Although rivers are the primary source of dissolved inorganic nitrogen (DIN) inputs to the Chesapeake Bay, direct atmospheric DIN deposition and DIN fluxes from the continental shelf can also significantly impact Chesapeake Bay hypoxia. The relative role of these additional sources of DIN has not previously been thoroughly quantified. In this study, the three-dimensional Estuarine-Carbon-Biogeochemistry model embedded in the Regional Ocean Modeling System (ChesROMS-ECB) is used to examine the relative impact of these three DIN sources. Model simulations highlight that DIN inputs from the atmosphere have roughly the same impact on hypoxia as the same gram for gram change in riverine DIN loading. DIN inputs from the shelf have a similar overall impact on hypoxia as those from the atmosphere (~0.2 mg L-1), however the mechanisms driving these impacts are different. While atmospheric DIN impacts dissolved oxygen (DO) primarily via the decomposition of autochthonous organic matter, coastal DIN also impacts DO via the decomposition of allochthonous organic matter entering the Bay from the continental shelf. The impacts of coastal and atmospheric DIN on estuarine hypoxia are greatest in the summer, and occur farther downstream (lower mesohaline) in wet years than in dry years (upper mesohaline). Integrated analyses of the relative contributions of all three DIN sources on summer bottom DO concentrations indicate that impacts of atmospheric deposition are largest in shallow near-shore regions, riverine DIN has dominant impacts in the largest tributaries and the oligohaline Bay, while coastal DIN fluxes are most influential in the polyhaline region. During the winter when estuarine circulation is strong and shelf DIN concentrations are relatively high, coastal DIN impacts bottom DO throughout the Bay.

The subterranean estuary (STE) is a subsurface ecosystem where fresh groundwater mixes with intruding, recirculated seawater at the coastline. Despite being present globally, STEs and their potential impacts as hotspots for biogeochemical processing, or as a source of nutrients to coastal systems, are not well understood. STEs have been recognized as highly reactive zones for biogeochemical reactions, which influence the fate and transport of nutrients, organic matter, and trace metals discharged to the coastal ocean. Biogeochemical processing of nitrogen (N) in STEs influences N in submarine groundwater discharge (SGD) including its availability for use by primary producers and cascading eutrophication. The overarching goal of this dissertation was to assess N cycling in STEs and to evaluate how these processes may impact exchanges of N with adjacent marine environments. In chapter two, seasonal, tidal, and spatial variation in geochemical gradients as well as N cycling rates were examined to determine their influence on nutrient fluxes in SGD in the Gloucester Point beach STE (GP-STE). Geochemical gradients varied significantly across seasons, but not over tidal and spatial scales, driving seasonal variance in STE nutrient concentrations and fluxes. The nitrate, ammonium, and dissolved oxygen gradients in the GP-STE suggested nitrification was a major biogeochemical process determining the fate of groundwater derived N. The GP-STE was identified as a source of N and phosphorus (P) to the overlying York River estuary in all seasons, but denitrification reduced N export. In chapter three, the microbial community of the sandy GP beach along with the composition and abundance of nitrifiers was examined with depth in four seasons. The microbial community varied significantly with depth, but not with season. Nitrifiers were present in the top one meter of the beach indicating the genetic potential for nitrification in the system, but their abundances decreased with depth. Multivariate analysis indicated that porewater nutrient concentrations, pH, and dissolved oxygen were major drivers of subsurface nitrifier abundance. In chapter four, STE nitrification rates were measured using conservative mixing models, an in situ tracer experiment, and ex situ sediment slurry incubations. All three methods indicated nitrification is occurring in the GP-STE; however, the in situ tracer experiment revealed variation in nitrification rates over space and time that was not captured by the mixing model calculations or slurry incubations. These data suggest that, due to heterogeneity in the subsurface environment, in situ experiments may be the best approach for estimating STE process rates. Chapter five used a global meta-dataset to examine the groundwater nutrient pool, determine STE behavior with regards to nutrients, and assess the impact STE processing has on groundwater fluxes to the global ocean. The composition and concentrations of the groundwater nutrients were influenced by sample salinity, latitude, land use, and site type. DON represented >30% of the groundwater N pool. STEs, at the global scale, produced DIN and DIP, but reduced DON concentrations in groundwater nutrients, resulting in higher DIN and DIP fluxes, but lower DON fluxes in fresh SGD to the global ocean. Total SGD fluxes of DIN and DON were estimated to be higher than riverine fluxes the ocean, but DIP fluxes from total SGD were half the riverine input. Overall, this dissertation reveals the importance of STE biogeochemical processes on exchanges of nutrients along the land-ocean continuum from groundwater to the coastal ocean.

Throughout the ocean, zooplankton transfer energy from primary producers to higher predators and transport carbon from surface waters to depth. The efficiency of these processes depends in part upon the taxonomic composition and trophic ecology of the zooplankton community. Zooplankton species abundance and distribution shifted over recent decades along the West Antarctic Peninsula during a period of rapid regional warming and sea-ice decline. Although conducted within the context of long-term change, this dissertation research focuses on zooplankton dynamics at finer temporal scales that have received less attention. I analyzed depth-stratified net samples to investigate zooplankton diel vertical migration during Antarctic summer. I further conducted twice-weekly sampling over three field seasons to characterize seasonal and interannual changes in coastal zooplankton composition. I also used field measurements, experimental incubations, and compound-specific stable isotope analysis to study the growth and trophic ecology of a dominant species – the Antarctic krill Euphausia superba – during its juvenile stage. Results indicate that several zooplankton taxa conducted diel vertical migration despite nearly continuous daylight during Antarctic summer. Other carnivorous, detritivorous, and seasonally migrating taxa were most abundant in the mesopelagic zone throughout the diel cycle. Vertically migrating zooplankton and mesopelagic residents likely have a substantial impact on vertical carbon flux, which should be better quantified in the Southern Ocean. Repeated shore-based sampling showed that seasonal peaks in coastal zooplankton biomass follow local phytoplankton blooms. Seasonal succession from larger, herbivorous species to smaller, omnivorous species was a consistent phenomenon across multiple taxonomic groups and years. Seasonal abundance patterns for various taxa shifted by a week or more between two consecutive years, consistent with a two-week shift in the timing of sea-ice breakup and the spring phytoplankton bloom. Flexible life history and trophic ecology may limit the risk of reproductive failure despite climate-induced phenology shifts. Exceptionally warm temperatures coincided with a bloom of the gelatinous salp Salpa thompsoni, and such conditions may become more common in future decades. Phytoplankton ingestion was insufficient to support rapid growth of juvenile krill during summer in coastal waters, and heterotrophic protists were a critical intermediate trophic link. Phytoplankton consumption was limited due to inefficient feeding on small cells that dominated the available autotrophic prey. Metazoan zooplankton were also important prey for juvenile krill, which are truly secondary consumers. This dissertation research revealed substantial shifts in the trophic ecology and composition of Antarctic zooplankton communities at diel to interannual scales, with implications for regional biogeochemical cycles and food web dynamics. Future work should consider these shorter time scales to detect and understand long-term change in Antarctic marine ecosystems.

The biological pump is a critical component of carbon transformation in aquatic ecosystems, but the role that zooplankton play in carbon production and vertical export is rarely studied in estuaries. Zooplankton produce carbon-rich fecal pellets which sink to depth and can fuel benthic community metabolism. The body size and taxonomic structure of the zooplankton community varies on interannual, seasonal, and diel time scales, and can lead to varying carbon production and export rates. We quantified fecal pellet carbon (FPC) production by the whole mesozooplankton community (> 200 µm) in the York River, a sub-estuary of Chesapeake Bay. Biomass and taxonomic composition of the near-surface zooplankton community was measured with paired day/night net tows conducted monthly over one year (Jun. 2019 - Nov. 2020). We also conducted live experiments to quantify FPC production rates of both the (size-fractionated) whole community and of dominant individual taxa. Zooplankton biomass generally increased in surface waters at night (2 to 29-fold) due to diel vertical migration. Biomass was low in the winter and high in the summer, with a peak in gelatinous zooplankton biomass in summer the most conspicuous seasonal shift in community composition. Acartia spp. copepods were consistently the most abundant taxon, with cladocerans and barnacle nauplii becoming equally abundant in the winter and spring. Whole community FPC production rates were higher (3- to 65-fold) at night than during the day. This was driven by increases in mesozooplankton biomass, especially Acartia spp., at night due to diel vertical migration, with the 0.5 – 1 mm size class comprised of Acartia spp. contributing 2-26% to FPC production in the day versus 40-70% at night. Daytime FPC production was dominated by the two smallest mesozooplankton size fractions - comprised mostly of Acartia and other copepods, barnacle nauplii, rotifers, and cladocerans. Increases in the relative contribution of larger size fractions to total FPC production occurred at night due to diel vertical migration into surface waters of larger animals such as mysids, which produced relatively large and carbon-rich fecal pellets. Seasonal estimates of community FPC production were highest in the fall, intermediate in the spring, and lowest in the summer. Surface FPC production was affected by seasonal shifts in the mesozooplankton community, including increases in the abundance of large migrating animals (mysids, chaetognaths, larval fishes) in the summer and relatively larger calanoid copepods in the fall. Gelatinous zooplankton may have contributed a top-down control limiting community FPC production rates in the summer. This study indicates that zooplankton FPC production in estuaries can surpass that in oceanic systems. Future research on the fate of fecal pellets produced in the surface is needed to understand the role of fecal pellets in vertical carbon export and benthic-pelagic coupling in the York River and other estuaries.

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Thesis (M. Sc.)--University of Hong Kong, 1995. / Includes bibliographical references (leaves 80-86).

A general mathematical equation relating variables affecting primary production has been developed to predict changes .in the vertical distribution of primary production in the oceans. The model is tested and shown to fit empirical observations from diverse oceanic areas.

In this study the ecology, biology and classification of the sea cucumber species of the Red Sea coast of Egypt and Gulf of Aqaba were examined in order to resolve some of the long standing question on the identification and classification of sea cucumber.The introduction of the new barcoding technique as a tool for sea cucumber identification was also tested in this study in order to assess its accuracy and potential of the technique in identifying sea cucumber individuals. A total of 18 different (species) of sea cucumber were collected from the Egyptian coast and examined for both morphological and molecular characteristics. One new species of sea cucumber were identified from the Egyptian coast of the Red Sea (Actinopyga.sp.nov). Cryptic species complex were also identified for the Holothuria atra population in the Red Sea using the molecular analysis of the mitochondrial COI gene.In this study another experiment were conducted in order to identify sea cucumber species from cooked or dried materials using the molecular techniques. As well as testing the possibility of using the DNA barcoding technique in order to identify badly/long period preserved museum specimens in order to try to identify the unknown specimens in the natural history museums around the globe.The use of the molecular DNA barcoding technique proves to be a good reliable method for sea cucumber ID; the technique was capable of resolving some of the standing taxonomic problems including the Holothuria fuscogilva /Holothuria nobilis species complex and the Pearsonthuria graeffei. The results also raised some questions about the classification of the genus Bohadchia and the Actinopyga crassa species in the Red Sea.

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