In the Chesapeake Bay, < 1% of the historic oyster population remains, and efforts have been increasing to restore oysters and the services they provide. Building reefs that successfully provide ecosystem services–especially habitat and foraging grounds–may require different restoration techniques than those previously used, and success may depend on reef morphology (complexity), location, and environmental conditions. Salinity and habitat complexity are two important factors that may interact to effect benthic communities and predator-prey interactions on restored reefs. The goals of this project were: (1) Characterize the benthic communities on restored oyster reefs in lower Chesapeake Bay, and (2) examine the effects of structural complexity and salinity on benthic communities and predator-prey interactions. A two-year field survey of restored reefs was carried out in four rivers in lower Chesapeake Bay to characterize faunal communities on restored reefs and to quantify the effect of reef complexity on faunal communities. A laboratory mesocosm experiment was conducted to examine the effect of reef complexity on predator foraging. In total, 61 macrofaunal species were identified among all samples, and restored reefs supported on average, 6,169 org/m2 and 67.88 g-AFDW/m2. There were significant differences in the community composition and diversity among the rivers, and salinity was the environmental factor that best explained the observed differences in species composition across the rivers. Salinity and rugosity (i.e., structural complexity) both positively affected diversity, while salinity negatively affected macrofaunal abundance and biomass. Oyster density and rugosity positively affected macrofaunal biomass, and oyster density positively affected mud crab, polychaete, and mussel densities. In the mesocosm experiment, predator foraging, measured by proportion and number of prey consumed, was significantly reduced in the presence of oyster shell structure. However, predators were able to consume more prey when prey density was increased, even in the presence of oyster shell structure. These results combine to enhance our understanding of the benefits of increased habitat complexity for both prey and predators on restored oyster reefs. Increasing complexity worked to increase the abundance, biomass, and diversity of organisms inhabiting restored reefs, and even though predator consumption was reduced in the presence of structure compared to non-structured habitat, predators were able to consume more prey individuals when prey density was increased. Therefore, increasing the structure of oyster reef habitat may benefit prey species by providing refuge habitat, and benefit predators by providing an increased abundance of available prey items.

While deeper estuaries typically demonstrate predictable responses to increased nutrient loads, responses in shallow systems are more varied, due in part to the presence of multiple benthic autotrophs. Shallow systems are particularly vulnerable to increases in watershed nutrient loads due to their position at the interface between land and open water. The prevailing conceptual model of eutrophication for shallow systems currently describes a succession in the dominant autotroph from seagrass to macroalgae to phytoplankton, but this model does not include benthic microalgae, which can sequester nutrients in photic systems. The Virginia Eastern Shore is characterized by shallow lagoons connected to upland watersheds through small tidal creeks, where the main source of fresh water and nutrients is groundwater. While some studies have characterized the response of the lagoons to nutrient loads, little is known about the tidal creeks and whether they act as filters, transformers, or conduits for land-based nutrients. We examined the role tidal creeks play in modulating watershed nutrient inputs in the Great Machipongo River (GMR) system, the largest tidal creek complex on the seaside of the Virginia Eastern Shore. We developed a field monitoring program that provided data to calibrate a reduced complexity Estuarine Ecosystem Model (EEM). Production, respiration, and net ecosystem metabolism were quantified, using both the open water and component methods, seasonally at three sites within this system. These rates together with monthly concentrations of standing stock nutrients and water column chlorophyll, monthly DataFlow surveys of physiochemical parameters, seasonally and spatially-intensive benthic chlorophyll surveys, and a bathymetric survey were used to develop and calibrate the EEM. The model was used to assess the degree to which tidal creeks export (via flushing), remove (via denitrification), or transform (via autotrophic uptake) land-based nutrient loads to the adjacent lagoons during baseflow and storm conditions. Component metabolism studies showed the system was overall net autotrophic, with increasing dominance of benthic processes towards the head of the estuary. Open water metabolism studies suggested the system was overall net heterotrophic, but we believe this conclusion is biased by the surrounding marshes and violations of the constant water mass assumption. The creek system exported 61,476 kg N y-1 as phytoplankton biomass, an amount approximately equal to inputs from the watershed and atmosphere, and imported 172,830 kg N y-1 in dissolved inorganic forms for a net import of 111,354 kg N y-1 from Hog Island Bay. Phytoplankton uptake, benthic microalgal uptake, and denitrification accounted for 216%, 343%, and 38% of the annual input of watershed and atmospheric N to the system, indicative of rapid cycling and advection of nutrients from Hog Island Bay. The storm simulation showed that almost all of the additional 28,635 kg N y-1 added from the watershed was flushed to Hog Island Bay and a small portion was denitrified. This study indicates that GMR system function is dominated by benthic processes, and the system acts as a transformer and filter of land-based nutrients during normal conditions and a conduit of nutrients during storm conditions.

This thesis developed from the VIMS Larval Fish Monitoring Program, which began in 2007 as part of a study comparing the larval fish assemblages of Chesapeake and Delaware Bays. Ribeiro et al. (2015) analyzed data from the first three years of this time series to describe the temporal variation in the larval fish assemblages. After this initial study was completed (three years in duration), the sampling continued at the fixed station near the mouth of the York River, which was used to represent the Chesapeake Bay. For this thesis, therefore, eight years of data (2007-2015) were available to investigate temporal changes in the larval fish assemblage, and to better evaluate intra-annual variation of the larval fish assemblage. Further, larval fish indexes of five target species of commercial and recreational importance in the Chesapeake Bay, were examined, including Anchovy (Anchoa spp.), Atlantic Menhaden (Brevoortia tyrannus), American Eel (Anguilla rostrata), Summer Flounder (Paralichthys dentatus), and Atlantic Croaker (Micropogonias undulatus). Regression models were used to evaluate the effect of different environmental and temporal variables on the larval fish density from the York River system. Results show a stable assemblage in the York River since 2007, with marked seasonal patterns in terms of composition and abundance of larval fishes. The assemblage from May to August is formed by estuarine species with high number of larval fishes (e.g., Anchovy, Green Goby, Naked Goby); the assemblage from September to April is characterized by a lower number of species, mainly coastal spawners such as Atlantic Croaker, Summer Flounder, and Atlantic Menhaden. at the species level, slight annual variations were found, although in general abundances were stable across the time series. Because the larval fish monitoring program sampled at a single fixed station located in the lower portion of the York River system, it is limited spatially even though it has good temporal resolution (eight years). One fixed station may capture only localized patterns and it is unclear if this is comparable to the larval fish assemblage in southern portion of the Chesapeake Bay generally. The second chapter of this thesis addresses the question of spatial variation of the larval fish assemblage, principally between the York River system and the mouth of the Chesapeake Bay. Samples taken in three locations were compared to determine if the assemblage varied among the sampling locations. Larval stages of two coastal spawners, Atlantic Menhaden and Atlantic Croaker, were the two most abundant at both all locations. Results indicate species specific differences among the locations, for example, Atlantic Croaker larvae were more abundant in the York River mouth (YRM) than in the Chesapeake Bay mouth (CBM), indicating significant spatial variation in larval fish assemblage composition over a distance of approximately 40 km, the distance between the YRM and CBM. This variation should be taken into account when generalizing the structure of the larval fish assemblage of the York River spatially.

Taking an ecosystem approach to fisheries requires the consideration of relevant ecological processes within research and assessment frameworks. Processes affecting ecosystem productivity can be categorized as biophysical (climate variability, primary production), exploitative (fishing), or trophodynamic (food web interactions). This dissertation incorporates these three governing processes to characterize spatiotemporal diversity and population abundance trends for multiple demersal fish and invertebrate species that inhabit the nearshore zone (15-30 ft. depth) along portions of the U.S. Atlantic east coast. Two large marine ecosystems (LMEs) encompass the U.S. East coast – the Southeast and Northeast U.S. Continental Shelf LMEs. The level of connectivity within and between these two ecosystems is well understood for some individual species, but not generally for the nearshore assemblage. The first research chapter of this dissertation is a spatial diversity analysis of 141 fish and invertebrate species that inhabit nearshore waters from Florida to New York. Latitudinal diversity patterns revealed multiple biotic ecotones, or areas of high species turnover. An ecotone was evident in northern spring near the Cape Hatteras border of the two LMEs, but this barrier dissipated as water temperatures homogenized and assemblage connectivity between ecosystems increased throughout the year. Multiple other biotic ecotones were evident within the Southeast U.S. LME and were explained by seasonality and the proximity and area of adjacent estuarine habitat. The second and third research chapters of this dissertation focus on explaining temporal abundance trends for multiple nearshore fish and invertebrate species within the Southeast U.S. LME. For the second research chapter, abundance trends for 71 species were analyzed during 1990-2013 within a univariate time series modeling framework with the goal of determining the relative importance of climate variability and fishing pressure as governing influences on abundance. A decrease in bycatch mortality explained changes for multiple species, while climate variability governed the dynamics for others. Multivariate ordination revealed similar trends for groups of taxonomically related species, indicating governing processes act on species with similar life histories. An extension of results from the second research chapter, research chapter three explores trophic interactions between the bonnethead shark (Sphyrna tiburo) and five of its prey species within Southeast U.S. LME nearshore waters. Multivariate time series modeling supports a negative effect of bycatch on bonnetheads, and population-level predation effects of larger sharks on multiple prey species. Abundance trends for most prey species were also explained by environmental variability associated with the Pacific Decadal Oscillation, although trophic effects were stronger. This body of work incorporates relevant ecological factors in characterizing diversity and abundance trends for fish and invertebrate species comprising the nearshore demersal assemblage within Southeast and Northeast U.S. LMEs. Results indicate seasonal connectivity between LMEs that require further exploration at multiple spatial scales. Abundance time series modeling for multiple species in the Southeast U.S. LME reveals that fishing and trophodynamics may be relatively more influential drivers than climate variability in this sub-tropical system.

Microorganisms are key players in the ecosystem functioning. In this thesis, we developed a framework to preprocess raw microbiome data, build a correlation network, and analyze co-occurrence patterns between microbes. We then applied this framework to a marine microbiome dataset. The dataset used in this study comes from a year-long time-series to characterize the microbial communities in our coastal waters off the Cal Poly Pier. In analyzing this dataset, we were able to observe and confirm previously discovered patterns of interactions and generate hypotheses about new patterns. The analysis of co-occurrences between prokaryotic and eukaryotic taxa is relatively novel and can provide new insight into how marine microbial communites are structured and interact.

Throughout the world, birds represent the primary type of wildlife that people experience on a daily basis. However, a growing body of evidence suggests that alterations to the acoustic environment can negatively affect birds as well as humans in a variety of ways, and altered acoustics from noise pollution has the potential to influence human interactions with wild birds. In this thesis, I investigated how anthropogenic noise impacts daily behavior as well as community structure of wild birds. In the first component of this thesis, I assessed the distance at which a bird initiates flight or escape behavior (i.e., flight initiation distance or FID) in varying acoustic conditions. I surveyed 12 songbird species from three foraging guilds, ground foragers, canopy gleaners, and hawking flycatchers, and I predicted FIDs to decrease, remain the same, and increase with noise exposure, respectively. Contrary to expectations, the canopy gleaning and flycatching guilds exhibited mixed responses, with some species exhibiting unchanged FIDs with noise while others exhibited increased FIDs with noise. However, FIDs of all ground foraging species and one canopy gleaner decreased with noise levels. In the second component, I examined the feeding of wild birds, an increasingly popular recreational activity throughout North America that promotes increased sense of wellbeing by connecting people with wildlife and nature. I tested how experimental noise influences abundance, species richness, community structure and foraging behavior of songbirds at maintained bird feeders. By measuring activity levels of all species that utilized the feeders exposed to intervals of quiet and noisy conditions, I found noise to be a significant predictor of community turnover. Specifically, noise exposure resulted in increased feeder activity for two species, and decreased activity for one species. I also confirmed previous research conducted in the laboratory indicating white-crowned sparrows decrease their foraging rate under noise conditions, presumably as a trade off with visual vigilance. Considering the interactions of humans and wild birds, the results from my two thesis components indicate that the acoustic environment can play a role in how species of different foraging guilds respond to birdwatchers and what species visit bird feeders.

The arroyo toad (Anaxyrus californicus) is a federally endangered species found on Fort Hunter Liggett, Monterey County, California. The species was discovered in 1996 and was determined to occupy 26.7 km of the San Antonio River from approximately 2.4 km northwest of the San Antonio Mission de Padua, to the river delta above the San Antonio Reservoir. The construction of the San Antonio Reservoir dam in 1963 isolated this northern population of arroyo toads. Through time, the Fort Hunter Liggett landscape has changed drastically. The land was heavily grazed by cattle until 1991, which considerably reduced vegetation in riparian areas. Military training following acquisition of the land in 1940 far exceeded current allowable training. Fire was used extensively to reduce unfavorable vegetation, and as a result, extreme tree loss occurred through the ranges. Today cattle grazing is prohibited and military activity is restricted from riparian corridors. While riparian vegetation continues to recover in the San Antonio River, habitat for breeding arroyo toads has become less suitable. To improve conservation efforts and management of this endangered species, I have provided a thorough assessment of the life history of arroyo toads specific to Fort Hunter Liggett and identified the status and current threats to the population on the installation. I have also prepared a habitat assessment of the San Antonio River in the arroyo toad range, quantified habitat conversion, and identified areas that may no longer provide suitable breeding habitat for the species. The research conducted for this report is preliminary to restoration efforts that are inevitable to ensure recovery of the endangered species at Fort Hunter Liggett.

Cephalopods provide forage to a wide range of predators in marine food-webs. Despite their ecological importance, a basic understanding of the mechanisms controlling predation risk and demand is lacking. This is true of one of the most common species of squid found in the northwest Atlantic, the longfin inshore squid (Loligo pealeii). In this dissertation, I address this shortcoming by investigating the role that size and behavior play in influencing squid’s vulnerability to predation. I used long-term food habits, population survey, and commercial landings data, to quantify size-based patterns of predation respective to 25 species of predators. Additionally, I estimated the amount of overlap between predatory consumption and the fishery catch for squid by size. I found that finfish and elasmobranchs generally consumed juvenile and sub-adult squid, while marine mammals primarily targeted adults. Consequently, marine mammals had the highest overlap with the fishing industry for squid size resources. Although large squid were not common in predator diets, predators did not appear to be gape-limited when feeding on squid. This suggested that other factors, including behavior, were important in shaping size-based patterns of predation. I used a laboratory-based approach to quantify attack and capture behaviors towards squid by two predators representing contrasting foraging tactics. Bluefish (Pomatomus saltatrix) and summer flounder (Paralichthys dentatus) were chosen as cruising and ambush predators, respectively. Patterns in attack rates suggested that sizeselection on squid was constrained by passive processes rather than active choice in both predators. Size-dependent profitability functions were calculated by combining capture success rates, handling times, and relative prey mass, and determined that bluefish was the more efficient predator of squid. Lastly, I evaluated the occurrence and effectiveness of anti-predator responses used by squid in the presence of bluefish and flounder. Squid behavior depended on the type of predator present, and the survival value of primary and secondary defense behaviors differed during interactions with each predator. The results of this project are intended to improve the quality of management of squid and their predators by providing a better understanding of predator-prey interactions in the northwest Atlantic.

A comparative study of the field populations of Crepidula lingulata, Crepidula nurnmaria, and Calyptraea fastigiata indicated all three preferred a rocky substrate but favored different size rocks. Their positions on the rocks varied but the greatest numbers were found attached to the undersides. Crepidula lingulata and C. nummaria preferred larger rocks and were found in intraspecific associations more often than C. fastigiata which preferred smaller rocks. These associations occurred with a 1:1 sex ratio; however, the overall population did not. Crepidula lingulata had a high female count and C. fastigiata a high male count. Males, of all three species, were smaller in size than females. Leptasterias hexactis and Evasterias troschellii were found to be possible predators. Protection was afforded those attached to the undersides of rocks. All three species used the radula to remove irritants from under the shell including the tube feet of attacking sea stars.

Three heteromyid rodent species were studied in relation to a large dry wash in Millard County, Utah, during the summer, 1974. Data were gathered with three trapping grids and analyzed to determine if the dry wash influenced rodent movement and distribution patterns. Dipodomys ordii and Dipodomys microps were distributed non-randomly in the dry wash and adjacent habitat, but Perognathus Zongimembris seemed to be randomly distributed. Dipodomys ordii was significantly correlated with wash habitat, but D. microps was found most frequently in upland areas. Soil and vegetative differences and competition were possible causes for the observed distribution. The wash was observed as a source of dispersing young D. ordii. It was concluded that the dry wash had little effect on daily movement of the rodents observed.