Methane-producing Archaea are of interest due to their contribution to atmospheric change and for their roles in technological applications including waste treatment and biofuel production. Although restricted to anaerobic environments, methanogens are found in a wide variety of habitats, where they commonly live in syntrophic relationships with bacterial partners. Owing to tight thermodynamic constraints of methanogenesis alone or in syntrophic metabolism, methanogens must carefully regulate their catabolic pathways including the regulation of RNA transcripts. The transcriptome is a dynamic and important control point in microbial systems. This paper assesses the impact of mRNA (transcriptome) studies on the understanding of methanogenesis with special consideration given to how methanogenesis is regulated to cope with nutrient limitation, environmental variability, and interactions with syntrophic partners. In comparison with traditional microarray-based transcriptome analyses, next-generation high-throughput RNA sequencing is greatly advantageous in assessing transcription start sites, the extent of 5′ untranslated regions, operonic structure, and the presence of small RNAs. We are still in the early stages of understanding RNA regulation but it is already clear that determinants beyond transcript abundance are highly relevant to the lifestyles of methanogens, requiring further study. 1. Introduction Methane- (CH4-) producing Archaea occupy an important position in the global carbon cycle and in atmospheric change by performing the final steps of biomass degradation in anaerobic systems, and releasing significant amounts of CH4 to the atmosphere every year [1]. Also, methanogenic Archaea are of interest due to their role in anaerobic degradation including waste treatment, biogenic gas production from coal, and other substrates that have potential for CH4 to be harvested for use as a fuel. Therefore, considerable environmental and economic benefits may come from understanding biological CH4 production. In terms of physiology, three major, partially overlapping, methanogenesis pathways are recognized: (i) methanogenesis from carbon dioxide (CO2) reduction with hydrogen (H2) (hydrogenotrophic pathway), (ii) methanogenesis from methylated compounds such as methanol and methylated amines (methylotrophic pathway), and (iii) methanogenesis from acetate cleavage (aceticlastic pathway). The biochemistry of methanogenesis was reviewed elsewhere [2–4] and is summarized in Figure 1. The only known biological producers of CH4 are a diverse range of anaerobic
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