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OWML: Microbial Source Tracking

Microbial Source Tracking at the Ohio Water Microbiology Laboratory.

What is Microbial Source Tracking?
Microbial source tracking is the science (and art) of distinguishing the origins of gut microbes based on source-specific characteristics. This has been accomplished by looking for individual species that are host specific (such as the bacterium Bacteroides thetaiotaomicron, found in humans), by looking for populations with host-related characteristics (such as E. coli that are resistant to the antibiotics commonly used by humans), or by looking for genetic markers relevant to host-microbe interactions (such as the adhesin gene esp in human-associated Enterococcus faecium).

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Identifying sources of fecal contamination.
Identifying sources of fecal contamination in a watershed is important for implementing appropriate remedial and control strategies and understanding human health risk of the water’s use. It is generally accepted that it is best to take a multi-tiered approach on source tracking (Boehm and others, 2003; Francy and others, 2006), moving from general to specific and from less to more expensive (Field and Samadpour, 2007). Steps to identify sources include (1) sanitary surveys, (2) determining distributions of bacterial indicators in the watershed, (3) understanding how hydrologic and meteorological processes affect these distributions, (4) identifying hot spots of fecal contamination, and (5) identifying the presence of specific pathogens or chemical contaminants and applying microbial source tracking (MST) techniques.

>Click to learn more about strategies for step 4

Microbial Source Tracking applications.
Microbial source tracking often is used to inform managers so they can control fecal-contamination sources and meet water-quality standards. Many MST tools are able to detect the presence of fecal material from animal sources (such as humans, ruminants, dogs, pigs, and others). At this time, there is no compelling evidence that current MST tools can quantify inputs from various sources (such as 47% from humans, 12% from cattle, and 41% from wildlife). Also, MST tools alone cannot differentiate among specific contaminant pathways (such as septic systems or wastewater treatment facilities) with the same animal source. Discrimination of specific pathways of contamination requires additional information and an appropriate sampling strategy.

Microbial Source Tracking at USGS.

The U.S. Geological Survey, in cooperation with other agencies, state, and local governments, has made significant contributions to the science of microbial source tracking. MST continues to be an active area of research at the Ohio Water Microbiology Laboratory, and in other locations at the USGS.

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Microbial Source Tracking Reviews

Meays, C.L., Broersma, K., Nordin, R., Mazumder, A. 2004. Source tracking fecal bacteria in water: a critical review of current methods. Journal of Environmental Management 73:71-9.

Scott, T.M., Rose, J.B., Jenkins, T.M., Farrah, S.R., Lukasik, J. 2002. Microbial source tracking: current methodology and future directions. Applied and Environmental Microbiology 68:5796-5803. 

Seurinck, S., Verstraete, W., Siciliano, S. 2005. Microbial source tracking for identification of fecal pollution. Rev. Environ. Sci. Bio/Tech. 4:19-37.

Simpson, J.M., Santo Domingo, J.W., Reasoner, D.J. 2002. Microbial source tracking: state of the science. Environmental Science and Technology 36:5279-5288. 

Sinton, L.W., Finlay, R.K., Hannah, D.J. 1998. Distinguishing human from animal fecal contamination in water: a review. Nature New Zealand Journal of Marine and Freshwater Research 32:323-348.

Yan, T., Sadowsky, M.J. 2006. Determining sources of fecal bacteria in waterways. Environmental Monitering and Assessment Oct 28.



MST studies from the USGS:

Products produced, in part, with support of the USGS cooperative water program.

Becker, M.F., Peter, K.D., Masoner, J. 2002. Possible sources of nitrate in ground water at swine licensed-managed feeding operations in Oklahoma, 2001.  USGS Water-Resources Investigations 2002-4257.

Davis, J.V. and Barr, Miya N. 2006. Assessment of possible sources of microbiological contamination in the water column and streambed sediment of the Jacks Fork, Ozark National Scenic Riverways, Missouri - Phase III.  USGS Scientific Investigations Report 2006-5161.

Davis, J.V., Richards, J.M. 2002. Assessment of possible sources of microbiological contamination and water-quality characteristics of the Jacks Fork, Ozark National Scenic Riverways, Missouri – pahse II. USGS Water-Resources Investigations 2002-4209.

Dumouchelle, D.H., 2006. Use of DNA Markers for Investigating Sources of Bacteria in Contaminated Ground Water: Wooster Township, Wayne County, Ohio.  USGS Open File Report 2006-1382.

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.  USGS Scientific Investigations Report 2006-5298.

Francy, D.S., Struffolino, P., Brady, A.M.G. and Dwyer, D.F. 2005.  A spatial, multivariable approach for identifying proximate sources of Escherichia coli to Maumee Bay, Lake Erie, Ohio.  USGS Open File Report 2005-1386.

Griffin, G.W., Stokes, R., Rose, J.B., Paul III, J.H. 2000. Bacterial indicator occurrence and the use of an F+ specific RNA coliphage assay to identify fecal sources of Homosassa Springs, Florida. Microbiology Ecology. 39(1):56-64.

Hartel, P.G., Frick, E.A., Funk, A.L., Hill, J.L., Summer, J.D., Gregory, M.B. 2004. Sharing of ribotype patterns of Escherichia coli isolates during baseflow and stormflow conditions.  USGS Scientific Investigations Report 2004-5004.

Hyer, K.E., Moyer, D.L. 2003. Patterns and sources of fecal coliform bacteria in three streams in Virginia, 1999-2000. USGS Water-Resources Investigations 2003-4115.

Lamendella, R., Santo Domingo, J.W., Oerther, D.B., Vogel, J.R., Stoeckel, D.M. 2007. Assessment of fecal pollution sources in a small northern-plains watershed using PCR and phylogenetic analyses of Bacteroidetes 16S rRNA gene. FEMS Microbiology Ecology 59 (3), 651–660.

Moyer, D.L., Hyer, K.E. 2003. Use of the Hydrological Simulation Program-FORTRAN and Bacterial Source Tracking for development of the fecal coliform Total Maximum Daily load (TMDL) for Accotink Creek, Fairfax County, Virginia. USGS Water-Resources Investigations 2003-4160.

Moyer, D.L., Hyer, K.E. 2003. Use of the Hydrological Simulation Program_FORTRAN and Bacterial Source Tracking for development of the fecal coliform Total Maximum Daily Load (TMDL) for Blacks Run, Rockingham County, Virginia. USGS Water-Resources Investigations 2003-4161.

Moyer, D.L., Hyer, K.E. 2003. Use of the Hydrological Simulation Program-FORTRAN and Bacterial Source Tracking for development of the fecal coliform Total Maximum Daily Load (TMDL) for Christians Creek, Augusta County, Virginia. USGS Water-Resources Investigations 2003-4162.

Schlottmann, J.L., Tanner, R.S., Samadpour, M. 2000. Reconnaissance of the hydrology, water quality, and sources of bacterial and nutrient contamination in the Ozark Plateaus Aquifer System and Cave Springs Branch of Honey Creek, Delaware County, Oklahoma, March 1999-March 2000. USGS Water-Resources Investigations 2000-4210.

Stoeckel, D.M., Mathes, M.V., Hyer, K.E., Hagedorn, C., Kator, H., Lukasik, J., O'Brien, T.L., Fenger, T.W., Samadpour, M., Strickler, K.M., Wiggins, B.A. 2004. Comparison of seven protocols. to identify fecal contamination sources using Escherichia coli.  Environmental Science and Technology 38(22):6109-17.

Vogel, J.R., Stoeckel, D.M., Lamendella, R., Zelt, R.B., Santo Domingo, J.W., Walker, S.R., and Oerther, D.B. 2007. Identifying fecal sources in a selected catchment reach using multiple source-tracking tools.  Journal of Environmental Quality 36:718-729.

Wicklein, S.M. 2004. Evaluation of water quality for two St. Johns River tributaries receiving septic tank effluent, Duval County, Florida. USGS Water-Resources Investigations 2003-4299.

Other products supported, in whole or in part, by USGS

Stoeckel, D.M., and Harwood, V.J. 2007. Performance, design, and analysis in microbial source tracking studies.  Applied and Environmental Microbiology 73:2405-2415. doi: 10.1128/AEM.02473-06.

Stoeckel, D.M. 2006. Selection and application of microbial source tracking tools for water-quality investigations. USGS Techniques and Methods 2-A3.

USEPA 2005. Microbial Source Tracking Guide Document. EPA 600/R-05/064.