Hundreds of stranded turtles wash up deceased on Virginia’s coastline each year, yet the causes of most stranding events are poorly understood. In this thesis, a carcass drift model was developed for the Chesapeake Bay, Virginia, to predict likely locations of mortality from coastal sea turtle stranding records. First, field studies were carried out to better parameterize the drift characteristics of buoyant sea turtle carcasses, namely, probable oceanic drift times and the impact of direct wind forcing on carcass drift. Based on the duration that tethered, free-floating turtle carcasses were buoyant, we determined that oceanic drift duration of turtle carcasses was highly dependent on water temperature and varied from 2-15 days during typical late spring to early fall bay water conditions. The importance of direct wind forcing for turtle carcass drift was assessed based on track divergence rates from multiple simultaneous deployments of three types of surface drifters: bucket drifters, artificial turtles and real turtle carcasses. Turtle drift along-wind leeway was found to vary from 1-4% of wind speed, representing an added drift velocity of approximately 0.03-0.1 m/s for typical bay wind conditions. The information obtained from these field studies were used to parameterize the oceanographic carcass drift model, which was applied to reported strandings during 2009-2014. Predicted origin of stranding records with probable cause of death identified as vessel strike were compared to commercial boating data. Locations of potential hazardous turtle-vessel interactions were identified in high traffic areas of the southeastern Chesapeake Bay and James River. Commercial fishing activity of various gear types with known sea turtle interactions were compared in space to predicted mortality locations for stranded turtles classified with no apparent injuries, suggesting possible fisheries-induced mortality. Probable mortality locations for these strandings were found to vary between spring peak and summer off-peak stranding periods, but two distinct hotpots were identified in the southwest and southeast portions of the lower bay. Spatial overlap was noted between potential mortality locations and gillnet, seine, pot, and pound net fisheries. These predictions provide clear space-time locations for focusing future research and prioritizing conservation efforts. Nevertheless, the lack of fine temporal and spatial resolution fishing data limited our ability to quantitatively assess most likely causes for specific stranding events. This study both highlights the importance of addressing these data gaps and provides a meaningful conservation and management tool that can be applied to stranding data of sea turtles and other marine megafauna around the globe.

Microbial communities associated with a particular space or habitat, or microbiomes, play significant roles in host health and the regulation of biogeochemical cycles. In oysters these microbiomes may be important contributors in the removal of biologically available nitrogen (N) from the coastal and marine environment through the process of denitrification. Denitrification is the microbially mediated step-wise reduction of nitrate (NO3-) or nitrite (NO2-) to N2 gas. Excess nitrogen in the Chesapeake Bay has been implicated in the increase of eutrophication and other detrimental effects including harmful algal blooms, hypoxia, and loss of benthic communities. Oyster reefs have been shown to enhance the rates of denitrification in nearby sediments, but little is known about the oyster microbiomes or associated microbes responsible for denitrification (denitrifiers). Furthermore, the identification of the oyster core microbiome, or set of resident microbes continually present in the oyster, is relatively unknown. Assessing the stable underlying core is necessary to evaluate and predict the effect of varying environmental conditions on the oyster microbiome and oyster denitrification. A combined 16S targeted metagenomic and metabolic inference approach was used in this study to investigate the gill, gut and shell microbiomes of the eastern oyster (Crassostrea virginica) and their associated denitrifiers in response to spatial and temporal changes. Denitrification activity was linked to community structure using methods such as quantitative PCR of nitrous oxide reductase genes (nosZ) and 15N isotope pairing technique with experimental flow-through design. The oyster gill, gut, and shell microbiomes all showed distinct and unique core microbiomes, suggesting an importance of the core to oyster function or health. Denitrifier abundance and activities were most consistent in the shell microbiomes indicating a stable, pool of potential denitrifiers for oyster denitrification. In comparison, oyster gill and gut denitrifier abundances and activities were highly variable and likely related to transient denitrifiers ingested with food particles. Additionally, denitrifiers demonstrated niche differentiation between the different oyster microbiomes, indicating different groups of denitrifiers are responsible for performing denitrification in the oyster. Assessing the stability and variability of the oyster microbiome and associated denitrifiers provides a greater understanding of the oyster’s role in denitrification and the mitigation of excess N in marine and coastal environments.

The effects of water quality and sediment composition on mid-Atlantic semi-annual and perennial Zostera marina reproductive success, seed-bank viability, and seed germination were elucidated using laboratory and in situ experiments, quantitative field observations, and ecological model simulations. The sediment seed-bank was found to play a large role in the recovery of perennial Z. marina beds in the Chesapeake Bay and in the yearly re-establishment of beds in North Carolina which were determined to have a semi-annual life history. However, the resiliency provided by sediment seed-bank for both semi-annual and perennial Z. marina beds was limited as seeds remained viable for less than one year. When comparing the two life forms, semi-annual Z. marina beds produced a greater proportion of flowering shoots and more seeds than nearby perennial beds. Seed germination was significantly affected by sediment type and burial depth with maximum germination of seeds occurring in sediments containing >3% organic content and buried at depths <3 cm. Model simulations indicate that York River Z. marina beds are currently at their maximum temperature threshold and that projected increases of >1??C in water temperature within the Chesapeake Bay may result in large scale declines. While the sediment seed-bank may provide a mechanism for recovery following one year of increased temperature stress, seed-banks are depleted following large scale germination events and may not provide resiliency to multiple consecutive years of stressful conditions. Further research into the interactive effects of sediment and water column conditions and seed physiology on seed viability are required to gain a more comprehensive understanding of seed-bank dynamics in Z. marina beds. Monitoring of semi-annual and perennial Z. marina beds in North Carolina indicated that multiple life history strategies may be found within one Z. marina bed. Shoots within the semiannual Z. marina bed germinated from seeds, a portion of seedlings flowered during their first year of growth, and all shoots completed their life cycle and died within one year of germination like a semi-annual plant; however, not all shoots flowered and shoots reproduced both sexually and asexually similar to a perennial plant. Since the individual plants found within the semiannual bed did not display the all of the defining characteristics of either perennial or annual Z. marina life histories, this population cannot be completely described by either life history strategy. Research into the development of a semi-annual life history strategy for Z. marina within this site and the possibility of this form occurring at other geographic regions requires additional research. Sexual reproduction is an important component of both semi-annual and perennial Z. marina populations that should be included in ecological studies and models. Although most perennial Z. marina beds rely on asexual reproduction as a primary form of bed maintenance, the ability to reproduce sexually is maintained and, as shown here, may play a large role in the recovery, maintenance, and expansion of these populations. For these reasons and due to the use of seeds in restoration of Z. marina beds within large systems such as the Chesapeake Bay, research into the dynamics of sexual reproduction within existing beds, a better understanding of seed physiology, and additional research into environmental effects (including the sediment) on seed germination and viability are essential.

Numerous studies have investigated the disease processes of Perkinsus marinus in the oyster, Crassostrea virginica. However, the transmission dynamics and factors affecting P. marinus infection are still unclear. The objectives of this study were to investigate: (1) the principal and most effective lifestage of P. marinus, (2) the synergistic effects of temperature, salinity and P. marinus dose on disease prevalence, (3) suppression of host reactive oxygen intermediates by P. marinus, (4) the localization of acid phosphatase in the parasite, (5) the effects of temperature and salinity on acid phosphatase secretion, and (6) the P. marinus lipid and fatty acid composition. Meronts were more infective than prezoosporangia, and infectivity was dose dependent (100 cells minimum). High temperatures, salinities and P. marinus doses increased infection prevalence and intensity. Temperature was the most important factor influencing disease susceptibility, followed by cell dosage and salinity. Both temperature and salinity significantly affected the host cellular and humoral factors in oysters. P. marinus suppression of hemocyte reactive oxygen intermediates production, as assessed by chemiluminescence was dose dependent. Zymosan stimulated hemocyte chemiluminescence was reduced, suggesting that live P. marinus cells or their extra-cellular products suppress host reactive oxygen intermediates production. Acid phosphatase activity in P. marinus cells increased with increasing temperature. Meronts had higher acid phosphatase activity than prezoosporangia. Extracellular acid phosphatase secretion by P. marinus was dose dependent, increasing with temperature and osmolality. Electron microscopy revealed that acid phosphatase activity was localized primarily in the nucleus, but was also present in the cell membrane. Lipid classes of meronts resembled those found in their media. Phospholipids were the major lipid class in meronts, while triacylglycerols were dominant in prezoosporangia isolated from infected oyster tissue. Results indicated that meronts may be capable of interconversion of lipid classes. Both meronts and prezoosporangia had much higher levels of arachidonic acid than the host.

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Sexual reproduction provides submerged aquatic vegetation (SAV) populations unique opportunities for dispersal, genetic mixing, and resilience in the event of catastrophic population declines. Relative to asexual reproduction, sexual reproduction is a risky resource investment and can have a lower probability of success. A wide variety of abiotic and biotic interactions common in both terrestrial and aquatic environments can lead to significant mortality of seeds and seedlings. The goal of this dissertation is to explore the diversity of biological interactions that influence seed and seedling survival in SAV that drive the population dynamics and restoration success of SAV species. A combination of survey and experimental methods were used to test if three biological interactions, disturbance, herbivory, and competition, compromised seedling recruitment for three different SAV species growing in three different coastal environments. Chapter One explored the influence of sediment bioturbators on seedling establishment for the seagrass Posidonia australis in a marine environment. Field surveys demonstrated that dispersed seeds of P. australis overlap with a suite of sediment bioturbators that disturb the sediment in the coastal lagoons of Western Australia. The movement of sediment bioturbators found in these areas (sand dollars, sea stars, and heart urchins) dislodged and moved recently settled P. australis seeds. The overlap in habitat suitability between these animals and P. australis seeds suggests high densities of these animals consistently disturb non-dormant P. australis seeds and may act as a bottleneck to seedling recruitment. Chapter Two explored the role of grazers on seedling recruitment of a freshwater angiosperm. Field surveys recorded high grazing levels of isolated Vallisneria americana propagules in oligohaline areas of the James and Chickahominy Rivers, VA. Camera surveys identified the blue crab, Callinectes sapidus, as a likely herbivore. Subsequent surveys and experiments suggested C. sapidus in this system consumes SAV as part of their diet. The emergence of non-native SAV in the system, but not V. americana, suggests grazing prevents the recruitment of some SAV, but not others. Chapter Three evaluated interactions between adult plants and seedlings and how they impacted seedling establishment of an estuarine seagrass species. Field surveys consistently recorded seedlings establishing among existing Zostera marina shoots in a meso/polyhaline region of Chesapeake Bay, VA. Concurrent experiments indicated that seed supply influenced seedling establishment rates in some areas. Further surveys and experiments showed that negative interactions between seedlings and adult shoots influenced the subsequent survival of these seedlings within existing Z. marina meadows. Results from the research studies in this dissertation, conducted across three diverse coastal habitats, demonstrate that interactions between SAV seeds or seedlings and other biota can be very important in ultimately determining seed or seedling survival. The diverse mechanisms through which biota compromise seedling recruitment and sexual reproduction for SAV observed here suggest there may be many additional, unexplored biological interactions affecting successful sexual recruitment for many SAV species. Because sexual reproduction provides substantial benefits to SAV populations, incorporating risks associated with seedling recruitment into population models and restoration strategies may help better predict SAV population health, resiliency and expansion as well as help optimize SAV restoration efforts.

Batrachoidiformes, the toadfishes, are benthic fishes that inhabit nearshore subtidal and intertidal habitats, characterized by their dorsoventrally flattened bodies and large pectoral fins. These fishes lack dispersive larvae, and larval development is retained in nests guarded by their parents. To date, 82 species and 23 genera are accepted as valid. Previous studies recognized a single family, Batrachoididae, with four subfamilies: Batrachoidinae, Porichthyinae, Thalassophryninae, and Halophryninae. Interrelationships among subfamilies, however, are unresolved and interrelationships among species are problematic. Despite being a conspicuous member of the coastal fauna, the internal morphology of most species of Batrachoidiformes is unknown, being intraspecific and ontogenetic variations not reported for most species. Several characters used in previous analyses were found to have problematic construction or be intraspecifically variable. This new study reassessed the morphology of 66 species of 22 genera, representing most of the diversity of subfamilies of Batrachoidiformes. This investigation also endeavored in accounting for intraspecific and ontogenetic variations, in order to recognize the potential phylogenetic characters. The first chapter investigated the caudal skeleton of Batrachoidiformes, the posteriormost region of the axial skeleton. Results found high intraspecific variation in this region, especially in the shape of the epurals and the parhypural flange. Despite the high intraspecific variability, potentially informative characters were identified, such as the presence of a hypurapophysis-like process in seven genera of Halophryninae. The second chapter investigated the series of intermuscular bones and tendons within Batrachoidiformes. Variation in this series of sesamoid bones is not only poorly known in toadfishes, but teleost fishes in general. Results show that variation in intermuscular bones is high and potentially phylogenetically informative. For example, Batrachoidinae, Thalassophryninae, and Halophryninae have the origin of the first epineural articulating with the neural spine of the first vertebra. In Porichthyinae and other representatives of Percomorphacea the origin of the first epineural articulates with the neural arch of the first vertebra. The third chapter described the early ontogenetic changes of the skeleton of Porichthys notatus (Porichthyinae). These completely novel descriptions include tables of sequence of ossification and appearance of cartilages. The fourth chapter is the phylogenetic analysis. Previous characters were modified and new characters were proposed, resulting in a dataset of 191 morphological characters. One of the main results of this analysis is that Halophryninae is not monophyletic, with Allenbatrachus, Batrachomoeus, and Halophryne being more closely related to Porichthyinae, Thalassophryninae, and Batrachoidinae. This new phylogenetic arrangement and its supporting synapomorphies are discussed, including potential implications in the classification within this order.

Relative to many highly migratory fishes, Striped Marlin, Kajikia audax, exhibit considerable stock structure. At least four genetically distinct stocks of Striped Marlin have been delineated in the Pacific and Indian oceans, although stock composition in the central North Pacific (CNP) remains unclear and the presence of an additional stock in the North Pacific has been suggested in two recent studies. The goals of this research were to clarify the number of Striped Marlin stocks in the North Pacific and utilize temporal sampling to better understand the stock dynamics of Striped Marlin exploited by the Hawaii-based pelagic longline fishery (HBPLLF). Fishery observers collected 417 samples of Striped Marlin from the HBPLLF from 2019-2020. Of these, 85 samples underwent genotyping-by-sequencing using DArTSeqTM and the data were co-analyzed with an existing single nucleotide polymorphism (SNP) dataset for 256 individuals of Striped Marlin collected from throughout the species’ range and reported in a previous study. Three of 12 Striped Marlin previously reported to comprise a putative second stock in the North Pacific and all with high observed heterozygosities were also re-sequenced to test the hypothesis that sample contamination resulted in the identification of a spurious stock. After re-sequencing, the observed heterozygosity of each of the three individuals was reduced by approximately 50%, confirming contamination and the original sequences for the 12 individuals comprising the putative second stock were removed from the dataset. Clustering analyses of the resulting dataset strongly supported a single North Pacific stock; the three re-sequenced individuals clustered into previously described stocks. The 73 (post-quality filtering) Striped Marlin sampled from the HBPLLF clustered into either the North Pacific (NPO; Japan, Taiwan, Hawaii, and California sample locations) or Oceania (New Zealand, western Australia, and eastern Australia sample locations) stocks, indicating mixing of the two stocks in the CNP. A panel of 48 SNPs with the highest power to discriminate between the two stocks was developed and 32 of these loci were used to genotype and assign an additional 325 Striped Marlin collected from the HBPLLF to stock of origin. Overall, 305 of these fish were assigned to stock of origin with high (> 90%) confidence and combined with DarTSeq-based assignments of the original 73 fish. Both stocks were present throughout the sampling period (NPO: 41.3%; Oceania: 58.7%). Temporal changes in stock composition were identified, with NPO fish dominant during the winter and spring, and Oceania fish dominant during the summer and fall. Although the HBPLLF is known to exploit mostly sub-adult Striped Marlin, 13 (3.1%) samples were found to be in an active spawning condition at the time of capture based on visual inspection. Of these, 10 assigned to NPO and two assigned to Oceania (the 13th fish assigned into Oceania but scores were below 90%). Factors that may influence the stock composition of Striped Marlin in the HBPLLF, including stock-specific movements to different spawning grounds and alternate feeding areas, as well as seasonally displaced recruitment to the HBPLLF, are discussed.