Fish in the Bay – July 2020: Lots of Crangon & Topsmelt, plus a Red Ceramium Bloom.

Trawl map.


Bay-side stations trawling results.


Upstream of Railroad Bridge.

Our July trawling weekend was quite an experience.  Spawning Anchovies, reported via a ‘Special Alert’ report, was the biggest of several shockers.  This regular July report covers the rest:

  • Pond A21 tiny fish explosion.
  • Red Ceramium blankets Lower South Bay
  • Crangon recruits congregate at Coy4
  • More Anchovy colors.
  • Shimofuri and Chameleon Gobies really are color-changing chameleons.
  • Interesting critters.


1. Pond A21 marsh is full of tiny fishes.

Micah Bisson sets the net for the trawl of Pond A21 borrow ditch.

Tide was low and falling at 8:22 AM on Saturday as we started the first trawl of the day.  Our semi-diurnal Pacific tides synch with Earth’s orbit around the Sun, so lowest low tide occurs in mid-day in mid-summer.  This makes for tricky trawling.  Restored ponds, like A21 are shallow to start with.

The borrow ditches around the perimeter cannot be trawled at low tide, and we were close to scraping the bottom after the end of this trawl.  Trawling the second station in Pond A21 was out of the question.     


Lots of tiny fishes!  Falling tide is the ideal trawling time.

Now we had to count thousands of fish.  Thirty minutes until we trawl the next station.  Count fast!


Results!  We caught 2,543 Topsmelt (Atherinops affinis)!


Pond A21 Fish Collage.

A note about small silvery fishes:  Most small silvery fishes we see here are generically called “Silversides” and are members of the Atherinopsidae family.  This is also known as the “Neotropical” or “New World” Silversides family of fishes that includes Jacksmelt, Topsmelt, Grunion, and Mississippi/Inland Silversides among others.

Topsmelt.  This was an excellent opportunity to gauge a common marsh fish that usually eludes the trawls.  Young Topsmelt hug close to the marsh and scatter into the reeds as the trawling boat approaches.  But, with a low and ebbing tide, they had no escape.  So, we caught a lot of them.  Like most species here, they hatch and recruit in brackish marsh then migrate out to the deep bay or sea.  These were all young recruits.


Mississippi Silversides/Inland Silversides (Menidia beryllina) were the next most populous fish caught in Pond A21.  Generally speaking, Mississippi and Inland Silversides are the same fish.  I use the names interchangeably.  Some papers describe minute phenotype and genetic differences.  But, for purposes here, there is no meaningful difference. They were first introduced into California at Clear Lake in 1967. 


Two of three Longjaw Mudsuckers from Pond A21.

Pond A21 was a desolate salt evaporator until it was breached for tidal circulation in March 2006.  It is now a fish hatchery!


2. Red Ceramium Bloom in Lower South Bay.

Red Ceramium at stations LSB1 and LSB2.

Ceramium.  We often see this fine thread-like red algae in the warm months, but we have never seen a bloom like this.  The net was clogged with the stuff at both deep Bay stations.  It was a bit of a mess as Micah and I picked small critters out of the red clumps.


Ceramium closeup.



We caught 6 Bat Rays at LSB1.  Micah pulled each one out from the Red Ceramium morass while avoiding getting stuck by their spiky tails.


Nudibranch.  This may be the first nudibranch we have caught in Lower South Bay trawls.  At least 100 different species of these shell-less gastropods live off the coast of California.  But, they rarely (almost never?) intrude so far south in SF Bay.  Does anybody recognize this Aeolid Nudibranch?

Philine snail.  Philines are nuisance invaders that we catch at LSB stations from time to time.  They are predatory gastropods that look like snot-balls, and we do not like them!

Decorator Crab.  Once again, we caught two Decorators.  Until this past year, they were uncommon here.  …  More discussion about crabs farther below


3. The Ghost Ship.


Low Tide at High Noon:  The Ghost-ship of Lower South Bay appears above the waves.

Ghost Ship.  This wrecked boat is visible when the vast mudflat exposes during lowest tide in summer.  See “Fish in the Bay,” May 2019, at very end of report:   

Here it is again.  It lies due west of the ‘Duck’s Beak’ and NNW of Moffet Field main airstrip.  It is a good reminder that this portion of the Bay is deceptively shallow

Warning to navigators: Do not stray from the main channel!


4. Crangon Shrimp Congregating at Coy4.


Coy4:  17,720 Crangon were caught mixed with more Ceramium

Young Crangon shrimp appear to be moving downstream as they grow.  The vast majority of them were collected at station Coy4. 

Also note: Crangon in July appear to be all Brown-tails (Crangon franciscorum).  The Black-tails are completely absent.


17,740 CrangonThis year is almost certain to beat our Crangon records.  With only six months of data, the 2020 Crangon count has almost matched the total numbers caught in our best years of either 2018 or 2014.  (For comparison, we only caught 1,529 Crangon in all of 2016!)

How to count 17,740 Crangon:  

  1. First, pick out any Anchovies, tiny gobies, or other shrimp species from the squirming mass. (Fortunately, this catch was almost pure Crangon.) 
  2. Second, count out a reasonably replicable pile of shrimp. Then, count piles.  In the past we found that a brimming full tray holds 3,000 to 5,000 shrimp, but unfortunately much depends on size (age) of shrimp and exact dimensions of each tray. 

We very rarely catch such huge numbers at one time.  But, who knows?  If these migrating shrimp become a permanent annual feature of marsh restoration and recovery, we will need to further streamline our counting methods!


Some Crangon caught at upstream station Coy1 on 12 July.

The relatively few Crangon caught at further upstream stations were also all Brown-tails. 


5. Colorful Anchovies.


Anchovies in LSB:  Youngish, bluish, with a bit of green.

Anchovies are generally bluer at downstream stations – with a lot of exceptions!

Most Anchovies caught at deep Bay stations seem to be young and mostly clear/translucent on the dorsal side.  On a few occasions in the past, larger solid greens or blues have been collected at these stations.  Presumably, those are adults migrating in from the ocean.  But, on this July weekend, all the deep Bay Anchovies were only weakly colored at best.

My guess is that young adults tend to loiter in the Bay for at least a year or two before migrating to the ocean.  Perhaps it takes a few years before full dorsal color develops?  Even in fully color-developed fish, the color fades away considerably when they stay in Lower South Bay.

  • Science Speculation: Guanine crystals in chromatophores form molecular planar structures that defract iridescent hues in Clupeiform fishes (and Salmonids too). Colors expressed range from blues and greens in saline water to browns and golds in fresher water across all these fishes.
  • Unlike the other fishes, Anchovies lose dorsal color altogether in fresher water. I suspect that chromatophores in Anchovy cells are conserved, but the cells simply cease producing guanine crystals in fresher water.  Does anyone know a molecular biologist interested in measuring this phenomenon?  
  • Also note: The color fades within minutes when the fish dies, and Anchovies are very difficult to keep live in a tank. So, this is a tricky problem to investigate.


Relatively higher salinity in the deep Bay to the mouth of Coyote Creek at station Coy4 appears to stimulate weak development of blue or blue-green hues.


Bi-colored Anchovies at Coy4.

Most Anchovies were weakly pigmented on Saturday, but there were notable exceptions.  The two shown above show bright areas of green and blue pigmented iridophores. 

Does this indicate Anchovies recently transitioning from higher to lower salinity?  If so, how long ago?


Green Anchovies at Alv1.

Somewhat counterintuitively, a small number of the greenest and most adult looking Anchovies were caught far upstream at station Alv1 on Saturday. 

  • Could these be adults migrating in from the ocean for spawning?
  • Would we find golden Anchovies spawning farther upstream in Alviso Slough/Guadalupe River like we did farther up Coyote Creek the next day???
  • More investigation is needed!


6. The Incredible (non-native) Chameleon Goby.

Chameleon Goby.  This Chameleon is showing its “watermelon” body stripes.  (This one was caught in surprisingly fresh water for a Chameleon.  

  • Young Shimo / Chameleon Gobies appear to lose their stripes after they grow a few inches long. They become chocolate brown with interesting banded or snake-like patterns. 
  • This one is a Chameleon, but I also learned that Shimofuri Gobies can change colors from light-striped to dark-banded at will. Who would have guessed?

Editor’s note 11/24/2023:  I originally mistakenly identified this fish as a Shimofuri Goby, and I neglected to correct this blog for a couple of years.  I was recently contacted by Munenori Kishida, in charge of scientific research support for His Majesty the Emperor Emeritus Akihito, at the Biological Laboratory of Imperial Palace (BLIP) of Japan regarding this error.  —  Mr. Kishida provided this additional guidance for identification:

  • “The large sparse white spots on the cheeks are the characteristics of the Chameleon goby (small dense white spots spreading to the throat area in Shimofuri goby).
  • The most conspicuous character of the species is the freely independent uppermost soft ray of the pectoral fin.”


These USGS Fact Sheets are confusing:

Allow me to translate:

  • Tridentiger trigonocephalus = Chameleon Goby. Rarely found in salinity less than 22 ppt. No white spots on lower portion of head, white margin & conspicuous stripes on 2nd dorsal and anal fins. 
  • Tridentiger bifasciatus = Shimofuri Goby. Generally found in fresher water; salinity of 22ppt or lower. White spots on lower portion of head, orange/red margin, and no conspicuous stripes on 2nd dorsal & anal fins in  bifasciatus.
  • “[The Chameleon Goby] gets its name from its ability to rapidly change colors from a striped to a barred pattern (Eschmeyer et al. 1983).” [Apparently the Shimofuri changes color too.  In fact, it is rumored that the two gobies may readily hybridize.]

Other color-changing gobies in England are described here: 

Note:  The color change mechanism in these Gobies is entirely different than that of Anchovies and other Clupeiform fishes – No relationship whatsoever!


7. Other interesting critters.

Harbor seal at Coy4.

We spotted at least three or four seals out hunting on Saturday.


Harbor seal at Coy3.


Dungeness Crab at Alv3; Oregon Mud Crab at Alv2

Dungeness Crab.  We found two more young Dungeness crabs plus two Decorator Crabs on Saturday.  Until this past year, these marine crabs were usually not seen in our trawls.  Now we are catching a few each month.

Oregon Mud Crab (aka Yellow Shore Crab).  We finally caught two Oregon Mud Crabs for the first time in well over a year.  For better or worse, this used to be one of the most commonly caught invertebrates in Lower South SF Bay decades ago.  We have also not seen any Harris Mud Crabs for some time!

Something continues to shake up Crab-World in Lower South Bay!


Mysid “shrimp” caught at Coy2.

Mysid closeup.  The lighting was just right to see the gleam in this mysid’s eye.  Also notice, she has a marsupium pouch full of eggs!


Mysid eyes!


Black-crowned Night Heron perched on California bulrush.

Speaking of eyes … This Black-crowned Night Heron had his eye on us as we cruised upstream on Dump Slough.


Another pregnant male Pipefish from Dump Slough.

Bay Pipefish.  It is always a delightful surprise to find a pipefish; especially a pregnant male.

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