Research Project: Improving Pre-harvest Produce Safety through Reduction of Pathogen Levels in Agricultural Environments and Development and Validation of Farm-Scale Microbial Quality Model for Irrigation Water Sources

Location: Environmental Microbial & Food Safety Laboratory

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Zero-valent iron and sand filtration reduces levels of Cyclospora cayetanensis surrogates,Eimeria tenella and acervulina, in water - (Peer Reviewed Journal)

Estimating concentrations of Escherichia coli across a farm pond from the sUAS-based RGB imagery and water quality variables with machine learning techniques - (Peer Reviewed Journal)
Hong, S., Morgan, B.J., Stocker, M.D., Smith, J.E., Kim, M.S., Cho, K., Pachepsky, Y.A. 2024. Estimating concentrations of Escherichia coli across a farm pond from the sUAS-based RGB imagery and water quality variables with machine learning techniques. Water Research. 260: Article e121861. https://doi.org/10.1016/j.watres.2024.121861.

On composite sampling for monitoring generic and antibiotic-resistant coliforms in irrigation ponds - (Peer Reviewed Journal)
Stocker, M.D., Smith, J., Pachepsky, Y.A. 2024. On composite sampling for monitoring generic and antibiotic-resistant coliforms in irrigation ponds. Frontiers in Water. 6. Article e1397630. https://doi.org/10.3389/frwa.2024.1397630.

An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: a systematic review - (Peer Reviewed Journal)
Mcconn, B.R., Kraft, A.L., Durso, L.M., Ibekwe, A.M., Frye, J.G., Wells, J., Tobey, E.M., Ritchie, S.M., Williams, C.F., Cook, K.L., Sharma, M. 2024. An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: a systematic review. Science of the Total Environment. 927. Article 172190. https://doi.org/10.1016/j.scitotenv.2024.172190.

Effects of sampling time and depth on phytoplankton metrics in irrigation ponds - (Peer Reviewed Journal)
Smith, J., Stocker, M.D., Wolny, J., Pachepsky, Y.A. 2024. Effects of sampling time and depth on phytoplankton metrics in irrigation ponds. Journal of Phycology. 11(4): Article e74. https://doi.org/10.3390/environments11040074.

Fine-scale spatiotemporal variations in bacterial community diversity in agricultural pond water - (Peer Reviewed Journal)
Stocker, M.D., Smith, J.E., Pachepsky, Y.A., Blaustein, R.A. 2024. Fine-scale spatiotemporal variations in bacterial community diversity in agricultural pond water. Applied and Environmental Microbiology. 915: Article e170143. https://doi.org/10.1016/j.scitotenv.2024.170143.

Estimating osmotic pressure in soil solutions of saline soils to evaluate the salinity effect on crop yields - (Peer Reviewed Journal)
Pachepsky, Y.A., Yakirevich, A., Ponizovsky, A., Gummatov, N. 2023. Estimating osmotic pressure in soil solutions of saline soils to evaluate the salinity effect on crop yields. Geoderma. 23(4); article e20299. https://doi.org/10.1002/vzj2.20299.

A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories - (Peer Reviewed Journal)
Kraft, A., Wells, J., Frye, J.G., Ibekwe, A.M., Durso, L.M., Hiott, L.M., East, C.L., McConn, B., Franklin, A.M., Boczek, L.A., Garland, J.L., Kabrera, C., McDermott, P., Ottesen, A.R., Zheng, J., Cook, K.L., Sharma, M. 2023. A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2023.167189.

Autonomous calibration of EFDC for predicting chlorophyll-a using reinforcement learning and a real-time monitoring system - (Peer Reviewed Journal)
Hong, S., Abbas, A., Kim, S., Kwon, D., Yoon, N., Yun, D., Lee, S., Pachepsky, Y.A., Pyo, J., Cho, K. 2023. Autonomous calibration of EFDC for predicting chlorophyll-a using reinforcement learning and a real-time monitoring system . Journal of Environmental Modeling and Software. 168. Article e105805. https://doi.org/10.1016/j.envsoft.2023.105805.

Biochar and zero-valent iron sand filtration simultaneously remove contaminants of emerging concern and Escherichia coli from wastewater effluent - (Peer Reviewed Journal)
Zhu, L., Chattopadhay, S., Akanbi, O.E., Lobo, S., Panthi, S., Malayil, L., Craddock, H., Allard, S.M., Sharma, M., Mongodin, E.F., Chiu, P.C., Sapkota, A., Sapkota, A.R. 2023. Biochar and zero-valent iron sand filtration simultaneously remove contaminants of emerging concern and Escherichia coli from wastewater effluent. Biochar . 5:41. https://doi.org/10.1007/s42773-023-00240-y.

Spatial variation of tetracycline-resistant E. coli and relationships with water quality variables in irrigation water: A pilot study - (Peer Reviewed Journal)
Stocker, M.D., Smith, J., Pachepsky, Y.A. 2023. Spatial variation of tetracycline-resistant E. coli and relationships with water quality variables in irrigation water: A pilot study. Journal of Applied Microbiology. 3(2):504-518. https://doi.org/10.3390/applmicrobiol3020036.

Coupled dynamics of fecal indicator bacteria in sandy sediments and the water column: a three-year high-frequency study at a Pennsylvania creek - (Peer Reviewed Journal)
Pachepsky, Y.A., Harriger, D.M., Panko Graff, C., Stocker, M.D., Smith, J.E. 2023. Coupled dynamics of fecal indicator bacteria in sandy sediments and the water column: a three-year high-frequency study at a Pennsylvania creek. Water, Air, and Soil Pollution. 234:398. https://doi.org/10.1007/s11270-023-06371-z.

Temporal stability of Salmonella enterica and Listeria monocytogenes in surface waters used for irrigation in the Mid-Atlantic United States - (Peer Reviewed Journal)
Kim, S., Pachepsky, Y.A., Micallef, S., Rosenberg-Goldstein, R., Hashem, F., Parveen, S., Kniel, K., Sapkota, A., Sharma, M. 2023. Temporal stability of Salmonella enterica and Listeria monocytogenes in surface waters used for irrigation in the Mid-Atlantic United States. Journal of Food Protection. 86(4). Article 100058. https://doi.org/10.1016/j.jfp.2023.100058.

Estimating phytoplankton concentrations in agricultural irrigation ponds from water quality measurements: a machine learning application - (Peer Reviewed Journal)
Smith, J., Hill, R., Wolny, J., Stocker, M., Pachepsky, Y.A. 2022. Estimating phytoplankton concentrations in agricultural irrigation ponds from water quality measurements: a machine learning application. Journal of Phycology. 9(11):142.

Variations in bacterial diversity and antibiotic resistance genes across diverse recycled and surface waters used for irrigation in the Mid-Atlantic and Southwest United States: A CONSERVE two-year field study - (Peer Reviewed Journal)
Malayil, L., Ramachandran, P., Chattopadhyay, S., Allard, S.M., Bui, A., Butron, J., Callahan, M., Craddock, H., Murray, R., East, C.L., Sharma, M., Kniel, K.E., Micallef, S.A., Hashem, F., Gerba, C., Ravishankar, S., Parveen, S., May, E., Handy, E.T., Kulkarni, P., Anderson-Coughlin, B., Craighead, S., Gartley, S., Vanore, A., Duncan, R., Foust, D., Haymaker, J., Betancourt, W., Zhu, L., Mongodin, E., Sapkota, A., Sapkota, A.R. 2022. Variations in bacterial diversity and antibiotic resistance genes across diverse recycled and surface waters used for irrigation in the Mid-Atlantic and Southwest United States: A CONSERVE two-year field study. Journal of Environmental Science and Technology. https://doi.org/10.1021/acs.est.2c02281 .

Phage biocontrol for reducing bacterial foodborne pathogens in produce and other foods - (Review Article)
Vikram, A., Callahan, M.L., Woolston, J.W., Sharma, M., Sulakvelidze, A. 2022. Phage biocontrol for reducing bacterial foodborne pathogens in produce and other foods. Current Opinion in Biotechnology. 78. Article 102805. https://doi.org/10.1016/j.copbio.2022.102805.

Depth-dependent concentrations of E. coli in agricultural irrigation ponds - (Peer Reviewed Journal)
Stocker, M.D., Smith, J.E., Pachepsky, Y.A. 2022. Depth-dependent concentrations of E. coli in agricultural irrigation ponds. Water. 14(14):2276. https://doi.org/10.3390/w14142276.

Listeria monocytogenes in irrigation water: an assessment of outbreaks, sources, prevalence, and persistence - (Peer Reviewed Journal)
Gartley, S., Anderson-Coughlin, B., Sharma, M., Kniel, K.E. 2022. Listeria monocytogenes in irrigation water: an assessment of outbreaks, sources, prevalence, and persistence. Microorganisms. https://doi.org/10.3390/microorganisms10071319.

Escherichia coli phylogroup distribution and prevalence of extended spectrum ß-lactamase (ESBL) producers in U.S. Mid-Atlantic surface and reclaimed water - (Peer Reviewed Journal)
Solaiman, S., Handy, E., Brinks, T., Good, K., Bollinger, C., Sapkota, A.R., Sharma, M., Micallef, S.A. 2022. Escherichia coli phylogroup distribution and prevalence of extended spectrum ß-lactamase (ESBL) producers in U.S. Mid-Atlantic surface and reclaimed water. Environmental Microbiology. https://doi.org/10.1128/AEM.00837-22.

The effect of a first-flush rainwater harvesting irrigation system on E. coli and pathogen concentrations in irrigation water, soil, and produce - (Peer Reviewed Journal)
Morgado, M.E., Hudson, C.L., Chattopadhay, S., Ta, K., East, C.L., Purser, N., Allard, S., Ferrier, D.M., Sapokata, A.R., Sharma, M., Rosenburg-Goldstien, R. 2022. The effect of a first-flush rainwater harvesting irrigation system on E. coli and pathogen concentrations in irrigation water, soil, and produce. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2022.156976.

Machine learning in vadose zone hydrology: a flashback - (Peer Reviewed Journal)
Ghanbaian, B., Pachepsky, Y.A. 2022. Machine learning in vadose zone hydrology: a flashback. Vadose Zone Journal. https://doi.org/10.1002/vzj2.20212.

Hierarchical deep learning model to simulate phytoplankton at phylum/class and genus levels and zooplankton at the genus level - (Peer Reviewed Journal)
Baek, S., Eun-Jung, Y., Pyo, J., Pachepsky, Y.A., Son, H., Cho, K. 2022. Hierarchical deep learning model to simulate phytoplankton at phylum/class and genus levels and zooplankton at the genus level. Water Research. https://doi.org/10.1016/j.watres.2022.118494.

Intra-daily variation of E. coli concentrations in agricultural irrigation ponds - (Peer Reviewed Journal)
Stocker, M., Smith, J., Hill, R., Pachepsky, Y.A. 2022. Intra-daily variation of E. coli concentrations in agricultural irrigation ponds. Journal of Environmental Quality. https://doi.org/10.1002/jeq2.20352.

AI4Water v1.0: an open-source python package for modeling hydrological time series using data-driven methods - (Peer Reviewed Journal)
Pyo, J., Pachepsky, Y.A., Kim, S., Abbas, A., Kim, M., Kwon, J., Ligaray, M., Cho, K. 2022. AI4Water v1.0: an open-source python package for modeling hydrological time series using data-driven methods. Geoscientific Model Development. 15(7):3021-3039.

Correcting coordinate-measurement mismatch of on-the-go field measurements by optimizing nearest neighbor statistics - (Peer Reviewed Journal)
Gonzalez Jimenez, A., Pachepsky, Y.A., Gomez Flores, J., Ramons Rodriguez, M., Vanderlinden, K. 2022. Correcting coordinate-measurement mismatch of on-the-go field measurements by optimizing nearest neighbor statistics. Sensors. 22(4):1496. https://doi.org/10.3390/s22041496.