TABLE 2.
Statistics of MAGs and reference genomes for each “Ca. Accumulibacter” species
| “Ca. Accumulibacter” speciesa | Pilot plant | IMG IDb | Strain nameg,h | dRep score | Sequencingc | Completeness (%) | Contamination (%) | Size (bp) | Contigs | Gc (%) | 16S rRNA copiesd | 23S rRNA copiesd |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| “Ca. A. regalis” | - | - | *UW3 | 102.1 | R, S, I | 99.94 | 0.03 | 4,329,894 | 6 | 63.9 | 0 | 0 |
| “Ca. A. adiacens” | - | - | *HKU1 | 79.0 | I | 90.06 | 2.54 | 3,625,256 | 824 | 63.9 | 0 | 0 |
| “Ca. A. appositus” | - | - | *BA-92 | 88.4 | I | 93.33 | 1.49 | 4,947,936 | 583 | 62.9 | 0 | 0 |
| “Ca. A. meliphilus” | - | - | *UW-LDO | 94.8 | N, I | 95.24 | 0.7 | 4,701,482 | 187 | 62.5 | 0 | 0 |
| AOia | 3300056759_486 | UW14 | 80.6 | PB | 95.24 | 4.02 | 5,539,002 | 26 | 62.5 | 2 | 2 | |
| “Ca. A. delftensis” | - | - | *Ca. Accumulibacter delftensis | 102.1 | I | 100 | 0.03 | 5,278,942 | 361 | 62.2 | 1+e | 1e |
| UCTca | 3300056625_186 | UW15 | 76.0 | PB | 96.44 | 5.27 | 5,074,113 | 15 | 62.4 | 3 | 3 | |
| “Ca. A. propinquus” | UCTca | 3300056624_334 | UW16 | 97.1 | PB | 97.62 | 0.77 | 5,011,213 | 2 | 62.3 | 2 | 2 |
| - | *OdNE_BAT3C.415 | 93.3 | N, I | 95.26 | 0.98 | 4,325,360 | 62 | 63 | 2 | 2 | ||
| AO-G | 3300056599_153 | UW24 | 54.0 | PB | 92.45 | 9.57 | 5,504,906 | 39 | 62.4 | 2 | 2 | |
| “Ca. A. aalborgensis” | - | - | *A_S1_v1 | 100.7 | I | 99.52 | 0.06 | 4,325,360 | 181 | 62.3 | 1 | 1 |
| “Ca. A. phosphatis” | - | - | *UW1 | 101.0 | R, S, I | 99.84 | 0.24 | 5,306,133 | 4 | 64.0 | 2 | 2 |
| “Ca. A. contiguus” | - | *SBR_L | 95.2 | IT | 96.85 | 0.98 | 5,024,437 | 167 | 61.7 | 0 | 0 | |
| UCTca | 3300056625_204 | UW17 | 95.1 | PB | 97.29 | 1.22 | 5,500,985 | 3 | 61.6 | 2 | 2 | |
| “Ca. Accumulibacter” UW18 | AOia | 3300055001_362 | UW18 | 87.3 | I | 98 | 2.54 | 4,846,527 | 172 | 62 | 0 | 0 |
| “Ca. A. cognatus” | - | *SSA1 | 95.9 | N | 99.05 | 1.11 | 5,169,514 | 3 | 61.4 | 1 | 1 | |
| “Ca. A. vicinus” | - | *UBA5574 | 93.9 | I | 93.65 | 0.24 | 4,283,242 | 326 | 62.0 | 1+ | 1+ | |
| “Ca. A. affinis” | - | *Fred_BAT3C.720 | 91.3 | N, I | 93.81 | 0.98 | 5,041,483 | 13 | 62.3 | 1 | 1 | |
| “Ca. A. proximus” | - | *EsbW_BATAC.285 | 82.1 | N, I | 96.67 | 3.63 | 5,402,764 | 40 | 62.7 | 1 | 1 | |
| “Ca. A. necessarius” | - | *UW12-POB | 95.9 | I | 98.1 | 0.98 | 4,564,207 | 91 | 62.7 | 0 | 0 | |
| AOia | 3300056623_77 | UW19 | 78.4 | PB | 80 | 0.98 | 4,180,114 | 5 | 62.1 | 2 | 2 | |
| AOia | 3300055001_422 | UW29 | 57.5 | I | 61.48 | 1.31 | 1,965,883 | 180 | 62.6 | 0 | 0 | |
| UCTca | 3300056624_146 | UW28 | 56.4 | PB | 95.24 | 9.31 | 5,512,878 | 20 | 62.6 | 2 | 2 | |
| “Ca. A. iunctus” | - | *UBA2327 | 92.4 | I | 92.43 | 0.29 | 4,431,027 | 325 | 65.2 | 1 | 1 | |
| “Ca. A. adjunctus” | - | *SK-12 | 94.0 | I | 92.6 | 0.05 | 4,412,715 | 331 | 65.8 | 0 | 0 | |
| “Ca. Accumulibacter” UW21 | AO-FF | 3300056999_35 | UW21 | 101.3 | PB | 98.1 | 0.03 | 5,194,397 | 1 | 65.8 | 2 | 2 |
| AO-G | 3300056626_235 | UW23 | 67.2 | PB | 72.99 | 1.72 | 4,288,616 | 14 | 65.5 | 1 | 1 | |
| “Ca. A. similis” | - | *SSB1 | 101.3 | N | 99.05 | 0.03 | 5,039,009 | - | 66 | 2 | 2 | |
| “Ca. A. conexus” | - | *UW7 | 85.3 | I | 98.97 | 3.04 | 4,870,756 | 102 | 66.3 | 1+ | 0 | |
| “Ca. Accumulibacter” UW20f | AO-FF | 3300056999_154 | UW20 | 98.9 | PB | 99.05 | 0.64 | 4,517,007 | 6 | 63.6 | 2 | 2 |
| AOia | 3300056827_258 | UW25 | 95.6 | PB | 97.25 | 1.05 | 4,226,414 | 3 | 63.4 | 2 | 2 | |
| AOia | 3300055001_270 | UW26 | 87.8 | I | 90.03 | 1.02 | 3,691,544 | 60 | 64.3 | 1 | 0 | |
| AOia | 3300057002_150 | UW27 | 76.1 | I | 77.34 | 0.77 | 2,776,145 | 183 | 64.7 | 0 | 0 |
MAGs are ordered to resemble the order of genome-resolved phylogenetic clusters in Fig. 2A.
For each MAG assembled in this study, the identification (ID) number in the Integrated Microbial Genomes (IMG) database is provided.
Sequencing platform: I = Illumina; PB = PacBio (6–10kb), N = Nanopore, IT = IonTorrent, R = Roche 454, S = Sanger.
+ denotes partial 16S rRNA gene sequence.
The “Ca. A. delftensis” reference genome also contains a full-length contaminant 16S rRNA sequence, and full-length and partial-length contaminant 23S rRNA sequences.
The “Ca. Accumulibacter” UW20 cluster is proposed to be named “Ca. Accumulibacter jenkinsii” sp. nov. in this study.
Asterisks denotes the MAGs used by Petriglieri et al. (13) as reference genomes to define the “Candidatus” species. Complete names and NCBI GenBank accession numbers can be found in their Data File S1 (28). The bolded font indicates MAGs assembled in this study.
A strain with a UW22 name is not used in the table because this name was assigned to a medium-quality MAG (IMG ID 3300056831_295; 50.8% completeness, 8.6% contamination) that was determined to be a hybrid of contigs belonging to “Ca. A. necessarius” and “Ca. A. propinquus.”