Organic and sustainable farming operations increasingly depend on biological soil amendments of animal origin to build soil health, improve nutrient availability, and sustain crop productivity without relying on synthetic fertilizers. Poultry litter, a mixture of manure, bedding material, feathers, and feed residues, is one of the most abundant and widely used of these amendments. In Georgia, one of the nation’s leading poultry-producing states, approximately two million tons of poultry litter are generated annually, making it an economically and agronomically important resource for vegetable growers across the state. Sweet onions, a signature Georgia crop, are frequently grown in soils amended with these materials.

The research team, which included Harsimran Kaur Kapoor of the University of Georgia and Abhinav Mishra of the university’s Department of Food Science & Technology, set out to answer a deceptively simple question: how long does E. coli remain viable in field soils treated with different poultry litter-based amendments, and how do environmental conditions modulate that survival? The answer matters because pathogenic strains of E. coli and related foodborne pathogens can persist on produce surfaces and within soil ecosystems long after the amendment is applied, creating a window of potential contamination that growers must manage.

Across two growing seasons, the researchers observed a consistent pattern. Soils amended with heat-treated poultry pellets and soils amended with composted poultry litter both supported longer survival of E. coli than untreated control soils. Heat treatment and composting are both intended to reduce pathogen loads in manure-based products, yet the study indicates that the amended soil environment itself, even when the amendment has been processed, can create conditions more favorable to bacterial persistence than unamended soil. Nutrient availability, moisture retention, and organic matter content are among the factors that researchers generally associate with improved microbial survival in amended soils, and the study’s results align with that broader understanding.

The weather findings add a layer of complexity that the authors argue is essential for risk management. The influence of weather differed between the two growing seasons analyzed, pointing to the importance of year-to-year variability. Higher humidity was associated with greater bacterial survival, while stronger winds generally reduced survival. Rain and warmer soil temperatures could promote bacterial persistence, whereas higher air temperature and wind speeds tended to reduce it. Taken together, the results suggest that extreme weather events, rather than average seasonal conditions alone, may play an important role in determining how long bacteria can survive in agricultural soils.

This distinction between averages and extremes carries real consequences for how food safety risk is modeled and managed. A season with a modest average temperature but several intense rainfall events may pose a different contamination profile than a season with a higher average temperature and steady winds. Risk-based approaches that rely solely on seasonal or monthly climate summaries could therefore underestimate the survival window of pathogens following specific extreme events. The authors note that understanding how amendment practices interact with extreme weather may help inform risk-based management approaches under real field conditions, where growers cannot control the weather but can adjust amendment type, timing, and application practices.

The crop at the center of the study is not an arbitrary choice. Onions have been linked to several major foodborne illness outbreaks in North America in recent years. In 2024, the U.S. Food and Drug Administration investigated an outbreak of E. coli O157:H7 associated with slivered onions served on McDonald’s Quarter Pounder burgers. Earlier incidents include a 2020 outbreak of Salmonella Newport linked to red onions across the United States and Canada, and a 2021 outbreak of Salmonella Oranienburg tied to whole fresh onions imported from Mexico. These outbreaks resulted in thousands of reported illnesses and hundreds of hospitalizations, underscoring that allium crops, long considered lower risk than leafy greens, can serve as vectors for serious foodborne disease.

Sweet onions present particular production considerations. They are typically grown in sandy soils with careful irrigation management, harvested after months in direct contact with the soil environment, and often consumed raw or with minimal processing, which means no kill step intervenes between field and consumer. Any pathogen that persists in the soil or on the bulb surface at harvest therefore represents a direct route into the food supply. Understanding whether and how poultry litter amendments extend the survival window of E. coli in these soils gives growers and regulators a concrete variable to work with when designing pre-harvest intervals, amendment application schedules, and water and soil testing regimes.

The regulatory context is also evolving. The authors note that regulators continue to seek data on the food safety implications of biological soil amendments of animal origin, a category that includes raw and processed manures, composts, and pelleted products. Field-scale studies like this one provide the kind of empirical evidence needed to calibrate standards that are both protective of public health and workable for growers who depend on these amendments for soil fertility. The interaction between amendment type and local environmental conditions that the study documents suggests that a one-size-fits-all national standard may be less effective than frameworks that account for regional climate, weather variability, and dominant amendment practices.

For Georgia’s sweet onion industry, and for produce growers in poultry-heavy regions more broadly, the study offers a practical takeaway: the combination of amendment choice and weather exposure deserves active attention in food safety planning. Growers who apply heat-treated poultry pellets or composted poultry litter may want to consider how upcoming rainfall, humidity, and wind patterns could extend or shorten pathogen survival in their fields. As extreme weather events become more frequent and more intense, the researchers’ central finding, that it is the extremes rather than the averages that shape bacterial persistence, is likely to grow in importance for anyone working at the intersection of soil health, agricultural productivity, and the safety of the fresh produce that reaches consumers’ tables.

Subject of Research: Survival of E. coli in poultry litter-amended soils under varying weather conditions in sweet onion production

Article Title: Study finds poultry litter-based soil amendments and weather influence E. coli survival in Georgia sweet onion production systems

Article References: Study finds poultry litter-based soil amendments and weather influence E. coli survival in Georgia sweet onion production systems. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: E. coli, poultry litter, soil amendments, sweet onions, food safety, extreme weather, Georgia agriculture, Risk Analysis, compost, foodborne illness, pathogen survival, produce safety

It doesn’t require a degree in ornithology, a lab test or even an app for most growers to determine whether bird poop near their crops presents a food safety risk. They just need to ask themselves a simple question: How big is it? 

That’s according to a study from the University of California, Davis, published today in the Journal of Applied Ecology. The study said an informed, nuanced view of food-safety risks and wild birds could help growers avoid crop losses and manage farms for food safety, biodiversity conservation and crop production.

Since 2006, when an E. coli outbreak devastated the U.S. leafy greens industry, growers have been pressured to remove natural habitat to keep wildlife — and the foodborne pathogens they sometimes carry — from visiting crops. Growers are often advised not to harvest crops within a roughly three-foot radius of any wildlife feces, lest they risk failing a food safety audit or losing a buyer contract. Growers often cite such concerns as a barrier to implementing conservation actions they would otherwise consider taking on their farms. 

“We wanted to find out the true risk of wild birds to food safety,” said lead author Austin Spence, a postdoctoral researcher in the UC Davis Department of Wildlife, Fish and Conservation Biology. “Which birds have pathogens, which birds are spending time on farms, and if a bird has a pathogen, does that pathogen survive long in bird poop? Our findings indicate that we can co-manage our areas for both agriculture and conservation.”

Where pathogens persist

Through field and greenhouse experiments, bird surveys, point counts and fecal transects, the authors assessed food-safety risks from nearly 10,000 birds across 29 lettuce farms on California’s Central Coast. They spent hours following turkeys, bluebirds and other wild birds at the UC Davis Student Farm and nearby Putah Creek, collecting hundreds of fecal samples. They compared E. coli survival in bird droppings on lettuce, soil and plastic mulch to measure pathogen persistence.

After all of these efforts, they landed on a simple finding: Smaller poops from smaller birds carry very low risk of foodborne pathogens, which were rare in birds overall. If a bird were to become infected, pathogen survival depends heavily on the bird’s size. 

“Birds that are large produce really big feces, and that’s where pathogens are more likely to survive,” said Spence. “Birds that are small have tiny feces, and the pathogens die off quickly. So farmers don’t have to know the species of bird it came from. They just need to know the size. If it’s the size of a quarter, don’t harvest near that. If it’s a tiny white speck, it’s very low risk and probably fine.”

Balancing conservation, crop yields, and food safety

Beyond fecal size, what the birds pooped on — be it the crop, soil or plastic — made a difference for pathogen survival. In the study, E. coli survived longer on lettuce itself than on soil or plastic mulch. 

Fortunately, about 90% of birds observed on the farms were small and tended to poop mostly on soil, where pathogens perish quickly. By avoiding no-harvest buffers when food-safety risks are low, growers of leafy greens could harvest about 10% more of their fields. 

“Birds generally present really low food-safety risks,” said senior author Daniel Karp, a UC Davis professor in the Department of Wildlife, Fish, and Conservation Biology. “The industry has been concerned about birds for a while. But pathogenic E. coli and Salmonella are vanishingly rare in wild, farmland birds. And we now know E. coli tends to die off quickly in most bird poop.”

The study opens up new strategies for growers to better balance conservation and food-safety risks. For example, growers could erect nest boxes to attract small, beneficial insect-eating birds, like bluebirds and swallows, that help control pests without risking food safety. 

The work also contributes to a growing body of research that suggests growers do not need to remove habitat to improve food safety. 

“There have been no studies to date that suggest habitat removal improves food safety,” Karp said. “Habitat around farms is actually likely to favor the small, insect-eating birds that are unlikely to carry pathogens. Studies like ours are giving farmers science-based permission to conserve habitat — and many species of wild birds — on their farms again.”

The study’s additional coauthors are Jeffery McGarvey and SangIn Lee at the USDA Agricultural Research Service, Olivia Smith at Michigan State University, Elissa Olimpi at Conservation Science Partners, and undergraduates Wentao Yang and Meirun Zhang at UC Davis. 

The study was funded through the Center for Produce Safety, the California Department of Food and Agriculture and the U.S. Department of Agriculture.