Supplementary Table 1: Origin of the samples used in this study, number of sequences
obtained after cleaning and Shannon index. Samples that were discarded because they had to
few sequences are shown in red.
Sample name
Bar_aqu_oak1
Cen_aqu_oak1
Top_aqu_oak1
Bar_aqu_pin1
Cen_aqu_pin1
Top_aqu_pin1
Bar_aqu_oak2
Cen_aqu_oak2
Top_aqu_oak2
Bar_aqu_pin2
Cen_aqu_pin2
Top_aqu_pin2
Bar_aqu_oak4
Cen_aqu_oak4
Top_aqu_oak4
Bar_aqu_pin4
Cen_aqu_pin4
Top_aqu_pin4
Cen_can_oak7r
1
Cen_can_oak7r
2
Cen_can_oak7r
3
Cen_can_pin7r
1
Cen_can_pin7r
2
Cen_can_pin7r
3
Bar_aqu_oak8
Cen_aqu_oak8
Top_aqu_oak8
Bar_aqu_pin8
Cen_aqu_pin8
Top_aqu_pin8
Bar_aqu_oak10
Cen_aqu_oak10
Top_aqu_oak10
Bar_aqu_pin10
Cen_aqu_pin10
Microhabitat
Month
Oak
Oak
Oak
Pine
Pine
Pine
Oak
Oak
Oak
Pine
Pine
Pine
Oak
Oak
Oak
Pine
Pine
Pine
Bark
Center
Top
Bark
Center
Top
Bark
Center
Top
Bark
Center
Top
Bark
Center
Top
Bark
Center
Top
1
1
1
1
1
1
2
2
2
2
2
2
4
4
4
4
4
4
Number of
sequences
5693
3092
3858
3261
2322
4944
4605
4182
3676
5315
3084
3222
4993
4013
3751
4483
3235
2965
Canyon
Oak
Center
7
3549
Canyon
Oak
Center
7
3453
Canyon
Oak
Center
7
3673
Canyon
Pine
Center
7
3631
Canyon
Pine
Center
7
3187
Canyon
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Pine
Oak
Oak
Oak
Pine
Pine
Pine
Oak
Oak
Oak
Pine
Pine
Center
Bark
Center
Top
Bark
Center
Top
Bark
Center
Top
Bark
Center
7
2505
8
8
8
8
8
8
10
10
10
10
10
4194
2331
1764
4460
3594
4144
4493
1663
3243
4819
3048
Origin
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Wood
Shannon
7.45
5.72
6.66
6.17
3.67
4.78
7.64
6.35
6.05
6.04
5.98
7.77
6.74
4.33
5.93
5.84
4.46
6.88
7.47
6.80
6.42
6.76
6.94
6.30
7.40
6.37
5.48
7.17
6.00
6.39
7.70
4.08
5.00
5.86
3.97
Top_aqu_pin10
Cen_can_oak12
r1
Cen_can_oak12
r2
Cen_can_oak12
r3
Cen_can_pin12
r1
Cen_can_pin12
r2
Cen_can_pin12
r3
Cen_aqu1_ITS
Top_aqu1_ITS
Bar_aqu1_ITS
Cen_aqu2_ITS
Top_aqu2_ITS
Bar_aqu2_ITS
Cen_can7r1_ITS
Cen_can7r2_ITS
Cen_can7r3_ITS
Cen_aqu8_ITS
Top_aqu8_ITS
Bar_aqu8_ITS
Cen_aqu1_ARC
Top_aqu1_ ARC
Bar_aqu1_ ARC
Cen_aqu2_ARC
Top_aqu2_ ARC
Bar_aqu2_ ARC
Cen_can7r1_AR
C
Cen_can7r2_AR
C
Cen_can7r3_AR
C
Cen_aqu8_ARC
Top_aqu8_ ARC
Bar_aqu8_ ARC
10
4426
12
3062
12
3845
12
2587
12
3978
12
3673
12
4588
1
1
1
2
2
2
7
7
7
8
8
8
1
1
1
2
2
2
1632
2788
1692
1683
1159
2939
362
526
415
0
93
842
1
979
215
336
1762
1451
Center
7
2580
Center
7
1809
7
581
8
8
8
0
0
3028
Aquarium
Pine
Top
Canyon
Oak
Center
Canyon
Oak
Center
Canyon
Oak
Center
Canyon
Pine
Center
Canyon
Pine
Center
Canyon
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Canyon
Canyon
Canyon
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Aquarium
Pine
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Oak
Center
Center
Top
Bark
Center
Top
Bark
Center
Center
Center
Center
Top
Bark
Center
Top
Bark
Center
Top
Bark
Canyon
Oak
Canyon
Oak
Canyon
Aquarium
Aquarium
Aquarium
Oak
Oak
Oak
Oak
Center
Center
Top
Bark
6.16
7.27
7.53
6.88
7.13
8.16
8.03
0.62
1.14
2.08
1.43
1.84
1.42
2.91
1.55
1.45
1.73
1.57
1.64
1.57
Supplementary Table 2: Discrete measurement of sulfide concentrations in the aquaria at the
interface between wood and seawater. All measurements were made on the biofilm that
develop at the interface.
Oak
Pine
Time in Days
Sulfide (µM)
21
4.2 +- 0.6
30
3.9 +- 2.3
30
4.4 +- 2
32
20.7 +- 2.6
32
14.1 +- 1.3
35
7.8 +- 1.4
35
2.6 +- 1
51
2.0 +- 0.4
78
29.1 +- 7.7
78
46.4 +- 6.2
78
12.4 +- 3.8
21
12.6+-2.5
30
30
30
32
32
32
35
35
38
38
122
122
12.8 +- 3.6
18.6 +- 5
0
0
28.6 +- 15
0
0
17.4 +- 7.4
0
0.7 +- 0.3
0
0
Supplementary Fig. 1: White microbial mat developing on oak wood surface in an aquarium
incubation. Wood powder in the centre originates from Teredinae bivalves boring activity.
Supplementary Fig. 2: Rarefaction curves for bacterial OTUs clustered at 97% similarity in
pine (a) and oak (b) wood samples.
Supplementary Fig. 3: Cluster analysis based on a Bray Curtis dissimilarity matrix of archaeal
OTUs in oak samples from the aquarium experiment (aqu) and from the in situ canyon
deployment (can). Numbers after the names indicate the time of incubation in months. r1 and
r2 are replicate samples. Bootstrap values are shown on the branches.
Supplementary Fig. 4: Cluster analysis based on a Bray Curtis dissimilarity matrix of fungal
OTUs in oak samples from the aquarium experiment (aqu). Numbers after the names indicate
the time of incubation in months. Bootstrap values are shown on the branches.
Supplementary Fig. 5: Sequence abundance of the five most abundant bacterial OTUs in each
sample for oak (1) and pine (2) wood and in the top (a), centre (b) and bark (c) microhabitats.
All samples are from the aquaria experiment.
Otu10983_Spirochaeta [Genus]
Otu06514_Desulfobacteraceae [Family]
Otu02907_Reinekea [Genus]
Otu05636_Bacteroidetes [Phylum]
Otu05637_Bacteroidetes [Phylum]
Otu02910_Reinekea [Genus]
Otu07261_Bacteria [Kingdom]
Otu04708_Gaetbulibacter [Genus]
Otu06515_Desulfovibrio [Genus]
Otu02906_Vibrionaceae [Family]
Otu02913_Gammaproteobacteria [Class]
Bar_aqu_oak1
Otu05639_Bacteroidetes [Phylum]
Otu04709_Maribacter [Genus]
Bar_aqu_oak2
Otu04710_Flavobacteriaceae [Family]
Otu06516_Desulfovibrio [Genus]
Bar_aqu_oak4
Otu07263_Bacteria [Kingdom]
Bar_aqu_oak8
Otu00747_Rhizobiales [Order]
Otu05635_Bacteroidetes [Phylum]
Bar_aqu_oak10
Otu07262_Bacteria [Kingdom]
Otu02920_Gammaproteobacteria [Class]
Cen_aqu_oak1
Otu00758_Alphaproteobacteria [Class]
Otu02908_Marinomonas [Genus]
Cen_aqu_oak2
Otu00762_Phyllobacterium [Genus]
Otu04715_Flavobacteriales [Order]
Cen_aqu_oak4
Otu00064_Proteobacteria [Phylum]
Cen_aqu_oak8
Otu07268_Bacteria [Kingdom]
Otu07265_Bacteria [Kingdom]
Cen_aqu_oak10
Otu05414_Olivibacter [Genus]
Otu06520_Desulfovibrio [Genus]
Top_aqu_oak1
Otu02816_Methylophilaceae [Family]
Otu00756_Altererythrobacter [Genus]
Top_aqu_oak2
Otu04723_Flavobacteriaceae [Family]
Otu02932_Enterobacteriaceae [Family]
Top_aqu_oak4
Otu00767_Rhodobacteraceae [Family]
Top_aqu_oak8
Otu02924_Gammaproteobacteria [Class]
Otu00757_Altererythrobacter [Genus]
Top_aqu_oak10
Otu00749_Alphaproteobacteria [Class]
Otu00774_Phyllobacterium [Genus]
Otu02931_Pseudoxanthomonas [Genus]
Otu00772_Rhodobacteraceae [Family]
Otu00773_Rhodobacteraceae [Family]
Otu00780_Alphaproteobacteria [Class]
Otu02914_Gammaproteobacteria [Class]
Otu10493_Brevibacterium [Genus]
Otu06530_Deltaproteobacteria [Class]
Otu02959_Gammaproteobacteria [Class]
Otu06526_Deltaproteobacteria [Class]
Otu04752_Aquimarina [Genus]
0
500
1000
2000
Number of Sequences
1500
2500
3000
3500
Supplementary Fig. 6: Proportion of the most abundant bacterial OTUs found in oak during
the aquaria experiment. Abundant OTU are defined as OTUs with > 1% sequence abundance
in at least 2 samples. The taxonomic assignation is based on the lowest annotated taxon.
Sample labels show the microhabitat (bark, top or center) and the time of incubation in
months (1,2,4,8 or 10).
Otu02906_Vibrionaceae [Family]
Otu05635_Bacteroidetes [Phylum]
Otu00747_Rhizobiales [Order]
Otu06515_Desulfovibrio [Genus]
Otu02909_Gammaproteobacteria [Class]
Otu10984_Spirochaeta [Genus]
Otu02908_Marinomonas [Genus]
Otu05413_Sphingobacteriales [Order]
Otu02912_Gammaproteobacteria [Class]
Otu06514_Desulfobacteraceae [Family]
Otu06404_Fusibacter [Genus]
Otu10983_Spirochaeta [Genus]
Bar_aqu_pin1
Otu00749_Alphaproteobacteria [Class]
Otu02915_Alteromonadales [Order]
Bar_aqu_pin2
Otu02914_Gammaproteobacteria [Class]
Otu10985_Spirochaeta [Genus]
Bar_aqu_pin4
Otu05638_Bacteroidetes [Phylum]
Bar_aqu_pin8
Otu00753_Porphyrobacter [Genus]
Otu02918_Alteromonas [Genus]
Bar_aqu_pin10
Otu04591_Arcobacter [Genus]
Otu02919_Alteromonadaceae [Family]
Cen_aqu_pin1
Otu04711_Flavobacteriaceae [Family]
Cen_aqu_pin2
Otu07262_Bacteria [Kingdom]
Otu00752_Hyphomonadaceae [Family]
Cen_aqu_pin4
Otu02916_Gammaproteobacteria [Class]
Otu02922_Marinomonas [Genus]
Cen_aqu_pin8
Otu02923_Marinomonas [Genus]
Otu02907_Reinekea [Genus]
Cen_aqu_pin10
Otu04718_Flavobacteriaceae [Family]
Top_aqu_pin1
Otu00021_Haloferula [Genus]
Otu00759_Rhodobacteraceae [Family]
Top_aqu_pin2
Otu07263_Bacteria [Kingdom]
Otu04719_Maribacter [Genus]
Top_aqu_pin4
Otu07266_Bacteria [Kingdom]
Top_aqu_pin8
Otu04593_Arcobacter [Genus]
Otu02926_Gammaproteobacteria [Class]
Top_aqu_pin10
Otu00763_Hirschia [Genus]
Otu00754_Rhodobacteraceae [Family]
Otu06405_Clostridiales [Order]
Otu02935_Gammaproteobacteria [Class]
Otu10986_Spirochaetales [Order]
Otu04594_Arcobacter [Genus]
Otu02934_Marinomonas [Genus]
Otu07271_Bacteria [Kingdom]
Otu02936_Glaciecola [Genus]
Otu02952_Gammaproteobacteria [Class]
0
200
400
600
800
1000
1200
1400
1600
1800
Number of Sequences
Supplementary Fig. 7: Proportion of the most abundant bacterial OTUs found in pine during
the aquaria experiment. Abundant OTU are defined as OTUs with >1% sequence abundance in
at least 2 samples. The taxonomic assignation is based on the lowest annotated taxon. Sample
labels show the microhabitat (bark, top or center) and the time of incubation in months
(1,2,4,8 or 10).
Otu00748_Alphaproteobacteria [Class]
Otu04706_Flavobacteriaceae [Family]
Otu04707_Algibacter [Genus]
Otu00750_Rhodobacteraceae [Family]
Otu04712_Sulfurovum [Genus]
Otu00751_Dasania [Genus]
Otu02917_Methylophilaceae [Family]
Otu04714_Flavobacteriaceae [Family]
Otu04713_Flavobacteriaceae [Family]
Otu06518_Deltaproteobacteria [Class]
Otu02921_Arenicella [Genus]
Otu00755_Rhodobacteraceae [Family]
Otu02816_Betaproteobacteria [Class]
Otu07264_Puniceicoccaceae [Family]
Cen_can_oak7r1
Otu00754_Hyphomonadaceae [Family]
Otu02923_Haloferula [Genus]
Cen_can_oak7r2
Otu07275_Bacteria [Kingdom]
Otu07269_Bacteria [Kingdom]
Cen_can_oak7r3
Otu05640_Psychroserpens [Genus]
Cen_can_oak12r1
Otu00757_Rhizobiales [Order]
Otu07266_Arcobacter [Genus]
Cen_can_oak12r2
Otu05415_Flavobacteriaceae [Family]
Otu00756_Altererythrobacter [Genus]
Cen_can_oak12r3
Otu04593_Epsilonproteobacteria [Class]
Otu00747_Rhodobacteraceae [Family]
Cen_can_pin7r1
Otu02937_Rhodobacteraceae [Family]
Cen_can_pin7r2
Otu00752_Alphaproteobacteria [Class]
Otu00021_Hirschia [Genus]
Cen_can_pin7r3
Otu00781_Myxococcales [Order]
Otu05642_Bacteroidetes [Phylum]
Cen_can_pin12r1
Otu10986_Spirochaetes [Class]
Cen_can_pin12r2
Otu02935_Gammaproteobacteria [Class]
Otu07271_Glaciecola [Genus]
Cen_can_pin12r3
Otu04728_Flammeovirgaceae [Family]
Otu10414_Rhizobiales [Order]
Otu00754_Alphaproteobacteria [Class]
Otu07264_Bacteria [Kingdom]
Otu00763_Rhodobacteraceae [Family]
Otu04597_Rhodobacteraceae [Family]
Otu02934_Marinomonas [Genus]
Otu05647_Bacteroidetes [Phylum]
Otu02912_Altererythrobacter [Genus]
Otu04594_Arcobacter [Genus]
Otu02936_Marinomonas [Genus]
Otu02952_Gammaproteobacteria [Class]
0
100
200
300
400
500
600
700
Number of Sequences
Supplementary Fig. 8: Proportion of the most abundant bacterial OTUs found in the canyon
experiment. Abundant OTU are defined as OTUs with > 1% sequences abundance in at least 2
samples. The taxonomic assignation is based on the lowest annotated taxon. Sample labels
show the type of wood (oak or pine), the time of incubation in months (7 or 12), replicate
samples (r) and replicate number (1, 2, 3).
Otu1_Candidatus_Nitrosopumilus [Genus]
Otu8_RC-V [Environmental cluster]
Cen_can7r1_ARC
Otu13_LDS [Environmental cluster]
Cen_can7r2_ARC
Otu35_Methanococcoides [Genus]
Bar_aqu2_ ARC
Bar_aqu8_ ARC
Otu34_Marine group I [Environmental cluster]
Top_aqu1_ ARC
Otu448_Marine group I [Environmental cluster]
Top_aqu2_ ARC
Otu406_Marine group I [Environmental cluster]
0
200
400
600
800
1000
1200
1400
1600
Number of Sequences
Supplementary Fig. 9: Proportion of the most abundant archaeal OTUs found in oak during
the canyon and aquarium experiment. Abundant OTU are defined as OTUs with > 1%
sequences abundance in at least 2 samples. The taxonomic assignation is based on the lowest
annotated taxon. Sample labels show the type of wood (oak or pine), the time of incubation in
months (7 or 12), replicate samples (r) and replicate number (1, 2, 3).
Supplementary Fig. 10: Proportion of the most abundant fungal OTUs found in oak during the
canyon and aquarium experiment. Abundant OTU are defined as OTUs with > 1% sequences
abundance in at least 2 samples. The taxonomic assignation is based on the lowest annotated
taxon. Sample labels show the microhabitat (bark, top or center), the sample site (canyon or
aquarium) and the time of incubation in months (1,2, or 8).