Fish in the Bay – December 2020: The Longfin Chronicles, Part 2.

Longfin trawl results from December 27th& 28th.

Longfin Smelt Broodstock Collection.

Operation “Save Our Smelt” 2020/21 continued through the last week of December and will continue into January.  The project goal is to collect 200 large Longfin male and female “keepers” this season.  These will be added to the breeding population at the UC Davis “Fish Conservation & Culture Laboratory” (FCCL) at Byron, CA.  With luck, this stock of reproducing smelt will conserve the gene-pool of the rapidly dwindling San Francisco Bay population.   

Step 1 – Collection of breeding-ready adult Longfins.  This step is labor-intensive but technically easy.  This is the third year that good quality breeding adults have been caught.

Step 2 – Persuading the fish to spawn in the lab.  The FCCL scientists have had little problem inducing the fish to do their thing.

Step 3 – Raising subsequent generations of lab-hatched Longfins into a sustainable breeding stock.  UC Davis scientists are learning with each trial, but so far the young do not survive to reproductive adulthood.  This continues to be a classic “race against time.”

The trawl maps above summarize the 27-28 December catches.  A total of 396 Longfin Smelt were caught (254 on Saturday + 142 on Sunday).   Only 49 of the largest fish were kept as “Broodstock” for delivery to FCCL lab.  The rest were released. 


Sunrise over Lower Coyote Creek.  The mouth of Alviso Slough lies center-right in the photo.

Trawls start early.  20-odd “keeper” fish are brought to the Alviso dock for transfer to FCCL staff by noon each day.  This allows for about an hour of road travel to Byron and then processing time to document and tag the fish before they are added to broodstock tanks at the lab.


Micah Bisson at the helm.  Caitlynn Klowen to the right.

Micah captains Broodstock collection expeditions.  On the weekend of 27-28 December, he was joined by Caitlynn (Catie) Klowen, a new employee at the UC Davis OG Fish Lab.


Micah and Catie Bring in the net.

Three-minute trawls.  As before, the duration of each trawl is limited to three minutes to minimize stress on the fish.


Selecting large Longfins for Broodstock.  The rejects are released.

Find the Longfins!  The otter trawl net is emptied into an aerated holding tub.  Longfins are carefully dip-netted then transferred to the chilled and aerated collection tank.


A large “keeper” smelt, probably a male, being lowered into the collection tank.


Micah and Catie check water quality in the collection tank.

Holding water is collected on-site. Water is oxygenated to 100% saturation and chilled to ambient temperature (around 10 to 12 degrees C) to keep the Longfins happy.


Happy male Longfin Smelt.  Collected on 27 Dec – trawl #7, at “the notch” in Pond A21.


Longfin eggs.  Physical handling of Longfin Smelt was restricted to dip-netting and cup-transfer to the collection tank or for release.  Examination was limited to eye-ball estimation of body length. 

However, during trawl #1 on December 28th, a packet of Longfin eggs was discovered with an adult female.  The female was alive and swimming and appeared to be otherwise unharmed. She was immediately released.  Abdominal pressure in the trawl net must have caused her to spontaneously abort.  The eggs were kept for further observation.


Know your tides!  On Saturday the 27th, ZERO Longfins were caught on the north side of Pond A21 at 8:22 (trawl #5).  At 10:59 (trawl #13), at practically the same location, 153 were collected.  The stage of tide may have made the difference. 

  • Tide was flooding in at 8:22 AM. Small fish, like Longfins, were presumably swimming into submerging spartina marsh to pick at food and/or spawn.  
  • Just after high tide at 10:47, ebbing water appears to have swept Longfins out of the marsh and into our net.
  • The difference was stark. Maybe it was just luck of the trawl.


Other Fishes & Bugs.


1. Anchovy Metamorphosis & Growth.

Two young (almost larval?) Anchovies from the vicinity of Coy3.

Spawning Anchovies were observed in LSB in summer through fall of 2020.  A key question is whether Anchovy larvae subsequently hatched (YES!) and to what extent the larvae survive through metamorphosis to juvenile stage roughly 60 to 75 days later. 

(Interestingly, fish survival through metamorphosis and early juvenile stage is the same bottleneck problem faced by UC Davis in attempting to sustain the Longfin Smelt Broodstock in the lab!)

It is already clear that many of our young Anchovies have survived to juvenile age!  However, these observations are only anecdotal.   More investigation is needed!

Culture and Growth of Northern Anchovy, Engraulis Mordax, Larvae. Anchovy metamorphosis is complete at 35mm standard length.  (To survive to metamorphosis, larvae had to be first fed Gymnodinium (naked dinoflagellates) and Brachionus rotifers up to 12 days.  From that point until about 20 days, rotifers were sufficient. After that, their diet shifts to copepods & nauplii.)  Hunter (1975) NOAA Fishery Bulletin: Vol. 74, No.1:

Behavior and Survival of Northern Anchovy Engraulis Mordax Larvae.  This paper summarizes the earlier feeding experiments.  Anchovies reach metamorphosis at 60 to 75 days at 16 degrees C.  Higher temperatures accelerate this growth.  Hunter (1975-1976) CalCofi Report, vol 19.

Larval growth & Metamorphosis.  European Anchovies begin schooling shortly after development of the caudal (tail) fin and inflation of the swim bladder at about 12 days.  Somarakis & Nikolioudakis (2010)

Feeding experiments on Cape Anchovy.  Rotifers, ciliates, and copepods alone are not sufficient food for “first feeding.”  (Also see p.185:  “… the brain and dorso-cranial musculature [in larval pilchard] were abnormally red, reminiscent of the symptoms described by Blaxter et al. (1974) in captive herring suffering from deficiencies in B-complex vitamins.”)  C. L. Brownell (1983)


Juvenile Anchovies at different growth stages.

FIRST FOOD.  Anchovy larvae must find their first food 2 days after hatch.  If they don’t find fairly specific tiny food, like naked dinoflagellates or something very similar, they will starve before the end of their first week. 

Somehow, our anchovies are surviving in the absence of rain!  What is their First Food here?

After they find their first food, they begin schooling at only 10mm, even before metamorphosis.  Eyes, scales, and internal organs, especially the digestive tract, develop. After roughly 75 days, when they reach 35 mm in length, they metamorphosize to juveniles; basically a smaller version of the adult fish form.

Young anchovies near metamorphosis age and older were observed in Ponds A19 and A21!  … they are present at almost all stations in the Alviso Marsh complex.


A pair of juvenile Anchovies, 28 Dec – Trawl #3, at the mouth of Mud Slough.

Young Anchovy Dorsal Color Development. 

  • At low salinity, juvenile Anchovies do NOT develop dorsal color.
  • If salinity is sufficiently high, young Anchovies begin to express blue or green colors at the crowns of their heads perhaps only days after metamorphosis. The color deepens and extends along the lateral line as time passes if salinity remains sufficiently high.
  • Anchovy dorsal colors may correspond with salinity thresholds seen in American Shad, eg. 14-19 ppt = green and 19+ ppt = blue.
  • Unlike Shad, Herring, or Sardines, Anchovies do NOT express brown color in chromatophores. Some turn golden, most simply lose color expression at low salinity. 

Like Shad and Herring, Anchovies can express color evenly across the entire dorsal side.  However, uniform dorsal coloring only appears in Anchovy adults returning from the ocean or deeper Bay.  Color fades away quickly as they remain in Lower South Bay.


American Shad & young-of-year Anchovies, 28 Dec – trawl #7, Mud Slough Channel.

Light intensity & angle is important for assessing iridescent fish colors.  Anchovies shown above appeared to be colorless “brown-backs” from a distance.  Closer examination revealed bright blue chromatophores at the crowns.


2. More Winter Run Anchovies?


A few big Blue-back Anchovies were seen on 27-28 Dec.

Adult Anchovies retain dorsal colors for days to weeks after exposure to intermittently fresher water.  Adults showing bright blue dorsal color, like those shown above, must have recently migrated in from the sea. 



Faded Blue-back Anchovy from Pond A21.

Northern Anchovies develop melanophore darkness over their dorsal sides as they age, in addition to chromatophore coloration (blue or green).  The darkness is analogous to a “suntan.”  Thus, faded blue or green-backs can still be identified by their dark gray dorsal sides even after the color disappears.  This large gray fish must have arrived earlier.  But, exactly when it arrived in the Bay is anyone’s guess at this point. 

Also note, water was saline (20.8 ppt), above the “Blue Shad” threshold, in Pond A21 when this big fish was caught.  However, salinity here varies widely.  Salinity at the same location ranged from 15 to 18 ppt the previous day during flooding tide.   


3. American Shad & Another Color Experiment.

Two American Shad, one large, one small, with other fish.  27 Dec, Trawl #1 at the mouth of Mud Slough.

Once in a great while, we catch large (for us) American Shad.  The bigger fish, shown above, appears to be about 3 years old.  That would put him (or her) in the year class that hatched in the wet years of 2017-2018. 

Non-native Shad were introduced into California in the late-1800s, but they have never been abundant in LSB.  However, their numbers increased at least 5-fold following the wet years of 2017 & 2018.

  • Comparable trawls at 20 stations in 2014 through 2016 caught 100 to 150 per year.
  • From 2017 through 2019, between 500 to over 800 American Shad were caught each year.
  • Only 237 were caught in regular monthly trawls in 2020.

El Nino/La Nina Cycle (or ENSO).  American Shad abundance in LSB seems to track with the Pacific Ocean’s ENSO cycle.  Shad were relatively scarce in LSB during dry years following a strong La Nina in 2011-12.  Their local population boomed in wet years after El Nino of 2014-2016.  The current intense, but short La Nina of 2020/21 seems to have again suppressed their numbers – at least through December.  We shall see … 


By random chance, we caught a DEAD American Shad in Pond A21 on December 28thAs LSB fishes go, American Shad are very hardy.  Regular monthly 10-minute otter trawls never harm them.  These 3-minute trawls for Longfin Smelt are particularly gentle, and this fish was already stiff from rigor mortis when collected. 

Regardless, this dead fish afforded an excellent subject for another Shad Dorsal Color experiment. 

  • Blue. The fish was netted in Pond A21 where pond water was 25 ppt.  When pulled from the net the Shad’s dorsal side was conspicuously bright celeste-to-indigo blue.
  • Brown. The fish was immersed in bottled drinking water (0 ppt) at 10:06 AM.  By 10:12, the dorsal side had turned dirt-brown.
  • Blue Restored. We placed the Shad back into a bucket of ambient Pond water at 10:12 AM.  When checked 18 minutes later, the Shad was blue again!
  • Exact timing of each color change was not measured in this experiment. (We were too busy with Longfin trawls.)  The color change in live American Shad, from fully-blue to fully-brown, has been documented in earlier experiments to take roughly 3-minutes. 

This dead Shad Experiment points out a few more important clues:

  1. In Shad, color change in chromatophore cells does NOT depend on the fish’s metabolism – THIS FISH WAS DEAD! Apparently, ambient salinity affected the orientation or distance between planar guanine crystals inside the cells.  Most likely, intercellular dehydration (to blueness) then rehydration (to brownness) is the mechanism causing the color changes.
  2. The mechanism of Anchovy color change must be a little different. Anchovy dorsal colors fade within minutes after death (10 minutes max based on crude observation.)  Somehow, Anchovy chromatophores are better insulated from ambient salinity and are completely dependent on the fish’s metabolism.    


4 . Predators lurk outside Pond A21.

Big sturgeon or leopard shark spotted on sonar just as we exited Pond A21.

Big fish learn where to hunt.  We spotted this really big fish just as we exited Pond A21 on December 27th.   Lots of smaller fish flow out of the pond as the tide ebbs.  Big fish figure this out.   


Another predator with two smaller shad.

Striped Bass are relatively rare catches in these slow and short-duration Longfin trawls.  Not surprisingly, the only bass we caught on the 27th was netted at the entrance “notch” at Pond A21 along with an American (top) and a Threadfin Shad (bottom).


 5. Flatfishes.

Juvenile Sanddab, 28 December near Coy3.

Speckled Sanddab.  This must be Sanddab recruitment season.  We are catching a few to several each day of trawling.



California Halibut with Staghorn Sculpin, American Shad, and three Anchovies.

California Halibut tend to recruit better in LSB in dry years.  Unfortunately, this did not seem to happen in 2020: only 78 were caught in regular monthly trawls.  That was only a slight improvement over the three prior wetter years.       


A parasitized English Sole, dorsal and ventral views, 28 Dec, Mud Slough Channel.

English Sole spawn offshore.  The juveniles migrate into the Bay to feed and recruit.  It is always rare to find one with no signs of disease!  They were documented to host over 2 dozen different kinds of parasites in a 1978 study in Oregon.  Also see Fish in the Bay, January 2019, section 3:

I cannot identify the affliction shown above.  So far we have spotted Lymophocystis virus (cauliflower looking lumps) and protozoan “X-cell disease” (pink bumps that grow into an amorphous-looking ooze).  This infection looks closer to X-cell disease, but it’s hard to tell.


 6. Topsmelt, Shrimp, & Ducks

Topsmelt populations exploded in Pond A21 in July 2020.  It may have been a fluke, but we continue to catch a few now and again.  As their name implies, Topsmelt tend to swim at the top of the water column so they often evade a bottom-dragging otter trawl net.   


Crangon females laden with eggs should be swarming Lower Coyote Creek by late December.  We have only caught a few so far this season.  We keep watching.


Lucky Ducky: Male Bufflehead being chased by six females near the north shore of Coyote Creek.

Male ducks always dress up in bright feathers to attract their mates.  Female ducks chase them.


End of Mission:  Anna Neill & Ana Felix pick up precious Longfin cargo for transport back to the FCCL lab.

140 Longfins sent to the lab so far, 60 more needed!

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