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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Environmental Microbial & Food Safety Laboratory » Research » Research Project #421065


Location: Environmental Microbial & Food Safety Laboratory

2015 Annual Report

1a. Objectives (from AD-416):
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.

1b. Approach (from AD-416):
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.

3. Progress Report:
Research was initiated to explain and interpret the presence of high concentrations of indicator microorganisms, E. coli and enterococci during the baseflow between rainfall events. Experiments were carried out with the release of tracers to two creeks at the Beltsville Agricultural Research Center and comparison of the dilution effects of tracer and bacteria concentrations. The preliminary results suggest the substantial influx of indicator microorganisms from bottom sediments to water column. This conclusion, if further confirmed, will substantially improve modeling microbial water quality for irrigation and recreation purposes. Research was carried out to elucidate the distribution of manure-borne microorganisms in soils after irrigation or precipitation events. In collaborative work with University of MD, we carried out controlled indoor experiments with manure application on grassed soil in specially designed boxes, and demonstrated the preferential accumulation of manure-borne microorganisms in the less than 1 cm-thin soil surface mixing layer, and therefore, excellent opportunity for them to be transferred from soil to runoff during following rainfall or irrigation. The results of this work indicate the need to revisit the bacterial survival patterns that are assumed in water quality models. Opportunities of improving watershed scale modeling of pathogenic and indicator microorganisms with the USDA Soil and Water Assessment Tool (SWAT) model were found when the time series of fecal coliform concentration observations were fecal coliform observations from four different sites in the U.S. and Korea. Seasonal dominance of bacteria growth or die-off in water and soil was found to be a plausible and efficient explanation of the observed bacteria concentration dynamics. Introducing the appropriate changes in the SWAT model led to the significant improvement in SWAT modeling results that are commonly used for design and evaluation of management policies and practices regarding microbial dynamics in watersheds. Scientists in Environmental Microbiology and Food Safety Laboratory, Beltsville, Maryland, continued to research the scale effect in removal of microorganisms from manured areas. Scientists repeated the large-scale field at the USDA-ARS Optimizing Production Inputs for Economic and Environmental Enhancement (OPE3) research site where the irrigation system was used to conduct irrigation events for applied fresh and aged manure, and companion plot-scale experiments. Results from two years show that although the scale effect is substantial for runoff amounts, it is not pronounced for E. coli and enterococci related from land-applied solid manure. These results are important in that they confirm the applicability of the data on microbial removal at research plots for the field-scale microbial removal that is typically simulated in farm and watershed scale studies of microbial quality of irrigation waters. Results of this work will contribute to further validation of the microbial release and transport model, Simulator of Transport With Infiltration and Runoff (STWIR), which is being adopted by the Environmental Protection Agency (EPA) and will be linked with the legacy water quality model. Fecal indicator organisms were shown to have high concentrations in the parts of surface water sources where algal accumulation was observed. Chl-a concentrations are often used as proxies to estimate the algae concentrations in surface water sources. Research was initiated to (a) compare E. coli and enterococci concentrations in areas covered and free of algae in pond, (b) to assess the applicability of biooptical algorithms used to estimate Chl-a concentrations across large water bodies from remote sensing data. The preliminary results show about one order of magnitude differences between E. coli concentrations in pond water with and without substantial algae populations. In collaborative work with Korean scientists, scientists showed the need and the feasibility of developing a correction to the existing biooptical algorithms for use in reservoir environments. Results of this work will contribute to the development of monitoring methodologies to evaluate microbial water quality in irrigation water sources. Literature data show that the release of microorganisms from solid manures occurs in a qualitatively different manner compared with slurries, liquid manures, and poultry litter. In particular, the release of microorganisms from solid manures cannot be predicted based on the total amount of irrigation or rain water. Scientists carried out research on E. coli and enterococci release from solid manure in indoor experiments with grasses and with membranes imitating soil surfaces. Scientists elucidated mechanisms and proposed a model for bacteria release from solid manure. Results of this work show that the substantial fraction of bacteria in manure is released to soil with infiltrating water before runoff begins to remove them from the application area. Results of this work show that substantially lower bacteria concentrations in runoff should be expected for solid manure as compared with slurry.

4. Accomplishments
1. Improved capability to estimate microbial water quality. Modeling of microbial water quality is dependent on estimates of microorganism survival after deposition on land in manure or animal wastes. ARS scientists from Beltsville, Maryland, completed the development of a sub-model to simulate fate and transport of microorganisms from land-applied manures and animal wastes. The sub-model was developed to be used with the existing watershed scale and farm-scale water quality models and includes state-of-the-art information about bacterial survival kinetics. It comes with the databases on survival of indicator microorganisms in surface waters, soils, land deposited manure, animal wastes, and bottom sediments. Different types of waters, soils, animal sources, application methods, and experimental conditions were represented. The database was pre-analyzed using predictive microbiology to provide default parameters for site-specific simulations. These results will lead to substantial improvements in accuracy of microbial water quality models used for assessment and predictions for safety of recreational and irrigation water sources.

Review Publications
Martinez, G., Pachepsky, Y.A., Whelan, G., Yakirevich, A., Guber, A., Gish, T. 2104. Rainfall-induced fecal indicator organisms transport from animal waste applied fields: Model sensitivity analysis. Environment International. 63:121-129.

Kim, K., Whelan, G., Purucker, T., Bohrmann, T., Cytersky, T., Molina, M., Gu, Y., Pachepsky, Y.A., Guber, A., Franklin, D.H. 2014. Rainfall-runoff model parameter estimation and uncertainty evaluation on small plots. Hydrological Processes. 28:5220-5235.

Guber, A., Pachepsky, Y.A., Yakirevich, A., Shelton, D.R., Whelan, G., Goodrich, D.C., Unkrich, C.L. 2014. Modeling runoff and microbial overland transport with KINEROS2/STWIR model: Accuracy and uncertainty as affected by source of infiltration parameters. Journal of Hydrology: 519.644-655.

Shelton, D.R., Pachepsky, Y.A., Kiefer, L., Blaustein, R.A., McCarty, G.W., Dao, T.H. 2014. Response of coliform populations in streambed sediment and water column to changes in nutrient concentrations in water. Water Research. 59:316-324.

Whelan, G., Kim, K., Pelton, M., Soller, J., Castleton, K., Molina, M., Pachepsky, Y.A., Zepp, R. 2014. An integrated environmental modeling framework for performing quantitative microbial risk assessments. Environmental Modelling & Software. 55:77-91.

Pachepsky, Y.A., Blaustein, R.A., Whelan, G., Shelton, D.R. 2014. Comparison of temperature effects on E. coli, Salmonella, and Enterococcus survival in surface waters. Letters in Applied Microbiology. 59:278-283.

Pachepsky, Y.A., Shelton, D.R., Dorner, S., Wjelan, G. 2014. Can E. coli or thermotolerant coliform concentrations predict pathogen presence or prevalence in irrigation waters? Critical Reviews in Microbiology. 42(3):384-393. doi:10.3109/1040841X.2014.954524.

Blaustein, R., Pachepsky, Y.A., Shelton, D.R., Hill, R. 2015. Release and removal of microorganisms from land-deposited animal waste and animal manures: A review of data and models. Journal of Environmental Quality. 44(5):1338-1354.

Blaustein, R., Pachepsky, Y.A., Hill, R., Shelton, D.R. 2015. Solid manure as a source of fecal indicator microorganisms: release under simulated rainfall. Environmental Science and Technology. 49(13):7860-7869.

Stocker, M.D., Pachepsky, Y.A., Hill, R., Shelton, D.R. 2015. Depth-dependent inactivation of Escherichia coli and Enterococcus faecalis in soil after manure application and simulated rainfall. Applied and Environmental Microbiology. 81(14):4801-4808.