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

Authors: DEVARAJAN, JARESH - University Of California; McGarvey, Jeffery - Jeff; SCOW, KATE - University Of California; JONES, MATTHEW - Washington State University; Lee, Sangin; SAMADDAR, SANDIPAN - University Of California; SCHMIDT, RODOMIR - University Of California; TRAN, THAO - Volunteer; KARP, DANIEL - University Of California

Submitted to: Journal of Applied Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2021
Publication Date: 4/6/2021
Citation: Devarajan, J., Mcgarvey, J.A., Scow, K., Jones, M., Lee, S., Samaddar, S., Schmidt, R., Tran, T., Karp, D. 2021. Cascading effects of composts and cover crops on soil chemistry, bacterial communities, and the survival of foodborne pathogens. Journal of Applied Microbiology. https://doi.org/10.1111/jam.15054.
DOI: https://doi.org/10.1111/jam.15054

Interpretive Summary: Many produce growers are reluctant to use composted animal manures due to fear of foodborne pathogen contamination of their crops. However composts are widely available and are known to improve soil health. Cover crops are also believed to improve soil health, but are also not commonly used. We collected soils that have been managed under organic and conventional methodologies with and without cover crops and analyzed them for their physical and chemical properties and their levels of microbial diversity. We also examined them for the ability to inhibit the persistence of the foodborne pathogens Salmonella enterica and Escherichia coli. We observed that the soils managed under organic cropping systems with cover crops contained more nutrients, greater microbial diversity and inhibited the persistence of pathogens significantly greater than those managed under conventional practices without cover crops.

Technical Abstract: Recent foodborne disease outbreaks have caused farmers to re-evaluate their practices. Faced with potential tradeoffs between improving soil health and mitigating pathogen contamination risk, many farmers have stopped applying animal-based composts to their fields. However, organic amendments— including animal-based composts and green waste from cover crops— often bolster soil microbial diversity and activity, which may help suppress foodborne pathogens in soils. Here, we couple a 27-year soil management experiment with lab experiments to 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 bacterial survival in soils. Specifically, organic soils managed with cover crops and composts hosted more macronutrients and bacterial communities that were better able to suppress foodborne pathogens. For example, soils without composts retained 4-5-fold more Salmonella after 10 days compared to compost amended soils. However, treatment effects dissipated as bacterial communities converged over the growing season. Understanding the generality of these findings requires experimentation in field conditions across cropping systems. Nonetheless, our results suggest that composts and cover crops may be used to build healthy soils while simultaneously suppressing foodborne pathogens.