Comparative genomics of two ‘Candidatus Accumulibacter’ clades performing biological phosphorus removal

Abstract

Members of the genus Candidatus Accumulibacter are important in many wastewater treatment systems performing enhanced biological phosphorus removal (EBPR). The Accumulibacter lineage can be subdivided phylogenetically into multiple clades, and previous work showed that these clades are ecologically distinct. The complete genome of Candidatus Accumulibacter phosphatis strain UW-1, a member of Clade IIA, was previously sequenced. Here, we report a draft genome sequence of Candidatus Accumulibacter spp. strain UW-2, a member of Clade IA, assembled following shotgun metagenomic sequencing of laboratory-scale bioreactor sludge. We estimate the genome to be 80–90% complete. Although the two clades share 16S rRNA sequence identity of >98.0%, we observed a remarkable lack of synteny between the two genomes. We identified 2317 genes shared between the two genomes, with an average nucleotide identity (ANI) of 78.3%, and accounting for 49% of genes in the UW-1 genome. Unlike UW-1, the UW-2 genome seemed to lack genes for nitrogen fixation and carbon fixation. Despite these differences, metabolic genes essential for denitrification and EBPR, including carbon storage polymer and polyphosphate metabolism, were conserved in both genomes. The ANI from genes associated with EBPR was statistically higher than that from genes not associated with EBPR, indicating a high selective pressure in EBPR systems. Further, we identified genomic islands of foreign origins including a near-complete lysogenic phage in the Clade IA genome. Interestingly, Clade IA appeared to be more phage susceptible based on it containing only a single Clustered Regularly Interspaced Short Palindromic Repeats locus as compared with the two found in Clade IIA. Overall, the comparative analysis provided a genetic basis to understand physiological differences and ecological niches of Accumulibacter populations, and highlights the importance of diversity in maintaining system functional resilience.

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis‐enriched floccular and granular biofilm

“…We did not detect any peptide hits to the novel cytochrome b/b6 that is proposed to provide the required anaerobic reoxidation of reduced quinones, indicating this was not a mechanism to release reducing power generated by anaerobic operation of the TCA cycle (García Martín et al, 2006;Flowers et al, 2013). All components of the tricarboxylic acid (TCA) cycle were detected, along with key enzymes involved in both the glyoxylate shunt and split TCA cycle (Hesselmann et al, 2000;Oehmen et al, 2007).…”

“…Recent studies have utilized the genomic information for proteomic and transcriptomic approaches to determine active metabolic pathways important for Accumulibacter growth (Wilmes, Wexler, et al, 2008;Wilmes, Andersson, et al, 2008;Burow et al, 2008;He & McMahon, 2011a). The phylogeny of Accumulibacter has been resolved to the strain level through analysis of the polyphosphate kinase gene (ppk1), grouping Accumulibacter into two major divisions (type I and II) each with multiple sub-divisions (type IA-IE, IIA-IIF) (He et al, 2007;Skennerton et al, 2014;Flowers et al, 2013). We found the Floc reactor to be dominated by Accumulibacter type IA, whereas the Gran reactor contained a mix of Accumulibacter types IIC, IC, and IIF (Skennerton et al, 2014).…”

Comparative genomics analyses on EPS biosynthesis genes required for floc formation of Zoogloea resiniphila and other activated sludge bacteria

“…We also conducted comparative genomics analyses among the closely related AS proteobacteria Zoogloea, Azoarcus, Thauera, Dechloromonas, Candidatus Accumulibacter and Nitrosospira strains. Our results indicate that those AS bacteria, including the yet-uncultured polyphosphate-accumulating Candidatus Accumulibacter phosphatis (CAP) strains (Hesselmann et al, 1999;Albertsen et al, 2012;Flowers et al, 2013), harbor the EPS biosynthesis gene cluster(s) required for formation of flocs, thereby facilitating their enrichment in the AS process.…”

“…Enhanced biological phosphorus removal (EBPR) technology had been designed based on bacterial phosphate uptake and polyphosphate synthesis (Bond et al, 1995;Mino et al, 1998;Garcia et al, 2006;Flowers et al, 2013). Z. resiniphila harbors two polyphosphate kinase (Ppk) genes and the polyphosphatase (Ppx) gene.…”

CRISPR/Cas9, a universal tool for genomic engineering

“…Технология была испробована на всех модельных организмах, включая дрозофилу (Bassett et al, 2013), аксолотля (Flowers et al, 2013), крысу и крупных животных, таких как макаки (Niu et al, 2014). Стоит отметить, что получение трансгенных приматов до этого являлось весьма трудной задачей.…”