A) Sm B) Sw C) Ss D) N1 114, Nitrospira 114, Nitrospira 24, Sytrophobacteraceae 146, Propionibacterineae 323, 26, Sytrophobacteraceae 161, 228, 333, Lactobacillales 67, KSB3 132, 23, Sytrophobacteraceae 21, TM6 23, Sytrophobacteraceae 143, Actinobacteridae 209, Chloroflexi 132, Acidobacteria 85, Bacteroidales 348, Firmicutes 10, Rhodocyclales 301, Firmicutes 114, Nitrospira 146, Propionibacterineae 79, Bacteroidales 23, Sytrophobacteraceae 61, Epsilon 224, Chloroflexi 146, Propionibacterineae 85, Bacteroidales 209, Chloroflexi 87, Bacteroidales 152, Propionibacterineae 113, Flexibacteraceae 351, OD2 208, Chloroflexi 85, Bacteroidales 128, 146, Propionibacterineae 213, Chloroflexi 186, Chlorobi 161, Spirochaetaceae 79, Bacteroidales 280, Clostridiaceae 250, Lachnospiraceae 138, others 196, Chloroflexi 114, Nitrospira 262, Lachnospiraceae 183, Chlorobi 213, Chloroflexi 24, Sytrophobacteraceae 340, Acidaminococcaceae 231, Chloroflexi 218, Chloroflexi 228, Chloroflexi 25, Sytrophobacteraceae 15, Rhodobacterales 333, Lactobacillales 25, Sytrophobacteraceae 13, Methylophilales 55, Desulfovibrionales 165, Spirochaetaceae 55, Desulfovibrionales 23, Sytrophobacteraceae 173, Spirochaetaceae 65, others 61, Epsilonproteobacteria 116, - 148, Propionibacterineae 1, Shewanella 132, Acidobacteria 158, Rubrobacteridae 157, Rubrobacteridae 2, Pseudomonadaceae 143, Actinobacteridae 83, Bacteroidales 85, Bacteroidales 3, Pseudomonadaceae 157, Rubrobacteridae 92, Bacteroidales 104, Bacteroidales 161, Spirochaetaceae 198, Chloroflexi 97, Bacteroidales 109, Flavobacteriales 71, Bacteroidales 199, Chloroflexi 98, Bacteroidales 110, Flavobacteriales 95, Bacteroidales 202, Chloroflexi 99, Bacteroidales 193, Chloroflexi 111, Flavobacteriales 106, Bacteroidales 205, Chloroflexi 195, Chloroflexi 184, Chlorobi 203, Chloroflexi 209, Chloroflexi 216, Chloroflexi 198, Chloroflexi 223, Chloroflexi 240, Chloroflexi 217, Chloroflexi 204, Chloroflexi 232, Chloroflexi 218, Chloroflexi 213, Chloroflexi 242, Chloroflexi 234, Chloroflexi 216, Chloroflexi 264, Lachnospiraceae 236, Chloroflexi 230, Chloroflexi 222, Chloroflexi 320, Firmicutes 237, Chloroflexi 233, Chloroflexi 226, Chloroflexi 325, Firmicutes 241, Chloroflexi 287, Firmicutes 240, Chloroflexi 344, Acidaminococcaceae 274, Lachnospiraceae 292, Firmicutes 261, Lachnospiraceae 30, TA-1 296, Firmicutes 313, Peptostreptococcaceae 268, Lachnospiraceae 49, Myxococcales 313, Peptostreptococcaceae 315, Peptostreptococcaceae 325, Firmicutes 345, Acidaminococcaceae 278, Lachnospiraceae 52, Desulfuromonadales 280, Clostridiaceae 341, Acidaminococcaceae 18, Sphingomonadales 58, Desulfovibrionales 281, Clostridiaceae 343, Acidaminococcaceae 5, Comamonadaceae 14, Moraxellaceae 282, Clostridiaceae 115, Nitrospira 8, Comamonadaceae 2, Pseudomonadaceae 292, Firmicutes 19, Alphaproteobacteria 27, Sytrophobacteraceae 3, Pseudomonadaceae 296, Firmicutes 20, Rhodospirillaceae 28, Sytrophobacteraceae 163, Spirochaetaceae 304, Firmicutes 7, Comamonadaceae 61, Epsilon proteobacteria 11, Nitrosomonadales 312, Peptostreptococcaceae 373, Deferribacteres 165, Spirochaetaceae 317, Peptostreptococcaceae 36, Delta proteobacteria 374, Deferribacteres 171, Spirochaetaceae 325, Firmicutes 59, Campylobacteraceae 361, others 178, 326, Firmicutes 4, Methylomonas 348, Firmicutes 0 5 10 15 20 25 30 175, 0 1 2 3 4 5 6 7 8 9 10 128, Planctomycetes 119, Verrucomicrobia-Chlamydiae 62, Epsilon proteobacteria 123, Verrucomicrobia-Chlamydiae 171, Spirochaetaceae 350, Caldicellulosiruptor 68, KSB3 66, Caldothrix 140, NKB19 365, OP10 353, OD2 244, OP9 354, OD2 376, Deferribacteres 0 1 2 3 4 5 6 7 8 9 356, WS6 141,others 0 2 4 6 8 10 12 14 16

Fig. S1. Rank abundances of bacterial phylotypes of 12 UASB granular sludges. Sludge samples were collected from the reactors A) Sm, B) Sw, C) Ss, D) N1, E) N2, F), Q, G) Hg, H) Hn, I) Yk, J) Ks, K) Hs, and L) Dt. The vertical axis shows the taxonomic affi liation and number of phylotypes found in the respective clone libraries (382 bacterial phylotypes in total). E) N2 F) Q G) Hg H) Hn

146, Propionibacterineae 182, Chlorobi 52, Desulfuromonadales 114, Nitrospira 23, Sytrophobacteraceae 114, Nitrospira 68, KSB3 138, others 161, Spirochaetaceae 142, others 25, Sytrophobacteraceae 85, Bacteroidales 211, Chloroflexi 213, Chloroflexi 52, Desulfuromonadales 52, Desulfuromonadales 26, Sytrophobacteraceae 224, Chloroflexi 68, KSB3 369, Deferribacteres 179, Leptospiraceae 24, Sytrophobacteraceae 114, Nitrospira 88, Bacteroidales 143, Actinobacteridae 35, Delta proteobacteria 244, OP9 93, Bacteroidales 93, Bacteroidales 130, others 85, Bacteroidales 210, Chloroflexi 126, Planctomycetes 151, Propionibacterineae 191, Chloroflexi 232, Chloroflexi 26, Sytrophobacteraceae 53, Desulfuromonadales 114, Nitrospira 189, Chloroflexi 170, Spirochaetaceae 146, Propionibacterineae 136, OS-K 197 ,Chloroflexi 79, Bacteroidales 79, Bacteroidales 64, others 214, Chloroflexi 88, Bacteroidales 194, Chloroflexi 70, Bacteroidales 227, Chloroflexi 188, Chloroflexi 201, Chloroflexi 85, Bacteroidales 239, Chloroflexi 226, Chloroflexi 229, Chloroflexi 29, TA-1 280, Clostridiaceae 245, Lachnospiraceae 297, Firmicutes 296, Firmicutes 44, Syntrophaceae 271, Lachnospiraceae 50, Myxococcales 347, Syntrophomonadaceae 16, Rhodobacterales 295, Firmicutes 132, Acidobacteria 23, Sytrophobacteraceae 77 ,Bacteroidales 339, Acidaminococcaceae 80, Bacteroidales 48, Myxococcales 37, Syntrophaceae 79, Bacteroidales 88, Bacteroidales 118, Verrucomicrobia-Chlamydiae 46, Syntrophaceae 81, Bacteroidales 90, Bacteroidales 373, Deferribacteres 375, Deferribacteres 85, Bacteroidales 105, Bacteroidales 146, Propionibacterineae 382, 91, Bacteroidales 185, Chlorobi 160, Coriobacteridae 142, others 201, Chloroflexi 154, Rubrobacteridae 206, Chloroflexi 132, Acidobacteria 209, Chloroflexi 78, Bacteroidales 215, Chloroflexi 145, Cellulomonadaceae 217, Chloroflexi 103, Bacteroidales 226, Chloroflexi 159, Rubrobacteridae 218, Chloroflexi 198, Chloroflexi 242, Chloroflexi 200, Chloroflexi 181, Chlorobi 225, Chloroflexi 252, Lachnospiraceae 208, Chloroflexi 191, Chloroflexi 228, Chloroflexi 321, Firmicutes 212, Chloroflexi 201, Chloroflexi 235, Chloroflexi 326, Firmicutes 213, Chloroflexi 328, Firmicutes 265, Lachnospiraceae 220, Chloroflexi 329, Firmicutes 331, Lactobacillales 332, Lactobacillales 27, Sytrophobacteraceae 238, Chloroflexi 251, Lachnospiraceae 333, Lactobacillales 334, Lactobacillales 30, TA-1 257, Lachnospiraceae 341, Acidaminococcaceae 17, Rhodobacterales 46, Syntrophaceae 292, Firmicutes 342, Acidaminococcaceae 25, Sytrophobacteraceae 162, Spirochaetaceae 293, Firmicutes 12, Methylophilales 56, Desulfovibrionales 172, Spirochaetaceae 297, Firmicutes 27, Sytrophobacteraceae 61, Epsilonproteobacteria 121, Verrucomicrobia-Chlamydiae 300, Firmicutes 29, TA-1 374, Deferribacteres 377, Deferribacteres 308, Peptostreptococcaceae 31, TA-1 379, Deferribacteres 63, 311, Peptostreptococcaceae 366, OP10 364, OP10 320, Firmicutes 39, Syntrophaceae 367, OP10 137, OP8 322, Firmicutes 45, Syntrophaceae 324, Firmicutes 357, TM7 65, others 162, Spirochaetaceae 325, Firmicutes 122, Verrucomicrobia-Chlamydiae 336, Firmicutes 0 5 10 15 20 25 30 35 40 0 2 4 6 8 10 12 14 16 244, OP9 35, Deltaproteobacteria 37, Syntrophaceae 131, others 53, Desulfuromonadales 0 5 10 15 20 25 30 35 164, Spirochaetaceae 177, Leptospiraceae 180, Leptospiraceae Verrucomicrobia-Chlamydiae Deferribacteres Deferribacteres Deferribacteres others others others 0 2 4 6 8 10 12 14 16

Fig. S1 (continued).Fig. S1. (continued). Narihiro et al. I) Yk J) Ks K) Hs L) Dt

59, Campylobacteraceae 27, Sytrophobacteraceae 90, Bacteroidales 368, Deferribacteres 322, Firmicutes 377, Deferribacteres 190, Chloroflexi 149, Propionibacterineae 318, Firmicutes 95, Bacteroidales 102, Bacteroidales 80, Bacteroidales 2, Pseudomonadaceae 26, Sytrophobacteraceae 187, Chloroflexi 377, Deferribacteres 335, Firmicutes 74, Bacteroidales 297, Firmicutes 150, Propionibacterineae 253, Lachnospiraceae 45, Syntrophaceae 26, Sytrophobacteraceae 292, Firmicutes 9, Oxalobacteraceae 369, Deferribacteres 54, Desulfuromonadales 373, Deferribacteres 73, Bacteroidales 138, others 164, Spirochaetaceae 208, Chloroflexi 256, Lachnospiraceae 79, Bacteroidales 283, Firmicutes 266, Lachnospiraceae 290, Firmicutes 16, Rhodobacterales 181, Chlorobi 296, Firmicutes 284, Firmicutes 306, Peptostreptococcaceae 146, Propionibacterineae 297, Firmicutes 319, Firmicutes 51, Bdellovibrionales 85, Bacteroidales 330, Firmicutes 51, Bdellovibrionales 162, Spirochaetaceae 41, Syntrophaceae 57, Desulfovibrionales 154, Rubrobacteridae 258, Lachnospiraceae 144, Cellulomonadaceae 371, Deferribacteres 155, Rubrobacteridae 275, Lachnospiraceae 221, Chloroflexi 359, Termite group I 33, TA-1 296, Firmicutes 323, Firmicutes 265, Lachnospiraceae 147, Propionibacterineae 176, Spirochaetes 69, Bacteroidales 243, OP9 330, Firmicutes 285, Firmicutes 16, Rhodobacterales 72, Bacteroidales 244, OP9 21, TM6 30, TA-1 86, Bacteroidales 156, Rubrobacteridae 133, Acidobacteria 37, Syntrophaceae 94, Bacteroidales 75, Bacteroidales 134, Acidobacteria 41, Syntrophaceae 245, Lachnospiraceae 76, Bacteroidales 47, Myxococcales 153, Propionibacterineae 247, Lachnospiraceae 88, Bacteroidales 58, Desulfovibrionales 82, Bacteroidales 248, Lachnospiraceae 89, Bacteroidales 373, Deferribacteres 84, Bacteroidales 249, Lachnospiraceae 91, Bacteroidales 377, Deferribacteres 254, Lachnospiraceae 99, Bacteroidales 93, Bacteroidales 135, Acidobacteria 100, Bacteroidales 255, Lachnospiraceae 96, Bacteroidales 85, Bacteroidales 112, Flavobacteriales 259, Lachnospiraceae 101, Bacteroidales 106, Bacteroidales 260, Lachnospiraceae 187, Chloroflexi 192, Chloroflexi 107, Bacteroidales 262, Lachnospiraceae 188, Chloroflexi 210, Chloroflexi 108, Bacteroidales 263, Lachnospiraceae 207, Chloroflexi 246, Lachnospiraceae 271, Lachnospiraceae 267, Lachnospiraceae 219, Chloroflexi 269, Lachnospiraceae 297, Firmicutes 272, Lachnospiraceae 242, Chloroflexi 270, Lachnospiraceae 314, Peptostreptococcaceae 273, Lachnospiraceae 276, Lachnospiraceae 273, Lachnospiraceae 10, Rhodocyclales 279, Clostridiaceae 294, Firmicutes 277, Lachnospiraceae 38, Syntrophaceae 280, Clostridiaceae 310, Peptostreptococcaceae 286, Firmicutes 52, Desulfuromonadales 288, Firmicutes 316, Peptostreptococcaceae 287, Firmicutes 292, Firmicutes 32, TA-1 53, Desulfuromonadales 289, Firmicutes 299, Firmicutes 38, Syntrophaceae 291, Firmicutes 165, Spirochaetaceae 302, Firmicutes 40, Syntrophaceae 292, Firmicutes 168, Spirochaetaceae 307, Peptostreptococcaceae 42, Syntrophaceae 294, Firmicutes 122, Verrucomicrobia-Chlamydiae 309, Peptostreptococcaceae 46, Syntrophaceae 298, Firmicutes 352, OD2 337, Firmicutes 52, Desulfuromonadales 303, Firmicutes 363, OP10 338, Acidaminococcaceae 54, Desulfuromonadales 305, Firmicutes 22, TM6 346, Syntrophomonadaceae 360, Termite group I 327, Firmicutes 349, Firmicutes 358, TM7 124, Planctomycetes 382, Thermotogae 125, Planctomycetes 64,others 6, Comamonadaceae 0 2 4 6 8 10 12 14 55, Desulfovibrionales 127, Planctomycetes 0 2 4 6 8 10 12 60, Campylobacteraceae 129, Planctomycetes 1, Shewanella 34, TA-1 3, Pseudomonadaceae 43, Syntrophaceae 169, Spirochaetaceae 52, Desulfuromonadales 368, Deferribacteres 166, Spirochaetaceae 167, Spirochaetaceae 370, Deferribacteres 168, Spirochaetaceae 372, Deferribacteres 174, Spirochaetes 377, Deferribacteres 177, Leptospiraceae 0 2 4 6 8 10 12 14 16 18 20 120, Verrucomicrobia-Chlamydiae 369, Deferribacteres 378, Deferribacteres 139, NKB19 382, Thermotogae 21, TM6 355, WS6 0 1 2 3 4 5 6 7 8

Fig. S1 (continued).Fig. S1. (continued). Narihiro et al. A) Sm B) Sw C) Ss D) N1

6, Methanosaetaceae 23, Methanobacteriaceae 1, Methanosaetaceae 29, Methanobacteriaceae 1, Methanosaetaceae 6, Methanosaetaceae 23, Methanobacteriaceae 1, Methanosaetaceae 23, Methanobacteriaceae 23, Methanobacteriaceae 1, Methanosaetaceae 2, Methanosaetaceae 12, Methanomicrobiales 14, Methanomicrobiales 12, Methanomicrobiales 12, Methanomicrobiales 2, Methanosaetaceae 24, Methanobacteriaceae 2, Methanosaetaceae 29, Methanobacteriaceae 11, Methanomicrobiales 9, Methanosarcinaceae 11, Methanomicrobiales 24, Methanobacteriaceae 10, Methanosarcinaceae 4, Methanosaetaceae 6, Methanosaetaceae 20, Methanospirillaceae 0 2 4 6 8 10 12 14 16 12, Methanomicrobiales 0 2 4 6 8 10 12 14 16 18 0 5 10 15 20 25 18, Methanomicrobiales 0 2 4 6 8 10 12 14

E) N2 F) Q G) Hg H) Hn

29, Methanobacteriaceae 1, Methanosaetaceae 1, Methanosaetaceae 1, Methanosaetaceae 23, Methanobacteriaceae 26, Methanobacteriaceae 29, Methanobacteriaceae 10, Methanosarcinaceae 1, Methanosaetaceae 23, Methanobacteriaceae 3, Methanosaetaceae 23, Methanobacteriaceae 24, Methanobacteriaceae 29, Methanobacteriaceae 6, Methanosaetaceae 29, Methanobacteriaceae 12, Methanomicrobiales 22, WSA2 12, Methanomicrobiales 6, Methanosaetaceae 14, Methanomicrobiales 24, Methanobacteriaceae 15, Methanomicrobiales 12, Methanomicrobiales 4, Methanosaetaceae 25, Methanobacteriaceae 2, Methanosaetaceae 13, Methanomicrobiales 5, Methanosaetaceae 0 5 10 15 20 25 30 35 14, Methanomicrobiales 26, Methanobacteriaceae 9, Methanosarcinaceae 23, Methanobacteriaceae 32, Methanobacteriaceae 28, Methanobacteriaceae 10, Methanosarcinaceae 0 5 10 15 20 25 30 35 40 0 5 10 15 20 25 22, WSA2 0 5 10 15 20 25 30

I) Yk J) Ks K) Hs L) Dt

1, Methanosaetaceae 30, Methanobacteriaceae 1, Methanosaetaceae 1, Methanosaetaceae

12, Methanomicrobiales 29, Methanobacteriaceae 6, Methanosaetaceae 15, Methanomicrobiales 23, Methanobacteriaceae 19, Methanomicrobiales 19, Methanomicrobiales 13, Methanomicrobiales 19, Methanomicrobiales 23, Methanobacteriaceae 1, Methanosaetaceae 20, Methanospirillaceae 14, Methanomicrobiales 26, Methanobacteriaceae 7, Methanosarcinaceae 23, Methanobacteriaceae 26, Methanobacteriaceae 28, Methanobacteriaceae 23, Methanobacteriaceae 15, Methanomicrobiales 28, Methanobacteriaceae 3, Methanosaetaceae 8, Methanosarcinaceae 20, Methanospirillaceae 17, Methanomicrobiales 0 10 20 30 40 50 60 22, WSA2 9, Methanosarcinaceae 0 5 10 15 20 25 30 35 40 0 5 10 15 20 25 30 35 16, Methanomicrobiales

21, Methanocorpusculaceae

27, Methanobacteriaceae

31, Methanobacteriaceae

0 5 10 15 20 25 30 35

Fig. S2. Rank abundances of archaeal phylotypes of 12 UASB granular sludges. Sludge samplesFig. were S2. collected Narihiro from et the al. reactors A) Sm, B) Sw, C) Ss, D) N1, E) N2, F), Q, G) Hg, H) Hn, I) Yk, J) Ks, K) Hs, and L) Dt. The vertical axis shows the taxonomic affi liation and number of phylotypes found in the respective clone libraries (32 archaeal phylotypes in total). Table S1. Bacterial phylotypes Phylotype Phylum order/family/ Clone No. Accession Nos. 1 Proteobacteria Shewanella 3 AB266937 2 Proteobacteria Pseudomonadaceae 11 AB267034 3 Proteobacteria Pseudomonadaceae 4 AB266924 4 Proteobacteria Methylomonas 1 AB291318 5 Proteobacteria Comamonadaceae 1 AB291335 6 Proteobacteria Comamonadaceae 1 AB291475 7 Proteobacteria Comamonadaceae 1 AB291302 8 Proteobacteria Comamonadaceae 1 AB291350 9 Proteobacteria Oxalobacteraceae 3 AB267030 10 Proteobacteria Rhodocyclales 5 AB266971 11 Proteobacteria Nitrosomonadales 1 AB291304 12 Proteobacteria Methylophilales 1 AB291418 13 Proteobacteria Methylophilales 2 AB291303 14 Proteobacteria Moraxellaceae 1 AB291292 15 Proteobacteria Rhodobacterales 2 AB266935 16 Proteobacteria Rhodobacterales 8 AB267060 17 Proteobacteria Rhodobacterales 1 AB291362 18 Proteobacteria Sphingomonadales 1 AB291340 19 Proteobacteria Alphaproteobacteria 1 AB291323 20 Proteobacteria Rhodospirillaceae 1 AB291301 21 TM6 7 AB266920 22 TM6 1 AB267027 23 Proteobacteria Sytrophobacteraceae 27 AB266947 24 Proteobacteria Sytrophobacteraceae 15 AB266958 25 Proteobacteria Sytrophobacteraceae 10 AB266997 26 Proteobacteria Sytrophobacteraceae 24 AB266942 27 Proteobacteria Sytrophobacteraceae 14 AB267023 28 Proteobacteria Sytrophobacteraceae 1 AB291342 29 Proteobacteria Group TA-1 3 AB266988 30 Proteobacteria Group TA-1 4 AB266983 31 Proteobacteria Group TA-1 1 AB291417 32 Proteobacteria Group TA-1 1 AB291496 33 Proteobacteria Group TA-1 2 AB291497 34 Proteobacteria Group TA-1 1 AB291504 35 Proteobacteria Deltaproteobacteria 4 AB266979 36 Proteobacteria Deltaproteobacteria 1 AB291314 37 Proteobacteria Syntrophaceae 5 AB267013 38 Proteobacteria Syntrophaceae 2 AB291493 39 Proteobacteria Syntrophaceae 1 AB291416 40 Proteobacteria Syntrophaceae 1 AB291491 41 Proteobacteria Syntrophaceae 5 AB267063 42 Proteobacteria Syntrophaceae 1 AB291481 43 Proteobacteria Syntrophaceae 1 AB291509 44 Proteobacteria Syntrophaceae 2 AB291380 45 Proteobacteria Syntrophaceae 5 AB267042 46 Proteobacteria Syntrophaceae 4 AB267005 Table S1 (continued). 47 Proteobacteria Myxococcales 2 AB267052 48 Proteobacteria Myxococcales 2 AB291397 49 Proteobacteria Myxococcales 1 AB266946 50 Proteobacteria Myxococcales 2 AB291370 51 Proteobacteria Bdellovibrionales 6 AB267045 52 Proteobacteria Desulfuromonadales 28 AB266993 53 Proteobacteria Desulfuromonadales 5 AB266989 54 Proteobacteria Desulfuromonadales 5 AB267053 55 Proteobacteria Desulfovibrionales 5 AB266926 56 Proteobacteria Desulfovibrionales 1 AB291366 57 Proteobacteria Desulfovibrionales 2 AB291465 58 Proteobacteria Desulfovibrionales 3 AB291293 59 Proteobacteria Campylobacteraceae 20 AB266960 60 Proteobacteria Campylobacteraceae 1 AB291449 61 Proteobacteria Epsilonproteobacteria 8 AB266932 62 Proteobacteria Epsilonproteobacteria 1 AB291286 63 Gemmatimonadetes 1 AB291371 64 unidentified 4 AB266992 65 unidentified 3 AB266955 66 Caldothrix 1 AB291312 67 KSB3 7 AB266941 68 KSB3 14 AB266927 69 Bacteroidales 1 AB291443 70 Bacteroidetes Bacteroidales 2 AB291388 71 Bacteroidetes Bacteroidales 1 AB291281 72 Bacteroidetes Bacteroidales 1 AB291479 73 Bacteroidetes Bacteroidales 2 AB267035 74 Bacteroidetes Bacteroidales 4 AB267041 75 Bacteroidetes Bacteroidales 1 AB291494 76 Bacteroidetes Bacteroidales 1 AB291501 77 Bacteroidetes Bacteroidales 1 AB291368 78 Bacteroidetes Bacteroidales 1 AB291403 79 Bacteroidetes Bacteroidales 13 AB267007 80 Bacteroidetes Bacteroidales 9 AB267020 81 Bacteroidetes Bacteroidales 1 AB291354 82 Bacteroidetes Bacteroidales 1 AB291440 83 Bacteroidetes Bacteroidales 1 AB291305 84 Bacteroidetes Bacteroidales 1 AB372571 85 Bacteroidetes Bacteroidales 27 AB266939 86 Bacteroidetes Bacteroidales 1 AB291445 87 Bacteroidetes Bacteroidales 2 AB291343 88 Bacteroidetes Bacteroidales 7 AB266999 89 Bacteroidetes Bacteroidales 1 AB291484 90 Bacteroidetes Bacteroidales 14 AB267044 91 Bacteroidetes Bacteroidales 2 AB291487 92 Bacteroidetes Bacteroidales 1 AB291322 93 Bacteroidetes Bacteroidales 7 AB267006 94 Bacteroidetes Bacteroidales 1 AB291457 Table S1 (continued). 95 Bacteroidetes Bacteroidales 6 AB267038 96 Bacteroidetes Bacteroidales 1 AB291495 97 Bacteroidetes Bacteroidales 1 AB291328 98 Bacteroidetes Bacteroidales 1 AB291309 99 Bacteroidetes Bacteroidales 2 AB291319 100 Bacteroidetes Bacteroidales 1 AB291435 101 Bacteroidetes Bacteroidales 1 AB291500 102 Bacteroidetes Bacteroidales 4 AB267061 103 Bacteroidetes Bacteroidales 1 AB291410 104 Bacteroidetes Bacteroidales 1 AB291344 105 Bacteroidetes Bacteroidales 1 AB291373 106 Bacteroidetes Bacteroidales 2 AB291512 107 Bacteroidetes Bacteroidales 1 AB291541 108 Bacteroidetes Bacteroidales 1 AB291538 109 Bacteroidetes Flavobacteriales 1 AB291339 110 Bacteroidetes Flavobacteriales 1 AB291334 111 Bacteroidetes Flavobacteriales 1 AB291300 112 Bacteroidetes Flavobacteriales 1 AB291429 113 Bacteroidetes Flexibacteraceae 3 AB266943 114 Nitrospira 96 AB266934 115 Nitrospira 1 AB291326 116 Verrucomicrobia-Chlamydiae 2 AB291299 117 Verrucomicrobia-Chlamydiae 1 AB291409 118 Verrucomicrobia-Chlamydiae 2 AB291391 119 Verrucomicrobia-Chlamydiae 1 AB291331 120 Verrucomicrobia-Chlamydiae 1 AB291539 121 Verrucomicrobia-Chlamydiae 1 AB291382 122 Verrucomicrobia-Chlamydiae 2 AB291423 123 Verrucomicrobia-Chlamydiae 1 AB291317 124 Planctomycetes 1 AB291455 125 Planctomycetes 1 AB291537 126 Planctomycetes 3 AB267012 127 Planctomycetes 1 AB291534 128 Planctomycetes 4 AB266921 129 Planctomycetes 1 AB291516 130 unidentified 4 AB266976 131 unidentified 1 AB291420 132 Acidobacteria 13 AB266922 133 Acidobacteria 1 AB267019 134 Acidobacteria 1 AB291434 135 Acidobacteria 1 AB291529 136 OS-K 3 AB266995 137 OP8 1 AB291385 138 unidentified 13 AB266952 139 NKB19 1 AB267067 140 NKB19 1 AB266925 141 unidentified 1 AB291279 142 unidentified 12 AB266986 Table S1 (continued). 143 Actinobacteridae 11 AB266950 144 Actinobacteria Cellulomonadaceae 2 AB291432 145 Actinobacteria Cellulomonadaceae 1 AB291424 146 Actinobacteria Propionibacterineae 57 AB266973 147 Actinobacteria Propionibacterineae 1 AB291473 148 Actinobacteria Propionibacterineae 1 AB291337 149 Actinobacteria Propionibacterineae 9 AB267014 150 Actinobacteria Propionibacterineae 5 AB267028 151 Actinobacteria Propionibacterineae 2 AB291363 152 Actinobacteria Propionibacterineae 2 AB291271 153 Actinobacteria Propionibacterineae 1 AB291438 154 Actinobacteria Rubrobacteridae 3 AB267039 155 Actinobacteria Rubrobacteridae 2 AB291482 156 Actinobacteria Rubrobacteridae 1 AB291480 157 Actinobacteria Rubrobacteridae 2 AB266969 158 Actinobacteria Rubrobacteridae 1 AB291327 159 Actinobacteria Rubrobacteridae 1 AB291428 160 Actinobacteria Coriobacteridae 1 AB291399 161 Spirochaetes Spirochaetaceae 20 AB266977 162 Spirochaetes Spirochaetaceae 5 AB267057 163 Spirochaetes Spirochaetaceae 1 AB291294 164 Spirochaetes Spirochaetaceae 5 AB267062 165 Spirochaetes Spirochaetaceae 4 AB266940 166 Spirochaetes Spirochaetaceae 1 AB291533 167 Spirochaetes Spirochaetaceae 1 AB291525 168 Spirochaetes Spirochaetaceae 2 AB267022 169 Spirochaetes Spirochaetaceae 1 AB291448 170 Spirochaetes Spirochaetaceae 3 AB267011 171 Spirochaetes Spirochaetaceae 2 AB291275 172 Spirochaetes Spirochaetaceae 1 AB291384 173 Spirochaetes Spirochaetaceae 2 AB291347 174 Spirochaetes 1 AB291510 175 Spirochaetes 1 AB291321 176 Spirochaetes 2 AB291486 177 Spirochaetes Leptospiraceae 2 AB291514 178 Spirochaetes Leptospiraceae 1 AB291348 179 Spirochaetes Leptospiraceae 4 AB267009 180 Spirochaetes Leptospiraceae 1 AB291413 181 Chlorobi 4 AB267051 182 Chlorobi 14 AB266987 183 Chlorobi 2 AB266953 184 Chlorobi 1 AB291264 185 Chlorobi 1 AB291283 186 Chlorobi 2 AB266928 187 Chloroflexi Anaerolineae 5 AB267065 188 Chloroflexi Anaerolineae 3 AB267008 189 Chloroflexi Anaerolineae 2 AB291361 190 Chloroflexi Anaerolineae 6 AB267066 Table S1 (continued). 191 Chloroflexi Anaerolineae 4 AB266980 192 Chloroflexi Anaerolineae 1 AB291433 193 Chloroflexi Anaerolineae 1 AB291349 194 Chloroflexi Anaerolineae 2 AB291376 195 Chloroflexi Anaerolineae 1 AB291341 196 Chloroflexi Anaerolineae 2 AB291313 197 Chloroflexi Anaerolineae 2 AB291351 198 Chloroflexi Anaerolineae 3 AB267002 199 Chloroflexi Anaerolineae 1 AB291296 200 Chloroflexi Anaerolineae 1 AB291401 201 Chloroflexi Anaerolineae 4 AB266985 202 Chloroflexi Anaerolineae 1 AB291290 203 Chloroflexi Anaerolineae 1 AB291330 204 Chloroflexi Anaerolineae 1 AB291285 205 Chloroflexi Anaerolineae 1 AB291288 206 Chloroflexi Anaerolineae 1 AB291372 207 Chloroflexi Anaerolineae 1 AB291498 208 Chloroflexi Anaerolineae 7 AB266972 209 Chloroflexi Anaerolineae 11 AB266968 210 Chloroflexi Anaerolineae 4 AB266990 211 Chloroflexi Anaerolineae 4 AB266991 212 Chloroflexi Anaerolineae 1 AB291400 213 Chloroflexi Anaerolineae 11 AB266975 214 Chloroflexi Anaerolineae 2 AB291352 215 Chloroflexi Anaerolineae 1 AB291377 216 Chloroflexi Anaerolineae 2 AB291274 217 Chloroflexi Anaerolineae 2 AB291345 218 Chloroflexi Anaerolineae 4 AB266962 219 Chloroflexi Anaerolineae 1 AB291490 220 Chloroflexi Anaerolineae 1 AB291392 221 Chloroflexi Anaerolineae 2 AB291436 222 Chloroflexi Anaerolineae 1 AB291269 223 Chloroflexi Anaerolineae 1 AB291310 224 Chloroflexi Anaerolineae 7 AB266967 225 Chloroflexi Anaerolineae 1 AB291367 226 Chloroflexi Anaerolineae 4 AB266998 227 Chloroflexi Anaerolineae 2 AB291357 228 Chloroflexi Anaerolineae 10 AB266966 229 Chloroflexi Anaerolineae 2 AB291426 230 Chloroflexi Anaerolineae 1 AB291346 231 Chloroflexi Anaerolineae 2 AB291291 232 Chloroflexi Anaerolineae 4 AB266994 233 Chloroflexi Anaerolineae 1 AB291338 234 Chloroflexi Anaerolineae 1 AB291306 235 Chloroflexi Anaerolineae 1 AB291355 236 Chloroflexi Anaerolineae 1 AB291329 237 Chloroflexi Anaerolineae 1 AB291308 238 Chloroflexi Anaerolineae 1 AB291394 Table S1 (continued). 239 Chloroflexi Anaerolineae 2 AB291360 240 Chloroflexi Anaerolineae 2 AB291295 241 Chloroflexi Anaerolineae 1 AB291316 242 Chloroflexi Chloroflexi subphylum I 3 AB266984 243 OP9 2 AB291499 244 OP9 9 AB266981 245 Firmicutes Lachnospiraceae 3 AB266996 246 Firmicutes Lachnospiraceae 1 AB291528 247 Firmicutes Lachnospiraceae 1 AB291471 248 Firmicutes Lachnospiraceae 1 AB291451 249 Firmicutes Lachnospiraceae 1 AB291461 250 Firmicutes Lachnospiraceae 2 AB291265 251 Firmicutes Lachnospiraceae 1 AB291407 252 Firmicutes Lachnospiraceae 1 AB291381 253 Firmicutes Lachnospiraceae 3 AB267037 254 Firmicutes Lachnospiraceae 1 AB291458 255 Firmicutes Lachnospiraceae 1 AB291466 256 Firmicutes Lachnospiraceae 2 AB291459 257 Firmicutes Lachnospiraceae 1 AB291402 258 Firmicutes Lachnospiraceae 2 AB291518 259 Firmicutes Lachnospiraceae 1 AB291446 260 Firmicutes Lachnospiraceae 1 AB291474 261 Firmicutes Lachnospiraceae 1 AB291277 262 Firmicutes Lachnospiraceae 3 AB266931 263 Firmicutes Lachnospiraceae 1 AB291467 264 Firmicutes Lachnospiraceae 1 AB291289 265 Firmicutes Lachnospiraceae 3 AB267021 266 Firmicutes Lachnospiraceae 2 AB291444 267 Firmicutes Lachnospiraceae 1 AB291472 268 Firmicutes Lachnospiraceae 1 AB291263 269 Firmicutes Lachnospiraceae 1 AB291536 270 Firmicutes Lachnospiraceae 1 AB291507 271 Firmicutes Lachnospiraceae 3 AB267001 272 Firmicutes Lachnospiraceae 1 AB291469 273 Firmicutes Lachnospiraceae 2 AB291521 274 Firmicutes Lachnospiraceae 1 AB291332 275 Firmicutes Lachnospiraceae 2 AB267054 276 Firmicutes Lachnospiraceae 1 AB291492 277 Firmicutes Lachnospiraceae 1 AB291511 278 Firmicutes Lachnospiraceae 1 AB291280 279 Firmicutes Clostridiaceae 1 AB291456 280 Firmicutes Clostridiaceae 6 AB266938 281 Firmicutes Clostridiaceae 1 AB291268 282 Firmicutes Clostridiaceae 1 AB291273 283 Firmicutes 3 AB267055 284 Firmicutes 3 AB267043 285 Firmicutes 2 AB291430 286 Firmicutes 1 AB291535 Table S1 (continued). 287 Firmicutes 2 AB291515 288 Firmicutes 1 AB291447 289 Firmicutes 1 AB291530 290 Firmicutes 3 AB291506 291 Firmicutes 1 AB291532 292 Firmicutes 10 AB267016 293 Firmicutes 1 AB291393 294 Firmicutes 2 AB291513 295 Firmicutes 2 AB291386 296 Firmicutes 8 AB267031 297 Firmicutes 10 AB267059 298 Firmicutes 1 AB291524 299 Firmicutes 1 AB291476 300 Firmicutes 1 AB291411 301 Firmicutes 3 AB266929 302 Firmicutes 1 AB291453 303 Firmicutes 1 AB291527 304 Firmicutes 1 AB291284 305 Firmicutes 1 AB291517 306 Firmicutes Peptostreptococcaceae 3 AB267056 307 Firmicutes Peptostreptococcaceae 1 AB291463 308 Firmicutes Peptostreptococcaceae 1 AB291406 309 Firmicutes Peptostreptococcaceae 1 AB291454 310 Firmicutes Peptostreptococcaceae 1 AB291488 311 Firmicutes Peptostreptococcaceae 1 AB291389 312 Firmicutes Peptostreptococcaceae 1 AB291287 313 Firmicutes Peptostreptococcaceae 2 AB291307 314 Firmicutes Peptostreptococcaceae 1 AB291442 315 Firmicutes Peptostreptococcaceae 1 AB291333 316 Firmicutes Peptostreptococcaceae 1 AB291503 317 Firmicutes Peptostreptococcaceae 1 AB291282 318 Firmicutes 12 AB267033 319 Firmicutes 3 AB267049 320 Firmicutes 2 AB291412 321 Firmicutes 1 AB291383 322 Firmicutes 16 AB267032 323 Firmicutes 10 AB266923 324 Firmicutes 1 AB291387 325 Firmicutes 4 AB267003 326 Firmicutes 2 AB291375 327 Firmicutes 1 AB291526 328 Firmicutes 1 AB291415 329 Firmicutes 1 AB291374 330 Firmicutes 4 AB267036 331 Firmicutes Lactobacillales 1 AB291427 332 Firmicutes Lactobacillales 1 AB291365 333 Firmicutes Lactobacillales 8 AB266930 334 Firmicutes Lactobacillales 1 AB291356 Table S1 (continued). 335 Firmicutes 4 AB267029 336 Firmicutes 1 AB291395 337 Firmicutes 1 AB291478 338 Firmicutes Acidaminococcaceae 1 AB291464 339 Firmicutes Acidaminococcaceae 2 AB291398 340 Firmicutes Acidaminococcaceae 2 AB291272 341 Firmicutes Acidaminococcaceae 2 AB291324 342 Firmicutes Acidaminococcaceae 1 AB291414 343 Firmicutes Acidaminococcaceae 1 AB291325 344 Firmicutes Acidaminococcaceae 1 AB291298 345 Firmicutes Acidaminococcaceae 1 AB291336 346 Firmicutes Syntrophomonadaceae 1 AB291477 347 Firmicutes Syntrophomonadaceae 2 AB291422 348 Firmicutes 6 AB266944 349 Firmicutes 1 AB291531 350 Caldicellulosiruptor 1 AB291315 351 OD2 3 AB266956 352 OD2 1 AB291441 353 OD2 1 AB291267 354 OD2 1 AB291278 355 WS6 1 AB291540 356 WS6 1 AB372572 357 TM7 1 AB291369 358 TM7 1 AB291437 359 Termite group I 2 AB291452 360 Termite group I 1 AB291483 361 unidentified 1 AB266954 362 unidentified 1 AB291405 363 OP10 1 AB291431 364 OP10 1 AB291379 365 OP10 1 AB291320 366 OP10 1 AB291358 367 OP10 1 AB291353 368 Deferribacteres 8 AB267058 369 Deferribacteres 9 AB267040 370 Deferribacteres 1 AB291470 371 Deferribacteres 2 AB291450 372 Deferribacteres 1 AB291460 373 Deferribacteres 10 AB266951 374 Deferribacteres 2 AB291297 375 Deferribacteres 2 AB291419 376 Deferribacteres 1 AB291270 377 Deferribacteres 20 AB267024 378 Deferribacteres 1 AB291519 379 Deferribacteres 2 AB291364 380 Deferribacteres 1 AB291390 381 Deferribacteres 1 AB291408 382 Thermotogae 4 AB267010 Table S2. Archaeal phylotypes Phylotype class order/family Clone No. Accession No. 1 Metanomicrobia Methanosaetaceae 267 AB266919 2 Metanomicrobia Methanosaetaceae 19 AB266894 3 Metanomicrobia Methanosaetaceae 12 AB266904 4 Metanomicrobia Methanosaetaceae 2 AB291247 5 Metanomicrobia Methanosaetaceae 1 AB291248 6 Metanomicrobia Methanosaetaceae 50 AB266892 7 Metanomicrobia Methanosarcinaceae 3 AB266912 8 Metanomicrobia Methanosarcinaceae 1 AB291255 9 Metanomicrobia Methanosarcinaceae 4 AB266896 10 Metanomicrobia Methanosarcinaceae 6 AB266905 11 Metanomicrobia Methanomicrobiales 4 AB266889 12 Metanomicrobia Methanomicrobiales 35 AB266893 13 Metanomicrobia Methanomicrobiales 11 AB266914 14 Metanomicrobia Methanomicrobiales 16 AB266899 15 Metanomicrobia Methanomicrobiales 12 AB266908 16 Metanomicrobia Methanomicrobiales 1 AB291256 17 Metanomicrobia Methanomicrobiales 1 AB291258 18 Metanomicrobia Methanomicrobiales 1 AB291246 19 Metanomicrobia Methanomicrobiales 14 AB266907 20 Metanomicrobia Methanospirillaceae 5 AB266913 21 Metanomicrobia Methanocorpusculacea 1 AB291254 22 WSA2 3 AB266909 23 Methanobacteria Methanobacteriaceae 93 AB266900 24 Methanobacteria Methanobacteriaceae 10 AB266898 25 Methanobacteria Methanobacteriaceae 1 AB291249 26 Methanobacteria Methanobacteriaceae 31 AB266903 27 Methanobacteria Methanobacteriaceae 1 AB291257 28 Methanobacteria Methanobacteriaceae 6 AB266916 29 Methanobacteria Methanobacteriaceae 77 AB266897 30 Methanobacteria Methanobacteriaceae 32 AB266911 31 Methanobacteria Methanobacteriaceae 1 AB291253 32 Methanobacteria Methanobacteriaceae 1 AB291251