Bridge at the End of Boardwalk


The New Chicago Marsh is a non-tidal salt marsh behind the Environmental Education Center of the Don Edwards San Francisco Bay National Wildlife Refuge. If you go out the back of the Environmental Education Center, you will find yourself on New Chicago Marsh Boardwalk.


The Bridge at the End of Boardwalk crosses a Non-tidal Slough which winds through the marsh, passing under the boardwalk in several places. The purpose of the boardwalk is to protect the marsh habitats.

BRIDGE at the end of Boardwalk

On the other side of the Bridge at the End of Boardwalk are steps up to the Levee that divides the New Chicago Marsh from a large Salt Pond. If you lean over the side of the bridge, you will see a long orange and green mat floating in the slough.

You may have thought of this as no more than a little “pond scum”, but it is actually its own habitat. Indeed, it is far richer in species than all of the large land plants and animals in the entire marsh.

DNA is the long genetic molecule that determines heredity. Using short regions of DNA as “DNA Barcodes”, environmental microbiologists have found as many as several thousand different species of bacteria, protozoa, algae, and microscopic animals in a single drop of marsh water.

Sampling the Mat at Bridge

I first sampled the water in the Non-Tidal Slough to determine how salty it was. I used a refractometer to measure salt content, just like the wine-grape growers use to measure sugar, except my refractometer is calibrated for salinity in Parts of salt-Per-Thousand-parts of water [PPT]. I found the slough water was almost as salty as the Bay usually is, about 32-PPT.

Then I sampled the orange and green Mat floating on the water just to the left of the bridge. This was a little harder, because the Mat is actually rather tough and several millimeters thick.

I clipped a small plastic sample vial to my staff land gently lifted out a tiny piece of the mat, along with a little water. Notice how many different colors you can see in the mat.

In this adventure, we will use a Field Microscope as our submarine to dive into the floating mat. These are our tools…

Tools Used

Down inside the mat is like a tangle of vines in a rain forest, but these vines move…! In fact, almost every microorganism in this microscopic world is motile.

Cyanobacteria and Purple Bacteria in the Mat

Here you can see at least two different sizes of Cyanobacteria. The large one is probably Oscillatoria, a common motile Cyanobacteria in San Francisco Bay salt marshes and in fresh water ponds and streams.

I have teased the Mat apart so we can see its components; otherwise, the tangle would be so dense that light for the microscope could not get through. When you look at the photomicrographs below, remember that most of these tiny creatures are swimming or crawling in a thick mat, not wandering around alone in open water.

Such mats are often called “Cyanobacterial Mats”, because various species of Cyanobacteria are the most common organism and make up the greatest biological mass. Oscillatoria is one of the most common of Cyanobacteria and is found in most pond mats.

Oscillatoria from Bridge.

Imagine the Mat as a fabric, woven of tangled Cyanobacteria. Some Cyanobacterial filaments can be several feet long, although most filaments in salt marsh mats are much shorter.

Here’s the surprise: Like almost all microorganisms in the Mat, Oscillatoria moves. In fact, it got its name from gently waving back and forth. In the videomicrograph below, click on the Black Triangle to see Cyanobacterial motion.

Now, imagine the threads in a fabric being constantly in motion, weaving across each other and along each other, down into, and up out of the mat. The Cyanobacterial Mat is a fabric in constant micro motion.

Those of you who read science fiction are familiar with the theme of humans meeting aliens from a culture thousands of years old, sometime, even, aliens that were traveling in space when humans were entering the stone age.

Well, Cyanobacteria are much older than that. There was a time when they dominated the earth, being the dinosaurs of their day. In the Proterozoic eon, about 2.5-billion years ago, they were thriving and forming large colonies that are preserved today as fossils called “Stromatolites”. It was a time when the atmosphere lacked oxygen and the moon was a giant orb much closer to earth.

Now it is our good fortune that Cyanobacteria are photosynthetic. That is, they use the energy of sunlight to “fix” carbon dioxide into organic compounds, releasing oxygen in the process. For countless millions of years, Cyanobacteria continued growing and releasing oxygen into the atmosphere. So, when you take a deep breath, thank the Cyanobacteria who gave us our oxygen atmosphere and made us oxygen-breathing animals possible.

The other bacteria that define this Mat “Micro-Community” are a species of purple-pigmented bacteria that grow in colonies held together by some sort of gel. These are one of the few members of the mat that do not move. The photomicrograph below was taken at 800X magnification.

Purple Bacteria.

I mentioned earlier that microorganisms can be distinguished by their DNA Barcode. The use of DNA for identification of bacterial species resulted in a great reorganization of bacterial taxonomy. One of the results was identification of a large group containing many bacteria that had previously been put in different taxons. This group is called “Proteobacteria” and has been subdivided into alpha, beta, gamma, and delta groups. We will meet some other members of the Proteobacteria further on. These Purple Bacteria are Purple Non-Sulfur alpha-Proteobacteria.

I have found these colony-forming Purple Bacteria in many small salt ponds in salt marshes around the Bay. Near Newark Slough, one large pond supported giant red colonies as large as a foot across. I have not been able to identify these bacteria further, but they have always been in floating Micro-Communities with Cyanobacteria. The gel that binds the individual bacteria into colonies may also give form to the large floating mats. When they are the dominent member of the Micro-Community, the mats range from pink to bright red or orange-red.

The Purple Bacteria are phototropic. That is, they use sunlight to fix carbon. According to the literature, they may also be able to use hydrogen sulfide in this process, which would make them “weak sulfur bacteria”. Unlike the hydrogen sulfide oxidizers which we will meet later, however, they do not tolerate strong hydrogen sulfide.

The Cyanobacteria and Purple Bacteria define the Mat Micro-Community. That is, they are the dominant members and provide both shelter and, possibly, nutrients to the minority members.

Two members of the gamma-Proteobacteria are the next most-common bacteria. These are sulfide-oxidizing bacteria that use sunlight to fix carbon, but they require hydrogen sulfide in the process. They are probably even more ancient than the Cyanobacteria.

Less common, but startling to watch are the gamma-Proteobacteria called Chromatium. These are large rod-shaped bacteria that scurry along in a sort of cork-screw tumbling motion. A dense culture results in a sort of frantic mass tumbling. Here is a single Chromatium rod at 800X magnification.


Look closely and you can see the yellow grains of elemental Sulfur in the large rod. The other two large objects are also Chromatium cells, the one below turned end-up and the one on the right slightly out of focus. The one end-up and the one out of focus clearly show the red color that gives Chromatium its name. Chromatium is sometimes call a “Purple Sulfur” bacterium because it requires hydrogen sulfide and sunlight to fix carbon.

Below is a videomicrograph of Chromatium, shot at 800X magnification. Click on the black triangle to view it and wait for a moment for the monster to appear [the title of this brief video was “Chasing Chromatium”].

The spinning is characteristic of Chromatium, as is the tumbling. Chromatium rises to the upper water in the morning to balance the sun and the hydrogen sulfide that has accumulated during the night. This bacterium is found in most salt marsh ponds around the Bay, but is the dominant hydrogen sulfide oxidizer in the Bayfront Park Salt Marsh. Samples collected from that marsh often have a dark red layer on top. It was moderately common in the floating mat, but the dominant hydrogen sulfide oxidizer is shown below:


These long gray bacteria are called Beggiatoa, and they are usually found in the salt marsh when there is a faint to strong smell of “rotton eggs”. Beggiatoa also rises to upper water in the early morning, but since it is not pigmented, the result is a gray-white scum or cloud near the surface. Shown below is a microvideograph of Beggiatoa in motion, much more sedate than Chromatium.

Last of the bacteria is a Spirochete, shown here at 800X magnification. The Spirochetes are very minority players, but I always find a few. Click on the black triangle to start this brief videomicrograph.

The role of Spirochetes in the Salt Marsh economy is not clear. This Spirochete seems to tolerate oxygen well, while other Spirochetes do not. Many Spirochetes are symbionts [aiding digestion in cockroaches and some clams] and some are parasites [causing such diseases as yaws and Lyme disease]. The strange “jinking” motion of Spirochetes is caused by internal flagella.

Although diatoms are usually plentiful in Salt Marsh waters, there seem to be both few species and few diatoms in floating Mats. The small diatom shown below appears in both floating Mats and bottom-layer Cyanobacterial Mats.

It seems to have some difficulty getting past the Beggiatoa sailing “upward” past it. Identifying Diatoms from a photomicrograph is quite difficult, since Diatom taxonomy is based on the little ridges and bumps on the silica [glass] shell.

Unlike the bacteria we have seen, Diatoms are fairly recent, evolving at about the same time as the mammals.

Ciliate Protozoa are common in San Francisco Bay Salt Marsh Micro-Communities. The photomicrograph below shows a large Ciliate from the Mat that illustrates the characteristics of marine Ciliates.

Large Ciliate

The rows of cilia are used to propel this protozoan. The cilia around the mouth groove are used to sweep up bacteria and other microorganisms. You can see this motion in the videomicrograph below:

Another, smaller, Ciliate Protozoan is shown in the next small movie.

This species appears to be twirling a mustache.

To be continued…

3 Responses to “Bridge at the End of Boardwalk”

  1. Cris Says:


    I stopped at that very same spot a couple of weeks ago. While I had no kite aloft and I took no samples, I did take six images of the mat surface with the intent of stitching them together. The final file is a whopping 7,500 pixels wide.

    Water surface panorama

    Check out the larger version on Flickr — a big print would be just the thing for a dining room wall.

  2. Wayne Says:

    Howdy, Cris…

    At moment unfinished, this will be my first post on Sunday’s supurb outing. I stopped by the Bridge at the End of Boardwalk before meeting with you at the Alviso Marina. Just a single quick sample and a brief demonstration to the folks at the Environmental Education Center. I haven’t yet finished this post and I haven’t yet gotten to the huge number of other samples [four at the Weep].

    I think this site will be an interesting one to follow during this fall and winter. I expect the Cyanobacterial Floating Mat to remain rather constant, based on the way the New Chicago Marsh Non-Tidal Slough is managed, but winter rains and run off may change the Mat character during the winter. I am beginning to see the New Chicago Non-Tidal Salt Marsh as a sort of “control” for the evolving Tidal Salt Marsh where the levee has been broken. I expect to re-visit it several times this fall.

    I like the very long image of the Cyanobacterial Floating Mat. It gives a clear sense that this is a more permanent element of the Salt Marsh, and the color variation shows its complex character.

    I still have not figured out where the continuing hydrogen sulfide is coming from. This morning my sample was white on top with Beggiatoa and smelled strongly of H2S. My Mat sample was small, only from the surface, and certainly did not contain any black mud [other that what might have been sticking to the bottom of the floating mat]. I have no interpretation yet. Detective work to do.

  3. Cris Says:

    I’ve found a couple of aerial shots that show the location of the mat that you sampled and provide some environmental context.

    Boardwalk bridge

    This first shot of the pedestrian bridge from the southeast gives a clear view of the borrow ditch that it spans. This ditch is aligned along an east-west line and comes to an end not too far from the right edge of the photograph. The ditch on the right side of the bridge has filled with material blown into that dead-end by the prvailing westerly winds.

    Boardwalk bridge

    In this second view of the bridge from the southwest you can see your sampling site on the near left corner of the structure. On the left side of the bridge the ditch has a generally open water surface.

    Incidentally, the aerial photo in Goggle Earth shows the channel surface as clear on both sides of the bridge.