The microbial communities of San Francisco Bay: location, location, location

A view of Rio Vista windmills from the Polaris.

I did my PhD research at the best field site one could ever hope for: the San Francisco Bay estuary. I had the ridiculously good fortune to be able to join USGS scientists on research cruises every month, taking the beautiful R/V Polaris on a transect between Rio Vista and Redwood City. For someone who grew up on the land part of the Bay Area, it was pretty spectacular to be able to witness the sunrise on the Delta, and to cruise under the Bay Bridge for a view of the San Francisco skyline from the water, all while doing science.


My purpose for spending all that time on the boat was to collect sediment samples, so we could study the microbes living there. For an estuary with such a rich history of ecological study, we know surprisingly little about microbial ecology in the Bay, especially the microscopic life at the bottom of it. In the Francis Lab, where I did my PhD work, we studied nitrogen-cycling bacteria and archaea, and my project was specifically focused on surveying the denitrifying bacteria in the estuary sediment.

The microbial nitrogen cycle, as portrayed in chocolate (on a post-thesis-defense cake). See Francis & Casciotti 2015 for greater detail.

Denitrifying bacteria have the ability to breathe nitrate (NO3) the same way humans breathe oxygen, and they do so in low-oxygen environments such as soils and sediments. When they breathe (reduce) nitrate, they take it through a series of transformations, eventually releasing much of it as dinitrogen gas (N2)—the same gas that makes up 78% of our atmosphere. Nitrate is an important nutrient for other bacteria, for plants, and for phytoplankton, whereas dinitrogen gas is pretty biologically inaccessible, so the activity of denitrifying bacteria has serious implications for nutrient availability and primary productivity in many ecosystems.

Les “infiniment petits.” Gayon & Dupetit, 1886.

We’ve known about denitrifiers since the 1800s, and have long appreciated their importance in wastewater treatment (where we encourage their activity to eliminate excess nitrogen from our waste) and in agriculture (where we try to minimize their tendency to volatilize the fertilizer we add to the soil). More recently, the fate of nitrogen has become a matter of particular concern in coastal ecosystems, where humans’ agricultural runoff and wastewater treatment plant effluent can add enormous amounts to the water, fertilizing algal blooms and leading to toxicity problems or dead zones. In San Francisco Bay, this wasn’t a problem for a long time, because suspended sediment left over from Gold Rush hydraulic mining activity (yes, STILL left over!) kept algal blooms at bay. But the water is finally becoming clearer, so nutrients are starting to matter more.

Algal bloom on the Delta.

The primary aim of my research was to get an idea of who was where, and how often things changed, in terms of nitrogen-cycling microbes in the Bay floor. I sampled sediment using a grab off the side of our research vessel, extracted DNA, sequenced functional genes (genes for nirK and nirS, two types of dissimilatory nitrite reductase) known to be specific to denitrifying bacteria, and compared groups of sequences from five different sites at different points during the year. And I happened to be doing this just around the time that next-generation sequencing was starting to become really affordable, so I had the chance to compare a smaller dataset generated with a more low-throughput method (Sanger sequencing) with an enormous dataset generated by the newer Ion Torrent platform, to see what, if anything, was different between the two.

Sample sites. Numbering by USGS. Background map from Stamen Maps.

Regardless of the method I used, I found that denitrifying bacteria are extremely site-specific. Just by looking at the community of denitrifiers in a sample (via the sequences of their nitrite reductase genes), you could probably tell which part of the bay that sample came from. Since we sampled along a salinity transect, these differences between sites also correlated with differences between freshwater and saltwater, and it’s a little difficult to say how important salinity is versus location. We do know, from studies in other environments, that salinity certainly makes a difference to microbial community composition.



You can explore some of the denitrifiers I found in San Francisco Bay: click on the trees below and they’ll bring you to my datasets on the Interactive Tree of Life, where you can pan and zoom to get the full view. Each branch with a cryptic name represents one sediment organism whose nitrite reductase gene I cloned and sequenced. Some of the branches have species names– those are the most closely-related cultured isolates, for reference. As you can tell, most of the organisms we found in Bay sediments aren’t closely related to known cultured organisms (a pretty typical situation for environmental microbes). The colored bars illustrate the sample site that each sequence came from. The full story on these datasets is in a paper I published in Microbial Ecology. Even better, I go way in-depth with just the nirS-type denitrifiers in a paper in Environmental Microbiology.


Phylogeny of nirK (Cu-type dissimilatory nitrite reductase) genes in San Francisco Bay sediments, color-coded by site.


Phylogeny of nirS (cytochrome cd1-type dissimilatory nitrite reductase) genes in San Francisco Bay sediments, color-coded by site.



Francis, C.A., and Casciotti, K.L. (2015). The Geomicrobiology of Nitrogen. In Ehrlich’s Geomicrobiology, H.L. Ehrlich, D.K. Newman, and A. Kappler, eds. (CRC Press), p. 281-296.

Gayon, M.U., and Dupetit, G. (1886). Recherches sur la réduction des nitrates par les infiniment petits. Mémoires de la Société des sciences physiques et naturelles de Bordeaux. 3, 201–308.

Lee JA, Francis CA. (2017) Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition. Environmental Microbiology 19: 4897–4912. [PDF]

Lee JA, Francis CA. (2017) Spatiotemporal characterization of San Francisco Bay denitrifying communities: a comparison of nirK and nirSdiversity and abundance. Microbial Ecology 73: 271–284. [PDF]

Rogers, P. (2013). San Francisco Bay waters are becoming clearer, but that may mean threats from algae growth. San Jose Mercury News, published online 30 November 2013.