Fish in the Bay – September 2019, UC Davis Trawls – Exopalaemon Blow-Out plus more Anchovy Color Investigation.

I did not join the September trawls, so the photo record is a little sparse.  It was an interesting month nonetheless.

UC Davis boat getting underway in Artesian Slough on Sunday, September 8th.


Trawl map.


Bay-side station trawling results.


Upstream of Railroad Bridge.

As summer temperatures dropped a degree or two, DO improved a bit at all upstream stations.  August through September tends to be the low DO time of year.  Summer warmth amps up all biological activity.  Photosynthesis by billions of single-celled phytoplankton (the phytos) churns out oxygen as soon as sunlight hits the water.  But the phytos are usually more than matched by oxygen-sucking respiration from billions upon billions of bacteria and larger critters … that feed on the phytos, as much as anything else.

Many of our bigger critters (like Anchovies) are adapted to life in low DO.  This is where the food is, so all they need is just enough DO for survival.  But, how low can they go?


1. Highlights from September trawls.


Mississippi / Inland Silversides caught at station Art2.

Inland / Mississippi Silversides.  Artesian Slough is currently the Inland Silverside hotspot.  All of the 152 Silversides caught in September were from stations Art2 and Art3.  I checked back through some early 2019 records though.  This fish found refuge in Ponds A19, A20, Dump Slough, and Alviso Slough when the weather was wetter.

Silversides invaded practically all of Northern California’s fresh water since introduction in Clear Lake in 1967.

According to Chernov et al. (1981) there are subtle differences between “Mississippi” (M. audens), “Inland” (M. beryllina), and even “Florida” (M. peninsulae) Silversides.  To me, these species identifications may be a distinction without much difference.  This is a highly adaptable fish, not unlike our native Sticklebacks or Northern Anchovies.  Adaptability is the secret to their success.


Starry Flounder, one of only two caught in September.

Starry Flounder are down!  The two Starries caught this month compare very poorly with 2017 and 2018 September catches.  We expect large numbers of young spawning Starries about this size to be congregating along the deep channels of Lower Coyote Creek by now.

In contrast, California Halibut may be doing a bit better this year: 13 were caught.  It is still not a good year for halibut, but the inverse correlation between Starries and Halibut is interesting.


Micah Bisson with a Striped Bass from UCoy1.

Striped Bass are a little down this year which might be a good thing.  They are not native.  Pretty much any native fish we care about, like Northern Anchovies, Pacific Herring, or Longfin Smelt, are forage food for this voracious predator.  Keep in mind that any Striped Bass much larger than the 14-incher shown here can easily outswim the otter trawl net, so there could well be big ones here that we never see.


Bay Pipefish from DMP2.

Bay Pipefish. So far, we have only seen 13 this year, far fewer than in previous years. This may be a fish that does not do as well in wet years.


Two Corbicula clams from UCoy1.

Good news: these non-native Corbicula clams continue to be rare odd-balls in our brackish marsh.  However, their presence here indicates there should be more of them upstream.  Since Corbicula are primarily freshwater clams, it is not entirely surprising to find them this far downstream in a wet year.


Harris Mud Crab from DMP2.

Trawl surveys in the 1980s recorded Harris Mud Crabs as the most commonly caught invertebrate in this area.  Now, they are not so common.  I often wonder what exactly changed with respect to mud crabs.


Wood Pallet caught at UCoy1.

Good news!  No tires were caught this month!


Fish and Bug Matrix.  This is the late-summer update to the Matrix.

  • So far, 2019 has been a very good year for Shad, Herring, and Longfin Smelt.
  • Striped Bass and Yellowfin Gobies have declined, at least temporarily, and may be a good thing.
  • Catches of Flatfishes Starry Flounder, Cal. Halibut, and Tonguefish have declined from previous years.
  • We have not yet seen a big Crangon shrimp rebound. Instead, Exopalaemon shrimp population is exploding, as explained further below.


2. Late-Summer Odd-Balls.


Pacific Herring.  All three Herring were caught in Ponds A19 and A21.  The vast majority of Herring caught in Lower South Bay are tiny baby recruits shortly after Herring-spawning-time in March.  Catching a Herring in September is rare, catching three or more between May through November has never happened until this year!

I briefly glanced back at datasheets from March and April 2019.  Baby Herring in March generally ranged 30-to-40mm in length.  By April, the range measured fish sizes widened: 25-to-50mm.  I presume this may have indicated an extended spawning/recruitment season corresponding with abundant and extended rains.

And now, three jumbo-sized 70-to-90mm long behemoths show up in September.*  Likely as not, these three may be Young-of-Year stragglers that missed the April through May seaward migration.

More importantly, 2019 appears to be a very good year for young Herring.  526 have been caught so far this year.  Some of this increase might be attributed to more thorough identification of baby fish by the UC Davis team the last few years.  But, on the other hand, these larger stragglers are easily identifiable and have not been seen in previous years.

(*Note: These September Herring are “behemoths” only by Alviso Marsh standards.  Adult Herring typically grow to 9 inches or longer.


Longfin Smelt.  Once again, a rare summertime/early-fall Longfin Smelt was caught on Saturday at station Coy3.   According to what we know about Longfin temperature and salinity tolerances, this fish should not be here in August or September.


White Sturgeon???  The Hummingbird depth finder detects large objects below the boat.  Once in a while, a big fish shows up.  This one got away.


3. Shrimp Wars 2019.


Big tub full of Exopalaemon from UCoy2.

2,862 Exopalaemon shrimp were counted.  This is over 1,000 more than have ever been caught on a survey weekend.   


Updated Shrimp Chart. In comparison to three of the previous five years, Crangon catches in August and September were pretty good.  But, following the big population surge in 2018, I continue to hope we will see a lot more of them soon.

Non-native Exopalaemon shrimp are booming closer to the fresher ends of the sloughs.  I have seen a few papers that state that Exopalaemon shrimp don’t tolerate salinity much above 4 ppt.  This is apparently WRONG!  Our Exos appear to be having no problem hanging out in double-digit salinity.  Nonetheless, Exos primarily inhabit the fresher water.


Updated Exo Chart.  Exos have only been in Lower South Bay sloughs since around 2012.  Their populations appear to be exploding since 2017.

(BTW: Exopalaemon modestus was reclassified into the Palaemon genus in 2013.  We continue to refer to them as Exopalaemon rather than change all the datasheets and tables.)


4. Pond A19 update.


Pond A19 on September 8th, 2019

Pond A19, still looking a little bare.  You may recall that winter rains freshened these marshes considerably last winter and spring.  By early summer, we saw numerous tall stands of California Bulrush for the first time in this pond.  But as expected, summertime salinity appears to have knocked down all but the hardiest bulrush stands.

Variable salinity plays a large role in keeping this pond sparsely vegetated.  During dry years, large clumps of spartina came close to covering most of the exposed mudflat.  Then, 2017’s late winter flushing knocked spartina down to the rhizomes.  Spartina rebounded quickly, but then the long-wet winter and spring of 2019 allowed extensive patches of California bulrush to recruit.  … Now, salinity has crushed the bulrush.  We appear to be back to square one.  Hopefully, mudflat elevation is slowly rising through all these vegetation swings.


5. Northern Anchovies and the Color Mystery


A collage showing three views of the same Anchovy.

Northern Anchovies. 340 Anchovies were caught in September.  Almost the same numbers were caught in September of 2016, 2017, and 2018.  So, we appear to be on track to have a fairly good Anchovy year in 2019.

Anchovy #2, two views.

Most of the Anchovies caught this year continue to show golden-green backs.  Very few deep greens or vivid blues seem to have been caught in 2019.

This summer’s Anchovies seem to have the shorter overall length and deeper bodies of estuarine brown-backs, but color traces at the crown of the heads and on the dorsal sides are unmistakably golden green.


Anchovy #3, two views.

Given the iridescence, is difficult to evaluate an Anchovy’s hue from one photo alone.  Colorful iridophores tend to express themselves in the crown of the head first, then along the lateral line, and finally over the entire dorsal surface – presumably in response to ocean temperature, salinity and possibly other environmental factors.  The colors are persistent, but difficult to see under different light angles.


6. Anchovy color supplement – August 2019.


Anchovy collage from station Alv2 on August 10th.

As mentioned in the August blog post, I attempted to document Anchovy colors more systematically.  I did not have time or space to include the results of my color survey then, so now is the time.


Anchovy collage from station Alv3.

On August 10th, Anchovies appeared from golden-green or brown at station Alv2, then little greener downstream at Alv3.   But, color variation from one fish to another is difficult to quantify.


Anchovy collage from station Pond A21 … #1

It got tougher when we got to Pond A21.  With 90 to 100 anchovies from each trawl, it was impossible to photograph each one in an organized way.  I attempted to line them up in the same direction in one hand and take photos with my free hand with mixed results.

Most Anchovies from the Pond also appear golden green, but there seem to be more colorless grays and browns in the mix.  Hard to tell.


Anchovy collage from station Pond A21 … #2

DO was low in August. These Anchovies were not holding up well from being held in a bucket then photographed.  Risk of Anchovy death increases with every second out of Bay water.  So, I attempted to speed up the process.  I went from photographing handfuls to taking their picture in the tray with water.  … But, it was still too slow.

(BTW:  I posed this question last month: Why do Anchovies routinely accept discomfort and stress of entering low DO water?  A retired former colleague called me to suggest that predator avoidance could be the reason.  It is not a bad suggestion.  Low DO in the ponds and sloughs literally throttles high-respiration predators like Leopard Sharks and Striped Bass.  Leopard Sharks and Bat Rays have a strong documented aversion to low DO areas, for example.  I am not convinced that Northern Anchovies are consciously aware that they are safer in a low DO zone.  But, there is little doubt that a pond or slough is literally a “safe harbor” from predators for a tiny fish able to tolerate low DO.)


Anchovy collage from station Pond A21 … #3

In desperation, I resorted to a “Shoot and Toss” method.  I simply grabbed handfuls of Anchovies and shot the photo as I heaved them overboard.  The problem with this method is that it gives no chance for closer examination.


Anchovy collage from LSB … the “deep Bay.”

When confronted with 157 Anchovies at station LSB1, I realized that photographing each fish with minimal casualties was not going to be possible.  So, I improvised a “Tubful” method.

However, I could immediately see a problem: brighter green anchovies are easier to see in the tub.  The less colorful ones fade into the background and are harder to count.  Plus, a large percentage get photographed at an odd angle that shows no dorsal color.


Anchovy collage from LSB – #2.

So, I returned to the “Shoot and Toss” method.

One firm conclusion:  Anchovies in the Deep Bay (aka, LSB stations) generally appear less yellow and more blueish, e.g. green color expressed at the crown of the head or along the lateral line looks more blue-green than golden-green.  Also, the dorsal-sides look a little more translucent/clear in the Deep Bay as opposed to brownish in the Pond and sloughs.


Anchovy collage from LSB – #3

A few Anchovies from the Deep Bay were clearly faded blue-backs. Most were greenish.  However, we have not seen many vivid Blue or Green-backs this year.


Anchovy collage from station Coy4

Returning to Coyote Creek stations, again it seemed apparent that Anchovy colors trended a bit more yellow to brownish.  The green hues a little further upstream looked more golden-green, less blue-green.

I will continue to investigate Anchovy colors, but not so rigorously in the future.  The fish don’t need the stress, and time is on our side for now.

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