By Kara Nuzback
Two rapidly advancing fields of scientific research are transforming the way we look at the natural world. Environmental DNA, or eDNA, offers a bird’s-eye view of the variety and complexity of life on Earth. Microbial ecology sheds light on poorly understood organismal interactions.
“Expertise in these fields keeps UMES on the cutting edge of research that carries profound implications for agriculture and use of living natural resources under changing ecological circumstances,” said Dr. Moses T. Kairo, dean of the UMES School of Agricultural and Natural Sciences.
The University of Maryland Eastern Shore brought on Drs. Gordon Custer, a microbial ecologist, and Justine Whitaker, an eDNA expert, in 2024.
“As these disciplines advance and align, they could provide solutions to many challenges in today’s rapidly changing natural world,” he said
What eDNA Can Tell Us About the Rare Atlantic Sturgeon
Just as modern DNA testing can help solve crimes of the past, environmental DNA, or eDNA, can shed light on species that have long been a mystery — even to scientists.
Atlantic sturgeon hasn’t changed much since it swam at the feet of dinosaurs more than 120 million years ago. It is credited as the primary food source that saved the Jamestown settlers during “The Starving Time” famine in the early 1600s. It once supported a massive commercial fishery for its caviar and meat.
Today, Atlantic sturgeon is listed as endangered; its rarity and protected status makes it difficult to study, despite being the largest fish native to the Chesapeake Bay.
Dr. Justine Whitaker, a UMES assistant professor of environmental science, has been testing water samples collected on the Delmarva Peninsula for eDNA, with the aim of investigating Atlantic sturgeon. She specializes in eDNA, conservation genomics, and biodiversity and genetic variation.
Rather than a traditional DNA sample, which would require catching the fish or its eggs, eDNA can be collected without disturbing what few members of the species remain. A water sample can be enough to show that Atlantic sturgeon are present.
Young Sturgeon Key to Recovery of Species
Whitaker recently joined a group of peers from the University of Maryland Center for Environmental Science (UMCES) and the Maryland Department of Natural Resources, who have studied the remaining members of the species in local waters for years.
One of those peers, former UMCES associate professor Louis V. Plough, who now works for NOAA, published a 2021 article in the journal Environmental DNA that reported he had detected sturgeon in the Nanticoke
River using eDNA. However, data at the time showed only adult sturgeon in the river during spawning season.
Atlantic sturgeon are anadromous fish, meaning they are born in freshwater, migrate to sea at maturity and make their way back to freshwater to spawn, normally to the same river in which they hatched.
Since no juvenile sturgeon were detected, the question is now whether sturgeon are spawning in the river, Whitaker said. Since the study was published, Maryland DNR has collected samples and tagged adult sturgeon in the Nanticoke River.
“They’ve never caught juveniles. They sampled with egg mats but didn’t find any eggs,” she said.
A Targeted Approach
Reusing water samples collected by Plough, Whitaker and intern Malachi Cox spent summer 2025 attempting a different method of eDNA collection to detect evidence of juveniles. In fall 2025, Myah Bowie, a NOAA Living Marine Resources Cooperative Science Center fellow and recent UMES graduate, joined the project.
There are two main procedures, or assays, for assessing the presence, amount or activity of an entity in eDNA collection: quantitative polymerase chain reaction, or qPCR, which is sensitive but detects only one species; and metabarcoding, which can identify numerous species from a sample.
Plough used a qPCR assay to detect Atlantic sturgeon in the water samples, which has been the gold standard for single species detection. With newer technology, Whitaker aims to develop an assay that is more sensitive than qPCR.
A targeted next-generation sequencing, or tNGS assay, takes the metabarcoding method and applies it to a single species, creating a more amplified and precise method of collecting data. The improved accuracy and increased depth of information in a tNGS assay can reveal more information about Atlantic sturgeon in the Nanticoke River, Whitaker said.
A tNGS approach would also be more cost-effective than using a qPCR with sequencing, while gleaning the same information, she said.
Whitaker said if she is successful in developing the new assay, it could be applied to monitoring other endangered or threatened species. For now, she hopes to find funding to grow the Atlantic sturgeon project to ensure the species is not lost.
“Sturgeon are my passion,” she said.
Can Bacteria, Fungi Mend Soil Health?
Just as humans have a skin microbiome and a stomach microbiome, plants have microbiomes in their roots, leaves and in the soil where they grow.
And just as a human would take a probiotic to improve their gut health, UMES Assistant Professor of Biology Gordon Custer is researching microbial treatments to improve soil health.
Custer took an interest in microbial ecology during his senior year of college while working with a professor who researched invasive plants and their effect on soil microbial communities.
“I thought it was fascinating there was this whole unseen world that you don’t ever think of,” he said.
As a graduate student at the University of Wyoming, Custer worked with Drs. William Stump and Linda van Diepen, researching plant and soil microbiomes and nutrient cycling. Custer then found work as a postdoctoral fellow at Penn State, where he worked with Dr. Francisco Dini-Andreote to look more broadly at the movement of microbiomes.
While working at Penn State in 2023 and 2024, Custer sought to experiment with adding bacteria to soil that was very low in phosphorus to improve both soil health and plant performance. Phosphorus is essential to plants in the processes of photosynthesis, root development, and flower and seed production.
Phosphorus is being depleted from soil more quickly than can be naturally replenished, leading to concerns about domestic food security and a potential reliance on imported fertilizer to meet phosphorus demand.
With the help of a grant from the U.S. Department of Agriculture’s National Institute of Food and Agriculture, Custer is continuing this research at UMES.
Red Spring Wheat
In September 2025, Custer planted hard red spring wheat in phosphorus deficient soils at the University of Maryland, College Park’s Research Greenhouse Facility. He and his research team plan to inoculate each plant
with different doses and frequencies of commercially available microbial inoculants and measure plant performance and phosphorus uptake.
Custer said he hopes the bacteria and fungi unlock more phosphorus in the soil. Beyond that, he aims to identify a dose and frequency of inoculation that results in long-term establishment in the soil microbiome — to the point that reapplication is not needed.
The project, scheduled to be completed in 2028, also involves outreach with students at a local high school. The A+ Garden Centre in Salisbury, Maryland, is a student-led commercial greenhouse that offers advanced
horticulture training opportunities to students in Wicomico County Public Schools.
The center uses many microbial inoculants in its production facility. Since the start of his collaboration in summer 2024, Custer has lectured before nearly 30 Parkside Career & Technology Education students and plans to offer student research internships in his lab at UMES to help carry out the grant-supported research.
Switchgrass and Drought
A second project Custer is undertaking, along with Dr. Jonathan Cumming, chair of the UMES Department of Natural Sciences, investigates the effect of drought on switchgrass through the lens of soil and root microbes.
Switchgrass is a biofuel stock that can grow on land that no longer supports corn or soybean growth because of salinization, drought or other environmental factors. But drought tolerance doesn’t equate to droughtproof, Custer said.
Through an Evans-Allen grant, Custer and Cumming will expose switchgrass to drought conditions, measure how that impacts the chemistry of the roots and learn how those changes influence microbial decomposition.
The goal of the project is to learn how drought affects plant-microbe interactions and use this information to make switchgrass more resilient to stress from extreme weather. They plan to have results by 2029.
The permanent rainout shelters constructed for this project can be used to simulate drought conditions for future research projects.
This work is supported by: Soil and microbes, no. 2024-67012-44745, U.S. Department of Agriculture. Switchgrass, no. NI251445XXXXG003, Evans-Allen capacity grant
