PMID- 35467400 OWN - NLM STAT- MEDLINE DCOM- 20221222 LR - 20221222 IS - 2379-5077 (Print) IS - 2379-5077 (Electronic) IS - 2379-5077 (Linking) VI - 7 IP - 3 DP - 2022 Jun 28 TI - Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus "Candidatus Accumulibacter". PG - e0001622 LID - 10.1128/msystems.00016-22 [doi] LID - e00016-22 AB - "Candidatus 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 "Candidatus Accumulibacter phosphatis," despite notable phylogenetic divergence. The ppk1 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, ppk1, and 16S rRNA gene-based approaches from comprehensive data sets. We identified 15 novel species, along with "Candidatus Accumulibacter phosphatis," "Candidatus Accumulibacter delftensis," and "Candidatus Accumulibacter aalborgensis." To compare the species in situ, we designed new species-specific fluorescence in situ hybridization (FISH) probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, "Ca. 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 "Ca. Accumulibacter" species, with detection in situ 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. IMPORTANCE "Candidatus 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, genome mining of genes and pathways of interest, validated in situ by application of a new set of FISH probes and Raman microspectroscopy, provided additional high-resolution metabolic insights into these organisms. FAU - Petriglieri, Francesca AU - Petriglieri F AUID- ORCID: 0000-0002-1676-7690 AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg Universitygrid.5117.2, Aalborg, Denmark. FAU - Singleton, Caitlin M AU - Singleton CM AUID- ORCID: 0000-0001-9688-8208 AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg Universitygrid.5117.2, Aalborg, Denmark. FAU - Kondrotaite, Zivile AU - Kondrotaite Z AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg Universitygrid.5117.2, Aalborg, Denmark. FAU - Dueholm, Morten K D AU - Dueholm MKD AUID- ORCID: 0000-0003-4135-2670 AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg Universitygrid.5117.2, Aalborg, Denmark. FAU - McDaniel, Elizabeth A AU - McDaniel EA AUID- ORCID: 0000-0003-4692-0913 AD - Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA. AD - Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA. FAU - McMahon, Katherine D AU - McMahon KD AD - Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA. AD - Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA. FAU - Nielsen, Per H AU - Nielsen PH AUID- ORCID: 0000-0002-6402-1877 AD - Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg Universitygrid.5117.2, Aalborg, Denmark. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20220425 PL - United States TA - mSystems JT - mSystems JID - 101680636 RN - 0 (RNA, Ribosomal, 16S) RN - 27YLU75U4W (Phosphorus) MH - Phylogeny MH - RNA, Ribosomal, 16S/genetics MH - In Situ Hybridization, Fluorescence MH - *Ecosystem MH - *Betaproteobacteria MH - Phosphorus/metabolism PMC - PMC9238405 OTO - NOTNLM OT - diversity OT - metagenome-assembled genome OT - phylogeny OT - ppk1 gene OT - "Candidatus Accumulibacter" COIS- The authors declare no conflict of interest. EDAT- 2022/04/26 06:00 MHDA- 2022/04/26 06:01 PMCR- 2022/04/25 CRDT- 2022/04/25 12:28 PHST- 2022/04/26 06:00 [pubmed] PHST- 2022/04/26 06:01 [medline] PHST- 2022/04/25 12:28 [entrez] PHST- 2022/04/25 00:00 [pmc-release] AID - 00016-22 [pii] AID - msystems.00016-22 [pii] AID - 10.1128/msystems.00016-22 [doi] PST - ppublish SO - mSystems. 2022 Jun 28;7(3):e0001622. doi: 10.1128/msystems.00016-22. Epub 2022 Apr 25.