Fish in the Bay – by James Ervin

19 November UC Davis Trawl – Part 1: May the Flush be with us. 

Hello everyone.  I spent nice sunny, albeit a bit chilly, day with the UC Davis/Hobbs crew on Sunday, 19 November.  I rode along for the Artesian Slough and upper side of Coyote Creek fish trawling this time.

Before UC Davis fish researchers showed up, I met with two of our Regional Wastewater Facility operators, Mike McLaughlin and Rami Hijazeen, as they were collecting samples at our outfall, AKA the “Weir-Bridge.”  This is the final point where roughly 80 million gallons per day of treated Regional Wastewater Facility effluent flows into Artesian Slough and the Bay.


Have you ever seen such crystal-clear effluent?  It is amazing to think that this water was “raw sewage” just 8 to 10 hours earlier.  Operators like Mike and Rami make it happen.



As I admired the outfall sample, a “gulp” of Double-Crested Cormorants few by.  Until that moment, I never thought that cormorants flew in large flocks.  I also did not know that a flock of cormorants is referred to as a “Gulp.”  But, there it is in the on-line dictionary.

Map of Saturday & Sunday trawl locations:

Saturday’s Catch – Downstream side:













Sunday’s Catch – Upstream side:












Dr. Levi Lewis managing the otter trawl net as we passed through Artesian Slough.

Native Crangon again outnumber non-native Palaemon shrimp. 

Abundance of Crangon shrimp reflects impact of freshwater in the system since the big Flush of February 2017.  More freshwater favors Crangons over Palaemons, and the trend continues.  Crangons got scarce during dry years, now they are abundant again.  The big spring flush apparently stimulated Crangon recruitment.  More recent rains in October and November are sustaining them.  Exopalaemons also like freshwater, but they tend to be constrained to upstream areas.  From an ecosystem perspective, it may not matter much which shrimp species dominate, but Crangons are native, so we like them more.

C. franciscorum up close:

Below – C. franciscorum at bottom, 5 Exopaleamon (rounded rostrums) at top

More American shad and Threadfin shad! 

(Shad are non-native, but we like them anyway.) Silvery and iridescent American shad is arguably the most beautiful fish we find in Lower South Bay.  Threadfin shad are miniature close-cousins of the Americans.  Both species are “Pelagic fishes” that have been in decline in the Sacramento/San Joaquin Delta over recent decades, so it is very good to see them here.  Their greater abundance is an aftershock of the big freshwater flush earlier in the year.

Comparing last November to this year:

  • 7 American shad were caught in November 2016 versus 65 this weekend.
  • 1 Threadfin shad was caught in November 2016 versus 52 this weekend.

Four Threadfin shad and one young American shad shown below.

The American shad is closest to my thumb.  It has five faint spots on its side versus the single prominent black spot seen on Threadfin shad.  Threadfins also have a long filament-like “thread” that extends from the base of the dorsal fin which can’t be seen in the photo.

American shad can grow to over 2 feet long.  This larger American shad was caught Lower Coyote Creek on Sunday.


More Striped bass! 

 Nine Striped bass were caught this weekend versus only 4 in November 2016 – not a huge difference considering the variability in Striped bass catch numbers, but still a difference.  Striped bass are a welcome but mixed blessing:  desirable sport fish, pelagic species otherwise in decline, but they are non-native and ferocious predators that eat everything else.

Longfin smelt!  

State threatened Longfin smelt have returned in larger numbers compared to last year.  You may recall that Dr. Hobbs documented larval Longfins in Artesian Slough and adjacent salt ponds for the first time in spring of 2017 following the February Flush.  The finding is supported by literature describing cold temperatures and low salinity as triggers stimulating Longfin spawning.

In the opinion of Jim Hobbs, some of those spring recruits are adding to the Longfin catch numbers now:

  • 4 Longfins were caught in November 2016 versus 20 this weekend.  (13 of the 20 Longfins were netted in restored ponds.)

Northern Anchovies are way down!  Some species don’t like freshwater flushes and Northern Anchovies are in that group.  Numbers from this weekend may be more confirmation that Bay-spawning “Brown-backs” got clobbered by freshwater last spring.  Ocean-going “Green-backs” were probably less affected, but they have mostly migrated back out to the open sea by now.  This makes a big difference in 2016 and 2017 fish totals:

  • 2450 Anchovies were caught in November 2016 versus 18 this year!

Photo below shows one of four Anchovies (a Green-back) found on Sunday, below a Longfin smelt; both fish caught in Pond A19.

Other random fishes.  

Young Starry flounder have migrated downstream, so only two were seen on Sunday.  This Starry from an Upper Coyote Creek station has several mysids stuck to its side and fins.

 Ubiquitous, and noxious invasive, Yellowfin gobies were seen at 15 of 20 stations this weekend in fairly typical numbers.  I tried to get this one to flare its colorful yellow fins for the photo, with mixed success.

Good news!  Fewer Corbula clams.

This weekend only 87 Corbula were caught in trawls versus almost 1000 just two months ago in September.  Admittedly, otter trawls are not a great survey method for clam populations, but fewer Corbula is better no matter how you measure them. (There was concern that the February Flush would cause Corbula populations to explode and there did seem to be a bump in Corbula numbers through summer this year.  Hopefully, low numbers collected in these November trawls reflect a Corbula crash.  No one wants more Corbula!)

Overall fish numbers for this November were way low compared to 2016, but this is entirely due to near-absence of Anchovies this weekend.  Otherwise, fish numbers were comparable to last year but tilted toward favoring fish that like it fresh.

Fish in the Bay –

19 November UC Davis Trawl – Part 2: Tiny Bugs & Carbon Cycling

Folks.  For November, I broke this fish report into two parts because; a) without the Anchovies, there were fewer fish this weekend, and b) we need to talk about Bugs & Carbon.

Carbon in the water.  November weekend (18-19th) was cool, sunny, and very calm.

Turbidity at slough stations ranged from around 15 to 30 cm.  I assume much, if not most, of the murkiness was due to phytoplankton in the water column. For example, here at the midpoint in Artesian Slough, where freshwater nudges against the tide, we can see soupy phyto scum against the water surface. That is some murky water!

Step one – Chlorophyll.  We (in San Jose) began taking twice per month Chlorophyll-a measurements since May of this year.  Chlorophyll is an index of phyto abundance that reflects densities of single-celled phytoplankton as they harness sunlight and carbon dioxide to synthesize sugars, carbohydrates & proteins via photosynthesis.  Data collected thus far in 2017 shows that chlorophyll-a in Lower Coyote Creek and nearby sloughs tends to be screamingly high.

Bay and Estuarine “normal” chlorophyll values are in the range of 5 to 20 ug/l.  Concentrations around 30 to 50 ug/l are considered “blooms.”  Based on the results shown in the graph below, one might characterize at least three of our stations as experiencing extreme phytoplankton bloom from June through at least October 2017. 

Chlorophyll numbers over 100 ug/l are usually considered insane!

Whether extreme phyto blooms are good or bad depends on where the carbon goes.  If huge numbers of diatoms eventually die then rot and feed bacteria, oxygen will be sucked out of the system and fish may die.  No one wants that!  But, if tiny bugs and fish feed off this phyto bonanza, and in-turn feed a thriving food web, then nature is doing what we want it to do by cycling carbon up from microbes to fish and birds.


(I am deliberately not discussing Harmful Algal Blooms (HABs) for the moment.  It has been proposed that high Chlorophyll concentrations may corelate to presence of HAB species, aka: “toxic phytos.”  We watch for HAB blooms as well.  And, thus far, no summer-time HAB “Blooms” or biological disturbances have been detected in data through June.  Knock on wood …)


Step2 – Bugs: Copepods and Mysids.  Tiny bugs are the next indicator needed to show whether phyto-synthesized organic carbon is cycling up to bigger things we like.

We see lots of bugs even in cruder, larger-scale otter trawling.  The photo below shows glassy bodied mysids stuck to a clump of mossy bryozoan pulled up by otter trawl on November 19th.  – Interestingly, the mossy bryozoan mass is itself a colony of thousands of tiny filter-feeding zooids that consume and assimilate phyto and bacterial carbon into their own body mass.  To a trained eye, this is a handful of living carbon!

But, otter trawls are for catching fish, not bugs.

To properly catch bugs, tiny nets are used.  Both UC Davis and our San Jose-Santa Clara RWF facility are collecting zooplankton samples at least monthly.  Below, Bryan Frueh is showing one of the tiny bug catching tow-sleds: a smaller Clarke-Bumpus net mounted at top collects the tiniest bugs higher in the water column, like copepods.  The larger “mysid net” at bottom scoops up slightly larger bugs, like mysids.


Jars at the end of mysid and Clarke-Bumpus nets strain and collect bug samples. Photo below shows Dr. Levi Lewis pouring concentrated bugs out of the mysid net receiving jar. 

The bug mass looks like clumps of oatmeal.  But, this is almost pure protein.  From a fish or bird perspective, this is pure food.

Below is a closeup of some of the clear-bodied mysids as found in the field:

These are some of the same mysids after being preserved (I call it “cooked”) in alcohol – next to a dime for size comparison:

Dr. Hobbs & UC Davis fish lab have been documenting mysids since at least 2011




(  Ongoing catches indicate that restored Salt Pond continue to foster these very important manifestations of carbon cycling.

Clarke-Bumpus net catches the tiniest bugs. 

The photo shows one of the Clarke-Bumpus net catch results on 19 November.  This is a mix of copepods and mysids:




These nets also occasionally also catch tiny fish that eat the tiniest bugs

In the example below, a baby Bay Pipefish was caught amongst mysids and copepods.  As you can see, this fish is way too small to eat mysids.  Even adult copepods are too large for that tiny mouth.  This fish must be feeding on naupli (baby copepods) or tinier creatures like rotifers and other ciliates. 

A week later, on the 27th, our San Jose mysid net sampling caught a slightly larger Pipefish yet another indication that we have a lot of fish that eat tiny bugs in our marsh area.







Tiniest bugs.  Numerous fish aquaculture web sites discuss importance of copepods as food for larval fish.  This is one example:

Below was my best copepod macro lens photo from bugs collected in the field on the 19th.


Near the lower middle of my finger tip, from left to right, you can barely make out two, one, and then two, individual copepods. 



Where the bugs are.  Lining up mysid net jars at end of day on the 19th showed where the bugs are.  Eyeball evaluation of bug-volumes concluded that tributary creek stations at “Alviso 3” and “Upper Coyote 2” have more bugs than Bay and Coyote Creek main stem stations.  Pond A21 was in a class by itself – two jars were needed to hold all the bugs.


(Note that some jars show a red color because they were treated with Rose-Bengal stain to aid later lab evaluation.)


Step 3 – Fish. 

If the system supports abundant fish food (eg: bugs), then you are likely to find lots of fish.  Arthur Barros was primary author of a recent UC Davis poster showing fish population comparisons for Alviso, Napa, Petaluma, and Sonoma River areas.  The poster was presented at the 2017 State of the Estuary Conference and is posted at the Hobbs Lab website here:

Hobbs lab data for 2015 through August 2017 clearly shows that Alviso Marsh area has the highest fish populations, however, it makes no conclusion as to why.  For me, this is no mystery at all.  More fish are here because we have MORE BUGS!!!    More bugs = More fish. 

Step 4 –Carbon feeds bigger creatures we like.  Big fish, like this striped bass caught in Pond A19 eat bugs (and small fish).


Big bass, in turn, get carried away by Bald Eagles.


(Ron Lam is a Facebook friend and one of our best photo documenters of our local Milpitas Bald Eagles.)


This Harbor Seal, seen hunting for fish in Pond A19 was also indirectly feasting off the bug bounty on Nov 19th.




The early morning gulp of cormorants, mentioned in my previous post, look for nest sites nearby because this is where the fish are.

Even these two guys, seen fishing in at the Pond A16 discharge point Artesian Slough as we motored out for our day of fish and bug sampling, are benefiting from Chlorophyll and Bug productivity.  (Actually, these two guys were fishing for sport only – catch and release. But, if they had been starving, they probably would have eaten some of the many striped bass we saw them snagging.)

Tiny bugs are important.  Tiny bugs are the carbon-transfer bridge between the microbial/phyto world and the world of bigger creatures we like.


We do not yet know enough about our bugs.




Hobbs Lab Attends Recent Conferences

James Hobbs, Christina Parker, Malte Willmes and Arthur Barros attended State of the Estuary on October 10-11, 2017 and presented the following posters:

Longfin Smelt Distribution: Abundance and Evidence of Spawning in San Francisco Bay Tributaries

Deep in the shallows: Environmental variability and habitat use by native and invasive fishes in San Francisco’s saltmarsh complexes

Thermal resilience of Delta Smelt: What can we learn from otoliths? MW_SOE_2017

Christian Denney attended Northern California Computational Biology Symposium  on October 7, 2017 and presented the following poster:

Use of Discrete Wavelet Transformations to identify groups in otolith chemistry profiles

Little Fish in Big Trouble: The Bay Delta’s Longfin Smelt

Longfin Smelt, is a small pelagic forage “baitfish” that was once one of the most abundant fishes in the San Francisco Estuary.  Our work on Longfin Smelt was recently featured by KCET’s Alistair Bland.  Here is the link to the news piece.

The extreme wet weather we’ve had during winter 16-17 turned the Lower South Bay Fresh for several months. This has resulted in the first successful reproductive event for Longfin Smelt in Lower South Bay since the 1982-1983 El Nino. Longfin Smelt have been encountered in our fish surveys of the Alviso Marsh during the winter months since we began our surveys in 2010.

Longfin Smelt typically arrive in late fall when temperatures begin to cool.  We see them every month during the winter through early spring.  This is typically the spawning season for Longfin Smelt.  We’ve been seeing them in large numbers inside the tidally restored salt ponds along Coyote Creek. They specialize on feeding on mysid shrimp, “estuarine krill”, which also typically increase in abundance in the winter and spring when Longfin Smelt are in the marsh.

Longfin Smelt seek out low-salinity or tidal freshwater habitats to spawn in the winter months. However, the Alviso Marsh in winter is typically too salty for Longfin to successfully reproduce.  In March of 2017 we found our first larval (baby) Longfin Smelt in the marsh. In our April Survey we captured over 200 of this little Longfin Smelt up to about 35mm about an inch and a half in length.  Our largest single catch of 59 fish occurred inside Pond A21, a tidally restored salt pond that was breached in summer of 2006.


Longfin Smelt were listed as threatened under the California Endangered Species Act in 2010 and as a result 8,000 acres of tidal wetland restoration was prescribed by the state to help mitigate the losses of fish in the giant pumps located in the South Delta.  These pumps are the key to California’s agricultural success.  Our work is demonstrating tidal restoration may provide additional habitat for the Longfin Smelt, however, it is unclear whether additional rearing habitat will bring Longfin Smelt abundance back to where it was before it was listed.  We will continue to monitor the abundance and growth of these fish in the coming months. Stay Tuned.



Monitoring Restoration in South San Francisco Bay Oct 1. 2016

Post by Dr. James Ervin, Compliance Manager for the San Jose-Santa Clara Regional Wastewater Facility

I joined UC Davis / Dr. Jim Hobbs fish monitoring survey on October 1st. I was on the Saturday run this time. As explained last month, monthly trawls are performed in Alviso Slough and Bay-side stations on Saturdays. On Sundays of the same weekend, the crew trawls the upstream half of Lower Coyote Creek. Saturday runs are always good for variety. The fish are fewer, but get bigger and weirder as you venture deeper into the Bay.

On this day, we launched from the public boat ramp at Alviso. This is what Alviso Slough looked like early in the morning. Can you see the gobs of white foam? Many people assume foam like this must be from detergent or some other form of pollution. Foam like this is quite common in sloughs of Lower South Bay. This is a result of billions of microbes cycling carbon. The microbes synthesize and lyse triglycerides, amino acids, proteins, etc. as they grow and die. This material becomes dissolved organic carbon (DOC) in the water column. The least bit of turbulence as Bay tide rushes in and out builds up globs of waxy foam that can persist for hours.

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Western Division AFS meeting in Reno 2016

Hobbs lab attended the AFS Cal/Neva and Western Division Meeting in Reno, Nevada March 21st to 24th, 2016. We presented seven posters on our work on Delta and Longfin Smelt and Jim gave a talk on the long-term ecological response of native smelt in the San Francisco Estuary.

All lab members in attendance participated in a field trip to Pyramid Lake or attended continuing education classes on fish passages and R for biologists at the start of the conference.  Plenty of networking opportunities presented themselves through after conference social events including a trip to the Discovery Center and the Monster Fish Exhibit. Of course, no group trip is complete with out some group bonding. We took advantage of the sunshine on Sunday before the conference to go check out the snow and go for a hike at Mount Rose.

A New Haven for the Leopard Shark

by Alessandra Bergamin on April 17, 2014

It is early morning at Eden Landing Ecological Reserve and in a pond designated as E9 by the managers of the South Bay Salt Pond Restoration Project, the water is cold and still. A leopard shark, around three feet long with distinct black and brown bands and spots mottled across a steel-gray body, rests on the pond’s silty floor. There is no real agenda for the day except, of course, to eat, but for one of the largest predators in the San Francisco Bay that shouldn’t be too much of a challenge. So the shark can afford to wait for the water to warm and the tide to come in before it starts its day.

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