Fish in the Bay – March 2019, UC Davis Trawls – Save the Whales! Larval fish trawl, plus a Sea Level Rise Rant.

First a Special Thanks:  I want to acknowledge and thank agencies that continue to support the Hobbs Lab work.  1) California Dept. of Water Resources (DWR) recently extended the larval Longfin Smelt contract through UC Davis.  2) City of San Jose has contracted to continue their Otter trawl sampling in Lower South Bay through the next year or two.  And, 3) NOAA Fisheries has advanced $50,000 to support this work as well.  This is very good news!  Until now, there was a serious possibility that trawling would cease by this month due to lack of funding!  THANKS TO ALL WHO CARED!

Tiny Fish and Bug Trawls this time.  This is the mid-March larval trawl report showing tiny fish and bug results from 20mm and Clarke-Bumpus nets. 

Waters were warming up by later March as you can see in chart above.
  • Warmer: Temperatures were just above Longfin Smelt spawning trigger by this time 
  • Still Fresh:  Salinity was still in single digits at almost all stations.  Juvenile longfins need low salinity for recruitment, says the literature.  So, baby Longfins already hatched continue to enjoy ideal nursery conditions as this wet winter turns to spring.

Since this was another 20mm larval fish trawl, I can’t quantify the catch other to say we caught buckets of tiny fish and bugs mainly to track Longfin Smelt spawning. However, there is much more at stake than just Longfin Smelt!

For that reason, I shall digress …

1. Whale Status.

Good News!  Populations of most species of whales continue to recover well around the world after a ban on international whale hunting in 1985.  Overall whale population assessment:

  • Humpback Assessment: According to NOAA Fisheries, most Humpback populations are recovering well, but I gather from the above graphic that our local migrating Mexican and Central American “Distinct Population Segments” (DPSs) are still in need of recovery: 
  • Gray Whale Assessment: NOAA Fisheries also reports that Gray Whales on this side of the Pacific are doing well.  They were delisted from endangered status in 1994:  (Gray Whales in the Western Pacific are still very much endangered.)

Farallon Islands.  More specifically, numbers of Humpback, Gray, and Blue Whales sighted near the Farallon Islands have been increasing since at least the 1970s. 

Humpback feeding off San Francisco in 2016, from DVC Inquirer article.

More good news: Humpbacks continue to feed in the Bay.  A 2016 article by “Diablo Valley College Inquirer” summarizes the Humpback situation at that time. 

Not so good news!  For better and for worse, “Golden Gate Cetacean Research” reports that San Francisco Bay itself has become a haven for small numbers of Humpback Whales since 2016:

Dead Gray Whale in San Pablo Bay as featured in the SF Chronicle article.

Terrible News!  Most recently, young Gray Whales have washed up dead in the Bay appearing severely malnourished  

2. Feed the Whales!

Generally, Humpbacks feed well with increased coastal upwelling and warmer waters.  Gray Whales tend to feed in colder waters.  Humpbacks seen near San Francisco Bay arrive in summer through fall for feeding.  Gray Whales tend to pass by as they migrate to and from southern breeding grounds from December to April.

Humpbacks eat small fish and krill:  I have mentioned before a few of the many reports indicating that Humpbacks near or inside the Golden Gate feed on migrating Anchovies.  Other reports identify Pacific Herring as another food source.

Gray Whales eat mysids: It is less well known, but well documented, that Gray Whales feed on mysids (very small shrimp-like crustaceans) more than anything else in temperate to sub-arctic waters.  The Grays are predominantly bottom-feeders that scoop up and filter mouthfuls of mud. In the Arctic, they mainly eat amphipods and bottom-dwelling shrimp, like Ghost Shrimp.  But, Grays are opportunistic feeders known to also eat small fish, clams, and crangon shrimp. 

Most importantly, female Grays basically starve as they migrate south to breeding lagoons off Mexico.  Calves born in those southern waters have little to eat once they are weaned off mother’s milk on the northward migration.  These whales often depend on coastal fueling stops on their way to feeding grounds near the Bering Sea:

Young blue-back Anchovy from LSB?  This young one shows predominantly blue with some traces of green.

Summer is when local adult Northern Anchovies migrate into the Bay from the sea.  Our anecdotal observations in Lower South Bay (LSB) record arrival of long-bodied blue-back Anchovies and perhaps green-backs as well.  By around December, adult Anchovies appear color-faded and somewhat emaciated.   

The recent 20mm trawls since December, including this current set, have solidly confirmed presence of many juvenile, and possibly larval, Northern Anchovies in LSB.  In addition, Dr. Hobbs tells me that yolk-sac anchovies have been identified in 20-mm net surveys here.  He also documented adult Anchovies with late-stage gonad development in the Alviso Marsh Complex in late-2016.  So, it is fairly certain Anchovies are spawning in the Alviso Marsh Complex and probably in Lower South Bay as well.

Hypothesis #1:  LSB is a food producing machine for Humpback Whales.

Researchers around the world track Anchovy hatching and recruitment.  This should be a high-priority research project here as well.  Hungry Humpbacks and sea surface temperature tracking should be more than enough motivation for people to study our local Anchovies.

Two young green-back anchovies from the LSB catch.

Northern Anchovies

  • Top panel above, descending order: Shokihaze Goby, Northern Anchovy, Three-spined Stickleback, Northern Anchovy.
  • Bottom panel: The two anchovies were green-backs when viewed from above.

We continue to search for more solid proof that our green and blue-backed anchovies in LSB migrate into the Bay from the sea. 

Much earlier studies identified Brown-backed Anchovies as local year-round residents.  Adult Anchovies are easy to identify by their bright hues.  But, young fish do not display much noticeable color.  All three anchovies shown in photos above would be misclassified as brown-backs without a closer look.   But, absent genetic or extensive otolith analysis, we may never be certain whether these different Anchovy color types are indeed separate populations.

Northern Anchovy young adult to juvenile in descending order.  (Pacific Herring juvenile at left.)

BTW:  The anchovy shown farther above was a bluish-green-back.  Another younger one caught in the same trawl was green.  I am not sure if we have seen any true brown-backs since November 2016.  But, only genetic analysis can really determine this.

More Humpback food:  Juvenile Pacific Herring caught on 23 March 2019.

Pacific Herring are not as numerous in Lower South Bay.  In all of the time that Jim Hobbs has been trawling in LSB, I don’t think either an egg-sack larva, nor a full adult Herring has ever been seen.  So, these young likely hatch further north then drift south as larvae. They certainly recruit (grow and fatten up) in LSB.  Either way, SF Bay functions as a Herring production habitat that supports all kinds of larger fish, birds, and likely Humpbacks as well.

More Whale food:  Mysids for Gray whales, juvenile Pacific Herring for Humpbacks.

Mysids.Gray whales could be coming into the Bay for Mysids.  Some species of mysids we have here are also the primary Gray Whale diet in coastal areas off British Colombia, Oregon and Washington State.

It is entirely possible that mysids are attracting Gray Whales into the Bay.  However, I do not know if our Lower South Bay mysid abundance is any indication of mysid presence up in Central and North Bay. 

Hypothesis #2:  LSB may produce food for Gray Whales too.

Investigation of Gray Whale diet in North and Central Bay is well beyond the scope of our LSB trawling studies, but someone should check!

Palaemon macrodactylus with eggs, 23 March 2019.

Shrimp.  San Francisco Bay has always hosted huge populations of Crangon shrimp, principally Crangon franciscorum (aka: Bay Shrimp, Grass Shrimp, some even call them ‘Sand Shrimp’).  But the situation became a little muddied in recent decades with arrival of non-native Palaemon and Exopalaemon shrimp. 

Both Humpbacks and Gray Whales are capable of eating crangon. Grays are known to do so. Crangon, as we have learned, recruit well with wet winter flushing.  We caught large numbers of Crangon in 2018 which likely recruited from the wet winter of 2016-2017.  We also witnessed a substantial Crangon winter brooding event between November 2018 through at least February 2019. 

We saw far fewer Crangon in the March larval trawls (none as I recall) which may be consistent with their migratory pattern:  Our winter brooding adult Crangon should now be out in Central Bay, or out to sea. 

Are Humpbacks and Gray Whales in the Bay feeding on our 2018-2019 bumper crop of Crangon?

Currently, we are seeing Palaemon shrimp laden with eggs.  I am not yet familiar with the Palaemon breeding cycle, or how this non-native shrimp is affecting Crangon populations.  Do whales eat Palaemon shrimp?  As near as I can tell, no one knows!  (BTW: Palaemon look tasty!  I would eat them.)

3. Food for Critters that Feed the Whales.

Copepods and other tiny bugs feed baby fish.

Tiny critters.  We see many millions of even tinier creatures, like those shown above, on every trip.  These are near microscopic crustaceans caught by pulling a fine-mesh Clarke-Bumpus net through one of the last truly productive estuarine marshes in SF Bay.  Even these tiny creatures are outnumbered by smaller microscopic life upon which they feed.  Why is this portion of the Bay so productive?  Is it productive enough?  We have whales to feed! 

4. More tiny fish.

Young fish:  American Shad (top), Staghorn Sculpin (lower left), Pacific Herring (everywhere else).

Carbon cycling starts at the bottom … all the way down to molecules and bacteria.  A complex food web follows multiple routes.  I see Copepods as the trophic bottleneck (or “crossroad” may be a better term) that cycles into most estuarine fishes, mysids and bigger shrimp.  For those larval and juvenile fish that don’t consume many copepods directly, in most cases, copepods feed the mysids or tiny fish that larger fish eat later in life.

Juvenile Longjaw Mudsucker resting on the back of a Pipefish.

Longjaw Mudsucker.Dr. Hobbs identified this mudsucker baby for me based on its pigmentation pattern.  (This one is even younger than the one I photographed in early March!!)

Longjaw Mudsuckers do not fit directly into the whale-feeding narrative, but they are important salt marsh sentinels nonetheless.  We always see a few straggler mudsuckers in slough trawls when healthy pickleweed marsh is nearby.  But, any fish this small probably eats a fair share of copepods.

Bay Pipefish from Pond A21.

Bay Pipefish.Like the mudsucker, pipefish are additional sentinels indicating that very tiny food must be present. 

Another young pipefish.

At risk of repeating myself: Pipefish have tiny tube-mouths.  A large adult copepod may be too big for them to eat.  Baby pipefish definitely require sub-copepod-sized food, like rotifers.  So, I regard presence of pipefish as a very good indication that the food web is churning.   

5. Sea Level Rise.

2019 update of tide gauge collage previously shown in 3 December 2017 “Fish in the Bay” blog post.

Sea Level Rise continues to be raised as an important issue.  To me, it is a bit of a distraction.  Regional and local tide gauges continue to indicate that we will see no more than several inches of Relative Sea Level Rise by year 2100.  That is 81 years from now, almost a large whale’s lifespan. 

Many people assert that it is likely or inevitable that seas will rise one to two meters.  This is very unlikely unless tide gauges start showing a SHARPLY upward bending curve starting TODAY. 

Tide gauge near New Orleans, Louisiana shows one of the highest rates of rise in the nation – still less than a meter projected there by 2100.

The math is simple.  To rise one meter over 81 years, gauges must show an annual rate of rise of 12.3 mm/year from this year on.  That would be a very large and visible shift in all gauge trends.  Even gauges closest to New Orleans have not reached that rate of rise after local lands subsided rapidly since the 1950s.   

If current trends do not change by, say 2050, the rate of rise will have to increase even more, to around 19 mm/year, to reach one meter by 2100.  Those very high rates are assessed as very unlikely by “Rising Seas in California” (2017) and various other IPCC, NOAA, and NRC reports.  (Rising Seas in California gives 5% or less probability for the one-meter rise scenarios.) Thus far, gauges remain steady and continue to show rise rates consistent with the LOW (RCP 2.6) scenario.

Please note:  I have carefully read recent papers asserting an acceleration in the rate sea level rise.  For example, Nerem, et al (2018):

In each case, authors either adjusted raw tide gauge or satellite data to match estimated Arctic & Antarctic ice loss or calculated future acceleration based on ice melt.  The papers either mention or reference the ‘problem’ that, so far, raw tide gauge and satellite altimetry records fail to show significant acceleration. I will happily discuss the published findings with anyone who desires more information.

On the other hand, I am deeply interested in marsh growth to facilitate food production.

Opening of the Pond A8 complex upstream of the Town of Alviso, starting in June 2011, has increased the tidal prism and tidal energy in Alviso Slough itself. 

Increased tidal energy has probably enhanced bank erosion.  Erosion would be compounded by river flushing during a wet year like this. 

Erosion yields to deposition where tidal velocity is slower. Moving downstream into the mouth of Alviso Slough and Lower South Bay, mud bank accumulation is evident.  But, is new marsh growing fast enough?  I believe it is. 

City of San Jose / HT Harvey Associates “Marsh Plant Associations” 1989 & 2012 maps.

I started casually tracking local marsh growth when I inherited oversight of City of San Jose’s mapping of marsh acreage downstream of the San Jose-Santa Clara Regional Wastewater Facility.  The actual assessment work was contracted to HT Harvey Associates.

You see, years ago the San Jose Santa Clara Regional Wastewater Facility was falsely accused of killing off pickleweed salt marsh by discharging too much fresh water.  As a result, the Regional Water Board required that San Jose pay for marsh mapping to show the extent of salt, brackish and freshwater marsh every few years for 23 years.  (The reports are available for inspection at: )

  • By 2012 it was clear:  We were INNOCENT!  Over 1,000 acres of new marsh had formed on accreting sediments, about 400 acres was salt marsh.  This documented marsh growth was separate and in addition to Salt Pond Restoration.
  • By 2018, I retired and joined Jim Hobbs and the ‘Environmental A-Team’ in hopes that I may someday clear my good name of this pickleweed-killing accusation.
1929 aerial composite photo of Alviso Marsh Complex.

In addition to the HT Harvey reports, it is very easy to line up historical and current Bay maps to assess past and present signs of marsh growth, or shrinkage.

2018 Google Maps view of Alviso Marsh Complex.  Dates of pond breaching indicated in parentheses.

Clearly, Lower South Bay has accumulated sediment for a very long time despite huge marsh loss to salt ponds, levee construction, and land subsidence.  As near as we can tell, the area continues to form new mud banks and marsh. 

The question of whether sedimentation and marsh growth can keep up with one or two meters of sea level rise is academic unless sea level rise rates jump to over 12 mm/year very soon.  If the rise rate doesn’t change, sedimentation and marsh growth appear sufficient so far. Albeit, the quality of marsh growth and succession are still important issues to resolve.

Calaveras Point Harbor Seals relaxing on a bed of spartina close to high tide.

Harbor Seals.  The seals shown above are resting on a shore that was in the middle of the mouth of Lower Coyote Creek in 1990!  This new land formed in an area that sank 2 to 3 feet in the early-to mid-1900s from local land subsidence according to Poland and Ireland (1988).  This appears to represent at least 3 feet of sediment accumulation (since 1990??)!!

BTW:  Not to change the subject, but this Calaveras colony of Seals was described in 1928!  … Records indicate they have been here since at least 1900.  They need to eat too!  See page 34:

6. We have many jars of work to do.

More larval fish catch from 23 March 2019.

Larval Catch

  • Top Panel: Juvenile Anchovies and mysids from 20mm net in March.
  • Bottom Panel: A juvenile Northern Anchovy (Per Dr. Hobbs: Identification confirmed by the paired row of melanophores (blacks spots) along the thoracic section and melanophores on the top of the swim bladder.) 

Personally, I think monitoring biological health and the many species of fish and bugs in this restoring area is much more urgent. 

Dr. Hobbs with yet another jar of 20mm net contents.

We have countless jars of biological material that must be evaluated.

Millions upon millions of tiny copepods remain uncounted and unclassified.
We must track many thousands of long-skinny baby Anchovies, Herring, and Longfin Smelt too!
Two jars were needed to hold all the mysids and baby fish in the 20mm net contents from Station Coy3.

Do we have sufficient funding and people to document all these fish and bugs?

A single day’s worth of jars to study!

Whales could starve if we don’t crack the mystery of this highly productive marsh system soon.  (Anything’s possible.) 

… On the other hand, any whale alive today will much more likely die of old age before catastrophic sea level rise is observed, according to IPCC, NOAA, NRC, and others – just a thought.

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