Alpha-I Alpha-II Alpha-III Alpha-IV Alpha-V Alpha-VI - Plos

89 81

79

82

FJ024324, clone 39

OTUb331 (4,6) KT748569, A10

OTUb473 (3,2)

EU491477, P0X4b2D12 DQ070833, JdFBGBact_73 X97691, Pedomicrobium manganicum ★ 96 X97693, Pedomicrobium australicum 76 100 OTUb222 (1) EU491718, EPR3968−O8a−Bc51 87 EF117253, Filomicrobium insigne 91 EU491581, EPR4059−B2−Bc81 100 OTUb311 (1) 93 HM127661, SINP713 88 KC682783, KiMba_C5 98 EU491656, EPR3970−MO1A−Bc69 92 89 OTUb483 (1) EU491704, EPR3968−O8a−Bc36 98 AB794104, Methyloceanibacter caenitepidi AY186071, EA1B4 98 51 EU491557, EPR4059-B2-Bc55 OTUb609 (3,2) 79 JX226796, NAB82 99 100 OTUb24 (8,1) EU491603, EPR3970−MO1A−Bc18 87 FJ024326, 8 98 85 OTUb221 (9) DQ070827, JdFBGBact_40 56 OTUb642 (2) 87 EU491636, EPR3970−MO1A−Bc5 88 OTUb500 (3,2) 100 EU491212, P9X2b7G10 AM997334, Ucm1508 89 EU491413, P0X4b3E05 54 100 OTUb368 (1) including Hyphomicrobiaceae, AM498744, Nitratireductor kimnyeongensis 87 AY598817, Hoeflea marina 70 Phyllobacteriaceae CP003358, Mesorhizobium australicum 79 and Rhodobiaceae EU491593, EPR4059−B2−Bc92 100 OTUb41 (3) OTUb501 (1) 83 100 OTUb584 (1) EU373869, HCM3MC80_7C_FL AWXZ01000027, Lutibaculum baratangense 72 GQ272328, Breoghania corrubedonensis 77 97 OTUb590 (2) EU491605, EPR3970−MO1A−Bc2 97 AM712634, Anderseniella baltica 92 OTUb259 (1) 91 KC682112, FLOCS_1301A−Basalt_A11 54 JN232991, IMS2R49 71 100 KT748580, C01 OTUb440 (1) 100 OTUb476 (1) JX227257, NCB220 57 97 KT748603, E10 OTUb252 (1) 100 JQ516560, 0907_Mf_HT3_B5 JQ678368, JdFBHP54 88 OTUb314 (1) 100 GU726974, SA_NR7_, SA_NR7_3 76 100 OTUb213 (1) JN233034, OS3BR46 99 EU491178, P9X2b7B12 100 KC534242, Citreicella manganoxidans ★ EU928765, Citreicella marina 98 DQ412071, Sulfitobacter sp. SPB−1 ★ 98 99 DQ223017, Roseobacter sp. AzwK−3b ★ JQ390520, Roseovarius litoreus DQ412059, Roseobacter sp. LOB−8 ★ 80 JQ844756, Thioclava dalianensis 92 CP004393, Celeribacter indicus 100 AAMT01000002, Maritimibacter alkaliphilus 91 OTUb275 (1) 85 100 GU302485, Out12bac60 EU491756, EPR3968−O8a−Bc89 63 100 OTUb145 (1) AWFH01000061, Hyphomonas atlantica 66 OTUb104 (1) 94 JN530600, SBZO_2028 100 JN233104, OS3SR5 96 KC682298, FLOCS_1301A−GWBasalt_H10 100 AB265822, Thalassospira tepidiphila OTUb143 (8) 51 98 OTUb120 (1) including Caulobacteraceae AB252199, Methylobacterium nodulans 100 and Kiloniellaceae 100 AY683045, Methylobacterium oryzae EU491830, EPR3967−O2−Bc84 100 OTUb315 (1) AY649762, Martelella mediterranea 97 U53824, Aurantimonas manganoxydans ★ 81 EF516517, FCPP475 84 100 GQ346863, SGPZ460 OTUb3 (1) 96 93 OTUb569 (1) 84 OTUb664 (7) 100 HM798941, PRTBB8505 CP002008, Caulobacter segnis 91 OTUb144 (1) 100 AF131295, Sphingomonas aquatilis OTUb530 (1,22) 100 AJ012461, Sphingomonas echinoides OTUb666 (1) 18 AY250869, FBP255 OTUb602 (3) 96 91 OTUb350 (1) 91 AY706935, Erythrobacter vulgaris 100 AF325445, Erythrobacter sp. SD−21 ★ including Sphingomonadaceae OTUb436 (3) 98 KJ870094, Erythrobacter sp. S−5 ★ 100 and Erythrobacteraceae 85 OTUb515 (1) GU061603, CE2−DCM−87 81 JF459982, Novosphingobium panipatense 53 ATUR01000005, Sphingopyxis baekryungensis AB524074, Parasphingopyxis lamellibrachiae 92 100 OTUb173 (1) JX879042, Postplume−III−1100m−003 86 AY162100, GMD21D06 95 EU491255, P9X2b2D09 96 EU491563, EPR4059−B2−Bc61 76 OTUb551 (1) 100 GU574708, Parvibaculum hydrocarboniclasticum 63 OTUb99 (1) 99 AB694249, OTU029_Xeno_Clone01 86 100 OTUb241 (1) AY682384, Kordiimonas gwangyangensis 94 including Kiloniellaceae, 100 OTUb633 (1) GU234715, SHFB1034 97 Kordiimonadaceae GQ903364, bore9 100 and Hyphomicrobiaceae AB474389, OC13S 100 100 OTUb262 (3) JX227116, NCB79 72 FJ746138, SPG12_343_353_B57 72 AB289439, Sneathiella glossodoripedis 98 DQ070828, JdFBGBact_41 98 OTUb559 (1,2) JX227094, NCB57 EU491852, EPR3965−I2−Bc30 99 OTUb634 (3) 98 JX227272, NCB235 OTUb626 (1) 84 100 OTUb69 (1) EU491648, EPR3970−MO1A−Bc60 95 100 OTUb399 (1) JF344387, OXIC−117 73 JF344637, ANOX−075 82 OTUb160 (1,1) GU118005, Acer_P06 100 85 FJ024323, clone 29 100 OTUb153 (1) EU491532, EPR4059-B2-Bc21 89 91 OTUb101 (1,1) EU373889, HCM3MC80_5D_FL OTUb109 (1) 78 OTUb185 (1) 86 86 OTUb102 (1) 90 AM997397, Ucm15282 KT748570, A12 98 EU491336, P9X2b2F07 97 100 OTUb31 (2,1) JF809788, RS−B96 78 OTUb586 (1) 99 HQ674346, F9P262000_S_B20 89 99 OTUb290 (1,1) FN553472, 251−33 83 100 OTUb445 (1) AB694211, OTU019_Common_Clone05 57 OTUb396 (1) 100 OTUb401 (3) EU236352, Hg91A9 GQ263965, WC2_50 OTUb162 (1) 99 OTUb297 (1) 87 KT748620, G11 99 FJ463255, Oceanibaculum pacificum 76 including Rhodospirillaceae 89 KC682820, KiMba_G7 DQ070812, 9NBGBact_80 99 OTUb600 (1) 92 99 OTUb579 (1) JX226888, NBB84 99 KT748606, F01 83 OTUb542 (1) 99 JQ516359, 0907_Mf_DT2_B71 90 OTUb55 (1) 99 FJ202709, SGUS651 95 96 OTUb267 (1) OTUb54 (1) 98 GU056079, DGS1−43 93 100 OTUb237 (1) EU491305, P9X2b8D09 73 100 OTUb329 (2) AM997739, Ucb1513 91 100 OTUb426 (1) JX227635, SCB163 77 100 OTUb376 (1,1) JN166353, HOT157_350m82 82 OTUb343 (1) 100 HQ673175, F9P41000_S_G24 99 87 OTUb648 (3) 80 AM997815, Ucb15153 EU491885, EPR3965−I2−Bc85 79 OTUb85 (1) 100 AM997870, Ucb15135 99 100 OTUb247 (1) OTUb499 (6,2) ● 96 92 OTUb198 (1) EU491883, EPR3965−I2−Bc83 97 DQ070832, JdFBGBact_66 85 GQ348193, SGSX1098 53 77 OTUb189 (2) 42 EU804840, 6C232806 AF510192, Pelagibacter ubique 95 82 OTUb379 (19) HQ674290, F9P261000_S_O24 90 100 OTUb233 (4) JQ678482, JdFBBkgd75 87 94 OTUb450 (3) OTUb554 (4) 96 DQ070781, 9NSWBact_2 91 97 OTUb621 (5) JN166304, HOT157_350m34 76 100 OTUb382 (1) 99 OTUb248 (5) 74 JN166299, HOT157_350m3 OTUb341 (4) 67 77 OTUb192 (2) HQ433381, 203−10−20 100 OTUb430 (2) 53 76 OTUb195 (4) 32 HQ674225, F9P261000_S_L14 OTUb273 (11) 97 98 OTUb663 (1) HQ433412, 191−2−09 76 99 OTUb538 (1) JN166266, HOT157_125m85 87 99 OTUb212 (6) 57 HM798902, PRTBB8456 95 JX879047, Postplume−III−1100m−014 OTUb640 (15) 85 OTUb516 (1) including Pelagibacteraceae 93 95 OTUb201 (3) 74 OTUb481 (1) 86 HQ672388, F9P4500_S_I16 98 OTUb87 (1) HQ673435, F9P41300_H05 100 OTUb485 (1) HQ433426, 211−17−24 77 OTUb577 (2) 93 GQ337189, CB1341b.50 OTUb532 (1) 100 OTUb525 (2) 93 DQ070785, 9NSWBact_10 89 DQ009261, SPOTSAUG01_5m781 88 AACY020487638, marine metagenome 100 OTUb133 (2) EU800729, 2C228907 99 OTUb325 (1) 78 82 GQ337303, NB2109b.27 95 OTUb620 (1) JX878932, Plumeprofile_1320m_084 61 OTUb190 (3) 100 JX879031, Prespill−800m−065 100 OTUb92 (3) HQ672365, F9P4500_S_H09 100 M73220, Anaplasma phagocytophilum OTUb183 (1) GU220759, ELSC−TVG13−B65 U00096, Escherichia coli CP000926, Pseudomonas putida 95

99

Alpha-I

Alpha-II

Alpha-III

Alpha-IV

Alpha-V

Alpha-VI

62

100 100

0.10

Fig. S3A

OTUb414 (1) JQ085819, W4−39b 97 EU491396, P0X3b5H04 100 OTUb306 (1) JX226764, NAB50 81 EU491591, EPR4059−B2−Bc90 98 KT748573, B04 77 94 EU491136, P9X2b3F03 92 EU491734, EPR3968−O8a−Bc67 OTUb302 (2) 89 OTUb469 (2,1) 99 AM997677, Ucp1487 94 OTUb384 (1) 81 OTUb228 (2) 78 AF317771, wb1_N15 99 100 OTUb74 (1) GU118825, Mfra_O14 56 OTUb459 (1) 57 95 OTUb594 (1) KC682610, TuiMs_LR3B1 84 DQ070808, 9NBGBact_71 94 100 EU491634, EPR3970−MO1A−Bc48 AB013830, NB1-i 85 GQ348094, SGST650 56 OTUb413 (1) Uncultured clone group 74 100EU491803, EPR3967−O2−Bc57 92 EU491229, P9X2b7C08 83 OTUb196 (1) 100 OTUb4 (1,2) 100 HQ674591, F9P262000_S_O19 100 AM997336, Ucm1577 100 OTUb657 (1) 95 DQ289938, LC1−13 OTUb383 (1) 92 99 AB013831, NB1-j OTUb286 (1,2) 99 EU491206, P9X2b7F08 OTUb15 (1) 80 100 OTUb95 (1) DQ070816, JdFBGBact_5 94 FJ024314, clone 2 EU491669, EPR3970−MO1A−Bc82 OTUb77 (1) 100 AM997788, Ucb15722 100 AJ233944, Kofleria flava 71 CP001804, Haliangium ochraceum KT748591, D05 OTUb616 (1) 100 OTUb56 (1) 100 AB694297, OTU044_Xeno_Clone01 97 AJ241020, Sva0679 95 OTUb447 (1) 97 EU050858, ss1_B_02_10 100 OTUb114 (1) 89 EF646143, N67e_155 Including Myxococcales AB847448, Vulgatibacter incomptus 85 AF382399, Anaeromyxobacter dehalogenans 96 DQ768119, Myxococcus virescens 99 OTUb91 (1) EF516099, FCPS738 100 OTUb474 (2) 97 JF344278, OXIC−008 57 OTUb261 (1) 100 OTUb477 (1) 83 JF809714, OMS−B65 OTUb210 (2) 64 EU491876, EPR3965−I2−Bc72 100 EU335390, BacC−u_043 75 OTUb540 (1) 100 OTUb296 (1) 100 EU050847, ss1_B_03_45 95 EF999343, TopBa4 Including Syntrophorhabdaceae 85 OTUb134 (1) 99 FN553502, 251−63 58 EF019725, Elev_16S_895 90 AB212873, Syntrophorhabdus aromaticivorans 100 OTUb139 (1) 100 HQ673051, F9P26500_S_P16 HM799022, PRTBB8612 99 Y11560, Desulfuromonas thiophila 95 U13928, Geobacter sulfurreducens 94 OTUb323 (1) 69 AB015549, BD3−7 98 EU491262, P9X2b2F12 81 AM997297, Ucm1535 OTUb48 (1) 79 97 KT748574, B05 94 KT748617, G08 OTUb234 (1,1) OTUb393 (1,1) 100 100 HM186019, HDB_SIOI924 80 OTUb494 (5) 84 OTUb508 (8) ● Uncultured clone group 100 DQ070830, JdFBGBact_43 90 EU491889, EPR3965−I2−Bc9 69 AB015242, JTB36 74 KT748563, A02 OTUb26 (3) 90 OTUb587 (2) 86 EU491265, P9X2b2H03 16 OTUb480 (15) 98 HQ674070, F9P261000_S_D02 100 OTUb174 (2) 96 U65908, Sar324 98 U65915, Sar276 95 OTUb220 (1) Uncultured clone group 98 AM997291, Ucm15292 99 EU491257, P9X2b2D12 100 FJ024327, clone 17 68 AJ240985, Sva0853 95 OTUb650 (1,2) 100 EU491606, EPR3970−MO1A−Bc20 69 JF809700, OMS−B31 OTUb50 (1) 94 100 OTUb580 (1) 71 JF809778, RS−B81 100 HM187394, HDB_SISU460 OTUb461 (1) 96 OTUb93 (1) 98 99 FM253681, H08−2 Uncultured clone group 99 KT748609, F04 OTUb181 (1) 86 OTUb495 (1) OTUb36 (1) 74 100 EU803844, 5C231481 43 FN396792, s5_0_V_10 JF344113, RODAS−135 92 AF418174, Desulfoarculus baarsii 82 AY651787, Syntrophobacter sulfatireducens 95 AF084854, Halobacteriovorax marinus 78 FR733673, Desulfobacter hydrogenophilus 84 CP000252, Syntrophus aciditrophicus 52 AJ292759, Bdellovibrio bacteriovorus 78 JQ612313, GBc108 100 HE817854, B5/GW947 76 OTUb338 (1) 98 AB353727, Desulfovibrio marinisediminis 100 DQ067421, Desulfohalobium utahense 100 OTUb407 (1) 56 EU735031, 127D70 100 EU491652, EPR3970−MO1A−Bc65 96 KT748625, H09 including Desulfovibrionaceae 100 OTUb443 (1) and Desulfurellaceae 84 KF827172, C−30−40 OTUb592 (1) 100 FJ905618, V19F5b 95 X72768, Desulfurella acetivorans 100 Y18292, Hippea maritima 100 OTUb171 (1) AY212738, 43ds5 55 EU491797, EPR3967-O2-Bc51 96 89 OTUb573 (4) AB021390, Curvibacter lanceolatus 100 59 OTUb225 (9) 97 OTUb408 (1) GQ140326, Delftia tsuruhatensis 100 100 OTUb352 (12) EU491323, P9X2b8C04 85 98 L33975, Leptothrix discophora ★ AEWG01000018, Rubrivivax benzoatilyticus 65 AY152824, Schlegelella thermodepolymerans 93 AB008801, Caldimonas manganoxidans ★ 72 HM798755, PRTAB7873 97 HQ773090, ELU0072−T477−S−NIPCRAMgANa_000153 OTUb667 (1) 99 83 OTUb298 (1) 100 OTUb385 (2) KC682321, FLOCS_1301A−GWPyrrhotite_H02 94 EU491796, EPR3967−O2−Bc49 84 AB681840, Derxia gummosa 87 81 OTUb489 (6) 85 OTUb668 (1) EU046556, Herbaspirillum huttiense 100 OTUb118 (7) JF496359, Massilia niastensis 58 79 OTUb361 (1) JN825219, DB60 100 94 OTUb377 (8,3) ● 76 OTUb46 (1) 71 KT748612, F10 98 EU491484, P0X4b2G08 DQ070800, 9NBGBact_38 97 CP000103, Nitrosospira multiformis U00096, Escherichia coli 100

Delta-I

Delta-II

Delta-III

Delta-V

Delta-VI

Delta-VII

Betaproteobacteria

0.10

Fig. S3B

Deltaproteobacteria

Delta-IV

OTUb165 (1) EU491211, P9X2b7G09 OTUb327 (1) KC682565, ABEba_2G2

92 95 73

OTUb58 (1)

94

EU491327, P9X2b8F07 100

OTUb643 (1)

EU491716, EPR3968−O8a−Bc49 JX227012, NBB208 OTUb66 (1) 98 EU491588, EPR4059−B2−Bc88 93 KT748582, C06 JX227240, NCB203 OTUb585 (1) 95 OTUb658 (1) 79 OTUb70 (1) 98 EU925872, 075F59 100 OTUb660 (1) 96 HM186130, HDB_SION1845 OTUb257 (1) EU044049, GASP−38KA−2−B01 88 EU491582, EPR4059−B2−Bc82 100 OTUb429 (1) 97 JQ579887, FII−TR092 OTUb256 (1) OTUb16 (1) 88 JX227321, SAB44 JN534585, SBZP_2813 86 OTUb142 (1) 94 JQ738927, SA_91 89 OTUb636 (2) including Coxiellaceae EU491542, EPR4059−B2−Bc36 100 OTUb106 (1) AM997495, Ulrdd_31 OTUb152 (1) 98 EU491490, P0X4b2H11 90 OTUb320 (1) 100 AACY023938188, marine metagenome 100 AHBH01000049, SAR86B 96 OTUb583 (1) 100 EU804827, 6C232792 89 OTUb340 (1) 100 AACY020398456, marine metagenome 100 GU474871, HF0130_23I23 100 OTUb11 (1) GU474891, HF4000_19M20 100 OTUb88 (3) 72 AJXC01067752, marine metagenome 90 OTUb364 (1) 86 KF798864, Woods−Hole_a4801 HQ241801, Sp02sw−22 99 AE016828, Coxiella burnetii OTUb229 (1) 88 EU491758, EPR3968−O8a−Bc91 96 OTUb470 (1) JX227284, SAB7 77 OTUb291 (1) 90 HE602882, YCaltP2E5 91 EU491737, EPR3968−O8a−Bc70 100 OTUb47 (1) 91 EU925916, 152H67 100 OTUb535 (2) 100 JQ678490, JdFBBkgd84 81 EU124668, Thioalkalibacter halophilus 99 OTUb34 (2) 90 AM997859, Ucb15697 93 OTUb83 (7,2) ● 99 JX227348, SAB71 98 KT748583, C08 88 EU491620, EPR3970−MO1A−Bc34 98 EU491197, P9X2b7E06 85 OTUb186 (2) OTUb511 (4) 78 EU491644, EPR3970−MO1A−Bc57 84 EU491366, P0X3b1B11 79 FJ024322, clone 14 88 OTUb319 (11,6) ● 94 DQ070815, JdFBGBact_3 96 OTUb258 (1) 100 EU491395, P0X3b5H03 95 KT748621, G12 76 OTUb310 (2) 95 EU491709, EPR3968−O8a−Bc42 89 DQ070798, 9NBGBact_23 77 OTUb348 (21,9) ● 78 JF344160, PET−036 AM997712, Ucs1544 100 DQ070821, JdFBGBact_18 79 OTUb567 (1) 96 FN553623, 285−43 EU491248, P9X2b2A08 89 OTUb333 (3) 93 JX227697, SCB225 99 EU491862, EPR3965−I2−Bc47 96 OTUb140 (1) 95 OTUb12 (5) 81 EU491609, EPR3970−MO1A−Bc24 Uncultured clone group 100 OTUb388 (1) 99 EU491745, EPR3968−O8a−Bc78 93 AM997418, Ucn1569 OTUb346 (1) HQ191008, WS322JS0307 86 JF344135, PET−011 84 OTUb116 (1) 100 OTUb514 (1) 89 EU491622, EPR3970−MO1A−Bc36 100 AM997951, Ucc15542 98 OTUb75 (1) 99 EU491633, EPR3970−MO1A−Bc47 97 OTUb317 (3,6) 89 GQ351153, J8P41000_1C02 59 OTUb389 (1) OTUb5 (1) 100 OTUb263 (4) 77 FN553487, 251−48 99 KT748615, G03 EU491545, EPR4059−B2−Bc39 99 OTUb606 (1,2) 74 EU491162, P9X2b7A04 87 OTUb232 (2) 100 HQ674079, F9P261000_S_D15 99 DQ009470, SPOTSMAY03_890m27 91 HQ673503, F9P41300_L15 96 OTUb630 (1) 51 KF799085, Woods−Hole_a5523 95 AAVT01000006, HTCC2143 94 OTUb558 (1) ATUS01000006, Spongiibacter tropicus 100 OTUb404 (1) 90 JX193306, D10902 JX226953, NBB149 99 OTUb539 (2) EU491750, EPR3968−O8a−Bc82 78 AUHJ01000047, Haliea salexigens 100 OTUb561 (1) 99 AM997950, Ucc1553 86 DQ070803, 9NBGBact_52 100 OTUb543 (1) 80 AB015537, BD2−7 including Spongiibacteraceae 99 OTUb460 (1) and Halieaceae 82 JQ678498, JdFBBkgd93 96 OTUb578 (1) 94 DQ351741, Belgica2005/10−120−6 100 EU491768, EPR3967−O2−Bc19 90 OTUb339 (2) 89 HM126898, SINI513 OTUb151 (1) 100 FM242420, 27 T12d−oil 77 EU491863, EPR3965−I2−Bc49 70 EU491902, EPR4055-N3-Bc22 80 CP007441, Pseudomonas stutzeri 97 OTUb194 (1) 94 CP007511, Pseudomonas balearica 97 EU491936, EPR4055-N3-Bc77 73 DQ412061, Pseudomonas sp. LOB−2 ★ EU491919, EPR4055-N3-Bc51 93 OTUb610 (3) 97 CP007152, Marinobacter salarius 100 DQ412064, Marinobacter sp. LOB−4 ★ 99 OTUb517 (2) AB617557, Marinobacter alkaliphilus 100 AB626730, Maricurvus nonylphenolicus 84 AB809161, Pseudomaricurvus alkylphenolicus 94 FJ203036, SHFG417 OTUb159 (1) 95 EU491790, EPR3967−O2−Bc43 86 CP000282, Saccharophagus degradans including Alteromonadaceae 100 DQ412068, Microbulbifer sp. KBB−1 78 AF500006, Microbulbifer elongatus and Alcanivoracaceae 89 OTUb124 (2,1) 78 OTUb627 (6) 100 JX227004, NBB200 64 EU491424, P0X4b3F12 69 EU491951, EPR4055-N3-Bc92 99 AF328762, Alcanivorax venustensis 81 OTUb613 (7) 100 EU536675, nbt249b03 95 CP003466, Alcanivorax dieselolei 98 OTUb242 (1) GU166134, Psychrobacter sp. BSw20963B 100 KJ475196, Psychrobacter submarinus 99 OTUb607 (2) 98 AB016057, Psychrobacter pacificensis 98 OTUb113 (2) 100 AB643594, Moraxella osloensis 87 DQ412066, Acinetobacter sp. LOB-6 ★ 94 HE651915, Acinetobacter haemolyticus including Moraxellaceae 98 OTUb625 (2) 82 OTUb180 (45) 99 OTUb6 (3 ) 95 AB101444, Acinetobacter junii 91 DQ412060, Pseudoalteromonas sp. LOB-10 ★ 96 AB720724, Pseudoalteromonas shioyasakiensis 100 DQ412078, Pseudoalteromonas sp. SPB−9 ★ 78 OTUb271 (5) 92 JQ218688, SPSHA19 DQ412067, Pseudoalteromonas sp. LOB-15 ★ 81 DQ412075, Alteromonas sp. SPB-5 73 DQ836766, Alteromonas simiduii 94 CP003841, Alteromonas macleodii 79 OTUb623 (8) 100 FJ024319, clone 21 96 DQ412077, Alteromonas sp. SPB-8 ★ 90 AJ252022, Moritella abyssi 100 U00096, Escherichia coli 96 OTUb33 (1) including Alteromonadaceae, 92 AF052740, Idiomarina abyssalis Colwelliaceae 89 OTUb44 (3) 60 OTUb179 (1) and Idiomarinaceae 98 AJ440214, Idiomarina baltica 91 EU491881, EPR3965-I2-Bc80 95 OTUb416 (1) 100 KF798487, Woods−Hole_a1671 93 AB094412, Colwellia piezophila 77 EU491950, EPR4055−N3−Bc91 94 EU513001, Neiella marina 79 OTUb423 (1) 100 L34955, Cycloclasticus pugetii 92 JN019017, 89−25 95 AF304195, Methylobacter luteus 83 OTUb265 (19) 79 OTUb370 (11) 94 AF212202, Halomonas neptunia EU491904, EPR4055-N3-Bc25 100 AJ564880, Halomonas alkaliantarctica including Halomonadaceae 88 JX524857, Halomonas sp. LOB−22 ★ 88 OTUb655 (1) 100 CP003023, Legionella pneumophila 94 FJ905683, V19F132b 92 HM798754, PRTAB7870 94 OTUb172 (3) 91 DQ070797, 9NBGBact_21 89 OTUb122 (1) 63 OTUb250 (1) 100 OTUb274 (1) 92 AM259847, TAA−10−33 100 JN113082, BAC−C110 Uncultured clone group 100 OTUb512 (1) 95 HQ433414, 191−2−15 97 OTUb219 (1) 85 OTUb53 (4,2) 88 EU491667, EPR3970−MO1A−Bc80 99 AY225635, AT−s80 96 KC682558, ABEba_2C4 68 FJ024318, clone 6 99 AF114783, Alkalispirillum mobile 100 AM943121, Ectothiorhodospira variabilis AGFD01000020, Thiorhodospira sibirica 95 GU056072GS1−36 100 OTUb125 (1) 80 OTUb422 (10) ● 73 EF117913, Thiohalomonas denitrificans 99 OTUb40 (1) including Thioalkalispiraceae 98 JQ287336, 7M24_063 and Ectothiorhodospiraceae 95 KC136313, Arenicella chitinivorans DQ070791, 9NBGBact_8 99 EU491567, EPR4059−B2−Bc67 100 OTUb82 (1,2) 100 EU925907, 133H37 86 AF481118, Thioalkalispira microaerophila 98 DQ469584, Thiohalophilus thiocyanatoxydans 94 OTUb321 (5,2) 91 OTUb400 (19,6) ● 82 EU491375, P0X3b1G06 KT748628, H12 80 OTUb527 (1) 97 EU491627, EPR3970−MO1A−Bc41 100 OTUb496 (1,3) 72 JX227077, NCB40 97 EU491112, P9X2b3C07 90 OTUb217 (2) 99 FJ024320, clone 23 100 OTUb591 (6) ● including Acidiferrobacteraceae 98 AF387301, Acidiferrobacter thiooxydans 99 OTUb240 (2) 100 HM798879, PRTBB8427 99 OTUb479 (1) 98 KC682738, ABEsO_D7 97 OTUb444 (1) 100 OTUb397 (1) 61 EU491429, P0X4b3H08 82 EU491600, EPR3970−MO1A−Bc15 99 OTUb188 (2) GU119320, Reef_L07 100 OTUb546 (1) 83 EU491165, P9X2b7A09 96 OTUb270 (1,1) 78 EU236403, Hg92D6 83 OTUb28 (1) 99 EU287170, P13−77 77 DQ070802, 9NBGBact_46 94 OTUb305 (1) 100 OTUb631 (1) 96 EU491287, P9X2b2F08 93 FJ712414, KZNMV−0−B19 99 AB016986, Thiorhodovibrio winogradskyi AJ010125, Thioflavicoccus mobilis 94 HM038001, Nitrococcus mobilis 86 FJ482231, Thiohalobacter thiocyanaticus 95 OTUb284 (2,3) 100 GQ261781, 70mos_20s_B2 EU491296, P9X2b8A11 77 AFOC01000137, endosymbiont of Riftia pachyptila AB189713, Ifremeria nautilei gill symbiont 62 AB468957, Thioprofundum lithotrophicum including Chromatiaceae 99 EU491662, EPR3970−MO1A−Bc76 KT748592, D06 and Thioalkalispiraceae 100 DQ070789, 9NBGBact_1 73 OTUb415 (1) 100 FJ024321, clone 11 87 OTUb10 (1) 100 DQ070817, JdFBGBact_9 64 OTUb105 (1) OTUb521 (2) OTUb524 (1) 89 OTUb522 (1,2) 89 OTUb405 (1) 84 OTUb466 (1) 100 EU491392, P0X3b5F08 93 OTUb550 (3) EU491486, P0X4b2G10 100 OTUb51 (1) JX226933, NBB129 AB118236, Thiovirga sulfuroxydans 99 AF465604, Acidithiobacillus ferrooxidans AJ459801, Thermithiobacillus tepidarius DQ469582, Thiohalorhabdus denitrificans AB021185, Bacillus flexus X90835, Marinococcus halophilus 100

51

99

Gamma-I

Gamma-II

Gamma-III

Gamma-IV

Gamma-V

Gamma-VI

Gamma-VII

Gamma-VIII

Gamma-IX

Gamma-X

Gamma-XI

85 100

100

94

0.10

Fig. S3C

96

OTUb29 (1)

JX227517, SCB45 OTUb456 (1) JX227389, SAB112 88 97 OTUb301 (1) 100 HQ673686, F9P121000_S_I05 95 EU491550, EPR4059-B2-Bc47 99 OTUb64 (1) 89 EU373935, HCM3MC78_8B_FL OTUb582 (1) 100 JX227289, SAB12 100 OTUb488 (1) 66 HM186788, HDB_SIOZ603 99 CP001472, Acidobacterium capsulatum 97 JN543507, Terriglobus tenax 100 OTUb335 (1) 98 AM997514, UncDee12 97 OTUb421 (1,1) 84 JX227616, SCB144 60 OTUb170 (1) AM997449, Ulr1549 97 OTUb182 (1) 75 AM997612, Ucd1550 79 JQ309130, Blastocatella fastidiosa 100 97 OTUb463 (1,2) EU491149, P9X2b3G06 100 OTUb7 (1 ) 83 GU474896, HF4000_26D02 87 96 FJ024305, clone 26 95 KT748589, D03 EU491345, P0X3b1D02 96 OTUb652 (4,4) 100 ( 1) 86 OTUb38 KC682557, ABEba_LR2A4 85 88 OTUb649 (1,1) KF741555, SIP12C_12F 93 99 OTUb214 (2,1) JX227485, SCB13 90 76 OTUb492 (2,1) 74 JX227638, SCB166 70 KT748627, H11 Acidobacteria EU491480, P0X4b2E11 97 95 OTUb598 (1,2) EU373956, HCM3MC83_3C_FL 99 65 OTUb611 (3) JX227490, SCB18 89 OTUb398 (2) EU491072, P7X3b4G03 99 OTUb209 (1) 89 EU491650, EPR3970−MO1A−Bc63 90 97 OTUb230 (1) JX227446, SBB51 82 OTUb14 (1) 98 EU287121, P13−28 99 (1,1) 99 OTUb57 AB694244, OTU027_Xeno_Clone02 95 OTUb428 (1) 100 HM187083, HDB_SIPO424 80 100 OTUb269 (2) EU491086, P7X3b1D06 90 OTUb164 (1) 96 AM997505, UncDeep3 81 OTUb22 (1) 90 JQ579942, FII−AN001 69 EU491320, P9X2b8B05 98 96 OTUb560 (1) DQ351815, Belgica2005/10−ZG−24 67 EU491807, EPR3967−O2−Bc60 OTUb202 (1) 99 OTUb576 (1) 84 EU373931, HCM3MC78_3D_FL OTUb59 (1) 90 96 OTUb107 (1) JX193423, Q10928 99 EU491394, P0X3b5G09 85 OTUb596 (1) 94 DQ070804, 9NBGBact_59 90 DQ070820, JdFBGBact_16 100 100 OTUb442 (1) JX227019, NBB215 89 OTUb80 (1) 99 EU491067, P7X3b4D03 90 EU491665, EPR3970−MO1A−Bc79 100 AB303221, Acanthopleuribacter pedis 92 OTUb358 (2) 87 OTUb378 (1,4,1) 67 EU491755, EPR3968−O8a−Bc88 HQ674237, F9P261000_S_M06 79 OTUb288 (1) 66 86 OTUb427 (1,4) AB694357, OTU085_Xeno_Clone01 92 (1) 95 OTUb62 AM997915, Ucb1576 83 OTUb360 (1) 95 OTUb381 (1) 92 100 OTUb158 (1) AB722094, BMS9AB13 90 82 OTUb433 (2) JX226892, NBB88 99 OTUb628 (1,1) 99 FJ416117, 101N27 95 99 OTUb563 (1) AB694358, OTU086_Xeno_Clone01 100 94 OTUb342 (2) JN018912, 65−11−18 84 (1) 99 OTUb60 AB694443, OTU174_Ref_Clone01 100 EU245438, MAT−CR−M1−F03 OTUb155 (1) AF317745, wb1_A18 OTUb67 (1) 100 GU056061, DGS1−22 75 85 FJ024313, clone 43 96 OTUb308 (1) EU491631, EPR3970-MO1A-Bc45 95 OTUb254 (2,1) 89 Gemmatimonadetes JX120390, UA_20 100 OTUb565 (1,2) EU374070, HCM3MC80_11C_FL 100 96 OTUb497 (1) AB694309, OTU050_Xeno_Clone01 98 AF186415, PAUC43f OTUb206 (1) 98 EU374069, HCM3MC78_6G_FL 98 KT748610, F07 99 OTUb486 (1) 82 OTUb108 (3) JF809756, RS−B52 OTUb127 (1) 100 OTUb330 (1) 60 JF809770, RS−B70 75 OTUb150 (2) 99 OTUb411 (1) EU491457, P0X4b3H02 99 100 OTUb344 (1) EU491639, EPR3970−MO1A−Bc52 65 100 OTUb475 (1) JF809765, RS−B63 98 OTUb403 (1) OTUb65 (1) 98 OTUb464 (1) 94 AY921922, AKYH548 98 OTUb374 (1) 71 OTUb614 (1) 99 AB072735, Gemmatimonas aurantiaca OTUb246 (1) 91 EU804764, 6C232724 96 FJ745242, SHWN_night2_16S_453 100 JX537830, 63−38 100 Cyanobacteria 100 OTUb412 (1,1) 100 CP000825, Prochlorococcus marinus DQ070784, 9NSWBact_8 16S U00096, Escherichia coli CP000926, Pseudomonas putida 100

100

96

96

0.10

Fig. S3D

OTUb504 (2) DQ070822, JdFBGBact_23 78 EU491412, P0X4b3E02 92 KT748607, F02 100 EU491619, EPR3970−MO1A−Bc33 OTUb434 (2) JX193358, D21027 57 CANL01000000, Candidatus Microthrix parvicella 93 93 EU491638, EPR3970−MO1A−Bc51 74 FJ024306, clone 12 94 OTUb211 (1) 95 OTUb548 (1) EU374087, HCM3MC78_8D_FL 92 OTUb132 (1) DQ070807, 9NBGBact_68 100 EU799057, 1C226612 83 65 OTUb555 (1) OTUb597 (1) 89 78 OTUb236 (1) 99 EU491728, EPR3968−O8a−Bc60 EU491214, P9X2b7H01 91 86 OTUb126 (1) 98 OTUb130 (1) EU491711, EPR3968−O8a−Bc44 100 GU451470, OTU139 88 AB360343, Ilumatobacter fluminis 76 AB360448, Iamia majanohamensis OTUb458 (1) 100 JN018760, 41−12−09 AACY020274567, marine metagenome AF186411, PAUC32f 97 100 OTUb618 (1) EU491645, EPR3970−MO1A−Bc58 74 JN233145, OS2BR65 93 AF251436, Ferrimicrobium acidiphilum 100 95 AY140237, Ferrithrix thermotolerans 86 AB517669, Aciditerrimonas ferrireducens AF329834, Arthrobacter crystallopoietes X80738, Arthrobacter crystallopoietes 95 CP001628, Micrococcus luteus 100 EF680886, Nesterenkonia flava 100 OTUb313 (1) AM778449, Microbacterium aquimaris 92 HM446115, WT98_067 100 OTUb366 (1) 100 HF922318, HP−Bac−B07 DQ412063, Rhodococcus sp. LOB-1 79 X79187, Rhodococcus fascians AE017283, Propionibacterium acnes 99 97 OTUb283 (1) EU491848, EPR3965−I2−Bc22 90 JQ580474, RII−AN095 98 OTUb484 (2) EU491398, P0X3b5H07 Actinobacteria 97 OTUb23 (1) 100 OTUb432 (1) 89 JF344146, PET−022 100 OTUb167 (1) 99 EU491546, PR4059-B2-Bc40 100 OTUb187 (6) 98 AB722111, BMS9AB65 93 DQ070796, 9NBGBact_19 AMFO01002406, microbial mat metagenome 97 OTUb431 (1) 74 OTUb588 (1) 97 EU491399, P0X3b5H09 90 EU491602, EPR3970−MO1A−Bc17 AB858545, BMS3BB25 84 86 OTUb639 (1) 33 AF110142, SAR432 100 DQ070780, 9NSWBact_1 99 KC811143, Candidatus Actinomarina minuta JQ579956, FII−AN015 97 OTUb528 (1) JX226756, NAB42 95 EU491208, P9X2b7F12 EU491616, EPR3970−MO1A−Bc30 100 100 OTUb304 (3) JF809760, RS−B57 100 99 OTUb205 (1) JX226869, NBB65 GQ866097, F1−20 97 94 OTUb347 (9,6) OTUb593 (1) 69 91 EU491408, P0X4b3C09 99 FJ024307, clone 44 EU491657, EPR3970−MO1A−Bc70 100 OTUb406 (1,1) 93 JF344188, PET−064 100 EU491878, EPR3965−I2−Bc74 64 FJ712481, KZNMV−5−B68 96 OTUb309 (1) 87 ( 1) OTUb2 100 EU491094, P9X2b3A06 100 EU491222, P9X2b7H10 98 EU491642, EPR3970−MO1A−Bc55 OTUb21 (1) 100 HM186223, HDB_SIOO1028 100 AJ458462, Thermoleiphilum album 78 EU491626, EPR3970-MO1A-Bc4 80 KT748613, F12 ( 2) 89 OTUb43 99 OTUb536 (3) FJ024310, clone 5 65 69 OTUb328 (3) 98 JX227400, SBB5 OTUb103 (1) 97 92 OTUb557 (1) 99 AM997690, Ucp1525 OTUb235 (1) 92 OTUb390 (1) 84 100 OTUb371 (1) AB015528, BD1−27 89 78 EU491599, EPR3970-MO1A-Bc14 93 OTUb491 (1) 100 DQ070826, JdFBGBact_34 KT748568, A09 OTUb292 (1) 97 EU627895, b2.1 52 AB681089, Reichenbachiella agariperforans 85 100 OTUb367 (1) HM128334, SINH888 94 OTUb435 (1) 99 EU236411, Hg92E12 100 AM746475, Ekhidna lutea 54 KC005305, Fabibacter pacificus 99 AY753206, Roseivirga echinicomitans 96 CP001102, Candidatus Amoebophilus asiaticus 97 ( 1) 74 OTUb68 100 KJ809384, BVESI3C14 EF407879, Sediminibacterium salmoneum 100 OTUb556 (1) 100 GQ264521, WW3_74 96 OTUb562 (1) 98 JQ287329, 7M24_054 88 100 OTUb533 (1) JN166984, Muricauda antarctica 99 KT748595, D10 99 OTUb453 (1) EU642844, Vitellibacter aestuarii 90 ( 1) 100 OTUb9 AM997730, Ucs1540 82 OTUb147 (1) 100 JX066803, Flavobacterium hauense 96 EU236375, Hg91G5 84 EU491731, EPR3968−O8a−Bc64 95 OTUb42 (2) 81 AB255368, Gilvibacter sediminis 99 AY243096, Ulvibacter litoralis 93 88 KT748565, A04 74 EU491866, EPR3965−I2−Bc52 HM798700, PRTAB7791 OTUb526 (1) OTUb641 (2) 100 AACY020458788, marine metagenome 94 JX412958, Flaviramulus ichthyoenteri 98 JF739861, Gaetbulibacter lutimaris 100 OTUb363 (1) 100 EU290161, Maritimimonas rapanae 95 FJ394546, Marinifilum fragile 94 AY918928, Prolixibacter bellariivorans 98 OTUb249 (2) 95 AB694383, OTU112_Xeno_Clone01 100 JQ678459, JdFBBkgd48 100 OTUb27 (1) 100 HE804134, Fuschna−P3−C07 98 99 OTUb110 (3) OTUb391 (1,1) (1 ) 100 OTUb76 JQ579799, FII−TR004 94 JN825435, Alchichica_AQ2_1_1B_43 89 (2,2) 97 OTUb72 DQ070835, JdFBGBact_79 100 JQ906088, Rubrivirga marina 91 OTUb231 (1) 100 AM997351, Ucm1541 100 EU491757, EPR3968−O8a−Bc90 78 EU491171, P9X2b7B03 89 89 OTUb177 (1) 100 OTUb448 (1) KC561141, Gracilimonas mengyeensis 80 KC686334, Gracilimonas rosea 100 OTUb279 (1) 92 83 FJ205251, B12F 100 EU491373, P0X3b1F08 AM086119, c5LKS28 Chlorobi HM186682, HDB_SIOT933 96 AB478415, Ignavibacterium album 55 CP000492, Chlorobium phaeobacteroides U00096, Escherichia coli CP000926, Pseudomonas putida 95

79

100

100

0.10

Fig. S3E

Bacteroidetes

96 93

OTUb318 (1) OTUb472 (1)

EU491491, P0X4b2H12 OTUb117 (1) AF317762, wb1_C17 100 OTUb581 (7,1) ● 58 FJ205238, B4A 99 OTUb169 (1) 84 EU491464, P0X4b2A08 85 EU084879, Candidatus Nitrospira bockiana 92 HM485589, Nitrospira calida 75 KF724505, Nitrospira lenta 90 HE603172, GCaltP6F10 OTUb387 (1) 55 AB818959, Nitrospira japonica 91 CZPZ01000003, Candidatus Nitrospira nitrificans 92 CZQA01000015, Candidatus Nitrospira nitrosa 100 X82558, Nitrospira moscoviensis 100 LN885086, Candidatus Nitrospira inopinata 86 EU491478, P0X4b2E01 79 FJ024315, clone 31 99 OTUb39 (1) 99 AB858540, BMS3BB16 Nitrospirae 98 X82559, Nitrospira marina 79 HQ686082, Nitrospira sp. Ecomares 2.1 OTUb637 (1) 100 KC682843, KiMba_LR2B9 JQ287208, 9M4I_072 98 EU491260, P9X2b2E08 93 KC706459, Candidatus Nitrospira salsa EF019030, Amb_16S_1574 OTUb519 (1) 100 AY734241, SDKAS1_13 92 EU491114, P9X2b3C09 100 AF356829, Leptospirillum ferriphilum 100 X86776, Leptospirillum ferrooxidans 100 GU979422, Candidatus Magnetoovum mohavensis 76 X71838, Candidatus Magnetobacterium bavaricum 100 FJ024316, clone 48 100 EF081294, Thermodesulfovibrio hydrogeniphilus X96726, Thermodesulfovibrio islandicus 74 OTUb410 (1) 100 OTUb599 (5) 67 EU491442, P0X4b3C05 51 KC682541, ABEba_E12 99 HM186569, HDB_SIOT1045 Caldithrix 95 OTUb608 (1) 87 AB694393, OTU123_Xeno_Clone01 93 AB722123, BMS9BB19 100 AJ430587, Caldithrix abyssi FJ999729, Caldithrix palaeochoryensis 74 KC682795, KiMba_D12 100 AM997732, Ucb1534 88 OTUb216 (2) 91 EF999358, TopBa32 97 EU491155, P9X2b3H03 78 OTUb661 (1) 100 HQ672611, F9P12500_S_F06 96 AQTY01000007, Nitrospina sp. SCGC AAA288−L16 100 OTUb575 (1) 85 GQ349320, SHAN761 Nitrospinae 89 AM997681, Ucp1537 86 OTUb17 (1) 73 OTUb81 (1) 99 EU491815, EPR3967−O2−Bc7 98 KC706458, Cb12 86 L35504, Nitrospina gracilis 98 AM997673, Ucp1528 OTUb18 (5,4) ● 88 FJ024329, clone 4 OTUb457 (1) 100 DQ070818, JdFBGBact_10 EF999360, TopBa51 100 OTUb156 (1) GQ452903, b31 94 EU491679, EPR3968−O8a−Bc1 100 AB331886, Persicirhabdus sediminis 100 OTUb218 (1) 95 FJ203597, SHFH683 100 EU491715, EPR3968−O8a−Bc48 100 OTUb191 (3) 100 OTUb638 (1) 99 HQ672640, F9P12500_S_H02 94 JN018863, 52−3−50 84 OTUb402 (1) 93 EU491625, EPR3970−MO1A−Bc39 KT748572, B03 77 OTUb224 (2) 89 JX227307, SAB30 98 AY114335, LD1−PB3 Verrucomicrobia 98 OTUb635 (1) 71 EU491673, EPR3970−MO1A−Bc86 96 DQ070799, 9NBGBact_30 94 OTUb264 (1) 96 JN490839, SBYX_5889 OTUb128 (1) 95 CP001998, Coraliomargarita akajimensis 73 KT748622, H01 60 AM997570, Ucd1579 100 OTUb659 (1) 53 FN553635, 285−60 89 AB694308, OTU049_Xeno_Clone02 100 OTUb604 (1) CP007053, Opitutaceae sp.TAV5 100 OTUb129 (1) AF042496, Waddlia chondrophila 86 Y07556, Parachlamydia acanthamoebae 93 OTUb409 (1) 57 OTUb547 (1) 59 GQ850567, d98 98 OTUb654 (1) 100 AY140911, Candidatus Fritschea eriococci Chlamydiae 56 U68460, Simkania negevensis 89 OTUb115 (1) 92 EU491566, EPR4059−B2−Bc66 97 OTUb345 (1) 85 OTUb98 (1) 100 OTUb498 (1) 84 D85708, Chlamydophila caviae 100 DQ011662, Chlamydia sp. CH301104 OTUb295 (1) 92 KJ630837, Bacillus rigiliprofundi 97 OTUb226 (1) HQ433471, Bacillus persicus 100 OTUb193 (2) 99 AB198719, Bacillus boroniphilus 94 AF326373, Bacillus sp. SG-1 94 DQ412062, Bacillus sp. LOB-3 Firmicutes 94 AY121439, Virgibacillus kekensis 100 OTUb449 (1) 100 JQ413413, Marinococcus tarijensis DQ221694, Caldalkalibacillus uzonensis 82 HE805640, Vallitalea guaymasensis 73 JN440981, SBYB_4236 100 KM410415, FS06−10−95 OTUb280 (2) U00096, Escherichia coli CP000926, Pseudomonas putida 97

53

79

92

95

100

97

100

0.10

Fig. S3F

OTUb131 (1,1) GU118977, Past_F20 100 OTUb268 (1) 99 EU374009, HCM3MC83_1E_FL 100 OTUb94 (1) 92 JX193417, Q10922 93 OTUb136 (1) 99 AY114326, LD1−PA40 58 EU491611, EPR3970−MO1A−Bc26 52 OTUb337 (2) 68 AM997399, Ucm15512 100 OTUb478 (1) 93 JX227010, NBB206 86 EU491649, EPR3970−MO1A−Bc61 90 OTUb100 (1) 99 JN536224, SBZP_1907 57 GU118227, Dstr_I07 94 OTUb392 (1) 94 EU491106, P9X2b3C01 98 EU491664, EPR3970−MO1A−Bc78 97 OTUb123 (1) 60 FJ024317, clone 88 78 OTUb166 (1) 98 DQ070794, 9NBGBact_17 98 OTUb223 (1) 82 EU491630, EPR3970−MO1A−Bc44 64 DQ070824, JdFBGBact_28 95 OTUb97 ( 1) 99 EU491748, EPR3968−O8a−Bc80 98 JN825611, Alchichica_AL52_2_1B_99 99 OTUb277 (1) 89 DQ070834, JdFBGBact_75 80 EU491597, EPR3970−MO1A−Bc12 JN518535, SBZH_2737 KT748601, E08 100 OTUb19 (1) 92 OTUb624 (1) FN667406, PS2666 90 EU491864, EPR3965−I2−Bc5 100 OTUb375 (1) 92 JX227656, SCB184 96 OTUb545 (2) 79 EU491565, EPR4059−B2−Bc65 78 JQ287351, 7M24_083 70 EU491677, EPR3970−MO1A−Bc9 92 OTUb418 (1) 100 EU491730, EPR3968−O8a−Bc62 97 AM997822, Ucb1621 100 OTUb518 (1) 100 OTUb84 (1) HM799018, PRTBB8608 98 EU491854, EPR3965−I2−Bc34 100 OTUb513 (1) 99 AJ231184, Planctomyces maris 87 EF018982, Amb_16S_1502 100 EU044518, GASP−77KB−802−B05 99 OTUb490 (1) 69 OTUb204 (1) 90 JN478565, SBYT_2295 95 EU491354, P0X3b5E01 72 OTUb617 (1) 88 OTUb629 (1) 88 JN825588, Alchichica_AL52_2_1B_131 100 OTUb135 (1) 60 OTUb417 (1) 99 JQ516422, 0907_Mf_DT3_B93 Planctomycetes OTUb255 (1) 78 JX227502, SCB30 100 OTUb63 (1) 94 DQ289897, LC1−1 77 OTUb653 (1) 100 JN476577, SBYS_6210 84 OTUb454 (1) 100 JN435867, SBXZ_4673 90 JN881631, PNG_TBG_B42 OTUb438 (2) 100 JF809766, RS−B64 93 OTUb282 (1) 100 AM997286, Ucm1561 OTUb467 (2) 96 FJ746293, SPG12_60_70_B39 87 EU491865, EPR3965−I2−Bc51 98 OTUb487 (1) 99 FJ455894, B103G10 100 OTUb149 (1) 98 OTUb534 (1) 100 OTUb419 (1) JX227186, NCB149 100 OTUb227 (1) 99 AM997692, Ucp1564 90 JN539828, SBZP_6733 87 OTUb45 (1 ) 100 FN553455, 251−15 100 OTUb651 (1) 85 OTUb89 (1) EU491431, P0X4b3H10 96 OTUb493 (1) 100 DQ833489, 35−49 94 HQ674339, F9P262000_S_B12 82 OTUb148 (1) 74 OTUb523 (1) OTUb510 (1) 100 AB694377, OTU106_Xeno_Clone01 88 EU491044, P7X3b4F03 88 OTUb276 (1) 99 JQ580298, RII−TR065 81 JQ580344, RII−TR111 21 OTUb332 (1) 100 JN522405, SBZI_3293 100 OTUb647 (1) 100 AM997478, Ulrdd_12 84 KT748596, E01 54 DQ070829, JdFBGBact_42 99 (2) OTUb1 100 HM798938, PRTBB8500 OTUb589 (1) 55 EU491753, EPR3968-O8a-Bc86 54 AF317785, wb1_D18 OTUb380 (1) 100 JQ287439, 3M34_018 95 OTUb137 (1) OTUb49 (1) 69 OTUb96 (1) 86 EU491279, P9X2b2C08 99 OTUb644 (1) 95 EU236408, Hg92E7 OTUb13 (1) 100 OTUb154 (1) 99 OTUb168 (1,1) JX227283, SAB6 87 OTUb175 (1) 93 AM997624, Ucp1602 92 EU491233, P9X2b7G07 95 OTUb197 (1,1) 99 OTUb356 (1) 96 HM185922, HDB_SIOH985 100 OTUb605 (1) 100 AM997888, Ucb15699 100 HM185993, HDB_SIOI798 Omnitrophica 98 OTUb278 (1) 100 AQSZ01000059, Omnitrophica bacterium SCGC AAA257−O07 OTUb595 (1) 67 HM187190, HDB_SIPO716 97 OTUb90 (1) 90 DQ070819, JdFBGBact_12 100 EU491266, P9X2b2H06 ASOC01000103, Candidatus Omnitrophus fodinae SCGC AAA011−A17 83 OTUb238 (2) 78 OTUb373 (1) 100 GQ337187, CB1341b.47 100 OTUb312 (1) 92 AM997774, Ucb1520 99 OTUb239 (2) 100 HQ674301, F9P261000_S_P14 60 AY534095, SAR256 99 OTUb351 (2) 53 GQ337207, CB1343b.36 90 OTUb289 (1) 100 ( 3) OTUb0 100 OTUb570 (1) 98 HQ674232, F9P261000_S_L23 88 OTUb253 (1) 100 JF809783, RS−B86 100 OTUb294 (1,2) 96 AF355053, Arctic96BD−6 39 OTUb334 (2,2) 87 U20797, SAR202 99 OTUb293 (1) 99 EU491393, P0X3b5F10 93 OTUb424 (1,3) 72 AJ567614, MBAE74 100 OTUb656 (1) 100 EU286996, B78−32 100 OTUb439 (1) 99 AM997765, Ucb1511 Chloroflexi 53 OTUb568 (2) 79 JN596666, XC1005 69 OTUb244 (2) 93 OTUb359 (1) 100 KF286103, BZ40D8f_b03 69 EU035922, KspoA5 OTUb299 (1) HM186501, HDB_SIOP878 OTUb272 (1) 87 FJ479355, p7h15ok 100 EU134062, FFCH4996 95 OTUb163 (1) 98 OTUb507 (1) 100 OTUb37 (1) EU491096, P9X2b3A11 100 EU134162, FFCH18756 98 OTUb119 (1) 96 OTUb505 (1) 80 DQ431896, 3G02−01 94 OTUb502 (1) 100 FJ905751, V1F129b 90 FJ905656, V19F63b JQ733906, Litorilinea aerophila U00096, Escherichia coli CP000926, Pseudomonas putida 93

94

100

100

0.10

Fig. S3G

(OP3)

OTUb52 (3,2) JX227479, SCB7 KT748567, A07 97 90 OTUb603 (6,6) ● AY225657, AT−s30 95 NC10 97 EU491346, P0X3b1D04 HM187379, HDB_SISU423 95 OTUb645 (4) 99 FJ621550, Ino-F12 96 FP565575, Candidatus Methylomirabilis oxyfera 98 OTUb207 (1) 80 FJ826302, A6−1−94 69 EU803175, 4C230611 95 ZB3 OTUb541 (1) 97 HQ674331, F9P262000_S_B04 100 EU491779, EPR3967−O2−Bc30 95 99 OTUb455 (1) JX227357, SAB80 100 64 EU491069, P7X3b4E06 NKB19 JN485309, SBYW_3552 100 100 OTUb353 (1) FN553459, 251−19 88 59 OTUb465 (1) KC432417, SEAB1BC051 100 96 EU491123, P9X2b3D08 NPL-UPA2 (BRC1) JN476608, SBYS_6244 100 97 OTUb615 (1) EU245888, MAT−CR−M7−F12 69 100 OTUb300 (1) JN506239, SBZC_2107 99 AF186412, PAUC34f 98 PAUC34f 93 OTUb425 (1) HQ270322, XB3A11F 100 88 EU491100, P9X2b3B05 64 OTUb303 (1) 100 GQ351144, J8P41000_1B04 AncK6 DQ513022, FS142−11B−02 90 100 OTUb386 (1) AY592156, Kazan−2B−32/BC19−2B−32 95 100 OTUb553 (1) EU925921, 159I30 80 WS3 100 OTUb662 (1) GQ259301, sediment_surface52 96 FJ478657, p27n12ok 96 87 OTUb251 (5) 99 JX227439, SBB44 Entotheonella FJ746180, SPG12_461_471_B46 100 EU373934, HCM3MC91_7D_FL 79 OTUb601 (1) 100 AJ301571, GR−296.II.45 100 AP011801, Candidatus Acetothermus autotrophicum Acetothermus (OP1) 96 FJ905663, V19F77b 100 FJ455902, B050B01 85 DQ070823, JdFBGBact_26 85 EU491485, P0X4b2G09 100 OTUb336 (1) EU236382, Hg91H5 76 KF926731, Dc−5 99 Entotheonella AZHW01000045, Candidatus Entotheonella sp. TSY1 100 99 OTUb215 (1) EU374043, HCM3MC83_9D_FL 98 JF344240, PET−116 97 57 OTUb199 (3) 89 GQ337210, CB1343b.51 97 OTUb452 (4) AACY020564058, marine metagenome 71 (1) 100 OTUb86 GU474892, HF4000_22B16 91 ( 1) 100 OTUb71 GQ337222, CB1648b.40 95 100 OTUb146 (1) Marinimicrobia (SAR406) HQ674241, F9P261000_S_M10 100 OTUb482 (3) JN166363, HOT157_350m91 100 OTUb564 (2) GQ375274, CB1341b.86 91 ASPI01000040, Marinimicrobia bacterium SCGC AAA003−E22 100 100 OTUb571 (1) HQ673826, F9P122000_S_E11 100 100 OTUb622 (1) HQ673270, F9P41000_S_M11 99 59 OTUb25 (1) 78 OTUb394 (2) KT748586, C11 100 JX226983, NBB179 71 DQ070831, JdFBGBact_44 77 OTUb544 (1) 75 TM6 AY792307, CrystalBog2E1 100 JN596648, XE3C12 100 96 OTUb471 (1) JX226849, NBB45 79 100 OTUb537 (2) EU491451, P0X4b3E01 51 100 OTUb420 (1) JX227326, SAB49 99 AY921882, AKYG853 Elusimicrobia 93 DQ676361, MVP−88 100 OTUb354 (1) 78 71 OTUb30 (1) JN825638, Alchichica_AQ1_2_1B_65 54 PRR-11 (BRC1) HM187263, HDB_SIPP525 100 GQ264471, WW3_178 94 90 KT748602, E09 72 OTUb365 (3) 90 EU491675, EPR3970−MO1A−Bc88 OTUb121 (1) 100 (3) 92 OTUb20 98 OTUb509 (1) EU491210, P9X2b7G08 64 98 OTUb324 (1) OTUb506 (1,2) AM935383, AMGC9 100 EU374027, HCM3MC83_1F_FL 55 86 OTUb612 (1) 100 JX227454, SBB59 SRB1093 100 OTUb665 (2) AM997666, Ucp1599 88 OTUb322 (1) 100 EU374029, HCM3MC91_5C_FL OTUb208 (11,3) ● 100 88 EU491524, EPR4059-B2-Bc12 OTUb632 (4,1) 100 FJ264768, so4B11 FJ024311, clone 25 85 OTUb285 (1) 97 HQ691926, Clip 24 OTUb503 (1) 95 JQ579864, FII−TR069 100 GN02 EU491859, EPR3965−I2−Bc40 92 OTUb178 (1) 60 JX521515, EPS09_OK_002_8 100 AACY023749576, marine metagenome 100 77 OTUb73 (1) EU246330, MARS−B06 69 AMFJ01036405, ACD_81C00166 62 EU491249, P9X2b2A10 OD1 93 OTUb574 (1) 100 AM997454, Ulr1480 100 ASKW01000012, Parcubacteria bacterium SCGC AAA010−E09 KF923319, ERBTW20082009OTU093 100 AF015925, OctSpA1−106 ASKL01000020, Fervidibacteria bacterium JGI 0000001−G10 96 Fervidibacteria 100 AB629129, Sm4hw054U OTUb349 (2) CP001710, Methanothermobacter marburgensis CP000866, Nitrosopumilus maritimus 98

95

100

100

0.10

Fig. S3H

OTUa520 (1) AXWL01000001, archaeon SCGC AAA282−K18 FJ487526, SPG11_3_4_A15 OTUa78 (1) 99 FJ487534, SPG11_3_4_A26 FJ487540, SPG11_3_4_A4 94 OTUa468 (20,13) ● 78 OTUa141 (1,4) 77 α 80 KF957664, Candidatus Nitrosopumilus sp. PS0 CP000866, Nitrosopumilus maritimus SCM1 91 OTUa372 (1) 80 80 FJ487525, SPG11_3_4_A12 97 OTUa451 (1,2) 100 EF069338, PS2ARC36 OTUa111 (2) 95 98 HQ331116, Candidatus Nitrosoarchaeum koreensis AEGP01000029, Candidatus Nitrosoarchaeum limnia OTUa355 (1,2) 99 FJ487504, SPG11_H2O_A34 90 100 OTUa566 (3) AF119134, APA1−0cm 59 95 OTUa362 (1,2) EF069354, PS2bARC10 93 OTUa549 (5,1) 92 FJ487542, SPG11_3_4_A41 85 94 OTUa161 (11,8) ● 99 OTUa243 (3,2) η−κ−υ FJ487518, SPG12_60_70_A22 99 83 OTUa307 (4,5) Thaumarchaeota OTUa32 (10,15) ● 97 EF069360, PS2ARC24 90 OTUa287 (2,5) 98 78 OTUa176 (3,10) (4,10) ● 91 OTUa35 99 FN553859, A251−22 AF119127, CRA8−11cm 83 89 OTUa441 (7,1) 96 EF069386, PS8ARC11 ε−ζ−θ 93 OTUa646 (33,21) ● GU270136, 30H−0S−5 99 OTUa572 (1) 77 (2,6) 100 OTUa79 FN553848, A251−11 74 OTUa369 (1) 100 KF901022, KM3_69_H10 71 OTUa669 (1) 98 OTUa245 (1) EU686624, AD1000−202−A 100 88 OTUa531 (19) γ AJ347777, ST−12K2A 99 97 OTUa552 (4) EU686623, AD1000−56−E4 87 100 OTUa437 (2) SAGMA-X FJ487487, SPG11_H2O_A87 100 100 OTUa446 (1) JQ085825, W5−61a 98 FJ150803, 083exp4 79 MBGA HM187473, HDBA_SISC414 100 1 ) ( OTUa266 95 FJ487456, SPG12_343_353_A93 100 OTUa200 (1) OTUa157 (1) 99 JWKV01000003, archaeon GW2011_AR16 94 FJ810531, JMYA24 66 OTUa529 (1) 96 AACY023847387, marine metagenome 93 CP010425, archaeon GW2011_AR15 OTUa260 (1) 99 (1) OTUa8 51 OTUa316 (1) 89 Woesearchaeota OTUa184 (1) 100 AF424534, MERTZ_21CM_64 99 OTUa281 (1) AY821999, CV1_A2_10 98 OTUa357 (1) 99 OTUa61 (1) 90 CP010426, archaeon GW2011_AR20 94 JF262383, YLA104 93 OTUa112 (1) 83 AB019751, pISA1 OTUa619 (2) 90 AF424528, MERTZ_2CM_6 100 Parvarchaeota AB424727, YdcGA50 88 AF424532, MERTZ_0CM_40 78 OTUa138 (1) 100 JN018542, 41−12−A−2 EU556724, DeepAnt−15E7 99 AACY020555882, marine metagenome 100 Euryarchaeota OTUa462 (1) 100 AB284823, F2apm1A36 68 CP005934, Candidatus Methanomassiliicoccus intestinalis 98 OTUa395 (1) AB329830, YS16Uc37 91 CP010424, archaeon GW2011_AR10 98 OTUa326 (1) 71 Diapherotrites ASMR01000001, Diapherotrites archaeon SCGC AAA011−K09 100 AQRS01000026, Candidatus Iainarchaeum andersonii SCGC AAA011−E11 U00096, Escherichia coli CP000926, Pseudomonas putida 90

97 89

Nitrosopumilaceae

84

75

100

100

0.10

Fig. S3I