Fish in the Bay – February 2019, UC Davis Trawls – LONGFIN ALERT! Spawning confirmed for 2019!

Folks, I write as the Atmospheric River pounds the Bay Area with much needed rain.  Urgent flood alerts have just been lifted in much of San Jose (14 Feb, Valentine’s Day), so we may have dodged a repeat of disastrous flooding that happened in February 2017.  Even better, this freshwater flushing is a lifeline for struggling populations of Longfin Smelt, not to mention Prickly Sculpin, Mysids, Starry Flounder, and other critters we like.


Female & five male Longfin Smelt from UCoy1.

LONGFIN SMELT SPAWNING AT STATION UCOY1!  The fat female at top left was extruding eggs when caught!  The five males show various degrees of post-milt release hollow bellies and elongated anal fins.  All fish display enhanced silvery reflectiveness and darker dorsal color indicating spawning readiness.

For context, for five long years (through 2012 to early 2017 at least) Dr. Hobbs searched in vain for any sign of Longfin Smelt spawning in the Alviso Marsh Complex (AMC).  Then, with the big February Freshwater Flush of 2017, all hell broke loose!  Huge rainstorms that threatened California dams and caused disastrous flooding also freshened our local marshes to the point that Longfins could spawn en-masse.  For the first time, the Hobbs team recovered female Longfins bearing eggs and freshly hatched Longfin larvae. 

Since then, Longfin Smelt in the AMC experienced a population rebound.  2017 flushing recruited a larger new generation of Longfins that appear to have returned to spawn a year later.**  The 2018 winter may have also been wet enough to continue the mini-population boom.  This year is even wetter, and the Longfins know it!   

(** The return of the Longfins is my supposition.  Even now, Dr. Hobbs is processing otoliths (ear stones) from current year adult Longfins at UC Davis labs.  Hopefully, the analysis will verify that these spawning adults hatched and recruited here.)

2. February Freshwater Flush – 2019.

Bay-side Station result:

Upstream of Railroad Bridge:

Freshwater Flush!  I highlighted in red the substantial salt-wedge at stations Coy2, Coy3, and Coy4.  As freshwater flowed, salinity varied by 10 to 12 parts per thousand (ppt) over just a few feet of depth in segments of Lower Coyote Creek!  Tidal velocity is huge here, so we assume that salinities were changing minute-by-minute in any specific place.  Can you imagine the osmotic stress this exerts on tiny fish and bugs?  Only hardy adapted survivors endure.  All others must flee or die. 

Even fresher.  I highlighted in blue salinity values below 1 ppt in the second table.  Much of Coyote Creek upstream of the Railroad Bridge was as fresh as public drinking water on Sunday.   

Blast from the Past; the Flush of 2017.  I highlighted above surface salinities recorded from April 2017 for comparison.  At that time, the freshwater flush was receding.  A big factor for Longfin Smelt recruitment will be the length of time that our current freshwater flush endures.  Longfin hatchlings tolerate 2 to 6 ppt and up to 8 ppt within 5 or 6 weeks (40 days is one literature benchmark).  But Longfins are just one estuarine species that need the Freshwater Flush.

Freshwater Flushing affects everything!  I will not have space in this report to discuss every change we see when the rain comes, but I will mention a few highlights:

  • Crangon (shrimp) numbers dropped from over 10,000 in January to just over 1,200 by Feb.  The Great Crangon Brooding Migration of 2018/19 is officially over.  I presume the huge mass of breeding-age crangon have retreated further north to saltier parts of the Bay – pending further investigation …
  • Corbula (clams) also dropped from several hundred in January to only 43 this month!  This is very good news because we don’t like corbula.  But, where did they go?  We saw no shells, no nothing!  I believe this is a diving duck story – more to follow in later reports …
  • New and odd species for Lower South Bay.  Dr. Hobbs maintains an official list of all species caught in Lower South Bay monthly surveys.  In December, he added Pacific Tomcod and a Red Swamp Crayfish to the list.  I highlighted oddballs in red in above tables:  Bonehead Sculpin, Pacific Tomcod (first sighting), Green Sunfish (only seen once before in June 2017), and a Red Swamp Crayfish that washed down from Coyote Creek.

GOOD NEWS for Longfin Smelt!  An additional Valentine’s day flush occurred just a few days after our last trawls: 

3. Global Context:  Polar Vortices and Atmospheric Rivers.

Polar Vortex and Atmospheric River are now part of our daily lexicon.  These are planetary weather patterns that have existed since time began (metaphorically speaking), and yet, I was unfamiliar until now.  Suddenly, I realiz that the fish have been telling me this for at least six years.  I just didn’t know the language.

Until recently, I did not know that a breakup of the stratospheric polar vortex would, in turn, push upper tropospheric jet streams southward and sometimes eastward across the Pacific. In some of our wettest years, warm and moist air masses from the mid-Pacific crash into California.  Rivers surge, sediments flow.  Microscopic phytoplankton and tiny bugs bloom on nutrients washing downstream.  Small fish feed on this stuff.  Young Prickly Sculpin, Lamprey, and Steelhead smolts tumble downstream to commence their lifetime migrations.  Adult Shad, Salmon, Lampreys, Herring, and others fight their way upstream to complete their spawning cycle. 

The current Atmospheric River event is also discussed here: 

I firmly believe we see hemispheric weather patterns reflected in our local fish and bug populations in near real time.  I am seeing it right now!

Most of our rain, 65 percent they say, comes in the form of Atmospheric Rivers (the old “Pineapple Express,” we used to call it).  Now we know it’s a hemispheric, if not global, phenomenon. 

This is the abstract to the Waliser & Guan (2017) paper on the subject:  Seemingly rare and random major storm events are actually not that rare or random.  Atmospheric Rivers are a fundamental component of our planet.  Fish and bugs figured this out at least a half a billion years ago.  We need to get with the program!

Absence of Atmospheric Rivers means DROUGHT in California and other parts of the world:

Twitter alerts regarding Guadalupe River flood risk from 14 Feb 2019.

Unfortunately, Polar Vortex breakup and Atmospheric Rivers also wreak havoc on human homes and infrastructure.   Above thread from Twitter feed linked here: 

4. Fish Food Grows When Creeks Flush.

Corphium at station Art2.

Corophium.  After rain, some of our favorite bugs come out in force.  These photos show some corophium picked up at station Art2.  We generally see large numbers of these bottom-dwelling bugs in vicinity of Artesian and Alviso sloughs.  These are important food for both fish and birds.

Corophium female with eggs.

Corophium with eggs!  Until now, I never thought a lot about the Corophium lifecycle.  These tiny wriggling bugs are hard to see and photograph.  I will have to pay closer attention in the future.

Corophium caught in the mysid net.

Another news flash: Swimming Corophium!  This is a close-up of the “Mysid Net” catch at station UCoy2 on 10 Feb.  The net was pulled near top of the water column for 5 minutes.  Corophium, shown here in the collection jar, were not hunkered down in mud-tubes as expected.  Instead, they were swimming near the surface. 

This is surprising, but not shocking.  Literature tells us that Corophium occasionally do swim for feeding and mate selection.  However, when and why they might choose to swim here is not known.  Swimming is dangerous activity for a Corophium.  We have seen them swim when stressed by low Dissolved Oxygen on the bottom.  But now, water is very fresh and oxygen rich.  Detritus and nutrients are flowing down the creek.  Maybe it is too fresh for most salt-water predators?  Is freshwater flow providing Corophium a food bonanza?  … Developing.  


Gammarid Amphipod from Art3.  Gammarids are just a little bigger than Corophium.  Both types of bugs are non-shrimp, but somewhat shrimp-like, amphipods.  Fish and birds eat them like candy.  I assume they all taste like shrimp or lobster. (This one has very pronounced, Corophium-like, antennae projecting from its snout. A little different from others I have seen.)

The air was full of midges at Art3.
Bugnado! Midge mating tornado in Artesian Slough.

Midges.  Rains bring midge blooms.  Midges here are basically like non-biting mosquitos: small flying insects that hatch and grow as larva in marsh water.  The larvae are highly desirable food for small fishes.  As adults in the air, many small birds, like swallows, eat them.  Adult midges were referred to as “Ghost Midges” in the past because their big white or grayish mating tornados look like ghosts walking across the marsh.

A clump of Mysids from Pond A19 on 10 Feb.

Mysids.  Rain flushing also feeds Mysid blooms.  Mysids are not true shrimp, but they look and act a lot like shrimp.  (They taste like shrimp, but I do not recommend eating them unless you know more about potential parasites than I do.)   As fish food, Mysids are ideal.  They are even sold as frozen or live food for home aquariums.    

Mysids collected in Guadalupe Slough on 19 Jan.  Too many for one sample jar!
Mysids from Alviso Slough in January.

Mysid Cakes in Alviso Slough.  We caught big clumps of mysids just upstream of the Town of Alviso and far up Guadalupe Slough during “Larval Survey” trawls on January 19th. So many mysids were collected here that only representative portions could be taken back to the lab for counting.   Altogether, this is clear documentation that Mysids congregate at some of the freshest and farthest upstream tidal slough locations.   

Mysid close-up.

5. Longfin Smelt Spawn When It Gets Cold and Fresh.

Longfin Smelt are triggered to spawn by cold water temperatures (usually below 12 degrees C) and fresher water (2 to 4 ppt).  Not coincidentally, a wide array of estuarine bugs (most of them microscopic and not shown above) also bloom about the same time.  No doubt, this arrangement was forged by evolution. 

Longfin males in spawning colors.

Longfin Smelt males showing spawning readiness.  Longfins, particularly males, turn darker and colorful as they get ready for mating.  These males also have elongated anal fins that are used to fan milt and eggs.  At least two of these fish have hollow bellies indicating that milt has been released.

In the photo above, you can see dark-pigmented melanophores on their heads and sides are very distinct.  The sides have “silvered up.”  Metallic-reflective iridophores along the dorsal side are showing bronze to greenish hues.

Same Longfin males flipped around.

Longfin Surprise!  (Same three males turned over.)  The surprise is the male in the middle. He appears to have formed a slimy ventral cup with his pelvic and anal fins (pectoral fins might be involved too.)  This looks a little similar to the ventral sucker cup that gobies form with their pelvic fins. 

Also, as near as I can tell by my amateur eye, this male appears to be extruding milt!  We may have caught him in mid-act.  If true, the photo is showing how the male may use his ventral-side fins to adhere to either the female or released eggs.

Female Longfin (middle) with two males.  The female was extruding eggs when caught. Interestingly, the male at top is small and looks young, possibly young-of-year, and yet he shows spawning colors.

Same female Longfin, front, with male behind.
Jim Hobbs recording Longfin Smelt vital signs for science.

6. Other Freshwater-Stimulated Oddballs.

Pacific Tomcod (Microgadus proximus)

Pacific Tomcod.  This fish is very common off the coast of California but a new catch for Lower South Bay. For some reason, this fish swam all the way to Station Coy3.  (Tomcod in photo above was caught and frozen the previous day – not live.)

Exopalaemon modestus

Exopalaemon shrimp with eggs.  As expected, non-native Exopalaemon shrimp (Siberian prawns) like it fresh.  Their numbers are up in upstream pockets of Artesian and Dump Sloughs.  I did not expect to see berried females though: all three shown above are full of eggs.  I don’t yet know the local Exopalaemon brooding cycle, and almost all other Exos did not have eggs on 10 Feb.

Procambarus clarkii

Red Swamp Crayfish (AKA, Louisiana Mudbug). This big bug was caught at UCoy2.  It was freshly dead, so I think that it was forcibly pushed downstream by surging currents.  Salt shock may have killed it upon entry to tidal water.  This is the first time we have seen one in Bay waters. I do not know if they are well established upstream in Coyote Creek. 

Red Swamp Crayfish have been seen in the Bay Area since at least the 1950s. 

Lepomis cyanellus

Green Sunfish.  This young noxious invader was caught at Art3.  Green Sunfish are native to Mississippi and the Great Lakes regions.  They have been introduced to watersheds all over the world. I presume this one also washed down from Coyote Creek.  Summertime salinity will push it back out of this area if nothing else does.

An interesting story by a rare person who doesn’t hate the Green Sunfish: 

Prickly Sculpin.  This was one of two native Pricklys caught on Sunday: one at UCoy1, the other at Dmp1.  This fish hatches and grows in freshwater creeks.  Winter flushing washes them downstream into tidal waters.  We don’t see them in dry years.  Both Pricklys caught in February were large adults.  As I understand the Prickly lifecycle, both these fish will soon be fighting their way upstream to find a spawning place. 

As always, more to follow …

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