By Haley R Moore
Beneath the calm surface of an agricultural pond in Maryland, an invisible world of microbes reveals insights that may reshape how we understand water safety in food production.
Researchers at the University of Maryland (UMD) and the United States Department of Agriculture (USDA) recently published a study on the complex microbial communities in irrigation water, showing how DNA sequencing helps understand which microbial species are present and how they interact within the dynamic water system. Their findings may offer farmers better tools for evaluating water quality and understanding food safety risks from agricultural water run-off.
Ryan Blaustein, assistant professor in the Department of Nutrition and Food Science at the College of Agriculture and Natural Resources, explained that their earlier study aimed to understand what microbes were present throughout the pond as a factor of sampling design, while the latest study used metagenome analysis to explore how these ‘microbiomes’ may function.
“Metagenomics lets us look at all the DNA in a sample,” Blaustein said. “If we think of DNA as puzzle pieces to a microbial genome, this approach allows us to rebuild many jigsaw puzzles all mixed together to identify the genes that each microbe carries.”
Researchers collected water samples from various depths and locations in an agricultural pond widely used for irrigation and conducting research at the Maryland Agricultural Experiment Station’s Wye Research and Education Center. Beyond the traditional surface samples, the team gathered data from the water column and sediment zones where microbes thrive.
By combining traditional microbial culture (counting live E. coli) with advanced metagenome sequencing, the team was able to expand their understanding of the microbial system. They further examined microbial traits like the ability to photosynthesize, metabolize nutrients, and resist antibiotics.
“This research is about more than just what is in the pond,” said Magaly Toro, associate research professor at UMD’s Joint Institute for Food Safety and Applied Nutrition, who conducted the genome sequencing. “It’s about understanding how bacteria like E. coli actually get there, how they move through the environment, and what makes them persist.”
Regulations require U.S. produce growers to monitor the quality of their irrigation water to prevent the spread of pathogens. Blaustein explained that there is a gray area for growers interpreting those regulations.
“There are regulatory recommendations but not always clear instructions,” Blaustein said. “Growers are told to test for indicators like E. coli, but are not always given specifics like ‘How often? How many samples? Where in the pond?’”
The team learned that sampling location and depth matter. The microbial community changed significantly depending on where and when the water was sampled. For example, photosynthesizing cyanobacteria dominated near the surface, while microbes deeper in the water, where E. coli may also lurk, were more associated with respiration and nutrient cycling.
“These findings suggest that growers and regulators need more nuanced strategies,” Toro said. “Maybe that means sampling after storms or using environmental conditions like turbidity as a proxy for microbial risk.”
The team also found that antimicrobial resistance (AMR) and virulence genes were present, including some previously undocumented in the pond. While they did not correlate directly with known foodborne illness risks, their presence highlights the potential for further research.
Microbial diversity itself may be an indirect indicator of water quality. The study suggests that combining simpler tests (like pH, temperature, or nutrient levels) might eventually be used to infer microbial risk — saving time and cost for farmers and producers.
By blending microbiology, environmental science, and hydrology, this study allows researchers to understand how microbes move through agricultural systems and offers a path forward for managing risk.
“This isn’t about making anyone afraid of irrigation water,” Blaustein said. “It’s about understanding the tiny life in that water and how it interacts with the food we eat.”