Field Microscopy from the KQED Quest Hike along the Weep


This is a report on the field and laboratory microscopy from our hike along the Weep near Drawbridge, with KQED Quest Interactive Producer Craig Rosa and Writer Anita Llewellyn.

The Weep is a perfect example of the paradigm behind “Hidden Ecologies” – that apparently nondescript, often unnoticed environments contain beauty and mystery. Most hikers and bikers pass quickly by the Weep. Few even glimpse the stunning beauty captured in Cris’s kite and pole photography; virtually none see its strange microscopic world.

Here, for example, is a true tale of terror and narrow escape from that world.

The shy explorer is a Ciliate protozoan found all along the Weep. So far, I have been unsuccessful in keying it out, so I don’t know its name. The microscope magnification is 200x.

The villain of the film is a Nauplius, the larva of some larger marine Crustacean. And, herein lies one of the deeper mysteries of Evolution. One Nauplius looks so much like any other Nauplius that even an experienced Marine Biologist has difficulty telling them apart. Yet the body plan of adult Crustacea is one of the most widely varying in the animal kingdom.

With no effort, we turn to another Weep mystery.


The blue-green clump growing around and to the left of the Pickleweed looks like moss. Touch it and it feels like moss. It has a velvety texture and is not slimy at all. Nothing to mistake for seaweed. Yet this moss-like critter and the seaweed along the shore are related, both being algae.

The dark green “moss” is a siphonous alga called Codium.

Algae with the siphonous [Greek for “tubular”] body plan are actually giant cells. Siphonous algae cells undergo repeated nuclear division without forming cell cross-walls. The result is a bundle of tubes with the multinuclear cytoplasm lining the cell wall. Shown here at 400x magnification is a tube from the Codium in the Weep:


The dark objects are the nuclei and the oval green structures are the chloroplasts in the giant cell [also called a “Coenocyte“].

Since all the tubes of the Codium are connected, when we stopped to feel the “moss’, we were actually feeling of a giant cell…!

Another, yet unsolved mystery of the Weep has to do with its dominant community. Salt marsh streams and ponds typically have a mat of organisms growing just on top of the bottom mud. Most often, this is a Cyanobacterial mat. Sometimes, it is a mat of Melosira diatoms.

A dark green or red bottom usually means a Cyanobacterial mat. A yellow or orange bottom is usually a sign of diatoms. Here is what the bottom looked like near where we sampled:


The lines of bird tracks show black mud under a yellow bottom. We had seen an orange bottom during our trip in August and had seen some large diatoms. We were sure we would see these diatoms again.

On the KQED Quest hike we found the bottom of the Weep has a community dominated by needle-like Diatoms called Cylindrotheca.

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These lovely and graceful diatoms were not the diatoms we had seen during the summer. Repeated samples from different areas showed the same Cylindrotheca. Clearly something had happened and we had a new dominant community.

In the videomicrograph below, you can see the Cylindrotheca of the bottom, along with another and very large Ciliate commonly found in almost all salt marsh ponds and streams of San Francisco Bay.

The Cylindrotheca are motile diatoms and, by themselves, move rather slowly. The rapid beating of the Ciliate’s cilia make it difficult to see that stately diatom movement.

With a little searching, we did find some of the Pennate Diatoms we had seen in the summer. Here a lone Pennate Diatom sails past the Cylindrotheca in a yellow-bottom sample.

The Pennate Diatoms were not totally gone, just vastly reduced and overtaken by the Cylindrotheca diatoms.

This is typical of salt marsh ponds and streams. One organism dominates and defines the micro-community, but the community contains many other organisms in the minority. I suspect that tiny environmental changes determine which organism dominates. Some change in the Weep environment, happening between the summer and the winter, selected against the larger Pennate Diatoms and for Cylindrotheca.

In addition to finding a few Pennate Diatoms on the yellow bottom of the Weep stream, we also found other diatoms, Cyanobacteria, and a species of marine Amoeba. Here Cynobacterial filaments move slowly along with the Cylindrotheca.

If you look closely, you can also see a Ciliate that has eaten some of the Cylindrotheca…!

Dominant organisms in a micro-community usually end up as fast food for some of the minority organisms. No doubt the Nauplius shown earlier and, even, the shy Ciliate it frightened also gobbled a few Cylindrotheca. It’s a dog-eat-dog world under the microscope…!

As it turned out…
There were Other Clues to the Mystery of the Vanishing Pennate Diatom…!

We found a small patch of orange mud at the North end of the Weep.


Sampling the surface of this mud turned up large numbers of the missing Pennate Diatoms:


Somehow, the original summer environmental conditions that held for the entire Weep stream still obtained in this tiny patch of mud and supported the rich growth of the Pennate Diatoms. Measurements showed no difference in salinity or temperature. Almost no Cylindrotheca were found in this patch, and those found may have simply washed in from the larger Weep stream.

A Patch of Green…
Not all was yellow and orange. We found several patches of green, such as the one shown below:


You can see the yellow-bottom of the Weep stream off to the lower left. The patch of green appeared in a depression in the stream bottom, next to a board. Perhaps something under the depression defined the environmental conditions that enabled a rich growth of…

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Green cells, probably a single-celled alga, some Cyanobacteria, a minority of Cylindrotheca, a few Pennate Diatoms that were not the same Pennate Diatom as in the orange mud, some Amoebae, some Ciliates, some Nematodes, some filaments of the bacterium Beggiatoa, and even some Flatworms. As well as a Mystery Organism…!

Here is a close-up of the Mystery Organism:

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It appears to be some sort of alga, perhaps a communal alga like Volvox. I have not been able to find out what it is, but there were quite a number of cells that looked like this.

The Beggiatoa may be a clue to the difference between this patch and the rest of the yellow-bottom Weep stream.


Beggiatoa are commonly found in Bay Area salt marsh ponds where sulfur compounds from decaying material in black mud under the bottom releases hydrogen sulfide through the action of sulfide reducing bacteria. Beggiatoa are photosynthetic bacteria that require sunlight, but also require hydrogen sulfide gas. They are motile and rise to the surface of streams and ponds in the early morning, when the sun rises. When this happens, clouds of Beggiatoa appear as a smoky scum on or just under the water’s surface.

The depression may have covered some decaying material, perhaps parts of a dead animal, that resulted in the hydrogen sulfide supporting growth of Beggiatoa. Decaying matter would also support the growth of many other kinds of bacteria, which in turn, would support the growth of bacteria-eating Ciliates, Nematodes, and Flatworms.

It is not clear to me why this would favor single-celled green algae and Cyanobacteria over the diatom Cylindrotheca, but the absence of large numbers of Cylindrotheca when they are common in the nearby stream, and the presence of various green algae cells on the bottom suggest this.

Here is the 800-lb Gorilla of this micro-community:

It is a Flatworm. Among the simplest of worms, this critter probably eats bacteria. It is, however, the largest microscopic creature around the Weep during the winter. That may change in the spring, but right now Flatworm is it. If you were a bacterium, and if bacteria had nerves [which they don’t], and if bacteria had hearts [which they don’t], then Flatworm would strike terror into your heart.

Here is the next biggest monster…

This heavy-hitter [shown at 100x magnification] is a bacteria-eating Nematode. Sometimes called a “round worm” to distinguish it from Flatworm. And yes, they always squirm like this. On a slide, pinned between slide and coverslip, the thrashing back and forth seems fruitless. On any free surface, from the bottom of a Petri plate to the bottom of a pond or stream, Nematodes can make record time [for their size]. They can also be difficult for the Field Microscopist. Just when you are ready to photograph that tiny Amoeba, they roar by and it’s “good bye Amoeba“…!

Where Flatworms, for the most part, are rather boring… Nematodes are very interesting. They can be tiny, but the biggest Nematode is more than 50-feet long and lives inside of a whale. Their sex lives are a study in endless variation. The nematode Caenorhabdus elegans starts out hermaphroditic, but becomes a male, by and by. In another species, the male is tiny and takes up residence for life inside the female.

Several thousand biologists, around the world, spend their time studying the nematode Caenorhabdus elegans. An astonishing number of them have won one or another Nobel Prize for so doing. Others who haven’t yet won it, have won other scientific awards, for such things as the study of aging, the genetics of development, and cancer.

The Nematode in the videomicrograph above is not C. elegans, which is a freshwater nematode, but it is a close relative.

No study of a pond or stream community is complete without an Amoeba.

The Biggest Mystery of All…

Why does the Weep persist?

When Cris Benton and I first walked along the Weep, we expected it to dry up soon. This was because we could find no inlet or outlet. We assumed that the inlet, perhaps a connection to either San Francisco Bay or Coyote Creek, had been obstructed during the work intended to open two former salterns to Bay tides.

Normal evaporation of salt ponds is rapid. Here are the results of a simple experiment to measure the increase in salinity when Bay water is exposed to ordinary wind and sun:


The important variable is wind, not temperature. The abrupt upward swing of the curve happened when the wind suddenly increased [and, the temperature went down]. What this curve shows is that salt concentration, which goes up with evaporation of the water, is quite rapid under ordinary field conditions.

The Weep stream is no more than inches at its deepest part. Most of it is less than 1-inch deep and only a few feet wide. The Weep is a few hundred yards long from start to end. Without salt water being regularly added, the Weep would gradually evaporate and turn into a salt pan within a matter of weeks. Addition of rain water would keep it from drying up, but the salt concentration would go down.

Since our first measurement in August, the Weep has remained at an approximately constant salinity of 40-PPT salt [“PPT” = parts per thousand]. It also appears to flow very slowly from north to south.

This tells us three things:

1. Water is flowing into the Weep from the north end at a sufficient average volume to prevent it from drying up;

2. The water is saline at least as salty as ordinary Bay water [about 34-ppt];

3. If the water is Bay water, then the flow is irregular and some evaporation takes place in between surges [because 40-ppt is higher than 34-ppt], or else the flow is constant and the inflowing water is about 40-ppt saline.

On the west side of the Weep there is a saltern separated from the Weep by high ground some 50-yards wide with the trail on it. On the east side of the Weep there is a saltern separated from the Weep by high ground about 5-yards wide with a layer of heavy gravel and railroad tracks on it. The north and south ends have some ponds, but are very far from either a saltern or Bay water.

Our working hypothesis is that salt water from the saltern on the east side, or a stream between the railroad tracks and the saltern, is seeping through the “dam” of the railroad earthworks to feed the Weep. We have not been able to confirm this, however.

That’s All Folks…

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