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GCE-LTER Theses & Dissertations

Albers, G. 2004. Applications of Island Biogeography: Plant Diversity and Soil Characteristics Among Back-Barrier Islands Near Sapelo Island, Georgia. M.S. Thesis, University of Georgia, Athens, Georgia. 113 pp.

Abstract
This work reviews Georgia coastal policy with respect to the bridging of back-barrier islands (BBIs), or marsh hammocks. It characterized plant and soil composition on BBIs near Sapelo Island, Georgia. Species richness of fourteen BBIs was examined according to the theory of island biogeography. Eighty-three species were observed in 52 100 m^2 plots. Quercus virginiana and Ilex vomitoria were the dominant overstory and understory plants, respectively, in these maritime forest communities. Linear regression analyses showed that biogeographic variables contributed to ~30% of the variance; island size and origin were important predictors of diversity. Soil analyses indicated fine sands with low nitrogen (<=2%) and variable carbon values (1.7-48%). Nonmetric multidimensional scaling showed differences in species composition based on plot location and soil C:N ratios that were not reflected in diversity analyses. Resource managers may use these findings to designate sensitive areas and develop policies that promote their sustainable use.

Angelini, C. 2014. Foundation species as drivers of ecosystem structure, multifunctionality, and resilience. Ph.D. Dissertation. University of Florida, Gainesville, FL. 164 pages.

Abstract
Foundation species are dominant, structure-forming organisms that modify physical and biotic conditions to facilitate associated communities { TC ABSTRACT }. Although foundation species nearly always co-occur, our understanding of how they interact with each other and collectively influence how ecosystems are structured, function, and respond to disturbance remains limited. Here, I synthesize research on foundation species interactions and quantify the effect that facilitation cascades, interaction chains in which primary foundation species facilitate secondary foundation species, have on ecosystem structure, functioning, and resilience. Many studies have either examined how competition and facilitative interactions drive spatial segregation and overlap, respectively, of foundation species, or what effects a single foundation species or functional group have on associated community characteristics. Integrating these complementary fields of research, I propose that the nature of interactions among foundation species controls landscape patterns in community structure. I then present results from experiments and surveys that assess mechanisms of facilitation that structure a tree (Quercus virginiana)- epiphyte (Tillandsia usneoides) cascade and 13 examine its effect on invertebrate species, functional group, and life stage diversity. I discovered that Tillandsia relies on physical stress reduction provided by Quercus, and secondarily reduces multiple stressors to enhance all aspects of arboreal invertebrate diversity. To assess whether the presence of multiple foundation species may also regulate ecosystem functioning, I tested how the density of ribbed mussels (Geukensia demissa) that occur in aggregations within salt marsh habitat formed by cordgrass (Spartina alterniflora) influences salt marsh invertebrate diversity, 7 ecosystem functions, and multifunctionality, the simultaneous performance of these functions. Using surveys of mussel distribution, I then extrapolated my experimental results to estimate the net effect of mussels, and the diverse invertebrate communities they facilitate, on multifunctionality at the landscape scale. In my final study, I used monitoring, model simulations, and experiments to demonstrate that the resilience of southeastern US salt marshes to drought hinges on the presence and spatial distribution of remnant cordgrass patches and that mussels, in facilitating cordgrass survival during drought, are likely playing a keystone role in regulating the resilience of this ecosystem. Combined, my research advances our understanding of how the interactions among foundation species regulates biodiversity, multifunctionality, and resilience within natural ecosystems.

Babcock-Adams, L. 2016. Elucidating natural and anthropogenic marine processes using molecular biomarkers. M.S. Thesis. University of Georgia, Athens, GA. 111 pages.

Biers, E.J. 2003. Microbial Interactions on Decomposing Spartina Alterniflora: Use of Fungally-Modified Leachate by Bacterial Communities in an Experimental Salt Marsh Decomposition System. M.S. Thesis, University of Georgia, Athens, Georgia. 144 pp

Abstract
Spartina alterniflora decomposition is an important route for carbon transfer to estuarine detrital food webs. The two major microbial groups of decomposers are fungi and bacteria, both studied separately in the Spartina decay system. By using flow-through microcosms, we studied how fungi affect Spartina decomposition products and how bacteria respond to the addition of these products as growth substrates. We found that fungi do not significantly alter leaf characteristics over < 40 day incubations, but fungi decrease Spartina particle removal and immobilize leached dissolved organic carbon (DOC), nitrogen, and phosphorus. Bacteria grown on these fungally-modified leachates did not respond numerically. However, bacterial operational taxonomic unit (OTU) diversity and ribotype diversity decreased with fungal influence. Leachates from fungally-modified Spartina leaves enhanced the relative proportion of alpha-Proteobacteria, the major Spartina-associated ribotype in nature. Overall, however, there was no conclusive evidence for antagonism between fungi and bacteria in the Spartina decay system.

Brittain, R. 2009. Trophic status, habitat use and climate change impacts on avian species of coastal, Georgia. Ph.D. Dissertation. Indiana University, Bloomington, IN. 195 pages.

Abstract
Plant, invertebrate and feather δ13 C and δ 15 N stable isotopic signatures were used to trace avian plant production sources and prey items in five habitats of coastal Georgia: tidal forest, oak forest, pine forest, shrub and saltmarsh. Isosource 1.3.1 mixing models of plant production sources were successful on Sapelo Island where there were large differences in photosynthetic pathways and hydrology, but failed in the Clayhole Swamp. Model sensitivity analysis indicated that the trophic position was the most important parameter to know for partitioning plant production sources and isotopic enrichment of δ 13 C and δ15 N in birds were equally important in determining prey items. Painted Buntings, the species of highest concern in the region, were almost as dependent on saltmarsh vegetation as they were on shrub and forest vegetation (∼40%). Greater dependence of young of year Yellow-throated Warblers, White-eyed Vireos and Brown-headed Nuthatches on C 3 saltmarsh vegetation suggests the saltmarsh may be providing an important source of protein for nestling birds across all habitats on Sapelo Island. Avian conservation efforts in coastal Georgia should include nearby saltmarsh to provide not only the necessary food resources for shrub-associated species, but also for forest interior species during the breeding season.Estimated habitat changes for 2100 due to climate change induced sea-level rise and coastal development indicate that sea-level rise is the greatest threat to saltmarsh and coastal shrub habitat, whereas accelerated urban development is the greatest threat to oak and pine forests. Tidal forests may serve as important refuges for closed-canopy species, such as Northern Parula, that will lose their preferred oak and pine habitats.

Buchan, A. 2001. Ecology and genetics of aromatic compound degradation in the ecologically important Roseobacter lineage of marine bacteria. Ph.D. Dissertation, University of Georgia, Athens, Georgia. 152 pp.

Abstract
The degradation of lignin-related aromatic compounds is an important ecological process in the highly productive salt marshes of the southeastern U. S., yet little is known of the mediating organisms or their catabolic pathways. An initial study of six isolates suggested that members of the roseobacter lineage, a dominant marine clade within the á-Proteobacteria, could degrade aromatic compounds via the beta-ketoadipate pathway, a catabolic route that has been well characterized in soil microbes. Four of the roseobacter group isolates had inducible protocatechuate 3,4-dioxygenase activity, a key enzyme in the pathway, in cell-free extracts when grown on p-hydroxybenzoate. The pcaHG genes encoding this ring-cleavage enzyme were cloned and sequenced from two isolates and in both cases the genes could be expressed in E. coli to yield dioxygenase activity. Evidence of genes encoding for protocatechuate 3,4-dioxygenase was found in all six roseobacter isolates by detection of pcaH by Southern hybridization or PCR amplification. These results suggested this ecologically important marine lineage compose a significant fraction of the aromatic compound degrading community in coastal systems. To test this hypothesis we investigated the diversity of pcaH amplified from bacterial communities associated with decaying Spartina alterniflora, the salt marsh grass dominating these coastal systems, as well as from enrichment cultures with aromatic substrates. Sequence analysis of 149 pcaH clones revealed 85 unique sequences. Fifty-eight percent of the clones matched sequences amplified from a collection of 36 bacterial isolates obtained from seawater or from senescent Spartina. Fifty-two percent of the pcaH clones could be assigned to the roseobacter group. Another 6% matched genes retrieved from non-roseobacter isolates cultured from decaying Spartina and 42% could not be assigned to a cultured bacterium based on sequence identity. These findings revealed a high diversity of genes encoding a single step in aromatic compound degradation in this coastal marsh and that many of the genes were indeed harbored by members of the roseobacter lineage. In a final study, we explored the genetic diversity of the beta-ketoadipate pathway among eight members of the roseobacter lineage (pairwise sequence identities of the 16S rDNA gene ranged from 92 to 99%). Genomic fragments containing gene clusters of this pathway were isolated and characterized by targeting pcaH. Sequence analysis revealed five unique gene arrangements. Identical gene clusters were found mostly between isolates demonstrating species-level identity (i.e. >99% similarity of 16S rDNA). In one isolate, six functionally related genes were identified: pcaQ, pobA, pcaD, -C, -H, and -G. The remaining seven isolates lacked at least one of these six genes within their respective gene clusters, however, gene order was consistent with this isolate s orientation. These results portray the dynamic nature of a set of genes that potentially play a central catabolic role in coastal marine environments.

Burns, C. 2018. Historical analysis of 70 years of salt marsh change at three coastal LTER sites. M.S. Thesis. University of Georgia, Athens, GA. 188 pages.

Abstract
Salt marshes are dynamic ecosystems that change in response to natural and human factors. This study used digitization of historical charts and imagery and the Analyzing Moving Boundaries Using R toolkit to measure approximately 70 years of change in lateral marsh extent and the distribution of interior features (ponds, upland, channels, and flats), in marshes of the Georgia Coastal Ecosystems (GCE), Virginia Coast Reserve (VCR), and Plum Island Ecosystems (PIE) LTER sites. Measuring the marsh edge exposed to high fetch and along channels was important for providing complete information on marsh change. Although GCE was dynamic, total marsh area was conserved. VCR experienced marsh loss to flat expansion, which was offset by marsh migration, and overall marsh area was conserved. PIE was erosional, losing marsh along the outer edge, channel widening, and ponding. GCE was considered the most resilient because of its tidal range, sediment supply, and elevation.

Carter, M. 2014. Characterization of Groundwater Discharge in a Back Barrier Tidal Creek. M.S. Thesis. Coastal Carolina University, Conway, SC. 66 pages.

Abstract
Groundwater discharge in the coastal environment is known to be a complex process. The driving mechanisms of groundwater discharge vary on spatial and temporal scales that can significantly impact coastal water chemistry and play a role in ecological zonation. Evolving combinations of observational and modeling approaches provide a basis to quantify groundwater discharge in a spatial and temporal sense. Here we employ a combination of geochemical (naturally occurring radon isotope) and geophysical (electrical resistivity) techniques to measure groundwater-surface water interactions along a back-barrier tidal creek. In addition to field measurements, a unique non-steadystate radon mass balance equation was developed to better constrain groundwater estimates. The radon mass balance shows spatial and temporal variance in groundwater composition along the tidal creek. Our estimates suggest that groundwater discharge is grater in the Upper Duplin compared to the Lower Duplin section. Spring tide conditions yielded greater groundwater discharge at all sites, but the Lower Duplin section had significantly greater discharge when compared to neap tide discharge. Electrical resistivity serves as a qualitative assessment to support the radon mass balance findingsof marsh zone water circulation on both daily and spring/neap cycles. Our observations proved baseline groundwater contributions to the Duplin River system. This can be used to constrain aquifer characteristic used in numerical simulations of chemical and nutrient transport the systems.

Crotty, S.M. 2019. Drivers and consequences of ribbed mussel spatial patterning in southeastern US salt marshes. Ph.D. Dissertation. University of Florida. 1-6 pages.

Davidson, K. 2019. Trade-offs between multiple ecosystem services in UK and US salt marshes. Ph.D. Dissertation. Swansea University, Swansea, Wales, United Kingdom.

Abstract
Salt marshes supply vital ecosystem services (ES), providing material goods and recreation space, regulating natural hazards, and supporting diverse wildlife. However, increases in the utilisation of one ES can lead to reductions or ‘trade-offs’ in others. Because salt marshes are commonly used for grazing livestock, it is important to understand how this grazing impacts the saltmarsh ecosystem, and the consequences for ES supply. This thesis (i) uses a global meta-analysis to investigate the effects of livestock grazing on saltmarsh properties, and finds multiple significant changes to soil, vegetation and fauna properties. The meta-analysis reveals that the response of soil carbon is context dependent – there is no effect in Europe but a reduction in the Americas. (ii) Extensive surveys of soil carbon in grazed and ungrazed US marshes, controlling for key covariates, confirm that grazing trades-off against carbon storage in US marshes. These observational surveys, together with 18-month experimental exclusion of horses from a salt marsh in Georgia, show that grazing also disrupts the plant community in US marshes, but has little effect on resident invertebrates. (iii) Focusing on bees in salt marshes, a three-year study in south Wales, UK shows that grazing trades-off against bee habitat by reducing the flower cover of two key food plants, and that increases in plant diversity with grazing do not compensate for this negative effect. (iv) Spatial analyses of seven saltmarsh ES supplied by an estuary complex in south Wales show that marshes are not achieving their potential as a bee habitat here, due to the predominance of grazing. These analyses also show that the provision of ES by salt marshes is spatially heterogeneous, dependent on management, size and location. As a whole, this thesis adds to the understanding of grazer impacts and ES trade-offs, and supplies crucial data to support evidence-based management of salt marshes.

Elston, S. 2005. Secondary Circulation in a Sinuous Coastal Plain Estuary. Ph.D. Dissertation, Georgia Institute of Technology, Atlanta, Georgia.

Abstract
Transport and mixing of momentum and salt in an estuary varies in time and space due to river discharge, changes in tidal amplitude and phase, wind stress, and lateral mixing processes. Lateral mixing commonly refers to poorly resolved, rarely quantified interaction(s) between flows induced by secondary circulation, river discharge, wind stress, and tidal forces. Modern instrumentation and better computational techniques have generated a resurgent interest in better comprehending such interactions. The intent of this dissertation is to observe, describe, parameterize, and quantifying secondary circulation using acoustic current meters in a sinuous coastal plain estuary. This endeavor is made to improve our general understanding of secondary circulation, to identify its primary driving forces, and to better parameterize key physical processes necessary for further study in current numerical models. Secondary circulation is a broad and often confusing term used to describe several mechanisms whose result is to vertically overturn the water column along the transverse axis of a channel. Most commonly, secondary circulation is generated by one or more of the following mechanisms: channel curvature, unusual bottom topography or channel geometry, planetary rotation, and/or the differential advection of density. Secondary circulation may be composed of one or more cells that can act to reduce or enhance local velocity and density gradients. A physical manifestation of secondary flow is often observed as foam or slick lines down the longitudinal axis of an estuary. Field data for this dissertation was collected in the naturally sinuous Satilla River in southeast Georgia during the spring of 1997 and during the spring and fall of 1999. A shallow coastal plain estuary, the Satilla is a typical partially-mixed estuary characterized by 2 - 2.5 meter range semidiurnal tides. It has a strong neap-to-spring axial current inequality ranging from 0.5 m s^-1 to 2.0 m s^-1 and, likewise, has strong neap-to-spring vertical salinity variations in the thalweg from 7 PSU to 2 PSU. The density structure of the Satilla River is most sensitive to variations in salinity. In the Satilla River, secondary circulation driven by channel curvature dominates the lateral momentum balance on time scales longer than the fortnightly tidal cycle. The signal of secondary circulation is modulated on the neap-to-spring cycle due to changes in the interaction of the vertical density gradient and the speed of the axial current. At neap, the vertical stratification can limit or halt the local transverse circulation. A first order inviscid balance between the lateral baroclinic gradient and centrifugal acceleration is sufficient to explain the observed modulation. Changes in freshwater discharge do not directly affect the strength and modulation of the transverse circulation, but rather, affect the location of the maximum axial and vertical salinity gradients. The balance of mechanisms responsible for the strength and location of secondary flows in the Satilla River varies with channel geometry, discharge conditions, fortnightly tidal cycle, ebb and flood tidal phase, and lateral cross-channel position. A steady-state momentum balance between the Coriolis acceleration, centrifugal acceleration, the lateral baroclinic gradient, and bottom stress is sufficient to explain the observed changes in secondary circulation on the tidal and fortnightly time scales in the Satilla River under widely different discharge conditions and in several differently curved channel reaches. The primary momentum balance at spring tide is between centrifugal acceleration and bottom stress. At neap tide, depending on local stratification and form drag, the primary momentum balance shifts from a two-way balance between centrifugal acceleration and the lateral baroclinic gradient at low drag states to a three-way balance between centrifugal acceleration, the lateral baroclinic gradient, and bottom stress at high drag states. The change in the balance of forces that drive secondary circulation in a channel cross-section varies with lateral position. In the thalweg, the dynamic balance is between the centrifugal acceleration and the lateral baroclinic pressure gradient. In the shallows and on the shoal flanks, the dynamic balance is between the centrifugal acceleration, the lateral baroclinic pressure gradient, and bottom stress. Bottom stress drives secondary circulation in the very shallow intertidal areas of the Satilla River where bathymetry changes rapidly, acting independently of tidal phase (ebb or flood). It is important to be able to understand what processes generate and limit the strength of secondary circulation in estuaries in order to predict the length of the salt intrusion, the locus of momentum transfer, and to determine the dispersion and distribution of various properties (e.g., larvae, sediment, and pollutants) in the estuarine environment.

First, M.R. 2008. Benthic Microbial Food Webs: Spatial and Temporal Variations and the Role of Heterotrophic Protists in Salt Marsh Sediments. Ph.D. Dissertation. University of Georgia, Athens, Georgia.

Abstract
In order to determine if the loss of bacterial biomass varies over time, I investigated the microbial food web structure at two time scales in the salt marsh sediments of Sapelo Island, Georgia. Samples were collected monthly for one year at three contrasting subtidal locations: a high energy sandy beach, a muddy Spartina marsh, and a tidal creek bed. Concentrations of benthic microalgae (BMA), bacteria, heterotrophic protists, and metazoan meiofauna were measured at each location. Additionally, short-term dynamics of sediment microbial populations and bacterivory rates were investigated over a diel period in an intertidal creek bed to determine if variable rates of protist grazing could significantly impact bacterial standing stock. Although bacterivory rates were variable throughout the day, there were no periods of the day when protists could effectively reduce bacterial biomass. Yearly sampling revealed high variation in the microbial food web structure, mostly among sample locations. However, I observed a shift from a BMA-dominated community in the spring/ early summer months to a bacterial-dominated food web in the late summer/fall at all locations. Bacteria and heterotrophic protist concentrations were significantly related to porewater volume (6.9±1.2 x 10 and 5.1±1.1 x 10 -1 cells ml, respectively, ±SE). The low abundance of protists (relative to high bacterial concentrations) may be due to top-down pressure by large ciliates and nematodes. This top-down pressure in the autumn months (when BMA are proportionally less abundant) may contribute to high concentrations of bacteria during this season. Microbenthos displayed a clumped distribution pattern in Fluorescently Labeled Embedded Cores (FLEC). The aggregation of microbenthos indicates that the importance of protists in microenvironments may be overlooked by their total concentrations in the sediments. The common benthic ciliate, Uronema marinum, was capable of ingestion of fluorescently-labeled dextran (a high molecular weight carbohydrate) at low concentrations (3 microM DOC). However, the ingestion of starch, glucose and acetate did not significantly improve the growth or biomass production for this ciliate. Instead, I hypothesize that the initial breakdown of recalcitrant organic carbon compounds (and egestion of fermentation byproducts) can stimulate sulfate reducing bacteria and indirectly benefit bacterivorous protists through increased bacterial production.

Gifford, S. 2011. Microbial Ecology and Biogeochemistry of the Coastal Ocean: New Insights from Metatranscriptomics. Ph.D. Dissertation. University of Georgia, Athens, Georgia. 163 pages.

Abstract
In the oceans, the transfer of energy and cycling of elements is predominantly controlled by bacterioplankton, such that any understanding of marine ecosystems requires knowledge about bacterial activities and functional capabilities. Metatranscriptomics, the direct retrieval and sequencing of environmental RNA, is a powerful tool that can identify active community members and their expressed functional capabilities. This dissertation is composed of three studies that used metatranscriptomics to gain fundamental insights into the ecology and biogeochemistry of coastal microbial communities. In the first study, an internal standard approach was developed to make absolute (per liter) estimates of transcript numbers, a significant advantage over proportional estimates. Expression levels of genes diagnostic for transformations in the marine nitrogen, phosphorus and sulfur cycles were determined, as well as the total size of the mRNA pool. By representing expression in absolute units, metatranscriptomics extends beyond relative comparisons, allowing for direct comparisons with other biogeochemical measurements. In the second study, a metatranscriptomic dataset revealed an unexpected abundance of transcripts to Candidatus Nitrosopumilus maritimus, an ammonia oxidizing Archaea whose presence has significant implications in the carbon and nitrogen cycles. Reads assigned to genes for ammonia uptake and oxidation accounted for 37% of N. maritimus transcripts. In contrast, transcripts from co-occurring ammonia oxidixing Bacteria were in much lower abundance, with no transcripts related to ammonia oxidation or carbon fixation. This study suggests that these two members of the ammonia oxidizing functional guild respond differently to the same environmental cues. The third study used metatranscriptomics to examine how differences in expression among taxa can be indicative of niche diversification. The sequencing of transcripts from four coastal bacterial communities revealed the expression and activity of thousands of different taxa. The genes carried by these taxa have extensive overlap, and the majority of highly expressed genes were for redundant functions. To identify unique ecological roles for these taxa, a method was developed to classify genes both by their expression level and their frequency in genomes. The results show clear functional delineations across broad phylogenetic groupings and provide insights into the diversity of lifestyle strategies that supports complex microbial assemblages.

Givens, C. 2012. A fish tale: comparison of the gut microbiome of 15 fish species and the influence of diet and temperature on its composition. Ph.D. Dissertation. University of Georgia, Athens, GA. 229 pages.

Abstract
This dissertation addresses four aspects of the biology of the fish gut. 1) What bacteria constitute the fish gut microbiome, how variable is the composition within a species; how different are the gut microflora of different fish species; and how do fish gut microbiomes different from those of other organisms that have been studied? 2) How do food quality and diet-associated bacteria affect the composition of the gut microbiome? 3) Ocean temperatures are expected to rise in the future in response to increased atmospheric CO2 concentrations, we know that the incidence of marine pathogenic Vibrios is higher during warm summer months and we know that Vibrios are common, and often dominant, taxa in the gut microbiome. Does increased habitat temperature influence the composition of the gut microbiome and specifically does the abundance of potentially pathogenic Vibrios increase when fish are held at higher water temperatures? 4) Conversely, can fish serve as refuges for these Vibrios when growth conditions are less favorable and as vectors for their distribution? We used 454-pyrosequencing to survey the 16S rRNA ribotypes in the gut microbiomes of 12 finfish and 3 shark species. Fish were selected to encompass herbivorous and carnivorous lifestyles, to have varied digestive physiologies, to represent pelagic and demersal species, and as representatives of a range of habitats from estuarine to marine. Proteobacteria ribotypes were present in all fish and often dominated the gut microflora community of many fish species. Firmicutes were also prevalent within the fish gut community, but at a lower relative abundance. Each species had a core gut microflora; however, no individual ribotype was present among all species suggesting that the gut microflora community is adapted to the autecological properties and physiological conditions of each fish species. We determined the effects of both diet quality and food-associated bacteria on gut microflora using mummichogs (F. heteroclitus) and pinfish (L. rhomboides) as model organisms. We identified a core gut microflora for these species and determined that food-associated microbiota strongly influenced the composition of the gut microflora in mummichogs, but not pinfish. We also tested the effect of temperature on the composition of gut microflora and on the occurrence of Vibrio spp. 16S rRNA and V. vulnificus vvh genes in the two model fish (mummichogs and pinfish) using clone libraries and quantitative PCR (qPCR). In a related set of experiments, we asked whether fish guts might serve as a refuge for Vibrio parahaemolyticus and Vibrio vulnificus during periods of sub-optimal environmental conditions. We found that both of these Vibrio species were present in the gut microbiome and that they could be transferred to other environmental reservoirs, implicating fish in the persistence and dispersal of these potential pathogens. Lastly, we examined the microbiome of the Atlantic blue crab (Callinectes sapidus) to address how the crab-associated bacterial community may affect crab, fish, and human health.

Guo, H. 2011. Organization of plant communities across estuarine landscapes in low-latitude tidal marshes. Ph.D. Dissertation. University of Houston, Houston, TX. 106 pages.

Abstract
Understanding the processes that influence the distribution of organisms and the structure of communities is a major goal of ecological research. The unprecedented loss of biodiversity and habitats due to the impacts from human activities and global changes has made this goal more essential to the conservation and restoration of ecosystem function and services. In this dissertation, I explored the underlying mechanisms that organize the plant communities in tidal marshes in the southeastern US, with a focus on three topics: 1) I investigated the abiotic and biotic factors that mediate plant distribution across estuarine landscapes. I found that the "competition-to-stress hypothesis" which states that the upstream limits of plant distributions are determined by competition and the downstream limits by abiotic stress, could not fully explain the plant distribution patterns. This illustrated that even apparently simple abiotic gradients can encompass surprisingly complex processes mediating plant distributions. 2) I explored the role of ecosystem engineers in influencing plant community distribution and structure. I demonstrated that oyster shell deposits play an important ecosystem engineering role in influencing salt marsh plant community by providing a unique niche for Suaeda linearis, which otherwise would be extremely rare or even absent in salt marshes in the southeastern US. 3) I evaluated the relative importance of deterministic (niche-based) and stochastic processes in structuring plant communities in tidal marshes across estuarine landscapes. I found that stochastic processes were relatively important in shaping plant community structure in freshwater marshes, whereas deterministic processes played a relatively strong role in structuring plant communities in brackish and salt marshes. At the estuarine scale, the community assembly of tidal marsh vegetation across the estuarine landscape was primarily driven by niche-based selective processes. The results of this dissertation suggest that deterministic processes related with selective forces play important roles in organizing plant communities in coastal wetlands, but that attention also needs to be paid to the non-neglectable stochastic aspects of community organization in tidal fresh marshes to better comprehend the mechanisms underlying the organization of plant communities in tidal marshes.

Hartmann, J. 2007. Determination of gas exchange velocities based on measurements of air-sea CO2 partial pressure gradients and direct chamber fluxes in the Duplin River, Sapelo Island, GA. M.S. Thesis. University of Georgia, Athens, Georgia. 84 pages.

Abstract
CO2 fluxes were determined directly, using a floating chamber for ten to fifteen minute intervals over the winter between 2006 and 2007 from Marsh Landing Dock on Sapleo Island, Georgia. Air-Sea pCO2 differences were measured alongside the fluxes using a coupled equilibrator and infrared gas detector whereby gas transfer velocities (k) were calculated. In addition, current speeds were measured using an acoustic doppler current profiler and correlated with gas transfer velocities along side wind speeds. In the Duplin River, with the exception of spring tides, wind is an important variable controlling k in agreement with prior empirical measurement of estuarine k values. However, bottom generated turbulence was responsible for more than half of the magnitude of measured gas transfer velocities for 17 out of 100 of the deployments. In addition, gas transfer velocities during spring tides may be able to substantially increase k, however independent verification with an un-tethered floating chamber is needed to verify this in the Duplin River.

Hembree, P.A. 2005. Defining science/defining stories: Teachers’ constructions of science knowledge through collaborations in field-based scientific research. Ph.D. Dissertation, University of Georgia, Athens, Georgia.

Abstract
This qualitative study investigated teacher understandings and experiences as they came to redefine science through their participation in a program that supports teacher-scientist collaborations in field-based scientific research. This summer residential experience in ecology for teachers was designed to answer the call for opportunities for teachers to conduct real world, long-term scientific inquiry projects and thus provide for greater teacher-as-scientist authenticity in the classroom. The program intended to connect several issues in recent science education literature: the conflict between real science and school science; science knowledge construction; and authentic science experiences for teachers and students. In this field-based research setting, teachers were challenged to expand their understanding of how science is conducted and how science knowledge is constructed. The teachers came to recognize the essential role of exchanging ideas and brainstorming in informal, social settings in the knowledge acquisition process. They recognized that research ideas and the designs of experiments within this research community were not considered rigid or procedural. Instead, they saw those ideas and designs as flexible and under continuous development and revision—open to outside suggestions and feedback. In trying to understanding the teachers’ experiences in the program and how their participation might subsequently influence their practice, I found that the events were empowering, transformative, and gave them confidence and a renewed energy to teach science in a way that paralleled the practice of science. The participants’ ideas of science knowledge construction were challenged and revised to include a more sophisticated, constructivist view of science learning and teaching as active, transitory, social, and local. This shift in understandings changed their self-view to include personal and professional empowerment and a new sense of comfort and pride in their practice.

Hensel, M.S. 2013. Cross-kingdom consumer diversity enhances multifunctionality of a coastal ecosystem. M.S. Thesis. University of Florida, Gainesville, FL. 34 pages.

Abstract
The global biodiversity crisis impairs the valuable benefits ecosystems provide human society. These nature-generated benefits (i.e. services) are defined by a multitude of different ecosystem functions that operate simultaneously. How species extinctions, either globally or locally, will affect simultaneous functioning (i.e. multifunctionality), remains unstudied in real-world food-web assemblages. Here, we investigated experimentally the extinction impacts of dominant and phylogenetically diverse salt marsh consumers (i.e., Kingdom Animalia and Fungi) and reveal that a diverse consumer assemblage significantly enhances ecosystem multifunctionality. High functional turnover among consumers was found to drive a positive diversity-function relationship, where each marsh consumer affected at least one different ecosystem function, but no individual function was affected by more than two consumers. Although overlooked in past food web-diversity studies, microbes (i.e. fungi) were significant forces driving enhanced ecosystem functioning. These results provide the first experimental evidence that maximizing ecosystem multifunctionality depends on maintaining high-levels of both functional and taxonomic consumer diversity. Moreover, it emphasizes the need to incorporate both micro- and macro-components of food webs to accurately predict biodiversity declines on integrated-ecosystem functioning.

Herbert, E. 2015. The effects of global change on the fate of soil organic matter in tidal freshwater wetlands. Ph.D. Dissertation. Indiana University, Bloomington, IN.

Abstract
Tidal wetlands are sentinel ecosystems for environmental change and human-induced degradation of natural systems. They have existed in a state of equilibrium with sea level rise (SLR) over the past 4,000 years by accumulating soil organic matter (SOM) produced by plants and trapping mineral sediment. Accumulation of SOM is controlled by the balance between plant productivity and decomposition. Both processes are susceptible to anthropogenic disturbance, including salinization caused by declining freshwater flows, eutrophication from fertilizer runoff, or accelerated SLR. I utilized field measurements and a stable-isotope tracer approach to examine how anthropogenic disturbances alter SOM through the direct effects of changes on microbial metabolism and the indirect effects mediated through changes in plant communities. Increased salinity and eutrophication accelerate microbial mineralization of organic matter by providing more energetically efficient metabolic pathways, sulfate reduction (salinity) and nitrate reduction (eutrophication). However, the microbial response is dwarfed by changes in plant productivity and biomass allocation. Salinity and eutrophication reduce total root biomass and allocation of carbon to the rooting zone. Incorporating the observed biogeochemical changes into models of marsh geomorphology reveals that increased salinity reduces the contribution of SOM to vertical accretion and reduces marsh resiliency to accelerated SLR. These results highlight the importance of the complex interactions between plant productivity, microbial activity, and geomorphic processes in tidal wetland landscapes. Because tidal wetlands integrate impacts to both freshwater and marine systems, their survival depends on maintaining the integrity in the continuum of landscapes from the headwaters of rivers to theocean.

Hladik, C.M. 2012. Use of Remote Sensing Data for Evaluating Elevation and Plant Distribution in a Southeastern Salt Marsh. Ph.D. Dissertation. University of Georgia, Athens, GA. 205 pages.

Abstract
Salt marshes are valuable ecosystems that are susceptible to habitat loss due to changes in sea level and coastal flooding, and there is growing interest in obtaining accurate habitat and elevation maps for these areas. Remote sensing techniques such as Light Detection and Ranging (LIDAR) can produce digital elevation models (DEMs), but the accuracy of LIDAR in salt marshes is limited by a combination of sensor resolution, instrument errors, and poor laser penetration in dense vegetation. I assessed the accuracy of a LIDAR-derived DEM for the salt marshes surrounding Sapelo Island, GA using real time kinematic (RTK) GPS. These observations were used to develop and validate species-specific correction factors for ten marsh cover classes, which ranged from 0.03 to 0.25 m. In order to apply these corrections to the 13 km2 study site, I classified hyperspectral imagery by cover class and combined this information with elevation in a decision tree. This produced both an accurate habitat classification (nine salt marsh habitat classes were mapped with a 90% overall accuracy) and a corrected DEM (overall mean error was reduced from 0.10 ± 0.12 (SD) to -0.003 ± 0.10 m (SD) and root mean squared error at the 68% confidence level decreased from 0.15 to 0.10 m) when validated with ground truth data. Finally, I evaluated the use of remote sensing-derived variables (DEM elevation, slope, distance metrics) versus field collected edaphic variables (soil organic matter, water content, salinity, redox) to develop predictive models of plant distributions with both linear discriminant analysis (LDA) and classification and regression trees (CART). Models that used remote sensing variables had accuracies of 0.78 and 0.79, whereas those for edaphic models were 0.63 and 0.72 for LDA and CART, respectively. Accuracies improved only slightly in the best models which combined remote sensing variables and soil organic matter (to 0.82 and 0.83 for LDA and CART, respectively), suggesting that remote sensing-derived variables alone can be effective predictors of marsh vegetation. Taken together, these findings show the potential for appropriately analyzed remote sensing data for evaluating elevation and habitat in marshes.

Ho, C.-K. 2008. Plant-herbivore interactions in U.S. Atlantic Coast salt marshes: the effect of omnivory and geographic location. Ph.D. Dissertation. University of Houston, Houston, TX. 116 pages.

Abstract
Plant-herbivore interactions are common and have been the focus of muchresearch. Ecologists have realized that in order to better understand the generality ofplant-herbivore interactions, there is a need to study factors that mediate theseinteractions. Here, I first address whether plant-herbivore interactions are affected byomnivores, second test whether latitudinal variation in plant quality might explainvariation in herbivore body size, and finally examine whether geographic origin of plants and herbivores affects herbivore performance.First, I examined the top-down impacts of an omnivorous crab, Armasescinereum, on the shrub Iva frutescens and its arthropod fauna. My hypothesis was that Armases would benefit Iva through a trophic cascade, and that this benefit would be stronger than the direct negative effect of Armases on Iva. Field and laboratory experiments both supported this hypothesis. Although Armases is an omnivore, it produced strong top-down forces and a trophic cascade because it fed preferentially on herbivores rather than plants when both were available. Second, I tested the hypothesis that latitudinal variation in plant quality might help explain Bergmann’s rule. I found that three herbivores grew bigger or faster when fed plants from high- versus low-latitude regions. For Prokelisia and Aplysia, plant quality alone could explain the variation in herbivore body size observed in the field. Third, I sampled plant and herbivore traits in the field to demonstrate that increased plant palatability at high latitudes likely reflects better plant quality for herbivores. I then conducted laboratory experiments to examine how the geographic origin of plants and herbivore would affect herbivore performance. The geographic origin of plants affected herbivore performance for 4 of 6 herbivores, and had a marginal effect for a fifth. The geographic origin of herbivores affected herbivore performance in all 6 cases, but the pattern was mixed with respect to which geographic region was best.These results suggest that the prevalence of omnivory in food webs and thegeographic location in which food webs are studied could both affect plant-herbivoreinteractions. To better understand plant-herbivore interactions, scientists must consider factors such as these that alter the nature of interactions in the field.

Jiang, L. 2009. Biogeochemical cycling of carbon dioxide in estuaries and the continental shelf of the southeastern United States. Ph.D. Dissertation. University of Georgia, Athens. 161 pages.

Abstract
In the first half of the dissertation, partial pressure of carbon dioxide (pCO2), dissolved inorganic carbon (DIC), and total alkalinity (TA) were measured at both high tide and low tide in the surface water of three Georgia estuaries from September 2002 to May 2004. Of the three estuaries, Sapelo and Doboy Sounds are marine-dominated estuaries, while Altamaha Sound is a river-dominated estuary. During all sampling months, the three estuaries were supersaturated in CO2 with respect to the atmosphere (390 - 3380 ?atm). The calculated annual air-water CO2 flux in Altamaha Sound (69.3 mmol m-2 d-1) is 2.4 times that of Sapelo and Doboy Sounds (28.7-29.4 mmol m-2 d-1). The higher CO2 degassing in the river-dominated estuary is largely fueled by CO2 loading from the river. Due to the substantial differences between river- and marine-dominated estuaries, current estimates of air-water CO2 fluxes in global estuaries (which are based almost entirely on river-dominated estuaries) could be overestimated. In the second half of the dissertation, surface water pCO2, as well as vertical distributions of DIC, TA, dissolved oxygen (DO), dissolved organic carbon (DOC), pH, nitrate (NO3-) plus nitrite (NO2-), phosphate (PO43-), silicic acid (H4SiO4), ?13C and ?14C of DIC, and ?D and ?18O of H2O, was measured over the entire continental shelf from North Carolina to Florida (also known as South Atlantic Bight, or SAB) during six months from January 2005 to May 2006. Results indicate that the SAB is a net sink of atmospheric CO2 on an annual and whole shelf basis (-0.48±0.21 mol m-2 yr-1). The inner shelf is a source of +1.20±0.24 mol m-2 yr-1, while the middle and outer shelves are sinks of -1.23±0.19 and -1.37±0.21 mol m-2 yr-1, respectively. After removing pCO2 variations due to the annual temperature cycle and air-sea gas exchange, residual pCO2 is calculated. Residual pCO2, along with salinity, DIC, DOC, is then used to evaluate mechanisms controlling pCO2 in this region. DIC results show that SAB is strongly controlled landside by carbon inputs and freshwater dilution from terrestrial sources, and seaside by biological activity on the middle and outer shelf.

Jung, Y. 2018. Modeling Growth and Production Dynamics of Spartina Alterniflora. Ph.D. Dissertation. University of Georgia, Athens, GA. 148 pages.

Abstract
The goal of this work is to investigate the growth and production dynamics of the dominant salt marsh grass in the southeastern United States, Spartina alterniflora, including documenting non-structural carbohydrate pools and investigating seasonal changes in translocated biomass between above- and below-ground tissues.In Chapter 2, the dynamics of several non-structural carbohydrates (NSC) stored in S. alterniflora is investigated. Results show that sucrose is the dominant NSC in both above- and below-ground tissues and that the total NSC as a percentage of total biomass is highest in the summer through to early winter. The study suggests that sucrose is likely used for long-term storage whereas glucose is preferentially utilized for short-term storage.In Chapter 3, the growth and production dynamics of short, medium, and tall height forms of S. alterniflora are investigated using a phenology-based growth model (PG model), which includes the effects of light, temperature, and salinity on plant production. The model is used in combination with field observations of biomass to estimate values of physiological parameters such as mass-specific rates of carbon translocation. Once parameterized, the model is used in forward mode to predict whole-plant production, growth, respiration, mortality, and translocation. Model results indicate that the short height form of S. alterniflora translocates a higher proportion of photosynthates or remobilization of assimilates to below-ground tissues during periods of growth and senescence periods than medium or tall S. alterniflora, although the absolute amount of carbon translocation to below-ground tissues is greatest in the tall form of S. alterniflora because of its larger above-ground biomass.In Chapter 4, the model is used to compare the production and translocation dynamics of S. alterniflora along a latitudinal gradient using sites in Delaware, South Carolina, and Louisiana. Model results indicate that photosynthates make up the main source of carbon translocated to below-ground tissues at low latitudes, whereas at high latitudes, both photosynthates and remobilization of assimilates in senescing shoots are preferentially used. This shows the importance of taking into account the different translocation dynamics of the plants when comparing growth and production across sites at different latitudes.

Kang, K. 2005. Waves, Turbulence, and Circulation in the Altamaha River Estuary, Georgia. Ph.D. Dissertation, University of Georgia, Athens, Georgia. 161 pp.

Abstract
Physical processes such as sea surface waves, turbulence, and residual circulation were studied in an estuarine environment using several observational data sets and modeling experiments in the Altamaha River Estuary, GA. The wave energy within the estuary becomes periodic in time showing wave energy during flood to high water phase of the tide and very little wave energy during ebb to low water. This periodic modulation is a direct result of enhanced depth and current-induced wave breaking that occurs at the ebb-shoaling region surrounding the Altamaha River mouth. Modeling results showed that depth-induced wave breaking is more important during the low water phase of the tide than current-induced wave breaking during the ebb phase of the tide. In this shallow environment these wave-current interactions lead to an increased bottom roughness, resulting in an enhanced bottom friction coefficient. An increase of river discharge changed the estuarine turbulence flow and density characteristics into a more ebb-dominated and stratified system. The Reynolds stress and turbulent kinetic energy (TKE) were increased due to increased river discharge. The spectral energy density of turbulent flow was deformed by surface waves and better satisfied the -5/3 slope for isotropic trublence when the wave-induced motions were removed. Buoyancy flux increased in magnitude with increased longitudinal density gradient and showed a weak energy source during flood tide and a relatively strong energy sink during ebb. A balance between production and dissipation of energy was not obtained, implying that turbulent transport of TKE is a consideration. Numerical modeling results revealed a complex depth dependence on turbulence intensity that varied with the tidal cycle and with the level of stratification. The mean flow is dominated by the semidiurnal lunar tidal component (M2) and the tidal phase showed fairly constant values in the center of the channel with strong variations in the shoaling regions. When the M2 component was removed, weak landward residual flows appeared on both slack waters, which may be a result of weak turbulent mixing and greater stratification, and strong seaward residual flow occurred during flood and ebb tides that may be attributed to strong turbulence levels.

Kaufman, G. 2011. Application of the Water Quality Analysis Simulation Program (WASP) to Evaluate Dissolved Nitrogen Concentrations in the Altamaha River Estuary, Georgia. M.S. Thesis. University of Georgia, Athens, Georgia. 227 pages.

Abstract
The Water Quality Analysis Simulation Program (WASP v.7.4) and a water flow model, SqueezeBox, were used to model concentrations of dissolved nitrogen (DN) in the Altamaha River estuary, Georgia. Model development was guided by previous studies using WASP, literature surveys, and sensitivity analyses. The model was calibrated and validated against observations from the Georgia Coastal Ecosystems Long Term Ecological Research project. Average error between model predicted and observed concentrations was 39.8 % for NH3, 23.6 % for NO3-, and 7.8 % for DON. Results from the calibrated model showed that riverine DN input had an approximately 6-fold greater influence on predicted DN in the estuary than either flow or temperature. Overall, predicted DN concentrations were highest for high DN input, high flows, and low and medium temperatures.

Kunza, A.E. 2006. Patterns of plant diversity in two salt marsh regions. M.S. Thesis. University of Houston, Houston, Texas. 70 pages.

Abstract
Although ecologists have been interested in explaining the diversity of ecological systems for many years, there is still no generally accepted theory to explain what determines diversity. Patterns of diversity are determined by which species are able to colonize a particular site and persist in a particular abiotic environment, and by biological interactions between species that may expand or contract their range across an abiotic gradient. By examining these patterns we can begin to understand which biotic and abiotic mechanisms are important for shaping the overall diversity of a system. I compared the salt marshes of Texas to those of Georgia to determine what differences in plant diversity patterns existed between these two systems with similar species pools and general abiotic environments. Both Gulf Coast and Atlantic Coast salt marshes are tidal systems and therefore plants must be tolerant to flooding, salinity, and anoxia. The major abiotic difference between the salt marshes of these two regions is the relatively irregular schedule and lower amplitude of tides in Texas. Tidal schedule and amplitude might affect plant distribution patterns by creating abiotic conditions that vary over time as much or more than over space, thereby altering competitive relationships between plant species.I quantified diversity patterns (richness and relative abundance) on transects across elevation at 59 salt marsh sites in Georgia and 49 sites in Texas. Diversity was measured at global, regional, site, and plot scales to consider processes occurring at all levels. Species pools were similar between regions. Texas had greater diversity at the site and plot scales, which was primarily due to processes occurring at the site level. The greater diversity of Texas was partially explained by the fact that Texas marshes had more middle marsh (a high diversity zone) and less low marsh (a low diversity zone) than Georgia marshes, and by the fact that most species were more widely distributed across the marsh landscape in Texas than in Georgia (i.e., zones were less discrete). Biomass data from a subset of plots and sites suggested that high diversity in Texas was not caused by lower productivity; instead, Texas marshes had greater standing biomass than Georgia marshes. Irregular flooding of Texas marshes might allow more species to exist in the marsh by making abiotic conditions more variable over time, thereby making the outcome of competitive interactions less predictable and rapid.This work suggests that Gulf Coast marshes may function differently in some ways than Atlantic Coast marshes. Managers of Gulf Coast marshes should not assume that paradigms based on the Atlantic Coast will automatically apply. In addition, because salt marsh diversity is determined by site-scale processes, protection efforts should focus on maintaining a range of different marsh types rather than simply maximizing the total marsh acreage protected in a region.

Ledoux, J.G. 2015. Drivers of groundwater flow at a back barrier island - marsh transect in coastal Georgia. M.S. Thesis. The University of Georgia, Athens. 104 pages.

Abstract
The tidal marsh connects terrestrial landscapes with the coastal ocean. Groundwater within this environment has the ability to move nutrients and influence plant distribution. Land-use change and Sea Level Rise (SLR) threaten to change these groundwater patterns. Monitoring wells recording conductivity, temperature, and water level across a back barrier island-marsh transect at Sapelo Island, GA, identified drivers of groundwater flow. Pressure propagation from tidal variations in creek water level was negligible at the study site. Density-driven flow had little impact on groundwatermovement. The saturated nature of the marsh allowed for the well nearest the tidal creek to be used as an inundation meter, and the effect of tidal flooding was identified using three different techniques. Filtering the tidal signal record demonstrated that precipitation, was a main factor for water level changes in the well nearest the upland.

Lee, R.Y. 2006. Primary production, nitrogen cycling and the ecosystem role of mangrove microbial mats on Twin Cays, Belize. Ph.D. Dissertation. University of Georgia, Athens, Georgia. 157 pages.

Abstract
The seasonal variability of porewater nutrient concentrations, metabolism, nitrogen cycling (denitrification and nitrogen fixation), and primary production (oxygenic and anoxygenic photosynthesis and chemoautotrophy) was examined in benthic mangrove environments on Twin Cays, Belize. Twin Cays mangroves exhibit a tree-height gradient from tall seaward fringe trees, through a transition of intermediate tree heights to short dwarf trees surrounding interior ponds and lagoons. Detailed investigations of steady state porewater profiles of nutrients and terminal metabolic products in dwarf mangrove soils revealed strong seasonal differences in salinity, organic carbon and nitrogen inventories, redox conditions and reduced manganese concentrations. Substantial rates of organic matter remineralization were coupled primarily to sulfate reduction. Redox conditions contributed to variability in mat nitrogen fixation and denitrification response to nutrient addition, while dissolved organic carbon did not. Nitrogen fixation was controlled primarily by the sensitivity of nitrogenase to oxygen inhibition, whereas denitrification was limited by nitrate availability. Community composition of photosynthetic organisms appeared to be controlled by light fluctuations due to mangrove canopy light gaps and by differential tolerance to environmental stresses such as desiccation or nitrogen limitation. Dwarf mangrove cyanobacteria-dominated microbial mats achieved a high biomass of photopigments in well-illuminated soils. Transition and fringe soils were more shaded and contained diatoms and green algae and less cyanobacteria and anoxygenic photosynthetic bacteria than in dwarf soils. Oxygenic photosynthesis was the primary mode of carbon fixation (56%) in all habitats under full sun, with a lesser contribution by anoxygenic photosynthesis (32%) and chemoautotrophy (12%). In situ light conditions underscore the gradient from highest rates of carbon fixation in dwarf mangrove habitat mats -2-1(0.21 g C m d) to diminished rates in shaded transition and fringe mangrove habitat mats (0.08 -2-1and 0.05 g C m d, respectively). Well-lit mats associated with dwarf mangrove habitats fix 18-20% of the net primary productivity of Twin Cays’ dwarf mangrove trees and can supply 5-28% of the nitrogen requirement of Twin Cays’ dwarf mangrove trees via nitrogen fixation. Light limitation restricts the fixation of carbon and nitrogen in transition and fringe mangrove habitat mats which account for only <0.3% of the net production and <2% of the nitrogen requirement of the respective mangrove trees.

Letourneau, M.L. 2020. Dissolved organic matter dynamics in coastal aquatic systems. Ph.D. Dissertation. University of Georgia, Athens, GA. 188 pages.

Li, F. 2017. Response and recovery of low-salinity marsh plant communities to constant and pulsed saline intrusion. Ph.D. Dissertation. University of Houston, Houston, TX, USA.

Abstract
The effects of climate change on environmental conditions will be manifest as both chronic changes and pulse changes of varying durations. In estuaries, future variation in sea level, freshwater withdrawal and drought will lead to saline intrusion into low-salinity tidal marshes. I sought to understand the responses to various salinization scenarios on individual, community and ecosystem levels. First, I used a mesocosm experiment to assess the responses of individual low-salinity marsh macrophytes to different durations of saline water exposure, without interspecific interactions. Second, I used another mesocosm experiment to assess the response of plant communities to saline water pulses of three salinities for five durations, and then assessed subsequent community recovery when the saline pulses were withdrawn. Third, I used a field experiment to explore the impacts on a freshwater marsh plant community of short- and long-term changes in salinity.I found that freshwater marsh plants varied in their tolerance to saline water addition. I ranked the species as follows, in order from least to most salt tolerant: L. peploides, P. hydropiperoides, P. cordata and Z. miliacea, followed by S. lancifolia and E. palustris in a tie. I found that community composition was increasingly affected by the more-saline and longer-duration treatments. In the second mesocosm experiment, most but not all of the plant species were able to recover from low-salinity, short-duration saline pulses in less than one year. Because not all the species recovered, post-disturbance community structure diverged among salinization treatments. In the field experiment, both presses and pulses of saline water addition caused the loss of L. repens, resulting in community composition diverging away from the controls. In the pressvtreatment, plant biomass and diversity was strongly suppressed. In the pulse treatment, community composition did not recover to the baseline conditions in between pulses of saline water, as L. repens failed to fully recover from pulses of salinity. In the second mesocosm experiment, shifts in community composition prevented long-term reductions in productivity. In the field experiment, however, salt-tolerant plants could not immigrate, and salinity presses caused significant decrease in aboveground biomass. In contrast, salinity pulses had no effect on plant production. These results show that species composition is more sensitive to environmental changes than overall ecosystem processes. However, changes in ecosystem structure due to pulse changes may not preclude recovery in ecosystem function.

Liu, Q. 2016. Biogeochemical cycling of polyamines in a coastal marine environment. Ph.D. Dissertation. University of Georgia, Athens, GA. 197 pages.

Abstract
Polyamines are a group of short-chain aliphatic compounds containing multiple primary or secondary amine groups. They are ubiquitous in aquatic environments with concentrations in the sub-nanomolar range, while their concentrations in cells are at millimolar levels. They are commonly regarded as important osmolytes, synthesized or assimilated by osmotrophs, like bacterioplankton. They play a key role in cellular growth and synthesis of nucleic acids and proteins, maintaining physiological functions. However, few studies have examined the role of polyamines in oceanic N cycling. In this study, I hypothesized that polyamines could contribute a significant amount of nitrogen to bacterial N production because of greater N: C ratio in polyamines than other labile organic nitrogen compounds. I determined the turnover rates of three polyamines (putrescine, spermidine and spermine) in water samples using 3 H-labeled compounds and measured their concentrations by HPLC in the South Atlantic Bight (SAB) from the inner continental shelf to the shelf-break at the edge of the Gulf Stream and in salt marsh estuaries. I sampled during different times of the years to assess temporal variability of polyamine dynamics. The data showed that polyamines were rapidly assimilated by bacterioplankton, especially in samples from salt marshes and the inner-shelf of the SAB. However, the low ambient concentrations of polyamines limited their contribution to bacterioplankton C (<5%) and N (10%) demand compared to dissolved free amino acids (L-arginine and L-glutamate) that were used as controls. My study of polyamine metabolism in phytoplankton suggested that bacterial uptake of polyamines was limited by the sources of polyamines. I found low concentrations (nmol-1 ) of dissolved polyamine pools in media of phytoplankton cultures, similar to concentrations measured in the field. My data suggested that the composition and concentration of dissolved polyamines is a result of low diffusion from intracellular pools, selective release and uptake by healthy phytoplankton cells, as well as modifications due to bacterioplankton uptake. Thaumarchaeota have been shown to oxidize polyamine nitrogen. This dissertation investigated the spatial and seasonal variability of the abundances and activity of Thaumarchaeota in the SAB by quantitative PCR of Thaumarchaeota 16S rRNA and Archaea ammonia monooxygenase subunit A (amoA) genes and simulated in situ incubations with 15NH4Cl. I found a peak in Thaumarchaeota abundance (>1000-fold increase) in mid-summer at inshore and nearshore stations, but rapid ammonia oxidation was constrained to the inner-shelf at the mouth of the estuaries, probably driven by the substrate availability.

Lynes, A.R. 2008. Centrifugal organization in a Georgia salt marsh plant community. M.S. Thesis. University of Houston, Houston, Texas. 67 pages.

Abstract
In this study I evaluate whether a centrifugal model helps explain vegetation patterns in a Georgia salt marsh using a combination of sampling data and manipulative experiments. The centrifugal model predicts that multiple stress gradients radiate out from a shared core habitat and that plants should occupy discrete ranges along these gradients. The results from this study indicated that there were two clear stress gradients, salinity and water-logging, along which species and habitats occupied discrete ranges, supporting the centrifugal model. The centrifugal model predicts that productivity should be greatest at the benign end of each stress gradient and least at the most stressful end. The results from this study generally supported the centrifugal model. Juncus and Borrichia, which occupied the most benign habitat, had the highest biomass. The stressful ends of the gradients, occupied by Salicornia virginica, short Spartina alterniflora and medium Spartina alterniflora, all had relatively low biomass. The centrifugal model predicts that diversity should be highest in intermediate levels of stress. Salicornia virginica and Spartina alterniflora zones always had the lowest species richness and diversity, supporting the centrifugal model. However, the Borrichia zone always had the greatest or second greatest level of species richness and diversity, not supporting the centrifugal model. The centrifugal model predicts that when species are transplanted outside of the benign habitat they will do poorly, with or without neighbors present, where species at the stressful ends of the gradients will do well when transplanted into the benign habitat without neighbors, but poorly when neighbors are present. The results of the transplant experiments strongly supported the centrifugal model. In conclusion, I found strong evidence that the centrifugal model was useful in explaining plant community structure in a Georgia salt marsh. This model also provides a unified theory for vegetation patterns in northeast and southeast USA salt marshes, where zonation due to high salinities caused by increased evapotranspiration in the low-latitude climates can be equated to the disturbance-caused temporary increases in salinity in high-latitude climates.

Lyons, J.I. 2007. Molecular description of ascomycete fungal communities on Spartina spp. in the U.S. Ph.D. Dissertation. University of Georgia, Athens, Georgia.

Abstract
Ascomycetous fungi play a crucial role in the decomposition of salt marsh vegetation. The first part of this research used molecular methods to examine whether physical associations exist between individual bacterial and common ascomycetous fungal species that co-occur on decaying smooth cordgrass, Spartina alterniflora, in a southeastern U.S. salt marsh. We found that bacterial communities were unaffected by the identity of initial fungal decomposers, suggesting that few species-specific associations exist between those members of the Spartina decomposer community. The next part of the study involved a characterization of ascomycetes involved in the decomposition of different species of Spartina in different environments. In California, the fungi associated with S. alterniflora, S. foliosa, the hybrid between them, and S. densiflora were all characterized using terminal restriction fragment length polymorphism (T-RFLP) analysis of their internal transcribed spacer (ITS) region of rRNA genes as well as clone libraries. Although we found no effect from the hybridization of two host species, we did see significant differences in the fungal decomposer communities both within and among species. S. densiflora hosted several unique ascomycetes. Two previously described ascomycetes, Phaeosphaeria spartinicola and Mycosphaerella, were ubiquitous on all samples analyzed. On the east coast, ascomycete communities on samples of S. alterniflora and S. patens collected in four states (Georgia, North Carolina, New York, and Massachusetts) were compared, again using T-RFLP analysis of the interspacer region. Results show that diversity of the ascomycete taxa on S. patens hosts a higher number of unique ascomycete species than S. alterniflora, and that it has significantly higher diversity, but there were no consistent differences among states. P. spartinicola and Mycosphaerella again dominated most T-RFLP profiles. The data suggest that two fragments (147 and 149 bp), although not confirmed to represent separate taxa, were specific to host plant species. Preliminary data from samples of the same species of grass collected in states along the Gulf coast (FL, LA, MS, AL) confirm all conclusions drawn for samples collected along the east coast, including the higher diversity on S. patens, omnipresence of P. spartinicola and P. halima, and species-specificity of fragments at 147 and 149 bp.

Marton, J.M. 2012. Ecosystem services of restored wetlands and riparian buffers---USDA conservation practices in the glaciated interior plains. Ph.D. Dissertation. Indiana University, Bloomington, IN. 138 pages.

Abstract
Wetlands provide valuable ecosystem services such as water quality improvement, carbon (C) sequestration, nutrient (nitrogen [N] and phosphorus [P]) retention, and biodiversity support. Throughout the Midwest, wetlands and riparian areas have been drained and cleared for conversion to row-crop agriculture. Through the United States Department of Agriculture, programs such as the Wetlands Reserve Program (WRP) and Conservation Reserve Program (CRP) provide landowners an opportunity to restore wetlands and riparian buffers with the goal of reintroducing ecosystem services lost during the conversion to agriculture. However, there has been little research on the effectiveness of WRP and CRP sites in returning ecosystem services to the landscape.To fill this knowledge gap, I measured water quality improvement functions (denitrification and P sorption), C sequestration, and nutrient (N,P) accumulation in natural and restored wetlands and riparian buffers in Indiana and Ohio. I also evaluated which of three USDA conservation practices (e.g., restored wetland, restored riparian, conserved riparian) provided the greatest relative level of water quality improvement functions. I then characterized fine-scale spatial variability of denitrification and associated soil properties in natural and restored wetlands to determine if restored wetlands had comparable heterogeneity relative to natural wetlands.Overall, riparian areas had higher rates of denitrification, P sorption, and C sequestration than depressional wetlands. Restored and natural riparian areas provided comparable services, whereas natural wetlands provided greater services than restored wetlands. Water quality improvement functions (N and P removal) were dependent upon the interactions between parent material (clayey vs. sandy soils), hydrologic connectivity (depressional vs. pulsed), and disturbance regime. First, greater connectivity to adjacent aquatic systems increased N and P removal and C sequestration. Second, finer-textured clayey soils facilitated greater denitrification and P sorption relative to sandier soils. Third, prescribed fires in the restored wetlands inhibited the accumulation of soil organic matter, which influences denitrification and P sorption. Continued enrollment of agricultural land into conservation practices will return ecosystem services to the landscape, although whether wetlands or riparian buffers should be restored will depend upon the desired ecosystem service.

McCall, B.D. 2011. Geographic Variation in the Structure of Salt Marsh Arthropod Communities. M.S. Thesis. University of Houston, Houston, Texas. 51 pages.

Abstract
The natural environment shows variation at multiple scales, and determining how large-scale patterns relate to the local community's structure and function is a fundamental goal of ecology. Salt marshes along the Atlantic and Gulf coasts are similar in many ways, and are inhabited by the same plant and insect species. However, the Atlantic and Gulf coast areas have different tidal regimes, which may result in the two areas not functioning exactly the same. In addition, abiotic factors that vary with latitude or longitude may lead to differences between northern and southern or eastern and western sites. I hypothesized that structure and function of the coastal salt marsh varies geographically. To test this, I characterized abiotic conditions and the plant and arthropod communities at 11 sites along each coast in the late summers of 2009 and 2010. I also manipulated wrack (dead plant stems) and nutrient availability in 2 x 3 m plots at each site to evaluate geographic differences in community response. The experiment was established in 2009 and allowed to run to 2010. My sampling documented that some abiotic factors varied geographically, as did plant height, nitrogen content, and thatch cover. Although the total number of arthropods collected did not differ geographically, the trophic composition of samples showed marked variation among regions. Large-scale differences in latitude and mean tidal range are likely driving much of this variation. Arthropod community structure was little affected by wrack addition, but responded strongly to fertilization; and, the effect of fertilization varied geographically for some trophic levels. Although salt marshes are superficially similar from Maine to Texas, they may be structured differently throughout this geographic range. Therefore, extrapolating results from one geographic region to another should be done with caution.

McFarlin, C.R. 2004. Impact of Fertilization on a Salt Marsh Food Web in Georgia. M.S. Thesis. University of Georgia, Athens, Georgia. 127 pages.

Abstract
I examined the response of a salt marsh food web to nutrients, and spatial variation in this response, at 19 sites on the Georgia coast. In fertilized treatments, Spartina alterniflora increased at the expense of Juncus roemerianus. Spartina dominance was reduced at sites with greater upland influence, regardless of fertilization. Because fertilization changes plant quantity and quality, it could also affect consumers of plants. Fertilization positively influenced herbivores (grasshoppers), had little effect on decomposers (fungi), and no effect on detritivores (snails). The two snail species Littoraria irrorata and Melampus bidentatus were negatively correlated with each other and likely compete. Natural variation among sites was typically similar or greater than impacts of fertilization. These results suggest that eutrophication of salt marshes is likely to have stronger impacts on plants and herbivores than on decomposers and detritivores, and that impacts are not likely to be much greater than variation among sites.

McFarlin, C.R. 2012. Salt Marsh Dieback: The response of Spartina alterniflora to disturbances and the consequences for marsh invertebrates. Ph.D. Dissertation. University of Georgia, Athens, GA. 238 pages.

Abstract
Spartina alterniflora is a foundation species that plays a disproportionately critical role in salt marshes, as it ameliorates chemical and physical stress to other plants and animals, provides essential habitat, protection from predators, and a source of organic matter to associated fauna. Disturbances including sudden dieback, herbivore overgrazing, and wrack deposition can lead to a loss of Spartina and thus, indirectly affect the invertebrate community. My goals were 1) to examine the effects on the invertebrate communities in 2 different geographical regions (GA, LA) and among 4 different disturbances within a region (GA), 2) to determine whether various disturbances would elicit a similar and predictable physiological response (the DMSO:DMSP ratio, and metal load) in Spartina that could be used as a sensitive and predictable indicator of stress among various disturbance types, and 3) to document the never before described long-term trajectory and patterns of recovery from sudden dieback in a Spartina and Juncus roemerianus marsh. Spartina loss in GA and LA led to similar decreases in Littoraria irrorata (periwinkle snails), but there were strong differences in the responses of infauna between the states and among years. These results suggested context-dependency in both the effect of foundation species within a geographical region and in the evaluation of the ecosystem service provided at the time of sampling. Overall and despite differing results, it was found that Spartina was ultimately important in maintaining the invertebrate communities in both states. However, within a geographical region, both the physiological response of Spartina and the indirect response of the invertebrates to Spartina loss were similar and predictable among four different disturbances. The DMSO:DMSP ratio and metal loads were increased in affected Spartina plants (often responsive in otherwise green leaves) and periwinkle snails and benthic macroinfauna (density, taxon richness, and diversity) were significantly decreased in affected areas, regardless of disturbance type. Vegetation recovery at sudden dieback is occurring slowly (on the order of a decade) via rhizomes extension from healthy areas, and thus understanding the effects to invertebrates is important, as disturbances such as these are expected to increase with climate change and anthropogenic effects.

McKay, P. 2008. Temporal and Spatial Variability of Transport and Mixing Mechanisms: Using Heat and Salt in the Duplin River, Georgia. Ph.D. Dissertation. University of Georgia, Athens GA. 217 pages.

Abstract
A study of the Duplin River, a shallow, sinuous, tidal creek which connects the salt marshes of Sapelo Island, on the central Georgia coast, with the waters of Doboy Sound and the coastal Atlantic Ocean, was conducted to quantify the physical processes which regulate the flux and zonation of heat and salt throughout the creek system.Three water masses are identified with differing temperature and salinity regimes. Hourly scale heat budgets are constructed for the upper (warmer) and lower (cooler) areas of the Duplin River showing the diminishing importance of tidal advection away from the mouth of the creek along with the concomitant increase in the importance of both direct atmospheric fluxes and of interactions with the marsh and side creeks. The heat budget is re-examined on daily averaged scales revealing the decreased importance of advective fluxes relative to direct atmospheric fluxes on this scale but the constant importance of marsh/creek interactions regardless of time scale or season. Tidally averaged along channel salt fluxes are calculated and a contrast is drawn between the lower and the upper Duplin. The main channel of the lower Duplin is bordered by creekless marsh, marsh hammocks and hard upland and salt fluxes are largely constrained to the main channel with salinity in the lower Duplin closely tracking observed salt fluxes. The upper Duplin is isolated from the lower Duplin by a sinuous channel and is subject to significant local fresh groundwater input. The upper Duplin acts as a reversing estuary on a fortnightly time scale. Salt fluxes are not constrained to the main channel but show a significant influence of the marsh. Vertical mixing is shown to be modulated on both M4 and fortnightly frequencies with turbulent stresses being generated near the bed and propagating into the water column on periods of max flood and ebb and being significantly greater on spring tide than on neap. Horizontal mixing is driven by tidal dispersion, which is modulated by the fortnightly spring/neap cycle. Net export of salt from the lower Duplin is shown to be due to residual advection modified by upstream tidal pumping which, in the absence of external forcing, exhibits a pulsating character with net export taking place for a short period on spring tide followed by a longer period of net import of salt.A box model is developed to explore subtidal inputs of groundwater and salt into the three water masses of the Duplin River. The results of this model are examined to draw insights into the magnitude and spatial distribution of these processes and their effect on the Duplin River water masses.

McKnight, C.J. 2016. A modelling study of horizontal transport and residence time in the Duplin River estuary, Sapelo Island GA. M.S. Thesis. University of Georgia, Athens, GA.

Abstract
A high-resolution, three-dimensional, hydrodynamic model of the Duplin River estuary on Sapelo Island Georgia has been developed using Finite Volume Community Ocean Model. Using a model to describe transport and retention is a good way to estimate the efficiency of an estuary at remediating contaminants. The model shows good agreement with time series of sea surface height and salinity from monitoring stations within the domain. The model does well at predicting tidal oscillations and subtidal SSH and salinity variations. However, there is room for improvement with regard to salinity variability in the upper model domain. A Lagrangian particle tracking analysis was carried out to study the effects of semi-diurnal tides, spring/neap tidal cycles, and seasonal forcings on residence times. Residence time is most sensitive to the stage of the tide (slack high or slack low) when starting the particle tracking and had maximum values on slack low water. Neap tides had characteristically longer residence times than spring tides. Residence time was also dependent on seasonal changes and was higher during periods of low river discharge which correspond to higher sea surface inundation than periods of high river discharge. An Eulerian salt flux analysis was carried out to study the relative roles of advective and dispersive flux on transport processes. The residual or advective flux, dominates the transport within the system and marsh circulation in the upper reaches shows net inward movement along the channel and net outward movement over the marsh. Tidal flux dominates the dispersive flux over estuarine exchange flux and thus controls the horizontal dispersion. The horizontal dispersion coefficient was dependent on seasonal river discharge as the horizontal salinity gradient switches from a positive to a negative estuary causing very large and highly variable values during periods of high river discharge. Alternatively, the horizontal dispersion coefficient was more periodic and controlled by the spring/neap cycle, showing maxima on spring tides during the season of low river discharge and high sea surface inundation.

Moreta, J.I.L. 2002. Diversity of laccase gene sequences and contributions of bacteria and ascomycetous fungi to lignocellulose degradation in a southeastern U.S. salt marsh. M.S. Thesis, University of Georgia, Athens, Georgia. 64 pp.

Abstract
In the first part of this study, we used molecular tools to create a database of protein sequences for laccase genes of salt marsh ascomycetes. Laccase is one of the enzymes shown to be involved in fungally-mediated lignin degradation. We then used this database to identify laccase sequences in the natural decomposer community on blades of Spartina alterniflora in two stages of decomposition. The sequences we collected contribute significantly to the relatively limited database of ascomycete sequences that currently exists. The second part of this study addressed the relative activity levels of bacterial and fungal decomposers by measuring rates of lignocellulose degradation in a simple microcosm system. The results of this study provide a tool for future evaluation of the effects of genetic manipulations on ecologically relevant decomposer organisms, including studies of gene function and degradative efficiency and interactions between bacterial and fungal decomposers.

Mou, X. 2006. Culture-independent Characterization Of DOC-Transforming Bacterioplankton in Coastal Seawater. Ph.D. Dissertation. University of Georgia, Athens, Georgia. 182 pages.

Abstract
Bacterially-mediated transformation of aromatic monomers and organic osmolytes, two important components of the dissolved organic (DOC) pool in coastal seawater, is significant in the biogeochemical cycling of essential elements including carbon, sulfur and nitrogen. A study of bacterioplankton responding to the addition of 20 uM dimethylsulfoniopropionate (DMSP), a sulfur-containing organic osmolyte, suggested that a subset of the bacterial community could degrade DMSP. Cells developing high nucleic acid content in the presence of DMSP included members of alpha-Proteobacteria (mainly in the Roseobacter clade), beta-Proteobacteria and gamma-Proteobacteria, and a lower number of Actinobacteria and Bacteroidetes. The relative importance of DMSP-active taxa varied seasonally. Another study tested whether aromatic monomers and organic osmolytes are transformed by specialist bacterial taxa. The taxonomy of coastal bacterioplankton responding to the addition of 100 nM organic osmolyte [DMSP or glycine betaine (GlyB)] or aromatic monomer [para-hydroxybenzoic acid (pHBA) or vanillic acid (VanA)] was determined using incorporation of bromodeoxyuridine (BrdU) to track actively growing cells. 16S rDNA clones of active bacterioplankton indicated that both types of DOC were transformed by bacterial assemblages composed of the same major taxa, including Actinobacteria, Bacteroidetes, alpha-Proteobacteria (mainly members of the Roseobacter clade), beta-Proteobacteria, and gamma-Proteobacteria (mainly members of Altermonadaceae, Chromatiaceae, Oceanospirillaceae and Pseudomonadaceae). The relative abundance of each taxon differed, however. Members of the OM60/241 and OM185, SAR11, SAR86 and SAR116 bacterioplankton groups in the active cell group indicated the ability to transport and metabolize these compounds by these ubiquitous but poorly described environmental clusters. In a final study, the phylogenetic diversity and functional capability of bacterioplankton stimulated by the addition of DMSP or VanA were explored by metagenomic analysis. Metagenomic sequences revealed a similar taxonomic structure for the bacterioplankton enriched with both DOC types, and were generally consistent with the PCR-based 16S rDNA analysis of the same template. Likewise, similar distribution patterns of functional gene categories were found for the two enriched bacterioplankton communities. These results indicate that DMSP and VanA were transformed by metabolic generalists capable of degrading both compounds. These studies provide insights into the response of coastal bacterial communities to changing environmental conditions in an ecological time frame.

Napora, K. 2021. Refining cultural and environmental temporalities at the late Archaic-early woodland transition along the Georgia coast, UGA. Ph.D. Dissertation. University of Georgia.

Nifong, J.C. 2014. Use of marine habitat and food resources by coastal inhabiting Alligator Mississipiensis (American Alligator): implications for food webs and community dynamics. Ph.D. Dissertation. University of Florida, Gainesville, FL. 201 pages.

Abstract
The American alligator (Alligator mississippiensis) is a widespread aquatic predator throughout the southeastern United States. Historically, the ecological interactions of A. mississippiensis have been studied in the context of freshwater ecosystems such as inland lakes. Lacking salt secreting glands maintained in closely related crocodiles (Crocodylidae), the occurrence of A. mississippiensis in higher salinity marine and estuarine ecosystems has often been considered aberrant and of no particular importance to ecological processes in these coastal systems. However, it is well known that top-predators have the potential to exhibit strong effects within foodwebs through their interactions with prey and movement between disparate ecosystems. Within this dissertation, I set out to demonstrate that the use of marine and estuarine ecosystems by A. mississippiensis is common and that these behaviors have the potential to affect isolated freshwater ponds and wetlands by transferring marinederived nutrients and salt marshes through their interactions with an importantmesopredator (Callinectes sapidus, Blue crab). First, I employed field studies using nightlight surveys, stomach content analysis, and stable isotope analysis to assess intra-population variation in the use of marine habitat and food resources by A. mississippiensis inhabiting an Atlantic barrier island.Second, I used GPS/VHF telemetry to assess the effect of abiotic factors on crossecosystem movement patterns of adult individuals. Third, I attached and deployed animal-borne imaging systems (Crittercam) to quantify prey attack and capture success rates as well as diel activity patterns and investigated variation in these parameters. Lastly, I experimentally tested the potential of A. mississippiensis to elicit a trophic cascade within a simplified salt marsh food web through consumptive and nonconsumptive interactions with the mesopredator C. sapidus.Results from this body of work will advance our understanding of the role A. mississippiensis serves in coastal ecosystems and provide essential data to predict consequences of changing environment conditions.

Ogburn, M.B. 2004. Salt marsh dieback in Georgia: Field survey and transplant experiments. M.S. Thesis, University of Georgia, Athens, Georgia. 108 pp.

Abstract
In winter 2002, portions of the salt marshes of coastal Georgia began experiencing dieback, affecting both Spartina alterniflora and Juncus roemerianus. During the summer of 2003, a field survey of 18 widely distributed sites along the coast was conducted to document the characteristics of and obvious patterns in dieback areas. Most dieback areas were small (<1 acre), did not show spatial patterns and occurred along the edges of tidal creeks. There were no consistent differences in soil salinity, pH or redox potential between dieback and healthy areas. A transplant study was carried out to determine if healthy plants can survive in dieback areas. Transplant survival was 100% from May to October 2003, and growth was observed in both dieback and healthy (control) areas. The results of this study suggest that drought, along with various contributing factors, was the ultimate cause of salt marsh dieback in coastal Georgia.

Pannill, V. 2018. Assessing the export of terrigenous dissolved organic matter in the South Atlantic Bight using CDOM analysis: 2014 and 2016 cruises. B.S. Thesis. University of Georgia, Athens, GA. 13 pages.

Porubsky, W.P. 2008. Biogeochemical dynamics in coastal sediments and shallow aquifers. Ph.D. Dissertation. University of Georgia, Athens, Georgia. 222 pages.

Abstract
Patterns of benthic metabolism and the relative importance of assimilatory and dissimilatory processes as sinks for nitrate (NO3-) in intertidal sediments were examined. Under illuminated, nitrogen (N)-replete conditions, sequential nutrient limitation of benthic microalgae (BMA) was observed, with N limitation preceding silicate limitation; and biological assimilation dominated nitrate uptake. Conversely, under dark hypoxic and anoxic conditions, water column NO3- uptake was dominated largely by three competing dissimilatory reductive processes; denitrification (DNF), dissimilatory nitrate reduction to ammonium (DNRA), and, on one occasion, anaerobic ammonium oxidation (anammox). High sulfide concentrations negatively impacted DNF and DNRA rates, while high dissolved organic carbon (DOC):NO3- ratios favored DNRA over DNF. Under baseline conditions sediments exhibited tight coupling between photosynthesis and respiration. Nitrogen addition shifted the metabolic status of the sediments from a balance between autotrophy and heterotrophy to net autotrophy, and the sediments became a source of DOC. The role of groundwater as a source of nutrients and organics to the coastal ocean was evaluated using a combination of radium isotopes and geochemical characterization. Geochemical data indicated significant spatial variations in groundwater chemical composition and radium activity ratios indicated geographically distinct hydrological regimes. Spatial variations in microbially mediated processes, DOC distribution, and/or groundwater residence time contributed to this pattern. Radium based geochemical loading rates illustrated a substantial groundwater contribution of organics, DIC, nutrients, methane and nitrous oxide to the Okatee estuary. The groundwater biogeochemical dynamics along a shallow monitoring well transect on a coastal hammock were evaluated by density-dependent reaction transport model. A switch in the redox status of the DIN pool occurred during the spring-neap tidal transition (spring high NO3- low NH4+; neap low NO3- high NH4+). The observed N redox-switch was evaluated with regard to the relative roles of nitrification, DNF, DNRA, ammonium adsorption, and variations in inflowing water geochemistry between spring and neap tides. The latter was found to most significantly affect the observed pattern in DIN dynamics. Additionally, the fate of DOC and DIN originating from a septic system was studied. Simulation results indicated that while DNF increased ~15 fold, higher N removal rates could not keep pace with the increase in DIN loading, resulting in higher export of DIN to coastal waters.

Ransom, B. 2008. Intestinal microbial community composition of six Actinopterygii fish species in the Southeastern United States. M.S. Thesis. University of Georgia, Athens, GA. 38 pages.

Abstract
The intestines of fish harbor a microbial community that aids digestion and prevents colonization by pathogens. Traditional methods of studying these communities have been cultivation dependent, yet many microorganisms are difficult to grow in the laboratory. In this study, gut microflora of six different Actinopterygii fish species from the southeastern United States were examined by PCR/DGGE analysis and cloning with primers specific for the 16S rRNA genes of Bacteria. Most fish species seem to have gut microflora dominated by either Firmicutes or proteobacteria. Sequences 92-93% similar to species of Mycoplasma were found in pinfish (Lagodon rhomboides) and red drum (Sciaenops ocellatus), while flounder (Paralichthys lethostigma) contained a majority of sequences most similar to Clostridium spp. The gut microflora of pipefish (Syngnathus scovelli) and silver perch (Bairdiella chrysoura) were dominated by members of the division proteobacteria, and speckled trout (Cynoscion nebulosus) were not dominated by either Firmicutes or proteobacteria.

Reader, H.E. 2011. Smouldering oceans: on the photochemically mediated oxidation of dissolved organic matter in coastal waters. Ph.D. Dissertation. University of Georgia, Athens, Georgia. 194 pages.

Abstract
Marine dissolved organic carbon (DOC) is one of the largest and most dynamic pools of reduced carbon on earth. Photochemical processes have the potential to significantly affect the content of this DOC pool. Photochemical oxidation to carbon monoxide and carbon dioxide are two direct pathways for the removal of DOC from the marine system. Indirectly, photochemical processes can lead to the removal of DOC through the alteration of chemical structures rendering them more biologically labile. In order to assess the influence of photochemistry on the coastal carbon cycle the variability of these processes must be well constrained. To calculate photochemical production in marine waters, it is crucial to know how light is absorbed by chromophoric dissolved organic matter (CDOM), as well as the spectral efficiency of the resulting photochemical reactions (i.e. the apparent quantum yield (AQY) spectra). The challenges of using visible wavelength CDOM absorption data to model ultraviolet absorption data are investigated. Direct measurements of ultraviolet absorption data model photochemical processes best. When this is not possible, visible data can be used with an accuracy of +/- 10% in coastal waters. Either a hyperbolic absorption model or one using correction factors applied to a traditional exponential model will allow for similar accuracy in the ultraviolet portion of the absorption spectrum. The variability of photochemical oxidation of dissolved organic carbon in a coastal system was studied in order to constrain remote sensing calculations. The variability of CO and CO2 AQY spectra were relatively well constrained in three estuaries of Georgia, USA. The AQY for CO varied within +/- 12.7% year-round while CO2 varied within +/- 33.6% year-round. Hyperspectral remote sensing reveals finescale hydrodynamic structure in estuarine systems and is readily adaptable to photochemical modeling applications. Defining the variability of photochemistry?s influence on the biological lability of DOC is a complex undertaking. Unlike direct photochemical oxidation of DOC to CO and CO2, the biologically labile products (BLPs) of incomplete oxidation can themselves be photochemically reactive. Competition between production and destruction of BLPs during irradiation is a significant consideration when determining the quantitative influence of photochemistry on marine systems.

Richards, C.L. 2004. Evolution in closely adjacent salt marsh environments. Ph.D. Dissertation. University of Georgia, Athens, Georgia. 141 pages.

Abstract
Environmental variation and its effect on phenotypic variation have long been of interest to evolutionary ecologists. Several hypotheses suggest how plants can live across steep environmental gradients. These include clonal integration, phenotypic plasticity and genetic differentiation. The main objective of this dissertation was to determine what strategies salt marsh plants use to live across the environmental gradients of the marsh. Field surveys of plant phenotypes, environmental parameters and allozyme patterns as well as a greenhouse study and a reciprocal transplant study were conducted to meet this objective.Field surveys of 12 species indicated that plant phenotypic variation is correlated to environmental variation. In contrast, allozyme patterns showed no association between alleles or genotypes with microhabitats. Similarly, levels of diversity did not differ across microhabitats along the gradient. Much of the variation in the distribution of genetic diversity, however, was predictable based on the gradient. In addition, genetic diversity was surprisingly high and clone size was limited. In both the greenhouse and field reciprocal transplant studies there was evidence of phenotypic plasticity for all traits measured. The greenhouse study on outcrossed seedlings revealed genetic variation for only final height and concentrations of leaf elements Na, P, and Mg. Alternatively, the field experiment on clones of field collected plants, found genetic variation in almost all salt tolerance traits. In high and low salt gardens, there was significant selection for increased total leaf area and water use efficiency (WUE). However, patterns of selection were significantly different in the two gardens only for stabilizing selection on WUE.These studies suggest that salt marsh plants are highly plastic. Although there is a lot of genetic variation for salt tolerance traits, and some evidence for differentiation between the two habitats, there is little evidence that these habitats select on traits differently. Differential selection in the two habitats on WUE was the one exception, however there was no evidence of differentiation for this trait. These studies therefore reveal the importance of phenotypic plasticity as the predominant strategy for living across the environmental gradients of the salt marsh.

Richards, T. 2018. A spatial and temporal investigation of estuarine and shelf flows on the Georgia Coast. M.S. Thesis. University of Georgia, Athens, GA.

Salgado, C. 2004. Latitudinal variation in palatability of salt marsh plants: Constitutive or induced? M.S. Thesis, University of Houston, Houston, Texas. 57 pp.

Abstract
A central biogeographic theory argues that consumer-prey interactions are more intense, and prey defenses better developed, at lower latitudes. Along the Atlantic Coast of the United States, southern salt marsh plants are less palatable than northern conspecifics. To test the hypothesis that latitudinal variation in palatability would occur in the absence of geographically-different environmental cues (i.e., that differences in palatability are constitutive rather than induced by climate or herbivore damage), I grew high- and low-latitude individuals of three species of salt marsh plants from seeds (Solidago sempervirens) or rhizome cuttings (Distichlis spicata and Spartina alterniflora) in a common-garden greenhouse environment, and compared their palatability to herbivores over time. I also quantified leaf toughness and nitrogen content of those plants in order to help explain results of feeding assays. My results document a pattern for northeastern salt marsh plants to be more palatable than southeastern conspecifics after being germinated in a greenhouse or kept under common-garden conditions for several clonal generations, suggesting that the latitudinal variation of salt marsh plants observed in the field is constitutive rather than induced by environmental cues. Latitudinal variation in plant traits depended on the plant species. Toughness varied as a function of latitude for Spartina and Distichlis, with southern plants being tougher than northern conspecifics across clonal generations. For all generations of Spartina and for seed-propagated Solidago, northern plants had higher nitrogen content than southern plants. Results are consistent with the theory that herbivory is a strong selective pressure that might be shaping geographical variation in plant palatability. However, many other factors, such as differences in growth season length and external disturbances could be of crucial importance in mediating this latitudinal pattern of palatability. Understanding the genetic and environmental bases of intraspecific variation and how they covary on broad geographic scales can provide important clues to how organisms adapt to different and changing environments.

Sanders, S.C. 2021. Groundwater flow and transport at the forest-marsh boundary: A modeling study. M.S. Thesis. University of South Carolina, Columbia SC USA. 50 pages.

Abstract
The forest-marsh boundary, where tidally influenced salt marshes meet a forested upland, is hydrologically complex due to its multiple water inputs. Groundwater flow and salinity transport at this boundary are not well understood. In order to make predictions about salinity at this boundary as it responds to climatic factors, a two-dimensional model was built to simulate groundwater flow and solute transport at a salt marsh on Sapelo Island, Georgia. After calibration based on observed data from wells at the study site, the model can be used to identify patterns in groundwater movement and solute transport that may influence the vegetation and consequently the migration of the forest-marsh boundary. Additionally, the model is designed to be a first step toward identifying the impacts of press and pulse disturbances, such as sea level rise or drought, on the marsh.

Schaefer, S.C. 2006 Nutrient budgets for watersheds on the southeastern Atlantic coast of the United States: temporal and spatial variation. M.S. Thesis, University of Georgia, Athens, Georgia, 105 pp.

Abstract
Nitrogen budgets were constructed for the watersheds of twelve rivers in the southeastern U.S. following the methodology of the SCOPE project. Total inputs ranged from 2,762-6,232 kg/km2/yr, with the largest contributions from fertilizer and net food/feed import. Export to the estuaries of these rivers was positively related to inputs and averaged 9%. In contrast, reported export to estuaries further north averaged 25%. These differences are consistent with temperature-driven changes in denitrifier activity and suggest a possible control for watershed nitrogen export. In order to evaluate changes in nutrient input over time, nitrogen and phosphorus budgets were constructed for the watershed of the Altamaha River estuary in Georgia for 1954, 1974, and 1992. Nutrient inputs increased between 1954 and 1974 and decreased in 1992 (from 2,007 to 3,553 to 2,977 kg N/km2/yr and 408 to 532 to 340 kg P/km2/yr). These changes were largely driven by trends in fertilizer use.

Schaefer, S.C. 2014. Controls on nitrogen inputs, loads, and in-stream concentrations in the Altamaha River, Georgia, and beyond. Ph.D. Dissertation. University of Georgia, Athens, GA.

Abstract
Human activity has increased the availability of reactive nitrogen (N), an element of critical importance to life. The broad goal of this dissertation was to understand which sources of N to a watershed reach rivers. Nitrogen input budgets were calculated for 18 watersheds on the United States west coast. Fertilizer was the most important source of new N, with atmospheric deposition second. N export was best correlated with streamflow variations, which explained 66% of the variance. Including inputs explained an additional 16% of the variance. Riverine N export averaged 12% of inputs. Percentage export was also best related to streamflow. These results were likely due to the large range of streamflows across the study region, which may have overwhelmed other factors contributing to N export. An in-depth examination of the Altamaha River watershed (Georgia, USA) found that riverine N concentrations and cumulative loads were best related to population density, rather than input factors. Concentrations were highest in the upper watershed and lowest in blackwater streams and a sampling station downstream of a dam. Isotopic analysis of nitrate suggested that most in-stream nitrate is derived from sewage or manure. Where the concentration was particularly low, an atmospheric signal was observed, suggesting that background nitrate is of atmospheric origin. N in this system appeared to be lost primarily on the watershed surface, as only a small proportion of inputs reached the stream, N was transported downstream conservatively, and an isotopic mixing model fit the data well. The Altamaha is comparable to other watersheds worldwide in its nitrate concentrations and population density. A metadata analysis of medium-sized (2,000-50,000 km2) watersheds, which are under-studied relative to large watersheds, revealed that nitrate concentrations are generally low (<25 µM). We found a relationship between population density and riverine NO3- concentration, which varied among continents and latitudinal zones. A combination of population density, population density without access to improved sanitation, temperature, precipitation, slope, and fertilizer use, explained 45% of the variation in nitrate concentrations. The relationship had less explanatory power than in large watersheds, potentially due to increased variation in NO3- concentrations with decreased watershed size.

Schultz, G.M. 2002. Hydrologic and Geophysical Characterization of Spatial and Temporal Variations in Coastal Aquifer Systems. Ph.D. Dissertation, Georgia Institute of Technology, Atlanta, Georgia. 329 pp.

Schutte, C. 2014. Nitrogen cycling and trace gas dynamics in shallow coastal aquifers. Ph.D. Dissertation. University of Georgia, Athens, GA.

Abstract
Since the industrial revolution, human activity has doubled the amount of carbon in Earth’s atmosphere and increased the rate of nitrogen supply to its biosphere by 40%. As a result, the climate is warming, sea level is rising, and fresh and saltwater resources are being threatened by eutrophication. Coastal areas are among the most vulnerable to these environmental challenges, and are economically critical zones that support tourism, fisheries, and half of the world’s population. Primary production in coastal waters tends to be nitrogen limited, so anthropogenic nitrogen inputs results in eutrophication and degraded coastal water quality. Groundwater discharge is the dominant source of nitrogen to the South Atlantic Bight and rivals riverine nitrogen loading in many coastalecosystems globally. However, groundwater must transit coastal aquifers prior to discharge where microbial communities have the potential to remove bioavailable nitrogen via coupled nitrification and denitrification or anammox. This microbial activity also generates methane and nitrous oxide, which are potent greenhouse gases. Thus, coastal groundwater influences both water quality and atmospheric chemistry. The goal of this work was to quantify patterns and rates of microbial processes in shallow coastal aquifers that contribute to the production and consumption of bioavailable nitrogen and the greenhouse gases nitrous oxide and methane. High nitrification rates (0.78 ± 0.26 mmol m-2 day-1) were found in shallow beach sand on a barrier island in coastal Georgia, USA. High nitrous oxide concentrations were also observed at this location (median = 282 nM, n = 32). Nitrous oxide production was supported by a nitrate loss rate of 11 mmol m-2 day-1, which in turn, was too high to be supported by the observed nitrification rate alone, suggesting that nitrogen fixation was also important at this site. A hotspot of methane was observed in the freshwater lens near the center of Cabretta Island (median = 587 µM) supported by high rates of methanogenesis (22.2 ±10.6 mmol m-2 day-1). However, most of this methane was consumed before it could be exported to the ocean due to active methanotrophy (18 ± 2.1 mmol m-2 day-1) in surficial beach sand. Finally, submarine groundwater discharge was shown to export roughly the same quantity of greenhouse gases from salt marsh soils as direct efflux to the atmosphere, the only export pathway recognized previously in theliterature.

Segarra, K. 2012. A study of methane-related processes in freshwater ecosystems. Ph.D. Dissertation. University of Georgia, Athens, GA.

Abstract
This dissertation seeks to understand the seasonal controls of methane cycling in freshwater sediments. Using a combination of field measurements, radiotracer incubations, porewater characterization, lipid biomarker analysis, and stable carbon isotopes, pronounced seasonal variations in microbial carbon turnover were documented in a freshwater sediment and in two peat wetlands. Constraints of the methane budget in shallow (< 40 cm) sediments revealed a seasonal imbalance between methane fluxes and methane production that may be relieved through tidal pumping of methane-laden porewaters derived from adjacent high marsh through the creekbank. Rate measurements of sulfate reduction and the anaerobic oxidation of methane (AOM), two processes not typically considered relevant in low salinity habitats, revealed their importance in freshwater settings. Seasonal variations in AOM may be driven by fluctuations in hydrogen and acetate dynamics generated by variations in other microbial metabolisms (e.g. sulfate reduction and methanogenesis). Lipid biomarker analysis revealed the presence of sulfate-reducing bacteria and archaea associated with methane cycling. However, seasonal variations in microbial metabolisms were not associated with changes in the lipid distribution. Stable carbon isotope analyses revealed the imprint of AOM on the signatures of methane and dissolved inorganic carbon. The influence of methanotrophy, however, was not as pronounced in the microbial lipid signatures. A potential AOM isotopic signal may have been diluted by methanogenesis and other autotrophic and heterotrophic processes, which may mask a clear methanotrophic signature. While sulfate reduction activity is sufficient to support all observed AOM activity, no conclusive evidence was found to link these processes. Long-term enrichments of coastal sediments with various electron acceptors demonstrated a positive influence of sulfate and ferric citrate additions on AOM. Other electron acceptors such as nitrate and manganese may also support AOM in these coastal settings. These studies advance the understanding of the seasonal controls on methane emissions, methane production, and methane consumption via AOM in freshwater ecosystems. Future efforts are aimed at closer examinations of these mediating factors, especially temperature changes and substrate availability.

Seminara, D.N. 2010. Synoptic comparison of salt marsh spatial structure using hyperspectral imagery at NOAA National Estuarine Research Reserves. M.S. Thesis. Creighton University, Omaha, NE. 177 pages.

Abstract
As a dynamic system, salt marshes are highly productive habitats. Exceedingly dependent on specific tolerances to tidal regimes, temperature, elevation, and salinity, the plant composition and structure of a salt marsh are highly variable. Due in part to their visible spatial patterns and the impracticality of large scale field observations, aerial and satellite remote sensing has provided an effective alternative for studying these plant communities. This research focused on the use of hyperspectral remote sensing to advance an overall understanding of salt marsh ecosystem productivity, diversity, and abundance within specific National Estuarine Research Reserves (NERRs) using AISA (Airborne Imaging Spectrometer for Different Applications) imagery.The overall goal of my thesis was to create a synoptic overview and site comparisons of salt marsh vegetation for seven NERRs, within their respective growing seasons, using three remote sensing vegetation indices. Additionally, within and between site geospatial patterns were examined using two landscape metrics. The seven sites were located in a range of climates, tidal, and river discharge regimes between Texas and Delaware.Across all sites, the NDVI and MSAVI indices were well suited for distinguishing structural differences and illustrating variations in relative biomass and plant vigor at each site. They both showed latitudinal and longitudinal shifts in histogram distributions, relatable to nutrient, tidal, and climate regimes. These indices were also useful for discriminating features unique to individual sites, such as exposed, intertidal mud flats (Georgia site) and robust Phramites australis stands (Delaware site).The VARIgreen index, more closely captured the photosynthetic capacity and "greenness" of salt marsh vegetation, and was more sensitive to phenological changes and foliage pigment densities. This index was more responsive to spring greening and late summer senescence. As a result, VARIgreen's distributional patterns appeared more sensitive to growing season patterns.Patches per unit area (PPU) was an effective landscape metric for measuring patchiness of vegetation index classes for the entire landscape. The Texas, Georgia, and South Carolina sites displayed the highest PPU values, while sites in Mississippi and West Florida had the lowest values. Although PPU illustrated the abundance of different patches in a single area, it was biased towards dominant classes. In comparison, the Shannon Diversity Index (SDI) captured the degree of equitability of all classes of patches. The largest class diversity and SDI values were found in the Delaware and West Florida sites.Ultimately, the vegetation indices and landscape metrics helped to show spatial variations at each site. As a result, site characterizations, unique to each site helped to explain the structure and productivity of the eight datasets.

Sharp, S. 2018. Disturbance and Recovery of Southeastern Salt Marshes: Drivers of Change and Ecosystem Service Dynamics. Ph.D. Dissertation. University of Florida, Gainesville, FL. 121 pages.

Slaughter, J.B. 2013. Factors influencing groundwater and surface water hydrogeochemistry with a special emphasis on the importance of sediment geology. M.S. Thesis. University of Georgia, Athens, GA.

Abstract
Historical data on groundwater and surface water nutrients and trace metal concentrations and water quality indicators were collected and examined in concert with aquifer, surficial geology and land use characteristics. A meta-analysis was conducted to better understand the factors affecting groundwater and surface water hydrogeochemistry and nutrients across variable conditions and scales. The primary goals were to compare (1) groundwater hydrogeochemistry and (2) groundwater vs. surface water geochemistry and nutrients for geologically and environmentally distinct wetland areas along the U.S Atlantic coast. The results demonstrate the influences of site geology, land use type, wetland extent and proximity to seawater inputs on the chemical signatures of the groundwater and surface water. Differences in microbial processes, oxygen and organic matter supply, and sources and sinks of dissolved constituents in groundwater and surface water wetland areas likely contribute to the variations in dissolved inorganic nutrients. These findings indicate the value of future studies of this nature.

Smith, C.B. 2001. Analysis of historic vegetation changes in two Georgia estuaries using aerial photography and GIS. M.S. Thesis, University of Georgia, Athens, Georgia. 93 pp.

Snyder, M. 2002. Geochemical trends associated with the seawater-freshwater mixing zone in a surficial coastal aquifer, Sapelo Island, GA. M.S Thesis, Georgia Institute of Technology, Atlanta, Georgia. 149 pp.

Thoresen, M. 2004. Temporal and spatial variation in seston available to oysters and the contribution of benthic diatoms to their diet in the Duplin River, Georgia. Ph.D. Dissertation, University of Georgia, Athens, Georgia. 220 pp.

Abstract
This study examined the quantity and quality of seston available to oysters and the contribution of benthic diatoms to their diets in the Duplin River, Georgia, and how it varied over different temporal and spatial scales. Average suspended particulate material (SPM), particulate organic carbon (POC), and chlorophyll a concentrations were significantly higher at the mouth (327.6 mg L^-1, 5.0 mg L^-1, 19.9 µg L^-1) than at the headwaters (93.4 mg L^-1, 1.6 mg L^-1, 9.4 mg L^-1). The quality of the seston was lower at the mouth with significantly higher carbon to nitrogen and POC to chlorophyll a ratios, but the seston was detrital-dominated throughout the inlet. Significant differences in seston characteristics were observed over tidal cycles at the mouth only, but all sites exhibited differences over lunar (spring tides greater than neap) and seasonal (spring and summer maxima) cycles. These differences were most consistent for SPM but were observed at some stations for other characteristics as well. Seston variability was greatest at the mouth at any temporal scale, but when compared within each site, the two sites closest to the mouth exhibited variability on tidal and lunar scales that was comparable to or even greater than seasonal scales, whereas at the up-river sites seasonal variability was the greatest. A significantly higher proportion of the diatoms were classified as benthic (pennate) at the headwaters as compared to the mouth in both seston (37% vs. 17%) and oysters (33% vs. 21%), although there was no evidence of selection for benthic forms. Microscopic observations of diatoms in seston and oysters were used to calculate the 13C and 34S values of oysters, assuming a diet of strictly diatoms, and these agreed well with observed values. This suggests that diatoms are a major food resource of oysters in this system and that benthic diatoms contribute to this pool. Oyster performance was evaluated at the study sites using shell height, dry tissue weight and condition index values. Oysters were significantly larger at the three up-river sites, which could be related to less than optimal feeding conditions and the high-energy physical regime near the mouth.

Tolar, B. 2014. The influence of environmental factors including reactive oxygen species on the spatial and temporal distribution of marine Thaumarchaeota. Ph.D. Dissertation. University of Georgia, Athens, GA. 418 pages.

Abstract
Thaumarchaeota ? formerly known as Marine Group I Crenarchaeota ? are highly abundant in the world?s oceans, making up ~20% of the total prokaryotic population. Members of the Thaumarchaeota are capable of oxidizing ammonia using the ammonia monooxygenase enzyme (amoA), which is the first step in nitrification and a key process in the global nitrogen cycle. They are most abundant in deeper, colder waters with appearances in surface waters generally limited to higher latitudes and polar oceans in winter. Reasons for this distribution have been postulated, but no definitive explanation has been found to date. A hypothesis tested with this work is that reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), play a role in exclusion of Thaumarchaeota from surface waters. This dissertation examines the spatial distribution of Thaumarchaeota in coastal and open-ocean, polar and temperate marine environments, where correlations with increased depth and decreased oxygen were common regardless of sample site. We also investigated the temporal distribution of Thaumarchaeota on Sapelo Island, Georgia, where annual spikes in abundance correlated to summer conditions (increased temperature; decreased pH, oxygen). The potential for Thaumarchaeota to use urea as an alternate substrate for ammonia oxidation was also investigated; our findings suggest that this is not a widespread attribute and is most likely due to removal of amine groups that are subsequently oxidized. Additionally, we found that nitrification is inhibited with increased [H2O2] in open ocean samples, with the most sensitive populations coming from the Southern Ocean. Populations from Sapelo Island, Georgia, were not as sensitive, but these microbial communities encounter high daily H2O2 concentrations. In conclusion, we have found that Thaumarchaeota distributions correlate to a variety of environmental factors and it is unlikely that any single one can be used to predict dynamics of the entire group. However, evidence from this work indicates that clades of Thaumarchaeota could be differentially affected by certain conditions, justifying the separation of this group into ecotypes for future studies. We have shown that direct oxidation of urea by Thaumarchaeota is unlikely, and that ROS can inhibit ammonia oxidation. This may explain why Thaumarchaeota are typically absent from surface waters.

Turck, J.A. 2011. Geoarchaeological analysis of two back-barrier islands and their relationship to the changing landscape of coastal Georgia, U.S.A. Ph.D. Dissertation. University of Georgia, Athens, GA. 239 pages. (DOI: 10.6073/pasta/d4e6577aa7dfcc6f2f36781f162a4124)

Abstract
This study examines the past human settlement system on the coast of Georgia from 12,000-1,000 B.P. (the Paleoindian through Late Woodland periods) in relation to landscape change. I take a landscape approach to understanding settlement, incorporating geomorphology, formation processes, a distributional approach to archaeological data, and landscape ecology metrics. Archaeological surveys of two back-barrier islands, Mary Hammock (9MC351) and Patterson Island (9MC493), are combined with non-archaeological paleoenvironmental data, and compared to changes in sea level, and to archaeological surveys from other environmental settings, to understand the change in human occupation in McIntosh County, GA. Numerous environmental datasets, including present-day elevations, former surfaces under the marsh, bathymetric data, soils, and wetlands, were incorporated together. These data were combined with changes in sea level over time, creating a dynamic model of landscape change. This model is used to create predictions about human settlement patterns in relation to the marsh-estuarine system for McIntosh County in general, and the back-barrier area specifically. These predictions were then tested with prehistoric site distributions of McIntosh County, as well as to prehistoric sherd densities of various surveys. Analysis revealed that terminal Middle Archaic sites (~5,000 B.P.) with evidence of coastal adaptations should be found within present-day McIntosh County. Because there are no such sites, I suggest that there may have been an abandonment of the coast at this time. The explosion in Late Archaic sites, then, may have been from an influx of people to the Georgia coast. Back-barrier islands were always part of the settlement system. The intensity of back-barrier island utilization may be related to their proximity to larger landmasses (the mainland and major barrier islands), and the different types of settlement systems associated with those landmasses. The intense utilization of back-barrier islands at certain times suggests that they may have been permanently settled. Another explanation for their intense use may be that these are relatively small islands where activities would have been concentrated. The predictions of the model were not always substantiated, indicating that changes in sea level and marsh-estuarine resources were not the only reason for changes in settlement and subsistence patterns.

Velasquez, L. 2005. The importance of benthic primary production in salt marsh carbon cycles. M.S. Thesis, University of Georgia, Athens, Georgia. 90 pp.

Abstract
Benthic microalgae are a central component of shallow coastal habitats and they may account for a significant fraction of the total primary production in these ecosystems. While several factors act in concert to generate the high photosynthetic rates observed in benthic microalgae, available data suggest light is of primary importance. Nutrient availability may also be important because increasing human population in the coastal zone has led to an oversupply of nutrients to aquatic habitats, in particular estuaries. The present study focused on the effects of light and nutrients on benthic primary production at two coastal Georgia sites: the Duplin River and the Satilla River. Benthic primary production and biomass along the Duplin varied over space and time. Nutrient addition experiments led to increased primary production by benthic microalgae (indicating nutrient limitation) with the addition of nitrogen and phosphorus at Sapelo Island but not at the Satilla River site.

Vu, H. 2016. Biophysical Feedbacks Mediate Tidal Creek Formation in Salt Marshes. Ph.D. Dissertation. University of Houston, Houston, Texas. 93 pages.

Abstract
How organisms and ecological systems respond to global change is of great interest to ecologists. These responses may or may not be beneficial because there might be positive or negative feedbacks that would make the impacts larger or smaller than expected. I conducted laboratory and field experiments to explore the mechanisms driving tidal creek formation in southeastern US salt marshes, focusing on three topics. 1) The effect of crabs on creek growth via four potential mechanisms: sediment excavation, plant removal, subterranean erosion, and decomposition. I found that Sesarma reticulatum (henceforth Sesarma) is the primary crab species mediating creek growth.Sesarma is concentrated at creek heads where plants are dying and creeks eroding.Sesarma excavated larger amounts of sediment through burrowing than other crabs, and is unique in creating burrow networks that likely increase belowground erosion and decomposition. Sesarma also is the only crab species that directly kills vegetation. Thus, Sesarma negatively impacts the marsh plant Spartina alterniflora and alters marsh geomorphology by engineering creek growth. 2) The factors mediating crab feeding preferences. I discovered that Sesarma did less damage to its food plant S. alterniflora in the presence of predators. Sesarma prefers and grows better consuming rhizomes than leaves; however, the cost of accessing rhizomes leads to higher mortality if rhizomes are the only diet option. A choice in feeding location allows Sesarma flexibility to balance the risks of predation, the nutritional benefit of feeding below-ground, and the survival costs of below-ground feeding. 3) The factors driving the aggregation and movement of Sesarma at creek heads. Creek heads are cooler, have higher dissolved oxygen levels, and lower hydrogen sulfide concentrations than elsewhere on the marsh. These superior conditions drive Sesarma aggregation. Additionally, I found that hydrology drives Sesarma aggregations when creek conditions were mimicked on the marsh platform. Theresults of this dissertation suggest that there is a biophysical feedback loop in marsh creek formation: creek growth is driven by a positive feedback between Sesarma crabs, which accelerate erosion, and creeks, which create abiotic conditions favorable for Sesarma crabs.

Wang, S. 2016. Inorganic carbon and oxygen dynamics in a marsh-dominated estuary. M.S. Thesis. University of Georgia, Athens, GA. 81 pages.

Abstract
We conducted a study to address uncertainties associated with the metabolism and netcarbon fluxes for the tidal wetland and estuarine portion of the coastal ocean because of thesezones disproportionately large role in ocean carbon dynamics. We measured open water diurnalO2 and CO2 dynamics seasonally in the Duplin River salt marsh-estuary in Georgia, USA with aparticular focus on the marsh-estuary linkage associated with tidal flooding. We observed that theoverall system was a net source of CO2 to the atmosphere and adjacent coastal ocean and a netsink for oceanic and atmospheric O2. Rates of metabolism were extremely high, with respiration(R: 43 mol/m2/yr) exceeding gross primary production (GPP: 28 mol/m2/yr). Rates of metabolismmeasured with CO2 were substantially higher than with O2. The net heterotrophy of the aquaticsalt marsh-estuary system is supported primarily by the net production of the salt marsh proper.

Wang, Y. 2016. Fronts and variability in the coastal ocean. Ph.D. Dissertation. University of Georgia, Athens, GA. 231 pages.

Abstract
The coastal ocean is characterized by strong gradients in water properties, which influences circulation and ocean-atmosphere interactions. Fronts and variability in the coastal ocean are studied using a combination of satellite observations and numerical model simulations. Satellite sea surface temperature (SST) and wind observations are used to describe the seasonal evolution of temperature fronts and their relation to wind forcing in Eastern Boundary Current Systems (EBCS). Front activity is closely related to seasonal variability in wind forcing and to the presence of topographic perturbations such as capes. Investigation of the coupling between SST gradients and wind variables in the global coastal ocean reveals that regions with strong front activity are generally also characterized by strong ocean-atmosphere interaction. Mid-latitude regions, especially in EBCS, are characterized by enhanced ocean-atmosphere coupling during local summer. In several low-latitude regions, however, the coupling is stronger during winter. Although the coupling between SST gradients and wind stress divergence is stronger at seasonal scales, intraseasonal variability associated with mesoscale eddies is stronger for the coupling between SST gradients and wind stress curl. Coastal regions can also present strong salinity gradients, especially near river mouths. The circulation at a complex estuarine system off Georgia is investigated using a numerical model. The estuary includes three major sounds that are connected by a network of channels, creeks and intertidal areas. Spatial and temporal variability in residence time and connectivity between the sounds are influenced primarily by the Altamaha River discharge, by seasonally-varying winds, and by tidal forcing.

Wang, Z. 2003. Biogeochemical Changes of Chemical Signals in the Georgia "Land-To-Ocean Continuum". M.S. Thesis, University of Georgia, Athens, Georgia. 187 pp.

Abstract
Major portion of this dissertation concentrated on interpreting and analyzing temporal and spatial variability of the CO2 system in the Georgia land-to-ocean continuum, which consists of Georgia marsh-influenced riverine and non-riverine estuaries and their adjacent continental shelf up to the shelf-break. Chapter 2 described an improved fiber optic pCO2 sensor based on a long pathlength liquid-core waveguide made by Teflon AF 2400. Three pronounced characteristics of the sensor are short response time, high sensitivity and long-time stability. Chapter 3 discussed the spatial and temporal variability of distributions of nitrogen nutrients in the five Georgia riverine estuaries. Estuarine nitrification and marsh denitrification are likely two major processes that modify spatial distributions of inorganic nitrogen within these estuaries. Seasonality of river discharge and temperature are apparently responsible for observed seasonal changes in distribution patterns of inorganic nitrogen. Chapter 4 examined CO2 dynamics in the South Atlantic Bight (SAB). The study found that this shelf region is a strong atmospheric CO2 source annually and an exporter of inorganic carbon to the open ocean. The carbon budget of the region indicated that the system is net heterotrophic annually. The annual CO2 source of the system to the atmosphere is likely maintained as a combined result of net heterotrophy, more intensive heating, and high discharge of inorganic carbon from coastal salt marshes. The research in Chapter 5 was centered on the seasonal variations of the CO2 system in Georgia estuary-marsh complexes. CO2 degassing and inorganic carbon export from a marsh-dominated tidal creek, the Duplin River, were quantified on a monthly basis in order to examine seasonality of marsh-estuary interaction. The study concluded that marsh export of inorganic carbon primarily supports CO2 degassing and inorganic carbon export in the marsh-dominated estuaries. Extrapolation of the Duplin River.s result to the entire SAB salt marshes indicated that marsh export of inorganic carbon likely has significant influence on the CO2 dynamics in the SAB. As a summary of carbon cycle in the Georgia "land-to-ocean continuum", a carbon mass balance and transport model and an "extended continental shelf pump" hypothesis were presented in Chapter 6.

Weston, N. 2005. Biogeochemistry in the coastal zone: changing land use, salinity intrusion, porewater stoichiometry and the mineralization of organic matter in estuarine sediments. Ph.D. Dissertation, University of Georgia, Athens, Georgia. 188 pp.

Abstract
Thirty years of population growth, land use change, and nutrient loading from the subwatersheds of the Altamaha River, GA were analyzed. Population growth, mainly in the upper watershed near the cities of Atlanta and Athens, resulted in increased nitrate delivery to the rivers and transport to the coastal zone. Delivery of freshwater appears to be declining, due to climate change and water withdrawal within the watershed. The effects of upriver salinity intrusion on the biogeochemistry of sediments from the tidal freshwater portion of the Altamaha River were investigated. Methanogenesis, which dominated in the freshwater sediments, declined quickly following salinity intrusion. Sulfate reduction was the dominant pathway of microbial organic matter mineralization within two weeks of salinity intrusion, although increased iron-oxide availability during initial salinity intrusion appears to have stimulated high rates of microbial iron reduction for a short period. Salinity-driven desorption of ammonium and increased rates of silica and phosphorus mineral dissolution following salinity intrusion increased overall export of ammonium, phosphate and silicate from salinity-impacted sediments. The mineralization of complex organic matter in sediments is mediated by a diverse consortium of microbes that hydrolyze, ferment, and terminally oxidize organic compounds. Patterns of estuarine sediment biogeochemistry, focusing on the role of dissolved organic carbon (DOC) and nitrogen, were determined with a multi-site, multi-season survey of estuarine porewater profiles in Georgia and South Carolina. This survey demonstrated system-scale correlations between the inorganic products of terminal metabolism (dissolved inorganic carbon, ammonium and phosphate) and sulfate depletion. DOC, as the substrate for terminal metabolism, was not correlated with other variables indicating that production and consumption of DOC were tightly coupled, and bulk DOC is largely a recalcitrant pool. Controls on the coupling between the hydrolytic/fermentative and terminal metabolic bacterial communities in estuarine sediments were further investigated using anaerobic flow-through bioreactors. We documented the temperature-driven decoupling of the production and consumption of key DOC intermediates due to variable temperature responses of these functional microbial groups. Production of labile DOC exceeded terminal oxidation at colder temperatures, resulting in accumulation of labile DOC. At higher temperatures, potential terminal oxidation rates exceeded those of labile DOC production and labile DOC availability limited rates of terminal oxidation.

Whitby, H. 2016. Identifying the factors affecting copper speciation in estuarine, coastal and open ocean waters. Ph.D. Dissertation. University of Liverpool, School of Environmental Sciences, Department of Earth, Ocean and Ecological Sciences, Liverpool, England. 181 pages.

Abstract
Copper (Cu) is an important micronutrient, predominantly occurring as organic complexes in marine waters. The composition of the ligands forming these metal complexes has implications for the bioavailability of the trace metals to marine microorganisms, both as nutrients and toxicants. A variety of samples from estuarine, coastal and open ocean waters were studied in an effort to further our understanding of the ligands responsible for controlling the bioavailability of copper. Presented here are findings on the nature and likely identity of such ligands, including humic substances and various thiols. A novel method was developed to measure copper-binding humic substances, which werediscovered to be synonymous with iron-binding humic substances. Using the new method on samples from the Mersey Estuary, humics were found to account for around 70% of the total ligand available for copper complexation in the estuarine and coastal samples. Samples from a very different estuarine environment, Sapelo Nature Reserve, Georgia, were then analysed in order to study potential copper limitation in blooms of Thaumarchaeota, prolific to the region and with a high copper requirement. Again, it was discovered that around 70% of the total available ligand for copper were humic substances, but that over 90% of the copper was complexed to thiourea-type thiols, also present in excess of the copper concentration. Comparing competitive ligand exchange (CLE) titrations to independent measurements of thiols and humic substances, the L1 and L2 ligand classes obtained viatitrations were found to correlate very well with thiols and humics respectively, providing an indication of the nature of the ligands responsible for copper complexation. Furthermore, these findings suggested that copper was predominantly complexed (90%) as Cu(I), contrary to our current understanding of copper speciation. A study across the seasonal cycle at these stations provided further insight into the complexities of copper speciation. Cu2+ was found to be exceptionally low throughout the study, at sub-femtomolar concentrations, and lowest during the Thaumarchaeota bloom itself. Although previously considered to be limited by Cu2+ concentrations lower than 2 x10-13 M (when induced by the presence of artificial ligands), here it was demonstrated that Thaumarchaeota must be able to access the naturally complexed copper in order to bloom at these levels, posing questions for our understanding of copper bioavailability to these organisms. Finally, the copper speciation of two profiles from Line P of the Northeast Pacific, coastal station P4 and open ocean station P26, were assessed in an attempt to characterise the ligands in ocean samples. Thiols and humic substances were detected at both stations but at concentrations lower than the ligand concentrations measured from titrations, suggesting additional ligands play a part in copper complexation in the open ocean.

White, S.N. 2004. Spartina species zonation along an estuarine gradient in Georgia: Exploring mechanisms controlling distribution. Ph.D. Dissertation, University of Georgia, Athens, Georgia. 206 pp.

Abstract
The general paradigm for the observed plant zonation in salt marshes is that a combination of abiotic stress and competition drive vegetation patterns within a single marsh, but there have been few studies investigating the bankside vegetation changes that occur along the longitudinal salinity gradient of estuaries. The main objectives of the research presented in this dissertation were to examine whether the same controls that explain the distribution of Spartina alterniflora in the salt marsh can be applied without modification to a longitudinal salinity gradient and to evaluate changes in Spartina distributions under drought conditions. Reciprocal transplant studies, greenhouse experiments, species removals in mixed Spartina stands, and vegetation surveys were conducted in the estuary of the Altamaha River, GA, where S. cynosusroides occurs upstream of S. alterniflora. In reciprocal transplant experiments, each plant survived and performed best in its natural habitat. The presence of conspecific neighbors slightly reduced S. alterniflora plant performance in the salt marsh whereas S. cynosuroides showed little response in either environment. The results of these and other experiments suggest the lower estuarine distribution of Spartina cynosuroides is controlled by abiotic conditions (salinity or sulfide concentrations). The upper estuarine distribution of S. alterniflora is not well understood, but seems to also be primarily controlled by abiotic factors (possibly a sulfate requirement). These outcomes challenge results from previous investigations of zonation controls in salt marshes and suggest that modifications to the salt marsh paradigm are necessary when describing vegetation distribution along an estuarine gradient. During an extended drought (2000-2002), Spartina alterniflora density increased to a greater extent than S. cynosuroides in mixed stands and the location where Spartina cover was 50% S. cynosuroides and 50% S. alterniflora shifted approximately 3 km upriver, suggesting that Spartina communities can respond rapidly to increasing estuarine salinity. These studies improve our understanding of the ecological linkages in estuaries and can aid coastal policymakers in making better management decisions and predictions concerning how changes in freshwater inflow might impact the distribution of estuarine organisms.

Wrona, A.B. 2004. Determining movement patterns and habitat use of blue crabs (Callinectes sapidus rathbun) in a Georgia saltmarsh estuary with the use of ultrasonic telemetry and a geographic information system (GIS). Ph.D. Dissertation, University of Georgia, Athens, Georgia. 178 pp.

Abstract
Estuarine habitat in Georgia is under increasing threat of degradation, which can negatively impact ecologically and commercially important species that reside there. Blue crabs (Callinectes sapidus) are the second highest valued fishery in Georgia yet little is known about their essential habitat requirements within either subtidal or intertidal areas. Ultrasonic telemetry was used to track 57 crabs, over 4 years, in the Duplin River estuary, near Sapelo Island, GA in order to assess movement patterns and habitat use. Crabs tagged with ultrasonic transmitters ranged in size from 4 to 13.3 cm CW and varied in sex and ontogenetic stage. Crab locations, substrate type, depth, and molting habitat was organized and analyzed within a geographic information system (GIS). Reproductively mature females used the greatest total area 1,052 m^2 on average over 8 days and movement was emigrational at average speeds of 657 m/day out of the estuary into the higher salinity Doboy sound. Male crabs did not, on average, use as large an area 108 m^2 on average over 7 days and movement patterns showed a high degree of meander and retention within the system. Movement speeds averaged 82 m/day. Immature female crabs were intermediate with a larger degree of meander than mature females with average movement speeds of 150 m/day, but used less total area (157 m^2 on average over 8 days). Crabs were tracked going onto and off of the flooded vegetated marsh surface and found on patches of oyster reefs located along edges of the subtidal zone indicating their habitat use. Crabs tagged with specialized molting transmitters were tracked to their molting habitat, which consisted of the vegetated marsh surface. The use of vegetated marsh edge is very important to crabs and was recoded frequently among all sexes and sixes of crabs. The adjacent marsh, therefore, is an essential part of blue crab habitat, it defines the subtidal creek habitat and provides essential habitat for molting crabs.

LTER
NSF

This material is based upon work supported by the National Science Foundation under grants OCE-9982133, OCE-0620959, OCE-1237140 and OCE-1832178. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.