Fish in the Bay – March 2025, Part2. Bottom fishes & bugs

As often happens, there was no room for discussion about bottom fishes and bugs in Part 1 of the March report.  The list of loose ends is long. 

1. Flatfishes.

California Halibut count = 16.  Halibut numbers fell a bit in March but still remain higher than what we typically see in most non-El Nino years.

• Fun Fact from Bruce Herbold’s Facebook post a few days ago: “Haly butte” is Old English for ‘holy fish’ and the Atlantic Halibut is a big flatfish that European Catholics preferred for Lent and holy days.”

English Sole count = 13.  English Sole are almost an “anti-Halibut.” 

• When English Sole numbers are high, Halibut counts tend to drop; and vice-versa.   
• English Sole recruit best in cool La Nina years; Halibut populations boom during warm El Ninos.
• English Sole spawn in coastal waters; Halibut spawn right here in the Bay.
• English Sole feed on small bottom-dwelling invertebrates; Halibut are ambush predators of pelagic fishes.

More fun facts from Bruce: 

1. The original British name for a similar looking flatfish was “Sole” … “cuz they look like the sole of a shoe.”
2. They are sometimes called “slime soles” …”
3. We can attest to fact #2 above … These baby Sole exude a lot of slime. We try to measure and release Sole quickly because their slime production makes the fish counting process rather icky.  Eventually Sole slime starts to suffocate other fishes in our measuring trays.  

Starry Flounder count = 2.  Only two Starry Flounder were caught in March.  These look to be young adults, possibly part of the population explosion we observed in mid-2023.  

• According to Kathy Hieb in an email from 2018: “Starry Flounder rear in the estuary for up to 4 years, with older fish found at higher salinities than the younger … The population declined substantially in the mid-1980s. We believe that most Starry Flounder now spawn in the ocean.”
• Overall Starry numbers in SF Bay, Monterey Bay, and Puget Sound are all way lower compared to catches in the 1980s. Some possible factors: 1) Population increases of seals and sea lions.  2) Decreases in freshwater flows to estuaries. 3) Estuarine habitat loss.

2. Gobies

Baby Goby count = 76.  Technically, these were all “Unidentified Gobies/Unidentified Larval fishes.”  Most were baby gobies.  Only a few were long skinny baby Clupeiforms or Smelt.

• These were early arrivals for our springtime baby fish bonanza.
• April is “Traditional Baby Fish Month” which is mostly fueled by hundreds to thousands of baby Yellowfin Gobies and Arrow Gobies.  
• Springtime is a general baby fish season which often includes baby Anchovies, Herring, Topsmelt, Striped Bass, and others.

Yellowfin Goby count = 20.  Fewer but larger Yellowfins are usually seen a month or two before the explosion of babies.  These are a few of the emaciated males and spent females who invested their energy to produce the next generation.

• Yellowfins are semi-catadromous – males swim a short distance downstream to stage for the spawn, females follow shortly after.

Shokihaze Gobies & Staghorns at Alv2, 2 March 2025.

Shokihaze Goby count = 27.   The Shokihaze rebound continues.  They declined severely after May 2021 as Shimofuri Goby numbers exploded.  Then, the situation reversed after July 2024: Shokihazes are up, Shimos are down!

Shimofuri Goby count = 20.  The Shimofuri population exploded up to hundreds per month in 2021. Then, it dropped sharply back down to a few dozen or less in 2024.

• Where did all the Shimos go? Will the population explode again?  

Chameleon Goby count = 5.  Chameleons are salty water close cousins of Shimofuri Gobies.  We almost always find them at LSB stations where salinity is higher.  By genetics and appearance, the young of both species are almost indistinguishable.  … Always remember:

• If salinity is above about 20 ppt, the fish is probably a Chameleon Goby. Dorsal and anal fins will have a red band.  The Japanese name for this goby is “Akaobi” – literally, “Red Band Goby.”
• If salinity is below 20 ppt, it is likely a Shimofuri. Dorsal and anal fins will have an orange margin. 

3. Corbula Clam Explosion & other Bad Bugs.

Corbula clam count = 5,860.  This is the highest monthly Corbula count we have seen since September 2012. 

• The vast majority of Corbula were scooped up in Alviso Slough.

Corbula size trend.  These clams tend to be biggest and probably most reproductive at relatively low salinity locations.

• We always find the biggest Corbula in the river channels where salinity generally ranges around 5 to 8 ppt.
• They get progressively smaller and younger farther downstream where salinity rises much higher.

Keep in mind – Salinity varies tremendously twice per day – with each sweep of the tide.  Nonetheless, big reproductive adults are reliably collected near stations UCoy1 to Coy1 on Coyote Creek and at upstream stations Alv1 to Alv2 in Alviso Slough.

Corbula size hypothesis:  Corbula amurensis (Amur River clams) tolerate a wide range of salinity at all life stages, but they rarely reach a ripe old age in the saltier water here. 

• The clams spawn at brackish upstream river locations. River currents wash Eggs, sperm, gametes, and free-swimming veliger larvae downstream.  Veliger larvae settle on the bottom about three weeks after fertilization.
• We consistently find smaller recruits at downstream stations, but mature adults are scarce downstream. The survival rate of young Corbula must be low at higher salinity locations due to predation and competition with other species.   
• Thompson (2010) Corbula amurensis Conceptual Model. https://www.vliz.be/imisdocs/publications/380118.pdf
  “If conditions allow the estuarine amphipod Ampelisca abdita or some other surface tube-dweller to invade, we see a threshold effect on the Corbula recruits as was seen with adult Corbula.  Nichols and Thompson (1985) reported a similar relationship between the bivalve Macoma balthica (now recognized as M. petalum) and A. abidita in the southern estuary. Although high abundances of adult Corbula can co-occur with A. abdita, recruits appear to be limited either by the flow disturbance of the tubes (Friedrichs et al. 2000) or the feeding activities of the suspension-feeding amphipod (Figure 8b).  … predators on juvenile Corbula include demersal fish, diving ducks in the shallow water, shrimp, and the exotic opisthobranch Philine auriformis in the more saline portion of the estuary (e.g. San Pablo Bay, Gosliner 1995).”

We can learn to control this pest!  Removal of adult Corbula clams from their spawning beds could be a sound management strategy. 

• At the very least, we must be careful not to inadvertently disperse and propagate Corbula clams as we sample from station to station in the Bay.

Other not-so-good bugs. 

• As expected, Atlantic Oyster Drills returned after an absence of several months. Seven were seen at LSB stations.  As their name suggests, they are predators of other mollusks.  Bad News: they are a major obstacle to restoring native oysters to San Francisco Bay.  Good News: they probably predate non-native Corbula clams and Musculista mussels as well.
• Eastern Mud Snails are always present. They replaced native California Horn Snails in most of SF Bay long ago.
• Tunicates are a mixed blessing; sometimes beneficial filter-feeders, sometimes fouling nuisances. We find only non-native Mogula manhattensis in Lower South Bay.  
• Japanese Littleneck Clams (a.k.a. Ruditapes philippinarum, Tapes japonica, or Manila clams). They are sold in Bay Area supermarkets. According to Wikipedia, these clams are “the second most important bivalve grown in aquaculture worldwide.”  (Maybe these clams are good bugs?)  https://en.wikipedia.org/wiki/Ruditapes_philippinarum  

4. Good Bugs.

Shrimp.  Shrimp counts were low in March, but Interestingly we found gravid females (“berried females”) amongst all three species. 

• Palaemon and Exopalaemon came from Northeast Asia. Females brood eggs through most of warm season in their native ranges.
• Crangon females swim into Lower South Bay around December and January to release their broods.  Straggler females occasionally arrive as late as March.

It should go without saying that crustaceans are delicious. The fish nursery in Lower South Bay depends on a robust sustained crop of shrimp.

Mysids in Pond A19, 1 March 2025.

Mysids bloom shortly after winter rains.  They tend to concentrate where waters move slower in dead-end sloughs and restored ponds.  These tiny shrimp-like crustaceans are a near perfect food for small fishes. 

Amphipods.  Not coincidentally, Amphipods tend to concentrate at some of the same locations where we find the biggest Corbula clams.  These busy bugs eat the same food and therefore compete directly with the nasty clam. 

• Amphipods are excellent food for fishes and birds.
• Corbula are horrible food: they have hard shells and are packed with selenium. 

The nitty gritty – https://www.youtube.com/watch?v=8S3Yt-NxY0E