BLACK POINT BOAT LAUNCH, NOVATO—The safety briefing on the research vessel Lonsme takes 30 seconds, because all this 23-foot boat contains is a steering console and a frame at the stern that’s used to tow a net. Keeping safe onboard boils down to not getting in the way.
“Oh, and don’t trip on that hose,” says Jim Hobbs, captain, researcher, co-principal investigator, and founder of the Otolith Geochemistry and Fish Ecology Lab at UC Davis. He’s the veteran of more hours on this boat, which he designed, than he may care to count.
Hobbs has spent 15 years steering the Lonsme, or its predecessor, through Bay waters, collecting and cataloguing whatever its trawl net catches. These are waters troubled by invasives, warmed by climate change—and the target of millions of dollars of restoration work, which requires monitoring. “You know what they say,” Hobbs tells me. “Don’t begin a long-term monitoring program. Don’t end one. And don’t ever change it once you’ve started!”
But he’s breaking that rule. We’re heading out to monitor fish for a very young long-term research program—the Wetland Regional Monitoring Program (WRMP). “Our goal is to be able to tell the story about how the estuary is changing over time,” Aviva Rossi, lead WRMP scientist with the San Francisco Estuary Institute, told me. The two-year-old program, led by the San Francisco Estuary Institute and the San Francisco Estuary Partnership, and funded by the U.S. Environmental Protection Agency and the San Francisco Bay Restoration Authority, unites and expands existing research projects to keep tabs on Bay Area wetlands. Other research includes everything from bird surveys to sea-level-rise studies to hyper-detailed laser mapping.
Hobbs and his crew are doing what they have long done, but now on a grander scale: counting what lives in the water. It’s not easy work, because a lot lives here. (70 native species of fish—and at least 32 invasive ones.) Because fish move around so much, it takes tons of data to say anything for sure. Getting that data needs a lot of time, money, energy, and love for (some of) the thousands of creatures that call the Bay home, from the spiky to squishy.
Also required: donuts—to sacrifice to Mother Nature for good weather. Today, Hobbs appeases her with a chocolate sprinkle. The Lonsme pushes off from the boat launch underneath State Route 37 into the mouth of the Petaluma River, toward the brilliant blue waters of San Pablo Bay. Twelve trawls lie ahead.
Trawl 1. Petaluma River. 7 fish, 168 shrimp, 54 mollusks, 3 comb jellies.
“Popping!” calls Alex Lama, an assistant specialist at the lab with four years of sampling under his belt. Sami Araya, another assistant specialist, five years of sampling, lowers the net from the A-frame at the back of the boat into the middle of the Petaluma River, a broad swath of water lined with golden cordgrass. Jim Ervin, a volunteer with the lab, stands at the ready.
“Dropping!” calls Lama. The 14-foot-wide, cone-shaped otter trawl net, designed to spread wide and sweep up anything on—or swimming above—the river bottom, sinks. “And … fishing!” Hobbs keeps the boat at a steady, puttering pace, towing the net behind us.
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After 300 seconds, Araya and Lama winch the net back in. Its trawl through the river has left it resembling a giant soggy brown sock. Araya upturns it into a black tub of water that’s sitting in the boat.
The catch seems to be mostly mud. Lama scoops through it with a tiny green hand-net, and dumps each scoop into three white trays to examine more closely. Not just muck, as it turns out: four species of shrimp and three species of fish wriggle out from the sediment, including a two-and-half-inch California halibut whose two compressed, beady eyes stare up at us. Everything is counted and summarily flicked back into the water. Take only data, leave only ripples.
Trawl 2. Bahia Slough. 5 fish, 136 shrimp, 208 mollusks, 4 comb jellies, boogers*.
*Shorthand for New Zealand mud snail eggs, which look like unidentifiable sacks of goo.
The real heft of biodiversity lies in the marshes, these surveys are finding. We navigate next into the pickleweed-lined Bahia Slough, a wetland that the Marin Audubon Society began restoring in 2010.
Few Bay Area marshes have been surveyed in such a concerted manner until now. Before the WRMP started, the lab’s surveys focused on the South Bay Salt Ponds, tracking how that longstanding, giant restoration project was progressing. As the surveys expand, these trawls are uncovering new fish hotspots across the Bay—including scores of babies. They expected these discoveries, says Levi Lewis, the lab’s other principal investigator. Wetlands are good nurseries, safe havens for young fish to grow and thrive. Restoring them should help reseed the Bay’s beleaguered waters.
Trawl 3. Bahia Slough. 15 fish, 95 shrimp, 1 mollusk, 9 crabs.
Pay dirt. Araya and Sama strain to haul the net onboard; we’ve caught a gigantic mudball. It’s almost two feet across, honeycombed with tunnels, and chock full of life. A plump-cheeked shokihaze goby peeks out from one crevice.
“It’s a marsh hotel!” says Ervin.
Trawl 4. Bahia Slough. 5 fish, 177 shrimp, 107 mollusks, 1 crab, 6 comb jellies, 1 tunicate, 1 scaleworm.
When Ervin sees the tunicate—which looks more like a dark lump than an animal—he exclaims, “Our closest living relative!” (Tunicates, also known as sea squirts, are the closest living relative of vertebrates.) He hops in place, which he tends to do when he gets excited. Ervin gets excited often.
Ervin, a Navy veteran, worked as a compliance manager for the San Jose wastewater treatment plant for decades, till his retirement. “I would have been a mediocre compliance manager at best,” he tells me later. But a chance encounter with the UC Davis lab’s fish monitoring at a conference sent him down an ecological rabbit hole. They took him out on a boat.
He got excited. He wrote an email summarizing the fish they saw in gleeful detail and sent it to every wastewater treatment manager he could think of. To him, the sheer numbers of fish they saw validated that their wastewater treatment was working. He kept going out on the boat. Later, when the lab’s money ran out, he persuaded the city of San Jose to fund sampling.
Ervin’s emails have now turned into monthly blog posts on the lab’s website. After 13 years on the water, he now knows as much if not more about our local fish—and isopods, and hydrozoans, and clams—as anyone else on board. Araya and Sama turn to him regularly with identification questions. Ervin has added several rows to the lab’s data sheet, including documenting the marsh floor for the WRMP.
“I feel responsible,” he quips to me later. “I’m the one who got them into this mess.” The mess in question being the WRMP fish monitoring itself, which Ervin estimates has tripled Hobbs’ nautical workload. Before the WRMP, the lab had two trawl days a month at the South Bay Salt Ponds. Now they’re out every other week. Lewis and other collaborators worked to include fish monitoring in the WRMP because it makes scientific sense: having fish data along with other measurements of wetland health helps restorationists figure out what’s working and what’s not. And also, Ervin says, the head of the EPA’s San Francisco Bay Water Quality Improvement Fund likes Ervin’s blog. (This was confirmed.)
Trawl 5. Novato Creek. 7 fish, 48 shrimp, 26 mollusks, 4 comb jellies, 1 nudibranch.
We enter the Novato Baylands, where more than $100 million has already been spent on flooding a former airstrip and planting native marsh species. The banks are dense with cordgrass, occasionally interspersed with pickleweed.
As we wait for this trawl to finish, they debate their most-hated fish. Hobbs has had a grudge against bat rays ever since one stabbed him through the hand. He was tagging it. “So to be fair,” Hobbs says, “I stabbed it first.”
Trawl 6. Novato Creek. 3 fish, 82 shrimp, 104 mollusks, 1 polychaete worm.
Moments later, the next net pulls up a two-foot-long bat ray. It flaps madly as if it might take flight. Araya measures its length and gently lowers it back into the green marsh waters. It dives and disappears in seconds.
I trip on the hose.
Trawl 7. Novato Creek. 4 fish, 29 shrimp, 7 mollusks, 4 comb jellies.
Navigating these sloughs depends on a captain’s ability to read the water and the wind, to understand the creep of the tides and the minute topographies of the sediment and what they mean for a small, not particularly maneuverable boat. Opportunities to get stuck abound—on an unexpected mud bank as the tides recede too fast, or in a tangle of marsh plants. That’s one of the reasons few other groups have embarked on surveys like this, Lewis says.
Hobbs steers while dancing. (He is a West Coast swing aficionado.) “Seventh trawl!” he says, and drums out a beat on the wheel. The whole boat bursts out into song. They are surprisingly in tune.
Take me out for a trawl day,
Take me out to the marsh!
Buy me some donuts and salty snacks,
I don’t care if we never go back!
So it’s trawl, trawl trawl for the longfin,
If we get stuck it’s a shame,
So it’s, one, two, three-four-five-six-seven-eight-nine-ten-eleven-twelve trawls we’re done,
On the old trawl day.
“You get bored here after a while,” Hobbs says. “After, you know, 15 years on the water.”
Trawl 8. Sonoma Baylands. 10 fish, 69 shrimp, 8 mollusks, 9 comb jellies, 1 isopod.
The next trawl hits gold—or rather, silver.
The first animal to rinse out of the net is a slender, shining fish: a longfin smelt.
“The song must have got it!” crows Hobbs. This endangered species, which lives its life between the open ocean and freshwater, focused most of the lab’s work—and funding—before the WRMP. Hobbs did his Ph.D. studying the longfin smelt’s even more beleaguered relative, the Delta smelt, before founding the lab.
Drought years, freshwater diversions, polluted waters, predation, and shrinking food sources have devastated both longfin and Delta smelt populations. But the Delta smelt is almost functionally extinct—Hobbs is the only one onboard to have ever seen them in the wild. (He says they smelled like cucumber.) Longfin smelt are hanging on, but barely: hundreds of thousands fish lived in the Bay in the 1970s. Maybe tens of thousands remain today. The lab breeds the fish on campus, to help supplement the dwindling wild population.
Before this smelt is returned to the Bay, Ervin takes another photograph. “You never know when it’s the last wild longfin you’ll ever see,” he says.
Trawl 9. Sonoma Baylands. 9 fish, 7 shrimp, 3 mollusks.
Ervin is never bored. He is measuring the largest Corbula clams, an increasingly prominent invasive species. He’s tracking how anchovies change from blue to greenish as waters freshen. Between each trawl, he records the color of the water. He is hoping to get an early warning of algal blooms like the one that caused the 2022 red tide. “Different Gold,” he decides, holding out his laminated color key against the Sonoma Baylands.
Ervin doesn’t care about research publications. “I don’t have a career,” Ervin says. “It’s just my own curiosity.”
Trawl 10. Sonoma Baylands. 1 fish, 2 shrimp, 3 mollusks, 1 crab, 1 comb jelly.
It’s not just fish out here. “Marsh treasure!” Araya hollers, and we detour to the very edge of a marsh to retrieve a large black buoy tangled in the pickleweed.
In the process, the boat gets stuck. Getting unstuck requires us to jump up and down on the back of the boat for several minutes. Hobbs, revving the engine, seems unfazed. “It’s not a survey day if you don’t fear for your life at least once.”
Hobbs left lab and Lonsme a few years ago to work for the California Department of Fish and Wildlife. He spent that time in Microsoft Teams meetings, mostly wondering, he says, what the meetings were about. “When the WRMP came online, I said okay, I’m coming back,” he says. “It’s a lot more fun getting outside.”
The Bay is a far cleaner place than it once was. Ervin recalls holding his breath whenever his family drove near the water in the 1970s. Advanced wastewater treatment, like where Ervin spent his real career, combined with cleanups, improved regulations, and trash-catching infrastructure in major cities, have made life better for some fish—though not all.
Trawl 11. Sonoma Baylands. 2 fish, 10 shrimp, 2 mollusks, 1 comb jelly.
Ervin points out a solitary, fingertip-sized mysid shrimp in his tray. “Kind of depressing,” he says. Mysids are the foundation of ocean ecosystems—nourishing creatures from rockfish to squid to blue whales. To find just one alone, for Ervin, symbolizes how much these ecosystems have constricted. The Bay has undergone centuries of settler-led development and pollution, and only a few decades of restoration. Invasives have overtaken these waters: more than 90 percent of species in the Bay aren’t from here. Now, it’s not always clear what’s native. Species like macoma clams might be Gold Rush introductions, or they might have been here all along.
“We did a lot of dumb stuff, our ancestors did,” says Hobbs.
Trawl 12. Sears Point. 13 fish, 32 shrimp, 11 mollusks, 1 comb jelly, 1 tunicate.
Sama hands me a piece of dark chocolate as a reward for making it to the last trawl of the day. The last nets lower at Sears Point, a decade-old restoration project that now, at high tide, looks like an inland lake. Hobbs thinks it will take decades for enough sediment to wash into this flooded farmland to create a real wetland. Fish by fish, these trawls could document that process—given luck, and funding. The WRMP supports this monitoring until 2027. No one knows what happens after that.
Right now, the boat’s researchers are focused on tonight. It’s time to sail home. The boat needs to be washed and stored. Hobbs, Araya, and Sama are deciding where to eat dinner. Ervin needs to beat rush-hour traffic for his 90-minute drive home to San Jose.
They’ll be back the next day to do it all again. “Every month, there’s something that’s surprising,” Ervin says. “It just depends on, how deep is your curiosity?”
