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Analytical Methods

References for Source Tracking Tools. July 2014

Bernhard, A.E., and Field, K.G., 2000, A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA: Applied and Environmental Microbiology, v. 66, no. 10, p. 4571–4574.

Boehm, A.B., Fuhrman, J.A., Morse, R.D., Grant, S.B., 2003, Tiered approach for identification of a human fecal pollution source at a recreational beach: Environmental Science and Technology, v. 37, p. 673–580.

Field, K.S., and Samadpour, M., 2007, Fecal source tracking, the indicator paradigm, and managing water quality: Water Research, v. 41, p. 3517–3538.

Dick, L.K., Bernhard, A.E., Brodeur, T.J., Santo Domingo, J.W., Simpson, J. M., Walters, S.P., and Field, K.G., 2005, Host distributions of uncultivated fecal Bacteroidales reveal genetic markers for fecal source identification: Applied and Environmental Microbiology, v. 71, no. 6, p. 3184–3191.

Francy, D.S., Bertke, E.E., Finnegan, D.P., Kephart, C.M., Sheets, R.A., Rhoades, J., and Stumpe, L., 2006, Use of spatial sampling and microbial source-tracking tools for understanding fecal contamination at two Lake Erie beaches, U.S. Geological Survey Scientific Investigations Report 2006–5298, 29 p.

Fremaux, B., Boa, T., and Yost, C.K., 2010, Quantitative real-time PCR assays for sensitive detection of Canada goose-specific fecal pollution in water samples: Applied and Environmental Microbiology, v. 76, no. 14, p. 4886–4889.

Glassmeyer, S.T., Furlong, E.T., Kolpin, D.W., Cahill, J.D., Zaugg, S.D., Werner, S.L., Meyer, M.T., and Cryak, D.D., 2005, Transport of chemical and microbial compounds from known wastewater discharges—potential for use as indicators of human fecal contamination: Environmental Science and technology, v. 39, no. 14, p. 5157–5169.

Green, H.C., Dick, L.K., Gilpin, B., Samadpour, M., and Field, K.G., 2012, Genetic markers for rapid PCR-based identification of gull, Canada goose, duck, and chicken fecal contamination in water: Applied and Environmental Microbiology, v. 78, no. 2, p. 503–510.

Griffin, J.F., Weisberg, S.B., and McGee, C.D., 2003, Evaluation of microbial source tracking methods using mixed fecal sources in aqueous test samples: Journal of Water and Health, v. 1, no. 4, p. 141–151.

Kildare, B.J., Leutenegger, C.M., McSwain, B.S., Bambic, D.G., Rajal, V.B., and Wuertz, S., 2007, 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: A Bayesian approach: Water Research, v. 41, p. 3701–3715.

Layton, Alice, McKay, L., Williams, D., Garrett, V., Gentry, R., and Sayler, G., 2006, Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water: Applied and Environmental Microbiology, v. 72, no. 6, p. 4214–4224.

Lu, J., Santo Domingo, J., Shanks, O.C., 2007, Identification of chicken-specific microbial sequences using a metagenomic approach: Water Research, v. 41, p. 3561–3574.
Lu, J., Santo Domingo, J.W., Lamendella, R., Edge, T., and Hill, S., 2008, Phylogenetic diversity and molecular detection of bacteria in gull feces: Applied and Environmental Microbiology, v. 74, no. 13, p. 3969–3976.

Santo Domingo, J.W., Bambic, D.G., Edge, T.A., and Wuertz, S., 2007, Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution: Water Research, v. 41, no. 16, p. 3639–3552.

Siefring S., Varma M., Atikovic E., Wymer L., and Haugland R., 2008, Improved real-time PCR assays for the detection of fecal indicator bacteria in surface waters with different instrument and reagent systems: Journal of Water and Health, v. 6, no. 2, p. 225–237.

Stewart, J.R., Ellender, R.D., Gooch, J.A., Jiang, S., Myoda, S.P., and Weisberg, S.B., 2003, Recommendations for microbial source tracking lessons learned from a methods comparison study: Journal of Water and health, v. 1, no. 4, p. 225–231.

Weidhaas, J.L., Macbeth, T.W., Olsen, R.L., Sadowsky, M.J., Norat, D., and Harwood, V.J., 2010, Identification of a Brevibacterium marker gene specific to poultry litter and development of a quantitative PCR assay: Journal of Applied Microbiology, v. 109, p. 334–347.

U.S. Environmental Protection Agency, 2010, Method B—Bacteroidales in water by TaqMan® quantitative polymerase chain reaction (qPCR) assay: Washington, D.C., EPA-822-R-10-003, 111 p. Accessed on February 7th, 2011 at

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