In the last decade, increased attention has been given to the physical and biological integrity of our nation’s water bodies. The 2000 National Water Quality Inventory reported that 39% of the rivers and streams evaluated were polluted, and pathogens are among the top three causes of impairment (http://www.epa.gov/305b/2000report/). In addition, the leading source of impairment was reported to be non-point-source pollution from urban and agricultural lands during periods of precipitation and runoff. Factors contributing to water impairment include increased land use and rural development which place receiving water bodies at high risk of contamination (25) and alterations in the hydrologic cycle, associated with global climate change, that are increasing the magnitude and frequency of runoff events (18, 25). States are addressing compromised water quality by identifying impaired water bodies and establishing total maximum daily load (TMDL) programs designed to limit pollution and restore water quality. An important part of a regional TMDL program is assessment of the relative microbial impacts of various potential waste inputs in a watershed, and a source-specific microbial indicator system would be an important component of such a program.

Enteric bacteria have traditionally been used as indicators of fecal contamination in source, drinking, and recreational waters. However, research has demonstrated that these bacteria may not be appropriate indicators of pathogenic viruses and protozoa (21, 23, 24), and the need for reliable index or indicator organisms for these pathogens has been widely recognized (12, 20; R. Karlin, R. Fayer, M Arrowood, C. Noss, and D. Schoenen, Proc. Am. Water Works Assoc. Source Water Prot. Symp.: Focus on Waterborne Pathogens, 1998 [on CD-ROM]). Coliphages, viruses that infect Escherichia coli bacteria, have been proposed by the U.S. Environmental Protection Agency as a viral indicator of fecal contamination of groundwater (35), and male-specific (F+) coliphages may provide the additional benefit of distinguishing human and animal fecal sources of pollution.

Coliphages infect coliform bacteria, are nonpathogenic to humans, and are more similar to enteric viruses with respect to physical characteristics, environmental persistence, and resistance to treatment processes than are indicator bacteria (5, 14, 20, 27, 32, 36). Coliphages are consistently present in domestic raw and treated sewage and have been reported to occur in concentrations ranging from 103 to 107 PFU/liter, depending on the level of sewage treatment (2, 5, 7, 11). In addition, a variety of domestic and feral animals also shed coliphages in their feces (2, 4, 8, 11, 22).

The coliphages can be divided into six major morphological groups, two of which infect only F+ male hosts through the F sex pilus (30). The two F+ coliphage families are the Leviviridae (small, icosahedral, single-stranded RNA phages) and the Inoviridae (filamentous, single-stranded DNA phages). F+ RNA coliphages have been highly correlated with virus concentrations in raw and treated wastewater, raw and partially treated drinking water, and surface and recreational waters (14). Other studies have found that F+ RNA coliphages behave similarly to enteric viruses in environmental waters and therefore may be used to indicate the viral safety of source waters (4, 9, 31). In addition, grouping of F+ RNA coliphages by serotyping or DNA oligoprobing may be used to identify and distinguish between human and nonhuman fecal contamination sources of F+ RNA coliphages (4, 11, 15). Griffin et al. (10) and Brion et al. (1) reported the use of F+ RNA coliphage analysis to confirm putative animal and human waste impacts on environmental waters.

In contrast to the F+ RNA coliphages, little is known about the ecology of F+ DNA coliphages (8). Research conducted in Massachusetts (19) and in other geographic areas by Sobsey and colleagues (personal communication) found F+ DNA coliphages in a variety of water sources impacted by human and animal fecal waste sources. Furthermore, the F+ DNA coliphages were commonly detected during warmer months, when F+ RNA coliphages were absent from surface water samples (19). Seasonal differences in the proportions of F+ DNA and RNA coliphage occurrence may reflect differential survival characteristics, changes in coliphage excretion patterns of hosts, or changes in land use in impacted watersheds.

This research investigated the presence, prevalence, and densities of F+ RNA and DNA coliphages in animal feces, animal wastewater from agricultural activities, and municipal wastewater. F+ RNA coliphage typing was used to distinguish fecal contamination sources. In addition, the densities and relative proportions of F+ RNA and DNA coliphages in surface waters were evaluated at well-defined sampling sites to determine their usefulness as a water quality surveillance tool with which to identify the most significant viral input sources (human versus animal).