Biology Theses and Dissertations

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    Assessing vertebrate biodiversity across the Chesapeake Bay using environmental DNA metabarcoding
    (2023) Rodriguez, Lauren Kelly; Bailey, Helen; Woodland, Ryan J; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Through the collection and sequencing of trace genomic evidence from environmental samples (e.g., water, air, and soil), environmental DNA (eDNA) metabarcoding can detect a range of vertebrates. Despite the dynamic characteristics of estuarine environments, which often hinder the persistence of genomic material, this project successfully employed metabarcoding to assess the distribution of vertebrates in the Chesapeake Bay. Primarily, the study evaluated the effects of using various eDNA sampling, laboratory, and post-hoc analysis techniques when investigating species presence and biodiversity of an area. This study also identified spatially-explicit fish communities along salinity gradients as described by a Generalized Additive Mixed Model (GAMM) and a Permutational Multivariate Analysis of Variance (PERMANOVA). Community compositions were similar to previous findings by traditional trawling and seining methods. This research supports the usefulness of eDNA metabarcoding to assess species presence across spatiotemporal extents, making it a promising tool for future biomonitoring efforts in the Chesapeake Bay.
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    Spatial and Temporal Variability in Suspended Sediment Characteristics in the Surface Layer of the Upper Chesapeake Bay
    (2020) Barletta, Stephanie Marie; Sanford, Lawrence P; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Periodic high discharge events flush suspended sediments from the Susquehanna River and Conowingo Dam reservoir into the upper Chesapeake Bay, which extends from the mouth of the Susquehanna River to the Bay Bridge near Annapolis, MD. Sediment characteristics in the surface layer of the upper Bay and changes in these characteristics with varying river discharge and distance downstream are not well known. In order to develop an integrated understanding of surface layer sediment dynamics, several in-situ data sets were examined at the Bay head and downstream along the Bay’s center channel, providing data on the spatial and temporal variability of suspended particle characteristics including concentration, settling speed, bulk density, and size. It was found that particles are entirely disaggregated at the Dam, later aggregating to a limited extent down Bay, and that downstream characteristics are more weakly linked to Susquehanna flow at lower flows and longer distances.
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    Nutrient effects on phytoplankton community composition in the eutrophic Anacostia River and a focus on diatom physiology
    (2019) Gleich, Samantha Julia; Glibert, Patricia M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The Anacostia River, Washington D.C., is a freshwater ecosystem that historically received high concentrations of nutrients from sewage and stormwater outfalls. Restoration efforts have been implemented recently that may improve water quality and alter the relative abundance of different phytoplankton taxa in the river. To determine the effects that environmental shifts may have on diatom abundance and phytoplankton community composition in the Anacostia River, a mesocosm experiment and laboratory studies were conducted. The results of the mesocosm study revealed that diatoms were consistently outcompeted by cyanobacteria. Additionally, phosphorus enrichment led to a 50% increase in cyanobacterial abundance and decreased the abundance of diatoms. In the culture study, shifts in water temperature and nutrient availability altered diatom growth rates, photosynthesis, silica deposition, and NO3- reduction. Together, these studies highlight the interactive effects that nutrient availability and temperature may have on the physiology and subsequent growth of diatoms in the Anacostia River.
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    Nitrogen Uptake and Denitrification in Restored and Degraded-Urban Streams: Impacts of Organic Carbon and Integrated Stormwater Management
    (2015) Newcomer Johnson, Tamara Ann; Kaushal, Sujay S.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Managing the N cycle and restoring urban infrastructure are major challenges especially in urban ecosystems. Organic carbon is important in regulating ecosystem function and its source and abundance may be altered by urbanization. My research focused on urban-degraded, restored, and forested watersheds at the Baltimore LTER in the Chesapeake Bay watershed. In Chapter 2, I investigated shifts in organic carbon quantity and quality associated with urbanization and ecosystem restoration, and its potential effects on denitrification at the riparian-stream interface. Denitrification enzyme assay experiments showed carbon was limiting in hyporheic sediments and variable carbon sources (grass clippings, decomposing leaves, and periphyton) stimulated denitrification differently. Evidence from stable isotopes, molar C:N ratios, and lipid biomarkers suggested that urbanization can influence organic carbon sources and quality in streams, which may have substantial downstream impacts on ecosystem services such as denitrification. In Chapter 3, I investigated whether stormwater best management practices (BMPs) integrated into restored and degraded urban stream networks can influence watershed N loads. I hypothesized that hydrologically connected floodplains and stormwater BMPs are “hot spots” for N retention through denitrification because they have ample organic carbon, low dissolved oxygen levels, and high residence time. I used reach-scale nitrogen mass balances, in-stream tracer injection studies, and 15N in situ denitrification to measure N retention in stormwater BMPs and their larger stream networks. There were high rates of in situ denitrification in both stormwater BMPs and floodplain features. Hydrologically connected floodplains can be important “hot spots” for N retention at a watershed and stream network scale because these areas likely receive perennial flow through the groundwater-surface water interface during both baseflow and storm events, while BMPs only receive intermittent flow associated with storm events. In Chapter 4, I conducted a literature review of N retention within hydrologically reconnected streams and floodplains. I reviewed 79 stream and floodplain restoration empirical studies from North America, Europe, and Asia and found that methods for measuring N retention varied considerably. I found many diverse strategies for promoting the ecosystem function of N retention in urban and agricultural watersheds.
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    THE DISTRIBUTION OF CALLINECTES SAPIDUS MEGALOPAE AT THE MOUTHS OF CHESAPEAKE AND DELAWARE BAYS: IMPLICATIONS FOR LARVAL INGRESS
    (2009) Biermann, Jeffery Lee; North, Elizabeth W; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Transport of Callinectes sapidus (blue crab) megalopae from the continental shelf into estuaries may influence recruitment variability of this economically important species. This research seeks to determine the vertical distribution of C. sapidus megalopae near the mouths of Chesapeake and Delaware Bays, and thereby infer swimming behaviors that may influence ingress to these estuaries. Megalopae and physical conditions were sampled at locations from ~10 km inshore of the estuary mouths to ~40 km offshore in coastal shelf waters in September 2005 and 2006. Megalopae were present in greater abundance and at shallower depths during night compared to day at all locations, suggesting a diurnal effect on distribution within the estuary and on the continental shelf. Unlike previous studies, offshore distributions did not indicate surface oriented behavior. Within the mouth of Delaware Bay, limited evidence suggests that megalopae presence in the upper portion of the water column increases in response to nocturnal flood tides. Results suggest photoinhibited swimming near the mouths of Chesapeake and Delaware Bays. In context of previous laboratory studies, these findings indicate that estuarine chemical cues at very low concentrations may induce changes in megalopae behaviors and stimulate molting at least 40 km offshore of estuarine mouths. Results suggest wind-forcing and density-induced subtidal flow are more likely mechanisms for ingress to Chesapeake and Delaware Bays than tidal-transport.
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    The Influence of Landscape Position on Coastal Marsh Loss
    (2004-04-29) Rogers, Andrew Stephen; Kearney, Michael S.; Marine-Estuarine-Environmental Sciences
    Coastal marshes are considered as important features of the landscape that are at risk of loss. Accurately assessing their prospects for survival is difficult in view of the wide possible causes of loss, the large areas involved and that most research is done on relatively small parcels. This project examined the probability of conversion of marsh surface parcels to open water as a function of distance from roadways across marshes, tidal creeks, and upland areas, and the distance upstream, and the size of a marsh parcel. These are understood to be stand-ins for hydrology, elevation and other factors that are more difficult to measure. The study area was divided into a MidAtlantic coastal region and a large bays region comprising the Chesapeake and Delaware Bays. A semi-automated system was developed for measuring the extent and severity of coastal marsh loss using Thematic Mapper (TM) data. The data derived from the TM analysis were used to develop algorithms to examine the impacts of the five factors listed above. The factors were examined individually using ordinary least squares (OLS) regression, and collectively using logistic regression. The OLS regression revealed that distance from uplands and distance from the nearest tidal creek were highly correlated with marsh loss in both areas. For the Atlantic Coast, however, the loss was negatively related to distance from tidal creeks, the opposite of what was expected. Distance upstream was negatively correlated with marsh loss as predicted. The relationship between distance from roads and marsh loss indicated that marshes are healthier near roads than farther away. The relationship between parcel size and marsh loss was non-linear, with small and large marshes having a lower probability of degradation than mid-sized marshes. The logistic regression model is useful for identifying areas with higher probabilities of conversion to open water. Sea level rise (SLR), tidal range, easting and northing were examined for use with the logistic models. SLR and tidal range added no information to the bay areas, but sea level rise was weakly negatively correlated with marsh loss on the Atlantic Coast and tidal range was weakly positively related.