Table S1 Phylogenetic relationships of the isolates

Table S1 Phylogenetic relationships of the isolates and clones in a clone library from the PLLA-acclimating activated sludge at 56 days of operation Analytical methods

Phylotypes/ Numbers of strain clones in total names 124 clones

PLLA-1a) PLLA-2a) PLLA-3 PLLA-4a) PLLA-5a) PLLA-6 PLLA-7 PLLA-8 PLLA-9 PLLA-10 PLLA-11 Clone library PLLA-12 analysis PLLA-13 PLLA-14 PLLA-15 PLLA-16 PLLA-17 PLLA-18 PLLA-19a) PLLA-20 PLLA-21 PLLA-22 PLLA-23 PLLA-24 DP-1a)

Numbers of isolates in Size (bp) Accession no. total 25 isolates

Closely relative species (type strain)

Comamonas badia strain IAM14839T (AB164432) Pseudacidovorax intermedius strain CC-CC21T(EF469609) Flavisolibacter ginsengiterrae strain Gsoil 492 T (AB267476 Comamonas kerstersii strain LMG3475T (AJ430347) Comamonas aquatica strain LMG2370T (AJ430344) Clostridium ganghwense strain HY-42-06T (AY903294) Pedobacter sandarakinus strain DS-27T (DQ235228) Caloramator fervidus strain RT4T (L09187) Cryomorpha ignava strain QSSC1-22T (AF170738) Gemmata obscuriglobus strain UQM2246T (X56305) Chitinophaga arvensicola strain DSM 3695T (AM237311) Empedobacter brevis strain LMG4011T (AM177497) Niastella yeongjuensis strain GR20-13T (DQ244076) Blastopirellula marina strain IFAM1313T (X62912) Caldilinea aerophila strain STL-6-O1T (AB067647) Ferruginibacter alkalilentus strain HU1-GD23T (FJ177530) Clostridium thermopalmarium T (X72869) Isosphaera pallida strain DSM9630T (AJ231195) Simplicispira limi strain EMB325T (DQ372987) Propionispora vibrioides strain FKBS1T (AJ279802) Pedobacter koreensis strain WPCB189T (DQ092871) Roseibacillus ponti strain YM27-130T (AB331889) Haematobacter massiliensis strain FramboiseT (AF452106) Fluviicola taffensis strain RW262T (AF493694)

22 17 14 12 9 9 6 5 5 3 3 2 2 2 2 2 2 1 1 1 1 1 1 1

-

1456 1450 1454 1453 1451 1431 1448 1455 1452 1452 1444 1450 1460 1423 1420 1453 1431 1446 1453 1480 1450 1457 1389 1444

AB596949 AB596950 AB596951 AB596952 AB596953 AB596954 AB596955 AB596956 AB596957 AB596958 AB596959 AB596960 AB596961 AB596962 AB596963 AB596964 AB596965 AB596966 AB596967 AB596968 AB596969 AB596970 AB596971 AB596972

-

16

1466

AB596973 Castellaniella denitrificans strain NKNTAUT (U82826)

% Sequence similarity of Taxonomy (phylum ) Quinone types isolates

93.6 97.5 95.1 98.9 99.1 100.0 100.0 100.0 86.1 85.4 99.3 79.6 100.0 100.0 84.0 93.2 96.6 90.9 98.8 99.9 87.3 86.6 96.3 86.0

Proteobacteria Proteobacteria Bacteroidetes Proteobacteria Proteobacteria Firmicutes Bacteroidetes Firmicutes Bacteroidetes Planctomycetes Bacteroidetes Bacteroidetes Bacteroidetes Planctomycetes Chloroflexi Bacteroidetes Firmicutes Planctomycetes Proteobacteria Firmicutes Bacteroidetes Verrucomicrobia Proteobacteria Bacteroidetes

-

99.1 Proteobacteria

Q-8

99.7 Proteobacteria

Q-8

98.5 Proteobacteria

Q-8

99.5 Proteobacteria

Q-8

2 1465 AB596977 Castellaniella denitrificans strain NKNTAU (U82826) DP-5 99.6 Proteobacteria a) T 99.3 Proteobacteria DP-6 1 1451 AB596978 Alicycliphilus denitrificans strain K601 (AJ418042) a) A phylogenetic tree with the 16S rRNA gene sequences of the members of families Comamonaceae and Alcaligeneaceae in Betaproteobacteria are shown in Fig. 5.

Q-8

Cultivation

DP-2

a)

DP-3

a)

DP-4

a) a)

-

2 2 2

1466 1453 1465

T

AB596974 Castellaniella denitrificans strain NKNTAU (U82826) T

AB596975 Acidovorax caeni strain R-24608 (AM084006) T

AB596976 Castellaniella denitrificans strain NKNTAU (U82826) T

Q-8