Molecular and Metagenomic Tools to Determine Primary and Secondary Sources of Fecal Bacteria in Waterways.

Many of the world’s rivers, lakes, and streams do not meet the water quality standard for fecal coliform bacteria. Sources of fecal coliform bacteria include runoff from feedlots and manure-amended agricultural land, wildlife, inadequate septic systems, urban runoff, and sewage discharges.  High levels of fecal bacteria in rivers, lakes, streams, and aquifers threaten the use of these water resources for swimming and drinking. A better understanding of the sources of fecal contamination in these waters will be a valuable tool in efforts to minimize the deleterious environmental consequences of fecal pollution.  The human health risks associated with the ingestion of water contaminated with human fecal materials is well documented.  Also, there is increasing concern about possible pathogens associated with fecal material from animal sources. The ability to distinguish between human and animal sources of fecal contamination is an important assessment tool.  From a public health perspective, fecal contamination originating from human sources poses a greater human health risk than that originating from animal sources.  Armed with knowledge about contamination sources, agencies could respond more quickly and more directly to inform that segment of the population at the greatest risk, without unnecessarily alarming people at low or insignificant risk.  From a water quality perspective the ability to narrow the source of fecal contamination among the many potential sources will facilitate more tailored and cost effective pollution abatement efforts. Since conventional microbiological methods cannot differentiate between sources of fecal pollution giving rise to elevated coliform counts. We have developed and utilized various genotypic methods to determine the source of water-borne fecal contamination. Here we report on the use of the horizontal fluorophore-enhanced HFERP DNA fingerprinting technique and DNA sequencing (metagenomic) methods,to examine sources and sinks of fecal bacteria in waterways. We also report on the use of these methods to determine if fecal bacteria in aquatic environments are sources of fecal bacteria on beaches, describe secondary habitats for many fecal bacteria and pathogens, and discuss the advantages and disadvantages of these approaches. Since E. coli and coliform bacteria appear to be ubiquitous in all environments examined, we also discuss why these organisms may not be useful indicators of fecal pollution and discuss strategies to overcome these deficiencies.