Figure 1

Neighbor-joining tree showing the phylogenetic relationships of all OTUs derived from the three libraries (UTC, BSD and CP) of treated soil based on 16S rRNA gene sequences for (a) the phyla Firmicutes and Proteobacteria , and (b) other phyla ( Acidobacteria , Verrucomicrobia , Bacteroidetes , Planctomycetes , Gemmatimonadetes , TM7 and others, Actinobacteria , and Chloroflexi ). Designation of clone names with C, W, and CP (deposited in the DDBJ/Genbank) corresponds to the clones belonging to the UTC, BSD and CP libraries, respectively. Bootstrap values (n = 1,000) above 70% are indicated at branch nodes. The scale bar represents 2% estimated difference in nucleotide sequence position. The name of each clone starts with designation of the respective clone libraries. As the outgroup, Sulfolobus acidocaldarius (D14053) (the domain Archaea) 16S rRNA gene sequence was used for both cases. Accession numbers of the species are shown in the parentheses. The phylogenetic groups of phyla and class levels are shown aside the close clusters. Numbers in the parentheses aside each clone name denote the number of clones assigned to the OTU. Each clone name without parenthesis represents one OTU with one clone. The squares marked with some clone clusters show the dominancy of major groups in the communities of the respective clone libraries.