Lake Merced – Preliminary Micro-community Findings


On February 19th, 2007, Susan Swartzenberg, Tim Waters, Cris Benton, and I made a field trip to Lake Merced in San Francisco. Click on the blue underlined [or red] names for earlier reports of this field trip, and for web information about Lake Merced.


I took this photograph of the Lake Merced shoreline during that field trip. Both Cris and Susan have much more detailed photographs of the lake, so I will not show more scenic pictures. I identified a north shoreline area of Lake Merced, just west of the Parking Lot at Fishermen’s Bridge, as Sample Site 01. Coordinates = N37.72847 W122.49525 degrees [decimal].

The photograph shows several features of the present lake shallows. First, the shallows water plants grow very richly. It is a dense area of water grasses and reeds. The water surface is covered with Duckweed. If you look down to the bottom center of the photograph, you can see that the submerged vegetation is thickly covered with a “furry” rust-red material.

I took several water and bottom samples from this site. I examined the samples with my field microscope on site, and with a larger laboratory microscope after I got home.

What I found was startling. First, the number of species in the bottom Micro-community was very limited. I saw a few filaments of Cyanobacteria, very few diatoms, very few protozoa, and some individual bacteria. By comparison, both salt marsh ponds around the Bay and various California lakes that I have examined reveal a rich bottom Micro-community. Typically there is either a Cyanobacterial mat, an algal mat, or a mat of diatoms over the bottom mud. Such mats shelter many different species of bacteria, diatoms, protozoa, algae, and insect larvae. Usually I find half-dozen species in the majority and many more minor species. Here was a microbiological desert.

The rust-red material covering submerged vegetation, which I had thought might be diatoms, turned out to be red flakes and particles that I could not identify at first. Among the red flakes and particles I found many small rod-shaped bacteria. Some were connected in longer filaments, characteristic of rapidly-dividing bacteria.

I had also identified another Sample Site, designated 02, on the south end of Lake Merced. This was also a shallow shoreline largely overgrown with water plants. Coordinates of Sample Site 02 were N37.72670 W122.50146 degrees [decimal]. Site 02 was similar in the sparse bottom Micro-community. It was different, however, in the absence of the thick rust-red coating on submerged vegetation. I did find some signs of the red flakes and particles along the bottom, but in nowhere near the quantities I observed in samples from Sample Site 01.

The best analogy was with water from a rusty water heater. Indeed, as it turned out, this is probably the correct analogy. In rural areas, people sometimes find such rusty red flakes coming out of well water and from the hot water system. The diagnosis is usually “Iron Bacteria“.

I returned to Sample Site 01 on Wednesday, February 21st, and re-sampled from the shallow shoreline along the trail between Fishermen’s Bridge and the Parking Lot. My sample area was next to a wood bridge along the trail, where I could easily reach the shallows.


Notice that the shallow water has a metallic sheen and the bottom and submerged vegetation are covered with the fuzzy rust-red material. Probing the metallic sheen was diagnostic: An oil slick does not fragment, the metallic sheen from Iron Bacteria does. You can also see the extent to which the fuzzy rust-red material covers everything under the water surface.

It was easy to isolate and examine fragments of the metallic sheen and red particles:


This photomicrograph shows a fragment of the metallic sheen with rust-red particles on it and some bacterial filaments projecting out of it. Examining the long bacterial filaments was more productive than looking at individual bacteria. Below is an example, identical to most of the filaments:


This photomicrograph was shot at 1,000x magnification and Hoffman Modulation Contrast optics. The camera was a Nikon Coolpix 885 set at 3x zoom for further magnification. I have included a 5-micron reference bar to show the size of the individual rod-shaped bacteria that make up the filament.

This photomicrograph also made a tentative identification possible, since only one common Iron Bacteria species has this morphology: Thiobacillus ferrooxidans. I should note here that this species name is also found spelled “Thiobacillus ferroxidans“.

From other web sites, I was able to identify the culture morphology, which closely resembles the site sample pictures. I was also able to find good descriptions of the biochemistry of Iron Bacteria.

Here is the “bottom line” about Lake Merced:

1. The metallic sheen [oil slick] is not oil. It is a biofilm. It breaks up in the manner of a film, rather than an oil slick, when disturbed. This is diagnostic for Iron Bacteria.

2. The rust-red material is probably Hematite [ferric oxide Fe2O3]. This is diagnostic for Iron Bacteria. The ferric oxidation state of iron is Fe3+. Iron Bacteria oxidizes various ferrous [Fe2+] compounds to ferric oxides such as Hematite.

3. I do find large numbers of bacteria that are about the size and shape of Thiobacillus ferrooxidans. Measurements showed a lower pH, which is also diagnostic for Iron Bacteria. I do not find any of the other species of Iron Bacteria that I know of.

4. The source of ferrous iron is probably ferrous sulfate [FeSO4]. This is a common component of both fertilizers and sewage treatment chemicals. I understand that the Golf Course, directly across a shallow narrows from Sample Site 01, has been recently renovated. This would require large amounts of fertilizer. This is certainly consistent with the rich growth of water plants in the shallows and the surface covering of Duckweed. Duckweed, in particular, requires fertilization for such heavy growth.

All this is slightly uncertain without further analysis and samples from many more sites. The clear finding, however, is that bottom samples from both Site 01 and Site 02 do not show the rich mats or mud communities I find in ponds and lakes elsewhere. I am increasingly certain that Lake Merced has an unhealthy micro-community. The most likely cause is fertilizer run-off, rich in ferrous sulfate, which has stimulated an equally rich growth of a single organism, Iron Bacteria.

One Response to “Lake Merced – Preliminary Micro-community Findings”

  1. Hidden Ecologies » Blog Archive » Case of the Missing Lake Merced Hematite Says:

    […] It was a bright and sunny Sunday, March 11th, out on Lake Merced. We were making a second survey of the lake to find out more about the rust red material we thought might indicate Iron Bacteria. For this part, you may want to take time to look back at my last Lake Merced Post. […]