Supplementary Online Material for Enhanced metabolic versatility of planktonic sulfur-oxidizing proteobacteria in an oxygen-deficient coastal upwelling ecosystem
Alejandro A. Murillo1, Salvador Ramírez-Flandes1, Edward F. DeLong2 and Osvaldo Ulloa1, * 1
Departmento de Oceanografía, Universidad de Concepción, Concepción, Chile
2
Department of Biological Engineering and Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
*To whom correspondence should be addressed. E-mail:
[email protected]
1
Table of Contents Figure S1: Water-column nutrient and oxygen profiles during the upwelling period in January 2009………………………………………………………………………………3 Figure S2 to S7: Taxonomic classification of 16S rRNA gene sequences………….…4-9 Figure S8: lysR-cbbM-cbbQ-cbbO organization for the RuBisCO operon………..……10 Figure S9: Phylogenetic tree of SucB………………………………………….…..……11 Figure S10: Phylogenetic tree of cytochrome bc1 subunit and cytochrome oxidase coxA subunit………………………………………………………………………………..13-14 Figure S11: NADH:ubiquinone oxidoreductase………………………………………...15 Figure S12: Fumarate reductase………………………………………………………...16 Figure S13: F-type ATPase………………………………………………………..…….17 Figure S14: Sulfur oxidation (Sox) system…………...………………………..………..18 Figure S15: Sulfur oxidation (Sox) B subunit……..…………………………………....19 Figure S16: Dissimilatory sulfite reductase operon (dsr)…………...…………………..20 Figure S17: Organization of the aprMBA-sat genes……………………………..……...21 Figure S18: Dissimilatory nitrate reductase (nar) operon………………………………23 Table S1: Sequences classification information of the metagenomic data……………...24 Tables S2 to S15: Taxonomic binning for the analyzed contigs…………………….25-34 Table S16: Single sequences not assembled in to contigs…………………………...34-47 Tables S17: 16S rRNA gene sequences recovered from each metagenomic survey……48 Tables 18-19: Identity analysis for the studied contigs……………………………...…..48 Table S20: ABC and TRAP transport systems………………………………………….49 Tables S21 to S30: Identity analysis for the studied contigs…………………….…..50-53
2
Figure S1: Water-column nutrient and oxygen profiles during the upwelling period in January 2009. The percentages of sequences assigned to major taxonomic groups of organisms derived fron the protein-coding sequences are shown for the 85 m metagenome in the colour coded stacked bar.
3
A
B
Figure S3: Taxonomic classification of 16S rRNA gene sequences, 35 m March 2009. (A) Percentage of sequences, of total Bacterial sequences, associated to a given Bacterial Phyla. (B) Percentage o sequences, of total γ-Proteobacteria Class, associated to a given
4
order. ARCTIC96BD-19 and SUP05 were considered as “orders” artificially separated, to be compared. The color codes start counterclockwise.
A
B
Figure S4: Taxonomic classification of 16S rRNA gene sequences, 50 m March 2009. (A) Percentage of sequences, of total Bacterial sequences, associated to a given Bacterial Phyla. (B) Percentage o sequences, of total γ-Proteobacteria Class, associated to a given
5
order. ARCTIC96BD-19 and SUP05 were considered as “orders” artificially separated, to be compared. The color codes start counterclockwise.
A
B
Figure S5: Taxonomic classification of 16S rRNA gene sequences, 85 m March 2009. (A) Percentage of sequences, of total Bacterial sequences, associated to a given Bacterial Phyla. (B) Percentage o sequences, of total γ-Proteobacteria Class, associated to a given
6
order. ARCTIC96BD-19 and SUP05 were considered as “orders” artificially separated, to be compared. The color codes start counterclockwise.
A
B
7
Figure S6: Taxonomic classification of 16S rRNA gene sequences, 50 m March 2011. (A) Percentage of sequences, of total Bacterial sequences, associated to a given Bacterial Phyla. (B) Percentage o sequences, of total γ-Proteobacteria Class, associated to a given order. ARCTIC96BD-19 and SUP05 were considered as “orders” artificially separated, to be compared. The color codes start counterclockwise.
8
A
B
Figure S7: Taxonomic classification of 16S rRNA gene sequences, 85 m March 2011. (A) Percentage of sequences, of total Bacterial sequences, associated to a given Bacterial
9
Phyla. (B) Percentage o sequences, of total γ-Proteobacteria Class, associated to a given order. ARCTIC96BD-19 and SUP05 were considered as “orders” artificially separated, to be compared. The color codes start counterclockwise.
Figure S8: lysR-cbbM-cbbQ-cbbO organization for the RuBisCO operon retrieved from metagenomic data (year 2011 sampling). RuBisCO operon (yellow) described for the (A) uncultured GB SUP05 cluster bacterium gb2_c20, (B) the uncultured ESP-GSO cluster Contig14992, and (C) for uncultured SI SUP05 clone FGYC_13J7. The operons are in synteny, but present differences in the genetic context of the surrounding genes. The identity between each gene segment is shown in white numbers. Genes in black are hypothetical proteins. Genes in green are part of the nar operon.
10
11
Figure S9: Phylogenetic tree of SucB. Amino acid sequences, translated from the sucB gene, were compared against - and -proteobacteria representatives for the 2oxoglutarate dehydrogenase, E2 subunit, dihydrolipoamide succinyltransferase. The tree was constructed using the “Bosque” software (Ramírez-Flandes and Ulloa, 2008), with PhyML for maximum likelihood phylogenies, an optimized tree topology, and bootstrap of 100.
12
A
B
13
Figure S10: Phylogenetic tree of (A) cytochrome bc1 subunit and (B) cytochrome oxidase coxA subunit of the oxidative phosphorylation pathway. Amino acid sequences, translated from the cytb and coxA genes, were compared against -, -, and proteobacteria representatives. The trees were constructed in the “Bosque” software, with PhyML for maximum likelihood phylogenies, an optimized tree topology, and bootstrap of 100.
14
Figure S11: NADH:ubiquinone oxidoreductase, complex
I of the oxidative
phosphorylation pathway. A) Comparison of the complex I (yellow) and the genomic context between the 2009 and 2011 contigs, and against the GB SUP05 subcluster gb1_c97 contig, SI SUP05 genomic scaffold (shown in green to denote de difference in size) and the symbionts Candidatus Ruthia magnifica and Candidatus Vesicomyosocius okutanii reference genomes. B) Specific annotation of the complex I and the flanking genes of contig generated with 2009 metagenomic data.
15
Figure S12: Fumarate reductase, complex II of the oxidative phosphorylation pathway. A) Comparison of the complex II (yellow) and the genomic context between the 2009 and 2011 contigs, and against the GB SUP05 subcluster gb1_c85 contig, SI SUP05 genomic scaffold and the symbionts Candidatus Ruthia magnifica and Candidatus Vesicomyosocius okutanii reference genomes. B) Specific annotation of the complex II and flanking genes of contig generated with 2009 metagenomic data.
16
Figure S13: F-type ATPase, complex V of the oxidative phosphorylation pathway. A) Comparison of the complex V (yellow) and the genomic context between the 2009 and 2011 contigs (99% of identity is represented by the black colour of synteny comparisons) and against the GB SUP05 subcluster gb1_c36 and gb2_65 contigs, SI SUP05 genomic scaffold
and
the
symbionts
Candidatus
Ruthia
magnifica
and
Candidatus
Vesicomyosocius okutanii reference genomes. B) Specific annotation of the complex V and flanking genes of contig generated with 2009 metagenomic data.
17
Figure S14: Sulfur oxidation (Sox) system. A) Incomplete soxAZYX cluster (yellow) associated to SUP05 lineage reconstructed in contigs from 2009 and 2011 metagenomic data, and compared with the GB SUP05 subcluster gb2_c35, SI SUP05 genomic scaffold and the symbionts Candidatus Ruthia magnifica and Candidatus Vesicomyosocius okutanii reference genomes. The soxB gene was recovered in a different contig suggesting a gen context different from the rest of the cluster, a classical organization described in other organisms. B) Specific annotation of sox genetic cluster coding in the contig retrieved from 2009 metagenomic data.
18
Figure S15: Sulfur oxidation (Sox) B subunit. A) Comparison of the soxB gene (yellow) and gene context of the contigs retrieved from 2009 and 2011 metagenomic data, against the GB SUP05 subclusters gb1_c23, gb1_c40 and gb2_c138 contigs, SI SUP05 genomic scaffold
and
the
symbionts
Candidatus
Ruthia
magnifica
and
Candidatus
Vesicomyosocius okutanii reference genomes. For 2009 data two contigs contain part of the soxB gene and present synteny with the described genomic context. B) Specific annotation of 2011 contig coding for soxB and the flanking genes.
19
Figure S16: Dissimilatory sulfite reductase operon (dsr). A) The dsr gene cluster generated with 2009 and 2011 metagenomic data (yellow, 99% of identity is represented by the black colour of synteny comparisons), compared against the reported operons for the GB SUP05 gb2_c106, SI SUP05 genomic scaffold and the symbionts Candidatus Ruthia magnifica and Candidatus Vesicomyosocius okutanii genomes. The dsr cluster retrieved from ESP SUP05 only lacks the dsrS gene compared to the canonical Allochromatium vinosum cluster and conserve synteny with the clusters described. B) Specific annotation of the dsr gene cluster and the flanking genes from the contig obtained with 2009 metagenomic data.
20
21
Figure S17: Organization of adenylyl-sulfate reductase aprMBA (yellow) and ATP sulfurylase sat (light cyan) genes, involved in the transformation of sulfite to sulfate + ATP. A) Comparison of de novo contigs generated from 2009 and 2011 metagenomic data, against the GB SUP05 subcluster gb1_c80, SI SUP05 genomic scaffolds and the symbionts Candidatus Ruthia magnifica and Candidatus Vesicomyosocius okutanii reference genomes. B) Specific annotation of the Sat-Apr complex and their flanking genes retrieved from 2011 data. C) Comparison of de novo contigs generated from 2009 and 2011 metagenomic data and the GB SUP05 subcluster gb1_c80, SI SUP05 genomic scaffolds, against the SCGC data of two ARCTIC96BD-19 representatives, AAA007O20 and AAA001-B15. The comparison shown low nuclotide identity of the sat-apr cluster between SUP05 and ARCTIC96BD-19 representatives and no synteny of the flanking genes, showing that our contig, for this gene cluster, are more closely related to SUP05 cluster.
22
Figure S18: Dissimilatory nitrate reductase (nar) operon. A) Organization of the membrane-bound nitrate reductase operon, the functional enzyme is encoding by narGHJI genes and is often linked to at least one narK gene encoding proteins belonging to the major facilitator superfamily of trans-membrane transporters. B) Histidine kinase nitrate/nitrite-specific regulators of nar operon, retrieved in a different contig and probable located in a different genomic context of the nar genes.
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Table S1: Number of sequences and sequences classification information of the metagenomic data
Samples
Total seqs
March 2009, 5m
323,081
Putative proteincoding filtered sequences1 239,276
January 2009, 85m
273,690
187,726
203
38.8%
March 2009, 35m
517,392
485,388
241
65.0%
March 2009, 50m
522,769
423,413
240
51.3%
March 2009, 85m
489,998
433,417
247
59.0%
March 2011, 5m
1,207,582
1,189,834
386
60.4%
March 2011, 25m
1,279,798
1,264,855
375
61.2%
March 2011, 50m
1,327,086
1,312,034
378
67.4%
March 2011, 85m
1,328,955
1,313,720
387
72.1%
Average sequence length2
NCBInr3
231
48.7%
Contigs4
Largest contig
299
76,353 bp
1,497
76,610 bp
1
Total of sequences filtered at 98% of similarity after RNA sequences extracted
2
Average sequences length (in base pairs) of the putative protein-coding sequences de-replicated
3
Percentages relative to the putative protein-coding or unknown sequences, i.e., total unique sequences 4
Contigs assembled with metagenomic data enriched in sequences assigned to sulfur-oxidizing organisms. The oxygenated depths were excluded from the assembling.
24
Table S2: Taxonomic binning for contig00465, coding the soxB gene. Organisms Vesicomyosocius okutanii Vesicomyosocius okutanii Ruthia magnifica Ruthia magnifica Ruthia magnifica SUP05 SUP05 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001
Contig start 1 3050 1 1577 3053 1 1636 1865 501 3294
Contig end 2982 3924 1456 2983 4292 1471 4293 2924 602 3326
E-value 0.0 5e-84 0.0 2e-115 2e-95 0.0 0.0 6e-26 0.001 0.004
Bit score 1281 311 998 416 349 994 810 118 44.6 42.8
Table S3: Taxonomic binning for contig31297, coding the soxXAYZ cluster for the oxidation of thiosulfate to sulfur. Organisms SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica
Contig start 44900 32580 2882 20195 8060 25370 38983 15399 27831 31309 43507 13552 24908 27069 13552 18301 14400 24128 42547 32757 22515 44900 24908 20187 38844 2840
Contig end 51536 38376 7942 23969 11719 27726 42074 18179 31151 32405 44695 14352 25275 28010 14286 18932 15378 24915 42966 32858 22811 51536 31151 23225 42073 5245
E-value 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 5e-172 2e-145 1e-128 8e-113 1e-97 3e-73 7e-57 3e-55 7e-25 3e-17 5e-08 5e-08 0.0 0.0 0.0 0.0 0.0
Bit score 4621 2910 2244 2089 1503 1422 1407 1404 982 607 518 462 410 360 279 224 219 118 93.3 62.6 62.6 4453 2778 1636 1317 1236
25
Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007
16815 35644 32631 5277 15481 13506 23344 43495 31883 24156 27280 22617 34953 21343 46564 24905 21037 2882 38829 16823 32572 35640 44899 31391 43495 15481 13425 24326 32591 42856 21876 2841 27 16835 7476 13477 46755 39314 15564 23338 20197 18468 24364 45944
18956 38252 34330 7864 16331 14347 23969 44695 32227 24878 27530 22718 35039 21924 51536 31168 23969 7900 41958 19154 34328 38406 46342 32373 44695 16330 14347 24806 32875 42971 21907 6104 1471 18158 7921 14385 47275 39922 16306 23992 20684 19167 24803 46075
0.0 0.0 0.0 0.0 3e-112 3e-111 1e-110 8e-107 3e-36 2e-32 1e-15 2e-07 2e-05 3e-04 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 7e-171 1e-135 9e-119 4e-110 8e-31 1e-09 2e-07 3e-04 0.0 0.0 0.0 8e-145 8e-107 2e-82 1e-73 1e-72 4e-66 3e-35 2e-31 7e-25 4e-22
1027 1005 962 737 408 405 403 390 156 143 87.8 60.8 53.6 50.0 3925 2742 1874 1671 1251 1050 1023 940 773 603 486 430 401 138 68.0 60.8 50.0 1195 843 664 517 390 309 280 277 255 152 140 118 109
26
ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001
46167 47284 759 38827 46581 765 49175 50797 50295 48203 31395 40877 39738 46576 47819 49809 13792 32121
46307 47536 904 39049 46669 844 49723 51091 50554 48487 31803 41117 39861 46751 47902 49921 13915 32334
6e-13 6e-13 2e-07 9e-05 0.001 0.004 1e-59 2e-32 9e-30 5e-27 5e-20 5e-20 3e-16 1e-15 2e-13 6e-13 8e-12 0.001
78.8 78.8 60.8 51.8 48.2 46.4 233 143 134 125 102 102 89.7 87.8 80.6 78.8 75.2 48.2
Table S4: Taxonomic binning for contig31001, coding the dissimilatory sulfite reductase (dsr) gene cluster. Organisms Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii
Contig start 2 19084 28044 33100 17696 24844 14287 22717 17210 24382 15757 18843 18833 610 19115 28047 22719 17210 33101 24844 14287
Contig end 13466 22593 31456 34034 18937 26527 15549 24024 17595 24628 16348 18924 18881 12998 22594 31403 24610 18937 33883 26527 15586
E-value 0.0 0.0 0.0 0.0 5e-139 6e-138 3e-116 2e-113 4e-32 6e-30 6e-24 8e-10 1e-06 0.0 0.0 0.0 2e-149 1e-139 7e-131 8e-130 2e-125
Bit score 7488 1921 1290 650 497 493 421 412 141 134 114 68.0 57.2 7068 1907 1272 531 499 470 466 452 27
Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007
2 33913 15729 18830 18839 1 32786 28117 29960 25062 27142 33913 18846 26878 18854 18837 29231 18819 18840 18847 32786 22878 18854
426 34045 16350 18924 18881 6908 33884 29623 31455 26567 27428 34046 18924 27119 18881 18875 29527 18920 18875 18890 32932 22931 18881
4e-76 1e-39 1e-39 3e-08 6e-05 0.0 0.0 0.0 9e-155 4e-121 8e-48 3e-47 6e-11 1e-07 0.002 0.009 9e-22 5e-06 7e-04 7e-04 3e-08 3e-08 0.002
288 167 167 62.6 51.8 4643 901 682 549 437 194 192 71.6 60.8 46.4 44.6 107 55.4 48.2 48.2 62.6 62.6 46.4
Table S5: Taxonomic binning for contig00369, coding the sat-aprMBA gene cluster, involved in the sulfite oxidation to sulfate and the ATP production. Organisms Ruthia magnifica Ruthia magnifica Ruthia magnifica Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii SUP05 SUP05 SUP05 SUP05 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007
Contig start 1311 46 4636 1324 46 4637 2543 39 1325 4634 2194 61
Contig end 4619 1270 5213 4619 1259 5209 4629 1270 2582 5218 4603 1061
E-value 0.0 0.0 2e-133 0.0 0.0 3e-106 0.0 0.0 0.0 1e-74 0.0 0.0
Bit score 3007 944 475 2996 897 385 1956 1209 1027 280 944 679
28
Table S6: Taxonomic binning for contig29238, coding the NADH:ubiquinone oxidoreductase gene cluster. Complex I of the oxidative phosphorylation pathway. Organisms Ruthia magnifica Ruthia magnifica Ruthia magnifica Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001
Contig start 2860 551 24402 2860 551 24402 2860 13099 578 26068 24404 22186 21769 19479 21348 24407 26409 27403 6236 27400 17408 6598 19817 13073 14515
Contig end 17065 2561 25460 17065 2534 25647 13092 17069 2561 26795 25278 22283 24204 20770 21681 24858 26680 27476 6363 27479 17481 6648 20184 13247 14659
E-value 0.0 0.0 8e-78 0.0 0.0 1e-89 0.0 0.0 0.0 3e-52 3e-46 0.002 0.0 0.0 1e-81 2e-54 6e-16 5e-11 2e-09 3e-07 1e-06 6e-04 3e-27 4e-12 2e-04
Bit score 7203 816 293 6937 765 333 5472 2426 890 208 188 46.4 971 865 306 215 87.8 71.6 66.2 59.0 57.2 48.2 125 75.2 50.0
Tables S7: Taxonomic binning for contig13071, coding the Succinate dehydrogenase/Fumarate reductase gene cluster. Complex II of the oxidative phosphorylation pathway. Organisms SUP05 SUP05 SUP05 SUP05 Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Ruthia magnifica Ruthia magnifica
Contig start 2849 4 2 22 1 22 6455 1 22
Contig end 5448 1570 107 76 1587 76 6531 1405 76
E-value 0.0 0.0 3e-35 6e-06 0.0 5e-07 6e-06 0.0 5e-07
Bit score 1281 830 150 53.6 953 57.2 53.6 913 57.2
29
ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001
193 1098 26 192 7431 193
268 1412 76 222 7460 222
3e-16 5e-13 2e-11 2e-04 8e-04 8e-04
87.8 77.0 71.6 48.2 46.4 46.4
Table S8: Taxonomic binning for contig01121, coding the Cytochrome bc1 gene cluster. Complex III of the oxidative phosphorylation pathway. Organisms Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001
Contig start 4702 208 2882 7274 33 2882 5119 7273 2883 38 6744 1009 661
Contig end 10707 2095 4598 10717 2095 4600 6192 10147 6313 2095 6872 1243 773
E-value 0.0 0.0 0.0 0.0 0.0 0.0 6e-119 0.0 0.0 0.0 6e-05 6e-24 1e-13
Bit score 1732 1012 958 1474 1162 1003 428 1312 1254 823 50.0 113 78.8
Table S9: Taxonomic binning for contig17720, coding the cytochrome c oxidase subunits I and II. Complex IV of the oxidative phosphorylation pathway. Organisms Ruthia magnifica Ruthia magnifica Vesicomyosocius okutanii Vesicomyosocius okutanii SUP05 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007
Contig start 1169 16 1179 13 4 148 475 4
Contig end 4325 703 4325 743 713 459 744 138
E-value 0.0 1e-21 0.0 2e-32 2e-57 4e-53 1e-47 1e-28
Bit score 1730 104 1579 140 223 208 190 127
30
Table S10: Taxonomic binning for contig13139, coding the ATP synthase (F-type ATPase). Complex V of the oxidative phosphorylation pathway. Organisms SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007
Contig start 22 22203 12624 16062 8010 11222 21539 10338 7031 40 18486 12601 16062 10793 8647 15405 10342 27 21539 4754 12601 16072 25105 10846 18486 8932 15405 20118 20919 10338 610 21540 4772 16098 13560 18537 25097 21 20100 12856
Contig end 6748 25804 15888 21360 10203 12452 22058 10679 7550 6796 25795 14448 17946 12310 10204 15890 10681 4453 24870 6759 14446 17945 25792 12293 19834 10201 15890 20663 21337 10686 4369 24875 6544 17919 14453 19762 25788 671 21337 13518
E-value 0.0 0.0 0.0 0.0 0.0 2e-160 1e-107 1e-50 4e-50 0.0 0.0 0.0 0.0 9e-166 1e-131 2e-73 4e-37 0.0 0.0 0.0 0.0 0.0 1e-158 2e-143 1e-132 2e-129 2e-84 1e-50 1e-38 2e-28 0.0 0.0 0.0 4e-177 6e-168 3e-166 2e-155 3e-128 7e-85 8e-78
Bit score 4376 1941 1878 1797 697 567 392 203 201 3990 2718 1002 839 585 471 279 158 3131 1452 1056 1003 884 562 511 475 464 315 203 163 129 2636 1261 719 623 592 587 551 461 316 293
31
ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001
15602 14991 7204 21554 15414 24322 13970 13967
15886 15484 7434 21883 15484 24375 14011 14028
3e-52 7e-34 3e-13 2e-27 8e-08 1e-05 1e-05 0.006
208 147 78.8 125 60.8 53.6 53.6 44.6
Table S11: Taxonomic binning for contig18758, coding the dissimilatory nitrate reductase pathway (nar) gene cluster, involved in the nitrate reduction to nitrite. Organisms SUP05 SUP05 Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Ruthia magnifica Ruthia magnifica ARCTIC96BD-19 AAA007
Contig start 164 7323 2105 6297 10660 5466 10660 9576 10665
Contig end 7316 10352 4936 7269 11212 5711 11191 9829 11146
E-value 0.0 0.0 0.0 1e-77 8e-74 4e-45 5e-82 1e-26 1e-70
Bit score 5663 2055 659 291 279 183 306 122 268
Table S12: Taxonomic binning for contig13237, coding the Nitrate reductase (nar) regulators narX/L and narQ. Organisms ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 SUP05 SUP05 SUP05 SUP05 SUP05 Ruthia magnifica Ruthia magnifica Vesicomyosocius okutanii Vesicomyosocius okutanii ARCTIC96BD-19 AAA001 ARCTIC96BD-19 AAA001
Contig start 10226 6996 4501 9709 1 471 4495 1 3014 419 1 431 1 6431 5778
Contig end 14083 9519 6904 10008 4339 2813 5718 362 4130 4339 300 4339 257 6727 5853
E-value 0.0 0.0 0.0 2e-31 0.0 0.0 8e-100 8e-81 3e-61 0.0 3e-73 0.0 1e-72 3e-16 8e-05
Bit score 2327 1956 874 138 1687 836 365 302 237 1350 277 1330 275 87.8 50.0
32
Table S13: Taxonomic binning for contig11209, coding the Nitrite reductase nirBD genes, involved in the reduction of nitrite in to ammonium. Organisms SUP05 SUP05 Ruthia magnifica Vesicomyosocius okutanii ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007
Contig start 362 5238 388 360 1 1 1
Contig end 3544 5641 3544 3544 63 63 55
E-value 0.0 1e-17 0.0 0.0 2e-16 5e-16 2e-09
Bit score 1487 91.5 1487 1402 87.8 86.0 64.4
Table S14: Taxonomic binning for contig14992, coding the RuBisCO operon genes. Organisms Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Vesicomyosocius okutanii Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica Ruthia magnifica SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 SUP05 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007 ARCTIC96BD-19 AAA007
Contig start 11479 8901 827 6181 4856 3799 11479 8901 968 4270 6209 3778 8470 14694 800 3770 4270 6120 8292 7327 3765 1208 6110 4270 8285 11580 3831
Contig end 14844 10632 2568 7296 5858 4173 14544 10632 2568 5861 7290 4174 8530 14755 3681 5861 5766 7283 9102 8071 4178 3146 7283 5849 9203 12130 4122
E-value 0.0 0.0 3e-162 6e-96 2e-94 3e-62 0.0 0.0 6e-165 1e-136 5e-71 4e-60 1e-09 2e-07 0.0 0.0 0.0 6e-140 3e-67 6e-64 3e-55 6e-115 1e-111 2e-107 7e-101 2e-64 1e-28
Bit score 2145 1245 572 352 347 241 1894 1139 581 488 269 233 66.2 59.0 937 879 762 499 257 246 217 416 405 390 369 248 129
33
ARCTIC96BD-19 AAA001
11586
11983
2e-44
181
Table S15: Taxonomic binning for contig19949, coding the sucB gene for the E2 subunit of the -ketoglutarate dehydrogenase complex. Organisms SUP05 SUP05 ARCTIC96BD-19 AAA001
Contig start 2902 4291 498
Contig end 4045 4961 703
E-value 9e-158 3e-49 1e-16
Bit score 556 196 87.8
Table S16: Single sequences not assembled into contigs, but with identity to some key functions in the uncultured ESP-GSO cluster bacterium. Sequence ID
Protein product
Taxonomic classification according BLASTX/NR
11159836
dissimilatory nitrite reductase
Pseudomonas entomophila L48
11181664
dissimilatory nitrite reductase
uncultured bacterium
11199038
dissimilatory nitrite reductase
uncultured bacterium
11219913
dissimilatory nitrite reductase
Nitrosopumilus maritimus SCM1
11221723
dissimilatory nitrite reductase
uncultured bacterium
11248601
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
11259125
dissimilatory nitrite reductase
uncultured SUP05 cluster bacterium
11273147
dissimilatory nitrite reductase
uncultured bacterium
11278075
dissimilatory nitrite reductase
uncultured bacterium
11280150
dissimilatory nitrite reductase
uncultured bacterium
11291573
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
11325924
dissimilatory nitrite reductase
Maritimibacter alkaliphilus HTCC2654
11350238
dissimilatory nitrite reductase
Nitrosopumilus maritimus SCM1
11356056
dissimilatory nitrite reductase
Shewanella loihica PV-4
34
11369742
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
8032425
dissimilatory nitrite reductase
Chelativorans sp. BNC1
8035716
dissimilatory nitrite reductase
Afipia sp. 1NLS2
8038572
dissimilatory nitrite reductase
uncultured bacterium
8057838
dissimilatory nitrite reductase
Afipia sp. 1NLS2
8070229
dissimilatory nitrite reductase
8097543
dissimilatory nitrite reductase
Rhodopseudomonas palustris CGA009
8098690
dissimilatory nitrite reductase
Silicibacter sp. TrichCH4B
8116699
dissimilatory nitrite reductase
Brucella suis 1330
8120022
dissimilatory nitrite reductase
Flavobacterium johnsoniae UW101
8120750
dissimilatory nitrite reductase
Candidatus Nitrosoarchaeum koreensis MY1
8130329
dissimilatory nitrite reductase
Nitrosopumilus maritimus SCM1
8147623
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
8163434
dissimilatory nitrite reductase
uncultured organism
8165180
dissimilatory nitrite reductase
uncultured marine crenarchaeote
8168758
dissimilatory nitrite reductase
Parvibaculum lavamentivorans DS-1
8173222
dissimilatory nitrite reductase
uncultured bacterium
8173740
dissimilatory nitrite reductase
Afipia sp. 1NLS2
8191672
dissimilatory nitrite reductase
uncultured organism
8196490
dissimilatory nitrite reductase
Mesorhizobium opportunistum WSM2075
8200688
dissimilatory nitrite reductase
Flavobacteriaceae bacterium 3519-10
8207551
dissimilatory nitrite reductase
Afipia sp. 1NLS2
8219546
dissimilatory nitrite reductase
Rhodopseudomonas palustris CGA009
8223320
dissimilatory nitrite reductase
uncultured bacterium
8231233
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
35
8247645
dissimilatory nitrite reductase
8257923
dissimilatory nitrite reductase
Rhodopseudomonas palustris CGA009
8280058
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
8286472
dissimilatory nitrite reductase
uncultured bacterium
8305217
dissimilatory nitrite reductase
Phaeobacter gallaeciensis 2.10
8324263
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
8328512
dissimilatory nitrite reductase
uncultured bacterium
8337452
dissimilatory nitrite reductase
uncultured bacterium
8339144
dissimilatory nitrite reductase
Flavobacterium johnsoniae UW101
8342357
dissimilatory nitrite reductase
Maritimibacter alkaliphilus HTCC2654
8353306
dissimilatory nitrite reductase
Nitrosopumilus maritimus SCM1
8362252
dissimilatory nitrite reductase
Nitrosomonas sp. AL212
8363598
dissimilatory nitrite reductase
Pseudomonas entomophila L48
8368866
dissimilatory nitrite reductase
Pseudomonas entomophila L48
8373915
dissimilatory nitrite reductase
Chelativorans sp. BNC1
8381021
dissimilatory nitrite reductase
Pseudomonas entomophila L48
8382760
dissimilatory nitrite reductase
Afipia sp. 1NLS2
8402569
dissimilatory nitrite reductase
uncultured marine crenarchaeote
8420320
dissimilatory nitrite reductase
uncultured marine crenarchaeote
8422412
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
8423452
dissimilatory nitrite reductase
Bradyrhizobium sp. BTAi1
8425568
dissimilatory nitrite reductase
Pseudomonas entomophila L48
8436312
dissimilatory nitrite reductase
Cardiobacterium hominis ATCC 15826
8453500
dissimilatory nitrite reductase
Pseudomonas entomophila L48
8462632
dissimilatory nitrite reductase
uncultured bacterium
8462948
dissimilatory nitrite reductase
uncultured bacterium
36
8491604
dissimilatory nitrite reductase
Candidatus Nitrosoarchaeum koreensis MY1
8496697
dissimilatory nitrite reductase
Phaeobacter gallaeciensis 2.10
8521757
dissimilatory nitrite reductase
uncultured marine crenarchaeote HF4000_APKG9M20
2324645
dissimilatory nitrite reductase
Brucella melitensis bv. 1 str. 16M
2334949
dissimilatory nitrite reductase
Chelativorans sp. BNC1
2361524
dissimilatory nitrite reductase
Nitrosopumilus maritimus SCM1
2383125
dissimilatory nitrite reductase
Candidatus Nitrosoarchaeum koreensis MY1
2395791
dissimilatory nitrite reductase
Nitrosococcus oceani ATCC 19707
2436641
dissimilatory nitrite reductase
Cardiobacterium hominis ATCC 15826
2499135
dissimilatory nitrite reductase
Thermaerobacter marianensis DSM 12885
2537340
dissimilatory nitrite reductase
uncultured bacterium
2561334
dissimilatory nitrite reductase
Chelativorans sp. BNC1
2670781
dissimilatory nitrite reductase
Maribacter sp. HTCC2170
2751723
dissimilatory nitrite reductase
uncultured bacterium
2754496
dissimilatory nitrite reductase
Nitrosopumilus maritimus SCM1
2764310
dissimilatory nitrite reductase
Hyphomicrobium denitrificans
8946891
dissimilatory nitrite reductase
Parvibaculum lavamentivorans DS-1
8975650
dissimilatory nitrite reductase
Candidatus Nitrosoarchaeum koreensis MY1
8982583
dissimilatory nitrite reductase
Afipia sp. 1NLS2
9052992
dissimilatory nitrite reductase
Pseudomonas entomophila L48
9119354
dissimilatory nitrite reductase
Leptospira biflexa serovar Patoc strain 'Patoc 1 (Ames)'
9137682
dissimilatory nitrite reductase
Chryseobacterium gleum ATCC 35910
9177387
dissimilatory nitrite reductase
Shewanella amazonensis SB2B
37
9188608
dissimilatory nitrite reductase
Shewanella loihica PV-4
9246590
dissimilatory nitrite reductase
Parvibaculum lavamentivorans DS-1
9260394
dissimilatory nitrite reductase
uncultured bacterium
9266233
dissimilatory nitrite reductase
Cardiobacterium hominis ATCC 15826
9287480
dissimilatory nitrite reductase
uncultured SUP05 cluster bacterium
9301358
dissimilatory nitrite reductase
Nitrosomonas sp. AL212
9322765
dissimilatory nitrite reductase
Achromobacter xylosoxidans A8
9355166
dissimilatory nitrite reductase
Bradyrhizobium japonicum USDA 110
9355806
dissimilatory nitrite reductase
Rhodopseudomonas palustris BisA53
9404577
dissimilatory nitrite reductase
Flavobacteriaceae bacterium 3519-10
11242745
flavocytochrome c subunit fccA gamma proteobacterium HTCC5015
11246329
flavocytochrome c subunit fccA Pseudomonas fluorescens Pf0-1
11257122
flavocytochrome c subunit fccA Sulfurimonas autotrophica DSM 16294
11258364
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
11285779
flavocytochrome c subunit fccA
11308428
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
11323521
flavocytochrome c subunit fccA
8092687
flavocytochrome c subunit fccA gamma proteobacterium HTCC2207
8119081
flavocytochrome c subunit fccA Nitrosococcus halophilus Nc4
8198572
flavocytochrome c subunit fccA Pseudomonas stutzeri
8215589
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
8241398
flavocytochrome c subunit fccA Psychromonas ingrahamii 37
8271633
flavocytochrome c subunit fccA
8294160
flavocytochrome c subunit fccA Psychromonas ingrahamii 37
Aeromonas hydrophila subsp. hydrophila ATCC 7966
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
38
8326594
flavocytochrome c subunit fccA Salinisphaera shabanensis E1L3A
8369349
flavocytochrome c subunit fccA Nitrosococcus oceani ATCC 19707
8498011
flavocytochrome c subunit fccA Photobacterium profundum SS9
8523317
flavocytochrome c subunit fccA Pseudomonas fluorescens WH6
2322874
flavocytochrome c subunit fccA Reinekea blandensis MED297
2327341
flavocytochrome c subunit fccA Methylophaga thiooxydans DMS010
2330440
flavocytochrome c subunit fccA Shewanella loihica PV-4
2343981
flavocytochrome c subunit fccA Neptuniibacter caesariensis
2374831
flavocytochrome c subunit fccA Neptuniibacter caesariensis
2375466
flavocytochrome c subunit fccA Pseudomonas fluorescens Pf0-1
2376379
flavocytochrome c subunit fccA
2389208
flavocytochrome c subunit fccA Neptuniibacter caesariensis
2443994
flavocytochrome c subunit fccA Pseudomonas fulva 12-X
2463254
flavocytochrome c subunit fccA Pseudomonas mendocina ymp
2491251
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
2499088
flavocytochrome c subunit fccA Psychromonas ingrahamii 37
2504309
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
2536778
flavocytochrome c subunit fccA Pseudomonas fluorescens Pf0-1
2549125
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
2580010
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
2601737
flavocytochrome c subunit fccA Shewanella loihica PV-4
2606017
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
2631764
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
2653539
flavocytochrome c subunit fccA
2664755
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
39
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
2682055
flavocytochrome c subunit fccA
2691848
flavocytochrome c subunit fccA Neptuniibacter caesariensis
2693110
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
2725821
flavocytochrome c subunit fccA
2736012
flavocytochrome c subunit fccA Pseudomonas fulva 12-X
2738672
flavocytochrome c subunit fccA Methylophaga thiooxydans DMS010
2752758
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
8944836
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
8945195
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
9001406
flavocytochrome c subunit fccA Pseudomonas mendocina NK-01
9012287
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
9013113
flavocytochrome c subunit fccA
9046437
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
9051215
flavocytochrome c subunit fccA Methylophaga thiooxydans DMS010
9067921
flavocytochrome c subunit fccA
9072026
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
9076749
flavocytochrome c subunit fccA Colwellia psychrerythraea 34H
9081830
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
9099316
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
9116415
flavocytochrome c subunit fccA Methylophaga thiooxydans DMS010
9214593
flavocytochrome c subunit fccA Pseudomonas fulva 12-X
9228153
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
9244952
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
9280540
flavocytochrome c subunit fccA Chloroherpeton thalassium ATCC 35110
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
40
9309643
flavocytochrome c subunit fccA Pseudomonas fluorescens Pf0-1
9310844
flavocytochrome c subunit fccA
9312058
flavocytochrome c subunit fccA Alcanivorax borkumensis SK2
9349829
flavocytochrome c subunit fccA Reinekea blandensis MED297
9370464
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
9372114
flavocytochrome c subunit fccA uncultured SUP05 cluster bacterium
9379209
flavocytochrome c subunit fccA Candidatus Vesicomyosocius okutanii HA
11319789
flavoprotein subunit of flavocytochrome c sulphide
uncultured SUP05 cluster bacterium
11344843
flavoprotein subunit of flavocytochrome c sulphide
uncultured SUP05 cluster bacterium
11354712
flavoprotein subunit of flavocytochrome c sulphide
Rhodobacterales bacterium HTCC2255
11365964
flavoprotein subunit of flavocytochrome c sulphide
Rhodobacterales bacterium HTCC2255
8156129
flavoprotein subunit of flavocytochrome c sulphide
Sulfitobacter sp. NAS-14.1
8162154
flavoprotein subunit of flavocytochrome c sulphide
Rhodobacterales bacterium HTCC2255
8358740
flavoprotein subunit of flavocytochrome c sulphide
Rhodobacterales bacterium HTCC2255
8399672
flavoprotein subunit of flavocytochrome c sulphide
Chlorobium phaeobacteroides DSM 266
8468178
flavoprotein subunit of flavocytochrome c sulphide
Rhodobacterales bacterium HTCC2255
8469424
flavoprotein subunit of flavocytochrome c sulphide
Rhodobacterales bacterium HTCC2255
2372352
flavoprotein subunit of flavocytochrome c sulphide
Chloroherpeton thalassium ATCC 35110
2483877
flavoprotein subunit of flavocytochrome c sulphide
uncultured SUP05 cluster bacterium
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
41
2584149
flavoprotein subunit of flavocytochrome c sulphide
Alkalilimnicola ehrlichii MLHE-1
2587797
flavoprotein subunit of flavocytochrome c sulphide
Roseovarius sp. 217
9231232
flavoprotein subunit of flavocytochrome c sulphide
Prosthecochloris aestuarii DSM 271
11185307
Nitric oxide reductase subunit, NorB
Magnetococcus sp. MC-1
11286654
Nitric oxide reductase subunit, NorB
Magnetococcus sp. MC-1
11289072
Nitric oxide reductase subunit, NorB
gamma proteobacterium HdN1
8091847
Nitric oxide reductase subunit, NorB
uncultured bacterium
8120821
Nitric oxide reductase subunit, NorB
Methylomonas methanica MC09
8441887
Nitric oxide reductase subunit, NorB
Aromatoleum aromaticum EbN1
2331831
Nitric oxide reductase subunit, NorB
Methylomicrobium album BG8
2336332
Nitric oxide reductase subunit, NorB
Gallionella capsiferriformans ES-2
2378688
Nitric oxide reductase subunit, NorB
gamma proteobacterium HdN1
2500966
Nitric oxide reductase subunit, NorB
Colwellia psychrerythraea 34H
2510708
Nitric oxide reductase subunit, NorB
gamma proteobacterium HdN1
2721593
Nitric oxide reductase subunit, NorB
Gallionella capsiferriformans ES-2
2721994
Nitric oxide reductase subunit, NorB
gamma proteobacterium HdN1
2727924
Nitric oxide reductase subunit,
gamma proteobacterium HdN1
42
NorB 8985531
Nitric oxide reductase subunit, NorB
Methylomonas methanica MC09
9041128
Nitric oxide reductase subunit, NorB
Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'
9103588
Nitric oxide reductase subunit, NorB
Aromatoleum aromaticum EbN1
9140247
Nitric oxide reductase subunit, NorB
Magnetococcus sp. MC-1
9158876
Nitric oxide reductase subunit, NorB
Bdellovibrio bacteriovorus HD100
9164437
Nitric oxide reductase subunit, NorB
Methylomicrobium album BG8
9235513
Nitric oxide reductase subunit, NorB
Pedobacter sp. BAL39
11249465
Nitric oxide reductase subunit, NorC
Magnetococcus sp. MC-1
8115371
Nitric oxide reductase subunit, NorC
Methylococcus capsulatus str. Bath
8391088
Nitric oxide reductase subunit, NorC
Methylococcus capsulatus str. Bath
2316996
Nitric oxide reductase subunit, NorC
Magnetococcus sp. MC-1
2350887
Nitric oxide reductase subunit, NorC
Methylomonas methanica MC09
11232163
Nitrous-oxide reductase
Dechloromonas aromatica RCB
11234792
Nitrous-oxide reductase
Magnetospirillum magnetotacticum MS-1
11235414
Nitrous-oxide reductase
Dechloromonas aromatica RCB
11285643
Nitrous-oxide reductase
uncultured bacterium
11296017
Nitrous-oxide reductase
Rhodothermus marinus DSM 4252
11381176
Nitrous-oxide reductase
Hahella chejuensis KCTC 2396
43
11402898
Nitrous-oxide reductase
Magnetospirillum magneticum AMB-1
8046329
Nitrous-oxide reductase
Maribacter sp. HTCC2170
8055048
Nitrous-oxide reductase
Maribacter sp. HTCC2170
8076239
Nitrous-oxide reductase
Nitratiruptor sp. SB155-2
8085108
Nitrous-oxide reductase
Gramella forsetii KT0803
8096494
Nitrous-oxide reductase
Psychroflexus torquis ATCC 700755
8111312
Nitrous-oxide reductase
Maribacter sp. HTCC2170
8156165
Nitrous-oxide reductase
Psychroflexus torquis ATCC 700755
8182399
Nitrous-oxide reductase
Photobacterium profundum SS9
8277709
Nitrous-oxide reductase
Wolinella succinogenes DSM 1740
8298441
Nitrous-oxide reductase
Flavobacteriales bacterium ALC-1
8303932
Nitrous-oxide reductase
Maribacter sp. HTCC2170
8306195
Nitrous-oxide reductase
Rhodothermus marinus DSM 4252
8307783
Nitrous-oxide reductase
Maribacter sp. HTCC2170
8308094
Nitrous-oxide reductase
Maritimibacter alkaliphilus HTCC2654
8330361
Nitrous-oxide reductase
Myxococcus xanthus DK 1622
8336016
Nitrous-oxide reductase
Gramella forsetii KT0803
8377024
Nitrous-oxide reductase
Ferroglobus placidus DSM 10642
8399485
Nitrous-oxide reductase
Maribacter sp. HTCC2170
8400245
Nitrous-oxide reductase
Maribacter sp. HTCC2170
8403529
Nitrous-oxide reductase
Maribacter sp. HTCC2170
8451430
Nitrous-oxide reductase
uncultured bacterium
2358589
Nitrous-oxide reductase
Psychroflexus torquis ATCC 700755
2366243
Nitrous-oxide reductase
Cellulophaga algicola DSM 14237
2376210
Nitrous-oxide reductase
Shewanella loihica PV-4
2382188
Nitrous-oxide reductase
Maribacter sp. HTCC2170
44
2422586
Nitrous-oxide reductase
uncultured bacterium
2438440
Nitrous-oxide reductase
Sulfurimonas autotrophica DSM 16294
2443143
Nitrous-oxide reductase
Shewanella loihica PV-4
2469536
Nitrous-oxide reductase
Maribacter sp. HTCC2170
2477207
Nitrous-oxide reductase
Shewanella denitrificans OS217
2485837
Nitrous-oxide reductase
Moritella sp. PE36
2495695
Nitrous-oxide reductase
Zobellia galactanivorans
2535266
Nitrous-oxide reductase
Maribacter sp. HTCC2170
2611256
Nitrous-oxide reductase
uncultured bacterium
2631356
Nitrous-oxide reductase
uncultured bacterium
2690590
Nitrous-oxide reductase
Sulfurovum sp. NBC37-1
2694698
Nitrous-oxide reductase
Maribacter sp. HTCC2170
2712371
Nitrous-oxide reductase
Maribacter sp. HTCC2170
2720000
Nitrous-oxide reductase
Magnetospirillum gryphiswaldense MSR1
2733021
Nitrous-oxide reductase
Pirellula staleyi DSM 6068
2738612
Nitrous-oxide reductase
Magnetospirillum gryphiswaldense MSR1
2747604
Nitrous-oxide reductase
Campylobacterales bacterium GD 1
2752776
Nitrous-oxide reductase
Shewanella loihica PV-4
8981882
Nitrous-oxide reductase
Psychroflexus torquis ATCC 700755
8985285
Nitrous-oxide reductase
Magnetospirillum magnetotacticum MS-1
9006200
Nitrous-oxide reductase
Maribacter sp. HTCC2170
9077861
Nitrous-oxide reductase
Photobacterium profundum 3TCK
9098179
Nitrous-oxide reductase
Cellulophaga algicola DSM 14237
9159337
Nitrous-oxide reductase
uncultured bacterium
9233865
Nitrous-oxide reductase
Maribacter sp. HTCC2170
45
9249483
Nitrous-oxide reductase
Symbiobacterium thermophilum IAM 14863
9279554
Nitrous-oxide reductase
Psychroflexus torquis ATCC 700755
9290434
Nitrous-oxide reductase
Shewanella denitrificans OS217
9302729
Nitrous-oxide reductase
Sphaerobacter thermophilus DSM 20745
9335967
Nitrous-oxide reductase
Runella slithyformis DSM 19594
9404653
Nitrous-oxide reductase
Rhodothermus marinus DSM 4252
9405883
Nitrous-oxide reductase
Pirellula staleyi DSM 6068
9412732
Nitrous-oxide reductase
Maribacter sp. HTCC2170
9421709
Nitrous-oxide reductase
Flavobacteriales bacterium ALC-1
11217942
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
8512804
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
2319233
Sulfide-quinone reductase
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
2343833
Sulfide-quinone reductase
delta proteobacterium MLMS-1
2356450
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
2463820
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
2519689
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
2558454
Sulfide-quinone reductase
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
2595635
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
2723841
Sulfide-quinone reductase
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
2745672
Sulfide-quinone reductase
2753815
Sulfide-quinone reductase
Magnetococcus sp. MC-1
2763953
Sulfide-quinone reductase
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
8942671
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
46
8951760
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
8966234
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
8976071
Sulfide-quinone reductase
Thiomicrospira crunogena XCL-2
9014270
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
9077682
Sulfide-quinone reductase
Candidatus Vesicomyosocius okutanii HA
9086110
Sulfide-quinone reductase
Candidatus Vesicomyosocius okutanii HA
9126841
Sulfide-quinone reductase
Candidatus Vesicomyosocius okutanii HA
9173928
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
9188922
Sulfide-quinone reductase
9228446
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
9277609
Sulfide-quinone reductase
Candidatus Vesicomyosocius okutanii HA
9325555
Sulfide-quinone reductase
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
9337096
Sulfide-quinone reductase
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
9354728
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
9396792
Sulfide-quinone reductase
uncultured SUP05 cluster bacterium
9420399
Sulfide-quinone reductase
Candidatus Ruthia magnifica str. Cm (Calyptogena magnifica)
47
Table S17: Number of 16S rRNA gene sequences recovered from each metagenomic survey.
Metagenome
Total 16S seq
Total 16S seq Bacteria (% of total)
Total 16S seq SUP05 (% of Bac)
Total 16S seq ARCTIC96BD19 (% of Bac)
Total 16S seq Archaea (% of total)
341
299 (87.68)
9 (3.01)
42 (14.05)
42 (12.32)
494
469 (94.94)
63 (13.43)
104 (22.17)
25 (5.06)
506
494 (97.63)
66 (13.36)
92 (18.62)
12 (2.37)
1611
1501 (93.17)
144 (9.59)
190 (12.66)
110 (6.83)
1674
1579 (94)
408 (25.84)
294 (18.62)
95 (5.67)
2009 March_35m 2009 March_50m 2009 March_85m 2011 March_50m 2011 March_85m
Table S18: Contig14992 RuBisCO cluster related genes. Identity at the amino acids level of ESP-GSO against the databases, first four hits. Contig length 14,886 bp, 1,981 sequences recruited, average coverage 30.96X and GC content of 34.8%. Gene lysR cbbM cbbQ cbbO
SI SUP05 66.5 89.8 89.3 76.2
GB SUP05 67.7 77.4 76.2 73.0
C. R. magnifica 51.4 87.2 82.8 74.1
C. V. okutanii 80.2 88.3 82.1 72.5
Table S19: TCA cycle related genes. Identity at the amino acids level of ESP-GSO against the databases, first four hits. Gene mdh sdhB sdhA fumC sucB sucC sucD 2-OG-Fe II iso/isop
SI SUP05
GB SUP05
C. R. magnifica
C. V. okutanii
Contig length (bp)
Average coverage
N° of sequences
Contig GC%
73.5 76.2 76.8 74.2 § § §
¶ 70.3 71.0 61.9 § § §
73.1 ¶ ¶ 65.3 § 70.6 70.1
72.9 ¶ ¶ 62.8 § 68.2 66.9
11,490 11,490 11,490 51,536 5,264 13,924 13,924
1,647 1,647 1,647 7.083 830 2,147 2,147
37.7 37.7 37.7 40.6 37.3 36.5 36.5
§
§
§
§
23,849
32.65X 32.65X 32.65X 32.26X 37.39X 36.21X 36.21X 33.04X
3,358
36.9
82.7
§
76.9
76.6
5,093
10.07X
230
36.0 48
dh iso dh ¶ ¶ 76.6 76.9 22,464 acnB 81.4 ¶ 76.6 73.9 18,443 § The gene sequence is not described for this organism.
32.92X 35.01X
3,149 2,770
39.9 37.6
¶ There was not hit against this organism.
Table S20: ABC and TRAP transport systems associated to the sulfur-oxidizing γProteobacteria uncultured ESP-GSO cluster bacterium. Transporter
Contig
Total contig length (bp)
Function related CDSs (total length bp)
09616
10,548
3 (3,094)
17570
5,149
3 (1,632)
10689
24,523
2 (1,912)
22062
4,807
3 (2,421)
13071
11,490
5 (4,846)
17723
26,967
4 (3,687)
22770
10,191
2 (985)
32011
8,975
5 (5,255)
04646
45,476
3 (3,493)
30874
12,223
4 (4,240)
23558
6,689
5 (3,528)
14418
68,244
4 (4613)
21516
4,341
1(120)
20767
34,001
3 (3,075)
25898
32,563
3 (3,003)
15847
37,142
1 (1,020)
00446
4,061
1 (1,368)
31001
34,585
1 (957)
Amino Acids, general
Amino Acids, branched chain
Carbohydrates
Polyamines Di-peptides Trap Compatible Solutes Antiporter
49
Table S21: Contig29238 NADH:ubiquinone oxidoreductase, complex I of the oxidative phosphorylation pathway. Identity at the amino acids level of ESP-GSO against the databases, first four hits. Contig length 27,560 bp, 3,872 sequences recruited, average coverage 33.43X and GC content of 36%. SI GB C. R. C. V. SUP05 SUP05 magnifica okutanii nuoA 80.0 80.1 80.0 74.1 nuoB 96.2 79.8 94.3 94.3 nuoC 74.7 70.4 71.7 71.2 nuoD 89.9 68.7 88.7 88.0 nuoE 75.2 73.0 68.8 70.1 nuoF 86.6 75.0 85.9 84.5 nuoG 64.7 68.0 59.5 58.6 nuoH 76.9 70.6 73.3 73.3 nuoI 78.0 70.7 81.0 81.6 nuoJ 58.9 67.9 54.5 54.0 nuoK 82.2 71.9 77.2 74.3 ¶ nuoL 74.1 75.5 73.6 § nuoM 80.9 81.9 80.4 § nuoN 76.1 70.1 66.4 § The gene sequence is not described for this organism. Gene
¶ There was not hit against this organism. Table S22: Contig13071 Fumarate reductase, complex II of the oxidative phosphorylation pathway. Identity at the amino acids level of ESP-GSO against the databases, first four hits. Contig length 11,490 bp, 1,647 sequences recruited, average coverage 32.65X and GC content of 37.7%. SI GB SUP05 SUP05 sdhA 86.2 71.0 sdhB 72.8 70.3 sdhC 48.7 61.9 ¶ There was not hit against this organism. Gene
C. R. magnifica ¶ ¶ ¶
C. V. okutanii ¶ ¶ ¶
Table S23: Contig01121 Cytochrome bc1, complex III of oxidative phosphorylation pathway. Identity at the amino acids level of ESP-GSO against the databases, first four hits. Contig length 10,717 bp, 1069 sequences recruited, average coverage 37.21X and GC content of 40.9%. Gene SUP05 isp cytb cyt1
§ § §
GB SUP05 67.3 72.1 69.6
C. R. magnifica 72.0 74.4 46.4
C. V. ARCTIC96BDokutanii 19 73.0 71.0 73.0 72.3 54.8 58.9 50
§ The gene sequence is not described for this organism.
Table S24: Contig17720 Cytochrome c oxidase, complex IV of the oxidative phosphorylation pathway. Identity at the amino acids level of ESP-GSO against the databases, first four hits. Contig length 4325 bp, 183 sequences recruited, average coverage 9.90X and GC content of 41%. SI GB C. R. C. V. SUP05 SUP05 magnifica okutanii coxB § 71.3 59.7 60.5 coxA § 76.3 87.9 87.6 coxC § 71.2 63.8 61.9 ctaG/cox11 § 73.8 73.1 70.9 § The gene sequence is not described for this organism. Gene
ARCTIC96BD19 § § 78.6 §
Table S25: Contig13139 F-type ATPase, complex V of the oxidative phosphorylation pathway. Identity at the amino acids level of ESP-GSO against the databases, first five hits. Contig length 25835 bp, 4,151 sequences recruited, average coverage 38.18X and GC content of 39.4%. SI GB GB C. R. C. V. SUP05 SUP05 gb1 SUP05 gb2 magnifica okutanii a 77.3 74.0 75.4 78.0 77.3 c 97.9 80.5 82.8 71.4 70.1 b 71.5 75.0 74.0 66.3 67.6 δ 56.9 67.6 67.4 50.3 46.4 α ¶ 77.6 78.8 85.1 83.7 γ 84.0 76.6 76.4 77.0 76.5 β 89.5 78.3 77.1 87.5 87.9 ε 77.0 76.8 76.7 72.6 75.5 ¶ There was not hit against this organism. Gene
Table S26: Contig31297 Sulfur oxidation (Sox) system and contig26956 soxB. Identity at the amino acids level of ESP-GSO against the databases, first four hits. Contig length 51,536 bp, 7,083 sequences recruited, average coverage 32.26X and GC content of 40.6%. SI GB SUP05 SUP05 soxA 43.6 58.3 soxZ 74.7 69.8 soxY 45.9 70.6 soxX 71.1 71.8 ¥ soxB 87.3 77.0 76.4€ 75.8£
Gene
C. R. magnifica 40.0 70.9 43.9 63.2 84.4
C. V. okutanii 38.6 67.1 43.2 61.4 80.9 51
¥ € £
Compared to GB SUP05 gb1_c23 Compared to GB SUP05 gb1_c40 Compared to GB SUP05 gb2_c138
Table S27: Contig31001 Dissimilatory sulfite reductase operon (dsr). Identity at the amino acids level of ESP-GSO against the databases, first four hits. Contig length 34,585 bp, 5,068 sequences recruited, average coverage 34.33X and GC content of 36.1%. SI GB C. R. C. V. SUP05 magnifica okutanii SUP05 dsrA ¶ 76.3 80.6 80.0 dsrB 87.4 79.3 84.6 83.5 dsrE 83.6 76.2 82.8 85.7 dsrF 85.8 80.5 83.6 82.1 80.5 dsrH 84.7 82.7 81.6 dsrC 89.7 79.3 85.0 86.0 dsrM 67.9 72.6 63.6 62.1 dsrK 84.0 75.8 81.3 82.0 dsrL § 75.2 80.8 79.1 dsrJ § 66.0 ¶ 51.7 dsrO § 71.6 74.1¥ 71.2 ¥ dsrP § 74.1 65.7 64.8 dsrN § 67.0 63.3¥ 61.2 ¥ dsrR § § 66.4 66.4 § The gene sequence is not described for this organism. Gene
¥ The sequence is described as hypothetical protein in this organism. ¶ There was not hit against this organism. Table S28: Contig21217 adenylyl-sulfate reductase and ATP sulfurylase genes. Identity at the amino acids level of ESP-GSO against the databases, first six hits. Contig length 51,536 bp, 650 sequences recruited, average coverage 24.20X and GC content of 42.2%. SI GB SUP05 SUP05 sat 92.1 81.3 aprM 66.7 62.9 aprB 95.7 80.1 aprA 82.4 82.9 ¥ Compared to SCGC AAA001-B15 Gene
C. R. magnifica 82.4 70.0 97.8 84.5
C. V. okutanii 79.7 67.2 98.9 84.9
ARCTIC96BD19 72.7¥ 72.4€ 38.4¥ 37.4€ ¥ 69.8 70.4€ 73.0¥ 72.7€
€ Compared to SCGC AAA007-O20
52
Table S29: Contigs18758 and 13237 dissimilatory nitrate reductase (nar) pathway. Identity at the amino acids level of ESP-GSO against the databases, first three hits. Contig length (bp)
Average coverage
N° of sequences
Contig GC%
dsrC11,251 78.1 37.4 36.48 like narI 72.7 § § 38.7 11,251 narJ 71.2 § § 33.9 11,251 narH 85.0 § § 66.9 11,251 narG 89.1 § § 58.8 11,251 narK 85.2 § § § 11,251 narK2 72.8 § § § 11,251 narX/L 78.5 § 78.5 77.2 14,083 narQ 70.6 § 66.3 64.4 14,083 § The gene sequence is not described for this organism.
32.05X
1,604
38.3
32.05X 32.05X 32.05X 32.05X 32.05X 32.05X 36.64X 36.64X
1,604 1,604 1,604 1,604 1,604 1,604 2,184 2,184
38.3 38.3 38.3 38.3 38.3 38.3 37.7 37.7
Gene
SI SUP05
GB SUP05 §
C. R. magnifica
C. V. okutanii
Table S30: Contig11209 nitrite reductase (NAD(P)H) nirBD genes. Identity at the amino acids level of ESP-GSO against the databases, first four hits. Contig length 6,599 bp, 344 sequences recruited, average coverage 11.79X and GC content of 39.4%. SI GB C. R. C. V. SUP05 SUP05 magnifica okutanii NO3-/NO274.1 89.1 70.0 69.4 Ser/Thr PK 66.4 § 63.4 62.8 nirB 57.8 58.0 57.2 57.1 nirD § § § § § The gene sequence is not described for this organism. Gene
53