Microbial Ecology at the Drawbridge Weep


The Drawbridge Weep consists of various apparently unconnected narrow stream-like ponds along a channel bounded by the Drawbridge trail on the west and the railroad tracks on the east. The north end of this channel begins below the bridge over Coyote Creek and extends south to Alviso. We have called it the “Weep” because the stream-like ponds have no obvious source or exit.

Since August of 2006, we have periodically observed the character, color, and microbial ecology of one area of the Weep, designated site DBWeep01. DBWeep01 = N37.44844-deg W121.97576-deg; and is about 1-mile north of the beginning of the Drawbridge trail at the Alviso Marina parking lot and 0.2-miles south of the bridge over Coyote Creek. Here is that site in December of 2006:

Weep in December

When the picture above was taken, the narrow stream-like pond shown at the end of the board and extending from left [north] to right [south] was well defined and about 3-cm deep. Although the bottom of the pond appears gray or blue in the photograph, looking down on it showed a rich orange-yellow color. The salinity was 40-PPT [parts-per-thousand] salt.

The picture below shows a close-up of the same area at the end of March, 2007.

End of March

In this end-of-March picture, the pond is almost completely dried up. The bottom retained some of the yellow color, but was pale in comparison. The salinity of the small amount of water wetting the mud was 82-PPT salt and the water pH = 7.25.

Compare these pictures with the more extensive aerial photographs Cris made during the same two outings.

Clearly, a substantial change took place along the Weep during the months of December, January, February, and March. This change had a massive impact on the microbial community living at the bottom of the stream-like pond.

For comparison, during visits in December and January samples were taken from the yellow-orange bottom of the stream-like pond, just at the end of the board in the first photograph above. These samples showed that the bottom community was dominated and defined by the needle-like diatom Cylindrotheca, sp. For a quick refresher, here is a photomicrograph of Cylindrotheca, along with a single long filament of Beggiatoa.

Cylindrotheca and Beggiatoa

If you clicked on the blue word “Cylindrotheca” in the paragraph above and read the earlier report, you will have learned that the bottom of the stream-like pond was covered with Cylindrotheca, which gave it the yellow-orange color. In addition, the bottom community also contained the sulfide-reducing bacteria Beggiatoa sp., along with many Ciliates, several other diatom species, Cyanobacteria, as well as nematodes and flatworms. In December and early January the bottom of the stream-like pond was a busy place.

Well, by the end of March the Cylindrotheca were almost gone. In their place was a new dominant organism, shown below:


The large green “Euglena-like Protists” were all over the bottom mud. Euglena, sp, are common fresh-water Protista that contain chloroplasts and are photosynthetic.

I have also indicated Spirochete bacteria. I did so because many fresh-water Euglena have a large flagellum at one end and I wanted to indicate that the little wiggly line was not a flagellum, but a bacterium. I also noted the presence of a colonial Purple Non-sulfur bacteria that we have observed in other San Francisco Bay salt marsh ponds. I will discuss both the Spirochete bacteria and Purple Non-sulfur bacteria further on.

Here the Euglena-like Protist is seen in motion, 200x magnification, Hoffman Modulation Contrast optics.

Observe that several small Ciliates dart past the large, Euglena-like Protista. Most of these Ciliates were observed in December, so at least one group of the December-January microbial community has persisted.

Euglena, sp, are also known for one or more red “eyespots“, which may be seen in at larger magnification in the photomicrograph shown below:

Euglena at 400x

The eyespot is not an image-processing “eye”, it is a light-detector that apparently enables Euglena to follow light. Light-responding pigments give it the red color.

I have used the term “Euglena-like“, since this is a salt-water tolerant species, apparently lacks a flagellum, and may belong to a different genus of the Euglena family. Because of its size, it proved rather difficult to photograph in complete focus.

Here is a videomicrograph of the Euglena-like Protist at 1,000x Hoffman Modulation Contrast optics.

This view of a single cell sailing past the camera lens gives some impression of the cellular anatomy of this Eukaryote microorganism.

The purple non-sulfur colonial bacteria are also somewhat new to the stream-like pond bottom. I observed a very few colonies along one edge of the Weep in December, but they were rare. Here these bacteria are shown at 1000x magnification:

Purple Non-sulfur Colonial Bacteria

These colonial bacteria are commonly designated Purple Non-sulfur Bacteria because they clearly belong with that group, but in San Francisco Bay salt marsh ponds they are usually associated with sulfide-oxidizing bacteria, either Beggiatoa or Chromatium. I have also noticed the Spirochete bacteria are often present in samples showing sulfide-oxidizing bacteria. I suspect, but have no conclusive evidence that the Spirochetes actually live down in the anaerobic black mud and release sulfides by digesting organic material or by reducing sulfate compounds.

As these remarks might indicate, Beggiatoa, sp. were found in this sample.

Beggiatoa with Euglena

This photomicrograph includes both Beggiatoa, sp., and Cyanobacteria. Generally Beggiatoa are large bacterial filament, but they still come in various sizes.

Beggiatoa loop

This rather delicate filament, probably also a Beggiatoa, sp., has coiled around a group of cells that are probably Cyanococcus, sp., a spherical Cyanobacteria that often shows in pairs, like two tennis balls pressed together.

Here are Spirochete bacteria in motion at 1,000x magnification.

I always think of them as “jittery bacteria” because of their movement. The reason for the irregular “jittery” motion is that their flagella are internal. When the internal flagella beat, they move the bacterial “sausage”, rather than beating against the exterior water [or other medium]. Many Spirochete species are pathogenic. It is very likely, however, that these salt marsh pond bacteria are not. For the bacteria, “species” is a slippery term. Loosely there are around 100 “species” of bacteria that are human pathogens. Recent DNA barcoding studies indicate that a drop of ordinary pond water may contain as many as several thousand identifiably different “species” of bacteria. There are, I imagine, at least 100-million different “species” of bacteria. That makes for 1,000,000:1 odds that the bacterium you meet will not be pathogenic for humans.

Sadly, the Codium, sp., we saw in December and January was almost completely gone. I found bleached and withered remains surround a tiny clump:

Codium remains

This Weep species of Codium somewhat resembles Codium Arabicum or Codium setchellii, in that it lacks “fingers”. Taxonomy by photo, however, is unreliable.

Since this coenocytic siphonous green algae is a common seaweed in many parts of the world, the loss of this species from the Weep is not an ecological disaster. The Weep site, however, is the only place I have seen any species of Codium in the San Francisco Bay Area. For all I know, this species may be unique and have unique properties.

Such speculation is not far fetched. Different species of Codium produce a wide range of food and pharmaceutical products. When you know little about a species, its loss cannot be evaluated.

Loss of a species and wholesale change in a microbial community is one problem well illustrated in the Weep. A cause was probably the dramatic rise in the salinity of the Weep water, accompanied by and driven by water loss through evaporation. That only moves the question one step further along:

Where did the water in the stream-like ponds come from in the first place? And, why did it go away during a rainy season?

Here is what we think we know.

[1] The dry areas along the Weep contain a lot of salt. So much that it sometimes forms a salty shell over the mud.

[2] There does not appear to be a tidal inlet anywhere along the Weep.

[3] On old aerial and satellite photographs the trail and railroad are together as a line between large salt ponds:

Google image of DBWeep area old aerial photo

Here I have used a circle around a “W” to mark the approximate location of the Weep site.

In the present-day Weep, a Profile through the Weep from east-to-west, cutting through the board shown in the photograph at the beginning of this report, would look something like this:

Profile through Weep.jpg

The black mud underlayment is silty. Gravel and rocks have been used to build the berm for the trail and for the Railroad. So, looking at the Profile, imagine the flow of water through the gravel, soil, and mud.

If the Weep stream-like pond is the lowest water around, then water may percolate through the gravel, soil, and mud from either pond or from the ditch and into the Weep. The actual hydrodynamics will depend on the relative water levels and on the porosity of the gravel, soil, and mud.

Return to the Weep.

Since I was finding more questions than answers, I decided another visit to the Weep was in order. I wend out on Wednesday, May 9th, 2007. It was a nice warm day, actually reaching 27-degC midafternoon, with a light breeze.

Interestingly, the stream-like pond in front of the board was deeper, about 1.5-cm, and much more extensive. The salt content, however, was much higher. At the board, I measured 185-PPT saline. On the other side of the railroad tracks, the ditch had almost dried out, with only sheltered ponds remaining. The ditch water was 27-PPT saline.

The water in the large pond, to the west of the Weep, was 128-PPT saline and also showed a dense population of the green dinoflagellates.

First the microbiology:

Sadly, the Codium is entirely gone. I found only dried remains.

Samples from the stream-like pond in front of the board showed the Euglena-like Protista were also gone. No doubt 185-PPT saline was too much for them. There were many more small green dinoflagellates of a kind often seen in the old salterns. These were probably Duniliella, sp. Also, there were many halophilic bacteria, probably a species of Halobacterium.

Someone had walked in the mud when it was drier, so water-filled footprints were evident. The water standing in the footprints was often quite green with the dinoflagellates.


This photomicrograph, taken at 1000x with Hoffman Modulation Contrast optics, shows both the dinoflagellates and halophilic bacteria.

Dinoflagellates and halophilic bacteria

Since the impression from this photomicrograph is of a few dinoflagellates and halobacteria, I am including a videomicrograph of the same sample [1000x] to convey just how active life in the green footprint was:

Other biota remained, including Beggiatoa and the small ciliates, as well as Cyanobacteria.

Measuring the Profile:

Part of the reason for the return visit was to put elevation numbers on my profile of the Weep. This turned out to be harder than I thought. Measurement with my GPS unit were too variable, although two measurements did serve to confirm other methods. I also brought a laser distance-measuring device, “FatMax” by Stanley. Although it worked well in the shop and around the house, it failed in the bright sunlight out on the Weep. Apparently the laser beam receiver had too low a signal-to-noise ratio to work. I could measure short distances to flat surfaces, but not long distances. I also brought a 16-ft Stanley Carpenter’s tape rule, just in case. As it turns out, that was just the case.

My measurements were crude, but informative. I used the tape rule for both distance and height. I used the railroad tracks [RRT] as reference because they are higher and because the two rails 5.2-ft apart enabled reasonably-accurate parallel sighting. I used my walking stick as the sighting tool, marking the stick at the point where both tracks came together when sighted from another point on the profile.

Here is what I found with reference to the railroad tracks:

The ditch was 16.1-ft east of the railroad track centerline.
The ditch water level was 4.0-ft below the railroad tracks.

The board was 21.6-ft west of the railroad track centerline.
The board was 4.0-ft below the railroad tracks.

The trail centerline was 72.1-ft west of the railroad track centerline.
The trail was 3.2-ft below the railroad tracks.

The trail berm west of the trail was 90.1-ft west of the railroad track centerline.
The trail berm west of the trail was 1.0-ft below the railroad tracks.

The water’s edge in the pond below the trail was 94.1-ft west of the railroad track centerline.
The water level in the pond was 3.75-ft below the railroad track.

These measurements were very crude, but bear on whether water from the pond or water from the ditch could be reaching the Weep by percolation through the soil.

Water from the ditch was on the same level as the board, 4.0-ft below the railroad tracks, and would have to travel 16.1+21.6=38.3-ft through soil and gravel to reach the stream-like pond at the end of the board. On this date, the ditch water was much reduced, being in discontinuous small ponds along the ditch. It was also very much less saline. It was about the same salinity the last time I was there, but at that time the ditch was full and the water level was probably a foot or more above the level of the board.

Water from the pond was only 0.25-ft above the level of the stream-like pond and would have to travel 90.1-21.6=68.5-ft through soil to reach the stream-like pond at the end of the board. The pond water is closer in salinity, and varies tidally. This was about mid-tide.

Either model is possible, but I am still reluctant to claim the water in the stream-like pond percolated from either the ditch or the pond.

Brief Report addendum after hike with Stanford Students on 15th May:

We used a surveying instrument and rod to confirm the relative elevations of the stream-like pond at the Board, the Ditch, and the Green Pond to the west of the Trail. Using the instrument, we were able to work from the bench mark on the trail to the east of the Railroad Tracks. The Ditch water was at, or below the elevation of the Board. The Green Pond water was well above the elevation of the Board.

As the afternoon progressed, we noticed that water seeped from the Green Pond, under the west Trail, and into the stream-like pond around the Board.

Water seeping under the trail from the green pond

At this time, the relative salinities were:

Green Pond = ~118-PPT
Weep Site Stream-like Pond at Board = ~122-PPT
Seep from Green Pond = ~128-PPT
Stream-like Pond north of Weep Site = ~87-PPT

See the next installment after more field study.

2 Responses to “Microbial Ecology at the Drawbridge Weep”

  1. Sharon Mooney Says:

    I found this microbe(protozoa?) last night –it has a red proto-eyespot, and I’ve seen this with Euglena. It has many features in common with Euglena.

    What am I looking at here?

    Anxiously awaiting identification.


    Thanks, Sharon

  2. Sharon Mooney Says:

    Once I learn of the identification, it will be easier to clip frames/stills from the original footage (some modifications to increase clarity) and voila, share photos on the web for those who are into education.

    Any help identifying this creature will be appreciated.