Eichmiller, Jessica J.2012-12-212012-12-212012-11https://hdl.handle.net/11299/141693University of Minnesota Ph.D. dissertation. November 2012. Major:Water Resources Science. Advisors: Michael J. Sadowsky, Randall E. Hicks. 1 computer file (PDF): xi, 182 pages.Fecal contamination of surface waters is a widespread environmental problem and a public health concern. The presence and degree of fecal contamination in surface waters is based on the abundance of culturable fecal indicator bacteria (FIB), such as Escherichia coli or Enterococcus spp. Culture-based methods, however, require 18 to 48 hr to process and are unable to determine sources and assess risk in real time. Advances in molecular methods has led to the development of several promising "real time" detection assays that quantify the abundance of genetic markers for FIB, but their distribution and persistence in freshwater environments is not well-studied. This work explores the use of rapid, culture-independent methods for the identification of fecal pollution. In particular, the application of rapid tools is considered for freshwater beaches, particularly those of Lake Superior. In this thesis I characterized the short time scale variation in goose/duck and human sources of fecal contamination, Salmonella spp., and pathogenic E. coli at three Duluth area beaches, examined the distribution of genetic markers of fecal pollution in sand and sediment of a Duluth-Superior Harbor beach near a wastewater outfall, measured the effects of temperature and moisture on the persistence of genetic markers in water, sand, and sediment, and compared the decay rates of genetic markers of fecal pollution and bacterial pathogens. Goose/duck-borne E. coli consistently made up 12 to 29% of E. coli at Duluth-Superior Harbor sites and 5% of E. coli at a Lake Superior beach. In contrast, a human-specific Bacteroides genetic marker exhibited high temporal variability, and was detected at great frequency in the water column at a site located on the inner harbor. Salmonella spp. and potentially pathogenic E. coli were infrequently detected at the study beaches. At a beach near a wastewater treatment plant outfall, effluent loading likely controlled the abundance of molecular indicators of fecal pollution in the water column. The concentration of enterococci and human-specific Bacteroides genetic markers in the water column was correlated to the abundance of genetic markers at some depths in sand and sediment. Sand and sediment contained more enterococci and total Bacteroides genetic markers on a per mass basis than water, whereas the concentration of human-specific Bacteroides was similar across sample types. In most instances, genetic markers were most abundant in the top 1 to 3 cm of sand and sediment. The decay of genetic markers of fecal pollution in sand and sediment was slow relative to the water column, and some genetic markers persisted or increased over time within sand and sediment. Molecular indicators decayed more rapidly at higher temperatures in all sample types and this decay was negatively correlated with sand moisture. The genetic marker for human-specific fecal contamination exhibited decay rates similar to markers for bacterial pathogens in sand, whereas non-source-specific markers decayed more slowly than bacterial pathogen markers under most conditions. Taken together, the relative sources of contamination, beach location, and other site-specific factors, such as the potential for resuspension of sand and sediment and pathogen abundance, should be considered in the choice of genetic markers for water quality monitoring on freshwater beaches.en-USBeachFecal indicator bacteriaLake SuperiorMolecular indicatorsPathogensPersistenceThesis or Dissertation