Fish in the Bay – January 2022: Anchovies and Longfins, yes! But, no Crangon brooding.

Good News!  Our streak of phenomenal finfish production continues.  This time last year, we were marveling over the uncharacteristic boost in Anchovy and Longfin Smelt numbers.  We speculated how the early 2021 drought could result in larval fish recruitment failure.  But, now a year later, Anchovy numbers have skyrocketed! Longfins are still way up.  And, Topsmelt set a new January record. 

Bad News!  Only 47 Crangon shrimp were counted.  We should have seen thousands of berried females after December.  The Crangon crash is an ongoing catastrophe!   


Northern Anchovies Last year, we counted a record 1,126 Anchovies in January.  Most were young juveniles in January 2021.  This year, the January count is 2,934 with many juveniles, but at least half are large adults congregating at upstream stations!     

The Upogebia mud shrimp explosion was already reported in early January.  See: 


Longfin Smelt are in their spawning season. This year’s January count of 417 is statistically equivalent to last year’s record January count of 456. In every year prior to 2018, no more than one or two dozen Longfins were ever counted in January.

Topsmelt counts also continue to be consistently high.  Both recruitment and long-term survival of small bait fishes seem to be trending well for the last few years.  We can only hope that these trends last.  


1. Perihelion

King Tide Weekend.  Once per year in early January, Earth passes closest to the Sun.  The highest-high tides of the year occur closer and closer to noon as we approach Perihelion.  … And, the highest monthly tides happen during ‘new’ and ‘full’ moons.

This year, Perihelion and “New Moon” almost coincided.  They were only off by 2 days!  It was a rare treat to see how close this highest of all high tides could come to swallowing the growing marsh in Pond A21.  The rising waters peaked as we trawled Pond A21 near noon.

It was a great perihelion weekend!  


Micah empties the net from a trawl in Pond A19


2. Northern Anchovies!

Ocean migrants versus Bay residents.  Once again, many, though not all, winter Anchovies have starkly different body shapes. 

  • ‘Long and skinnies’ are generally darker blue on the dorsal side and look like they have been starving. We rarely, if ever, see these skinny ones in the summertime.
  • Deeper-bodied chubby ones are likely Bay residents. Most Anchovies caught this month appeared to be the chubby variety.


Baby Anchovies!  Larval baitfish, like Anchovies, Herring, and Longfin Smelt, are essential routes of finfish production in this estuarine ecosystem.  Most of these baby fish are destined to be food for birds, big fish, harbor seals, and whales.  Abundance of baby Anchovies is a very good sign. 

However, we don’t specifically count babies versus adults.  Evaluating net Anchovy productivity is still guesswork.  With that in mind, the January Anchovy count looks very encouraging.


Only a small fraction of all Anchovies were measured for length.  Nonetheless, results again indicate a fairly consistent “Anchovy size gradient.” 

  • The longest and generally older fish congregate near upstream stations along Coyote Creek.
  • Smaller fish, mostly juveniles, are found downstream either in the deep Bay or at least closer to it.
  • The relatively few Anchovies in Alviso Slough did not follow this size gradient rule. This could indicate that adult Anchovies are seeking slightly fresher water (around 10 ppt – but not lower) in Coyote Creek or seeking the food that thrives there.


Do big Anchovies seek fresher water in winter?


Jumbo Anchovies.  Two, (perhaps several?) of this January’s 2,934 Anchovies were jumbo-sized adults well over 110 mm.  We suppose that these fish are at least 4 or 5-year-old survivors of multiple Bay-to-ocean migrations.  None showed any signs of eggs or milt, so they did not return for spawning. 


Sea Lice.  So far, fewer Caligidae Copepod parasites have been spotted compared to last year. These pests are a nightmare for fish farms around the world.  But, what can you do about them?   


3. Longfin Smelt.

Youngish-looking Longfins from Pond A21.

Longfin Smelt.  417 Longfins were caught in January.  Longfin numbers trended sharply upwards after 2017 which was also the same year that Longfin spawning was first confirmed here.

  • 2017 was the year of the big February Freshwater Flush when salinity dropped very low across the entire Bay. For at least a few years, we presumed (and feared) that the Longfin surge may have been strictly attributed to that rare flushing event.
  • Good news! Longfins are sticking around here and continuing to spawn in both wet years and dry!
  • We hope this trend continues.  


Presence of large males expressing milt should correlate closely with the precise locations of Longfin spawning grounds. 

  • Larger males guard the best spots on gravel beds or in patches of marsh reeds and roots. We found big males mainly at stations upstream stations: in Artesian Slough, Dump Slough, Pond A19, and Upper Coy. 
  • Longfin females tend to stage a little farther downstream until they are ready to release eggs,
  • The spawning frenzy may happen any night when the temps drop to around 13- or 14-degrees C, or lower. But for all we know, the lunar cycle and spring tides could also play a role in the timing.


Two dark male Longfin Smelt, UCoy1, 2 Jan 2022.

Longfin spawning colors.  Longfins turn progressively darker during the spawning cycle, at least the older ones do.  Blue or green iridescence darkens considerably along the dorsal side.  Males darken the most, but we have seen some older females in darker colors as well. 

(It is presumed that this darkening is a result of hormonal change during spawning.  But, could darkening result from extended exposure to low, single-digit PPT salinity?  That might be a good question for the UC Davis FCCL lab.) 


4. Pacific Herring.

Pacific Herring.  Two large adults and one smaller one in January!  A few more big adults were caught during Longfin Broodstock trawls later in the month – one with eggs!

  • This is a very good sign. Until the last few years, we caught only very young juveniles later in the spring but never adults. 
  • Now we are catching adults in winter.
  • These Herring look like they might be preparing for the spawn!


The other big adult herring was caught and released in Pond A19.


5. Other fishes.

Shiner Surfperch, LSB1, 1 Jan 2022.

Shiner Surfperch.  This was the first and only Shiner we have seen since last May.  Only seven Shiners were caught in 2021.  This is one of the few fishes whose numbers have been declining in Lower South Bay trawling records since 2014.    


Staghorn Sculpin.  We only caught four Staghorns in regular January trawls. At least several more were netted in Longfin Smelt Broodstock trawls later in the month.  All but a few were large adults.  We spotted many with fat bellies but none showing unambiguous signs of readiness for egg-laying. 

Hopefully, Staghorns are already spawning in sheltered hollows where our net cannot reach them.  


Seven of the nine Tomcods caught in January were from a single trawl in Pond A21.

Pacific Tomcod.  Last month, Tomcod was one of our new fishes.  Now, we caught a bunch more.  In addition to these January numbers, we caught five or six more during subsequent Broodstock trawls.     

  • Tomcods grow up to a foot long. These were all young fish.
  • Perhaps high salinity has drawn them into LSB? Or maybe, the coastal Tomcod population has exploded? 


These gill parasites came from the Tomcods caught in Pond A21.

Nearly all Tomcods were carrying parasites too.  Practically, every tomcod hosted one or two of these “Cymathoid” isopod gill parasites.  We see these a lot in fishes returning from the ocean. 

Think of Cymathoid parasites as swallows from Hell returning to Capistrano. I think the fresher water here tends to stun them out of their host.  But, that is just a guess.  For all we know, these bugs might jump from one host to another quite readily when they sense stress. 

  • They are energetic swimmers. At least some of them target a new host almost as quickly as they abandon another.
  • Bad Cymothoid or Boprid Isopod parasites have been known to overturn entire ecosystems. Always keep an eye on them!


6. More Bugs.

Not all isopods are bad.  Most are non-parasitic and somewhat similar to common garden pill bugs and sowbugs (aka “woodlice”).  In lower salinity waters we tend to find Sphaeromatid varieties. Aside from those and from parasitic Cymothoids during winter fish migration season, Synodotea (not shown) are our most common isopods.   


Mysids and Corophium amphipods are fundamental fish and bird food.  The Mysid count remains alarmingly low this winter. 

Corophium are similar-sized bugs that live in burrows just below the surface of the mud.  Flocks of Stilts and Avocets commonly hunt for them as tidewaters rise and fall.


Swollen anemones at Alv1, 1 Jan 2022.

Anemones.  We spotted a number of anemones (likely Diadumene franciscana or D. lineata) in Alviso Slough.  They were unusually easy to see in the shell hash this month because they were all bloated like marshmallows.  It is likely that freshwater flushing from November and December rains was making life hard for them.  None appeared dead, but they definitely did not look healthy!


A couple more puffy Anemones from Alviso Slough.

Wintertime freshwater flushing is probably nature’s way of eradicating anemones from the upstream reaches here.  Again, none of the anemones were dead, but I will be surprised if they survive this.


Few Crangon – no brooders, Alv3, 1 Jan 2022,

Crangon Shrimp.   The severity of the current Crangon crisis is hard to fathom.  We found no brooders in December or January trawls.  A few brooding females were spotted at LSB stations later in the month – just a few! 

Two of the three shown above show a yellowish/tan mass growing under the shell, just behind the head.  That is the developing egg mass.  These shrimp, and thousands more, should have been fully berried and releasing young into Lower Coyote Creek by now!  We continue to hope for a Crangon rebound, but this situation is looking grimmer every month.   


7. Sonar Vision.

White Sturgeon.  Sturgeon are always present this time of year.  We sometimes net one, but we see many more on sonar.  This Alviso Marsh Complex is a Sturgeon feeding ground, and they are THE popular recreational sport fish here.

Best fed Sturgeon in San Francisco Bay?  Over the past month we met two local anglers.  One of them told us he caught a Sturgeon with gobies in its belly.  The other guy reported finding lots of Anchovies in two different Sturgeon that he caught.  Anchovies!!!  Contrary to popular opinion, Sturgeon often prefer to eat fish:   


Also, see Zeug et al (2014). “Ancient fish and recent invaders: …” 

  • White Sturgeon in North San Francisco Bay experienced a significant change in diet following the Corbula clam invasion in 1987.
  • Prior to the Corbula explosion, Sturgeon ate mostly Herring eggs, small fishes, and barnacles.
  • After the invasion, Sturgeon switched to eating Corbula clams, crayfish, and crabs.
  • The authors suggest that this was a bad change of diet: Corbula are hard-shelled clams that occasionally pass through the Sturgeon gut alive and undigested, plus Corbula are packed with selenium!

… Since relatively high numbers of the clams are not digested, white sturgeon may have to expend more energy on average to acquire the same caloric value as with more easily digested prey items. Furthermore, this bivalve readily accumulates the trace element selenium (Schlekat et al. 2000, Stewart et al. 2004, 2013, Lee et al. 2006) to levels that have been shown to result in reproductive toxicity in surrogate species (Stewart et al. 2013). Greater clam consumption in the post-invasion period could result in reduced juvenile growth and increased reproductive damage in sturgeon (Linville 2006) and may pose risks to their predators (humans). Stewart et al. (2004) reported greater selenium concentrations in trophic pathways leading to SFE white sturgeon relative to other top predators.”

Corbula clams are very bad food for Sturgeon!!!


Harbor Seal. A youngish-looking seal took some time to check out the boat while we were counting fish in between trawls at station Coy1. It kept ducking under the water whenever I tried to take a photo. It then swam under the boat and we could see it with our Sonar Vision.  We waited with the motor in idle until she surfaced again on the other side of the creek so we could continue trawling!


8. Ducks.

January Duck Collage:  Goldeneyes at Alv1 shown at top, Ruddy ducks and a Northern Shoveler at Art1 shown at bottom.

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