SCIENCE IN SHORT: Longfin smelt, the little fish that gets around

Near the bottom of the San Francisco Estuary’s food web is a small fish about the size of a herring or an anchovy. And although this species has been listed as threatened by California’s standards since 2009, it only became a federally-listed endangered species in July of 2024. In this Science-in-Short episode reporter Ashleigh Papp interviews three scientists about longfin smelt. Listeners will also hear these experts share their insights into how the species uses Delta, Bay and ocean habitats, including restored marshes, during different parts of its life cycle.

Full Transcript: 

Host Ashleigh Papp: The San Francisco Estuary is an intricate, interconnected ecosystem. Fresh water meets salty water, and life teems above and below the surface. 

Near the bottom of the estuary food web is a small fish about the size of a herring or an anchovy. And although this species has been listed as threatened by California’s standards since 2009, it only became a federally-listed endangered species in July of 2024. In this episode I’ll be talking with experts that cover some of the different habitats where this tiny fish, the longfin smelt, is known to be.  

Fish Ecologist, Levi Lewis: When you catch them, in certain times of the year, they can appear goldish in color, and then in other parts of the year, they’ll actually turn kind of purplish and iridescent. And they’re absolutely gorgeous. They have giant fit pectoral fins that look like wings, not quite as big as a flying fish, but they’re much bigger than most other bait fishes their size, and that’s where they get their name from, longfin smelt.

Papp: That’s Levi Lewis, a research scientist at UC Davis who runs a fish ecology laboratory. The lab studies a lot of things related to longfin smelt, including the structures inside the inner ear’s of fish, called otoliths, which can provide a lot of insight into the life of a fish and how it migrates to different parts of the estuary throughout its life. 

With the recent federal listing, interest in figuring out just where and how the longfin smelt makes use of the estuary has increased. We’ll hear more from Lewis later in this episode, but for now, let’s get a big picture view of the longfin’s home bases throughout the bay and beyond.  

U.S. Fish and Wildlife Service Biologist: Longfin smelt really use all parts of the San Francisco estuary, but they use different parts of the estuary during different parts of their life cycle.

Papp: That’s a U.S. Fish and Wildlife Service Biologist, who I spoke with in November 2024. Her work focuses on longfin smelt in the Bay Area. 

USFWS Biologist: When they’re spawning, they use really fresh water, the low salinity marshes that are kind of further inland, usually kind of outside of the tidal range of the estuary. So they’re really using those freshwater marshes in the winter and the spring for spawning. And then once the eggs hatch, the larvae tend to center around what we call the low salinity zone, which is where the fresh water from the river mixes with the salt water from the ocean.

Papp: In the San Francisco estuary, the areas with the freshest water are where the longfin smelt go to spawn, or release the eggs that contain the next generation of fish. 

USFWS Biologist: So we don’t 100% know where the spawning is happening, or where the eggs are hanging out. We do know a lot about that by inferring it from other things, though. So we know that longfin eggs hatch between December and May. [The eggs are] heavier than the water, so they’re sitting on the bottom until they hatch. We know that they’re in marshes, because that’s where we find some of the earliest larvae. There’s other fish hanging out in there, probably that would like to eat them (laugh). You know, it’s tough to be a little fish in the estuary when there’s all that structure for other predators to hang out in.

Papp: Understanding these spawning and hatching details is important because it helps researchers paint a more complete picture of the longfin’s life cycle. And this biologist brings a special angle to the work — a mathematical rigor. She uses statistics to do science. 

USFWS Biologist: Having this, like, huge amount of data, and how do you find patterns in that data that can help you answer ecological questions and management questions that help us really do better things for the environment.

Papp: Right now this biologist’s expertise is aimed at developing new analytical tools to understand where and how longfin smelt use the various ecosystems in the area. And she’s doing it with the help of multiple research partners.

USFWS Biologist: It’s an interagency collaboration to build a life cycle model for longfin smelt. So that involves several of us with statistical experience at the Fish and Wildlife Service, and then we have some partners at other agencies, like the Department of Water Resources and California Department of Fish and Wildlife, as well as some of the water contractors are involved in an advisory capacity for that as well. So it’s this really big interagency collaboration. And the idea is to develop a tool that will help us answer some management questions in an experimental way.

We’ve really seen an increase in interest in learning more about how we can do things to help manage the species better, and thinking more about recovery, because we’ve been watching this decline in the longfin smelt population for a long time. We’re concerned about it, we want to help.

Papp: One really impactful way that scientists are trying to help is by better understanding the details of how a longfin smelt lives in their different habitats. These fish, similar to some trout and salmon, are anadromous. This means that they spend part of their lives in fresh water and others, in salt water. 

So, let’s head downstream now to the Pacific Ocean, to hear more about what this tiny yet mighty fish does as a juvenile making its first big migration …

Fish Biologist, Matthew Young: They pass out underneath the Golden Gate. They go out in the ocean, and then they come back a couple months to a year and a half later, and very, very little is understood about what happens when they’re in the ocean.

Papp: That’s Matthew Young, a fish biologist with the US Geological Survey who is also a collaborator in the Fish & Wildlife Service work. He’s been studying fish in California since 2007, and longfin smelt specifically since 2016 with a focus on the part of their lives spent out at sea. 

Young: It’s a very interesting life history strategy — it’s energetically intensive, right? You’re moving a long way. You’re exposed to all sorts of risks, both in transit and then in your new environment. And the reason why it’s worth it is, generally speaking, it’s because the habitat you would spend your formative years or year in, in this case, for salmon or longfin smelt, the ocean is just so much more productive than the habitat in which you were born. So there’s just like a lot of food out there, you’re able to grow fast and get as big as you need to [in order] to maximize your reproductive potential, and then you go back into a safer or otherwise more appropriate environment to reproduce.

Papp: In the fresh and brackish waters of the San Francisco Estuary, longfin smelt are observed and monitored regularly through visual observations. But these fish are too tiny to attach GPS trackers to, so once they head out into the ocean depths, researchers like Young don’t really know much about what happens. 

Young: Essentially, they leave our monitoring networks. They go out into this big, wide, open world of the ocean, and we don’t know what they do, we don’t know where they go, we don’t know what they eat. And we know nothing about how ocean conditions or any marine or ocean drivers influence what we see in the estuary in terms of population size or reproductive fitness or recruitment success. It’s like this big black box.

Papp: So Young and his colleagues are working to bring some color to that “black box” of the longfin smelt’s life cycle. 

Young: There was a fantastic paper in the California Department Fish and Wildlife journal, by Rebecca Garwood. What they wanted to do is compile all of the observations of longfin smelt in the Pacific Ocean, in California. And so they went through and pulled together like a whole bunch of records dating back many decades, just showing that, okay, this is when and where we see longfin smelt in the ocean off the California coast. And what colleagues and I set out to do is to expand this and build from it.

Papp: Young and the team pulled longfin smelt observations from old museum records and previous monitoring efforts ranging from Kodiak, Alaska, all the way down to Southern California. And they put all of this information into a massive database. 

Young: And we used that database to then define what might be good longfin smelt habitat. We were able to build a species distribution model, a statistical model, saying like, what is the probability that longfin smelt would live here?

Papp: All in all, the work took Young about three years, and right as he was getting started, the COVID-19 pandemic forced all of us to shelter in place. Which, ended up working out ok for the initial steps in his process …

Young: I emailed hundreds of fisheries, biologists, and managers on the Pacific Coast who were also stuck in their office and happy to talk to a stranger from California.

Not only did I get to think about statistical models and data that I wasn’t immediately familiar with, but I also got to think about how fish use glacial fjords off of the coast of British Columbia. So California is interesting. We have these bar-built estuaries that make up most of the estuaries on the coast, you know, think of things like Humboldt Bay. There are large sand jetties that separate the bay from the ocean. But as you go up the coastline, it gets really rugged and rocky and steep, and there’s glaciers, and there’s this whole other type of estuary that longfin smelt also use. And thinking about how longfin smelt habitat changes at these ocean estuary interfaces across thousands and thousands of miles was just so fun to think about.

Papp: After factoring in all of the data points, Young got to work analyzing the information and looking for trends. 

Young: And what we found, basically, [is] that high temperature years, years in which ocean conditions are warmer than normal off the California coast lead to a substantial contraction in the amount of habitat that longfin smelt could use. And this is a first step in sort of figuring out how ocean conditions might influence longfin smelt population dynamics.

Papp: There are still a lot of unknowns about the longfin smelt’s life cycle when they’re out in the ocean. 

Young: The work that we’re talking about here is very much a habitat suitability question. Can the habitat feasibly support longfin smelt? Presumably they have to eat, presumably they have to avoid predators, and presumably they have to make decisions about returning to estuaries when it’s time to do so. We can make some pretty educated guesses about what they might eat because of what closely related species eat. We don’t know what triggers their return for spawning, migrations into the estuary, whether it’s you know, is it a temperature threshold in the ocean? Is it something about day length? Possibly, is it something about outflow from the estuary that triggers them to come back?

Papp: By understanding more about the longfin smelt’s life at sea, Young is hopeful that researchers can help the species thrive in all of its environments.

Young: One of the reasons why it’s important to understand what goes on in the ocean is that, we don’t have a lot of management levers that can be adjusted to change conditions. We can’t magically make more food in the ocean or change ocean temperatures, however, there are lots of management actions that can be taken in the estuary, things I’m not advocating for or anything, but things like modifying outflow or pollution or habitat restoration. There’s a lot of specific actions that can be taken in an estuary on small scales that could influence longfin smelt population success, and it is difficult to evaluate the success of those actions if we can’t at least account for other parts of their life cycle.

There is another part of the longfin’s life cycle that is quickly becoming less of a mysterious black box. Next up, let’s hear from Levi Lewis, the fish ecologist who shared the colorful description of the longfin smelt in the beginning of this episode. He’s been monitoring inside the estuary, especially around the large wetland restorations of the South bay salt ponds. 

Because as Levi and his colleagues discovered, more of these tiny fish are hanging out in this area than anyone ever imagined. So, what is it about the South Bay that’s so desirable for longfin smelt? 

Lewis: We don’t know for sure, but we can certainly hypothesize. So, one is that the lower part of South San Francisco Bay is somewhat lagoonal, it has a very high residence time, it has a lot of nutrients coming in and it is extremely productive. And so there’s lots and lots of food, like an order of magnitude more food down there.

Papp: Longfin smelt can eat a number of things, but their preferred diet is pretty strictly made up of mysid shrimp, a tiny shrimp-like crustacean that drifts along in the water, and eurytemora, a tiny animal that also drifts, and is part of a larger group called copepods. 

Although it’s yet to be thoroughly investigated, Lewis is thinking that these preferred foods may be readily available in the restored wetlands of the South Bay. 

Lewis: The other hypothesis is that they just cue into wetland signals. They may be generally homing on those kinds of wetland habitats where they can smell the vegetation, they can smell the fresh water mixing with salt water. And in years when we get a lot more fresh water flow, we may see a lot more fish moving into these kind of external, smaller wetland habitats, whereas in drier years when they don’t have enough flow coming into them, we may see the majority of the fish moving in, for example, to the Delta, where you always have fresh water coming in. We don’t know that for sure. But again, these are all just kind of theories and hypotheses. Right now, we’re still just trying to quantify, like, how many fish are coming in, how often are they coming in, and what relative contribution spawning in this habitat might be paying to the overall population dynamics of the species.

Papp: Back in 2016, Lewis started working with his mentor and predecessor at UC Davis, Dr. James Hobbs. Hobbs had been a part of an ambitious effort to restore more than 10,000 acres of salt ponds in the South Bay for more than a decade. And when Lewis officially joined, they would go out into the areas that were converted from salt ponds back to wetlands to track the changes. 

Lewis: And it was during those initial sampling events, during the winter time Dr. Hobbs started noticing really high densities of longfin smelt every single year, even in years when folks would say that longfin smelt were fairly rare, he would see pretty large aggregations of longfin smelt in some of these shallow sloughs in lower South San Francisco Bay.

Papp: According to Lewis, it’s hard to say right now if the restoration work is the major influencer, or if perhaps longfin smelt have always been visiting and spawning in the South Bay. But in the decade or so since scientists have been monitoring this area, there have been three successful longfin smelt spawns and they were all tied to years when there was a lot of rain, which meant a lot of freshwater flowing into the south bay waterways. 

Lewis: There are many different hypotheses for why longfin smelt do so well when they have lots of fresh water, but we don’t really have a for sure answer yet. But what we do know is that more fresh water generally means more longfin smelt. And so I think the interaction of having more fresh water and having more healthy wetlands together likely does a lot of good for the species, but any one of them by themselves, only fresh water or only wetlands probably isn’t really sufficient.

Papp: In 2019, when Lewis and a team of researchers published their discovery of longfin smelt in the South Bay, it was a pretty big deal. Today, they’re stepping up longfin monitoring in that area to drill down into more of the questions scientists have about what keeps longfin healthy in the estuary. 

Lewis: The listing provides additional potential funding to go into research and conservation actions. Conservation actions may include improving hydrology. It could include additional habitat restoration, and it could include additional science. Whether or not more resources means more success is to be determined. But I don’t think it’s going to hurt to have some additional funding and some additional brains and minds thinking about how we can do better for this species.

Papp: To learn more about this topic and see photos of the work, check out our website at mavensnotebook.com. Science in Short is a quarterly podcast written and produced by me, Ashleigh Papp! With editing support from Ariel Rubissow Okamoto and the Estuary News Group, and with funding from the Delta Stewardship Council. For Maven’s Notebook, I’m Ashleigh Papp. Thanks for listening!

Note from the editor:

All three scientists were interviewed for this story in Fall 2024. By our publication date in 2025, we were unable to include all their names.

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