Supplementary data
Table S1: Data related to the number of 16S rRNA PCR sequences.
Bulk soil
Rhizosphere
C1BS
C2BS
C3BS
C1R
C2R
C3R
N° of 16S rDNA sequences
50609
56025
62022
42925
37358
52948
Maximum read length (bp)
362
323
315
322
308
304
Shortest read length (bp)
250
250
250
250
250
250
Average read length (bp)
265
266
266
264
265
264
Table S2: Estimate of the number of sequences required to reach the plateau
OTUsMin* observed OTUs observed OTUs estimated (Chao1) Estimated number of sequences **
Low 95%
Up 95%
C1BS
8,281
9,872
18,365
484,079
942,174
C1R
4,886
5,264
9,738
264,745
458,860
C2BS
7,752
9,740
17,882
414,744
692,231
C2R
7,550
7,551
14,191
220,909
333,102
C3BS
5,178
6,830
12,570
399,458
670,394
C3R
5,619
6,843
12,995
444,985
923,719
* OTUs
Min:
OTUs observed when the numbers of sequences were normalized with the sample harboring the
smallest number of sequences (C2R= 37358 sequences).
** the theoretical number of sequences required to reach the plateau was generated by combining the observed
number of OTUs, the observed number of sequences and the theoretical number of OTUs (obtained with nonparametric Chao1 estimate ; lower and upper 95% confidence intervals). The theoretical number of sequences
(bold) was obtained using linear equations as presented in figure S2 for the C2BS sample.
Table S3: Number of sequences classified to be within known mineral weathering bacterial genera
For each group, the number of sequences was evaluated at a 80% confidence threshold (bold upper value). The
three independent samples are presented as follow: C1, C2 and C3. BS: bulk soil; R: rhizosphere. For each
functional bacterial genus, a one-factor ANOVA (relative distribution values) and a Bonferroni-Dun test (p=0.05)
were performed on the relative distribution values. Statistical analysis showed that there was significantly more
Burkholderia (p=0.008) and Collimonas (p=0.045) in the rhizosphere than in the bulk soil.
C1
C2
C3
BS
R
BS
R
BS
R
Burkholderia
431
1045
567
971
622
870
Collimonas
4
22
4
6
3
12
Mineral weathering bacteria
Table S4: The ten most abundant genera in each of the six soils sampled as percent of total sequences
from each soil.
Bulk soil
Rhizosphere
Phylum
Statistic
Genus
C1
C2
C3
C1
C2
C3
Acidobacterium
28.83
27.87
24.55
25.57
28.67
21.95
Acidobacteria
n.s.
Rhodoplanes
6.88
7.58
7.05
5.57
5.02
6.08
Alphaproteobacteria
P=0.0132 (BS>R)
Bradyrhizobium
3.34
3.54
4.22
4.06
3.42
4.56
Alphaproteobacteria
n.s.
Burkholderia
1.12
1.2
1.19
2.84
3.08
1.96
Betaproteobacteria
P=0.008 (R>BS)
Alterococcus
0.26
0.28
1.4
2.57
0.55
2.18
Gammaproteobacteria
n.s.
Chitinophaga
0.73
0.88
1.36
1.51
1.36
1.57
Bacteroidetes
n.s.
Mycobacterium
1.82
3.19
1.21
1.5
2.1
1.26
Actinobacteria
n.s.
Conexibacter
1.46
1.19
1.62
1.3
1.1
1.5
Actinobacteria
n.s.
Gemmatimonas
1.24
0.76
1.73
1.22
0.9
0.98
Gemmatimonadetes
n.s.
Spirillospora
0.55
0.41
0.77
0.92
0.76
0.91
Actinobacteria
n.s.
0.17
0.2
0.17
0.19
0.23
0.95
Planctomycetes
0.87
0.79
1
0.8
0.55
0.69
Actinobacteria
Planctomyces
Acidimicrobium
n.s.
n.s.
Titles and legends to fgures of the supplementary data:
Figure S1 : Number of OTUs and Richness estimators
a. Number of OTUs obtained. b. Shannon estimate; c. Chao1 estimate. The number of OTUs was determined
using the RDP pyrosequencing pipeline. The non-parametric estimates were calculated using the EstimateS
package. No significant differences were observed for any of these observed or theoretical indexes according to
a one-factor ANOVA and the Bonferroni-Dun test (p=0.05). The solid circles and the open squares present bulk
soil and Rhizosphere samples respectively.
Figure S2: Presentation of the inverse values of the number of observed sequences and observed OTUs
from C2BS sample. The last hundred values observed (OTUs and sequences) and presented in figure 1, were
used to draw this graph. From this graph a linear regression was generated and a linear equation (y=ax+b) was
obtained. The same approach was performed for each sample. For each sample, a linear equation was
generated.
Figure S3: Relative clone frequencies in Proteobacteria groups of the sequences from the oak
rhizosphere and the surrounding soil. Soil samples are presented as follow at field-scale (C1, C2 and C3) and
at micro-scale (BS: bulk soil and R: rhizosphere). One factor ANOVA (p=0.05) and a Bonferroni-Dun test
performed on the relative distribution values evidenced that there was significantly more -,- and unclassifiedproteobacteria in the rhizosphere than in the bulk soil. -proteobacteria, p=0.0071 (R>BS); -proteobacteria,
p=0.0482 (R>BS); unclassified-proteobacteria, p=0.0166 (R>BS).