Fish in the Bay – December 2019: Part 2, Gobies and more wet-season erosion.

Some additional December observations and 2019 end of year clean up.

Fish & Bug Matrix: Six good years of comparable monthly trawling data.

2019: another year of data in the bag.  The table has been updated to show 2019 end-of-year totals. Some nice surprises:

  1. Yellowfin Goby and Corbula Clam populations declined somewhat. Yellowfin numbers are lowest ever!
  2. Crangon shrimp are doing well – not as good as last year, but still very good.

Interesting surprise:  Exopalaemon shrimp populations continue to grow in fresher upstream areas, for better or for worse.

  • Remember, these are raw critter counts unadjusted for QC or rare missing trawls during a given month – like when we couldn’t trawl station LSB2 due to heavy weather a few months ago!   Take it all with a large grain of uncertainty!
  • 2014 Exception: all trawls in 2014 were 5-minutes as opposed to 10-minute-trawls all subsequent years. So, simply double all raw numbers shown for 2014 to make them comparable in terms of “Catch Per Unit Effort” (CPUE).
  • The UC Davis lab has additional monthly trawling data going back to 2010, but stations and trawling times were less standardized. I do not feel comfortable displaying earlier data at this point.


1. Longfin Smelt and a new paper by the UC Davis “OG Fish Lab.”

Another Longfin Smelt from Pond A19 caught on December 8th.

Bad News:  Longfins have not yet rebounded this season.  Only 71 have been caught after last February.  We were hoping for a bigger bounce this November or December.  This fish is rapidly disappearing from SF Bay.

These last wild-caught fish are sent back to one lab or another.  Otoliths, livers, and stomach contents are studied at UC Davis’ Otolith Geochemistry & Fish Ecology Laboratory (OG Fish Lab) to determine the secrets of their survival.  Other fish are collected for broodstock at the UC Davis FCCL lab in Byron in case all else fails.  Time is running out!


ATTENTION:  Dr. Levi Lewis, manager of OG Fish Lab ( announces posting of two recent open-access articles published by the Ecological Society of America (links below).

The articles document discovery of rare Longfin Smelt spawning habitat in ponds restored under the South Bay Salt Pond Restoration Project near San Jose/Silicon Valley.  Title: “Newly discovered spawning and recruitment of threatened Longfin Smelt in restored and underexplored tidal wetlands.”

Paper is linked here: and here

Photo illustrations by Levi here:


2. Shrimp and Mysids.

Exopalaemon shrimp, station DMP2, December 8th, 2019.

Exopalaemon shrimp continue to dominate fresher upstream stations.  These shrimp first invaded North Bay around year 2000.  By 2012, they had spread to this area along Upper Coyote Creek.   They are our newest significant invaders in this system (aside from Bald Eagles!).  Like it or not, they are here to stay!


Jon Kuntz sorts through a small pile of mysids in Artesian Slough.

I am showing a few more December photos of juicy “Neomysis kadiakensis” mysids because they are so important.  From what I read last month, the big fat females swim into the marshes from the channels to deliver their broods.  In the North Bay, near China Camp, they were documented as brooding three times per year, or more.  Here, our most noticeable brooding, or at least the population explosion seems to coincide with the rainy season.


Close up of big fat mysids in the tray.  Each mysid is roughly 1 cm long.

Practically all the big Mysids this month have a tan/yellow mass behind the head.  In theory, all the big ones should be females entering the upstream marshes to release young.  Mysids are also called “Opossum Shrimp” because they have an opossum-like pouch for holding larval young.  Perhaps the yellowish masses we see this time are batches of young???


Tiny mysids from the mysid net.

Tiny mysids, about the size of brine shrimp, were caught in the finer “Mysid Net” at various stations.  Are these, shown above in the collection jar, some of the recently released next generation?  We may know from mysid counts in a few months whether 2020 will be a good or bad year.

Mysids are important food for Longfin Smelt.  Unfortunately, all the other critters eat mysids too.


3. Goby World.


Yellowfin Goby at Alv3 on 7 Dec

Noxious and invasive Yellowfin Gobies were first reported in SF Bay in 1963.  They have been our dominant goby for many years.  (Presumably, most tiny “Unidentified Gobies” counted in past years were also baby Yellowfins.)

There may have been an upset in 2019.  Yellowfin numbers fell again in the local area.  From 2015 through 2017, roughly 2800 Yellowfins were caught per year on average in all Lower South Bay trawls.  The number dropped to 1432 in 2018, then dropped again to 692 this past year.  Baby fish month in April was not quite so big in 2019, and we seem to be seeing more baby Shimofuri and Shokihaze gobies.

Are Yellowfins on their way out?  Or, will their population rebound?  Time will tell.


Shokihaze Gobies photographed at Coy1 on November 11th, 2019.

Shokihaze Goby (non-native).  According to reports, this is our most recent goby invader.  They were first reported in the Bay in 1997.  Shokihazis have been our second most common goby for at least several years.  They may take the top goby spot if Yellowfins continue to decline.


Shimofuri Goby (non-native).  Top: puffy-cheeked buccal respiration-mode.  Bottom, same Shimo, catching its breath in the photarium.

You can see how the Shimo’s cheeks are puffed out in the top photo.  The fish is respiring with his buccal cavity.  It is not a natural look, but it helps a goby survive out of water.

Fused pelvic fins on its underside make a sucker disk.  Most gobies, including Yellowfins, have that pelvic sucker.  They use it to hang on rocks against currents and mild tide surges.


Shimo at Dump slough.  Top: in the hand and breathing hard.  Bottom: flaring its fins next to a Prickly Sculpin in the Photarium.

Shimofuri or Chameleon?  The color of the border-stripe on the anal fin distinguishes a Shimofuri Goby from a Chameleon goby.  Unfortunately, the anal fin is usually folded and hard to see.  Orange or white?  The stripe shown above is pale, but look more orange than white to me … Orange means it is a Shimofuri, I suppose.

How often are these two gobies misidentified?  I am not confident that we can yet distinguish our Shimofuris from Chameleons.


Baby Shimos on December 7th.

Baby Shimofuri Gobies.  Young Shimos (and Chameleons) have longitudinal stripes.  We continue to catch a few baby shimos at several stations.  They were getting bigger by December.  Shimos are still far outnumbered by Shokihazis and Yellowfins, but they are becoming more common.


Gobies caught in South Bay Otter Trawls from Bay Study data.

Gobies are changing in the bigger South Bay too!  I made this clustered-column chart from CDFW’s Bay Study Data: 

Monthly catches of four species from 1980 through 2017 are depicted:  Chameleon Gobies (CHAGOB in green), Shimofuri Gobies (SHIGOB in blue), Shokihaze Gobies (SHOGOB in red), and Yellowfin Gobies (YELGOB in yellow).

  • Yellowfin Gobies (yellow) were usually the most numerous gobies before the mid-1980s.
  • Chameleon Gobies (green) dominate after 1997 with few exceptions.
  • Shokihaze Gobies (red) surged after the mid-2000s. A huge spike of Shokihazes in late-2014 through 2015 may have coincided with warm sea temperatures or dry conditions.

Some additional thoughts: 

  • South Bay otter trawls are in much deeper water – not marshes. It is very possible that Yellowfins simply don’t inhabit those depths in great numbers.
  • Fewer South Bay trawls were performed in 2016 and 2017 which artificially contributes to the apparent decline in numbers.
  • Clearly, Shokehaze and Chameleon Goby populations exploded over recent decades. A Shimofuri explosion might be buried in these data as well.


Arrow Goby caught in Artesian Slough on December 8th.

Native Arrow goby.  Long sinuous body and a big mouth.  Corner of the mouth extends beneath and well behind the eye.


Cheekspot Goby from LSB1 on December 7th. 

Native Cheekspot Goby.  Small mouth + iridescent blue-black spot on the cheek.

There is a lost native Goby: “Bay Goby.”  Bay Gobies were commonly caught in Lower South Bay trawls in the 1980s.  We have not seen a Bay Goby here for at least two years!!!  Albeit, they are still found in South Bay to the north of us.  Why did they leave?

Summary of Goby invaders.  (One invader to SF Bay per decade from the 1960s through 1990s.)

  1. Yellowfin Goby – Large goby with a longer snout.  Invaded in 1963.
  2. Chameleon Goby – WHITE stripe on the anal fin. Invaded in 1978.
  3. Shimofuri Goby – ORANGE stripe on the anal fin. Invaded in 1985.
  4. Shokihaze Goby – aka “Bearded Goby.”  Invaded in 1997.


4. A Whale’s-Eye View.

Sonar vision at Coy3!  In 2019 it became increasingly clear that our modern-day acoustical depth finder gear has become comparable to the sonic vision of a toothed whale or porpoise.  We can see big fish, and even some little fish, as they get beamed by our Sperm Whale Eye.


Composite of Sonar Vision images from five different stations.

I started grabbing screenshots every chance I got.  These are all big fish (or seals) missed by our trawling surveys.


5. Good Vibrations.

Allen Hyunh and Jon Kuntz taking a break as we motored to another trawling station.


Pregnant? Potbellied prickly sculpin from Alv1

We caught two potbellied Pricklys at upstream stations over the weekend.  I am guessing that the one shown above is a pregnant female.  If so, she will be seeking an eligible male for spawning.

From what I read, spawning should usually be a little farther upstream, but who knows?  Eggs are laid in stream-side rocky or vegetated sheltered places.  Males guard the eggs until they hatch.

As always, Prickly Sculpin are good indicators of healthy upstream water quality.


Bay Pipefish from December.

Bay Pipefish bounced back a bit, but we have not been catching as many last two years, … possibly owing to wetter weather?  I always assume pipefish are good indicators of abundance of copepods, rotifers and the other tiny critters that they eat.


Red Algae and green Ulva samples from December.

Red algae must be an important component of the food web here.  It also might be dense enough to provide subtidal mudbank cohesion against erosion.  I know for certain that these red algae serve as an anchoring matrix for snail eggs and tunicates.  I can think of a lot of important things this subtidal red weed might be doing.

A couple of highlights:

  • Coy4 (top right panel): Broadleaf portion of Cryptopleura.  I had not seen this before.  I get lost in all the google search images of red algae.  If any red algae experts know what this growth represents, feel free to chime in.
  • Coy2 (bottom left) Cryptopleura turns green? Portions of this robust ball of Cryptopleura are green.  This link from UC Berkeley mentions that some species of red algae turn green when phycoerythrin pigment levels are low.   Does direct sunlight exposure at the surface cause his algae to green-up?


6. Marsh-Level Rise Continues?

Baylands & Creeks of South San Francisco Bay

Historical Baylands Map courtesy of the Oakland Museum:


Modern Google Map of the same geographic area

Update on Marsh Growth and Geology.  The entire marsh area north of the town of Alviso subsided at least two feet from the 1930s through 1968 according to Poland and Ireland (1988):

Two feet of subsidence, combined with at least 4 or 5 inches of sea-level rise and completion of several dams that shut off significant sediment supply, should have resulted in drowned marshes across the area. … However, against all expectations, marshes grew and encroached into all the channels over several decades – so it seems.

Calaveras Point, where the seals haul out, and “Mud Island” (my name for it – I don’t know its formal name) have both emerged from the Lower Coyote Creek open channel while I watched over the last 30 years.  We all know that marsh rises.  But, how fast?  More importantly, do marshes rise fast enough to outpace “sea-level rise?” 


This shot was taken near location 1, “south bank of Lower Coyote Creek.”  The higher ground 100 feet in the background is the Pond A15 levee.  I believe this fringing marsh was open water in the 1930s or 1940s when that levee was built.

As happened last year, winter rains softened marsh soils leading to sloughing of large chunks of mud and vegetation into Lower Coyote Creek.


This photo looks eastward along the marsh shore from roughly the same location #1.  From visible appearance, I would assume that this crumbling shore must be receding from erosion.  But, historic maps indicate marsh expansion.  I continue to wonder if land here is advancing due to plant-driven carbon sequestration.


Location 2 from the map: western tip of Mud Island.  Mud Island was an unvegetated subtidal mudflat in the early 1990s.  It only poked above the waves during the lowest of low tides. Today, it is covered in pickleweed, cordgrass, and other plants, and stands well above Mean High Water.  … And now this: Giant mud chunks sloughing off Mud Island!

Plant growth and decay must be contributing to Marsh-Level Rise.  I don’t think sedimentation alone explains it.  Is this marsh growing faster than sea level rise?


Location 3:  West Bank of Alviso Slough.  As noted earlier in 2019; long portions of Alviso Slough’s west bank are clearly crumbling.  But, I don’t detect expanding width in the slough itself from naked-eye observation.

Pond A6 downstream, and the large Pond A8 Complex upstream, were opened to circulation into Alviso Slough after 2010.  All that extra acreage of tidal ponds adds to velocity and volume of tides that slosh through Alviso slough.  This likely accelerated local erosion.  Nonetheless, the marsh does not appear to be diminishing as near as I can tell.

Let’s keep watching!

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