Active Research Projects

> Coastal
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> Extreme Environments
> Mangrove Biogeochemistry
> Saline Lakes
> Salt Marsh and Estuarine Biogeochemistry

Research conducted by Joye's group examines the biogeochemical cycling of nutrients (nitrogen and phosphorus), trace metals (iron and manganese), carbon, sulfur and oxygen in a variety of systems, ranging from saline lakes to coastal environments to deep ocean sediments. Several projects include parallel studies of biogeochemical and molecular ecological dynamics with the aim of identifying fundamental links between environmental variables, bacterial community composition and bacterial activity. Areas of focus include coastal ecology and the study of microbial metabolism in and adaptation to "extreme" environments (a.k.a. astrobiology)

Coastal Ecology

We strive to identify and understand the environmental and physiological controls on elemental cycling (e. g., N, P, C, O, S, Fe, Mn ...) and ecosystem metabolism in coastal regions. A primary goal of this work is to identify how coastal ecosystems respond to global change and various natural and anthropogenic forcing functions.

We utilize a broad, cross-disciplinary approach to address biogeochemical research questions. We value innovative technologies and incorporate new methodologies and approaches into our research program as they become available. Our work exploits traditional biogeochemical (e.g., radio- and stable- isotopic tracers, physiological inhibitor-based studies), microbiological (e.g., enrichment culture work, microbial isolations), molecular biological (e.g., PCR, cloning and sequencing), and geochemical (e.g., rate measurements, stable isotopes, and constituent concentration profiles) to examine rates of individual processes at local and system-wide scales. Significant effort is put towards developing novel approaches and techniques to address research questions.

We have worked or are working in a variety of coastal environments, including salt marshes along the coast of Georgia, South Carolina and Massachusetts, California, North Carolina, Georgia and Texas, and mangrove forests in Belize and Panama. Current projects are summarized briefly below. If you have questions, comments or would like additional information, please contact Mandy Joye at mjoye@uga.edu.

Our coastal ecology research is supported by the National Science Foundation's Georgia Coastal Ecosystems LTER program and the Biocomplexity in the Environment program, by the Environmental Protection Agency's Climate Change program and by NOAA Sea Grant programs in Georgia and South Carolina.

Salt Marsh and Estuarine Ecology

Groundwater Biogeochemistry
As human population has grown and agricultural, commercial, and industrial activities have expanded in coastal watersheds, loading of anthropogenic wastes from localized (e.g., sewage, industrial effluent) and diffuse (e.g., agricultural run-off) sources to surface waters and groundwater has increased. Ultimately, these materials end up in coastal waters, where they cause eutrophication, the increase in labile organic matter supply to an ecosystem. Today, increases in the frequency of harmful algal blooms, water column hypoxia/anoxia, fish kills, and reduced water quality are clear signs of eutrophication in the coastal zone. Understanding the response of the coastal ecosystem to eutrophication is one of the most important research challenges facing marine scientists today.

Many factors, including land use (natural vs. developed, e.g., residential, agricultural or commercial), soil type and erosion rate, influence water quality. To date, the scientific effort has focused largely on documenting the composition and flow of surface waters (e.g., rivers, streams), the most conspicuous component of the hydrologic cycle. However, predicting the response of coastal ecosystems to land use change and eutrophication requires robust models that include all relevant sources of nutrients and organic materials. Among these, groundwater isan important, but poorly understood, source of nutrients and organics to coastal waters. Groundwater-derived fluxes need to be quantified, particularly in Southeastern U.S., coastal systems where such data are rare. The lack of information regarding groundwater flux and groundwater quality in coastal systems makes it impossible to predict how the quality (chemistry) or quantity (freshwater flux) of this "input" or "source term" will respond to increased development pressures in coastal regions.

We are assessing the flux of groundwater to coastal systems using a variety of approaches, including seepage chambers (see figures to the left and below; seepage meters are the brown circles beneath the water surface). We collaborate with Dr. Carolyn Ruppel at Georgia Tech, who uses indirect geophysical techniques to estimate groundwater fluxes, and researchers at the University of South Carolina (Drs. Marj Aelion and Billy Moore), who use geochemical and microbiological techniques to evaluate the fate of groundwater derived materials. An integrated effort is being made to quantify the impact of coastal development and land use change on ecological, chemical, and physical processes through the study of both groundwater and surface water components in Georgia and South Carolina. In the course of this project, we will quantify the flux and chemical signature of shallow coastal groundwater and contrast the chemical composition of groundwater and surface waters. The impact of groundwater flux on a suite of biological processes will be evaluated in the marsh and in estuarine waters (tidal creeks). These data will be integrated into a GIS-based modeling framework, with the aim of predicting the response of groundwater-derived fluxes to land use change.

Sediment Biogeochemistry
To evalaute the role of groundwater-derived nutrient loading in an ecosystem-level context, we characterize sediment biogeochemical regimes, determine rates processes like denitrification, and quantify benthic fluxes. We are examining sites where surface and/or groundwater quality has been altered to varying degrees due to development in the upper (or adjacent) watershed. Over the past 50 years, increased population density and industrial and agricultural activity in coastal watersheds has elevated the loading rates of nutrients, particularly nitrogen (N) and phosphorus (P), to coastal waters resulting in the eutrophication of many nearshore environments. Identifying ways to improve coastalenvironmental quality and formulating a suite of systematic environmental quality indicators are primary objectives of coastal managers around the globe.

Sound management decisions require a basic understanding of the structure and function of coastal ecosystems. However, such basic information is lacking for many systems and scientists are unable to predict how they will respond to future perturbations. Examining the biogeochemical response of coastal sediments to increased nutrient loading provides a mechanism to assess how these critical habitats may respond to future perturbation and may allow us to identify important feedback mechanisms necessary for improving coastal environmental quality in the future.

Salt marsh and mudflat habitats, the interface between terrestrial and oceanic ecosystems, serve as filters of materials exchanged between these two end-members. These regions may act as sources, sinks and/or transformers of organic materials and nutrients. Determining which role they play and elucidating the factors that control net nutrient exchanges have important implications for understanding nutrient flux and production dynamics in both estuarine and coastal oceanic environments. In this project, we are assessing spatio-temporal patterns in sediment metabolism and nutrient dynamics at sites within two intertidal marsh-mudflat complexes along the Georgia coast. We have chosen to study sediment processes because they determine net fluxes of materials between the water column and sediment and as a group are capable of significantly altering net metabolism on the ecosystem scale in shallow coastal regions.

Our hypotheses concern linkages between benthic primary production, net sediment metabolism, and the cycling of nitrogen and phosphorus. We will investigate interactions among processes on various time and space scales, but will focus our efforts on documenting diel (day-night) and seasonal trends in carbon (C), N and P dynamics. With the recent emergence of ephemeral microalgal blooms in the pristine Satilla River, understanding the mechanisms leading to the proliferation of benthic microalgae and on how their activity influences N and P processing has never been more critical. We will quantify rates of benthic metabolism and N and P fluxes as well as rates of "indicator" processes, specifically, benthic primary production and denitrification, in marshes at the mouth of Satilla River and adjacent to Sapelo Island.

Impacts of Climate Change on Coastal Ecosystem Dynamics {Learn More}

Conceptual models will be used to develop a framework for examining how ecosystem services of tidal marshes vary along the salinity gradient and how climate change will alter the delivery of ecosystem services. We hypothesize that tidal freshwater marshes provide higher levels of regulation, habitat and (plant) production functions relative to salt marshes. Salt marshes though provide higher levels of disturbance regulation and fisheries habitat. Accelerated sea level rise is predicted to reduce the area of tidal marsh through submergence and conversion of tidal freshwater marsh to brackish and salt marsh. The result is a reduction in ecosystem services of salt and brackish marshes along with a complete loss of services of tidal freshwater marshes. Predicted greater inter-annual variability of climate in the future will lead to greater frequency of drought that reduces delivery of ecosystem services and episodic freshwater pulsing which we predict will enhance delivery of ecosystem services.

We will test the effects of rising sea level and greater inter-annual variability of climate on alteration of area and ecosystem services of tidal marshes in three watersheds (Altamaha, Satilla and Savannah Rivers, Georgia) of the South Atlantic coast. Ecosystem services related to disturbance regulation (shoreline protection), gas regulation (CO₂ & CH₄ flux), soil formation (C sequestration), nutrient regulation (N, P retention) and waste treatment (sediment deposition, denitrification), refugium and food (production & diversity of macrophytes & marsh nekton) will be measured in replicate (n=2) salt, brackish and tidal freshwater marshes of each watershed. GIS in conjunction the SLAMM model will be employed to predict changes in marsh area resulting from submergence and habitat conversion. Overlay of ecosystem-scale measurements will be used to predict how the cumulative delivery of ecosystem services in each watershed is altered in response to rising sea level. SLAMM also will be used to predict changes in shoreline protection potential of tidal marshes, commercial shrimp yields and the effects of alternate management scenarios (maintenance of existing dikes, construction of new dikes) on delivery of ecosystem services.

This work will provide a basis to understand how ecosystem services vary among salt-, brackish- and tidal fresh-water marshes, predicts how sea level rise alters marsh area and delivery of ecosystem services, compares the effects of diking (to protect marshes) on delivery of ecoystem services and elucidates how climate variability affects temporal patterns of primary production & diversity, sediment deposition and marsh accretion.

Mangrove Biogeochemistry {Learn More}

Microbial and nutrient controls in mangrove ecosystems
[this Biocomplexity project is directed by Dr. Candy Feller at the Smithsonian Environmental Research Center]

Mangrove forests, the intertidal, tree-dominated communities characteristic of tropical coasts, are often described as "simple systems." This is a relative description, however, perhaps due to the apparent greater complexity of terrestrial systems with larger numbers of plant species. Nonetheless, these tidal wetlands are systems with complex trophic structures and sharp gradients in nutrient dynamics. Furthermore, mangroveorganisms exhibit intricate physiological and structural adaptations to stresses and environmental variables associated with the zone of overlap between marine and terrestrial ecosystems. Ecological interactions and physiological processes in mangrove forests are complex and controlled by interactions among the microbial community structure, function, and interaction of higher trophic groups, and feedback among different trophic levels. Hydrology, physico-chemical factors, and the physiological tolerances of mangrove ecosystem species mediate these interactions. We propose to elucidate the linkages and feedback loops among mangrove community components and place them in the context of forest structure and trophic (grazing and detrital) connections in mangrove ecosystems. Our major goal is to determine how the interactions controlling structure and function at a number of trophic levels act to produce the emergent properties that characterize mangrove forests.

Our Biocomplexity program seeks to answer the question,"What are the functional relationships among microorganisms, geochemical processes, hydrology, and nutrient availability in mangrove forests, and how do these relationships interact to generate biological complexity in this ecosystem?" We will qualify and quantify a set of potentially interactive ecological and physiological processes that span multiple levels of organization and scale, i.e., microbial community structure, microbially-mediated nutrient transformations, soil physico-chemical properties, primary productivity, plant physiology and stress adaptations, within-plant and ecosystem-level nutrient cycling, and primary and detrital consumption. Using an established fertilization experiment in Belize and a multidisciplinary approach, our objectives are to determine how these processes are interrelated by examining the effects of increased availability of limiting nutrients on feedback relationships among hydro-edaphic conditions; microbial, plant, and animal communities: primary production and decomposition; and peat formation. The proposed study site is a range of mangrove-dominated islands located in an oligotrophic setting, remote from anthropogenic influences. This system is nitrogen (N) limited at the mangrove fringe, phosphorus (P) limited in the interior, and both N and P limited in a transition zone.

To unify our study, we will use both diagenetic modeling of sediment processes and Network Analysis. Diagenetic model information will feed into the Network Analysis to add robustness to nutrient cycling components. The latter provides a powerful set of mathematical tools to determine direct and indirect interactions of one ecosystem compartment with another, to produce a synopsis of the trophic structure, to enumerate and quantify routes via which nutrients are recycled, and to define the overall status of system activity.

Extreme Environments

Examining the interrelationships between organisms and the environments within which they exist is a basic goal of biogeochemistry. When such studies focus on life-supporting environments that exist near the extremes of planetary conditions, new insight can be obtained regarding the evolution of life on Earth and the ability of microorganisms to adapt to a variety of physiological extremes, e.g., temperature, salinity, pressure, etc. The study of extreme environments is often referred to as "Astrobiology".

Our research in extreme environments examines chemoautotrophic processes, mainly methane oxidation, nitrification and nitrification. We use traditional biogeochemical approaches and molecular biological and organic geochemical methods to quantify rates of specific processes, access microbial diversity and genetic potential, and to identify novel microorganisms with unique physiologies.

This research is funded by the National Science Foundation's Microbial Observatory and Life in Extreme Environments programs, by NOAA's National Undersea Research Program, and by the American Chemical Society's Petroleum Research Fund.

Cold Seeps {Learn More}

Molecular ecology and biogeochemistry of methane hydrates and brine pools in the Gulf of Mexico.

Low molecular weight hydrocarbons (methane through pentane) and hydrogen sulfide form ice-like clathrates with water called "gas hydrates". Frequently, methane is the dominant gas, so these structures are referred to as "methane hydrates" or "methane clathrates". Submarine methane hydrates comprise a large reservoir of labile organic carbon. Methane hydrate forms under conditions of methane saturation, high pressure and low temperature by the inclusion of gas molecules, primarily methane but also higher hydrocarbon gases up to pentane, into a lattice of water molecules. The resulting solid is stable at temperatures below about 7 ºC and pressures greater than about 50 bar. The widespread occurrence of gas hydrates became apparent when deeply buried layers, known as bottom simulation reflectors (BSR), were detected by seismic and deep-sea drilling studies. BSR features are widely distributed at the base of continental margins at sub-bottom depths of about 300m. In the Gulf of Mexico, hydrates occur as shallow layers and vein-filling plugs that breach the sediment interface and slowly decompose in contact with seawater. The "extreme" nature of the hydrate niche includes low temperature and high pressure, limited carbon sources (C1-C5), and desiccation (little available free water). Thus microbes living in this environment require special adaptations.

Little is known about the types of microorganisms dwelling in hydrate environments, their phylogenetic diversity, taxonomy, ecology or ecophysiology. This project will test the hypotheses that hydrate microbes inhabit distinct microbial niches requiring specialized adaptation, that these niches have predictable temporal and spatial characteristics, and that there is dynamic interaction between microbial activity and the geochemistry of the system. We will use molecular biological and organic geochemical techniques to assess the microbial community composition and identify 'new' microorganisms. Rates of processes will be determined using classic biogeochemical methods.

Saline Lakes {Learn More}

Mono Lake Microbial Observatory

What might the microbial ecology of Mono Lake have to do with microbial life on Mars? Present day alkaline (or soda), hypersaline lakes on Earth are believed to be good analogs to the ancient seas of Earth and Mars (shown to the right). Studying the microbial ecology of soda lakes like Mono Lake may provide insight to the types and physiology of microbes that inhabited early Earth and Martian oceans.

Available data suggests that early in the history of Mars, climatic conditions could have supported development of a microbial biosphere. Degassing of volatiles from the Martian interior would have generated shallow oceans (from depths of 50 m to 0.5 km on the surface) and a dense atmosphere rich in carbon dioxide. Martian "oceans" were probably standing water bodies that filled impact craters and thus were quite different from Earth's oceans. Nonetheless, liquid water was present on the surface (as evidence by the canyon shown to the left). A carbon dioxide-rich atmosphere would have generated a greenhouse sufficient to maintain liquid water for millions to hundreds of millions of years. A carbon dioxide rich atmosphere would have also resulted in surface waters rich in carbonate and bicarbonate, important anions in present-day soda lakes. During this period, microbial life could have evolved on Mars. Geological evidence suggests that Earth's microbial biosphere developed in about a hundred billion years. When conditions on the Martian surface deteriorated, the microbial biosphere would have become extinct.