Microbial mats; Cyanobacteria; Circadian clock; Metatranscriptome; Metagenome; Photosynthesis; Dinitrogen fixation
To understand the ecological role of circadian rhythms in prokaryotes, we often move from an initial observation in nature to an in-depth analysis of isolated species under laboratory conditions. The other way around is less common: newly found insights on circadian control of microbial physiology and metabolic interactions are rarely tested in the original ecosystem. This is partly due to the general inability to use laboratory-type analytical tools and controlled conditions in the environment. Thanks to novel developments in high-throughput DNA and RNA sequencing and meta-proteomic approaches, we now have tools to determine the extant activity of individual genes and expressed proteins in the natural community. We apply this approach to photosynthetic microbial mats, unique millimeter-scale ecosystems that are dominated by circadian clock-controlled Cyanobacteria. The rhythmic activities of cyanobacteria related to photosynthesis and dinitrogen fixation have been well documented. Therefore, microbial mats form ideal model systems that are easily accessible, well-characterized, have a constant community composition in the short term, and can be mimicked under laboratory conditions. Here we will provide an overview on these diverse microbial ecosystems and describe our studies on rhythmic processes in coastal microbial mats.