Supplemental Table 1. Quantification of the single ... - Caltech Authors

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

Conserved single-copy marker gene PB-SRB1 PB-PSB1 recA 1 1 RpoB 1 1 DNA gyrase A 1 1 DNA gyrase B 1 1 ffh signal recognition particle protein 1 1 Chaperone protein HtpG 1 1 YgjD/Kae1/Qri7 family metalloendopeptidase 1 1 phosphoribosylformylglycinamidine cyclo-ligase 1 1 Porphobilinogen deaminase 1 1 ribonuclease HII 1 1 phenylalanyl-tRNA synthetase alpha subunit 1 1 phenylalanyl-tRNA synthetase beta subunit 1 1 tRNA pseudouridine synthase B 1 1 translation elongation factor EF-2 2 1 translation initiation factor IF-2 1 1 ribosomal protein S2 1 1 ribosomal protein S3 1 1 ribosomal protein S5 1 1 ribosomal protein S7 1 1 ribosomal protein S8 1 1 ribosomal protein S9 1 1 ribosomal protein S10 1 1 ribosomal protein S11 1 1 ribosomal protein S12/S23 1 1 ribosomal protein S13 1 1 ribosomal protein S15P 1 1 ribosomal protein S17 1 1 ribosomal protein S19 1 1 ribosomal protein L1 1 1 ribosomal protein L2 1 1 ribosomal protein L3 1 1 ribosomal protein L4/L1e 1 1 ribosomal protein L5 1 1 ribosomal protein L6 1 1 ribosomal protein L10 1 1 ribosomal protein L11 1 1 ribosomal protein L13 1 1 ribosomal protein L14b 1 1 ribosomal protein L15 1 1 ribosomal protein L16 1 1 ribosomal protein L18P/L5E 1 1 ribosomal protein L22 1 1 ribosomal protein L24 1 1 ribosomal protein L25/L23 1 1 ribosomal protein L29 1 1

1

Thiocapsa pendens AJ002797 Thiocapsa marina FM178270 Lamprocystis purpurea AJ223235

0.44

Thiodictyon elegans EF999973

1

Thiodictyon bacillosum EF999974

0.93 0.97

Thiocystis gelatinosa Y11317 Thiocystis minor Y12372 Allochromatium vinosum CP001896

0.99

Chromatium okenii Y12376 1 0.96

Marichromatium indicum AJ543328 Marichromatium gracile X93473

Thiorhodococcus bheemlicus AM282559 0.89 0.91

0.74

Rhabdochromatium marinum X84316 Thiorhodovibrio winogradskyi Y12368 1

0.8

0.75

0.99

Thioflavicoccus mobilis AJ010126 Thiococcus pfennigii Y12373

Halochromatium roseum AM283535 Halochromatium salexigens X98597

Halochromatium glycolicum X93472 Thiohalocapsa marina AM491592 0.83

PB-PSB1 Pirry PSB KF513139

Thiohalocapsa halophila AM903380 Ectothiorhodospira variabilis AM943125 0.02

Supplemental Figure 1. Maximum likelihood phylogeny (rooted) constructed from 16S rRNA gene sequences 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 the number of estimated changes per position for a unit of branch length.

Supplemental Figure 2. Maximum likelihood phylogeny (mid-point rooted) constructed from 16S rRNA gene sequences of pink berry Bacteroidetes phylotypes OTUs (pink), cultured isolates (blue), and uncultured environmental amplicon. 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. Marked with red stars are the dominant pink berry phylotypes. Note that the relative scarcity of cultured isolates and abundance of related sequences from diverse sulfur-cycling habitats

1 0.98 1

0.99

1

1

1 0.45

0.91 0.08

0.8

0.45

0.26

1

0.99 0.93

0.98 0.76

0.97

0.35

1

1 1

0.99 0.54

0.98

1

0.98

0.98

1

1

0.97

1 0.87 0.14

1

0.89 0.97 1

0.98

0.1 1 0.36 0.38 0.93 0.16 0.93

1

0.52 0.01

0.66 1 0.96 0.96 0.99

0.33

1 1 1

0.36

0.91

1 0.06 0.89

1 0.99

0.44

1 0

0.95

0.95

0.2 0.92

1

0.65 0.71

0.96 0.94 0.99 0.14

1 0.88

CP001699 Chitinophaga pinensis DSM 2588 EU854577 Flavihumibacter petaseus KF512935 52_OTU GQ441322 marine microbial mats from a sandy intertidal beach AM286229 Lewinella agarilytica GU451591 macroalgal surface AB476226 ventral setae of Shinkaia crosnieri FJ535337 Fe-rich mats submarine volcanoes along the Kermadec Arc GU451583 macroalgal surface DQ270658 carbonate chimney in Lost City Hydrothermal Field EF106030 Guerrero Negro evaporitic crust DQ330419 Guerrero Negro hypersaline microbial mat HM798914 ocean water collected from 6000m depth within the Puerto Rico Trench EU245266 hypersaline microbial mat KF512925 44_OTU GU235037 Chemolithotrophy in bacterioplankon Antarctic sea water collected from 5m DQ103648 hypersaline endoevaporitic microbial mat in Eilat Israel KF513052 63_OTU KF513105 41_OTU GQ348350 Saanich Inlet 200 m depth GU145535 Black sea particulates potential density 16 AB078063 Flexibacter roseolus DQ330420 Guerrero Negro hypersaline microbial mat EU236422 Marine sponge-associaed Haliclona KF512957 9_OTU JF272224 biofilms CU466744 anoxic basin of a municipal wastewater treatment plant EU340220 Thiotrix-dominated macrophte Sedge Bay Yellowstone HQ163185 Saanich Inlet 100 m depth DQ836305 Fulvivirga kasyanovii AB058919 Reichenbachiella agariperforans GU235101 Chemolithotrophy in bacterioplankon Antarctic sea water collected from 5m EU236350 Marine sponge-associaed Haliclona GU119029 Coral-associated Porites astreoides KF513076 56_OTU FJ205237 inactive hydrothermal field sediments depth 2350m East Lau AM997690 deep-sea surface sediment South-Atlantic Ocean Cape Basin AY627533 sediment near Urania brine lake Eastern Mediterranean 3km depth GQ259254 deep sediments from an arctic fjord of svalbard KF513081 61_OTU EU245160 hypersaline microbial mat HQ153837 white microbial film in aphotic zone of shallow hydrothermal vent South Tonga DQ415767 Frasassi sulfidic cave stream biofilm FJ640814 hydrothermal vent chimney 4143-1 Mothra field Juan de Fuca Ridge 2267m depth GQ261768 deep sea sediment associated with whale falls KF513000 10_OTU KF512962 45_OTU FJ905765 Fe-oxide sediments submarine Volcano 1 Tonga Arc GU118272 Coral-associated Diploria strigosa CU923026 mesophilic anaerobic digester which treats municipal wastewater sludge GU472712 meromictic sulfur-cycling Lake Pavin HQ116750 Butyric acid and DMS assimilating biofilter biofilm EU104280 activated sludge AY693832 granular sludge treating cassava starch wastewater NS9 “marine” HQ640607 partial nitrifying-ANAMMOX municipal wastewater reactor HQ843694 nitrifying bioreactor group DQ309373 effluent treatment plant high salinity bioreactor-type FM174355 biotrickling filter treating high loads of H2S FN433410 marine water North Atlantic GQ349627 Saanich Inlet 10 m depth EF645942 particle-associated anammox bacteria Namibian upwelling system GU234835 Chemolithotrophy in bacterioplankon Antarctic sea water (5m) GQ348086 Saanich Inlet 100 m depth HQ671953 OMZ subarctic Pacific Ocean 10m depth GU145411 Black sea particulates potential density 15.3 GU145430 Black sea particulates potential density 15.7 KF512918 2_OTU KF513029 64_OTU NS9 marine HQ153895 white biofilm in aphotic zone of shallow hydrothermal vent South Tonga GU119272 Coral-associated surrounding water group GQ346748 Saanich Inlet 10 m depth EF645959 particle-associated anammox bacteria Namibian upwelling system FJ497472 Fe-rich mats and basaltic rock Vailulu'u Seamount GQ350671 Saanich Inlet 120 m depth AM997863 deep-sea surface sediment South-Atlantic Ocean Guinea Basin DQ153141 surface biofilm in estuarine seawater AB476278 ventral setae of Shinkaia crosnieri EU544843 1.0-60 um size fraction small-suspended particles of Arctic seawater EU919815 marine bacterioplankton in Kongsfjorden FJ716938 lungworm bioturbated sediments UK FJ744798 surface water at the UGA Marine Institute CU466753 anoxic basin of a municipal wastewater treatment plant AB078042 Crocinitomix catalasitica EU236348 Marine sponge-associaed Haliclona

0.58 0.9 0.8 0.97

0.98

0.97 0.49

0.51 1

1 0.98 0.97

1

1 0.86

0.79

0.57 0.98 0.92

1

0.42 0.810.99 0.93 0.99 0.96

0.1

1 0.98 0.88 0.95 0.82 0.45 0.7

0.83

0.98

1

0.54

0.8 0.770.72 0.86

1 0.32 0.72 0.38

0.93

0.98

1

0.06

0.320.85 0.94

0.99 1

0.7

1

1 0.85

0.99 1 0.96 0.750.42 1 1 0.88 0.98 1 0.9 0.75 0.86 0.9

0

0.98 0.88 0.96

0.14

0.86 0.93 0.5

1 0.95 0.96 0.38

0.87

1

0.99

0.94 0.86 0.87

0.25

1

0.85 0.44 0.94

0.93

1

1 0.85 0.78

0.06

1 1

FJ497615 Fe-rich mats and basaltic rock Vailulu'u Seamount GU118830 Coral-associated Montastraea franksi HQ326365 biofilm on SWRO membranes KF513024 46_OTU FJ615160 Saanich Inlet 100 m depth EU290161 Tenacibaculum marinus GU197418 Tubificoides benedii associated S-symbionts GQ259310 surface sediments from an arctic fjord of svalbard EU592341 Salton sea hypersaline water KF512961 39_OTU EU236393 Marine sponge-associaed Haliclona FJ264580 methane seep sediment GQ349579 Saanich Inlet 10 m depth DQ071072 surface water glycolate oxidase diveristy GQ347908 Saanich Inlet 10 m depth AM997600 deep-sea surface sediment South-Atlantic Ocean Cape Basin AY243096 Ulvibacter litoralis AY274841 Delaware River estuary EF554364 Ulvibacter antarcticus EU626642 Sea urchin associated AY883937 Gaetbulibacter saemankumensis DQ361033 Flaviramulus basaltis EF108219 Gaetbulibacter marinus GQ249487 Bay of Cadiz marine sediment 0-2 cm layer KF513005 36_OTU AY521224 Winodgradskyella epiphytica AB232533 Alvinocaris longirostris gill S-oxidizing environment FJ264752 methane seep sediment AM279207 marine plankton JF272048 biofilms FJ595484 Winogradskyella exlils sp. 022-2-26 AY848823 Winogradskyella poriferorum FJ203309 Coral associated Montastraea faveolata KF513008 28_OTU KF513104 25_OTU KF513019 59_OTU GQ259266 deep sediments from an arctic fjord of svalbard GU302483 Beggiatoa mat at methane seep Gulf of Mexico GQ357029 methane seep sediment GQ347258 Saanich Inlet 125 m depth EU487896 Seagrass bed associated with lucinid bivalves EU488045 Seagrass bed associated with lucinid bivalves HQ153921 white microbial film in aphotic zone of shallow hydrothermal vent South Tonga FJ264575 methane seep sediment BD2-2 group AF419690 methanotrophic hydrothermal sediments in the Guaymas Basin GQ261783 deep sea sediment associated with whale falls FJ814752 Thioploca sheath associated Carmel Canyon FN820306 mud volcano Gulf of Cadiz DQ330451 Guerrero Negro hypersaline microbial mat FJ437895 Fayetteville Green Lake at 25 m water depth EU662514 microbial mat from sulfidic cave stream DQ103643 hypersaline endoevaporitic microbial mat in Eilat Israel EU245346 hypersaline microbial mat EF687374 sulfide-oxidizing mat Chefren mud volcano AB240238 Phragmites marsh reeds rhizosphere sediment GQ339154 FeII-rich seep AJ307947 String -of-pearls consortia from sulfur spring EF467452 Frasassi sulfidic cave stream biofilm EU662423 microbial mat from sulfidic cave stream HQ153966 white filamentous microbial mat photic zone shallow hydrothermal vent South Tonga EU622300 Eel River Basin methane seep 520 m depth GQ261765 deep sea sediment associated with whale falls KF512950 1_OTU AJ441220 Paralvinella palmiformis mucus secretions FN658701 Rimicaris exoculata epibiont AY531558 scaly snail epibiont Indian Ocean hydrothermal vent GU584511 marine hydrocarbon seep sediment DQ103645 hypersaline endoevaporitic microbial mat in Eilat Israel FJ536453 hypersaline mats KF648879 17_OTU DQ330454 Guerrero Negro hypersaline microbial mat EU245320 hypersaline microbial mat GU145487 Black sea particulates potential density 15.81 AJ431253 Enrichments from Alvinella pompejana white tubes FJ264590 methane seep sediment AJ441241 Paralvinella palmiformis mucus secretions FJ814757 Thioploca sheath associated Carmel Canyon WCHB1-69 DQ330455 Guerrero Negro hypersaline microbial mat DQ415785 Frasassi sulfidic cave stream biofilm group DQ415754 Frasassi sulfidic cave stream biofilm FJ712490 Kazan Mud Volcano Anaximander Mountains East Mediterranean Sea GQ249617 Bay of Cadiz marine sediment 18-20 cm layer FJ437881 Fayetteville Green Lake at 25 m water depth EU245231 hypersaline microbial mat EU488064 Seagrass bed associated with lucinid bivalves AY280418 exterior of a deep-sea hydrothermal vent chimney Juan de Fuca Ridge GQ357018 methane seep sediment HQ588376 Amsterdam mud volcano sediment AY548995 whale fall VC2.1 Bac22 EU580684 Marine sediment Sulfurimonas-associated group AF419687 methanotrophic hydrothermal sediments in the Guaymas Basin HM141161 S-biomineralization in supraglacial spring HQ405619 anaerobic oxidation of methane enrichment FJ497562 Fe-rich mats and basaltic rock Vailulu'u Seamount GQ261786 deep sea sediment associated with whale falls FM179880 methane seeps Gullfaks and Tommeliten North Sea AJ535256 marine sediment hydrate ridge Oregon GQ261811 deep sea sediment associated with whale falls GU302447 Beggiatoa mat at methane seep Gulf of Mexico KF648877 13_OTU KF513061 48_OTU AY510257 microbial mat in sulfidic cave spring of Lower Kane Cave EF467588 Frasassi sulfidic cave stream biofilm

OTU_13 KF517015 1

0.94 0.69 0.9 1 0.84

OTU_53 KF517009

Dinophyceae gen. sp. MIY-01 AB092336 Prorocentrum emarginatum Y16239 Dinoflagellates Prorocentrum concavum Y16237 OTU_06 KF516999 Prorocentrum levis DQ238043 1 Prorocentrum sp. RAV2 EU287488 OTU_09 KF517000 0.98 Lyrella sp. LM2002 AJ535149 0.63 OTU_64 KF517014 0.97 OTU_59 KF516997 0.9 OTU_92 KF517004 Stenopterobia curvula HQ912416 1 Surirella splendida HQ912415 0.96 1 Raphid pennate Cocconeis convexa HQ852032 0.97 Amphora pediculus AM501960 diatoms 1 Amphora cf. fogediana AM502022 0.31 Amphora sp. AT-221.04 AM501957 0.99 Amphora lybica AM501959 0.74 Phaeodactylum tricornutum GQ421691 0.91 Cymbella hybrida HQ680549 1 Cymbella lata HQ680558 Cymbella laevis HQ680557 Fallacia pygmaea HQ912605 0.98 Fallacia monoculata HQ912596 0.55 0.6 Rossia sp. CH2 AJ535144 1 OTU_61 KF517001 0.84 OTU_77 KF517011 Navicula cryptocephala AM501973 0.54 0.94 Navicula sp. AT-201Gel01 AM501999 0.84 1 Navicula cryptotenella AM502011 Pseudogomphonema sp. LM-2002 AF525663 0.09 OTU_74 KF517007 0.97 OTU_68 KF516998 0.7 0.96 OTU_75 KF517012 uncultured marine eukaryote GU385607 OTU_67 KF517005 1 0.63 OTU_07 KF517002 0.92 OTU_39 KF517003 Araphid pennate 0.8 OTU_29 KF517006 0.75 diatoms Staurosira elliptica EF423414 0.92 Nanofrustulum cf. shiloi HQ912578 1 OTU_72 KF517017 0.27 Nanofrustulum shiloi AM746971 0.91 Pseudostaurosira zeilleri var. elliptica EF465473 0.04

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.

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. DESULFOVIBRIO_DESULFURICANS[115117] DESULFOVIBRIO_INTESTINALIS[58621] DESULFOVIBRIO_SIMPLEX[54565] DESULFOVIBRIO_DESULFURICANS[115117] 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_DESULFURICANS[115117] DESULFOVIBRIO_HALOPHILUS[45629] DESULFOVIBRIO_OXYCLINAE[63560] DESULFOVIBRIO_AESPOEENSIS[182210] DESULFOVIBRIO_LONGUS[889] DESULFOVIBRIO_ZOSTERAE[82171] DESULFOVIBRIO_AMINOPHILUS[81425] UNCULTURED_PROKARYOTE[198431] 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]

DESULFOBACTERIUM_AUTOTROPHICUM[2296] DESULFOBACTERIUM_VACUOLATUM[2298] DESULFOBOTULUS_SAPOVORANS[888] DESULFOCELLA_HALOPHILA[66835] DESULFOFABA_GELIDA[84981] DESULFOSARCINA_CETONICA[90730] DESULFOSARCINA_VARIABILIS_STR._MONTPELLIER[859321]

UNCULTURED_PROKARYOTE[198431] DESULFOCOCCUS_MULTIVORANS[897] DESULFONEMA_LIMICOLA_STR._JADEBUSEN[859314] DESULFONEMA_ISHIMOTONII[45657] DESULFATIBACILLUM_ALKENIVORANS[259354] DESULFOCOCCUS_OLEOVORANS_HXD3[96561] UNCULTURED_PROKARYOTE[198431] DESULFOMONILE_TIEDJEI_DSM_6799[706587] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] 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] UNCULTURED_PROKARYOTE[198431]

UNCULTURED_PROKARYOTE[198431] SYNTROPHOBACTER_WOLINII[29527] SYNTROPHOBACTER_FUMAROXIDANS_MPOB[335543] DESULFOVIRGA_ADIPICA[149712] DESULFORHABDUS_AMNIGENA[40218] DESULFACINUM_INFERNUM[35837] THERMODESULFORHABDUS_NORVEGICA[39841] UNCULTURED_PROKARYOTE[198431] DESULFARCULUS_BAARSII_DSM_2075[644282] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] DESULFOBACCA_ACETOXIDANS[60893] THERMODESULFOVIBRIO_YELLOWSTONII[28262] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_PROKARYOTE[198431] UNCULTURED_SULFATE_REDUCING_BACTERIUM[153939] UNCULTURED_SULFATE_REDUCING_BACTERIUM[153939] UNCULTURED_SULFATE_REDUCING_BACTERIUM[153939] UNCULTURED_PROKARYOTE[198431] 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] METAGENOME_SEQUENCE[256318] THIOTHRIX_NIVEA_DSM_5205[870187] UNCULTURED_BACTERIUM[77133] UNCULTURED_BACTERIUM[77133] METAGENOME_SEQUENCE[256318] UNCULTURED_BACTERIUM_BAC13K9BAC[332979] METAGENOME_SEQUENCE[256318] METAGENOME_SEQUENCE[256318] UNCULTURED_BACTERIUM[77133] 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] UNCULTURED_BACTERIUM[77133] UNCULTURED_BACTERIUM[77133] UNCULTURED_BACTERIUM[77133] UNCULTURED_BACTERIUM[77133] UNCULTURED_BACTERIUM[77133] 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]

hypotheticals

soxYZ

scaffold_341 Thiocapsa marina Thiorhodococcus drewsii Marichromatium purpuratum Thiocystis violascens Thiorhodovibrio sp. 970 Ectothiorhodospira sp. PHS-1 Thioalkalivibrio sp. HL-EbGR7 Thioalkalivibrio sp. HL-EbGR7 Halothiobacillus neapolitanus Thioalkalivibrio nitratireducens Thioalkalivibrio thiocyanoxidans Thioalkalivibrio sp. K90mix Halorhodospira halophila

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 Chromatiales hypothetical gene cluster upstream from soxYZ (7,12,10,3).

dsrC-like

dsrABEF(H)

dsrCMKL(J)

dsrOPN RS

scaffold_619 scaffold_659 scaffold_285 Thiorhodovibrio sp. 970 Thiocapsa marina Thiorhodococcus drewsii Thiocystis violascens Thioflavicoccus mobilis Marichromatium purpuratum Thioalkalivibrio sp. HLEbGR7 Thioalkalivibrio nitratireducens Thioalkalivibrio thiocyanoxidans Alkalilimnicola ehrlichii Vesicomyosocius okutanii Thiobacillus denitrificans Halorhodospira halophila

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).

hypothetical

aprM

scaffold_71

aprBA

FKBP-type peptidyl-prolyl cistrans isomerase SlyD (EC 5.2.1.8)

Thiorhodococcus drewsii Thioflavicoccus mobilis

sat

Thiorhodovibrio sp. 970 Thiocapsa marina Thiobacillus denitrificans Thioalkalivibrio sp. K90mix

sat

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.

ftsK

aprBA

qmoABC

scaffold_149 Desulfotalea psychrophila Desulfocapsa sulfexigens Desulfobulbus propionicus Desulfatibacillum alkenivorans Desulfococcus oleovorans Desulfohalobium retbaense Desulfovibrio vulgaris vulgaris DP4 Desulfovibrio desulfuricans. ATCC 27774 Desulfomicrobium baculatum Desulfovibrio desulfuricans G20

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.

dsrABD scaffold_206 Desulfocapsa sulfexigens Desulfotalea psychrophila Desulfobulbus propionicus Desulfohalobium retbaense Desulfotomaculum acetoxidans Desulfomicrobium baculatum Desulfococcus oleovorans Desulfatibacillum alkenivorans Moorella thermoacetica Desulfovibrio vulgaris Miyazaki F Desulfovibrio desulfuricans ATCC 27774

Syntrophobacter fumaroxidans

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. Set 6 8 10 11 14 15 28 30

Gene annotation Glucose-6-phosphate isomerase (EC 5.3.1.9) Ribulose-phosphate 3-epimerase (EC 5.1.3.1) Rossmann fold nucleotide-binding protein Smf RNA polymerase sigma factor RpoD DNA primase (EC 2.7.7.-) Biotin-protein ligase (EC 6.3.4.15) Alcohol dehydrogenase (EC 1.1.1.1) S-adenosylmethionine synthetase (EC 2.5.1.6

dsrC scaffold_372 Desulfotalea psychrophila Desulfobulbus propionicus Desulfocapsa sulfexigens Desulfohalobium retbaense Desulfovibrio desulfuricans G20 Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough Desulfovibrio vulgaris subsp. vulgaris DP4

Desulfatibacillum alkenivorans

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. Set 1 2 4 25

Annotated function dsrC Peptidyl-prolyl cis-trans isomerase ppiD (EC 5.2.1.8) COG0553: Superfamily II DNA/RNA helicases, SNF2 family Uroporphyrinogen-III methyltransferase (EC 2.1.1.107) / Uroporphyrinogen-III synthase (EC 4.2.1.75)

hypothetical

dsrMKJOP

scaffold_12 Desulfobulbus propionicus Desulfocapsa sulfexigens Desulfotalea psychrophila Desulfovibrio vulgaris Miyazaki F Desulfohalobium retbaense Syntrophobacter fumaroxidans Desulfococcus oleovorans

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.

1400

δ34S (‰, V-CDT)

1200 1000 800 600 400 200 0 -200

labeled

‰ V-CDT mean standard deviation Biological replicates

labeled 1135.98 193 3

labeled + molybdate labeled + molybdate -15.42 0.00 2

unlabeled unlabeled + molybdate unlabeled -22.88 0.27 3

unlabeled + molybdate -24.86 2.03 2

Native

Native -14.8 1.19 3

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.