By Alastair Bland
Federal wildlife officials formally listed the San Francisco Estuary longfin smelt as an endangered species in July. Whether the action is a first step toward recovery or just an administrative milestone on the path to extinction is too early to say, but one thing is already clear: The longfin smelt is ominously close to vanishing. Now, as its existential clock ticks, scientists are hustling to better understand the species’ biology and environmental requirements and, with luck, safeguard its future.
The estuary’s population of longfin smelt—Spirinchus thaleichthys, a species that can live in saltwater and ranges as far north as Alaska—has been declining for several decades, with an accelerated dip starting around the turn of this century. Once plentiful enough to be a target for commercial fishers, it now shows a feeble presence in annual sampling programs. The longfin smelt was listed by the state as a threatened species in 2009. The same year, the federal government rejected a petition for formal protection. Since then, the longfin smelt’s slip toward oblivion has continued, becoming too dire to ignore last decade. Its new status on the federal Endangered Species List—which specifically applies to the San Francisco Bay-Delta population—ushers it to the apex of protective regulations.
It also opens the doors to new, and urgently needed, pathways of research as state and federal biologists tasked with protecting the fish try to learn more about it.
“As dreary as it is to say that a species needs listing, one of the benefits of doing so is it allocates a lot of funding and resources towards research,” said Michael Eakin, a senior environmental scientist with the California Department of Fish and Wildlife.
The longfin smelt, named for its remarkably long pectoral fins, lives two to three years and can attain a maximum length of about 15 centimeters. The fish spawn throughout the Bay and Delta, and—like Pacific salmon—they die after laying and fertilizing their eggs. Spawning season spans the winter and seems to peak in February.
But there is a great deal that remains unknown about the species. For instance, researchers don’t entirely understand the fish’s relationship to freshwater flows. As with other species native to the Bay and Delta, longfin smelt numbers tend to spike following periods of relatively high Delta outflow—generally the result of wet winters—according to data collected by the Department of Fish and Wildlife.
This suggests that strategically managing flows may be the key to recovery. But more information is necessary, scientists say, to ensure that added flows—typically produced by curbing Delta water exports—are provided at the right time and place. Brian Schreier, environmental program manager with the California Department of Water Resources, explained that the relationship between abundance and flow amounts to a correlation, without a known causal explanation.
“Despite knowing about this relationship and the strength of this relationship for several decades, the exact mechanisms that support this observation are still unclear,” he said.
He hopes to help identify and close data gaps in the longfin smelt’s life cycle, and those of the invertebrates on which they feed, which also respond positively to flow increases.
“Understanding those mechanisms will help us be more targeted and efficient with future management actions that could be helpful to the species,” Schreier said.
Stressors for a Small Fish
Reduced Delta outflow is just one factor related to the longfin smelt’s decline. Also upsetting to the smelt and its ecosystem have been loss of wetland habitat, water pollution, and the appearance several decades ago of two Asian clams. These invasive filter feeders have had a silent but devastating impact, stripping the estuary’s water column of so much phytoplankton and other nutrition that creatures farther up the food chain have been left with less to eat.
Climate change is now emerging as another great threat. Droughts are growing more extreme, and temperatures are rising—trends threatening not just the longfin smelt but also its cousin and fellow endangered species the Delta smelt, both green and white sturgeon, Central Valley steelhead, and several distinct runs of Chinook salmon that migrate through the Bay and Delta.
“This is the southern extent of all of their ranges, the San Francisco Estuary, and [rising temperatures] will be something we have to deal with in managing all these species moving forward,” Schreier said.
Eakin noted that the same environmental changes now testing the evolutionary fabric of native fish species are providing invasive competitor species, including black bass, silversides, and aquatic weeds, with an edge. Many are partial to slow-moving, warm water and are poised to thrive in the changing estuary .
“Not only do we get conditions that are not good for our native species, but we get conditions that are good for the nonnative species,” he said.
If warming trends squeeze the San Francisco Estuary off the range map for its native fishes, total extinction will likely claim the Delta smelt, which is endemic to the estuary and naturally lives nowhere else. For the longfin smelt, it’s a different story. Such a shift would amount to extirpation—regional extinction—with the probability that they would persist farther north. Small populations with clear genetic links to the San Francisco Bay population occur in estuaries up the coast, and a larger independent population lives around the Columbia River mouth, Eakin explained. There are even at least two landlocked freshwater populations in the Pacific Northwest.
In fact, the species’ adaptability in a dynamic environment has made it relatively difficult to study and understand compared to the Delta smelt, which only resides in the Sacramento-San Joaquin Delta. Eakin explained that several annual surveys are specifically designed to capture Delta smelt. Moreover, they sample the entire known range of the fish.
Longfin smelt are a little trickier to study.
“Only one of our monitoring programs was specifically designed and implemented for longfin, and up until 2022, that survey only sampled the upper estuary,” he said.
It turns out, in fact, that for many years scientists may have been overlooking a large area of suitable habitat in the south end of San Francisco Bay. It’s here that, in 2017, researchers found hundreds of longfin smelt larvae in restored salt evaporation ponds, confirming that the fish use the area for spawning. (Eakin noted that it is still not certain to scientists on what type of substrate longfin females deposit their eggs.)
The 2017 discovery raises questions of how wetland restoration efforts in the Bay and Delta might help the species in ways that researchers did not previously foresee. Schreier and Eakin said several projects, both underway and completed, in the Suisun Bay and Delta regions could offer benefits to the species. These include Tule Red on the eastern shore of Grizzly Bay, Chipps Island in Suisun Bay, and Winter Island near Pittsburg.
Ecosystem on Edge
The longfin smelt’s plight in the San Francisco Estuary isn’t exactly surprising to experts. To the contrary, it is consistent with other changes affecting the ecosystem.
“The longfin smelt is the next species in the queue of fishes at risk of extinction,” said U.C. Davis biologist Peter Moyle, who has studied California’s inland fishes for more than 50 years. “That so many species that require the Delta in one way or another are declining like this tells you that the whole ecosystem is in trouble.”
Since about 2002, the longfin smelt has declined rapidly in tandem with a handful of other fishes—part of the phenomenon biologists began calling the “POD,” for “pelagic organism decline,” shortly after it was first observed and described. That downward trend continued as an extraordinary drought began in 2012. During the five-year dry spell that followed, the numbers of longfin and Delta smelt captured in the annual Fall Midwater Trawl Survey each dropped to the single digits. While the longfin smelt index—which historically ranged in the thousands—has since bumped back into the low hundreds, Delta smelt have almost entirely disappeared; none have been captured since 2017.
That year, Moyle and colleague James Hobbs examined the longfin and Delta smelts’ troubles in a review paper published in San Francisco Estuary and Watershed Science. They questioned whether extinction is inevitable for the San Francisco Estuary’s beleaguered smelts, and the answer, they concluded, is twofold: Extinction is potentially avoidable in the short-term, but survival and continued existence for each may eventually depend upon human support—assuming, that is, we care enough to intervene.
“We regard the fate of these species to be a test of society’s will to pull threatened and endangered species back from the brink of extinction and further, to bring about recovery of native fishes,” the scientists wrote.
With consideration of the collapsing ecosystem, Moyle and Hobbs advised that “[i]ncreasing freshwater outflow to the estuary should be the ultimate priority for promoting resilience in the Delta’s native species.”
Such concise recommendations on water management in the Delta are uncommon among state and federal officials. Steven Detwiler, a listing and recovery program supervisor with the U.S. Fish and Wildlife Service, acknowledged the clear connection between flows and abundance for longfin smelt, but said actions to more sustainably manage Delta water exports must be taken within a framework of established human uses.
“We are committed to working with all our partners in the Bay Delta ecosystem to create durable approaches to water management for the benefit of listed and native species, while respecting the needs of communities and agriculture who are also reliant on the delta,” he said in a statement.
Can Better Tech and More Science Help?
Efforts to breed longfin smelt in captivity have been underway for almost 15 years, though with poor results. The captive adult fish, scientists have reported, have been exceedingly picky about food, rejecting most dried feed products and preferring harder-to-get natural items, like the mysid shrimp they eat in the wild. (Even in the wild, Eakin noted, “they’re incredibly food-specific.”)
Worse, the fish simply don’t live long in tanks.
“[M]ost adult broodstock die due to unknown reasons within a month after arrival … in captivity,” wrote the authors of the Longfin Smelt Science Plan 2020-2030, a collaboration between the departments of Water Resources and Fish and Wildlife, the State Water Contractors, and the U.S. Fish and Wildlife Service.
As captive breeding potentially offers a shield against extirpation, scientists continue to monitor the wild population. Hand-counting fish sifted from trawl nets is the traditional approach, but it is being augmented with new innovations. One, Schreier explained, is the micro-acoustic tag. Conventional acoustic tags are tiny enough to be inserted into juvenile salmon but too large for the slender, fragile bodies of smelt. Now, a new generation of super-small acoustic tags, about a fourth the size of their predecessors, is becoming available to researchers.
“That is going to open up a whole new world of seeing how these fish respond to different cues in their environment and different flow patterns,” Schreier said.
The use of these tags could help researchers map out key habitat in high resolution. So might environmental DNA analysis. Catching fish in nets can be difficult, and as certain species grow scarcer, it can become less and less effective. This is where eDNA may come in. It is easy to collect, typically gathered up with small water samples and with minimal field effort. It reveals little or nothing about the health, size, or life status of the individual from which the DNA originated. It also can be difficult to interpret, since a DNA molecule collected in one place may have originated miles away—especially in an ecosystem governed by tides and currents like the San Francisco Estuary. But eDNA analysis can help rule out extinction, or confirm it, for a species for which trawl data has flatlined.
In fact, experts are already discussing how and when to declare a dwindling species extinct, with particular attention on the Delta smelt. The longfin smelt may one day become the focus of the same discourse. In their 2017 paper, Moyle and Hobbs addressed the administrative and clerical logistics of deciding when a species has officially slipped away. One challenge they foresaw involved potential inconsistencies between state and federal protections; one government agency could delist a species assumed to be extinct while another maintained regulatory protections, leading to confusing and conflicting rules on operating the Delta water pumps. The scientists also stressed the importance of continuing to sample smelt populations “to avoid premature extinction declarations.”
Recovery—not just delaying extinction or accurately announcing it—is ostensibly the goal of listing a species as threatened or endangered. However, it’s a rare outcome. Of more than 1,300 species listed under the federal act, barely 3% have officially recovered. The Delta smelt has been listed for three decades, first as threatened and then as endangered, but its downslide has continued. This trend, likely to play out for the longfin smelt as well, signals an unrelenting ecological collapse.
It also implies a caveat to our own cultural values: While we typically lament the decline of a species and root for its recovery, sometimes—especially if the creature is cryptic enough and the road to recovery steep enough—we’re okay with extinction.
This story was produced by Estuary News Group with support from the Delta Stewardship Council.
