Fish in the Bay – October 2019, UC Davis Trawls (Part2) – Big Fish in a Little Pond; plus a Shrimp update.

This is part 2 from our latest trawling weekend, 5 & 6 October.  See previous post for datasheets.

Bay Study.  I am beginning to compare and contrast some of our local UC Davis trawl data with the much bigger “San Francisco Bay Study.”  Until now, I have been a little intimidated by the size of the database.

The Bay Study tracks populations of critters in the bigger South, Central, San Pablo, and Suisun Bays and includes the lower Delta portions of the estuary.  SF Bay Study data can be downloaded at this link:

So far, I have only graphed South Bay shrimp data – see section 3, “Shrimp Wars,” below.

Dr. Levi Lewis’ presentation at the 2019 State of the Estuary made a strong case that UC Davis otter trawls from Napa, Sonoma, Petaluma, and Alviso marshes fill important geographic gaps in the longer-running “Bay Study” effort.  I see his point!


1. The Big Fish in LSB.

More baby bat rays at Coy3!  We caught 14 bat rays in October.  The largest Bat Ray caught in October was 900mm (35 inches) nose to tail flaps.  (I don’t show a photo of the big one because the babies are cuter.)

You can also see a 13-inch (standard length) striped bass in this tub.


Leopard Shark at LSB1.  This was our most charismatic megafauna for Saturday: Leopard Shark or Triakis semifasciata.

This little guy was 16.5 inches long, so he is most likely young-of-year. Leopard Sharks are about 12 to 18 inches long when born (Unlike most fish, they are live-born, not hatched.)  They grow about one inch per year.

He is a boy!  You can see claspers along the anal vent.  – An article here briefly describes the structure and purpose of shark claspers: (Warning, adult theme!)


Is he a heathy shark?  He felt muscular and strong.  His sandpapery hide did not have any visible parasites, but I did not look very closely as he was getting out of breath – so to speak.  It was time to toss him back.

What do they eat?  The UC Davis team, under Dr. Hobbs, performed a diet study of Leopard Sharks in local restoring salt pond – 2010-2014:

  • Shark stomach contents were collected via “gastric lavage.” (I call it the “Shark Barf” study.)
  • Not surprisingly, the study found that our SF Bay Leopard Sharks eat polychaete worms, small crabs, shrimp, and unidentifiable plant material more than anything else.
  • They eat small fish like Longjaw Mudsuckers, Yellowfin Gobies, and others if they can catch them.
  • Adult Leopard sharks grow to around 5 feet. The world record is a 6-footer caught off San Diego:


California Halibut continue to show up this wetter than average year.  Sixteen juveniles were caught on the October weekend.  As mentioned before, CDFW reports that this is a better than average recruitment year owing to a large population of adults that recruited several years ago during the “Warm water Blob” event around 2014-2015.  This was documented in this poster by Giannetta et al. (2016):

Halibut get quite large (but not in our little pond).  They are true California / West Coast natives and very edible and desirable sport fish.  The young ones shown above have juvenile mottled spots.  The spots fade as they age.  Young Halibut migrate north into the bigger Bay as they increase in size.


Striped Bass from Art3 on October 6th. This one has the characteristic full belly of a happy bass.  He/She will grow large here.  Bigger stripers live in these marshes, but they can outrun the net, so we never see them in otter trawls. … but, I have seen the big ones …

Striped Bass – blast from the past.  Due to an unfortunate event in 2014, I documented a large number of dead 5 to 20-pounders that had unintentionally broke into fenced-off Pond A18.  The incident was immediately reported and corrected!  So, I know bigger ones visit here.

(BTW: The 2014 incident was caused by a rare extended Dissolved Oxygen (DO) crash in the warm late-summer season.  Many large bass, about 750 of them, broke into a shallow pond with no way out.  Photosynthesis shuts off at night, and then we experienced a couple of hot days with unseasonable cloudiness.  Phytoplankton could not produce enough oxygen for all the respiring critters.  DO bottomed out at ZERO mg/l from 2 AM until Noon the next day, two days in a row.  It was a disaster!)

Striped Bass are tenacious.  They are very good at wriggling into little ponds and eating everything!  Then you have a little pond full of large striped bass and very few other fish.

  • A record 45-pounder was caught in Los Vaqueros reservoir in 2009. This article mentions that stripers were never planted there:
  • As long as the local forage fish birth rate exceeds Striped Bass growth rate in our area, we should be OK.


White Sturgeon caught at Art2 on 6 Oct 2019.  We catch a big sturgeon about once per year in LSB trawls.  Local sport anglers catch them regularly.  This fish was 1.2 meters long (just under 4 feet).

This Sturgeon was caught in Artesian Slough just downstream from the San Jose-Santa Clara Regional Wastewater Facility that treats wastewater from 1/5th of the Bay Area’s human population (1.4 million people!)  Excellent wastewater treatment like this is essential for maintaining the health of our ecosystem.

(Full Disclosure:  I retired from this facility.  It still makes me very proud to see giant dinosaur fish living happily in our wastewater plant effluent channel.  This is a mark of treatment plant excellence that should never be ignored!  –  Having said that, many may point out that contaminants in fish tissue is the other unseen standard.

Selenium:  I know from studies, that South Bay Sturgeon flesh tends to be a little lower in selenium even though ambient selenium is higher in the south part of the Bay.  I suspect we don’t have a big Sturgeon-selenium problem because South Bay Sturgeon don’t eat as many Corbula clams.  Corbula are notorious selenium-accumulators!  We must control Corbula!

Mercury: All Bay Sturgeon are generally on the “DO NOT EAT,” or “ONLY EAT IF YOU ARE OLDER”  lists due to legacy gold-rush era Mercury in addition to industrial-era PCBs.  The longer and older the fish, the more mercury it contains.


White Sturgeon – one that got away.  Our Hummingbird depth finder caught a glimpse of another sturgeon cruising the bottom at UCoy2 on the same day.  … Improved echo location gear on recreational fishing boats could be horrible news for big slow-moving fish like Sturgeon!


2. Odd Invertebrates and Red Algae.

Just a couple of updates.

Unidentified polychaete in LSB2. This roughly 3 to 4 cm-long worm is shorter and very different from our usual “Pile Worms” aka neried polychaetes.  Someone suggested that it might be a type of “scale worm.”  But, it doesn’t look scaly enough to me.  Does anyone else have ideas about what species this is? 


Corbula Clams at Alv3 and UCoy2. As usual, most Corbula were scraped up at the detrital-deposition zones in Alviso and Coyote Sloughs and stations a little further upstream.

Good News!  The total 2019 count of these noxious invaders is only 2,500 so far.  We caught over 6,000 in each of the previous three years.  Something seems to be keeping their numbers in check.  Aside from Sturgeon, Winter Diving Ducks are now arriving to clobber the Corbula.  I hope Corbula stay under control.  I kill them on sight!


Red algae update.  These red algae chunks and ribbons were churned up with bottom material near the foot of Alviso Slough.  Red algae encountered here appears to be our major “Submerged Aquatic Vegetation: (SAV).   We do not encounter Eel Grass in LSB trawls.


3. Shrimp Wars.

Raw Shrimp data – unprocessed.

Bug stew at Alv2. Micah Bisson shows what’s left after fish, detritus, and dirt clods are removed.  It’s like panning for gold … Shrimp gold that is.


Shrimp sorted and counted.

LSB shrimp come in three flavors: Native Crangon, plus non-native Palaemon and Exopalaemon.

Shrimp-graph.  I created a living visual aid to conceptualize the rough proportions of this month’s shrimp catch at top. It’s meant to be artistic, but not necessarily mathematically correct.

Pie Charts.  To be scientific, I added two pie charts showing exact total proportions for each trawling day.  These show the relative amounts and final counts of Crangon, Palaemon and Exos caught from the ten stations downstream of the railroad bridge versus the ten upstream stations.

  • Crangon still rule in the saltier bay.
  • Exos are now in the lead in fresher waters.
  • Palaemon are struggling.

What a difference a few years makes. Palaemon shrimp outnumbered the others in 2015 and 2016.  Then the wet 2017 brought Crangon rushing back.  Meanwhile, the Exos that invaded Lower Coyote Creek in 2012 have been multiplying.  Wet years help them a lot too.  Now, Exos dominate the upper tidal waters.


Exopalaemon Shrimp (Palaemon modestus) from Coy2

Exopalaemon (Palaemon modestus) used to be called the Siberian Prawn.  It is a caridean shrimp, not a prawn, that invaded the Bay-Delta sometime around year 2000.

Last month I blog-posted that most literature indicates that Exos don’t tolerate much above 4 ppt.  I forgot that I had seen the Tiffany Brown and Kathy Heib 2006 Exopalaemon poster showing that Exos have been caught in up to 18 ppt salinity in the Delta.  Here is the link again:


Palaemon macrodactylus from Coy4

Palaemon macrodactylus are the Korean War-era invader with the steak-knife rostrum. I am still not competent in reading the exact age these shrimp might be.  I guess the lower two are “teen-agers” about six or eight months old???  The bigger, darker, egg-laden, female at top might be about a year old – maybe?


Young Crangon franciscorum from Coy4.

Crangon franciscorum – the Bay Shrimp, Sand Shrimp, or Grass Shrimp. These are sandy brown Crangon franciscorum.  I am guessing that these young ones are progeny from our Great Crangon Brooding Event last Dec 2018 – Feb 2019.

Crangon also come in three flavors: C. franciscorum, C nigricauda (Black-tailed), and C. nigromaculata (Black-Spot.)  The Black-tailed and Black-spot Crangon are seen in LSB at times, but usually as minor percentage of the shrimp catch. Literature tells us that both types are more common further north and out to sea.  — See, Fish in the Bay December Report for more detailed description of Crangon varieties:


Bay Study Data: Shrimp in South Bay. The above stacked-bar-graph shows the three species of Crangon caught at 12 stations in South Bay, just north of Lower South Bay (LSB).  Again, the Dumbarton Bridge is the dividing line between South bay and LSB.  This is a small summary from the Bay Study fish and bug counts that have been collected and curated by Kathy Hieb for many years.

  • Crangon franciscorum – red.
  • Crangon nigricauda (Black-tails) – black.
  • Crangon nigromaculata (Black-spots) – yellow.
  • Heptacarpus and Palaemon shrimp – blue and green.
  • Exopalaemon have NEVER been caught in bigger South Bay, north of the Dumbarton Bridge, according to Bay Study Data!!!

Good News: The long-term record does not show any alarming shrimp population crash.  (Admittedly, 2015 does not look good and in 2016 only 5 months were sampled.)

Interesting News: A number of research papers document that populations of Crangon franciscorum (red) increase in the Bay during wetter years.  Crangon nigricauda (Black-tails, in black) tend to dominate when it’s drier. Crangon nigromaculata (yellow) and H. stimpsoni (blue) are both considered coastal shrimp that intrude into the bay during dry years.  For that reason, brown and black circles show documented wet and dry periods in the above graph.


Crangon & Palaemon in South Bay.  The above collage shows salinity and temperature ranges in which four species of shimp were caught in South Bay from 1980 to 1996.  The shrimp are arranged left to right by preferences: salty versus fresh, cool versus warm.  Temperature and salinity profiles are cut and pasted from a 1999 article by Kathy Hieb.

All four species can tolerate ocean-level salinity (up to 34 ppt), but evidently, C. franciscorum and P. macrodactylus are caught in freshwater down to 0 ppt.

All local Crangon species live one to two years. Males over one year are rarely found.  Females appear to live to two years.  Like other species of shrimp and some fish, male and female Crangon tend to segregate by temperature and salinity at different stages of their life cycle.

Kathy Hieb and other researchers report that C. franciscorum may be “a protandrous hermaphrodite, with males transitioning to females at approximately 1 year (Gavio 1994).”

This suggests that young Crangon we catch in LSB may tend to be largely, or exclusively, male.  ALL of the thousands of berried Crangon we caught between December and February were certainly female.  More investigation needed!

A fragment of an article from Online Archive of Calif. (AOC) tells us how to determine the sex of adult Crangon shrimp:   “In both Crangon franciscorum and C. nigricauda, the sex can be determined easily in the larger shrimp by the structure of the inner ramus of the first pleopod or abdominal leg.


4. Pond A19.

American Avocets picking at scurrying Corophium during receding tide on Pond A19.

Pond A19 is one of several former salt evaporation ponds in this area.  This 265-acre pond was breached to Bay water in March 2006 for passive restoration.  Last month, I was a little alarmed by a few photos showing relatively bare mudflat, so in October, I investigated.

  • Moderate expanses of mudflat dotted with stands of spartina and pickleweed lie at the western and southeastern corners.
  • Spartina fields appear to be expanding over most of the middle areas.
  • A, possibly fresher?, duck pond is forming in the middle.
  • California bulrush has established as large, apparently perennial, colonies along the Eastern side.


Duckpond in the middle of Pond A19.

Duckpond in A19. From a distance with telephoto, I could make out Northern Shoveler, American Widgeon, and possibly some Green-winged Teal too.

I suspect a similar “pond within the pond” creation is happening in nearby Pond A21 as well: Spartina and bulrush grow dense along the outer fringes that are regularly inundated by tidewater.  Over time, the dense stands of vegetation impound water in the middle and apparently create a pond within the newly created marsh.


California bulrush in Pond A19!

California bulrush (Schoeneoplectus californicus).  A large dense colony of California bulrush suddenly became well-established on the eastern side of Pond A19 in 2019.  This taller, fresher brackish water plant provides refugia and bug food production for many kinds of marsh birds.

Presence of California bulrush here indicates that this portion of the pond may be a little fresher on average.


Gulls in Pond A19!

Gulls loafing in Pond A19.  We continue to have a Gull problem that started around 1980.  It was around that time that falling water levels in Mono Lake caused colonies of California Gulls to flee to new nesting areas.  The nomad Gulls of Mono Lake discovered vast landfill feeding troughs in SF Bay.  Very quickly, SF Bay went from practically NO NESTING GULLS to permanent colonies in the tens of thousands.  And, that’s why local landfills have Gull Abatement programs.

Unfortunately, Pond A19 lies less than 2,000 feet from Newby Island Landfill.  Lazy Gulls like to loaf on Pond A19 marshes at low tide.  This would not be a problem if Gulls were not such tough birds.  Hungry Gulls eat a lot of things aside from garbage, including eggs and baby birds if they find them.

Hopefully, rising and falling tide keeps these gulls a little off-balance.  They loaf on exposed mud between tides, but they do not nest here.


Baby Seal in Pond A19.

Harbor Seal.  As we motored out of Pond A19, we spotted a Harbor seal cruising in the borrow ditch lagoon.  Seconds later, Pat Crain spotted a rogue wave running through the water toward our seal.  “There goes another seal!” said Pat.  … Until I blew up my telephoto image at home, I did not realize that the surfaced seal was a Baby.  The submerged seal we couldn’t see was almost certainly Mama Seal.

Mama Seal was teaching her pup to hunt.  We saw the same thing last May in Alviso Slough, see Fish in the Bay, May report:

I assume Seal foraging in pond A19 is a good sign?    It seems like we saw a lot more new pups at the Calaveras Pont Seal Colony this year.


Summary of significant observations in Pond A19 on October 6th.


5. Up Coyote & Dump Sloughs.

Starry Flounder with tubercles at UCoy2

This Starry is covered the sandpapery starry-looking tubercles that give the fish its name.  This time of year, they crawl upstream along the mud bottom of the deepest channel of Coyote slough (the “thalweg”) to find good spawning areas at the creek’s end.

This was our 50th Starry of 2019.  Not a bad year, but not great.  2017 was the “Year of the Starry:” 407 were caught in LSB trawls.


Shiner Surfperch (top) and Bay Pipefish (bottom) from DMP2

Dump Slough has become a magically restored wetland sandwiched between the region’s largest landfill and the wastewater treatment plant.  Officially, “Dump Slough” is known as the Coyote Creek Bypass Channel.  It was a small drainage ditch until Santa Clara Valley Water District completed large flood control project in 1988.  Our monthly trawls here continue to find a very good diversity of fish and bugs.


Red-winged Blackbirds (Agelaius phoeniceus)?  OR Tricolored Blackbirds (Agelaius tricolor)???  Micah noticed the colorful male blackbirds as we rounded Dump Slough near station DMP1.  Red-winged Blackbirds are common in tall tules like cattails or California bulrush.


Yellow epaulets?  According to various sources:

  • Yellow epaulets = Red-winged Blackbird;
  • White epaulets = Tricolored Blackbird.
  • I can’t tell the difference from studying on-line photos, but I will admit, these epaulets look a little more yellow than white to me.

For local marsh ecology, I don’t think it matters, but it would be very cool to find Tricolors in Dump Slough!  —  ATTENTION BIRDERS:  Please take a look at these blackbird photos.  Could these be Tricolors?? 

I will pay closer attention in November!

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