The Florida Microbiome Project: Mapping Microbial Communities to Support Environmental Health

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- by Ky Miller
New College Student Cara Ruhnke, and Alumni Marcela Prado Zapata and Elliott Schenker, work on the Florida Microbiome Project

Just beneath our feet—from downtown Sarasota’s urban backyards to the Myakka River’s tannin-rich floodwaters—a complex network of species, invisible to the human eye, is working around the clock. This network helps plants grow the food we eat, filter nutrient pollution and even fight climate change.

Since 2019, the Florida Microbiome Project—led by New College Assistant Professor of Biology and Environmental Studies Erika Díaz-Almeyda, Ph.D., and a cadre of dedicated students—has explored how these unseen microbial communities support livelihoods and habitat health throughout Sarasota and the state of Florida.

“We want to answer the questions: How are microbes changing with different land uses? And how are microbes indicators of overall environmental health?,” Díaz-Almeyda said. “There are few sites in Florida where researchers are doing long-term ecological sampling of the microbiome, and none are coastal.”

By keeping the exact same methods and sampling sizes to generate baseline data over a long time period, and making this data open-access, the team will be able to observe how different management practices have changed local ecosystems. This work will help maintain soil and water health, as well as inform decisions in the coming decades.

Little is known about Florida’s plant and soil microbiome, which is made up of thousands of tiny species called microorganisms that help plants photosynthesize and uptake nutrients (such as phosphorus and nitrogen) in the soil.

Much like a study from Mote Marine Laboratory and Aquarium’s Randall Wells, Ph.D., which traced the health of local dolphin populations over more than 50 years in Sarasota Bay, the findings from Díaz-Almeyda’s long-term study will shed light on an understudied but thriving ecological community. This community is the foundation for the health of Sarasota’s environment, which, in turn, is the foundation for the region’s communities and economy.

For example, nutrient pollution in one area can affect ecosystems miles away as it leaks into surrounding water bodies and slowly makes its way into the bay. It fuels the red tide algal blooms that wreak havoc on Sarasota’s beach-tourism-dependent economy. 

“Microbes provide many different ecosystem services, but among those is nutrient cycling,” said John Lambie, the founder of Southface Sarasota, an eco-conscious nonprofit organization. “For instance, there is a variety of common bacteria that converts water-soluble nitrogen fertilizer to nitrogen gas and sends it back to the atmosphere instead of the bay, while other microbes transform food waste to compost, prey on pathogens that may make us sick, and perform untold vital ecosystem services. Yet, we know so little about the interactions between microbes, fungi and plants that are actually making that happen.”

In 2019, Díaz-Almeyda’s Florida Microbiome Project studied the effects of urban food gardens on the city of Sarasota’s soils at Southface and found more than 100 different species of microorganisms diligently working to process nutrients and sequester carbon in the soil.

Now, in a new phase of the project, Díaz-Almeyda’s team of New College undergraduates and recent alumni is analyzing how similar microbial processes affect environmental health—and how human activity alters those processes—at the Triangle Ranch conservation easement in Myakka.

In 2016, Sarasota philanthropist Elizabeth Moore purchased Triangle Ranch’s 1,143 acres of sprawling fields and forests (which buffer the Myakka River State Park), with the support of the Conservation Foundation of the Gulf Coast and the Southwest Florida Water Management District. The goal was to protect the biodiversity-rich land from expanding development in the region.

Moore—who is also the president of the TREE Foundation and a member of Southface Sarasota’s board of directors—has been instrumental in the success of the Florida Microbiome Project and the broader ecological conservation efforts in the region.

“We are a part of nature, not separate from it. The data this project generates will inform local policymakers and the public about how we move forward with the decisions we make as a community, and as a region, for our environment,” Moore said. “We are all connected through biology on a macro and micro scale.”

The connection between the microbial world and social/environmental wellbeing in the Sarasota community is a lived reality for Triangle Ranch Manager Jason McKendree. His livelihood raising cattle is directly affected by the health of the ranch’s soil and water, and he has collaborated with Díaz-Almeyda to survey the ranchland.

“Phosphate mining in the Myakka head area is only about 20 miles away from here at the Mosaic-owned Wingate Creek Mine,” McKendree said. “This ranch is the last piece of property before [the Myakka River] flows into the state park. This makes it really essential for the water quality and wildlife habitat in this area.”

More than three miles of the Myakka River wind through the ranch’s rolling fields, and 120-plus species of plants and animals (including the endangered Florida panther) call Triangle Ranch home. Just as important are the microbial communities that the land, which is now permanently protected thanks to Moore, supports.

Applying the long-term data that the Florida Microbiome Project generates, Triangle Ranch may ultimately be able to become a species reservoir—one that could help restore the microbial communities in other areas of Sarasota and Florida as widespread development destroys habitats once rich with microbial diversity.

Because Triangle Ranch hosts many of the most common habitats of Central Florida’s ecosystems (such as oak hammocks, pastures and marshes), findings from the project will not only have an impact on ecosystems in the immediate area but also on the way scientists manage diverse ecosystems throughout Florida.

Beyond the statewide implications of Díaz-Almeyda’s study—from the professor’s early work with urban microbes at Southface Sarasota to her recent endeavors at Triangle Ranch—one thing has remained a constant at the community level: New College has been a nexus for community engagement and hands-on student research opportunities.

Marcela Prado Zapata, a 2021 New College marine biology graduate, now works as a research assistant to Díaz-Almeyda. Prado Zapata described her exposure to a diverse range of perspectives that reach beyond academia (working closely with local community members, for example) as one of the most enlightening elements of the project.

“The stakeholders at [Triangle Ranch] have been here for years; they are firsthand witnesses to seasonality changes. They know what the vegetation has looked like over the years, what major changes have been made to the environment, what organisms are common or uncommon to the area on a regular basis, and how the community itself interacts with the ranch,” Prado Zapata said. “As a student, research assistant and academic, I consistently work with people in my field who have similar access to information. But, by working with the community, you get to see the way your work applies to others and, more importantly, you get information that is not accessible in any journal or manual.”

Prado Zapata, along with 2021 New College graduate Elliott Schenker and thesis student Cara Ruhnke, have also had the opportunity to gain experience with rigorous procedures—both in the lab and the field. These include soil and water sample collection, DNA extraction and analysis techniques for both types of samples, and analysis of nutrient and sequencing data.

As a research assistant, Schenker performs microbial DNA extractions to explore the makeup of the microbes living in Triangle Ranch’s fertile soils. This will provide critical insight into how the ranch’s microbial communities are affected by flooding and excess nutrients in waterways.

“The whole idea is that we are bringing students into a legacy project, where everybody brings their own perspective and contributes a small part each year, as we train the next generation of scientists to recognize that environmental health equals human health and that we all have the right to healthy microbial communities,” Díaz-Almeyda said. “We are making an investment in the future of our students and our communities.”

With each passing year that Díaz-Almeyda and her team of young scientists collect data, the project gains momentum to advance local knowledge about the effects of human activity on the microbiome at a breakneck pace.

As the Sarasota region faces threats from nutrient pollution, climate change and development to meet the needs of Florida’s growing population, Díaz-Almeyda’s Florida Microbiome Project will inform land management and environmental planning in Sarasota County for decades to come.

For more information on Díaz-Almeyda and the Florida Microbiome Project, visit

Ky Miller, a 2021 New College graduate, is a contributing writer for the Office of Communications & Marketing.