Fish in the Bay – Special Report: Suisun Bay Broodstock Trawls, December 2024.

I accompanied the UC Davis crew on a “Longfin Smelt Broodstock” trawling expedition in north San Francisco Bay in December 2024. 

Longfin Broodstock background:  For several years, the UC Davis “OGFL” team has collected adult Longfin Smelt to serve as “Broodstock.  The ultimate goal is to cultivate self-sustaining Longfin populations in university laboratory aquariums as a hedge against possible extirpation or extinction of the species. 

• Difficult, but not impossible. The UC Davis Fish Conservation and Culture Lab (FCCL) in Byron California perfected raising of Delta Smelt from broodstock some years ago.  https://fccl.ucdavis.edu/ 
• This blog post from 2020 described the Longfin Smelt Broodstock project at that time. https://www.ogfishlab.com/2020/12/20/fish-in-the-bay-december-2020-the-longfin-chronicles-part-1/

This report describes some of the fishes, bugs, and plants encountered in the far north of the Bay.

Brave new world:  Suisun Bay is roughly 60 miles north of “Lower South Bay” (LSB).  The extreme northern and southern ends of SF Bay are very different:

• North Bay / Suisun Bay functions as a “River Dominated Estuary / Salt-wedge Estuary. The Sacramento and San Joaquin Rivers drain almost 40 percent of California’s total land area.  A huge volume of freshwater flows through the delta system and Suisun Bay on its way to the ocean.
• Lower South Bay is a “Tidal Lagoon.” Various creeks and rivers drain into LSB, but they are all tiny compared to the rivers in California’s Central Valley.  Freshwater entering LSB sloshes back and forth with the tides for up to a month or more (on average) as it slowly oozes its way northward up SF Bay and outward to the ocean.
• See: Conomos et al (1985) https://www.usgs.gov/publications/environmental-setting-san-francisco-bay  “San Francisco Bay, the largest bay on the California coast, is a broad, shallow, turbid estuary comprising two geographically and hydrologically distinct subestuaries … The northern reach is a partially mixed estuary dominated by seasonally varying river inflow, and the South Bay is a tidally oscillating lagoon-type estuary.” 

A few caveats: 

1) We call these “Suisun Bay trawls.”  However, we were technically in “Grizzly Bay” which is a northern lobe of Suisun Bay. 

2) We also say we were in “Suisun Slough” even though the trawls were conducted between the mouths of Montezuma and Suisun Sloughs.  (A bypass channel was carved between both sloughs decades ago.  The sloughs exchange water below the bypass.)  See map above for clarification.

Fishes and Bugs.  The table summarizes one day of sampling in North Bay in mid-December. Salinity at all stations was low by LSB standards: around 4 ppt.  Each trawl was short in duration; just a few minutes as opposed to 10-minute trawls for regular LSB fish monitoring surveys. 

1. Familiar Fishes & Bugs.

Bad News?  Non-native fishes predominated. 

• Striped Bass were the number one fish by far. 43 Bass were caught and released over the 13 trawls on Dec 18th.
• Threadfin Shad were number two. 10 were netted over the morning.
• No Anchovies, Halibut, or Herring were caught! Monthly upstream trawls of LSB over the same period caught many individuals of all three native species.   — But keep in mind, trawl durations, depths, and spatial distributions were targeted on collecting Longfins.  This was NOT intended to be a representative survey of Suisun/Grizzly Bay fishes and bugs.   

Bugs:

• Native Crangon and non-native Exopalaemon shrimp were collected in equal numbers. This could suggest that this area does not support robust Crangon recruitment.  (In LSB, we continue to catch more Crangon per Exopalaemon at these levels of salinity.
• No Palaemon shrimp (Palaemon macrodactylus). Absence of Palaemon was probably due to low salinity.
• Corbula Clams! Corbula were collected at 8 of 13 stations.  This is not good, but also not unexpected.  These ecosystem-destroying clams inhabit a narrow range of salinity in SF Bay.  Unfortunately, the geographic extent of this brackish range is large in Suisun Bay.  Corbula are squeezed into a much smaller area in LSB. 

A Longfin Smelt caught at Trawl #3.  

Longfin Smelt were the number three fish of the day.  Twelve Longfins were caught.  Four were deemed suitable for collection as Broodstock specimens.  All the rest were released with minimal handling.   

Other familiar fishes included: 9 Yellowfin Gobies, 2 Starry Flounder, and 1 Shokihaze Goby.

2. Unfamiliar Plants.

Submerged Aquatic Vegetation. Underwater plants are very different in this river-dominated estuary.  We never see these green plants in LSB. 

Left panel above: Elodea / Brazilian Waterweed is non-native. 

• This was a common freshwater plant sold in tropical fish aquarium stores when I was young. “… Elodea densa is a popular aquarium plant, but is no longer sold in some areas due to its invasive potential.”
• Elodea was also a standard specimen presented to middle school students for microscopic examination of plant cells in the 1970s and 1980s. I vaguely recall looking at Elodea cells in my 9^th grade school microscope.    

Elodea escaped and invaded the Sacramento / San Joaquin Delta system decades ago. 

• USFWS – Brazilian Waterweed (Egeria densa). Ecological Risk Screening Summary: https://www.fws.gov/sites/default/files/documents/Ecological-Risk-Screening-Summary-Brazilian-Waterweed.pdf “From Swearingen and Bargeron (2016): “This plant was first introduced into the United States in the late 1800s as an aquarium plant.”
• Wikipedia – Elodea densa: https://en.wikipedia.org/wiki/Elodea_densa 
  “Elodea densa, the large-flowered waterweed or Brazilian waterweed, is a species of Elodea native to warm temperate South America in southeastern Brazil, Argentina, Chile, and Uruguay.  It is considered a problematic invasive species due to its use in home aquariums and subsequent release into non-native ecosystems.”  
  • Invasive species: “Elodea densa has escaped from cultivation and become naturalized and invasive in many warm temperate to subtropical regions of the world … In the Sacramento-San Joaquin Delta  of California, it was introduced in the 1960s and has since had a significant adverse impact on the local ecosystem. The plant currently infests 2,400 ha (5,900 acres), or 12% of the total surface area of the delta …”

Right panel = Mystery weed.  I am not familiar with this aquatic plant.  If anyone knows the identity, please send comments.

Other algae and plant-like organisms under the water.

• Filamentous green algae is occasionally found in upstream sloughs of LSB – more often in Artesian Slough than anywhere else.
• Mossy Bryozoan is a colonial animal, sort of like soft coral. We regularly find clumps of it at upstream stations in LSB:  Alv1 in Alviso Slough and UCoy2 in Coyote Creek.  The presence of it at the mouths of Suisun and Montezuma Sloughs indicates that conditions like salinity and food availability are similar here. 

Dense stands of Phragmites or “Common Reed” (Phragmites australis) line the edges of Suisun Slough just upstream of the Broodstock trawling locations.   

• This plant is known to be present in most counties surrounding San Francisco Bay: https://www.calflora.org/app/countytaxon?crn=6465.  However, it has been rare or absent where we trawl in LSB.  We have only recently noticed a few small patches of tall reed with feathery tassels popping up in Pond A19.  It looks to be the same plant.   Perhaps, “Common Reed” is now starting to spread in LSB as well?
• Wikipedia: https://en.wikipedia.org/wiki/Phragmites_australis 
• Suisun Marsh Vegetation Guidebook: https://suisunrcd.org/wp-content/uploads/IMPappendices/AppendixR/Appendix-R-Key-Wetland-Plants-and-Growth-Requirements.pdf 

3. New Fishes.

Sacramento Splittail.  Six Splittail were caught and released. 

I was very interested to see this fish.  According to reports, this fish was last seen in LSB, specifically in Coyote Creek, in 1980.  … 

• Wikipedia: https://en.wikipedia.org/wiki/Sacramento_splittail  They were once caught from southern San Francisco Bay and in Coyote Creek (Santa Clara County) but are now restricted to the Sacramento Delta, Suisun Bay, and the lower parts of Sonoma Creek, Petaluma River, and Napa River.  
• UC Davis, California Fish Website. https://calfish.ucdavis.edu/species/?uid=83&ds=241  “Sacramento splittail are hearty minnows that live in fluctuating environments and can tolerate relatively high salinities and low oxygen levels (< 1.0 mg/L). Typically they are found in estuarine environments and are commonly found in water with salinities from 10-18 ppt.”
• Splittail need seasonal floodplains for feeding and spawning. Loss of floodplains eventually doomed the population that once lived in Coyote Creek!

Food for thought:  Should we consider bringing Splittail back to Coyote Creek in Lower South Bay?

• Since 1980, at least a few hundred acres of brackish marsh areas have been restored in Coyote Lagoon, Coyote Bypass Channel, and Pond A19. Could these restorations be sufficient to again sustain a small Splittail population?
• Native versus non-native fishes. In the absence of Splittail, non-native Shad, Shimofuri Gobies, and other non-native fishes have been taking over.
• Minimal cost: Several healthy adult Splittail from San Pablo Bay shipped in two or three 5-gallon buckets + battery aerators is all that would be needed.

Sacramento Pikeminnow.  One Pikeminnow was netted on our tenth trawl.  This native ‘freshwater barracuda’ is never seen in LSB.  Pikeminnows are voracious predators that eat almost any smaller fish or bug, including Salmon and Steelhead.  For that reason, Pikeminnows are not particularly desirable.  (Ironically, non-native Striped Bass still remain desirable?) 

• Fun fact: Until 1998, this fish was called the “Sacramento Squawfish.”  The old name was abandoned because, frankly, the old name was insulting to both humans and the fish. 
• Wikipedia – Sacramento Pikeminnow: https://en.wikipedia.org/wiki/Sacramento_pikeminnow 
• UC Davis, California Fish Website. https://calfish.ucdavis.edu/location/?ds=694&uid=113 

4. Eagles!

Bald Eagles nest here!  We spotted a Bald Eagle adding material to his/her nest in a tall Eucalyptus tree off the east bank of Suisun Slough as we motored down to our trawling site.  This bird did not exist here when I was young!

• Bald Eagles in California https://wildlife.ca.gov/Conservation/Birds/Bald-Eagle    “By the late 1960s and early 1970s, when the bald eagle was listed as an endangered species, fewer than 30 nesting pairs remained in California–all in the northern third of the State.”
• Bald Eagles have been present in Suisun marshes for almost 20 years now.  https://suisunwildlife.org/eagle2008.html 

Another nest?  On our return trip up Suisun Slough, we spotted another (???) pair of Bald Eagles.  They were perched in tall trees far south of the nest we observed earlier in the morning. 

• Are these the same eagles? Or a different pair?
• They gazed at each other from opposite trees. There is no doubt they were a bonded pair.  They were probably shrieking love songs at each other, but given the distance and the hum of the boat motor, we could not hear their vocalizations.    

We have our own pair of Bald Eagles in LSB.  They first arrived and built their nest at Curtner Elementary School in Milpitas in late 2017.  Several chicks have hatched and fledged since then.  https://www.youtube.com/watch?v=nZ99DMX3A5E

Yes – Roundabout Lyrics  https://www.youtube.com/watch?v=on5t06ExbBc

“Catching the swirling wind the sailor sees the rim of the land,
The eagle’s dancing wings create as weather spins out of hand.”