1

Supplementary Figures

Supplementary Figure 1. Abundance of Fe related gene transcripts. Abundance of Fe

related gene transcripts in plume and background are calculated based on mapping

transcripts from Illumina (a) and 454 (b) datasets to protein sequences involved in ten

pathways of Fe uptake.

0 500 1000 1500 2000 2500 3000 3500 4000 4500

Fe3+ uptake

Fe2+ uptake

Heme uptake

Fe storge

Relative abuance of transcripts

0 50 100 150 200 250

Fe3+ uptake

Fe2+ uptake

Heme uptake

Fe storge

Relative abundance of transcripts

Background

Plume

a b

Biological functions

Unspecified Fe transport

Siderophore regulation

Siderophore uptake

Siderophore systhesis

Biological functions

Unspecified Fe transport

Siderophore regulation

Siderophore uptake

Siderophore systhesis

2

Supplementary Figure 2. Phylogeny of Alteromonas population. Phylogenetic analysis

of Alteromonas population in the GB hydrothermal plume are analyzed based on 16S

rRNA (a) and two housekeeping genes encoding DNA gyrase subunit B (gyrB, b) and

RNA polymerase (rpoB, c). Black and white bars indicate the relative abundance of

transcripts (normalized number) for each gene in the plume (black) and background

(white) metatranscriptomic datasets. The red, blue and green circles indicate the

environmental source of Alteromonas sequences, from hydrothermal vent, surface, and

deep seawater, respectively. In panel (a), the identifiers of 16S rRNA gene sequences

from the GB hydrothermal plume are shown in red text (265 and 87).

A.macleodii LS9 (FJ937879)

A. macleodii 29-C (GQ203115)

A. macleodii ST716 (X85174)

A.macleodii 24082 (AM885870)

A. macleodii HJ-14 (AB238950)

265

A. macleodii LMG 24081 (AM885867)

A. macleodii HYD657 (AJ319537)

A.macleodii MS907 (AJ414399)

Uncultured Alteromonas sp. (HQ012277)

GB plume A (1996 m) 1E-074 (FJ980825)

GB plume A (1996 m) 1E-083 (FJ980834)

A. macleodii (AB376669)

A. macleodii R-28696 (AM885869)

GB plume A (1996 m) clone 1E-149 (FJ980896)

A. macleodii LMG 24080 (AM885868)

A. macleodii IAM 12920T (X82145)

Uncultured Alteromonas sp. (HQ012273)

Uncultured Alteromonas sp. (HQ012274)

GBAlt-1

A. macleodii (NC_011138)

A. macleodii (NC_011138)

GB plume A (1996 m) 1E-106 (FJ980857)

GB plume A (1996 m) 1E-172 (FJ980917)

Uncultured Alteromonas sp. (HQ012278)

A. macleodii 'Deep ecotype' (AAOD01000049)

A.macleodii (NC_011138)

Background B (2000 m) 3E-008 (FJ981336)

Uncultured Alteromonas sp. (HQ012269)

GBAlt-2

GB plume A (1996 m) 1E-144 (FJ980891)

GB background A (1503 m) 2E-116 (FJ981143)

GB background A (1503 m) 2E-084 (FJ981111)

Alteromonas sp. str. JAM-GA15 (AB526338)

87

GBAlt-3

Alteromonas sp. str. K (AB040465)

0.01

0 400000 800000 1200000 1600000

!"

#"

$"

#"

$"

%"

&"Plume

Background

0 400000 800000 1200000 1600000

!"

#"

$"

%"

&"Plume

Background

400000

AD45 (AY831592)c91343 (2236427302)c78005 (2236416039)

U4 (AY831581)H94-8 (AY831597)AND3 (AY831594)H84-3 (AY831596)8 (EU379757)7 (EU379756)11 (EU379758)621 (EU379760)

ATCC 27126 (AY831593)AND1 (AY831595)

673 (EU379761)U8 (AY831583)Adriatic 2 (AY831585)UM4b (AY831587)UM8 (AY831589)MED64 (AY831591)U7 (AY831582)U12 (AY831584)UM7 (AY831586)Adriatic 1 (AY831588)615 (EU379759)

AltDE (NC_011138)U10 (AY831590)

63

72

86

52

0.02 1000

U12 (AY831567)615 (EU379817)U7 (AY831565)U4 (AY831564)U8 (AY831566)

MED64 (AY831574)Adriatic 2 (AY831568)

UM7 (AY831569)Adriatic 1(AY831571)U10 (AY831573)UM4b (AY831570)UM8 (AY831572)

c56582 (2236397735) 11 (EU379816)7 (EU379814)8 (EU379815)H84-3 (AY831579)H94-8 (AY831580)

ATCC 27126 (AY831576)AND1 (AY831577)673 (EU379819)

c47962 (2236390278)AND2 (AY831578)AD45 (AY831575)

621 (EU379818)

99

97

99

67

100

63

0.02 500

0 1000 2000

Normalized

number of cDNA

reads mapped

Plume

Background

0 1000 2000

Normalized

number of cDNA

reads mapped

Plume

Background

0 1000 2000

Normalized

number of cDNA

reads mapped

Plume

Background

0 500 1000 1500

Normolized

number of cDNA

Plu

0 500 1000

Normolized

number of cDNA

0 500 1000 1500

Normolized

number of cDNA

Plu

a

b

c

3

Supplementary Figure 3. Genome comparison of GBAlt. Gene sequence identities of

GBAlt (2549 mRNA) are compared to the deep ecotype (AltDE) and surface ecotype

(ATCC 27126) of A. macleodii. Each circle represents one gene of GBAlt with BLASTn

bit score greater than 50 to genes of the other two ecotypes.

75%

80%

85%

90%

95%

100%

75% 80% 85% 90% 95% 100%

Gen

e id

enti

ty b

ewte

en G

BA

lt a

nd A

. m

acl

eodii

AT

CC

27126

Gene identity bewteen GBAlt and A. macleodii AltDE

4

A

5

B

Supplementary Figure 4. TonB-dependent and ABC type transporters of GBAlt.

Functional prediction of TonB-dependent (a) and ABC type transporters (b) of

Alteromonas population in the GB hydrothermal plume is performed according to Tang et

al.41

. The relative abundance of gene transcripts was normalized to the length of gene

fragments and total number of transcripts. The gene ID number for Alteromonas

population of GB hydrothermal plume was assigned from gene annotation by JGI

IMG/MER database.

6

Supplementary Figure 5. Thermodynamic modeling. Mineral concentration in mineral

and aqueous phase in the GB plume is predicted by thermodynamic modeling.

10-31

10-26

10-21

10-15

10-11

10-6

10-1

1 10 100 M

iner

als

(m

mo

l/k

g)

Temperature (o C)

Clacite

Sphalerite

Bomite-H

Pyrite

Talc

Anhydrite

Chalcocite

Magenesite

Pyrolusite

Iron-hydroxyide

Fe2+

Fe3+

FeCl+

FeCl2+

FeCl2(aq)

FeO

FeOH+

FeOH2+

HFeO2-

Minerals

Phase

Aqueous

Phase

7

Supplementary Figure 6. STXM images and elemental maps. Scanning transmission X-

ray microscopy (STXM) images and C, N, Mn, and Fe elemental maps (white scale) for

three regions of a Guaymas Basin plume sample were shown. The scale bars are 2 μm

are Area 1 and 1 μm for Area 2 and 3. The maximum optical density values for each

elemental map, in order of C, N, Mn, and Fe, are: Area 1) 1.57, 1.28, 2.51, 0.60; Area 2)

0.90, 0.92, 1.84, and 2.21; and Area 3) 1.22, 0.29, 1.57, and 1.38.

0 Maximum optical density value

8

Supplementary Figure 7. X-ray fluorescence maps. The maps are showing the

distribution of: a) Fe (red) and Mn (green); b) Fe (red), Mn (green), and Ca (blue); c) V

(red), Ti (green), and Ca (blue); and d) Fe (red), Mn (green), and Zn (blue). White stars

labeled Fe0 to Fe3 are locations of Fe XANES spectroscopy. All scale bars are 200 μm.

9

Supplementary Figure 8. C 1s XANES spectrum. A representative C 1s XANES

spectrum collected from Guaymas Basin plume particulates is shown.

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

1.8

280 290 300 310 320 330 340

Energy (eV)

No

rmal

ized

Ab

sorb

ance

10

Supplementary Table 1 Summary of samples and sequencing in this study.

Cast Location Depth

(m) Total Mn

(nM) O2

(μM) Temp. (°C)

Number of reads

11-2#14 27°0.823 N

111°24.654 W 1996 356 27.4 2.96 576,187 (454 DNA)

21-6#2 27°2.240 N

111°21.790 W 1963 315 26.1 2.93 664,240 (454 cDNA)

12-27a#1 27°30.360 N

111°20.818 W 1950 288 27.7 2.93

894,665 (454 cDNA)

206,157,516 (Illumina cDNA)

34-2#7 26°22.755 N

110°43.433 W 1900 21 46.5 2.59

406,533 (454 DNA)

504,086 (454 cDNA)

11-1#8 27°1.852 N

111°24.000 W 1775 257 27 2.95 563,818 (454 DNA)

12-8#12 27°29.174 N

111°21.844 W 1600 55 28.5 2.97

358,335 (454 DNA)

514,607 (454 cDNA)

2,4451,9176 (Illumina cDNA)

The bold highlighted samples are samples that are used for de novo metatranscriptomic

assembly with Illumina cDNA sequences in the current study (after Lesniewski et al.21

and Anantharaman et al.34

).

11

Supplementary Table 2 Guaymas Basin hydrothermal plume particle elemental concentrations*

Sample Location Depth

(m) Vol (L) Al/(Fe+Mn+Al) Mn Fe Al Ti P Zn Ni Cu Cr U

GOCAL

31-12A

27° 1.892 N

111° 25.891 W 1890 80 0.15 54.9 6.75 10.74 2.42 4.68 0.355 0.346 0.137 <DL <DL

GOCAL

31-17A

27° 0.774 N

111° 24.984 W 1959 90 0.43 33.3 4.15 28.65 9.69 3.33 0.906 <DL 0.162 <DL 0.758

GOCAL

31-2A

27° 1.240 N

111° 24.789 W 1900 100 0.17 65.4 15.78 17.19 <DL 4.49 1.029 1.027 0.292 2.68 <DL

GOCAL

32-10A

27° 30.090 N

111° 21.210 W 1891 50 <DL 48.1 7.47 <DL 0.97 4.49 0.638 <DL 0.219 <DL <DL

*All concentrations in nmol per kg seawater. Detection limits (DL, nmol per kg seawater): Mn (0.08), Fe (0.08), Al (1.70), Ti (0.10), P

(0.30), Zn (0.04), Ni (0.04), Cu (0.01), Cr (0.18) and U (0.10).