Fish in the Bay – December 2020: Anchovy Rebound & Blue Fish.

Trawl map.

A Longfin Smelt “Alert” was posted earlier concerning egg-bearing Longfins we caught in December.  This post addresses all the other interesting fish and bugs from December trawls.

  1. Winter-time San Jose “Bowl” returns.
  2. Anchovy Rebound: Baby Anchovy explosion + plus possible Winter Run Anchovies.
  3. Blue Fish: American Shad and Anchovies turn blue as salinity rises.
  4. Winter Sturgeon, and so on …


Bay-side stations trawling results.


Upstream of Railroad Bridge.


1. December boaters & “The Bowl.”

Busy Saturday morning at the docks.

Boating activity at Alviso increases in winter due to duck season and sturgeon.


The “San Jose Bowl” — or the “Alviso Bowl.”  Either name fits.

“The Bowl.”  Is it just us, or does it seem like less rain falls directly into Lower South Bay?

Joanna De Sa, our former manager of the SJ-SC Regional Wastewater Facility, first alerted me to this atmospheric effect.  Most often, when it rains around Lower South Bay, less rain falls in northern San Jose!  Years of sewer flow data from the San Jose-Santa Clara Regional Wastewater Facility seemed to back this up at the time.


From the sloughs we often see clouds stacked up to the west, and clouds stacked up to the east, against the inner and outer coastal mountains that ring Silicon Valley.  But, skies remain fairly clear in the middle space just above us.  Many times we approach the boat docks for a day of trawling, and it feels like the predicted rainy day becomes more pleasant – still partly cloudy, just not as inundated by rainstorms around us.

  • This bowl effect may be strongest in the AM when surface winds from the Bay are low.
  • Maybe an urban heat island over America’s 10th largest city contributes to this clear-sky bubble?
  • Clouds are hard to read. Maybe our imaginations are playing tricks on us? 


2. Anchovy Rebound.

Young of year Anchovies at Alv3.  These are at least a few months old.

Northern Anchovies.  The early November cold-snap caused an Anchovy crash:  numbers dropped from the hundreds to only twelve (12) in November trawls.  In December, the number bounced back up to 237!   

Most of this bounce is due to many baby Anchovies!  As hoped, the Anchovy spawn we observed July-thru-October appears to have resulted in successful hatch and recruitment.


Young blue anchovies in pond A21.

Young Anchovies develop a small amount of blue or green iridescent color in the crowns of their heads as they grow.  There may also be a genetic component, but so far, the salinity connection is very strong.  


Baby Anchovy at LSB1.

We caught many Baby Anchovies as well.  Albeit, the otter trawl net has very large mesh that does not catch them efficiently.  The baby shown above hatched just weeks ago!


More baby & juvenile Anchovies at LSB2.


Copepod parasite on young-of-year anchovy.

Anchovy parasites.  A few of our Anchovies were afflicted with copepod parasites, aka “Sea Lice.” The little vampires show up in winter when temperatures and salinity are more like the ocean.  Until now, I assumed they live in higher salinity, far out to sea.  But now, we are seeing them on young Anchovies that hatched here. 

Don’t ignore them!  Sea Lice can be lethal to young fish.  They are a serious environmental problem for farmed salmon around the world. 


Big blue adult Anchovies.  These fish were almost purple!  Bigger, bluer adults may represent a separate winter-migrant population.


3. Blue Fish

The Bay is still salty: American Shad & Northern Anchovy showing bluer dorsal hues.

Blue fish are a good indicator of high salinity in our estuarine marshes: this year rain is late, and our fish are still blue.  In 2019, our Shad and Anchovies “browned-down” after the first rains in November. 


Northern Anchovies and American Shad at Dmp2

Blue Fish = High Salinity: 23.3 ppt in Dump Slough!  Shad and Anchovies “blue-up” when salinity rises over 19 or 20 ppt. 


Shad Experiment – year 2.

American Shad are “poster-fish” for demonstrating salinity-induced color change in Clupeiform fishes.  Dorsal colors in both American and Threadfin Shad change color quickly and reliably in response to a range of salinity between 10 to 20 ppt.  

American Shad, shown above, were collected at our farthest upstream Coyote Creek station, UCoy1.  Water was relatively fresh at around 12 ppt.  

  • The dorsal sides of both Shad were initially fresher-water brown in 12 ppt water. 
  • Water in the measuring tray was saltier (18 ppt).  It had been collected downstream prior to the trawl.  The Shad turned green as we counted and measured other fish.
  • We drew saltier water (22 ppt) at station UCoy2 as we headed back downstream. The Shad turned blue (“celeste or aqua”) within a few minutes after immersion.  Both fish were then released unharmed.


Why do Shad change color as salinity changes?  I attempted to explain this before.  I will keep trying until I get it right:

Iridophores.  Shimmery metallic colors originate in specialized chromatophore cells known as “iridophores.” These are buried under the fish’s dorsal scales.

Guanine Crystals.  Iridophores develop and shape guanine crystals.  “Guanine crystals are rhombic platelets composed of multiple transparent layers, but they have a high index of refraction that partially reflects and transmits light from layer to layer,”

Guanine crystals form as thin plates in fish iridophores.   “The thin crystal plates stack into layers. … The thickness of the plates and the distance between each plate corresponds to the wavelength of visible light … to create the iridescent metallic lustre of fish skin.”

Venetian Blind versus Accordion model?  See Gur, Palmer, et al. (2015), The mechanism of color change in the neon tetra fish: a light-induced tunable photonic crystal array: “The colors are produced by constructive interference of light reflected from stacks of intracellular guanine crystals, forming tunable photonic crystal arrays. … reversible variations in crystal tilt within individual arrays are responsible for the light-induced color variations. These results settle a long-standing debate between the two proposed models, the “Venetian blinds” model, and the “accordion” model.”

I continue to be a fan of the “Accordion Model” for American Shad.  Color change in American Shad and other clupeiformes is clearly salt-induced, as opposed to light-induced in Neon Tetras.  However, either model could be at work here. 


4. Winter Sturgeon.

Sturgeon.  We see a few to several sturgeon on the fish-finder sonar each trawling day this time of year.  I try to catch a screen-shot, but I always miss a few.  Anglers usually bring at least a few to the Alviso Dock each day of sport fishing. 


5. Shrimp Wars.

Crangon with developing egg masses at Alv3.

Crangon Shrimp.  We were having a great Crangon year until August.  After that, we had a terrible year: monthly numbers crashed from over 18,000 in July to less than 1,000 each month since then. 

Thousands of egg-bearing females should arrive by December.  Instead, we caught less than 700.  Many shrimp we catch have visible yellowish egg masses growing behind their heads, but only a couple of fully-berried females have been seen so far. 


Palaemon shrimp from station Alv2.

Non-native Palaemon Shrimp numbers increased dramatically and unexpectedly by fall.  October through December catches were in the thousands and made this our best Palaemon year on record.  This is not good!


Blue-spot Crangon (Crangon nigromaculata).   Interestingly, we found Blue-spot Crangon at Coy4 and LSB stations.  This species is the coastal/marine version of our more familiar “Bay Shrimp” or Crangon franciscorum.  High salinity is drawing them in.


6. Other odd critters.

Scale worm, LSB1

Scale Worm.  Until recently, we caught these worms so rarely that we didn’t know what they were.  They are small, fragile, and hard to see in the net or in the measuring tray.  Maybe we just missed them.


Ctenophore or “Comb Jelly,” LSB1

Comb Jellies.  Only 11 were caught this month.  We should be seeing more of them.  Comb Jellies are drawn in by cold temperatures and high salinity.  It is both colder and saltier now than at this time last year when we netted dozens to hundreds.  They eat near-microscopic crustaceans.  Lack of food could be an issue. 


Philine snails at Coy4.

Philine Snails.  For multiple months we have collected Philines outside their normal range.  High salinity seems to have pulled them upstream in Coyote Creek.


Halibut at LSB1

California Halibut are still few in number.  However, the few halibut we see seem to be bigger.  Some are older fish that normally migrate out to the deeper bay. 


Red-eye Jellyfish from LSB1.

Polyorchis penicillatus – the Red-eye Jelly.  This attractive jelly stands about 3 inches high and 2 inches wide.  Medusa-type jellies are fragile.  Most get torn apart in the net as we pull them in.  Fortunately, this one survived unscathed for close examination. 

  • Little eyes. This jelly has at least several dozen bright magenta-red and pinpoint small Ocelli (eye-spots). The eye-spots are at the base of each small tentacle just below the edge of the bell.  This animal has many eyes! 
  • Big eyes. We can also see larger patches of magenta eye-pigment a little higher up the bell.  These are associated with eight larger tentacles spaced evenly around the circumference.  I would guess that all these (100+) eyes sense only light and dark: Red-eye jellies have a diel cycle: they tend to lay on the bottom in daytime then swim up at night.  If a shadow flashes by, they speed up their swimming pace. 
  • The mouth and stomach is that dangly thing hanging from the top of the “subumbrella” space.
  • Gonads are small filaments extending from four “radial canals” just above the stomach.

Fun Fact:  This Jelly inhabits bays and estuaries up and down the West Coast.  But, a very closely related specimen was featured on a 1990s-era postage stamp issued by Azerbaijan.

Polyorchis penicillatus fact sheets:


7. Bad Signs

Bent fish watch – another case of Scoliosis at Alv1

Scoliosis, or Bent-fish phenomenon was mentioned in last month’s blog.  Since then, I was reminded that the Pond A8 complex was known to have a high number of bent Silversides prior to initial discharge several years ago.  At the time, they thought the deformity might result from high concentrations of Mercury, Selenium, or something else. 

Nowadays, we catch a bent fish or two a couple of times per year.  We see it in American Shad, Shimofuri Goby, and Inland Silverside – all non-native species. 

  • Perhaps these foreign fish are not adapted to the high selenium concentrations that are, at least partially, natural near alluvial fans from eroding coastal mountains on North America’s West Coast.
  • Or, perhaps their bent spines result from legacy Mercury contamination.
  • We will pay closer attention from now on.


Mylar balloons in Dump Slough.

This is wrong on many levels.

After we played with them a bit, we popped the balloons and put them in the trash. 

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