Exploring Establishment and Persistence of Enterococci in Agricultural Soils under Controlled Abiotic and Biotic Conditions

Soil biodiversity is increasingly recognized as an important part of the One Health framework. It is known to be pivotal not only for sustaining agricultural productivity, but also as a biological barrier limiting the establishment and persistence of livestock-associated pathogens. While direct transmission pathways between animals and humans are well documented, the role of soil microbial communities in regulating pathogen survival outside hosts remains poorly understood.

We investigate how abiotic soil properties and native microbial biodiversity interact to constrain the environmental persistence of emerging zoonotic pathogens. Enterococci were used as a model for fecal-derived, opportunistic pathogens in agricultural systems. Combining field observations with controlled microcosm experiments, we studied soils from a free-range and a conventional pig farm representing contrasting management practices and soil textures. Enterococcal abundance was quantified using genus-specific qPCR, while bacterial community composition was assessed via 16S rRNA amplicon sequencing to characterize the ecological context of potential pathogen establishment.

Enterococcal DNA was detected across multiple management zones in freshly collected soils, with highest abundances in areas of recent pig activity. However, few viable cells were found across the samples. In sterile soil microcosms, Enterococcus lactis and E. sulfureus proliferated strongly in both sandy and silty soils, demonstrating that abiotic conditions alone do not prevent enterococcal growth. These results indicate that biotic interactions, rather than physicochemical constraints, are likely the dominant factor limiting enterococcal persistence in natural soils.

Ongoing experiments manipulate native microbial diversity gradients to disentangle mechanisms of biotic suppression, while integrated DNA/RNA analyses will distinguish active growth from residual necromass. By linking microbial community composition to pathogen exclusion, our work highlights soil biodiversity as a key ecosystem function contributing to “pathogen-resistant” soils. The experimental framework established here is broadly transferable to other soil-borne or fecal-associated pathogens, supporting risk assessment and sustainable soil management in agricultural landscapes.