Fish in the Bay – January 2020: Part 2, More Winter Bugs & Fishes.

Full Moon and perihelion.   As mentioned in Part 1, we were experiencing the second or third highest-high tide of the year on Saturday.  Earth passes closest to the Sun in the first week of January.  The combination of new or full moon spring tides at that time makes for very high-highs in the day and low-lows at night.

This higher-high tide event allowed us to establish the elevation of what I call “Mud Island” that sits off the south shore of Lower Coyote Creek, just east of Alviso Slough.  This island was subtidal mudflat in the early 1990s, exposed only during the lowest-low tides.  Judging from this day’s tide, Mud Island’s elevation must be close to 9.4 feet NAVD; well above all but the year’s highest “king” tides.   


Predicted tide at 12:22 pm as shown on the Hummingbird depth finder display.

A good GPS unit would precisely establish Mud Island’s elevation.  But, we don’t have one on hand, so I used the tide.  Close enough for now. 


1. Longfin Alert!  – Spawning Longfin Smelt Again Caught on Camera.

Spawning Longfin Smelt!!  Once again, we caught a female Longfin extruding eggs.  As in recent years past, we found either milting males and/or egg extruding females between stations UCoy1 and UCoy2. 

Last year, we also captured a pair of spawning longfins at ALV1.  These locations are at lower creek marshes where freshwater meets the tides.  Longfins may spawn farther upstream as well, but we are again certain that they spawn here

In early 2018, UC Davis researchers also caught an egg-extruding female nearby in Artesian Slough, just 300 feet downstream of the San Jose-Santa Clara Regional Wastewater Facility discharge point, in early 2018, but that is another story confounded by the environmental benefits of tertiary treated wastewater!   

This is a Longfin Spawning place.

Also notice that spawning Longfin dorsal color becomes darker and emerald green (roughly Pantone 17-5641?).  The color change happens in both male and female fish.  I thought that this color change was caused by reproductive hormones.  However, in light of last month’s Shad Experiment, it is possible that low salinity alone might cause the darkening.  I will have to check with the UC Davis FCCL lab people to see what they think. 


2. Flat fishes on Saturday.

Baby Halibut and Speckled Sanddabs at LSB1.

Halibut and Sanddabs must also have been spawning out in the Bay recently.  Larvae and juveniles migrate upstream (south in this case) to recruit.


Speckled Sanddab – top.  California Halibut – bottom.


Baby Halibut closeup.  According to identification keys: the lateral line in California Halibut curves just behind the operculum.  In this photo, the lateral line bends sharply upward then arcs back downward toward the centerline of the body.


Halibut at LSB2: Slightly older, but still very young.

The Halibut total for January was 15.  This is still on the low side for LSB trawls. 


English Sole from Alv3 showing a nasty parasite infection (dorsal and ventral sides shown).

English Sole.  This was the only Sole caught.  Young English Sole should be swimming in from the ocean with cool winter temperatures.  Hopefully, we will see more soon.

Most of the Sole we catch here show conspicuous infections, like this one.

Reminder: as blog reported in January 2019, English Sole in Oregon have been documented as being infected by at least 29 species of parasites: microsporidians (fungi), nematodes, trematodes, acanthocephalans, leeches, and copepods, among others.  (See Fish in the Bay, Parasite Paradise –


3. Mysids and Fish that eat them in Artesian Slough on Sunday.

Levi shows off a large Striped Bass at Art1.  500mm!!  …  Almost 20 inches.

Striped Bass.  Our only Striped Bass caught over the weekend was caught first on first trawl on Sunday immediately downstream from the SJ-SC Regional Wastewater Facility discharge . He was a big one for us.  Striped Bass this size or larger easily outrun the trawling net.


California Halibut (top) and Starry Flounder (bottom) also at Art1.

Both Halibut and Starry Flounder were a little unexpected at this station.  Halibut are usually out in the Bay.  Flounder generally migrate up the main stems of the creeks.  These two probably took the Artesian Slough detour for the food. 


Handful of mysids at Art1.

Mysids = Fish Food.  As always, winter rains bring mysids.  But, there has been little rain over the past month.  Mysids congregate close to freshwater sources this time of year – like the Regional Wastewater Facility.  Then big fish follow.


A mysid casserole at Art1.

Mysids by the trayful.  Experienced aquarists know that live Mysids are the best food for most aquarium fish.  They are expensive if you can find them. 


Two Corophium amphipods from Art3.  Female with small arm-like antennae above.  Male at bottom.

Corophium amphipods; the other fish and bird food.  We found more Corophium farther downstream at Art3.  Corophium also seem more numerous in the cold wet season, but I don’t yet know much about their life cycle.  These mysid-sized bugs live in u-shaped mud burrows along the sides and bottom of the channel.  They probably taste like crab or shrimp like most crustaceans. 


Dr. Lewis shows off the smaller mysid catch from Pond A21.

It’s all about the food! (… and, the food chases the freshwater!)


4. Colorful Shad.

Aquamarine American Shad at Coy3.  Water was salty; about 24ppt.

I took many pictures of American Shad in preparation for the Shad Experiment.  The range of colors, from Aquamarine to Brown, and the correlation with ambient salinity is striking.


Brown American Shad in Pond A19.  Water was fresher at around 10ppt.


Threadfin Shad caught in Artesian Slough – two views of the same pair.

Threadfin Shad are smaller and deeper bodied cousins of American Shad.  Other than size, the two fish look very similar.  The Threadfin has a single black spot on each side and a long “thread” extending from the base of its dorsal fin. – We caught 19 Threadfin Shad in January.  This compares with 117 American Shad from the same trawls.


Three violet-brown Threadfin Shad compared against American Shad in the tray.

Threadfin dorsal color usually has a purplish or violet sheen where American Shad are olive or brown.  Until January weekend, I assumed that Threadfin color does not change.


This violet-brown Threadfin from Artesian Slough was exposed to higher salinity water in the Photarium.  It turned olive green! (Pantone 17-05305)  However, I did not carefully record the start color, salinity, nor time duration.  Result was rejected from Shad Experiment for lack of Quality Control.

However, on close examination Threadfin Shad dorsal colors appeared to roughly match those of American Shad at each station; from violet-brown through olive-green. I have not seen aquamarine Threadfins, and we rarely catch them at high salinity.  I doubt their colors range into blue territory.  But, you never know!


5. Anchovies

Blue and green Anchovies from three different stations.

The January Anchovy count was 33.  This is a record six-year low for a January, albeit January counts in 2017 and 2018 were in the 40s. 

As usual, adult anchovies colors were faded and ranged from blue to green.  Anchovy colors loosely correlate with salinity.  Unlike Shad, Anchovies appear to have “long-term color memory” or “low color plasticity,” depending on how you look at it.      


Baby Anchovies at LSB2.

Very young juvenile anchovies were also caught.  Those netted in high-salinity water in the deep Bay again tend to show a blue crown when color first develops. 


Juvenile Anchovy with a green crown from Artesian Slough.

This baby anchovy with a green crown was caught at a fresher water station.  Otolith (ear-stone) examination could determine the salinity of water in which this Anchovy was reared.  Perhaps someday soon we will read the history of these young fish simply by looking at the color in their crowns.


6. More Marsh Life.

Comb Jellies (Ctenophores) next to an Aquamarine American Shad from Pond A21.

203 Comb Jellies were caught in January.  Many of them were caught far upstream.  Once again, this is a clear reflection of lack of rain / high salinity.


Crangon Franciscorum with eggs.  Brooding Crangon!

Crangon franciscorum – brooding again.  The photo shows one of the many berried females we caught over the weekend.  This brooding event is much smaller than the one seen last year, but still a good sign.


American Avocets and Least Sandpipers feasting on Mysids & Corophium in Pond A19.


7. Historic sites.

Whitten Boat Shed as seen from Pond A21.

I learned from Ceal Craig that this barn was once the Witten Boathouse. 

(Note: The presentation, near the end, asserts that “too much freshwater is going into the Bay.”  This is INCORRECT!  This was a misperception from the early 1990s.  At that time, Regional Water Board and other agencies believed that Lower South Bay salt marsh habitat was in steep decline due to freshwater discharges. 

Over subsequent decades, it has become clear that local land subsidence and levee building from the 1930s through the late-1960s caused marsh disappearance.  After land subsidence was arrested around 1968, sediments slowly accumulated and new lands and marshes – like Mud Island! – started to appear.  Salt marshes fringing the Alviso Marsh Complex continue to expand.

Other than that small error, Ceal provides a great presentation about Drawbridge.)


Ritchie’s water tower and house. 

In it’s heyday, Drawbridge was supplied with water from a well at the Sprung Hotel.  When the well dried up, so did the town.  … Sinking land and nearby raw sewage discharge contributed to Drawbridge’s decline as well.

The old ghost town now mainly provides perches for Red-tailed Hawks as it dissolves into the restored marsh. 

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