Fish in the Bay – September 2021: Operation Guadalupe, Part 2.

Operation Guadalupe trawl stations.

Operation Guadalupe. Continued.  For this second installment, we examine some of the fishes in Alviso Slough and the lower (downstream) parts of Coyote Creek. 


Part II: Alviso Slough and Lower Coyote Creek results. 

Alviso Slough and Lower Coyote Creek trawls.

The map above shows the trawling sequence in Alviso Slough and Lower Coyote Creek.  As with Guadalupe Slough and LSB described in the previous blog post, a series of three 15-minute trawls were conducted at each station on four different dates between mid-August thru mid-September.  (15 minutes x 3 trawls x 4 dates = one hour of trawling time for each station.)

Results shown above are presented as Catch Per Unit Effort (CPUE).  Raw numbers were adjusted to be comparable to regular monthly 10-minute trawls (Operation Guadalupe total/6).  This gives an idea of fish density in terms we normally see.  In all other instances, raw unadjusted catch numbers are used throughout the rest of this blog.  


Summary of the most commonly caught critters during Operation Guadalupe.

These fish and bugs know where they want to be.  The above table is a rough reflection of critter preferences as quantified from Operation Guadalupe trawl results.

  • Alviso Slough had the highest number of Anchovies and Shimofuri Gobies.
  • The lower portion of Coyote Creek was off the chart for both Leopard Sharks and Palaemon Shrimp.



Alviso Slough was #1 for Anchovies

We found egg and milt-bearing Anchovies at all stations in nearly every trawl throughout Operation Guadalupe.  But generally, Anchovies were bigger and more colorful at downstream creek mouth stations.  The big ones were usually more numerous there.


One of the Big Mamas.  Dark and blue/green on top with very silvery sides.

Nutrients tend to accumulate where creeks flush into the estuary.  That’s where microscopic food production is highest. It is likely that spawning-ready Anchovies, particularly females with developing eggs, are targeting maximum protein wherever they can find it.   


More big and colorful Anchovies at Alv3.

Adult Anchovies migrate upstream from the North SF Bay and the ocean in summer. Their dorsal sides are deep blue or green as a result of recent exposure to marine salinity.


A mix of both large and small, young and old Anchovies at Coy3

For Alviso Slough, half the Anchovies were caught downstream at Alv3, and 20 to 30 percent were found at each upstream station.  The Anchovy distribution seems to be roughly similar for the main stem of Coyote Creek as well. 



A few of the largest Anchovies were documented at Coy3. 

  • Eggs were loose and watery, likely indicating not ready for release.
  • Or perhaps, eggs in the bigger females just always look that way.

I suspect females feed and stage downstream as they swell with eggs.  Then, they swim or drift upstream every several days as a new batch of eggs nears time for release.  But, this is based only on anecdotal observations and could be wrong. 

How will we document Anchovy spawning behavior here?


Two of the longest/oldest Anchovies.

It is important to note that total Anchovy numbers at each station were highly variable.  We caught a lot of them at station Alv3 on two of four dates, for example.  Then, more at stations Alv1 or Alv2 on the alternate dates. 

Anchovies are constantly swimming around, and they probably drift with the tide as well.


Rays and Sharks.

Bat Rays work here. East bank of Alviso Slough near Alv2.

Alviso Slough and Lower Coyote Creek host robust populations of Bat Rays.  At most times of year at low tide, we see pits and trenches in the muddy banks that are made by schools of Rays foraging here. 


Seven Bat Rays caught at Alv3 on August 29th.

Bat Ray pupping season continues.  All but a few of the Rays caught during Operation Guadalupe were babies.  Many were newborns.


Micah and Leticia measuring newborn Baby Bat Rays in Mud Slough.


Leopard Sharks, Coy3b, August 29th.

24 out of 57 Leopard Sharks were caught at Lower Coyote Stations (Coy1, Coy3, and Mud) during the month-long operation. 

  • All were babies at around one foot in length.
  • An additional, three Brown Smoothhound Sharks were netted at Coy3 on September 12th.
  • This area also had the highest concentration of shrimp, a common diet item for these sharks.



Another Leopard Shark at station Mud b on 29 August.



Lower Coyote is the Shrimp Capital of Lower South Bay.  We always catch the most native and/or non-native shrimp at stations along the main stem of Lower Coyote Creek in regular monthly trawls.  This was also true during Operation Guadalupe. 

The only anomaly is that Palaemon Shrimp (Palaemon macrodactylus) have overtaken the native Crangon variety this year. 

  • We presume that high salinity caused the abrupt crash in Crangon populations we observed after June.
  • Crangon will hopefully return for their upstream brooding migration from December through March.
  • That should be the same time that Palaemon die back or go dormant during the cold season.  


Some of the 2250 Palaemon Shrimp at Coy3c on August 29th.

Regardless of species, these shrimp feed the sharks and other big fishes that live here.


Shimofuri Gobies.

Alviso Slough has the dubious honor of hosting the most non-native Shimofuri Gobies – by far.  We first noticed the Shimofuri population explosion at Station Alv1 in early August and it continued throughout Operation Guadalupe. 

Until this year, Shimos were just a minor presence amongst the several species of gobies we count.  Then in August, KABOOM!  We began collecting hundreds to thousands of them at the upstream end of Alviso Slough.  Where did they come from?  Why at this station?  Why now?   


Shimofuris ultimately came from North-East Asia.  They are the most attractive of the three “Tridentiger” goby species we have here: Shokihaze, Chameleon, and Shimofuri Gobies.  (“Tridentiger” means triple-toothed as a reference to the tricuspid teeth that distinguish this family of gobies.)

  • Shimos were first seen in San Francisco Bay in the late 1980s.
  • They have been common but not particularly abundant here in Lower South Bay for at least several years.
  • All of the sudden, they became overwhelmingly abundant at Alv1 in August.  
  • What impact will they have on our spawning native fishes?


Other common and not so common species encountered.

Prickly Sculpin.  Three Pricklys were counted in Alviso Slough and four more in Upper Coyote during Operation Guadalupe.  

  • Usually, Pricklys disperse from the creeks and show up in our nets as a result of rain and creek flushing.
  • Seeing any of them in August when there had been no rain was an unexpected surprise.


Two Oregon Mud Crabs at Alv3c.


White Croaker.  This was the first adult White Croaker (aka “Kingfish”) we have seen in ten years of trawling!  They were a common fish in Lower South Bay at least through the 1980s.  We have caught a few to several baby White Croakers in each of the last few years in springtime.  Are White Croakers returning?  And, why did this native fish disappear from Lower South Bay in the first place?

  • I am of the opinion that the near-complete loss of marsh habitat in earlier decades might have ultimately extirpated the Croaker from this area. If so, this could be a very good sign for restoration.
  • Croakers are members of the Sciaenidae family of fishes.   


Tires!  As a result of the expanded monitoring regime, the UC Davis crew picked up many tires.  Tires and concrete chunks are often picked up when new stretches of slough are trawled.  From visual inspection, these tires appear to have been here since at least the 1980s or earlier.


Red Algae Watch.

Red Gracilaria found in Mud Slough.

Red Gracilaria.  We found a few sprigs of Red Gracilaria in Mud Slough and a few other locations during Operation Guadalupe.  It is an edible and beneficial red alga according to all I have read.   

In contrast, Red Ceramium, the other more hair-like red algae, continued to clog nets farther downstream.  So far, all species of red algae that we encounter appear in mid-to-late summer and completely die back in winter.


Two new critters continue to show up.


Enosima Aeloid (Sakuraeolis enosimensis).  This nudibranch is probably native to East Asia.  We saw our first one in May or June.  Then, we caught at least 2 or three more of these during Operation Guadalupe.  For better or worse, this is our new nudibranch in Lower South Bay. 



Diadumene franciscana, or D. lineata anemones.  At least a few more of these tiny anemones were spotted in Alviso, Coyote, and Mud Sloughs.  Some were orange, others were green. Some were round-bottomed and detached.  Most attach themselves to shell, or plant material.

Until this year, we only found these at LSB stations in the Deep Bay.  Now, they are at nearly all stations.


Summary Tables.

Operation Guadalupe – Alviso Slough trawling results.

Alviso Slough Results.  A few overall trends here were also typical in all slough segments:

  • Palaemon Shrimp were more numerous at downstream (saltier) stations.
  • Corbula Clams were usually more numerous upstream in other sloughs. But, this trend is not seen in Alviso Slough, and very few Corbula were caught here.
  • Anchovies were generally more numerous near the downstream creek mouths, but they appear to drift up and down each slough segment at random.
  • This dry summer, or something, decimated Crangon shrimp. And, at the same time, Palaemon shrimp population has exploded.

A Shimofuri Goby population explosion near station Alv1 was first observed in early August and it continued throughout Operation Guadalupe.  In 10 years of trawling, we have never seen Shimofuri numbers like those shown above.


Operation Guadalupe – Lower stem of Coyote Creek trawling results.

Lower Coyote Slough Results. Similar trends: 

  • Palaemon shrimp congregated at downstream stations,
  • Corbula Clams tended to be upstream, and
  • Anchovies varied from few to many at each station in the main stem.


A Great Blue Heron takes flight near Alv3.

Years of trawl monitoring are bringing the underwater critters of Lower South Bay into sharper focus.

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