Activity, diversity and community structure of aerobic methane oxidizing and carbon dioxide producing bacteria in soils from the Canadian high Arctic

The fate of soil organic carbon stocked in permafrost environments is a major concern in the context of global warming. In this thesis, the bacterial populations implicated in two important aerobic microbially-driven processes of the carbon cycle, aerobic methane oxidation and carbon dioxide production, were studied in different soils from the Canadian high Arctic. A protocol for the safe and sensitive detection of DNA in cesium chloride density gradients for stable isotope probing of DNA, a recent and widely used technique in microbial ecology allowing for the identification of microorganisms implicated in the degradation of a specific substrate, was developed. Using this protocol, active methanotrophic bacteria from the genera Methylobacter and Methylomonas were identified in active layer soils from Eureka, in the Canadian high Arctic. These soils had the capacity to oxidize methane at 4°C and at room temperature (RT), but the oxidation rates were greater at RT and were significantly enhanced by nutrient amendment. Bacterial populations implicated in aerobic methane oxidation and carbon dioxide production were studied in three different soils with highly distinctive physico-chemical characteristics from Axel Heiberg Island, in the Canadian high Arctic. Using microarray and clone library analyses of the particulate methane monooxygenase gene (pmoA), putative atmospheric methane oxidizers from the uncultured genotypes "upland soil cluster gamma" and "upland soil cluster alpha" were detected for the first time in Arctic soils and were associated with near neutral and acidic pH conditions, respectively. The overall methanotrophic bacterial diversity in these soils was higher than previously described for other Arctic soils and the community composition differed depending on the soil type. Potential methane oxidation rates of the soils at low and high methane concentrations were positively correlated to the relative abundance of genotype "upland soil cluster gamma". Differences in the bacterial community structure in the three soils from Axel Heiberg Island were detected at the genera/species levels using microarrays of the 16S rRNA gene and were related to soil pH and seasonal changes. Shifts in community structure were also detected at the phyla/classes levels by real-time PCR (qPCR) of the 16S rRNA gene, with the soil carbon dioxide production rate being positively correlated to the relative abundance of bacterial groups previously described as copiotrophs (Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria). The results from this study indicated that bacterial communities in high Arctic soils play an important role in two aerobic processes of the carbon cycle, methane oxidation and carbon dioxide production. Methanotrophic bacteria and methane oxidation were detected in these soils and might be implicated in the reduction of methane emissions from the melting permafrost in the context of global warming. Beside, the relatively higher abundance of copiotrophic bacterial taxa in high Arctic soils with high organic matter content might lead, upon warming, to a rapid increase in soil carbon dioxide production. Further research is needed to assess the relevance of these findings under in situ conditions in a warming climate.

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