Fish in the Bay – November 2023, Part 2 – Micro World.

Sami and Janai loading the net on Saturday morning.

For this second part of the November report, Janai gave us a short glimpse of the microbial world in Lower South San Francisco Bay – and a major discovery. 


1. Water colors.

Water colors had changed dramatically.  In October, waters were uniformly “Luau Green” (Sherwin Williams #27) at almost all stations.  By 11-12 November, water colors had turned slightly browner and much more variable.  Colors ranged from “Bengal Grass” to “Melange Green.” 

Water clarity also dropped considerably in November. (Turbidity was higher.)   For example, Secchi depths at stations Coy2, 3, 4 and LSB1 & 2 ranged between 50 – 80 cm in October.  By November, the values had dropped to 22 – 42 cm. 
Most likely, this change was due to Neap Tide versus Spring Tide. 
The Moon was at 3rd quarter on October 7th & 8th and tidal flushing was mild (neap tide).  When we returned to trawl on November 11th & 12th the Moon was new and tides were strong (spring tide).   


Greenness at the water surface can intensify when the Sun is bright and waters are calm and stratified.  Diatoms and other photosynthetic phytoplankton compete for surface habitat to feed on sunlight and nutrients.  Spring tide turbulence complicates their strategy.

  • This minor lunar upheaval happens every other week!


A Great Egret on the bank of Alviso Slough on Saturday morning.  Murky swirls in the water betray the drama just below.


2. Phytos & other Microscopic Creatures.

Janai Southworth again joined us for our trawls on November 11thShe is a highly experienced wizard of microscopy. 


Janai focused her “magic eye” (Em1 Portable Microscope – ) on tiny water samples collected in her plankton net on Saturday.  The results were striking as always: many types of Diatoms immediately came into view.  These organisms are responsible for most of the green and brown colors in the water!    

Diatoms, like Bacillaria, shown above, are very common.


More examples of diatoms from Janai’s field examination.


Higher-definition images from Janai’s home-lab examinations.

Janai collected and chilled samples for more rigorous and higher-magnification analysis back at home.  The typical result is a 4-to-5-hour streaming video that is available to view for up to a few weeks on her Twitch channel at this link:

More phytos seen in November:

  • Thalassiosira or Coscinodiscus. (Centric diatom – top left).  Notes from Janai: “Because the specimen is still alive, full of chloroplasts, and not attached in a chain, the genus cannot be discerned.  It is either Thalassiosira (T) or Coscinodiscus (C).  T forms chains, C does not.  Because chloroplasts are still present, minute features on the valve face are not visible: T would show studded spiked processes near the edge of the valve face; C would show a central rosette and slightly spiral pattern.  Both genera are common centric diatoms that comprise a hundred or more species each, e.g.
  • Pleurosigma or Gyrosigma. (Penate diatom – bottom left). Both of these penates are also common.  The alignment of minute striations on the frustule (not visible in this image) distinguish the two. or


3. Hydrozoan – A new Cnidarian!

Believe it or not, I puzzled over this strange brownish plant-like material since 2019.  It is always present.  We pick up bigger gobs of the stuff from upstream sloughs each cool season. 

  • We usually find these bumpy filaments growing from woody plant material below the waterline. They look like roots, so I presumed they might be plant roots. Or maybe, they were some kind of bryozoan? 
  • What the devil is this stuff??? – I wondered for so long.


I posed this question to Janai in November.  Janai immediately suspected hydrozoa, specifically, Thecate Hydrozoans:  She suggested immersing a bunch of it in water to see if tiny polyps would emerge. … Polyps emerged!  They were easy to see using cell phone camera magnification. 

Hydrozoa was confirmed! Janai solved this mystery.


Hydrozoan colony at Coy1, 12 Nov 2023.

I duplicated Janai’s photographic techniques the next day.  These organisms are fairly attractive once you know what to look for.  Since the colonies appear to grow bigger in winter, they must feed on microscopic critters and particulate material flushing from creeks and marshes.  


Gastrozooids look like sea anemones. Blastostyles look like loose grape clusters in this photo.

I suspect we are finding at least two major varieties of Obelia Hydrozoa in Coyote Creek and surrounding sloughs.  There could be dozens of varieties.  

  • What exactly does it eat? –  How does it fit in the local carbon cycle?
  • Anyone out there with Hydrozoa experience, please chime in!!!


 4. Some Bigger Critters.

Copepod nauplii at Coy4.  (Photo by Janai)


Bigger Bottom Critters. 

The overall shrimp picture has improved each month.  Native Crangon continue to increase.  The non-native types are also doing well, but not quite as well.

  • Crangon shrimp count = 10,206. The Crangon YTD count is now just over 50,000.  This is not a record but still very good. 
  • Palaemon count = 2,347.
  • Exopalaemon count = 225.

Corbula Clam count = 3,541.  This big Corbula surge in November brought the YTD count up to 5,380 which is just a little less than average for years 2020 and prior.  This reverses the recent 2-year decline and supports the hypothesis that stormwater flushing stimulates propagation of non-native Corbula clams.


Hydrozoa!!!   Another puzzle piece falls into place!


Extra good news – 20 Nov 2023: 

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