Probing Functional Diversity of Thermophilic Cyanobacteria in Microbial Mats

In recent years there has been growing appreciation of the unexpected genetic diversity of microbes in the environment. This diversity has important implications for our understanding of photosynthesis in populations and in the environment. Conventional methodologies often cannot effectively capture this aspect. This chapter describes new approaches including comparative genomic and metagenomic approaches combined with a more detailed understanding of the metabolism and functionalities of cyanobacteria. This approach, which can be defined broadly as "functional ecogenomics" is partly motivated by the availability of high-throughput sequence data, which are steadily being acquired. The focus is on unicellular cyanobacteria in the hot spring microbial mats of Yellowstone National Park, which are primary producers in this prokaryotic community. We took a three-pronged approach, in which we (a) acquired complete genome sequences from two dominant Synechococcus sp. and carried out a comparative genomic analysis to understand the functional differences between these temperature adapted isolates; (b) produced a metagenome dataset that allows us to place genomic information in the context of the community within which these cyanobacteria grow and evolve; and (c) obtained pure isolates of some dominant organisms that allow us to manipulate them in a well-defined laboratory setting. In situ transcriptomics has allowed quantification of transcripts during the diel cycle. These diverse approaches and the ability to measure environmental parameters such as light and O-2 levels allow us detailed insight into the microbial mat system. Such an approach could be used to study a wide array of photosynthetic microorganisms as populations and interacting communities. As sequencing capacity, single cell capture techniques, proteomics and imaging techniques become more widely accessible we expect to obtain ever more detailed information about natural communities.