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. 2004 Oct;2(10):e303.
doi: 10.1371/journal.pbio.0020303. Epub 2004 Sep 21.

Genomic Insights Into Methanotrophy: The Complete Genome Sequence of Methylococcus Capsulatus (Bath)

Free PMC article

Genomic Insights Into Methanotrophy: The Complete Genome Sequence of Methylococcus Capsulatus (Bath)

Naomi Ward et al. PLoS Biol. .
Free PMC article


Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.

Conflict of interest statement

The authors have declared that no conflicts of interest exist.


Figure 1
Figure 1. Global Methane Cycle
Methane is oxidized either photochemically in the atmosphere or biologically in terrestrial and aquatic systems. The ocean, grasslands, and desert form major methane sinks, whereas wetlands, agricultural and grazing lands, and other anthropogenic sources such as landfills, are major sources. The cow depicted in the figure represents diverse ruminants. Anthropogenic inputs of nitrogen in the form of ammonia compete for MMOs, reducing methane oxidation and leading to the formation of nitrous oxide, another greenhouse gas.
Figure 2
Figure 2. Predicted Central Metabolic Pathways of M. capsulatus
Genomic information was used to predict the flow of carbon from methanotrophy pathways into carbon fixation pathways, and thence into glycolysis/gluconeogenesis and the TCA cycle. Locus names are indicated next to key steps. Some intermediates are omitted.

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