Fish in the Bay – February 2021: Tales from the Coral Reef and the Spawning Ground.

Trawl map.

Good news, a new season of spawning fish arrived!  Read on.


Bay-side stations trawling results.

Rare, odd-ball fish are highlighted in red.  These are usually common marine species that have ventured south into Lower South Bay.


Upstream of Railroad Bridge.

Salinities 12 ppt and less are highlighted in blue.  That is a rough threshold for successful Longfin Smelt recruitment.  Good news: most Coyote Creek stations continue to show near single-digit salinities despite the lack of rain. 


1. English Sole, Sanddabs, and Herring have returned.

English sole, Staghorn Sculpin, and a Cheekspot Goby at Alv2.

English Sole.  We counted 64 English Sole in February.  That is more than we caught in the entire years of 2015, 2016, 2017, 2019, and 2020.  Stay tuned, we might be going for the English Sole record this La Nina year!

Speckled Sanddabs.  23 Sanddabs were counted (not shown).  We realized early in the weekend that very young Sanddabs and English Sole are hard to distinguish.  Close examination was necessary.  We have been seeing a lot of very small flatfishes.


Baby Pacific Herring from Art2 on 14 Jan 2021.

Pacific Herring.  We caught 32 baby Herring at upstream stations this month.  That is a lot for February. 

The San Francisco Bay Herring spawn happens this time every year.  You may recall that we saw 4 possibly gravid Herring adults in January: one from regular monthly trawls and three more during Longfin Smelt trawling.  The spawn is happening now! 

Pelagic fish numbers look very good so far in 2021.  Anchovies, Herring, and Longfin Smelt are all doing well.


2. A growing reef in Lower South San Francisco Bay.

Big chunks of bryozoan reef continue to be picked up at LSB stations.  I still think this is a new and growing hard-bottom habitat that hosts a number of marine species.  At the very least, it seems to draw in critters that we have not seen here before!

Tunicates shown above are “Sea Grapes” or Molgula manhattensis: They anchor to underwater plants and algae, but hard substrates support many more of them. 

  • Tunicates are not new to us. They tend to bloom in winter then bust in summer. 
  • These simple animals arrived as ballast water and/or oyster barrels by the 1940s. They are efficient filter-feeders of plankton and serve as food for sharks and such.

Scale worm (Halosydna brevisetosa?).  We see more scale worms in recent years, but granted, we look harder for them now.  They seem to like the caves and cervices that the Bryozoan reef provides.  Scale worms are extremely common detritus-eaters in the world’s oceans. 


Red Beard Sponge (Clathria prolifera).  This is the first sponge we have ever seen.  It is common in the northern parts of San Francisco Bay, but new here.


3. Other organisms like the hard bottom.

Plainfin Midshipman.  This was our first full-sized adult midshipman caught in at least several years of trawling.  We see a few to several babies each year, but never adults, until now.  Yes, this is the “Singing Toadfish.”  He grunted warning songs at me as I held him.


Bonehead Sculpin is the coastal marine oddball that shows up at least once every winter at one of the LSB stations. 

Brown Rockfish.  This small juvenile is the first Rockfish we have seen in several years of trawling.  However, rockfish are very common just north of Dumbarton Bridge.    



Orange-striped Anemone (Diadumene franciscana?), “the San Francisco Anemone.”  We continue to find many of these tiny orange blobs stuck to oyster shells at LSB stations.  The big surprise was finding this one at station Art3 in Artesian Slough, far upstream of any others we have seen before. 


Chameleon and Shimofuri Gobies.  We continue to loosely track Chameleon and Shimo populations,  But, the counts on data sheets will always be confused.  These two gobies are genetically very closely related.  To the naked eye, identification is difficult. The distinguishing marks can be seen only under careful close examination.  It is also possible that these two species may hybridize!

Through January, we caught many Chameleons at stations far upstream on Coyote Creek.  This month, we found a number of Shimos living nearly side-by-side with Chameleons at downstream LSB stations!

  • Chameleons prefer marine salinity and are usually caught only at stations LSB1 and LSB2. The growing hard bottom in LSB provides refuge and nesting caves for Chameleon Gobies.
  • Shimofuri Gobies live upstream in brackish water.
  • Male Chameleon Gobies are known to turn dark, almost black, when they court females and tend eggs in their hard substrate caves. The dark Chameleon shown in photos above and below is one of those guys!


Same three Chameleon Gobies with one Shimo at LSB2.

Both species are non-native from Japan.  They invaded only a few decades ago.  I can’t see any direct harm they cause, but they must compete with natives.  They are the prettiest gobies by far.


Bay Goby (Lepidogobius Lepidus).  This is our second winter that baby Bay Gobies have shown up in LSB.  We don’t know what is causing this native Bay Goby rebound, but we hope it continues. 

Bay Gobies spawn in January through March in small bays along the California coast.  Like most gobid-type fishes, adult males swim downstream into saltier Bay water to dig burrows where they attract females to lay eggs.  Males tend the eggs for around three weeks until hatch.   

See:  Gary D. Grossman (1979), “Demographic characteristics of an intertidal bay goby (Lepidogobius lepidus)”


4. Spawning Grounds in Upstream Marshes!

Another bunch of golden-orange fish eggs at station Alv2.  We found loose eggs like this near this same location on January 9th.  We still don’t know which fish might produce these eggs.


Adult male(?) Staghorn Sculpin and two younger sculpins at Art3

Pacific Staghorn Sculpin mostly live along the coast.  But, they migrate far up into the Bay to release eggs.  Some stick around for most of the year, but we always see a small surge of bigger fatter adults around December, then lots of babies a month or two later.

For years, we have wondered why some adult Staghorns have bright white patches over their eyes.  These must be the males!  Pregnant females do not have the white spots – see below.  


We caught this gravid female Staghorn amongst many juveniles and babies in February.  Several more pregnant females were caught through the month of January.


A few more gravid female Sculpin from January trawls.


Artistic representation of the scene at Art2: Western Grebe above & bird food below, Art2 on 14 Feb.

This place used to feed millions of birds before all the bad stuff happened.  Many little sculpins will survive and many won’t. 


Baby Sculpin, Coy2

Teeny-tiny Baby Staghorn Sculpin!!  We see babies like these around the upper stations along Coyote Creek.  This means that fat-bellied females are releasing eggs into muddy caves along this slough. Males we catch must be recovering from the egg-tending ordeal.  This is a Staghorn spawning zone!


Pregnant Yellowfin Goby from Dump Slough, 16 Jan 2021.

Yellowfin Goby.  30 Yellowfins were recorded for February.  That is a typical winter catch.  Many females are swelling up with eggs they need to release. 

Yellowfin courtship and egg-tending are almost identical to that of all Gobies, Sculpins, and Midshipmen:  Yellowfin males usually swim downstream to seek ideal brackish salinity to build underwater burrows.  Females lay eggs on ceilings of mating caves.  Males guard eggs for almost a month, sometimes with female help.


Anchovies, young and very young in Pond A21 on 13 Feb 2021.

Northern Anchovies.  Nearly all the 371 Anchovies caught in February were babies. These nearly transparent larval fish are maturing into juveniles and young adults mainly at stations in LSB, Dump Slough, and Ponds A19 and A21.  They probably migrate out to the deeper Bay as they age.


Longfin Smelt.  Our threatened species is spawning here!  Many of the 225 Longfins caught in February were adult breeders. The adults were in an extreme state of reproductive readiness!  The female shown above was visibly extruding eggs.  Several males, with long sweeping anal fins and deep dark green and brown iridescent dorsal color, appeared to be seeping milt. 

This is consistent with the notion that longfin males stage at mating sites upstream.  The male uses his long anal fin to sweep out a spot.  He then induces a female to drop sticky eggs as he exudes milt just above the spot.  The eggs then stick to sand, gravel, or plant material as they incubate.

  • See Yi-Jiun Jean Tsai et al (2021). Researchers at the UC Davis Fish Conservation and Culture Lab (FCCL) for the first time witnessed spawning behavior in related Delta Smelt.  Longfin spawning behavior could be very similar: Delta Smelt spawning happens in darkness at night.  Two to five fish swim side-by-side against the current.  They release eggs and milt during multiple bouts through the night.  It paints a picture.


Coyote Creek, between stations UCoy1 to UCoy2, is a year-round spawning ground!

Another schematic artwork to celebrate this discovery:  Over the past year, we found signs that Anchovies, Longfins, and now Staghorn Sculpin all spawn in this exact spot.  What could be better than that?  This marsh is a finfish production machine!   

  • Oddly enough, we thought that super-dry winter would have decimated the Longfin population by now. It hasn’t so far. Longfin spawner numbers are up from recent years.  But, the next question will be whether the fry survive. 
  • This place could end up being the last stand for Longfin Smelt in the San Francisco Estuary. … Or, their salvation. 


5. Lampreys!  – signs of another spawning zone far upstream.

Pacific Lamprey.  This macropthalmia-age Lamprey hatched upstream and lived for the last 5 to 7 years as a blind worm-like larva in mud or sand on a creek bottom.  As a young Ammocoete, this Lamprey performed the same function as earthworms do in garden soil. 


Three more Lampreys were caught near station Coy4 during supplemental Longfin Smelt Broodstock trawls in January.  They were all also at the macropthalmia-age and migrating out to sea. 

Lampreys are boneless and extremely high in protein.  They are the ideal food for White Sturgeon. There are few animals as valuable as a Lamprey to the ecosystem.   


6. Boogers!

Boogers.  We see these jelly-like blobs from time to time. 27 of them were caught in Pond A21 this month. We have always considered them to be “jellyfish fragments.”  They are common enough that they must play an ecological role. 

  • What if these are entire organisms, not fragments?
  • What the devil are they? … Salps? … Jellies? … Something else? 


Two more boogers caught on 13 Feb.

Boogers are fragile and often nearly transparent. They are roughly cylindrical in shape: around 1 inch wide and 2 to 3 inches long.   Many more of them may disintegrate in the net before we ever see them. 


Closeup of Booger fragment from 23 Jan 2021.  What is this Boogery structure?

Boogers have a fibrous structure inside the jelly bag.  The golden fibers link chains of small beads – possibly bacterial cocci?  Could these boogers be some form of cyanobacterial colony like planktothrix?

  • Practically all “Medusa Jellies” we tally in data sheets are actually these boogers. I don’t think these are jellies at all. 
  • Can anyone identify these boogers?


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