Supplementary Information

Supplementary Information Microbial Population Dynamics in Membrane Bioreactor with Quorum Quenching Hak-Woo Kim 1, Hyun-Suk Oh 1, Sang-Ryoung Kim 1, Ki-Baek Lee 1, Kyung-Min Yeon 1, Chung-Hak Lee 1, Seil Kim 2 and Jung-Kee Lee 3 1 School of Chemical and Biological Engineering, Seoul National University, Seoul 151-744, Korea 2 Clean Energy Research Center, Korea Institute of Science and Technology, Seoul 136-791, Korea 3 Departments of Life Science and Genetic Engineering, Paichai University, Daejeon 302-735, Korea E-MAIL: leech@snu.ac.kr, TEL: +82-2-874-0896, FAX: +82-2-874-0896 E-MAIL: stapler@kist.re.kr, TEL: +82-2-958-5266, FAX: +82-2-958-6858 1

Fig. S1 Size distribution of MIEX and MEC. 2

Fig. S2 2D SDS-PAGE gel images from (a) control channel and (b) quorum quenching channel 3

Table S1 Total reads and OTUs data C start C1 broth C2 broth Q start Q1 broth Q2 broth C1 biofilm C2 biofilm Q1 biofilm Q2 biofilm Total reads (all sequence) 633 6532 4018 3277 2215 1520 1386 1386 7715 6824 OTUs (CDHit) 103 764 295 249 158 129 135 129 392 574 4

Table S2 SIMPER analysis data for microorganisms in the broth and biofilm based on all ten samples Taxonomic a Average Abundance of b Average Abundance of c Average Average Dissimilarity Contribution Cumulative Phylotype Rank Control Group (%) Quorum quenching Group (%) Dissimilarity / Standard Deviation (%) contribution (%) Gammaproteobacteria Class 6.41 47.9 3.76 7.28 6.87 6.87 Enterobacteriales Order 1.09 26.54 2.32 12.75 4.23 11.1 Enterobacteriaceae Family 1.07 26.45 2.31 13.08 4.21 15.31 Proteobacteria Phylum 46.37 65.06 1.7 3.61 3.09 18.4 Pseudomonadales Order 0.24 17 1.52 2.6 2.76 21.17 FJ755943_g Genus 0.36 13.68 1.21 10.23 2.21 23.38 FJ755943_s Species 0.35 13.44 1.19 10.12 2.17 25.56 Alphaproteobacteria Class 24.87 13.06 1.07 2.4 1.96 27.52 Pseudomonadaceae Family 0.18 11.86 1.06 3.36 1.93 29.45 Pseudomonas Genus 0.17 11.74 1.05 3.28 1.91 31.36 Enterobacter Genus 0.62 12 1.04 8.8 1.89 33.25 Rhizobiales Order 16.83 6.35 0.95 2.59 1.74 34.99 Sphingobacteria Class 17.4 8.36 0.82 4.32 1.5 36.49 Solibacteres Class 12.48 3.62 0.8 2.42 1.47 37.95 FJ479064_o Order 12.46 3.61 0.8 2.41 1.46 39.42 DQ532145_f Family 12.39 3.59 0.8 2.4 1.46 40.87 DQ532145_g Genus 12.33 3.55 0.8 2.33 1.45 42.33 FJ710748_s Species 12.31 3.54 0.8 2.32 1.45 43.78 Acidobacteria Phylum 12.83 4.13 0.79 2.46 1.44 45.22 Sphaerotilus_f Family 9.02 0.78 0.75 4.49 1.36 46.58 Sphingobacteriales Order 16.4 8.16 0.75 3.37 1.36 47.94 Bradyrhizobiaceae Family 11.01 3.23 0.71 2.74 1.3 49.24 Pseudomonas monteilii Species 0.06 7.75 0.7 3 1.27 50.51 Flavobacteriales Order 0.45 7.93 0.68 1.89 1.23 51.74 Betaproteobacteria Class 10.56 3.23 0.66 3.89 1.21 52.96 Burkholderiales Order 10.01 2.68 0.66 4.04 1.21 54.17 5

Flavobacteria Class 2.64 9.9 0.66 2.06 1.2 55.37 Flavobacteriaceae Family 0.45 7.71 0.66 1.73 1.2 56.56 Chitinophagaceae Family 15.21 7.99 0.65 3.35 1.19 57.76 Bradyrhizobium Genus 9.9 2.82 0.64 3.49 1.18 58.93 Bacteroidetes Phylum 27.46 21.54 0.56 1.8 1.03 59.96 Ferruginibacter Genus 7.1 1.11 0.54 1.66 0.98 60.95 Methylibium Genus 5.89 0.35 0.5 3.17 0.92 61.86 Enterobacter asburiae Species 0.17 5.43 0.48 4.71 0.87 62.74 Moraxellaceae Family 0.06 5.05 0.45 1.26 0.82 63.56 Acinetobacter Genus 0.06 5.05 0.45 1.26 0.82 64.38 Rhizobium lupini Species 6.75 1.92 0.44 3.39 0.8 65.18 Cytophagia Class 7.39 2.72 0.44 1.97 0.8 65.98 Cytophagales Order 7.17 2.65 0.42 2 0.77 66.74 Acinetobacter guillouiae Species 0.05 4.5 0.4 1.25 0.73 67.47 Elizabethkingia Genus 0.27 4.13 0.35 1.72 0.64 68.11 Elizabethkingia miricola Species 0.26 4.08 0.35 1.72 0.63 68.74 Pseudomonas fuscovaginae Species 0.1 3.65 0.32 1.11 0.58 69.32 Deltaproteobacteria Class 4.19 0.78 0.31 1.24 0.57 69.89 Chryseobacterium Genus 0.17 3.51 0.3 1.17 0.55 70.44 Enterobacter cancerogenus Species 0.04 3.35 0.3 6.21 0.55 71 Armatimonadetes Phylum 3.79 0.73 0.28 1.9 0.51 71.51 AF368184_c Class 3.77 0.73 0.28 1.9 0.51 72.01 AF368184_o Order 3.77 0.73 0.28 1.91 0.51 72.52 AF418954_f Family 3.75 0.72 0.28 1.93 0.5 73.02 AF418954_g Genus 3.73 0.72 0.28 1.94 0.5 73.53 AY792299_s Species 3.03 0.2 0.27 1.27 0.49 74.01 Sphingomonadaceae Family 5.38 2.49 0.26 2.8 0.48 74.49 Sphingomonadales Order 5.39 2.51 0.26 2.85 0.48 74.97 AF418954_s Species 3.53 0.69 0.26 1.92 0.47 75.45 Methylibium petroleiphilum Species 2.99 0.16 0.26 2.57 0.47 75.91 Chloroflexi Phylum 3.13 5.6 0.24 1.05 0.44 76.36 Caldilineae Class 3.12 5.59 0.24 1.05 0.44 76.8 6

EF516688_s Species 2.83 0.18 0.24 3.15 0.44 77.24 Caldilineales Order 3.1 5.53 0.24 1.05 0.43 77.67 DQ906906_o Order 2.73 0.33 0.22 1.18 0.39 78.06 Paracaedibacter_o Order 0.06 2.33 0.21 1.17 0.38 78.44 Cytophagaceae Family 2.63 0.4 0.2 1.39 0.37 78.81 Enterobacter ludwigii Species 0.42 2.62 0.2 0.97 0.36 79.18 Bradyrhizobium canariense Species 3.05 0.86 0.2 3.56 0.36 79.54 AJ867903_f Family 0.01 2.13 0.2 1.14 0.36 79.9 AJ867903_g Genus 0.01 2.11 0.19 1.14 0.35 80.25 AB240353_s Species 2.33 0.31 0.19 1.44 0.34 80.6 AB240353_g Genus 2.33 0.31 0.19 1.44 0.34 80.94 Hyphomicrobiaceae Family 3.59 1.54 0.19 2.35 0.34 81.28 Hyphomicrobium Genus 3.54 1.52 0.18 2.37 0.34 81.62 Sphingopyxis Genus 2.95 0.96 0.18 1.78 0.33 81.94 DQ336985_s Species 0.01 1.94 0.18 1.16 0.32 82.27 Sphingopyxis ummariensis Species 2.87 0.95 0.17 1.72 0.32 82.59 Xanthomonadales Order 4.49 3.21 0.13 1.06 0.24 82.83 Terrimonas Genus 5.9 5.4 0.13 1.64 0.24 83.07 Xanthomonadaceae Family 4.12 3.12 0.12 1.11 0.23 83.29 AY945920_s Species 1.24 0.08 0.1 3.28 0.19 83.49 Aquincola Genus 1.27 0.11 0.1 3.32 0.19 83.68 Nitrospira_g1 Genus 1.46 0.33 0.1 2.66 0.19 83.87 Nitrospirales Order 1.48 0.35 0.1 2.54 0.19 84.05 Nitrospiraceae Family 1.48 0.35 0.1 2.55 0.19 84.24 Nitrospirae Phylum 1.49 0.36 0.1 2.51 0.19 84.43 Nitrospira_c Class 1.49 0.36 0.1 2.51 0.19 84.61 AB252940_s Species 1.4 0.32 0.1 2.78 0.18 84.79 Chlorobi Phylum 1.23 0.49 0.09 1.18 0.17 84.96 OPB56 Class 1.23 0.49 0.09 1.18 0.17 85.13 OPB56_o Order 1.23 0.49 0.09 1.18 0.17 85.3 AJ630296_f Family 1.23 0.49 0.09 1.18 0.17 85.47 AJ630296_g Genus 1.23 0.49 0.09 1.18 0.17 85.63 7

AJ630296_s Species 1.23 0.49 0.09 1.18 0.17 85.8 GQ088353_s Species 4.3 4.68 0.09 1.31 0.17 85.97 Comamonas Genus 0.11 1.09 0.09 1.54 0.16 86.13 AY218694_g Genus 1.61 1.38 0.09 1.42 0.16 86.3 Sphingomonas Genus 2.34 1.44 0.09 1.7 0.16 86.46 Comamonadaceae Family 0.95 1.84 0.09 1.23 0.16 86.62 EU881309_f Family 0.98 0.04 0.09 1.94 0.16 86.77 Sphingomonas koreensis Genus 2.07 1.27 0.08 1.55 0.15 86.92 GQ093804_s Species 0.99 0.43 0.08 1.38 0.15 87.07 EU937987_s Species 1.25 0.49 0.08 1.78 0.15 87.22 EU234264_o Order 0.93 0.17 0.08 1.35 0.15 87.36 EU234264_f Family 0.93 0.17 0.08 1.35 0.15 87.51 EU234264_g Genus 0.93 0.17 0.08 1.35 0.15 87.66 Myxococcales Order 0.86 0 0.08 1.14 0.14 87.8 Polyangiaceae Family 0.85 0 0.08 1.12 0.14 87.94 Chondromyces Genus 0.85 0 0.08 1.12 0.14 88.08 Rhodospirillales Order 1.33 0.51 0.08 1.73 0.14 88.21 Piscinibacter Genus 0.84 0.03 0.07 3.18 0.13 88.35 Verrucomicrobia Phylum 0.95 0.14 0.07 2.24 0.13 88.48 Piscinibacter aquaticus Species 0.83 0.03 0.07 3.11 0.13 88.61 AB286578_s Species 0.84 0.15 0.07 1.37 0.13 88.75 Comamonas testosteroni Species 0.07 0.81 0.07 1.36 0.13 88.87 EU134489_f Family 0.76 0.02 0.07 0.94 0.12 88.99 AY693832_o Order 1.83 1.35 0.06 1.3 0.12 89.11 AY693832_f Family 1.8 1.34 0.06 1.3 0.11 89.22 EF203200_o Order 0.36 0.6 0.06 0.94 0.11 89.34 DQ309373_g Genus 1.74 1.32 0.06 1.32 0.11 89.44 EF203200_f Family 0.34 0.58 0.06 0.94 0.11 89.55 AB252934_s Species 1.18 0.77 0.06 1.27 0.11 89.66 AY491576_s Species 1.71 1.28 0.06 1.26 0.1 89.76 AB286618_f Family 0.78 0.21 0.06 1.25 0.1 89.86 Alysiosphaera_f Family 0.98 0.37 0.06 1.52 0.1 89.96 8

DQ413135_s Species 0.93 0.33 0.05 1.8 0.1 90.06 a Average Abundance of Broth Group: The average value of the abundances in broth samples in control and quorum quenching MBR (Cstart, C1 broth, C2 broth, Qstart, Q1 broth, Q2 broth) b Average Abundance of Biofilm Group: The average value of the abundances in biofilm samples in control and quorum quenching MBR (C1 biofilm, C2 biofilm, Q1 biofilm, Q2 biofilm) c Average Dissimilarity: The contribution of the specific taxon to the he average Bray-Curtis dissimilarity between broth group samples and biofilm group samples (The average dissimilarity between broth group samples and biofilm group samples was 54.81%.) 9

Table S3 SIMPER analysis data of microorganisms in the control and quorum quenching MBRs based on all ten samples Taxonomic a Average Abundance of b Average Abundance of c Average Average Dissimilarity Contribution Cumulative Phylotype Rank Control Group (%) Quorum quenching Group (%) Dissimilarity / Standard Deviation (%) contribution (%) Gammaproteobacteria Class 20.95 25.06 2 1.11 5.32 5.32 Enterobacteriales Order 11.79 10.74 1.17 1.02 3.11 8.44 Enterobacteriaceae Family 11.72 10.72 1.16 1.02 3.1 11.53 Proteobacteria Phylum 53.48 54.22 1.03 1.36 2.75 14.28 Pseudomonadales Order 4.9 8.98 0.88 1.07 2.34 16.62 Alphaproteobacteria Class 20.5 19.78 0.76 1.71 2.02 18.64 Rhizobiales Order 12.98 12.3 0.67 1.79 1.78 20.42 FJ755943_g Genus 5.85 5.52 0.62 1.04 1.65 22.07 FJ755943_s Species 5.76 5.41 0.61 1.04 1.62 23.68 Pseudomonadaceae Family 4.18 5.52 0.58 1.05 1.54 25.22 FJ710748_s Species 9.86 7.75 0.58 1.59 1.53 26.76 DQ532145_g Genus 9.87 7.77 0.57 1.58 1.53 28.29 Pseudomonas Species 4.1 5.5 0.57 1.05 1.53 29.82 FJ479064_o Order 9.98 7.87 0.57 1.58 1.53 31.34 Solibacteres Class 10 7.87 0.57 1.57 1.53 32.87 DQ532145_f Family 9.9 7.84 0.57 1.58 1.52 34.39 Acidobacteria Order 10.39 8.31 0.56 1.53 1.48 35.87 Enterobacter Genus 5.43 4.91 0.53 1.05 1.42 37.29 Sphingobacteria Class 14.3 13.26 0.49 1.37 1.32 38.6 Sphingobacteriales Order 13.95 12.25 0.48 1.44 1.28 39.88 Bradyrhizobiaceae Family 7.81 7.99 0.47 1.53 1.26 41.14 Bacteroidetes Phylum 23.7 26.48 0.47 1.59 1.25 42.39 Ferruginibacter Genus 6.61 2.8 0.46 1.37 1.23 43.62 Sphaerotilus_f Family 6.3 5.15 0.45 1.36 1.2 44.82 Chitinophagaceae Family 13.18 11.46 0.43 1.49 1.14 45.96 Flavobacteria Class 4.51 6.58 0.43 1.2 1.14 47.1 Flavobacteriales Order 2.45 4.44 0.42 1.02 1.11 48.21 Flavobacteriaceae Family 2.27 4.43 0.41 0.99 1.1 49.31 Betaproteobacteria Class 8.13 7.12 0.41 1.42 1.09 50.4 Burkholderiales Order 7.5 6.66 0.4 1.35 1.07 51.47 10

Bradyrhizobium Genus 7.29 6.85 0.4 1.42 1.06 52.53 Pseudomonas monteilii Species 3.17 3.1 0.38 1.03 1.02 53.55 Cytophagia Class 4.88 6.16 0.36 2.12 0.95 54.5 Cytophagales Order 4.82 5.91 0.34 2.07 0.9 55.4 Methylibium Genus 4.24 3.1 0.33 1.42 0.87 56.27 Acinetobacter Genus 0.68 3.42 0.31 0.88 0.84 57.11 Moraxellaceae Family 0.69 3.43 0.31 0.88 0.84 57.95 Deltaproteobacteria Class 3.69 1.96 0.29 1.24 0.77 58.72 Acinetobacter guillouiae Species 0.62 3.04 0.28 0.87 0.75 59.46 Rhizobium lupini Species 4.85 4.77 0.28 1.46 0.74 60.2 AY792299_s Species 3.08 0.72 0.26 1.21 0.7 60.89 Enterobacter asburiae Species 2.42 2.12 0.25 1.06 0.68 61.57 Elizabethkingia Genus 1.44 2.18 0.22 0.99 0.58 62.15 Pseudomonas fuscovaginae Species 0.74 2.29 0.22 0.77 0.58 62.72 Armatimonadetes Genus 1.98 3.14 0.22 1.46 0.58 63.3 AF368184_c Class 1.98 3.13 0.21 1.46 0.57 63.87 AF368184_o Order 1.98 3.13 0.21 1.46 0.57 64.44 Elizabethkingia miricola Species 1.42 2.15 0.21 0.99 0.57 65.01 AF418954_f Family 1.97 3.1 0.21 1.46 0.57 65.58 AF418954_g Genus 1.97 3.09 0.21 1.46 0.56 66.14 Chloroflexi Phylum 4.45 3.8 0.21 1.08 0.55 66.69 DQ906906_o Order 2.53 1.01 0.2 1.16 0.54 67.23 Caldilineae Family 4.43 3.79 0.2 1.08 0.54 67.78 Chryseobacterium Species 0.78 2.23 0.2 0.79 0.53 68.31 AF418954_s Order 1.85 2.94 0.2 1.45 0.53 68.84 Caldilineales Family 4.38 3.76 0.2 1.07 0.53 69.38 Cytophagaceae Family 2.55 0.92 0.19 1.23 0.5 69.88 Sphingomonadaceae Family 4.19 4.26 0.18 1.64 0.47 70.34 Sphingomonadales Order 4.21 4.27 0.17 1.61 0.46 70.81 AB240353_s Species 2.21 0.82 0.17 1.27 0.46 71.27 AB240353_g Genus 2.21 0.82 0.17 1.27 0.46 71.73 Methylibium petroleiphilum Species 2.17 1.54 0.17 1.36 0.46 72.18 Terrimonas Genus 4.95 6.45 0.16 1.91 0.43 72.61 Enterobacter cancerogenus Species 1.53 1.19 0.16 1.09 0.43 73.04 Sphingopyxis Genus 2.55 1.74 0.16 2.03 0.42 73.46 11

EF516688_s Species 2.07 1.47 0.16 1.41 0.42 73.87 Sphingopyxis ummariensis Species 2.5 1.7 0.15 2.05 0.41 74.28 Enterobacter ludwigii Species 1.08 1.52 0.15 0.85 0.4 74.68 Xanthomonadales Order 3.61 4.35 0.14 1.32 0.37 75.05 Paracaedibacter_o Order 1.34 0.59 0.14 0.81 0.37 75.42 Xanthomonadaceae Family 3.34 4.1 0.14 1.38 0.37 75.79 Hyphomicrobiaceae Family 3.09 2.46 0.13 1.52 0.35 76.14 Hyphomicrobium Genus 3.07 2.4 0.13 1.53 0.35 76.48 AJ867903_f Family 1.2 0.51 0.13 0.78 0.35 76.83 AJ867903_g Genus 1.18 0.51 0.13 0.79 0.34 77.17 Bradyrhizobium canariense Species 2.36 1.98 0.12 1.36 0.33 77.5 DQ336985_s Species 1.08 0.49 0.12 0.79 0.31 77.81 AY218694_g Genus 0.99 2.05 0.11 1.64 0.3 78.11 GQ088353_s Species 3.87 5.04 0.11 1.42 0.29 78.4 Chlorobi Phylum 1.36 0.51 0.1 1.18 0.27 78.67 OPB56 Class 1.36 0.51 0.1 1.18 0.27 78.94 OPB56_o Order 1.36 0.51 0.1 1.18 0.27 79.21 AJ630296_f Family 1.36 0.51 0.1 1.18 0.27 79.47 AJ630296_g Genus 1.36 0.51 0.1 1.18 0.27 79.74 AJ630296_s Species 1.36 0.51 0.1 1.18 0.27 80.01 Sphingomonas Genus 1.54 2.42 0.09 1.69 0.24 80.25 Sphingomonas koreensis Species 1.3 2.19 0.09 1.66 0.23 80.48 GQ093804_s Species 0.48 1.05 0.09 1.49 0.23 80.71 Comamonadaceae Family 1.16 1.46 0.08 1.75 0.22 80.92 EU234264_o Order 0.32 0.93 0.08 1.3 0.21 81.13 EU234264_f Family 0.32 0.93 0.08 1.3 0.21 81.34 EU234264_g Genus 0.32 0.92 0.08 1.3 0.21 81.55 AB252934_s Species 1.43 0.6 0.08 1.69 0.2 81.75 Myxococcales Order 0.84 0.19 0.07 1.09 0.2 81.95 Polyangiaceae Family 0.83 0.19 0.07 1.08 0.2 82.15 Chondromyces Genus 0.83 0.19 0.07 1.08 0.2 82.35 EU134489_f Family 0.82 0.11 0.07 0.97 0.19 82.54 AB286578_s Species 0.28 0.85 0.07 1.34 0.19 82.73 Nitrospirales Order 1.22 0.84 0.07 1.4 0.19 82.92 Nitrospirae Phylum 1.23 0.85 0.07 1.41 0.19 83.1 12

Nitrospira_c Class 1.23 0.85 0.07 1.41 0.19 83.29 Nitrospiraceae Family 1.22 0.83 0.07 1.41 0.19 83.48 Nitrospira_g1 Genus 1.2 0.81 0.07 1.41 0.19 83.67 EU937987_s Genus 0.79 1.11 0.07 1.46 0.18 83.85 Aquincola Species 0.93 0.67 0.07 1.38 0.18 84.03 AY945920_s Species 0.89 0.66 0.07 1.38 0.18 84.21 AB252940_s Species 1.15 0.79 0.07 1.42 0.18 84.38 Rhodospirillales Order 0.85 1.15 0.06 1.69 0.16 84.55 EU881309_f Family 0.58 0.62 0.06 1.3 0.16 84.71 AY693832_o Order 1.57 1.7 0.06 1.55 0.16 84.87 Comamonas Genus 0.61 0.4 0.06 1.01 0.16 85.03 AY693832_f Family 1.56 1.67 0.06 1.54 0.16 85.18 EF203200_o Order 0.49 0.42 0.06 0.99 0.15 85.34 Afipia Genus 0.43 0.84 0.06 1.04 0.15 85.49 AB286618_f Family 0.72 0.38 0.06 1.38 0.15 85.63 DQ309373_g Genus 1.54 1.61 0.06 1.47 0.15 85.78 EF203200_f Family 0.47 0.41 0.05 0.99 0.15 85.93 Verrucomicrobia Phylum 0.79 0.47 0.05 1.45 0.14 86.07 AY491576_s Species 1.49 1.59 0.05 1.47 0.14 86.21 Rhizobiaceae Family 0.82 0.36 0.05 1.16 0.14 86.35 Rickettsiales Order 0.55 0.43 0.05 1.29 0.14 86.48 Rickettsiaceae Family 0.54 0.36 0.05 1.27 0.14 86.62 Hyphomicrobium denitrificans Species 0.48 0.76 0.05 1.27 0.13 86.74 DQ404664_g Genus 0.38 0.32 0.05 0.97 0.13 86.87 Mesorhizobium Genus 0.63 0.13 0.05 1.09 0.13 87 Comamonas testosteroni Species 0.49 0.24 0.05 0.95 0.12 87.12 Pseudomonas carboxydohydrogena Species 0.18 0.55 0.05 1.04 0.12 87.25 Piscinibacter Genus 0.49 0.55 0.05 1.36 0.12 87.37 Piscinibacter aquaticus Species 0.48 0.53 0.05 1.33 0.12 87.49 Opitutales Order 0.61 0.27 0.05 1.52 0.12 87.61 Opitutae Class 0.61 0.27 0.05 1.53 0.12 87.73 Opitutaceae Family 0.6 0.26 0.04 1.49 0.12 87.85 EF520417_g Genus 0.47 0.26 0.04 1.25 0.12 87.97 Opitutus Genus 0.59 0.25 0.04 1.48 0.12 88.09 Alysiosphaera_f Family 0.68 0.79 0.04 1.34 0.12 88.2 13

Bacteroidia Class 0 0.48 0.04 0.53 0.11 88.32 Bacteroidales Order 0 0.48 0.04 0.53 0.11 88.43 AB286342_f Family 0.41 0.22 0.04 1.26 0.11 88.55 Alysiomicrobium Genus 0.68 0.78 0.04 1.35 0.11 88.66 EF520417_s Species 0.45 0.25 0.04 1.24 0.11 88.77 Mesorhizobium plurifarium Species 0.54 0.09 0.04 1.01 0.11 88.88 Caulobacterales Order 0.38 0.72 0.04 0.79 0.11 88.99 Caulobacteraceae Family 0.38 0.72 0.04 0.79 0.11 89.1 DQ413135_s Species 0.67 0.71 0.04 1.37 0.11 89.21 Prevotellaceae Family 0 0.45 0.04 0.49 0.11 89.32 Prevotella Genus 0 0.45 0.04 0.49 0.11 89.42 DQ337099_f Family 0.24 0.39 0.04 1.46 0.11 89.53 Thiotrichales Order 0.27 0.4 0.04 1.44 0.1 89.63 Rudaea Genus 0.6 0.36 0.04 1.29 0.1 89.73 Desulfuromonadales Order 0.27 0.52 0.04 1.24 0.1 89.83 AB240359_f Family 0.27 0.52 0.04 1.24 0.1 89.93 Rudaea cellulosilytica Species 0.58 0.34 0.04 1.32 0.1 90.03 a Average Abundance of Control Group: The average value of the abundances in broth and biofilm samples in control MBR (Cstart, C1 broth, C2 broth, C1 biofilm, C2 biofilm) b Average Abundance of Quorum Quenching Group: The average value of the abundances in broth and biofilm samples in quorum quenching MBR (Qstart, Q1 broth, Q2 broth, Q1 biofilm, Q2 biofilm) c Average Dissimilarity: The contribution of the specific taxon to the average Bray-Curtis dissimilarity between control group samples and quorum quenching group samples (The average dissimilarity between control group samples and quorum quenching group samples was 37.51%.) 14

Table S4. The composition of major taxa in the microbial community Taxonomic rank Name C start C1 broth C2 broth Q start Q1 broth Q2 broth C1 biofilm C2 biofilm Q1 biofilm Q2 biofilm Phylum Armatimonadetes 4.58 5.39 4.73 4.61 1.9 1.51 0.58 0.43 0.43 1.47 Class AF368184_c 4.58 5.37 4.7 4.58 1.9 1.51 0.58 0.43 0.43 1.47 Order AF368184_o 4.58 5.34 4.7 4.58 1.9 1.51 0.58 0.43 0.43 1.47 Family AF418954_f 4.58 5.21 4.7 4.58 1.9 1.51 0.58 0.43 0.43 1.45 Genus AF418954_g 4.58 5.14 4.7 4.55 1.9 1.51 0.58 0.43 0.43 1.44 Phylum Chloroflexi 2.21 4.42 4.48 3.3 2.35 2.04 4.26 3.61 4.87 9.67 Class Caldilineae 2.21 4.41 4.45 3.27 2.35 2.04 4.26 3.61 4.85 9.63 Order Caldilineales 2.21 4.29 4.43 3.27 2.35 2.04 4.26 3.61 4.77 9.48 Phylum Proteobacteria 40.13 49.69 49.73 41.17 46.86 50.66 66.96 64.57 68.4 60.3 Class Betaproteobacteria 10.74 8.91 11.2 8.12 13 11.38 2.6 2.16 3.18 4.97 Order Burkholderiales 10.43 7.91 10.48 7.78 12.42 11.05 2.38 2.09 2.1 4.16 Family Sphaerotilus_f 9.16 6.51 9.01 6.93 11.74 10.79 0.43 0.65 0.92 1.13 Genus Methylibium 4.74 4.39 6.02 3.94 8.94 7.3 0.22 0.14 0.54 0.48 Species Methylibium petroleiphilum 3 1.7 2.94 1.86 5.01 3.42 0.07 0 0.39 0.19 Class Gammaproteobacteria 5.21 8.63 8.79 6.59 5.37 3.88 52.09 50.58 51.3 37.62 Order Enterobacteriales 1.42 1.06 1.07 1.46 1.04 0.46 25.69 24.46 29.37 26.64 Family Enterobacteriaceae 1.42 1.03 1.02 1.46 1.04 0.46 25.69 24.46 29.28 26.35 Genus Enterobacter 0.63 0.41 0.4 0.92 0.95 0.39 12.99 10.1 13.21 11.69 Species Enterobacter ludwigii 0.47 0.08 0.1 0.73 0.72 0.39 6.28 0.65 2.68 0.86 Species Enterobacter asburiae 0.16 0.23 0.25 0.18 0.18 0 3.61 6.35 5.92 5.82 Genus FJ755943_g 0.47 0.47 0.62 0.46 0.05 0.07 11.76 14.29 15.07 13.61 Species FJ755943_s 0.47 0.46 0.6 0.46 0.05 0.07 11.54 14 14.85 13.38 Order Pseudomonadales 0 0.4 0.35 0.43 0.27 0 22.73 21.43 17.46 6.36 Family Pseudomonadaceae 0 0.31 0.25 0.34 0.18 0 12.05 15.01 14.27 6.11 Genus Pseudomonas 0 0.26 0.25 0.34 0.18 0 11.98 15.01 14.04 5.92 Species Pseudomonas fuscovaginae 0 0.23 0.2 0.12 0.05 0 2.09 8.95 2.76 0.79 Species Pseudomonas monteilii 0 0.03 0.02 0.21 0.09 0 9.74 5.7 10.78 4.76 Family Moraxellaceae 0 0.08 0.1 0.09 0.09 0 10.61 6.35 3.07 0.18 15

Genus Acinetobacter 0 0.06 0.1 0.09 0.09 0 10.61 6.35 3.05 0.18 Species Acinetobacter guillouiae 0 0.06 0.07 0.09 0.09 0 9.6 5.48 2.72 0.18 Order Xanthomonadales 3.32 6.23 6.42 4.06 3.7 3.22 2.02 3.75 3.43 3.62 Family Xanthomonadaceae 2.84 5.71 6.25 3.72 3.39 2.83 2.02 3.68 3.29 3.49 Class Alphaproteobacteria 18.64 30.62 28.02 23.07 22.53 26.32 11.18 10.46 13.13 17.45 Order Rhizobiales 11.37 21.79 19.56 14.95 15.76 17.57 5.05 3.75 8.48 8.13 Family Bradyrhizobiaceae 7.42 15.46 12.15 9.34 10.52 11.18 3.32 1.59 3.34 4.65 Genus Bradyrhizobium 7.11 12.63 10.23 8.7 9.93 10.79 2.89 1.37 3.01 4.02 Species Rhizobium lupini 4.9 8.86 7.22 5.86 6.46 7.17 1.73 1.15 2.01 2.77 Order Sphingomonadales 4.9 4.85 5.18 5.19 5.33 6.91 3.1 3.32 1.72 1.91 Family Sphingomonadaceae 4.9 4.81 5.15 5.19 5.33 6.91 3.1 3.32 1.69 1.83 Order Paracaedibacter_o 0 0.06 0.15 0.03 0.09 0 2.45 0.29 1.31 5.26 Class Deltaproteobacteria 5.21 1.01 1.19 3.02 5.87 8.82 1.01 1.37 0.65 0.1 Order DQ906906_o 2.84 0.7 0.55 1.92 4.11 6.25 0.51 0.43 0.32 0.06 Phylum Acidobacteria 16.11 8.44 7.77 13.85 14.99 15.79 5.48 3.75 3.75 3.55 Class Solibacteres 15.32 7.99 7.32 13.7 14.85 15.72 5.34 3.39 3.27 2.48 Order FJ479064_o 15.32 7.96 7.32 13.61 14.85 15.72 5.34 3.39 3.27 2.43 Family DQ532145_f 15.32 7.84 7.29 13.58 14.85 15.46 5.34 3.39 3.25 2.36 Genus DQ532145_g 15.32 7.5 7.29 13.58 14.85 15.46 5.34 3.39 3.23 2.24 Species FJ710748_s 15.32 7.42 7.27 13.55 14.85 15.46 5.34 3.39 3.2 2.23 Phylum Bacteroidetes 30.96 28.03 29.12 30.03 24.38 22.24 19.48 24.82 19.78 22.07 Class Sphingobacteria 19.75 15.17 15.08 19.68 18.24 16.45 8.66 7.65 7.47 9.67 Order Sphingobacteriales 18.64 13.35 13.02 18.68 18.24 16.45 8.59 7.65 7.45 8.94 Family Chitinophagaceae 16.59 12.43 12.27 17.52 16.66 15.79 8.37 7.65 7.14 8.79 Genus Terrimonas 6.16 6.61 7.29 7.05 4.29 4.01 6.93 5.27 4.73 4.67 Species GQ088353_s 4.74 4.36 5.13 4.64 3.97 2.96 6.2 4.76 4.28 3.49 Genus Ferruginibacter 7.74 2.54 2.22 8.42 11.15 10.53 0.79 0.72 0.99 1.95 Species AY792299_s 3 0.03 0 3.33 6.5 5.33 0.36 0.22 0.21 0.01 Class Flavobacteria 2.21 3.48 4.6 2.53 1.53 1.51 7.22 15.37 9.77 7.22 Order Flavobacteriales 0.16 0.78 0.9 0.61 0.18 0.07 6.57 13.78 8.37 3 Family Flavobacteriaceae 0.16 0.75 0.9 0.61 0.18 0.07 6.57 13.78 8.2 2.27 Genus Elizabethkingia 0.16 0.41 0.5 0.37 0.09 0.07 4.47 5.34 6.22 0.47 16

Species Elizabethkingia miricola 0.16 0.38 0.47 0.37 0.09 0.07 4.47 5.27 6.14 0.45 Genus Chryseobacterium 0 0.29 0.4 0.24 0.09 0 2.09 8.37 1.94 1.64 Class Cytophagia 8.85 9.35 9.43 7.81 4.6 4.28 1.37 1.8 2.53 5.17 Order Cytophagales 8.53 8.77 9.13 7.69 4.6 4.28 1.3 1.8 2.44 5.07 17