Cultural eutrophication (CE) is the allochthonous input introduction of a quantity of matter, such as sediments, organic material, or nutrients, into a water body over the pre-anthropogenic (natural) levels. In most coastal estuaries CE has come to refer primarily to an increase in the concentration of phyto-nutrients. CE has been identified as the cause of very graphic phenomena such as hypoxia and fish kills. In this work I examine the potential for CE to alter the composition of the primary producer community and potentially alter or disrupt the benthic food web, using Macoma balthica as an indicator species. A series of surveys and experiments identified that clams in areas with greater than average nutrient concentrations had lower health, slower growth, and greater non-predatory mortality than clams in less eutrophic areas. Primary production, as estimated from chlorophyll a concentration, was greater at higher nutrient locations while the health and growth of clams was lower. The phytoplankton community in the more eutrophic areas had a lower proportion of diatoms relative to dinoflagellates. A biochemical analysis of clam tissue indicated that the clams from the less nutrient rich sites had a greater proportion of Eicosapentaenoic acid (EPA) relative to other fatty acids. Diatoms are rich in EPA compared to dinoflagellates. Thus, we hypothesize that CE induced shifts from diatom based production toward dinoflagellates may be limiting trophic transfer due to a lack of EPA. Using a series of models we were able to predict that trophic disruption could significantly reduce the scope for growth of the blue crab, Callenecties sapidus . Thus it is possible that the CE induced changes to primary producer community could disrupt the food web creating a trophic bottleneck.

Carbonate sands are an integral part of coral reef environments but their role in the cycling of matter in the reef is understudied. Methods such as micro-profiling, core incubations, in-situ chamber incubations, and aquatic eddy covariance measurements can be used to study solute fluxes and biogeochemistry of these sediments. The interfacial fluxes can reveal production and degradation processes in the sands and thereby provide key information on the role of these sediments in the cycles of matter in the coral reef. To date, the eddy covariance technique is the most advanced method for measuring the solute fluxes noninvasively. The traditional eddy covariance method employs a solute sensor (e.g. oxygen sensors) and an Acoustic Doppler Velocimeter (ADV). We developed a triple O2-sensor-eddy covariance instrument that provides a hardware solution minimizing time-lag errors arising from the physical separation of the O2 sensor and the velocity sensor measuring volume, which affects the measurements in the traditional instrument. These errors are most pronounced in environments with currents and waves, and are difficult to correct through data processing. Oxygen flux measurements with the aquatic eddy covariance technique in benthic environments with wave action and/or highly varying current direction can lead to erroneous flux estimates due to the transient time-lag between the velocity and oxygen concentration measurements. By positioning the oxygen sensors in the same horizontal plane and with 120 degrees radial spacing around the center point where current flow is measured, synoptic oxygen measurements are recorded with opposing time-lags. Averaging of the three sensor signals at each time point produces an oxygen concentration closely corresponding to that at the flow measuring point, and thus, at a position that does not require time-lag correction. Field tests with the new instrument in a coral reef sand flat affected by waves demonstrated the advantages of the new instrument setup, and simultaneously allowed evaluation of the magnitude of errors that are associated with the traditional time-lag correction. Model simulations of the 3 sensors system in a known oscillating oxygen distribution field suggests that the new 3 oxygen sensor eddy covariance (3OEC) system can reduce time-lag error by at least five-fold. We conclude that the new system can improve oxygen flux estimates significantly, while simplifying the processing of the aquatic eddy covariance data. Another factor that may impose errors in the calculated fluxes by the aquatic eddy covariance method is the slow response of the solute sensors which may dampen the recorded dataset. To overcome this issue, we developed an instrument by which reliable and reproducible measurements of the response time of the sensors is possible. We used this method to select the sensors that we installed on our improved eddy covariance instrument. We used the improved aquatic eddy covariance instrument in a Florida coral reef sand flat to quantify benthic oxygen fluxes as proxy for benthic metabolism. The non-invasive measurements characterize the carbonate sands as sites of intensive organic matter production and consumption, and underline their dependency on key environmental drivers such as light, water current velocity, and significant wave height. The positive response to light and increasing light intensity were characterized by large temporal dynamics even at ~9 m water depth. Daytime fluxes reached 2.3 ± 2.0 (Mean ± SE) mmol m-2 h-1 and nighttime fluxes -2.0 ± 0.7 (Mean ± SE) mmol m-2 h-1. Spring deployments indicated net autotrophy of the sedimentary environment, while summer and winter measurements implied a metabolic balance. During summer, an increase in bottom currents correlated with an increase in sediment oxygen uptake during daytime and nighttime, reflecting enhanced benthic organic matter mineralization activity during the warm season. The oxygen fluxes reveal their role in the reef sands as hotspots of benthic carbon cycling. / A Dissertation submitted to the Department of Earth, Ocean, and Atmospheric Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / 2019 / November 8, 2019. / Aquatic eddy covariance, Benthic oxygen flux, Carbonate sediments, Ocean engineering, Permeable sediments, Sediment biogeochemistry / Includes bibliographical references. / Markus Huettel, Professor Directing Dissertation; Janie Wulff, University Representative; Amy Baco-Taylor, Committee Member; Peter Berg, Committee Member; Sven Kranz, Committee Member; Kevin Speer, Committee Member.

Includes abstract. / Includes bibliographical references. / The life history strategy of the Cape horse mackerel, Trachurus capensis in the southern Benguela, relating to distribution and reproductive ecology, was re-evaluated. It is possible that certain aspects of the species' life history may have changed since the previous assessment by Barange et al. (1998), as a result in this study, the conceptual hypotheses about the life history of horse mackerel proposed by Barange et al. (1998) were re-evaluated and possible revisions proposed. Distribution patterns were analysed using acoustic and midwater trawl data (1997-2010), and demersal trawl data (1984-2011) collected during biannual surveys of pelagic and demersal fish.

A two-year zooplankton survey of lower Chesapeake Bay was conducted from August 1971 to August 1973. Twenty-four stations extending from the Rappahannock River mouth to the Bay entrance were sampled each month, using paired bongo nets with a 202 μm mesh. Marine Cladocera comprised >68% of the total zooplankton during two months of the survey, and were 36-40% by number three other times. The mean abundance over the whole study area of all cladoceran species combined was >62,000 m-3 in August 1971 and was >1000 m-3 on six other occasions. Of the six species of marine Cladocera found, Podon polyphemoides was most eurythermal and euryhaline, being found in abundance at temperatures of 7-26°C and salinities of 11.5-27 0/00. It was found in all months of the year with a peak occurrence in May and a smaller peak in January. Peak densities of P. polyphemoides always followed periods of rapidly changing temperatures. Podon leuckarti was found only near the Bay mouth, nearly always at densities of latitude, cold water species which requires spring conditions for its emergence, restricting its appearance to the month of May in Chesapeake Bay. Podon intermedius occurred only in the bay mouth area, at densities of 18.3-26.4°C and a minimum salinity of 20.42 0/00. Although appearing to be a warm-water organism in Chesapeake Bay, the species is found at much lower temperatures elsewhere. An inverse temperature-salinity relationship may influence the worldwide distribution of this species, with its warm water occurrences being at relatively low salinities, and vice versa. Evadne nordmanni is a high-latitude species neeaing spring conditions to develop. It does not persist throughout the summer in regions where temperatures are >21°C for two months or more. E.nordmanni occurred from late winter through June, with a peak in May. It appeared throughout the study area with highest concentrations (>100 m-3) at the bay mouth at 15-19°C and 17-26 0/00-salinity. Evadne tergestina and Penilia avirostris usually occurred at densities of >100,000 m-3 at some stations, with a mean of 30,000 m-3 over the entire area. Densities of both species were greatly reduced by September and they disappeared in October. The species reappeared in August 1972 in greatly reduced numbers, being >1000 m- 3 only at the bay mouth. Numbers were higher in August 1973 but were still an order of magnitude less than in 1971. The freshwater runoff from Tropical Storm Agnes was responsible for the great reduction in populations of Podon polyphemoides, Evadne tergestina and Penilia avirostris in the summer of 1972 as compared to 1971 and 1973. Biological influences on cladoceran populations included predation by ctenophores, which limited P. polyphemoides to the bay mouth in June, and predation by chaetognaths, a probable cause of the great reduction in E. tergestina and P. avirostris densities between August and September. Day and night sampling over the entire study area and a 24-hour station at the York River mouth showed that Evadne tergestina releases its young from the brood pouch just before dawn. An individual of E. tergestina releases its first brood of young when two days old. The parthenogenetic reproduction of Cladocera makes them among the most opportunistic of marine zooplankters and is probably partially responsible for their comparative lack of speciation in marine waters. This dissertation is from the Joint Program Degree from the College of William & Mary and University of Virginia and awarded by the University of Virginia.

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At the time of the Deepwater Horizon oil spill in 2010, very little was known about the inshore bottlenose dolphin (Tursiops truncatus) populations hit hardest by the spill. Without previous population demographic data impacts were challenging to assess. My dissertation was designed to build research capacity moving forward by helping to fill data gaps in the western Florida Panhandle. The first study presented here resulted in the first system-wide assessment of seasonal abundance, survival, and site fidelity patterns of bottlenose dolphins that inhabit the Pensacola Bay system. In contrast to a previous study that reported only 33 dolphins, results from mark-recapture analyses estimated abundance ranging from 220-310 individuals, which consisted of a high proportion (43%) of transients. The second study revealed fine-scale genetic population structure (detected using both microsatellite and mitochondrial DNA markers) among five inshore systems in the Florida Panhandle. Migration rates were variable among populations with higher gene flow moving from east to west than in the reverse direction, and into St. Andrews Bay than coming out of it. There was no evidence of sex-biased dispersal. Finally, a 100-year flood (20 inches over 30 hours) occurred unexpectedly in the middle of my field work, after which dolphins were seen with extensive skin lesions. The event resulted in a unique natural experiment from which to evaluate the potential impacts of sustained freshwater exposure on local dolphin population health. Despite the persistence of a near freshwater environment for several months, skin lesions were not widespread but extensive and persistent for only some individuals, the reasons of which remain unknown. This body of work offers an updated perspective on the ecological and evolutionary connectivity of inshore dolphin populations in the Florida Panhandle, information of which is crucial for understanding how to best manage populations and assess new potential threats moving forward.

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The objective of my research was to examine the physiology and behavior of metamorphosing oysters, Crassostrea virginica, and to investigate the effects of low oxygen stress on metamorphic processes. Specifically, I examined the effects of hypoxia (20% of air saturation) and microxia (&<&1% of air saturation) on settlement, survival, growth, morphology, metabolic rate and feeding on post-settlement oysters. All of the functions I measured were adversely affected by hypoxia and microxia, compared to normoxic controls. Survival times indicate that, like larvae and adults, post-settlement oysters are capable of anaerobic metabolism. The 2 week period following settlement is especially critical to recruitment. Low oxygen conditions increases mortality and have detrimental effects on the development and growth of post-settlement oysters. Oysters have the ability to feed at nearly all stages of settlement and metamorphosis. While hypoxic conditions reduce feeding only in the youngest metamorphosing oysters, microxic conditions affect all ages. Not only does weight-specific metabolism decrease as the oysters grow, but metabolic responses to low oxygen change from relatively oxygen independent to oxygen dependent. I conclude that oyster distribution may be influenced by low oxygen, especially in those areas that experience prolonged (24-48 h) hypoxia or severe microxic events. Low oxygen events may control recruitment into the adult population directly, because of larval settlement failure and post-settlement mortality, and indirectly, because of reduction in feeding, development rate, and growth of post-settlement oysters.