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.


Notwithstanding a small amount of foam, the “Alviso Marina County Park” is a lovely place to visit if you have never been there.  Trish Mulvey recently sent a link to a promotional video by Tandem featuring the Don Edwards Wildlife Refuge:  John Bourgeois and others are featured.


Unfortunately, the public notice board at the boat launch must remind us that some of the best fish in this area cannot be safely eaten due to mercury and PCBs contamination that persists to this day. (A small caveat: adult males and women over childbearing age can safely eat a filet per week of sturgeon, leopard shark, and white croaker.)



The station map shows below shows you the geographic locations of the Saturday and Sunday trawls.


Below are the two data tables showing fish caught on October 1st (Bay-side) and October 2nd (Upstream).  By looking between the map and the tables, you get a sense of where different fish hang out in a given month based on these 10 minute otter trawl surveys.

Bay-side trawls:


Upstream trawls:


Think of trawls as showing fish density at each station.  Any fish not fast enough to evade the net get sucked up and counted.  The density of fish at fresher upstream stations was pretty close to 10 times higher compared to salty parts of the Bay.  The higher fish density is overwhelmingly driven by tiny silversides, sticklebacks and anchovies.  The bigger sea monsters loiter where salinity is higher.  In terms of biomass, leopard sharks, bat rays, and the single massive sturgeon that were caught further downstream greatly outweighed the 1000-plus tiny fish – just to be fair.

Gobies.  You always find some bottom-dwelling gobies unless the water gets very fresh.  Over the past century, Shokihaze, Shimofuri, and large Yellowfin gobies invaded and have become very common.  Nonetheless, native Arrow and Cheekspot gobies are still present, if not reasonably common.  The only big loser in the goby wars seems to be the native Bay Goby.  They were commonly caught in this part of the Bay in the early 1980s.  Now, it is very rare to see a Bay Goby near Lower Coyote Creek.  This is my “Goby Collage” summarizing the best of the Saturday catch:


Shrimp.  The Hobbs data includes shrimp although I did not summarize invertebrate results in the tables above. Non-native Palaemon macrodactylus were again far more common than native Crangon species.  This is typical in late summer as the lower bay dries out.  These “Korean” or “Oriental” shrimp were first collected in the Bay in 1957 (Cohen & Carleton, 1995).  Palaemon are highly edible for fish and humans and don’t seem to cause much harm.  Get used to them, they are not going away.

As noted before, Palaemon shrimp have clear bodies.


Native Crangon shrimp are sandy colored.  Crangon franciscorum is the more common Crangon to be found.  On this weekend, we did catch a few specimens of the other two varieties: C. nigricauda and C. nigromaculata.


Mysids.  After full sized shrimp, mysids are next down the food chain.  Many sources document mysids as a principal food for Palaemon and Crangon shrimp. Mysids are also important, if not critical food for all types of fingerling-sized fish such as anchovies, longfin smelt, and young striped bass.  The importance of mysids to a productive fish nursery cannot be overstated.


Early October is not the typical mysid bloom period, so we did not see a lot of them.  But those that were caught do seem to be getting bigger and fatter as the year progresses.

One of my goals is to make more mysid photos available to people concerned about Bay and Delta ecology. It is hard to describe this critical link in the food web to people who have never seen them.


Tunicates.  We are starting to see tunicates (sea squirts or “sea grapes”) again.  I don’t know if this is a typical seasonal pattern.  We had buckets full of them last December after winter rains seemed to turn Bay waters notably greenish with phytoplankton.  Then, I hadn’t noticed them at all until this time out.  Are sea squirts strictly a winter-time phenomenon in the Lower South Bay?


Bat Rays.  A large pregnant female bat ray was caught near the confluence of Alviso Slough with Lower Coyote Creek.  She was not happy; flicking her tail like a big floppy-finned scorpion.


A baby male bat ray was caught in the same net with copious amounts of bat ray slime.  Dr. Hobbs’ first suspicion was that the baby boy had just been born.  Bat rays are ovoviviprous, so this is possible.  But, on second examination the baby boy appears a little large to be newly born. Who knows?


By the way, the photos below show how you can easily determine the sex of all sharks and rays: males have “claspers.” (Examine carefully: even baby bat rays have a stinging spine.  Jim assures me that a bat ray sting is extremely painful.)  13 bat rays were caught on Saturday: 5 males, 8 females.

Harbor Seals (not caught in nets – we observed them as they observed us).  The seals have used a muddy haul out site on Calaveras Point at least since I started working here in the early 1990s.  The haul out is located along the north shore of Lower Coyote Creek opposite Pond A6.  Fortunately, these big guys stay well clear of the otter trawl nets.


The seals come in at least three distinct colors – mottled gray, black and red.  I would swear that I used to see a lot more red ones many years ago, but I never paid a lot of attention.  From what I read, the red color is attributed to high concentrations of iron or selenium in water.  (But…, if metals in the water causes the red color, shouldn’t they all be uniformly reddish?)


Clams.  Otter trawling picks up clams, crabs, and amphipods if they live near the mud surface.  Surface dwelling bivalves like Potamocorbula, Musculista, and Japanese Littlenecks are commonly collected. The Hobbs crew is seeing some Corbula this year due to the El Nino rains, but the density of Corbula remains very low. The largest number, 126 Corbula, was collected at the Coy-1 station this weekend.  That seems like a lot until you consider that the trawl net scrapes up an area roughly 10 feet wide and several hundred feet long. A hundred or so Corbula over that amount of area is very low density for clams.

These were some of the surface, or near-surface, dwelling clams we saw in Lower Coyote Creek and Pond A21:



The shark tank.  Further out in the Bay, at station LSB-1, we typically pull up a large amount of oyster shell “hash.”  These are dead shells that remain from commercial oyster farming over a century ago.  The shell hash is popular with some benthic organisms and the sharks that eat them.


Dr. Hobbs netted a leopard shark and a brown smooth hound shark at both LSB-1 and LSB-2 stations. This was the first of two leopard sharks of the day:


The brown smoothhounds were a little smaller than the leopards.  Brown smoothhounds are not rare in California. However, they are rarely caught in Lower South Bay, so this was a nice surprise.  (BTW, brown smoothhounds are supposedly good eating, but in other estuaries, the same mercury advisories that apply to leopard sharks also apply to brownsmoothounds.)


Emily Trites shows off a brownsmoothhound:


I got to hold one too.


Guitarfish. The biggest surprise of the day was a baby guitarfish.  Again, not rare on the California coast, but this is only the second one Jim Hobbs has caught in Lower South Bay.  As you can see, Guitarfish have a body shape halfway between a shark and a ray. They are bottom feeders, so this fish is here to eat clams, crabs and other benthic bugs.  I like to speculate that this fish is yet another indicator of increasing Bay ecological diversity, but Dr. Hobbs did caution me that data is a little sparse to jump to that conclusion based on one or two fish.


Sturgeon.  A big surprise, in terms of body mass, was a 1.4 meter long sturgeon caught at station Coy-2.  The white color of the scutes, bony armor on the sides, tells you that this is a white sturgeon.  Sturgeon are the largest freshwater fish in North America.


Plainfin Midshipmen pulled up at station Coy-3.  This is another deep sea oddity.  Jim catches midshipmen once every month or so.  They live much of their life in the deep ocean and commonly spawn on rocky shores from California to Washington and further.  This fish is bioluminescent: you can clearly see the rows of shiny phosphorescent dots on his top and bottom sides.  Midshipmen have little biological importance in the Bay except that the male midshipmen summer-time mating song disturbs human houseboat dwellers docked at Sausalito.  Unlike most vertebrates, midshipmen come in three sexes: Female, Male 1, and Male 2.  This is possibly the freakiest fish you will find in the Bay.


As always, I saw more amazing things than can be summarized in a single email blog.  I will close with a mundane factoid that is probably of greater biological significance.

Anchovies. Dr. Hobbs continues to find strong indication that Northern Anchovies successfully spawn in Lower South Bay.  He documented male and female anchovies at full reproductive readiness this month and last.  In addition, a number of young-of-year anchovies were collected.  The photo below shows a mix of adult and very young fish caught at station LSB-2.


These are a few close ups of young anchovies:


I couldn’t help but notice that the greenish color we see on the backs of some adult anchovies in mid-summer appears to turn blue this time of year.  Dr. Hobbs suggested that the color may have a relationship to spawning readiness.  … yet another mystery to solve.