The genome sequence of Methylococcus capsulatus – a species typical of methane-breathing bacteria commonly found in soils, landfills, sediments and peat bogs – includes a full and at times redundant toolkit of genes for using methane as an energy and carbon source. Such methane-consuming microbes are called methanotrophs.
The study, to be published in the October issue of PLoS Biology and posted online this week, found an unexpected flexibility in M. capsulatus metabolic pathways, hinting that the bacterium is capable of responding to changes in its environment by functioning through different chemical pathways for using methane. That finding, if confirmed by later experiments, may increase the bacterium's potential as a biotech workhorse.
Methanotrophs play an important role in the global energy cycle because they consume methane, a gas that is produced mostly by chemical processes in landfills, in the guts of ruminant livestock such as cows, and by oil and natural gas processing plants.
In recent years, environmental scientists have shown increasing interest in methanotrophs because their use of methane as a sole source of carbon and energy could possibly be harnessed to play an important role in efforts to reduce methane emissions that are generated by biological sources such as ruminants and landfills.
The PLoS Biology study found that M. capsulatus has multiple pathways for different stages in the oxidation of methane. They also found genes that suggest metabolic flexibility, including the microbe's likely ability to grow on sugars, to oxidize sulfur, and to live in reduced-oxygen environments.
"We now have a much better picture of the relationship between M. capsulatus and its environment," says Naomi Ward, the paper's first author. "It is important for us to know under what conditions methane can be removed from the ecosystem before it accumulates as a greenhouse gas."
Ward is an Assistant Investigator at The Institute for Genomic Research (TIGR), which led the genomic sequencing and conducted the analysis with scientific collaborators at the University of Bergen in Norway.
While noting that "there is a clear need for experimental validation" of the metabolic pathways suggested by the genome, the study's authors suggest that their analysis "deepens our understanding of methanotroph biology, its relationship to global carbon cycles, and its potential for biotechnological applications."
Johan Lillehaug, the Norwegian scientist who oversaw the University of Bergen's role in the project, says the genome analysis found that M. capsulatus has a novel strategy for scavenging copper, an essential element for regulating methane oxidation. "We found that M. capsulatus is a good model for studying how microbes adapt to varying copper concentrations," he says, noting that M. capsulatus uses two separate systems – at high and low copper concentrations – for oxidizing methane.
Scientists say the organism's potential significance for biotechnology include the use of bacteriophage (viruses that infect bacteria) that have made a home in the genome. Such phages could be exploited to genetically manipulate M. capsulatus to more efficiently produce microbial protein for commercial animal feed.
The study's senior author, TIGR Investigator Jonathan Eisen, says the analysis of M. capsulatus also will help scientists learn more about some methane-fixing bacteria – those that live inside of animals such as clams and mussels in deep-sea methane seeps – that are extremely difficult to study. Such methane-fixing bacterial symbionts allow their host animals to feed off of the methane collected in seeps.
"The methane-fixing symbionts are very important ecologically but we know little about how they work since they live inside of animals and cannot be grown in pure cultures on their own,"says Eisen. "Since the symbionts are closely related evolutionarily and biologically to Methylococcus capsulatus, we can now use the information gleaned from this genome sequence to make predictions about the symbionts."
TIGR's half of the study was funded by the U.S. Department of Energy's Office of Biological Energy Research; the Norwegian half was funded by the University of Bergen Research Foundation, the Norwegian Research Council, and the Melzer Foundation.
The Institute for Genomic Research (TIGR) is a not-for-profit research institute based in Rockville, Maryland. TIGR, which sequenced the first complete genome of a free-living organism in 1995, has been at the forefront of the genomic revolution since the institute was founded in 1992. TIGR conducts research involving the structural, functional, and comparative analysis of genomes and gene products in viruses, bacteria, archaea, and eukaryotes.