Fig. 4

Phylogenetic tree generated using the neighbor-joining method to analyze 178 deduced amino acid sequences of archaeal amoA-like genes from microbes trapped in the 10-µm-pore filter for throughfall of Cj1 (red clone name N2-throughfall, AB873108–AB873179) and phyllospheric microbes on the leaves of C. japonica [Cj1 (blue clone name N2, AB650007–AB650012), Cj2 (green clone name N3, AB622267–AB622275), and Cj3 (purple clone name N1, AB649997–AB650012)]. The bar represents a 2 % evolutionary distance, and bootstrap values above 50 % are shown. Node percentages represent the bootstrap values based on neighbor-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML)