Fish in the Bay – March 2022: A Crazy & mixed up month!

March was an unusual month that we still have not completely figured out.  We are in the start of a second back-to-back La Nina year.  Two natural forces from the land and sea directions seem be shaping fish world in unusual ways.

  • On the sea-side, cool ocean upwelling should be stimulating finfish production.
  • On the land side, a second year of drought and very dry January and February must be hammering certain fish and bugs.

March highlights:

  • English Sole babies surged.
  • It was a March record for Anchovies and Longfin Smelt.
  • Shimofuri Goby population exploded once again.
  • Three Sturgeon were spotted on sonar … and much more.


Critters in decline:

  • We counted NO baby Herring and few Staghorn Sculpin in March. Both Herring and Staghorn adults are known to benefit from La Nina upwelling, but it did not help them this season.  Perhaps the drought clobbered their winter spawning.
  • Corbula Clams have practically disappeared. (THIS IS VERY GOOD NEWS! Non-native Corbula are ecosystem killers.  We do not like them!)  Either the drought disrupted their winter recruitment, or cool ocean upwelling may have boosted populations of fishes and crabs that eat Corbula.  
  • Philine sea slugs were also rare and there were no Atlantic Oyster Drills.
  • Ctenophores (Comb Jellies) have also been practically absent this season. Their populations usually bloom sometime in late winter through spring when they consume excess zooplankton.  Is something else consuming zooplankton?  Or, is the zooplankton population depressed?

Critters on the rise …

  • Shimofuri Gobies were not expected to rebound so quickly, but they are our #1 goby once again. We have a persistent population of Shimos upstream on Alviso Slough.

Good News:  Anchovies and Longfin Smelt were particularly abundant at upstream stations. 

This is the crazy and mixed up part: Normally, March is a very low month for Anchovies. Longfin numbers should have declined as well; instead we caught A LOT of both.  What happened?    

Crangon shrimp also rebounded a bit. 352 Crangon is pretty good for a March.  The majority of Crangon we saw were tiny babies.  This means that brood release and some recruitment happened despite the alarming low count of berried females from December through February.      


1. Red Tide strikes again???

Brownish-red water at Alv1= Dinoflagellates? Green water at Art1= Diatoms?

Red tide at Alv1.  In February, we noted a turbid reddish-brown tint in the water at station Alv3.  In March, we saw the same thing farther upstream at station Alv2.  Both events were accompanied with supersaturated Dissolved Oxygen (DO).  I realize these are probably not “red tides” in the classically toxic and alarming sense.  These are merely “reddish” looking tides that may indicate some new and amazing aspect of the primary production here. 

Phyto Power.  Intense phytoplankton blooms typically happen in late winter through spring in this marsh.  The tiny phytos absorb solar energy that cascades up the trophic levels. This is particularly important as we approach Baby Fish Month in April. Baby fish need tiny food. Dinoflagellates, Diatoms, Copepod nauplii, and Rotifers can be among the best foods for fishes with tiny mouths. If the phytos are not right, the system will collapse.     

What are these phytos?  From a naked eye vantage point, water color can vary from reddish to brown to green depending on which phytos are present.  In a productive estuary like this one, there can be up to tens of billions of phytos in each milliliter of water.  The entire ecosystem depends on them! 

We must understand our phytos!


2. Some Flatfishes.

English Sole at Alv2 on 6 Mar 2022.  (A young Starry Flounder at top left.)

English Sole.  We caught 377 Sole in March. These were all small juveniles that swim and drift in from the sea soon after hatch.  Similar to Flounder and Turbots, English Sole young migrate to estuarine creek mouths as places to feed and grow. 


English Sole.  Many English Sole arrive in LSB at near larval stage!


Speckled Sanddab (top) and English Sole (bottom) at Coy4.

Speckled Sanddab and English Sole.  5 Speckled Sanddabs were spotted amongst the gobs of young Sole.  It can be hard to tell the two apart.  English Sole have a more sharply pointed mouth and eyes on the right side.  Sanddabs have a more rounded shape and eyes on the left. 

These small flatfishes are highly edible.  Sharks, Sturgeon, and Harbor Seals feed on them. 


Young California Halibut at Alv1

California Halibut.  Only 3 very young Halibut were seen.  Their life cycle is similar to Sole and Sanddabs.  The young hatch far out in the Bay or off the coast then migrate inland to recruit.  La Nina cool ocean upwelling tends to favor English Sole hatch and recruitment.  Halibut usually do better in warmer El Nino years … that’s the theory anyway. 


Starry Flounder at UCoy1.

Starry Flounder.  8 Starries were netted in March.  Unlike all the other flatfishes here, Starries spawn upstream near the creek mouths.  The young migrate downstream as they feed and grow.  They become reproductive after only a year or two, so even these little ones are capable of spawning.   


3. Shimofuri Gobies.

Some of the 257 Shimofuri Gobies at Alv1 on 6 Mar 2022.

Shimofuri Gobies.  A total of 414 Shimos were caught in March.  The upper reaches of Alviso Slough are a persistent hotspot.  Shimofuri Gobies first came onto the scene in Lower South Bay in 2012.   They surpassed the Yellowfin Goby as our most common goby in 2021.  So far, Shimos are way out in front in 2022 as well. 

Tridentiger Invaders.  Three gobies of the Asian “Tridentiger” genera invaded SF Bay:  Yellowfin Gobies by the early 1960s, Chameleon Gobies in the 1980s, and Shimofuris around year 2000.  For the last several decades, Yellowfin Gobies were the most common “Cockroaches of the Bay.”  Fortunately, aside from displacing native Bay Gobies, the Yellowfins are pretty much fully integrated into the local ecosystem. Now, for better or for worse, their distant cousins, the Shimofuris seem to have taken over.


4. Longfin Smelt.

Longfin Smelt.  We caught an astounding 539 Longfin Smelt in March. (Only a few were kept for analysis, the vast majority were immediately released.)  This March catch was second only to the record catch of 907 in February. 

“Belly flaps” on these males (technically a fleshy ridge at the base of the anal fin) indicate that they are ready for spawning.  Males stage upstream to prepare nesting sites where they attempt to attract females to deposit their eggs.  Each male we find tells us that we have found a functioning spawning ground! 


 5. Anchovies.

Northern Anchovies.  March has always been a low Anchovy month: sometimes single digits, never more than double digits.  This year is very different: 1227 Anchovies were netted and released!

We found mostly smaller young and smaller Anchovies at the LSB stations: mainly around 40 to 70 mm.  These are successful recruits from the summer-through-fall spawn.  It is well documented that baby Anchovy survival hinges on success in finding “first food” immediately after yolk sac absorption about 4 days after hatch. Researchers have identified Dinoflagellates as the most important “first food” for Anchovies in other spawning areas.  What is our “first food” here?  


Young and old Anchovies in Dump Slough on March 6th.

The range of Anchovy sizes was greater at upstream stations.  Both young and old Anchovies were present, but upstream stations always hosted the largest Anchovies, up to 80 and 90 mm. It is unknown why these bigger fishes did not flee the area after November as they usually do.    


Pelagic fishes plus a few dimersals at Dmp2.

Our upstream trawls monitor fish and bugs in three tributary segments and a restored pond: Artesian Slough, Upper Coyote, Dump Slough, and Pond A19. It is always interesting to see which segment will host the most fishes any given month.

In March, Dump Slough was the winner!  378 anchovies, 170 Longfin Smelt, 6 Staghorn Sculpin, 12 Threadfin Shad, 10 American Shad, 3 Bay Pipefish, and 30 assorted Gobies.  (It was the out-of-season Anchovies that put Dump Slough over the top!)


6. Leopard Shark.

Micah examines a Leopard Shark at LSB1.

Leopard Shark.  This is our first shark of 2022.  He was probably born the previous spring or summer judging from his size: 520 mm or 20.5 inches.    


Same Leopard Shark at LSB1. The pair of claspers next to his anal vent tell us that he is a boy.


7. Oddballs.

Mud Shrimp (Upogebia major) at LSB1 on 6 Mar 2022.

Upogebia.  We caught another Asian mud shrimp (Upogebia major).  This one was way out in the middle of Lower South Bay. This variety of Mud Shrimp replaced our native Upogebia pugettensis about a decade ago.  Mud shrimp, aka “mud lobsters,” are highly beneficial ecosystem engineers and extremely delicious to big fishes like Sturgeon. 

The mud shrimp story is a long one, and I told it last January: )  

To summarize: any mud shrimp is a good mud shrimp even if non-native.  They are extremely beneficial ecosystem engineers that live in deep burrows under the mudflats and marshes.  They rarely venture outside their protected homes, and for that reason, we don’t often see them.


Pacific Tomcod.  We caught one Tomcod in March.  Until this season, we had seen this coastal fish only once before.  For some reason, we netted a few to several Tomcods in December, January, February, and now this one in March.

Bay Goby.  One very small Bay Goby showed up at LSB2.  A few of very young ones have shown up each of the past few springs.  We keep hoping these native gobies will recover. They are very hard to identify at this size.  


Bread Crumb Sponge at LSB1.

Bead Crumb Sponge.  We have only found one or two small sponges in each of the last few years, so they are still quite rare in Lower South Bay.  This one, and the others we have seen, are non-native but probably beneficial as living water filters. 

From the “Field Guide to Common Benthic Species:”  “Halichondria bowerbanki … Shares the common name “bread crumb sponge” with another sponge, H. panicea. … introduced to the Pacific Coast of North America in shipments of commercial oysters. First observed in northern California (Sacramento/Stockton Delta) in 1950. … This species is easily confused with another species, Halichondria panicea, that appears greenish in certain light and produces a characteristic smell of gunpowder when touched.” 

Unfortunately, I did not crush and sniff it for the smell of gunpowder.   


8. White Sturgeon.

Two of three Sturgeon seen on sonar at UCoy1.

White Sturgeon.  We spotted three Sturgeon on sonar at UCoy1.  They appeared to be in feeding mode; probing and sucking up benthic fish and bugs with their flexible vacuum cleaner mouths.  These Sturgeon are well fed.   A few anglers have told us that they have found Gobies and even Anchovies in the stomachs of local Sturgeon. 


9. Bonus Fish.

A few of the 15 Bay Pipefish caught and released at Art2 in March.

Bay Pipefish.  31 Pipefish were netted in March.  23 of them were caught in Artesian Slough. The Pipefish have really bloomed this spring! 


10. Bonus Invertebrate.

California Horn Snail shell at Alv3.

California Horn Snail!  Alas, this was only a dead shell.  For three years I have searched for a living Horn Snail.  They are among the last benthic invertebrates known to be native here.

I am afraid they are gone.  Horn Snails cannot compete against Eastern Mudsnails  (Ilyanassa obsoleta) and other non-natives that invaded over the last century or so.  However, it is rumored that small pocket colonies of Horn Snails may still persist in slightly higher and drier margins of the marsh where eastern mudsnails can’t compete.   …   The search goes on.


“The mystery of life isn’t a problem to solve, but a reality to experience.  A process that cannot be understood by stopping it.  We must move with the flow of the process.”    – Dune 2021

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