Fish in the Bay – 18-19 August 2018 UC Davis Trawls – Shrimp Explosion.

Hello again.  This is the August Lower South Bay fish report. 

Very good news!  We encountered a shrimp population explosion in August.  As explained further below, the summer of 2018 has been very good for shrimp of all kinds, but particularly for native Crangon (aka: grass shrimp or Bay shrimp).

Saturday, 18 August – Bay-side trawls

Sunday, 19 August – upstream and east of Railroad Bridge

Measuring the salt-wedge:  In the temperature line above I note “s” for “start” and “e” for “end” to indicate which values for DO, Salinity, and Temperature were used.  Normally, I use end-of-trawl, top of water column numbers to characterize water quality at a given station.  When the Hobbs team trawls across the stratified tidal salt wedge differences can be extreme. In those cases, I have to choose between up to four different measurements: (1) start and (2) end of trawl; (3) top and (4) bottom of water column.  I try to pick the most characteristic numbers.  In some cases, I show Top/Bottom for either start or end of the trawl.  I don’t have space or interest in showing FOUR different numbers for each parameter, so that’s the best I can do for now.

I have said it before: this is an extreme estuarine environment.  Any critters living here must endure wild swings in temp, salinity and DO within each several-hour tidal cycle.


Shrimp by the tub-full on Saturday.  Yikes!  What the heck happened!  August weekend was a shrimp blowout.  Even Dr. Hobbs commented that he has not seen shrimp numbers this high in over 8 years of trawling.  Usual summer time trawl numbers are 2,000 to 3,000 in a good month; 5,000 to 6,000, as caught last April, is a big month.  21,000 shrimp of all types were caught in August.  This is insane.  There were so many shrimp that Jim and Rachel Fichman had to improvise an estimated counting system: Shrimp were counted to fill one plastic tray to the brim = 500 shrimp.  Then trays were repeatedly filled and counted as 500.  Where did they come from?  Why was August 2018 so special?

Bat Rays also by the tub-full on Saturday.  These were the 14 baby bat rays caught at station Coy3.  These are newborns; at 12 to 14 inches across, this is about as small as they get.  Bat rays are born live with their wings curled up.  Mama bat rays birth a few to several young depending on the size and age of the mama.  In all, 29 bat rays were caught on Saturday from Alviso Slough out to the middle of Lower South Bay.

Seven leopard sharks were also caught out in Lower South Bay. (unfortunately, no photos)

Other highlights of the August weekend:

  1. Former San Jose workmate and current Compliance Manager at the SJ-SC Regional Wastewater Facility, Eric Dunlavey, joined the Hobbs crew on Saturday, the big shrimp day.
  2. Sunday got off to a rocky start as it was discovered that someone had stolen the trailer hitch ball off the truck the previous night. This caused some delay and expense requiring Jim Hobbs, Pat Crain, and Rachel Fichman to run to Home Depot for a replacement.
  3. A second unfortunate event was the mid-morning catch of a tire at station UCoy2. Full of mud and barnacles, this tire weighed at least 150 pounds.  It had to be wrestled out of the net, the net reset, then the station re-trawled.  Note that this location, near the salt-wedge focal point, is the abundant sweet-spot for shrimp, clams, and occasional tires.  This is where sloshing tides concentrate food in the Coyote Creek system for the benefit of benthic filter feeders and detritivores.

Pond A19.  I chose to join the Sunday Upstream-side trawls to update myself on Pond A19 restoration progression.  A-19 was a barren gypsum salt-plain when first breached in March 2006.  It is now year-12 since its opening to circulation and restoration.  (Photo: Great Blue Heron against stands of spartina on the A19 mudflat.)

Restoration of Pond A19 to densely vegetated marsh proceeds steadily but slowly.  The pond is filling steadily with sediment, albeit more slowly than nearby Pond A21, owing to A19’s more upstream location.  Stands of spartina, pickleweed, and occasional fat hen have taken firm root in the new soil.  I noticed in early 2017 that emergent marsh got temporarily flattened in due to the big freshwater flush that winter.  But, marsh plants grew back from buried root-stock.  Nonetheless, a substantial area of A19 remains mud flat. Tall marsh in the surrounding area indicates that dense vegetation will grow in the pond eventually.  In the meantime, the mudflat attracts and supports denser and more diverse bird groups pretty much any time I visit.  (Photo: from background to foreground; spartina, pickleweed, and fat hen (Atriplex prostrata) in A19 mud just after high tide.)

Small fish in Pond A19.  The above photo shows an assortment of tiny fish from A19: Left, top to bottom:  Stickleback, Killifish, Stickleback, Silverside, and three Arrow gobies.  Right: three Sticklebacks.

In A19 and elsewhere, we saw some return of Inland Silversides (aka: Mississippi Silversides) and Rainwater Killifish.  Both types had been almost absent since last summer.  They are both non-native and among the hardiest of survivors.  When local marsh gets a little drier and saltier, their populations explode.

Above: a better collage to show three principle types of tiny marsh fish in the Alviso Marsh Complex.

Arrow Gobies still doing better than normal.  And, more good news: Yellowfin Goby numbers have dropped again.  In June, we counted 840 Yellowfins.  In August, 1001 unidentified gobies were caught.  Where did they all go?  I don’t know, but good riddance!  (Arrow goby shown above.)


Longjaw Mudsuckers in A19.  The photo above is showing 5 or 6 of the seven Mudsuckers caught in Pond A19.  (The other 2 or 3 larger fish are Yellowfin Gobies.)  Mudsuckers seek refuge in muddy holes amongst the pickleweed.  Consequently, they are less apt to be caught in trawling nets.  So, if you see mudsuckers in your trawl, it means there must be a lot of mudsuckers in the pickleweed, and that is a good thing.

Longjaw Mudsuckers in my hand.  Mudsuckers is are really slippery.  You can distinguish Yellowfin Gobies from Mudsuckers by touch alone.  In this photo, I was attempting to see how many Mudsuckers I could hold in one hand while taking a picture with the other.  Three was the max.  These fish are just too slippery.

Also, notice the top fish in the photo.  See how two or three Synidotea isopods (bugs) have attached to the mudsucker’s mid-section?  We think of Synidotea as strict detritivores, but I have often noticed that they cling tightly to fish if they can get their little claws into them.  I suspect that armies of Synidotea on channel bottoms quickly devour any struggling fish that does not have an adequate defense against them.  On the other hand, I have handled thousands of Synidotea, and I can assure you, they do not bite humans.  (I always pry them off any fish they grab like this, btw)


Anchovies.  The tally of Northern Anchovies was fairly normal for August = 182.  This is less than the occasional huge 1,000+ numbers we saw prior to the 2016/2017 winter flush.  I presume that the population of marsh year-round resident anchovies is still re-building.  (Above: Green and Brown-backs from Pond A-19.)

Green-backs shown above.

Gold-backs?  As discussed in previous posts, and on Facebook, marsh resident Anchovies have brown backs.  I am wondering if we are now witnessing a year-by-year natural selection of Green to Brown backedness as ocean migrating populations recolonize Alviso Marsh Complex post flush.   I doubt that my anecdotal and amateurish photos will prove this thesis, but you got to start somewhere!  (Above: Two gold-backs from Coyote Creek? … Half green, half brown?)

Bay Pipefish.  We only counted two Bay Pipefish on Sunday, but we saw many more.  This healthy male pipefish was caught in the main channel of Lower Coyote Creek.  How do we know it was a male??  Because …

This Pipefish had a belly-pouch full of babies.  Male pipefish tend the babies in their belly-pouch.  Looking back at some of my photos over the past three years, I can see that baby pipefish and “pregnant” males are caught in summer months.  (Photo shows Rachel displaying the pipefish pouch.)

But, there were even more pipefish …

A baby pipefish was caught amongst the copepods and mysids in the smaller mysid net.   And…

Even tinier baby pipefish appear to have been in the same jar.  I believe we can see two, possibly three, very tiny pipefish floating just barely above the main mass of copepods.  This suggests that there are a lot of pipefish in Alviso Marsh Complex even if most don’t survive to adulthood.

Crangon exploded in Lower Coyote Creek and Lower Alviso Slough!  (Photo above:  A lone Crangon shrimp from Dump Slough.)  There were almost 18,000 Crangon caught on Saturday!  This has been an extraordinary summer for Crangon: roughly 5,200 caught in May, 2,800 in June, 2,400 in July, now close to 18,000.  I don’t know why the Crangon population boomed this summer, but I hope the trend continues.  This 2014 article from BayNature summarizes the long history of the rise and fall of Crangon in San Francisco Bay, and may provide some clues:

Shrimp gradient.  Last month, I inaugurated a “Shrimp Gradient” table to show where populations of our three flavors of shrimp concentrate from Bay salt water to creek fresh water along the main stem of Lower Coyote Creek.  Here I expanded and repeated the table to show shrimp results for both July and August.  (Shrimp caught in Alviso, Artesian, and Dump Sloughs not shown in these tables.)

Palaemon shrimp drifted downstream between July and August.  We don’t usually see large numbers of them far out into LSB, but in August many were caught at LSB1.  (Photos above shows two Palaemon shrimp from Coyote Creek. Both appear to be carrying eggs.)

Exopalaemon shrimp numbers greatly increased at UCoy2.  The August gradient table does not show the extra 354 Exopalaemons caught in Dump Slough or the 157 from Artesian Slough.  The lower-most Exo shown in the photo above is full of eggs.

Exopalaemons have the curved shaped rostrum on their foreheads.  I have long noticed that the rostrum shape and number of serrations seem to vary a bit.  I don’t know if that is a function of age, sex, or maybe we have a few different kinds of Exos in this area.  Notice that the eye can be big and pitch black in some individuals and smaller and sandy or tan colored in others.

Exopalaemon with smaller sandy eye.  It could be that the different looking Exo eyes might just be the way Exos focus their vision or retract eyeballs into eye stalks – they look really different.

Exopalaemon shrimp with blue antennae!  Something else to ponder.  Of the 157 Exos caught in Artesian Slough, many had blue antennae. This could be very normal, it’s just the first time I ever noticed it.  Note the two different looking eyeballs among these three shrimp.

Corbula clams.  The photo above shows Rachel racing to tally 1,466 clams from UCoy2 before we reached our next station.  693 more were caught in Alviso Slough.

Both Alviso Slough and UCoy2 stations are consistent corbula hotspots.  But, only a single corbula clam was caught in Alviso Slough in July.  The 693 clams caught in Alviso Slough in August are older than one month old.  Nearly all were greater than 10 mm in size.  So, this must mean these clams move around en masse!!!

About a year ago, Jim Hobbs pointed out to me that dense beds of corbula appear to jump around in Alviso Slough from one station to another, month-by-month.  It might be more accurate to say they roll around.  Unlike other clams, corbula rest at the surface of the mud bottom.  We THINK, maybe even as adults, these clams let tidal and river currents push them around until they find the sweet spot, sort of like tumbleweeds of the clam world.  It makes me wonder if adult clams might also have some ability to control their buoyancy.

A Pile Worm (polychaete).  Rachel pointed out this small polychaete to me. They are common and very important in the food web, but they usually get torn up in the trawling net so I rarely get a chance to look at them closely.  This was a nice intact specimen even if a little smaller than usual.  (I left a portion of my thumb in the photo to show scale.  This worm was perhaps 2 inches long.)

Look closely. This worm has eyes!  Until now, I did not know polychaetes had eyes. I never thought about it, although I do recall hearing that they are attracted to light at night.  Here is a note about polychaete eyes:

It is said that vision has evolved independently dozens of times in over 30 phyla of life in the evolutionary record.  Mollusks, Jellyfish, and Planarians (flatworms) all have eyes. Even single-celled euglena and dinoflagellates have eyespots.  More recent research shows that vision is based on a small family of proteins called “opsins” which have been with us since earliest times.  Thanks to revolutions in the sciences of genomics, x-ray crystallography, organic chemistry, etc., researchers are now tracing the evolutionary history of proteins in living cells!  And, if you follow the science of bio-proteins, you should be aware that the SHAPE of the protein is all-important:

Polychaetes are amongst the most ancient of multicellular lifeforms. They have been around since late Ediacaran or early Cambrian eras at least 550 million years ago.  That makes polychaetes and their body-form older than dragonflies!  Even older than trilobites!  Polychaetes are some of our earliest distant multicellular cousins on the evolutionary tree of life.

Here is something even more fascinating; body segmentation in annelids (like earthworms and polychaetes) and arthropods (like centipedes and millipedes) may have evolved through similar genes but completely separately:

One more amazing polychaete fact: an entire genus of whale bone-eating polychaetes was discovered by the Monterey Bay Aquarium Research Institute in 2002. Based on that discovery Swedish researchers found a new species of that genus feeding on dead Minke whale bones in their waters a few years later: they called it, I kid you not, the Osedax mucofloris, literally the “Bone-Eating Snot Flower.”

Marine pillbug (Sphaeromatid Isopod). This is another interesting bug I have seen before, but never commented on – I also posted an album of photos on Facebook.  A dozen or more were caught in Dump Slough on Sunday, but I have seen them in Alviso Slough on other weekends.  These are marine versions of your common garden pillbug or “rolly polly.”  They fold into tight little balls when disturbed.

These critters are rarely documented.  The set of images to the right is from a reprinting of a paper by Milton A. Miller, UC Davis, 1968, in which this same species was identified as endemic to SF Bay.  This could be a rare SF Bay native amongst benthic species. But then, who really knows?


American Shad.  Seven were caught in August.  The four shown here were about 7 inches long.  (You can barely see my fingers to the left of them for scale.)  As shad get scarcer, they are getting larger.  This indicates that we are still seeing the population cohort that recruited with the big flush 18 months ago; few, if any, younger ones appear to be recruiting with drier weather.

Striped Bass.  We did not see many striped bass in August, but those that were caught were large for otter trawls.  When bass get this size, they are strong enough swimmers to outrun the net.  More likely than not, the low Dissolved Oxygen slowed these big guys down.  Also, water temperatures were climbing up near the 25 degree C threshold that induces heat stress in Striped Bass.

In any case, these bigger fish gave Jim his chance to throw down a dramatic sport-fisherman type of pose.  These were big ones that did NOT get away.  (Yes, they were released unharmed after the photo op.)

Happy fishing!


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