Risk Factors Associated with Generic E. coli Survival in Soils from Certified Organic Farms

Untreated manure is commonly used as a biological soil amendment of animal origin in organic production but may introduce foodborne pathogens into the farm environment. In this multi-regional study, generic E. coli was used as an indicator of fecal contamination to identify factors associated with its in manure-amended soils. The analysis included samples from 19 certified organic farms in California, Maine, Minnesota, and Maryland collected over two growing seasons. A zero-inflated linear mixed model was used to assess the association between generic E. coli concentration in soil, farm-related practices, soil and environmental factors. Generic E. coli concentration in the soil rapidly declined in the first 60 days after manure application (β: -1.00, CI₉₅: -1.17, -0.83) before a secondary increase through Day 180. Manure management practices, including use of different types of animal manure and manure application rates, were significantly associated with generic E. coli in soil. Soil nutrients (phosphorus (β: 0.22, CI₉₅: 0.15, 0.30)) and micronutrients (zinc (β: 0.03, CI₉₅: 0.01, 0.04) and manganese (β: 0.02, CI₉₅: 0.01, 0.02)), elevated moisture content (β: 0.13, CI₉₅: 0.07, 0.19), and Salmonella (β: 1.79, CI₉₅: 1.31,2.23) or Listeria monocytogenes (β: 0.24, CI₉₅: 0.03, 0.44) also showed positive association with generic E. coli in soil. Lower wind speed (β: -0.12, CI₉₅: -0.19, -0.06), increased precipitation (β: 0.03, CI₉₅: 0.01, 0.05), and increased UV index (β: 0.24, CI₉₅: 0.15, 0.34) were found to be associated with higher E. coli concentration in manured soil. Overall, the persistence of generic E. coli in manure-amended soil was multifactorial. Effective microbial risk management should incorporate considerations for origin of manure, management, environmental and meteorological factors alongside current USDA National Organic Program standards (90-120 days) regarding the interval of application of raw manure to harvest of the edible portion of food crops.