Cascading effects of composts and cover crops on soil chemistry, bacterial communities and the survival of foodborne pathogens

AIMS: Recent foodborne disease outbreaks have caused farmers to re‐evaluate their practices. In particular, concern that soil amendments could introduce foodborne pathogens onto farms and promote their survival in soils has led farmers to reduce or eliminate the application of animal‐based composts. However, organic amendments (such as composts and cover crops) could bolster food safety by increasing soil microbial diversity and activity, which can act as competitors or antagonists and reduce pathogen survival. METHODS AND RESULTS: Leveraging a study of a 27‐year experiment comparing organic and conventional soil management, we evaluate the impacts of composted poultry litter and cover crops on soil chemistry, bacterial communities and survival of Salmonella enterica and Listeria monocytogenes. We found that bacterial community composition strongly affected pathogen survival in soils. Specifically, organic soils managed with cover crops and composts hosted more macronutrients and bacterial communities that were better able to suppress Salmonella and Listeria. For example, after incubating soils for 10 days at 20°C, soils without composts retained fourfold to fivefold more Salmonella compared to compost‐amended soils. However, treatment effects dissipated as bacterial communities converged over the growing season. CONCLUSIONS: Our results suggest that composts and cover crops may be used to build healthy soils without increasing foodborne pathogen survival. SIGNIFICANCE AND IMPACT OF THE STUDY: Our work suggests that animal‐based composts do not promote pathogen survival and may even promote bacterial communities that suppress pathogens. Critically, proper composting techniques are known to reduce pathogen populations in biological soil amendments of animal origin, which can reduce the risks of introducing pathogens to farm fields in soil amendments. Thus, animal‐based composts and cover crops may be a safe alternative to conventional fertilizers, both because of the known benefits of composts for soil health and because it may be possible to apply amendments in such a way that food‐safety risks are mitigated rather than exacerbated.