Why Sequence Beijerinckiaceae?

Methane is a major greenhouse gas and a potential alternative fuel. In the environment, methane is oxidized by aerobic methanotrophic bacteria. Most methanotrophic bacteria are unable to grow on any substrate containing a carbon-carbon bond, and are therefore termed “obligate methanotrophs”. The only known exception is the recently discovered facultative methanotroph Methylocella, which grows on some organic acids and alcohols as well as on methane. The reason for the obligate nature of methanotrophy in all known species except Methylocella is a long-standing scientific mystery. In order to examine this mystery, JGI will sequence the facultative methanotroph Methylocella silvestris BL2, the obligate methanotroph Methylocapsa acidiphila B2, and the nonmethanotrophic chemoorganotroph Beijerinckia indica subsp. indica, all members of the family Beijerinckiaceae.

The family Beijerinckiaceae presents an ideal opportunity for a comparative genomic study into the evolution and biochemistry of obligate methanotrophy. This is the only bacterial family containing methanotrophic and nonmethanotrophic bacteria, and the only family where an intermediate phenotype, a facultative methanotroph, is present. These all belong in a tight phylogenetic cluster of maximum 3.8% 16S rRNA gene sequence divergence, and all were isolated from acidic soil environments. Our collaborators hypothesize that much of the genetic variability among them is related to their different metabolic lifestyles, and that genome comparisons would provide insight into the genetic and metabolic tradeoffs required for a specialized methanotrophic lifestyle compared to more generalist chemoorganotrophic lifestyles. The recent discovery of facultative methanotrophy in Methylocella has considerable environmental and biotechnological implications as well, and its complete genome sequence could provide robust data to develop a platform for biotechnological and environmental exploitation of facultative methanotrophs.

Principal Investigators: Peter Dunfield (Inst. of Geological and Nuclear Sciences), Colin Murrell (Univ. of Warwick), Werner Liesack (Max Planck Inst. for Terrestrial Microbiology), Svetlana Dedysh (Russian Acad. of Sciences), and Maqsudul Alam (Univ. of Hawaii)