SRA

Settleability of particles in activated sludge systems can be impaired by an overgrowth of filamentous bacteria, a problem known as bulking. These filaments are often members of the phylum Chloroflexi, which can account for up to 30% of the biovolume. The uncultured Chloroflexi phylotype, Candidatus Amarilinum, has been observed in high abundances in Danish full-scale activated sludge systems by 16S rRNA gene amplicon surveys, where it has been associated with bulking. In this study, fluorescence in situ hybridization was applied to confirm their high abundance, filamentous morphology, and also their contribution to the interfloc bridging that characterizes filamentous bulking, in several full-scale activated sludge systems. Furthermore, genome-centric metagenomics using both Illumina and Oxford Nanopore sequencing, was used to obtain a near complete population genome (5.7 Mbp) of the Ca. Amarilinum phylotype, which is also the first representative of the SJA-15 class of Chloroflexi. Annotation of the genome indicated that the phylotype is capable of aerobic respiration, fermentation and dissimilatory nitrate reduction to ammonia. The name Candidatus Amarilinum aalborgensis is proposed for the species.