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United States Department of Agriculture

Agricultural Research Service

Research Project: Protection of Food and Water Supplies from Pathogen Contamination
2011 Annual Report


1a.Objectives (from AD-416)
Determine the relationships between manure management and populations of human pathogens and antibiotic resistant bacteria (ARB) that result in new recommendations for best management practices (BMPs); Develop effective methods and practices to protect crops from pathogen contamination; Develop management practices to minimize the transport of pathogens (e.g. E. coli O157:H7, Cryptosporidium, enterococcus, Salmonella) from concentrated dairy and beef cattle operations to water resources.


1b.Approach (from AD-416)
Conduct laboratory and field experiments to examine the important biological, chemical, and physical processes affecting the prevalence and distribution of pathogenic and antibiotic resistant bacteria on representative farms in the Santa Ana River watershed. Studies will be conducted at various scales to determine the persistence (survival) of E. coli O157:H7 in its sources on these farms and assess potential factors influencing pathogen survival in the root zone and contamination of leafy greens. Laboratory scale study will be conducted to quantify critical processes influencing the dissemination of pathogens in the watershed by runoff, streams and rivers. Factors influencing the treatment of contaminated surface waters by sand filtration will also be investigated to more fully assess its capabilities and potential weaknesses. Data obtained from these studies will be used to develop best management practices (BMPs) and low cost treatment technologies for immobilization and inactivation of pathogens from concentrated animal feeding operations (CAFOs) to water and food resources.


3.Progress Report
Objective 1 a/b: We have initiated studies to assess prevalence, distribution, and antibiotic resistance of pathogenic and generic E. coli strains on a representative farm with a university collaborator. Comprehensive information on the E. coli strains will be collected from this farm for a period of 24 months to fully assess in situ characteristics. We have also identified locations for in situ survival studies of E. coli O15:H7 on this farm using sentinel chambers.

Objective 2a: Survival of E. coli O157:H7 was studied in organic and conventional soils of produce growing areas of California and Arizona to determine stress levels under salinity conditions before plants are introduced. Principal component analysis, artificial neural network analysis, stepwise regression analysis, and topological data analysis showed that overall survival of E. coli O157:H7 in soils were strongly affected by salinity, water soluble organic carbon, and total nitrogen with salinity being the dominant factor. Survival of E. coli O157:H7 in all soils decreased significantly with moderate to high salinity and in a laboratory experiment with soils spiked with increasing salts concentrations, the survival time decreased with increasing salinity levels. Further analysis confirmed that high concentrations of sodium in soil water extracts significantly decreased the survival of E. coli O157:H7 especially in conventional soils.

Objective 2B: An overland flow chamber (3 m long, 15 cm high, and 18 cm wide) was designed to study pathogen transport with runoff water. Preliminary transport studies using a conservative tracer (bromide) and E. coli O157:H7 will help to refine experimental protocols. Studies have been initiated to examine the influence of solution chemistry on the transport and release of E. coli O157:H7 in runoff water. A model has been developed to simulate water flow and pathogen transport in overland flow and in variably saturated soils under a wide range of conditions and is being used to examine: (1) the influence of the surface mixing zone, surface topography, and depression storage on pathogen removal; (2) the interactions of surface and subsurface water flow on pathogen transport; (3) the influence of pathogen size; and (4) and the role of pathogen retention parameters. Preliminary modeling results reveal that pathogen removal from runoff water is controlled by exchange with the soil which is a function of soil texture and structure, and surface topography. Results from these studies are expected aid in the design of vegetative buffer strips for removing pathogens.

Objective 2D: We have coupled the dual permeability pathogen transport model described in the accomplishment section below to solution ionic strength (IS). The relevant retention model parameters (sticking efficiency, maximum retention capacity, and release rate) are continuously updated at each time step to reflect differences in solution IS. We successfully developed theory and used this model to simulate previously measured colloid and microorganism (E. coli D21 g and coliphage fX174) release behavior with transients in IS. A manuscript is in preparation on this topic.


4.Accomplishments
1. Public health officials use E. coli bacteria as an indicator of water quality. E. coli from human sources are more diverse and carry more multiple resistances to different antibiotics than E. coli from animal sources (dairy). This research was conducted at the USDA-ARS-U.S Salinity laboratory in Riverside to investigate prevalence, genetic diversity and antimicrobial susceptibility of E. coli isolates obtained from surface water and sediment along the middle Santa Ana River watershed of southern California, USA. This was accomplished through the analysis of 600 E. coli isolates collected from human and animal sources throughout the watershed. The occurrence of greater numbers of E. coli with multiple antibiotic resistances from urban runoff sources than agricultural sources in this watershed provides useful evidence in planning strategies for water quality management and public health protection.

2. Mathematical model for pathogen transport and retention developed. Existing mathematical models to simulate the movement of pathogens through agricultural soils and groundwater do not provide reliable predictions even under relatively simple, well defined conditions. Researchers at the USDA-ARS-US Salinity and the University of California in Riverside have developed a mathematical model for pathogen transport and retention that accounts for observed trends in pathogen and soil size, velocity, chemical interactions, and concentration. Our approach considers pathogen transport in the bulk water and adjacent to the soil surface, and pathogen retention on only a fraction of the solid surface. The model provides a clear conceptual explanation for many incompletely understood observations of pathogen transport and retention in soils, and helps to identify areas where additional research and theory development are still needed. This information will be of interest to scientists and engineers concerned with predicting the fate of pathogens in soils and aquifers.


Review Publications
Bradford, S.A., Kim, H.K. 2010. Implications of cation exchange on clay release and colloid-facilitated transport in porous media. Journal of Environmental Quality. 39(6):2040-2046.

Bradford, S.A., Torkzaban, S., Wiegmann, A. 2011. Pore-scale simulations to determine the applied hydrodynamic torque and colloid immobilization. Vadose Zone Journal. 10:252-261.

Ibekwe, A.M., Papiernik, S.K., Grieve, C.M., Yang, C. 2010. Quantification of persistence of Escherichia coli O157:H7 in contrasting soils. Internationl Journal of Microbiology. Available: http://www.hindawi.com/journals/ijmb/2011/421379.html.

Ma, J., Ibekwe, A.M., Yi, X., Wang, H., Yamazaki, A., Crowley, D.E., Yang, C. 2011. Persistence of escherichia coli O157:H7 and its mutants in soils. PLoS One. 6(8):1-8.

Zeng, Q., Ibekwe, A.M., Biddle, E., Yang, C.H. 2010. Regulatory mechanisms of exoribonuclease PNPase and regulatory small RNA on T3SS of dickeya dadantii. Molecular Plant-Microbe Interactions. 23(10):1345-1355.

Last Modified: 4/18/2014
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