This depository contains datasets, R scripts, and outputs from a study on the persistence of enteric pathogens in agricultural soil.
This work is licensed under the Creative Commons CC BY 4.0 license.
- If you use this repository, please cite the manuscript (in-production): Yusuf et al. Human norovirus persists longer than Escherichia coli in sandy soil, independent of plant decaying materials. Scientific Reports. DOI : 10.1038/s41598-025-31728-1.
Obj2_modeling_NM120825.pdf: Rendered R scripts and outputs supporting this research.
The following data files are included in this repository and permanently archived on Zenodo https://doi.org/10.5281/zenodo.16230597
obj2_dat.RDS: Triplicate microbial data collected during experiments.FAWN_report_2022_2025_daily.csv: Average daily weather and soil property data.FAWN_report_seven_day_hourly.csv: Average hourly weather and soil property data from 7 days before each sampling date.
| Column Name | Type | Description |
|---|---|---|
day |
Numerical | Sampling intervals in days |
assay |
Categorical | The assays used for the quantification of each microbial target |
matrix |
Categorical | Microbe-suspended matrix to be studied |
microbe |
Categorical | Microbial groups |
replicate |
Numerical | Number of each biological replicate |
survival |
Numerical | Microbial survival |
temp |
Categorical | Temperature in which the soil samples were incubated (set to 12ºC) |
week |
Numerical | Sampling intervals in weeks |
week_fac |
Categorical | Sampling intervals in weeks |
| Category | Levels | Description | Unit |
|---|---|---|---|
assay |
plate |
Total plate count | log10 Colony-Forming Units (CFU)/g |
tcid50 |
50% Tissue Culture Infectious Dose (TCID50) | log10 TCID50/g | |
pcr |
RNase RT-qPCR | log10 Genome Copies (GC)/g | |
matrix |
p |
Soil without decaying plant materials, served as control | - |
ps |
Soil with decaying plant materials | - | |
microbe |
ec |
Enteric bacteria: Escherichia coli TVS 353 | - |
nv |
Enteric virus: Human norovirus GII (HuNoV GII) | - | |
tv |
Enteric virus: Tulane virus (a surrogate for human norovirus) | - |