Fears that leaky septic systems had for years caused levels of fecal bacteria exceeding state standards for recreation at a ditch on Chicken Ranch Beach were put to rest last week, when cutting edge DNA test results ruled out human waste as the culprit.
Scientists who analyzed the tests believe that traditional testing methods employed by the county, which use a few bacteria to indicate the potential presence of harmful pathogens, were detecting naturally occurring microbial communities in soils. But some West Marin residents and the nonprofit Tomales Bay Watershed Council still want to see the county—at a cost of hundreds of thousands of dollars—restore the area’s former ecological function as a wetland. Meanwhile the county says its priority for the beach is not habitat restoration, but ensuring the safety of beach-goers.
John Hulls, a project director for the Nicasio-based Carbon Cycle Institute who co-authored the report on the Chicken Ranch D.N.A. testing, said traditional bacteria tests were designed for large cities where pollution from point sources—like sewage from treatment plants or urban storm water runoff—is more likely. And they might not be as useful in rural areas.
“We’re finding out that there are lots of naturally occurring E. coli and enterococcus, which can regrow in the natural environment and are capable of triggering the state tests,” said Mr. Hulls, a Point Reyes Station resident.
The analysis relied on a device called a PhyloChip, which can analyze the DNA of over 60,000 different kinds of bacteria. The study of the Chicken Ranch samples searched for two bacteria—clostridia and bacteriodales—which comprise more than 90 percent of bacteria in the human gut. But the device found virtually none in the 12 samples taken from January to August. “The PhyloChip community structure analysis showed no indication of any human source contamination in any of the samples despite indicating a complex microbial community especially in Channel B,” the report said.
Mr. Hulls explained that rain events can trigger complex interactions between creeks, rivers and stream bank reservoirs by pulling a diverse array of microbes from the soil into rivers, which he believes can set off traditional tests. Although scientists have only recently begun to study these interactions, DNA testing “does demonstrate the considerable possibility of error if sources are not identified, especially in cases where there may be significant influence from complex natural communities, as opposed to humans and wildlife,” Mr. Hulls said.
“It’s just a fascinating time to be involved in microbial technology because we’ve never been able to look at this chain in such a dynamic way. We’re learning so much so quickly. Maybe regulators will eventually catch up,” he added.
In accordance with state law, the county tests 28 beaches and recreational waters weekly from April to October, using traditional tests for fecal coliform bacteria, E. coli and enterococcus. Warnings are issued and posted when those levels exceed state-established safety limits. Last week, for instance, samples from the Green Bridge, Inkwells and a site in Samuel P. Taylor State Park, all along Lagunitas Creek, were above that limit; Green Bridge has been elevated for five weeks in a row, while tests at Inkwells has been elevated in four of the past five weekly tests. (In a 2011 report on another study undertaken by the county, the PhyloChip found “evidence of contamination from human, bird and grazer sources” at Inkwells, though their proportional contributions were unclear.)
But traditional tests, which work by culturing the tiny fraction of bacteria that can successfully grow in a lab, can’t pinpoint the source of the fecal bacteria, which could theoretically come from humans, grazing animals, wildlife or natural microbial communities in the soil. In fact, the cultured bacteria in themselves aren’t harmful, but instead act as indicators of the possible presence of other bacteria or viruses that can make people ill.
Yet in order to maximize safety for beach goers, the safety limits established by the state assume the worst-case scenario: that the bacteria come from human waste.
“Some animals, like cattle in particular, can produce human impacts and health impacts as strong as human wastes; other animals less so,” said Michael Gjerde, a coordinator for the State Water Resources Control Board’s Clean Beaches program. Some studies, he said, have indicated that gull waste doesn’t constitute the same health threat that human waste does. (Though he added that the risk is not zero and that “no one wants to swim in a bathtub filled with bird poop, anyway.”)
Mr. Hulls explained that although some diseases can jump from animals to humans, human waste presents the greatest risk. “If you don’t detect a human source, you’ve essentially eliminated the risk of all the pathogens that live in the human gut, and those are the major sources of infection. So when we see gut bacteria from another source, in most cases, there’s dramatically less risk associated with that,” he said.
But Mr. Gjerde said that because there are no full analyses of exactly how risks from different waste sources compare, and because traditional tests themselves don’t determine the source, “we treat it all as an indicator [for human waste].” (The state-established safety levels, however, do assume some base amount of fecal coliform coming from wildlife.)
Because the PhyloChip can distinguish between difference sources—or at least rule one out—a cadre of locals asked the county this spring to determine whether failing septic systems were contaminating Chicken Ranch’s Channel B, causing the high fecal levels seen in traditional tests.
The county parks department signed a contract for $6,500 with the Carbon Cycle Institute to take a suite of 10 water samples from Chicken Ranch in July. Those samples, along with two more collected by the county in January and April, were analyzed at the Lawrence Berkeley National Laboratory, which developed the PhyloChip.
The county didn’t request a full-blown analysis of the bacterial community—only whether or not it came from human waste. To that end, the report asserts that the county’s January sample shows that traditional tests found a “false positive” because the PhyloChip discovered no human gut bacteria while the traditional tests, which assume high levels indicate human influence, failed state standards for enterococcus.
Mr. Gjerde, however, noted that that many cities and regional water boards in Southern California are also using genetic testing to determine sources of fecal bacteria with the hope that the state might someday adjust limits in areas with waters deemed less susceptible to the risk of human contamination.
The Chicken Ranch report says a more thorough analysis, assessing all potential sources, “would be required to make a fully informed decision as to both the necessity for remediation measures”—such as restoration—“to meet existing standards and, should such measures be implemented, their likelihood of achieving the desired impact on water quality testing outcomes.”
The Tomales Bay Watershed Council finished a proposed restoration plan for Chicken Ranch Beach in 2013, which it says would cost around $350,000 to implement, not including permits or environmental studies. (The county parks department disputed that estimate last year, believing it would cost at least twice that amount.) The council asked the county in a letter last year to take on the project. The plan, which outlines how to improve the area’s floodplain function, restore habitat and reduce sediment loads into the bay, is meant to address high bacteria levels but also seeks to eliminate them as one of its goals.
Neysa King, the coordinator for the council, says that restoring natural functions could address those historically high levels. She said that although the council was not part of the push to determine whether or not the bacteria came from septic systems, she is happy to have more information and assurance that human waste is not the problem.
“One element [of the restoration plan] would address the drainage ditches that comprise Channels A and B, and replace these structures with a wetland complex,” she said. Third Valley Creek could spill out into a historic floodplain and allow for better spread and filtration of waters potentially containing the high bacteria loads, she added.
Tom Gaman, an Inverness resident who, along with others, pushed the county to do the tests, says he is happy human waste is not making its way to Chicken Ranch, but he also hopes the county will take on the restoration plan.
“It is an exciting development to hear it’s not a human septic tank problem. [It’s also] pretty exciting because it could mean that restoring the natural wetlands process… can result in natural processes cleaning the perennial [fecal bacteria] we’ve seen at Chicken Ranch,” Mr. Gaman said.
For Linda Dahl, the general manager of the county parks department, the PhyloChip results, in combination with the absence of water violations at Chicken Ranch since April testing began, underscore the county’s lack of interest in a restoration. The county would only pay for more specific tests to determine the contamination source if traditional testing again started to exceed state limits for recreation. (The ditch is often not sampled because it only fills during rain events.)
“I think that until and unless a health threat reemerges, we’ll keep an eye on it and we’ll keep testing,” Ms. Dahl said. “The immediate concern was a health threat, and if there’s no health threat, that goal has gone away.”
The parks department, she went on, has limited funds and it is now focusing efforts on restoring the Bolinas Wye, at the north end of Bolinas Lagoon. The lagoon has been designated a wetland of international importance, Ms. Dahl pointed out. Chicken Ranch, in comparison, is managed largely as a county park where people flock on weekends to swim, play with their kids and picnic. “I think the biggest difference between [the two] is that Chicken Ranch Beach is a dramatically altered area because of the private development…so in terms of what’s left to save, it’s less about habitat and more about public health,” Ms. Dahl said.