21Candidatus Accumulibacter phosphatis (CAP) and its sub-clades-level diversity has been 22 associated and implicated in successful phosphorus removal performance in enhanced biological 23 phosphorus removal (EBPR). Development of high-throughput untargeted methods to 24 characterize clades of CAP in EBPR communities can enable a better understanding of 25 Accumulibacter ecology at a higher-resolution beyond OTU-level in wastewater resource 26 recovery facilities (WRRFs). In this study, for the first time, using integrated 16S rRNA gene 27 sequencing, oligotyping and genome-resolved metagenomics, we were able to reveal clade-level 28 differences in Accumulibacter communities and associate the differences with two different full-29 scale EBPR configurations. The results led to the identification and characterization of a distinct 30 and dominant Accumulibacter oligotype -Oligotype 2 (belonging to Clade IIC) and its matching 31 MAG (RC14) associated with side-stream EBPR configuration. We are also able to extract 32 MAGs belonging to CAP clades IIB (RCAB4-2) and II (RC18) which did not have 33 representative genomes before. This study demonstrates and validates the use of a high-34 throughput approach of oligotyping analysis of 16S rRNA gene sequences to elucidate CAP 35 clade-level diversity. We also show the existence of a previously uncharacterized diversity of 36 CAP clades in full-scale EBPR communities through extraction of MAGs, for the first time from 37 full-scale facilities. 38
Introduction
39Enhanced biological phosphorus removal (EBPR) has been a promising technology for 40 phosphorus removal from municipal wastewater, due to its sustainable nature and P recovery 41 potential in comparison to chemical precipitation and adsorption-based approaches [1]. However, 42 conventional EBPR processes face challenges related to system stability and susceptibility to 43 variations and fluctuations in influent loading conditions such as unfavorable carbon to P (C/P) 44 ratios [2]. A new emerging process, namely, side-stream EBPR (S2EBPR) features an anaerobic 45 side-stream reactor that allows a portion of the return activated sludge (RAS) to undergo 46 hydrolysis and fermentation thus enabling influent carbon-independent enrichment and selection 47 of polyphosphate accumulation organisms (PAO). Facilities that have operated or piloted 48 S2EBPR showed improved and more stable performance [3][4][5][6]. However, several key 49 knowledge gaps still exist for this process including lack of understanding of the fundamental 50 mechanisms governing the process and differences in microbial ecology, particularly 51 functionally relevant key populations such as PAOs between the conventional and the S2EBPR 52 processes. Several studies that have characterized the microbial ecology of different process 53 configurations using 16S rRNA gene amplicon sequencing, fluorescence in-situ hybridization 54 (FISH) and quantitative polymerase chain reaction (qPCR) have failed to associate differences in 55 PAO microbial ecology with proc...