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Whodunnit? Finding the Source of E. coli in Pocatello’s Mink Creek

Thousands of recreational enthusiasts descend upon Mink Creek, near Pocatello, every summer. With the discovery that the creek and its tributaries contain high levels of E. coli, the U.S. Forest Service Caribou-Targhee National Forest (USFS)  — aided by researchers at the University of Idaho — were on the hunt to solve a mystery: Who or what is contaminating the water?

In the summer of 2018, in order to create an effective management plan around Mink Creek, the USFS. began to address the question. Through the Idaho Department of Environmental Quality (IDEQ), the USFS discovered that the levels of E. coli in Mink Creek and its tributaries exceeded standards for secondary contact.

The two main suspects in this whodunnit mystery were cattle — which use the area for grazing — and humans — who use recreational areas in the creek during the summer months. The clues were all in the water.

“When the DEQ brought up their E. coli contamination concerns, we knew we had to look closely at the source of the problem,” said Robbert Mickelsen, USFS Ecosystem Branch Chief at the Caribou-Targhee National Forest. “Our mission is to provide clean water for people to enjoy, and it was very important to us to be able to manage this issue correctly.”

If a living organism deposits fecal matter near the water, it will get washed in the waterway and contaminate it. Previous data collected by IDEQ suggested cattle as the culprit because high E. coli levels tended to overlap with the presence of cattle. However, there were spikes of E. coli weeks or even months after the cattle had left the area. Given that wildlife and humans periodically inhabit areas within the watershed, the dominant source of E. coli in the watershed remained unresolved.

Eric Winford, with the Rangeland Center collects water samples in Mink Creek.
Eric Winford, with the Rangeland Center collects water samples in Mink Creek.

U of I Water Research Team Finds the Answer

The investigation was not conducted by a conventional detective. Instead, the USFS partnered with the University of Idaho, asking the university to conduct the research necessary to identify the culprit.

Eric Winford, associate director of the U of I Rangeland Center, put together a team of experts and researchers from several departments across the university to compile and analyze water samples to solve the mystery.

“As in any mystery, in scenarios like these you often have a number of possible alternatives, that’s your set of suspects. Science uses hypothesis testing to look at each suspect and see who did it,” said Alan Kolok, director of the Idaho Water Resources Research Institute. “You ask a ‘yes’ and ‘no’ question and hypothesis testing allows scientists to find the answers. In this case, our suspects were cattle and humans, and we were able to answer ‘who did it’ by collecting data from the water during late spring, summer and early fall.”

Results from the data found that humans played a larger role in the presence of E. coli in the water than any other organism. Human DNA was found at 64% of the sites that had high levels of the bacteria. The data also show that the presence of a holiday had a positive influence on the levels of E. coli. Cattle DNA was found at 11% of the sites. The rest of the samples (29%) could not be identified and possibly came from other wildlife sources.

Scientists analyze water samples in a lab.
Scientists analyze water samples in a lab. By using microbial source tracking (MST) they’ll helps determine whether the fecal bacteria present in the water came from cattle or humans.

To conduct their analysis, the researchers selected 14 locations across the watershed based on the use of land by cattle and recreationists. Using microbial source tracking (MST) — which helps determine whether the fecal bacteria present in the water came from cattle or humans — they sampled the water before and after selected dates in 2019 to capture the movement of the cattle and the use of the watershed by recreationists after key summer holidays.

“MST is a gold standard technique — even used in forensics — that picks up DNA from the water samples and links it to the source organism who left it behind,” said U of I College of Agricultural and Life Sciences researcher Jane Lucas, who ran much of the lab work and analysis of samples in the study. “You can’t see the DNA, but you can pick up and identify its signature just like you can do with fingerprints in a crime scene.”

The collaboration with U of I was a very productive and positive experience, said Mickelsen.

“It provided us with the information we needed to help us focus on the real issue in the watershed and to direct our efforts to solve it,” he said.

An E. coli mystery solved with DNA

U of I researchers help solve a water contamination mystery. Video by the Idaho Rangeland Resources Commission.

Management Implications

The U of I team presented a report to the USFS in early August, which include recommendations for public land and recreational areas management, such as moving cattle farther from the stream by grazing at higher elevations when temperatures are high, herding cattle where spring water is available or developing off-stream water sources. Since humans were responsible for the majority of the high levels of E. coli in this study, the suggestions included keeping public toilets clean and available, increasing public toilets at certain dates and locations or educating the public about the risks of contamination via kiosks.

Mickelsen said the USFS is already adapting some of these strategies.

“We are working to find ways to improve the recreation facilities in the area to reduce contamination in the streams,” said Mickelsen. “We might add new facilities and will make sure the existing ones are well designed and well maintained. National Forest staff also started to educate the public through appearances in the media.”

The report “Relationships among fecal coliforms, the location of cattle in a mixed-land-sed rangeland watershed, and microbial source racking markers,” was funded by a $25,000 grant from the USFS and matching $6,800 from IWRRI and the U of I Rangeland Center.

Magnifying Glass

Meet the U of I Team of Researchers

  • Reed Findlay, U of I Extension Eastern District educator, Crops and Horticulture
  • Naveen Joseph, postdoctoral fellow, Idaho Water Resources Research Institute (IWRRI)
  • Alan Kolok, IWRRI director
  • Jane Lucas, Soil and Water Systems Research postdoctoral associate, College of Agricultural and Life Sciences
  • Jim Sprinkle, research faculty and Extension specialist, Nancy Cummings Research Extension and Education Center
  • Michael Strickland, Soil and Water Systems Research associate professor, College of Agricultural and Life Sciences
  • Nikhil Vishwanath, doctoral candidate, IWRRI
  • Eric Winford, associate director, U of I Rangeland Center

Article by Maria Ortega, University of Idaho Boise.

Published October 2020.

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