Fish in the Bay – March 2020, part 2: The Shrimp Gradient (post SARS-CoV-2 lock-down edition).

Hello again folks.  This is a belated part 2 to the March fish report.  Coronavirus/COVID-19 crisis forced a hiatus in my fish reporting. 

No, I have not been exposed to SARS-CoV-2 (the virus), nor have I come down with COVID-19 (the illness).  But, safety concerns regarding COVID-19 required UC Davis to limit boat crews and research teams to essential personnel only.  And, I agree that the volunteer fish photographer is not essential at the height of a general shutdown/social distancing period.   I wouldn’t want to catch the virus, and I do not want to play any part in spreading it.  Hopefully, we will all feel safe in allowing a volunteer to ride along again soon.


1. California Water News.

Dr. Bruce Herbold, retired USEPA fish biologist & UC Davis alum, testified as expert witness via Zoom hearing on May 8th in Calfornia’s lawsuit against federal rules meant to protect, but potentially endangering, Delta Smelt, Winter-run Chinook Salmon, and other endangered fish in the Delta.   

U.S. District Court Judge Dale Drozd heard testimony from Bruce and others about fish and river flows during the nine-hour hearing.  The following week, the judge granted California’s request for a preliminary injunction to stop increased pumping by the Central Valley Project from May 11-31.

As Bruce testified, and as we have seen here in Lower South Bay (LSB), there is a lower limit of river flushing flows needed to sustain native fish and bugs.  We don’t know the exact lower limit here, but there is a lower limit.  We must leave some water for the fish!


2. Charismatic megafauna.

Micah carefully untangling a baby Bat Ray and its stinger from the net.

Bat Rays. It was unusual to see so many of them while still in the cooler part of the year on March 7th.  14 Bat Rays were caught: 4 at station Alv3, 10 at stations LSB1 and LSB2 out in the middle of Lower South Bay.  The photo above shows the tub of 9 Bat Rays from LSB1.  With the exception of one large male, these were all young to baby-sized rays.


Mid-sized Bat Ray being measured.

We usually expect Bat Rays in warm summer months, not in early March.  We can only speculate that the lack of rain, and unseasonable high salinity up to that point, brought them in early this year.


Decorator Crab from LSB2.

Decorator Crab.  Just for the record, we caught 3 more Decorator Crabs at LSB2 in March.  This was the third month in a row for a crab that, until now, we rarely see in Lower South Bay.


Colorful male Longfin Smelt from Pond A19.

Longfin Smelt.  Longfin Smelt “darken up” (turn blue-green) on the dorsal side when they are ready to spawn.  This blue**, gold, and silver male was even extruding milt at the time of catch!  Do Longfins spawn in Pond A19?  A milting male is a strong piece of evidence that they might.

Bad news:  This was the only Longfin Smelt caught in March!  So far, Lower South Bay trawls have only caught twenty-one (21) Longfins in 2020.  This is not good!  For comparison, in January thru March in 2018 and 2019 we netted 67 and 661 Longfins respectively. 

** (In January, we caught an egg-extruding female Longfin nearby at UCoy1.  Her dorsal color was close to “emerald green,” roughly Pantone 17-5641.  The dorsal hue on this male looks like “blue quartz” (pantone 19-3964) perhaps?)


We also caught two tires, both on Saturday.


 3. A shrimp gradient (across three species.)

Palaemon upstream at Alv1.

Palaemon shrimp bounced back a bit in March: 765 Palaemon compared to 4781 Crangon and 2227 Exopalaemon.  Palaemon have been in decline the last two years.  They are non-native, so their decline is not a huge concern.  

  • Top photo in collage: About this time last year, I noticed that Palaemon shrimp turn greenish-brown in the fresher upstream sloughs.  Now they are doing it again.  I still do not know if this is caused by diet or a stage of sexual maturity.  
  • Bottom: A berried female full of eggs.  Many Palaemon at Alv1 were either berried adult females with big chelated forelimbs or slightly younger females with signs of a growing egg mass behind the head.


Palaemon shrimp a bit further downstream at Alv2.  One Crangon shrimp is at lower left.

Clear/Pinkish Palaemon shrimp downstream.  Station Alv2 is immediately downstream from Alv1.  At this station, young Palaemon generally appear lighter pink to translucent in color.  Adults, especially females(?) are redder.

These pinkish shrimp were only separated from the darker greenish-brown ones by about a mile of narrow Alviso Slough channel.  Nonetheless, the difference in appearance was fairly stark.  The same change in color was seen in Lower Coyote Creek in 2019 and now again in 2020.  What causes this two-tone color change?

Palaemon at Coy1.

Station Coy1, just upstream of the railroad bridge, was the equilibrium point for pinkish versus greenish-brown Palaemon shrimp on the March weekend.  From eyeball examination there appeared to be almost equal numbers of each.  All had the characteristic steak knife rostrum. 

The dark Palaemon were a bit larger and more often had chelated forelimbs, albeit rigorous measurements were NOT taken in the interest of time, sparing shrimp lives, and more important things to do. 

I would guess that pinkish/translucent Palaemon are younger.  The darker (female??) ones appear more mature, and often as not, seem to be carrying eggs.  Are we witnessing an annual Palaemon brooding migration?  Do egg-bearing Palaemon shrimp mamas swim upstream to release their broods like Crangon and Mysids? 

More observation is needed.


Crangon in the middle of LSB –  LSB1

Crangon shrimp follow a similar salinity/color gradient, but instead of brown to pink, Crangon generally get darker with higher salinity.  The unusual lack of winter rain up through March 2020 resulted in slightly higher Bay salinity, and hence it seems, darker Crangon.  As mentioned in the February blog-post, many of this year’s darker Crangon are showing light-colored bands, or “tiger-stripes.” 

For well over a century, researchers have described the two or three species of Crangon that are native to SF Bay.  For example:

  1. A 1979 guide attributed to University of Oregon:
  2. Richard Wahle (1995) described different feeding habits of C. franciscorum and C. nigricauda in San Pablo Bay:

For refresher, the three local Crangon species are:

  • Crangon franciscorum, aka Bay Shrimp, aka “Brown-tails.”
  • Crangon nigricauda, aka Black Shrimp, aka “Black-tails.”
  • Crangon nigromaculata, aka “Blue-spot.”

In Lower South Bay, C. franciscorum (Brown-tails) are far more common.  C. nigricauda (Black-tails) show up in winter when salinity is relatively high.  C. Nigromaculata (Black-spots) are mainly a coastal species. They are rare odd-balls here.


C. nigricauda at LSB2

Crangon nigricauda in LSB.  As discussed before, it is sometimes hard to distinguish Black-tails from Brown-tails with naked-eye observation.  But generally, salty water brings blacker Crangon.  Hence, on the March trawling weekend, almost all Crangon caught at downstream/Bay-side stations were conspicuously Black-tails.  But, as always there were a few exceptions. 


More C. nigricauda (“Black-tails”) at Alv3.


Classic examples of “Brown-tail” versus “Black-tail” Crangon at Alv3.  C. franciscorum is usually described as slightly larger than C. nigricauda.

On the March weekend, roughly equal numbers of Black-tails and Brown-tails were caught in the vicinity of station Alv3 at the mouth of Alviso Slough.  However, it is safe to assume that the informal boundary between these two species moves with each sweep of the tide. 


Lighter colored “brown-tail” Crangon at Coy3.

Crangon franciscorum upstream.  As we proceeded upstream along Lower Coyote Creek, Black-tails disappeared and were replaced by young-looking brown-tails.  However, some still had dark grey telsons (tails) despite an overall lighter colored beige-brown appearance.

I continue to wonder whether higher salinity tends to darken up the regular brown-tails – many of these had dark gray telsons (tails).


Crangon at Coy1.

Crangon franciscorum at Coy1 – totally brown, no dark telsons at all.  According to literature, Crangon segregate by sex around brooding migration time (winter for us).  But, are we seeing some amount of size and sex segregation over much of the year?


Young Crangon at Art2.

Crangon farther upstream.  Only small, young Crangon were caught at the farthest upstream stations.  This seems to be typical.  These represent the new generation of recruits that hatched over the past winter.   

As seen previously, some of these new recruits have black tails, some are brown.  How do we classify these?  Are both young C. franciscorum and C. nigricauda present this far upstream? 


Exopalaemon Shrimp (Exos) in A19.

Exopalaemon shrimp dominate at most far upstream stations. Yellow-green eggs and growing egg masses are visible in many of these shrimp.  At least one had fully-formed eggs.

Exopalaemon shrimp are our newest invader in LSB creeks.  According to our data, they arrived here sometime around 2012, though they had been in North Bay creeks since around year 2000 or slightly prior.    


Exos at Art2.

According to Brown and Hieb (2014), Exos reproduce in the San Francisco estuary from March through December.  Like Crangon, females migrate upstream, adult males tend to loiter farther downstream.

All of our trawls are conducted in downstream tidal sections of Coyote Creek and Alviso Slough/Guadalupe River.  For that reason, I am guessing that most of these adult Exos are male.  Females may generally swim farther upstream to release broods.  Nonetheless, we often catch at least a few berried females down here in the warmer months.


Exos at UCoy1, the furthest upstream trawling station on Coyote Creek (One Palaemon and three young Crangon at far right in the photo.)


4. Mysid supplement.

A pregnant Mysid from Art2.  Belly pouch is full of eggs or larvae!

I turned my macro lens on some Mysids in the Photarium while we were motoring between stations in Artesian Slough. 

You may recall that Mysids are tiny shrimp-like crustaceans.  They are about the size of a jumbo-sized ant, termite, midge, or mosquito.  They serve roughly the same ecological purpose: they are food for larger critters. (They have other purposes, but food for fish and shrimp is the big one.)  As discussed in the January blog post, marsh ecological success or failure depends on the annual Mysid “bloom.” 

Even ducks eat Mysids!


Mysids are sometimes called “Opossum Shrimp” because they have a “marsupium.”  That is the brooding pouch that holds eggs and larvae until ready for release.  I photographed at least several Mysids with marsupiums full of eggs. 

Apparently, Mysids migrate upstream into fresher water in winter to release their broods much like the bigger shrimp.  In 2019, when rains were abundant, we documented phenomenal Mysid “blooms” in Alviso, Artesian, Dump, and Coyote Sloughs.  (See February 2019 Fish in the Bay report, “Bug Bonanza::


5. Anchovies.

Northern Anchovies from Pond A19: one faded Green-back, one faded Blue-back.

66 Northern Anchovies were caught in March trawls.  That is actually a large number.  March tends to have the lowest monthly count of the year.  (Only one (1) anchovy was caught in each March of 2017 and 2019!)   As usual, the Anchovy count generally goes up in LSB when rain is scarce and down again in abundant rain. 

As discussed before, high salinity must play a role in whether an Anchovy becomes a blue-back or a green-back.  But the effect is always delayed or indirect, otherwise, how could we find both blues and greens in the same pond on the same day?  What is the secret of these colorful Anchovies?


Green-back anchovy with younger uncolored ones from Pond A19 and Alv2.

Most Anchovies caught in March were young and colorless.  They are the year’s new recruits.  However, we see at least some young throughout the year.  This continues to indicate that Anchovies are spawning here, or further north in the Bay, during much of the year. 


6. California bulrush continues to spread across Pond A19.

California bulrush on the west side of pond A19, looking northeast toward the East Bay hills over Milpitas and Fremont.

California bulrush continues to establish on the salty western side of Pond A19.  This is a surprise to me.  I expected these patches to turn dry as straw from the higher salinity caused by lack of rain.  This was now two months ago, so it is possible that these bulrush stands may have succumbed since then.  A large dense area of California bulrush is now well established on the eastern (fresher) side of the pond, and it is in no danger of desiccating. 

California bulrush makes a taller and nicer marsh.  A lot more interesting bird species roost, nest and hide in California bulrush.  More midge white tornados emerge from California bulrush as well.  It’s good stuff.


7. American Avocets going crazy on a falling tide.

The falling tide at 3:45 PM, March 7th: Risky time for bugs; a bonanza for shorebirds.

As the tide receded on Saturday afternoon, Avocets crowded just below the waterline.  It is a common sight if you stop to watch at the right time. 


Falling tide is Avocet feeding time.

Hungry Avocets were probing for moving amphipods (bugs).  I presume that Corophium are the major target here.  According to literature, Corophium scurry back to mud tubes as the tide falls.  The Avocet’s sharp upturned beak and long legs are very specifically evolved for catching these bugs.   

As far as I know, Avocets could be probing for any of the local amphipods: Corophium, Gamarids, Ampilesca, or a combination of all three.  A random polychaete worm would be a welcome treat as well.  Someday, we should probe this mud to determine exactly what they are eating. 


Avocet feeding train.  Silicon Valley in the background.

There must be some advantage for Avocets to form a long feeding-train as they probe for bugs.  It is a common behavior.  Sometimes, it looks like a feeding frenzy.  Do bigger birds at the head of the train soften the mud for those near the rear?  Or, maybe later birds simply see their friends feasting and want to jump in on the good deal?  What exactly is going on here?


North shore of Pond A14 outer levee bank from Alviso Slough.

Avocets get so focused on catching bugs at times like this that they tend not to notice our boat gliding by.  It allows us to get closer for a good look.

That’s all for now.  Sorry for the delay in reporting.  Unfortunately, the SARS-CoV-2 emergency forced a hiatus in both blogging and trawling.  This leaves a gap in the ongoing monthly data record.  Gaps make seasonal and year-by-year comparisons more difficult to see no matter what statistical tools are employed.  Fish and bug behaviors correlate with so many variables like rainfall, atmospheric rivers, ENSO cycles, invading species, climate change, and sea-level rise or fall.  It could take many more decades to figure this all out if we do not consistently monitor our fish and bugs.

Good News!  UC Davis trawls have reportedly resumed!

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