Molecular ecology and biogeography of methanotrophic bacteria in wetland rice fields

Methanotrophic bacteria perform a central function in our climate system representing the only biogenic sink for the greenhouse gas methane. In wetland rice fields, they function as bio-filters preventing methane produced in anoxic layers escaping into the atmosphere, attenuating the potential methane emission by up to 90%. Despite intensive studies in the past, molecular approaches have barely started to explore the full diversity of methanotrophs. Furthermore, only little is known on their ecological niche differentiation and the factors influencing their community structure. This thesis focuses on the aerobic methanotrophic communities in the wetland rice ecosystem using the pmoA gene as a functional and phylogenetic marker to detect these bacteria in the environment. A high diversity could be recorded dominated by Methylocystis and Methylosinus species (type II) and yet uncultivated bacteria grouping within type Ib methanotrophs. The rice paddy cluster 1 (RPC-1) forms the largest cluster consisting entirely of sequences obtained from paddy fields located around the world. It is only distantly related to cultivated species and might form a new genus of methanotrophs specifically adapted to wetland rice fields. Methanotrophic communities showed no large scale horizontal distribution patterns within an Italian paddy field; thus, a reduced sampling effort is sufficient to extrapolate to the field scale. However, different methanotrophic communities were detected on the rice roots compared to the field soil and the communities in different fields differed significantly. The rice roots were characterized by a high abundance of type I methanotrophs and different rice cultivars were shown to have an effect on these communities. This effect could be correlated to the plant genotype and enables to select specific cultivars for in-depth studies. Re-evaluating the pmoA gene as a phylogenetic marker for methanotrophs revealed a good correlation of the pmoA to the 16S rRNA phylogeny. Nevertheless, some exceptions suggests that methanotrophy might be evolutionary more complicated having been even exchanged between species. Furthermore, a meta-analysis of pmoA sequences from various environments revealed distinct correlations of genotypes and habitats