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Project Overview

Full Title
Fate and transport of pathogenic microorganisms and nutrients originating from livestock animal manures applied to agricultural lands

Location
 Wake County, NC

Cooperating Agencies
U.S. Environmental Protection Agency, National Risk Management Laboratory, Land Remediation and Pollution Control Division, Cincinnati, Ohio

Project Chief
Stephen Harden

Period of Project
October 2009 September 2012

Team Members
Doug Smith
Scott Caldwell
Shane Rogers (EPA)

Science Topic
Agriculture and Water Quality

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Fate and transport of pathogens and nutrients from land-applied animal manures

This project was completed in 2012. These pages are for historical purposes only.

Project Summary

The overall objectives of the work planned by USEPA and USGS at the LWRFL are to examine:

spraying

Active spraying in application field.

  1. pathogen survival in agricultural land applications of livestock manure,
  2. the effect of rainfall on overland transport and infiltration into soils of pathogens, antimicrobial-resistant bacteria, nutrients, and
  3. the relationship between the fate and transport of host-specific PCR biomarkers, bacterial pathogens, and fecal indicators.

This scope of work is being established to support USEPA’s research activities at the LWRFL site over a 2-year period, beginning in October 2009 (FY10) and ending in September 2011 (FY11). Field data collection activities are planned for the first year (FY10). Water-quality sampling sites will be established at the swine operation at the LWRFL. Water-quality samples of source waste materials and surface water will be collected for laboratory analysis of fecal indicator bacteria, pathogens, host-specific PCR biomarkers, antibiotic resistant bacteria, antibiotic resistant genes (ARGs), and nutrients (tables 1 and 2). In the final year of the project (FY11), the field site will be decommissioned and the USGS and USEPA will work collaboratively to develop a final project report that compiles results of data collection activities at the LWRFL.

The specific objectives of the USGS and USEPA research proposed at the LWRFL are to:

  1. measure the survival of bacterial indicator organisms and pathogens and the persistence of host-specific molecular biomarkers in soils receiving applications of swine waste materials, and

  2. assess transport of microorganisms and nutrients through overland runoff and from waste-application fields to adjacent streams.

As part of field data collection activities, the USGS has installed stream gages to monitor flow and automated samplers to collect stormwater-runoff samples at five surface-water sites (fig. 1). Samples at the stormwater monitoring stations will be collected during approximately 6 storm events. Soil samples will be collected following applications of lagoon effluent in the spray fields. A rain gage will be installed to record rainfall data at the LWRFL. The USGS will collect and provide samples to USEPA for analysis of fecal indicator bacteria, pathogens, host-specific PCR biomarkers, antibiotic resistant bacteria, and ARGs (table 1). USGS also will collect and analyze samples for nutrient concentrations (table 2).

Approach

The following tasks and data collection activities will be performed to meet the project objectives.

Task 1: Establish hydrologic and water-quality monitoring stations

Five monitoring sites at the LWRFL (fig. 1 and table 3) have been established for use in collecting water-quality samples and continuous discharge data. Monitoring sites ST1A, SR1, SR2, and ST1D were established to monitor stormwater runoff at the swine facility. Monitoring site BR1 was established in an agricultural field with no animal waste inputs to generate background data for use in examining relative differences in bacteria and nutrient loadings associated with sites SR1 and SR2 that receive overland runoff from the swine waste application fields. A rain gage was installed at site ST1A for recording continuous data on precipitation at the LWRFL.

ST1D SR1
Downstream monitoring station ST1D. Overland runoff monitoring station SR1.

Task 2: Continuously measure water stage at each water-quality monitoring station

At each monitoring site established as part of task 1, USGS will continuously measure water stage and perform discharge measurements to develop continuous records of discharge at each site. Pre-fabricated flumes have been installed at overland runoff sites BR1, SR1, and SR2 (fig. 1 and table 3). Discharge rating curves for the flumes will be used in combination with continuous stage measurements in each flume to determine continuous discharge records for each site.

Task 3: Characterization of animal wastes

Samples of fecal waste-material will be collected from the animal waste-storage lagoons at the swine operation for laboratory analyses (fig. 1). Samples of swine waste applied by spraying of lagoon effluent also will be collected in the waste application fields. The samples will be analyzed primarily for fecal bacterial indicators, pathogens, molecular biomarkers, and antimicrobial resistance (table 1). Select samples will be analyzed for nutrients (table 2).

Task 4: Collect soil samples for survivability testing of pathogenic microorganisms

Samples of surface soil material will be collected from the swine waste application fields for laboratory analysis of pathogens, fecal indicator bacteria, and antibiotic resistance bacteria, and host specific molecular biomarkers (fig. 1, table 1). Ideally, a soil sampling event will be conducted in coordination with the spraying of lagoon effluent in the application fields. Samples are proposed to be collected the day before spraying, the day of spraying, and then at 3, 7, 14, and 28 days following the application event.

Task 5: Perform rainfall-associated sample collection for evaluation of bacteria and nutrients at each water-quality monitoring station

At the five monitoring stations (fig. 1), automated samplers will be used to collect water samples during approximately 6 rainfall-runoff events during the one year monitoring period. For each event, approximately 5 samples will be collected at each site for microbiological and chemical analyses (table 1 and table 2). The water quality samples will be analyzed primarily for fecal bacterial indicators, pathogens, molecular biomarkers, antimicrobial resistance, and nutrients.

Task 6: Perform routine baseline sample collection for evaluation of bacteria and nutrients at each study area

In addition to storm-event sampling, instantaneous water samples will be collected on approximately a bi-weekly basis to establish baseline water-quality information. Samples will be collected at the upstream and downstream automated monitoring stations (sites ST1A and ST1D) and at two additional baseline sites (sites ST1B and ST1C) not included in the runoff monitoring network (fig. 1 and table 3). Discharge measurements will be performed at the time of sampling. The water samples will be analyzed primarily for fecal bacterial indicators, pathogens, molecular biomarkers, antimicrobial resistance, and nutrients (table 1 and table 2).

Task 7: Compile site use information

USGS staff will work with LWRFL staff to obtain available information on past and present activities at the swine operation that may be beneficial to interpreting data results obtained during the study. To the extent possible, USGS will compile information on waste applications (manure types and amounts, timing, and field locations), inorganic fertilizer applications, crop rotations, livestock populations, and historical pharmaceutical use for the swine operation.

Task 8: Prepare final report

Upon completion of field data collection activities, the USGS will work in collaboration with EPA to jointly complete an USGS Open-File Report (available online) that compiles and summarizes results of data collection activities at the LWRFL. The study results will provide animal producers, public health officials, and water-resource managers, at local and national levels, with beneficial information in designing and implementing best management practices for reducing the load of pathogenic microorganisms, nutrients, and OWCs reaching the environment.

Table 1. Summary of biological laboratory analyses for manure, water, and soil samples collected at the swine operation at the NCSU Lake Wheeler Road Field Laboratory, Wake County, North Carolina.
Laboratory Analyses and Constituents Method/Reference
Fecal Indicator Bacteria
Total Coliform Bacteria, MPN 1 Idexx ColiSure®
Escherichia coli, MPN Idexx ColiSure®
Enterococci, MPN Idexx Enterolert®
Enterococci, qPCR 2 Ludwig and Schleifer, 2000
Fecal Bacteroidetes, qPCR Dick and Field, 2004
Bacterial Pathogens
Salmonella spp., ± 3 Dynal Dynabeads, Anti-Salmonella®
Salmonella spp., qPCR Malorny et al., 2004
E. coli O157:H7, ± Dynal Dynabeads, Anti-O157®
E. coli O157:H7, qPCR Ibekwe et al., 2002; Heuvelink et al., 2007
Campylobacter spp., qPCR Lund et al., 2004
Antibiotic-resistant Bacteria
Antibiotic-resistant E. coli Broth microdilution, Trek Diagnostics Gram Negative Veterinary NARMS panel®
Antibiotic-resistant Enterococcus spp. Broth microdilution, Trek Diagnostics Gram Positive Veterinary NARMS panel®
Antibiotic resistant genes 4, qPCR Smith et al., 2004; Volkmann et al, 2003; Chen et al., 2007; Pei et al., 2006
Host-specific PCR Biomarkers 4
Cattle: M2, M3, CF128, CF193’ Shanks et al., 2008; Bernard and Field, 2000; Gourmelon et al., 2007
Pig: Pig-1-Bac, Pig-2-Bac, PF163 Mieszkin et al., 2009; Dick et al., 2005
Human: hum163, hum336, HF134, HF183 Bernard and Field, 2000

1. MPN = Most Probable Number

2. qPCR = quantitative real-time polymerase chain reaction

3. ± = presence/absence assay, cultivation-based

4. Partial listing, other gene targets may be explored as they emerge or as warranted by analysis of source fecal material

Table 2. Summary of chemical laboratory analyses for manure, water, and soil samples collected at the swine operation at the NCSU Lake Wheeler Road Field Laboratory, Wake County, North Carolina.
Laboratory Analyses and Constituents Method/Reference
Nutrients and Solids
Dissolved ammonia Fishman, 1993
Dissolved nitrite + nitrate Fishman, 1993
Total nitrogen, filtered (NH3+Organic N) Patton and Truitt, 2000
Total nitrogen, unfiltered (NH3+Organic N) Patton and Truitt, 2000
Dissolved phosphorus USEPA, 1993
Total phosphorus USEPA, 1993
Total suspended solids, residue at 105 ºC Fishman and Friedman, 1989

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