Cyanobacterial Mats


A Cyanobacterial mat is a layer of Cyanobacteria resting on the mud at the bottom of a salt marsh pond. Cyanobacteria that form mats range from individual Cyanobacterial cells forming a soft, gelatinous mat to long filaments that can form very tough, thick hard mats. The photograph below shows an area 4.3-cm X 7.9-cm of the Cyanobacterial mat on the bottom of a Heron’s Head Park salt marsh pond, San Francisco Bay. The 609 bubbles are essentially pure oxygen, generated by Cyanobacterial photosynthesis. This represents about 2.7-liters of oxygen per square meter.


The 1-cm scale bar was created from a reference in the original photograph. Bubble volume was estimated from the average diameter of 6-bubbles. Bubble counts were made from a printed photograph, using a mechanical counter and marking pen to avoid duplicate counting. Two larger bubbles were seen to detach from the mat and rise to the surface while the photograph was being taken, but this observation does not permit more than a minimal estimate of 2.7-liters oxygen per square meter produced during a day of sunlight.

Heron’s Head Park has an area of 11-acres, but only about 60% consists of wetlands. Still, the minimal estimate amounts to a daily Heron’s Head Park oxygen production of at least 72,115-liters [~103-kg] of oxygen. By comparison, a large tree [30-in base trunk diameter] produces just slightly less oxygen per year. So the wetlands of Heron’s Head minimally produce about as much oxygen per day as a forest of around 365 large trees. Put another way, the average human requires about 0.84-kg oxygen per day, so Heron’s Head Park minimally provides enough oxygen to support 123-people [tree data from Arboculture and Urban Forestry 2007.33:220.] Pretty good for a stinky salt marsh…!

A simplified chemical equation for photosynthesis gives 6-molecules of carbon dioxide [O=C=O] from the air interacting with 12-molecules of water [H-O-H], in the presence of light, to produce 6-molecules of oxygen [O=O] in the bubbles, 6-molecules of water, and 6-molecules of “fixed” carbon, which we can represent by
Usually the equation specifies a single molecule of the 6-carbon sugar glucose, instead of six “fixed” carbons composed of some highly variable structure involving one carbon atom, two hydrogen atoms, and one oxygen atom, but what I want to emphasize here is that “fixed” carbon can follow any number of metabolic pathways into the complex carbon compounds of life, from glucose to protein to fats, or burned as metabolic energy. My grandson Joe refers to this molecule, which can be assembled into so many different structures, as CHHO and points out that most of life is composed of CHHO.

Since the carbon dioxide comes from the atmosphere, we see that salt marsh pond Cyanobacterial photosynthesis removes some of the carbon added to the atmosphere by human activities. In fact, from these figures, the Heron’s Head salt marsh removes every year an amount of carbon equal to the carbon output of seven Americans.

Admittedly, part of that carbon is returned to the air as carbon dioxide produced by metabolism, but some of it remains in the salt marsh and is sequestered, over very long periods of time, in the form of Peat. Indeed, over 30% of the world’s sequestered carbon is held in peat bogs or peat marshes.

So, what is this Cyanobacterial mat and how does it work…?

The example described is one common Cyanobacterial mat found in salt marsh ponds throughout San Francisco Bay. The dominant microbial population is composed of Cyanobacteria which are are a species of Oscillatoria. Here is a sample of Oscillatoria from a Heron’s Head Park salt marsh pond.


The filaments, or Trichomes, can be short with only a few cells, or they can grow to be quite long in undisturbed environments. I have seen Trichomes up to several feet long in run-off streams from hot springs. Because salt marsh ponds are often disturbed by tides, or by rapid changes in salinity, the Trichomes are rarely more than several millimeters in length.

A cell in this species is about 3-microns thick and 25-microns in diameter. One cell grows and divides along its thickness, creating two stacked disks where one was before. Sometimes cells die. A Trichome can break into smaller segments at the site of a dead cell, or simply because some shear stress is sufficient to break two cells apart.

Each cell is filled with membranes supporting the chlorophyll-based photosynthetic apparatus. Because Oscillatoria are prokaryotes, indeed, an ancient prokaryote more than 3.5-billion years old, their cells are not organized into a nucleus, chloroplasts, and other organelles. One evolutionary theory, by now well supported and usefully predictive, is that chloroplasts are actually the descendants of free-living Cyanobacteria that became included in larger cells, took up residence as symbionts, and have now become dependent organelles.

In a mat, the Trichomes lie horizontally – sort of like spaghetti on a flat plate. Since sunlight is necessary for photosynthesis, the filaments of Cyanobacteria are in constant motion, seeking light or higher carbon dioxide concentrations. The result is a dynamic mat, constantly in motion as moving Trichomes slide past each other. The videomicrograph below shows this motion and has been put to music intended to capture continued restless movement over the more than 3.5-billion years this species has existed [turn your sound on if you want to hear it].

You can now estimate the speed of Oscillatoria movement. Simply count the number of cells passing any point during a time noted on your watch, and you can calculate the speed as microns per minute. Hmmmm… Turns out to be a bit more tricky than I thought. In one trial, I got 8-cells in 19-seconds [0.4211-cells/sec]; in the next, I got 7-cells in 17-seconds [0.4118-cells/sec]. Taking the average, I find 0.4164-cells/sec X 3-microns/cell X 60-seconds/minute = 74.95-microns/minute. Say 75-microns/minute, or about 4-mm/hour.

Exactly how such a filament of Oscillatoria cells moves is not well understood. Many bacteria are propelled by flagella, which are whip-like structures that project from the bacterial cell. Most flagella actually spin, driven by a little molecular motor. The gliding motion of Oscillatoria filaments, however, cannot be the result of flagella because these bacteria lack flagella. One or more proteins are involved in the gliding motion of Oscillatoria because mutants lacking these proteins do not move, but how the identified proteins form a motor and how that motor operates is not known.

The next question is why Oscillatoria filaments move. The word “why” is not meant to imply they think about what they are doing, just whether they are responding to physical or chemical signals.

Earlier above I mentioned that their movement in the pond bottom mat seemed to be in response to light or carbon dioxide. To examine this, when I started writing this report I “domesticated” some Oscillatoria from a Heron’s Head Park salt marsh pond and watched them growing and moving on clear sea water agar. Microbiologists use the term “domesticated” to recognize that growing bacteria in the laboratory results in adaptation to the growth medium and culture conditions which may change the bacteria from their ancestors in the wild. Still, working with an organism in the laboratory may be the only way to get at some questions.

Transferring the Oscillatoria filaments to sea water agar resulted in short to medium-length filaments scattered over the Petri plate. Within a day, almost all of the filaments had done something unexpected. You can see that in this sequence of photomicrographs:


These pictures were taken at 100x magnification by putting the Petri plate on the stage of the microscope and moving stage up until the filament was almost touching and in focus. No cover glass was used.

Start with the picture in the upper left. Some very short filaments remained straight, but filaments of a few hundred cells, or more, quickly formed loops. As the loops coiled tighter and tighter, other filaments joined the loops, as seen in the upper right-hand picture and lower left-hand picture. Within a few days, columns of filaments began to branch out of the coil, sometimes joining other coils and sometimes meandering over the Petri plate for considerable distances.

With time, filaments began crawling over each other, even though there was plenty of room on the Petri plate for the forming “mat” to remain only one layer thick.


When microbes appear to respond to some sort of chemical, tactile, or physical signal by moving toward or away from it, their action is called a “taxis”. This was a deliberately-coined new word to avoid any implication of motive, or intent. A taxis is simply a physical response to a physical or chemical stimulus. The word “taxis” carries no implication as to how the microbe detects the stimulus or responds to the stimulus. In some types of “chemotaxis” that are well understood, the stimulus is purely chemical and results in no more than greater activity, e.g., faster spinning of a flagellum motor. This may seem a dumb way to get somewhere, but if the motor slows down when the microbe gets farther away and speeds up when it gets closer, then random motion can still bring the bacterium closer to the stimulus.

A positive taxis is movement toward the stimulus; a negative taxis is movement away from a stimulus. In this instance, it appears that Oscillatoria filaments have a positive taxis to the mechanical stimuli of touch [thigmotaxis] or, possibly, to some chemical attractant they, themselves, produce [chemotaxis]. This would explain the coiling into larger and larger disks, until they are even coiling over themselves.

At the beginning of my discussion of Oscillatoria filaments moving, I noted that one hypothesis was movement toward more intense light [phototropotaxis] and another was movement toward greater concentrations of carbon dioxide [chemotaxis]. I do not have the tools to test the latter hypothesis, but I have increasing doubts that Oscillatoria filaments exhibit phototropotaxis. Observing that the filaments moved all over a Petri plate, I covered half of a Petri plate with aluminum foil and oriented the plate in various directions toward sunlight. I expected to observe a net movement into the well-lighted area. This did not happen; the distribution of coils and filaments remained random, rather than concentrating in either the lighted area or the area in shadow.

These experiments only hint at the conditions necessary for Cyanobacterial mat formation, for they introduced two artifacts that cloud interpretation of Oscillatoria movement. The first was that there was no water over the agar surface, as there is usually water over the mud in a salt marsh pond [except in extreme evaporation]. The second was that growth of the Oscillatoria was rather limited. I had expected to see a substantial increase in filaments until the surface of the agar was covered as the mud bottom of a pond is covered by the mat. This has not happened, suggesting that seawater agar may lack sufficient mineral nutrients. The mud under San Francisco Bay salt marsh ponds is typically much richer in iron compounds, copper compounds, magnesium, and sulfur compounds, than the seawater used to hydrate the agar.

I am starting a series of experiments in which the seawater agar is supplemented with various mineral nutrients and, even, filtered extracts of mud. In some dishes, the enriched agar is then covered with a layer of ordinary seawater after inoculation with Cyanobacteria. These experiments will enable me to better determine the parameters necessary for good Cyanobacterial mat formation.

One Response to “Cyanobacterial Mats”

  1. Noreen Weeden Says:

    Recently I went on a walk with some of the folks from LEJ at Heron’s Head Park in San Francisco and Myla Ablog mentioned Hidden Ecologies. Golden Gate Audubon has been restoring a wetland at Pier 94 in San Francisco since 2002 and I was wondering if you might be available to take a look at this wetland site along SF Bay? There are 2 ponds on this 6.5 acre site,
    Please contact me if this is of interest. Thank you.