A deeply branched novel phylotype found in Japanese paddy soils

Novel 16S rDNA clones which possibly constitute a sister clade from the two known archaeal lineages, Crenarchaeota and Euryarchaeota, were found in pa ddy soil environments. Overall signature sequences showed that the clone se quences shared a majority of signature sequence features with the Archaea a nd Eukarya. However, there were at least nine nucleotides which distinguish ed the novel clones from the domains Archaea and Eukarya. Phylogenetic tree s, drawn by maximum-parsimony, neighbour-joining and maximum-likelihead met hods, also supported the unique phylogenetic position of the clones. Both s ignature sequence and phylogenetic analyses strongly suggest that the novel organisms constitute a new group and their phylogenetic positions are dist ant from the Crenarchaeota and Euryarchaeota. A specific primer set was des igned to detect the presence of the novel group of organisms in terrestrial environments. Specific DNA fragments were amplified from all paddy soil DN As, suggesting that the novel organisms are widely distributed in rice padd y fields in Japan.