Small subunit (SSU) ribosomal RNA (rRNA) genes of four Gordona (Nocardia) amarae strains were sequenced and compared to the sequence of the G. amarae type strain obtained from the Ribosomal Database Project (RDP). Comparative sequence analysis showed that the five strains represent two lines of evolutionary descent: Group 1 consists of strains NM23 and ASAC1 and Group 2 contains strains SE-6, SE102, and ASF3. To determine the abundance of G. amarae in activated sludge systems, we designed three oligonucleotide probes: a species-specific probe for G. amarae, a probe specific for Group 1 and a probe targeting Group 2. The probes were characterized by performing dissociation temperature and specificity studies. Using these probes, two other strains, strains SE-149B and RBI, also were found to be part of Group 1. We used these probes along with previously designed probes in membrane hybridizations to determine the abundance of G. amarae, Group 1, Group 2, Bacteria, Mycobacterium complex, and Gordona in samples from foaming episodes. We demonstrated that the Mycobacterium complex, the genus Gordona, and G. amarae strains were present in significantly greater concentrations in activated sludge foam than in mixed liquor.

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