Mark J. Brush

Toward Ecosystem-Based Fisheries Management

Abstract Considerable effort has been directed in the last decade towards the development of multispecies, ecosystem-based approaches to fisheries management. One aspect of this is the development of models that take into account direct and indirect ecological interactions among species and their environment. We review four multispecies modeling approaches that we feel have great potential for use in fisheries management: multispecies production models, multispecies virtual population analysis, Ecopath with Ecosim, and multispecies bioenergetics models. All four can predict biomass trajectories over time and under various fishing pressures, but with different spatial, temporal, and biological resolution, quantitative/qualitative nature of the results, and insight into system function. We present the data requirements of each model and give examples of field programs that have provided data for model construction and validation. We conclude with a set of issues to consider when designing a coupled field-mo...

Impacts of Climate-Related Drivers on the Benthic Nutrient Filter in a Shallow Photic Estuary

In shallow photic systems, the benthic filter, including microphytobenthos and denitrifiers, is important in preventing or reducing release of remineralized NH4+ to the water column. Its effectiveness can be impacted by climate-related drivers, including temperature and storminess, which by increasing wind and freshwater delivery can resuspend sediment, reduce salinity and deliver nutrients, total suspended solids, and chromophoric dissolved organic matter (CDOM) to coastal systems. Increases in temperature and freshwater delivery may initiate a cascade of responses affecting benthic metabolism with impacts on sediment properties, which in turn regulate nitrogen cycling processes that either sequester (via microphytobenthos), remove (via denitrification), or increase sediment nitrogen (via remineralization, nitrogen fixation, and dissimilatory nitrate reduction to ammonium). We conducted a seasonal study at shallow stations to assess the effects of freshwater inflow, temperature, wind, light, and CDOM on sediment properties, benthic metabolism, nitrogen cycling processes, and the effectiveness of the benthic filter. We also conducted a depth study to constrain seasonally varying parameters such as temperature to better assess the effects of light availability and water depth on benthic processes. Based on relationships observed between climatic drivers and response variables, we predict a reduction in the effectiveness of the benthic filter over the long term with feedbacks that will increase effluxes of N to the water column with the potential to contribute to system eutrophication. This may push shallow systems past a tipping point where trophic status moves from net autotrophy toward net heterotrophy, with new baselines characterized by degraded water quality.

Progress and Challenges in Coupled Hydrodynamic-Ecological Estuarine Modeling

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.

Drivers of Change in Shallow Coastal Photic Systems: An Introduction to a Special Issue

Coastal ecosystems are characterized by relatively deep, plankton-based estuaries and much shallower systems where light reaches the bottom. These latter systems, including lagoons, bar-built estuaries, the fringing regions of deeper systems, and other systems of only a few meters deep, are characterized by a variety of benthic primary producers that augment and, in many cases, dominate the production supplied by phytoplankton. These “shallow coastal photic systems” are subject to a wide variety of both natural and anthropogenic drivers and possess numerous natural “filters” that modulate their response to these drivers; in many cases, the responses are much different from those in deeper estuaries. Natural drivers include meteorological forcing, freshwater inflow, episodic events such as storms, wet/dry periods, and background loading of optically active constituents. Anthropogenic drivers include accelerated inputs of nutrients and sediments, chemical contaminants, physical alteration and hydrodynamic manipulation, climate change, the presence of intensive aquaculture, fishery harvests, and introduction of exotic species. The response of these systems is modulated by a number of factors, notably bathymetry, physical flushing, fetch, sediment type, background light attenuation, and the presence of benthic autotrophs, suspension feeding bivalves, and fringing tidal wetlands. Finally, responses to stressors in these systems, particularly anthropogenic nutrient enrichment, consist of blooms of phytoplankton, macroalgae, and epiphytic algae, including harmful algal blooms, subsequent declines in submerged aquatic vegetation and loss of critical habitat, development of hypoxia/anoxia particularly on short time scales (i.e., “diel-cycling”), fish kills, and loss of secondary production. This special issue of Estuaries and Coasts serves to integrate current understanding of the structure and function of shallow coastal photic systems, illustrate the many drivers that cause change in these systems, and synthesize their varied responses.

Contribution of Nutrient and Organic Matter Sources to the Development of Periodic Hypoxia in a Tributary Estuary

The seasonal formation of periodic hypoxia within tributary estuaries is influenced by multiple nutrient and organic matter sources, both autochthonous and allochthonous. In contrast to lakes and flowing rivers, allochthonous inputs to estuaries include those from near-field sources in the watershed as well as far-field sources from adjacent marine systems that contribute nutrients, organic matter, and hypoxic water via estuarine circulation. This study utilized a reduced-complexity eutrophication model to quantify the contribution of individual sources to hypoxia in the York River estuary (YRE), and assess the reductions necessary to mitigate hypoxic conditions. Results indicate that portions of the oligohaline YRE are influenced by organic loading from the watershed, while the lower mesohaline region is influenced by both internal phytoplankton production and watershed loads. In the high mesohaline, watershed organic matter and internal phytoplankton production play an equally important role during the spring; however, in summer and fall oxygen concentrations appear to respond strongly to dissolved organic carbon (DOC) entering via advection from Chesapeake Bay (CB). The polyhaline region, which is frequently the site of reoccurring hypoxia, responded primarily to advected DOC from CB. Results indicate that different regions of the YRE may require different management strategies, and highlight the strong relationship between periodic hypoxia in the lower YRE and advection of labile organic matter from CB, a far-field input that requires a regional management approach. A cross-system comparison of nutrient budgets indicates that far-field sources can comprise a large portion of total system inputs in numerous tributary estuaries.

Simulated Short-Term Impacts of the Atlantic Menhaden Reduction Fishery on Chesapeake Bay Water Quality

Abstract Atlantic menhaden Brevoortia tyrannus support an intense fishery in Chesapeake Bay, an estuary that is impaired by eutrophication and excess phytoplankton biomass. Since Atlantic menhaden are filter-feeding fish that consume plankton, including phytoplankton, fishery removals may negatively affect water quality and may therefore hinder bay restoration efforts. We performed a simulation to estimate the short-term (monthly and annual) water quality impacts caused by the reduction fishery harvesting its current total allowable catch of Atlantic menhaden in Chesapeake Bay (109,020 metric tons/year). A theoretical loss in net nitrogen removal (Nt ) due to the fishery was estimated for each month, and the simulation was repeated for several scenarios to account for uncertainties associated with Atlantic menhaden feeding behavior. The largest potential impact of the fishery (i.e., absolute value of Nt ) occurred in August for all scenarios, but depending on the value assumed for average feeding rate the...

Dedication: Dr. Scott W. Nixon (1943–2012)

In May 2012, the coastal marine research community unexpectedly lost one of its most influential members and deepest thinkers with the passing of Dr. Scott W. Nixon. Scott’s contributions spanned over four decades and resulted in many of the most frequently cited papers in our field. Using the novel systems approach of his inspirational graduate advisor, Howard T. Odum, Scott made wide-ranging contributions to the study of estuaries, lagoons, marshes, and other coastal ecosystems on topics including their productivity, metabolism, and nutrient cycling; carbon, nutrient, and energy budgets; eutrophication and oligotrophication; and the effect of climate change on estuarine functioning. These advances came through a diverse combination of field studies, mesocosm experiments, simulation models, and synthetic and comparative ecosystem analyses. Scott was a clear thinker who communicated his results in an elegant fashion that did more than simply present the science; rather the data were used to tell a story. As a result, many of Scott’s contributions provided a clear focus that guided the research and management communities for years. Fortunately for us all, this influence will continue for years to come. Following his Ph.D. from the University of North Carolina at Chapel Hill, Scott spent the duration of his professional career at the University of Rhode Island Graduate School of Oceanography, serving as director of the Rhode Island Sea Grant College Program from 1986 to 2000 and most recently as the UNESCO-Cousteau Chair of Coastal Ecology and Global Assessment. A list of Scott’s professional activities and accolades would go on for pages, but given that this dedication is printed in the pages of Estuaries and Coasts, it seems appropriate to mention that Scott was a long-time member and fervent supporter of the Coastal and Estuarine Research Federation (CERF), his regional affiliate society, the New England Estuarine Research Society (NEERS), a longtime (1988–2005) co-Editor-in-Chief of Estuaries, and the recipient of the NEERS Achievement Award in 2000 and the CERF Odum Award for Lifetime Achievement in 2003. Scott’s character, humility, and penchant for treating those around him with total respect made him an esteemed colleague, successful Sea Grant director, and beloved mentor. His low-key, positive approach influenced the careers of numerous colleagues. Scott derived a special pleasure from mentoring his graduate students, always quick to delight in their success and step back to, as he would say, “bask in the reflected glow of the limelight.” Scott created a unique, enriching, and truly inspirational space for us to grow academically, modeled after his own time with H.T. Odum; his unique mentoring style and total dedication to our success fostered a strong sense of academic family that lives on in his absence. In total, Scott mentored 39 graduate students for a total of 17 M.S. and 22 Ph.D. degrees, with 2 final Ph.D. degrees pending. Communicated by Wayne S. Gardner

A Reduced Complexity, Hybrid Empirical-Mechanistic Model of Eutrophication and Hypoxia in Shallow Marine Ecosystems

Numerical simulation models have a long history as research tools for the study of coastal marine ecosystems, and are increasingly being used to inform management, particularly related to nutrient-fueled eutrophication. Demand for modeling assessments is rapidly increasing, and managers need generally applicable tools that can be rapidly applied with limited resources. Additionally, a variety of calls have been made for the development of reduced complexity models for use in parallel with more complex models. We propose a simplified, empirically constrained modeling approach that simulates the first-order processes involved in estuarine eutrophication, contains a small number of aggregated state variables and a reduced set of parameters, and combines traditional mechanistic formulations with robust, data-driven, empirical functions shown to apply across multiple systems. The model was applied to Greenwich Bay, RI (USA), a subestuary of Narragansett Bay, and reproduced the annual cycles of phytoplankton biomass, dissolved inorganic nutrients, and dissolved oxygen, events including phytoplankton blooms and development of hypoxia, and the rate of annual primary production. While the model was relatively robust to changes in parameter values and initial conditions, sensitivity analysis revealed the need for better constraint of the phytoplankton carbon-to-chlorophyll ratio, temperature dependence of phytoplankton production, and parameters associated with our formulations for water column respiration and the flux of phytoplankton carbon to the sediments. This reduced complexity, hybrid empirical-mechanistic approach provides a rapidly deployable modeling tool applicable to a wide variety of shallow estuarine systems.