Fish in the Bay – February 2019, UC Davis Trawls – Bug Bonanza! Winter rains bring more bugs!

Hi everyone.   I again accompanied the UC Davis / Hobbs team on Saturday, 23 February, for “20-milimeter Larval Fish Trawls.”  This is the winter-time search for larval Longfin Smelt that I have accompanied and reported on at other times before.  The only significant difference between these trawls and regular monthly “Otter Trawls” is the type of net used.  The Otter net has larger mesh so tends to catch larger fish.  The 20-mm survey net has smaller mesh theoretically optimized to catch fish larvae that are around 20 mm long. 

As we shall see, the 20-mm net catches more bugs, plus a few fish too.    

Locations and water quality conditions at the 10 stations sampled.

Good news for Longfin Smelt.  Longfin adults are triggered to spawn when temperatures fall to around 12 degrees C and salinity drops to 2 parts per thousand (ppt) or lower.  We are in the “Longfin Spawning Zone” at all stations upstream of Lower South Bay (LSB): both temperature and salinity are perfect.

This begs a big question in my mind: Why are Longfin Smelt adapted to spawn at low temperature and salinity? 

For that matter, why are native Crangon shrimp also triggered by low water temperature to swim upstream to drop eggs?  Young English Sole make similar temperature and freshwater triggered journeys to the mouths of creeks.  Then also consider the ducks. Why do ducks fly thousands of miles to winter in San Francisco Bay.  What is the purpose?  What drives their timing?  I think the answer is summed up in one word: BUGS!

Bar graph from the San Jose-Santa Clara Regional Wastewater Facility (SJ-SC RWF) 2018 Annual Report, p. 47.  

Spring-Bloom Time!  Of course, it’s more than just bugs.  Microscopic phytoplankton multiply to dense concentrations in marshes and sloughs.  These are tiny single-celled plants, or plant-like animals, that harvest sunlight to energy. 

The bar chart above indicates two bloom periods from 2018 data: a big spring bloom (February – March) and a smaller fall bloom (October – November).  The blooms are measured as concentrations of Chlorophyll-a in micrograms per liter (ug/l).  In estuarine ecology, and specifically in San Francisco Bay, Chlorophyll-a concentrations around 20 to 40 ug/l is a substantial bloom.  Here, we occasionally see more than double those numbers.

Bottom-up Trophic Cascade.   The early-spring (I still think of February as “winter”) explosion of phytoplankton feeds a bottom-up trophic cascade.  ( Microscopic animals, like rotifers, ciliates, clam and shrimp larvae, and others feed on the blooming phytoplankton and, in turn multiply.  Marsh waters rapidly become a thick broth of tiny food particles.  But, what feasts on this micro-buffet?  … BUGS!

Jon Kuntz releasing lines as we got underway from Alviso Launch.

The larval fish and bug net. The 20-mm net is the large white hoop-shaped contraption mounted on the back of the boat in the above photo.  A smaller “Clarke-Bumpus” net (not shown) was also attached to capture the tiniest bugs and hopefully some fish eggs too.

1. Birds

Even before we put a net in the water, winter birds provided evidence that there must be a lot of food or something attractive.

Goldeneye ducks in Alviso Slough.

Goldeneyes!  Like many of our recruiting fish, ducks arrive this time of year to fatten up on the same stuff:  bugs, and/or clams and worms, that eat the blooming phytoplankton.  This photo was taken looking upstream from Alviso Launch along the banks of the Town of Alviso.  I am not a duck expert, but I am pretty sure these are Goldeneye ducks.  Goldeneyes are diving ducks that feed on shrimp, crustaceans, worms, small fish, and other bottom dwelling critters.    

Avocets at the water’s edge on a falling tide.

Avocets!   Avocets and other shorebirds pick at Corophium and other amphipods during the ebbing tide.  If you read much about Corophium, you learn that ebb tide is the time when male Corophium tend to briefly crawl out of their holes to seek females.  Shorebirds figured this out a long time ago

Buffleheads in the deeper water near station Coy4.

Buffleheads!  A raft of deeper diving male and female Bufflehead ducks were loitering in the vicinity of station Coy4 and much of Lower Coyote main stem.  Like Goldeneyes, Buffleheads are diving ducks. I think Buffleheads are more inclined to feed on mollusks (clams) compared to Goldeneyes.  Sometimes, I see Goldeneyes and Buffleheads paddling around together, but this day I did not.

Surf Scoters in Lower South San Francisco Bay on February 23rd.

Surf Scoters!  Farther out in Lower South Bay, we could see thousands of Surf Scoters along with a few more Buffleheads.  Surf Scoters are primarily clam-eaters, but they relish polychaete worms and crustaceans as well. 

A side note about Corbula clams. These diving ducks (also referred to as “sea ducks”) are a big reason invasive corbula clams ( have not taken over in Lower South Bay.  However, diving ducks are only present in winter.  The other year-round “secret weapon” against corbula is reported to be invasive Philine (“snotball” or “tortellini”) snails (  But, the snail only ranges out in the middle of Lower South Bay, not at upstream creek locations. 

Further up the creeks and sloughs, diving ducks are comprised of Ruddy Ducks, Goldeneyes, and some scaup, but no Philine snails.  This may explain why corbula clams continue to appear in large concentrations further upstream in Alviso Slough and Coyote Creek in summer, then disappear in winter.

Surf Scoters in, and above, the Bay.

Surf Scoters are a very good sign.  There has been concern that Surf Scoter populations have been decline in recent decades.   I do not know if the decline continues.  But I will say, I have never seen so many Scoters in Lower South Bay, and I have been watching for them the past two winters.

In the photo background, you can see a long line of various types of ducks: Scoters, Scaup, Canvasbacks, Redheads, and Buffleheads.  I call it a “duck island,” running along the west side of Lower South Bay.  Corbula clams have no chance here!

2. Bugs

20mm net being deployed.
Jon trying to figure out what to do with all the Mysids – the jar overflowed!

Station Coy4: Mysids!  The biggest shocker this trip was the dense concentrations of blooming mysids at all stations in the main stem of Coyote Creek and in Pond A21. 

Only a few weeks before, on January 19th, the Mysid explosion was observed at the farthest upstream stations in Alviso and Guadalupe Sloughs where freshwater met the tides.  Considerable freshwater flushing and dam releases over intervening weeks appear to have moved the epicenter of the Mysid explosion a few miles further downstream.

This is what a bug explosion looks like: the collection jar overflowed after a 10-minute trawl.   In fact, all trawls in Coyote Creek had to be limited to 5 minutes to avoid over-stuffing the net with bugs.  Too many bugs!

Juicy bugs – a near perfect fish food.
Mysid close-up
Jon showing another jar full of bugs from station LSB1.
Synidotea on a bed of Mysids from station LSB2.

We found slightly fewer Mysids out in the middle of Lower South Bay, but there were still a lot of them.   I can’t quantify exact “catch per unit effort” at deep Bay stations except to say that after a 10-minute trawl, all Mysids fit into one jar.  

Synidotea isopods were also collected at all stations, but highest numbers were at the deep Bay stations.  From the Boyd paper linked below, I gather that our Synidotea do not tolerate freshwater well.  This explains the lower numbers at upstream stations.  The author also suggests that our (also non-native here) San Francisco Bay Synitodea may have invaded Delaware Bay via ballast water.

Synidotea side-note:  I have wondered what Synidotea eat.  They are generally described as detritivores and occasional carnivores.  The Boyd paper documents some of the diet: worms, branching bryozoans, zooplankton, dead oysters, ulva (sea lettuce) and dead spartina, among other things.  

Another thing I noticed: our Synidotea in February look younger and bright orange or tan.  As late as January, most I saw were brown and crusty looking and perhaps a little larger, suggesting they were old adults.

An old crusty Synidotea caught in January.
Pond A21.  Almost 100 percent Mysids!  Again, too many for one jar.
Pile of Mysids from Station Coy2

At stations Coy2 and 3 – the mysid explosion continued.  Some stations had to be re-trawled at 5-minutes only.

Dr. Hobbs peering into the mysid jar.

3. Tinier Bugs

Small bugs with tiny bugs from the Clarke-Bumpus net.

The finer-mesh Clarke-Bumpus net (CB net) was pulled in tandem with the 20-mm survey net.  The CB net catches very tiny creatures, like copepods.  This gives us some idea about what the bigger bugs might be eating.

The photo above shows the results from one CB trawl.  Some of the larger small bugs are indicated.  The brownish specks and sludges are comprised of a combination of copepods, phytoplankton, and many other near-microscopic critters that will have to be identified in the lab.

Mysids silhouetted by copepods and phytoplankton.

The results of another CB trawl are shown against a filter screen above.  You can see the outline of Mysid bodies through the mass of copepod and phytoplankton sludge.

4. Fish and bigger critters.

Some bigger critters found buried in the mysid catch.

As expected, the 20-mm net catches smaller fish and bugs.  Some examples of the February 23rd catch are shown above.

More critters from the 20-mm survey.

The photo shows (top to bottom) an Inland (or Mississippi) Silverside, a Rainwater Killifish, and a Palaemon shrimp along with more Mysids.  The Palaemon is laden with eggs.

Inland Silversides and Topsmelt.

I always find it difficult to distinguish Inland Silversides from young Topsmelt.  Both have a distinct silver band running lengthwise down their sides.  Topsmelt tend to be a little plumper and the mouth is not quite so sharply up-turned.  The arrangement of their fins is the real key, but you can’t always see that in photos.  … So, if I am not mistaken, the very top two fish are Topsmelt.  The next two below are Inland Silversides.  The solitary fish in the bottom photo is another Topsmelt.  I have noticed a slightly blue tint to Topsmelt before.  If I have not mixed up my fish, I think I have documented Topsmelt-blue here.    

Inland Silversides were introduced into Blue Lake and Clear Lake in 1967.  Since then, they have managed to invade most corners of California.   

More tiny fish from 20-mm trawling.

The collage above shows a few more examples of tiny fish.  Two things to point out:

  1. There are very few photos of Arrow Gobies or Cheekspot Gobies on the internet.  It is difficult to distinguish the two.  In the top photo, this tiny goby has a reflective patch on its operculum (gill cover).  Is this an Arrow, or a Cheekspot?
  2. Dr. Hobbs identified the fish in the middle photo as a very young Longjaw Mudsucker.  This may be the smallest mudsucker I have photographed. 

5. Larval Fish.

Larval fish & bugs.

We did see some larval fish.  In particular, we were looking for long and skinny, snake-like looking larvae.  Longfin Smelt, Pacific Herring, and Northern Anchovy larvae all look long and skinny compared to many other larval fish.  All three species spawn here.  So, at this point, unless we see something more specific, like a triangular-shaped swim bladder, or an adipose fin, we do not yet know if any Longfin larvae were caught.

Searching for long-skinnies in the collection jar.

Some kind of fishes were spawning here.  But, were they Longfins?

6. Odds and Ends.

Northern Harrier (I think) cruising over Pond A21.  Whitten boat shed, one of the last remaining structures from the ghost town of Drawbridge, is in the background.

I am finding Northern Harriers very difficult to photograph.  They fly erratically over the marsh as they hunt for small mammals. Red-tailed Hawks like to venture into the marsh territory for the same prey.  A Red-tailed Hawk fooled me a few months ago, and I have been trying to make up for it.  It’s not easy.

Weekend anglers show off a White Sturgeon they just caught.

I am constantly amazed at the number of White Sturgeon that are being caught in Lower South Bay.  The photo shows some folks that pulled up a Sturgeon as we were finishing the last of the larval trawls.  (I obscured the human faces even though this was a legal and permitted catch, and they were rightfully proud of their fishing prowess.)

Cinnamon Seals of Lower South Bay.

I am equally amazed by the herd of red harbor seals that beach themselves on the mudflats at Calaveras Point.  I call them Cinnamon Seals. They were looking redder than usual that day.

(I also want to note, these photos were taken from mid-channel in Lower Coyote Creek with extreme telephoto.  We do not harass the seals!)

More Cinnamon Seals.

Life is good for us at the apex of the food pyramid.  Blissfully unaware of the infinite biological activity that supports us.

Best news of all (for fish and bugs, not necessarily for humans living near the creeks), as I write, yet another atmospheric river has arrived in the Bay Area.  This means more fresh water is coming. 

The Hobbs team captured spawning longfins on February 9th.  Egg development takes a month before hatch.  Longfin hatchlings require very low salinity for at least a few weeks.  They gradually become more salt-water tolerant as they grow to the 20 mm threshold.  According to most sources, Longfin larvae need salinity to stay below 8 ppt for six to eight weeks. 

If salinity remains in the current low range for another month or two, we should see a very good Longfin recruitment this year.   

Pray for rain!

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