Research Projects

Current and recent Center for Environmental Diagnostics and Bioremediation research projects.

Effects of biodegradation on allelopathy

The production and release of bioactive secondary metabolites, or allelochemicals, by plants serves myriad ecological functions including plant-plant competition, antiherbivory, and communication between plant roots and microbial members of the rhizosphere. Bacteria in the rhizosphere that biodegrade the allelochemicals control their flux and thus exert a major impact on plant chemical ecology. Although allelopathic chemicals are natural products, little is known about their biodegradation by bacteria. This project involves discovering the microbes involved in biodegradation of agriculturally important allelochemicals and establishing their molecular mechanisms and ecological roles. Current studies focus on biodegradation of juglone, a toxic compound produced by black walnut to inhibit growth of competitors.

Biodegradation of synthetic organic pollutants

Bioremediation is a powerful technology for elimination of organic pollutants in terrestrial and marine environments. Although virtually all natural organic compounds are biodegradable, synthetic pollutants such as pesticides, solvents and propellants are often resistant to biodegradation. This project focuses on discovery of bacteria able to biodegrade synthetic chemicals with man-made halogen or nitro substituents. Determination of biodegradation mechanisms, evolution and ecological roles of the bacteria provides the basis for application of bioremediation strategies in a variety of habitats.

Gas Hydrate Contribution to the Ross Sea Carbon Budget; Shallow Sediment to Water Column; Present and Future

Understanding Earth warming requires significant insight on geochemical and geobiological cycles in both polar regions and many environments in between. Most of the precious work has focused on the Arctic. More recently, however, the Antarctic Ross Sea has been recognized to have an extensive bottom ocean layer – sediment interface that is one of the most rapidly warming regions on Earth. Our goal is to determine the significance of a vast ephemeral reservoir of gas hydrate carbon present in the Ross Sea and provide the first thorough assessment of Earth warming with a Southern Hemisphere focus.

We will examine methane since it is abundant in ocean sediments and can be a significant source of carbon dioxide with approximately 25 times greater heat absorption than carbon dioxide. Comparison of carbon source(s) and cycling will include phytoplankton, land based and glacier ice transport, shallow sediment organoclastic carbon, and deep sediment petroleum dissolved and methane trapped in gas hydrates. Data collection will include seismic profiling, light element isotope and broad geochemical data, geology, and geo-microbiology. Data obtained will provide a new understanding of climate change and the effect on the ocean carbon budget that will serve as groundwork for future research in ocean carbon models and interpretation of past paleo-oceanographic cycles.

We bring together an international team of experts in geophysics, geology, ocean chemistry, geomicrobiology and isotope geochemistry. Expectations from this research include: 1) a coastal assessment of the relative contributions of methane, phytoplankton, glacial ice, and sediment carbon to surface sediment and overlying water column carbon cycling, 2) an expanded Antarctica coastal seismic data set with attention on gas hydrates and hydrocarbons, and 3) initial geochemical evaluation of Antarctica coastal sediment gas hydrate inventory. A detailed analysis of carbon pools and cycling in both the water column and sediments will allow the development of a model to better allow predicted climate change effects as each of the carbon pools responds to changing climate conditions. This will greatly expand our understanding of these processes beyond the Arctic.

Pensacola Beach Time Series

This project began in 2015 during our work related to the Deepwater Horizon Oil spill. Our goal was to determine whether there was a seasonal response of marine microbes to crude oil exposure. For 12 months, students collected water samples from the end of the Pensacola beach pier and determined the seasonal relative sensitivity to oil. After the first year’s sampling was complete, students working in the Jeffrey lab wanted to continue the sampling regime. As a result, students have collected water samples from the pier every 2 weeks and measured a suite of standard microbial ecology parameters including temperature and salinity, bacterial production, phytoplankton photosynthesis, bacterial cell numbers, chla concentrations, nutrients, water clarity, and microbial diversity based on DNA sequencing. The project serves as a training program for students interested in marine microbial ecology. Long term trends are beginning to appear and we hope to continue this data set for years to come.

Bacterial survival under the polyextreme conditions of the Atacama Desert and the Chilean Altiplano

Although commonly referred to as the driest place on earth, there are areas known as salars or lagoons where water percolates to the surface of the Atacama Desert and the Chilean Altiplano. The resulting ponds and springs may be hydrothermal or hypersaline, but all are exposed to very high levels of solar ultraviolet radiation.

High-altitude hydrothermal springs offer windows into life’s adaptation to extreme physicochemical gradients, yet the mechanisms by which microorganisms adjust their metabolism to such conditions remain incompletely understood. We investigated this question, by combining field geochemistry, equilibrium thermodynamic modelling and sedimentary stable-isotope analysis across six pools (53–75°C) at 4,000 m elevation in Chile’s Altiplano (~0.6 atm).

Photoheterotrophy in Gulf coastal and estuarine waters

Dr. Waidner, along with three other faculty from other Florida universities, is working on development of a rapid tool for assessing Vibrio vulnificus abundances in Gulf coast estuaries and coasts. Numerous UWF undergraduate and graduate students, in both Biology and Earth and Environmental Sciences majors, are involved in sample collection, in situ data monitoring, open-source data analyses, and laboratory analyses. Vibrio vulnificus infections are particularly news-worthy in Florida during summer tourist seasons, not only locally (Escambia and Santa Rosa Counties), but also in other parts of the state (Ft. Meyers press article with Waidner's FGCU collaborator on this project). This prediction tool development, based on CEDB work to enumerate Vibrio in oysters, along with the FIT researchers' metabolomics data, will be an important first step in mitigating risk factors. Data based on controlled, aquaculture-raised oysters indicate specific metabolite pathways are up- or down-regulated in the presence of Vibrio toxin, as described in this publication: Babaee, S., et al. (2025) Metabolomics analysis of eastern oysters (Crassostrea virginica) exposed to Vibrio cholerae toxin.

Drs. Waidner and Jeffrey work with UWF undergraduate and graduate students to track the ecological factors contributing to distribution and abundances of aerobic anoxygenic phototrophic bacteria and proteorhodopsin bacteria in local inland and coastal areas. This area of basic research is important for understanding environmental perturbations' impacts on heterotrophic bacteria activities, particularly those related to sea surface temperatures, intensification of storm events and water column turbidity. The most recent student project, Effects of seagrass density on water turbidity and abundances of aerobic anoxygenic phototrophic bacteria, earned the 2^nd place UWF SURP Student award (July 2026).

Diet Analysis of Flathead Catfish in the rivers of Northwest Florida

Flathead Catfish Pylodictis olivaris are considered a nonnative species in Florida. This species was first documented in Florida in the early 1950’s (Apalachicola) and was established throughout north Florida by the 1990s. Ecological concerns have emerged regarding their impacts via direct predation on native fish species. Flathead Catfish are obligate carnivores (primarily piscivores) and have been connected to declining populations of native fishes, particularly ictalurids, post introduction into systems. Invasive species introductions are widely recognized as a leading driver of biodiversity loss and ecosystem degradation worldwide.

Diet analysis of Flathead Catfish in the Flint River, Georgia demonstrated ontogenetic shifts in feeding ecology, with young-of-the-year individuals consuming aquatic insects and small benthic fishes, including darters (Etheostoma spp.), and larger size classes exhibiting increased piscivory, with gizzard shad (Dorosoma cepedianum) becoming a primary teleost prey item (Quinn 1987). These findings are particularly relevant to the rivers of northwest Florida, where several darter species are designated as Species of Greatest Conservation Need (SGCN), including the Crystal Darter (Crystallaria asprella) and Saddleback Darter (Etheostoma erythrozonum). In addition to darters, anadromous clupeids such as the Alabama Shad (Alosa alabamae) and native catfish such as the Spotted Bullhead (Ameiurus serracanthus), are also listed as a SGCN, which are vulnerable to large piscivores.

The Croteau Coastal Ecology Lab is collaborating with the Florida Fish and Wildlife Conservation Commission to examine Flathead Catfish diets in the rivers of Northwest Florida, to determine the impact to our native fish communities.

Common Snook Range Expansion into the Florida Panhandle

Common Snook Centropomus undecimalis are an estuarine dependent species that is sensitive to temperatures below 18°C. However, observed increases in daily minimum temperatures during the winter creates the possibility for northern range expansion of tropical species, including Snook. In the northern Gulf, this could include migration of coastal species along Florida’s west coast and the Texas coast. Snook have been reported by anglers in several of our local bays, but it is unknown whether these are sustained resident populations (reproducing and able to over-winter) or new additions that have migrated into the region when conditions are favorable.

The Croteau Coastal Ecology Lab has created a Panhandle Snook database using angler derived data to map the spatial and temporal sightings of Snook in our region. Have you caught or observed a snook in the Panhandle? Report your sighting here

Mapping Snook Recruitment and Distribution in Choctawhatchee Bay

The Croteau Coastal Ecology Lab with support from the Choctawhatchee Basin Alliance Estuary Program is conducting a larval drift study and snook survey throughout Choctawhatchee Bay and its tidal tributaries. Crews will be sampling juvenile habitat and potential overwintering habitats for juvenile and adult snook. Multiple drift card releases will be conducted to understand where larval snook may be transported and settle.

Response to Whole Lake Restoration

Whole lake restoration projects involving water level draw downs and the removal of vegetation and sediment provide an excellent opportunity to observe successional plankton community dynamics and water quality changes following restoration. Locklin Lake is a small urban lake in Milton, FL. It has a 3000-acre watershed and receives water from two small creeks and stormwater runoff. Lake water levels are maintained by a dam on the east side of the lake.

In the fall of 2024, the dam was opened and the lake was drained to survey and restore the lake using mechanical dredging to remove sediment accumulated from runoff and invasive vegetation and recontour the shoreline to prevent future erosion.

In October 2025, restoration activities were completed and the dam was closed. The lake refilled quickly following a large rain event, and weekly monitoring of the water quality and zooplankton community began immediately after water levels stabilized. The two tributary creeks feeding the lake are also sampled for comparison. These findings may inform future restoration projects by understanding water quality and successional community dynamics after similar dredging events.

Peripheral Oyster Habitat

In the Pensacola Bay system oyster populations have seen a decline in recent decades due to the significant loss of oyster reefs and subsequent factors hindering their recovery. This has created an increase in efforts to study and restore oyster populations both for harvesting and environmental restoration. Peripheral oysters are those growing outside of reefs, which may include bridge pilings, docks, seawalls, and marsh vegetation. When reef-building populations have been lost, peripheral oysters may remain and continue to perform vital ecosystem services. An initial peripheral oyster survey of Santa Rosa Sound and Bayou Grande was conducted by researchers at Northwest Florida State College (NWFSC) in 2023 to determine their substrate preferences, population densities, and distributions (Smith 2023). Bayou Grande was resurveyed by members of the Croteau Coastal Ecology Lab in collaboration with NWFSC 2026 and 64% of the original sampling locations were revisited. Relative abundance was categorized, ambient water conditions (salinity, temperature, dissolved oxygen, and pH) were recorded, and water column videos were recorded. Still images at surface depth, 0.5m and 1.0m depths were captured from the videos and analyzed for oyster abundance and average size. This study will help us quantify the contribution of peripheral oysters in urban bayous and provide useful information about settlement for future restoration projects.

Watershed Monitoring of Aquatic Insects

Aquatic insects spend all or a portion of their life cycle in freshwater aquatic environments. They process organic matter, can be micro predators, and serve as a food source for higher trophic levels. Many species have limited mobility making them a model bioindicator of location specific ecosystem health and water quality. EPT taxa (Ephemeroptera, Plecoptera, and Trichoptera) are pollution-sensitive and are used a baseline for water quality. Students in the Croteau Coastal Ecology Lab and Watershed Ecology course are monitoring waterbodies in the Pensacola Bay watershed for aquatic insects and other freshwater macroinvertebrates. This study will be part of a long-term dataset that can be used to assess ecosystem health and long-term trends.