Fish in the Bay – August 2020: Red Ceramium, Tricolored Blackbirds, & more Spawning Anchovies.

Hello again.  This is a bit of an “odds and ends” clean up post. 

I was unable to join the downstream “deep Bay” trawls, so fish photography was limited.  But on the other hand, Anchovies were still spawning, Red Ceramium continued to bloom, and Tricolored Blackbirds have returned!  Not a bad month despite low fish counts.

Trawl map.


Bay-side stations trawling results.

Return to normal = “Triple Bummer in the Summer.”  The first thing you notice about the August trawl results is that the total fish count fell from over 7,000 to only 877.  That’s mainly because July was an unusual kick-ass month.  The August count is a little closer to the summer norm. 

Rising tide = less fish caught.  A big factor was that August trawls were pulled into the rising tide versus a mostly ebbing and low tide in July.  That alone probably accounts for the lower Topsmelt count in August: only one (1) Topsmelt was caught in August versus 2,555 netted in July!  (Of course, Topsmelt lifecycle migration must play a role as well.  They flee the marsh as they grow like most of the other fish here.

The triple bummer:

  1. Fewer Anchovies. The Anchovy count fell from 2,148 to 636 between July to August.  Again, a rising tide may account for some of that decrease, but for all we know, it may also reflect a typical (or atypical) Anchovy annual migration pattern.
  2. Far fewer Crangon Shrimp. We caught well over 18,000 young Crangon in July.  The August count was only 1,113.  This may accurately represent the annual Crangon migration.  It is a ‘Charlotte’s Web’ type of story – with a twist.  Our young male Crangon are now swimming out to the deep Bay and the ocean.  Most of them will end up as bird, fish, or even Gray Whale food.  Nonetheless, many will return next December, or probably the December after next, as mature females laden with eggs.  That is what protandry is all about!
  3. No unusual marine crabs in August. We did not catch any Dungeness or Decorator Crabs in August.  This again is a return to normal and probably not very significant. 


Young Crangon Shrimp on a bed of red Ceramium.  (This photograph from July 11th since I was unable to join Bay-side trawls in August.)

Ceramium Red Algae – A Growing Weirdness:  Ceramium again clogged the net at stations LSB1, LSB2, and Alv3.  As reported last month, this is unusual and very weird.  We have photographed small sprigs of Ceramium only as far back as 2017.  Until now, we have never netted buckets full of this fine filamentous material in several years of trawling. 

Red algae is generally good.  But, could this be too much of a good thing?


Upstream of Railroad Bridge.


Good News!  Anchovies were still spawning as of August 1st.  According to literature, Anchovies spawn repeatedly, with female dropping eggs every 7 to 10 days, when conditions are favorable.  So, now we know conditions continued to be favorable at least through early August.  Hopefully, we may see more.  

To avoid torturing casual readers, I will file a separate supplemental Anchovy spawning report in a few days – Here are a few preliminary conclusions:

  • Limited observation on August 1st suggests that blue, green, and gold Anchovies all spawn together indiscriminately. This may blow away the Hubbs notion from 1925 that green-backed and clear, or brown-backed, Anchovies represented separate ‘races’ or subspecies.  (I was hoping that Carl Hubb’s proposed “Engradulus mordax nanus Girard” (the ‘Brown-back’) would be confirmed as a unique San Francisco Bay subspecies.  – Maybe it was in 1925, but the brown-back Anchovy seems to be less of a separate population nowadays. ** Also note: Carl Hubbs observed likely interbreeding of Bay and Ocean ‘races’ of Anchovies even in 1925. See pp 20-21:
  • Some Anchovies seen in August exuded eggs that are plump and pinkish. These are assumed to ready, or near ready, for release.
  • Eggs that look scrawny and white may need a few to several more days for growth and hydration.


1. Artesian Slough

Two guys fishing downstream of the SJ/SC RWF discharge.

The site shown above is one of two early morning launch points for our weekend trawls.  The UC Davis research boat is hidden behind bulrush on the right bank of the channel.

San Jose-Santa Clara Regional Wastewater Facility (SJ-SC RWF). This is the point from which roughly 80 to 100 million gallons of clean, fresh, treated wastewater is discharged 24/7/365.  The largest Striped Bass and even some Largemouth Bass are usually caught here; which once again explains the anglers shown in the photo.

I have long noted that discharge from the SJ-SC RWF does not appear to degrade, and may actually enhance, environment and habitat quality in these surrounding waters. 


Striped Bass, with suspiciously full belly, and two anchovies, Art2, 1 Aug 2020.


Relatively fresh water in Artesian Slough consistently turns green-backed Anchovies into Golden Anchovies and eventually into “colorless” brown-backs if the fish loiter here long enough.  The same color-changing process occurs in the other nearby sloughs, but the freshwater flow here is more consistent here, hence, the Anchovies are reliably more golden or brown. 

Again, the occasional presence of a green Anchovy indicates that this population mixes with migrants from saltier waters.  The Anchovy color change is a slow process of unknown duration.

In August, many Anchovies were observed extruding eggs further upstream at Pond A19, Upper Coyote Creek, and Dump Slough stations.  However, there was no evidence of spawning Anchovies in Artesian Slough this month. 


 2. Shimofuri Gobies

Darkish colored Shimofuri Goby, station Art3

Shimofuri Goby.  I learned last month that Chameleon Gobies, and closely related Shimofuri Gobies, can change from dark to light brown coloration at will and within minutes.  Two dark brown stripes that run longitudinally along each side are harder to see when the goby turns dark. 

Shimofuri Goby identification, a review:

  • An orange-red border is SOMETIMES seen on the anal and second dorsal fins of larger Shimos. It may be a sign of maturity of even sexual display.    
  • Both Chameleons and Shimos have light-colored spots on the face. Shimos have additional spots below the jaw-line.  “Shimorfuri” means “marbled” in Japanese.  I assume that is a reference to the marbled face. 
  • Our gobies must be Shimos! According to literature, Chameleon Gobies are rarely present in waters less than 22 ppt in salinity.  Shimofuris greatly prefer lower salinity.  For that reason alone, our gobies are almost certainly Shimos.


Two lighter colored Shimofuri Gobies with three Arrow Gobies from station Coy1.

Lighter colored Shimos.  The tone of the dark stripes doesn’t change, so they show up starkly when the fish assumes the lighter color. 

(Note:  We have not directly observed any of our Shimofuris actually changing color.  I will try to watch a few of these interesting gobies more closely in the near future to document this amazing process!)


Baby Shimofuri Goby


3. Decapods.

Palaemon shrimp, station Coy1. Top-down photography reveals that six of seven Palaemon shrimp in this photo are pregnant females!

Palaemon Shrimp.  We caught 901 Palaemons in August, which isn’t particularly low despite a general Palaemon population decline after 2018. 

Both Palaemon and Exopalaemon shrimp females brood eggs and release young through most of the summer.  In this instance, egg masses in berried females in the photo above makes the abdomen look dark gray.  A smaller Palaemon, second from left, has no egg mass.


Two berried female Palaemon shrimp, side-view in the photarium.


Exopalaemon Shrimp females are also reproductive through most of the warm months.  Yellow-green egg masses are visible in the two smaller shrimp to the left in the top panel. 


Crangon shrimp.  As mentioned above, native Crangon shrimp numbers dropped from well over 18,000 in July to only 1,113 in August.  This was very disappointing.  But we must remember, Crangon counts were much lower in dry-year Augusts before 2017: 

Crangon Counts in August
Aug 2019=2,246, Aug 2018=17,852, Aug 2017=1042, Aug 2016=7, Aug 2015=21, Aug 2014=480

Literature and our own six-years of data suggest that good Crangon recruitment depends on rainfall the previous year.  Pray for rain!


Harris Mud Crab (Rhithropanopeus harrisii). For some reason both Harris and Oregon Mud Crabs had been rare or missing or since 2019.  In August we caught one of each, in contrast to the marine Decorator and Dungeness crabs we had been seeing most of this year.  The non-native Harris, shown here, originates from the Atlantic Coast.  It invaded many estuaries around the world over the last century. 

This crab is one of the hardiest of survivors, particularly where bigger fish and bird predators cannot control it.  Take for example, the Baltic Sea, where invading Harris Mud Crabs turned the ecosystem upside down by feeding on otherwise defenseless bivalves and gastropods: 

“ … profound ecosystem changes are being caused by the recent introduction of the mud crab R. harrisii into the Baltic Sea, a bottom-up driven ecosystem where no equivalent predators ever existed. In doing so we demonstrate how the addition of a novel predator can trigger a regime shift through strong top-down control of suspension-feeding invertebrates, modulating pelagic nutrient availability and increasing the magnitude and frequency of phytoplankton blooms.”

The Harris Mud Crab was the most common invertebrate caught in otter trawls here in the 1980s.  I suspect that Harris Mud Crab dominance was a reflection of marsh sickness (not enough sewage treatment & inadequate habitat) that has since been alleviated and facilitated by healthy marsh recovery.  …  However, it is complicated!  We cannot rule out recent additional conflict and competition from non-native Corbula clams (with harder shells), Exopalaemon shrimp and Shimo and Shokihaze gobies.


4. Other tiny fish.

One of two Bay Pipefish from station UCoy2.


Cheekspot Gobies, UCoy2.

Cheekspot Gobies.  Altogether, we caught 13 Arrow and Cheekspot Gobies on August 1st, then another 41 on August 2nd. These two native gobies differentiate each other by habitat type even within very small geographic areas.  That seems to be the reason we often find both types in the same trawl.  Cheekspots prefer cooler water, which usually implies deeper channels, and harder substrate.


Arrow Gobies, Coy1.

Arrow Gobies prefer warmer, shallower, muddier habitat.  The restored ponds should be ideal for them, but both Arrows and Cheekspots seem to be fairly adaptable.  Almost every slough channel and borrow ditch has both warm muddy shallows and cool shell-hash deeps. 

These tiny gobies continue to be very difficult to identify in the field.  They are hard to photograph too. The big mouths of the Arrows and hunched backs on the Cheekspots are somewhat easier to see with macro photography.   


5. Updates from UC Davis OG fish lab

At least a dozen members of the UC Davis Otolith Geochemistry and Fish Ecology Lab presented posters for the Interagency Ecological Program (IEP) 2020 Annual Workshop.  Two posters, in the Delta and Longfin Smelt category, focused on our Alviso Marsh here in Lower South Bay:

Poster #1:   An Estuary-Wide Synthesis of the Distribution of Larval and Adult Longfin Smelt.

Excerpt from poster. My highlights in red.

This poster summarizes Otter Trawl data (top) and 20mm Trawl data (bottom).  Results show that sloughs surrounding San Francisco Bay are important recruitment habitats for threatened Longfin Smelt – especially in wet years.  The Alviso Marsh area was a particular Longfin Smelt hotspot in wet year otter trawls. 


Poster #2: Larval and Juvenile Longfin Smelt Feeding in Restored Tidal Habitats

The huge biomass of zooplankton explains why Alviso Marsh area is such a magnet for fish spawning. 

  • This is where the tiny fish food is!
  • Longfin Smelt spawn here in winter.
  • Topsmelt spawn in spring.
  • Anchovies in summer.

Be sure to check out this short and interesting TikTok video by Arthur Barros here:

6. Tricolored Blackbirds along Dump Slough

Tricolored Blackbirds (Agelaius tricolor).  In October and November 2019, we observed threatened Tricolored Blackbirds (or possibly the California Bicolored variant) in Dump Slough.  Now again this August, we spotted a small tribe of 15 to 20 birds with odd flashes of yellow or white epaulets.  They are hard to identify amongst the tall tassels of California bulrush that line the slough.   


Tricolor Sociability.  Perhaps the best indicator that these are Tricolors may be their compact gathering.  Tricolors are notably gregarious, unlike the more common Red-winged Blackbirds where males defend territories.  We listened for any bird vocalizations as we passed but did not hear any.  We also could not see any signs of nests or young birds, so this location is probably a post-season roosting area for them.   (


Dumpsters at Newby Island Recyclery: Audubon Society volunteers identified one or two Tricolored Blackbirds amongst a mixed flock of foraging Starlings, Brewers Blackbirds and Red-winged Blackbirds here in December 2019.

Audubon Society Confirmation in 2019.  Late last year, SCVAS birders reported at least one or two Tricolors foraging the dumpsters at the nearby Newby Island Landfill Recyclery facility (, during the Christmas Bird Count on 15 December 2019.  This makes it more certain that our birds are Tricolors.


7. Additional bird notes from readers:

Guillemots and Tonguefish.  Victoria “Tori” Seher emailed on July 11th to tell us that ‘Pidgeon Guillemots nesting on Alcatraz Island eat a lot of California Tonguefish,’ in addition to sculpin, shrimp, and other flatfish.  (In contrast, Farallon Island Guillemots eat mainly rockfish.)  

Tori is a Natural Resource Specialist at the John Muir National Historic Site. In a previous job she studied the 50 pairs of Guillemots that live on Alcatraz.


Least Terns.  In Marine biology, we tend to appreciate tiny critters specifically because they serve as food for bigger animals that everybody likes.  Another case in point:  Mark Rauzon posted a few FB photos taken on 9 August showing a Least Tern feeding its chick a young Topsmelt at Alameda South Shore.  (Note:  At first, I thought the fish was an Anchovy. But, on close examination in expanded computer view, the silver stripe on the side says otherwise!)

We commonly see Terns (more likely Caspians and Forster’s) dive-bombing and catching tiny fish as we trawl Lower South Bay marshes.  But, the birds are too fast and too far away from us to see the catch.


Stay tuned for the August Anchovy spawning supplement.

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