Activated sludge foaming is a worldwide problem in wastewater treatment plants that results in poor quality effluent, increased difficulty in sludge management, and increased maintenance costs.  The etiological agents of these foams are members of the Mycolata; Gram-positive, hydrophobic, filamentous bacteria embracing the genera Gordonia, Mycobacterium, Nocardia, Rhodococcus, Skermania, and Tsukamurella. No universal methods exist yet to control these foams rationally.

Fifty-three phages infective for members of the Mycolata were isolated, and fourteen then investigated for their potential use in phage therapy to control this foaming.  Whole genome sequencing of these Siphoviridae phages revealed novel dsDNA sequences ranging from 14, 270 to 103, 424 kb in size and containing many novel and often unexpected genes.  Nucleotide and amino acid sequence similarity levels  between these phages suggested their evolutionary relatedness and revealed evidence of recombination events in their evolution.  Most appeared obligately lytic and thus suitable candidates for foam bio-control.

Presence of temperate phages infecting Mycolata species was also examined as was their potential for foam bio-control following their induction in their hosts.  In silico analysis of 259 Mycolata sequences revealed that 83 % of Mycolata genomes contained putative genes of phage origin, and 26 % appeared to possess intact and inducible temperate phages.  Studies with Mycolata strains isolated from activated sludge foams supported these trends, as both spontaneous and mitomycin C mitigated prophage induction was achieved in G. alkanivorans, G. malaquae, and T. paurometabola strains. Whole genome sequencing of these suggested an ecological role for them as some encoded genes that might enhance host fitness.  Should an induction agent suitable for wastewater treatment plants be identified their selective induction en masse presents a novel method of biologically controlling foams.