1
Supplementary information
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Legends of supplementary figures
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Fig. S1. Relative abundances of the dominant fungal (a) and bacterial (b) phylotypes,
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and their major variations in soil rhizosphere of cotton seedlings (Zhong-38 and
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NAU-10) grown in two different monocropped soils and control soil. Relative
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abundances are calculated as the percentage of individual taxa to the total number
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of 16S rRNA gene or ITS sequence reads respectively. CK, control soil without cotton
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cropping event; CC4, soil cropped with cotton for 4 years; CC15, soil cropped with
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cotton for 15 years. Others comprise of all the rare remaining taxa.
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Fig. S2. Redundancy analysis (RDA) performed on the representative fungal (a) and
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bacterial (b) taxa and the underlying cotton growth. Arrows indicate the correlation
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between the taxa abundance and cotton growth. Tinctorial symbols on the plots
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indicate the growth status of cotton, which was determined based on the plant
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growth parameters and disease indices. CK, control soil without cotton cropping
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event; CC4, soil cropped with cotton for 4 years; CC15, soil cropped with cotton for
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15 years. The figure showed that most rhizosphere fungal taxa were associated with
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cotton grown in monocropped soils, of which the abundance of S. chartarum, V.
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dahliae, A. sclerotigenum, F. oxysporum f. sp. vasinfectumand F. merismoides var.
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merismoides had the strongest correlation (a). In comparison, most rhizobacterial
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taxa contributed to the growth performance of both cotton varieties grown in the
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control soil, of which the abundance of Xanthomonadaceae, Comamonadaceae,
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Oxalobacteraceae and Opitutaceae made the strongest contribution. But few
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rhizobacterial taxa appeared to be correlated with the growth performance of cotton
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grown in monocropped soils, in which the abundance of Flavobacteriaceae,
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Sphingomonadaceae and Streptomycetaceae had the strongest correlation (b).
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Fig. S3. Effects of root exudates of Zhong-38 and NAU-10 seedlings on the sporulation
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(a) and spore germination (b) of F. oxysporum. The mean values and standard errors
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of three replicates are presented. Significant differences of variable means are
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indicated by different letters (P < 0.05).
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Table S1. PCR conditions and primers used for the majority of amplifications
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Primer
Primer sequence
Target gene
Thermal Profile
Reference
Name
ITS5
95 °C for 10 min; 35 cycles of
5’-TCCTCCGCTTATTGATATGC-3’
Soil fungi
95 °C for 1 5 s, 52 °C for 30 s,
Schoch et al.,
and 72 °C for 1.5 s; 72 °C for
2012
ITS1+ITS2
ITS4
5’-GGA AGTAAAAGTCGTAACAAGG-3’
7 min; and 4 °C on hold
Soil
bacteria
515F
806R
5’-GTGCCAGCMGCCGCG G-3’
5’-CCGTCA ATTCMTTTRAGTTT-3’
Universal
94°C for 3min; 32 cycles of 94°C for
16S rRNA
45s, 50°C for 60s, and 72°C for 90s;
genes
72°C for 10min; and 4 °C on hold
Caporaso et al.,
2011
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Table S2. Results of two-factorial analyses of variance on differences of the main
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phylotypes among the rhizosphere soils and cotton varieties. Degrees of freedom
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were 2 for cotton and 3 for soil (n=18). F- and p-values and associated are listed.
Taxa
Factors
Soilb
F values
p values
3.142
0.075
15.929
0.001
Soil
1.000
0.393
Cotton
0.250
0.625
51.888
0.000
1.301
0.273
36.106
0.000
Cotton
1.092
0.314
Soil
6.938
0.008
Cotton
47.320
0.000
Soil
11.961
0.001
Cotton
9.315
0.009
Soil
9.333
0.003
Cotton
5.250
0.038
Soil
1.366
0.287
Cotton
0.085
0.774
Soil
0.203
0.163
Cotton
0.654
0.651
72.711
0.000
1.268
0.293
60.608
0.000
3.559
0.096
Gammaproteobacteria
Cottona
Deltaproteobacteria
Soil
Betaproteobacteria
Cotton
Soil
Alphaproteobacteria
Actinobacteria
Bacteroidetes
Verrucomicrobia
Firmicutes
Acidobacteria
Soil
Sordariomycetes
Cotton
Soil
An uncultured fungus
Cotton
4
Soil
9.300
0.008
14.628
0.005
Dothideomycetes
Cotton
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Note: a “soil” denotes comparison among the three soils; b “cotton” denotes
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Zhong-38 vs. NAU-10.
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Table S3. Results of one-way ANOVA on the means of the main fungal and bacterial
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phylotypes of both cotton varieties among the monocropped and control soils.
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Degrees of freedom were 3 for soil (n=18). F- and p-values and associated are listed.
F2,17
p
*
F2,17
p
values
values
76.9
<0.001
7.5
0.006
10.2
0.002
23.5
<0.001
23.9
<0.001
*
Fungal Taxa
Bacterial Taxa
values
values
Stachybotrys chartarum
46.3
<0.001
F. oxysporum f. sp. vasinfectum
7.4
0.006
Sphingomonadaceae
A taxon within
Sphingomonadales
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Verticillium dahliae
18.7
<0.001
Rhizobiaceae
Acremonium sclerotigenum
86.5
<0.001
F. solani
5.5
0.016
Pyrenochaetopsis decipiens
20.9
<0.001
Methylophilaceae
23.2
<0.001
Bionectria ochroleuca
3.8
0.047
Rhodocyclaceae
5.8
0.014
F. merismoides var. merismoides
25.1
<0.001
Xanthomonadaceae
24.6
<0.001
Acremonium charticola
43.4
<0.001
Alteromonadaceae
4.2
0.035
F. equiseti
20.0
<0.001
Opitutaceae
4.1
0.038
Glomerales
31.6
<0.001
Verrucomicrobiaceae
5.0
0.022
Streptomycetaceae
5.0
0.022
Flavobacteriaceae
6.1
0.012
Comamonadaceae
Oxalobacteraceae
Note: * denotes comparisons among the three soils.
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Table S4 Spearman’s correlations between the components of root exudates and the
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main taxa in cotton rhizosphere soil
Verticillium
Fusarium oxysporum
dahliae
f. sp. vasinfectum
Xanthomonadaceae
Components
Comamonadaceae
Oxalobacteraceae
r
p
r
p
r
p
r
p
r
p
Glucose
-0.886
0.019
-0.657
0.156
0.429
0.397
0.657
0.156
0.657
0.156
Fructose
-0.429
0.397
-0.886
0.019
0.771
0.072
0.543
0.266
0.886
0.019
Vanillic acid
-0.200
0.704
-0.657
0.156
0.600
0.208
0.486
0.329
0.657
0.156
Ferulic acid
-0.543
0.266
-0.943
0.005
0.829
0.042
0.714
0.111
0.943
0.005
Asp
0.257
0.623
0.486
0.329
-0.314
0.544
-0.771
0.072
-0.486
0.329
Glu
0.543
0.266
0.829
0.042
-0.771
0.072
-0.100
0.000
-0.829
0.042
Gly
0.714
0.111
0.771
0.072
-0.714
0.111
-0.943
0.005
-0.771
0.072
Ala
0.771
0.072
0.829
0.042
-0.657
0.156
-0.771
0.072
-0.829
0.042
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Note: Significance was at p<0.05
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Fig. S1
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Fig. S2
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Fig. S3
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