Phylogenetically distinct methanotrophs modulate methane oxidation in rice paddies across Taiwan

Rice paddies are considerable sources of methane because of the highly reduced soil oxidation–reduction conditions during rice cultivation. In this ecosystem, active methane-oxidizing bacteria are important, because they consume methane while reducing the overall emissions from rice paddy soils. However, the biogeographic distribution of active methanotrophs in paddy soils across Taiwan remains poorly understood. We used DNA-based stable isotope probing (DNA-SIP) to show that phylogenetically distinct type I and type II methanotrophs dominated methane oxidation in geographically different paddy soils across Taiwan. High-throughput sequencing of soil 16S rRNA and pmoA genes under field conditions revealed that a type II methanotroph, Methylocystis, was predominant in rice paddy soils. In addition, an uncultured novel type I methanotroph cluster (Rice Paddy Clusters) was detected with the closest relatedness to Methylocaldum 16S rRNA genes in all rice field soils tested. SIP microcosm incubation, however, suggested that the type I methanotrophs Methylosarcina and Methylobacter were significantly stimulated during the consumption of high-concentration methane in five paddy soils with pH > 6.07, whereas the Methylosinus-like microorganisms of type II methanotrophs dominated aerobic methane-oxidizing communities in acidic soil with pH = 5.17. Furthermore, high-throughput sequencing of 13C-pmoA genes indicated the presence of novel methanotrophs that are phylogenetically distantly related to the type I methanotrophs Methylosarcina in four out of five non-acidic paddy soils studied, and the high proportions in the 13C-DNA suggested that these uncultured methanotrophs play an important role in methane oxidation. These results provide strong evidence for the environmental selection of phylogenetically distinct methanotrophs under field conditions. Moreover, community shifts in active methanotrophs likely occurred in response to environmental variations with fluctuating methane concentrations.