Fish in the Bay – November 2018 UC Davis Trawls – Longfin Season’s Greetings

An early Merry Christmas!  Longfin Smelt returned to Lower South San Francisco Bay!  First arrival of Longfins occurred in October when 5 were caught.  For November, the count increased to 75!  This was our second biggest weekend catch in eight years.

45 of the Longfins were caught in the east corner Pond A21 alone.  Jim Hobbs thinks this may be his biggest single-trawl catch on record.  And, they were beauties too!  We saw big ones likely ready to spawn, and small ones, probably hatched this year, everywhere we trawled.

Longfins beauties.  Above, Dr. Levi Lewis showing some of the catch from Pond A21 on November 25th.  These appear to be members of a cohort that hatched here early in 2017 in response to the Freshwater Flush.  These fish were preserved and sent to UC Davis laboratories where they will be analyzed to determine exact age and origin.  We will soon know for certain if they were hatched here, or if they came down from North Bay.

This once plentiful fish is threatened according to State of California (albeit not yet Federally listed):  A few years ago, Dr. Hobbs discovered that a small, possibly remnant, population of longfins lives here in Lower South Bay.  Earlier records indicate that this heretofore unknown population been here at least since the early 1980s.


Trawl map.


November trawl dates are a little wonky.  I accompanied the Hobbs crew twice in November.  The trawling weekend was originally scheduled for November 10th and 11th.  But, a blown seal in a boat trailer wheel hub canceled trawling on November 10th.  Instead, we trawled upstream of the railroad bridge on November 11th.  Then Jim Hobbs, Emily, and Levi Lewis returned to trawl on the Bayside two weeks later, on November 25th.


Sunday, 25 November – Bay-side trawls following light rain from 21 November to the 23rd.


Sunday, 11 November – upstream and east of Railroad Bridge

Longfins like the rain.  They spawn in cold fresher marsh water.  The bigger Longfin catch on 24 November (table farther above) correlates with the first seasonal rain event on 21 through 23 November which brought about an inch of rain throughout the Lower Bay Area.  The longfin spawning preference for cool, low-salinity, water is well established in literature, and we see it here.



The first November Longfin was caught at Station Art2.  I owe much joy and job-satisfaction to this fish.

It was Hobbs’ discovery of Longfins in Artesian Slough by 2012 that first caught my attention.  As Compliance Manager for the San Jose-Santa Clara Regional Wastewater Facility, the largest discharger in the Bay Area, I deduced that presence of this threatened fish downstream of our treatment plant was a clear sign that we must have gotten something right.

We must understand what keeps these smelt hanging on here when they seem to be slowly disappearing everywhere else in the Bay and Delta.  (BTW: I retired earlier this year.  I am now repaying my debt to the Longfin.)



A second batch of Longfins was caught further down Artesian Slough on the 11th.  The above photo shows a mature fish with five younger Longfins from station Art3.  Pending confirmatory otolith analysis, it is presumed that the bigger, bright silver fish is a two-year-old.  The little translucent guys probably hatched earlier in 2018.  Hopefully, we will soon know if the two-year-olds were locally hatched and now returning to spawn.


Jim Hobbs records data for three Longfins caught in Dump Slough on 11 November.  This is very exciting.  Dump Slough originates from the Lower Coyote Creek bypass channel on the south side of Newby Island Landfill (hence the unofficial name “Dump Slough”).  The fresher marsh here did not exist until the bypass was constructed by the Santa Clara Valley Water District in 1988, so this is relatively new restored habitat for smelt – and it’s working!


Four of the five Longfins caught in Pond A19 later the same day.  Here again we can see at least two age classes, young-of-year and older.  Literature tells us that Longfins typically live two years, occasionally surviving to the third year.  It would be amazing if Hobbs Lab discovers a three-year-old fish in this bunch.

Remember that Ponds A19 and A21 were breached in March 2006.  This 12-year-old restored habitat is already supporting multiple generations of a threatened fish!  Someone deserves a gold star for this one.


Birds in Pond A19.  Pond A19 mudflats also feed a large number of shorebirds as tides surge in and out.  The above photo was taken as high tide was rolling in.  American Avocets pick at benthic amphipods and other invertebrates which, in turn, are scrambling to collect food or search for mates in the incoming water.

I presume most of the bird food is comprised of corophium.  But, I would not be shocked if other types of gammarid amphipods or pile worms were also on the menu.


Avocets browse right along the water’s edge as the tide rises.


Sometimes I see Avocets march as a group right along the waterline, picking and walking like a little freight train.


Smaller birds, like these Least Sandpipers, forage over higher parts of exposed mud.


Avocets have a particular advantage that they can continue to forage the deeper water as the tide continues to rise.


Meanwhile, dabbling ducks also loaf and feed in the Pond’s deeper waters.


Our favorite bugs – Corophium and Mysids.  The birds point out that sloshing tide is the pump that keeps this carbon-loop cycling.  Dissolved oxygen, phytoplankton, and zooplankton are constantly replenished.  Millions of slightly larger amphipods, like corophium, or pelagic bugs like mysids, feed off the cycling food supply.  Then birds and Longfins feed off mid-sized bugs.  The sun provides most of the energy that drives the system.  But, we must not ignore the energy contributed by the tides.

Bird Food?  Local records consistently identify Americorophium spinicorne as our endemic type of corophium.  But, several types that live here, and around the world, look and function about the same.  I have mentioned before, that corophium are identified as a keystone species influencing mudflat sediment dynamics in other parts of the world.  Example here:

Fish Food!  Jim Hobbs has identified at least four species of mysids in Alviso Marsh Complex that bloom at different parts of the year and always seem to be present.  Mysids are a well-known food for estuarine fish.

If you are a fish fancier, you can buy mysids:  Or, you can even raise them yourself:


Longfin raw data as of 11 November.  Thus far in 2018, Jim Hobbs’ Longfin Study is showing that our local South Bay “Alviso Marsh Complex” is hosting a significant population, possibly the biggest population, of Longfins in San Francisco Bay.  But, we do not know yet whether this group is separate and self-sustaining or if it is part of a spill-over population from North Bay.


25 November:  Two age classes of Longfins at Station Alv3.  Examination of otoliths (ear stones) will confirm the exact date of hatch for the above fish and hatch-month for the fish at bottom.  Additional otolith chemistry may tell us whether these fish hatched here in the Alviso Marsh Complex or whether they hatched in the North Bay.   And, if otoliths can’t tell us, genetics will.

Notice the older fish has “silvered up.”  Age, and exposure to saltier water, appears to contribute to the silvery appearance in many species of fishes – says Dr. Lewis.   And, we see it here.


We entered Pond A21 at close to 1:00 pm just before higher-high tide.  The moon was full two days prior, on 23 November, and Earth is approaching perihelion, closest orbital point with the sun just after New Year.  Those two factors contribute to this being one of the higher-high tides of the year.  All but the tallest spartina was submerged.


The tide was so high …  that I could look over the Pond levee and watch two hunters motoring down Mud Slough on the north side.  It’s a weird feeling floating over so much water in the pond.  The combination of spring tide and perihelion only happens on the Winter side of the year. And then, you only have a few hours during a few days near full moon to experience it.


Silvery two-year-old beauties caught in Pond A21 on 25 November.


Longfin suntan?  I started tracking color development in Anchovies, Shad, Herring.  It is basic biology that fish develop color for camouflage, UV protection, and for mating display through dispersal of combinations of different types of chromatophores in the epidermis.

I think we are seeing “melanophores.”  Melanophores are the type of chromatophore that expresses black or brown color.  These black punctilations over the top of an older smelt may be providing some degree of UV protection and/or camouflage.  There are also a few glimmers of blue-green that could indicate traces of guanine crystals in iridophores which I don’t expect in this species of smelt.   Maybe some smelt specialist could help explain what we see here?



Longfin suntan in a different fish. 


Another Longfin from Pond A21 with a very full belly.  Literature tells us that Longfins eat tiny crustaceans.  From Jim Hobbs’ work, we know that mysids (tiny shrimp-like crustaceans) are an important part of the diet and are abundant here.  Saving the Longfin may depend just as much on saving the mysid and everything the mysid eats.


Longfin bonanza from Pond A21.  The majority of these fish appear to be the older second-year cohort which may portend a very good spawning year.


Pond A21 Longfins bagged and tagged.  It is ironic and sad that we must sacrifice increasingly rare Longfins in order to save them.  Fish collected this day will be used to characterize the life history of this population.

A 2015 article authored by Hobbs and Moyle gives a good summary of Longfin status and the importance of monitoring this splinter population:

Later in December, the Hobbs team will commence what I call “Operation Smelt Rescue.”  This will be a complex operation to capture and transport live smelt to an aquaculture facility in Tracy.  Hopefully, some fish will survive as human-raised brood-stock that can be used as a hedge against extinction.


Jim Hobbs recording more Longfin vital data on 25 November.  


Pond A21 at high tide is a haven for dabbling ducks too.  Ducks are shy, so I have a hard time getting a decent photo of them.   From distant blurry photos, I could make out Northern Shovelers, American Widgeon, Green-winged Teal, and possibly Gadwalls.   Pond A21 is off-limits for hunting, and ducks figure this out pretty quickly.

It appears that tidal habitat is good for both birds and Longfins.


Emily Trites watching as we pass by people out for Sunday fishing on the 25th.    We observed many other biological wonders over this broken weekend, like another unprecedented 11,000 crangon shrimp for 2018.  But, I must save the rest for a second posting.  The smelt, birds, and restored ponds needed a post of their own.

If we save the Longfin, it will be with the help of a community of bugs, fish, birds, and people.

Stand by for Operation Smelt Rescue!  Or, Save Our Smelt (SOS)!





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