Investigating the Prevalence of Salmonella and E. coli in Florida’s Soil and Identifying Key Environmental Factors

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Foodborne outbreaks linked to contamination from soil identified a need to investigate regional, environmental factors that impact pathogen prevalence in the soil. This research was conducted to evaluate the prevalence of foodborne pathogens in unamended soils, complementing previous studies and providing a more complete picture of the potential risk of produce contamination from soils in Florida. The prevalence of Salmonella and the prevalence and concentration of generic E. coli in Florida’s agricultural soils was evaluated to understand the risk of microbial contamination at the pre-harvest level. A longitudinal field study was performed in three geographically distributed agricultural areas across Florida. At each location, 20 unique 5 × 5 m field blocks were selected, soil was collected and evaluated for Salmonella presence (25 g) and E. coli and coliform enumeration (5 g). Complementary data included weather, adjacent land use, soil macro- and micronutrients, and field management practices from October 2021 to April 2022. Dried soil was sent to Waters Agricultural Laboratories, Inc. in Camilla, GA for analysis of the following elements total carbon (TC), total nitrogen (TN), organic matter, pH, aluminum (Al), calcium (Ca), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), molybdenum (Mo), sodium (Na), phosphorus (P), sulfur (S), and zinc (Zn). Dried soil from each farmwas also sent to Waters Agricultural Laboratories in Camilla, GA for soil texture analysis. Data on the type of soil in eachsampling plot was collected using the USDA Web Soil Survey. An initial questionnaire was completed by the farm managers prior to the start of the sampling period to collect data on farm management practices. An observational questionnaire was also completed during each sampling trip, for each sampling plot, to collect additional farm management data. Weather data, including average, maximum and minimum air temperature (2 m), soil temperature (10 cm), precipitation, relative humidity (2 m), dew point (2 m) solar radiation (2 m), and wind speed (10 m) were obtained from the Florida Automated Weather Network (FAWN) weather station at each location for each sampling trip. Data onland use adjacent to each farm was collected using data from the2019 National Land Cover Database and ArcGIS Pro. The overall prevalence of Salmonella and generic E. coli were0.418% (1/239) and 11.3% (27/239), respectively; mean E. colipopulation levels in positive samples were 1.56 log CFU/g. FarmA had the highest prevalence of generic E. coli, 22.8% (18/79);followed by Farm B, 10% (8/80); and Farm C 1.25% (1/80). Thelow prevalence of Salmonella in the soil was not expected basedon a previous study where prevalence of Salmonella in SouthFlorida’s soil was 62.5%.Investigation of the relationship between farm and samplingtrip through a two-way analysis of variance showed that bothfarm and sampling trip were significant (P < 0.05) for generic E.coli and coliforms and the interaction between farm and samplingtrip was significant (P < 0.05) for coliforms only. Variation inthe prevalence of generic E. coli and changes in coliform populationsbetween farms suggests the factors influencing the soilenvironment at the three farms are different. Pearson’s correlationanalysis of farm management variables and generic E. coli andcoliform concentrations identified positive correlations with fieldstatus, soil disturbance, the staking of crops, and the presence ofcrop residues. Analysis of variance and Tukey post-hoc testingidentified the fall as being statistically significant (P < 0.05) inthe variation of generic E. coli showing seasonal temperaturefluctuations impact soil microbial communities. An analysis ofvariance also identified soil type as significant for both generic E.coli (P < 0.001) and coliforms (P = 0.00685). Post-hoc analysesshowed that Pahokee muck soil was statistically different thanthe sandy soils for generic E. coli. The post-hoc analysis for coliformsindicated a statistically difference between Pahokee mucksoil and both Zolfo and Immokalee fine sand, with no statisticaldifferences between the four sandy soils. While Salmonella wasonly identified once, generic E. coli was detected in Florida soilsthroughout the duration of the growing season meaning activitiesthat limit contact between soil and crops should continue to beemphasized. The influence of local environmental factors on theprevalence of indicator organisms in the soil presents a uniquechallenge when evaluating the applicability of more globalmodels to predict pathogen prevalence in pre-harvest produceenvironments.

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