Purpose: A longitudinal survey was conducted to quantify the extent to which soils from different fields suppress survival of E. coli O157 and to characterize important microbial groups in the soil that may be responsible for altering this suppression.
Methods: Soil was collected at planting and during harvest from twelve specialty crop fields in Ohio. Heat-treated and unheated subsamples were assayed for anti-E. coli O157 effects by inoculating the soil with gfp-labelled E. coli O157 and following the fate of these bacteria over 48 h. In order to understand the biological basis for pathogen suppression, differences in microbial community structure associated with E. coli O157 suppressive soils were determined by sequencing of the V4 region of the 16S rRNA gene and ITS-1 of fungal targets by Illumina MiSeq platform. Analysis was performed using QIIME.
Results: Heat-sensitive microorganisms were largely responsible for the suppression of E. coli O157 regardless of the season, region, or chemical composition of the soil. Soil pH, moisture content, and levels of soil organic matter (SOM) of the samples varied widely across regions and seasons. Likewise, relative suppression of the samples varied within each region and season. Although not statistically significant, this suppression appeared to be more frequently observed at harvest than at planting. Across the different fields, the composition of the microbiota varied and, within a single field, seasonal changes within the soil microbiota were also observed.
Significance: The results of this project support that a novel biocontrol soil additive to enhance natural foodborne pathogen suppression in specialty crop soils has potential as a means of controlling foodborne pathogens on small fruits and vegetables.