Fish in the Bay – Special Report: Lower South Bay Broodstock Trawls, Jan 2025 – Return to Oz.

Longfin Smelt Broodstock trawls continued over numerous days through January, February, and even into the first weeks of March. 

• I only attended three of the events: one in Suisun/Grizzly Bay and two more in our home territory of Lower South Bay.

The other UC Davis crew members were Broodstocking over the entire period. (https://www.ogfishlab.com/people/)   The UC Davis OGFL team ultimately achieved this year’s goal of collecting over 1,000 reproductive Longfin Smelt adults for breeding in university labs.

This report describes the Broodstock effort in Lower South San Francisco Bay (LSB) on 22 & 23 January. 

This was just a month after I had participated in similar trawls in Suisun Bay.  The difference felt stark.  Suisun Bay was comparatively cold, colorless, and gray.   https://www.ogfishlab.com/2025/03/10/fish-in-the-bay-special-report-suisun-bay-broodstock-trawls-december-2024/ 

Daybreak in Mud Slough, 23 Jan 2025.

The contrast between Suisun and Lower South Bay was like jumping from sepia-toned Kansas into the Technicolor ‘Land of Oz.’  It was good to be back home.

• The impression could have been accidental: an overcast day in Suisun versus a sunny day in LSB.
• Or more than coincidence?
  • I suspect sunny days are much more common in LSB due to the rain shadow effect from the coastal mountains.
  • Water was a degree or two warmer in this South Bay tidal lagoon.
  • Green water suggests that food production is high here.

All that aside, there were vastly more fishes and more bugs of various types in LSB. (Striped Bass were a notable exception).  LSB is a fish and bug wonderland. 

Sami searches for Longfin Smelt in the net full of Clupeiforms from trawl #9 on 22 Jan 2025.

All Broodstock trawls are 5 minutes in duration using the same equipment and protocols.  Thus, trawl results in Suisun and LSB are reasonably comparable. 

• 13 trawls were conducted in Suisun on 18 December – versus:
• 14 and 15 trawls in LSB on 22 and 23 January.

Results are discussed below …

1. Colorful Clupeiforms.

Anchovy count = 286 downstream / 32 upstream in LSB – versus ZERO in Suisun Bay.  Anchovies were the overall most numerous fish in LSB.  As should be expected, they were most numerous in saltier downstream waters.  Low salinity may also explain why we found no Anchovies in Suisun / Grizzly Bay Broodstock trawls on December 18th.

Pacific Herring count = 5 downstream / 2 upstream in LSB – versus ZERO in Suisun Bay.  The explanation is the same as above.  Both Herring and Anchovies often spawn in low salinity water.  And, both fishes migrate to saltier waters fairly quickly after spawn.    

Green and brown Shad at UCoy1 on 23 Jan 2025.

American Shad count = 14 downstream / 57 upstream in LSB – versus 1 in Suisun Bay.

Threadfin Shad count = 26 downstream / 102 upstream in LSB – versus 10 in Suisun Bay.

We were experiencing a “Shaduary” Shad explosion in January and February.  We still do not know why their populations peaked this year.  Shad migrate to fresher water each winter. 

• Roughly four times more Shad were caught at upstream versus downstream stations in LSB. (This seems to beg a question: why so few Shad in Suisun/Grizzly Bay?)    

2. Longfin Smelt.

Longfin Smelt count = 64 downstream / 78 upstream in LSB – versus 12 in Suisun Bay.  Most Longfins in LSB were caught near the railroad bridge, e.g. at stations Coy 1 and Coy2.  This is NOT the typical distribution.  

Lack of rain in December and most of January seems to have disrupted Longfin spawning habits.  Usually, females and juveniles stage in restored ponds A19 and A21 and farther downstream in Coyote Creek.  Instead, we found most Longfins loitering in a narrow segment of Coyote Creek in the middle of the main stem.

Overall, Broodstock collections on 22 and 23 January were fairly successful: 13 reproductive Longfins were taken at downstream stations and another 24 were picked up upstream.  This compares with only four (4) Longfin breeders from comparable trawls in Suisun Bay on December 18^th.   

However, once again, Longfin distribution and total numbers were disappointing:  Only two males and two females of sufficient breeding readiness were collected near upstream spawning grounds at station UCoy1 on January 23^rd.  This same location had been a prime male Longfin staging place for spawning in recent years. 

• Water quality data indicated that Coyote Creek salinity may not have dropped low enough to trigger much male Longfin staging this year.
• Literature says Longfin spawning success is strongly tied to robust rainwater flushing.
  • Lewis et al. (2019). https://pmc.ncbi.nlm.nih.gov/articles/PMC9285352/
    “Postlarval recruits (Fig. 2d) were also observed in April–May of 2017 and 2019, with each of these years characterized by anomalously high precipitation and freshwater outflow (and persistent low‐salinity spawning and rearing habitat). Thus, the potential for spawning was apparent in all years, whereas recruitment success appeared to be limited by freshwater outflow, …”
  • Rahman et al. (2023).  https://onlinelibrary.wiley.com/doi/10.1155/2023/9984382#:~:text=Here%2C%20we%20found%20that%20longfin,was%20highest%20at%20lower%20salinities.  “Eggs that were fertilized in freshwater (0.4 ppt) exhibited a significantly higher fertilization rate (81%) than those fertilized in brackish water (62% at 5 ppt), …”

3. Some brown bottom fishes.

Speckled Sanddab with two Threadfin Shad & various shrimp at Coy1, trawl #12 on 23 Jan 2025.

Speckled Sanddab & English Sole count = 1 each in LSB versus ZERO in Suisun.  However, in fairness, two Starry Flounder were caught in Suisun on Dec 18^th versus no Starries in LSB.

Unlike regular monthly fish monitoring, Broodstock trawls are optimized for catching Longfins: trawls are operated to minimize collection of unwanted bottom critters.  Consequently, flatfish catches were relatively low in both Suisun and LSB.

Shokihaze Goby count = 1. – versus 1 in Suisun. Judging from the swollen head and puffy cheeks, this is likely a male Shokihaze in his spawning season display.  We have seen a number of small ones over the past year, but few large adults until now. 

California Halibut count = 2 downstream / 4 upstream in LSB – versus ZERO in Suisun Bay.  As almost always, we caught young Halibut in LSB.  

• Nursery habitat for native Halibut is a major ecological service that LSB provides.

4. Wicked Witches!

Silversides and Shad at UCoy1 – trawl #10 on 23 Jan 2025.

Mississippi Silverside count = 246.  Non-native Silversides were present at four upstream stations in LSB.  We caught a lot of them in Pond A19 and at UCoy1 where we normally expect to find spawning Longfin Smelt.  This continues to be a very bad sign.  Silverside populations are a threat to our spawning Anchovies, Herring, and Longfin Smelt.  They should be controlled.

Good News?  We saw ZERO Silversides in the Suisun/Grizzly Bay trawls.  However, since Silversides tend to congregate in upstream dead-end sloughs, it is likely we were simply not trawling in the right place to catch them there.

Striped Bass count = 2.  From a combined total of 29 Broodstock trawls in LSB on 22 & 23 January, we caught only two baby Striped Bass! 

Compare this to the 43 mostly adult Bass that were netted from 13 trawls in Suisun/Grizzly Bay on 18 December.  A Sacramento Pikeminnow was also picked up in the Suisun trawls.

• Absence of these voracious predators could partially explain why we find so many Anchovies, Herring, Shad, and Longfin Smelt in LSB.
• From a small pelagic fish’s point of view, non-native Striped Bass are Wicked Witches of the East. Pikeminnows are Witches of the West.  (Or maybe they are flying monkeys?)

5. Emerald City: Bottom-up productivity!

Green water.  We were experiencing neap tides a few days after “third Quarter Moon” in January.  (3Q+1 & 3Q+2)   Slower moving water during neap tide reduces the amount of sediment that gets resuspended.  Water becomes clearer.  The green glow of phytoplankton stands out as the sediment settles.  (Yes.  Water color changes in response to moon phases here!)

Green is good.  Tiny bugs graze on billions and billions of single-celled plant-like organisms that feed on sunlight.  Small fishes eat tiny bugs. 

Crangon shrimp = bigger bugs for bigger fishes.  Large numbers of brooding Crangon females full of eggs were found in the main stem of Coyote Creek between stations Coy1 to Coy4.  – versus relatively few Crangon in Suisun and no brooders.

White Sturgeon count = 10 spotted on sonar + one seen jumping.  Sturgeon were also lurking near the middle section of Coyote Creek.  Shrimp and small fishes are a wintertime smorgasbord for big Sturgeon here. 

We did not see any Sturgeon on sonar in Suisun on Dec 18^th, but that was likely just a matter of where we were trawling.  Large numbers of Sturgeon have been observed in Suisun/Grizzly Bay sloughs at other times in the past.  It is presumed that North Bay hosts a much larger Sturgeon population than LSB.

Dorothy awakens: “But it wasn’t a dream.  It was a place. … this was a real truly live place.  I remember that some of it was not very nice, but most of it was beautiful … But anyway Toto, we’re home!
… There’s no place like Home!”

Music – 1981 – Austin City Limits – Willie Nelson – Somewhere Over the Rainbow  https://www.youtube.com/watch?v=2jfWrbvmPdg