of 19
1
Table of Contents
Supplementary Figure 1
.
Taxonomic separation of syntrophic sulfate reducing
bacteria using average nucleotide identity
2
Supplementary Figure
2
.
Comparison of 16S rRNA and 23S rRNA phylogeny of
organisms from the phylum Desulfobacterota.
3
Supplementary Figure
3
. Phylogeny of RpoB from organisms within the phylum
Desulfobacterota.
4
Supplementary Figure
4
.
Placement of various Seep
-
SRB1 clades w
ithin the phylum
Desulfobacterota.
5
Supplementary Figure 5. Pan
-
genome analysis of Seep
-
SRB1a metagenomes.
6
Supplementary Figure 6. Pan
-
genome analysis of Seep
-
SRB2 metagenomes.
7
Supplementary Figure 7
.
Phylogenetic placement of the outer membrane beta barrel,
OetI
from the putative DIET cluster
.
8
Supplementary Figure 8
.
The Tmc complex in Seep
-
SRB1a and Seep
-
SRB1g are
divergent
.
9
Supplementary Figure 9. Distribution of QrcABCD and RnfABCDEG in
Desu
lfobacterota.
10
Supplementary Figure 10. Gene neighborhoods of various HdrA containing
complexes and carbon fixation pathways in syntrophic SRB.
11
Supplementary Figure 11. Operons of Flx
-
Hdr
complexes and gene neighborhood of
putative formate utilizing proteins.
12
Supplementary Figure 12. Putatively polysaccharide biosynthesis pathways in Seep
-
SRB1a
13
Supplementary Figure 13. Putatively polysaccharide biosynthesis pathways in
Seep
-
SRB1g
14
Supplementary Figure 14. Putatively polysaccharide biosynthesis pathways in Seep
-
SRB2
15
Supplementary Figure 15. Putatively polysaccharide biosynthesis pathways in
HotSeep
-
1
16
Supplementary Figure 16. Presence of extracellular contractil
e injection systems
(eCIS) in ANME and SRB.
17
Supplementary Figure 17. Phylogeny of afp10, the spike protein from the
extracellular contractile injection system.
18
Supplementary Figure 18. Phylogeny of afp11, a base plate protein from the
extracellular contractile injection system.
19
2
Supplementary Figure 1
.
Taxonomic separation of syntrophic sulfate reducing bacteria
using average nucleotide identity
.
The average nucleotide identity of genomes from each clade
of the syntrophic sulfate reducing bacteria and some related bacteria were computed using the
PyANI program available through Anvi’o. The different clades of syntrophic SRB
HotSeep1,
Seep
-
SRB2, S
eep
-
SRB1a and Seep
-
SRB1g are colored according to the attached legend. The
Seep
-
SRB1a genomes in particular are differently colored depending on whether they partner
Desulfofervidales_sp._FWG156
Desulfofervidaceae_sp._str._NA091.008_B6
Desulfofervidaceae_sp._str._FWG155
HotSeep1_FWG170
HotSeep_1_draft_B50
Candidatus_Desulfofervidus_auxilii
HotSeep1_E50_DN
HotSeep1_E37_DN
Dissulfurirhabdus_thermomarina_ASM1049943v1
DTYO01_sp012961845
Seep-SRB2_sp._1_str._G37
Seep-SRB2_sp._1_str._Meg22_1214_Bin_80
Seep-SRB2_sp._2_str._FWG174
Seep-SRB2_sp._7_str._ML8_D
Seep-SRB2_sp._8_str._Meg22_1618_Bin_149
Seep-SRB2_sp._8_str._Meg22_1012_Bin_335
Seep-SRB2_sp._6_str._Meg22_02_Bin_69
Seep-SRB2_sp._3_str._002367355
Seep-SRB2_sp._5_str._003645605
Seep-SRB2_sp._4_str._E20
Seep-SRB1g_sp_CR10073A
C00003106_sp001751015
Seep-SRB1g_S7142MS4
B60-G16_sp003647275
C00003060_sp001751085
B23-G16_sp003647435
S7086C20_sp001751075
Desulfobacter_hydrogenophilus
JACNLL01_sp014381545
JACNLL01_sp013202725
ETH-SRB1_sp004193555
Eth-SRB1_sp019313565
Eth-SRB1_sp019314185
Seep-SRB1a_sp._1_str._013792055
Seep-SRB1a_sp._4_str._FWG172
Seep-SRB1a_sp._2_str._CR9063A
Seep-SRB1a_sp._9_str._Meg22_02_Bin_90
Seep-SRB1a_sp._6_str._003647525
Seep-SRB1a_sp._8_str._AB_03_Bin_172
Seep-SRB1a_sp._3_str._014237365
Seep-SRB1a_sp._7_str._FWG171
Seep-SRB1a_sp._5_str._SM7059A
Seep-SRB1a_sp._5_str._20073_SRB
Seep-SRB1a_sp._5_str._S7142MS3
1
0.71 0.7 0.71 0.72 0.71 0.72 0.72 0.67 0.67 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.67 0.67 0.67 0.68 0.68 0.67 0.68 0.68 0.67 0.67 0.66 0.67 0.67 0.67 0.67 0.67
0.67 0.68 0.67 0.68 0.67 0.67 0.67 0.67 0.68 0.68 0.67
0.71
1
0.72 0.74 0.74 0.74 0.74 0.74 0.79 0.66 0.68 0.67 0.68 0.68 0.67 0.67 0.67 0.67 0.67 0.68 0.67 0.67 0.66 0.67 0.67 0.67 0.68 0.68 0.67 0.67 0.68 0.67 0.67 0.6
7 0.67 0.68 0.67 0.67 0.67 0.68 0.67 0.67 0.68 0.67
0.7 0.72
1
0.73 0.73 0.73 0.73 0.73 0.7 0.67 0.68 0.67 0.68 0.67 0.67 0.67 0.67 0.67 0.67 0.68 0.68 0.67 0.67 0.68 0.68 0.68 0.68 0.69 0.68 0.67 0.68 0.68 0.68 0.67 0.67
0.68 0.68 0.68 0.67 0.68 0.67 0.67 0.68 0.67
0.71 0.74 0.73
1 0.96 0.96 0.96 0.96
0.66 0.67 0.69 0.69 0.68 0.67 0.68 0.67 0.67 0.67 0.67 0.67 0.67 0.66 0.66 0.68 0.67 0.68 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.68 0.68 0.68 0.68 0.67 0.68 0.6
7 0.67 0.68 0.68 0.67
0.71 0.74 0.73
0.96 1 0.98 0.98 0.98
0.73 0.66 0.69 0.68 0.69 0.67 0.68 0.67 0.67 0.67 0.67 0.68 0.67 0.67 0.66 0.67 0.67 0.68 0.68 0.7 0.67 0.68 0.68 0.67 0.67 0.68 0.68 0.68 0.68 0.67 0.67 0.67
0.67 0.68 0.68 0.68
0.71 0.74 0.73
0.96 0.99 1 0.99 0.99
0.72 0.67 0.69 0.68 0.7 0.67 0.68 0.67 0.67 0.67 0.67 0.68 0.68 0.68 0.66 0.67 0.68 0.67 0.68 0.69 0.67 0.67 0.68 0.67 0.67 0.68 0.68 0.68 0.68 0.67 0.68 0.67
0.67 0.68 0.68 0.68
0.72 0.74 0.73
0.96 0.99 0.99 1 0.99
0.75 0.66 0.7 0.68 0.7 0.67 0.68 0.67 0.67 0.67 0.66 0.69 0.68 0.67 0.67 0.68 0.69 0.67 0.68 0.71 0.67 0.67 0.68 0.67 0.68 0.68 0.68 0.69 0.69 0.67 0.66 0.67 0
.66 0.68 0.69 0.68
0.71 0.74 0.73
0.96 0.99 0.99 0.99 1
0.7 0.67 0.69 0.68 0.69 0.67 0.68 0.67 0.67 0.67 0.67 0.68 0.67 0.67 0.67 0.68 0.67 0.67 0.68 0.68 0.67 0.67 0.68 0.67 0.67 0.68 0.68 0.68 0.68 0.67 0.67 0.67
0.67 0.67 0.68 0.68
0.66 0.77 0.69 0.65 0.72 0.72 0.75 0.73
1
0.7 0.7 0.7 0.7 0.69 0.7 0.69 0.69 0.7 0.7 0.7 0.69 0.69 0.68 0.68 0.68 0.68 0.69 0.69 0.69 0.69 0.7 0.68 0.68 0.68 0.67 0.7 0.67 0.67 0.68 0.67 0.67 0.68 0.68 0
.67
0.67 0.66 0.68 0.67 0.67 0.68 0.68 0.67 0.7
1
0.71 0.71 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.71 0.68 0.68 0.69 0.68 0.68 0.68 0.68 0.69 0.69 0.68 0.69 0.68 0.68 0.69 0.68 0.68 0.69 0.68 0.68 0.69 0.69 0.69 0.69 0.
69
0.67 0.68 0.67 0.68 0.69 0.69 0.69 0.69 0.7 0.71
1 0.99 0.87
0.8
0.84 0.84 0.85 0.86 0.85 0.85
0.71 0.7 0.69 0.71 0.73 0.71 0.7 0.69 0.7 0.7 0.71 0.69 0.69 0.7 0.7 0.7 0.7 0.69 0.71 0.7 0.71 0.7 0.71 0.71
0.67 0.67 0.67 0.69 0.69 0.69 0.69 0.69 0.7 0.71
0.99 1 0.87
0.8
0.85 0.84 0.85 0.86 0.85 0.85
0.71 0.71 0.7 0.72 0.73 0.72 0.69 0.69 0.69 0.69 0.7 0.69 0.69 0.7 0.72 0.71 0.7 0.69 0.71 0.7 0.71 0.71 0.71 0.71
0.67 0.68 0.68 0.67 0.7 0.7 0.7 0.69 0.7 0.7
0.87 0.87 1
0.81
0.88 0.88 0.88 0.9 0.88 0.88
0.73 0.71 0.7 0.72 0.75 0.73 0.71 0.69 0.69 0.69 0.71 0.7 0.71 0.71 0.71 0.72 0.71 0.7 0.73 0.71 0.72 0.72 0.71 0.72
0.68 0.67 0.68 0.67 0.67 0.67 0.67 0.67 0.69 0.7 0.79 0.8 0.81
1 0.83 0.84 0.83 0.83 0.82 0.82
0.7 0.69 0.68 0.7 0.71 0.68 0.69 0.68 0.69 0.69 0.7 0.69 0.7 0.7 0.7 0.7 0.69 0.68 0.71 0.69 0.69 0.7 0.69 0.69
0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.7 0.7
0.85 0.84 0.88 0.84 1 1 0.9 0.9 0.89 0.89
0.73 0.7 0.69 0.71 0.73 0.7 0.7 0.69 0.7 0.69 0.72 0.71 0.71 0.71 0.73 0.72 0.71 0.69 0.72 0.72 0.71 0.72 0.7 0.7
0.68 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.7 0.7
0.84 0.84 0.88 0.84 1 1 0.9 0.9 0.89 0.89
0.72 0.7 0.7 0.71 0.73 0.69 0.71 0.68 0.7 0.69 0.7 0.7 0.7 0.71 0.72 0.71 0.7 0.7 0.71 0.71 0.71 0.71 0.7 0.71
0.68 0.67 0.67 0.66 0.67 0.67 0.66 0.67 0.7 0.7
0.85 0.85 0.89 0.83 0.91 0.91 1 0.92 0.91 0.91
0.71 0.69 0.69 0.69 0.73 0.72 0.7 0.69 0.7 0.69 0.7 0.7 0.69 0.7 0.7 0.7 0.71 0.71 0.74 0.7 0.7 0.71 0.7 0.71
0.67 0.67 0.68 0.67 0.67 0.67 0.67 0.67 0.7 0.7
0.86 0.86 0.89 0.83 0.9 0.9 0.91 1 0.92 0.92
0.74 0.71 0.7 0.71 0.73 0.72 0.69 0.69 0.69 0.7 0.72 0.71 0.71 0.72 0.7 0.73 0.73 0.71 0.74 0.71 0.71 0.73 0.71 0.71
0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.7 0.7
0.85 0.85 0.88 0.83 0.89 0.89 0.91 0.92 1 0.93
0.72 0.7 0.7 0.7 0.72 0.71 0.69 0.68 0.7 0.73 0.7 0.69 0.7 0.69 0.7 0.71 0.72 0.68 0.71 0.69 0.72 0.71 0.7 0.68
0.67 0.68 0.68 0.67 0.68 0.68 0.69 0.69 0.7 0.7
0.85 0.85 0.88 0.82 0.89 0.89 0.9 0.92 0.93 1
0.75 0.72 0.71 0.71 0.75 0.7 0.7 0.69 0.71 0.7 0.72 0.71 0.72 0.72 0.73 0.73 0.73 0.72 0.73 0.72 0.73 0.73 0.72 0.72
0.67 0.67 0.67 0.67 0.68 0.67 0.68 0.68 0.69 0.68 0.72 0.71 0.74 0.7 0.73 0.72 0.71 0.74 0.72 0.75
1 0.98 0.98
0.7 0.71 0.7 0.69 0.69 0.71 0.7 0.73 0.71 0.73 0.71 0.73 0.75 0.74 0.73 0.77 0.74 0.75 0.76 0.73 0.74
0.67 0.67 0.67 0.66 0.68 0.68 0.68 0.68 0.69 0.68 0.71 0.71 0.72 0.7 0.71 0.7 0.71 0.72 0.71 0.73
0.98 1 0.99
0.7 0.71 0.69 0.69 0.69 0.7 0.7 0.7 0.7 0.71 0.7 0.71 0.72 0.72 0.72 0.74 0.72 0.72 0.72 0.72 0.72
0.67 0.66 0.67 0.68 0.69 0.68 0.67 0.68 0.68 0.69 0.69 0.7 0.71 0.69 0.7 0.69 0.68 0.71 0.71 0.71
0.98 0.99 1
0.7 0.7 0.69 0.69 0.68 0.7 0.7 0.7 0.7 0.7 0.7 0.71 0.73 0.72 0.71 0.73 0.71 0.7 0.72 0.71 0.71
0.67 0.67 0.68 0.68 0.68 0.68 0.69 0.68 0.69 0.68 0.71 0.72 0.72 0.7 0.71 0.71 0.69 0.71 0.7 0.71 0.7 0.7 0.7
1
0.79 0.73 0.72 0.68 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69
0.67 0.67 0.68 0.67 0.68 0.67 0.68 0.67 0.68 0.67 0.74 0.73 0.75 0.72 0.74 0.74 0.74 0.74 0.73 0.75 0.71 0.7 0.7 0.79
1
0.72 0.72 0.68 0.69 0.69 0.69 0.69 0.7 0.7 0.7 0.71 0.7 0.7 0.72 0.7 0.7 0.71 0.7 0.7
0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.68 0.68 0.72 0.73 0.73 0.69 0.69 0.69 0.72 0.72 0.71 0.71 0.7 0.69 0.69 0.73 0.72
1
0.7 0.68 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69
0.67 0.68 0.68 0.66 0.68 0.68 0.68 0.68 0.7 0.67 0.7 0.7 0.71 0.69 0.7 0.7 0.69 0.7 0.69 0.7 0.69 0.69 0.68 0.72 0.72 0.7
1
0.68 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.7 0.69 0.69 0.71 0.7 0.69 0.69 0.69 0.69
0.66 0.71 0.72 0.66 0.72 0.72 0.74 0.72 0.73 0.67 0.71 0.68 0.72 0.68 0.69 0.67 0.68 0.69 0.67 0.7 0.69 0.7 0.68 0.69 0.68 0.67 0.7
1
0.68 0.68 0.7 0.68 0.68 0.68 0.68 0.69 0.69 0.68 0.68 0.68 0.68 0.68 0.69 0.68
0.67 0.68 0.67 0.67 0.67 0.67 0.67 0.67 0.69 0.68 0.7 0.7 0.7 0.7 0.7 0.7 0.69 0.7 0.7 0.71 0.71 0.7 0.7 0.69 0.69 0.69 0.69 0.69
1 0.91
0.8 0.79 0.79 0.74 0.74 0.74 0.74 0.74 0.75 0.74 0.74 0.74 0.75 0.74
0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.69 0.69 0.69 0.69 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.71 0.7 0.71 0.7 0.69 0.69 0.69 0.69
0.91 1
0.8 0.79 0.79 0.75 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.75 0.75
0.67 0.69 0.69 0.67 0.69 0.69 0.69 0.69 0.71 0.68 0.71 0.69 0.72 0.7 0.71 0.69 0.7 0.72 0.7 0.73 0.73 0.7 0.7 0.69 0.69 0.69 0.69 0.69 0.8 0.8
1 0.86 0.87
0.74 0.74 0.76 0.75 0.76 0.77 0.74 0.75 0.76 0.76 0.75
0.67 0.67 0.68 0.67 0.67 0.67 0.67 0.67 0.68 0.68 0.7 0.69 0.7 0.7 0.7 0.69 0.7 0.7 0.69 0.71 0.71 0.7 0.7 0.7 0.69 0.69 0.69 0.69 0.79 0.78
0.86 1 0.98
0.76 0.76 0.78 0.8 0.77 0.8 0.76 0.76 0.78 0.77 0.78
0.67 0.68 0.68 0.67 0.68 0.68 0.68 0.68 0.69 0.68 0.7 0.69 0.71 0.71 0.72 0.7 0.7 0.72 0.7 0.73 0.73 0.71 0.7 0.7 0.7 0.69 0.69 0.69 0.79 0.79
0.86 0.99 1
0.75 0.75 0.77 0.77 0.76 0.81 0.76 0.76 0.78 0.76 0.76
0.67 0.67 0.67 0.68 0.68 0.68 0.68 0.68 0.67 0.68 0.7 0.7 0.71 0.7 0.71 0.7 0.71 0.72 0.69 0.71 0.71 0.7 0.7 0.7 0.7 0.69 0.69 0.69 0.74 0.75 0.74 0.75 0.74
1 0.86 0.88 0.87 0.88 0.87 0.87 0.86 0.88 0.88 0.88
0.67 0.68 0.67 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.7 0.7 0.71 0.71 0.73 0.71 0.71 0.7 0.7 0.72 0.73 0.71 0.71 0.69 0.7 0.69 0.69 0.68 0.74 0.74 0.74 0.75 0.75
0.86 1 0.91 0.9 0.9 0.9 0.9 0.87 0.91 0.92 0.92
0.67 0.68 0.68 0.68 0.68 0.68 0.69 0.68 0.7 0.68 0.71 0.71 0.72 0.7 0.72 0.7 0.7 0.72 0.7 0.73 0.75 0.72 0.72 0.69 0.7 0.69 0.7 0.68 0.74 0.74 0.75 0.77 0.76
0.88 0.91 1 0.93 0.92 0.91 0.91 0.88 0.93 0.94 0.94
0.67 0.68 0.68 0.68 0.68 0.69 0.68 0.69 0.69 0.68 0.7 0.69 0.71 0.7 0.71 0.7 0.71 0.73 0.7 0.73 0.74 0.71 0.72 0.7 0.7 0.69 0.7 0.69 0.74 0.74 0.75 0.78 0.76
0.87 0.9 0.93 1 0.92 0.91 0.91 0.88 0.93 0.94 0.94
0.67 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.69 0.68 0.69 0.69 0.69 0.69 0.69 0.71 0.69 0.72 0.73 0.7 0.7 0.69 0.69 0.69 0.69 0.69 0.74 0.74 0.76 0.76 0
.76
0.88 0.9 0.92 0.92 1 0.92 0.91 0.87 0.92 0.93 0.93
0.69 0.69 0.69 0.68 0.68 0.68 0.68 0.68 0.68 0.69 0.72 0.7 0.73 0.72 0.72 0.7 0.72 0.74 0.71 0.73 0.78 0.73 0.75 0.69 0.71 0.69 0.7 0.69 0.76 0.76 0.77 0.8 0.8
1
0.87 0.9 0.92 0.91 0.92 1 0.9 0.87 0.91 0.92 0.92
0.67 0.68 0.68 0.67 0.67 0.68 0.67 0.67 0.68 0.69 0.71 0.71 0.71 0.7 0.71 0.72 0.71 0.71 0.7 0.73 0.75 0.72 0.74 0.69 0.7 0.69 0.7 0.68 0.74 0.74 0.75 0.76 0.7
5
0.87 0.9 0.92 0.91 0.91 0.9 1 0.88 0.91 0.93 0.92
0.67 0.67 0.68 0.67 0.67 0.67 0.67 0.67 0.66 0.69 0.71 0.71 0.71 0.7 0.71 0.71 0.7 0.71 0.7 0.73 0.75 0.71 0.71 0.69 0.7 0.69 0.69 0.69 0.74 0.74 0.75 0.76 0.7
5
0.86 0.87 0.88 0.87 0.87 0.87 0.87 1 0.88 0.88 0.88
0.67 0.67 0.67 0.68 0.67 0.67 0.68 0.68 0.67 0.69 0.7 0.7 0.7 0.7 0.72 0.71 0.71 0.72 0.71 0.73 0.75 0.71 0.72 0.69 0.7 0.69 0.69 0.68 0.75 0.74 0.76 0.77 0.77
0.88 0.91 0.93 0.93 0.92 0.91 0.91 0.88 1 0.97 0.98
0.67 0.68 0.68 0.68 0.69 0.68 0.69 0.69 0.7 0.68 0.7 0.7 0.72 0.69 0.71 0.7 0.7 0.71 0.7 0.72 0.73 0.71 0.71 0.69 0.7 0.69 0.7 0.69 0.75 0.75 0.76 0.77 0.75
0.89 0.92 0.95 0.94 0.93 0.92 0.93 0.89 0.97 1 0.98
0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.68 0.67 0.68 0.71 0.7 0.72 0.7 0.71 0.71 0.7 0.72 0.7 0.73 0.74 0.71 0.71 0.7 0.69 0.69 0.69 0.68 0.75 0.74 0.76 0.77 0.76
0.89 0.92 0.94 0.94 0.93 0.92 0.92 0.89 0.98 0.97 1
Seep-SRB1a sp. 5 str. S7142MS3
Seep-SRB1a sp. 5 str. 20073 SRB
Seep-SRB1a sp. 5 str. SM7059A
Seep-SRB1a sp. 7 str. FWG171
Seep-SRB1a sp. 3 str. 014237365
Seep-SRB1a sp. 8 str. AB 03 Bin 172
Seep-SRB1a sp. 6 str. 003647525
Seep-SRB1a sp. 9 str. Meg22 02 Bin 90
Seep-SRB1a sp. 2 str. CR9063A
Seep-SRB1a sp. 4 str. FWG172
Seep-SRB1a sp. 1 str. 013792055
Eth-SRB1 sp019314185
Eth-SRB1 sp019313565
ETH-SRB1 sp004193555
JACNLL01 sp013202725
JACNLL01 sp014381545
Desulfobacter hydrogenophilus
S7086C20 sp001751075
B23-G16 sp003647435
C00003060 sp001751085
B60-G16 sp003647275
Seep-SRB1g S7142MS4
C00003106 sp001751015
Seep-SRB1g sp CR10073A
Seep-SRB2 sp. 4 str. E20
Seep-SRB2 sp. 5 str. 003645605
Seep-SRB2 sp. 3 str. 002367355
Seep-SRB2 sp. 6 str. Meg22 02 Bin 69
Seep-SRB2 sp. 8 str. Meg22 1012 Bin 335
Seep-SRB2 sp. 8 str. Meg22 1618 Bin 149
Seep-SRB2 sp. 7 str. ML8 D
Seep-SRB2 sp. 2 str. FWG174
Seep-SRB2 sp. 1 str. Meg22 1214 Bin 80
Seep-SRB2 sp. 1 str. G37
DTYO01 sp012961845
Dissulfurirhabdus thermomarina
HotSeep1 E37 DN
HotSeep1 E50 DN
Candidatus
Desulfofervidus auxilii
HotSeep 1 draft B50
HotSeep1 FWG170
Desulfofervidaceae sp. str. FWG155
Desulfofervidaceae sp. str. NA091.008 B6
Desulfofervidales sp. FWG156
1
1
1
0.996
1
1
1
0.73
1
1
1
1
1
1
0.991
0.635
1
0.997
1
1
0.488
0.925
1
0.917
1
1
1
1
1
1
1
1
1
1
1
1
1
0.995
1
1
1
Pescadero Basin hydrothermal vent site
Guayamas Basin hydrothermal vent site
Costa Rica cold methane seep site
Elba marine coastal sediment
Hydrate Ridge methane seeps
Santa Monica cold methane seep sites
Coal oil point, Santa Barbara
Gulf of Cadiz mud volcano
Deep subsurface groundwater in Olkiluoto, Finland
Mahoney Lake, saline lake
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
ANME-1 partner
ANME-2c partner
ANME-2a partner
ANME-2b partner
HotSeep-1
Seep-SRB2
Seep-SRB1g
Seep-SRB1a
3
ANME
-
2a or ANME
-
2c respectively. The geographic location from which each genome was
extrac
ted is indicated on each node or clade in the tree.
Supplementary Figure
2
.
Comparison of 16S rRNA and 23S rRNA phylogeny of organisms
from the phylum Desulfobacterota.
16S rRNA and 23S rRNA sequences were extracted from
all organisms from the phylum Desulfobacterota available in GTDB release 95, and from
4
syntrophic SRB. These sequences were aligned using MUSCLE and a tree was inferred using
IQTREE2. Hot
-
Seep1 is placed a
djacent to the order Thermodesulfbacteriales in both these trees.
Supplementary Figure
3
. Phylogeny of RpoB from organisms within the phylum
Desulfobacterota.
Sequences of RNA Polymerase, subunit B were extracted from all organisms
from the phylum Desul
fobacterota available in GTDB release 95, and from syntrophic SRB
using BLASTP with an e
-
value cut
-
off of e
-
30 and appropriate query sequences. The sequences
were confirmed to RpoB by manual inspection of a multiple sequence alignment generated using
5
MUSCL
E and the tree was inferred using IQTREE2. In this tree, Hot
-
Seep1 is found adjacent to
the order Desulfovibrionales.
6
Supplementary Figure
4
.
Placement of various Seep
-
SRB1 clades within the phylum
Desulfobacterota.
A phylogenetic tree of full length 16S sequences from various Seep
-
SRB1
clades including the
original
16S rR
NA sequences used to define the Seep
-
SRB1(a
-
f) clades
.
Supplementary Fig
ure 5.
Pan
-
genome analysis of Seep
-
SRB1a metagenomes.
Fourteen
genomes from nine Seep
-
SRB1a species were analyzed using the Anvi’o pan
-
genome analysis
pipeline. Five
gene cluster
bins were annotated based on genes that were identified as part of the
core m
etagenome, unique to Seep
-
SRB1a sp. 2, Seep
-
SRB1a sp. 3, Seep
-
SRB1a sp. 5 and from
the Seep
-
SRB1a sp. 4 and 7.
7
Supplementary Figure 6. Pan
-
genome analysis of Seep
-
SRB2 metagenomes.
Fourteen
genomes from nine Seep
-
SRB1a species were analyzed using the Anvi’o pan
-
genome analysis
pipeline.
Three
gene cluster
bins were annotated based on genes that were identified as p
art of the
core metagenome,
present in Seep
-
SRB2 sp. 1 and absent in Seep
-
SRB2 sp.1
8
Supplementary Figure 7
.
Phylogenetic placement of the outer membrane beta barrel,
OetI
from the putative DIET cluster
.
A multiple sequence alignment,
Supplementary multiple
sequence alignment MSA2
of the
OetI
protein sequences extracted from the genomes of
syntrophic SRB and the NCBI database was generated using MUSCLE. This alignment was used
to infer a phylogenetic tree
using IQ
-
Tree2 and visualized on the iTOL web server. a. The
phylogenetic placement of
OetI
from E20 Seep
-
SRB2 next to
OetI
from Thermodesulfobacteria
and
Dissulfurirhabdus thermomarina
demonstrates that it was possibly vertically acquired from a
gene tran
sfer that was ancestral to the Seep
-
SRB2 and then vertically transferred. b. The
phylogenetic placement of Seep
-
SRB1a and Seep
-
SRB1g
OetI
suggests that they are related.
Additionally, the placement of
OetI
from G37 Seep
-
SRB2 next to
OetI
from Desulfofervid
ales,
suggests that the Seep
-
SRB2 partner of ANME
-
1 acquired its DIET cluster from HotSeep1.
MBU1232963.1 Proteobacteria bacterium
MBU1138639.1 Proteobacteria bacterium
MBU0945753.1 Proteobacteria bacterium
MBU1060414.1 Proteobacteria bacterium
HFQ88617.1 Desulfobulbus sp.
HEB51214.1 Desulfobulbus sp.
HEB68685.1 Desulfobulbus sp.
NOX81122.1 Deltaproteobacteria bacterium
GBE53412.1 bacterium BMS3Bbin14
HHO47316.1 Desulfobacteraceae bacterium
RJX24390.1 Desulfobulbus sp.
KPK25464.1 Desulfobacterales bacterium SG8 35 2
MBW2466307.1 Deltaproteobacteria bacterium
WP 155890653.1 Desulfuromonas sp. TF
WP 191156331.1 Pelobacter sp. M08fum
MBE0598469.1 Desulfuromonadales bacterium
MBI5441499.1 Deltaproteobacteria bacterium
WP 013162639.1 Desulfurivibrio alkaliphilus
PXF57835.1 Seep-SRB2 E20 sp003194495
DFBQ01000012.1 21 Seep-SRB2 sp002367355
WP 169755419.1 Dissulfurirhabdus thermomarina
WP 163297689.1 Dissulfurirhabdus thermomarina ASM1049943v1
MBU4262709.1 Proteobacteria bacterium
MBU0968432.1 Proteobacteria bacterium
RJX27786.1 Desulfurivibrio sp.
MBI5557136.1 Deltaproteobacteria bacterium
OKY74846.1 Desulfobulbaceae bacterium DB1
OGQ99171.1 Deltaproteobacteria bacterium RIFOXYD12 FULL 57 12
TDB36203.1 Deltaproteobacteria bacterium
MBU4408368.1 Proteobacteria bacterium
MBU2620385.1 Proteobacteria bacterium
MBU1405738.1 Proteobacteria bacterium
MBA3002646.1 Desulfurivibrio sp.
MBU4118553.1 Proteobacteria bacterium
MBU4033621.1 Proteobacteria bacterium
MBU2536953.1 Proteobacteria bacterium
WP 013162994.1 Desulfurivibrio alkaliphilus
HET98732.1 Desulfurivibrio alkaliphilus
PLX50880.1 Desulfobulbaceae bacterium
MBU0682461.1 Proteobacteria bacterium
HIJ78263.1 Deltaproteobacteria bacterium
MBA3015988.1 Desulfobulbaceae bacterium
MBF0220885.1 Desulfobulbaceae bacterium
HFQ80997.1 Desulfobacterales bacterium
MBU0484585.1 Proteobacteria bacterium
NTV13056.1 Desulfobulbaceae bacterium
MBU0481026.1 Proteobacteria bacterium
MBU0673827.1 Proteobacteria bacterium
MBU0730581.1 Proteobacteria bacterium
MBU1711259.1 Proteobacteria bacterium
AEH45646.1 Thermodesulfatator indicus DSM 15286
WP 169311170.1 Thermodesulfatator indicus
WP 157627868.1 Thermodesulfatator autotrophicus
OAG27706.1 Thermodesulfatator autotrophicus
WP 157608117.1 Thermodesulfatator atlanticus
HHI98139.1 Thermodesulfatator atlanticus
WP 166032768.1 Thermosulfuriphilus ammonigenes
NPA15986.1 Deferribacteres bacterium
WP 221171603.1 Thermosulfurimonas sp. F29
HFC97555.1 Thermosulfurimonas dismutans
RLG11305.1 Candidatus Pacearchaeota archaeon
WP 038055358.1 Thermodesulfobacterium hydrogeniphilum
RLD97851.1 Aquificae bacterium
RLD93460.1 Aquificae bacterium
HDN67453.1 Firmicutes bacterium
WP 068548857.1 Thermosulfidibacter takaii
WP 072905028.1 Malonomonas rubra
WP 040201235.1 Geoalkalibacter subterraneus
OEU69584.1 Desulfuromonadales bacterium C00003093
NOQ51159.1 Desulfuromonadaceae bacterium
OHB29066.1 Desulfuromonadaceae bacterium GWC2 58 13
WP 140396645.1 Desulfuromonas acetexigens
WP 155875644.1 Desulfuromonas sp. AOP6
BCA79346.1 Desulfuromonas sp. AOP6
MBN1930614.1 Desulfobacterales bacterium
PLX89823.1 Desulfuromonas sp.
NPA25898.1 Deltaproteobacteria bacterium
MBN2808880.1 Deltaproteobacteria bacterium
MBN2332177.1 Deltaproteobacteria bacterium
WP 005999027.1 Desulfuromonas acetoxidans
PLX96191.1 Desulfuromonas sp.
OEU73148.1 Desulfuromonadales bacterium C00003068
100
93
100
100
100
100
96
100
100
100
100
93
100
100
100
85
100
100
100
100
83
99
100
69
100
100
100
100
72
100
100
100
100
70
100
100
97
70
97
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
83
44
93
100
100
99
100
100
100
67
100
100
82
100
100
100
40
97
100
100
100
100
100
100
100
Tree scale: 1
a.
a
.
Phylogenetic placement of the outer membrane beta barrel from Seep-SRB2 (E20)
P
h
y
l
o
g
e
n
e
t
i
c
p
l
a
c
e
m
e
n
t
o
f
t
h
e
o
u
t
e
r
m
e
m
b
r
a
n
e
b
e
t
a
b
a
r
r
e
l
f
r
o
m
S
e
e
p
-
S
R
B
2
(
E
2
0
)
MBT9439656.1 Seep-SRB1a sp. S7142MS3
Ga0402080 bin2 589 Seep-SRB1a SM7059A
MBW2739412.1 Seep-SRB1a sp. AB_03_Bin_172
RLC24913.1 Seep-SRB1a sp003647525
MBW2737301.1 Seep-SRB1a sp. AB 03 Bin 172
OEU78978.1 Desulfobulbaceae bacterium C00003063
MBN1840865.1 Seep-SRB1c sp016930875
MBW1675111.1 Seep-SRB1c Meg22_810_Bin_246
HID30861.1 Seep-SRB1c sp012962685
NVL90216.1 JABXJX01 sp013375375
RLB82945.1 B60-G16 sp003647275
MBW1740403.1 Seep-SRB1c sp. B60-G16 sp003647275
MBA3018034.1 Seep-SRB1a sp013792055
MBU4209345.1 Seep-SRB1a sp013792055
MBW2624018.1 Adiutricales bacterium
MBC2694390.1 B13-G4 sp014237365a
Ga0402054 bin3 1853 Seep-SRB1a sp. CR9063A
Ga0402030 bin2 2261 Seep-SRB1g sp. CR10073B
MBT9448005.1 Seep-SRB1g sp. S7142MS4
OEU53602.1 Desulfobacterales bacterium C00003106
OEU57520.1 Desulfobacterales bacterium C00003104
WP 126376166.1 Desulfovibrio ferrophilus
BBD07179.1 Desulfovibrio ferrophilus
MBU1001577.1 Desulfocurvus sp. MM_PC_MetaG.mb.39
OGQ35877.1 Deltaproteobacteria bacterium RIFCSPLOWO2 02 FULL 42 39
OGP43475.1 Deltaproteobacteria bacterium GWD2 42 10
OGQ27541.1 Deltaproteobacteria bacterium RIFCSPHIGHO2 02 FULL 42 44
OGQ75995.1 Deltaproteobacteria bacterium RIFOXYA2 FULL 42 10
HCY18496.1 Deltaproteobacteria bacterium
MBI3754384.1 Deltaproteobacteria bacterium
MBI5875013.1 Deltaproteobacteria bacterium
OGQ11666.1 Deltaproteobacteria bacterium RIFCSPHIGHO2 02 FULL 43 33
MBI5903770.1 Deltaproteobacteria bacterium
MBI5235716.1 Deltaproteobacteria bacterium
MBI5237919.1 Deltaproteobacteria bacterium
HHL40056.1 Deltaproteobacteria bacterium
MBI5560673.1 Deltaproteobacteria bacterium
MBI5599503.1 Deltaproteobacteria bacterium
HHD11522.1 Deltaproteobacteria bacterium
MBI5748741.1 Nitrospinae bacterium
MBI3584845.1 Nitrospinae bacterium
OGW06831.1 Nitrospinae bacterium RIFCSPLOWO2 01 FULL 39 10
OGW07740.1 Nitrospinae bacterium RIFCSPLOWO2 12 39 16
OGV97810.1 Nitrospinae bacterium RIFCSPHIGHO2 02 39 11
OGW07482.1 Nitrospinae bacterium RIFCSPLOWO2 12 39 15
OGW06292.1 Nitrospinae bacterium RIFCSPLOWO2 02 39 17
MBI5182766.1 Nitrospinae bacterium
AMM40356.1 Candidatus Desulfofervidus auxilii
IEOPGEAI 00603 Candidatus Desulfofervidus auxilli sp. B50
WP 066060692.1 Candidatus Desulfofervidus auxilii
CAD7783700.1 Candidatus Desulfofervidus auxilii EN37
CAD7772292.1 Candidatus Desulfofervidus auxilii EN50
BEFNOMPG 00388 Candidatus Desulfofervidus auxilli sp. PB12019FWG170
MBW1937369.1 Seep-SRB2 sp019307905
MBW1718516.1 Seep-SRB2 sp019306525
MBW1670749.1 Seep-SRB2 sp019306545
PXF54096.1 Seep-SRB2 G37 sp003194485
MBW1966863.1 Seep-SRB2 sp019308155
RLB12608.1 Deltaproteobacteria bacterium (o_Desulfatiglandales)
GLOGJPLJ 00704 Desulfofervidaceae sp. PB NA091.008 B6
OLHCEBFO 00969 Desulfofervidaceae sp. PB11946FWG155
RLA81695.1 Deltaproteobacteria bacterium
MBI2876984.1 Candidatus Tectomicrobia bacterium
Cdidt
100
100
100
99
99
99
100
99
91
100
83
76
74
94
100
100
99
98
100
100
100
100
94
92
100
99
100
100
100
99
100
100
100
100
51
99
100
100
100
99
51
100
100
100
100
100
98
98
100
100
100
100
100
99
95
100
92
42
100
100
63
100
100
95
51
100
100
b.
b
.
Phylogenetic placement of outer membrane beta barrel, omb from other syntrophic SRB
P
h
y
l
o
g
e
n
e
t
i
c
p
l
a
c
e
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e
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m
e
m
b
r
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e
b
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t
a
b
a
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l
,
o
m
b
f
r
o
m
o
t
h
e
r
s
y
n
t
r
o
p
h
i
c
S
R
B
Seep-SRB1c
Seep-SRB1a
Hot-Seep1
Seep-SRB2
Seep-SRB1g
Seep-SRB1a (omb with deletion)