Diversity in Microbial Communities

Our initial physiological findings, coupled with the genetic diversity of microbes, provide a unique and exciting opportunity to explore, in real time, how evolution and adaptation work in the microbial world at temperatures exceeding 50oC. I believe that cyanobacterial interactions in the environment provide an excellent paradigm for dissecting the survival, functional diversity and evolution of microbial communities in a variety of harsh environmental settings and how the diversification within the community reflects the integrated utilization of limiting resources. The biogeochemical and regulatory processes underlying these microbial communities can now be queried by a number of sophisticated tools.

Exploiting comparative genomics/metagenomics:

Comparative genomics/ metagenomics is a very powerful tool and with the advent of high throughput/low cost sequencing it is possible to explore this at a level that was not feasible even a few years ago. Even with our limited analysis we have seen that genomic variability is extensive in the closely related cyanobacteria that we study. Taking this to the next logical step requires a deeper focus on specific questions. One such example which we are currently pursuing is the adaptation of cyanobacteria to high temperatures. In the microbial mats, there is a gradient of temperature (from ~50C to 70C) that the cyanobacteria have adapted to in various as yet unknown ways. This natural temperature gradient and moderately simple assemblage of organisms provides an excellent setting for probing this question.

Exploring diversity at the single cell level:

Extending from our results from the microbial mats it might not be too much of a stretch to say that bacterial populations in the environment are genetically varied and far from clonal. This raises the obvious question of how we can best assess this variability. A few years ago we initiated a collaboration with Dick Zare’s group in Chemistry to exploit the power of microfluidic cell chambers and single cell capture, followed by capillary electrophoresis to count single molecules (in this case the highly fluorescent phycobiliproteins in cyanobacteria). This led to interesting observations of variability in phycobiliprotein content in single cells and the conclusion that clonality is not necessarily the norm (put in another way, it says that averaging cellular output, although powerful, can conceal these single cell variations).

Ecophysiology of cyanobacteria:

Beyond comparative genomics lies the question of how these differences in gene content impact the ecophysiology of cyanobacteria in the environment. For instance, we identified an entire nitrogenase (nif) gene cluster in these organisms suggesting that these unicellular cyanobacteria may be capable of nitrogen fixation. Nitrogen fixation reduces nitrogen gas to biomass, and is of paramount importance in biogeochemical cycling of nitrogen. To address this point, we analyzed nif transcript levels and nitrogenase activity of the Synechococcus ecotypes, over the diel cycle in the microbial mat of an alkaline hot spring in Yellowstone National Park. Nif transcripts rise in the evening, with a subsequent decline over the course of the night. In contrast, the level of the NifH polypeptide remained stable during the night, and only declined when the mat became oxic in the morning. Nitrogenase activity was low throughout the night; however, it exhibited two peaks, a small one in the evening and a large one in the early morning, when light began to stimulate cyanobacterial photosynthetic activity, but oxygen consumption by respiration still exceeded the rate of oxygen evolution. Transcripts for proteins associated with energy-producing metabolisms in the cell also followed diel patterns, with fermentation-related transcripts accumulating at night, photosynthesis- and respiration-related transcripts accumulating during the day and late afternoon, respectively. This study, among others, suggests that a multi-faceted approach to understand microbial communities can provide insights into the regulation of metabolism. Combining eco-physiology with experiments using clean Synechococcus isolates is also an approach we are actively developing. We have recently characterized a number of responses of these isolates to nutrient stress and to high light.