Fish in the Bay – 20 October 2018 UC Davis Trawls – Duck Hunter’s Weekend.

Hello again everyone.  I joined the Hobbs group for a day of lovely weather in late October.

This was a duck hunter’s weekend.  I learned that 20 October was opening day for duck and geese hunting in San Francisco Bay.  There we were for the big event.  Even better, the A3, A7, and A8 pond complexes were open for hunting on Saturday and Sunday, so we got a floating front row seat, so to speak, for opening day.

I don’t hunt myself.  Frankly, I greatly appreciate the modern-day luxury of not having to personally kill my own prey.  But, my dad was an avid duck hunter, and I grew up accompanying him on many hunts.  I always notice that the human population that directly experiences and appreciates local marshes is relatively small.  If people want to come here (and pay) to hunt ducks, I say the more the merrier.  BTW:  This is the Don Edwards website info on waterfowl hunting:

Happy Dogs.  We also saw several very happy dogs this day.  We all know that Labradors were bred for hunting.  It is something else to see them doing what they were born to do.

California Fish and Wildlife Service wardens were also out in force.  They were making sure hunting regulations and bag limits were understood and respected. (Hard to see in the photo, but another happy Labrador is shown at the midpoint of the boat.)



Saturday, 20 October – Bay-side trawls

Sunday, 21 October – upstream and east of Railroad Bridge

We had a full boat. In addition to Jim Hobbs (behind the secchi stick sacrificing a sprinkle donut), Levi Lewis (back toward me),and Pat Crain at the helm, we were joined by John Kuntz from Hobbs Lab who is a new member of the otter trawling experience.


First catch. This is how the raw data looks fresh out of the net: a mixed bag of gobies, sculpin, corbula clams and three flavors of shrimp.  Over medium flame with some tomato, garlic, and ham this could have made a fine Zarzuela de Mariscos.   ( )  However, this catch is not destined for gourmet dining.  All were sorted, counted, then released.


The tastiest treats of all: two crangon along side five exopalaemon shrimp.  The most amazing shrimp summer on record continues.  The October catch again netted over 10,000 shrimp which were mostly native crangon.


A pair of Staghorn Sculpin.  The 26 Staghorns caught in October are looking larger and fatter.

You may recall, we saw “big” adult sculpin through December 2017 and January 2018 (a “big” staghorn in this part of the Bay is roughly 100 to 130 mm).  Then, in March and April, the Hobbs crew caught large numbers of teeny-tiny baby staghorns.  By May, staghorns were fewer but growing to mid-adult size.  I presume, the two shown above may be some of the spring 2018 recruits that will complete the spawning cycle next spring.


Marine Leeches!  Levi Lewis pointed out that this sculpin from Alviso Slough is being parasitized by leeches.  Until seeing this, I never considered salt water leeches.  Apparently they are quite common, typically infesting sharks, skates, flatfish, cod, salmon, and rockfish.

Also, some basic biology:  Segmented worms are called Annelids.  I remember from 9th grade biology class that the phylum “annelida” was one of my favorites.  But, until Dr. Lewis reminded me, I had forgotten that leeches (family Hirudinea) are a subgroup of Oligochaets (like earthworms) which in turn are a subgroup of Polychaets (like our Bay pile worms) with all three groups falling under phylum Annelida.

I also remember my 9th grade science teacher, Mr. Wong, telling us that annelids are roughly at the half-way point of sophistication between simple bacteria and the most complex reptiles, birds, and mammals.  I often wondered since middle school if these worms really are the half-way point, versus say, three-eighths or seven-sixteenths, for example.  I will check on this someday.


Shokihaze gobies.  78 shokihazes were caught in October.  This is the largest number caught in 2018 so far, but not a record for this fish.  Judging from the last couple of years of data, shokihazes are always present.



Only 4 Arrow Gobies were caught in October.  I was hoping more Arrow Gobies would continue to show up.  But alas, it was not to be.  The specimen on the right (two views) had silver-blue iridescence on the operculum which could be a signal of adult (male?) spawning readiness perhaps?

A native Cheekspot Goby is about the same size, with “an iridescent blue-black blotch on gill cover.”  However, the fish shown above are clearly Arrow Gobies.  These tiny fish are not often photographed, so I do not know if the blue patch is a normal adult, or seasonal, color pattern.

Goby table.  I filled in a few missing months of my goby table.  As you can see, shokihazes are up even as arrow and yellowfin numbers declining to winter-time lows. (BTW: I just noticed that shokihazes seem to be winter gobies here – more than the other types at least.)

During the past month, Levi shared a Breitburg (2002) paper with me: Effects of Hypoxia, and the Balance between Hypoxia and Enrichment, on Coastal Fishes and Fisheries.   The paper is available at either of these two links:

The Breitburg (2002) paper, among other things, describes how nutrient over-enrichment can result in declines in demersal fish (bottom fish, like gobies) even as production of pelagic fish (like anchovies) increases.

As near as I can tell, Lower South Bay currently has lots of both types of fish. But, wouldn’t it be interesting if we could build and track a pelagic/demersal fish index?  Such an index may give us quite a bit on information about ecosystem dynamics even if nutrient/nitrogen over-enrichment is not currently disruptive.  Going beyond a simple index, the Beitburg paper gives examples of species-specific behaviors in response to anthropogenic disturbance.  Much food for thought.  I will try to work on this.


Bat Rays.  These were three of the six bat rays caught on Saturday.  These three from station Alv3.  All were newborn baby bat rays.  I do not know how old, but they do not get any smaller than this.  I think they are weeks old, or less.  Notice the stinger spine in photo #2 – handle with care!

I assembled this bat ray photo montage to show that all were released back to the Bay.  I get asked about that often – here’s the proof.


Baby Bat Ray from Coy2 station.  John Kuntz is carefully holding another baby bat ray by the tail a little later in the morning.  Baby bat rays are cute, but they will sting.


Top Smelt versus Silverside:  Similar but not the same!  This photo shows a native Top Smelt (top) and non-native Mississippi (or Inland) Silverside (bottom).  These two fish were caught in Pond A21.  Both are pelagic fish with big saucer shaped eyes and a bright reflective silver stripe along their sides.  But beyond that, body shapes and fin characteristics are very different.  Nonetheless, because they are so small and reflective, it can be hard to tell the two apart in a wriggling mass of tiny fish!


Ruddy Duck.  This young male ruddy duck was paddling around in front of us as we trawled Pond A21.  He is showing his non-breeding season colors.  Sometime in spring or early summer his bill will turn sky blue and his back will become brick red (ruddy color).  That will be his mating display to attract a female ruddy.

Ruddy Ducks are also known as “stiff-tailed ducks.”  They use that stiff tail as a rudder as they swim under water to forage clams and bugs on the bottom.  Roughly one hundred years ago, ruddy ducks were considered one of the best eating ducks.  Nowadays hunters avoid shooting them because of their strong gamey flavor.

Ruddy ducks are very high on the cuteness scale, as you can see.


Seaweed.  Much of San Francisco Bay is noted for being seaweed deficient.  The technical term used for seaweed here is “Submerged Aquatic Vegetation (SAV).”  Seaweed provides both food and refuge for many types of fish and invertebrates.  Some types of seaweed / SAV can also grow out of control if, say, the Bay has too much nitrogen nutrient.

For these reasons, I try to note good or bad indications of new seaweed.  Generally, we want more seaweed here, and red algae is almost always a good thing.  Once, in November 2016, we found wide-spread clumps of the green algae, Codium fragile (aka: “Dead Man’s Fingers” or “Oyster Thief”), which could be a very bad sign. But the codium disappeared, and we haven’t seen it since.

  • The broad-leafed darker red algae shown above is likely Cryptopleura lobulifera.  C. lobulifera is endemic along the California coast, and this leaf shape looks about right.  However, there are other Cryptopleura varieties, and this is not my field of expertise.  As far as I know, it could be C. ramosa, C. ruprechtiana, or something similar.  We also picked up Cryptopleura in Pond A21 last year (September 2017), so it may be here to stay.
    Cryptopleura lobulifera:
    Cryptopleura ramosa:
    Cryptopleura ruprechtiana:
  • The thinner, lighter colored, and more tubular looking red algae is most likely some species of Gracilaria (aka: Red Gracilaria). I have mentioned before, gracilaria is very good food for some types of fish (people too). I noted sightings of this wonderful seaweed in our Lower South Bay trawls in October 2016 and September 2017 – so apparently, fall is its season.
  • The green stuff is clearly Ulva, or “sea lettuce.” We see ulva covering portions of the Ponds A19 and A21 mudflats during each warm season.  Ulva appears to tolerate being exposed to sun and wind for hours during low tides.


A better close-up of Red Gracilaria.


A new seaweed! Ceramium?  A new type of very fine filamentous red algae was collected at nearly all stations below Alviso Slough.  You can see it next to the fish in photos of longfin smelt, on the snout of the brown smoothhound, and with the anchovies further below.  It seems to be everywhere.  This is the same red algae noted at some stations in September as well.  Levi suggested to me that this new red algae may be a type of Ceramium   But, so far, I haven’t found an image of a species that exactly matches.


Baby Bay Pipefish in Ceramium.  A closeup of the mysid net jar shows a tiny goby and a longer Bay Pipefish, maybe about 3 centimeters long.  These fish probably simply got scooped up in the net along with the algae and everything else, but it suggests an intriguing possibility that Ceramium could be used as refugia.  If I were a baby pipefish, I would definitely conceal myself in this kind of material.



Longfin Smelt.  Jim Hobbs captured the first longfins of the season in October.  Three were caught on Saturday and two more on Sunday.  (My data tables show only two Saturday longfins.  This was my miscount that I hope to resolve soon.)  As expected adult longfins are returning to marshes and fresher water for spawning.  The arrival this early was a little unexpected because water temperatures at 19 to 20 degrees centigrade are a little warm for this fish.

Longfins are in trouble.  Other than Jim Hobb’s discovery of this breeding population of longfins in the Alviso Marsh Complex, most of the news about longfins in the Bay and Delta has not been good.  These fish suffer long-term population declines as seen in Delta Smelt and other pelagic fishes.  This Lower South Bay population offers a slim ray of hope that the fish will not be extirpated from the Bay for at least a few more years, maybe a decade or two with luck.

Even worse news:  The other disheartening news is that funding that supports UC Davis fish monitoring in Lower South Bay will run out by April or May 2019.  No new funding is in sight.   The Hobbs team will continue to be funded by California Department of Water Resources to monitor longfin smelt IN WINTER ONLY, but nothing else.

Too much of fisheries research specifically focuses on species or conditions only after the situation is dire.  And, by that time it is usually too late and impossible to determine what the ecosystem looked like when it was healthy.  … Then finger-pointing ensues, and another species heads toward oblivion.

I wish there was a better way!


Starry Flounder.  26 starrys were caught in October.  Like most of the others, this one was caught in the main stem of Coyote Creek (Coy3 station).  And, all the rest were found further upstream.  This was a particularly colorful specimen with tubercles indicating spawning readiness.


Plainfin Midshipman.  This single baby Midshipman was caught at station Coy4.

Midshipman versus Shokihaze.  As I was looking at the tiny Midshipman, I noticed how similar it looked to an equally young Shokihaze Goby.  Macro photography sees the clear differences in eyes, body shape, and belly color.  But, to the unaided eye in a tray full of fish, these two can be hard to tell apart.


Harbor seals.  As always, harbor seals watch as we pass by.  At least 9 of the eleven seals shown in this photo have the reddish cinnamon or ginger color that is claimed to be unique to seals in San Francisco Bay.  On the cuteness scale, these guys rank very close to ruddy ducks.


Brown Smoothhound.  This shark was caught at station Coy4.  Note the red Ceramium algae on the snout and in the tray.


“Anthuroidea” isopod!  As I turned over a piece of debris from the net at station LSB1, I noticed this creepy little worm-like creature, about one centimeter long.  I am always incredibly lucky to have one or more distinguished PhD fish biologists within arm’s length when I see this kind of thing.  Dr Levi Lewis immediately recognized that this is not a worm nor a larval insect, but rather a type of long skinny isopod.  I later discovered that long skinny isopods of the family “Anthuroidea” are numerous and common around the world.  Some species, like Paranthura japonica, are also widely invasive.

I do not know if this individual is native or, more likely, yet another San Francisco Bay invader.  I could have, and should have, put it in a jar with alcohol for later microscopic examination, but I didn’t.

General Anthuroidea information:

An interesting poster telling about invasion of Paranthura japonica into the Mediterranean:

This link has a very colorful photo documentary of many marine isopods.  It is in French, but I highly recommend you browse through it.  One thing that shocks me is the number of isopods that are fish parasites.  I often wonder if our local synodotea would, or could, predate or parasitize fish.  I think the answer is perhaps YES!


Northern Anchovies with red Ceramium from station LSB2.  I planned to say much more about anchovies, but I will save that for another installment.  A good case can be made that anchovies are the key indicator of ecosystem health here, and we know too little about them.


Returning duck hunters and happy dogs.  We came back up Alviso Slough in the afternoon much as we went out: with a steady traffic of hunting teams comprised of humans and dogs.  Many would judge this is yet another sign of a healthy functioning ecosystem as long as everything remains in balance.


Stay tuned for part 2:  San Francisco Bay Anchovies.


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