Microbes that reduce carbon dioxide to methane catalyze a significant component of the carbon cycle on Earth and are responsible for most of the methane in the atmospere. Since methane contributes significantly to the greenhouse effect, understanding the biological controls on emissions of methane may provide the opportunity to compensate for the emission of other important trace gases, such as CO₂. In addition, methane is a common fuel, and the biological production of methane catalyzed by these bacteria has great potential as an alternative fuel source. This application is of special significance because it is "CO₂ neutral", i.e., it does not result in the net emissions of greenhouse gases to the earth's atmosphere. Methanogenesis also has great potential in waste treatment, especially of dilute waste waters typical of many sewage and chemical wastes. Moreover, methanogens have a robust hydrogen metabolism and are a potential source of catalysts for hydrogen production and consumption. This alternative fuel may gain widespread use in the near future.

Methanocaldococcus [Methanococcus] jannaschii was the first archaeon whose genome was sequenced. Since that time, its biochemistry has become among the best characterized among the archaea. However, very little is known about the other thermophilic (favoring temperatures between 60 and 80 degrees C) and hyperthermophilic (favoring temperatures above 80 degrees C) methanococci, and the evolutionary and biological context for interpreting this biochemical data is largely absent. Thus, DOE-JGI will be sequencing the genomes of seven organisms from this group in order to enable comparative genomic analyses within the thermophilic methanococci and comparative analyses between the thermophilic and mesophilic (favoring moderate temperatures) methanococci. These studies are expected to provide new insights into gene function among the hyperthermophiles as well as the adaptations of microorganisms to thermophily. They will also provide additional sequences of heat-stable genes for industrial applications. Because these organisms are abundant within deep-sea hydrothermal vent communities, these sequences will also facilitate metagenomic analyses of these communities. The organisms selected for this project include Methanothermococcus okinawensis IH1, Methanotorris igneus Kol 5, Methanotorris formicicus Mc-S-70, Methanocaldococcus fervens AG86, Methanocaldococcus infernus ME, Methanocaldococcus vulcanius M7, and Methanocaldococcus sp. FS406-22.