Found worldwide, microbial mat communities are often the pioneering species in perturbed environments and can represent the only biota in extreme habitats. These associations are well-adapted to a range of harsh conditions that include extremes of temperature, salinity, high or low oxygen levels, and nutrient deprivation. In many cases, microbial mats are highly productive biochemical ‘factories’ exhibiting enormous genetic diversity, which gives rise to an equally wide array of biotic interactions. The proposed sequencing effort emphasizes transcriptomics of several model microbial communities where a genomic foundation exists to map these reads and interpret specific expression signals in terms of metabolic community network models. Organisms from high-temperature and hypersaline environments contain enzymes and metabolic pathways that have potential application in energy production and or biochemical processing.