Food Safety Research Information Office
Title:Pathogen Fate and Transport in Irrigation Waters
Objective:

Objective 1: Elucidate and quantify mechanisms and factors of pathogen and indicator bacteria fate and transport from animal sources to irrigation waters. Evaluate the effects of soil and vegetation properties on parameters of pathogen fate and transport with surface runoff to irrigation water sources. Assess contribution of bottom sediments as potential pathogen reservoirs in agricultural landscapes. Research the fate and transport of pathogen and indicator bacteria in irrigation water delivery systems.

Objective 2: Develop models and computer-based tools to recommend and implement site-specific diagnostics, monitoring, and prediction of the fate and transport of pathogen and indicator bacteria that affect the microbiological condition of irrigation water. Develop bacteria fate and transport components for USDA-ARS hydrologic models to simulate the effect of bottom sediments, periphyton, and bank soils on microbiological quality of surface waters intended for irrigation. Develop a farm-scale irrigation system model that will use site specific environmental and management data to provide input data for quantitative microbial risk assessment of irrigation waters.

More Info:
Approach: An integrated approach including laboratory research, field research on irrigation systems, and mathematical modeling will be used. Experiments and monitoring will be carried out to (a) evaluate the effects of soil and vegetation properties on pathogen fate and transport with surface runoff to irrigation water sources, (b) understand and quantify pathogen and indicator bacteria fate in potential pathogen reservoirs associated with irrigation systems, such as bottom sediments in surface waters, and biofilms in irrigation equipment, and (b) microbial exchange between these reservoirs and flowing or stagnant waters. Mechanistic models will be developed to allow for (a) analyzing possible changes in pathogen and indicator bacteria concentrations along hydrologic pathways from animal sources to fields, and (b) improving resource allocation to monitor pathogen and indicator bacteria occurrence along the pathways.
Funding Source:United States Department of Agriculture (USDA), Agricultural Research Service (ARS)
Type:Appropriated
Start Date:2011
End Date:2016
Project Number:1245-12630-008-00
Accession Number:421065
Institutions:USDA/ARS - Beltsville Area Research Center
Investigators:Pachepsky , Yakov
Shelton, Daniel
Project Reports:2013 Annual Report
2012 Annual Report
2011 Annual Report
Published Journal
Articles USDA
ARS (NP 108):
Temporal stability of soil water content as affected by climate and soil hydraulic properties: a simulation study
Martinez G, Pachepsky YA, Vereecken H.
Hydrol Process. 2014 Feb;28(4):1899-915.
Evaluating manure release parameters for nonpoint contaminant transport model KINEROS2/STWIR
Guber A, Pachepsky YA, Dao TH, Shelton DR, Sadeghi AM .
Ecol Model. 2013 Aug 10;263:126-38.
Modeling transport of Escherichia coli in a creek during and after artificial high-flow events: three-year study and analysis
Yakirevich A, Pachepsky YA, Guber AK, Gish TJ, Shelton DR, Cho KH.
Water Res. 2013 May 15;47(8):2676-88.
Using the Q10 model to simulate E. coli survival in cowpats on grazing lands
Martinez G, Pachepsky YA, Shelton DR, Whelan G, Zepp R, Molina M, Panhorst K.
Environ Int. 2013 Apr;54:1-10.
Modeling local control effects on the temporal stability of soil water content
Martinez G, Pachepsky YA, Vereecken H, Hardelauf H, Herbst M, Vanderlinden K.
J Hydrol. 2013 Feb 25;481:106-18.
Escherichia coli survival in waters: temperature dependence
Blaustein RA, Pachepsky Y, Hill RL, Shelton DR, Whelan G.
Water Res. 2013 Feb 1;47(2):569-78.
The modified SWAT model for predicting fecal coliforms in the Wachusett Reservoir Watershed, USA
Cho KH, Pachepsky YA, Kim JH, Kim JW, Park MH.
Water Res. 2012 Oct 1;46(15):4750-60.
Persistence of Escherichia coli introduced into streambed sediments with goose, deer and bovine animal waste
Kiefer LA, Shelton DR, Pachepsky Y, Blaustein R, Santin-Duran M.
Lett Appl Microbiol. 2012 Sep 7;55(5):345-53.
Single collector attachment efficiency of colloid capture by a cylindrical collector in laminar overland flow
Wu L, Gao B, Muñoz-Carpena R, Pachepsky YA.
Environ Sci Technol. 2012 Aug 21;46(16):8878-86.
Coliform retention and release in biofilms formed on new and weathered irrigation pipes
Shelton DR, Kiefer LA, Pachepsky YA, Blaustein RA, Martinez G.
Irrig Sci. 2012 Aug 5;31:971-81.
Quasi 3D modeling of water flow in vadose zone and groundwater
Kuznetsov M, Yakirevich A, Pachepsky YA, Sorek S, Weisbrod N.
J Hydrol. 2012 Jul 11;450-451:140-9.
Temporal Stability of Soil Water Contents: A Review of Data and Analyses
Vanderlinden K, Vereecken H, Hardelauf H, Herbst M, Martinez G, Cosh MH, Pachepsky YA.
Vadose Zone J. 2012 Jun 6;11(4):1-19.
Estimating Topsoil Water Content of Clay Soils With Data From Time-Lapse Electrical Conductivity Surveys
Garcia GM, Vanderlinden K, Pachepsky Y, Cervera JVG, Perez AJE.
Soil Sci. 2012 Jun;177(6):369-76.
Data assimilation with soil water content sensors and pedotransfer functions in soil water flow modeling
Pan F, Pachepsky Y, Jacques D, Guber A, Hill RL.
Soil Sci Soc Am J. 2012 May;76(3):829-44.
Scale effects on information theory-based measures applied to streamflow patterns in two rural watersheds
Pan F, Pachepsky YA, Guber AK, McPherson BJ, Hill RL.
J Hydrol. 2012 Jan 11;414-415:99-107.
Detection of E. coli O157:H7 by immunomagnetic separation coupled with fluorescence immunoassay
Zhu P, Shelton DR, Li S, Adams DL, Karns JS, Amstutz P, Tang CM.
Biosens Bioelectron. 2011 Dec 15;30(1):337-41.
Kirkham’s legacy and contemporary challenges in soil physics research
Jury WA, Or D, Pachepsky Y, Vereecken H, Hopmans JW, Ahuja LR, Clothier BE, Bristow KL, Kluitenberg GJ, Moldrup P, Simunek J, van Genuchten MTh, Horton R.
Soil Sci Soc Am J. 2011 Sep;75(5):1589-601.
Non-journal publications:
Comparing dependencies of E. coli, Salmonella, and Enterococci survival on temperature in surface waters - (Abstract Only)
Blaustein, R.A., Pachepsky, Y.A., Hill, R., Whelan, G., Shelton, D.R. 2013. Comparing dependencies of E. coli, Salmonella, and Enterococci survival on temperature in surface waters. BARC Poster Day.
Developing new bacteria subroutines in the SWAT model - (Abstract Only)
Accepted Publication (04-Mar-13)
Integrating model abstraction into monitoring strategies - (Government Publication)
Accepted Publication (20-Feb-13)
SSDA code to apply data assimilation in soil water flow modeling: Documentation and user manual - (Government Publication)
Martinez, G., Feng, P., Pachepsky, Y.A. 2013. SSDA code to apply data assimilation in soil water flow modeling: Documentation and user manual. Software and User Manual Public Release. Available: http://www.ars.usda.gov/research/docs.htm?docid=23018.
On the effect of soil hydraulic properties on the relationship between spatial variation and spatial mean of soil water contents - (Abstract Only)
Martinez, G., Pachepsky, Y.A., Vereecken, H. 2013. On the effect of soil hydraulic properties on the relationship between spatial variation and spatial mean of soil water contents. [abstract] European Geophysical Society; American Geophysical Union; European Union of Geosciences. Vol 15.
Survival and release of animal waste-borne E. Coli in field conditions - (Abstract Only)
Martinez, G., Pachepsky, Y.A., Shelton, D.R., Whelan, G., Molina, M., Zepp, R., Jeong, J., Williams, J. 2012. Survival and release of animal waste-borne E. Coli in field conditions. [abstract]. Paper No. 83-2.
The arrhenius equation as means to simulate E. Coli survival in waters - (Abstract Only)
Blaustein, R., Pachepsky, Y.A., Hill Robert, Whelan, G., Molina, M., Zepp, R., Sadeghi, A.M. 2012. The arrhenius equation as means to simulate E. Coli survival in waters. [abstract]. Paper No. 357-3.
Modeling E. Coli release and transport in a creek during artificial high-flow events - (Abstract Only)
Yakirevich, A., Pachepsky, Y.A., Gish, T.J., Gho, K., Kuznetsov, M. 2012. Modeling E. Coli release and transport in a creek during artificial high-flow events. [abstract].
How can climate, soil, and monitoring schedule affect temporal stability of soil water contents - (Abstract Only)
Martinez, G., Pachepsky, Y.A., Vereecken, H. 2012. How can climate, soil, and monitoring schedule affect temporal stability of soil water contents. [abstract].
Applying model abstraction techniques to optimize monitoring networks for detecting subsurface contaminant transport - (Abstract Only)
Pachepsky, Y.A., Guber, A., Gish, T.J., Yakirevich, A., Nicholson, T., Cady, R. 2012. Applying model abstraction techniques to optimize monitoring networks for detecting subsurface contaminant transport. [abstract].
Geophysics applications in critical zone science: emerging topics - (Abstract Only)
Pachepsky, Y.A., Martinez, G., Guber, A., Walthall, C.L., Vereecken, H. 2012. Geophysics applications in critical zone science: emerging topics. [abstract].
Ensemble modeling with pedotransfer functions in the hydropedological context - (Abstract Only)
Accepted Publication (29-May-12)
Temporal stability of soil water contents as affected by weather patterns: a simulation study. - (Abstract Only)
Martinez, G., Pachepsky, Y.A., Vereecken, H., Hardelauf, H., Herbst, M., Vaderlinden, K. 2012. Temporal stability of soil water contents as affected by weather patterns: a simulation study.[abstract]. Paper No.74041.
Environmental research to improve food safety - (Other)
Pachepsky, L., Pachepsky, Y.A., Shelton, D.R., Van Kessel, J.S. 2012. Environmental research to improve food safety. Internet Web Page. Available: www.ars.usda.gov/research/docs.htm?docid=22497
An information theory application to improve understanding of subsurface flow and transport conditions at the BARC OPE3 site - (Abstract Only)
Yakirevich, A., Gish, T.J., Pachepsky, Y.A., Guber, A.K., Cady, R., Nicholson, T. 2012. An information theory application to improve understanding of subsurface flow and transport conditions at the BARC OPE3 site. BARC Poster Day.
E. coli survival in waters: applicability of the Arrhenius equation - (Abstract Only)
Blaustein, R.A., Pachepsky, Y.A., Whelan, G., Hill, R., Shelton, D.R., Sadeghi, A.M. 2012. E. coli survival in waters: applicability of the Arrhenius equation. [abstract]. BARC Poster Day. p.14.
Survival and release of Escherichia coli in land-applied animal manure: models and parameters - (Abstract Only)
Martinez, G., Pachepsky, Y.A., Shelton, D.R., Dao, T.H., Whelan, G., Kim, K., Williams, J., Jaehak, J. 2012. Survival and release of Escherichia coli in land-applied animal manure: models and parameters. [abstract]. BARC Poster Day. p. 40.
Upscaling with data assimilation in soil hydrology - (Abstract Only)
Pachepsky, Y.A., Gish, T.J., Daughtry, C.S., Jacques, D., Cady, R., Nicholson, T. 2012. Upscaling with data assimilation in soil hydrology. [abstract]Proceedings of PEDOFRACT. p.13.
Biofilms in irrigation pipes affect the microbial quality of irrigation water - (Abstract Only)
Pachepsky, Y.A., Shelton, D.R. 2012. Biofilms in irrigation pipes affect the microbial quality of irrigation water [abstract] p. 13-14.
Parameter estimation and uncertainty in scaling KINEROS2 runoff parameters - (Abstract Only)
Kim, K., Whelan, G., Purucker, T., Cyterski, M., Marirosa, M., Gu, Y., Pachepsky, Y.A., Guber, A., Franklin, D.H. 2011. Parameter estimation and uncertainty in scaling KINEROS2 runoff parameters. [abstract]. Abstract book 1741B-1032.
Non-local controls on spatial and temporal variability of soil water content in heavy clay soils - (Abstract Only)
Vanderlinden, K., Pedrera-Parrilla, A., Martinez, G., Espejo, A., Giraldez, J., Pachepsky, Y.A. 2011. Non-local controls on spatial and temporal variability of soil water content in heavy clay soils. [abstract]. Abstract book 1731M-02.
Augmenting an observation network to facilitate flow and transport model discrimination. - (Abstract Only)
Pachepsky, Y.A., Kuznetsov, M., Guber, A., Yakirevich, A., Martinez, G., Gish, T.J., Cady, R., Nicholson, T. 2011. Augmenting an observation network to facilitate flow and transport model discrimination. [abstract]. American Geophysical Union. H23H-1372.
Estimating spatial variations in water content of clay soils from time-lapse electrical conductivity surveys - (Abstract Only)
Martinez, G., Pachepsky, Y.A., Vanderlinden, K., Giraldez, J. 2011. Estimating spatial variations in water content of clay soils from time-lapse electrical conductivity surveys. [abstract]. Abstract book. H42F-05.
Is it enough to have one ECa map for the site-specific management delineation? - (Abstract Only)
Martinez, G., Pachepsky, Y.A., Vanderlinden, K., Giraldez, J. 2011. Is it enough to have one ECa map for the site-specific management delineation?. ASA-CSSA-SSSA Proceedings. Paper No. 67335.
Using passive capillary lysimeter water flux measurements to improve flow predictions in variably saturated soils. - (Abstract Only)
Pachepsky, Y.A., Guber, A.K., Diederik, J., Van Genuchten, M., Cady, R., Nicholson, T. 2011. Using passive capillary lysimeter water flux measurements to improve flow predictions in variably saturated soils.[abstract] ASA-CSSA-SSSA Annual Meeting Abstracts. Paper No. 67149.
Status of the database on microorganism inactivation in environmental media (DIMEM) - (Abstract Only)
Bolster, C.H., Pachepsky, Y.A., Sadeghi, A.M., Shelton, D.R. 2011. Status of the database on microorganism inactivation in environmental media (DIMEM) [abstract]. ASA-CSSA-SSSA Annual Meeting Abstracts. Paper No. 67154.
Modeling rainfall-induced release of manure constituents from surface-applied liquid dairy manure - (Abstract Only)
Guber, A.K., Pachepsky, Y.A., Shelton, D.R. 2011. Modeling rainfall-induced release of manure constituents from surface-applied liquid dairy manure. [abstract]. ASA-CSSA-SSSA Annual Meeting. Paper No. 67329.
Irrigation waters as a source of pathogenic microorganisms in produce: a review Reprint Icon - (Review Article)
Pachepsky, Y.A., Shelton, D.R., Mclain, J.E., Patel, J.R., Mandrell, R.E. 2011. Irrigation waters as a source of pathogenic microorganisms in produce: a review. Advances in Agronomy. 113:73-138.
Ultra-sensitive detection using integrated waveguide technologies - (Book / Chapter)
Li, S., Kiefer, L., Zhu, P., Shelton, D.R., Amstutz, P., Tang, C. 2011. Ultra-sensitive detection using integrated waveguide technologies. In: Somerset, V. Environmental Biosensors. Rijeka, Croatia: InTech. p.305-313.
Measurement challenges of detecting enteric organisms in food and water - (Abstract Only)
Shelton, D.R. 2011. Measurement challenges of detecting enteric organisms in food and water. [abstract].
Pilot study of the effect of biofilms in irrigation pipes on the microbial water quality of irrigation water - (Abstract Only)
Davies, G.E., Downey, A., Guber, A.K., Morrow, J., Pachepsky, Y.A., Rowland, R.A., Shelton, D.R. 2011. Pilot study of the effect of biofilms in irrigation pipes on the microbial water quality of irrigation water. BARC Poster Day. #10.
Information and complexity measures for hydrologic model evaluation - (Abstract Only)
Pan, F., Wagener, T., Pachepsky, Y.A., Hill, R. 2011. Information and complexity measures for hydrologic model evaluation. BARC Poster Day. 39.
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