Productivity, diversity and survival of estuaries are threatened by explosive coastal population growth and associated recreational activities. One major area of recreational growth has been the number of small pleasure craft motoring in shallow waters at high speeds. On the east coast of Central Florida in the Indian River Lagoon system, intense boating activity occurs year-round and intertidal reefs of the eastern oyster Crassostrea virginica with dead margins (piles of disarticulated shells) on their seaward edges are commonly found adjacent to major boating channels. The cause(s) of the dead margins is unclear. However, the disarticulated shells may be reducing reef sustainability if these surfaces are unavailable for larvae. Recruitment trials were run on eight reefs (4 with dead margins, 4 without) in three 8-week trials in 2001/2002. Significant differences were found for location on reef and season. For survival of recruits, significant differences were found for reef type, location on reef, and season. Sediment loads, percent silt/clay, and relative water motion were all found to be significantly higher on impacted reefs. Spring months were found to be the optimal time for larval recruitment to increase larval set and survival and to also decrease the effects of sedimentation and water motion. Based on these results, experimental restoration began May 2003 to develop an ecologically and economically feasible restoration protocol for this intertidal region. Four different densities of shells (0, 16, 25, 36) were attached to vexar mesh mats (45 X 45 cm) displaying shells perpendicular to the substrate. 360 mats were randomly deployed at one of six dentified optimum recruitment locations. Recruitment increased through June and was significantly higher on mats with 36 shells. This was followed by a large, expected decline in recruitment and survival in July/August, due to competition, predation and/or extreme high temperatures. Total live oysters on the restoration mats significantly increased during October 2003 through February 2003. These newly-created oyster reefs are moveable and provide optimal substrate and larval set to be transported post-recruitment to areas resource managers have slated for restoration to aid in reef sustainability. To determine the potential negative effects of flow and sediment levels on oyster larval settlement, which may be associated with an increase in boating actitivity, laboratory experiments were conducted. Eighteen trials, with competent oyster larvae, nine in flowing-water and nine in still-water were run at three sediment levels: no sediment, low sediment, and high sediment loads. Larval settlement was significantly higher in the still-water trials and both high and low sediment loads significantly reduced larval settlement.

Copano Bay is a shallow (< 2-3 m), microtidal estuary in south central Texas. In an effort to both determine the distribution as well as investigate the controls on the distribution of oyster reefs, a geophysical survey of Copano Bay was conducted in June and July 2007. Surficial sediment analysis confirms that the recent sedimentation in Copano Bay is comprised of mostly estuarine mud with little sand or shell, large extents of oyster reefs and smaller areas of sand. Seismic stratigraphy analyses verify that the first oyster reefs in Copano Bay formed atop topographic highs in the Pleistocene surface. About 6 ka, sea level rise slowed to near its present rate and sediment supply decreased tremendously to Copano Bay decreasing the amount of suspended sediment. The first oyster reefs began forming around this time using these fluvial terraces as suitable substrate. Once the initial reefs were established, additional reefs began forming atop these initial reefs, or on the eroded shell hash material from the initial reefs. During this time of slow sea level rise and low sediment input to the bay, oyster reefs thrived and reef and shell hash material covered a majority of the bay surface. Once climate change increased sediment input to the bay, the reefs began to decrease in size due to siltation. The reefs have continued to decrease in size causing a 64 percent reduction in oyster reef and shell hash area from approximately 4.8 ka to today.

As the world continues to experience substantial rates of habitat loss, habitat restoration has become of prime interest to ecologists worldwide. Restoration has shown to be successful in recovering targeted components of certain ecosystems but it is important to achieve a holistic understanding of the resulting ecological impacts it has on communities. To address this, four oyster reefs and three living shorelines were restored during the summer of 2017. These sites, along with four dead oyster reefs, four living oyster reefs, and three undisturbed (control) living shorelines, were sampled before restoration and regularly post-restoration for one year using lift nets. Macroinvertebrates were collected and enumerated in the lab. Diversity indices, community composition, and similarity percentages were then calculated and compared across treatments, time, and treatment-by-time. Live reefs displayed significantly higher species richness and Shannon diversity than restored and dead reefs. Simpson diversity did not differ between live and restored oyster reefs but both were significantly higher than dead reefs. Though not statistically detectable, species richness and Shannon diversity on restored reefs were relatively similar to dead reefs before restoration but became increasingly similar to live reefs over the course of the study. Additionally, analyses revealed significantly different community compositions between live reefs and restored reefs, as well as between live and dead reefs. Living shorelines showed no significant differences in diversity indices but did experience similar seasonal fluctuations in diversity across treatments. Just as with oyster reefs, restored and control living shorelines harbored significantly different communities across time. The findings of this study emphasize the need for dedication to thorough monitoring and multi-metric evaluation of success in restoration efforts. This study and future research will equip resource managers with ways to quantify the effects of restoration that will consider several important ecosystem components.

The heterogeneity provided by structured habitats is important in supporting diverse and dense fish communities. The biogenic reefs created by the native Eastern Oyster, Crassostrea virginica, were once the dominant structural habitat in Chesapeake Bay, and have since declined to less than 1% of historic estimates. Conflicting results on the effects of oyster reef restoration on pelagic fish assemblages make further investigation necessary. Incorporating multiple sampling strategies may help elucidate oyster reef habitat influence on fish assemblages. This study used multi-panel gillnets, hydroacoustic technology, and day-night sampling to describe pelagic fish assemblages on and off oyster reef habitat in the lower Piankatank River, VA. Data from oyster reef habitat, adjacent sandy-mud bottom habitat, and unstructured sandy habitat outside of a reef restoration area compared fish diversity, species composition, and density among habitat types. A multivariate analysis using day of the year, day or night, and habitat type as model terms found temporal factors explained variation in fish distribution more than habitat. Fish diversity varied significantly with day or night and habitat type. Diversity and density were significantly higher at night, demonstrating the necessity of nocturnal sampling in fish assemblage research. Results from this study conclude that fish assemblages were not significantly more diverse or denser on reef than non-reef habitat. We suggest that future work should concentrate on studying areas where oyster reef habitat comprises a larger proportion of the study area.

Oyster reef habitats have declined from historic levels due to a variety of reasons, including overharvest, disease, and degraded water quality. The harvesting of oysters has led to a loss of reef habitat for both oysters and reef-associated fauna. When oysters spawn, the larval oysters, or spat, depend on hard substrate for settlement and growth. Oyster shell is the preferred substrate for use in restoration because it most closely matches natural reef habitat, but it is often expensive and in limited supply. This study incorporated field and laboratory experiments to assess the relative habitat value of alternative substrates (crushed concrete, porcelain, crushed limestone, and river rock, as well as oyster shell) for larval oyster recruitment as well as reef resident fishes and macro-invertebrates. Replicate trays of each substrate type were deployed in St. Charles Bay, TX for four months during spring and summer 2012 and assessed for oyster recruitment and faunal diversity and density. Concrete, river rock, limestone and porcelain had similar spat recruitment densities compared to oyster shell (1300-2300 spat). Spat shell heights were also larger on these substrates (13-16 mm), while spat on porcelain substrates were slightly smaller (10-13 mm). All substrates except bare sediment had similar fauna species densities (200-500 individuals m-2). Limestone had lower fauna diversity (H’; 0-1) than concrete and shell (1-2). Laboratory experiments compared the effectiveness of these substrates in providing prey refuge from pinfish and blue crab predators. All substrates performed similarly resulting in very low (<20 %) prey mortality rates for either predator. Results may enable future restoration plans to be implemented at a lower cost while providing similar habitat functions.

Pattern formation in ecological systems refers to a nonuniform distribution of animal and plant species across a landscape. Pattern formation can be observed in many aquatic and terrestrial systems and can provide important insights into their dynamics and ability to cope with environmental changes. In this dissertation, we focus on pattern formation in tidal marshes and oyster reefs, two important habitats that provide a number of essential ecosystem services. Both of these systems have also experienced dramatic losses, prompting much research to investigate their dynamics as and viable restoration and management strategies. The first part of this dissertation focuses on understanding the spatial patterning of the marsh shoreline, which can range from a uniform to a more wave-like shoreline. We present a mathematical framework for modeling the spatial variation of the shoreline as a result of interactions between marsh vegetation, mussels and their impact on marsh sedimentation and erosion. While both species are known to significantly impact marsh dynamics, no mathematical model describing this phenomenon has been previously proposed. Numerical and analytical investigation of our model indicates that the interactions between these species can drive the spatial variation of the marsh edge, increase the system’s productivity and allow it to withstand harsh erosion conditions. The second part of this dissertation focuses on pattern formation in intertidal oyster reef communities, where both round and elongated reefs of various orientations dominate the landscape. Most of what is currently known about reef geometry has been anecdotal, with no comprehensive, quantitative study of reef pattern formation carried out. In particular, the interaction of oyster reefs of various geometric configuration with tidal flow remains poorly understood. This is important in reef restoration, where understanding the interaction of reef geometry with flow and other environmental factors can inform the construction of artificial oyster reefs. In this dissertation, we present a comprehensive analysis of remotely sensed aerial imagery of an intertidal oyster reef network in conjunction with information on tidal flow dynamics and bathymetry. Using texture and color properties of the aerial imagery, we identify and delineate over six thousand individual reefs. We then classify reefs into natural classes based on geometric attributes such as reef shape, size and orientation. Finally, we use multiple spatial analysis techniques to determine the spatial clustering of different reef types and investigate the role of flow and bathymetry in their spatial distribution.

Efforts to mitigate shoreline erosion through living shoreline methods along the USA Atlantic seaboard have often incorporated the cultivation and transplantation of smooth cordgrass, Spartina alterniflora. Assessments of these transplants at several sites in the Indian River Lagoon have shown that survival is variable after a year (survival: 10-93%). Lower survival has been attributed to environmental variables such as dislodgement by wave energy, and transplant shock due to salinity changes from cultivation to estuarine conditions. To improve living shoreline projects, we examined the effects of cultivation salinity (0 ppt, 15ppt) on transplantation success, and the success of anchoring plants to biodegradable mats (Jute mesh, 5 individuals per 50 cm2) and utilizing oyster bags as breakwaters in facilitating reestablishment of new transplants. Spartina alterniflora individuals were grown under salinity treatments for 20 weeks; plants grown in 15 ppt produced new shoots with significantly greater heights than those grown in freshwater. The plants were then transplanted to two sites in the IRL, and monitored after four weeks. After four weeks there was a greater net increase in stem density and larger decrease in plant height for plants grown in 15 ppt. Jute-mesh mats and oyster bags did not impact growth or survival of transplants. Low-saline (15 ppt) conditions increased shoot growth of the project by 50% in four weeks at a cost of 30 cents per additional shoot produced by an individual. Longer-term monitoring will determine if benefits persist or decrease over time, and if the cost is justified by the benefits.

Oyster reefs are important estuarine ecosystems that provide habitat to many species including threatened and endangered wading birds and commercially important fishes and crabs. Infaunal organisms (i.e. small, aquatic animals that burrow in the sediment) are also supported by oyster reef habitats. Infaunal organisms are critical to marine food webs and are consumed by many important species that inhabit coastal estuaries. However, over the past century 85% of shellfish reef habitats have been lost, making restoration of these areas vital. Due to their important role in coastal food webs, infauna is hypothesized to be a strong indicator of habitat productivity to document the transition from a dead to a restored and living intertidal oyster reef. Research was conducted in Mosquito Lagoon of the northern Indian River Lagoon system. Three replicate samples were collected from 12 intertidal oyster reefs (four dead, four live, four restored). Samples were collected one-week pre-restoration and one month and six months post-restoration. Infauna was counted and sorted into six taxonomic categories: polychaetes, amphipods, isopods, gastropods, bivalves, and decapods. Reef infaunal abundance increased following restoration: restored reefs became more similar to live reefs one month following restoration. Six months after restoration restored reefs were also significantly different than dead reefs. Live reefs consistently had high infaunal abundance and dead reefs consistently had low abundance, while restored reefs were intermediate. These data suggest restored reefs are more productive than their dead counterparts, with restoration showing a positive trajectory to impact numerous infaunal species and their associated food webs.

This study aims to review thirteen coastal restoration projects considering the various ecosystem services provided by restoration and estimates the economic value of one of the ecosystem services of restoration. These ecosystem services include water quality improvement, fish and benthic species productivity, shoreline stabilization, oyster abundance, and marsh growth. The projects represent a set of large-scale projects within Alabama and Mississippi, with construction and monitoring costs ranging from $2.3 million to $50 million per project. To determine the economic value of one of the ecosystem services of coastal restoration projects, I used the meta-analysis method to estimate the willingness to pay (WTP) for coastal water quality improvements. The estimated function from the meta-analysis is applied to parameters specific to the study area. The WTP for improved coastal water quality, from a baseline of fishable but likely to degrade, to an improved fishing catch rate, is $203 per household annually among residents of Alabama and Mississippi.