Pathogens in Soil and Water

Researchers involved:
Rick Holley
Denis Krause
Joel Walkty
Ainsley Little
Stephanie Cheng
Bu Dengpan


A common concern regarding livestock manure management is potential for pathogens to move from manure into the soil and surface or ground water. There have been a number of high-profile incidents of water contamination with E. coli and food contamination with Salmonella in recent years, as well as growing concern regarding antibiotic resistance caused by routine use of antibiotics in intensive livestock production systems. Therefore, an important aspect of the La Broquerie Research Project is to monitor the presence and movement of pathogens in a system where hog manure is applied to forage land for cattle production.

Two studies on pathogens were carried out as part of the La Broquerie Research Project.

Study 1

The objectives of the first study were:

  • to follow the persistence of pathogens and their movement in the environment
  • to determine if cattle grazing on a hog manure-treated pasture can become infected with organisms from the hog manure

E. coli and Salmonella are the best-known pathogens associated with manure management and human poisonings. Therefore, these two organisms were the focus of this part of the La Broquerie Research Project. A third, less-known organism, Yersinia enterocolitica, is also common in large-scale hog operations, and was included in the study as well.

Study 2

The objective of the second study was to determine if antibiotic-resistant organisms were making their way into groundwater from hog manure applied on forage land, by comparing microorganisms present in the hog manure and in the groundwater.

Materials and Methods

Study 1

In order to attempt to trace the movement of pathogenic organisms through the system, samples were taken from a number of points in the system at various times:

  • hog manure - samples taken from the tanker during the application process
  • soil and vegetation -
    • 2004: sampled before and after manure application (1-14 days)
    • 2005: sampled before and after manure application (1 day), as well as just before cattle grazing (23-25 days after manure application
  • cattle feces - sampled before and at monthly intervals after grazing forages where manure had been applied. Samples were also taken from cattle grazed on non-manure-treated plots.
  • ground water - sampled from wells located throughout the research site in late April, mid-July, late September and early November in 2005.

Microorganisms were identified with DNA fingerprinting techniques to see if the same strains or serotypes were present in more than one component of the system.

Study 2

Samples were taken from hog manure after manure was applied to plots. Ground water samples were taken from wells located in each plot as noted above.

Samples were cultured in order to identify any microbes present. Microbes in both manure and water samples were resuscitated in buffered peptone water and then cultured in media containing various antibiotics. DNA analysis allowed researchers to determine the number of antibiotic resistant species of microbes and estimate the abundance of each species.


Study 1

The organism Yersinia was not found in any samples, indicating that the hog barn producing the manure used in this study is free of this pathogen.

Salmonella was found in hog manure and on the vegetation after manure was applied, in both 2004 and 2005. In 2004, the Salmonella serotype found on vegetation did not match the serotype found in the hog manure; in 2005, the serotypes in manure and on vegetation matched. Salmonella was not found in soil or cattle at any time. Salmonella was not found in groundwater samples taken throughout the summer of 2005, but it was found in samples taken in November (20 days after manure application). The Salmonella serotypes identified in these samples could not be traced to the serotypes found in the hog manure and so the source of the Salmonella in the water is not clear. Water may have been contaminated with Salmonella from manure applied to adjacent fields.

E. coli was found in hog manure and on vegetation after manure was applied in both years. It was also found in soil in some plots before manure was applied and in most plots immediately after manure was applied. In only a few cases was E. coli found in soil just before cattle were put on plots. E. coli was identified in cattle feces in both 2004 and 2005. However, when E. coli serovars were compared with DNA fingerprinting, there was only one case where the serovar in hog manure matched the one in cattle (in sampling period 1 in 2005). In all other cases, no link could be found between the E. coli in the hog manure and the E. coli in the soil or the cattle. E. coli was also identified in groundwater samples from one background well (beside the research site) and two wells within the research area before manure application in 2005. This was likely a result of contamination from adjacent fields.

Study 2

Microbes resistant to various antibiotics were identified in hog manure samples (Table 1). Microbes were most resistant to Aureomycin and Sulfamethazine. A low level of multi-drug resistant organisms were present in hog manure from the La Broquerie Research Project.

Table 1. Prevalence of Antibiotic Resistant Microbes in Hog Manure
Antibiotic Treatment Number of Antibiotic Resistant Microbes
Tetracycline 15
Erythromycin 21
Erythromycin and Tetracycline 5
Aureomycin 27
Sulfamethazine 40
Penicillin G 21
Aureomycin and Sulfamethazine and Penicillin G 8

When groundwater samples were cultured and analyzed in the same way as hog manure samples, antibiotic resistant microbes were found to be present but in much lower quantities than in hog manure (Table 2). Less than 53% of antibiotic resistant microbes found in hog manure were also found in ground water, indicating that over time and through soil filtration, many of the antibiotic resistant microorganisms are removed.

Table 2. Percentage of Antibiotic Resistant Microbes from Hog Manure found in Ground Water
Antibiotic Treatment Percentage of Antibiotic Resistant Microbes
Tetracycline 7 - 53%
Erythromycin 10 - 33%
Erythromycin and Tetracycline 0%
Aureomycin 0 - 30%
Sulfamethazine 0 - 30%
Penicillin G 0 - 43%
Aureomycin and Sulfamethazine and Penicillin G 0 - 38%

Not all plots in the La Broquerie Research Project contained antibiotic resistant microbes. Detection of these bacteria did not seem to be related to manure appliction, since antibiotic resistant bacteria were found in groundwater not only from manured plots but also from plots where no hog manure was applied. In fact, the no-manure grazed treatment was one of the treatments containing the highest number of antibiotic resistant microbes in groundwater samples. These microbes may have moved into this treatment through groundwater crossflow. Because of groundwater movement, it is difficult to identify the source of antibiotic resistant organisms in groundwater.


  • Yersinia enterocolitica was absent from all samples.
  • Salmonella and E. coli were present in hog manure and on vegetation shortly after manure application.
  • E. coli was present in low numbers on soil and vegetation.
  • Salmonella and E. coli did not appear to be transferred from hog manure to cattle grazing on manure-treated fields.
  • Salmonella and E. coli were detected in wells within and outside the research area in 2005. This contamination was probably from adjacent fields also treated with hog manure.
  • Antibiotic resistant bacteria may get into the groundwater from hog manure, but this contamination is not extensive.
  • It is difficult to determine precisely where the antibiotic resistant microbes come from in groundwater because of cross flow.

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