supplemental table 1. quantification of the single copy...

Conserved single-copy marker gene PB-SRB1 PB-PSB1recA 1 1

RpoB 1 1DNA gyrase A 1 1DNA gyrase B 1 1

ffh signal recognition particle protein 1 1Chaperone protein HtpG 1 1

YgjD/Kae1/Qri7 family metalloendopeptidase 1 1phosphoribosylformylglycinamidine cyclo-ligase 1 1

Porphobilinogen deaminase 1 1ribonuclease HII 1 1

phenylalanyl-tRNA synthetase alpha subunit 1 1phenylalanyl-tRNA synthetase beta subunit 1 1

tRNA pseudouridine synthase B 1 1translation elongation factor EF-2 2 1

translation initiation factor IF-2 1 1ribosomal protein S2 1 1ribosomal protein S3 1 1ribosomal protein S5 1 1ribosomal protein S7 1 1ribosomal protein S8 1 1ribosomal protein S9 1 1

ribosomal protein S10 1 1ribosomal protein S11 1 1

ribosomal protein S12/S23 1 1ribosomal protein S13 1 1

ribosomal protein S15P 1 1ribosomal protein S17 1 1ribosomal protein S19 1 1

ribosomal protein L1 1 1ribosomal protein L2 1 1ribosomal protein L3 1 1

ribosomal protein L4/L1e 1 1ribosomal protein L5 1 1ribosomal protein L6 1 1

ribosomal protein L10 1 1ribosomal protein L11 1 1ribosomal protein L13 1 1

ribosomal protein L14b 1 1ribosomal protein L15 1 1ribosomal protein L16 1 1

ribosomal protein L18P/L5E 1 1ribosomal protein L22 1 1ribosomal protein L24 1 1

ribosomal protein L25/L23 1 1ribosomal protein L29 1 1

Supplemental Table 1. Quantification of the single copy phylogenetic marker genes for estimating genome completion and number of genomes per bin of the PB-SRB1 and PB-PSB1 associated bins. Note that translation elongation factor EF-2 is duplicated in the closely related Desulfobulbaceae genomes

0.02

Thiococcus pfennigii Y12373

Ectothiorhodospira variabilis AM943125

Thiocystis minor Y12372

Thiocystis gelatinosa Y11317

Allochromatium vinosum CP001896

Thiocapsa pendens AJ002797

Thiohalocapsa halophila AM903380

Marichromatium indicum AJ543328

Thiocapsa marina FM178270

Thiodictyon bacillosum EF999974

Halochromatium glycolicum X93472

Chromatium okenii Y12376

Thioflavicoccus mobilis AJ010126

Rhabdochromatium marinum X84316

Pirry PSB

Halochromatium salexigens X98597

Thiohalocapsa marina AM491592

Thiorhodovibrio winogradskyi Y12368

Thiodictyon elegans EF999973

Thiorhodococcus bheemlicus AM282559

Halochromatium roseum AM283535

Lamprocystis purpurea AJ223235

Marichromatium gracile X93473

0.75

0.91

1

0.44

1

0.97

1

0.99

0.93

0.99

0.83

0.74

1

0.89

0.96

0.8

Supplemental Figure 1. Maximum likelihood phylogeny (rooted) constructed from 16S rRNA genesequences of pink berry purple sulfur bacteria PB-PSB1 and cultured Chromatiales relatives. Phylogeny was constructed with FastTree using the approximate maximum likelihood method (Price et al., 2010) and GTRCAT approximation with 20 rate categories. Values at the nodes are SH-like local supports (1000) computed by FastTree and used as condiference values of tree branches. Scale bar represents thenumber of estimated changes per position for a unit of branch length.

PB-PSB1 KF513139

EU854577 Flavihumibacter petaseus

HQ640607 partial nitrifying-ANAMMOX municipal wastewater reactor

GQ441322 marine microbial mats from a sandy intertidal beachAM286229 Lewinella agarilytica

FJ535337 Fe-rich mats submarine volcanoes along the Kermadec Arc

HQ153837 white microbial film in aphotic zone of shallow hydrothermal vent South Tonga

FJ905765 Fe-oxide sediments submarine Volcano 1 Tonga Arc

EU919815 marine bacterioplankton in Kongsfjorden

EU245266 hypersaline microbial mat

CU466753 anoxic basin of a municipal wastewater treatment plant

CU923026 mesophilic anaerobic digester which treats municipal wastewater sludge

EU236348 Marine sponge-associaed Haliclona

GU118272 Coral-associated Diploria strigosa

CP001699 Chitinophaga pinensis DSM 2588

CU466744 anoxic basin of a municipal wastewater treatment plant

FJ716938 lungworm bioturbated sediments UK

GU472712 meromictic sulfur-cycling Lake PavinHQ116750 Butyric acid and DMS assimilating biofilter biofilm

KF513076 56_OTU

KF512962 45_OTU

AM997690 deep-sea surface sediment South-Atlantic Ocean Cape Basin

EU544843 1.0-60 um size fraction small-suspended particles of Arctic seawater

EF645959 particle-associated anammox bacteria Namibian upwelling system

FM174355 biotrickling filter treating high loads of H2S

FJ205237 inactive hydrothermal field sediments depth 2350m East Lau

DQ836305 Fulvivirga kasyanovii

KF512957 9_OTU

DQ330420 Guerrero Negro hypersaline microbial mat

FJ744798 surface water at the UGA Marine Institute

KF512925 44_OTU


EU340220 Thiotrix-dominated macrophte Sedge Bay Yellowstone

GQ259254 deep sediments from an arctic fjord of svalbard

EU104280 activated sludge


GQ348350 Saanich Inlet 200 m depth


HQ163185 Saanich Inlet 100 m depth


EF106030 Guerrero Negro evaporitic crust

GU145411 Black sea particulates potential density 15.3

AM997863 deep-sea surface sediment South-Atlantic Ocean Guinea Basin

AY693832 granular sludge treating cassava starch wastewater

DQ153141 surface biofilm in estuarine seawater

DQ103648 hypersaline endoevaporitic microbial mat in Eilat Israel

GU119029 Coral-associated Porites astreoides

KF512918 2_OTU

AB058919 Reichenbachiella agariperforans

AB078042 Crocinitomix catalasitica

JF272224 biofilms

GU451591 macroalgal surface

KF513000 10_OTU

HQ671953 OMZ subarctic Pacific Ocean 10m depth

GU451583 macroalgal surface

KF513052 63_OTUKF513105 41_OTU

HM798914 ocean water collected from 6000m depth within the Puerto Rico Trench

HQ153895 white biofilm in aphotic zone of shallow hydrothermal vent South Tonga

DQ270658 carbonate chimney in Lost City Hydrothermal Field

AY627533 sediment near Urania brine lake Eastern Mediterranean 3km depth

AB078063 Flexibacter roseolus

FJ640814 hydrothermal vent chimney 4143-1 Mothra field Juan de Fuca Ridge 2267m depth


GU234835 Chemolithotrophy in bacterioplankon Antarctic sea water (5m)

GU119272 Coral-associated surrounding water

KF513029 64_OTU

EF645942 particle-associated anammox bacteria Namibian upwelling system


GU235037 Chemolithotrophy in bacterioplankon Antarctic sea water collected from 5m

GQ261768 deep sea sediment associated with whale falls

DQ415767 Frasassi sulfidic cave stream biofilm


KF513081 61_OTU

AB476278 ventral setae of Shinkaia crosnieri

AB476226 ventral setae of Shinkaia crosnieri

FJ497472 Fe-rich mats and basaltic rock Vailulu'u Seamount

FN433410 marine water North Atlantic


HQ843694 nitrifying bioreactor

GU145535 Black sea particulates potential density 16

KF512935 52_OTU


GU235101 Chemolithotrophy in bacterioplankon Antarctic sea water collected from 5m

DQ309373 effluent treatment plant high salinity

1

0.8

0.99

1

0.01

1

0.99

1

1

0.97

0.52

0.96

0.2

0.33

0.45

1

0.95

0.92

0.98

0.66

1

0.97

0.98

1

0

0.65

1

0.36

0.16

0.89

1

0.93

0.45

1

0.87

1

0.44

0.93

0.96

0.06

1

1

0.91

0.98

1

0.99

0.961

1

0.14

0.08

0.93

0.71

1

1

1

1

0.88

1

0.98

1

0.99

0.36

0.98

0.14

0.26

0.99

0.54

0.98

0.97

0.99

0.89

0.76

0.38

0.91

0.35

10.1

1

1

0.94

0.95

NS9 marine group

NS9 “marine” groupbioreactor-type

Supplemental Figure 2. Maximum likelihood phylogeny (mid-point rooted) constructed from 16S rRNAgene sequences of pink berry Bacteroidetes phylotypes OTUs (pink), cultured isolates (blue), and unculturedenvironmental amplicon. Phylogeny was constructed with FastTree using the approximate maximum likelihoodmethod (Price et al., 2010) and GTRCAT approximation with 20 rate categories. Values at the nodes are SH-likelocal supports (1000) computed by FastTree and used as condiference values of tree branches. Scale bar representsthe number of estimated changes per position for a unit of branch length. Marked with red stars are the dominantpink berry phylotypes. Note that the relative scarcity of cultured isolates and abundance of related sequencesfrom diverse sulfur-cycling habitats

HQ153966 white filamentous microbial mat photic zone shallow hydrothermal vent South Tonga

HQ588376 Amsterdam mud volcano sediment

AY883937 Gaetbulibacter saemankumensis

FJ264752 methane seep sediment

AJ441220 Paralvinella palmiformis mucus secretions

AY848823 Winogradskyella poriferorum



AY510257 microbial mat in sulfidic cave spring of Lower Kane Cave

EU488064 Seagrass bed associated with lucinid bivalves

EF687374 sulfide-oxidizing mat Chefren mud volcano

p g


GQ259266 deep sediments from an arctic fjord of svalbard


GQ357029 methane seep sediment

AF419687 methanotrophic hydrothermal sediments in the Guaymas Basin

GQ249487 Bay of Cadiz marine sediment 0-2 cm layer

EU662423 microbial mat from sulfidic cave stream

EF108219 Gaetbulibacter marinus



KF513024 46_OTU

EF554364 Ulvibacter antarcticus

EU622300 Eel River Basin methane seep 520 m depth

FJ437895 Fayetteville Green Lake at 25 m water depth

HM141161 S-biomineralization in supraglacial spring

AY274841 Delaware River estuary

EU626642 Sea urchin associated

AJ307947 String -of-pearls consortia from sulfur spring


DQ071072 surface water glycolate oxidase diveristy

HQ405619 anaerobic oxidation of methane enrichment

FJ615160 Saanich Inlet 100 m depth

FJ536453 hypersaline mats

GU118830 Coral-associated Montastraea franksi

KF512950 1_OTU


EF467588 Frasassi sulfidic cave stream biofilm

AF419690 methanotrophic hydrothermal sediments in the Guaymas Basin

AJ431253 Enrichments from Alvinella pompejana white tubes


KF512961 39_OTU



AY531558 scaly snail epibiont Indian Ocean hydrothermal vent

AY280418 exterior of a deep-sea hydrothermal vent chimney Juan de Fuca Ridge

HQ326365 biofilm on SWRO membranes

GU197418 Tubificoides benedii associated S-symbionts


GU584511 marine hydrocarbon seep sediment

EU290161 Tenacibaculum marinus

EF467452 Frasassi sulfidic cave stream biofilm


GQ249617 Bay of Cadiz marine sediment 18-20 cm layer

FN658701 Rimicaris exoculata epibiont


FM179880 methane seeps Gullfaks and Tommeliten North Sea

KF513104 25_OTU KF513019 59_OTU

GQ357018 methane seep sediment

AJ441241 Paralvinella palmiformis mucus secretions

GQ339154 FeII-rich seep

AY243096 Ulvibacter litoralisAM997600 deep-sea surface sediment South-Atlantic Ocean Cape Basin



FJ203309 Coral associated Montastraea faveolata



FJ595484 Winogradskyella exlils sp. 022-2-26

FJ814757 Thioploca sheath associated Carmel Canyon


FJ814752 Thioploca sheath associated Carmel Canyon

EU592341 Salton sea hypersaline water


AB240238 Phragmites marsh reeds rhizosphere sediment

GU302447 Beggiatoa mat at methane seep Gulf of Mexico

KF513061 48_OTU

EU662514 microbial mat from sulfidic cave stream

JF272048 biofilms


AB232533 Alvinocaris longirostris gill S-oxidizing environment

AJ535256 marine sediment hydrate ridge Oregon

EU580684 Marine sediment Sulfurimonas-associated

KF513008 28_OTU

FN820306 mud volcano Gulf of Cadiz


AY521224 Winodgradskyella epiphytica

FJ437881 Fayetteville Green Lake at 25 m water depth

FJ712490 Kazan Mud Volcano Anaximander Mountains East Mediterranean Sea



KF648877 13_OTU

HQ153921 white microbial film in aphotic zone of shallow hydrothermal vent South Tonga

GU302483 Beggiatoa mat at methane seep Gulf of Mexico

AY548995 whale fall

KF648879 17_OTU

DQ361033 Flaviramulus basaltis

GQ259310 surface sediments from an arctic fjord of svalbard

AM279207 marine plankton



KF513005 36_OTU

0.75

0.94

1

0.97

1

0.8

0.83

1

0.9

1

0.72

0.88

0.85

0.99

0.99

0.38

0.5

0.1

0.99

0.32

0.06

1

0.7

1

0.93

0.93

0.85

0.88

0.99

0.88

0.58

1

1

0.98

0.8

1

1

1

0.96

0.98

1

1

0.25

0.38

0.79

0.98

0.75

0.98

0.96

0.9

0.77

0.42

0.971

1

1

0.93

0.87

0.98

0.96

0.86

1

0.85

0.98

0.98

1

0.9

0.78

0.99

1

0.14

0.51

1

0.87

1

0

0.95

0.93

0.57

0.82

0.49

0.85

0.42

0.45

1

0.72

0.86

0.86

0.94

0.7

0.94

0.54

0.95

0.98

0.81

0.92

0.44

1

0.86

0.97

0.96

0.86

0.32

BD2-2 group

WCHB1-69 group

VC2.1 Bac22 group

0.06

0.04

OTU_13 KF517015

OTU_29 KF517006

Amphora cf. fogediana AM502022

OTU_59 KF516997

Nanofrustulum cf. shiloi HQ912578

Cymbella hybrida HQ680549

Pseudostaurosira zeilleri var. elliptica EF465473

Amphora lybica AM501959

Lyrella sp. LM2002 AJ535149

OTU_92 KF517004

OTU_67 KF517005

Dinophyceae gen. sp. MIY-01 AB092336

Stenopterobia curvula HQ912416

Amphora pediculus AM501960

OTU_53 KF517009

Prorocentrum sp. RAV2 EU287488

OTU_75 KF517012

Surirella splendida HQ912415

Prorocentrum emarginatum Y16239

Staurosira elliptica EF423414

Nanofrustulum shiloi AM746971

OTU_06 KF516999

OTU_39 KF517003

Phaeodactylum tricornutum GQ421691

OTU_72 KF517017

OTU_07 KF517002

OTU_09 KF517000

OTU_68 KF516998

Prorocentrum levis DQ238043

Navicula sp. AT-201Gel01 AM501999

Fallacia monoculata HQ912596

OTU_64 KF517014

Pseudogomphonema sp. LM-2002 AF525663

uncultured marine eukaryote GU385607

Rossia sp. CH2 AJ535144

OTU_77 KF517011

Prorocentrum concavum Y16237

Cocconeis convexa HQ852032

Cymbella lata HQ680558

Fallacia pygmaea HQ912605

Navicula cryptocephala AM501973

OTU_74 KF517007

Amphora sp. AT-221.04 AM501957

Navicula cryptotenella AM502011

Cymbella laevis HQ680557

OTU_61 KF517001

0.63

0.6

0.98

0.92

0.92

0.91

0.8

1

0.63

1

0.9

1

0.97

1

0.7

0.09

0.9

1

0.84

1

0.97

0.54

0.74

1

0.69

0.91

1

1

0.99

0.96

0.75

0.94

0.84

0.27

1

0.94

0.31

0.84

0.550.98

0.96

0.97

1

Dinoflagellates

Raphid pennatediatoms

Araphid pennatediatoms

Supplemental Figure 3. Maximum likelihood phylogeny (mid-point rooted) constructed from 18S rRNA gene sequences of pink berry eukaryotes OTUs and cultured relatives. Phylogeny was constructed with FastTree using the approximate maximum likelihood method (Price et al., 2010) and GTRCAT approximation with 20 rate categories. Values at the nodes are SH-like local supports (1000) computed by FastTree and used as condiference values of tree branches. Scale bar represents the number of estimated changes per position for a unit of branch length.

Supplemental Figure 4. Epifluorescence microscopy of CARD-FISH hybridization of sectioned pink berries with a nonsense probe (NON338, panel A), and a Gammaproteobacteria probe (GAM42a, panel B). The left side of each panel shows the Alexa 488 probe signal and background autofluorescence, the right side of the panel shows the DAPI stain.

DESULFOVIBRIO_DESULFURICANS[115117]

DESULFOVIBRIO_INTESTINALIS[58621]

DESULFOVIBRIO_SIMPLEX[54565]


DESULFOVIBRIO_PIGER_ATCC_29098[411464]

BILOPHILA_WADSWORTHIA[35833]

DESULFOVIBRIO_CUNEATUS[159728]

DESULFOVIBRIO_VULGARIS_STR._HILDENBOROUGH[882]

DESULFOVIBRIO_SP._PT_2[77909]

DESULFOVIBRIO_TERMITIDIS_HI1[644897]

DESULFOEUBACTERIUM_AMINOVORUM[252248]

DESULFOVIBRIO_DESULFURICANS_AESTUARII[126333]

DESULFOVIBRIO_ALASKENSIS_G20[207559]

UNCULTURED_PROKARYOTE[198431]

DESULFOVIBRIO_CARBINOLICUS[296842]

DESULFOVIBRIO_FRUCTOSOVORANS_JJ[596151]

DESULFOVIBRIO_GABONENSIS[42056]

DESULFOVIBRIO_AFRICANUS[873]


DESULFOVIBRIO_HALOPHILUS[45629]

DESULFOVIBRIO_OXYCLINAE[63560]

DESULFOVIBRIO_AESPOEENSIS[182210]

DESULFOVIBRIO_LONGUS[889]

DESULFOVIBRIO_ZOSTERAE[82171]

DESULFOVIBRIO_AMINOPHILUS[81425]


DESULFONATRONUM_LACUSTRE_DSM_10312[935942]

DESULFOMICROBIUM_BACULATUM_DSM_4028[525897]

UNCULTURED_DELTA_PROTEOBACTERIUM[34034]

DESULFOHALOBIUM_RETBAENSE_DSM_5692[485915]

DESULFONATRONOVIBRIO_HYDROGENOVORANS[53245]

DESULFOBACTER_CURVATUS[2290]

DESULFOBACTER_LATUS[2292]

DESULFOBACTER_POSTGATEI_2AC9[879212]

DESULFOBACTER_VIBRIOFORMIS[34031]

DESULFOBACULA_PHENOLICA[90732]

DESULFOSPIRA_JOERGENSENII[53329]

DESULFOTIGNUM_BALTICUM[115781]

Supplemental Figure 5. Maximum likelihood phylogeny (FastTree) constructed from an alignment of full length dsrAB gene sequences (Loy et al., 2009). Illumina sequence reads were processed withthe Phylosift pipeline which placed them onto this fixed, full length reference tree using pplacer (Matsen et al., 2010). Branches with reads placed are in red, and with a branch line width proportional to the number of assigned seqeunces.

DESULFOBACTERIUM_AUTOTROPHICUM[2296]

DESULFOBACTERIUM_VACUOLATUM[2298]

DESULFOBOTULUS_SAPOVORANS[888]

DESULFOCELLA_HALOPHILA[66835]

DESULFOFABA_GELIDA[84981]

DESULFOSARCINA_CETONICA[90730]

DESULFOSARCINA_VARIABILIS_STR._MONTPELLIER[859321]


DESULFOCOCCUS_MULTIVORANS[897]

DESULFONEMA_LIMICOLA_STR._JADEBUSEN[859314]

DESULFONEMA_ISHIMOTONII[45657]

DESULFATIBACILLUM_ALKENIVORANS[259354]

DESULFOCOCCUS_OLEOVORANS_HXD3[96561]


DESULFOMONILE_TIEDJEI_DSM_6799[706587]







SULFATE_REDUCING_BACTERIUM_MXYS1[77631]

DESULFOBACTERIUM_ANILINI[90728]

DESULFOTOMACULUM_THERMOSAPOVORANS[58137]

SPOROTOMACULUM_HYDROXYBENZOICUM[68035]

DESULFOTOMACULUM_GEOTHERMICUM[39060]

DESULFOTOMACULUM_ACETOXIDANS[58138]

DESULFOTOMACULUM_THERMOACETOXIDANS[58136]

DESULFOTOMACULUM_THERMOBENZOICUM[29376]

DESULFOTOMACULUM_KUZNETSOVII_DSM_6115[760568]

DESULFOTOMACULUM_THERMOCISTERNUM[42471]

DESULFOBULBUS_ELONGATUS[53332]

DESULFOBULBUS_PROPIONICUS[894]

DESULFOBULBUS_RHABDOFORMIS[34032]

DESULFOBULBUS_SP._DSM_2058[168134]

DESULFORHOPALUS_VACUOLATUS[40414]

DESULFOTALEA_ARCTICA[84979]

DESULFOTALEA_PSYCHROPHILA_LSV54[177439]

DESULFOFUSTIS_GLYCOLICUS[51195]

DESULFORHOPALUS_SINGAPORENSIS[91360]

DELTA_PROTEOBACTERIUM_MLMS_1[262489]

THERMODESULFOBACTERIUM_COMMUNE[289377]

THERMODESULFOBACTERIUM_THERMOPHILUM[886]



SYNTROPHOBACTER_WOLINII[29527]

SYNTROPHOBACTER_FUMAROXIDANS_MPOB[335543]

DESULFOVIRGA_ADIPICA[149712]

DESULFORHABDUS_AMNIGENA[40218]

DESULFACINUM_INFERNUM[35837]

THERMODESULFORHABDUS_NORVEGICA[39841]


DESULFARCULUS_BAARSII_DSM_2075[644282]






DESULFOBACCA_ACETOXIDANS[60893]

THERMODESULFOVIBRIO_YELLOWSTONII[28262]







UNCULTURED_SULFATE_REDUCING_BACTERIUM[153939]




DESULFOTOMACULUM_AERONAUTICUM[53343]

DESULFOTOMACULUM_RUMINIS_DSM_2154[696281]

DESULFOTOMACULUM_REDUCENS_MI_1[349161]

DESULFOTOMACULUM_PUTEI[74701]

DESULFOTOMACULUM_NIGRIFICANS_DSM_574[696369]

DESULFOTOMACULUM_ALKALIPHILUM[105483]

DESULFOTOMACULUM_HALOPHILUM[57172]

PELOTOMACULUM_PROPIONICICUM[258475]

THERMOSINUS_CARBOXYDIVORANS_NOR1[401526]

CARBOXYDOTHERMUS_HYDROGENOFORMANS_Z_2901[246194]

DESULFITOBACTERIUM_DEHALOGENANS_ATCC_51507[756499]

DESULFITOBACTERIUM_HAFNIENSE_DCB_2[272564]

DESULFOSPOROSINUS_ORIENTIS[1563]

THERMODESULFOBIUM_NARUGENSE_DSM_14796[747365]

ARCHAEOGLOBUS_FULGIDUS[2234]

ARCHAEOGLOBUS_VENEFICUS[58290]

ARCHAEOGLOBUS_PROFUNDUS_DSM_5631[572546]

ALLOCHROMATIUM_VINOSUM[1049]

THIOCAPSA_MARINA_5811[768671]

THIOCYSTIS_VIOLACEA[13725]

THIOCYSTIS_GELATINOSA[46450]

THIOCAPSA_ROSEOPERSICINA[1058]

THIOCAPSA_ROSEOPERSICINA[1058]

HALOCHROMATIUM_SALEXIGENS[49447]

METAGENOME_SEQUENCE[256318]

UNCULTURED_BACTERIUM[77133]


THIOTHRIX_NIVEA_DSM_5205[870187]




UNCULTURED_BACTERIUM_BAC13K9BAC[332979]




CANDIDATUS_RUTHIA_MAGNIFICA[413404]

CANDIDATUS_VESICOMYOSOCIUS_OKUTANII_HA[412965]

ALKALILIMNICOLA_EHRLICHII_MLHE_1[187272]

HALORHODOSPIRA_HALOPHILA_SL1[349124]

ENDORIFTIA_PERSEPHONE[394104]

MAGNETOSPIRILLUM_MAGNETICUM_AMB_1[342108]

MAGNETOSPIRILLUM_MAGNETOTACTICUM_MS_1[272627]

MAGNETOSPIRILLUM_GRYPHISWALDENSE_MSR_1[431944]






THIOBACILLUS_THIOPARUS[931]

THIOBACILLUS_DENITRIFICANS_ATCC_25259[292415]

CHLOROBIUM_LIMICOLA[1092]

CHLOROBIUM_TEPIDUM_TLS[194439]

PROSTHECOCHLORIS_AESTUARII_DSM_271[290512]

CHLOROBIUM_LIMICOLA_DSM_245[290315]

CHLOROBIUM_PHAEOBACTEROIDES_DSM_266[290317]

CHLOROBIUM_CHLOROCHROMATII_CAD3[340177]

PELODICTYON_PHAEOCLATHRATIFORME_BU_1[324925]

CHLOROBIUM_LUTEOLUM_DSM_273[319225]

CHLOROBIUM_PHAEOVIBRIOIDES_DSM_265[290318]

CHLOROBIUM_PHAEOBACTEROIDES_BS1[331678]

MAGNETOCOCCUS_MARINUS_MC_1[156889]

MOORELLA_THERMOACETICA_ATCC_39073[264732]

PYROBACULUM_AEROPHILUM_STR._IM2[178306]

PYROBACULUM_ISLANDICUM_DSM_4184[384616]

Supplemental Figure 6. Chromatiales soxYZ gene. Generated by RAST synteny viewer using 1e-20 BLASTP similarity cutoff to define and color gene sets (each set has unique number and color). Ordered according to % aa similarity to scaffold_341 soxY query. Note the conserved Chromatialeshypothetical gene cluster upstream from soxYZ (7,12,10,3).

Thiorhodococcusdrewsii

Thiorhodovibrio sp. 970

Thiocapsa marina

Thioalkalivibriothiocyanoxidans

Ectothiorhodospira sp. PHS-1

Thiocystis violascens

Marichromatium purpuratum

Thioalkalivibrio sp. HL-EbGR7

Halorhodospira halophila

scaffold_341

Thioalkalivibrionitratireducens

Halothiobacillus neapolitanus

Thioalkalivibrio sp. K90mix


soxYZ hypotheticals

scaffold_285

Thiorhodococcus drewsii

Thioflavicoccus mobilis


Thiocapsa marina

Thiobacillus denitrificans

Thioalkalivibriothiocyanoxidans

Vesicomyosocius okutanii

Thioalkalivibrionitratireducens

Thiocystis violascens

Marichromatiumpurpuratum


Alkalilimnicola ehrlichii

Halorhodospira halophila

scaffold_659

scaffold_619

dsrABEF(H) dsrCMKL(J) dsrOPN RSdsrC-like

Supplemental Figure 7. Chromatiales dsrABEFHCMKLJOPNRS gene cluster is represented in three distinct metagenomic contigs from PB-PSB1. Generated by RAST synteny viewer using 1e-20 BLASTP similarity cutoff to define and color gene sets (each set has unique number and color). Ordered according to % aa similarity to scaffold_285 dsrA query. Genes shown in parenthesis at top (dsrH and dsrJ) were not annotated on metagenomic contigs by RAST but are identifiable as gene-fragments using independent BLASTP queries. Also, note the conserved Chromatiales hypothetical gene cluster upstream from dsrAB (10,17,16/18).

aprBA aprM FKBP-type peptidyl-prolyl cis-trans isomerase SlyD (EC 5.2.1.8)

hypothetical

sat

sat

scaffold_71

Thiorhodococcus drewsii

Thioflavicoccus mobilis


Thiocapsa marina

Thiobacillus denitrificans

Thioalkalivibrio sp. K90mix

Thioalkalivibrio thiocyanoxidans

Vesicomyosocius okutanii

Thioalkalivibrio nitratireducens

Candidatus Ruthia magnifica (Calyptogena magnifica)

Supplemental Figure 8. Genomic context of aprM-aprBA gene cluster in PB-PSB1. Generated by RAST synteny viewer using 1e-20 BLASTP similarity cutoff to define and color gene sets (each set has unique number and color). Ordered according to % aa similarity to the scaffold_71 aprB query.

scaffold_149

Desulfotalea psychrophila

Desulfovibrio vulgaris vulgaris DP4

Desulfohalobium retbaense

Desulfococcus oleovorans

Desulfatibacillum alkenivorans

Desulfobulbus propionicus

Desulfocapsa sulfexigens

Desulfovibrio desulfuricans. ATCC 27774

Desulfomicrobium baculatum

Desulfovibrio desulfuricans G20

ftsK qmoABC

Supplemental Figure 9. Genomic context of aprAB-qmoABC gene cluster in PB-SRB1.Generated by RAST synteny viewer using 1e-20 BLASTP similarity cutoff to define and color gene sets (each set has unique number and color). Ordered according to % aa similarity to the scaffold 149 aprA query.

aprBA

scaffold_206


Desulfovibrio vulgaris Miyazaki F






Desulfomicrobium baculatum

Syntrophobacter fumaroxidans

Moorella thermoacetica

Desulfovibrio desulfuricans ATCC 27774

Desulfotomaculum acetoxidans

dsrABD

Set Gene annotation 6 Glucose-6-phosphate isomerase (EC 5.3.1.9) 8 Ribulose-phosphate 3-epimerase (EC 5.1.3.1)

10 Rossmann fold nucleotide-binding protein Smf 11 RNA polymerase sigma factor RpoD 14 DNA primase (EC 2.7.7.-) 15 Biotin-protein ligase (EC 6.3.4.15) 28 Alcohol dehydrogenase (EC 1.1.1.1) 30 S-adenosylmethionine synthetase (EC 2.5.1.6

Supplemental Figure 10. Genomic context of dsrAB PB-SRB1. Generated by RAST synteny viewer using 1e-20 BLASTP similarity cutoff to define gene sets (each set has unique number and color). Table below shows annotations for Desulfobulbaceae-conserved genes in this genomic region. Ordered according to % aa similarity to scaffold 206 dsrA query.

dsrC scaffold_372


Desulfobulbus propionicus Desulfocapsa sulfexigens



Desulfovibrio desulfuricans G20

Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough

Desulfovibrio vulgaris subsp. vulgaris DP4

Set Annotated function 1 dsrC 2 Peptidyl-prolyl cis-trans isomerase ppiD (EC 5.2.1.8) 4 COG0553: Superfamily II DNA/RNA helicases, SNF2 family

25 Uroporphyrinogen-III methyltransferase (EC 2.1.1.107) / Uroporphyrinogen-III synthase (EC 4.2.1.75)

Supplemental Figure 11. Genomic context of dsrC PB-SRB1. Generated by RAST synteny viewer using 1e-20 BLASTP similarity cutoff to define gene sets (each set has unique number and color). Table below shows annotations for conserved genes in PB-SRB1 in this genomic region. Ordered according to % aa similarity to the scaffold_372 dsrC query.

scaffold_12





Desulfovibrio vulgaris Miyazaki F

Syntrophobacter fumaroxidans


dsrMKJOP hypothetical

Supplemental Figure 12. Genomic context of dsrMKJOP gene cluster in PB-SRB1. Generated by RAST synteny viewer using 1e-20 BLASTP similarity cutoff to define and color gene sets (each set has unique number and color). . Ordered according to % aa similarity to the scaffold_12 dsrM query.

Supplemental Figure 13. Elemental analyzer-isotope ratio mass spectrometry (EA-IRMS) of pooled berry biomass from dark incubations with either added 34S-enriched sulfate (“labelled”) or standard sulfate (“unlabeled”). Incubations were conducted both with and without 10 mM molybdate. Also shown are three different measurements of pooled berry biomass taken directly from the marsh (“native”). Values shown are per mil V-CDT the mean of biological replicates, error bars show standard deviation between these replicates.

-200

0

200

400

600

800

1000

1200

1400

labeled labeled +molybdate

unlabeled unlabeled +molybdate

Native

δ34S

(‰

, V-C

DT)

‰ V-CDT labeled

labeled + molybdate unlabeled

unlabeled + molybdate Native

mean 1135.98 -15.42 -22.88 -24.86 -14.8 standard deviation 193 0.00 0.27 2.03 1.19

Biological replicates 3 2 3 2 3

supplemental table 1. quantification of the single copy...

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