Dupont et al, supplemental materials
Materials and Methods
Primary production: Photosynthesis (primary production) was estimated from
radiolabelled carbon tracer incorporation during 24 h on-deck incubations. Briefly, water
samples were collected into 60 ml polycarbonate bottles and inoculated with 10 μCi of
14
C bicarbonate solution. For each station, one replicate surface sample was filtered
immediately to provide time-zero controls. The remaining samples were incubated for
24 h on deck in acrylic incubators screened with blue plus neutral density stage screening
to achieve a given percentage of surface irradiance that corresponded to the depth from
which they were taken, nominally 100%, 47%, 30%, 16%, 10% and 1%. The depth of
each light level was calculated using an inverse analytical radiative transfer model as
previous described (Johnson et al 2002). Incubator temperatures were maintained by a
continuous flow of surface seawater. After incubation, duplicate samples were filtered
onto 0.2 μm polycarbonate or Whatman GF/F filters then acidified with 0.5 ml of 0.5 N
HCl for 24 h to liberate unincorporated inorganic 14C. Ecolume scintillation fluid (7 ml)
was added and activity quantified using a Tri-Carb 2900TR liquid scintillation counter
(Packard Bioscience, Waltham, MA). Total added 14C, was quantified in select inoculated
subsamples prior to filtering. Primary production was estimated from the activity of the
total and filtered samples using standard calculations (Barber et al 1996). When an exact
depth match was not present, primary production values were linearly interpolated
between nearest neighbor depths to the depth of the interest.
1
Nitrogen uptake rates: Eight 500mL polycarbonate bottles were filled for each of six
depths collected 2 hours before dawn. Spikes of 100 nM 15NH4+, 15N-urea, or 15NO3- (all
99% 15N, Sigma) were added to duplicate bottles for each depth and the bottles were
transferred to on-deck incubators cooled with surface seawater and shaded to 30%
ambient light. After two hours, the entire contents of each bottle was filtered onto a
precombusted GF/F (Whatman) filter at low pressure with subsequent storage at-20oC in
a dessicator. Filters were dried (3 hours at 50oC) and packaged in tin for mass
spectrometry analysis at the UC Davis Stable isotope facility. Separately, 1L from each
of the six depths was filtered gently onto pre-combusted GF/F filters, which were
subsequently dried and packaged in tin. The total carbon and total nitrogen captured on
these filters were determined at the Scripps Institution of Oceanography analytical
facility with a Costech 4010 Elemental combustion analyzer. Uptake rates were
determined using the equations described in Dugdale et al (Dugdale and Goering 1967,
Dugdale and Wilkerson 1986). In the case where the nutrient concentrations were below
the analytical detection limits (100 nM), an ambient concentration of 100nM was
assumed.
Electron microscopy: Cells in log phase, grown at room temperature at 30 uE (daylight
fluorescent bulbs) on a rotary shaker (125 rev/min) were pelleted; a small aliquot was
transferred by toothpick to a cushioning material and dropped onto a liquid He-cooled
copper block (4 deg K); the frozen material was transferred to liquid nitrogen and
fractured, etched at -80°C for 2 min, and Pt/C rotary replicated as described previously
(*). The replicas were examined with a JEOL electron microscope, model JEM
2
1400, equipped with an AMTV601 digital camera. The images are photographic
negatives; hence, protuberant elements of the fractured/etched surface are most heavily
coated with platinum and appear white.
Pigment measurements: Two liters of seawater was gently filtered onto a Whatman GF/F
filter, which was placed in a cryogenic vial and stored in liquid nitrogen until analysis as
described in Goericke and Montoya (1998) and Dupont et al. (2010).
3
Table 1: Number of sequences generated for each library and annotation statistics .
Schmidt filtering removes duplicate reads. Taxonomic annotation refers to having a
match in PhyloDB. Cluster indicates if a sequence is recruited to the GOS protein
clusters. KEGG, PFAM, and TIGRFAM indicate the percentage of reads annotated by
the indicated families of HMMs.
Library
GS265_454_0.1
GS265_454_0.8
GS265_454_3.0
GS265_polyA mRNA
GS265_total mRNA
GS265_sanger_0.1
GS266_454_0.1
GS266_454_0.8
GS266_454_3.0
GS266_polyA mRNA
GS266_total mRNA
GS266_sanger_0.1
GS267_454_0.1
GS267_454_0.8
GS267_454_3.0
GS267_polyA mRNA
GS267_total mRNA
GS267_sanger_0.1
GS268_454_0.1
GS268_454_0.8
GS268_454_3.0
GS268_polyA mRNA
GS268_total mRNA
GS268_sanger_0.1
GS269_454_0.1
GS269_454_0.8
GS269_454_3.0
GS269_polyA mRNA
GS269_total mRNA
GS269_sanger_0.1
GS270_454_0.1
GS270_454_0.8
GS270_454_3.0
GS270_polyA mRNA
GS270_total mRNA
GS270_sanger_0.1
GS271_454_0.1
GS271_454_0.8
GS271_454_3.0
GS271_polyA mRNA
GS271_total mRNA
GS271_sanger_0.1
GS272_454_0.1
GS272_454_0.8
GS272_454_3.0
GS272_polyA mRNA
GS272_total mRNA
GS272_sanger_0.1
Genome/Transcriptome
Genome
Genome
Genome
Transcriptome
Transcriptome
Genome
Genome
Genome
Genome
Transcriptome
Transcriptome
Genome
Genome
Genome
Genome
Transcriptome
Transcriptome
Genome
Genome
Genome
Genome
Transcriptome
Transcriptome
Genome
Genome
Genome
Genome
Transcriptome
Transcriptome
Genome
Genome
Genome
Genome
Transcriptome
Transcriptome
Genome
Genome
Genome
Genome
Transcriptome
Transcriptome
Genome
Genome
Genome
Genome
Transcriptome
Transcriptome
Genome
Read length (median)
422
406
376
349
157
1021
422
397
351
374
375
1027
457
414
377
424
116
1028
460
365
336
376
287
1025
409
449
432
454
319
1030
426
432
385
336
337
1027
407
411
338
398
397
1036
447
427
402
325
90
1030
Raw Reads
260734
220031
334337
415501
112564
46654
244716
175015
174055
889091
249623
45757
145239
272874
250090
453751
202368
46531
223789
189181
206976
946195
161315
46588
286048
230045
335849
206753
160020
45458
247242
221331
324771
772491
95082
46311
310047
236896
304775
770314
563599
44347
209455
183007
391736
500776
112047
45475
Schmidt filtered Post rRNA removal
250390
158324
235993
412298
96293
46651
235087
130529
127098
874427
209920
45745
135257
233648
211894
450932
182244
46502
208138
129164
143681
914645
128030
46585
276953
220521
314465
206280
133069
45457
239167
203542
294927
758859
77791
46310
291740
201973
251684
752922
163326
44266
198247
146134
308436
499770
95364
45456
4
Percentages based on post schmidt and rRNA removal
Library
% taxonomic
Cluster
GS265_454_0.1
73
181550
GS265_454_0.8
56
84095
GS265_454_3.0
24
53285
GS265_polyA mRNA
27
92214
GS265_total mRNA
25
21676
GS265_sanger_0.1
92
42712
GS266_454_0.1
69
161365
GS266_454_0.8
56
69699
GS266_454_3.0
17
20305
GS266_polyA mRNA
29
212449
GS266_total mRNA
35
62700
GS266_sanger_0.1
88
40240
GS267_454_0.1
76
103105
GS267_454_0.8
52
119862
GS267_454_3.0
18
37100
GS267_polyA mRNA
29
112637
GS267_total mRNA
21
35994
GS267_sanger_0.1
92
42813
GS268_454_0.1
64
132924
GS268_454_0.8
51
62077
GS268_454_3.0
21
28999
GS268_polyA mRNA
31
240658
GS268_total mRNA
39
45851
GS268_sanger_0.1
86
40038
GS269_454_0.1
71
196327
GS269_454_0.8
35
72098
GS269_454_3.0
20
60242
GS269_polyA mRNA
32
56862
GS269_total mRNA
32
38848
GS269_sanger_0.1
92
41844
GS270_454_0.1
56
132104
GS270_454_0.8
47
81786
GS270_454_3.0
13
33308
GS270_polyA mRNA
35
213496
GS270_total mRNA
60
44375
GS270_sanger_0.1
88
40436
GS271_454_0.1
67
194088
GS271_454_0.8
50
94403
GS271_454_3.0
17
40473
GS271_polyA mRNA
36
226759
GS271_total mRNA
49
73323
GS271_sanger_0.1
88
38897
GS272_454_0.1
67
132216
GS272_454_0.8
59
84280
GS272_454_3.0
26
76638
GS272_polyA mRNA
29
130192
GS272_total mRNA
15
12940
GS272_sanger_0.1
90
40599
%cluster
73
53
23
22
23
92
69
53
16
24
30
88
76
51
18
25
20
92
64
48
20
26
36
86
71
33
19
28
29
92
55
40
11
28
57
87
67
47
16
30
45
88
67
58
25
26
14
89
Kegg
118236
43221
23919
32722
11377
28086
103852
32683
7226
76698
26233
25181
68685
68456
16510
41830
19310
28988
76815
28222
8136
89046
26302
23699
133271
31458
23733
20849
19159
28319
78944
29430
9462
73090
12213
25102
120461
47466
16678
79645
32036
25525
79324
46043
32926
43057
6350
25142
% Kegg
47
27
10
8
12
60
44
25
6
9
12
55
51
29
8
9
11
62
37
22
6
10
21
51
48
14
8
10
14
62
33
14
3
10
16
54
41
24
7
11
20
58
40
32
11
9
7
55
PFAM
158305
70679
42218
83797
19555
37195
139017
53412
13943
191578
57044
33752
89292
101789
28216
101338
32212
37242
108111
46987
17659
216205
39639
32354
172318
58489
44676
50924
34628
36518
111778
63402
23021
193408
34016
33858
163347
79679
31912
206113
54364
33996
109095
70710
57885
113916
11627
33680
PFAM%
63
45
18
20
20
80
59
41
11
22
27
74
66
44
13
22
18
80
52
36
12
24
31
69
62
27
14
25
26
80
47
31
8
25
44
73
56
39
13
27
33
77
55
48
19
23
12
74
TIGRFAM
74459
27773
15397
14560
7993
17088
65017
21170
4527
37100
15658
15236
42154
44193
10417
18125
11897
17582
47447
18576
5094
42931
18236
14287
84382
19062
14801
8773
11659
17448
48366
17468
5458
36729
9204
15275
74866
30622
10498
36899
22575
15659
49795
29695
20826
20289
3813
15355
TIGR%
30
18
7
4
8
37
28
16
4
4
7
33
31
19
5
4
7
38
23
14
4
5
14
31
30
9
5
4
9
38
20
9
2
5
12
33
26
15
4
5
14
35
25
20
7
4
4
34
5
Table 2: Genomes enriched in the largest size fraction, the SCM, and the surface ocean.
No genomes are enriched in the smallest size fraction. All of these genomes are
statistically enriched according to multiple methods with p scores less than 0.001 (Chi2
test and FDR). Many more genomes are enriched in each environment. The total
metagenomic abundance is shown along with total transcriptome abundance. Finally, the
percent amino acid identity of the translated transcripts and metagenome reads to each
genome is shown.
3.0 enriched bacteria
Synechococcus sp. CC9311
Akkermansia muciniphila ATCC BAA-835
Alteromonas macleodii ATCC 27126
Alteromonas macleodii str. 'Deep ecotype'
Coraliomargarita akajimensis DSM 45221
Synechococcus sp. CC9902
Synechococcus sp. BL107
Lacinutrix sp. 5H-3-7-4
Verrucomicrobium spinosum DSM 4136
Flavobacteriales bacterium ALC-1
Lentisphaera araneosa HTCC2155
Chthoniobacter flavus Ellin428
Verrucomicrobiae bacterium DG1235
Synechococcus sp. WH 7803
Ulvibacter SCB49
SCM enriched bacteria
Prochlorococcus marinus str. NATL1A
Prochlorococcus marinus str. NATL2A
Prochlorococcus marinus str. CCMP1375
Synechococcus sp. CC9311
Prochlorococcus marinus str. MIT 9313
Acidimicrobium ferrooxidans DSM 10331
Prochlorococcus marinus str. MIT 9303
Prochlorococcus marinus str. MIT 9211
Frankia sp. EUN1f
delta proteobacterium MLMS-1
Candidatus Ruthia magnifica str. Cm
Frankia sp. EuI1c
Pedosphaera parvula Ellin514
Candidatus Vesicomyosocius okutanii HA
Frankia alni ACN14a
Surface enriched bacteria
Prochlorococcus marinus CCMP1986
Coraliomargarita akajimensis DSM 45221
Prochlorococcus marinus str. MIT 9515
Candidatus Puniceispirillum marinum IMCC1322
gamma proteobacterium HTCC2207
Hyphomonas neptunium ATCC 15444
alpha proteobacterium HIMB114
Roseobacter litoralis Och 149
Octadecabacter antarcticus 307
Candidatus Pelagibacter sp. IMCC9063
Prochlorococcus marinus str. MIT 9301
Ruegeria pomeroyi DSS-3
Roseovarius sp. 217
Roseobacter denitrificans OCh 114
Candidatus Pelagibacter HTCC 7211
0.1/3.0
0.00
0.01
0.01
0.01
0.01
0.01
0.02
0.02
0.02
0.02
0.02
0.02
0.02
0.02
0.02
surface/SCM
0.01
0.02
0.09
0.13
0.14
0.16
0.18
0.19
0.20
0.20
0.20
0.22
0.24
0.24
0.25
surface/SCM
13.27
6.58
5.74
3.82
3.79
2.69
2.57
2.22
2.21
2.18
2.16
2.16
2.14
2.12
2.05
Meta %
0.58
0.16
0.20
0.20
2.47
0.57
0.34
0.95
0.42
1.08
0.45
0.28
0.41
0.07
0.35
Meta %
3.25
1.38
0.13
0.58
0.03
0.16
0.08
0.08
0.03
0.04
0.14
0.06
0.32
0.10
0.03
Meta %
4.23
2.47
0.77
1.78
1.52
0.17
0.65
0.13
0.12
0.62
0.09
0.24
0.11
0.18
8.22
Tran %
1.52
0.07
1.81
1.80
0.34
2.41
1.19
0.18
0.16
0.19
0.09
0.10
0.17
0.18
0.07
Tran %
5.56
0.68
0.31
1.52
0.07
0.07
0.25
0.31
0.02
0.02
0.10
0.05
0.26
0.08
0.02
Tran %
1.41
0.34
0.64
3.00
0.57
0.19
0.25
0.08
0.11
0.26
0.06
0.20
0.09
0.14
1.67
% ID to ref
91
61
83
93
68
91
89
74
62
64
47
56
50
82
74
% ID to ref
93
91
92
91
90
68
92
86
42
66
76
50
52
73
52
% ID to ref
91
68
93
81
64
70
74
78
70
76
85
71
89
75
81
6
Table 3: Most expressed genes for several of the most abundant genomes.
SAR86 subtype A, clade I (78% AA identity)
Puniceispirillum marinum IMCC1322 (75% AA identity)
Ton B Receptor
sugar ABC transporter periplasmic sugar-binding protein
Cytochrome C and Quinol oxidase polypeptide I
hypothetical protein
Hypothetical protein
cytochrome-c oxidase subunit I protein
Peroxidase
membrane protease subunit HflK
EF-Tu
ATP synthase F1 subunit alpha
RNA polymerase Rpb2
cell division protein FtsH
Inorganic H+ pyrophosphatase
DNA-directed RNA polymerase subunit beta
Ribosomal protein L10
DNA-directed RNA polymerase
D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
molecular chaperone DnaK
Ton B Receptor
chaperonin GroEL
Pelagibacter HTCC7211 (81% AA identity)
Erythrobacter sp. SD-21 (83% AA identity)
bacteriorhodopsin
ribosomal protein L4/L1 family
Na+/solute symporter, Ssf family
ATP synthase F0, A subunit
Bacterial extracellular solute-binding protein, family 7
50S ribosomal protein L3
glycine betaine-binding lipoprotein, putative
translation elongation factor G
V-type H(+)-translocating pyrophosphatase
ribosomal protein S14p/S29e
receptor family ligand-binding protein
30S ribosomal protein S13
putative porin
ribosomal protein S2
trap dicarboxylate transporter - dctp subunit
hypothetical protein
translation elongation factor Tu
ATP synthase F1, alpha subunit
glutamate synthase large subunit
protein-export membrane protein SecF
SAR324 clade bacteria, surface branch (69% AA identity)
Alteromonadales bacterium TW-7 (89% AA identity)
LacI periplasm sugar binding protein
ribosomal protein L6
Bacterial extracellular solute-binding protein
Bacterial flagellin N-terminus
TCP-1/cpn60 chaperonin family
protein TolR
Hypothetical protein
ribosomal protein S1
Bacterial extracellular solute-binding protein
ribosomal protein L7/L12
Bacterial extracellular solute-binding proteins, family 3
DNA-directed RNA polymerase, beta subunit
Bacterial extracellular solute-binding proteins, family 3
ribosomal protein L4/L1 family
Sodium/hydrogen exchanger family
ribosomal protein L10
Hypothetical protein
translation elongation factor G
Bacterial extracellular solute-binding proteins
50S ribosomal protein L3
Prochlorococcus NATL1A (93% AA identity)
Synechococcus CC9311 (91% AA identity)
light-harvesting complex protein
porin
rplC
psbA-3
psbD
porin
light-harvesting protein PcbH
porin
rpl
cpaB-2
porin-like protein
psaB
rbcL
psaA
psbC
psbA-1
psbB
psbB
F0F1 ATP synthase subunit B'
NADH dehydrogenase
7
Table 4: Genomes whose abundance correlated (r2>0.7) with measurements of primary
production, nitrate uptake, and chl a. Also shown is the metagenomic abundance of the
genomes, its enrichment factor in the largest size fraction, and the CDNA to DNA ratio
for each genome.
Primary production
Species
Synechococcus sp. CC9902
Synechococcus sp. CC9311
Synechococcus sp. BL107
Synechococcus sp. WH 8109
Candidatus Ruthia magnifica str. Cm
Methylophilales bacterium HTCC2181
Runella slithyformis DSM 19594
Candidatus Vesicomyosocius okutanii HA
unidentified eubacterium SCB49
Parabacteroides distasonis ATCC 8503
Synechococcus sp. CC9605
Trans %
2.41
1.52
1.19
0.39
0.10
0.08
0.04
0.08
0.07
0.01
0.49
Genome % CDNA/DNA
0.57
4.25
0.58
2.63
0.34
3.47
0.10
4.06
0.14
0.70
0.23
0.36
0.15
0.26
0.10
0.82
0.35
0.21
0.03
0.23
0.17
2.91
0.1/3.0
0.19
0.03
0.24
0.47
8.69
10.17
0.73
6.49
0.34
0.46
0.39
Surf/chl max
0.35
0.13
0.38
1.12
0.20
1.74
0.72
0.24
0.71
0.69
0.98
Nitrate uptake
Species
Synechococcus sp. WH 8109
Synechococcus sp. WH 8102
Synechococcus sp. CC9605
Methylophilales bacterium HTCC2181
Sar86 B
Trans %
0.39
0.32
0.49
0.08
0.44
Genome % CDNA/DNA
0.10
4.06
0.21
1.54
0.17
2.91
0.23
0.36
2.35
0.19
0.1/3.0
0.47
0.39
0.39
10.17
3.22
Surf/chl max
1.12
1.09
0.98
1.74
1.69
Chlorophyll a
Species
Runella slithyformis DSM 19594
Parabacteroides distasonis ATCC 8503
Synechococcus sp. CC9311
Synechococcus sp. RS9917
Candidatus Vesicomyosocius okutanii HA
Synechococcus sp. WH 7805
Candidatus Ruthia magnifica str. Cm.
Synechococcus sp. RS9916
Methylovorus sp. MP688
Spirosoma linguale DSM 74
Synechococcus sp. CB0101
Bacteroidetes oral taxon 274 str. F0058
Haliscomenobacter hydrossis DSM 1100
Synechococcus sp. WH 7803
Chthoniobacter flavus Ellin428
Akkermansia muciniphila ATCC BAA-835
Pedosphaera parvula Ellin514
Odoribacter splanchnicus DSM 20712
Synechococcus sp. RCC307
Chitinophaga pinensis DSM 2588
Verrucomicrobium spinosum DSM 4136
Microscilla marina ATCC 23134
Blastopirellula marina DSM 3645
Trans %
0.04
0.01
1.52
0.06
0.08
0.11
0.10
0.13
0.01
0.05
0.03
0.01
0.13
0.18
0.10
0.07
0.26
0.03
0.04
0.05
0.16
0.08
0.10
Genome % CDNA/DNA
0.15
0.26
0.03
0.23
0.58
2.63
0.05
1.27
0.10
0.82
0.07
1.57
0.14
0.70
0.08
1.63
0.02
0.69
0.13
0.39
0.03
0.85
0.03
0.46
0.28
0.46
0.07
2.65
0.28
0.36
0.16
0.44
0.32
0.81
0.09
0.37
0.04
1.18
0.15
0.35
0.42
0.38
0.28
0.28
0.20
0.48
0.1/3.0
0.73
0.46
0.03
0.71
6.49
0.43
8.69
0.49
3.38
0.73
0.45
0.61
0.52
0.34
0.33
0.13
0.50
0.44
0.42
0.54
0.28
0.62
0.61
Surf/chl max
0.72
0.69
0.13
0.40
0.24
0.41
0.20
0.40
0.76
0.68
0.29
0.58
0.68
0.35
0.54
0.67
0.24
0.50
0.37
0.60
0.56
0.65
0.35
8
Figure S1: Depth profiles of particulate carbon, nitrogen, chlorophyll a, and the C:Chl a
at each site where metagenomic and metatranscriptomic samples were taken.
Particulate Carbon (ug/L)
0.00
0
Particulate nitrogen (ug/L)
50.00 100.00 150.00 200.00 250.00 300.00
20
20
40
40
60
60
80
10.00
20.00
60.00
100
120
120
140
140
160
160
Particulate chl a (ug/L)
0.00
0
30.00 40.00 50.00
80
93.40
93.110
93.120
93.80
100
Dept h (m)
0.00
0
0.20
0.40
0.60
0.80
1.00
C:Chl a (ug/ug)
1.20
0.00
0
20
20
40
40
60
60
80
80
100
100
120
120
140
140
160
160
500.00
1000.00
1500.00
2000.00
9
Figure S2: Taxonomic breakdown at the domain level for reads that received a
taxonomic annotation via BLAST to PhyloDB for each library.
Surface
0%
Chl a maximum
100% 0%
50%
50%
100%
93.40
93.80
93.110
93.120
0.1-0.8 um
metagenome
93.40
93.80
93.110
93.120
0.8-3.0 um
metagenome
93.40
93.80
93.110
93.120
3.0-20 um
metagenome
93.40
93.80
93.110
93.120
polyA mRNA
metatranscriptome
93.40
93.80
93.110
93.120
total mRNA
metatranscriptome
Archaea
Bacteria
Eukarya
Virus
Scripps Figure 3
10
Figure S3: Top panel: Taxonomic breakdown of all annotated reads of putative viral
origin for each size class. Bottom panel: Taxonomic breakdown of all annotated
reads of putative viral origin for the surface and SCM samples. Only the most
abundant taxonomic categories are shown for clarity of legend, thus the histograms
do not add up to 100%.
100
Taterapox virus
Synechococcus phage Syn5
Cyanophage PSS2
90
Roseobacter phage SIO1
OCTOPUS_SMPL_20031004
80
Vibrio phage KVP40
% of total annotated reads of viral origin
Micromonas sp. RCC1109 virus MpV1
70
BEARPAW_SMPL_20031007
Bathycoccus sp. RCC1105 virus BpV1
60
Enterobacteria phage EPS7
Enterobacteria phage T5
Acanthamoeba polyphaga mimivirus
50
GIS_HUMAN_FECAL_VIRUS_RNA_SMPL
Cafeteria roenbergensis virus BV-PW1
40
Prochlorococcus phage P-SSP7
SDSU_MISSION_BAY_VIRUS_SMPL
30
SDSU_MARINE_SEDIMENT_VIRUS_SMPL
Synechococcus phage syn9
20
Synechococcus phage S-PM2
Synechococcus phage S-RSM4
Prochlorococcus phage P-SSM4
10
SDSU_SCRIPPS_PIER_MARINE_VIRUS_SMPL
Prochlorococcus phage P-SSM2
0
sum (0.1)
sum (0.8)
sum (3.0)
Aeromonas phage phiAS5
100
90
Xanthomonas phage Xp15
Emiliania huxleyi virus 86
Synechococcus phage Syn5
80
Rhodothermus phage RM378
Ostreococcus virus OsV5
Cyanophage PSS2
Shigella phage phiSboM-AG3
Acanthocystis turfacea Chlorella virus 1
OCTOPUS_SMPL_20031004
70
% of annotated viral reads
UDEL_CHESAPEAKE_VIROPLANKTON_SMPL
Ostreococcus tauri virus 2
Ostreococcus lucimarinus virus OlV1
Roseobacter phage SIO1
60
Micromonas sp. RCC1109 virus MpV1
BEARPAW_SMPL_20031007
Vibrio phage KVP40
Bathycoccus sp. RCC1105 virus BpV1
GIS_HUMAN_FECAL_VIRUS_RNA_SMPL
50
Enterobacteria phage T5
Acanthamoeba polyphaga mimivirus
Enterobacteria phage EPS7
40
Prochlorococcus phage P-SSP7
Cafeteria roenbergensis virus BV-PW1
30
Synechococcus phage S-RSM4
20
Synechococcus phage S-PM2
Synechococcus phage syn9
SDSU_MISSION_BAY_VIRUS_SMPL
10
Prochlorococcus phage P-SSM4
SDSU_MARINE_SEDIMENT_VIRUS_SMPL
SDSU_SCRIPPS_PIER_MARINE_VIRUS_SMPL
Prochlorococcus phage P-SSM2
UDEL_CHESAPEAKE_VIROPLANKTON_SMPL
0
Surface
SCM
11
Figure S4: Representation of various eukaryotic (left column) and bacterial (right
column) in pooled metagenomes (top four panels) and the two types of
transcriptomes. A similar comparison for the two types of transcriptomes is shown
in the bottom two panels.
12
Figure S5: Freeze etch micrographs of the basal body (upper panel) and axoneme
(lower) structure in Pelagomonas calceolate CCMP1756
13
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