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Two white hands holding a small silvery fish
The delta smelt, once the most abundant fish in California’s San Francisco estuary, is now critically endangered. An experimental hatchery project aims to save the species. Photo by Cavan Images/Alamy Stock Photo

Something Fishy Is Happening Inside the Ears of Delta Smelt

Abnormalities in the ear bones of hatchery-reared delta smelt could challenge efforts to save the endangered fish.

Authored by

by Annie Roth

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Conservationists have spent decades trying to prevent the extinction of the delta smelt, a tiny transparent fish that smells vaguely of cucumbers. The funky fish is native to California’s San Francisco estuary, a series of bays and river deltas covering more than 4,000 square kilometers between Sacramento and the Golden Gate Bridge. The delta smelt was once the most abundant fish in the estuary but is now approaching extinction, with few fish left in the wild. Over the past two years, scientists have surveyed the estuary thousands of times but caught just one wild fish.

In December 2021, researchers at the University of California, Davis, started to experimentally release hatchery-reared delta smelt into the wild. The California Department of Fish and Wildlife (CDFW), which oversees the project, hopes the experiment will boost numbers, giving people more time to address the root causes of the fish’s decline, which include pollution, invasive species, and habitat loss caused by dams and agriculture.

However, mere months into the project, fish ecologist Levi Lewis and laboratory technician Jonathan Huang, both then at the University of California, Davis, noticed something fishy about the hatchery-reared delta smelt that raises questions about the project’s effectiveness.

Lewis, Huang, and their colleagues conducted a study that found a large percentage of delta smelt reared at the university’s hatchery had abnormalities in their inner ear bones, which are also known as otoliths. The tiny stone-like structures are usually made of the mineral aragonite and are opaque, with alternating rings of light and dark. But many of the hatchery fish’s otoliths were crystalline, a trademark characteristic of the mineral vaterite. While both aragonite and vaterite are forms of calcium carbonate, with the same number of calcium, carbon, and oxygen atoms, they have different structures and properties.

Two brown otoliths side by side on a white background.

A normal delta smelt ear bone (first photo), formed from aragonite, has concentric light and dark rings, like a tree core. A malformed otolith (second photo) has an outer layer of vaterite, which appears glassy and pale. Photos courtesy of Levi Lewis

When Lewis and Huang compared the otoliths of hatchery-reared delta smelt with those of wild fish, they found that the cultured fish were 80 times more likely to have at least one vateritic otolith. The researchers also observed that the paired ear bones in cultured fish were more likely to be lopsided, compared with normal otoliths, which are the same size and shape on both sides of a fish’s head.

To date, scientists can’t explain what triggers this type of otolith malformation, but vaterite is a problem for hatchery-reared fishes of other species, such as lake trout, and Atlantic and chinook salmon. Malformed otoliths have been shown to impact hearing, swimming ability, and predator avoidance in those species. The scarcity of abnormalities among wild delta smelt in Lewis and Huang’s study suggests that fish with irregular otoliths are quickly weeded out in the wild.

“Physiologically, otoliths are really important,” says Lewis. “A fish might be deaf or have vertigo or some sort of disequilibrium if their otoliths are forming abnormally.” While scientists still don’t know if vaterite affects delta smelt in similar ways as other species, they agree that otolith abnormalities are a cause for concern.

The results of this study are a grim reminder that we can’t rely solely on supplementation to save dwindling fish populations, says Alec Lackmann, an aquatic ecologist at the University of Minnesota who was not involved in the new study. The problem with breeding endangered fish in captivity and releasing them into the wild, Lackmann says, is that hatchery-reared fish are rarely identical to wild fish. “Nature is very complicated, and it’s hard to mimic everything in a lab setting.”

If delta smelt with malformed otoliths are likely to die soon after release, it would challenge hatchery efforts to save the population. Yet other hatchery programs have produced fish with similar abnormalities and still managed to achieve their goals.

Even if only one-third of hatchery-reared delta smelt pass on their genes, “that is still a net win,” says Jereme Gaeta, a freshwater fisheries scientist with CDFW. Those offspring would vastly outnumber the young that wild delta smelt could produce without supplementation.

Around 60,000 cultured delta smelt have now been released into the wild, and while it remains to be seen what percent survived long enough to breed, biologists caught more than a dozen of the fish during a survey in late January 2022. If the experimental releases succeed in bolstering the population, CDFW plans to launch a formal supplementation program to release more fish into the estuary each year.

Despite the concerns raised by his findings, Lewis agrees that releasing fish is worthwhile. “Our analysis doesn’t in any way undermine the utility or the value,” he says. “In the absence of a better option, the supplementation program may be the only way for us to save the species at this point in time.”