FIG. 2
Dissociation (DNA-DNA) kinetics for probes to clusters of Nitrosospira (a to c) and Nitrosomonas (d) detected on DGGE gels: NspCL2_458 (a), NspCL3_454 (b), NspCL4_446 (c), and NmoCL6a_205 (d). The rDNA targets used for Nitrosospira were derived from Nitrosospira briensis (accession no., M96396) and clones pH4.2A/K2 (accession no., Z69167), pH4.2A/C (accession no., Z69159), pH4.2A/J2 (accession no., Z69166), pH7C/30 (accession no., Z69191), pH4.2A/19 (accession no., Z69150), and EnvB1-7 (accession no., Z69102). Nitrosospira sp. strains B6, T7, KI, and GM41 are described by Utåaker et al. (28). The rDNA targets for Nitrosomonas were derived from N. europaea (accession no., M96399) and clones pH7C/54 (accession no., Z69196), pH4.2A/23 (accession no., Z69151), pH7C/56 (accession no., Z69197), DT1.9 (accession no., U62884), pH4.2A/3E (accession no., Z69155), and pH4.2/17 (accession no., Z69149). + denotes the cognate target sequence, and ○ and ▵ represent the closest available nontarget sequences. Asterisks denote that the sequence is identical to the top sequence in that position. Differences are denoted by the replacement nucleotides shown below the target sequence. Probes were named to agree as closely as possible with the scheme used by Mobarry et al. (18), except that the position of the 5′ nucleotide complementary to the 3′ probe nucleotide is given as a suffix (E. coli numbering [3]).