Theses and Dissertations from UMD
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Item NITROGEN, MICROBES, PARTICLES AND OXYGEN DEFICIENT ZONES(2024) Huanca Valenzuela, Paulina Alejandra; Fuchsman, Clara A.; Cram, Jacob A.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Single-celled microbes mediate most biogeochemical cycling in the ocean. Ammonium is generally the preferred reduced nitrogen form microbes use for assimilation and growth. However, ammonium is often removed to undetectable levels from offshore waters. Microorganisms can metabolize alternative organic reduced nitrogen forms in the absence of ammonium, if they possess genes encoding for the enzymes cyanase (cynS), and urease (ureC), which catalyze the decomposition of cyanate and urea respectively. It is unknown which microbes contain these genes in the environment.In my first chapter, I quantified the microbes that can use cyanate and/or urea in oxic and anoxic (ODZ) environments by using a phylogenetic read placement technique. First, I explored depth profiles of metagenomes from two Pacific Ocean regions: an oxic region represented by the nutrient limited Hawaii Ocean Time series, and two ODZ environments represented by the Eastern Tropical South and the North Pacific. A larger proportion of N2 producing anammox bacteria in ODZs have the ability to utilize cyanate than urea, while a larger proportion of nitrite oxidizing Nitrospina have the ability to utilize urea than cyanate. Ammonia-oxidizing Thaumarchaeota had the ability to use urea in deep oxic waters. Contrastingly, the majority of heterotrophic SAR11 bacteria had the ability to use urea in surface waters, but none did in deep waters. This structuring of who can utilize which reduced N form could reflect competition between microbes and N availability. For my second chapter, I examined microbial ability to use urea and cyanate across time and space using metagenomes from two oceanic Geotraces transects in the North Atlantic; GA02 a North-South spring transect, and GA03, a Fall West to East transect. The two transects differed in nutrient concentrations, affecting the composition of phytoplankton communities. Though eukaryotic phytoplankton were abundant on the spring GA02 transect, they did not have the ability to use urea or cyanate, probably because ammonia was present. However, the ability to use urea was still common in SAR11. Cyanobacteria Synechococcus was abundant on this transect and had the ability to use cyanate. In the nutrient limited fall GA03 transect, the results were similar to oxic waters in chapter 1 except that towards the east, cyanobacteria Prochlorococcus gained the ability to utilize cyanate. Both seasonal and spatial changes were observed in the distribution of ureC and cynS genes in microbial groups in the North Atlantic. My third chapter focuses on organisms living on suspended particles. Marine particles constitute a niche that provides ample nutrient and carbon sources. Large particles have been postulated to support anaerobic metabolism that cannot occur in the surrounding water. We examined how microbial diversity changes among a range of 7 different particle sizes in a depth profile at the East Pacific Rise, an area of the ocean with a distinct oxygen minimum. By combining a quantitative 16S rRNA amplicon sequencing dataset with size fractionated organic matter concentrations, we estimated numbers of each microbial taxa per gram of carbon. Results show differences in microbial composition at different particle sizes and depths.Item INTERACTIONS BETWEEN NITROGEN AND TEMPERATURE ON THE METABOLISM OF THE RED-TIDE MIXOTROPHIC DINOFLAGELLATE KARENIA SPP. IN SUPPORT OF PREDICTIVE MODELS: IMPLICATIONS FOR BLOOM DYNAMICS ON THE WEST FLORIDA SHELF(2023) Ahn, So Hyun; Glibert, Patricia; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The toxic mixotrophic dinoflagellate Karenia spp. forms blooms almost annually in the Gulf of Mexico, especially on the West Florida Shelf (WFS). Blooms typically initiate in early fall but can persist from months to years. Daily, Karenia vertically migrates to the surface water during the day, possibly experiencing changes in temperature, light, nitrogen (N), and prey type and availability. Therefore, this dissertation aimed to examine the interplay between Karenia’s photo-autotrophic and phago-mixotrophic metabolism and the short-term fluctuations in environmental conditions to understand how these factors may relate to the conditions under which Karenia spp. are found in the WFS.Title of Dissertation: INTERACTIONS BETWEEN NITROGEN AND TEMPERATURE ON THE METABOLISM OF THE RED-TIDE MIXOTROPHIC DINOFLAGELLATE KARENIA SPP. IN SUPPORT OF PREDICTIVE MODELS: IMPLICATIONS FOR BLOOM DYNAMICS ON THE WEST FLORIDA SHELF So Hyun (Sophia) Ahn, Doctor of Philosophy, 2023 Dissertation directed by: Professor Patricia M. Glibert, Marine Estuarine Environment Sciences A culture of K. mikimotoi balanced photon flux pressure (light availability) with consumption in overall metabolism when pulsed with 15N-NO3-, 15N-NH4+, or 15N-urea over the range of 15-25°C as shown by photosynthetic fluorescence. However, when shifted to 30°C, cells were significantly stressed, but urea-enriched cells showed a smaller decline in fluorescence, implying that urea might induce a photoprotective mechanism by increasing metabolic “pull.” Studies conducted with natural K. brevis winter and summer populations during 2021 showed that thermal history played a critical role. Unusually, summer blooms had higher biomass but were stressed photosynthetically and nutritionally. However, 15N-urea enriched summer cells had higher uptake rates as well as carbon (C) and N cell-1, especially in warmer waters, showing differential thermal responses based on N forms. Mixotrophy grazing measurements showed that K. brevis grazed both the picoplankter Synechococcus as well as the cryptophyte Rhodomonas. Grazing did not selectively target specific qualities of Synechococcus (based on differing N and P of the prey growth media), but ingestion rates were a function of prey-to-grazer ratios (R2=0.76) as well as prey amounts (R2=0.71). NanoSIMS confirmed 15N incorporation from Synechococcus in K. brevis. In natural communities of K. brevis, ingestion rates were also significantly related to prey-to-grazer ratios (p < 0.01) and by temperatures (p < 0.05) to a lesser degree (R2= 0.75) when incubated at ambient (24°C) and ambient temperature ± 5°C (19, 29°C). The grazer effects on the photosynthetic performance of grazer and prey were also examined. Grazing on Synechococcus indirectly reduce the photosynthetic performance of prey, especially at warmer temperatures but had little or no effect on the photosynthesis of K. brevis itself.Item Impact of Plant-Derived Allelochemicals on Harmful Algal Blooms(2023) Armstrong, Christen Taylor; Place, Allen; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Harmful algal blooms (HABs) are a global concern in both freshwater and coastal systems; creating dire consequences for public health, water resources, and local economies. Thus, there is a focus among scientists and environmental managers on HAB prediction, prevention, and mitigation. Current chemical mitigation methods include algicides such as copper sulphate, chlorination, and hydrogen peroxide, which can have high financial costs and secondary pollution associated with them. The use of natural allelochemicals produced by plants and bacteria has received considerable attention as an alternative to synthetic algicides, as they can have negligible toxins, be highly selective, and easily degraded in the environment. This dissertation is a coalition of research looking into new sources of plant allelochemicals and whether natural levels of allelochemicals in the water column, can impact phytoplankton communities and the presence of toxin-producing algal species. The first objective focused on the use of the waste product: brewer’s spent grain (BSG), as a new control mechanism to inhibit the growth of toxic algae. BSG extract of doses higher than 250mg/L inhibited the growth of freshwater and marine toxin-producing cyanobacteria and dinoflagellate species (Microcystis aeruginosa and Karenia brevis), while not impacting the diatom and chlorophyte tested (Scenedesmus obliquus and Prorocentrum tricornutum). This same dosage of BSG caused cyanobacteria abundance in lake water to decline by 90% within 4 days and chlorophytes to dominate the community by day 6 during a microcosm study. However, an experiment controlling bacteria levels demonstrated that the decline of K. brevis growth was likely due to the increase in abundance or presence of certain types of bacteria growing with exposure to BSG extract rather than due to chemicals released from the BSG. The second and third objectives shifted focus to the New Jersey Pinelands and whether the chemicals released into the water from terrestrial and marine plants in these waters, like phenolic compounds, impact the phytoplankton community and toxin-producing species. The second objective focused on the spatial and temporal distribution of phycotoxins along two New Jersey estuaries using passive samplers and whether the utility of passive samplers was impacted by the excess phenolic compounds in the water. By utilizing passive samplers in New Jersey, phycotoxins not previously reported in the area were described, such as azaspiracids, goniodomin-A and yessotoxins. However, this objective also showed some of the caveats of passive samplers, especially at sites with high phenolic compounds. The third objective focused on identifying the primary environmental drivers of chlorophyll a concentration and phytoplankton community along the freshwater – marine continuum of two New Jersey Estuaries with varying levels of disturbance. This dissertation explored BSG as a novel control method of HABs, and provided new information for monitoring, managing, and modeling HABs based on phenolic content measured in the water.Item TOOL DEVELOPMENT TO CONSTRAIN AND OPTIMIZE SHELLFISH AQUACULTURE GEAR PERFORMANCE(2022) Campbell, Brendan; Gray, Matthew W; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)To produce virginica cultured Crassostrea more efficiently, current grow out techniques require better understanding to allow for more consistent growth and quality. While the basic physical conditions that influence shellfish growth have been well researched, there are limited studies that consider how physical conditions (i.e. water flow and wave motion) influence shellfish growth within the context of an off-bottom aquaculture farm. Since oysters are suspension feeders, they require food to be delivered to their siphons through ambient processes. Changes in water flow can influence the overall survival, growth rate, and quality of oysters. Additionally, the motion, or jostling, of cages are thought to cause chipping on the outer portion of oyster shells, influencing the overall shape and growth of oysters. There are many techniques and equipment that have the potential to influence the water delivery and movement of oysters in containerized culture; however, little research has addressed how culture practices influence physical forcing surrounding cultured oysters and what impact those changes have on oyster performance. The biophysical relationship occurring in shellfish aquaculture is not being properly characterized partially due to a lack of affordable tools capable of monitoring physical forces in constrained spaces. This dissertation summarizes the current understanding of how culture practices influence oyster aquaculture production and demonstrates the novel use of affordable and commonly available tools that can be utilized in shellfish aquaculture research across multiple operational scales. The development of a novel clod card method and predictive model was attempted for use in characterizing mass transfer rate of water. The clod card, along with accelerometer loggers were utilized to understand the effects of physical forcing on the production of off-bottom cultured oysters when exposed to a range of biofouling mitigation treatments, grown using different culture methods, and spatially across an active shellfish aquaculture lease. These experiments validated the value in characterizing physical forcing in shellfish aquaculture and identified trade-offs between oyster shell growth and market quality that are linked to changes in the physical environment, which were produced by changing culture practices. Additionally, these validation experiments determined that variability in oyster growth and performance can change over small spatial scales, smaller than the typical grow-out shellfish aquaculture lease, which can influence water movement inside cages, water quality, and the efficiency of a commercial shellfish operation. By considering the local physical environment, growers can strategically employ culture practices that optimize the water flow through and movement of oysters to enhance farm profitability.Item USING A HIGH RESOLUTION, MECHANISTIC MODEL OF FILTRATION, BIODEPOSITION, HYDRODYNAMICS, AND SEDIMENT BIODGEOCHEMISTRY IN ORDER TO UNDERSTAND THE DRIVING FORCES BEHIND NITROGEN DYNAMICS ON OYSTER REEFS(2022) Kahover, Kevin James; Harris, Lora; Testa, Jeremy; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The overarching goal of this work was to develop a modeling tool that can provide quantitative predictions of ecosystem services related to N removal and biomass production using oyster restoration metrics such as reef size and oyster planting densities. I expanded the predictive capability of an existing advection-diffusion model of particle capture on an oyster reef to incorporate oyster biodeposit production, transport, and relationship to nutrient cycling. The resulting oyster reef filtration, biodeposition, and ecosystem services model (ReeFBioDES) utilizes modeled or measured current velocities, temperature, salinity, and chlorophyll-a in a given reef environment (reef length, oyster size and density) to predict spatial patterns of biodeposition production, transport, and denitrification. I applied the model at Little Neck Reef in Harris Creek (Choptank River) over an annual cycle for a range of oyster densities and found the model reproduced both the spatial dynamics of along-reef water-column concentrations of TSS, as well as generating rates of on-reef denitrification that are comparable to recently measured rates in experimental incubations of intact oyster clumps from Harris Creek. The model is now available for scenarios simulations to quantify ecosystem services associated with ongoing and future oyster restoration sites in Chesapeake Bay and other temperate coastal ecosystems that C. virginica occupies.Item Marsh-ing Through Time: Resolving the temporal and spatial variability of tidal marsh sediment dissolved organic carbon sorption(2021) Morrissette, Hannah; Hood, Raleigh; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Tidal marsh ecosystems are among the most economically and ecologically valuable environments in the world, providing critical ecosystem services and a continuous exchange of carbon between these systems and their surrounding environments. Tidal marshes are an important overall net carbon sink, while simultaneously being a substantial source of dissolved organic carbon (DOC) to estuaries and the coastal ocean. The temporal and spatial variability in these carbon fluxes is large, difficult to measure, and currently considered to be one of the most daunting challenges to carbon exchange quantification. Sorption, despite being known as a dominant DOC exchange process at the sediment-water interface, is still understudied in tidal marsh ecosystems, with exchange kinetics largely unquantified. This research combined observational data with sediment flux modeling to answer a suite of questions addressing sorption speed, its variability, and its impacts to DOC fluxes between sediments and adjacent waters. Sediment flux models must incorporate sorption processes to more accurately simulate DOC fluxes between tidal marsh sediments and adjacent waters. Kinetics of these processes were quantified for the first time through a set of 24 hour sorption laboratory experiments, from which results showed that the majority of sorption processes occur rapidly, within 15 minutes of sediment exposure to water. Sorption rate parameters were determined through a numerical modeling study that simulated the laboratory experiments. These rates were used to parameterize a sediment flux model that included sorption processes formulated with varying degrees of complexity. The sorption kinetics of individual pools of DOC (colored and non-colored) were also measured, revealing that these separate pools sorb quickly but independently of one another, with preferential adsorption of humic colored DOC over time, and preferential desorption of native non-colored DOC over time. Sorption kinetics were also shown to be spatially variable within a marsh site, with adsorption decreasing with sediment depth and distance from the creek edge. This research provided important new information on sorption in tidal marsh sediments that allows these processes to be incorporated into models, which will, ultimately, facilitate efforts to simulate and quantify coastal carbon fluxes.Item Nutrients, chlorophyll, and emergent harmful algal bloom species of concern in coastal waters of Assateague Island National Seashore(2021) Ross, Morgan O; O'Neil, Judith M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The Atlantic Ocean coastal zone of Maryland is important both ecologically and economically. Due to water quality issues, the coastal lagoons of Maryland have received considerable research attention, but little corresponding research in the coastal waters that exchange with the coastal lagoons. To better understand the linkages between the coastal ocean and the potential impacts of human activity on Maryland’s coastal zone, 5 research cruises (2018-2019) were completed to investigate concentrations of nutrients and emergent harmful algal bloom (HAB) species of concern (Dinophysis, Karenia, Pseudo-nitzschia). Nutrient and HAB species had high intra-annual variability, as well as geographic variability with relation to the inlets, coastal lagoons, and offshore discharge sites. The most significant determinants across all sampling locations, depths, and times were nitrate and ammonium. Continued eutrophication and climate change, as well as the impact of connected waterways, presents challenges for managing regional water quality issues in the coastal ocean.Item The significance of sea ice algae in the Pacific Arctic determined by highly branched isoprenoid biomarkers(2021) Koch, Chelsea Wegner; Cooper, Lee W; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Our current understanding of ice algae as a carbon source at the base of the Arctic food web is limited because of difficulties unequivocally distinguishing sympagic (sea ice) from pelagic primary production once assimilated by consumers. For this study, I tested the utility of highly branched isoprenoids (HBI), which are unusual lipids produced by diatoms. This includes a biomarker found exclusively in Arctic sea ice termed the ice proxy with 25-carbon atoms (IP25) and two other HBIs with sea ice and pelagic sources. HBI measurements in the Pacific Arctic (the northern Bering and Chukchi seas) were sparse compared to the rest of the Arctic prior to this investigation. Analysis of surface sediments and cores collected across the continental shelf revealed a latitudinal gradient of increasing sympagic HBIs. Some of the highest concentrations of IP25 recorded in the Arctic were found in the Chukchi Sea. Fluxes of IP25 indicated year-round export of ice algal lipids in this region. Persistent diatom fluxes and rapid burial of sympagic carbon are likely a sustaining resource for infaunal communities throughout the year. As such, HBIs were measured in benthic primary consumers and indicated an elevated utilization of ice algae by surface and subsurface deposit feeders, while suspension feeders by contrast showed greater pelagic organic carbon utilization. Sympagic organic carbon signatures were largely influenced by the HBI content in local sediments. This led to the identification of two species with possible dependencies on ice algae. This method was extended to transient, higher trophic organisms by measurement of HBIs in Pacific walrus livers harvested during subsistence hunting activities. Relative HBI proportions were shown to relate to foraging location and revealed a higher reliance on sympagic organic carbon by female and juvenile Pacific walruses relative to males. This is likely due to a greater requirement for sea ice habitat by females and calves in the Bering and Chukchi seas. This study showed that HBI biomarkers can robustly track sea ice organic carbon contributions through the Pacific Arctic food web and should be considered alongside other trophic markers in future monitoring efforts in response to climate change.Item Evaluating white perch (Morone americana) fecundity in select Chesapeake Bay tributaries in repsonse to pathology and fitness(2020) Shaner, Jacob; Harrell, Reginal M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Fecundity studies have emerged as a complement to generalized stock assessment methods in an effort to more accurately determine reproductive potential, as well as explain a lack of stock recovery in some cases. The Chesapeake Bay presents an interesting case study, in that widespread anthropogenic influence has created the potential to reduce reproductive fitness among resident species, including white perch (Morone americana). This study seeks to investigate white perch population fecundity in response to habitat quality, as well as disease and nutrition, through the use of stereological and automated counting methods to assess agreement between stock assessments and reproductive potential. Results indicate lack of impact on fecundity from degraded habitat, limited impact of individual nutrition, and no conclusive effect from disease. These findings, coupled with stable recruitment, indicate that white perch reproduction in the Chesapeake Bay is unaffected by increased population stress.Item Phenology of cyanobacterial blooms in three catchments of the Laurentian Great Lakes(2020) Wynne, Timothy; Hood, Raleigh R; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This dissertation discusses the cyanobacterial bloom phenology in three anthropogenically impacted regions of the Great Lakes: western Lake Erie, Saginaw Bay, and Green Bay. A detection algorithm was applied to ocean color satellite imagery, and a timeseries was constricted from each of the basins using either data from the MODIS sensor (Saginaw Bay), the MERIS sensor (Green Bay), or a combination of the two (western Lake Erie). The sensors have a high temporal resolution, collecting imagery several times a week. The algorithm used, the Cyanobacterial Index (CI), was applied to the imagery. The CI imagery was then sampled into fifteen 10-day composites throughout the bloom season (defined here as June 1 – October 31). Each of the five months will have three composites (each spanning ~10 days). From this point the bloom climatology is shown and the variability of each region is addressed. The interannual variability of the cyanobacterial blooms can be low (factor of ~2 in Saginaw Bay) or high (differing by a factor of ~20 in Green Bay and western Lake Erie). Various ancillary datasets describing the physical environment of each region were assembled including: field data, modeled data, remotely sensed data, or some combination therein. Impacts of associated cyanobacterial biotoxins were addressed and statistical models were formulated to explain any variability. The dissertation will also cross compare the three basins with one another in an effort to determine the similarities as well as differences among the regions. Management recommendations are given at the end of each of the three subsequent chapters to deter potential detrimental impacts of the blooms and their associated toxins.