French Broad River

DNA source testing of E. coli could become a powerful new tool for N.C. riverkeepers

July 15, 2021 by Greg Barnes

DNA source testing of E. coli could become a powerful new tool for N.C. riverkeepers - North Carolina Health News

For decades, industrial farms have blamed people, not their animals, for much of the fecal bacteria that gets into the state’s rivers and streams. The riverkeepers think DNA testing will help them prove who is actually responsible on a case-by-case basis.

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.

Gauging the lead threat in NC waters and aquatic life

November 14, 2020 by Carolina Public Press

Gauging the lead threat in NC waters and aquatic life - North Carolina Health News

Upcoming federal trial of Brevard city official over handling of lead contamination highlights a concern that affects other NC communities.

by Dan DeWit, Carolina Public Press

Carolina Public Press is an independent, in-depth and investigative nonprofit news service for North Carolina.

When MountainTrue organized opposition to a Henderson County Sheriff’s Office firing range near Saluda in 2018, it was not just because of obvious environmental concerns: Would highly toxic lead seep from the range into the nearby, pristine Green River? Could it be absorbed by plants and wildlife? Did it pose a long-term threat to public drinking supplies?

The environmental group also fought the project near the Henderson-Polk county line because the lack of regulation of outdoor firing ranges made these questions almost impossible to answer.

“The problem with lead is there are just so many ways it can get into the environment and find an exposure pathway to humans,” said Gray Jernigan, MountainTrue’s Green Riverkeeper, who helped convince the Henderson County Commission to abandon plans for the project.

“To us, there was just too much uncertainty.”

Scenarios presented as future possibilities in Henderson County are already pressing in nearby Brevard, a city of 8,000 a few miles to the west in Transylvania County.

Brevard’s public works director, David Lutz, is due to stand trial in January on federal charges of mishandling soil from an abandoned Police Department firing range measured at more than 25 times the federal hazardous waste threshold.

Meanwhile, the state has ordered the city to clean up the remaining lead-laden soil at this range, on the French Broad River, as well as at an older city shooting range on otherwise pristine Cathey’s Creek, which is the sole source of the city’s drinking water.

These mandates came after years of lead accumulation and only because somebody spoke up, in this case a neighbor of one of the ranges who complained to the state.

Someone speaking up is about the only way cleanups can be mandated, according to federal environmental policy that says government agencies can order remediation but cannot regulate them as producers of solid waste.

“This broad exemption from environmental statutes is producing thousands of highly contaminated toxic waste sites at firing ranges across the country,” according to a 2001 report from the Environmental Working Group that Jernigan submitted to support his opposition to the Saluda range.

The date of that report is another, indirect, symptom of this exemption. Without the permit applications, inspection reports and test results generated by regulation, scientists and environmentalists have little documentation on which to base research or position papers.

As a result, Jernigan was forced to rely on reports that were more than a decade old or from foreign countries.

But these studies raise issues that remain relevant over time and distance, including the extreme toxicity of lead and the large amounts of it that can be pumped into firing range “backstops” — the soil piled behind targets to catch fired ammunition.

“Lead is considered the number one environmental threat to children’s health by the federal government” and, even “at very low levels, is linked to subtle developmental delays and reduced IQ in children,” the Working Group report said, echoing the current guidance from the U.S. Environmental Protection Agency that any level of lead in the blood of children is unsafe.

A conservative estimate of use at the roughly 1,800 outdoor ranges in the U.S. “would put nearly nine million pounds of lead into the environment per year,” the Working Group report said.

The activity at ranges and the number of them has likely grown significantly in recent years with shooting’s increasing popularity, according to the National Shooting Sports Foundation industry group.

Concentrations of lead in range backstops globally have routinely been found to exceed 10,000 parts per million, according to a 2002 report from a researcher at New Zealand’s Lincoln University. By comparison, the N.C. Department of Environmental Quality requires remediation of soil measured at more than 270 parts per million of lead.

That report also addresses the more complicated question of how much of that lead migrates into the environment. Typically, about 90% of lead at ranges is contained in stable lead slugs, the report said. But much of the remaining 10%, corroded by rain and chemicals in the soil, can make its way into groundwater.

And given the often high overall concentrations of lead in the soil, the Lincoln University report says, “The corrosion products represent a large reservoir of highly soluble lead.”

Testing in North Carolina, though far from comprehensive, has revealed little evidence that significant amounts of lead from ranges have seeped into ground or surface waters.

DEQ’s routine monitoring of rivers does not sample for lead or other heavy metals, said Anna Gurney, spokeswoman for the agency’s Division of Water Resources. The division’s random sampling program, which does test for metals, has not surveyed streams near the few range sites, including those owned by Brevard, that have been scrutinized by the state because of known lead contamination.

But the city has tested runoff from both sites and found it free of lead, as was drinking water measured at taps throughout the city.

Avner Vengosh, a Duke University professor of geochemistry and water quality, led a study that tested groundwater at hundreds of sites throughout North Carolina over the last decade. Lead shows up far less often than some other toxins, including arsenic, which in North Carolina is often naturally occurring.

“We don’t commonly see lead in groundwater unless it’s coming from people’s pipes, which is a different ballgame,” he said.

Soil and rainwater are usually not acidic enough to dissolve lead, he said. Lead also quickly settles out of both ground and surface water because of its lack of buoyancy, said Shea Tuberty, a biology professor at Appalachian State University, and a past president of the Carolina Society of Environmental Toxicology and Chemistry.

“It’s called a heavy metal for a reason,” he said.

Along with the volume of water in large rivers, this property makes it unlikely that, for example, Brevard’s abandoned range on the French Broad would lead to significant contamination of the river’s water, especially miles downstream.

“I’m sure you’ve heard the old paradigm, ‘Dilution is the solution to pollution,’” he said. “With lead, it works pretty well.”

Not just the water

But water is not lead’s only pathway to humans. Tuberty and his students have tested for lead in both the water and aquatic life of the Broad River near Mooresboro, to the east in Cleveland County, as part of an ongoing study of contamination from a zinc recycling plant and an old Duke Energy coal ash pond.

Because of their feeding patterns, sunfish showed especially high concentrations of lead, as much as 2.3 parts per million, or several times the level considered safe for human consumption.

Lead that settles on the riverbed is taken up by algae, which is consumed by snails and tiny fingernail clams, a favorite food of sunfish, which, alarmingly, are a favorite game fish of young, novice anglers.

“If you’re using a Zebco with a bobber and a weight, that’s the fish you’re going to catch,” he said.

What does all this say about the hazard of lead in the soil of range sites such as Brevard’s?

“You can’t just say, there’s lead in the ground, so this is the worst thing ever,” he said, “but you can’t assume there’s no impact, ever.”

The path to improvement

There’s one upside to the discovery of lead-tainted soil at Brevard’s sites: It might raise awareness of the potential for impact and start to shed light on the extent of it.

The investigation already highlighted the potential for contamination in the soil at firing ranges. Even after the removal of the soil with the highest lead concentration from the Broad River site, some of the remaining soil there, as well as at the older abandoned range on Cathey’s Creek, was measured at above the state’s remediation standard.

The city recently approved $451,000 to complete the cleanup of these sites. As this work proceeds, the state will require the city’s consultant to regularly test lead levels in the river and creek, providing at least a partial picture of the potential for lead to seep from the soil.

As Lutz’s case progresses, Jernigan also anticipates testimony and documents will fill in more gaps in the public’s knowledge of how lead accumulates at ranges and the danger presented by contaminated soil.

“This reveals that there is a lot we just don’t know about this issue,” Jernigan said.

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