Alligators as Bioindicators for Contaminants

Written by Hailey Murphy, interviews conducted by Mary Lide Wallace; S.C. Sea Grant Consortium.

American alligator swimming in a pond at Huntington Beach State Park, Murrells Inlet, S.C. Photo credit: Morgan Treon/S.C. Sea Grant Consortium.

A Southern Icon

The sun is setting, the warmth of the mud flat you’ve been sunbathing on is fading, and it’s about time for something to eat. You’re an ambush predator: you’ll submerge yourself in the sediment-rich water near the bank and let dinner find you, lunging at just the right moment and using your many (about 80) teeth and powerful bite force to incapacitate prey. Fish, shrimp, snails, or blue crabs are on the menu here by the coast, though if you moved inland, maybe you’d go for some turtles or unwary birds. Maybe even a feral hog. You’re not picky, and you haven’t had a meal in days. There—you see something floating your way. Let’s see if it’s edible.

American alligators (Alligator mississippiensis) are one of the most iconic animals of the Southeast. A regular sight in South Carolina’s wetland ecosystems, American alligators can live to be over 80 years old and grow over 14 feet long. These stealthy megafauna consume all parts of their prey and can digest even the toughest materials, like the bones of a whole adult deer. Alligators often take the stage of our collective imagination, but now they are also the spotlight for water quality research in South Carolina and Georgia.

Murky Waters

As plastics and other aquatic and marine debris become more present in our ecosystems, alligators’ diets increasingly include items off their natural menu. Either directly consumed or ingested indirectly via prey, plastics and the coatings on plastic materials can be digested by living organisms, breaking down into microplastics and other contaminants of emerging concern (CECs). Microplastics are plastic particles ranging in size from 5 millimeters, which is about the size of a sesame seed, to 1 nanometer, about the size of a strand of human DNA. CECs include multiple classes of chemicals such as pharmaceuticals, personal care products, and microplastics. One of the types of chemicals designated as CECs is polyfluoroalkyl substances (PFAS), which research indicates have become increasingly prevalent in the environment. Many CECs lack regulatory standards or are only partially regulated, in part because research is still evolving as new compounds emerge, health impacts are attributed, and exposure levels are becoming more understood. Knowing how these contaminants are distributed and how abundant they are in wetland ecosystems has become a crucial step in determining the risk they pose to humans, wildlife, and environmental health, and informing future regulations.

This is the focus of the Consortium’s collaborative research project, “Elucidating Patterns of Microplastic and PFAS Contamination Using Alligators to Explore Exposure and Fate of Contaminants of Emerging Concern in Wetlands,” led by Principal Investigator Jim Anderson, Ph.D., director of the Baruch Institute of Coastal Ecology and Forest Science at Clemson University. The project team seeks to explore alligators as a new indicator of CECs in the Southeast and to use data from alligators to understand potential impacts of sea level rise, precipitation, and flooding on CEC distribution and abundance in aquatic systems.

Top of the Food Chain

To learn more about pollutants and the state of the environment, scientists regularly sample certain species, a method called biomonitoring or bioindication. Typical aquatic bioindicator species—often fish, shellfish, or crustaceans—are selected for ease and reliability in sampling for comprehensive and long-term water quality monitoring of specific ecosystems.

It’s unusual to select southeastern predatory megafauna such as sharks, alligators, and bears for bioindicators due to the challenges associated with the capture and handling of large animals, the lower average population sizes of these species, and, in some cases, their protection status. Yet this research team believes they may yield significant data on contaminants and ecosystem health.

“Alligators are a long-lived species,” explained Anderson. “They’re top of the food chain in these aquatic and wetland systems. Thinking about bioaccumulation, it makes sense to pick something towards the top.”

By virtue of living as long as humans, eating just about anything that crosses their path, and being remarkably resilient and adaptive to natural hazards, alligators are an excellent candidate for data on bioaccumulation, or the buildup of substances in the body. Testing the prevalence of CECs or microplastics in the stomach contents, blood, or tissue samples of alligators from a range of ages can provide a clear picture of that organism’s total exposure to a substance and how that exposure has changed from generation to generation. Compared to fish or crustaceans, alligator lifespans more closely resemble those of humans, as they live 60 to 80+ years in the wild, so data on their exposure to contaminants over decades may be revealing for public health research as well.

Miriam Boucher, Ph.D. student, and Anna Chobot, undergraduate student, both at Clemson University, on their way to collect water and sediment samples for PFAS and microplastic analysis on the Black River, Georgetown County, S.C. Photo credit: Dorothy Aldridge, Clemson University.

Prowling for Samples

Once overhunted for its hides in the late-19th and early-20th centuries, the American alligator population has rebounded thanks to conservation efforts and legal protections established in 1967 when the species was classified as endangered. By 1987, the American alligator was considered stable in enough U.S. states to be delisted as an endangered species. However, because they resemble species that are still in peril, such as some crocodiles and caimans, the American alligator is listed as “Threatened by Similarity in Appearance” throughout its entire range. This designation means that American alligators remain closely managed to ensure that look-alike endangered species don’t experience population loss due to misidentification.

Anderson and his team, including Ph.D. student Miriam Boucher at Clemson University, employ non-lethal sampling methods, including capture-and-release collection of blood, claw, stomach contents through flushing, tissue samples, and the collection of eggs from nests. Repeated sampling of the same target populations or individuals helps scientists identify patterns of contaminant exposure and the rate of bioaccumulation. Alligators are marked and released, with recapture rates based on their tendency to return to familiar habitats.

“Alligators, like most creatures, are creatures of habit,” explained Anderson. “They have a home range, and so if you go to a waterbody this year and you capture it and you go back next year, unless something drastic has happened, there’s a pretty good likelihood that it’s still in that waterbody.”

Boucher described a leading example of a past study that utilized this method: “As part of a long-term mark-recapture study led by Thomas Rainwater, Ph.D., at the Tom Yawkey Wildlife Center in Georgetown County, S.C., hundreds of alligators have been captured, sampled, and released since the late-1970s. Many individuals have been recaptured several times, usually in the same general location as their previous captures.”

Anderson and his research team do not conduct lethal sampling of alligators. They collaborate with the S.C. Department of Natural Resources (SCDNR) and Georgia Department of Natural Resources (GADNR) to engage licensed recreation hunters, private landowners, state-licensed trappers, and game processors to collect samples from harvested alligators. This method of monitoring became possible first in Georgia in 2003, when the GADNR determined that the population had recovered to the point that a sport hunting season for the species could be established. In 2008, SCDNR adopted a highly managed, limited public draw hunting season. Additionally, nuisance alligators, though uncommon, are reported and culled in both states by the appropriate agencies.

These management practices provide unique opportunities for researchers to collect entire organs and systems for a clearer picture of exposure and bioaccumulation of contaminants, including microplastics and PFAS. Previous studies have relied on the state-managed hunter-harvest of alligators in South Carolina to analyze concentrations of PFAS in consumable tail muscle tissue (Tipton et al., 2017). Though limited in scope, this research laid the groundwork to demonstrate that alligators are effective bioaccumulators of PFAS. Anderson’s team is building on those findings while addressing sampling biases by broadening the type and amount of data collected, and exploring the appropriateness of alligators as longer-term, replicable monitoring tools.

Anna Chobot, undergraduate research assistant at Clemson University, processing sediment samples under a laboratory hood. Photo credit: Miriam Boucher, M.Sc., Clemson University.

This project builds on a larger dataset created by Boucher, who began collecting samples in 2023 and now has over 600 total samples, representing nine states. Of these, 134 samples were collected from South Carolina and Georgia. From South Carolina, 124 samples—derived from 59 live alligators and 65 harvested alligators—were sourced from fixed study sites or through the annual alligator hunting season. The remaining 10 samples were collected from live alligators in Georgia.

Funding from the Consortium has since allowed the team to expand this dataset, with 25 sampling sites in S.C., including locations in Georgetown, Charleston, and the ACE Basin, and four sampling sites in Georgia at the Savannah River, Harris Neck National Wildlife Refuge, Champney River Park, and Jekyll Island.

Stomachs of Steel

Alligator stomach contents are analyzed by using a sieve to isolate diet items greater than 0.5 mm in size, then freezing and saving the remaining contents for microplastic analysis based on methods modified from pioneering studies on oysters and alligator scat in the lab of Stefanie Whitmire, Ph.D., during the early days of microplastic research in organisms. Diet items are weighed and counted, using the Percent Index of Relative Importance (%IRI) to standardize them across samples and states. Organic material is removed from the saved stomach contents through chemical digestion using a solution of potassium hydroxide, followed by a solution of hydrogen peroxide, until the samples appear clear and no longer react. At this stage, organic material is almost entirely removed from the sample, making it clearer to detect inorganic pollutants. The samples are placed into vials of 99% ethanol and analyzed for microplastics and other synthetic materials using a Laser Direct InfraRed (LDIR) instrument. As of early 2026, an initial project analyzing the diets of 33 hunter-harvested alligators from South Carolina was completed, with over 100 samples prepped for diet analysis.

For PFAS analysis, the team works with John Bowden, Ph.D., at the University of Florida, whose lab uses an advanced two-stage technique called liquid chromatography-tandem mass spectrometry to isolate individual compounds and identify PFAS in the alligator samples. As of 2025, the team has analyzed samples from 152 total individual South Carolina alligators—derived from 99 live alligators and 53 harvested alligators. Samples from an additional 267 individual alligators, representing eight states, have been prepared for PFAS analysis.

Boucher holding glass sample jars containing alligator stomach contents undergoing chemical digestion prior to microplastic analysis. Photo credit: Hailey Murphy/S.C. Sea Grant Consortium.

Findings

In South Carolina, coastal alligator diets consist predominantly of Atlantic blue crab (Callinectes sapidus) and shrimp (Palaemonetes spp. and Litopenaeus spp.). Inland alligator diets appear more generalized, including a wider range of fish, mammals, birds, and reptiles such as snakes and turtles.

This project team’s analysis of the diet samples so far suggests a few surprising menu items on the alligator diet: “Our analyses identify rubber tire wear particles as the most prevalent and abundant synthetic particle found in alligator stomach contents,” said Anderson.

Microrubber, considered a subgroup of microplastics, has made frequent appearances in environmental studies across the world. In South Carolina, tire wear particles have regularly been found in water and samples of sediment. Studies in the Charleston Harbor and coastal stormwater ponds, including a 2020-2022 Consortium-funded study, have demonstrated the toxicity of tire wear particles on both estuarine fish and freshwater fish.

“As we drive, our tires naturally wear, shedding microrubber onto road surfaces,” explained Boucher. “These particles are washed into waterways. Either through indirect consumption or transfer from prey items, rubber ends up in gator stomachs.”

Though normal wear and tear of tires from regular driving activity is likely the primary contributor to tire wear particles entering the environment, there are also protections in place to reduce other environmental impacts from tires. Laws in South Carolina prohibit dumping tires improperly, and the South Carolina Department of Environmental Services (SCDES) manages tire recycling or disposal to help prevent pollution and control South Carolina’s most infamous insect—the mosquito, which uses pockets of water caught in tires to lay eggs. To reduce the rate of wear on tires, it’s important to follow recommended guidelines for vehicle tire inflation, maintenance, and daily use.

In addition to tire wear particles, Anderson’s team reported other plastics and synthetic materials: “Notable plastic particles include acrylonitrile butadiene styrene (ABS plastic), polytetrafluoroethylene (PTFE), and polyamide (nylon). We also observed magnesium stearate in some samples, a salt that acts as a surfactant and is used in thermoplastic molding, as well as in commercial and domestic applications.”

A juvenile American alligator sunbathing on a log on the edge of a managed rice impoundment at Caw Caw Interpretive Center in Ravenel, S.C. Photo credit: Morgan Treon/S.C. Sea Grant Consortium.

Another unique find? Whole shotgun shells. Boucher said, “What we do find with frequency are shotgun shells and wadding left by hunters. Alligators consume these whole, and we’ve recovered them from alligators in South Carolina.”

But microplastics and larger particles found in the stomach samples are just one part of the picture. Many of these materials leach chemicals or break down after digestion into other contaminants, such as PFAS. There are hundreds of confirmed PFAS compounds, with thousands more suspected, but scientists are still working to identify and categorize these compounds. Most labs that analyze samples for PFAS have the capacity to identify only a fraction of these.

“Of the 30 PFAS we analyze in our samples,” wrote Anderson, “perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) are among the most common and are currently the only PFAS for which state and federal regulations exist. Long-chain PFOS, a variant that bioaccumulates more readily than its short-chain congeners, is found in all of our samples in varying concentrations. The highest concentrations currently found in our samples follow the drainage of the Cooper River from Columbia to Charleston.” The Cooper River flows Southeast to the Atlantic Ocean from an outflow of Lake Moultrie, which connects through a series of lakes, tributaries, and floodplains to the watersheds surrounding the urban center of Columbia.

Anderson described preliminary findings from repetitive sampling in live alligators that suggest mercury may bioaccumulate differently between males and females. “The next year, with the recapture of the males, the concentrations were basically the same or a little bit higher, which is what you would expect… [but concentrations in] the females actually dropped.”

Anderson hypothesized that reproduction may be the reason for this difference: “Females are laying eggs, and so that would indicate most likely that this transfer from the females to the embryos, to the eggs, and so now the young are coming out contaminated, but that’s a way for the females to offload some contaminants.” It is still unclear if PFAS may be offloaded in this way.

Aldridge and Chobot conducting lab work. Photo credit: Miriam Boucher, M.Sc., Clemson University.

What’s Next?

“Our future analyses will seek to incorporate spatial variables as predictors for PFAS in alligators and environmental samples,” said Anderson. “We anticipate that this trend is related to industry and human development.”

Using this multi-state dataset of alligator diet and PFAS and microplastic contamination in alligators and their wetland habitats, the next step is to integrate environmental sampling data pulled from surface water and sediment samples, as well as spatial data on wetland type, land cover, and urbanization of sample sites. With the data they have so far, there isn’t one clear reason for the differences between South Carolina and Georgia’s contamination levels in alligators.

“There are certainly differences among states,” Anderson explained, “But I don’t think it’s a state issue; it’s more of a water boundary issue… I’m guessing it has to do a lot with historical and current manufacturing, population densities, and road densities within those watersheds.”

Along with creating indices for their alligator contamination dataset, hotspot maps, and blood-muscle contaminants, they hope to model future conditions and create interactive web-based scenarios for CEC distribution and exposure under various climatic and land-use conditions.

“We’re hoping to use some of the existing climate prediction models, incorporating our data to look at basically hotspots,” said Anderson. “Where would you expect to have the greatest issues? It’s where we have the highest hydrologic input, whether that’s from sea level rise or flooding from upstream in the watershed coming downstream, or widespread precipitation events.”

Outreach and Impact

Anderson, Boucher, Chabot, and Aldridge are all working to make their findings about CECs known and understood by the scientific community, but they are also hoping to use the data to inform the public. “I think people are becoming more aware,” said Anderson. “We do a lot of outreach in terms of going to schools, going to public events, and several of our students have talked about PFAS, microplastics, and other contaminants. Younger kids indicate that they seem to know more about it than older people. It’s not universal; a lot of people don’t know anything about it, and some know quite a bit.”

The team hopes their research will inform curriculum for both an undergraduate creative inquiry course and K–12 lesson plans on CECs offered by Clemson University. The team attends conferences, meetings, and outreach events all over the region where they share posters, give presentations, and participate in webinars—such as the Consortium’s Science in Session series—that focus on ecosystem health, water quality, and wildlife. They hope to publish their work in a variety of formats, including articles, newsletters, and social media.

Aldridge leading education and outreach programming with elementary students at Hobcaw Barony. Photo credit: Miriam Boucher, M.Sc., Clemson University.

More than Megafauna

Alligators have always had a powerful hold on the hearts and minds of South Carolina’s residents and visitors, and our relationship with them has led to their near-extinction, protection, and recovery, and now to a more nuanced give-and-take as coinhabitors of this landscape.

We can respect this dynamic better by giving alligators plenty of space, supervising children and pets when playing in or around water, and swimming only during daylight hours in designated swimming areas. Note that it is illegal to kill, harass, touch, or attempt to move alligators without the appropriate licensing and direction from SCDNR. It is also illegal to feed alligators, as they may overcome their natural shyness and become accustomed to or attracted to humans when fed, possibly becoming nuisance alligators.

We can help reduce the exposure of alligators and other wildlife to contaminants by following best practices for recycling or disposing of unwanted materials, such as household waste, plastics, tires, and other items. Southeastern state agencies have launched a Gator Wise program to help support human-gator coexistence.

“I hope that we can reframe how we look at alligators,” said Boucher. “They’re not just a tourist icon or a backyard neighbor; they are an integral part of our ecosystem, relying on the same water resources we do. By learning about the alligators around us and what is impacting them, we also have a chance to learn and reflect on what those impacts may mean for us.”

You may learn more about the contaminants of emerging concern program by reaching out to Brooke Saari, Coastal Environmental Quality and Extension Services specialist for the Consortium. You may also reach out to Principal Investigator Jim Anderson, Ph.D., at Clemson University.

Co-Investigators and Project Partners

– Thomas Rainwater, Ph.D., Tom Yawkey Wildlife Center and Clemson University.
– Stefanie Whitmire, Ph.D., Baruch Institute of Coastal Ecology and Forest Science, Clemson University.
– John A. Bowden, Ph.D., Bowden Laboratory, University of Florida.
– Debabrata Sahoo, Ph.D., PE, P.H., Cooperative Extension Service, Clemson University.
– Nemours Wildlife Foundation.
Students assisting with this research include:
– Miriam Boucher, Ph.D. student, Clemson University.
– Dorothy Aldridge, M.S. student, Clemson University.
– Anna Chobot, undergraduate student, Clemson University.

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