Schmid, M.C., Hooper, A.B., Klotz, M.G., Woebken, D., Lam, P., Kuypers, M.M.M., ... Welsh, A., Chee-Sanford, J.C., Connor, L.M., Löffler, F.E., and Sanford, R.A. ...
Supporting information
Table S1. Primers and thermal cycling conditions for quantification of 16S rRNA and nitrogen cycling genes, and 454 pyrosequencing of nosZI and nosZII Sequences (5’-3’)
References
Thermal cycling
16S rRNA 341F 534R
CCT ACG GGA GGC AGC AG ATT ACC GCG GCT GCT GGC A
López-Gutiérrez et al., 2004
(95C, 7 min) x 1 (95C, 15 s; 60C, 30 s; 72C, 30 s; 80C, 30 s) x 40 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1
105
hzo hzocl1F1 hzocl1R2
TGY AAG ACY TGY CAY TGG ACT CCA GAT RTG CTG ACC
Schmid et al., 2008
(95C, 7 min) x 1 (95C, 15 s; 52.5C, 30 s; 72C, 30 s; 77C, 30 s) x 35 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1
79
Respiratory ammonification
nrfA nrfAF2aw nrfAR1
CAR TGY CAY GTB GAR TA TWN GGC ATR TGR CAR TC
Welsh et al., 2014 Mohan et al., 2004
(95C, 5 min) x 1 (95C, 15 s; 57C, 30 s; 72C, 30 s) x 7 (95C, 15 s; 52C, 35 s; 72C, 35 s; 80C, 15 s) x 35 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1
Nitrification (archaeal)
amoA crenamoA23F crenamoA616R
ATG GTC TGG CTW AGA CG GCC ATC CAT CTG TAT GTC CA
Tourna et al., 2008
(95C, 5 min) x 1 (95C, 15 s; 55C, 30 s; 72C, 40 s; 80C, 10 s) x 35 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1
75
Nitrification (bacterial)
amoA AmoA1F AmoA2R
GGG GTT TCT ACT GGT GGT CCC CTC KGS AAA GCC TTC TTC
Rotthauwe et al., 1997
(95C, 5 min) x 1 (95C, 15 s; 55C, 30 s; 72C, 40 s; 80C, 10 s) x 35 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1
85
Denitrification Nitrate reduction
nirK nirK F1aCu nirK R3Cu
ATCATGGTSCTGCCGCG GCCTCGATCAGRTTGTGGTT
Hallin and Lindgren, 1999
Denitrification Nitrate reduction
nirS nirS cd3aFm nirS R3cdm
AACGYSAAGGARACSGG GASTTCGGRTGSGTCTTSAYGAA
Throbäck et al., 2004
Process/Taxa
Genes Primer names
Bacteria
Anammox*
(95C, 7 min) x 1 (95C, 15 s; (63C – 58C, -1/cycle), 30 s; 72C, 30 s) x 6 (95C, 15 s; 58C, 30 s; 72C, 30 s; 80C, 30 s) x 35 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1 (95C, 7 min) x 1 (95C, 15 s; (65C – 60C, -1/cycle), 30 s; 72C, 30 s) x 6 (95C, 15 s; 60C, 30 s; 72C, 30 s; 80C, 30 s) x 35 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1
Efficiency (%)
78
80
63
1
Cont. Denitrification Nitrous oxide reduction
nosZI 1840F 2090R
Denitrification Nitrous oxide reduction
nosZII nosZII-F nosZII-R
Denitrification
nosZI pyrosequencing nosZF1-mod2 nosZ2R-mod
Nitrous oxide reduction Denitrification Nitrous oxide reduction
nosZII pyrosequencing nosZII-F nosZII-R
CGC RAC GGC AAS AAG GTS MSS GT CAK RTG CAK SGC RTG GCA GAA
CTI GGI CCI YTK CAY AC GCI GAR CAR AAI TCB GTR C
CGC TST TYM TIG AYA GYC AG CAK RTG CAI SGC RTG GCA GAA
CTI GGI CCI YTK CAY AC GCI GAR CAR AAI TCB GTR C
Henry et al., 2004
Jones et al., 2013
mod. from Philippot et al., 2013
Jones et al., 2013
(95C, 7 min) x 1 (95C, 15 s; (65C – 60C, -1/cycle), 30 s; 72C, 30 s) x6 (95C, 15 s; 60C, 30 s; 72C, 30 s; 80C, 30 s) x 35 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1 (95C, 7 min) x 1 (95C, 15 s; 54C, 30 s; 72C, 30 s; 80C, 30 s) x 40 (95°C, 15 s;(60 to 95° C, 10 s, increment 0.5°)), x 1
78
74
(95C, 7 min) x 1 (95C, 45 s; 54C, 60 s; 72C, 60 s) x 20+20 (72C , 60 s) x 1
na
(95C, 7 min) x 1 (95C, 45 s; 54C, 60 s; 72C, 60 s) x 20+15 (72C , 60 s) x 1
na
*Anammox: Anaerobic ammonium oxidation
2
Table S2 Abundances of nitrogen cycling genes in seed communities (t0) and sediments subject to different oxygen regimes expressed as copies per ng DNA (x103; mean ± SD, oxygen regimes: n=4, t0: n=2). Oxygen regime
nirS
nirK
nosZI
nosZII
hzo
nrfA
amoA (archaeal)
amoA (bacterial)
Anoxic
11.8±1.15
2.33±0.54
4.45±0.5
0.22±0.04
0.84±0.1
Oscox*
15.8±1.04
2.82±0.30 7.83±1.25 0.32±0.04
0.92±0.09 9.12±1.15 0.78±0.05 4.28±0.33
Oscan*
14.9±0.86
2.93±0.87 7.11±1.01 0.26±0.05
0.97±0.06 10.8±1.10 0.90±0.14 5.77±1.14
Oxic
12.2±1.05
2.49±0.46 5.64±0.40 0.22±0.04
1.02±0.12 8.49±1.23 1.17±0.13 7.98±0.37
t0 *
15.6±2.85
2.52±0.64 3.65±1.28 0.24±0.04
1.01±0.14 9.74±1.84 0.41±0.03
9.88±1.14 0.52±0.04 3.13±0.38
3.08±0.25
*Oscox: Oscillating oxygen regimes starting oxic; Oscan: Oscillating oxygen regimes starting anoxic, t0: before incubation
Table S3. Dissimilarity distances of the N2O reducing community at 97% sequence identity level 1st Qu.
Median
Mean
3rd Qu.
Sörensen Morisita-Horn
0.35 0.08
0.38 0.15
0.38 0.15
0.41 0.20
Sörensen Morisita-Horn
0.33 0.02
0.34 0.05
0.35 0.08
0.36 0.15
nosZI
nosZII
3
Figures Fig. S1. Phylogenetic placement of nosZI reads of the seed community into the reference phylogeny. Pyrosequencing and initial sequence processing and analysis were performed as described by Jones et al. (2014). The full set of 9 281 high quality reads was mapped into the reference phylogeny using pplacer (Matsen et al., 2010) with the LG+Γ substitution model (Le and Gascuel, 2008). The resulting placements were summarized (-fat command in ‘guppy’) and visualized with Archeaopteryx (Han and Zmasek, 2009). Red colored branches indicate the placement of reads onto that edge and branch thickness is proportional to the number of placements on that edge. The clade consisting of nosZII sequences is collapsed. Fig. S2. Phylogenetic placement of nosZI reads from the samples after incubation under the four different oxygen regimes into the reference phylogeny. Pyrosequencing and initial sequence processing and analysis were performed as described by Jones et al. (2014). The full set of 149 138 high quality reads was mapped into the reference phylogeny using pplacer (Matsen et al., 2010) with the LG+Γ substitution model (Le and Gascuel, 2008). The resulting placements were summarized (-fat command in ‘guppy’) and visualized with the Archeaopteryx (Han and Zmasek, 2009). Red colored branches indicate the placement of reads onto that edge and branch thickness is proportional to the number of placements on that edge. The clade consisting of nosZII sequences is collapsed. Fig. S3. Phylogenetic placement of nosZII reads of the seed community into the reference phylogeny. Pyrosequencing and initial sequence processing and analysis were performed as described by Jones et al. (2014). The full set of 19 882 high quality reads was mapped into the reference phylogeny using pplacer (Matsen et al., 2010) with the LG+Γ substitution model (Le and Gascuel, 2008). The resulting placements were summarized (-fat command in ‘guppy’) and visualized with the Archeaopteryx (Han and Zmasek, 2009). Red colored branches indicate the placement of reads onto that edge and branch thickness is proportional to the number of placements on that edge. The clade consisting of nosZI sequences is collapsed. Fig. S4. Phylogenetic placement of nosZII reads from the samples after incubation under the four different oxygen regimes into the reference phylogeny. Pyrosequencing and initial sequence processing and analysis were performed as described by Jones et al. (2014). The full set of 146 517 high quality reads was mapped into the reference phylogeny using pplacer (Matsen et al., 2010) with the LG+Γ substitution model (Le and Gascuel, 2008). The resulting placements were summarized (-fat command in ‘guppy’) and visualized with the Archeaopteryx (Han and Zmasek, 2009). Red colored branches indicate the placement of reads onto that edge and branch thickness is proportional to the number of placements on that edge. The clade consisting of nosZI sequences is collapsed. Fig. S5. Relative contribution of individual edges in the reference phylogeny to the first principal component (PC1) of the nosZI ePCA. The color of the branches correspond to changes along PC1 in Figure 3a in a positive (orange) and negative (green) direction and the thickness to their magnitudes. The clade consisting of nosZII sequences is collapsed. Fig. S6. Relative contribution of individual edges in the reference phylogeny to the second principal component (PC2) of the nosZI ePCA. The color of the branches correspond to changes along PC2 in Figure 3a in a positive (orange) and negative (green) direction and the thickness to their magnitudes. The clade consisting of nosZII sequences is collapsed. 4
Fig. S7. Relative contribution of individual edges in the reference phylogeny to the first principal component (PC1) of the nosZII ePCA. The color of the branches correspond to changes along PC1 in Figure 3b in a positive (orange) and negative (green) direction and the thickness to their magnitudes. The clade consisting of nosZI sequences is collapsed. Fig. S8. Relative contribution of individual edges in the reference phylogeny to the second principal component (PC2) of the nosZII ePCA. The color of the branches correspond to changes along PC2 in Figure 3b in a positive (orange) and negative (green) direction and the thickness to their magnitudes. The clade consisting of nosZI sequences is collapsed.
5
References Hallin, S. and Lindgren, P.-E. (1999) PCR Detection of Genes Encoding Nitrite Reductase in Denitrifying Bacteria. Appl. Envir. Microbiol. 65: 1652–1657. Han, M. V and Zmasek, C.M. (2009) phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10: 356. Henry, S., Baudoin, E., López-Gutiérrez, J.C., Martin-Laurent, F., Brauman, A., and Philippot, L. (2004) Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. J. Microbiol. Methods 59: 327–335. Jones, C.M., Graf, D.R.H., Bru, D., Philippot, L., and Hallin, S. (2013) The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. ISME J. 7: 417–426. Jones, C.M., Spor, A., Brennan, F.P., Breuil, M.-C., Bru, D., Lemanceau, P., et al. (2014) Recently identified microbial guild mediates soil N2O sink capacity. Nat. Clim. Chang. 4: 801–805. Le, S. and Gascuel, O. (2008) An improved general amino acid replacement matrix. Mol. Biol. Evol. 25: 1307–1320. López-Gutiérrez, J.C., Henry, S., Hallet, S., Martin-Laurent, F., Catroux, G., and Philippot, L. (2004) Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR. J. Microbiol. Methods 57: 399–407. Matsen, F.A., Kodner, R.B., and Armbrust, E.V. (2010) pplacer: linear time maximumlikelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 11: 538. Mohan, S.B., Schmid, M., Jetten, M., and Cole, J. (2004) Detection and widespread distribution of the nrfA gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. FEMS Microbiol. Ecol. 49: 433–443. Philippot, L., Spor, A., Hénault, C., Bru, D., Bizouard, F., Jones, C.M., et al. (2013) Loss in microbial diversity affects nitrogen cycling in soil. ISME J. 7: 1609–1619. Rotthauwe, J., Witzel, K., and Liesack, W. (1997) The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammoniaoxidizing populations. Appl. Environ. Microbiol. 63: 4704–4712. Schmid, M.C., Hooper, A.B., Klotz, M.G., Woebken, D., Lam, P., Kuypers, M.M.M., et al. (2008) Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria. Environ. Microbiol. 10: 3140–3149. Throbäck, I.N., Enwall, K., Jarvis, A., and Hallin, S. (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol. Ecol. 49: 401–417. Tourna, M., Freitag, T.E., Nicol, G.W., and Prosser, J.I. (2008) Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ. Microbiol. 10: 1357–1364. Welsh, A., Chee-Sanford, J.C., Connor, L.M., Löffler, F.E., and Sanford, R.A. (2014) Refined NrfA phylogeny improves PCR-based nrfA gene detection. Appl. Environ. Microbiol. 80: 2110–2119.
6
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Figure S1
1940_nosZI 156_Halobacterium_sp 149_Haloarcula_amylolytica 150_Haloarcula_argentinensis 151_Haloarcula_hispnica 152_Haloarcula_japonica 153_Haloarcula_sinaiiensis 154_Haloarcula_vallismortis 160_halophilic_archaeon 159_Halogeometricum_borinquense 174_Haloferax_denitrificans 175_Haloferax_larsenii 176_Haloferax_mediterranei 169_Halorubrum_lacuspofundi 171_Halorubrum_saccharovorum 246_Natronococcus_amylolyticus 249_Natrialba_hulunbeirensis 158_Halobiforma_nitratireducens 248_Natronococcus_occultus 167_Halorubrum_aidingense 170_Halorubrum_lipolyticum 168_Halorubrum_hochstenium 172_Halorubrum_terrestre 250_Natrinema_altunense 166_Halopiger_xanaduensis 247_Natronococcus_jeotgali 164_Halopiger_sp 157_Halobiforma_lacisalsi 165_Halopiger_sp 1215_nosZI 500_nosZI 1733_nosZI 1293_nosZI 1404_nosZI 182_Janthinobacterium_sp 1149_nosZI 225_Methylotenera_mobilis 328_Pseudogulbenkiania_sp 069_Burkholderia_kururiensis 070_Burkholderia_pseudomallei 071_Burkholderia_thailandensis 039_Azoarcus_sp 030_Aromatoleum_aromaticum 041_Azoarcus_toluclasticus 009_Aedes_aegypti 1732_nosZI 350_Rhodoferax_ferrireducens 427_Thiobacillus_denitrificans 426_Thiobacillus_denitrificans 428_Thiobacillus_thioparus 416_Thauera_aminoaromatica 422_Thauera_sp 424_Thauera_terpenica 327_Pseudogulbenkiania_ferrooxidans 138_gamma_proteobacterium 188_Lautropia_mirabilis 040_Azoarcus_sp 418_Thauera_linaloolentis 421_Thauera_sp 423_Thauera_sp 018_Alicycliphilus_denitrificans 002_Acidovorax_ebreus 007_Acidovorax_sp 005_Acidovorax_sp 004_Acidovorax_sp 008_Aedes_aegypti 380_Rubrivivax_gelatinosus 006_Acidovorax_sp 003_Acidovorax_radicis 032_Azohydromonas_australica 191_Leptothrix_cholodnii 438_uncultured_bacterium 001_Acidovorax_delafieldii 437_uncultured_bacterium 330_Pseudoperonospra_cubensis 338_Ralstonia_eutropha 104_Cupriavidus_sp 340_Ralstonia_pickettii 049_beta_proteobacterium 105_Cupriavidus_sp 103_Cupriavidus_basilensis 339_Ralstonia_pickettii 342_Ralstonia_solanacearum 1169_nosZI 341_Ralstonia_solanacearum 431_Thioalkalivibrio_sulfidophilus 429_Thioalkalivibrio_nitratireducens 432_Thioalkalivibrio_thiocyanoxidans 1558_nosZI 162_Halomonas_sp 163_Halomonas_sp 207_Marinobacter_daepoensis 208_Marinobacter_hydrocarbonoclasticus 211_Marinobacter_santoriniensis 210_Marinobacter_manganoxydans 209_Marinobacter_lipolyticus 212_Marinobacter_sp 147_Hahella_chejuensis 148_Hahella_ganghwensis 020_Alcanivorax_dieselolei 299_Pseudomonas_caeni 307_Pseudomonas_pelagia 314_Pseudomonas_stutzeri 298_Pseudomonas_brassicacearum 301_Pseudomonas_extremaustralis 326_Pseudomonas_veronii 304_Pseudomonas_fluorescens 308_Pseudomonas_sp 302_Pseudomonas_fluorescens 303_Pseudomonas_fluorescens 305_Pseudomonas_mandelii 311_Pseudomonas_sp 312_Pseudomonas_sp 012_Aeromonas_salmonicida 315_Pseudomonas_stutzeri 316_Pseudomonas_stutzeri 320_Pseudomonas_stutzeri 323_Pseudomonas_stutzeri 322_Pseudomonas_stutzeri 325_Pseudomonas_stutzeri 313_Pseudomonas_stutzeri 324_Pseudomonas_stutzeri 318_Pseudomonas_stutzeri 319_Pseudomonas_stutzeri 306_Pseudomonas_mendocina 321_Pseudomonas_stutzeri 317_Pseudomonas_stutzeri 309_Pseudomonas_sp 300_Pseudomonas_denitrificans 297_Pseudomonas_aeruginosa 310_Pseudomonas_sp 1840_nosZI 019_Alkalilimnicola_ehrlichii 430_Thioalkalivibrio_sp 433_Thioalkalivibrio_thiocyanodenitrificans 294_Psychromonas_ingrahamii 362_Rhodanobacter_sp 358_Rhodanobacter_spthiphylli 357_Rhodanobacter_fulvus 363_Rhodanobacter_thiooxydans 360_Rhodanobacter_sp 359_Rhodanobacter_sp 361_Rhodanobacter_sp 343_Reinekea_blandensis 1201_nosZI 1334_nosZI 261_Osedax_symbiont 262_Osedax_symbiont 021_Amphritea_japonica 241_Neptunomonas_japonica 101_Colwellia_piezophila 102_Colwellia_psychrerythraea 392_Shewanella_denitrificans 393_Shewanella_loihica 440_Vibrio_orientalis 441_Vibrio_tubiashii 218_Moritella_sp 216_Moritella_dasanensis 217_Moritella_marina 100_Colwellia_piezophila 293_Psychromonas_hadalis 292_Psychromonas_aquimarina 295_Psychromonas_ossibalaenae 277_Photobacterium_profundum 278_Photobacterium_profundum 1403_nosZI 179_Hyphomicrobium_zavarzinii 439_nosZI 279_Pleomorphomonas_koreensis 280_Pleomorphomonas_oryzae 063_Bradyrhizobium_sp 056_Bradyrhizobium_japonicum 173_nosZI 065_Bradyrhizobium_sp 062_Bradyrhizobium_sp 061_Bradyrhizobium_sp 057_Bradyrhizobium_oligotrophicum 066_Bradyrhizobium_sp 064_Bradyrhizobium_sp 058_Bradyrhizobium_sp 054_Bradyrhizobium_japonicum 059_Bradyrhizobium_sp 060_Bradyrhizobium_sp 053_Bradyrhizobium_japonicum 052_Bradyrhizobium_japonicum 067_Bradyrhizobium_yuanmingense 055_Bradyrhizobium_japonicum 013_Afipia_birgiae 348_Rhodopseudomonas_palustris 349_Rhodopseudomonas_palustris 347_Rhodopseudomonas_palustris 345_Rhodopseudomonas_palustris 346_Rhodopseudomonas_palustris 014_Afipia_sp 177_Hyphomicrobium_denitrificans 178_Hyphomicrobium_denitrificans 258_Oligotropha_carboxidovorans 215_Methylobacterium_sp 094_Chelatococcus_sp 329_Pseudochrobactrum_sp 068_Brucella_ceti 253_Ochrobactrum_anthropi 214_Mesorhizobium_loti 268_Paracoccus_sp 396_Sinorhizobium_fredii 354_Rhizobium_sp 397_Sinorhizobium_meliloti 353_Rhizobium_leguminosarum 352_Rhizobium_giardinii 355_Rhizobium_sp 264_Pantholops_hodgsonii 356_Rhizobium_sullae 296_Pseudovibrio_sp 1321_nosZI 183_Kiloniella_laminariae 265_Pantholops_hodgsonii 034_Azosprillum_amazonense 035_Azosprillum_brasilense 036_Azosprillum_brasilense 038_Azosprillum_lipoferum 037_Azosprillum_halopraeferens 368_Rhodosprillum_centenum 088_Cardiobacterium_hominis 089_Cardiobacterium_valvarum 256_Oligella_ureolytica 257_Oligella_urethralis 051_Bordetella_petrii 445_Achromobacter_arsenitoxydans 446_Achromobacter_xylosoxidans 447_Achromobacter_xylosoxidans 015_Alcaligenes_faecalis 016_Alcaligenes_faecalis 186_Kingella_oralis 185_Kingella_kingae 184_Kingella_denitrificans 395_Simonsiella_muelleri 236_Neisseria_macacae 239_Neisseria_sp 237_Neisseria_mucosa 238_Neisseria_sicca 233_Neisseria_flavescens 240_Neisseria_subflava 232_Neisseria_cinerea 234_Neisseria_flavescens 235_Neisseria_gonorrhoeae 436_Thalassospra_xiamenensis 029_Arhodomonas_aquaeolei 402_Salinispaera_shabanensis 252_Nitratireductor_indicus 222_Maritimibacter_alkaliphilus 403_Salipiger_mucosus 689_nosZI 1513_nosZI 242_Nesiotobacter_exalbescens 098_Celeribacter_baekdonensis 390_Sediminimonas_qiaohouensis 1022_nosZI 1548_nosZI 1001_nosZI 1809_nosZI 1359_nosZI 1691_nosZI 364_Rhodobacter_capsulatus 367_Rhodobacter_spaeroides 365_Rhodobacter_sp 366_Rhodobacter_spaeroides 1306_nosZI 266_Paracoccus_denitrificans 090_Catellibacterium_nectariphilum 267_Paracoccus_sp 1755_nosZI 375_Roseovarius_sp 376_Roseovarius_sp 2010_nosZI 281_Pannonibacter_phragmitetus 273_Phaeobacter_arcticus 254_Oceaniovalibus_guishaninsula 331_Pseudorhodobacter_ferrugineus 096_Citreicella_sp 115_Dinoroseobacter_shibae 1879_nosZI 382_Ruegeria_pomeroyi 379_Roseobacter_sp 189_Leisingera_aquimarina 344_Rhodobacterales_bacterium 274_Phaeobacter_caeruleus 275_Phaeobacter_gallaeciensis 282_Polymorphum_gilvum 220_Maritalea_myrionectae 187_Labrenzia_aggregata 244_Nisaea_denitrificans 237_nosZI 377_Roseobacter_denitrificans 378_Roseobacter_litoralis 190_Leisingera_nanhaiensis 394_Silicibacter_lacuscaerulensis 1044_nosZI 383_Ruegeria_sp
[238]
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Figure S2
1940_nosZI 156_Halobacterium_sp 149_Haloarcula_amylolytica 150_Haloarcula_argentinensis 151_Haloarcula_hispnica 152_Haloarcula_japonica 153_Haloarcula_sinaiiensis 154_Haloarcula_vallismortis 160_halophilic_archaeon 159_Halogeometricum_borinquense 174_Haloferax_denitrificans 175_Haloferax_larsenii 176_Haloferax_mediterranei 169_Halorubrum_lacuspofundi 171_Halorubrum_saccharovorum 246_Natronococcus_amylolyticus 249_Natrialba_hulunbeirensis 158_Halobiforma_nitratireducens 248_Natronococcus_occultus 167_Halorubrum_aidingense 170_Halorubrum_lipolyticum 168_Halorubrum_hochstenium 172_Halorubrum_terrestre 250_Natrinema_altunense 166_Halopiger_xanaduensis 247_Natronococcus_jeotgali 164_Halopiger_sp 157_Halobiforma_lacisalsi 165_Halopiger_sp 1215_nosZI 500_nosZI 1733_nosZI 1293_nosZI 1404_nosZI 182_Janthinobacterium_sp 1149_nosZI 225_Methylotenera_mobilis 328_Pseudogulbenkiania_sp 069_Burkholderia_kururiensis 070_Burkholderia_pseudomallei 071_Burkholderia_thailandensis 039_Azoarcus_sp 030_Aromatoleum_aromaticum 041_Azoarcus_toluclasticus 009_Aedes_aegypti 1732_nosZI 350_Rhodoferax_ferrireducens 427_Thiobacillus_denitrificans 426_Thiobacillus_denitrificans 428_Thiobacillus_thioparus 416_Thauera_aminoaromatica 422_Thauera_sp 424_Thauera_terpenica 327_Pseudogulbenkiania_ferrooxidans 138_gamma_proteobacterium 188_Lautropia_mirabilis 040_Azoarcus_sp 418_Thauera_linaloolentis 421_Thauera_sp 423_Thauera_sp 018_Alicycliphilus_denitrificans 002_Acidovorax_ebreus 007_Acidovorax_sp 005_Acidovorax_sp 004_Acidovorax_sp 008_Aedes_aegypti 380_Rubrivivax_gelatinosus 006_Acidovorax_sp 003_Acidovorax_radicis 032_Azohydromonas_australica 191_Leptothrix_cholodnii 438_uncultured_bacterium 001_Acidovorax_delafieldii 437_uncultured_bacterium 330_Pseudoperonospra_cubensis 338_Ralstonia_eutropha 104_Cupriavidus_sp 340_Ralstonia_pickettii 049_beta_proteobacterium 105_Cupriavidus_sp 103_Cupriavidus_basilensis 339_Ralstonia_pickettii 342_Ralstonia_solanacearum 1169_nosZI 341_Ralstonia_solanacearum 431_Thioalkalivibrio_sulfidophilus 429_Thioalkalivibrio_nitratireducens 432_Thioalkalivibrio_thiocyanoxidans 1558_nosZI 162_Halomonas_sp 163_Halomonas_sp 207_Marinobacter_daepoensis 208_Marinobacter_hydrocarbonoclasticus 211_Marinobacter_santoriniensis 210_Marinobacter_manganoxydans 209_Marinobacter_lipolyticus 212_Marinobacter_sp 147_Hahella_chejuensis 148_Hahella_ganghwensis 020_Alcanivorax_dieselolei 299_Pseudomonas_caeni 307_Pseudomonas_pelagia 314_Pseudomonas_stutzeri 298_Pseudomonas_brassicacearum 301_Pseudomonas_extremaustralis 326_Pseudomonas_veronii 304_Pseudomonas_fluorescens 308_Pseudomonas_sp 302_Pseudomonas_fluorescens 303_Pseudomonas_fluorescens 305_Pseudomonas_mandelii 311_Pseudomonas_sp 312_Pseudomonas_sp 012_Aeromonas_salmonicida 315_Pseudomonas_stutzeri 316_Pseudomonas_stutzeri 320_Pseudomonas_stutzeri 323_Pseudomonas_stutzeri 322_Pseudomonas_stutzeri 325_Pseudomonas_stutzeri 313_Pseudomonas_stutzeri 324_Pseudomonas_stutzeri 318_Pseudomonas_stutzeri 319_Pseudomonas_stutzeri 306_Pseudomonas_mendocina 321_Pseudomonas_stutzeri 317_Pseudomonas_stutzeri 309_Pseudomonas_sp 300_Pseudomonas_denitrificans 297_Pseudomonas_aeruginosa 310_Pseudomonas_sp 1840_nosZI 019_Alkalilimnicola_ehrlichii 430_Thioalkalivibrio_sp 433_Thioalkalivibrio_thiocyanodenitrificans 294_Psychromonas_ingrahamii 362_Rhodanobacter_sp 358_Rhodanobacter_spthiphylli 357_Rhodanobacter_fulvus 363_Rhodanobacter_thiooxydans 360_Rhodanobacter_sp 359_Rhodanobacter_sp 361_Rhodanobacter_sp 343_Reinekea_blandensis 1201_nosZI 1334_nosZI 261_Osedax_symbiont 262_Osedax_symbiont 021_Amphritea_japonica 241_Neptunomonas_japonica 101_Colwellia_piezophila 102_Colwellia_psychrerythraea 392_Shewanella_denitrificans 393_Shewanella_loihica 440_Vibrio_orientalis 441_Vibrio_tubiashii 218_Moritella_sp 216_Moritella_dasanensis 217_Moritella_marina 100_Colwellia_piezophila 293_Psychromonas_hadalis 292_Psychromonas_aquimarina 295_Psychromonas_ossibalaenae 277_Photobacterium_profundum 278_Photobacterium_profundum 1403_nosZI 179_Hyphomicrobium_zavarzinii 439_nosZI 279_Pleomorphomonas_koreensis 280_Pleomorphomonas_oryzae 063_Bradyrhizobium_sp 056_Bradyrhizobium_japonicum 173_nosZI 065_Bradyrhizobium_sp 062_Bradyrhizobium_sp 061_Bradyrhizobium_sp 057_Bradyrhizobium_oligotrophicum 066_Bradyrhizobium_sp 064_Bradyrhizobium_sp 058_Bradyrhizobium_sp 054_Bradyrhizobium_japonicum 059_Bradyrhizobium_sp 060_Bradyrhizobium_sp 053_Bradyrhizobium_japonicum 052_Bradyrhizobium_japonicum 067_Bradyrhizobium_yuanmingense 055_Bradyrhizobium_japonicum 013_Afipia_birgiae 348_Rhodopseudomonas_palustris 349_Rhodopseudomonas_palustris 347_Rhodopseudomonas_palustris 345_Rhodopseudomonas_palustris 346_Rhodopseudomonas_palustris 014_Afipia_sp 177_Hyphomicrobium_denitrificans 178_Hyphomicrobium_denitrificans 258_Oligotropha_carboxidovorans 215_Methylobacterium_sp 094_Chelatococcus_sp 329_Pseudochrobactrum_sp 068_Brucella_ceti 253_Ochrobactrum_anthropi 214_Mesorhizobium_loti 268_Paracoccus_sp 396_Sinorhizobium_fredii 354_Rhizobium_sp 397_Sinorhizobium_meliloti 353_Rhizobium_leguminosarum 352_Rhizobium_giardinii 355_Rhizobium_sp 264_Pantholops_hodgsonii 356_Rhizobium_sullae 296_Pseudovibrio_sp 1321_nosZI 183_Kiloniella_laminariae 265_Pantholops_hodgsonii 034_Azosprillum_amazonense 035_Azosprillum_brasilense 036_Azosprillum_brasilense 038_Azosprillum_lipoferum 037_Azosprillum_halopraeferens 368_Rhodosprillum_centenum 088_Cardiobacterium_hominis 089_Cardiobacterium_valvarum 256_Oligella_ureolytica 257_Oligella_urethralis 051_Bordetella_petrii 445_Achromobacter_arsenitoxydans 446_Achromobacter_xylosoxidans 447_Achromobacter_xylosoxidans 015_Alcaligenes_faecalis 016_Alcaligenes_faecalis 186_Kingella_oralis 185_Kingella_kingae 184_Kingella_denitrificans 395_Simonsiella_muelleri 236_Neisseria_macacae 239_Neisseria_sp 237_Neisseria_mucosa 238_Neisseria_sicca 233_Neisseria_flavescens 240_Neisseria_subflava 232_Neisseria_cinerea 234_Neisseria_flavescens 235_Neisseria_gonorrhoeae 436_Thalassospra_xiamenensis 029_Arhodomonas_aquaeolei 402_Salinispaera_shabanensis 252_Nitratireductor_indicus 222_Maritimibacter_alkaliphilus 403_Salipiger_mucosus 689_nosZI 1513_nosZI 242_Nesiotobacter_exalbescens 098_Celeribacter_baekdonensis 390_Sediminimonas_qiaohouensis 1022_nosZI 1548_nosZI 1001_nosZI 1809_nosZI 1359_nosZI 1691_nosZI 364_Rhodobacter_capsulatus 367_Rhodobacter_spaeroides 365_Rhodobacter_sp 366_Rhodobacter_spaeroides 1306_nosZI 266_Paracoccus_denitrificans 090_Catellibacterium_nectariphilum 267_Paracoccus_sp 1755_nosZI 375_Roseovarius_sp 376_Roseovarius_sp 2010_nosZI 281_Pannonibacter_phragmitetus 273_Phaeobacter_arcticus 254_Oceaniovalibus_guishaninsula 331_Pseudorhodobacter_ferrugineus 096_Citreicella_sp 115_Dinoroseobacter_shibae 1879_nosZI 382_Ruegeria_pomeroyi 379_Roseobacter_sp 189_Leisingera_aquimarina 344_Rhodobacterales_bacterium 274_Phaeobacter_caeruleus 275_Phaeobacter_gallaeciensis 282_Polymorphum_gilvum 220_Maritalea_myrionectae 187_Labrenzia_aggregata 244_Nisaea_denitrificans 237_nosZI 377_Roseobacter_denitrificans 378_Roseobacter_litoralis 190_Leisingera_nanhaiensis 394_Silicibacter_lacuscaerulensis 1044_nosZI 383_Ruegeria_sp
[298]
0.1
Figure S3
1315_nosZII 1777_nosZII 360_nosZII 968_nosZII 1570_nosZII 255_Olavius_algarvensis 122_endosymbiont_of 387_Sedimenticola_selenatireducens 1426_nosZII 425_Thiocapsa_marina 1610_nosZII 417_Thauera_linaloolentis 419_Thauera_phenylacetica 420_Thauera_selenatis 033_Azonexus_hydrophilus 404_Sulfuricella_denitrificans 106_Dechlorosoma_suillum 108_Dechloromonas_aromatica 082_Candidatus_Accumulibacter 107_Dechlorosoma_suillum 205_Magnetosprillum_magneticum 206_Magnetosprillum_sp. 410_Sulfurimonas_denitrificans 389_sediment_metagenome 412_Sulfurimonas_sp 245_Nitratiruptor_sp 251_Nitratifractor_salsuginis 398_Sulfurovum_sp 408_Sulfurimonas_autotrophica 413_Sulfurimonas_sp 409_Sulfurimonas_denitrificans 411_Sulfurimonas_gotlandica 110_Denitrovibrio_acetiphilus 076_Campylobacter_gracilis 414_Sutterella_sp 444__ 081_Campylobacter_sp 075_Campylobacter_curvus 073_Campylobacter_concisus 074_Campylobacter_concisus 079_Campylobacter_showae 078_Campylobacter_showae 077_Campylobacter_rectus 080_Campylobacter_showae 072_Calescamantes_bacterium 627_nosZII 1252_nosZII 844_nosZII 1485_nosZII 1778_nosZII 1464_nosZII 160_nosZII 1363_nosZII 1960_nosZII 923_nosZII 789_nosZII 1364_nosZII 534_nosZII 1238_nosZII 1604_nosZII 1305_nosZII 124_Ferroglobus_placidus 337_Pyrobaculum_sp 099_candidate_division 336_Pyrobaculum_calidifontis 1097_nosZII 884_nosZII 1269_nosZII 1986_nosZII 2003_nosZII 622_nosZII 1525_nosZII 61_nosZII 1760_nosZII 435_Thermomicrobium_roseum 369_Rhodothermus_marinus 370_Rhodothermus_marinus 407_Sphaerobacter_thermophilus 1071_nosZII 1646_nosZII 097_Caldilinea_aerophila 1052_nosZII 1799_nosZII 1226_nosZII 1157_nosZII 317_nosZII 1755_nosZII 1474_nosZII 1433_nosZII 871_nosZII 044_Bacillus_azotoformans 046_Bacillus_sp 117_Desulfotomaculum_ruminis 119_Desulfosprosinus_meridiei 114_Desulfitobacterium_sp 111_Desulfitobacterium_dichloroeliminans 120_Desulfosprosinus_youngiae 112_Desulfitobacterium_hafniense 113_Desulfitobacterium_hafniense 109_Deinococcus_ficus 042_Bacillus_azotoformans 045_Bacillus_massiliosenegalensis 043_Bacillus_azotoformans 047_Bacillus_sp 025_Anoxybacillus_flavithermus 141_Geobacillus_caldoxylosilyticus 142_Geobacillus_sp 143_Geobacillus_thermodenitrificans 118_Desulfomonile_tiedjei 022_Anaeromyxobacter_dehalogenans 023_Anaeromyxobacter_dehalogenans 024_Anaeromyxobacter_sp 1762_nosZII 386_Salinibacter_ruber 405_Salisaeta_longa 116_Diplospaera_colitermitum 260_Opitutaceae_bacterium 1011_nosZII 259_Opitutus_terrae 1973_nosZII 1688_nosZII 1641_nosZII 751_nosZII 093_Cesiribacter_andamanensis 286_Pontibacter_sp 284_Pontibacter_roseus 283_Pontibacter_roseus 285_Pontibacter_sp 2029_nosZII 1852_nosZII 2073_nosZII 269_Pedobacter_arcticus 406_Solitalea_canadensis 1721_nosZII 276_Phocaeicola_abscessus 289_Prevotella_multisaccharivorax 290_Prevotella_oulorum 287_Prevotella_denticola 288_Prevotella_histicola 291_Prevotella_veroralis 271_Pedobacter_saltans 017_Algoriphagus_mannitolivorans 351_Rhodonellum_psychrophilum 048_Belliella_baltica 091_Cecembia_lonarensis 221_Mariniradius_saccharolyticus 1896_nosZII 173_Haliscomenobacter_hydrossis 385_Runella_zeae 384_Runella_slithyformis 381_Rudanella_lutea 388_Sediminibacterium_sp 243_Niastella_koreensis 391_Segetibacter_koreensis 121_Dyadobacter_fermentans 031_Arcticibacter_svalbardensis 270_Pedobacter_oryzae 231_Niabella_soli 373_Riemerella_columbina 371_Riemerella_anatipestifer 372_Riemerella_anatipestifer 095_Chryseobacterium_palustre 132_Flavobacteriaceae_bacterium 126_Flavobacterium_denitrificans 129_Flavobacterium_sp 128_Flavobacterium_gelidilacus 130_Flavobacterium_suncheonense 125_Flavobacterium_columnare 127_Flavobacterium_filum 140_Gemmatimonas_aurantiaca 434_Thermonema_rossianum 180_Ignavibacterium_album 998_nosZII 213_Melioribacter_roseus 399_Sulfurihydrogenibium_sp 155_Hydrogenobacter_thermophilus 272_Persephonella_marina 439_uncultured_bacterium 1636_nosZII 2042_nosZII 194_Leptonema_illini 201_Leptospra_terpstrae 202_Leptospra_vanthielii 199_Leptospra_meyeri 195_Leptospra_biflexa 204_Leptospra_yanagawae 200_Leptospra_sp. 203_Leptospra_wolffii 198_Leptospra_inadai 196_Leptospra_broomii 197_Leptospra_fainei 230_Nafulsella_turpanensis 263_Owenweeksia_hongkongensis 133_Flexithrix_dorotheae 136_Fulvivirga_imtechensis 192_Lewinella_cohaerens 181_Imtechella_halotolerans 1996_nosZII 193_Lewinella_persica 223_Marivirga_tractuosa 083_Capnocytophaga_cynodegmi 087_Capnocytophaga_sp 084_Capnocytophaga_gingivalis 085_Capnocytophaga_granulosa 086_Capnocytophaga_sp 137_Gaetbulibacter_saemankumensis 554_nosZII 026_Aquimarina_muelleri 219_Maribacter_sp 144_Gillisia_limnaea 400_Salinimicrobium_terrae 229_Myroides_odoratus 227_Myroides_injenensis 228_Myroides_odoratimimus 1283_nosZII 139_Gelidibacter_mesophilus 010_Aequorivita_capsosiphonis 011_Aequorivita_sublithincola 131_Flavobacteriaceae_bacterium 335_Psychroflexus_tropicus 333_Psychroflexus_gondwanensis 334_Psychroflexus_torquis 332_Psychroserpens_burtonensis 134_Flavobacteriales_bacterium 224_Mesoflavibacter_zeaxanthinifaciens 401_Salinimicrobium_xinjiangense 027_Arenibacter_certesii 028_Arenibacter_latericius 092_Cellulophaga_algicola 443_Zobellia_galactanivorans 226_Muricauda_ruestringensis 123_Eudoraea_adriatica 374_Robiginitalea_biformata 145_Gillisia_sp 146_Gramella_forsetii 415_Tenacibaculum_ovolyticum 050_Bizionia_argentinensis 135_Formosa_sp
[298]
0.1
Figure S4
1315_nosZII 1777_nosZII 360_nosZII 968_nosZII 1570_nosZII 255_Olavius_algarvensis 122_endosymbiont_of 387_Sedimenticola_selenatireducens 1426_nosZII 425_Thiocapsa_marina 1610_nosZII 417_Thauera_linaloolentis 419_Thauera_phenylacetica 420_Thauera_selenatis 033_Azonexus_hydrophilus 404_Sulfuricella_denitrificans 106_Dechlorosoma_suillum 108_Dechloromonas_aromatica 082_Candidatus_Accumulibacter 107_Dechlorosoma_suillum 205_Magnetosprillum_magneticum 206_Magnetosprillum_sp. 410_Sulfurimonas_denitrificans 389_sediment_metagenome 412_Sulfurimonas_sp 245_Nitratiruptor_sp 251_Nitratifractor_salsuginis 398_Sulfurovum_sp 408_Sulfurimonas_autotrophica 413_Sulfurimonas_sp 409_Sulfurimonas_denitrificans 411_Sulfurimonas_gotlandica 110_Denitrovibrio_acetiphilus 076_Campylobacter_gracilis 414_Sutterella_sp 444__ 081_Campylobacter_sp 075_Campylobacter_curvus 073_Campylobacter_concisus 074_Campylobacter_concisus 079_Campylobacter_showae 078_Campylobacter_showae 077_Campylobacter_rectus 080_Campylobacter_showae 072_Calescamantes_bacterium 627_nosZII 1252_nosZII 844_nosZII 1485_nosZII 1778_nosZII 1464_nosZII 160_nosZII 1363_nosZII 1960_nosZII 923_nosZII 789_nosZII 1364_nosZII 534_nosZII 1238_nosZII 1604_nosZII 1305_nosZII 124_Ferroglobus_placidus 337_Pyrobaculum_sp 099_candidate_division 336_Pyrobaculum_calidifontis 1097_nosZII 884_nosZII 1269_nosZII 1986_nosZII 2003_nosZII 622_nosZII 1525_nosZII 61_nosZII 1760_nosZII 435_Thermomicrobium_roseum 369_Rhodothermus_marinus 370_Rhodothermus_marinus 407_Sphaerobacter_thermophilus 1071_nosZII 1646_nosZII 097_Caldilinea_aerophila 1052_nosZII 1799_nosZII 1226_nosZII 1157_nosZII 317_nosZII 1755_nosZII 1474_nosZII 1433_nosZII 871_nosZII 044_Bacillus_azotoformans 046_Bacillus_sp 117_Desulfotomaculum_ruminis 119_Desulfosprosinus_meridiei 114_Desulfitobacterium_sp 111_Desulfitobacterium_dichloroeliminans 120_Desulfosprosinus_youngiae 112_Desulfitobacterium_hafniense 113_Desulfitobacterium_hafniense 109_Deinococcus_ficus 042_Bacillus_azotoformans 045_Bacillus_massiliosenegalensis 043_Bacillus_azotoformans 047_Bacillus_sp 025_Anoxybacillus_flavithermus 141_Geobacillus_caldoxylosilyticus 142_Geobacillus_sp 143_Geobacillus_thermodenitrificans 118_Desulfomonile_tiedjei 022_Anaeromyxobacter_dehalogenans 023_Anaeromyxobacter_dehalogenans 024_Anaeromyxobacter_sp 1762_nosZII 386_Salinibacter_ruber 405_Salisaeta_longa 116_Diplospaera_colitermitum 260_Opitutaceae_bacterium 1011_nosZII 259_Opitutus_terrae 1973_nosZII 1688_nosZII 1641_nosZII 751_nosZII 093_Cesiribacter_andamanensis 286_Pontibacter_sp 284_Pontibacter_roseus 283_Pontibacter_roseus 285_Pontibacter_sp 2029_nosZII 1852_nosZII 2073_nosZII 269_Pedobacter_arcticus 406_Solitalea_canadensis 1721_nosZII 276_Phocaeicola_abscessus 289_Prevotella_multisaccharivorax 290_Prevotella_oulorum 287_Prevotella_denticola 288_Prevotella_histicola 291_Prevotella_veroralis 271_Pedobacter_saltans 017_Algoriphagus_mannitolivorans 351_Rhodonellum_psychrophilum 048_Belliella_baltica 091_Cecembia_lonarensis 221_Mariniradius_saccharolyticus 1896_nosZII 173_Haliscomenobacter_hydrossis 385_Runella_zeae 384_Runella_slithyformis 381_Rudanella_lutea 388_Sediminibacterium_sp 243_Niastella_koreensis 391_Segetibacter_koreensis 121_Dyadobacter_fermentans 031_Arcticibacter_svalbardensis 270_Pedobacter_oryzae 231_Niabella_soli 373_Riemerella_columbina 371_Riemerella_anatipestifer 372_Riemerella_anatipestifer 095_Chryseobacterium_palustre 132_Flavobacteriaceae_bacterium 126_Flavobacterium_denitrificans 129_Flavobacterium_sp 128_Flavobacterium_gelidilacus 130_Flavobacterium_suncheonense 125_Flavobacterium_columnare 127_Flavobacterium_filum 140_Gemmatimonas_aurantiaca 434_Thermonema_rossianum 180_Ignavibacterium_album 998_nosZII 213_Melioribacter_roseus 399_Sulfurihydrogenibium_sp 155_Hydrogenobacter_thermophilus 272_Persephonella_marina 439_uncultured_bacterium 1636_nosZII 2042_nosZII 194_Leptonema_illini 201_Leptospra_terpstrae 202_Leptospra_vanthielii 199_Leptospra_meyeri 195_Leptospra_biflexa 204_Leptospra_yanagawae 200_Leptospra_sp. 203_Leptospra_wolffii 198_Leptospra_inadai 196_Leptospra_broomii 197_Leptospra_fainei 230_Nafulsella_turpanensis 263_Owenweeksia_hongkongensis 133_Flexithrix_dorotheae 136_Fulvivirga_imtechensis 192_Lewinella_cohaerens 181_Imtechella_halotolerans 1996_nosZII 193_Lewinella_persica 223_Marivirga_tractuosa 083_Capnocytophaga_cynodegmi 087_Capnocytophaga_sp 084_Capnocytophaga_gingivalis 085_Capnocytophaga_granulosa 086_Capnocytophaga_sp 137_Gaetbulibacter_saemankumensis 554_nosZII 026_Aquimarina_muelleri 219_Maribacter_sp 144_Gillisia_limnaea 400_Salinimicrobium_terrae 229_Myroides_odoratus 227_Myroides_injenensis 228_Myroides_odoratimimus 1283_nosZII 139_Gelidibacter_mesophilus 010_Aequorivita_capsosiphonis 011_Aequorivita_sublithincola 131_Flavobacteriaceae_bacterium 335_Psychroflexus_tropicus 333_Psychroflexus_gondwanensis 334_Psychroflexus_torquis 332_Psychroserpens_burtonensis 134_Flavobacteriales_bacterium 224_Mesoflavibacter_zeaxanthinifaciens 401_Salinimicrobium_xinjiangense 027_Arenibacter_certesii 028_Arenibacter_latericius 092_Cellulophaga_algicola 443_Zobellia_galactanivorans 226_Muricauda_ruestringensis 123_Eudoraea_adriatica 374_Robiginitalea_biformata 145_Gillisia_sp 146_Gramella_forsetii 415_Tenacibaculum_ovolyticum 050_Bizionia_argentinensis 135_Formosa_sp
[238] 1940_nosZI 156_Halobacterium_sp 149_Haloarcula_amylolytica 150_Haloarcula_argentinensis 151_Haloarcula_hispnica
Figure S5
152_Haloarcula_japonica 153_Haloarcula_sinaiiensis 154_Haloarcula_vallismortis 160_halophilic_archaeon 159_Halogeometricum_borinquense 174_Haloferax_denitrificans 175_Haloferax_larsenii 176_Haloferax_mediterranei 169_Halorubrum_lacuspofundi 171_Halorubrum_saccharovorum 246_Natronococcus_amylolyticus 249_Natrialba_hulunbeirensis 158_Halobiforma_nitratireducens 248_Natronococcus_occultus 167_Halorubrum_aidingense 170_Halorubrum_lipolyticum 168_Halorubrum_hochstenium 172_Halorubrum_terrestre 250_Natrinema_altunense 166_Halopiger_xanaduensis 247_Natronococcus_jeotgali 164_Halopiger_sp 157_Halobiforma_lacisalsi 165_Halopiger_sp 1215_nosZI
0.1
500_nosZI 1733_nosZI 1293_nosZI 1404_nosZI 182_Janthinobacterium_sp 1149_nosZI 225_Methylotenera_mobilis 328_Pseudogulbenkiania_sp 069_Burkholderia_kururiensis 070_Burkholderia_pseudomallei 071_Burkholderia_thailandensis 039_Azoarcus_sp 030_Aromatoleum_aromaticum 041_Azoarcus_toluclasticus 009_Aedes_aegypti 1732_nosZI 350_Rhodoferax_ferrireducens 427_Thiobacillus_denitrificans 426_Thiobacillus_denitrificans 428_Thiobacillus_thioparus 416_Thauera_aminoaromatica 422_Thauera_sp 424_Thauera_terpenica 327_Pseudogulbenkiania_ferrooxidans 138_gamma_proteobacterium 188_Lautropia_mirabilis 040_Azoarcus_sp 418_Thauera_linaloolentis 421_Thauera_sp 423_Thauera_sp 018_Alicycliphilus_denitrificans 002_Acidovorax_ebreus 007_Acidovorax_sp 005_Acidovorax_sp 004_Acidovorax_sp 008_Aedes_aegypti 380_Rubrivivax_gelatinosus 006_Acidovorax_sp 003_Acidovorax_radicis 032_Azohydromonas_australica 191_Leptothrix_cholodnii 438_uncultured_bacterium 001_Acidovorax_delafieldii 437_uncultured_bacterium 330_Pseudoperonospra_cubensis 338_Ralstonia_eutropha 104_Cupriavidus_sp 340_Ralstonia_pickettii 049_beta_proteobacterium 105_Cupriavidus_sp 103_Cupriavidus_basilensis 339_Ralstonia_pickettii 342_Ralstonia_solanacearum 1169_nosZI 341_Ralstonia_solanacearum 431_Thioalkalivibrio_sulfidophilus 429_Thioalkalivibrio_nitratireducens 432_Thioalkalivibrio_thiocyanoxidans 1558_nosZI 162_Halomonas_sp 163_Halomonas_sp 207_Marinobacter_daepoensis 208_Marinobacter_hydrocarbonoclasticus 211_Marinobacter_santoriniensis 210_Marinobacter_manganoxydans 209_Marinobacter_lipolyticus 212_Marinobacter_sp 147_Hahella_chejuensis 148_Hahella_ganghwensis 020_Alcanivorax_dieselolei 299_Pseudomonas_caeni 307_Pseudomonas_pelagia 314_Pseudomonas_stutzeri 298_Pseudomonas_brassicacearum 301_Pseudomonas_extremaustralis 326_Pseudomonas_veronii 304_Pseudomonas_fluorescens 308_Pseudomonas_sp 302_Pseudomonas_fluorescens 303_Pseudomonas_fluorescens 305_Pseudomonas_mandelii 311_Pseudomonas_sp 312_Pseudomonas_sp 012_Aeromonas_salmonicida 315_Pseudomonas_stutzeri 316_Pseudomonas_stutzeri 320_Pseudomonas_stutzeri 323_Pseudomonas_stutzeri 322_Pseudomonas_stutzeri 325_Pseudomonas_stutzeri 313_Pseudomonas_stutzeri 324_Pseudomonas_stutzeri 318_Pseudomonas_stutzeri 319_Pseudomonas_stutzeri 306_Pseudomonas_mendocina 321_Pseudomonas_stutzeri 317_Pseudomonas_stutzeri 309_Pseudomonas_sp 300_Pseudomonas_denitrificans 297_Pseudomonas_aeruginosa 310_Pseudomonas_sp 1840_nosZI 019_Alkalilimnicola_ehrlichii 430_Thioalkalivibrio_sp 433_Thioalkalivibrio_thiocyanodenitrificans 294_Psychromonas_ingrahamii 362_Rhodanobacter_sp 358_Rhodanobacter_spthiphylli 357_Rhodanobacter_fulvus 363_Rhodanobacter_thiooxydans 360_Rhodanobacter_sp 359_Rhodanobacter_sp 361_Rhodanobacter_sp 343_Reinekea_blandensis 1201_nosZI 1334_nosZI 261_Osedax_symbiont 262_Osedax_symbiont 021_Amphritea_japonica 241_Neptunomonas_japonica 101_Colwellia_piezophila 102_Colwellia_psychrerythraea 392_Shewanella_denitrificans 393_Shewanella_loihica 440_Vibrio_orientalis 441_Vibrio_tubiashii 218_Moritella_sp 216_Moritella_dasanensis 217_Moritella_marina 100_Colwellia_piezophila 293_Psychromonas_hadalis 292_Psychromonas_aquimarina 295_Psychromonas_ossibalaenae 277_Photobacterium_profundum 278_Photobacterium_profundum 1403_nosZI 179_Hyphomicrobium_zavarzinii 439_nosZI 279_Pleomorphomonas_koreensis 280_Pleomorphomonas_oryzae 063_Bradyrhizobium_sp 056_Bradyrhizobium_japonicum 173_nosZI 065_Bradyrhizobium_sp 062_Bradyrhizobium_sp 061_Bradyrhizobium_sp 057_Bradyrhizobium_oligotrophicum 066_Bradyrhizobium_sp 064_Bradyrhizobium_sp 058_Bradyrhizobium_sp 054_Bradyrhizobium_japonicum 059_Bradyrhizobium_sp 060_Bradyrhizobium_sp 053_Bradyrhizobium_japonicum 052_Bradyrhizobium_japonicum 067_Bradyrhizobium_yuanmingense 055_Bradyrhizobium_japonicum 013_Afipia_birgiae 348_Rhodopseudomonas_palustris 349_Rhodopseudomonas_palustris 347_Rhodopseudomonas_palustris 345_Rhodopseudomonas_palustris 346_Rhodopseudomonas_palustris 014_Afipia_sp 177_Hyphomicrobium_denitrificans 178_Hyphomicrobium_denitrificans 258_Oligotropha_carboxidovorans 215_Methylobacterium_sp 094_Chelatococcus_sp 329_Pseudochrobactrum_sp 068_Brucella_ceti 253_Ochrobactrum_anthropi 214_Mesorhizobium_loti 268_Paracoccus_sp 396_Sinorhizobium_fredii 354_Rhizobium_sp 397_Sinorhizobium_meliloti 353_Rhizobium_leguminosarum 352_Rhizobium_giardinii 355_Rhizobium_sp 264_Pantholops_hodgsonii 356_Rhizobium_sullae 296_Pseudovibrio_sp 1321_nosZI 183_Kiloniella_laminariae 265_Pantholops_hodgsonii 034_Azosprillum_amazonense 035_Azosprillum_brasilense 036_Azosprillum_brasilense 038_Azosprillum_lipoferum 037_Azosprillum_halopraeferens 368_Rhodosprillum_centenum 088_Cardiobacterium_hominis 089_Cardiobacterium_valvarum 256_Oligella_ureolytica 257_Oligella_urethralis 051_Bordetella_petrii 445_Achromobacter_arsenitoxydans 446_Achromobacter_xylosoxidans 447_Achromobacter_xylosoxidans 015_Alcaligenes_faecalis 016_Alcaligenes_faecalis 186_Kingella_oralis 185_Kingella_kingae 184_Kingella_denitrificans 395_Simonsiella_muelleri 236_Neisseria_macacae 239_Neisseria_sp 237_Neisseria_mucosa 238_Neisseria_sicca 233_Neisseria_flavescens 240_Neisseria_subflava 232_Neisseria_cinerea 234_Neisseria_flavescens 235_Neisseria_gonorrhoeae 436_Thalassospra_xiamenensis 029_Arhodomonas_aquaeolei 402_Salinispaera_shabanensis 252_Nitratireductor_indicus 222_Maritimibacter_alkaliphilus 403_Salipiger_mucosus 689_nosZI 1513_nosZI 242_Nesiotobacter_exalbescens 098_Celeribacter_baekdonensis 390_Sediminimonas_qiaohouensis 1022_nosZI 1548_nosZI 1001_nosZI 1809_nosZI 1359_nosZI 1691_nosZI 364_Rhodobacter_capsulatus 367_Rhodobacter_spaeroides 365_Rhodobacter_sp 366_Rhodobacter_spaeroides 1306_nosZI 266_Paracoccus_denitrificans 090_Catellibacterium_nectariphilum 267_Paracoccus_sp 1755_nosZI 375_Roseovarius_sp 376_Roseovarius_sp 2010_nosZI 281_Pannonibacter_phragmitetus 273_Phaeobacter_arcticus 254_Oceaniovalibus_guishaninsula 331_Pseudorhodobacter_ferrugineus 096_Citreicella_sp 115_Dinoroseobacter_shibae 1879_nosZI 382_Ruegeria_pomeroyi 379_Roseobacter_sp 189_Leisingera_aquimarina 344_Rhodobacterales_bacterium 274_Phaeobacter_caeruleus 275_Phaeobacter_gallaeciensis 282_Polymorphum_gilvum 220_Maritalea_myrionectae 187_Labrenzia_aggregata 244_Nisaea_denitrificans 237_nosZI 377_Roseobacter_denitrificans 378_Roseobacter_litoralis 190_Leisingera_nanhaiensis 394_Silicibacter_lacuscaerulensis 1044_nosZI 383_Ruegeria_sp
[238] 1940_nosZI 156_Halobacterium_sp 149_Haloarcula_amylolytica 150_Haloarcula_argentinensis 151_Haloarcula_hispnica
Figure S6
152_Haloarcula_japonica 153_Haloarcula_sinaiiensis 154_Haloarcula_vallismortis 160_halophilic_archaeon 159_Halogeometricum_borinquense 174_Haloferax_denitrificans 175_Haloferax_larsenii 176_Haloferax_mediterranei 169_Halorubrum_lacuspofundi 171_Halorubrum_saccharovorum 246_Natronococcus_amylolyticus 249_Natrialba_hulunbeirensis 158_Halobiforma_nitratireducens 248_Natronococcus_occultus 167_Halorubrum_aidingense 170_Halorubrum_lipolyticum 168_Halorubrum_hochstenium 172_Halorubrum_terrestre 250_Natrinema_altunense 166_Halopiger_xanaduensis 247_Natronococcus_jeotgali 164_Halopiger_sp 157_Halobiforma_lacisalsi 165_Halopiger_sp 1215_nosZI
0.1
500_nosZI 1733_nosZI 1293_nosZI 1404_nosZI 182_Janthinobacterium_sp 1149_nosZI 225_Methylotenera_mobilis 328_Pseudogulbenkiania_sp 069_Burkholderia_kururiensis 070_Burkholderia_pseudomallei 071_Burkholderia_thailandensis 039_Azoarcus_sp 030_Aromatoleum_aromaticum 041_Azoarcus_toluclasticus 009_Aedes_aegypti 1732_nosZI 350_Rhodoferax_ferrireducens 427_Thiobacillus_denitrificans 426_Thiobacillus_denitrificans 428_Thiobacillus_thioparus 416_Thauera_aminoaromatica 422_Thauera_sp 424_Thauera_terpenica 327_Pseudogulbenkiania_ferrooxidans 138_gamma_proteobacterium 188_Lautropia_mirabilis 040_Azoarcus_sp 418_Thauera_linaloolentis 421_Thauera_sp 423_Thauera_sp 018_Alicycliphilus_denitrificans 002_Acidovorax_ebreus 007_Acidovorax_sp 005_Acidovorax_sp 004_Acidovorax_sp 008_Aedes_aegypti 380_Rubrivivax_gelatinosus 006_Acidovorax_sp 003_Acidovorax_radicis 032_Azohydromonas_australica 191_Leptothrix_cholodnii 438_uncultured_bacterium 001_Acidovorax_delafieldii 437_uncultured_bacterium 330_Pseudoperonospra_cubensis 338_Ralstonia_eutropha 104_Cupriavidus_sp 340_Ralstonia_pickettii 049_beta_proteobacterium 105_Cupriavidus_sp 103_Cupriavidus_basilensis 339_Ralstonia_pickettii 342_Ralstonia_solanacearum 1169_nosZI 341_Ralstonia_solanacearum 431_Thioalkalivibrio_sulfidophilus 429_Thioalkalivibrio_nitratireducens 432_Thioalkalivibrio_thiocyanoxidans 1558_nosZI 162_Halomonas_sp 163_Halomonas_sp 207_Marinobacter_daepoensis 208_Marinobacter_hydrocarbonoclasticus 211_Marinobacter_santoriniensis 210_Marinobacter_manganoxydans 209_Marinobacter_lipolyticus 212_Marinobacter_sp 147_Hahella_chejuensis 148_Hahella_ganghwensis 020_Alcanivorax_dieselolei 299_Pseudomonas_caeni 307_Pseudomonas_pelagia 314_Pseudomonas_stutzeri 298_Pseudomonas_brassicacearum 301_Pseudomonas_extremaustralis 326_Pseudomonas_veronii 304_Pseudomonas_fluorescens 308_Pseudomonas_sp 302_Pseudomonas_fluorescens 303_Pseudomonas_fluorescens 305_Pseudomonas_mandelii 311_Pseudomonas_sp 312_Pseudomonas_sp 012_Aeromonas_salmonicida 315_Pseudomonas_stutzeri 316_Pseudomonas_stutzeri 320_Pseudomonas_stutzeri 323_Pseudomonas_stutzeri 322_Pseudomonas_stutzeri 325_Pseudomonas_stutzeri 313_Pseudomonas_stutzeri 324_Pseudomonas_stutzeri 318_Pseudomonas_stutzeri 319_Pseudomonas_stutzeri 306_Pseudomonas_mendocina 321_Pseudomonas_stutzeri 317_Pseudomonas_stutzeri 309_Pseudomonas_sp 300_Pseudomonas_denitrificans 297_Pseudomonas_aeruginosa 310_Pseudomonas_sp 1840_nosZI 019_Alkalilimnicola_ehrlichii 430_Thioalkalivibrio_sp 433_Thioalkalivibrio_thiocyanodenitrificans 294_Psychromonas_ingrahamii 362_Rhodanobacter_sp 358_Rhodanobacter_spthiphylli 357_Rhodanobacter_fulvus 363_Rhodanobacter_thiooxydans 360_Rhodanobacter_sp 359_Rhodanobacter_sp 361_Rhodanobacter_sp 343_Reinekea_blandensis 1201_nosZI 1334_nosZI 261_Osedax_symbiont 262_Osedax_symbiont 021_Amphritea_japonica 241_Neptunomonas_japonica 101_Colwellia_piezophila 102_Colwellia_psychrerythraea 392_Shewanella_denitrificans 393_Shewanella_loihica 440_Vibrio_orientalis 441_Vibrio_tubiashii 218_Moritella_sp 216_Moritella_dasanensis 217_Moritella_marina 100_Colwellia_piezophila 293_Psychromonas_hadalis 292_Psychromonas_aquimarina 295_Psychromonas_ossibalaenae 277_Photobacterium_profundum 278_Photobacterium_profundum 1403_nosZI 179_Hyphomicrobium_zavarzinii 439_nosZI 279_Pleomorphomonas_koreensis 280_Pleomorphomonas_oryzae 063_Bradyrhizobium_sp 056_Bradyrhizobium_japonicum 173_nosZI 065_Bradyrhizobium_sp 062_Bradyrhizobium_sp 061_Bradyrhizobium_sp 057_Bradyrhizobium_oligotrophicum 066_Bradyrhizobium_sp 064_Bradyrhizobium_sp 058_Bradyrhizobium_sp 054_Bradyrhizobium_japonicum 059_Bradyrhizobium_sp 060_Bradyrhizobium_sp 053_Bradyrhizobium_japonicum 052_Bradyrhizobium_japonicum 067_Bradyrhizobium_yuanmingense 055_Bradyrhizobium_japonicum 013_Afipia_birgiae 348_Rhodopseudomonas_palustris 349_Rhodopseudomonas_palustris 347_Rhodopseudomonas_palustris 345_Rhodopseudomonas_palustris 346_Rhodopseudomonas_palustris 014_Afipia_sp 177_Hyphomicrobium_denitrificans 178_Hyphomicrobium_denitrificans 258_Oligotropha_carboxidovorans 215_Methylobacterium_sp 094_Chelatococcus_sp 329_Pseudochrobactrum_sp 068_Brucella_ceti 253_Ochrobactrum_anthropi 214_Mesorhizobium_loti 268_Paracoccus_sp 396_Sinorhizobium_fredii 354_Rhizobium_sp 397_Sinorhizobium_meliloti 353_Rhizobium_leguminosarum 352_Rhizobium_giardinii 355_Rhizobium_sp 264_Pantholops_hodgsonii 356_Rhizobium_sullae 296_Pseudovibrio_sp 1321_nosZI 183_Kiloniella_laminariae 265_Pantholops_hodgsonii 034_Azosprillum_amazonense 035_Azosprillum_brasilense 036_Azosprillum_brasilense 038_Azosprillum_lipoferum 037_Azosprillum_halopraeferens 368_Rhodosprillum_centenum 088_Cardiobacterium_hominis 089_Cardiobacterium_valvarum 256_Oligella_ureolytica 257_Oligella_urethralis 051_Bordetella_petrii 445_Achromobacter_arsenitoxydans 446_Achromobacter_xylosoxidans 447_Achromobacter_xylosoxidans 015_Alcaligenes_faecalis 016_Alcaligenes_faecalis 186_Kingella_oralis 185_Kingella_kingae 184_Kingella_denitrificans 395_Simonsiella_muelleri 236_Neisseria_macacae 239_Neisseria_sp 237_Neisseria_mucosa 238_Neisseria_sicca 233_Neisseria_flavescens 240_Neisseria_subflava 232_Neisseria_cinerea 234_Neisseria_flavescens 235_Neisseria_gonorrhoeae 436_Thalassospra_xiamenensis 029_Arhodomonas_aquaeolei 402_Salinispaera_shabanensis 252_Nitratireductor_indicus 222_Maritimibacter_alkaliphilus 403_Salipiger_mucosus 689_nosZI 1513_nosZI 242_Nesiotobacter_exalbescens 098_Celeribacter_baekdonensis 390_Sediminimonas_qiaohouensis 1022_nosZI 1548_nosZI 1001_nosZI 1809_nosZI 1359_nosZI 1691_nosZI 364_Rhodobacter_capsulatus 367_Rhodobacter_spaeroides 365_Rhodobacter_sp 366_Rhodobacter_spaeroides 1306_nosZI 266_Paracoccus_denitrificans 090_Catellibacterium_nectariphilum 267_Paracoccus_sp 1755_nosZI 375_Roseovarius_sp 376_Roseovarius_sp 2010_nosZI 281_Pannonibacter_phragmitetus 273_Phaeobacter_arcticus 254_Oceaniovalibus_guishaninsula 331_Pseudorhodobacter_ferrugineus 096_Citreicella_sp 115_Dinoroseobacter_shibae 1879_nosZI 382_Ruegeria_pomeroyi 379_Roseobacter_sp 189_Leisingera_aquimarina 344_Rhodobacterales_bacterium 274_Phaeobacter_caeruleus 275_Phaeobacter_gallaeciensis 282_Polymorphum_gilvum 220_Maritalea_myrionectae 187_Labrenzia_aggregata 244_Nisaea_denitrificans 237_nosZI 377_Roseobacter_denitrificans 378_Roseobacter_litoralis 190_Leisingera_nanhaiensis 394_Silicibacter_lacuscaerulensis 1044_nosZI 383_Ruegeria_sp
[298] 1315_nosZII 1777_nosZII
Figure S7
360_nosZII
0.1
968_nosZII 1570_nosZII 255_Olavius_algarvensis 122_endosymbiont_of 387_Sedimenticola_selenatireducens 1426_nosZII 425_Thiocapsa_marina 1610_nosZII 417_Thauera_linaloolentis 419_Thauera_phenylacetica 420_Thauera_selenatis 033_Azonexus_hydrophilus 404_Sulfuricella_denitrificans 106_Dechlorosoma_suillum 108_Dechloromonas_aromatica 082_Candidatus_Accumulibacter 107_Dechlorosoma_suillum 205_Magnetosprillum_magneticum 206_Magnetosprillum_sp. 410_Sulfurimonas_denitrificans 389_sediment_metagenome 412_Sulfurimonas_sp 245_Nitratiruptor_sp 251_Nitratifractor_salsuginis 398_Sulfurovum_sp 408_Sulfurimonas_autotrophica 413_Sulfurimonas_sp 409_Sulfurimonas_denitrificans 411_Sulfurimonas_gotlandica 110_Denitrovibrio_acetiphilus 076_Campylobacter_gracilis 414_Sutterella_sp 444__ 081_Campylobacter_sp 075_Campylobacter_curvus 073_Campylobacter_concisus 074_Campylobacter_concisus 079_Campylobacter_showae 078_Campylobacter_showae 077_Campylobacter_rectus 080_Campylobacter_showae 072_Calescamantes_bacterium 627_nosZII 1252_nosZII 844_nosZII 1485_nosZII 1778_nosZII 1464_nosZII 160_nosZII 1363_nosZII 1960_nosZII 923_nosZII 789_nosZII 1364_nosZII 534_nosZII 1238_nosZII 1604_nosZII 1305_nosZII 124_Ferroglobus_placidus 337_Pyrobaculum_sp 099_candidate_division 336_Pyrobaculum_calidifontis 1097_nosZII 884_nosZII 1269_nosZII 1986_nosZII 2003_nosZII 622_nosZII 1525_nosZII 61_nosZII 1760_nosZII 435_Thermomicrobium_roseum 369_Rhodothermus_marinus 370_Rhodothermus_marinus 407_Sphaerobacter_thermophilus 1071_nosZII 1646_nosZII 097_Caldilinea_aerophila 1052_nosZII 1799_nosZII 1226_nosZII 1157_nosZII 317_nosZII 1755_nosZII 1474_nosZII 1433_nosZII 871_nosZII 044_Bacillus_azotoformans 046_Bacillus_sp 117_Desulfotomaculum_ruminis 119_Desulfosprosinus_meridiei 114_Desulfitobacterium_sp 111_Desulfitobacterium_dichloroeliminans 120_Desulfosprosinus_youngiae 112_Desulfitobacterium_hafniense 113_Desulfitobacterium_hafniense 109_Deinococcus_ficus 042_Bacillus_azotoformans 045_Bacillus_massiliosenegalensis 043_Bacillus_azotoformans 047_Bacillus_sp 025_Anoxybacillus_flavithermus 141_Geobacillus_caldoxylosilyticus 142_Geobacillus_sp 143_Geobacillus_thermodenitrificans 118_Desulfomonile_tiedjei 022_Anaeromyxobacter_dehalogenans 023_Anaeromyxobacter_dehalogenans 024_Anaeromyxobacter_sp 1762_nosZII 386_Salinibacter_ruber 405_Salisaeta_longa 116_Diplospaera_colitermitum 260_Opitutaceae_bacterium 1011_nosZII 259_Opitutus_terrae 1973_nosZII 1688_nosZII 1641_nosZII 751_nosZII 093_Cesiribacter_andamanensis 286_Pontibacter_sp 284_Pontibacter_roseus 283_Pontibacter_roseus 285_Pontibacter_sp 2029_nosZII 1852_nosZII 2073_nosZII 269_Pedobacter_arcticus 406_Solitalea_canadensis 1721_nosZII 276_Phocaeicola_abscessus 289_Prevotella_multisaccharivorax 290_Prevotella_oulorum 287_Prevotella_denticola 288_Prevotella_histicola 291_Prevotella_veroralis 271_Pedobacter_saltans 017_Algoriphagus_mannitolivorans 351_Rhodonellum_psychrophilum 048_Belliella_baltica 091_Cecembia_lonarensis 221_Mariniradius_saccharolyticus 1896_nosZII 173_Haliscomenobacter_hydrossis 385_Runella_zeae 384_Runella_slithyformis 381_Rudanella_lutea 388_Sediminibacterium_sp 243_Niastella_koreensis 391_Segetibacter_koreensis 121_Dyadobacter_fermentans 031_Arcticibacter_svalbardensis 270_Pedobacter_oryzae 231_Niabella_soli 373_Riemerella_columbina 371_Riemerella_anatipestifer 372_Riemerella_anatipestifer 095_Chryseobacterium_palustre 132_Flavobacteriaceae_bacterium 126_Flavobacterium_denitrificans 129_Flavobacterium_sp 128_Flavobacterium_gelidilacus 130_Flavobacterium_suncheonense 125_Flavobacterium_columnare 127_Flavobacterium_filum 140_Gemmatimonas_aurantiaca 434_Thermonema_rossianum 180_Ignavibacterium_album 998_nosZII 213_Melioribacter_roseus 399_Sulfurihydrogenibium_sp 155_Hydrogenobacter_thermophilus 272_Persephonella_marina 439_uncultured_bacterium 1636_nosZII 2042_nosZII 194_Leptonema_illini 201_Leptospra_terpstrae 202_Leptospra_vanthielii 199_Leptospra_meyeri 195_Leptospra_biflexa 204_Leptospra_yanagawae 200_Leptospra_sp. 203_Leptospra_wolffii 198_Leptospra_inadai 196_Leptospra_broomii 197_Leptospra_fainei 230_Nafulsella_turpanensis 263_Owenweeksia_hongkongensis 133_Flexithrix_dorotheae 136_Fulvivirga_imtechensis 192_Lewinella_cohaerens 181_Imtechella_halotolerans 1996_nosZII 193_Lewinella_persica 223_Marivirga_tractuosa 083_Capnocytophaga_cynodegmi 087_Capnocytophaga_sp 084_Capnocytophaga_gingivalis 085_Capnocytophaga_granulosa 086_Capnocytophaga_sp 137_Gaetbulibacter_saemankumensis 554_nosZII 026_Aquimarina_muelleri 219_Maribacter_sp 144_Gillisia_limnaea 400_Salinimicrobium_terrae 229_Myroides_odoratus 227_Myroides_injenensis 228_Myroides_odoratimimus 1283_nosZII 139_Gelidibacter_mesophilus 010_Aequorivita_capsosiphonis 011_Aequorivita_sublithincola 131_Flavobacteriaceae_bacterium 335_Psychroflexus_tropicus 333_Psychroflexus_gondwanensis 334_Psychroflexus_torquis 332_Psychroserpens_burtonensis 134_Flavobacteriales_bacterium 224_Mesoflavibacter_zeaxanthinifaciens 401_Salinimicrobium_xinjiangense 027_Arenibacter_certesii 028_Arenibacter_latericius 092_Cellulophaga_algicola 443_Zobellia_galactanivorans 226_Muricauda_ruestringensis 123_Eudoraea_adriatica 374_Robiginitalea_biformata 145_Gillisia_sp 146_Gramella_forsetii 415_Tenacibaculum_ovolyticum 050_Bizionia_argentinensis 135_Formosa_sp
[298] 1315_nosZII 1777_nosZII
Figure S8
360_nosZII
0.1
968_nosZII 1570_nosZII 255_Olavius_algarvensis 122_endosymbiont_of 387_Sedimenticola_selenatireducens 1426_nosZII 425_Thiocapsa_marina 1610_nosZII 417_Thauera_linaloolentis 419_Thauera_phenylacetica 420_Thauera_selenatis 033_Azonexus_hydrophilus 404_Sulfuricella_denitrificans 106_Dechlorosoma_suillum 108_Dechloromonas_aromatica 082_Candidatus_Accumulibacter 107_Dechlorosoma_suillum 205_Magnetosprillum_magneticum 206_Magnetosprillum_sp. 410_Sulfurimonas_denitrificans 389_sediment_metagenome 412_Sulfurimonas_sp 245_Nitratiruptor_sp 251_Nitratifractor_salsuginis 398_Sulfurovum_sp 408_Sulfurimonas_autotrophica 413_Sulfurimonas_sp 409_Sulfurimonas_denitrificans 411_Sulfurimonas_gotlandica 110_Denitrovibrio_acetiphilus 076_Campylobacter_gracilis 414_Sutterella_sp 444__ 081_Campylobacter_sp 075_Campylobacter_curvus 073_Campylobacter_concisus 074_Campylobacter_concisus 079_Campylobacter_showae 078_Campylobacter_showae 077_Campylobacter_rectus 080_Campylobacter_showae 072_Calescamantes_bacterium 627_nosZII 1252_nosZII 844_nosZII 1485_nosZII 1778_nosZII 1464_nosZII 160_nosZII 1363_nosZII 1960_nosZII 923_nosZII 789_nosZII 1364_nosZII 534_nosZII 1238_nosZII 1604_nosZII 1305_nosZII 124_Ferroglobus_placidus 337_Pyrobaculum_sp 099_candidate_division 336_Pyrobaculum_calidifontis 1097_nosZII 884_nosZII 1269_nosZII 1986_nosZII 2003_nosZII 622_nosZII 1525_nosZII 61_nosZII 1760_nosZII 435_Thermomicrobium_roseum 369_Rhodothermus_marinus 370_Rhodothermus_marinus 407_Sphaerobacter_thermophilus 1071_nosZII 1646_nosZII 097_Caldilinea_aerophila 1052_nosZII 1799_nosZII 1226_nosZII 1157_nosZII 317_nosZII 1755_nosZII 1474_nosZII 1433_nosZII 871_nosZII 044_Bacillus_azotoformans 046_Bacillus_sp 117_Desulfotomaculum_ruminis 119_Desulfosprosinus_meridiei 114_Desulfitobacterium_sp 111_Desulfitobacterium_dichloroeliminans 120_Desulfosprosinus_youngiae 112_Desulfitobacterium_hafniense 113_Desulfitobacterium_hafniense 109_Deinococcus_ficus 042_Bacillus_azotoformans 045_Bacillus_massiliosenegalensis 043_Bacillus_azotoformans 047_Bacillus_sp 025_Anoxybacillus_flavithermus 141_Geobacillus_caldoxylosilyticus 142_Geobacillus_sp 143_Geobacillus_thermodenitrificans 118_Desulfomonile_tiedjei 022_Anaeromyxobacter_dehalogenans 023_Anaeromyxobacter_dehalogenans 024_Anaeromyxobacter_sp 1762_nosZII 386_Salinibacter_ruber 405_Salisaeta_longa 116_Diplospaera_colitermitum 260_Opitutaceae_bacterium 1011_nosZII 259_Opitutus_terrae 1973_nosZII 1688_nosZII 1641_nosZII 751_nosZII 093_Cesiribacter_andamanensis 286_Pontibacter_sp 284_Pontibacter_roseus 283_Pontibacter_roseus 285_Pontibacter_sp 2029_nosZII 1852_nosZII 2073_nosZII 269_Pedobacter_arcticus 406_Solitalea_canadensis 1721_nosZII 276_Phocaeicola_abscessus 289_Prevotella_multisaccharivorax 290_Prevotella_oulorum 287_Prevotella_denticola 288_Prevotella_histicola 291_Prevotella_veroralis 271_Pedobacter_saltans 017_Algoriphagus_mannitolivorans 351_Rhodonellum_psychrophilum 048_Belliella_baltica 091_Cecembia_lonarensis 221_Mariniradius_saccharolyticus 1896_nosZII 173_Haliscomenobacter_hydrossis 385_Runella_zeae 384_Runella_slithyformis 381_Rudanella_lutea 388_Sediminibacterium_sp 243_Niastella_koreensis 391_Segetibacter_koreensis 121_Dyadobacter_fermentans 031_Arcticibacter_svalbardensis 270_Pedobacter_oryzae 231_Niabella_soli 373_Riemerella_columbina 371_Riemerella_anatipestifer 372_Riemerella_anatipestifer 095_Chryseobacterium_palustre 132_Flavobacteriaceae_bacterium 126_Flavobacterium_denitrificans 129_Flavobacterium_sp 128_Flavobacterium_gelidilacus 130_Flavobacterium_suncheonense 125_Flavobacterium_columnare 127_Flavobacterium_filum 140_Gemmatimonas_aurantiaca 434_Thermonema_rossianum 180_Ignavibacterium_album 998_nosZII 213_Melioribacter_roseus 399_Sulfurihydrogenibium_sp 155_Hydrogenobacter_thermophilus 272_Persephonella_marina 439_uncultured_bacterium 1636_nosZII 2042_nosZII 194_Leptonema_illini 201_Leptospra_terpstrae 202_Leptospra_vanthielii 199_Leptospra_meyeri 195_Leptospra_biflexa 204_Leptospra_yanagawae 200_Leptospra_sp. 203_Leptospra_wolffii 198_Leptospra_inadai 196_Leptospra_broomii 197_Leptospra_fainei 230_Nafulsella_turpanensis 263_Owenweeksia_hongkongensis 133_Flexithrix_dorotheae 136_Fulvivirga_imtechensis 192_Lewinella_cohaerens 181_Imtechella_halotolerans 1996_nosZII 193_Lewinella_persica 223_Marivirga_tractuosa 083_Capnocytophaga_cynodegmi 087_Capnocytophaga_sp 084_Capnocytophaga_gingivalis 085_Capnocytophaga_granulosa 086_Capnocytophaga_sp 137_Gaetbulibacter_saemankumensis 554_nosZII 026_Aquimarina_muelleri 219_Maribacter_sp 144_Gillisia_limnaea 400_Salinimicrobium_terrae 229_Myroides_odoratus 227_Myroides_injenensis 228_Myroides_odoratimimus 1283_nosZII 139_Gelidibacter_mesophilus 010_Aequorivita_capsosiphonis 011_Aequorivita_sublithincola 131_Flavobacteriaceae_bacterium 335_Psychroflexus_tropicus 333_Psychroflexus_gondwanensis 334_Psychroflexus_torquis 332_Psychroserpens_burtonensis 134_Flavobacteriales_bacterium 224_Mesoflavibacter_zeaxanthinifaciens 401_Salinimicrobium_xinjiangense 027_Arenibacter_certesii 028_Arenibacter_latericius 092_Cellulophaga_algicola 443_Zobellia_galactanivorans 226_Muricauda_ruestringensis 123_Eudoraea_adriatica 374_Robiginitalea_biformata 145_Gillisia_sp 146_Gramella_forsetii 415_Tenacibaculum_ovolyticum 050_Bizionia_argentinensis 135_Formosa_sp
