Organic farmers often rely on animal manure to build soil health and fertility. While these amendments improve soil structure, nutrient cycling, and long-term productivity for growers, they can carry pathogens. 

A recent two-year, multi-state study published in the Journal of Food Protection addressed this consideration by determining the farm conditions that are more likely to result in fecal indicator bacteria detected on produce. Researchers tracked generic E. coli (a common indicator of fecal contamination risk) on produce grown on USDA Organic certified farms using untreated manure. They gathered 509 produce samples from 19 farms across California, Maine, Minnesota, and Maryland, collecting crops from 30 to 180 days after manure application and pairing those samples with farm management surveys, soil and water testing, and local weather data. Across all samples, 22% tested positive for generic E. coli. However, contamination odds weren’t evenly distributed. Weather, crop type, field history, and manure use timing all influenced contamination risk.

Supporting a field reality, rainfall stood out as a consistent risk signal. These conditions result in higher soil to plant transfer from runoff and splash. Results indicated that for every increase in precipitation in the 7 days prior to sampling, the odds of detecting generic E. coli on produce increased. Crop type also mattered. Compared to fruits (where the edible portion typically doesn’t touch soil), leafy greens had ~13x higher odds of generic E. coli presence and root vegetables had ~20x higher odds. Interestingly, fields with previous non-agricultural land use had higher odds of generic E. coli on produce, pointing to land-use history as a meaningful risk factor worth considering in site assessments. The study also found that time after manure spread influenced detection odds, with a notable drop by Day 60. Importantly, the overall pattern did not indicate elevated risk beyond the 90-120-day rule used in USDA organic standards for manure application.

These results reinforce the idea that risk is not a “one size fits all” for organic systems. It is shaped by factors such as crop contact with soil, field history, and manure application timing, emphasizing that weather-aware and crop-specific risk management may further reduce contamination likelihood.

It’s important to note that generic E. coli is an indicator organism, not a direct measure of pathogens like Salmonella, or Listeria. Still, it’s a useful early warning for conditions that can increase contamination risk. This study reinforces the strength of the National Organic Program, highlighting the evidence-based importance of safe harvesting, storage, and handling practices within organic production systems. 

Photos by Glen Hayoge and Eryxson Fonseca on Unsplash