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Additional File 1 Additional file 1 Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys Jialin Hou, Stefan M. Sievert, Yinzhao Wang, Jeff S. Seewald, Vengadesh Perumal Natarajan Fengping Wang*, Xiang Xiao* a b 100 100 75 75 Taxa Alphaproteobacteria Taxa Betaproteobacteria Aquificae Deinococcus-Thermus Campylobacteria Deltaproteobacteria 50 Euryarchaeata 50 Euryarchaeata Others Gammaproteobacteria Percentage Percentage Thermodesulfobacterium Muproteobacteria Unclassified Nitrospirae Others Unclassified 25 25 0 0 aclA aclB cdhA cdhC napA napB norB nosZ sat soxA soxC soxY soxZ sqr aprA aprB dsrA dsrB narG nirB PRK rbcL rbcS Gene Gene Figure S1 Taxonomic classification of key functional genes retrieved from the L- and M-vent chimeny.(a) The key genes enriched in the active L-vent chimney. (b) The key genes enriched in the recently inactive M-vent chimney. Reductive bacterial type Reductive archaeal type Chlorobi group Archaeoglobus(3) Oxidative bacterial type Crenarchaeota Alphaproteobacteria(1/16) Nitrospirae(12) Acidobacteria(1/14) Betaproteobacteria Firmicutes groups Gammaproteobacteria (20) Tree scale: 1 Deltaproteobacteria(9/10) Reductive bacterial type Figure S2 Maximum-likelihood phylogeny of dsrA genes retrieved from L- and M-vent chimney. The red branches represent the dsrA genes recovered from active the L-vent chimney, while the blue ones are those from recently inactive M-vent chimney. Numbers of dsrA gene for each sample are displayed in the parenthesis after the clade name. W W W W W W W WP P P W 4 P WP P P P P 2 0 0 007601690 1 thiosulfohydrolase SoxB Bradyrhizobium sp WSM1253 P W W 0 003614695 1 MUL 008967367 1 thiosulfohydrolase SoxB Bradyrhizobium sp STM 3843 6 1 063684315 1 thiosulfohydrolase SoxB Bradyrhizobium stylosanthis W W W 7 0 057197484 1 thiosulfohydrolase SoxB Bradyrhizobium sp Leaf396 5 WP W 0 0 3 W P P 6 1 P P 4 P 9 2 2 06311 012752908 1 thiosulfohydrolase SoxB Methylobacterium extorquens P 2 3 037019901 1 thiosulfohydrolase SoxB RhizobialesP bacterium 015821 1 1 0 041750721 1 thiosulfohydrolase SoxB Bradyrhizobium sp BT N 1 WP 056910972 1 thiosulfohydrolase SoxB Pseudolabrys 0504233 sp Root14621 WP 1 5 056201494 1 thiosulfohydrolase SoxB Methylobacterium sp Leaf123 4 0 1 C W 4 9 7 8 3 W S 2 8 W 5 4 P 068025945 1 thiosulfohydrolase SoxB Rhodoplanes sp Z2 5 5 069275816 1 thiosulfohydrolase SoxB Bradyrhizobium elkanii 6 6 3 4 p 4 P 0 02 P 1224 1 thiosulfohydrolase SoxB Methylobacterium radiotolerans Aquificae Gammaproteobacteria 5 9 3 s 1 4 1 W C 063987252 1 thiosulfohydrolase SoxB Methylobacterium populi 8 3 0 7 159 1 thiosulfohydrolase SoxB Methylobacterium extorquens 1 1 A t 1 4080312 1 t C P 1 m af07 h h 1 t W 1 3 L u W R V t 0 i h i i o h o t 1 1 1 thiosulfohydrolase SoxB Bradyrhizobium tropiciagri r i h p P p p s o 6 P i s W 6 e o Afipia s s i s t 850 008389056 1 u e u s o 029031962 1 thiosulfohydrolase SoxB Salinarimonas rosea 5 W W s P c l u l a s a 7 TISPECIES thiosulfohydrolase SoxB Methylosinus f a u f a o 046021260 1 thiosulfohydrolaseP SoxB Magnetospira sp QH 2 o l u P e e 9 e f W W l b f 3 h o h l s 0 s 069189482 1 thiosulfohydrolase SoxB s 7 26 o f 560 1 th o y h y o o P o P l o h T W W 28879728 1 t ngens d 1 Actinobacteria y Campylobacteria d t h y B 047029550 1 t B hiosulfo y 5 02 B a W r d r y h P d 5 P t o YS 1r o W t r h d B B 2 B 054309588P 1 r l o 7284263 1 thiosulfohydrola l 0647 e a i o r x a x W x P o ardiphaga sp l W o s a l o 0 o s o M T s 03553062 a l P e Afipia sp P52 10 s m sp N 404492 e um W a i S P u S osulfohydrolase So s S D4 v 03 e B Afipia broomeae s l thiosulfohydrolase SoxB Rhodovulum sp PH10 e 043 S 89 hy S Afipia sp Root123D2 m barat f P e e x e e o biu S gil o s o s 0 S s W o 1 HTCC2 8034880 drolase SoxB Magnetospiril h o 185 S x o a bium marinum x a a o l S l P 24588 y l m B m 6 B x o 646 B hiosulfohydr o x o d o o u richSK drii u 01 B O e 41 1 thiosulfohydrolase SoxB Hoeflea phototrophica r x r onas coralicida Deinococcus-Thermus Chlorobi r B B r T n H s B d 1 o d hios d lla pfennigii NS P ph 7 r 8 a y y 17 y X W l y r 0 l e xa a thi t a s 21 1 H Ad13 r p h h hiosulfohydrol h a e 053 1 thiosulfohyd o d o P 13 s l h r y o o o o ulfohydrolase SoxB Hoeflea sp n bae y s e 1 thi f f oxB Rhiz a 0 f Afif zia sp i p l d o l s l bacteri t r t W 557 n h y h s h h u 3 ul m S u a u o sp thi 1 xB Lutibaculu i 0V17 MB20 o s e h i s P 80 o Aurantim m s o foh z trifican E os thiosu i b o c o u c o m o se S ale osulf x o i i f 014515003W 58 1 i ibri r lum olas o l r a So i B b h ulfohy h o h ydr xB i eni t m u h thiosulfoh t c e c P t rolase SoxB Nitratireductor pacificus ov i 17 b d u s s t cte r Alphaproteobacteria Betaproteobacteria 038 S d m sp e 1 i 1 i o SoxB 1 op m a o o c u e So W ol t Magnetospir i olase SoxB Rhizobium sp Root482 u 4 r l b d a b hydro s r r 9 i m 3 W fohy 1 TISPECIES thiosulfohydrolase SoxB 1 h ase S o f bi a i o onas sp 2 P ase Sox r l W e t sis d e SoxB Polymo seud dr 6 u rol 6 L 7 0 k o b 0241 P t S u s d m atlantic n i 1 P m d 5 5 P 47 e a 1 im olas i su 0 hio xB t i u e a u 0 e 8 icr o e SoxB Labre 3 01 d y o z oroseobacter sh a B Nisaea ri 09 8 1 1 se SoxB Ho m s 80 lase So 5 z ola n 3 t rola a 5 yd x o lfohyd n uv h 1 8 s oxB r l R 8 te a i 3 2 um g tim 0 B Rubritepid o thios T T e 46292 0 1945 1 ulf e SoxB t l A 3 1 t n c h 1 W v lum r n 9 erasakiella spe PR1 3 9 r p 1 f Sox oxB 4 i drolase SoxB Labrenzia sp CP4 a o olase f a 9 B Mes a i o M s f 2 oh rasakiella pusilla 4 i 6 h osu Def P 0 r hydr 1664487 1 thiosulfohydrolase SoxB Rhodopseudomonas palustris y b i c S A KPD29122 1 t e SoxB v c r s 4 0 ovu 6 T 0 luen d 0 01 i ase SoxB Candidatus Filomicr ti DI z ydrola i W ul e 1 thiosulfohy hi c l B gr c 1504631 1 thiosulfohydrolase SoxB Rhodopseudomonas palustris h illum m a yd e d ubr W 7 1 t 5 T 056714039 1 thiosulfohydrolase SoxB Bosea sp Leaf344 lfo c Acidithiobacillia Deltaproteobacteria h 057191334 1 thiosulfohydrolase SoxB Bosea sp Root483D1 055728613 1 thiosulfohydrolase SoxB Bosea thiooxidans ia philum YIM 77505 i h nf r N xB Cae u 047574680 1 thiosulfohydrolase SoxB Methylobacterium sp ZNC0032 x W l 1 OL 65 1 thiosulfohy h fohydrolaseiosu So P e n se 5 n P 01 drolase SoxB Labrenzlase P n P l u al Ai1 027279129 1 thiosulfohydrolase SoxB Rhodopseudomonas palustris A o D P 84 a 044409978 1 thiosulfohydrolase SoxB Rhodopseudomonas palustris 1 t o A rola s i y ho a 1 047308425 1 thiosulfohydrolase SoxB Rhodopseudomonas palustris 083 1 thiosulfohydrolase SoxB Stappia stellulata y i s M s P YC6860 s la ch SoxB Ma i 0 lfo ra 027 Thermopet assospira pro i ro W Co W 041798973 1 thiosulfohydrolase SoxB Rhodopseudomonas palustris or phiswaldense W 0 O 7 os h WP 068732006 1 thiosulfohydrolase SoxB o rm 02 61 t WP i u d K WP 034463065 1 thiosulfohydrolase SoxB 38 lfoh WP 8664 oh WP e ios h efl 063676819 1 thiosulfohydrolase SoxB Bradyrhizobium neotropicale 63 hydro se hizobium sp 1M WP m ZK WP 006019993 1 thiosulfohydrolase SoxB lf h A WP o 876 38 iosul 056301239 1 thiosulfohydrolase SoxB hy nticu t 1 u 2 0 o WP th ydro xB R aschi s sp t s M scaffold21824 WP li ea sp BAL378 a f 062314242 1 thiosulfohydrolase SoxB Bradyrhizobium sp CCH10 C7 lf ase S SoxB oxB a sp 3 isop 2 7 ulfoh S n WP 67333538 1 thiosulfohydrolase SoxB Stappia indica 1 o u a 91 1 6 ydrolase s WP 024919724 1 MU su i W 8 i IMCC20628 859 33 1 thiosulfohydrolase SoxB Fulvimarina pelagi u S m M L 9 0505 1 thiosu is hoef WP o oh ol x C0 g 6 878 coviens WP P s ell 8 1 th ox locculans 0 02905 6 i f hydrolase SoxB Rho So Jannas u P 4 WP l i n M hi fo p h o o ase rib 55 WP P 138 1 thiosulfohydrolase hydrolase SoxB Di va Eh o s 4 M M g 00 63404 f a l 027881 ydrolas h B i W 67 1 l xB tan B u 1 1 t o ne rill M scaffold31746 gene9 052639129 1 thiosulfohydrola o ase vi e 1 u rol l k i p um H e 7 s y scaffold10 r l W 037153841 1 thiosulfohydrolase SoxB Rhizobium0 sp M vax atla C i Th scaffo ea sp 2 05 20 1 thios hiosulf lase crob s 1 thio os d obact WP P ohydr d i n t ulf xB um 53436 7430 1 thiosulfoh6 vi m C i drolase SoxB M toco WP P y oxB Jann hiosulfoh r M 023430402 1 thiosulfohydrola 1 thi hiosu Lo u andonensig h u ola S fund W P 07 6 8 1 t xB ose i cus o ermu s 026379258 1 thiosulfohydrolase SoxB dro h lim p i e W ydro o l hia t W io hy lfoh T sca 0 1 t R s rru s oxB salinarum W thios fo h osei c r w 193 1 s e S se caf 13 415 0744 1 t l s e rc P he c WP P 02435 48 iosulf oxB cter f a ul sulfoh drol l er sp 624 8 1 u a ter 008 y d5787 cus m i WP 0 h lfo cte r l So s mar WW 67 51 t lfohy s lase S se S S f f drola oxB rm fo ffold454 1 W P 0 79364 u ae bacteria o oh T a 06 e Rube nn ac 1 WP 4 1 thiosulf1 s ro a b h yd as he P a cte r ant 285 thiosul us mylo ld544 W 55 64 982 6 o d oxB R o a s yd yd xB gen P 009469448 1 thiosulfohydrolase3177 SoxB Roseibium sp J ob ace d te W ydro 63 TC1 i W 0 4 6 thio 1 partial y xB b aquimarie W r e Sox s P 4669 29 hi se SoxB o r o s T r ar hiosu 1 lfohydrolase So o d P 94 o rolase s m ge W 94 t t ydrol a e S Roseibaod ter ac i P l e S hermusThe thermophil 4 P 0 7 ne u oh So h rh d ter l ase Thermus thermophilusp inu W gene8 f h ol o b ro 0 01 a u liqu gene8 e5 P 063 1 1 s r as o o W 1 9 se la CC s 0 g W ul o SoxB xB d e fohydrol g n P 028 21 7 9 io f rh d P 2 1 S s B o r cal W ge s o u o o 9 W 0 e x m e9 s P 00803 h o fohydrolas obac 0125 6 t 88 SoxB Meio e ene1 en W 25 sul l hyd S d hi oxB S T B B P 70 se rh a 4 P S u fa W 01 9 157 hi o o rolase u o c osulfoh o herm idi 0358441 253205 t i lf d SoxB Rhodobac r spha i 1 1 oxB Th s ig US3 UF1 cie e9 P 1 olase se P d hod t W 4 0 17 xB W 53 54 8 1 t h y
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