FIG. 3.

Maximum-likelihood tree of deduced amino acid sequences of pmoA and amoA genes amplified from ¹³C-DNA or ¹²C-DNA fractions. Clones obtained from the ¹³C-DNA fraction are prefixed with “LOPA13” when amplified with the A189-A682 (•) primer set or with “LOPB13” when amplified with the A189/mb661 (⧫) primer set. Clones obtained from the ¹²C-DNA fraction and amplified with the A189-A682 (○) primer set are prefixed with “LOPA12.” The tree was constructed with a filter (163 aligned amino acid positions; this excludes ambiguities and missing data), and the PmoA sequence of the environmental clone RA21 as an outgroup. Multifurcations indicate branch points where the topology between maximum-likelihood, evolutionary-distance, and maximum-parsimony analyses of the data set were not supported by a strict consensus rule. The number of clones (50 in each library) assigned to each OTU by RFLP analysis is shown in parentheses.