Fish in the Bay – January 2024, Part 2 – A January food chain.

Part 2 of the January 2024 report:

1. Green water & some reddish fish in Artesian Slough.

Clear green water of Artesian Slough. Artesian Slough was the only significant oasis of bird life around here from the later 1960s through 1999.  Access to the slough was restricted part of the year due to its official designation as a critical Heron and Egret rookery.  I never gave this much thought for the first decade that I worked at the SJ-SC RWF facility.  It was just the way it was.

One day in 1999, City of San Jose received letter notification from CDFW: Artesian Slough was no longer restricted.  Local Herons and Egrets had discovered new restored marsh areas around the Coyote Creek Riparian Corridor.  Artesian Slough was still a rookery; it was just no longer critical. 

Artesian Slough is always a little different: a little fresher, greener, and less turbid than anywhere else.  Marsh plants grow taller, bugs, fish, and birds are usually a little more robust and abundant.  I may be biased, but that is what I usually see here. 

– Except this weekend.  Restored Pond A21 was the pelagic fish winner!  See notes farther below.


Three-spined Stickleback count = 32.  Sticklebacks prefer fresher water.  Two-thirds of those we caught in January were from Artesian Slough alone.  At least two of the group shown above were males showing their cherry-red mating colors.

Sticklebacks are very charismatic for such a tiny fish. They rarely measure over an inch or inch-and-a-half.  Males develop red coloring on their lower jaw and upper belly when in reproductive mood.  They build mating-tunnels by glueing bits of detritus into a tube-shaped nest.  They then seduce bulging females to deposit eggs.  This bunch was released after a few photos.


Yellowfin Goby count = 21.  The Yellowfin count is a bit low for this time of year. Their numbers seem to expand during drier years and decline a bit when we have big rains.    

Yellowfins are also wintertime spawners.  Males excavate y-shaped burrows. On perhaps three occasions in winter, we have caught Red-headed Yellowfins like the one shown above.  We surmise that red-heads are mating-ready males.  Their red heads could result from burrowing activity.  Or perhaps, redness is a mating display like we see in Sticklebacks. Does red = romance here?


2. Devil-Bug note.

Cymothoid Isopod Gill Parasite (Devil Bug) count = 10+????  Devil Bugs are difficult to count.  These quick-moving, hyper intelligent parasites infest pelagic fishes that arrive in winter: Herring, Shad, and Longfin Smelt.  Pacific Tomcods are particularly favored as hosts by Devil Bugs.

These bugs are capable of vacating one host and then immediately chasing down and entering another one.  We often observe Devil Bugs abandoning their hosts as we count and measure fish in the trays.  Who knows how many of these tricky bugs we likely miss?

Devil Bugs can impose a severe burden on our native fishes.  Sami has begun collecting and preserving the bugs at the UC Davis OGFL Fish Lab so that future generations may study them as well.    


3. Wintertime Pelagic Fishes.

Restored Pond A21 was the ‘fish abundance’ winner in January.  Anchovy and Herring numbers were high.  The Longfin Smelt count alone put Pond A21 way over the top. 


Fish abundance at UCoy1:  showing 6 of 31 Longfins, 8 of 24 American Shad, and 2 of 86 Starry Flounder.

American Shad count = 238.  The Shad count was a bit on the low side compared to recent Januarys.  (Prior to 2019, 238 would be a record-breaking count.)  As usual, American Shad tended to congregate more heavily at creek locations farther upstream compared to most Anchovies, Herring, and even Longfin Smelt.


Increasing numbers of Anchovies, Shad, and Herring enable us to hone our Clupeiform Color observations.  Each of the three species expresses slightly different dorsal colors at given salinity levels.

General Clupeiform Color Rule:  Clupeiform fishes “Blue up” in high salinity at or above around 18 ppt.  They “Brown down” in brackish water at or below about 14 ppt.  They express green dorsal color between the blue & brown thresholds – give or take a few ppt.


Pacific Herring count = 151.  As in December, this 2023/24 Herring cohort is all made up of yearlings, about 3 inches long.  All were between about 68 to 82mm.

Clupeiform Color Hierarchy:  Based on recent observations, it appears that Herring tend to be browner at any given salinity.  Anchovies tend to be bluer.  American and Threadfin Shad are most often in the greenish middle of this range all else being equal. 


During April 2023 ‘Baby Fish Month,’ we counted 2010 Herring hatchlings.  We are guessing that these yearlings we are seeing now likely originated from that hatch. 

  • Could Pacific Herring become yet another regularly spawning pelagic fish in these restored marshes?


Amongst Clupeiforms, Anchovies tend to retain the deepest indigo blues at lower salinity levels.  They “Brown down,” but it seems to take more time and slightly lower salinity to moderate their blueness.


It is equally interesting that Herring always retain a bit of greenness at all but full marine salinity concentrations. 

  • As always, keep in mind that Anchovies are the rule-breakers of this group. Lower and variable salinity causes Anchovies to lose dorsal color altogether.  Anchovies cannot be trusted.
  • Science marches on.


4. Tomcods and Flatfishes.

Three Pacific Tomcods from Alv3 on 15 Jan 2024.

Pacific Tomcod count = 42.  Tomcod numbers have increased each year.  Tomcods are the smallest members of the Cod family of fishes.  They grow up to roughly a foot long.  We caught our first young Tomcod in 2019.  Since then, we have caught several to a dozen young ones each winter.


English Sole count = 8.  Sole hatch off the coast.  Newly hatched recruits migrate to fresher water upstream.  For that reason, our Sole counts are highly dependent on offshore ocean cycles and coastal upwelling productivity.

California Halibut count = 31.  This is our second highest January Halibut count after 2016 – the year after a big El Nino.  All Halibut caught this January were tiny babies as shown above.  We just experienced a moderately strong, albeit short-lived El Nino these last several months.  Halibut populations increase during El Nino years. 

Staghorn Sculpin note:  Some adult Staghorns have bright patches over each eye.  I call the patches “headlights.”  “Headlights” might be a mating-ready signal primarily for male Staghorns.  Otherwise, it seems suicidally risky for a bottom-dwelling marsh fish to exhibit such a flashy display.  

Philine “bubble snail,” aka “snot-ball snail,” aka “New Zealand Sea Slug” count = 14.  Philine Snails are one of many non-native nuisances.  Their numbers have declined a bit over the last few years.   


5. Extreme Fishes.

Saddleback Gunnel count = 2.  Saddleback Gunnels (Pholis ornate) are common on the coast.  We caught our first one in December 2022 at station Coy1.  Salinity was 21.6 ppt at the bottom.  It was described at the bottom of this report: 

  • Now, we have picked up two more at UCoy2. Bottom salinity was 18.9 ppt. Why would a normally marine fish travel so far upstream?  How do they tolerate the freshness?
  • Saddleback Gunnel per Wikipedia:    


Bay Pipefish at Coy2. 

Bay Pipefish count = 9.  Winter – or maybe late fall, seems to be spawning time for these long skinny seahorses.  A gravid female is shown above. 

  • Sometime soon, she will need to convince one or more willing males to accept her eggs.
  • Pipefish Males fertilize and brood eggs and young until after hatch.  

Two anglers snagged a Sturgeon at Coy2 as we passed by.

White Sturgeon count = 7.  Sturgeon counts were entirely based on sonar sightings plus one observation of a sport fishing catch.

Local marshes feed Sturgeon.  Sturgeon spawn and hatch at the upstream ends of big rivers in the Central Valley. They come to feed in Lower South Bay when temperatures are low. Sturgeon eagerly eat Lampreys, shrimp, gobies, Anchovies and probably Longfin Smelt as well.    

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