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Time to settle the score:
Retrieving the genome of a novel Chloroflexi associated with bulking in activated sludge
Martin H. Andersen, Simon J. McIlroy, Marta Nierychlo, Per H. Nielsen and Mads Albertsen
Albertsen Lab, Center for Microbial Communities, Aalborg University, Denmark
Variable regions: Ashelford K E et al. Appl. Environ. Microbiol. 2005;71:
AAU
Conclusions
Introduction
Settleability of particles in activated sludge systems can be impaired by an overgrowth of filamentous bacteria, a problem known as bulking. The uncultured Chloroflexi phylotype Candidatus
First genome of the novel family Amarolineaceae in the Chloroflexi phylum, providing an important reference for expression studies
High-quality draft genome assembled with Illumina and Nanopore reads. Genome of 5.7 Mbp on 80 contigs and 95.5% completeness
Possibly capable of reducing nitrate to ammonia, fermentation and glycogen storage. May compete with PAOs and could cause bulking
Amarolinea has been associated with bulking in Danish full-scale activated sludge systems. In this study, a near-complete genome of Ca. Amarolinea aalborgensis was obtained using genome-centric metagenomics
Identification of a novel Chloroflexi
Metabolic potentials
mmgenome2
Nanopore +
Hybrid workflow
Illumina
Genome-centric metagenomics applied in a hybrid workflow. Differential coverage binning used through mmgenome2 to extract a bin. Reassembly with Unicycler, recruiting Nanopore reads for scaffolding, reduced the contig count from 467 to 80 and gave a 5.7 Mbp high-quality draft genome of 95.5% completeness.
Selected annotated metabolic pathways for Ca. Amarolinea aalborgensis. Annotation supported a typical Chloroflexi physiology with genes for fermentation, glycolysis/gluconeogenesis and a complete TCA cycle were annotated. The phylotype is facultative anaerobe and likely capable of dissimilatory nitrate reduction to ammonia. Capable of glycogen storage under anaerobic conditions, competing with the key polyphosphate-accumulating organisms (PAO), their overgrowth may be detrimental to enhanced biological phosphate removal (EBPR) activated sludge systems.
Perspectives
Targeting and obtaining genomes for the “most wanted” of activated sludge will allow future online surveillance for process optimization. This will in turn provide actionable information to plant operators, e.g. via an alert when process-critical Bacteria reach high abundances.
Phylogenetic tree based on the Genome Tree Database (GTDB). The right, outermost brackets contain class-level classifications, while the inner brackets contain order-level classifications. Ca. Amarolinea aalborgensis is placed in a novel family within the Caldilineales order, relegated from class in GTDB. Based on two-way AAI, the most similar phylotype was the “Ground water MAG” (below Amarolinea aalborgensis) at 51% AAI (1646 proteins). The scale bar represents amino acid substitutions per site.
Microbial community
Alert
Time
Bacteria (genus)
Action
Ca. Microthrix
Ca. Amarolinea
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