Jamie M.P. Vaudrey

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.

Biology and Ecology of Long Island Sound

Many compelling management issues in Long Island Sound (LIS) focus on how organisms respond to stresses such as commercial and recreational harvesting, eutrophication, hypoxia, habitat degradation, invasion of non-native species, ocean acidification, and climate change. In order to address these complex problems, we must first understand the factors controlling biological processes and how organisms interact ecologically. This chapter provides an overview of the major groups of organisms occupying the dominant habitats of LIS.

Effects of oyster depuration gear on eelgrass (Zostera marina L.) in a low density aquaculture site in Long Island Sound.

ABSTRACT Oyster (Crassostrea virginica) aquaculture has a long history and tradition in Long Island Sound (Connecticut, USA). Although most of the producers practice traditional on-bottom aquaculture, there are a growing number of individuals utilizing bottom gear for cultivation and depuration. The use of this gear presents a potential conflict in eastern Long Island Sound where the last remaining populations of eelgrass (Zostera marina L.) exist. Shellfish aquaculture activity has been identified as a potential source for negative impacts to eelgrass populations. However, bivalve aquaculture has also been shown to provide an equivalent or greater degree of ecosystem services as submerged aquatic vegetation. The effects of short-term oyster depuration activity were gauged by comparing eelgrass reference sites and experimental plots (eelgrass areas containing oyster depuration cages with and without oysters) in triplicate. Changes in sheath length of the eelgrass 1 m from the cages were used as a proxy for growth rate. The aquaculture gear had no effect on this measure of growth rate of eelgrass in any of the deployments. Sediment characteristics (sediment chlorophyll, sediment % organics) in the cage footprint and 1m from the cages also failed to show an effect of the depuration cages on the local environment. Video monitoring of the footprints and local area indicated little physical damage to the eelgrass beds as a result of the short deployment of the aquaculture gear. The water column at all three sites was vertically well mixed and no effect of the cages on water column light and other characteristics was detectable. The results of this study indicated that at the current level of activity, short-term depuration of oysters has minimal effect on eelgrass growth, water quality and the sediment characteristics measured. However, if depuration activity expands in terms of the amount of gear and/or individual operations, it may result in measurable effects. Understanding the interactions between shellfish aquaculture activity and the marine environment is necessary for sustainable growth of the industry.

The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation

Benthic microeukaryotes are key ecosystem drivers in marine sandy beaches, an important and dynamic environment; however, little is known about their diversity and biogeography on a large spatial scale. Here, we investigated the community composition and geographical distributions of benthic microeukaryotes using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors and spatial separation on the distribution patterns of both rare and abundant taxa. We collected 36 intertidal samples at 12 sandy beaches from four regions that spanned distances from 0.001 to 12,000 km. We found 12,890 operational taxonomic units (OTUs; 97% sequence identity level) including members of all eukaryotic super-groups and several phyla of uncertain position. Arthropoda and Diatomeae dominated the sequence reads in abundance, but Ciliophora and Discoba were the most diverse groups across all samples. About one-third of the OTUs could not be definitively classified at a similarity level of 80%, supporting the view that a large number of rare and minute marine species may have escaped previous characterization. We found generally similar geographical patterns for abundant and rare microeukaryotic sub-communities, and both showed a significant distance-decay similarity trend. Variation partitioning showed that both rare and abundant sub-communities exhibited a slightly stronger response to environmental factors than spatial (distance) factors. However, the abundant sub-community was strongly correlated with variations in spatial, environmental and sediment grain size factors (66% of variance explained), but the rare assemblage was not (16%). This suggests that different or more complex mechanisms generate and maintain diversity in the rare biosphere in this habitat.

Advancing Coastal Habitat Resiliency Through Landscape-Scale Assessment

ABSTRACT Coastal areas are among the most biologically rich regions in the world. They provide tremendous benefit to people through ecological services like pollution filtration, carbon sequestration, and storm protection. However, human activity has decreased the ability of ecosystems to provide these services, and in many coastal areas, restoration is not as effective as it could be. Limited success is largely attributed to vague goals and a lack of holistic, science-informed planning. Quantifying coastal habitat health can aid in setting better restoration goals and lead to greater restoration success. The Long Island Sound Study National Estuary Program conducted the first comprehensive look at coastal habitat health for the Long Island Sound Estuary. In this study we also reviewed landscape-scale habitat assessment progress within other coastal programs. Results can be applied to establish ecosystem health-oriented goals that improve habitat function and resilience across coastal areas.