Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus " Candidatus Accumulibacter"

• Published in: mSystems 2022-06, Vol.7 (3), p.e0001622-e0001622
• Main Authors: Petriglieri, Francesca, Singleton, Caitlin M, Kondrotaite, Zivile, Dueholm, Morten K D, McDaniel, Elizabeth A, McMahon, Katherine D, Nielsen, Per H
• Format: Article
• Language: English
• Subjects: Betaproteobacteria; Candidatus Accumulibacter; diversity; Ecosystem; Environmental Microbiology; In Situ Hybridization, Fluorescence; metagenome-assembled genome; Phosphorus - metabolism; Phylogeny; ppk1 gene; Research Article; RNA, Ribosomal, 16S - genetics
• ISSN: 2379-5077; 2379-5077
• DOI: 10.1128/msystems.00016-22

" Accumulibacter" was the first microorganism identified as a polyphosphate-accumulating organism (PAO) important for phosphorus removal from wastewater. Members of this genus are diverse, and the current phylogeny and taxonomic framework appear complicated, with most publicly available genomes classified as " Accumulibacter phosphatis," despite notable phylogenetic divergence. The marker gene allows for a finer-scale differentiation into different "types" and "clades"; nevertheless, taxonomic assignments remain inconsistent across studies. Therefore, a comprehensive reevaluation is needed to establish a common understanding of this genus, in terms of both naming and basic conserved physiological traits. Here, we provide this reassessment using a comparison of genome, , and 16S rRNA gene-based approaches from comprehensive data sets. We identified 15 novel species, along with " Accumulibacter phosphatis," " Accumulibacter delftensis," and " Accumulibacter aalborgensis." To compare the species , we designed new species-specific fluorescence hybridization (FISH) probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, " . Accumulibacter" species were widespread in wastewater treatment plants (WWTPs) with phosphorus removal, indicating process design as a major driver for their abundance. Genome mining for PAO-related pathways and FISH-Raman microspectroscopy confirmed the potential for PAO metabolism in all " . Accumulibacter" species, with detection of the typical PAO storage polymers. Genome annotation further revealed differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal. " Accumulibacter" is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to phylogeny based on the 16S rRNA gene and other phylogenetic markers, we obtained a higher-resolution taxonomy and established a common understanding of this genus. Furthermore, gen