Salt marshes remove nitrogen (N) from tidal water via denitrification (DNF) but simultaneously retain N in sediments via dissimilatory nitrate reduction to ammonium (DNRA). The rate of N removal may be governed by NO3 - supply through nitrification and tidal exchange and the relative partitioning of NO3 - to DNF or DNRA. Although both DNF and nitrification are inhibited by sulfide (H2S), DNRA may be favored by high H2S and dissolved organic carbon to nitrate (DOC:NO3 -) ratios, conditions often found in pore water of low-elevation interior marshes. We compared seasonal rates of DNF and DNRA in control and fertilized plots across three locations with varying geochemical characteristics. Fertilization stimulated DNF regardless of location, whereas DNRA responses to fertilization were variable. DNRA rates ranged 0%-90% and averaged 21.6% of total nitrate reduction but varied by season, location, and N enrichment status. Structural equation modeling suggested that DNF rates were directly influenced by fertilization, DOC:NO3 - ratio, and temperature, but DNRA rates were promoted primarily by temperature and sulfide. This indicates that high sulfide concentrations may promote DNRA as an important pathway for NO3 - reduction. This study highlights how nitrogen removal (via DNF) and nitrogen retention (via DNRA) are regulated by distinct biogeochemical factors. This indicates that salt marshes do not universally act as nitrogen sinks; their function may be location-specific and influenced by environmental conditions such as temperature, sulfide concentrations, and DOC:NO3 - ratios.

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 (

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 with 15NH4+ tracer injection, and ex situ sediment slurry incubations with 15NH4+ 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−1 based on mixing models, 94.2–225 μmol N m−2 d−1 in the in situ tracer experiment, and 36.6–109 μmol N m−2 d−1 slurry 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 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−1 for 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.

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 −1 for 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.

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 of amoA genes. 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.

Harmful algal blooms (HABs) cause damage to fisheries, aquaculture, and human health around the globe. However, the impact of HABs on water column microbiomes and biogeochemistry is poorly understood. This study examined the impacts of consecutive blooms of the ichthyotoxic dinoflagellates Margalefidinium polykrikoides and Alexandrium monilatum on the water microbiome in the York River Estuary, Chesapeake Bay, USA. The samples dominated by single dinoflagellate species and by a mix of the two dinoflagellates had different microbiome compositions than the ones with low levels of both species. The M. polykrikoides bloom was co-dominated by Winogradskyella and had increased concentrations of dissolved organic carbon. The A. monilatum bloom had little impact on the prokaryotic portion of the whole community but was associated with a specific group of prokaryotes in the particle-attached (>3 µm) fraction including Candidatus Nitrosopumilus, Candidatus Actinomarina, SAR11 Clade Ia, Candidatus Bealeia, and Rhodobacteraceae HIMB11. Thus, blooms of these two algal species impacted the estuarine microbiome in different ways, likely leading to shifts in estuarine carbon and nutrient cycling, with M. polykrikoides potentially having a greater impact on carbon cycling in the estuarine ecosystem than A. monilatum.

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.

Denitrification, anaerobic ammonium oxidation and dissimilatory nitrate reduction to ammonium (DNRA) are important microbial processes determining the fate of nitrogen (N) in estuaries. This study examined these processes in sediments of the York River Estuary, a tributary of Chesapeake Bay, and investigated environmental and microbial drivers of the rates of denitrification and DNRA. Nitrate reduction followed a consistent pattern throughout the year and across the estuary with nitrogen removal, primarily through denitrification, decreasing from the head of the estuary to the mouth and nitrogen retention, through DNRA, following the opposite pattern. At the mouth of the estuary, nitrogen retention was consistently higher than nitrogen removal. Denitrification rates showed strong linear relationships with concentrations of organic matter, nitrate and chlorophyll a, and the abundance of the nirS gene. DNRA rates were best correlated with the relative abundance of three bacterial families, Anaerolineaceae, Ectothiorhodospiraceae and Prolixibacteraceae, which carry the nrfA gene. The controls responsible for retention or removal of N from an estuary are complex, involving both geochemical and microbial factors. The N retained within estuaries may support primary production and seasonal algae blooms and result in estuarine eutrophication.

The Defense Coastal/Estuarine Research Program (DCERP) was a 10-year multi-investigator project funded by the Department of Defense to improve understanding of ecosystem processes and their interactions with natural and anthropogenic stressors at the Marine Corps Base Camp Lejeune (MCBCL) located in coastal North Carolina. The project was aimed at facilitating ecosystem-based management (EBM) at the MCBCL and other coastal military installations. Because of its scope, interdisciplinary character, and duration, DCERP embodied many of the opportunities and challenges associated with EBM, including the need for explicit goals, system models, long-term perspectives, systems complexity, change inevitability, consideration of humans as ecosystem components, and program adaptability and accountability. We describe key elements of this program, its contributions to coastal EBM, and its relevance as an exemplar of EBM.

The resilience of salt marshes to sea level rise depends on vertical accretion through belowground biomass production and sediment deposition to maintain elevation above sea level. Increased nitrogen (N) availability from anthropogenic sources may stimulate aboveground biomass production and sediment deposition and, thus, accretion; however, increased N may also negatively impact marsh accretion by decreasing belowground biomass and increasing net CO 2 emissions. A study was conducted in Spartina alterniflora ‐dominated salt marshes in North Carolina, USA, to determine how responses to fertilization vary across locations with different physical and chemical characteristics. Pore water residence time, inundation time, and proximity to tidal creeks drove spatial differences in pore water sulfide, ammonium, and dissolved carbon concentrations. Although annual respiration and gross primary production were greater at the creek edge than interior marsh sites, net ecosystem CO 2 exchange (NEE) was nearly balanced at all the sites. Fertilization decreased belowground biomass in the interior sites but not on the creek edge. Aboveground biomass, respiration, gross primary production, and net CO 2 emissions increased in response to fertilization, but responses were diminished in interior marsh locations with high pore water sulfide. Hourly NEE measured by chambers were similar to hourly NEE observed by a nearby eddy covariance tower, but correcting for inundation depth relative to plant height was critical for accurate extrapolation to annual fluxes. The impact of fertilization on biomass and NEE, and thus marsh resilience, varied across marsh locations depending upon location‐specific pore water sulfide concentrations.

Salt marshes have among the highest carbon (C) burial rates of any ecosystem and often rely on C accumulation to gain elevation and persist in locations with accelerating sea level rise. Net ecosystem carbon balance (NECB), the accumulation or loss of C resulting from vertical CO 2 and CH 4 gas fluxes, lateral C fluxes, and sediment C inputs, varies across salt marshes; thus, extrapolation of NECB to an entire marsh is challenging. Anthropogenic nitrogen (N) inputs to salt marshes impact NECB by influencing each component of NECB, but differences in the impacts of fertilization between edge and interior marsh must be considered when scaling up. NECB was estimated for the 0.5 km 2 Spartina alterniflora marsh area of Freeman Creek, NC, under control and fertilized conditions at both interior and edge berm sites. Annual CO 2 fluxes were nearly balanced at control sites, but fertilization significantly increased net CO 2 emissions at edge sites. Lateral C export, modeled using respiration rates, represented a significant C loss that increased with fertilization in both edge and interior marsh. Sediment C input was a significant C source in the interior, nearly doubling with fertilization, but represented a small source on the edge. When extrapolating C exchanges to the entire marsh, including edge which comprised 17% of the marsh area, the marsh displayed net loss of C despite a net C gain in the interior. Fertilization increased net C loss fivefold. Extrapolation of NECB to whole marshes requires inclusion of C fluxes for both edge and interior marsh.

Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.

In coastal ecosystems, suspension-feeding bivalves can remove nitrogen though uptake and assimilation or enhanced denitrification. Bivalves may also retain nitrogen through increased mineralization and dissimilatory nitrate reduction to ammonium (DNRA). This study investigated the effects of oyster reefs and clam aquaculture on denitrification, DNRA, and nutrient fluxes (NO x , NH 4 + , O 2 ). Core incubations were conducted seasonally on sediments adjacent to restored oyster reefs ( Crassostrea virginica ), clam aquaculture beds ( Mercenaria mercenaria ) which contained live clams, and bare sediments from Smith Island Bay, Virginia, USA. Denitrification was significantly higher at oyster reef sediments and clam aquaculture site than bare sediment in the summer; however, DNRA was not enhanced. The clam aquaculture site had the highest ammonium production due to clam excretion. While oyster reef and bare sediments exhibited seasonal differences in rate processes, there was no effect of season on denitrification, or dissimilatory nitrate reduction to ammonium (DNRA) or ammonium flux at the clam aquaculture site. This suggests that farm management practices or bivalve metabolism and excretion may override seasonal differences. When water column nitrate concentration was elevated, denitrification increased in clam aquaculture site and oyster reef sediments but not in bare sediment; DNRA was only stimulated at the clam aquaculture site. This, along with a significant and positive relationship between denitrification and sediment organic matter, suggests that labile carbon limited nitrate reduction at the bare sediment site. Bivalve systems can serve as either net sinks or sources of nitrogen to coastal ecosystems, depending mainly on the type of bivalve, location, and management practices.

As bivalve aquaculture expands globally, an understanding of how it alters nitrogen is important to minimize impacts. This study investigated nitrogen cycling associated with clam aquaculture in the Sacca di Goro, Italy (Ruditapes philipinarum) and the Eastern Shore, USA (Mercenaria mercenaria). Ammonium and dissolved oxygen fluxes were positively correlated with clam biomass; R. philippinarum consumed ~ 6 times more oxygen and excreted ~ 5 times more NH4+ than M. mercenaria. There was no direct effect of clams on denitrification or dissimilatory nitrate reduction to ammonium (DNRA); rather, nitrate availability controlled the competition between these microbial pathways. Highest denitrification rates were measured at sites where both water column nitrate and nitrification were elevated due to high densities of a burrowing amphipod (Corophium sp.). DNRA exceeded denitrification where water column nitrate was low and nitrification was suppressed in highly reduced sediment, potentially due to low hydrologic flow and high clam densities.

A comprehensive carbon budget was constructed to quantify carbon flows through the freshwater-marine continuum of a temperate, microtidal estuary. We performed coordinated measurements of dissolved inorganic carbon and total organic carbon fluxes to resolve spatial variability between and along the channel and shoals and diel variability across the entire estuary for 2 yr. Net ecosystem metabolism (NEM) was the most significant control on carbon flow within estuary regions. However, metabolic rates were spatially coupled such that counteracting fluxes across the channel-shoal gradient or along the river-ocean gradient resulted in system-wide NEM that was closely in balance (-3.0 +/- 3.3 to 1.1 +/- 4.4 molC m(-2) yr(-1)). Similarly, large diel and seasonal variability in air-water CO2 fluxes were observed during 72 spatial surveys, but these short-term variations generally cancelled out when aggregated to annual budget terms. Although atmospheric exchanges were small (-0.2 +/- 0.1 to 2.0 +/- 0.4 molC m(-2) yr(-1)), they were subject to large errors (+/- 4 molC m(-2) yr(-1)) if diel variability was neglected. Internal mechanisms that maintained balanced carbon flows were strongly impacted by river discharge and were only apparent by separately quantifying channel and shoal fluxes. Notably, metabolic responses of the shoal to river forcing outweighed the responses of the channel, and the net impact was contrary to prior relationships derived from synthesis of lower-resolution carbon budgets. Our budget demonstrates that resolution of carbon fluxes at appropriate scales, including channel-shoal and diel variability, is critical to characterizing ecosystem function and the fate of carbon within the river-ocean continuum.

Riverine loading of nutrients and organic matter act in concert to modulate CO2 fluxes in estuaries, yet quantitative relationships between these factors remain poorly defined. This study explored watershed‐scale mechanisms responsible for the relatively low CO2 fluxes observed in two microtidal, lagoonal estuaries. Air‐water CO2 fluxes were quantified with 74 high‐resolution spatial surveys in the neighboring New River Estuary (NewRE) and Neuse River Estuary (NeuseRE), North Carolina, which experience a common climatology but differ in marine versus riverine influence. Annually, both estuaries were relatively small sources of CO2 to the atmosphere, 12.5 and 16.3 mmol C m−2 d−1 in the NeuseRE and NewRE, respectively. Large‐scale pCO2 variations were driven by changes in freshwater age, which modulates nutrient and organic carbon supply and phytoplankton flushing. Greatest pCO2 undersaturation was observed at intermediate freshwater ages, between 2 and 3 weeks. Biological controls on CO2 fluxes were obscured by variable inputs of river‐borne CO2, which drove CO2 degassing in the river‐dominated NeuseRE. Internally produced CO2 exceeded river‐borne CO2 in the marine‐dominated NewRE, suggesting that net ecosystem heterotrophy, rather than riverine inputs, drove CO2 fluxes in this system. Variations in riverine alkalinity and inorganic carbon loading caused zones of minimum buffering capacity to occur at different locations in each estuary, enhancing the sensitivity of estuarine inorganic C chemistry to acidification. Although annual CO2 fluxes were similar between systems, watershed‐specific hydrologic factors led to disparate controls on internal carbonate chemistry, which can influence ecosystem biogeochemical cycling, trophic state, and response to future perturbations.

As bivalve aquaculture expands worldwide, an understanding of its role in nutrient cycling is necessary to ensure ecological sustainability and determine the potential of using bivalves for nutrient mitigation. Whereas several studies, primarily of epifaunal bivalves, have assessed denitrification, few have considered nutrient regeneration processes such as dissimilatory nitrate reduction to ammonium (DNRA), which competes with denitrification for nitrate and results in nitrogen retention rather than loss. This study compares sediment nitrogen cycling including mineralization, DNRA, and denitrification within U.S. clam aquaculture sediments to nearby uncultivated sediments, seasonally. Clam aquaculture significantly increased sediment ammonium and phosphate effluxes relative to uncultivated sediments. Both DNRA and denitrification were significantly enhanced at clam beds compared to uncultivated sediments in July and November, while in May only DNRA was increased. The ratio of DNRA to denitrification was significantly higher at clam beds compared to uncultivated sediments, demonstrating that DNRA may be favored due to a ready supply of labile organic carbon relative to nitrate and perhaps sulfidic conditions. Functional gene abundances, nrfA (DNRA) and nirS (denitrification) followed similar patterns to nitrate respiration rates with highest nrfA abundances in the clam sediments and similar nirS abundances across seasons and sediment type. Ultimately clam sediments were found to be a significant source of nutrients to the water column whereas uncultivated sediments retained ammonium produced by microbial mineralization. Thus, clam cultivation may promote local eutrophication (i.e., increased primary production) by facilitating nutrient regeneration and retention of ammonium in the sediments.

Increased interest in using bivalve cultivation to mitigate eutrophication requires a comprehensive understanding of the net carbon (C) and nitrogen (N) budgets associated with cultivation on an ecosystem scale. This study quantified C and N processes related to clam (Mercenaria mercenaria) aquaculture in a shallow coastal environment (Cherrystone Inlet, VA) where the industry has rapidly increased. Clam physiological rates were compared with basin-wide ecosystem fluxes including primary production, benthic nutrient regeneration, and respiration. Although clam beds occupy only 3 % of the ecosystem's surface area, clams filtered 7–44 % of the system's volume daily, consumed an annual average of 103 % of the phytoplankton production, creating a large flux of particulate C and N to the sediments. Annually, N regenerated and C respired by clam and microbial metabolism in clam beds were ∼3- and ∼1.5-fold higher, respectively, than N and C removed through harvest. Due to the short water residence time, the low watershed load, and the close vicinity of clam beds to the mouth of Cherrystone Inlet, cultivated clams are likely subsidized by phytoplankton from the Chesapeake Bay. Consequently, much of the N released by mineralization associated with clam cultivation is "new" N as it would not be present in the system without bivalve facilitation. Macroalgae that are fueled by the enhanced N regeneration from clams represents a eutrophying process resulting from aquaculture. This synthesis demonstrates the importance of considering impacts of bivalve aquaculture in an ecosystem context especially relative to the potential of bivalves to remove nutrients and enhance C sinks.