FIG. 4.

16S rRNA gene phylogenetic consensus tree based on maximum-likelihood analysis (Tree-puzzle) performed with a 50% conservation filter for the “Betaproteobacteria.” The tree shows the affiliation of clone sequences (boldface type) retrieved from the sewage treatment plant Kraftisried by using “Rhodocyclales” subgroup-selective primer pairs A (KRA clones), R (KRR clones), and Z (KRZ clones) for PCR. The grey box shows affiliation to a “Rhodocyclales” lineage. The bar indicates 10% estimated sequence divergence. Polytomic nodes connect branches for which a relative order could not be determined unambiguously by applying neighbor-joining, maximum-parsimony, and maximum-likelihood treeing methods. The percent reliability value of each internal branch indicates how often the corresponding cluster was found among 50,000 intermediate trees during quartet puzzling. Values below 70% are not shown. Parentheses indicate the perfect-match target organisms of the probes. Probe S-*-OTU1-1415-a-A-20 (OTU1-1415) (Table 5) is depicted in bold and was used for quantitative FISH analysis. The microarray position is depicted after the probe name. Probes RHC630, RHC143, RHC222, RHC175a, and RHC175b, perfectly matching some of the Kraftisried clones, are not shown to enhance clarity.