Publications by authors named "Yakov A Pachepsky"

26 Publications

  • Page 1 of 1

Modeling the photoinactivation and transport of somatic and F-specific coliphages at a Great Lakes beach.

J Environ Qual 2020 Nov 5;49(6):1612-1623. Epub 2020 Nov 5.

Dep. of Civil & Environmental Engineering, Michigan State Univ., East Lansing, MI, 48824, USA.

Fecal indicator organisms (FIOs), such as Escherichia coli and enterococci, are often used as surrogates of contamination in the context of beach management; however, bacteriophages may be more reliable indicators than FIO due to their similarity to viral pathogens in terms of size and persistence in the environment. In the past, mechanistic modeling of environmental contamination has focused on FIOs, with virus and bacteriophage modeling efforts remaining limited. In this paper, we describe the development and application of a fate and transport model of somatic and F-specific coliphages for the Washington Park beach in Lake Michigan, which is affected by riverine outputs from the nearby Trail Creek. A three-dimensional model of coliphage transport and photoinactivation was tested and compared with a previously reported E. coli fate and transport model. The light-based inactivation of the phages was modeled using organism-specific action spectra. Results indicate that the coliphage models outperformed the E. coli model in terms of reliably predicting observed E. coli/coliphage concentrations at the beach. This is possibly due to the presence of additional E. coli sources that were not accounted for in the modeling. The coliphage models can be used to test hypotheses about potential sources and their behavior and for predictive modeling.
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http://dx.doi.org/10.1002/jeq2.20153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7859910PMC
November 2020

Depth-Dependent Response of Fecal Indicator Bacteria in Sediments to Changes in Water Column Nutrient Levels.

J Environ Qual 2019 Jul;48(4):1074-1081

Concentrations of in bottom sediments can influence the assessment of microbial stream water quality. Runoff events bring nutrients to streams that can support the growth of in sediments. The objective of this work was to evaluate depth-dependent changes in populations after nutrients are introduced to the water column. Bovine feces were collected fresh and mixed into sediment. Studies were performed in a microcosm system with continuous flow of synthetic stream water over inoculated sediment. Dilutions of autoclaved bovine manure were added to water on Day 16 at two concentrations, and KBr tracer was introduced into the water column to evaluate ion diffusion. Concentrations of , total coliforms, and total aerobic heterotrophic bacteria, along with orthophosphate-P and ammonium N, were monitored in water and sediment for 32 d. Sediment samples were analyzed in 0- to 1-cm and 1- to 3-cm sectioned depths. Concentrations of and total coliforms in top sediments were approximately one order of magnitude greater than in bottom sediments throughout the experiment. Introduction of nutrients to the water column triggered an increase of nutrient levels in both top and bottom sediments and increased concentrations of bacteria in the water. However, the added nutrients had a limited effect on in sediment where bacterial inactivation continued. Vertical gradients of concentrations in sediments persisted during the inactivation periods both before and after nutrient addition to the water column.
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http://dx.doi.org/10.2134/jeq2018.12.0450DOI Listing
July 2019

Evaluating the influence of climate change on the fate and transport of fecal coliform bacteria using the modified SWAT model.

Sci Total Environ 2019 Mar 14;658:753-762. Epub 2018 Dec 14.

School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea. Electronic address:

Fecal coliform bacteria (FCB) contamination of natural waters is a serious public health issue. Therefore, understanding and anticipating the fate and transport of FCB are important for reducing the risk of contracting diseases. The objective of this study was to analyze the impacts of climate change on the fate and transport of FCB. We modified both the soil and the in-stream bacteria modules in the soil and water assessment tool (SWAT) model and verified the prediction accuracy of seasonal variability of FCB loads using observations. Forty bias-correcting GCM-RCM projections were applied in the modified SWAT model to examine various future climate conditions at the end of this century (2076-2100). Lastly, we also compared the variability of FCB loads under current and future weather conditions using multi-model ensemble simulations (MMES). The modified SWAT model yielded a satisfactory performance with regard to the seasonal variability of FCB amounts in the soil and FCB loading to water bodies. The modified SWAT model presented substantial proliferation of FCB in the soil (30.1%-147.5%) due to an increase in temperature (25.1%). Also, increase in precipitation (53.3%) led to an increase in FCB loads (96.0%-115.5%) from the soil to water body. In the in-stream environment, resuspension from the stream bed was the dominant process affecting the amount of FCB in stream. Therefore, the final FCB loads increased by 71.2% because of the growing peak channel velocity and volume of water used due to an increase in precipitation. Based on the results of MMES, we concluded that the level of FCB would increase simultaneously in the soil as well as in stream by the end of this century. This study will aid in understanding the future variability of FCB loads as well as in preparing an effective management plan for FCB levels in natural waters.
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http://dx.doi.org/10.1016/j.scitotenv.2018.12.213DOI Listing
March 2019

Export from Manured Fields Depends on the Time between the Start of Rainfall and Runoff Initiation.

J Environ Qual 2018 09;47(5):1293-1297

After rainfall or irrigation begins, surface-applied chemicals and manure-borne microorganisms typically enter the soil with infiltration until the soil saturates, after which time the chemicals and microbes are exported from the field in the overland flow. This process is viewed as a reason for the dependence of chemical export on the time between rainfall start and runoff initiation that has been documented for agricultural chemicals. The objective of this work was to observe and quantify such dependence for released from solid farmyard dairy manure in field conditions. Experiments were performed for 6 yr and consisted of manure application followed by an immediate simulated rainfall event and a second event 1 wk later. The nonlinearity of the release seen in laboratory and plot studies did not manifest itself in the field. The number of exported cells in runoff was proportional to rainfall depth after runoff initiation in each trial. The proportionality coefficient, termed export rate, demonstrated a strong dependence on the runoff delay time that could be approximated with the exponential decrease. The export rate decreased by one order of magnitude when the rainfall depth at runoff initiation increased from 18 to 42 mm. The same dependence could approximate data from the simulated rainfall event 1 wk after the manure application, assuming that the initial content in manure after 1 wk of weathering was 10% of the initial content. Overall, accounting for the dependence of manure-borne export on the runoff delay time should improve the accuracy of export predictions related to the assessment of agricultural practices on microbial water quality.
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http://dx.doi.org/10.2134/jeq2018.02.0081DOI Listing
September 2018

Spatial Patterns of Concentrations in Sediment before and after High-Flow Events in a First-Order Creek.

J Environ Qual 2018 09;47(5):958-966

Understanding spatial patterns of in freshwater sediments is necessary to characterize sediments as microbial reservoirs and to evaluate the impact of sediment resuspension on microbial water quality in watersheds. Sediment particle size distributions and streambed concentrations were measured along a 500-m-long reach of a first-order creek 1 d before and on Days 1, 3, 6, and 10 after each of two artificial high-flow events, with natural high-flow events also occurring within the sampling periods. Spatial variability of was greater in sediments than in water within any given sampling; however, variation between sampling days was greater for water than for sediment. The mean relative difference analysis revealed temporally stable patterns of concentrations in sediments. rich locations along the reach corresponded to areas with higher organic matter and fine particle contents. Although low ( < 0.5 d) or negative survival rates were observed at most locations along the reach during times where no precipitation was recorded, a small number of locations showed such large concentration increase that on average the survival rate remained positive at the reach scale. The studied creek appears to have hot spots of concentration increase, where conditions for populations to increase are much more favorable than in most other locations across the reach. The effect of this increase can be seen at the reach scale but is difficult to discern without individual sampling that is dense in space and time.
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http://dx.doi.org/10.2134/jeq2017.11.0451DOI Listing
September 2018

Capturing Microbial Sources Distributed in a Mixed-use Watershed within an Integrated Environmental Modeling Workflow.

Environ Model Softw 2018 Jan;99:126-146

U.S. Department of Agriculture, Agricultural Research Service, Marshfield, WI USA.

Many watershed models simulate overland and instream microbial fate and transport, but few provide loading rates on land surfaces and point sources to the waterbody network. This paper describes the underlying equations for microbial loading rates associated with 1) land-applied manure on undeveloped areas from domestic animals; 2) direct shedding (excretion) on undeveloped lands by domestic animals and wildlife; 3) urban or engineered areas; and 4) point sources that directly discharge to streams from septic systems and shedding by domestic animals. A microbial source module, which houses these formulations, is part of a workflow containing multiple models and databases that form a loosely configured modeling infrastructure which supports watershed-scale microbial source-to-receptor modeling by focusing on animal- and human-impacted catchments. A hypothetical application - accessing, retrieving, and using real-world data - demonstrates how the infrastructure can automate many of the manual steps associated with a standard watershed assessment, culminating in calibrated flow and microbial densities at the watershed's pour point.
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http://dx.doi.org/10.1016/j.envsoft.2017.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069999PMC
January 2018

Development and evaluation of the bacterial fate and transport module for the Agricultural Policy/Environmental eXtender (APEX) model.

Sci Total Environ 2018 Feb 17;615:47-58. Epub 2017 Oct 17.

USDA-ARS, Environmental Microbial and Food Safety Lab, 10300 Baltimore Avenue, BARC-East Bldg. 173, Beltsville, MD 20705, USA. Electronic address:

The Agricultural Policy/Environmental eXtender (APEX) is a watershed-scale water quality model that includes detailed representation of agricultural management. The objective of this work was to develop a process-based model for simulating the fate and transport of manure-borne bacteria on land and in streams with the APEX model. The bacteria model utilizes manure erosion rates to estimate the amount of edge-of-field bacteria export. Bacteria survival in manure is simulated as a two-stage process separately for each manure application event. In-stream microbial fate and transport processes include bacteria release from streambeds due to sediment resuspension during high flow events, active release from the streambed sediment during low flow periods, bacteria settling with sediment, and survival. Default parameter values were selected from published databases and evaluated based on field observations. The APEX model with the newly developed microbial fate and transport module was applied to simulate fate and transport of the fecal indicator bacterium Escherichia coli in the Toenepi watershed, New Zealand that was monitored for seven years. The stream network of the watershed ran through grazing lands with daily bovine waste deposition. Results show that the APEX with the bacteria module reproduced well the monitored pattern of E. coli concentrations at the watershed outlet. The APEX with the microbial fate and transport module will be utilized for predicting microbial quality of water as affected by various agricultural practices, evaluating monitoring protocols, and supporting the selection of management practices based on regulations that rely on fecal indicator bacteria concentrations.
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http://dx.doi.org/10.1016/j.scitotenv.2017.09.231DOI Listing
February 2018

Hydrological modeling of Fecal Indicator Bacteria in a tropical mountain catchment.

Water Res 2017 08 15;119:102-113. Epub 2017 Apr 15.

Géosciences Environnement Toulouse, Université de Toulouse, CNES, CNRS, IRD, UPS, 31400 Toulouse, France.

The occurrence of pathogen bacteria in surface waters is a threat to public health worldwide. In particular, inadequate sanitation resulting in high contamination of surface water with pathogens of fecal origin is a serious issue in developing countries such as Lao P.D.R. Despite the health implications of the consumption of contaminated surface water, the environmental fate and transport of pathogens of fecal origin and their indicators (Fecal Indicator Bacteria or FIB) are still poorly known in tropical areas. In this study, we used measurements of flow rates, suspended sediments and of the FIB Escherichia coli (E. coli) in a 60-ha catchment in Northern Laos to explore the ability of the Soil and Water Assessment Tool (SWAT) to simulate watershed-scale FIB fate and transport. We assessed the influences of 3 in-stream processes, namely bacteria deposition and resuspension, bacterial regrowth, and hyporheic exchange (i.e. transient storage) on predicted FIB numbers. We showed that the SWAT model in its original version does not correctly simulate small E. coli numbers during the dry season. We showed that model's performance could be improved when considering the release of E. coli together with sediment resuspension. We demonstrated that the hyporheic exchange of bacteria across the Sediment-Water Interface (SWI) should be considered when simulating FIB concentration not only during wet weather, but also during the dry season, or baseflow period. In contrast, the implementation of the regrowth process did not improve the model during the dry season without inducing an overestimation during the wet season. This work thus underlines the importance of taking into account in-stream processes, such as deposition and resuspension, regrowth and hyporheic exchange, when using SWAT to simulate FIB dynamics in surface waters.
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http://dx.doi.org/10.1016/j.watres.2017.04.038DOI Listing
August 2017

Modeling the interannual variability of microbial quality metrics of irrigation water in a Pennsylvania stream.

J Environ Manage 2017 Feb 29;187:253-264. Epub 2016 Nov 29.

Farm Systems & Environment, AgResearch Ltd, Invermay Research Centre, Private Bag 50034, Mosgiel 9053, New Zealand.

Knowledge of the microbial quality of irrigation waters is extremely limited. For this reason, the US FDA has promulgated the Produce Rule, mandating the testing of irrigation water sources for many farms. The rule requires the collection and analysis of at least 20 water samples over two to four years to adequately evaluate the quality of water intended for produce irrigation. The objective of this work was to evaluate the effect of interannual weather variability on surface water microbial quality. We used the Soil and Water Assessment Tool model to simulate E. coli concentrations in the Little Cove Creek; this is a perennial creek located in an agricultural watershed in south-eastern Pennsylvania. The model performance was evaluated using the US FDA regulatory microbial water quality metrics of geometric mean (GM) and the statistical threshold value (STV). Using the 90-year time series of weather observations, we simulated and randomly sampled the time series of E. coli concentrations. We found that weather conditions of a specific year may strongly affect the evaluation of microbial quality and that the long-term assessment of microbial water quality may be quite different from the evaluation based on short-term observations. The variations in microbial concentrations and water quality metrics were affected by location, wetness of the hydrological years, and seasonality, with 15.7-70.1% of samples exceeding the regulatory threshold. The results of this work demonstrate the value of using modeling to design and evaluate monitoring protocols to assess the microbial quality of water used for produce irrigation.
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http://dx.doi.org/10.1016/j.jenvman.2016.11.054DOI Listing
February 2017

Modeling fate and transport of fecally-derived microorganisms at the watershed scale: State of the science and future opportunities.

Water Res 2016 09 29;100:38-56. Epub 2016 Apr 29.

USDA-ARS, Environmental Microbial and Food Safety Laboratory, 10300 Baltimore Ave. Building 173, BARC-EAST, Beltsville, MD 20705, USA.

Natural waters serve as habitat for a wide range of microorganisms, a proportion of which may be derived from fecal material. A number of watershed models have been developed to understand and predict the fate and transport of fecal microorganisms within complex watersheds, as well as to determine whether microbial water quality standards can be satisfied under site-specific meteorological and/or management conditions. The aim of this review is to highlight and critically evaluate developments in the modeling of microbial water quality of surface waters over the last 10 years and to discuss the future of model development and application at the watershed scale, with a particular focus on fecal indicator organisms (FIOs). In doing so, an agenda of research opportunities is identified to help deliver improvements in the modeling of microbial water quality draining through complex landscape systems. This comprehensive review therefore provides a timely steer to help strengthen future modeling capability of FIOs in surface water environments and provides a useful resource to complement the development of risk management strategies to reduce microbial impairment of freshwater sources.
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http://dx.doi.org/10.1016/j.watres.2016.04.064DOI Listing
September 2016

Irrigation waters and pipe-based biofilms as sources for antibiotic-resistant bacteria.

Environ Monit Assess 2016 Jan 24;188(1):56. Epub 2015 Dec 24.

USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Ave. Bldg. 173, Beltsville, MD, 20705, USA.

The presence of antibiotic-resistant bacteria in environmental surface waters has gained recent attention. Wastewater and drinking water distribution systems are known to disseminate antibiotic-resistant bacteria, with the biofilms that form on the inner-surfaces of the pipeline as a hot spot for proliferation and gene exchange. Pipe-based irrigation systems that utilize surface waters may contribute to the dissemination of antibiotic-resistant bacteria in a similar manner. We conducted irrigation events at a perennial stream on a weekly basis for 1 month, and the concentrations of total heterotrophic bacteria, total coliforms, and fecal coliforms, as well as the concentrations of these bacterial groups that were resistant to ampicillin and tetracycline, were monitored at the intake water. Prior to each of the latter three events, residual pipe water was sampled and 6-in. sections of pipeline (coupons) were detached from the system, and biofilm from the inner-wall was removed and analyzed for total protein content and the above bacteria. Isolates of biofilm-associated bacteria were screened for resistance to a panel of seven antibiotics, representing five antibiotic classes. All of the monitored bacteria grew substantially in the residual water between irrigation events, and the biomass of the biofilm steadily increased from week to week. The percentages of biofilm-associated isolates that were resistant to antibiotics on the panel sometimes increased between events. Multiple-drug resistance was observed for all bacterial groups, most often for fecal coliforms, and the distributions of the numbers of antibiotics that the total coliforms and fecal coliforms were resistant to were subject to change from week to week. Results from this study highlight irrigation waters as a potential source for antibiotic-resistant bacteria, which can subsequently become incorporated into and proliferate within irrigation pipe-based biofilms.
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http://dx.doi.org/10.1007/s10661-015-5067-4DOI Listing
January 2016

Predicting microbial water quality with models: Over-arching questions for managing risk in agricultural catchments.

Sci Total Environ 2016 Feb 3;544:39-47. Epub 2015 Dec 3.

Biological & Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK.

The application of models to predict concentrations of faecal indicator organisms (FIOs) in environmental systems plays an important role for guiding decision-making associated with the management of microbial water quality. In recent years there has been an increasing demand by policy-makers for models to help inform FIO dynamics in order to prioritise efforts for environmental and human-health protection. However, given the limited evidence-base on which FIO models are built relative to other agricultural pollutants (e.g. nutrients) it is imperative that the end-user expectations of FIO models are appropriately managed. In response, this commentary highlights four over-arching questions associated with: (i) model purpose; (ii) modelling approach; (iii) data availability; and (iv) model application, that must be considered as part of good practice prior to the deployment of any modelling approach to predict FIO behaviour in catchment systems. A series of short and longer-term research priorities are proposed in response to these questions in order to promote better model deployment in the field of catchment microbial dynamics.
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http://dx.doi.org/10.1016/j.scitotenv.2015.11.086DOI Listing
February 2016

Release and Removal of Microorganisms from Land-Deposited Animal Waste and Animal Manures: A Review of Data and Models.

J Environ Qual 2015 Sep;44(5):1338-54

Microbial pathogens present a leading cause of impairment to rivers, bays, and estuaries in the United States, and agriculture is often viewed as the major contributor to such contamination. Microbial indicators and pathogens are released from land-applied animal manure during precipitation and irrigation events and are carried in overland and subsurface flow that can reach and contaminate surface waters and ground water used for human recreation and food production. Simulating the release and removal of manure-borne pathogens and indicator microorganisms is an essential component of microbial fate and transport modeling regarding food safety and water quality. Although microbial release controls the quantities of available pathogens and indicators that move toward human exposure, a literature review on this topic is lacking. This critical review on microbial release and subsequent removal from manure and animal waste application areas includes sections on microbial release processes and release-affecting factors, such as differences in the release of microbial species or groups; bacterial attachment in turbid suspensions; animal source; animal waste composition; waste aging; manure application method; manure treatment effect; rainfall intensity, duration, and energy; rainfall recurrence; dissolved salts and temperature; vegetation and soil; and spatial and temporal scale. Differences in microbial release from liquid and solid manures are illustrated, and the influential processes are discussed. Models used for simulating release and removal and current knowledge gaps are presented, and avenues for future research are suggested.
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http://dx.doi.org/10.2134/jeq2015.02.0077DOI Listing
September 2015

Rainfall intensity effects on removal of fecal indicator bacteria from solid dairy manure applied over grass-covered soil.

Sci Total Environ 2016 Jan 18;539:583-591. Epub 2015 Sep 18.

USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, USA.

The rainfall-induced release of pathogens and microbial indicators from land-applied manure and their subsequent removal with runoff and infiltration precedes the impairment of surface and groundwater resources. It has been assumed that rainfall intensity and changes in intensity during rainfall do not affect microbial removal when expressed as a function of rainfall depth. The objective of this work was to test this assumption by measuring the removal of Escherichia coli, enterococci, total coliforms, and chloride ion from dairy manure applied in soil boxes containing fescue, under 3, 6, and 9cmh(-1) of rainfall. Runoff and leachate were collected at increasing time intervals during rainfall, and post-rainfall soil samples were taken at 0, 2, 5, and 10cm depths. Three kinetic-based models were fitted to the data on manure-constituent removal with runoff. Rainfall intensity appeared to have positive effects on rainwater partitioning to runoff, and removal with this effluent type occurred in two stages. While rainfall intensity generally did not impact the parameters of runoff-removal models, it had significant, inverse effects on the numbers of bacteria remaining in soil after rainfall. As rainfall intensity and soil profile depth increased, the numbers of indicator bacteria tended to decrease. The cumulative removal of E. coli from manure exceeded that of enterococci, especially in the form of removal with infiltration. This work may be used to improve the parameterization of models for bacteria removal with runoff and to advance estimations of depths of bacteria removal with infiltration, both of which are critical to risk assessment of microbial fate and transport in the environment.
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http://dx.doi.org/10.1016/j.scitotenv.2015.07.108DOI Listing
January 2016

Solid Manure As a Source of Fecal Indicator Microorganisms: Release under Simulated Rainfall.

Environ Sci Technol 2015 Jul 8;49(13):7860-9. Epub 2015 Jun 8.

‡USDA-ARS Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland 20705, United States.

Understanding and quantifying microbial release from manure is a precondition to estimation and management of microbial water quality. The objectives of this work were to determine the effects of rainfall intensity and surface slope on the release of Escherichia coli, enterococci, total coliforms, and dissolved chloride from solid dairy manure and to assess the performance of the one-parametric exponential model and the two-parametric Bradford-Schijven model when simulating the observed release. A controlled-intensity rainfall simulator induced 1 h of release in runoff/leachate partitioning boxes at three rainfall intensities (30, 60, and 90 mm h(-1)) and two surface slopes (5% and 20%). Bacterial concentrations in initial release were more than 1 order of magnitude lower than their starting concentrations in manure. As bacteria were released, they were partitioned into runoff and leachate at similar concentrations, but in different volumes, depending on slope. Bacterial release occurred in two stages that corresponded to mechanisms associated with release of manure liquid- and solid-phases. Parameters of the two models fitted to the bacterial release dependencies on rainfall depth were not significantly affected by rainfall intensity or slope. Based on model performance tests, the Bradford-Schijven model is recommended for simulating bacterial release from solid manure.
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http://dx.doi.org/10.1021/acs.est.5b01095DOI Listing
July 2015

Colloid filtration in surface dense vegetation: experimental results and theoretical predictions.

Environ Sci Technol 2014 Apr 14;48(7):3883-90. Epub 2014 Mar 14.

Department of Agricultural and Biological Engineering, University of Florida , Gainesville, Florida 32611, United States.

Understanding colloid and colloid-facilitated contaminant transport in overland flow through dense vegetation is important to protect water quality in the environment, especially for water bodies receiving agricultural and urban runoff. In previous studies, a single-stem efficiency theory for rigid and clean stem systems was developed to predict colloid filtration by plant stems of vegetation in laminar overland flow. Hence, in order to improve the accuracy of the single-stem efficiency theory to real dense vegetation system, we incorporated the effect of natural organic matter (NOM) on the filtration of colloids by stems. Laboratory dense vegetation flow chamber experiments and model simulations were used to determine the kinetic deposition (filtration) rate of colloids under various conditions. The results show that, in addition to flow hydrodynamics and solution chemistry, steric repulsion afforded by NOM layer on the plants stem surface also plays a significant role in controlling colloid deposition on vegetation in overland flow. For the first time, a refined single-stem efficiency theory with considerations of the NOM effect is developed that describes the experimental data with good accuracy. This theory can be used to not only help construct and refine mathematical models of colloid transport in real vegetation systems in overland flow, but also inform the development of theories of colloid deposition on NOM-coated surfaces in natural, engineered, and biomedical systems.
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http://dx.doi.org/10.1021/es404603gDOI Listing
April 2014

Rainfall-induced fecal indicator organisms transport from manured fields: model sensitivity analysis.

Environ Int 2014 Feb 28;63:121-9. Epub 2013 Nov 28.

USDA-ARS Hydrology and Remote Sensing Laboratory, Beltsville, MD, 20705, USA.

Microbial quality of surface waters attracts attention due to food- and waterborne disease outbreaks. Fecal indicator organisms (FIOs) are commonly used for the microbial pollution level evaluation. Models predicting the fate and transport of FIOs are required to design and evaluate best management practices that reduce the microbial pollution in ecosystems and water sources and thus help to predict the risk of food and waterborne diseases. In this study we performed a sensitivity analysis for the KINEROS/STWIR model developed to predict the FIOs transport out of manured fields to other fields and water bodies in order to identify input variables that control the transport uncertainty. The distributions of model input parameters were set to encompass values found from three-year experiments at the USDA-ARS OPE3 experimental site in Beltsville and publicly available information. Sobol' indices and complementary regression trees were used to perform the global sensitivity analysis of the model and to explore the interactions between model input parameters on the proportion of FIO removed from fields. Regression trees provided a useful visualization of the differences in sensitivity of the model output in different parts of the input variable domain. Environmental controls such as soil saturation, rainfall duration and rainfall intensity had the largest influence in the model behavior, whereas soil and manure properties ranked lower. The field length had only moderate effect on the model output sensitivity to the model inputs. Among the manure-related properties the parameter determining the shape of the FIO release kinetic curve had the largest influence on the removal of FIOs from the fields. That underscored the need to better characterize the FIO release kinetics. Since the most sensitive model inputs are available in soil and weather databases or can be obtained using soil water models, results indicate the opportunity of obtaining large-scale estimates of FIO transport from fields based on publicly available rather than site-specific information.
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http://dx.doi.org/10.1016/j.envint.2013.11.003DOI Listing
February 2014

Using the Q10 model to simulate E. coli survival in cowpats on grazing lands.

Environ Int 2013 Apr 31;54:1-10. Epub 2013 Jan 31.

Department of Agronomy, University of Cordoba, 14071, Cordoba, Spain.

Microbiological quality of surface waters can be affected by microbial load in runoff from grazing lands. This effect, with other factors, depends on the survival of microorganisms in animal waste deposited on pastures. Since temperature is a leading environmental parameter affecting survival, it indirectly impacts water microbial quality. The Q10 model is widely used to predict the effect of temperature on rates of biological processes, including survival. Objectives of this work were to (i) evaluate the applicability of the Q10 model to Escherichia coli inactivation in bovine manure deposited on grazing land (i.e., cowpats) and (ii) identify explanatory variables for the previously reported E. coli survival dynamics in cowpats. Data utilized in this study include published results on E. coli concentrations in natural and repacked cowpats from research conducted the U.S. (Virginia and Maryland), New Zealand, and the United Kingdom. Inspection of the datasets led to conceptualizing E. coli survival (in cowpats) as a two-stage process, in which the initial stage was due to growth, inactivation or stationary state of the population and the second stage was the approximately first-order inactivation. Applying the Q10 model to these datasets showed a remarkable similarity in inactivation rates, using the thermal time. The reference inactivation rate constant of 0.042 (thermal days)(-1) at 20 °C gave a good approximation (R(2)=0.88) of all inactivation stage data with Q10=1.48. The reference inactivation rate constants in individual studies were no different from the one obtained by pooling all data (P<0.05). The rate of logarithm of the E. coli concentration change during the first stage depended on temperature. Duration of the first stage, prior to the first-order inactivation stage and the initial concentration of E. coli in cowpats, could not be predicted from available data. Diet and age are probable factors affecting these two parameters however, until their environmental and management predictors are known, microbial water quality modeling must treat them as a stochastic source of uncertainty in simulation results.
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http://dx.doi.org/10.1016/j.envint.2012.12.013DOI Listing
April 2013

Single collector attachment efficiency of colloid capture by a cylindrical collector in laminar overland flow.

Environ Sci Technol 2012 Aug 27;46(16):8878-86. Epub 2012 Jul 27.

Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida 32611, United States.

Little research has been conducted to investigate the fate and transport of colloids in shallow overland flow through dense vegetation under unfavorable chemical conditions. In this work, the single collector attachment efficiency (α) of colloid capture by a simulated plant stem (i.e., cylindrical collector) in laminar overland flow was measured directly in laboratory flow chamber experiments. Fluorescent microspheres of two sizes were used as experimental colloids. The colloid suspensions flowed toward a glass cylindrical rod installed in a small size flow channel at different laminar flow rates. Different solution ionic strengths (IS) were used in the experiments to simulate unfavorable attachment conditions. Our results showed that α increased with IS and decreased with flow velocity. Existing theoretical and empirical models of colloid attachment efficiency for porous media were used to simulate the experimental measurements in α and found to fall short in matching the experimental data. A new dimensionless (regression) equation was proposed that predicts the α of colloid capture by a cylindrical collector in laminar overland flow with reasonable accuracy. In addition, the equation was also effective in predicting the attachment efficiency of colloid deposition in porous media.
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http://dx.doi.org/10.1021/es301365fDOI Listing
August 2012

The modified SWAT model for predicting fecal coliforms in the Wachusett Reservoir Watershed, USA.

Water Res 2012 Oct 28;46(15):4750-60. Epub 2012 Jun 28.

Department of Civil and Environmental Engineering, University of Massachusetts, 130 Natural Resources Road, Amherst, MA 01003, USA.

This study assessed fecal coliform contamination in the Wachusett Reservoir Watershed in Massachusetts, USA using Soil and Water Assessment Tool (SWAT) because bacteria are one of the major water quality parameters of concern. The bacteria subroutine in SWAT, considering in-stream bacteria die-off only, was modified in this study to include solar radiation-associated die-off and the contribution of wildlife. The result of sensitivity analysis demonstrates that solar radiation is one of the most significant fate factors of fecal coliform. A water temperature-associated function to represent the contribution of beaver activity in the watershed to fecal contamination improved prediction accuracy. The modified SWAT model provides an improved estimate of bacteria from the watershed. Our approach will be useful for simulating bacterial concentrations to provide predictive and reliable information of fecal contamination thus facilitating the implementation of effective watershed management.
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http://dx.doi.org/10.1016/j.watres.2012.05.057DOI Listing
October 2012

Prediction of contamination potential of groundwater arsenic in Cambodia, Laos, and Thailand using artificial neural network.

Water Res 2011 Nov 27;45(17):5535-44. Epub 2011 Aug 27.

Department of Civil and Environmental Engineering, University of Massachusetts, Amherst, Amherst, MA 01003, USA.

The arsenic (As) contamination of groundwater has increasingly been recognized as a major global issue of concern. As groundwater resources are one of most important freshwater sources for water supplies in Southeast Asian countries, it is important to investigate the spatial distribution of As contamination and evaluate the health risk of As for these countries. The detection of As contamination in groundwater resources, however, can create a substantial labor and cost burden for Southeast Asian countries. Therefore, modeling approaches for As concentration using conventional on-site measurement data can be an alternative to quantify the As contamination. The objective of this study is to evaluate the predictive performance of four different models; specifically, multiple linear regression (MLR), principal component regression (PCR), artificial neural network (ANN), and the combination of principal components and an artificial neural network (PC-ANN) in the prediction of As concentration, and to provide assessment tools for Southeast Asian countries including Cambodia, Laos, and Thailand. The modeling results show that the prediction accuracy of PC-ANN (Nash-Sutcliffe model efficiency coefficients: 0.98 (traning step) and 0.71 (validation step)) is superior among the four different models. This finding can be explained by the fact that the PC-ANN not only solves the problem of collinearity of input variables, but also reflects the presence of high variability in observed As concentrations. We expect that the model developed in this work can be used to predict As concentrations using conventional water quality data obtained from on-site measurements, and can further provide reliable and predictive information for public health management policies.
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http://dx.doi.org/10.1016/j.watres.2011.08.010DOI Listing
November 2011

Relationship between eae and stx virulence genes and Escherichia coli in an agricultural watershed: implications for irrigation water standards and leafy green commodities.

J Food Prot 2011 Jan;74(1):18-23

U.S. Department of Agriculture, Agricultural Research Service, Environmental Microbial and Food Safety Laboratory, Building 173, Beltsville Agricultural Research Center-East, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA.

The California Leafy Greens Marketing Agreement (LGMA) was adopted in an effort to minimize the risk of contamination of leafy greens with enteric pathogens from a variety of sources, including ground and surface irrigation waters. The LGMA contains standards similar to those established for recreational waters, based on Escherichia coli concentrations. However, no correlation between E. coli and any specific waterborne pathogen(s) has been reported. We conducted this monitoring study in an agricultural watershed to (i) evaluate spatial and temporal fluctuations in E. coli populations and virulence genes associated with pathogenic E. coli and (ii) investigate whether a relationship could be established between E. coli and virulence genes. The virulence genes targeted for analysis were the eae and stx genes, encoding for intimin and Shiga-like toxins, respectively; they were detected with PCR methods. E. coli concentrations and eae and stx prevalence varied both spatially and temporally. In general, both were higher in agricultural than in forested areas and were higher in the summer and fall seasons than in winter. The eae and stx genes were prevalent throughout the watershed. However, in the absence of actual isolates, no conclusions could be drawn regarding the prevalence of specific pathogenic E. coli. No correlation was observed between E. coli concentrations and virulence genes; lower E. coli concentrations were not necessarily associated with decreased prevalence of eae and stx genes. These results suggest that the LGMA standards might not adequately address the issue of waterborne contamination, and that alternative criteria might be required.
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http://dx.doi.org/10.4315/0362-028X.JFP-10-241DOI Listing
January 2011

Biofilm morphology as related to the porous media clogging.

Water Res 2010 Feb 2;44(4):1193-201. Epub 2009 Jul 2.

Environmental Microbial and Food Safety Laboratory, USDA-ARS, 10300 Baltimore Ave., Beltsville, MD 20705, USA.

Aquifer recharge for the wastewater reuse has been considered and studied as a promising process to cope with the worldwide water scarcity. Soil clogging by an excessive growth of bacteria is often accompanied with the aquifer recharge. In this study, biofilm morphology and hydraulic conductivity were concurrently characterized at two flow rates and two levels of substrate concentrations. The experiments were conducted using a biofilm flow cell that was filled with glass beads. The biofilm images taken by confocal laser scanning microscopy (CLSM) were quantified by textural, areal, and fractal parameters. Hydraulic conductivity was monitored during the experiments. The flow velocity influenced the superficial morphology of biofilms and initial clogging time, while the substrate concentration affected biofilm density and clogging rate. Three different clogging mechanisms were suggested depending on the flow rate and substrate concentration: (1) clogging at a high flow rate can be accelerated by entrapped and accumulated biofilms, and can be easily eliminated by high shear force, (2) clogging at a low flow rate can be delayed for the time of local biofilm growths in the narrow pore necks, but the biofilm is rigid enough not to be sloughed, and (3) clogging in a solution with high substrate concentrations cannot be easily eliminated because of the growth of dense biofilms. The depicted biological clogging mechanisms will play a role in supporting studies about aquifer recharge.
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http://dx.doi.org/10.1016/j.watres.2009.05.049DOI Listing
February 2010

Size distributions of manure particles released under simulated rainfall.

J Environ Manage 2009 Mar 16;90(3):1365-9. Epub 2008 Sep 16.

USDA-ARS, Environmental Microbial Safety Laboratory, 10300 Baltimore Avenue, Building 173, Barc-East, Beltsville, MD 20705, USA.

Manure and animal waste deposited on cropland and grazing lands serve as a source of microorganisms, some of which may be pathogenic. These microorganisms are released along with particles of dissolved manure during rainfall events. Relatively little if anything is known about the amounts and sizes of manure particles released during rainfall, that subsequently may serve as carriers, abode, and nutritional source for microorganisms. The objective of this work was to obtain and present the first experimental data on sizes of bovine manure particles released to runoff during simulated rainfall and leached through soil during subsequent infiltration. Experiments were conducted using 200 cm long boxes containing turfgrass soil sod; the boxes were designed so that rates of manure dissolution and subsequent infiltration and runoff could be monitored independently. Dairy manure was applied on the upper portion of boxes. Simulated rainfall (ca. 32.4 mm h(-1)) was applied for 90 min on boxes with stands of either live or dead grass. Electrical conductivity, turbidity, and particle size distributions obtained from laser diffractometry were determined in manure runoff and soil leachate samples. Turbidity of leachates and manure runoff samples decreased exponentially. Turbidity of manure runoff samples was on average 20% less than turbidity of soil leachate samples. Turbidity of leachate samples from boxes with dead grass was on average 30% less than from boxes with live grass. Particle size distributions in manure runoff and leachate suspensions remained remarkably stable after 15 min of runoff initiation, although the turbidity continued to decrease. Particles had the median diameter of 3.8 microm, and 90% of particles were between 0.6 and 17.8 microm. The particle size distributions were not affected by the grass status. Because manure particles are known to affect transport and retention of microbial pathogens in soil, more information needs to be collected about the concurrent release of pathogens and manure particles during rainfall events.
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http://dx.doi.org/10.1016/j.jenvman.2008.08.001DOI Listing
March 2009

Effect of bovine manure on fecal coliform attachment to soil and soil particles of different sizes.

Appl Environ Microbiol 2007 May 16;73(10):3363-70. Epub 2007 Mar 16.

A135 Bourns Hall, Department of Environmental Sciences, University of California, Riverside, CA 92521, USA.

Manure-borne bacteria can be transported in runoff as free cells, cells attached to soil particles, and cells attached to manure particles. The objectives of this work were to compare the attachment of fecal coliforms (FC) to different soils and soil fractions and to assess the effect of bovine manure on FC attachment to soil and soil fractions. Three sand fractions of different sizes, the silt fraction, and the clay fraction of loam and sandy clay loam soils were separated and used along with soil samples in batch attachment experiments with water-FC suspensions and water-manure-FC suspensions. In the absence of manure colloids, bacterial attachment to soil, silt, and clay particles was much higher than the attachment to sand particles having no organic coating. The attachment to the coated sand particles was similar to the attachment to silt and clay. Manure colloids in suspensions decreased bacterial attachment to soils, clay and silt fractions, and coated sand fractions, but did not decrease the attachment to sand fractions without the coating. The low attachment of bacteria to silt and clay particles in the presence of manure colloids may cause predominantly free-cell transport of manure-borne FC in runoff.
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http://dx.doi.org/10.1128/AEM.02434-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1907106PMC
May 2007

Estimation of viable Escherichia coli O157 in surface waters using enrichment in conjunction with immunological detection.

J Microbiol Methods 2004 Aug;58(2):223-31

U.S. Department of Agriculture, Agricultural Research Service, Animal and Natural Resources Institute, Environmental Microbial Safety Laboratory, Building 173, BARC-East, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA.

The use of a minimal lactose enrichment broth (MLB) in conjunction with immunomagnetic electrochemiluminescence detection (IM-ECL) was evaluated for the estimation of viable Escherichia coli O157 populations in surface water samples. In principle, E. coli O157 populations (C(initial E. coli O157)) can be derived from enrichment data according to the equation: C(initial E. coli O157) = C(initial coliforms) x C(final E. coli O157)/C(final coliforms)), assuming that the growth rates and lag times of water-borne E. coli O157 and collective coliforms are sufficiently comparable, or at least consistent. We have previously described a protocol for determining C(final E. coli O157) in MLB-enriched water samples. In the present study, 80% of coliforms (red/pink colonies on MacConkey Agar) grew in MLB, indicating that this provides reasonably accurate estimates of C(initial coliforms). Estimates of C(final coliforms) were determined from turbidity data. Initial E. coli O157 populations (C(initial E. coli O157)) were calculated for 33 Baltimore watershed samples giving a positive IM-ECL response. The majority of samples contained E. coli O157 concentrations of < 1 cell per 100 ml. These data indicate that E. coli O157 are present in surface water samples but at very low levels. Growth rates for MLB-enriched coliforms were highly variable (k= 0.47 +/- 0.13 h(-1), n= 72). There was no correlation between growth rates and any measured water parameter, suggesting that coliform populations in water samples are spatially and temporally unique. Although variability in growth rates was expected to yield some low values, the fact that most E. coli O157 concentrations were < 1 suggests that other factor(s) were also responsible. Studies with E. coli O157:H7 and wild-type E. coli suggest that increased lag times due to starvation were at least partially responsible for the observed data. Based on estimates of C(initial coliforms) and k(coliforms), MLB was evaluated for sensitivity and quantitativeness. Simulated populations of E. coli O157:H7 at stationary phase varied from ca. 10(3) to 10(8) cells ml(-1) enrichment culture. Although not suitable for quantitation, MLB enrichment in conjunction with IM-ECL can detect as few as one viable water-borne E. coli O157 cell per 100 ml surface water. Experiments are in progress to evaluate alternative media for sensitivity and quantitative detection of enterohemorrhagic E. coli.
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http://dx.doi.org/10.1016/j.mimet.2004.03.017DOI Listing
August 2004
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