Aggregative boot cover sampling may be a more representative, practical, and powerful method for preharvest produce soil testing than grab sampling because boot covers aggregate soil from larger areas. Our study tests if boot cover sampling results reflect quality and safety indicator organisms and community diversity of grab sampling. We collected soil samples from commercial romaine lettuce fields spanning 5060 m2 using boot covers (n = 28, m = 1.1 ± 0.4 g; wearing boot covers and walking along the path), composite grabs (n = 28, m = 231 ± 24 g; consisting of 60 grabs of 3–5 g each), and high-resolution grabs (n = 72, m = 56 ± 4 g; taking one sample per stratum). Means and standard deviations of log-transformed aerobic plate counts (APCs) were 7.0 ± 0.3, 7.1 ± 0.2, and 7.3 ± 0.2 log(CFU/g) for boot covers, composite grabs, and high-resolution grabs, respectively. APCs did not show biologically meaningful differences between sample types. Boot covers recovered on average 0.6 log(CFU/g) more total coliforms than both grabs (p < 0.001) where means and standard deviations of log-transformed counts were 3.2 ± 1.0, 2.6 ± 0.6, and 2.6 ± 1.0 log(CFU/g) for boot covers, composite grabs, and high-resolution grabs, respectively. There were no generic E. coli detected in any sample by enumeration methods with LODs of 1.3–2.1 log(CFU/g) for boot covers and 0.5 log(CFU/g) for both grabs. By 16S rRNA sequencing, community species diversity (alpha diversity) was not significantly different within collection methods. While communities differed (p < 0.001) between soil sampling methods (beta diversity), variance in microbial communities was not significantly different. Of the 28 phyla and 297 genera detected, 25 phyla (89%) and 258 genera (87%) were found by all methods. Overall, aggregative boot cover sampling is similar to both grab methods for recovering quality and safety indicator organisms and representative microbiomes. This justifies future work testing aggregative soil sampling for foodborne pathogen detection.
Data analysis was performed in R and RStudio Desktop with the following packages:
- datasets
- ggplot2
- multcompView
- dplyr
- ggpubr
- tidyverse
- gapminder
- plotly
- grid
- car
- rstatix
You can view the list of authors in the AUTHORS file.
Corresponding author: Matthew J. Stasiewicz
103 Agricultural Bioprocess Lab
1302 W. Pennsylvania
Urbana, IL, 1361801
USA
+1-217-265-0963
[email protected]
Wu, J., R. J. Gathman, J. Quintanilla Portillo, C. Gaulke, M. Kim, and M. J. Stasiewicz. 2023. Aggregative Soil Sampling Using Boot Covers Compared to Soil Grabs From Commercial Romaine Fields Shows Similar Indicator Organism and Microbial Community Recoveries. Journal of Food Protection. 86:100177.
This project's code is licensed under the GNU General Public License v3.0 and dataset is licensed the Creative Commons Attribution Share Alike 4.0 International license. Please see the LICENSE.code and LICENSE.dataset files for details.
This study was funded by the USDA National Institute of Food and Agriculture, Agricultural and Food Research Initiative Competitive Program – Food Safety and Defense Program, grant number: 2021-67017-33828 https://portal.nifa.usda.gov/web/crisprojectpages/1024000-aggregative-sampling-for-powerful-preharvest-leafy-green-food-safety-testing.html.