By Greg Barnes

In May, Katy Hunt jumped out of her truck alongside a small stream in Lenoir County and knew instantly that something was wrong.

“I was smacked in the face with the smell of waste,” said Hunt, the Lower Neuse River riverkeeper. “The water smelled foul. The air smelled foul. The water looked funny. It had this reddish-like orange and brownish sheen to the surface.”

Hunt said she took samples in the creek to test for Escherichia, a common type of fecal bacteria also known as E. coli, and reported her findings to the state Department of Environmental Quality. The samples exceeded 2,400 Most Probable Number of  E. coli, more than 10 times what the U.S. Environmental Protection Agency considers safe for recreational waters.

Initially, Hunt said she suspected the contamination was coming from a large nearby hog farm, but she has since learned that the farm is downstream from the contamination. She said she continues to investigate the source, but her efforts are hamstrung because the DEQ cannot legally share its findings with her.

“I feel like I’ve been trying to solve a 1,000-piece puzzle without even knowing what the picture is supposed to look like,” Hunt said. “So, it’s really hard to figure out what’s going on in this stream when I don’t have all of the information available to me that I could.”

The reason? A law passed by the General Assembly in 2014 prohibits the DEQ from sharing information with Hunt or the public unless and until it issues a notice of violation against the polluter. That means the DEQ couldn’t share information with Hunt or the state’s 14 other riverkeepers even if it wanted to. 

But Hunt has a new tool now.  For the first time, she used DNA testing in an effort to determine whether the E-coli in the creek came from hogs, poultry, people, pets or nature. It’s a tool that Hunt and other riverkeepers plan to use regularly starting this month to help them identify sources of fecal contamination.

The blame game

When fecal bacteria is found in the state’s rivers and streams, the hog and poultry industries often try to place the blame on public sewer systems or private septic tanks.

There’s no arguing that a tremendous amount of human fecal waste gets into the state’s waterways from old and leaking sewer pipes, sewer overflows and wastewater treatment plant bypasses that happen when heavy rains overwhelm the systems.

Last year alone, sewer overflows resulted in 74 million gallons of raw sewage spilling into the state’s surface waters, figures from the N.C. Department of Environmental Quality show.

Common causes of sewer overflows are line breaks and blockages, sewer defects that allow stormwater and groundwater to overwhelm a system, power failures, and improper sewer design. The state estimates that it would cost $11 billion to fix all of the aging sewer systems in North Carolina.

But fecal waste from industrial farms housing thousands upon thousands of swine, chickens, turkeys and cattle — commonly referred to as concentrated animal feeding operations or CAFOs — share some of the blame, too.

“A lot of times when we talk about the hog farms and the poultry farms and how they contribute to pollution a lot of people are out there like, ‘It’s not the hog farms, it’s the wastewater treatment plants in the city, they’re the ones who are spilling waste and, you know, dumping in this that and the other thing.’ ”  Hunt said. “It’s very frustrating because it’s, ‘Yes. You both are doing it.’ ” 

Hunt and the other riverkeepers say they hope the DNA testing will help them definitively determine that E. coli bacteria in a stream or a river came from humans or swine or whatever and then to use that scientific information to help them pinpoint the source — be it a sewer line, a farm or something entirely different.

“Hopefully, this DNA testing will show, ‘Yeah, it is coming from your facility, and we can prove that as a result of DNA testing,’ ” said Larry Baldwin, the Pure Farms Pure Water NC Campaign coordinator for Waterkeeper Alliance and a former riverkeeper.

How DNA testing works

Before DNA testing became available, the riverkeepers were checking only for E. coli in rivers, creeks and streams without a definitive way to say where it came from. They were finding the bacteria — often in large numbers — throughout the state. 

A report released in May by Waterkeeper Alliance and Waterkeepers North Carolina found that every river basin in North Carolina failed the EPA’s safe E. coli criteria at least once last summer, and at least 20 failures occurred every week.

“Although not all E. coli bacteria are harmful, numerous studies have demonstrated that E. coli concentrations are the best predictor of swimming-associated gastrointestinal illness,” according to the report. “Additionally, illnesses such as eye infections, skin irritations, and respiratory disease are common in people who come into contact with fecal-contaminated water.”

Beginning this month, the state’s riverkeepers plan to start taking samples of suspected E. coli contamination and sending them to a company in Colorado called Jonah Ventures for DNA analysis. The company has been in business since 2014 and started doing environmental DNA testing about a year ago, said Joe Craine, a company co-founder.

Craine said the testing methods Jonah Ventures uses are similar to the polymerase chain reaction (PCR) testing used to determine whether someone has COVID-19.

“We’ll actually look for the DNA of the hosts,” Craine said. “So we’re going to look for the mitochondria of chickens in humans and cattle and pigs, for example. And so if you see elevated E. coli and then also at the same time see elevated mitochondria for cattle, then the simplest explanation for that is that those E. coli came from the cattle.”

Craine said that although the technology could be used to trace the source of E. coli contamination to a specific farm or a specific septic tank, in practice it doesn’t get used that way. 

“To use this technology to do that you would have to sample upstream and downstream of a farm and see E. coli levels jump, as well as source DNA,” he said. “Potentially, you can do that if you sample often enough along a stream or river, that you can start to pin down spatially, geographically, that source.

“But we tend not to use the technology to the point where we can look at the DNA in the same way that we’re doing forensics for a crime … So instead we just say it’s cattle DNA or it’s chicken DNA, pig DNA, human DNA.”

Craine said the technology can be used relatively well to lessen or lower, but not necessarily rule out, the probability of a source.

“But if you have a situation where there’s uncertainty about where the E. coli levels are coming from — chicken waste or pig waste or cow waste or somebody’s septic system — and all we see is high levels of one particular host, then more than likely those two things are connected. That would be the way that I’d recommend it get used.”

The technology isn’t cheap, however. Craine said testing for E. coli in a stream, like the riverkeepers do now, typically costs about $25. The DNA testing costs $125 per sample, he said.

Some riverkeepers said they are defraying the costs through grants, donations and foundation funding. In the mountains, the General Assembly approved a bill in 2019 that allocated $100,000 for DNA testing. Craine said MountainTrue Riverkeeper Carson Hartwell got the other riverkeepers excited about using DNA testing. 

DNA testing in the mountains

Hartwell, the riverkeeper for the French Broad River in the western mountains, said he has been using DNA testing for about a year. He said it helped determine that much of the E. coli in the river is coming from cattle. 

“I thought it was cow and human but I didn’t know that cow would be quite as prevalent as it was,” Hartwell said.

Initially, MountainTrue took samples from more than 30 locations on the French Broad. Cattle DNA was found in 44 of the 55 samples, according to the Asheville Citizen-Times. Waste from cattle often gets into creeks and streams on farms and then flows into the French Broad. 

As a result of the testing, Hartwell said, his office is now advocating that the state provide more funding to soil and water conservation districts, which help farmers fence in cattle, provide stream crossings and do other best-management practices to keep E. coli out of the French Broad.

DNA testing and a subsequent DEQ investigation appear to have ruled out hogs as the source of pollution in the Lenoir County stream that Hunt, the Lower Neuse riverkeeper, continues to investigate.

“We don’t believe it has anything to do with the hog farm,” Anna Gurney, a spokeswoman for the DEQ, told NC Health News. “We actually feel like it’s probably naturally occurring due to, you know, rains and organic matter and wild animals, that kind of stuff.”

Gurney said the DEQ will monitor the site more regularly, “to figure out if there’s an issue there, but we found nothing that was sort of out of the ordinary, if you will.”

Regardless of those findings, Jill Howell, the Pamlico-Tar riverkeeper for Sound Rivers, is convinced that DNA testing will become a valuable tool as she begins to implement it this month.

One of the most common problems Howell sees in the Pamlico and Tar rivers are fecal bacteria, algal blooms and fish kills caused by excessive nutrients.

“This is a way to confirm that it’s coming from humans or it’s coming from farms or it’s coming from both, just another way to bolster the data that we’re already collecting,” Howell said.

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Greg Barnes retired in 2018 from The Fayetteville Observer, where he worked as senior reporter, editor, columnist and reporter for more than 30 years. Contact him at: gregbarnes401 at