Direct measurements of light attenuation by epiphytes on eelgrass \u3cem\u3eZostera marina\u3c/em\u3e

Declines in the seagrass Zostera marina L. in estuaries and lagoons have been attributed in part to reductions in irradiance reaching the seagrass blades. Epiphytes growing on Z. marina have the potential to attenuate a large fraction of the light that would otherwise reach the blades. This problem has previously been studied by measuring light penetration through homogenized epiphytic slurries or through glass slides fouled with epiphytes. However, the latter may not represent the natural succession or species composition found on live Z. marina leaves and the former does not preserve the structure of the epiphytic complex. Further, past studies have not measured attenuation across the full range of epiphytic densities found in the field. In this study, we measured light penetration across a wide range of epiphytic densities by holding scraped and unscraped Z. marina blades over a submerged light sensor. Results compared well with past studies at low epiphyte densities, with strong reductions in light penetration as density increased. However, at higher densities, penetration leveled off to a relatively constant value as the epiphytes floated out from the edges of the blade. Studies using slurries did not capture this phenomenon and thus predicted decreasing penetration down to 0%

Modeling the Effect of Hypoxia on Macrobenthos Production in the Lower Rappahannock River, Chesapeake Bay, USA

Hypoxia in Chesapeake Bay has substantially increased in recent decades, with detrimental effects on macrobenthic production; the production of these fauna link energy transfer from primary consumers to epibenthic and demersal predators. As such, the development of accurate predictive models that determine the impact of hypoxia on macrobenthic production is important. A continuous-time, biomass-based model was developed for the lower Rappahannock River, a Bay tributary prone to seasonal hypoxia. Phytoplankton, zooplankton, and macrobenthic state variables were modeled, with a focus on quantitatively constraining the effect of hypoxia on macrobenthic biomass. This was accomplished through regression with Z\u27: a sigmoidal function between macrobenthic biomass and dissolved oxygen concentration, derived using macrobenthic data collected from the Rappahannock River during the summers of 2007 and 2008, and applied to compute hypoxia-induced mortality as a rate process. The model was verified using independent monitoring data collected by the Chesapeake Bay Program. Simulations showed that macrobenthic biomass was strongly linked to dissolved oxygen concentrations, with fluctuations in biomass related to the duration and severity of hypoxia. Our model demonstrated that hypoxia negatively affected macrobenthic biomass, as longer durations of hypoxia and greater hypoxic severity resulted in an increasing loss in biomass. This exercise represents an important contribution to modeling anthropogenically impacted coastal ecosystems, by providing an empirically constrained relationship between hypoxia and macrobenthic biomass, and applying that empirical relationship in a mechanistic model to quantify the effect of the severity, duration, and frequency of hypoxia on benthic biomass dynamics

Impacts of Harmful Algal Blooms on Dissolved Organic Carbon in the Lower York River Estuary

Estuaries are important sites of carbon cycling; however, the impact of increasingly prevalent harmful algal blooms (HABs) on cycling in these systems remains unclear. To examine the impact of two bloom species, Alexandrium monilatum and Margalefidinium polykrikoides on the quantity and composition of the dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) pools and rates of benthic and pelagic microbial respiration in the lower York River Estuary, VA, a series field samplings and laboratory incubations were performed. The two HAB species greatly increased the size of the DOC and CDOM pools and altered the character of the CDOM pool, causing it to shift towards higher molecular weights and lower levels of aromaticity. DOC released by A. monilatum and M. polykrikoides both stimulated increased respiration by pelagic microbes, but displayed different levels of microbial lability in the DOC produced suggesting species level differences in how HABs affect DOC cycling. HAB produced organic matter did not stimulate increased levels of benthic microbial respiration as measured in sediment core incubations, suggesting that benthic microbial communities are not carbon limited. These findings show that HABs alter the quality and quantity of the DOC pool which in turn affects pelagic microbial respiration. This study also highlighted the need for species level analysis of HABs to be factored in to future estuarine carbon budgets in HAB affected systems

An updated model for estimating the TMDL-related benefits of oyster reef restoration Harris Creek, Maryland, USA

In 2014, a user-friendly, web-accessible model was developed that allowed restoration practitioners and resource managers to easily estimate the TMDLrelated benefits of oyster reef (Crassostrea virginica) restoration per unit area, run restoration scenarios in Harris Creek, MD to optimize restoration planning and implementation, and calculate the benefits of the chosen plan. The model was rooted in scientifically defensible data and was readily transferrable to systems throughout the Chesapeake Bay and Eastern Shore. The model operated in five vertically well-mixed boxes along the main axis of the creek. Exchanges among creeks were computed using a tidal prism approach and were compared to exchanges provided from a high resolution 3D hydrodynamic model. Watershed inputs for the model were obtained for the Harris Creek sub-watershed from the Phase V Chesapeake Bay Program Watershed Model. The base model simulated daily concentrations over an annual cycle of chlorophyll-a, dissolved inorganic nitrogen (N) and phosphorus (P), dissolved oxygen, total suspended solids, the biomass of benthic microalgae, and the water column and sediment pools of labile organic carbon (C) and associated N and P. Water quality data for model forcing and calibration were obtained from the Chesapeake Bay Program, the Choptank Riverkeeper, the University of Maryland Center for Environmental Science, and the Maryland Department of Natural Resources. An oyster sub-model was coupled to this base model to compute the volume of water filtered, removal of phytoplankton, suspended solids, and associated nutrients via filtration, recycling of nutrients and consumption of oxygen by oyster respiration, production of feces, N and P accumulation in oyster tissues and shell, oyster-enhanced denitrification, and N and P burial associated with restored reefs. The completed model was served online and operated through a web browser, enabling users to conduct scenario analysis by entering box-specific values for acres restored, restored oyster density, and restored oyster size, as well as the economic value of associated N and P removal. The updated model incorporates all aspects of the previous model but replaces oyster related data collected outside Harris Creek with site-specific data, and now includes restored oyster populations and water quality data through 2016. It also incorporates the impacts of two common, reef-associated filter feeding organisms: the hooked mussel Ischadium recurvum and the sea squirt Molgula manhattensis. Additional data collected in Harris Creek and incorporated into the model include: biomass of benthic microalgae, biogeochemical fluxes in relation to oyster biomass, and the biomass density and distribution of the dominant non-oyster reef filter feeders (I. recurvum, and M. manhattensis). The revised model incorporates an improved estimate of annual oyster growth, uses an improved method for estimating N and P sequestered in tissues and shells, and accounts for the prerestoration oyster population in Harris Creek. The model also incorporates data on the filtration capacity of I. recurvum and M. manhattensis in relation to C. virginica collected as part of a previous study (not in Harris Creek) by Kellogg and Newell (unpublished data)

Reconstructing primary production in a changing estuary: A mass balance modeling approach

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

Opportunities and Challenges for Including Oyster-Mediated Denitrification in Nitrogen Management Plans

Nitrogen pollution is one of the primary threats to coastal water quality globally, and governmental regulations and marine policy are increasingly requiring nitrogen remediation in management programs. Traditional mitigation strategies (e.g., advanced wastewater treatment) are not always enough to meet reduction goals. Novel opportunities for additional nitrogen reduction are needed to develop a portfolio of long-term solutions. Increasingly, in situ nitrogen reduction practices are providing a complementary management approach to the traditional source control and treatment, including recognition of potential contributions of coastal bivalve shellfish. While policy interest in bivalves has focused primarily on nitrogen removal via biomass harvest, bivalves can also contribute to nitrogen removal by enhancing denitrification (the microbial driven process of bioavailable nitrogen transformation to di-nitrogen gas). Recent evidence suggests that nitrogen removed via enhanced denitrification may eclipse nitrogen removal through biomass harvest alone. With a few exceptions, bivalve-enhanced denitrification has yet to be incorporated into water quality policy. Here,we focus on oysters in considering how this issue may be addressed.We discuss policy options to support expansion of oyster mediated denitrification, describe the practical considerations for incorporation into nitrogen management, and summarize the current state of the field in accounting for denitrification in oyster habitats. When considered against alternative nitrogen control strategies, we argue that enhanced denitrification associated with oysters should be included in a full suite of nitrogen removal strategies, but with the recognition that denitrification associated with oyster habitats will not alone solve our excess nitrogen loading problem

A review of how we assess denitrification in oyster habitats and proposed guidelines for future studies

Excess nitrogen (N) loading and resulting eutrophication plague coastal ecosystems globally. Much work is being done to remove N before it enters coastal receiving waters, yet these efforts are not enough. Novel techniques to remove N from within the coastal ecosystem are now being explored. One of these techniques involves using oysters and their habitats to remove N via denitrification. There is substantial interest in incorporating oyster-mediated enhancement of benthic denitrification into N management plans and trading schemes. Measuring denitrification, however, is expensive and time consuming. For large-scale adoption of oyster-mediated denitrification into nutrient management plans, we need an accurate model that can be applied across ecosystems. Despite significant effort to measure and report rates of denitrification in oyster habitats, we are unable to create such a model, due to methodological differences between studies, incomplete data reporting, and inconsistent measurements of environmental variables that may be used to predict denitrification. To make a model that can predict denitrification in oyster habitats a reality, a common sampling and reporting scheme is needed across studies. Here, we provide relevant background on how oysters may stimulate denitrification, and the importance of oyster-mediated denitrification in remediating excess N loading to coastal systems. We then summarize methods commonly used to measure denitrification in oyster habitats, discuss the importance of various environmental variables that may be useful for predicting denitrification, and present a set of guidelines for measuring denitrification in oyster habitats, allowing development of models to support incorporation of oyster-mediated denitrification into future policy decisions

Quantifying the effects of commercial clam aquaculture on C and N cycling : an integrated ecosystem approach

Author Posting. © The Author(s), 2016. This is the author's version of the work. It is posted here by permission of Coastal and Estuarine Research Federation for personal use, not for redistribution. The definitive version was published in Estuaries and Coasts 39 (2016): 1746–1761, doi: 10.1007/s12237-016-0106-0.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-fold 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.This work was supported by Virginia Sea Grant (NA10OAR4170085, #R/71515W, #R/715168), the NSF GK12 Fellowship (DGE-0840804), the Strategic Environmental Research and Development Program – Defense Coastal/Estuarine Research Program Project SI-1413, and NSF Virginia Coast Reserve LTER Project (DEB 0080381, DEB 0621014).2017-05-1

Progress and challenges in coupled hydrodynamic-ecological estuarine modeling

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Estuaries and Coasts 39 (2016): 311-332, doi:10.1007/s12237-015-0011-y.Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review, we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.NKG, ALA, and RPS acknowledge support from the USGS Coastal and Marine Geology Program. DKR gratefully acknowledges support from NSF (OCE-1314642) and NIEHS (1P50-ES021923-01). MJB and JMPV gratefully acknowledge support from NOAA NOS NCCOS (NA05NOS4781201 and NA11NOS4780043). MJB and SJL gratefully acknowledge support from the Strategic Environmental Research and Development Program—Defense Coastal/Estuarine Research Program (RC-1413 and RC-2245)