Fish in the Bay – November 2018 UC Davis Trawls – Amazing Bugs, Red Algae, Beautiful Fish

Hi Everyone. 

This posting is a mixed bag of loose ends from November and early December.  (Monthly Data Tables are in the previous November post.)

November/December is always busy.  Late-fall is busy fish and bug month in the Bay.  As temperatures continue to drop, we will witness:

  • Shrimp migrating upstream bearing eggs (I will discuss this more later in December.)
  • Shad apparently moving upstream for spawning
  • Adult sculpin, young starry flounder and Longfin Smelt congregating here for spawning
  • Baby English Sole arriving from the sea to recruit.
  • With luck, we might see substantial blooms of tunicates and comb jellies, but maybe not until a little later in January.

Fish and bug migration mirrors migratory bird season above the water, but for opposite reasons.  Migratory birds flee Arctic cold temperatures.  Here in the Bay, most of the abundant fish and bugs thrive in the cold (I think Anchovies and Halibut may be a few weird exceptions).

FIRST: A big Thank You!  As mentioned previously, the scheduled November weekend was disrupted by a boat trailer malfunction.  A blown wheel hub seal was discovered in wee morning hours of Saturday 10 November.  Quick action by Emily Trites and her friends at Gone Fishin’ Marine in Dixon, CA, saved the day.  Mechanics at Gone Fishin’ Marine scrambled on a Saturday morning to get the Hobbs Lab boat trailer back in shape in time to salvage half our initial trawling weekend.

Gone Fishin’ Marine:   also on Facebook:


Part 1:  Work on the boat.  (This is not all fun and games!)

Sunday, 11 November was a bright sunny day.  Here, Jim Hobbs sacrifices the sprinkle donut to ensure good trawling.  (OK, some of this is fun and games.)

On 11 November, an old tree trunk was drifting mid-channel right in the path of our first trawl.  Emily lassoed it, while Jim gaffed it so, so we could tow the snag to a firm resting place along the shore.  Tires and debris complicate the survey work.

Speaking of Tires …  Tires again slowed us down on both 11 November at Station Art3 and again on 8 December at Station Alv1.   In the photo above, Levi Lewis pulls a barnacle-encrusted tire from the net at Alv1.  A mixed blessing: it is back-breaking work to pick up a mud-filled and clean it, but tires usually shelter hundreds of tiny fish and critters.

Jim taking water chemistry fingerprinting samples.  This is the time-consuming start of a tedious process to catalog strontium and oxygen isotopes. This water data can then be compared to isotopes in fish otoliths to determine EXACTLY where fish hatched, recruited, and roamed.  It is not as interesting as fish to me, but I understand the importance.


Part 2: Amazing Bugs.  (A small selection of invertebrates caught in November-December.)

Copepods & mysids.  Tiny bugs are caught in the smaller fine mesh nets.  In this photo, copepods are light colored, semi-transparent, and about the size of coarse grains of sand.

Dr. Hobbs told me this weekend that copepod density in this Alviso Marsh Complex is “off the charts” compared to other parts of the Bay.  Abundant copepods are key to productive fish rearing.

Harris Mud Crab.  In 1980s-era otter trawls, these were the most commonly caught invertebrate after shrimp.  Now they are uncommon to rare.  Their rarity is not necessarily a bad sign: there may be either less dead material for feeding crabs or more competition from other detritivores.  I hesitate to say that fewer Harris Crabs might be a good sign – maybe, maybe not!

Generally, I don’t care for crabs.  They are crabby.  This one is pinching my thumb!

Marine pill bug (Sphaeromatid Isopod).  I first showed a picture of one of these in August.  More were netted in November and December.  These little bugs do not appear to be particularly important, but they are kind of interesting and little known.  I think this is a native bug.  It seems to occupy a rare nitch that hasn’t attracted a stronger invasive bug from some other part of the planet.

Pile Worm: aka, Polychaete specifically, Neanthes succinea.  Levi handed me this worm from the Alv1 haul.  This is a common polychaete here.  You can step into Laine’s Bait in Alviso and buy them as bait.  This worm is also an important component of the local food web.  This species is non-native, but benign as far as I know.  What was benthic life like here before this worm arrived?  I don’t think we know!

In August, I photographed a smaller Pile Worm and discovered it had tiny eyes.  I read that many polychaetes have eyes, some don’t, and some lose their eyes as they grow.  Until now, I never noticed eyes in the big adult worms.  This time I did.  Creepy, yet intriguing.

Corbula with barnacles from UCoy2.  Corbula clams are the potential nuclear bomb of invasive pests we find here.  They can literally suck the life out of this system by filtering and consuming practically every microscopic living thing, phytoplankton, zooplankton, rotifers, the works!  Then they multiply until all that is left are corbula blanketing the bottom.  I cannot allow that to happen, so I bucket them for disposal and splash them with ethanol to make sure they don’t survive.  I don’t expect my meager efforts to make any difference, but I can only do what I can do.

I took the photo of corbula with barnacles to try to gauge how old a one-to-two-centimeter corbula could be.  A few of these clams have barnacles on top of barnacles.  Their numbers seem to peak and fall each year, especially at the Alviso Slough and UCoy2 stations, but with enormous variability.  Where do they go?  How do they keep returning?  What keeps them in check?

Good News: As long-time readers know corbula have not proliferated in Lower South Bay like they did up north in Suisun Bay.

Bad News: Corbula are not going away – see table below.

Older data shows: 17,774 Corbula clams were caught in 2012 even though fewer stations were trawled back then.  Then, Corbula numbers crashed in 2013 through 2015.

  • Dry, rainless years may crush Corbula populations, but the Corbula resurgence of 2016 (still a dry year) does not fit that pattern.
  • Bat Rays and Starry Flounder eat Corbula, but their numbers don’t match the Cobula crash and boom either.
  • Salt pond restoration increased diving duck populations, which also eat Corbula, after the early 2010s.

But despite all that, Corbula numbers rebounded in 2016 and since.  What’s going on here?

Part 3:  Red Algae

Submerged Aquatic Vegetation (SAV).  Like last month, and at scattered times in the past, we are seeing fragments of red algae.  The algae seems to be more prevalent each November and December, but my observations are limited.  I think this is a very, very good sign.

SAV update for December.  We pulled up even more red algae in December.  Big clumps of Red Gracilaria and Cryptopleura were found in Pond A21.  There were fragments of Ceramium at stations in the main stem of Coyote Creek and in the middle of LSB.


Part 4. Beautiful Fish

First trawl in Alviso Slough on 25 November.  To my spotty anecdotal observations, Alviso Slough has evolved into a productive fish and bug factory as the Pond A8 complex was gradually opened for discharge over the last few years.  I could be wrong, but it seems fish are getting bigger on average and more numerous.  Here we see:

  • Two Pacific Staghorn Sculpin as big and fat as they get in this part of the Bay. These will be spawning in the next few months.
  • Two Yellowfin Gobies (one nearly hidden at far right). These are also adults.
  • Two American Shad showing the golden-brownish river color on their backs. These are the beautiful fish that we saw only rarely prior to the 2017 Freshwater Flush.
  • One Starry Flounder young adult ready for spawning.


Staghorn Sculpin from Alviso Slough.  The top photo is the natural sculpin pose, standing on the two pectoral fins, that I rarely capture.  The bottom photo of a different sculpin shows off dorsal fins.

Bonehead (or Bonyhead) Sculpin, 25 November.  BINGO!  A new fish species for Lower South Bay.

Actually, this fish is not exactly new: records show that another Bonehead was caught at the same station, LSB1 in February 2016.  Until we saw the one shown above, we had not seen a Bonehead before or since.  Boneheads are common on the coast, but rare here.

Bonehead Sculpin UPDATE.  Our December trawling weekend picked up four more Bonehead Sculpins at LSB2!  (Boneheads look a little like horned toad lizards to me.)

Yellowfin Goby – a really old one.  Until now, I had never seen a really big, mature yellowfin.  Then we picked up this monster from Alviso Slough on November 24th.  Look at those teeth!

Monster Yellowfin!  A second look.  In all gobies, the head and jaws get very large, particularly in males.  I presume this one is a male.  Yellowfins are noxious invasive pests that disrupt our local ecosystem.  Nonetheless, I still can’t quite bring myself to destroy them.  After these photographs, I tossed him back to the Bay.

Yellowfin Gobies from Artesian Slough, 11 Nov. These are more typically-sized adults.  At this size, they are not so dragon-like.  Around 1,500 yellowfin gobies were caught this year which is about half the annual numbers of 2015, 2016, and 2017.  A yellowfin population drop is a good sign, but I doubt it will last.


Bay Pipefish.  This pipefish was caught in Artesian Slough.  Another was caught further up Coyote Creek.

Pipefish were rare here in the 1980s.  Only 9 were caught in similar trawls performed over 5 years, from 1981 to 1986.  Granted, the 1980s trawls covered fewer stations.  But, that compares to 17 pipefish caught in trawls this year alone, not counting additional baby pipefish caught in larval fish and Clarke-Bumpus trawls.  More pipefish may indicate more cordgrass marsh on the fringes and more tiny ciliate, rotifer, and copepod food in general.

Shimofuri Gobies.  These were five caught in November, the biggest one, at bottom right, from Artesian slough.  

I learned earlier this year that we have a Shimofuri identity crisis.  Young Shimos are longitudinally-striped and look EXACTLY like Chameleon Gobies until they lose the stripes.  Barring genetic analysis, we literally cannot tell the two species apart when Shimos are young.  Thus, we cannot be certain in historic records, or even now, to what extent Chameleon Gobies are present.

California Halibut at LSB1 on 25 November then another at LSB2 on 8 Dec.  These are two of only four California Halibut caught in 2018.  Since the Freshwater Flush in February 2017, halibut fell from common catch, several hundred to over 1000 per year, to practically gone in this local area. The few we continue to catch are getting larger and older.  Halibut are a cold ocean fish, but they avoid Lower South Bay when it gets fresher and cooler.

Pat Crain tells me that halibut lose spots as they age.  The fish at bottom is about 2½ inches longer and is less intensely spotted.

Starry Flounder in November.  This pair was caught in Dump Slough on 25 November.

More Starry Flounder.  We caught 17 more Starries at station Alv1 on 8 December.  These are young but sexually mature Starries swimming upstream to spawn.  Starries and English Sole like it fresh and cooler, and we have seen more of these since the rains returned.


Striped Bass – one of only two caught in November and December.  This bass is showing nasty wounds on both sides.  Bass this size often have ulcerations which may be caused by lampreys or bacterial infection.  But, these wounds are different.  They are partially healed, and they look like tooth marks.  I suspect a harbor seal may have bit this bass.

Anchovy and Shad colors.  Photo above showing, top to bottom: Anchovy, American Shad, American Shad, Anchovy.

This rainbow of colors is brought to you by guanine crystals in iridophores.  Some set of conditions makes these fish express bright metallic blue and green hues. I took photos of this arrangement at slightly different angles.  The blue, green, or goldish to red-orange hues remain fairly constant even as reflection and iridescence change the color intensity.

Anchovy with scattering of blue iridophores along the back and with silver sides.  Have you ever wondered, “What makes a fish silvery?

Both iridophore blue and reflective silver scales and skin are caused by quanine crystals. In fact, guanine was first extracted from the scales of a fish.  Albeit, isolation of the chemical compound, from seabird guano, came two centuries later:

“In 1656 in Paris, a Mr. Jaquin extracted from the scales of the fish Alburnus alburnus so-called “pearl essence”,[8] which is crystalline guanine.[9] In the cosmetics industry, crystalline guanine is used as an additive to various products (e.g., shampoos), where it provides a pearly iridescent effect. It is also used in metallic paints and simulated pearls and plastics. It provides shimmering luster to eye shadow and nail polish. Facial treatments using the droppings, or guano, from Japanese nightingales have been used in Japan and elsewhere, reportedly because the guanine in the droppings produces a clear, “bright” skin tone[10] that users desire. 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, thus producing a pearly luster. It can be applied by spray, painting, or dipping.” 

People may laugh, but there is serious science and history behind these fish beautiful fish colors!  Serious beauty tip: apply this silvery fish essence If you want your skin and hair to radiate a beautiful glow!

Threadfin Shad from Dump Slough.  At 122 mm, almost 5 inches, this is about as big as a Threadfin gets.  It’s also about as colorful as they get.

I tried to capture the shimmering silver and steel blue glint off the scales.  There is so little time to capture a good photo, and the fish struggles and gasps for breath.  I take three to five shots at different light angles and hope for the best as I toss the fish back in the Bay.

Shiner Surfperch (or shiner perch).  This pregnant female Shiner was caught in Pond A21.  In another month or so, she will give birth to several to a dozen live babies. (They don’t lay eggs like most fish.)

Shiners were much more abundant in the 1980s.  Now, we see them rarely.   … Another mystery!

More info about the surfperch family:  To date, the Hobbs crew has caught three types of surfperches in Lower South Bay: Shiner, Barred and Walleye.

The work never stops.  Even as I write today, Jim Hobbs and crew are out again attempting to net elusive Longfin Smelt as part of Operation “Save Our Smelt” (SOS).

This newest project will attempt to collect and transport 150 adult Longfins from different marshes in San Francisco Bay to “UC Davis Fish Conservation and Culture Lab” aquaculture tanks:

More news soon!

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