The formation of a stable, dark, viscous foam or scum on activated sludge aeration basin surfaces is a recent and increasing problem. Microscopically, the foam is comprised of a predominance of one of a few different types of filamentous bacteria. The diversity of filaments found in the foam is increasing with time. However, two prominent foaming organisms in Australia are Nocardia amarae and Nocardia pinensis. Although these nocardioforms can be microscopically differentiated, N. amarae is indistinguishable from other foaming filaments such as Rhodococcus rhodochrous and Tsukamurella paurometabolum. Morphology is the cardinal character used in differentiating bulking filamentous microorganisms. However, microorganism morphology is a notoriously poor descriptive attribute that can vary widely depending upon nutritional conditions. The past decade has witnessed the use of molecular biological techniques as the dominant approach for the detection of microorganisms that are difficult to identify by conventional culture techniques or microscopy. The most common nucleic acid target sequences for molecular probes are found in conserved genes such as 16S rDNA. Genomic DNA was isolated from strains of N. amarae and N. pinensis. The 16S rDNA was amplified by the polymerase chain reaction and sequenced using an automated DNA sequencing machine. The sequences were compared and regions that could be exploited for oligonucleotide probes were highlighted. These regions can differentiate the two species and by comparison with sequences available in Genbank, they can differentiate N. amarae from other foaming nocardioforms for which 16S rDNA sequence information is available.

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