terrestrial sources into coastal waters, resulting in lower rates of DOM degradation especially under cool conditions. While these findings provide evidence for seasonal variation in DOM degradation, shifting environmental conditions (e.g., increasing temperatures and precipitation) due to climate change may also have interactive effects on the magnitude and composition of DOM exported to estuaries and its subsequent reactivity. 

Abstract Subterranean estuaries (STEs) form in the subsurface where fresh groundwater and seawater meet and mix. Subterranean estuaries support a variety of biogeochemical processes including those transforming nitrogen (N). Groundwater is often enriched with dissolved inorganic nitrogen (DIN), and transformations in the STE determine the fate of that DIN, which may be discharged to coastal waters. Nitrification oxidizes ammonium (NH₄⁺) to nitrate, making DIN available for N removal via denitrification. We measured nitrification at an STE, in Virginia, USA using in situ and ex situ methods including conservative mixing models informed by in situ geochemical profiles, an in situ experiment with¹⁵NH₄⁺tracer injection, and ex situ sediment slurry incubations with¹⁵NH₄⁺tracer addition. All methods indicated nitrification in the STE, but the ex situ sediment slurries revealed higher rates than both the in situ tracr experiment and mixing model estimations. Nitrification rates ranged 55.0–183.16 μmol N m⁻² d⁻¹based on mixing models, 94.2–225 μmol N m⁻² d⁻¹in the in situ tracer experiment, and 36.6–109 μmol N m⁻² d⁻¹slurry incubations. The in situ tracer experiment revealed higher rates and spatial variation not captured by the other methods. The geochemical complexity of the STE makes it difficult to replicate in situ conditions with incubations and calculations based on chemical profiles integrate over longer timescales, therefore, in situ approaches may best quantify transformation rates. Our data suggest that STE nitrification produces NO₃⁻, altering the DIN pool discharged to overlying water via submarine groundwater discharge. 

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 Coastal habitat‐forming species provide protection and essential habitat for fisheries but their ability to maintain these services are under threat from novel stressors including rising temperatures. Coastal habitat restoration is a powerful tool to help mitigate the loss of habitat‐forming species, however, many efforts focus on reintroducing a single, imperilled species instead of incorporating alternatives that are more conducive to current and future conditions. Seagrass restoration has seen mixed success in halting local meadow declines but could begin to specifically utilize generalist seagrasses with climate change‐tolerant and opportunistic life history traits including high reproduction rates and rapid growth.Here, we built on decades of successful eelgrass (Zostera marina) restoration in the Chesapeake Bay by experimentally testing seed‐based restoration potential of widgeongrass (Ruppia maritima)—a globally distributed seagrass that can withstand wide ranges of salinities and temperatures. Using field experiments, we evaluated which seeding methods yielded highest widgeongrass survival and growth, tested if seeding widgeongrass adjacent to eelgrass can increase restoration success, and quantified how either seagrass species changes restored bed structure, invertebrate communities, and nitrogen cycling.We found that widgeongrass can be restored via direct seeding in the fall, and that seeding both species maximized total viable restored area. Our pilot restoration area increased by 98% because we seeded widgeongrass in shallow, high temperature waters that are currently unsuitable for eelgrass survival and thus, would remain unseeded via only eelgrass restoration efforts. Restored widgeongrass had higher faunal diversity and double animal abundance per plant biomass than restored eelgrass, whereas restored eelgrass produced three times greater plant biomass per unit area and higher nitrogen recycling in the sediment.Synthesis and applications.Overall, we provide evidence that supplementing opportunistic, generalist species into habitat restoration is a proactive approach to combat climate change impacts. Specifically, these species can increase trait diversity which, for our study, increased total habitat area restored—a key factor to promote seagrass beds' facilitation cascades, stability, and grass persistence through changing environments. Now, we call for tests to determine if the benefits of restoration with generalist species alone or in conjunction with historically dominant taxa are broadly transferrable to restoration in other marine and terrestrial habitats. 

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. 

Abstract Terrestrial groundwater travels through subterranean estuaries before reaching the sea. Groundwater‐derived nutrients drive coastal water quality, primary production, and eutrophication. We determined how dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP), and dissolved organic nitrogen (DON) are transformed within subterranean estuaries and estimated submarine groundwater discharge (SGD) nutrient loads compiling > 10,000 groundwater samples from 216 sites worldwide. Nutrients exhibited complex, nonconservative behavior in subterranean estuaries. Fresh groundwater DIN and DIP are usually produced, and DON is consumed during transport. Median total SGD (saline and fresh) fluxes globally were 5.4, 2.6, and 0.18 Tmol yr⁻¹for DIN, DON, and DIP, respectively. Despite large natural variability, total SGD fluxes likely exceed global riverine nutrient export. Fresh SGD is a small source of new nutrients, but saline SGD is an important source of mostly recycled nutrients. Nutrients exported via SGD via subterranean estuaries are critical to coastal biogeochemistry and a significant nutrient source to the oceans. 

Abstract Marine cable bacteria (Candidatus Electrothrix) and large colorless sulfur‐oxidizing bacteria (e.g., Beggiatoaceae) are widespread thiotrophs in coastal environments but may exert different influences on biogeochemical cycling. Yet, the factors governing their niche partitioning remain poorly understood. To map their distribution and evaluate their growth constraints in a natural setting, we examined surface sediments across seasons at two sites with contrasting levels of seasonal oxygen depletion in Chesapeake Bay using microscopy coupled with 16S rRNA gene amplicon sequencing and biogeochemical characterization. We found that cable bacteria, dominated by a single phylotype closely affiliated toCandidatus Electrothrixcommunis, flourished during winter and spring at a central channel site which experiences summer anoxia. Here, cable bacteria density was positively correlated with surface sediment chlorophyll, a proxy of phytodetritus sedimentation. Cable bacteria were also present with a lower areal density at an adjacent shoal site which supports bioturbating macrofauna. Beggiatoaceae were more abundant at this site, where their biomass was positively correlated with sediment respiration, but additionally potentially inhibited by sulfide accumulation which was evident during one summer. A springtime phytodetritus sedimentation event was associated with a proliferation of Beggiatoaceae and multipleCandidatus Electrothrixphylotypes, with cable bacteria reaching 1000 m length cm⁻². These observations indicate the potential impact of a spring bloom in driving a hot moment of cryptic sulfur cycling. Our results suggest complex interactions between benthic thiotroph populations, with bioturbation and seasonal oscillations in bottom water dissolved oxygen, sediment sulfide, and organic matter influx as important drivers of their distribution. 

Abstract Estuarine primary production (PP) is a critical rate process for understanding ecosystem function and response to environmental change. PP is fundamentally linked to estuarine eutrophication, and as such should respond to ongoing efforts to reduce nutrient inputs to estuaries globally. However, concurrent changes including warming, altered hydrology, reduced input of sediments, and emergence of harmful algal blooms (HABs) could interact with nutrient management to produce unexpected changes in PP. Despite its fundamental importance, estuarine PP is rarely measured. We reconstructed PP in the York River Estuary with a novel mass balance model based on dissolved inorganic nitrogen (DIN) for the period 1994–2018. Modeled PP compared well to previous estimates and demonstrated a long‐term increase and down‐estuary shift over the study period. This increase occurred despite reductions in discharge, flushing time, DIN loading, and DIN standing stock over the same period. Increased PP corresponded to increased water temperature, decreased turbidity and light attenuation, and increased photic depth and assimilation ratio, suggesting that phytoplankton in the York River Estuary have become more efficient at converting nutrients into biomass primarily due to a release from light limitation. The increase in PP also coincided with the increasing occurrence of late summer HABs in the lower York River Estuary, including the emergence of a second bloom‐forming dinoflagellate in 2007. Results demonstrate how changes concurrent with nutrient management could alter expected system responses and illustrate the utility of the mass balance approach for estimating critical rate processes like PP in the absence of observations. 

Abstract Microplastics are ubiquitous in estuarine, coastal, and deep sea sediments. The impacts of microplastics on sedimentary microbial ecosystems and biogeochemical carbon and nitrogen cycles, however, have not been well reported. To evaluate if microplastics influence the composition and function of sedimentary microbial communities, we conducted a microcosm experiment using salt marsh sediment amended with polyethylene (PE), polyvinyl chloride (PVC), polyurethane foam (PUF) or polylactic acid (PLA) microplastics. We report that the presence of microplastics alters sediment microbial community composition and nitrogen cycling processes. Compared to control sediments without microplastic, PUF- and PLA-amended sediments promote nitrification and denitrification, while PVC amendment inhibits both processes. These results indicate that nitrogen cycling processes in sediments can be significantly affected by different microplastics, which may serve as organic carbon substrates for microbial communities. Considering this evidence and increasing microplastic pollution, the impact of plastics on global ecosystems and biogeochemical cycling merits critical investigation.