Fish in the Bay – May 2025, Extra Baby Fish Month

Extra Baby Fish Month!  It happened again.  Every once in a while, we see a bigger goby baby boom in May instead of April.  This month, we counted 714 baby gobies versus only 308 in April.  We experienced similar inversions in April/May of 2022 and 2018.  In scientific terms, this represents the variability in what we call “Traditional Baby Fish Month.”

• All kidding aside, Extra Baby Fish Month was good news.  The April total was disappointingly low.  The extra babies help bring the spring bloom numbers up a bit. 

Corbula clam explosion continues!  The Corbula count jumped to 26,155 in May – the highest count since at least 2012 or before.  This is very bad news. 

Egg and milt-bearing Anchovies showed up in May.  The 2025 Anchovy “Summer of Love” is just beginning.

As usual, the Corbula clam explosion is largely contained in the main stems of Coyote Creek (stations Coy1 & UCoy2 and Alviso Slough (Alv1 & Alv2).

A couple of changes: 

• The UC Davis crew began recording counts of Mysids, Amphipods, and Isopods (in addition to order ranking) a few months ago.  Mysids and Amphipods are important fish food.  They are now added to the spreadsheets. 
• The new Wetland Regional Monitoring Program (WRMP) added three new “reference sites” to the upstream LSB area.  Fish and bug counts at these new stations are listed above but were not added to the overall totals in the far-right column of the spreadsheet.    

Station Alv1 was the epicenter of the Corbula explosion in May.  These clams tend to grow to jumbo size there.

1. Corbula Clams.

Corbula Clam count = 26,155.  These non-native clams sequester enormous quantities of phytoplankton and tiny zooplankton into their own hard-shelled biomass.  As a result, there is less food for baby and pelagic fishes, small birds, or pretty much any other organism that can’t consume a Corbula.  To make matters worse, Corbula can accumulate selenium to toxic concentrations. 
This is a very bad clam!

We again attempted crude measurement of Corbula size at each station.  Corbula thrive at some sweet spot between high and low salinities in the main stems of the major river channels.  So far, the correlation between Corbula size and specific bottom salinities has proven to be elusive.  Other factors must also play a role here.

2. Striped Bass.

Striped Bass count = 26.  This was our highest monthly count of Stripers in LSB since June 2021.  

Lamprey bites?  Two Stripers at Art1 were showing conspicuous oval-shaped wounds on their right sides.  If not Lamprey, what else could have done that?

More Striped Bass in May.

3. Small Bugs in the Green Marsh.

We estimate 5,900 Amphipods in this “termite mound” at Art1.

Amphipod count = 10,885.  Amphipods and Mysids are essential basic food for fishes and birds. They represent almost an entire trophic level of primary and secondary consumers.  But, it is also extremely difficult to count these tiny wriggling “insect-sized” creatures.

• Counting them is akin to estimating the number of ants in a colony, bees in a hive, or termites in a mound.  Nonetheless, even rough estimates are far more informative than no numbers at all.     

The big spring bloom.  We usually visit these marshy places only once per month.  As a result, the blooming greenness seems to erupt all at once.  At least, it feels that way.  Marsh plants that died back to roots and rhizomes over the winter suddenly (plus or minus a month) leaf out across the landscape. 

• Fresher water in upstream areas supports taller bulrushes.

Downstream plants are exposed to higher salinity.  Tall Bulrushes give way to shorter stands of Pickleweed and Spartina.

• Even the saltier salt marsh turns extraordinarily green this time of year.

4. Baby Fishes.

Unidentified/Baby gobies in Pond A21, 7 May 2025.

Unidentified/Baby goby count = 714.   Restored salt ponds A17, A19, and A21 are baby goby factories.  The vast majority of springtime baby gobies are caught in the restored ponds. 

• We also catch most summertime spawning Anchovies and wintertime spawning Longfin Smelt in the ponds.   

Tiny fishes photographed by Sami.  I was unable to join the trawls in May.  Consequently, almost all these photos were taken by Sami on his cell phone. 

• I was stunned by the quality.  Sami is a master of this art!      

5. Gobies & Sculpin.

More high-quality photos by Sami.

Shimofuri Goby count = 4.  Shimofuri Goby numbers continue to be very low. 

Both Shimofuris and their arch-rivals, the Shokihaze Gobies, appear to be in a state of spawning readiness throughout the warmer season from perhaps April (or earlier) until November.   

California Halibut & Shokihaze Gobies at Coy2 on 7 May 2025.

Shokihaze Goby count = 25.  Shokihaze goby counts remain high for the eighth consecutive month.  More Shokihazes mean fewer Shimos, and vice versa. 

Staghorn Sculpin count = 288.  The Staghorn-La Nina rebound continues.  The numbers are not yet huge, but still significantly higher than what we see during warm SST El Nino times.

Flatfishes & Bat Rays.

California Halibut count = 18.  Young Halibut are still showing up even through mildly La Nina conditions this spring.  

Halibut melanophore spots: Young California Halibut display a particular spotted pattern across their ocular sides: Five darker spots along the dorsal side (above the eyes), three to five darker spots on the ventral side, and three larger irregular splotches in the middle of the body (in addition to many other irregular speckles and spots).

• Could Halibut spots and splotches be used to evaluate Halibut diet and health?  – Yes, for extreme malformations like albinism, but this is a complicated subject.
  
  
• Hamre, Holen, & Moren (2007) Pigmentation and eye migration in Atlantic halibut (Hippoglossus hippoglossus L.) larvae: new findings and hypotheses  https://onlinelibrary.wiley.com/doi/10.1111/j.1365-2095.2007.00467.x
  
  “Atlantic halibut juveniles, which have been fed Artemia during larval development, frequently demonstrate malpigmentation and impaired eye migration. This is in contrast to the high percentage of normally developed larvae fed copepods, reared under similar conditions. Nutrition is therefore an important component influencing larval development.
  
  Analyses of the nutrient composition of Artemia and copepods show that Atlantic halibut larvae fed Artemia probably receive sufficient amounts of vitamin A by converting canthaxanthin, while iodine may be deficient, possibly leading to interrupted thyroid hormone synthesis. An unbalanced fatty acid composition, such as high levels of arachidonic acid and low levels of docosahexaenoic acid, can be another limiting factor in Artemia.
  
  Vitamin A, fatty acids and thyroid hormones have all been shown to affect pigmentation in flatfish. They are ligands to nuclear receptors, thyroid hormone receptors, retinoic acid receptors, retinoic X receptors and peroxisomal proliferator-activated receptors, which are members of the superfamily of steroid hormone receptors. The receptors interact with each other to promote gene expression that modulates proliferation and differentiation of cells.”
  
  
• Bolker and Hill (2000)  Pigmentation development in hatchery-reared flatfishes.  https://scholars.unh.edu/cgi/viewcontent.cgi?referer=&httpsredir=1&article=1238&context=nhaes
  
  “Pigmentation development in flatfishes occurs in two phases. First, during embryonic and larval stages     pigment cells differentiate on both sides of the body. Second, at metamorphosis, larval melanophores disappear, and adult melanophores differentiate on the ocular but not on the blind side.
  
  Malpigmentation seems to result from disruptions of the second phase, and may take the form of albinism on the ocular side or darkening of the blind side. Both types of aberration may be related to aspects of the hatchery environment such as lighting, substratum, and diet. Larval nutrition appears to be a key factor and enrichment of larval diets with fatty acids and Vitamin A can greatly reduce malpigmentation rates …”
  

More Halibut showing similar spot patterns.

English Sole count = 18.  We are near the end of baby English Sole season.  These babies will migrate back to the ocean soon.  We rarely see them after June.   

English Sole have spots as well:  Baby English Sole show a similar loose line of melanophore dots along their dorsal and ventral margins. In Sole, there appear to be as many as 6 dorsal and maybe 5 ventral spots.  

• Apparently, these lines of dark melanophore spots (or nodes) are characteristic of all flatfishes. 

Starry Flounder count = 8.  This is roughly an average Starry count for a May – not bad compared to the last decade or so, but pitifully weak compared to numbers in the 1970s or 80s.

Starries have melanophore spots too!  Again, notice the lines of four to five melanophore dots along the dorsal and ventral margins. These dark spots appear to roughly correspond with the dark patches in Starry dorsal and anal fins as well.  (I did not highlight the dark spots in this Starry collage. Look closely – use your imagination.)      

• Hundreds of published papers examine the color-changing abilities of flatfish species and/or the biochemical processes by which flatfish ocular sides turn brown and blind sides remain unpigmented during early development. However, very few papers describe the ocular-side spot patterns we see here. After some search, I found only a couple of helpful references:
  
  
• Lanzing (1977) Reassessment of chromatophore pattern regulation in two species of flatfish (Scophthalamus maximus; Pleuronectes platessa)  https://www.sciencedirect.com/science/article/abs/pii/0077757977900084
  
  “Observations were carried out on the disposition and types of chromatophore patterns in the turbot (Scophthalmus maximus), the plaice (Pleuronectes platessa) and, to a lesser extent, the sole (Solea solea). … The distribution of distinct chromatophore spots in the skin of the ocular side appears permanent and predictable, although some spots are often not visible due to aggregation. … Attention is drawn to the fact that the chromatophore spots on the ventral half of the ocular side form the mirror image of those located on the dorsal side, with the lateral line as the axis of symmetry.”
  
  
• Darius et al (2013) Coordinated Regulation of Chromatophore Differentiation and Melanogenesis during the Ontogeny of Skin Pigmentation of Solea senegalensis (Kaup, 1858)  https://pmc.ncbi.nlm.nih.gov/articles/PMC3650040/
  
  “… we have evaluated eleven genes related to two different processes of pigmentation: melanophore differentiation, and melanin production. …
  
  [Fig. 3 notes]  Red circles show 3 stripes of 5 patches of chromatophores conforming the juvenile pattern of skin color in the ocular side of the fish. Clusters of iridophores delimit these patches of melanophores, xanthophores and leucophores. Fins also follow the same distribution of chromatophores. …  The distribution of chromatophores was restricted to two bands on either side of the vertebral column and in the distal parts of the trunk, close to the beginning of the dorsal and anal fins. Some melanophores grouped to form a patch in the middle of the trunk. Two patches of chromatophores could be distinguished in the dorsal fin and another one in the ventral fin (Fig. 2G).”

Conclusion:  At a very early age, all flatfishes develop melanophore spots on their ocular sides.  The pattern of spots is species-specific, and the spots tend to fade or become obscured as each fish ages.  Beyond that, very few researchers bother to mention them.     

Bat Ray count = 32.  Summertime Baby Bat Ray season is off to a great start.  32 is the new record number for a May. 

• Bat Rays are one of the few creatures in LSB capable of consuming Corbula clams.  This is very good news.

7. New WRMP Reference Sites in Lower South SF Bay.

New Station: Warm Springs Marsh (WSM).  WSM is one of three new “reference sites” introduced by the WRMP.   

• We found an additional 6 Striped Bass, 12 baby gobies, and a baby Starry here!
• Reference sites are surveyed using shorter-duration 5-minute trawls. So in theory, these fish numbers should be doubled to match the “Catch per Unit Effort” (CPUE) of regular LSB stations.

New Station: UCoy1.5.   This second WRMP reference site is located at the confluence of Coyote Creek with a small channel we call “Truck Tire Slough” owing to the collection of old truck tires embedded in the muddy bank that become visible at low tide.  Geographically, it is midway between UCoy1 and UCoy2. 

• These side channels and ponds are important rearing habitats for tiny fishes.

New Station: Pond A17.  The third new reference site is restored salt pond A17.  This pond was initially opened to tidal flows in 2005 and then reconfigured and reopened in 2013. 

• Marsh vegetation in A17 has not yet colonized as robustly as in other nearby restored Ponds, but fish and bug counts look good: 153 baby gobies and many Mysids.  
• Restored ponds generate lots of tiny fishes and bugs.

These reference sites are just a small taste of many additions that the WRMP partnership has introduced to the UC Davis fish and bug monitoring program.  More discussion will follow in upcoming blog posts.