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Home > Protecting Our Lands & Waters > Clean Water Fund > Clean Water Research Program > 7 Mile Creek Watershed

Growth, Survival, and Genetic Structure of E. coli found in Ditch Sediments and Water at the Seven Mile Creek Watershed

Principal Investigator: Michael Sadowsky
Organization(s): University of Minnesota, Department of Soil, Water, and Climate
Sponsor: Clean Water Legacy Act
Award Amount: $192,804
Start Date: 7/1/2008 | End Date: 6/30/2010
Project Manager(s): Adam Birr

FINAL REPORT: Growth, Survival, and Structure of E.coli found in Ditch Sediments (PDF: 1.4 MB/45 pages)


Escherichia coli (E. coli) is currently used as an indicator of fecal contamination in freshwater systems. The presence of E. coli in water is thought to indicate recent fecal contamination and in turn signal the possible presence of pathogens. However, several studies have reported the presence of naturalized or indigenous E. coli strains that persist and potentially grow in the environment, regardless of new inputs.

  • Sources of fecal contamination include sewage and septic systems, livestock feedlots, wildlife, and run off from urban and agricultural land

In this study, researchers used molecular techniques to determine the sources of E. coli contamination and to examine the growth and survival of E. coli  in a drainage ditch located within the Seven Mile Creek (SMC) watershed situated in eastern Nicollet County, Minnesota. The purpose of this study was to:

  1. The bacteria E.coli under a microscopeExamine the spatial and temporal distribution of E. coli in water and sediments of the SMC
  2. Examine the persistence and transport of these bacteria in the SMC
  3. Use DNA fingerprinting analyses to examine the genetic structure of E. coli populations obtained from water and sediment samples to determine if these bacteria are likely growing in this environment or if they arise as a result of new inputs
  4. Determine potential sources of fecal contamination in the SMC by using molecular biological tools


Samples were collected in 2008 (July - October), 2009 (April - October), and 2010 (April -June). Detailed methods describing sample collection and processing, enumeration of E. coli, E.coli isolation, and DNA extraction and analysis is in the methods section of the Final Report.

This project uses the polymerase chain reaction (PCR) method.  PCR is a molecular biology analysis use to amplify a segment of DNA which can then be used to examine a specific genetic sequence.


  • E. coli counts varied considerably across sites and by dates and were likely affected by seasonal parameters, such as temperature and rainfall.
  • Host specific PCR assays indicated that cattle were likely major contributors to the fecal loading of the SMC, although swine and poultry fecal markers were also detected sporadically. There was no indication of contamination from human waste.
  • DNA analysis indicated that the E. coli populations present in SMC were very diverse, but consisted of both transient and persistent strains. Persistent strains are likely indigenous to the sites and may grow in the sediment and/or water.
  • Water and sediment isolates are closely related in each year, suggesting that there is mixing of E. coli strains in the sediment and water column. This may contribute to elevated E.coli counts.
  • Mixing and transport of E. coli isolates occur between sites during flow events.
  • Flow rate, temperature effects, rainfall and run-off events are likely factors influencing the distribution of E.coli populations in SMC.
    • E. coli counts were  higher during the summer than the rest of the sampling period.
  • Indigenous E. coli stains are likely present in SMC sediments and some strains appear to grow in the sediments. Results show that both newly acquired and indigenous E. coli strains are present in the SMC.

Overall, researchers found that not all E. coli strains originated from fecal matter and many of these bacteria naturally occur in sediments. This means that in the absence of any inputs, a population of E. coli could still be present. Often the presence of any E. coli is associated with a recent contamination; while this study showed that specific strains are likely indigenous to a site and may not be the best indicator of contamination.

Tables of results can be found at the end of the Final Report.


  • Examine ditch sediment and water samples for the presence and numbers of E. coli over a two year period;
  • Determine the proportion of the E. coli population that are stable members of the microbial community (i.e. indigenous) and those which are likely to be transient (i.e. newly acquired) due to run-off; and
  • Use DNA hybridization, PCR, and DNA fingerprint approaches in an attempt to determine the potential sources of E. coli present in ditch sediment and water samples.  

MDA Contact

Margaret Wagner
Supervisor, Clean Water Technical Unit