Fish in the Bay – 6 November 2016 UC Davis trawl – the upstream run

Report from Sunday trawling.  UC Davis Sunday trawls motor through waters east of the railroad bridge.

Fresher water fish and spawning fish looking for fresh to brackish nursery habitat are found on this side.  It makes sense when you think about it.  If you were a tiny ocean-going fish, would you want to hatch your clouds of young in the salty ocean full of hungry predators?  I don’t think so!  The winning strategy would appear to be moving up into water too fresh for predators to follow … somewhere with lots of tiny food for baby fish.

Bay-side trawls:

Upstream trawls:

A couple of observations right off the bat. 

  1. In the top chart, I blue fonted differences in top and bottom Dissolved Oxygen (DO), Salinity, and Temperature.  This demonstrates some water column stratification during low thru flood tides as salt water flows into Lower South Bay and Lower Coyote Creek.  Heavier salt water slides under less dense freshwater from Guadalupe River and Coyote Creek.  The top and bottom difference in salinity at station COY2 was 10 ppt!  Any large or small critter living near that location must tolerate a wide range of salinity or be able to move quick at least twice per day.
  2. Low DO. In the bottom chart (Artesian & Lower Coyote Creek), Dissolved Oxygen (DO) was below 5.0 mg/l at every station on Sunday, 6 November. It was mostly an overcast day, so the drop in sunlight probably cut the rate of photosynthesis from phytoplankton well up in to Coyote Creek and side sloughs.  Despite the low DO, fish appeared unaffected.  The highest number of anchovies on Sunday were caught at Station ART3 where DO was only 2.2 mg/l.   But, there was food – more about this later.

A side-note regarding ducks.  Before Hobbs & crew showed up on Sunday morning, I photo surveyed our SJ/SC RWF Biosolids lagoons for ducks.  Lower South Bay is the southern terminus for much of the migratory duck populations that use the Pacific Flyway, and this is the migratory season.  Lower South Bay marshes are a very important North American duck wintering location. Tens of thousands of them fatten up here for later spring and summer nesting in the prairie potholes of the Northern US and Canada. Dabbling ducks show up starting in the last week of August and the numbers increase as winter gets colder.  Diving ducks tend to arrive much later, mainly in December or by January.  Over previous two winters, I observed up to 15 dabbling and diving duck species on our Facility property alone. Below is a photo montage of duck species seen on Sunday, 6 November, before the boat arrived.  These were amongst roughly 2,000 ducks spotted.  Ruddy ducks are the only diving ducks represented so far.  The rest are dabblers.  As typical, shovelers far outnumber the other types in our freshwater ponds.

Duck numbers will continue to increase over the next few months.  Males are increasingly taking on their brightest colors as winter approaches.  Females seek attractive male ducks and bond in preparation for northern nesting.  (It’s counterintuitive to think of females as the instigators, but if you watch ducks much during this season, you will see females stalking males.  Males tend to act aloof and just look pretty.)

Coots, rail-related marsh birds, arrive early in the season with the shovelers.  They migrate at the same time as dabbling ducks, but don’t flock with them. Coots are not as flashy.

Jim Hobbs, Emily Trites, and Pat Crain arrived at our boat launch on Artesian Slough at 8:00 AM, ready for a day of trawling.

Oyster thief!  – see below.

Submerged Aquatic Vegetation.  I saw the weird rubbery green algae at least a year ago in the deeper Bay.  The nets caught small clumps of it at different stations on Sunday.  It is almost certainly a noxious non-native seaweed known as “Dead Man’s Fingers’” or “Oyster Thief.”  (  and )  We seemed to find lose fragments of the stuff sloshing along the bottom with the tide.  Literature indicates this green algae is not particularly good for anything.  It is also known as Oyster Thief because it has a habit of anchoring to oyster shells and floating them if they break loose.

The other red mystery “plant” was discovered the previous month in October in the Pond A21 borrow ditch.  It is a red algae.  From photos, it is very likely Red Gracilaria; a good nitrate absorber and can be a high quality fish food.  …  and!/2012/12/ipsf-tang-heaven.html .  People actually pay for the red stuff to feed their aquarium reef fish!  But, do any fish eat it in Lower South Bay?

Mossy Bryozoan – not vegetation! We pulled up clumps of Mossy Bryozoan at almost all stations, as normal.  These colonial animals are somewhat analogous to corals.  They live on the muddy bottom in clumps, possibly attached to rocks or plant material.  Once you wash the mud off, they are interesting to look at.  Each link in the branches or stalks contains a tiny filter-feeding zooid animal inside a leathery sheath. The bryozoa zooids consume phytoplankton and are in turn consumed by mollusks and crustaceans of various types. Bryozoans are so common they must serve as a significant component of the food web here.

Corophium.  Like mysids, corophium are so tiny that we tend to miss them.  But, when they are plentiful, the mud literally crawls with them.  An interesting web page that describes them as a keystone species on Bay of Fundy mud flats can be found here:  Keystone species??!!?!?  Who would have thought rice-grain-sized bugs could be so important?  They are important food for sandpipers on the mud banks at the very least.  A surprising variety of fish eat them too.

The steel deck was littered with corophium after Dr. Hobbs rinsed the net.


Anchovies.  At the third trawl location in Artesian Slough, we found fish.   You can see on the chart, 433 anchovies were netted here.  This was not as many as the 1445 pulled up the previous day in the middle of Lower South Bay, but still a respectable haul.  Most of this group look to be the “brown race” (presumably Bay-spawning) variety of anchovy.

At least a few “green race” (green-backed) anchovies were caught in this group.  The UC Davis group is commissioning genetic evaluations of these two types of anchovies to see if they really do represent two distinct groups.

Very low DO!  Dissolved Oxygen at this location was very low: 2.2 mg/l at bottom.  This was the lowest DO reading of the day.  As far as I know, no literature suggests that anchovies will tolerate, much less migrate toward, such low DO.  Why were they congregating here?  As Dr. Hobbs opened anchovy stomachs we seemed to find the answer.  Stomachs had corophium in them.

Anchovies eat corophium! At first look, this is puzzling.  Anchovies are filter-feeding fish. They swim with their mouths open to scoop up planktonic plants and animals:    Anchovies are not expected to burrow in mud looking for larger bugs like corophium.

We believe these hungry anchovies were attracted to swimming corophium.  But, corophium shouldn’t be swimming during daylight, especially when predators are near.  It appears that corophium are swimming to get a gulp of oxygen because DO is so low at the bottom.  The anchovies take advantage of the situation to frenzy feed.  I think of it as a “Robins after a rainstorm effect.”  Robins are attracted to grassy fields after rain because earthworms and other bugs must surface for air.  Wouldn’t fish respond to a similar situation in the estuary?  In any case, we can be certain that the anchovies were not attracted to the low DO.

Continued signs of spawning.  Dr. Hobbs examined a small selection of the anchovies for spawning readiness.  This requires evaluation of female egg sacks and male testes.  Rankings are given 1 to 5, with 5 being ready to spawn right now.  Of 15 anchovies examined this way, seven were ranked at spawning readiness “stage 4.”  The other eight fish were either too young to spawn or “spent” – had already spawned.

UC Davis researchers continue to confirm the conclusion drawn by McGowan’s egg and larval fish surveys that anchovies spawn in the Bay (Fishery Bulletin: Vol. 84, No. 4, 1986)  A related 1981 paper by Sally Richardson (Fishery Bulletin: Vol. 78, No. 4, 1981) discusses the three Northern Anchovy subpopulations, “Northern,” “Central”, and “Southern”, extending from Alaska down to Baja:  Richardson cites Hubbs 1925 as identifying the San Francisco Bay anchovy population as “a separate subspecies, E. mordax nanus …”

Huge schools of anchovies are sometimes seen along the California coast, like this one filmed off San Diego in 2014:

Anchovies are major consumers of plankton (and occasionally bigger things like Corophium).  Larval anchovies absolutely depend on tiny diatom and dinoflagellate phytoplankton for survival.  According to Reuben Lasker’s1978 paper, a larval anchovy has 1.5 days to find sufficient density of food particles around 50 micrometers in size.  If they don’t find sufficient tiny food, they die and recruitment can’t happen.  Like most fishes, anchovies graduate to bigger food as they grow.  Large masses of adults, no doubt consume large quantities of zooplankton, like copepods, or even bigger food, like corophium, and in doing so help keep those smaller phytoplankton consumers in check.  A healthy anchovy population may be an excellent indicator of a healthy Bay.

Two American Shad were caught on Sunday.  This is one of the non-native sport fish imported to California in the late 1800s.

Threadfin Shad.  Threadfins are also non-native, having been first introduced in San Diego County in 1953.  Threadfins are one of the four fish species noted for being impacted by Pelagic Organism Decline (POD) in the Delta.

Longfin Smelt.  The longfin is the California endangered species second after the Delta Smelt being threatened by POD.  The photo below shows a longfin caught on Sunday below an anchovy and a three-spined stickleback.  Despite his ragged appearance, this fish was alive and kicking as I took the photograph.  He swam away vigorously when I tossed him back into Coyote Creek.

Two Longjaw Mudsuckers were caught on Sunday.  The one shown below is displaying typical Mudsucker behavior out of water: gaping mouth with operculae spread.  He is maximizing the surface area of the buccopharyngeal chamber in his throat to absorb oxygen from the air.  Mudsuckers are gobids, and other gobies have this ability as well, but the Mudsucker is a particular air-breathing specialist.  The Wikipedia article mentions this breathing mechanism but does not describe it. .

According to Fishes: An Introduction to Ichthyology by Moyle and Chech, “At least 374 species of air-breathing fishes (49 families) have been described! (Graham1997). Almost all air-breathing fishes retain the ability to breathe water also and are categorized as bimodal breathers.”  The authors cite the American Mudsucker as making use of “modified areas of the mouth for aerial gas exchange.  In their discussion of fish species that have “evolved bimodal breathing capabilities to feed or escape predators by moving out of the water.”  Moyle and Check point out that air breathing comes at a price for a fish unless or until oxygen concentration in water goes very low:

“Kramer et al. (1983) determined that overall survival of [strictly] water-breathing fishes was significantly higher than that of bimodal breathers when exposed to a predatory green heron (Butorides striatus) when water oxygen levels approximated 20% air saturation … because of water-breathers’ superior ability to breathe hypoxic water, avoiding the water surface.  However, bimodal breathers’ survival exceeded that of the water breathers when the water held insufficient oxygen (ca. 6% of air saturation…).”

The Mudsucker had a Synidotea isopod clamped on his back.  I’ve mentioned Synidotea before, and they bear mentioning again.  Otter trawl nets scrape a chain across the mud bottom and pull up buckets full of these crawlies.  They are just a little larger and about as innocuous as sowbugs / potato bugs you see at home.  I have held many, and they don’t seem to be able to bite.  However, I have also seen many examples of a Synidotea clamping on a small fish so tightly that they have to be pried off.  Synidotea are mainly detritivores, but they are noted for also eating carrion.  Giant deep-sea isopods have been documented as being occasional predators and even eating live fish in nets.  I assume this tinier variety behaves the same.  In turn, many species of estuarine fish are known to eat Synidotea, at least occasionally.  Because there are always so many of them, I further assume Synidotea play a significant role in the Lower South Bay food web.

California Halibut.  Of the 11 halibut collected on Sunday, several were such tiny juveniles that it was difficult to tell if they were halibut or another flatfish species.  This portion of the Bay is the halibut nursery.

Starry Flounder.  Only two small Starry Flounder were caught on Sunday.  We saw a lot of them in 2013 and 2014, but not as many the past two years.  This pair is interesting: one is right-eyed, the other is left-eyed.  Like California Halibut, Starry Flounder can be either left or right-eyed on the California coast.  But, the same flounder species, on the other side of the ocean near Japan and Korea, is nearly 100% left-eyed.

Jim Hobbs continues to collect tiny organisms using the larval fish net and finer Clarke-Bumpus net.  The contents from these nets are initially preserved in formalin and Rose Bengal dye. The jars shown here are from the four Saturday surveys further downstream.  The larger jars generally contain larval fish and mysids.

The second jar from left shows results from the COY2 station just downstream of Pond A21.  Apparently there were a lot more mysids and critters at that location on 5 November.  The smaller jars hold copepod-sized organisms caught in the Clarke-Bumpus net.

I like to experiment with my macro lens to see if I can pick out any identifiable near microscopic life.  It quickly becomes impossible. I can see them, but I can’t identify them!

That’s all for now.





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