By Karrigan Börk, John Durand, Nann Fangue, and Levi Lewis

Late last summer, on August 29th, 2024, the United States Fish and Wildlife Service listed the San Francisco Bay-Delta distinct population segment of longfin smelt (Spirinchus thaleichthys) as ‘endangered’ under the federal Endangered Species Act (ESA). With this decision, the Longfin Smelt joins the Delta Smelt (Hypomesus transpacificus) , the longfin’s infamous cousin species, as a list species under the ESA.  Longfin smelt had already been listed as ‘threatened’ under the California Endangered Species Act (CESA), but the new federal listing is a sign of the challenges that smelt and the broader Delta ecosystem face. The listing brings additional protections and new regulatory requirements that may further complicate water management in the Delta. This blog post provides an overview of this population of Longfin Smelt, explains what listing means, and then discusses ongoing work at UC Davis and beyond to recover Longfin Smelt populations.

About the Longfin Smelt

The Longfin Smelt is a small (~10 cm) migratory forage fish within the true smelt family Osmeridae that occurs in coastal habitats from Central California to Alaska. Spawning, hatching, and larval rearing occur in tidal fresh and low-salinity estuarine habitats, with juveniles migrating to higher-salinity bay and coastal marine habitats where they forage on mesozooplankton until returning to estuaries to spawn at 2-3 years of age. The San Francisco Estuary (SFE) Longfin Smelt population represents the southernmost spawning population of the species. This population may have been an important component of SFE food webs, from freshwater to marine habitats, given its former abundance (Nobriga and Rosenfield 2016). Because the SFE population has declined to < 1% of its 1970s abundance levels, the listing reflects concerns that it could be rapidly heading toward extinction (Hobbs et al. 2017; USFWS 2022).  

Regulatory Impact

What happens when a species is listed as endangered? Listing brings protections under several different sections of the ESA. 

First, under Section 10, the ESA bars any “take” of endangered species, absent a special permit. “Take” a technical term that includes direct harm, harassment, or “significant habitat modification or degradation where it actually kills or injures wildlife by significantly impairing essential behavioral patterns, including breeding, feeding or sheltering.” (50 C.F.R. § 17.3 (2017)). This means that the 2024 ESA listing imposes new permitting requirements on any activities that might result in incidental take of Longfin Smelt. Because the smelt was already listed as threatened under the CESA, permitting requirements aren’t entirely new, but any actions involving take will now require both state and federal permits, potentially with even stricter limitations that extend across their entire range, including freshwater, estuarine, bay, and coastal habitats. If past practice is a guide, this may not be too onerous; California may decide that permits issued under the ESA will count for CESA compliance as well. Most research and construction activities in the SFE already require both federal, state, and regional permits because of the plethora of currently listed species that occur there. 

Second, ESA Section 7 adds a requirement that federal agencies ensure “that any action authorized, funded, or carried out by such agency . . . is not likely to jeopardize the continued existence of any endangered species or threatened species or result in the destruction or adverse modification of [critical] habitat of such species.” (16 U.S.C. § 1536(a)(2).) This second provision requires analysis of the impacts of actions funded, undertaken, or approved by a federal agency, like the Coordinated Long-term Operation Plan for the Central Valley Project (CVP) and the State Water Project (SWP) (which determines how the two largest Delta water export projects operate) permits to fill, restore, or modify wetlands issued by the U.S. Army Corps of Engineers. When the agencies determine that an action is likely to impact the Longfin Smelt, FWS must prepare a Biological Opinion analyzing the impacts to the local population  and including protective measures to reduce impacts to an acceptable level. It’s a lot of analysis, all designed to protect threatened or endangered species, and it tends to be controversial, with many Biological Opinions resulting in protracted litigation. Litigants include the entire political spectrum of SFE stakeholders, from water export and delivery contractors, water districts, counties, the state of California, and environmentalists.  Most regulatory actions in the Delta already end up in court, so the listing is unlikely to lead to an overall increase in litigation, but it will make the litigation even more complicated. If Delta smelt are driven to extinction and thereby are excluded from future consideration in permitting decisions and litigation, the Longfin Smelt represents another hurdle. Like its cousin, Longfin Smelt requires fresh water flows and open water habitat, ensuring continued litigation in its name, along with other listed species like steelhead, salmon and sturgeon. 

Third, although existing investments by the state of California (e.g., CDFW, DWR) toward the conservation of Longfin Smelt have been foundational, the new ‘endangered’ listing under the federal ESA may bring an infusion of additional federal funding and attention. As we have noted in other blogs, conflict motivates collaboration: the threat of litigation and a background threat of increased regulation are often necessary antecedents to cooperation that improves ecosystem conditions. Increased spending on research and recovery efforts, combined with stakeholders’ willingness to come to the table, may help to improve the status of Longfin Smelt. Should the federal government withdraw from its regulatory oversight, these large cooperative incentives may disappear, resulting in less certainty and more litigation to resolve stakeholder differences.

Recovery Efforts at UC Davis and Beyond

One key approach to reduce extinction risk is to develop aquaculture practices and reserve populations of? listed species.  Aquaculture of Longfin Smelt has its origin with The Fish Conservation and Culture Laboratory (FCCL) in Byron, CA, at the University of California Davis (UCD).  In 2009, the FCCL began to develop a captive culture program for Longfin Smelt conservation based on their extensive knowledge of Delta Smelt culture. However, rearing protocols developed for Delta Smelt were not entirely suitable for Longfin Smelt, due to differences in life histories or other unknowns.  Early efforts to rear Longfin Smelt in captivity were successful to 400 days post hatch (dph; immature adults, Y1), but fish production numbers were limited to fewer than 400 fish per year from a few families/crosses; on average, 200-250 wild adults were collected each year to produce these fish, and variation in wild fish spawning condition was high.  Investing in 200-250 adults to produce only 400 fish for the next generation is a very poor investment, by hatchery standards, so clearly, improvements in culture methods were needed. Until 2023, spawning of fish reared exclusively in the laboratory (F1s to F2s) had been unsuccessful and the captive life-cycle for Longfin Smelt had not been closed.  

In 2021, the Department of Water Resources (DWR) established a program to formalize and further develop Longfin Smelt culture methods as part of the Longfin Smelt Science Plan.  Dr. Fangue is the Principle Investigator of the project, leading her research team in the culturing of Longfin Smelt on the UCD campus and at the Bodega Marine Lab.  Dr. Levi Lewis is a co-PI on the project; his team (the OGFL) leads the collection and transport of wild Longfin Smelt broodstock to the culture facilities each year.  Dr. Tien-Chieh Hung continues to advance culture methods at the FCCL. Every year, advancements in key steps of the Longfin Smelt life cycle are made, and just this Winter, we spawned our second fully captive reared fish offering great promise for this program.  

Effective ecosystem targets for Longfin smelt

Regulation, litigation, and cultivation are only short-term approaches for addressing the plight of Longfin Smelt and other aquatic species native to the San Francisco Estuary. The Delta smelt, for example, has continued its decline toward extinction under the current conservation framework. The transformation of the Bay and Delta ecosystems that began during the 19th Century has never really been addressed in a comprehensive way. Turning around the SFE ecosystem decline for Longfin Smelt will require the return of sediment fluxes; thoughtful reduction of aquatic vegetation in the freshwater Delta; targeted flows of fresh water from the Sacramento River and small regional watersheds like Alviso and Ulatis creeks; and restoration of spawning habitats in the SFE. 

Conclusion

Adding the Longfin Smelt to the rolls of the Endangered Species Act further complicates the already fraught water management in California’s Delta and reflects poorly on our lack of success in Delta conservation thus far. We will continue our efforts to restore the Longfin Smelt populations through science, aquaculture, and habitat improvements, in hopes that this listing will add to the push for Delta restoration. 

About the Authors

UC Davis Professor of Law Karrigan Börk’s publications run the gamut from California minimum streamflow requirements to a hatchery and genetic management plan for the reintroduction of spring-run Chinook salmon in the San Joaquin River. Prof. Börk graduated with Distinction and Pro Bono Distinction from Stanford Law School in 2009 and completed his Ph.D. dissertation in Ecology at UC Davis in September 2011. His current work focuses on western water law.

UC Davis Professor and Chair Nann A. Fangue studies California native fish physiology and conservation.  With her team of students and staff, their work focuses on understanding how changes in the environment influence fish responses and how we can use our understanding of these responses to find creative solutions to tough environmental problems.  Prof. Fangue received her PhD from the University of British Columbia in 2007, joined the UC Davis faculty in 2009, and is a UC Davis Chancellor’s Fellow.  

UC Davis Research Scientist and Director of the OGFL, Levi Lewis, uses field sampling, otoliths, and geochemical approaches to study the age, growth, distribution, and migrations of endangered fishes across the globe. Dr. Lewis received his PhD from Scripps Institution of Oceanography, UC San Diego in 2016 and became director of the OGFL in WFCB in 2019.

UC Davis Research Scientist John Durand studies food webs, fish assemblages and restoration outcomes in estuarine wetlands, with a focus on California and the SFE in particular. He received his Ph.D. at UC Davis in 2014. 

Further Reading

U.S. Fish and Wildlife Service. 2022. Species Status Assessment for the San Francisco Bay-Delta Distinct Population Segment of the Longfin Smelt. Prepared by: E. Chen V. Tobias, M. Eakin J. Hobbs A. Roessler; Edited by: S. Detwiler & M. Nobriga. https://ecos.fws.gov/ServCat/DownloadFile/223002

Matthew L. Nobriga, Jonathan A. Rosenfield, Population Dynamics of an Estuarine Forage Fish: Disaggregating Forces Driving Long‐Term Decline of Longfin Smelt in California’s San Francisco Estuary, Transactions of the American Fisheries Society, Volume 145, Issue 1, January 2016, Pages 44–58, https://doi.org/10.1080/00028487.2015.1100136

Hobbs, J., Moyle, P. B., Fangue, N., & Connon, R. E. (2017). Is extinction inevitable for Delta Smelt and Longfin Smelt? An opinion and recommendations for recovery. San Francisco Estuary and Watershed Science, 15(2).