Heron’s Head Park Salt Marsh – July and August in 2006


Salt pond observations in Heron’s Head, made July 15 and August 22, 2006, show some startling


Compared here are the Tide Plots for July 15 and August 22, 2006.


These dates are slightly more than a month apart and the two tide plots are markedly different. In mid-July the tidal excursion was more regular and less frequently exceeded 2-meters above the datum. Toward the end of August, the tidal excursion was irregular and tides exceeded 2-m above datum about every 24-hours.

Many of the ponds in the Heron’s Head Park Salt Marsh are slightly higher than the 2-m level, so they are only washed by San Francisco Bay water during the extreme tides that rise well above the 2-m mark. Each tidal washing resets the salinity of the pond to that of the Bay water. In between tidal washing, the evaporation in the ponds raises the salinity above the Bay water average.

During the summer, Bay water salinity averages between 30-ppt [parts per thousand] and 34-ppt. In 2005, the average Bay water salinity was regularly 34-ppt. This resulted in an excursion in salinity of Heron’s Head Salt Marsh ponds from 34-ppt up to around 48-ppt, and then back down again with the next extreme tide.

In 2006, however, my measurements of Bay water salinity have all been around 30-ppt. We had a very wet winter and spring 2006, during which substantial quantities of fresh water, mostly from the Sierra Mountains snow melt, flowed into the bay. Frequently the winter and spring Bay water fell to, or below, 19-ppt salinity. Release of water impounded in dams during the winter and spring may be continuing and this could be the cause of lower Bay water salinities of this summer.

Similar differences between the summer of 2005 and this summer were found in the salt marsh pond communities. In earlier posts, I have described substantial changes that took place in Heron’s Head Salt Marsh pond Micro-communities between the summer of 2005 and the spring of 2006. Most obvious now is that during this summer Heron’s Head Salt Marsh ponds have not completely regained the well-defined Cyanobacterial-Mat communities of 2005.

Most startling, however, has been the change in one pond, now called the “Big Pond Site“, that is just east of the previously-studied pond sites. The photograph below was taken on July 15.

Big Pond in July.

BIG POND SITE… Cris, Marina, and I hiked in Heron’s Head Park on July 15, and were startled to find this pond almost completely covered in a very thick floating mat. In some areas, the mat was as thick as 10-cm [almost 4-inches], although most of the mat was slighly less than 4-cm thick [about 1.5-in]. Parts of the mat were yellow, but large areas were completely white and some areas were a rich blue-green.

hh-060715 bigpond verythickmat-cu-center 024-txt-s.JPG

The close-up photograph above gives some idea of the thickness of the mat, as well as its color variation. I took a sample of the Bleached White area, show below.

Close up of thick white mat.

The tip of my hiking stick gives an idea of the mat thickness. The diameter of the rubber tip is almost exactly 5-cm. My sample for microscopy was taken from the dense white mat material in front of the hiking stick tip.

Earlier in the spring, I had found that the Cyanobacterial Mat of the previous summer had vanished in the two smaller ponds sampled, to be replaced by a thick velvet cover of the colonial diatom Melosira. For this reason, I expected the white mat material to be a tangle of bleached and dead Melosira filaments. Below is shown what I found at 400X magnification of a slide preparation of the white filaments.

Bleached algae in the white mat.

Shown is a filament of multicellular algae. Where the algae had grown profusely, the filaments were thicker and branched. Various colonies of bacteria, the bleached remains of dinoflagellates, and the bleached remains of diatoms were scattered among the algal filaments, but the defining organism of the mat was this filamentous alga.

I have observed a very similar filamentous alga in salt ponds of the marsh near Newark Slough in the Don Edwards San Francisco Bay National Wildlife Refuge. In several of those ponds this filamentous alga forms both a bottom mat and floating colonies. Before this, however, I had never seen such thick and dense algal mats in a Salt Marsh pond.

If you look at the earlier photograph of the mat, you will notice some dark blue-green areas. Close up, those areas looked like this:

Thick green mat CU

I sampled the area show to determine if this was composed of unbleached green algae. What I found is shown in the photomicrograph below:

Cyanobacteria in the green thick mat

Not algae at all, but Cyanobacteria…! Cyanobacteria a bit the worse for wear and cluttered with the remains of diatoms and dinoflagellates, but remarkably free of the algal filaments I found in the the bleached white mat areas.

To see that this is not a truly healthy Cyanobacterial mat, compare the photomicrograph above with the photomicrograph below, made from a sample taken from the small pond we are now calling New Site-1.

New Site-1 Cyanobacteria.

This is the same Pond Site-1 discussed in earlier posts of this year, in which the Cyanobacterial mat had vanished, to be replaced by a bottom velvet of Melosira, the colonial diatom. The original Cyanobacterial mat had not fully returned by July 15, but the sparse growth of tiny fragments of Cyanobacterial filaments had become healthy Cyanobacteria mixed in with the Melosira [which you can see on the right].

The thick, rich floating mat shown in the first photographs of the Big Pond Site seemed to be somewhat unhealthy, but so completely covered the pond that we expected to see it persist throughout the summer. Well, here is what I found on August 22:

Mat-free Big Pond of August 22

BIG POND SITE IN AUGUST… Big surprise…! Compare this August 22 photograph of the Big Pond Site with the July 15 photograph. Things come and go pretty fast in the microscopic world, resulting in big changes in biomass. It was difficult to estimate the total wet weight of the original full-pond mat, but I would guess at least 1,000-lb. A good part would be cellulose from the cell walls of the algal component. If true, that would represent the complete decomposition of biomass at around 27-lb per day.

Sequence of photomicrographs from Heron’s Head Salt Marsh – Big Pond Site on August 22, 2006:

Cyanobacteria, Beggiatoa, and Dinoflagellate – A mix from the mat.

HH Big Pond Mix

This photomicrograph shows the dominant members of the Cyanobacterial Mat Community. The large Cyanobacterium is probably Oscillatoria, a motile bacterial filament. Each of the lines across the bacterial filament marks an individual bacterial cell.

The Cyanobacteria are among Earth’s oldest living creatures, and are found petrified in rocks almost 3-billion years old. Cyanobacteria are photosynthetic, using the energy of sunlight to split carbon from carbon dioxide [CO2] and hydrogen from water [H2O] to release oxygen [O2] and produce [CHx]n carbon compounds for life. The continual release of oxygen over the last 3-billion years has resulted in today’s rich oxygen atmosphere.

The Dinoflagellate is a motile single-celled alga. Like the Cyanobacteria, this alga uses sunlight to fix Carbon Dioxide. Unlike the Cyanbacteria, it evolved much more recently and is a Eukaryote [true cell] organism.

The long, thin gray filaments are sulfide-oxidizing gamma-proteobacteria called Beggiatoa.

Beggiatoa are important in the Heron’s Head Salt Marsh because quantities of Hydrogen Sulfide [H2S] are produced in the black mud below the Cyanobacterial mat. Like the Cyanobacteria, Beggiatoa uses sunlight to fix Carbon Dioxide, but it gets its hydrogen from the “rotten-egg smell” gas Hydrogen Sulfide.

Each Beggiatoa filament is a single cell, so it is a very large bacterium. The filaments rise up through the Cyanobacterial Mat early in the morning, when the concentration of H2S is great and the sun is just rising. During the day, as the sun becomes more intense and much of the H2S from the black mud has been consumed, the Beggiatoa filaments sink back down into the mat.

The photomicrograph below shows a Dinoflagellate, probably Gonyaulax sp. Dinoflagellates are algae with two flagella. The flagella grow out of the groove around the body of this organism, and are oriented at right angles to each other. As a result, when the flagella beat, the cell is propelled with a lurching motion.

Notice the red-golden rod on the righthand side of the photomicrograph. This is a rod-shaped bacterium, probably Chromatium. Like the Beggiatoa, shown in the photomicrograph above this one, Chromatium is an oxidizer of Hydrogen Sulfide [H2S].

hh bigpondsite samp-2 dino_gony-good 033_060822_txt-s.JPG

Two Ciliates. What have they been eating…? Notice that you can see the cilia, not only around the edge, but in rows acoss the protozoan body.

hh bigpondsite samp2 cilliates_threads 066_060822-txt-s.JPG
Ciliates are busy critters, racing around eating everything in sight. The marine Ciliate Protozoa shown in the videomicrograph below are not Paramecium, a fresh-water organism, but they are very similar. Look for the cilia beating around their edges and in rows. Look for a mouth groove similar to Paramecium. What have these Ciliates been eating? Look closely for moving Cyanobacteria, and Dinoflagellates in this video.Click on the BLACK TRIANGLE to play.

To see a Ciliate Protozoan from the Big Pond Site that looks entirely different, click on the BLACK TRIANGLE below:

The clear “envelope” around the Ciliate Protozoan is called a “lorica” and it is made of organic material, but sometimes also containes embedded inorganic material. Sometimes the shape and nature of the lorica is useful for identifying the Ciliate species.

Throughout Heron’s Head Salt Marsh, in both ponds and in the soil, are thousands of millions of tiny round worms called Nematodes. Most of these marine nematodes a very small, only a few hundred cells in their body, and most eat bacteria. A roundworm is, essentially, a tube of cells around a gut. See if you can find the gut in this frantic roundworm. Play the videomicrograph by clicking on the BLACK TRIANGLE.

Since I have already displayed Cyanobacteria from New Site-1, I will next show a close of of New Site-1 on August 22, and then continue to a series of photomicrographs from New Site-1.

New Site-1 shown close up.

THE POND AT NEW SITE-1… In the photograph above, the tell-tale orange color of Melosira sp. is apparent. As late as the end of August, the New Site-1 Pond has not fully recovered from the rich growth of this colonial diatom that replaced the Cyanobacterial Mat on the bottom during the winter and spring of 2006.

Now both Cyanobacteria and Melosira are growing together. At the time this picture was taken, the pond salinity was 39-ppt and the water temperature was 20.8-degC. My notes say, however, that the water was clear and the bottom had a good mat of Cyanobacteria.

The next photomicrograph shows a healthy example of Melosira.

New Site-1 Beggiatoa

I have observed Melosira growing in ponds on the bottom, on marsh grass standing in water, and on the underside of boat docks. It seems to have a very broad tolerance for salinity and thick growth, although it does not form a mat, still provides shelter for many other microorganisms. When it is growing in places like a boat dock, most people spotting its creamy yellow color, think of it as “sea weed”. Diatoms are a form of algae, as “sea weed is”, but each cell also has a 2-part glass shell. Feeling of Melosira, when its growth is thick and the filaments very long, does not give the slimy feeling of “sea weed”, but, rather a slightly gritty feeling.

The winter Melosira community also supported many large diatoms that were not evident during the summer of 2005. Some of these diatoms were still around in New Site-1 on August 22. One is shown below:


In the next section, which shows samples from the Old Site-1 pond, you will see this diatom again in a videomicrograph. In the meantime, we first look at an organism found in every Heron’s Head Salt Marsh pond, Beggiatoa

New Site-1 Beggiatoa

The majestic movement of Beggiatoa is easily shown in the videomicrograph below. Just click on the BLACK TRIANGLE.

The final pond site exmined on August 22 was Old Site-1.

The peculiar designation of Old Site-1 and New Site-1 came from an error in note taking during the winter of 2006. The two salt pond sites are about 12-meters apart, at the same elevation and distance from the trail. The error was subsequently discovered, but the notes already identified both sites as Site-1. The site first designated HERON-S1 on the GPS receiver was renamed HH-OLDS-01 and the site later designated HH-SITE-01 was renamed HH-NEWS-01.

HH-NEWS-01 = N 37.73769 deg by W 122.37413 deg and is West of…

HH-OLDS-01 = N 37.73763 deg W 122.37394 deg, which is shown below:

Old Site Sample area.

THE POND AT OLD SITE-1… This pond site, also, had a few surprises.

First, it had a floating mat of Cyanobacteria, as well as the usual Cyanobacterial mat on the bottom. The members of the floating mat community were the usual Cyanobacterial mat dwellers of small diatoms, a few beggiatoa. and a few very large diatoms.

Cyanobacteria from floating mat with large diatom.

The sample above was from the floating mat and shows both a big diatom and Cyanobacteria. This diatom is the same species as the big diatom shown earlier from New Site-1, but here it is turned on its side so it appears more pointed and pennate.

In addition, I found a number of red patches in the floating mat that turned out to be a tightly colonial Purple Non-Sulfur Bacteria. One of those colonies is shown below:

Purple Non-Sulfur Bacteria Old Site-1

The individual bacterial cells are small [this photomicrograph was taken at 400X magnification], and they appear to produce a gel that holds the colony together. We have found floating colonies of these Purple Non-Sulfur Bacteria in salt marshes of the Don Edwards San Francisco Bay National Wildlife Refuge.

And… Along came a Spirochete. Spirochetes are ancient bacteria that have internal flagella. When the little flagella motors turn, it gives the Spirochete a peculiar twiching motion that sometimes appears a bit frantic and is always odd looking. Go to “Images” in the top menu and select “Cast of Critters” for more information about Spirochetes. Here is a little videomicrograph of a Spirochete visiting the colony of Purple Non-Sulfur Bacteria – Click on the BLACK TRIANGLE.

Another startling find was the motile colonial diatom with the delightful name of Bacillaria paxillifera. Here are a few diatom cells of the colony:

Bacillaria paxillifera good shot.

Notice that the cells are long and narrow, generally termed “pennate”. Each cell is “stuck” against the side of the next cell in the colonial chain. Well, so much for a still life photomicrograph.

In real life, the cells move in a coordinated way, each sliding along the next one in line, rather like a carpentier’s ruler extending out. The diatom ruler extend way out in one direction… Then collapses into a stack… And then extends way out in the other direction.

And, below, you can click on the little BLACK TRIANGLE in the middle of the picture and… presto, you can see what I have described in a videomicrograph:

Finally, I found that some diatoms had attached along their edges colonies of bacteria and even some other, smaller, diatoms. This is shown in the photomicrograph below:

Diatom with fur.

If you look closely, you can see little “hairs” sticking off the long, pennate diatom. The “hairs” are actually rod-shaped bacteria.

I find this frequently, both for diatoms and Cyanobacteria. Being photosynthetic, they produce a surplus of oxygen in the course of fixing carbon dioxide into sugars and other carbon compounds. I think the bacteria gather along the diatom cell because it is an area rich in oxygen.

One can actually show this in the laboratory with filamentous algae, which often gather “bacterial hair” when rapidly undergoing photosynthesis. I am not sure why the small diatoms also gather along the larger diatom, they may just be using it as a surface to stick to.


2 Responses to “Heron’s Head Park Salt Marsh – July and August in 2006”

  1. Cris Says:


    This fine write up inspired me to gather and post aerial images from the July ’06 walk out at Heron’s Head.


    Take a look at the set. There you will find aerial shots of your sampling sites and their context. Some of the very wide angle images are stitched panoramas. All are available in higher resolution.

    The slide show below displays a Flickr set that contains regular images and stitched panoramas.

  2. Kolette Says:

    Halo Wayne, I have followed your report here with great interest, even though I am not much into cyanobacteria myself. However, I have started a marine phytoplankton monitoring project last year along the southern part of our coast off Namibia (look at the southwest of Africa on a map if you wonder where on earth Namibia is! :-)). I am busy putting together an ID guide for phytoplankton species in our local waters. Since we are a small research office, much of my work is self taught through books and especially internet, and whatever local expertees I can get hold of. One of the species I struggle to identify I have now seen on your images above: Beggiatoa. I have various images of these organisms from samples in our waters and of similar looking organisms, which I would like to e-mail to you with the hope that could help me identify them. You can respond to my email address above if you are interested to help. It will be most appreciated. Thanks, Kolette Grobler