Mystery by the Bay

Marine biologists try to find the source of bacteria contaminating Morro Bay’s estuary

BY KATHY JOHNSTON

Peering into his powerful spotting scope perched at the water’s edge, Matt Oliver focuses on a single sandpiper. He watches, waits, then rushes across the muddy shore with gloves and a vial. Scooping up the whitish blob, he carefully packs it on ice for its long journey to a renowned laboratory.

It’s a process the Cal Poly graduate biology student has repeated 500 times, tracking and collecting the waste from birds, cattle, dogs, deer, marine mammals, and even humans who live around the shores of the Morro Bay estuary.

"It has to be fresh," Oliver explained. "You can’t get an old dried one."

These samples play a key role in a marine detective story, where a team of gumshoes in gumboots is working to solve a mystery: What is the source of the fecal bacteria that’s contaminating Morro Bay’s oyster farm?

DNA fingerprinting provides some clues in this investigation, bringing sophisticated scientific techniques to match the bacteria in the waste samples Oliver has collected with the ones state health officials have found in the oyster tissue.

It’s not just a matter of ensuring that Embarcadero restaurants can safely serve the distinctive mollusks. Whether or not you enjoy gobbling oyster shooters or oysters-on-the-half-shell, the health of these shellfish reflects the overall health of the Morro Bay estuary, one of the most productive ecosystems in the world.

"You can look at oysters as sentinels in the bay," said Marc Commandatore, public health biologist with the California Department of Health Services. "If you think about it, if you can eat out of your bay, it’s an indication of how healthy it is. If you can’t, you really have to ask yourself what’s going on."

Although the overall water quality in the bay is generally good, unexplained spikes of bacteria found in a few water samples from the oyster-growing leases are making state health officials nervous. One area across the water from the Morro Bay State Park marina has been closed for oyster farming, while other areas are being closely monitored.

As filter-feeders, oysters can concentrate any disease-causing organisms from the waters in which they grow, creating the potential for outbreaks of illness if they are consumed by humans.

Acting under the state Shellfish Protection Act of 1993, the Central Coast Regional Water Quality Control Board has set up a technical advisory committee, bringing together a range of interests and expertise to tackle the issue of where the bacteria is coming from and what can be done about it.

The line-up of suspects in the fecal bacteria investigation includes boaters and liveaboards, failing Los Osos septic tanks, cattle and wildlife in the watershed, seals, seabirds, and shorebirds. All are potential contributors of the fecal coliform bacteria known as E.coli, which state health officials use to determine the safety of oyster-growing areas.

"The Regional Board wanted to set policies to reduce the amount of bacteria entering Morro Bay, but everybody said, ‘It’s not my E.coli,’" explained Dr. Christopher Kitts, a microbial ecologist in Cal Poly’s biology department. Dr. Kitts, who serves on the technical advisory committee, came up with the idea of DNA fingerprinting to help identify the sources of the fecal bacteria.

He’s working with a University of Washington epidemiologist, Dr. Mansour Samadpour, who has made it his life work to collect a library of more than 30,000 DNA samples from a variety of sources.

"That’s the key to DNA fingerprinting. To find a match, you have to have a database to compare the DNA to the set you’ve got," Kitts said.

Because the strains of bacteria in the intestines of animals and humans can vary by geographical location, waste samples had to be specifically collected from the Morro Bay area to add to the DNA database.

"To get the ‘fingerprint,’ you look for E.coli in the sample and see how the DNA is organized in its genome. The technical name is ribotype. It’s kind of like a bar code you can read, and if it lines up you’ve got a match," he explained.

With fingers pointing at Los Osos septic tanks as a possible pollution source in the estuary, more data is needed. Recently, as Los Osos property owners voted to form a sewer assessment district [see page 17 for related story], Cal Poly biology graduate student Noah Doughty worked with Oliver to collect more DNA samples.

Sloshing through the mud along the shoreline at the end of Third Street in Los Osos, the two stopped at a seep flowing off the land into the estuary. With long tongs wrapped around a jar, Doughty dipped into the flow to grab a sample of the water.

"This looks clear, but it’s chock full of bacteria, a hundred times more concentrated than what’s found in the bay," said Oliver. The sample will be shipped to Washington, where its E.coli bacteria will be DNA fingerprinted to see if it matches any found in the oyster farm across the water.

People on boats answering the call of nature, including hunters and liveaboards, are another suspected source of fecal contamination in the estuary. "With hunters staying out on the water for hours and hours, a lot of people think, "Over the boat it goes,’" Oliver said.

Boat owners who make their vessel their permanent residence are strictly regulated by the Morro Bay Harbor District, and must have "appropriate waste facilities" on their boats, according to harbor director Rick Algert.

But these regulations apply only within the City of Morro Bay boundaries, which cover the estuary area along the Embarcadero. Boats moored off the Inn at Morro Bay in Windy Cove, the State Park marina and further back in the bay are not covered by the Harbor District’s waste-disposal restrictions.

Folks who live aboard their boats in these areas are "tweeners in the cracks," Algert said. "But in my opinion, 99 percent of people who live on vessels are even more concerned about their environment than average. They live on the water and view it as their home."

Unlike some other California harbors, though, boats visiting Morro Bay are not required to seal or put dye tablets in their holding tanks to guarantee they don’t dump any pollutants into the water.

"You just don’t know what goes on behind closed doors on boats," said public health biologist Gregg Langlois of the State Department of Health Services as he gazed out over the estuary. "Beyond the city limits, there are no controls and no oversight, even at the marina."

He added, "Honestly, when you look at a boat with two people and they pull the plug on their holding tank, it would take out the whole bay for shellfish growing. People just don’t understand how significant small amounts of contamination are."

For example, in another oyster farming area, Tomales Bay North of San Francisco, contaminated oysters caused a disease outbreak that affected hundreds of people. The bay’s water quality tested clean just one day before the suspect oysters were harvested.

That outbreak could have been caused by an overboard discharge of excrement or vomit from a boat or kayak, or even a disposable diaper thrown overboard, Langlois said, adding, "We’ll never know. But it shows how small an impact is needed to create a devastating situation."

The concern rises as recreational use increases. Tomales Bay, like Morro Bay, has seen more and more kayakers, with no facilities provided for their waste. "You’ve got all these pressures increasing, and the oyster growing is literally in the downstream end of all of this," he noted.

Another obvious source of fecal bacteria in Morro Bay estuary is birds, many of which perch on the floats that support the mesh bags containing the growing oysters. "The oyster growers put up structures as part of their business, and that attracts birds and marine mammals. They’re creating a nuisance for their own business," Langlois said.

Local oyster growers are working with the Morro Bay National Estuary Program to obtain funding to develop a system of unstable floats that won’t work as bird perches.

That design work was started by the late Bill Williams, a colorful Morro Bay character who set up Williams Shellfish Company and obtained leases for his oyster farm in several areas of the bay. Known for his love of the bay and his year-round attire in shorts, Williams sold his oysters at local restaurants and farmers markets and supervised the annual oyster eating contest at the Morro Bay Harbor Festival.

When Williams died unexpectedly a year ago, his daughters Diane Ramos and Denise Resco and their husbands Chuck and Echo vowed to carry on the oyster operation, in spite of a steep learning curve.

"Dad had a lot of knowledge he didn’t share. He knew everything about oysters, all the quirks. He called them his babies. We’re all learning from scratch," Denise said. Her sister, Diane, added, "Dad would talk on and on about his oysters, and I’d be listening like, ‘yeah, yeah, uh huh.’ Now I wish I had listened more closely."

The two couples spent months obtaining the required certifications to take over the oyster business, as well as attending meeting after meeting where they had to learn the acronyms thrown around by water quality officials, plus the finer points of DNA fingerprinting and analysis.

"Basically, they stick the oysters in a blender and make a big milk shake to get the DNA out," Denise explained with a laugh.

Her husband Chuck spends two days a week out on the bay, caring for and harvesting the oysters growing in mesh bags suspended in the water. Hauling the heavy bags onto his boat, he whisks the live oysters straight to local restaurants, including the Galley and Outrigger on the Embarcadero and Sakura’s in San Luis Obispo.

He proudly reports that some of the 36,000 baby oysters (just 1/8-inch across) that the couples planted in October are nearly ready for harvest. "We must have done something right," he said with a smile, as he steers his boat towards the oyster processing unit in the middle of the bay.

Pacific oysters have been grown commercially in Morro Bay for nearly 70 years, although the shellfish are not native to the area. Local water temperatures mean they can’t reproduce here, so baby oysters are brought in to grow fat and succulent in the nutrient-rich waters.

"It’s not very often you run across a bay like this that has a farm," noted Denise. "If we can grow oysters here and sell them to eat, we’ve got something really special."

Her father Bill especially appreciated the fragile nature of the estuary and worked to keep it clean, she said.

The technical committee of shellfish called Sherlocks plans to continue their detective work to find the culprits responsible for fecal bacteria in the bay’s oyster farm through the summer, with results of the DNA fingerprinting analysis expected in October.

But even then, it may be difficult to pinpoint exactly what’s going on.

"You can’t tell everything," Kitts said. "The data you get just gives you a little window."

Results will show comparative contributions to the E.coli counts, he said, such as 30 percent from birds, 20 percent from humans, 40 percent from cattle.

Action plans can then be put into place to clean up each of these sources, work that is already ongoing through the National Estuary Program.

"Morro Bay is one place where restoration is doable," said Regina Wilson, who supervises a network of volunteer water monitors for the NEP. "There’s a sense of ‘wow’, across the whole United States; ‘there’s no place like this.’ If there was a model of how to make it all work, with cooperation among the volunteer monitors, the fishing community, the boating community, the farming community, this would be the place."

Clean water is the responsibility not just of boaters but of everybody, according to harbor director Algert: "We are all the source of pollution in the bay. Everything we drop into our drains and our creeks or put on our lawn ends up here. Everybody ought to think about changing the way we do things."

When it comes to ensuring that the sparkling waters of the estuary are clean and safe, the oyster is our world. Æ

SLO County freelance journalist Kathy Johnston has also written about DNA fingerprinting for the respected British science journal Nature, where the discovery of DNA was first reported.