Could manure and compost act like probiotics, reducing antibiotic resistance in urban soils?

Urban soils often contain chemical contaminants, such as heavy metals or trace amounts of antibiotics, along with higher levels of antibiotic-resistant bacteria. New research from the University of Maryland suggests that, in some cases, boosting urban soil health with compost and treated manure may reduce the amount of “bad” bacteria. Understanding these dynamics has important implications for improving the quality and safety of fresh produce in urban agriculture. The study was published online July 13, 2024, in the Journal of Food Protection.

“Urban farming brings people together and now we see that it can help clean up the environment, at least from certain antibiotic-resistant bacteria,” said Ryan Blaustein, an assistant professor in the Department of Nutrition and Food Science at UMD and an author of the study. “Growing organically may promote healthier vegetable ‘microbiomes’ that we are exposed to as consumers.”

Urban farmers and community gardeners often amend their soil with biological additives, like animal manure, or composts made from mixtures of plant material and food scraps that may include fruits and vegetables, eggs, milk, meat, or shellfish waste. These types of soil amendments are regulated, and must be properly composted or pasteurized before application, because they carry a risk of introducing microbes like salmonella and E. coli, which cause food-borne illness. But little is known about the potential effects of using organic soil amendments on antibiotic resistance in bacteria in urban food systems.

To help fill this gap, Blaustein and his colleagues analyzed soils and leafy green vegetables like kale and lettuce from seven urban farms and community gardens around Washington, D.C.  They tested for levels of total bacteria and bacteria resistant to antibiotics like ampicillin and tetracycline. At each location, they tested leafy greens as well as soil that had been treated with manure or compost and soil that had not been treated.

Their results showed that amended soils treated with manure or compost had much more total bacteria than untreated soils, but not necessarily more harmful bacteria or antibiotic-resistant strains. Meaning, the proportion of resistant bacteria and food safety indicators were actually lower in the amended soil. Further studies need to be done to determine the long-term impacts, but their results suggest that manure and compost could act like probiotics for the soil, perhaps introducing or stimulating beneficial bacteria that outcompetes and suppresses the antibiotic-resistant bacteria.

The researchers also found that the pH in soil was strongly associated with concentrations of tetracycline-resistant bacteria, suggesting that managing pH has applications for controlling associated risks. In addition, they saw large differences in bacteria levels between sites, sometimes within the same farm, depending on what amendments were used and what greens were grown. Blaustein said these results highlight the need to build a systems-level understanding of soils in urban farming environments.

This information has important implications for understanding the role of compost and manure for improving soil health and managing harmful bacteria and ensuring a healthy food supply from urban agricultural settings.