Soil Ecology Research Laboratory

Combining an optical strip-assay biosensor with ribotyping for bacterial source tracking of Enterococcus faecalis in the Lower Hudson River basin

Project summary:

As population pressure along the Hudson increases, the capacity to manage wastes effectively diminishes. Sub-urban lands begin to abut agricultural lands and when water quality is at risk, the finger-pointing begins. Agricultural operations that field apply animal manure are coming under increasing fire as potential sources for bacterial contamination of waterways. This problem was highlighted in a recent news article on WSTM-TV, Syracuse, entitled "Factory Farms Under Fire Over Waste Handling". At the same time sewage treatment plants run close to capacity. Public perception is that farms are responsible, in part or in full measure, for significant non-point source fecal pollution of the state's waterways, whereas sewage treatment plants represent significant potential point sources. In order to determine both point and nonpoint sources of fecal contamination in a water body, a means to track the source of fecal indicator bacteria must be devised. Several laboratories nationwide have developed effective genetic fingerprinting techniques that can be used to characterize fecal bacteria; specifically E. coli, at the strain or isolate level. The genetic fingerprints generated from field isolates and from animal feces are stored in a database and used to compare with samples taken from the environment. This allows one to determine the likely source of the bacteria when closely matching samples are found. Efforts to develop E. coli fingerprint databases in other regions of the country (Dombek et al. 2000); (Hartel et al. 2002) have shown that a database developed in one region is not useful for tracking E. coli from other regions, due to the high genetic plasticity of the organism. In essence, to effectively track the source of fecal contamination within a region requires intense targeting sampling combined with a local fingerprint database. I am currently collaborating on a Multi-state research project, which has seed-funding through the Federal Formula Funds Program at Cornell University, entitled "Soil Microbial Taxonomic and Functional Diversity as Affected by Land Use and Management", Project S-297. In this project, I am examining molecular approaches to bacterial source tracking in impaired waters and their potential use in monitoring total maximum daily loads using E. coli as the indicator species for database development. Recent work out of the Hartel laboratory at the University of Georgia (Wheeler et al. 2002; Kuntz et al. in review) indicates that Enterococcus faecalis, found in the human gut, may be a better indicator organism for the presence of fecal contamination due to human sources than E. coli. Enterococcus faecalis as defined by isolation on selective media appears to be unique to the digestive tracts of humans and some birds in field tests conducted to date (Kuntz et al. in review). I would like to extend the studies currently underway in the S-297 project to test this hypothesis in the two nominated tributaries in the Lower Hudson River Basin and to develop a portable, field-based biosensor to detect this pathogen in environmental samples.

Objectives:

1. To ribotype isolates of Enterococcus faecalis from water and suspected sources of contamination in order to develop a pathogen tracker database and to validate that the indicator species has a limited host range.
2. To use the database to identify the source(s) of fecal contamination in the Wappinger and Stoney Creek tributaries
3. To develop a species-specific ribosomal DNA gene biosensor for rapid detection of Enterococcus faecalis from environmental samples (water and human feces).
4. To correlate detection limits of target DNA with the number of Enterococcus faecalis cells/mL for usew in TDML studies in other parts of New York State.

Project staff:

Principal investigator: Janice Thies, Cornell University