Fish in the Bay – December 2018 UC Davis Trawls – Save Our Smelt (SOS)

This is another special edition of Fish in the Bay. 

While most of us Christmas shop or prepare to leave town for the holiday break, the UC Davis Hobbs Lab crew is collecting holiday cheer in the form of ripe, fertile adult and endangered Longfin Smelt.

For those who may not be aware, Longfin Smelt in the San Francisco Bay and Delta have been disappearing for decades, not unlike the Delta Smelt.  Coincidence?  We think not!



The good news from the Alviso Marsh Complex in Lower South San Francisco Bay is that we have a small but robust population of reproducing Longfins here.  Winter rains attract them to the marsh and cold temperatures induce them to spawn.

Map above shows numbers of Longfin Smelt caught at each station on 8 and 9 December.  Almost two-thirds of Longfins in December trawls were netted in restored ponds A19 and A21.  This was habitat that did not exist prior to pond breaching in March 2006.  Now, at least two restored ponds host one of the largest remaining remnants of Longfins remaining in San Francisco Bay!


Photo above:  Five adult Longfin with two Young-of-Year Smelt caught in Pond A19 on 9 December – photographed by Levi Lewis.


Jim Hobbs has been tracking this small straggler population of winter Longfins for several years.  Finally, after robust rain in early 2017, Jim confirmed that spawning was happening at several locations in this area.  More spawning was detected in early 2018, and the Longfin catch increased each of the past two winters.


UC Davis research boat pushes off from Alviso Launch for operation “Save Our Smelt” on 10 December.


The grim news is that Longfins, once one of the most numerous fish in the Estuary, have been disappearing for decades.

A 2017 article by Hobbs, Moyle, Fangue, and Connon, “Is Extinction Inevitable for Delta Smelt and Longfin Smelt?” describes the smelt situation and makes several management recommendations:

I have even heard anecdotal tales; one from an old Alviso resident that smelt were once abundant in Alviso Slough next to the town in the 1940s – essentially at same launch location shown in the photo above.   Even my mother remembers “smelting,” almost certainly for Longfins, near Redwood City in the late-1950s, for another example.  On a human-scale, both accounts happened long, long ago, but in geologic, evolutionary, or ecosystem history, that was yesterday.

How could we lose the most abundant forage fishes, Longfin and Delta Smelt, and not profoundly change the entire ecosystem?



Operation Save Our Smelt is a mission to capture adult spawning Longfin Smelt from 1) Alviso, 2) Napa-Petaluma, and 3) Sonoma Creek marshes for transport to the UC Davis Fish Conservation and Culture Lab (FCCL) at Byron pump station near Tracy CA.  If successful, captured Longfin adults will be used as broodstock to give humans a chance to preserve this species if things continue to go very badly in the wild.

You can peruse the FCCL webpage here:



Photo from: 


UC Davis Fish Conservation and Culture Lab (FCCL) is located at the State of California “Harvey O. Banks Pumping Plant” facility on the west side of Clifton Court Forebay.

The pump station lifts Delta water into the California Aqueduct to supply State Water Project (SWP).  A nearby federal pump station on Old River supplies the Federal Central Valley Project (CVP).

This LA Times article from earlier this year summarizes the fate of the Delta Smelt with respect to California water management:

This longer April 2018 article features Peter Moyle and describes California water diversions in greater detail:



The UC Davis FCCL has raised endangered (some say functionally extinct) Delta Smelt in tubs and tanks at the pumping plant since 2004.  The three Delta Smelt production tanks shown above host roughly 2000 fish each.  I surmise from recent catch data that these three tanks alone hold a significant portion of all remaining Delta Smelt! 



These Delta Smelt are now “broodstock.”  The fish are genetically identified from fin clips and tagged.  As they mature, these adult fish are transferred to the “Adult Lab” where temperature, salinity, and other factors are controlled to stimulate spawning: Cool temperature is the main criterion.  Delta Smelt spawn at around 12 degrees centigrade.



Galen Tigan, Assistant Manager at the FCCL, is able to induce Delta Smelt to spawn at least two to three times per year.  When Galen is ready to move adult fish to breeding tanks, he calls tag numbers in to the UC Davis Genomic Variation Lab (GVL).   The GVL then messages Galen with Smelt ID numbers to match to ensure optimum genetic diversity.


Galen Tigan (second from left) showing Jim Hobbs, Jon Kuntz and Alec Scott the adult Delta Smelt in one of the breeding tanks. 


Delta Smelt in an adult lab tank above: some of the last of their kind.


Wild-caught Longfin Smelt from Station A21-1 on 8 December.

In recognition that Longfin Smelt are getting equally vulnerable to extirpation if not extinction, the FCCL Lab started researching ways to also sustain Longfins in tanks in 2008.  Once methods were refined, facilities were expanded, and new production and breeding tanks were set up for Longfins.




Hobbs Team to the rescue!  This is where UC Davis Department of Wildlife, Fish and Conservation Biology and Hobbs Lab comes into the picture.

From years of tracking remaining Longfin populations in San Francisco Bay, Dr. Hobbs knows where they are, when they show up, and he knows how to catch and handle them.  He also has boats, nets, and a bunch of motivated team members.


Step one: catch the fish. 

Otter trawling is the most efficient way to bag Longfins.  It’s rough on the fish, but time spent in the net is very limited – less than 10 minutes for a 5-minute trawl.  Beach seines and Fyke nets would work well, but considerations of labor, logistics, or habitat disturbance can weigh against those methods.



Step 2: Find the Longfins. 

Recent wet years have been very good for Crangon shrimp, American Shad, Starry Flounder and some other species.  The tub above contains the typical catch from Station Coy3: 1000+ crangon shrimp and assorted fish.  With luck there may be 2 to 6 adult Longfins (greater than one year old) hidden somewhere in this mass of shrimp.



Success!  An adult Longfin.



Double success: Longfin female dropping EGGS!!!


Above: Cylindrical containers are used to hold Longfins after netting and through transport to the Culture Lab in the Central Valley.   (Note battery powered aerators on closer tank.)


Jim Hobbs (right) and Jon Kuntz (left) carting live Longfins from Alviso Launch on 11 December.


Step 3:  Keep them alive until they get to the FCCL. 

Longfin Smelt, like most smelt, are a fragile fish.  They do not hold up well to netting and extensive handling, like say, Striped Bass, gobies, or Staghorn Sculpin.   For this reason, the operation had to be carefully planned:

  • Shorter 5-minute trawls to reduce fish stress.
  • Two Longfin deliveries per day, at noon and evening, to reduce holding time and avoid peak Bay Area traffic.
  • Two 20-gallon tanks, one aerated, one for makeup water, to assure survival.
  • Prior coordination with the Culture Lab so that tanks, tags, and fish food were ready to accept delivery.

The Longfin capture strategy is frustrated by the fact that most Longfins are at locations distant and a bit difficult from the Alviso Launch.  Pond A21 is a particular hot-spot, but the Pond can only be trawled at daylight high tide which only occurs after noon at this time of year.



(L to R) Jim Hobbs, Alex Scot, and Jon Kuntz securing the Longfin container for transport on 10 December. 

Moving the fish.  If no one else is available for transport duties, Hobbs and crew park the boat and transport the fish to the FCCL near Byron themselves.


First delivery on 10 December: Galen Tigan (far right) with Jim Hobbs lifting the Longfin tank off the tailgate at the UC Davis FCCL Lab facility.


Alec, Jim, and Jon inspecting the new temporary home for Longfin broodstock.

Step 4:  Give them a new home.



Eleven Longfin breeders delivered on day one with no casualties. 

Jim Hobbs’ original goal was to deliver 50 adult Longfins each from Alviso, Napa-Petaluma, and Sonoma Creek marshes to ensure good genetic diversity.  However, early success in Alviso Marsh Complex motivated Dr. Hobbs to increase the Lower South Bay contribution 100 breeders – just in case the northern marshes yield less fish.


Step 5: Keep them fed.

The FCCL Lab also raises smelt food.  Smelt are small fish that eat tiny food.  Galen maintains separate tanks for raising Artemia (brine shrimp), Mysids (also a small shrimp), and rotifers.  These are the same types of food organisms that smelt eat in the wild.

According to Galen, Copepods are not on the menu because, for the time being, they can’t be raised fast enough with available equipment to provide a meaningful food supply.




Other fish caught during Operation SOS.  As always, a variety of fish are caught in Alviso Marsh Complex.  It would be misguided to ignore additional fish data generated by all the extra trawls since they help define suitable Longfin habitat and competitive pressures.  Examples above include, clockwise from top left:

  1. English Sole – This was the first English Sole detected for winter 2018-19.
  2. Northern Anchovy – Examples of both brown-back and blue-back varieties shown here.
  3. Starry Flounder – This pair photographed by Levi Lewis.
  4. California Halibut – Halibut are uncommon in Lower South Bay now that winters are wet again.
  5. Three-spined Stickleback (center).


Table above summarizes all fish caught in SOS 5-minute trawls the first two mornings of the operation. 


This is a rare chance to compare results from repeated trawls in the same area:

  • Most trawls were conducted near Station Coy3 on the two different dates.
  • Longfins Smelt were counted either as Young-of-Year or mature (Year-2).
  • Despite considerable variability in numbers of commonly caught fish, Longfin Smelt, Northern Anchovy, Yellowfin Goby, the averages are surprisingly similar.
  • Of the fifteen fish species caught, at least 4 were uncommon one-offs: Threadfin Shad, Bonehead Sculpin, California Halibut, Plainfin Midshipman, and Arrow Goby.

A little too warm:  Longfin Smelt generally do not spawn above around 12 degrees centigrade, though some sources claim that spawning can occur as high as 14.5 degrees.

Still too salty:  Larval Longfin Smelt tolerate 2 to 6 ppt of salinity when first hatched and 8 ppt within weeks.*  Salinities in Alviso Marsh Complex are falling with each winter rainstorm but still may have a way to go before successful spawning can happen this year.

We experienced a BIG Freshwater Flush in early 2017.  Then, BOOM, Longfins started spawning as local salinity dropped!  By late February, local salinity fell as low as 0.5 ppt!  Salinity that low is extraordinarily rare for the Lower Coyote Creek area, and Longfins don’t need it that low, but the experience shows us the potential benefits of significant flushing here.

* According to a 2012 USFWS 12-month finding that cites Baxter 2011a, pers comm.  



It may be silly, but I can’t help making this comparison:  The 1972 movie “Silent Running,” starring Bruce Dern portrayed a dark dystopian future in which all significant plant life had been moved to spaceship arboretums because future Earth no longer supported forests:

The “Silent Running” movie future was set in year 2008, so we dodged a major bullet in that respect.  Nonetheless, despite our delayed timeline, we are gradually moving in that direction.  The last representatives of yet another once numerous species may soon exist only in a culture facility in Central California.  This is not good!


 Photo from 8 December: an adult breeder Longfin alongside two “Young of Year” (YOY). 


We still have hope!  Over the past December week, the Hobbs team successfully captured and transferred live Longfin Smelt to the UC Davis FCCL labs near Byron.  At this point, I do not know if the same efforts in Napa-Petaluma and Sonoma Creek marshes will be so fruitful.

More importantly, the Lower South Bay / Alviso Marsh Complex population of Longfins, though small, appears to be robust and reproductive.  There is an equally good chance we can learn to manage and further enhance marshes around Lower Coyote Creek to sustain SF Bay Longfins here in the wild.


Merry Fishmas and Happy New Year!






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