Summary Notes on the Weep Site and Pond A21


These Notes were started after the May 26th hike to Drawbridge with Cris and Maria, during which we visited both the Pond A21 Site, near Drawbridge, and the Weep Site. Changes at both sites were so puzzling, however, that posting was delayed. First, until after two subsequent trips to the Weep Site, on Wednesday, 4th June, with Prof. Sarah Lewison of Illinois State University, then on Thursday with Sarah, Prof. Amy Franceschini of the University of San Francisco, and members of the environmental group Future Farmers. Then, anticipating further changes, until after a return to the Weep on July 25th. And, finally, after another visit to the Weep Site on August 27th.

Our first impression, back in May, was… The Weep Site we had been studying for almost two years was drying up…! We had seen low water before, but what had often appeared as a stream was, on May 26th, little more than damp mud surrounded by dry, salt-crusted soil.


When salt ponds evaporate the salinity skyrockets. Sure enough, the salinity of the thin half-centimeter layer of water covering the wet mud shown in the photograph above of the Weep Site was 250-PPT [Parts per Thousand]. Sea water salinity is about 34-PPT, so this water was more than seven-times as salty.

Few organisms can tolerate this intense salinity. As we expected, we found a dense population of Dinoflagellates and halophilic bacteria, with virtually no other organisms.

The Dinoflagellate population consisted of a species of Dunaliella, commonly found throughout the salt marsh ponds of the Don Edwards San Francisco Bay National Wildlife Reserve. The halophilic bacteria were a species of Hallobacterium. Both of these organisms are shown in the photomicrograph below, taken at 1,000X magnification with Hoffman Modulation Contrast optics.


In this photomicrograph I have inserted a scale marker showing 10-micrometers [microns]. The Dunaliella are around 5-microns X 7-microns and the Hallobacterium are even smaller. Both of these organisms are photosynthetic, making their living by using sunlight to fix carbon dioxide into sugars and energy, while releasing oxygen.

I have also inserted a line drawing of the Dunaliella cell, showing its two whirling flagella [Dino-flagellate, where the Greek and Latin roots confuse us with “di” = two (L); “dino” = terrible (G); but, actually, “dinos” = whirling (G); and, “flagellum” = whip (L)]. These flagella are arranged at right angles to each other, so when they beat, or rotate, they move the Dinoflagellate cell in an abrupt and whirling motion.

Like this videomicrograph, also taken at 1,000x magnification…

There are a number of things to notice in this videomicrograph of Dunaliella “swimming”. First, the motion is jerky and whirling. Somehow, it works for them.

Second, notice that a little group of cells in the center are not moving very much. This is because their flagella are intertwined, holding them together for conjugation.

Dunaliella are Eukaryotes, which means they are true cells with actual chromosomes and such cellular organelles as chloroplasts. Dunaliella cells are also haploid in their normal condition. Periodically, apparently the result of environmental conditions, they conjugate, combining their two haploid sets of chromosomes into a diploid zygote. The zygote, as in most microorganisms, is both a sex cell and a cryptic persistent cell. That is, the zygote rests in an apparently lifeless state so it can persist in an adverse environment [such as a dried-up pond]. When the good times roll, the zygote undergoes reduction division and releases a flock of little haploid Dunaliella cells, which grow up into Dunaliella. This is a very good strategy in an environment like the salt marsh, where ponds dry up and tides roll in.

Tides, however, do not explain the Weep.

We understand evaporation – where the water goes, but we do not fully understand where the Weep water comes from.

We have circumnavigated the Weep trough from its northern-most point, along both sides, to its southern-most point in the water east and south of the Alviso Marina parking lot. At no point does this trough directly connect with other ponds, sloughs, culverts, or streams. The presence of water in the Weep and its associated trough does not result directly from tides, nor directly from the release of impound water.

All the observations and evidence suggest the seepage of water into the trough and into the Weep area from the ditch east of the Railroad tracks by flowing under the Railroad tracks [which bound the trough on the east side] and from the large pond on the west, flowing under the levee berm on which the north-south road runs. This seepage appears to be intermittent from both sources, rather than continuous.

The diagram below shows a W-E transect profile through the Weep Site. It was not drawn exactly to scale, but the relative elevations are approximately correct. Elevations have been twice surveyed, using different instruments, and the datum was referenced to a USGS marker just east of the ditch.

Profile through Weep

The two surveys did not exactly coincide because of problems linking all measurements to the reference USGS marker, but do support the conclusion that the level of water in Pond A15 and the level of water in the ditch are both higher than the Weep water. This suggests seepage of water from the ditch to the Weep Site, through the earth and gravel berm supporting the railroad, is possible. It also suggests seepage of water from Pond A15 to the Weep Site, under the road berm, is possible.

Two observations support seepage from Pond A15. Probing the ground west of the Weep Site shows wet mud only a few centimeters below the dry earth surface. In some earlier visits to the Weep Site, water has been observed and photographed trickling out of the road berm and flowing down to the Weep Site.

Evidence of seepage from the ditch is supported by salinity measurements. The salinity of the water in the ditch that runs north-south on the east side of the Railroad is, at most, 15-PPT. Most recently, on August 27th, I measured it at 8-PPT.

Near the north end of the Weep Site is a small “refuge” pool bounded by the gravel of the Railroad berm on the east, slightly higher than the rest of the Weep, and with a slight rim on the west that isolates it from the rest of the Weep Site during times of low water. This refuge pool has consistently remained at lower salinity than the rest of the Weep Site 01, except at times of very high water when it is flooded by the water from the larger Weep Site. When I visited in June, I found this refuge pool showed a salinity of 10-PPT, compared to the Weep Site 01 salinity of 114-PPT. At that time I designated the refuge pool = Weep Site 02, about 30-m north of Weep Site 01. In August, the refuge pool = Weep Site 02 still showed a salinity of 10-PPT, while Weep Site 01 had fallen to around 60-PPT. This suggests that the refuge pool is being fed directly by seepage from the ditch, so it maintains its low salinity.

The salinity of the water in pond A15, immediately west of the Weep and on the other side of the road berm, has remained constant in the region of 140-PPT for the last two years. Most recently, I measured it at 130-PPT.

Since we observe wide swings in the overall Weep salinity, we conclude that seepage may contribute to the Weep water supply, but the primary determinant of Weep salinity is evaporation and a high residual salt content in the mud.

The general layout of the Weep can be seen from the following sequence of photographs:

View facing east in front of the Weep Site:


View facing south showing the Weep and the trough along the Railroad track [on the left].


View facing north toward Drawbridge while standing next to the Weep.


This is about as bleak as we have ever seen the Weep Site area. It is certainly a considerable change from my visit on Feburary 18th, when the salinity of the Weep Site at the end of the board was 52-PPT, and there was a good run of water in the Weep trough.

Stepping back in time to February 18th, look at this same view, north from the Weep Site:

This is as great a contrast as one can imagine.

Tracking the salinity of Weep Site 01 at the pyramid rock over the three years 2006, 2007, and 2008, we see how the salinity has varied:


These data are inadequate to prove a clear pattern, but it does appear that the peak salinity occurs in the late spring, rising over the winter and falling as the summer progresses. There is no tidal access to the Weep and this is the peak rainy season, so we must conclude that increasing salinity results from a change in the balance of water seeping [or raining] into the Weep and evaporation of water from the Weep.

This is a puzzling pattern. In tidally washed salt marsh ponds, such as I have reported for Heron’s Head Park salt marsh ponds elsewhere in this Hidden Ecologies BLOG, the time of low salinity is during the late winter and early spring, when the Sierra snow melt and the release of impound water floods San Francisco Bay with large amounts of fresh water. During that time, the normally 34-PPT Bay Water can drop in salinity to 19-PPT, as around one-third of a cubic mile of fresh water flows per day from the Sacramento River and other tributaries into the Bay. High tides tend to reset tidally-washed ponds to the Bay salinity.

The result is a constantly-changing salt marsh pond micro-community. Typically the mat on the bottom of a salt marsh pond is dominated during the summer and fall by Cyanobacteria, usually a species of the genus Oscillatoria. Minor components of this micro-community, such as ciliates and Diatoms vary according to the salinity as it swings between the normal Bay 34-PPT and 40-PPT to 50-PPT resulting from evaporation between very high tides.

As the winter rains and, most importantly, thaw from snow melt, dumps fresh water into the Bay, the salt marsh pond is usually dominated by various species of the communial Diatom Melosira, which forms a fuzzy mat displacing the Cyanobacterial mat. In some higher salt marsh ponds, a thick surface mat of filamentous algae dominates. This latter change in dominant biomass can amount to many tons appearing in only a week or two in even a small pond.

These salt marsh pond micro-community changes described are regular with both tides and seasons. Knowing the history of a particular tidally-washed salt marsh pond enables one to predict micro-community changes based on the time of year and time of the most recent very high tide.

Such prediction of micro-community changes does not appear to be possible for the Weep Site. Above I showed the Dinoflagellate/Hallobacterium micro-community we found in May.

If we go back in time to September of 2006, the Weep Site 01 salinity was about 48-PPT and the bottom was a yellow-orange mat of large sigmoidal pennate Diatoms that looked like this:


By December of that year, the orange-yellow mat composed of the sigmoidal Diatoms had retreated to a small patch at the north end of the Weep and the larger Weep area had a yellow mat composed of Beggiatoa and a dense population of a species of the lovely Diatom Cylindrotheca:


In March of 2007, the lovely Cylindrotheca had become a distinct minority, with the dominant population being a strange species of marine Euglena:

DBWeep marine euglena 125t

By May of 2007, the Euglena were completely gone, replaced by an assortment of Beggiatoa, an assortment of Dinoflagellates, and a few Cylindrotheca.

Skipping ahead to 2008, the low salinity of January and February resulted in the population shown here:

How startling a difference. This giant Amoeba flowing over Cyanobacteria was observed in a sample from the North end of the Weep Site in February, 2008. At low salinities I have observed a wide variety Amoebae species in the Weep, but none this large before.

The Cyanobacteria were also interesting. Of similar size and general appearance, they came in two “flavors”:


Most were not motile and had a distinct sheath, as shown above. A few, however, looked identical, but were without the sheath:


By all indicators, this flavor was a species of Oscillatoria. How it is related to the non-motile Cyanobacteria with a sheath is not clear to me. It may be simply two different expressions of the same species, or they may represent entirely different species. In any event, both are more slender than most salt marsh Cyanobacteria species and were more frequently found in short filaments that usual.

In any event, the smaller Weep Cyanobacteria were certainly motile, as shown below at 200x magnification, and were the dominant part of a rich micro-community.

This rich assembly of Cyanobacteria, Amoebae, and Diatoms had vanished with the spike in salinity of May, 2008 [see the beginning of this post]. In its place were two salt marsh microorganisms able to tolerate such extreme salinity, Dinoflagellates and Halobacteria.

Then, as water in the Weep increased from June to August of 2008, and the salinity fell, a new micro-community appeared. Both of the Cyanobacteria found earlier in February, 2008, returned. They were not, however, a major component of the Weep Site micro-community.

The bottom appeared to be coated with a slightly “fuzzy” yellow mat. Sampling the mat, the small Pennate Diatom shown below at 1000x magnification [10-micron scale bar for reference] was, at least by numbers, the dominant member of the micro-community.


This diatom is motile and was quite active, as this brief videomicrograph shows [also at 1000x]:

Another member of the micro-community, not in as large numbers as the small Pennate Diatom, but much larger in size, was this bright yellow organism [shown here at 200x magnification, with a 50-micron scale bar for reference]. It did not appear to be motile.


I have not yet identified it, although I have sometimes seen it in the salt marsh before in very small numbers.

Here I mention a species of Cyanobacteria that was very much a minority of the microbial population of the Weep Site, but because it is both rare to see in a San Francisco Bay salt marsh pond, I include:


This is a species of the Cyanobacterium Chroococcus. It is found in fresh water, salt water, sludge, and free-floating in the ocean. Indeed, it makes up the world’s largest population, either by numbers or by weight. It is also one of the major sources of oxygen for the world’s atmosphere and a major sink for carbon dioxide. It is, therefore, an essential component in regulating carbon in the atmosphere.

The only other place I have found Chroococcus is in a Heron’s Head Park salt marsh pond, that example shown here because its components are identified:


I have written above about the “Refuge” Pool – Weep Site 02. This is a small pool located in the north-eastern end of the larger Weep Site, bounded on the east by the gravel of the Railroad track berm and on the west by a slight rise, sufficient to isolate it from the rest of the Weep when evaporation reduced the water level. It is largely protected from wind and bright sun by the Railroad berm and large rocks.

Apparently, the refuge pool is continually fed by brackish water seeping through the gravel under the Railroad tracks from the ditch on the east side. The ditch has remained between 5-PPT and 15-PPT salinity at all visits during. I only discovered this in May of 2008, so I do not know how long it has persisted. My measurements showed about 10-PPT salinity at each visit this year. This photograph was taken in August:


The size of the pool can be estimated by the end of my walking stick, showing in the photograph. The dark green mass on the left is a dense growth of Cyanobacteria – the kind shown in the photomicrographs earlier in this post. Sampling the large dark green mass showed almost all the Cyanobacterial filaments were sheathed and not motile. However, when I left the sample sitting in a small partially-open vial, filaments climbing up the walls were observed within 24-hours. Samples from these filaments were not sheathed and were quite motile.

Samples from the bottom mat showed a rich assortment of microbial fauna and flora, from Cyanobacteria to Diatoms to various protozoa. Close to and supported by the rocks and mixed with the Cyanobacterial mass was a healthy growth of a species of the coenocytic siphonous green algae Codium, rare in the San Francisco Bay area.

The reason I have called this pool a “refuge” is that its constant low salinity may provide just that for many of the species of the Weep micro-community, especially during times of very low water and very high salinity in the larger Weep area.

A refuge provides an instant and fairly dense population of microorganisms for populating the larger Weep area when rains or seeps occur. This may, effectively, determine the population of the Weep.

The concept of “refuge” is widely used in the ecology of larger organisms, particularly plant populations.

Pond A21

The Pond A21 Site remains an enigma. This was a salt pond until the dike was broken in June of 2006. We reported on this pond in September of that year at the time of a very high tide. It was clear, at that time, that microbial studies were unlikely to be productive until things settled down. Bottom erosion was considerable during the extreme high tides.

One of my goals was to study the succession of micro-communities in Pond A21 as it evolved from a maintained saltern pond to a tidally-washed salt marsh. I had no idea what to expect, or how long it would take to see results.

The visit on May 26th of this year was the first time I have made any serious effort to sample mat communities in Pond A21 since the visit in September of 2006. I was startled to find the pond salinity was only 10-PPT, essentially brackish water. Just across the berm to the north, an older healthy pickleweed salt marsh yielded small tidally-washed ponds with a salinity of about 40-PPT [it had been awhile since a tide sufficiently high to was these small ponds, so evaporation had driven the salinity up]. The comparison was startling.

The bottom of Pond A21 showed a large number of Diatoms similar to those found in brackish water or fresh water, as well as many ciliates and Nematodes. There was no obvious “bottom mat”, just slick mud with a slight yellowish cast.


Across the berm, the salinity 40-PPT salt marsh pond, surrounded by pickleweed, yielded the usual large Cyanobacteria in a typical well-established mat, with a few Diatoms and no ciliates. The flora of this small pond could be found from Heron’s Head salt marsh around the Bay to the tidally-washed ponds around Newark Slough.


I have not been able to get back to Pond A21, and neither Cris nor I know where enough fresh water could come from to drive the salinity of the water standing in Pond A21 down to 10-PPT.

Clearly this area is ready for a much more concentrated study.

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