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United States Department of Agriculture

Agricultural Research Service

Research Project: Protection of Food and Water Supplies from Pathogen Contamination
2013 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. Replaces 5310-32000-002-00D (1/11).


3.Progress Report:
Substantial progress was made on all of the objectives during this reporting period. Data on contamination of surface waters in a large urban watershed are limited due to the complexity of sources and different contaminants and their by-products. Using two polymerase chain reaction methods, the relationships between manure management and populations of fecal enterococci and E. coli into the Santa Ana River were determined, and the data were correlated with the presence of 16 antibiotics, their resistant genes and the presence of multiply resistant genes (Objective 1A). Further analysis of resistant gene pattern indicated that the most resistant genes were dominated in sources from urban or agricultural environment. A follow up study was done to determine the population structure of E. coli from manure storage through a surface flow constructed wetland (Objective 1B). E. coli was enumerated, characterized, and typed from samples collected from manure storage throughout the different sections of the wetland, and to the final effluent. The presence of E.coli O157 was also monitored throughout the process and the data showed that most of the E. coli strains were without the Shiga toxin genes, but with high distribution of resistant phenotypes. Studies were done to compare the persistence of E. coli O157:H7 and non O157 in preharvest environment collected from three major fresh produce growing areas (Objective 2A). Results showed that the nonpathogenic E. coli O157:H7 4554 survived longer than the pathogenic E. coli O157:H7 EDL933 in all soil tested from the three regions. Also, two non O157 (E. coli O26:H21 and E. coli O103:H2) survived significantly longer than E. coli O157:H7. Additional experiments and analysis were performed to investigate the influence of solution chemistry on the transport, retention, and release of E.coli D21g and coliphage fX174 in runoff water (Objective 2B). The transport and release of microbes were demonstrated to be sensitive to the solution chemistry. Significant amounts of E.coli D21g were released in runoff when the ionic strength (IS) was reduced, and this release was strongly correlated with the solution optical density (e.g., sediment content). However, addition of small amounts of calcium to the soil significantly reduced the release of E.coli D21g with a reduction in IS. Research was conducted to improve our understanding of blocking/filling processes during pathogen retention and to better understand mechanisms of pathogen retention (Objective 2D). In particular, an improved modeling approach was developed to determine the fraction of the solid surface area that contributes to pathogen retention on heterogeneous surfaces. This information is needed to predict blocking behavior. In this theoretical model we use colloids as a surrogate for microbes, and simulation results demonstrate that attachment is more important for higher solution IS, for more flexible colloids, for greater variations in surface charge, and for smaller colloids and water velocities. Conversely, straining at roughness locations and grain-grain contacts will be more important for the opposite conditions.


4.Accomplishments
1. Application of deep sequencing technology on survival of E. coli O157:H7. To determine the survival of E. coli O157:H7 in soils from California and Arizona, ARS Researchers at Riverside, California, correlated the survival time of E. coli O157:H7 in soils with deep sequencing based bacterial community composition. Kohonen self-organizing map of survival and associated soil chemical, physical and biological variables using artificial neural network analysis showed that survival of E. coli O157:H7 in soils was negatively correlated with salinity, but positively correlated with total nitrogen and water soluble organic carbon. Bacterial diversity as determined by the Shannon diversity index had no significant effect on survival, but individual bacterial groups had different effects. The survival of E. coli O157:H7 was positively correlated with the abundances of two major bacterial groups (Actinobacteria and Acidobacteria), and negatively correlated with another two groups (Proteobacteria and Bacteroidetes). Our data showed that specific groups of bacteria may impact the persistence of E. coli O157:H7 in soils, thus opening new ways to study the influence of certain bacterial groups on survival of this pathogen and other related pathogens in complex environments. This information will be of interest to scientists and growers who are concerned with food safety.

2. Microbial interaction energies on physically and chemically heterogeneous porous media. Microbial interactions with porous media play a critical role in determining their environmental transport and fate, and small scale variations in roughness and/or charge on the microbe or soil are known to influence these interactions. Colloids and microbes with similar shape, roughness, and charge characteristic have the same interactions. We therefore use colloids as a proxy for microbes and predict their interactions in heterogeneous porous media. Simulation results demonstrate that roughness and variations in charge can enhance colloid interactions and retention, in comparison to uniform surfaces. The interactions were found to be strong functions of the solution chemistry and the colloid size. The findings from this study will be of interest to scientists and engineers concerned with predicting the fate of microbes, colloids, and nanoparticles in environmental and industrial applications.


Review Publications
Bradford, S.A., Morales, V.L., Zhang, W., Harvey, R.W., Packman, A.I., Mohanram, A., Welty, C. 2013. Transport and fate of microbial pathogens in agricultural settings. Critical Reviews in Environmental Science Technology. 43(8):775-893.

Ma, J., Ibekwe, A.M., Crowley, D.E., Yang, C-H. 2012. Persistence of Escherichia coli O157:H7 in major leafy green producing soils. Environmental Science and Technology. 46:12154-12161.

Harris, L.J., Bihn, E.A., Bender, J., Blessington, T., Danyluk, M.D., Delaquis, P., Ibekwe, A.M., Goodridge, L., Ilic, S., Kniel, K., Lejeune, J.T., Schaffner, D., Stoeckel, D., Suslow, T. 2012. A framework for developing research protocols for evaluation of microbial hazards and controls during production that pertain to the quality of agricultural water contacting fresh produce that may be consumed raw. Journal of Food Protection. 75(12):2251-2273.

Bradford, S.A., Torkzaban, S. 2013. Colloid interaction energies for physically and chemically heterogeneous porous media. Langmuir. 29(11):3668-3676.

Bradford, S.A., Torkzaban, S., Kim, H., Simunek, J. 2012. Modeling colloid and microorganism transport and release with transients in solution ionic strength. Water Resources Research. doi:10.1029/2012WR012468.

Bradford, S.A., Torkzaban, S. 2012. Colloid adhesive parameters for chemical heterogeneous porous media. Langmuir. 28:13643-13651.

Bradford, S.A., Torkzaban, S., Shapiro, A. 2013. A theoretical analysis of colloid attachment and straining in chemically heterogeneous porous media. Langmuir. 29:6944-6952.

Wang, Y., Bradford, S.A., Simunek, J. 2013. Transport and fate of microorganisms in soils with preferential flow under different solution chemistry conditions. Water Resources Research. doi:10.1002/wrcr.20174.

Ma, J., Ibekwe, A.M., Yang, C., Crowley, D.E. 2013. Influence of bacterial communities based on 454-pyrosequencing on the survival of Escherichia coli O157:H7 in soils. FEMS Microbiology Ecology. 84(3):542-554.

Last Modified: 7/23/2014
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