Progress 04/03/10 to 01/29/15
Outputs
Progress Report 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. 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. This is the final report for the project which was terminated in January of 2015. The next five year research plan will undergo Office of Scientific Quality Review in 2016. Please see the bridging project, 2036- 32000-004-00D, for further information. Over the 5 years of this project, substantial progress was made toward meeting the goals and objectives of NP214 (currently 212) Problem Area 1: Fate and Transport Characteristics of Animal and Zoonotic Pathogens from Animal Agriculture. This progress is evidenced by the substantial experimental, theoretical, field, growth chamber, laboratory, and modeling results realized over the 5 years of this project, and also by the publication list which includes over 65 peer reviewed publications and one invention disclosure. Research accomplishments encompassed a diversity of topics related to pathogens and/or antibiotics resistant bacteria and antibiotics resistance genes in the agro-environment, including: (1) Microbial transport, retention, and survival in the subsurface; (2) Microorganism release under steady-state and transient physicochemical and/or water saturation conditions; (3) Preferential transport of microbes; (4) Transport of microbes in runoff water and their exchange with the subsurface; (5) Identification of greater number of E. coli with multiple antibiotic resistance genes from urban runoff sources than agricultural sources; (6) Role of different bacterial phyla in soil on survival of E. coli O157; (7) Detection of Shiga Toxin-producing E. coli using Recombinase Polymerase Amplification. This research has resulted in new concepts and principles related to the movement and survival of pathogens in the vadose zone, in ground water systems, and in surface/runoff waters. New and more accurate descriptions of transport and fate processes have subsequently been developed and incorporated into mathematical models to reliably simulate pathogen and antibiotic resistant bacteria migration in soil and water systems at different scales, to assess risks, and to develop best management practices to protect food and drinking-water supplies. The detection method using Recombinase Polymerase Amplification has successfully demonstrated for the first time that this method could be used for real- time detection of 1 to 10 cells of E. coli O157 within 10 minutes, compared to several hours needed for polymerase chain reaction (PCR) detection. This has resulted in the filing of an invention disclosure and we believe that the commercial potential of our technology is high and is likely to be accepted by the produce industry and water utility agencies for point of use detection of Shiga Toxin producing E. coli. This technology will allow the produce industry to make informed decisions regarding the distribution and marketing of fresh produce throughout the country. The magnitude of the market will far exceed the costs of commercialization sufficient to warrant a patent, especially considering Recombinase Polymerase Amplification detection platform can easily be adapted to onsite detection of Shiga Toxin producing E. coli. This patent would allow the licensing and commercialization of the technology that in turn would provide farmers and water utility agencies access to a more precise mechanism to detect the presence of Shiga Toxin producing E. coli in minutes rather than in days, and determine the presence of this pathogen in their fields or processing facilities resulting in millions or billions of dollars saved by farmers.
Impacts
(N/A)
Publications
- Abakpa, G.O., Umoh, V.J., Ameh, J.B., Yakubu, S.E., Kwaga, J.K., Ibekwe, A. M. 2014. Occurrence of enteric pathogens on fresh produce grown on irrigated soils. British Microbiology Research Journal. 6(1):13-23.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report 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. 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. Substantial progress was made on all of the objectives during this reporting period. Data on contamination of surface waters by pathogens originating from farm/lagoon water are limited due to the complexity of different contaminants and low-abundance species. Current identification methods rely on culturing. Novel approaches for microbial pathogen detection from lagoon water and wetland effluent were accessed using next generation sequencing (Objective 1A, Objective 1B). The computer software and bioinformatics analyses facilitated the identification of pathogens and non-pathogens in lagoon water. The experiment produced very large datasets for monitoring and correlating the abundance and diversity of pathogens to environmental factors. Detection and quantification of microbial pathogens using next- generation sequencing is providing the fastest method to identify different bacterial pathogens without culturing. Three commercially available DNA extraction methods for identification and quantification of human bacterial pathogens (E. coli O157) and other microbial genera for water quality assessment using next generation sequencing platform and real-time polymerase chain reaction (PCR) were evaluated (Objective 2A). Significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same lagoon sample with different extraction kits were determined. The optimization of this assay has provided the first step in preparing high-quality DNA for pathogen identifications using next generation sequencing and accurate downstream bioinformatics analyses. Runoff has been reported to be the primary transport route for pathogen dissemination on hillslopes. Tracer and indicator microbe runoff experiments were conducted to investigate the influence of solution chemistry on the transport, retention, and release of E. coli D21g (Objective 2C). The runoff breakthrough curves (BTCs) for D21g were sensitive to the soil slope and the solution chemistry. Greater amounts of cell retention occurred for higher chamber slopes because of enhanced exchange with the soil, and at higher solution ionic strength (IS) because of an increase in the adhesive interaction with the soil. Retained cells were slowly released from the soil to the runoff water when the IS of the runoff water was reduced, especially at the highest chamber slope that had the greatest amount of retained cells. Pathogen release from soils and sediments depend on a wide variety of physical, chemical, and microbiological factors that change with time. Equilibrium, kinetic, combined equilibrium and kinetic, and two-site kinetic models of pathogen release during transient physicochemical conditions were developed (Objective 2D). The modeling approach relates pathogen release under transient conditions to changes in the fraction of the solid surface area that contributes to retention. The developed models were subsequently used to investigate the influence of variations in ionic strength (IS), pH, cation exchange, and water velocity on release of E. coli D21g. Collectively, experimental and modeling results indicate that episodic pathogen transport in the subsurface is expected because of transient conditions. Significant Activities that Support Special Target Populations: ARS scientists from Riverside, California, provided a presentation and laboratory tour on March 1, 2014, to student winners of the Riverside Unified School District science fair competition. Approximately 30 individuals (students and parents) attended, including women and minority groups. The presentation covered research activities and products developed at the U.S. Salinity Laboratory, as well as potential career opportunities in science fields. An ARS scientist from Riverside, California, is helping to mentor a woman PhD student from the Environmental Science Department and a Hispanic undergraduate student at the University of California, Riverside. An ARS scientist from Riverside, California, was elected incoming chair of The Diversity Committee in Agronomy which is committed to enhancing participation of underrepresented students and professionals in the Tri- Societies, thereby strengthening and diversifying the potential workforce in agricultural and environmental sciences and recruiting high school students into careers in agriculture and environmental sciences through the Gateway Scholars Program. An ARS scientist from Riverside, California, worked with faculty and students from California State Polytechnic University-Pomona (Hispanic serving institution) and California State Polytechnic � San Luis Obispo to obtain a National Institute of Food and Agriculture (NIFA) Agriculture and Food Research Initiative (AFRI) grant (CO-PI) and another as Co- Investigator from California State University Agricultural Research Initiative (ARI). Funds from this grant are used in part at California State Polytechnic University-Pomona to support two minority students whom the ARS scientist is mentoring. An ARS scientist from Riverside, California, worked with faculty and students from Tuskegee University to successfully get a manuscript published in a peer reviewed journal. Accomplishments 01 Preferential transport of E. coli D21. ARS researchers at Riverside, California, conducted laboratory and numerical studies to investigate the transport and fate of E. coli D21g in saturated soils with preferential flow paths (e.g., worm holes) under different solution chemistry conditions. The length and configuration of preferential flow pathways had a strong influence on the transport of D21g, especially when salts were present in water. A model that accounted for fast and slow flow rates in soil provided an accurate description of the observed preferential transport. An approach was developed to estimate and predict the effects of preferential transport in agricultural fields with different amounts and types of preferential flow. This method provided a satisfactory prediction of hypothetical field results under the tested cases. This information will help to quantify the risks of concentrated animal feeding operation waste (manure, runoff, wash water) in agricultural fields on groundwater quality. 02 Release of E. coli D21g from soil. ARS researchers at Riverside, California, investigated the release of E. coli D21g from soil under varying water saturation and solution chemistry conditions that commonly occur at the soil surface. Results demonstrate that D21g release and transport toward groundwater was highly sensitive to changes in water saturation and solution chemistry. The amount of bacteria released and transported through the soil strongly depended on the initial number of bacteria in the soil, the solution chemistry, and changes in the water saturation. Increased risks of microbial contamination from concentrated animal feeding operation waste (manure, runoff, washwater) to groundwater resources are expected as a result of changes in water saturation and solution chemistry in surface soils. 03 Detection of Shiga toxin producing Escherichia coli O157. Laboratory studies were conducted to investigate the detection of Shiga toxin producing Escherichia coli. ARS researchers at Riverside, California, along with collaborators from California Polytechnic University, Pomona, California designed and evaluated primers and probes for detection of Shiga toxin producing Escherichia coli at constant temperature. The assay detected Shiga toxin producing Escherichia coli in real-time (within 5-10 minutes) at 39 degrees C. Limits of detection of 5 to 50 colony forming units per milliliter were achieved in culture media and 100 to 1000 colony forming units per milliliter were obtained from manure lagoon samples. When fully optimized, the protocol could be used directly in the field and at the point-of-care for rapid real-time detection of pathogens.
Impacts
(N/A)
Publications
- Ibekwe, A.M., Leddy, M., Murinda, S.E. 2013. Potential human pathogenic bacteria in a mixed urban watershed as revealed by pyrosequencing. PLoS One. DOI: 10.1371/journal.pone.0079490.
- Wang, Y., Bradford, S.A., Simunek, J. 2014. Physicochemical factors influencing the preferential transport of Escherichia coli in soils. Vadose Zone Journal. DOI: 10.2136/vzj2013.07.0120.
- Wang, Y., Bradford, S.A., Simunek, J. 2014. Estimation and upscaling of dual-permeability model parameters for the transport of E.coli D21g in soils with preferential flow. Journal of Contaminant Hydrology. 159:57-66.
- Shange, R., Haugabrooks, E.M., Ankumah, R.O., Ibekwe, A.M., Smith, R.C., Dowd, S. 2013. Assessing the diversity and composition of bacterial communities across a wetland, transition, upland gradient in Macon County Alabama. Diversity. 5(3):461-478.
- Bradford, S.A., Wang, Y., Kim, H., Torkzaban, S., Simunek, J. 2014. Modeling microorganism transport and survival in the subsurface. Journal of Environmental Quality. 43(2):421-440.
- Wang, Y., Bradford, S.A., Simunek, J. 2014. Release of E.coli D21g with transients in water content. Journal of Environmental Science and Technology. 48:9349-9357.
- Murinda, S.E., Ibekwe, A.M., Zulkaffly, S., Cruz, A., Park, S., Razak, N., Paudzai, F.M., Ab Samad, L., Baquir, K., Muthaiyah, K., Santiago, B., Rusli, A., Balkcom, S. 2014. Real-time isothermal detection of Shiga toxin- producing Escherichia coli using recombinase polymerase amplification. Foodborne Pathogens and Disease. 11(7):529-536.
- Ma, J., Ibekwe, A.M., Crowley, D.E., Yang, C. 2014. Persistence of Escherichia coli O157 and non-O157 strains in agricultural soils. Science of the Total Environment. 490:822-829.
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Progress 10/01/12 to 09/30/13
Outputs
Progress Report 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. 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). 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. Significant Activities that Support Special Target Populations: ARS scientists from Riverside, California, provided a motivational talk to �Gateway Scholars� at the 2012 Annual meetings of the Tri-Societies (ASA, CSSA and SSSA) in Cincinnati. The goal was to introduce the next generation of scientists to different research areas and identify and motivate the future leaders in sciences. About 50 minority students and teachers from three schools, Withrow University High School; Woodward Career Technical High School; and Aiken College & Career High School, participated on October 23, 2012 during the Annual Meetings of ASA-CSSA- SSSA at Cincinnati. An ARS scientist from Riverside, California, served as a panelist during the �Careers for Life Science Majors� panel on 02/12/2013 during the University of California, Riverside (UCR) career day. A total of 59 students were present and 15 students stayed behind to discuss career opportunities in science field and in ARS. ARS scientists from Riverside, California, worked with the faculty and students from Tuskegee University to successfully get a manuscript submitted in a peer reviewed journal in July, 2013. An ARS scientist from Riverside, California, worked with one faculty and a minority Ph.D. student from the University of Wisconsin, Milwaukee for the successful completion of a Ph.D. in Biological Sciences �Cellullar Metabolism and its effect on the type III secretion system of Dickeya dadantii 3937�. ARS scientists from Riverside, California, provided a presentation and laboratory tour on March 2, 2013, to student winners of the Riverside Unified School District science fair competition. Approximately 30 individuals (students and parents) attended, including women and minority groups. The presentation covered research activities and products developed at the US Salinity Laboratory, as well as potential career opportunities in science fields. An ARS scientist from Riverside, California, served on the Math and Physical Science Career Panel at the University of California, Riverside, on February 11, 2013. Information about careers in ARS was distributed to 75 interested students (including women and minority groups) and a resume was forwarded to individuals involved in nanoparticle research. Accomplishments 01 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. 02 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.
Impacts
(N/A)
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.
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report 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. 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. Mathematical models to simulate the movement of pathogens through aquifers and soils frequently do not consider the significant influence of transients in solution ionic strength (IS) and velocity on pathogen fate. A sophisticated transport model was modified and theory was developed to mechanistically account for the transport, retention, and release of pathogens with transients in IS and velocity. The calibrated model provided a satisfactory description of the observed release behavior for a range of microbe types and sizes. Furthermore, analysis of fitted model parameters indicates that microscopic heterogeneities on the soil and/or microbe played an important role in pathogen interactions, especially for smaller sized microorganisms. This information will be of interest to scientists and engineers concerned with predicting the fate of pathogens in soils and aquifers. Data on E. coli O157:H7 persistence in major fresh produce-growing soils are limited due to the complexity in datasets generated from different environmental variables and bacterial taxa. Using the Ayasdi Iris platform, which employs Topological Data Analysis (TDA) methods, we have reconstructed the relationship structure of E. coli O157:H7 survival in 32 soils (16 organically, 16 conventionally managed soils) from California (CA) and Arizona (AZ) with a multi-resolution output. Here, we constructed our topological data using three E. coli O157, and three non- E. coli O157 strains to test their persistence in typical agricultural soils collected from 3 major fresh produce growing areas of California and Arizona. This information will be of interest to scientists and growers interested in understanding fate and survival of E. coli O157 and non-E. coli O157 in organically and conventionally managed soils. Significant Activities that Support Special Target Populations: Provided a presentation and laboratory tour to student winners of the Riverside Unified School District (RUSD) science fair competition, and served as a USDA mentor for the day to students from the Riverside Community College (RCC) in the Soil Science Management course (Biology 14) . This project is funded in part by a grant from USDA CSREES Hispanic Serving Institution Education Grants Program entitled �Building Bridges Across Riverside through Water Quality Research� by faculty at RCC and the University of California Riverside (UCR). The presentation and tour took place on February 25, 2012 at the US Salinity Laboratory. Approximately 35 people attended (20 RUSD students and parents, 10 RCC students and faculty, and 5 UCR graduate students and faculty). Worked with one faculty and one Ph.D. student from Tuskegee University to successfully get a manuscript published in peer reviewed journal in July, 2012 (see #11 of publications for this report). Accomplishments 01 Determining pathogen transport parameters on heterogeneous surfaces. Th transport and retention of pathogenic microorganisms are strongly influenced by small scale variations in charge on the surfaces of the so grains and microbes. A modeling approach was developed to predict pathog transport parameters on these heterogeneous surfaces. Simulation results demonstrate that microbe transport parameters are complex functions that are sensitive to the size, charge, and amount of heterogeneity on the surfaces, the microbe size, the solution chemistry, and the water veloci The findings from this study have important implications for predicting microbe transport and retention in soils and aquifers. This information will be of interest to scientists and engineers concerned with pathogen risk assessment and in the development of mitigation approaches. 02 Treatment and removal of contaminants by surface flow constructed wetlan To assess the impacts of seasonal variations and the mechanism of the wetland layout/operations on E. coli populations, we compared the geneti diversity and antibiotic resistance of the bacteria in a surface flow constructed wetlands used for treating swine waste. E. coli was enumerat and their genetic differences from samples collected from the swine hous source water, storage lagoon, storage tank, surface flow constructed wetland environment, and the final effluence using polymerase chain reaction and antibiotics resistant methods. None of the isolates were confirmed as pathogenic E. coli O157, but as other types of E. coli that are not as pathogenic as E. coli O157. Our data showed that most of the coli strains were without the toxin genes, but with high distribution of resistant genes. Therefore, the occurrence of E. coli with multiple resistances in the wetland is a matter of great concern due to possible transfer of resistant genes from nonpathogenic to pathogenic strains tha may result in increased duration and severity of illness. This informati will benefit water quality managers and scientists who are working on different best management strategies for water quality improvement.
Impacts
(N/A)
Publications
- Bradford, S.A., Torkzaban, S., Simunek, J. 2011. Modeling colloid transport and retention in saturated porous media under unfavorable attachment conditions. Water Resources Research. 47:W10503. DOI:10. 1029/2011WR010812.
- Ibekwe, A.M., Leddy, M.B., Bold, R.M., Graves, A.K. 2011. Bacterial community composition in low-flowing river water with different sources of pollutants. FEMS Microbiology Ecology. 79:155-166.
- Ibekwe, A.M., Murinda, S.E., Graves, A.K. 2011. Genetic diversity and antimicrobial resistance of Escherichia coli from human and animal sources uncovers multiple resistances from human sources. PLoS One. 6(6):1-12.
- Ibekwe, A.M., Murinda, S.E., Graves, A.K. 2011. Microbiological evaluation of water quality from urban watersheds for domestic water supply improvement. International Journal of Environmental Research and Public Health. 8:4460-4476.
- Torkzaban, S., Wan, J., Tokunaga, T.K., Bradford, S.A. 2012. Impacts of bridging complexation on the transport of surface-modified nanoparticles in saturated sand. Journal of Contaminant Hydrology. 136-137:86-95.
- Ibekwe, A.M., Lesch, S.M., Bold, R.M., Leddy, M.B., Graves, A.K. 2011. Variations of indicator bacteria in a large urban watershed. Transactions of the ASABE. 54(6):2227-2236.
- Wang, D., Paradelo, M., Bradford, S.A., Peijnenburg, W.J., Chu, L., Zhou, D. 2011. Facilitated transport of Cu with hydroxyapatite nanoparticles in saturated sand: Effects of solution ionic strength and composition. Water Research. 45:5905-5915.
- Ma, J., Ibekwe, A.M., Wang, H., Xu, J., Leddy, M., Yang, C., Crowley, D.E. 2012. Assimilable organic carbon (AOC) in soil water extracts using Vibrio Harveyi BB721 and its implication for microbial biomass. PLoS One. 7(5): e28519. DOI: 10.1371/journal.pone.0028519.
- Wang, D., Bradford, S.A., Harvey, R.W., Hao, X., Zhou, D. 2012. Transport of ARS-labeled hydroxyapatite nanoparticles in saturated granular media is influenced by surface charge variability even in the presence of humic acid. Journal of Hazardous Materials. 229-230:179-176.
- Ibekwe, A.M., Leddy, M.B., Bold, R.M., Graves, A.K. 2011. Bacterial composition in sediment and surface water as indicators for pollution in a mixed watershed. FEMS Microbiology Ecology. 79:155-166.
- Shange, R.S., Ankumah, R.O., Ibekwe, A.M., Zabawa, R., Dowd, S.E. 2012. Distinct soil bacterial communities revealed under a diversely managed agroecosystem. PLoS One. 7(7):e40338. doi:10.1371/journal.pone.0040338.
- Bradford, S.A., Kim, H. 2012. Causes and implications of colloid and microorganism retention hysteresis. Journal of Contaminant Hydrology. 138- 139:83-92.
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