Table S1 Primers used in PCR amplication of genes encoded antibiotics.
Primer
Sequence
G+C
(%)
Tm
(°C)
Position*
Phl2a
GAGGACGTCGAAGACCACCA
60
73
1915
Phl2b
ACCGCAGCATCGTGTATGAG
55
72
2660
PCA2a
TTGCCAAGCCTCGCTCCAAC
60
79
3191
PCA3b
CCGCGTTGTTCCTCGTTCAT
55
76
4341
PLTC1
AACAGATCGCCCCGGTACAGAACG
58.3
74.2
12282
PLTC2
AGGCCCGGACACTCAAGAAACTCG
58.3
73.8
12720
PRND1
GGGGCGGGCCGTGGTGATGGA
76.2
82.4
5269
PRND2
YCCCGCSGCCTGYCTGGTCTG
66.6
74.2
6055
PHZ1
GGCGACATGGTCAACGG
64.7
52.4
PHZ2
CGGCTGGCGGCGTATTC
70.6
* Position of the 5P-end of the primer in the database sequence.
57.3
1
Product
length (bp)
Reference
745
(Raaijmakers et al. 1997)
1150
(Raaijmakers et al. 1997)
438
(Souza and Raaijmakers 2003)
786
(Souza and Raaijmakers 2003)
1408
(Raaijmakers et al. 1997)
Table S2 Using ability of different carbon and nitrogen sources of endophytic bacterium and pathogenic fungus.
Only nutrient source
D-fructose
D-glucose
D-raffinose
xylose trehalose sucrose
ALEB 7B
+
+
+
+
−
−
+
SY4
+
+
+
+
+
+
+
Only nutrient
source
L-histidine
L-alanine
L-serine
L-arginine
L-glutamic
ALEB 7B
−
+
+
+
SY4
+
+
−
+
acid
D-melibiose
L-phenylalanine
L-prolina
L-threonine
L-leucine
L-methionine
+
+
+
+
+
+
+
−
+
+
+
+
2
Figure S1 Results of agarose gel electrophoresis and plate spread using tissue homogenates of
seedlings with / without inoculation. (a) Agarose gel electrophoresis of 16S rDNA fragments
amplified using tissue homogenates of seedlings with / without endophytic bacterial
inoculation as models. (b) Plate spread with tissue homogenates of sterile seedlings. (c) Plate
spread with tissue homogenates of seedlings inoculated with endophytic bacterium P.
fluorescens. (d) Plate spread with tissue homogenates of seedlings inoculated with pathogenic
fungus A. rolfsii SY4.
3
Figure S2 Designs of different experimental systems. (a) Design of the co-culture of
endophytic P. fluorescens ALEB 7B and pathogenic A. rolfsii SY4. (b) Design of the co-culture
system to test effects of volatile organic compounds from endophytic P. fluorescens ALEB 7B
on pathogenic A. rolfsii SY4.
4
Figure S3 Gas chromatograms of standard substances and VOCs / dichloromethane (DCM)
extracts of LB medium and P. fluorescens ALEB 7B. (a) Gas chromatogram of VOCs from LB
agar. (b) Gas chromatogram of VOCs released by P. fluorescens ALEB 7B. Number 1 shows
the peak of dimethyl disulfide (DMDS) and number 2 shows the peak of 1-undecene. (c) Gas
chromatograms of DMDS and 1-undecene. (d) Gas chromatogram of DCM extracts of LB
broth. (e) Gas chromatogram of DCM extracts of P. fluorescens ALEB 7B cell-free culture
filtrates. Arrow shows the peak of 2-piperidinone. (f) Gas chromatogram of 2-piperidinone.
5
Figure S4 Phylogenetic position, colonial morphology, sclerotia and hyphal characteristics of
A. rolfsii SY4. (a) The dendrogram of A. rolfsii SY4 constructed based on the 18S rDNA
sequence. The dendrogram are generated by the neighbor-joining method. The bar indicates
sequence divergence and present bootstrap values of more than 50% (from 1,000 replicates) are
indicated at the nodes. (b) The colony morphology of A. rolfsii SY4. (c, d) The color of
sclerotia turns white to dark brown by the time. (e) Mycelial characteristics of A. rolfsii SY4
amplifying 20 times. Scale bar = 20 μm.
6
Figure S5 The phylogenetic position of endophytic bacterium ALEB 7B. Dendrograms are
constructed based on sequences of 16S rDNA (a), rpoD (b) and gyrB (c) genes, separately.
Dendrograms are generated by the neighbor-joining method. Xanthomonas campestris pv.
campestris is used as an outgroup in dendrograms based on rpoD and gyrB genes. The bars
indicate sequence divergence and present bootstrap values of more than 50% (from 1,000
replicates) are indicated at nodes.
7
Figure S6 Inhibitory effect of DMDS and 1-undecene on A. rolfsii colony growth. (a, b) A.
rolfsii colony diameters after exposure to different amounts of DMDS and 1-undecene. (c, d) A.
rolfsii colony morphology after exposure to different amounts of DMDS and 1-undecene.
8
Figure S7 Inhibitory effect of 2-piperidinone on colony growth of A. rolfsii. (a) A. rolfsii
colony diameters when exposed to different amounts of 2-piperidinone. (b) A. rolfsii colonial
morphologies when exposed to different amounts of 2-piperidinone.
9
Figure S8 Agarose gel electrophoresis of potential genes encoded antibiotics and the
dendrogram constructed based on phlD gene. (a) Agarose gel electrophoresis of potential genes
encoded antibiotics. The first lane and the last lane are DNA ladders. White arrows point the
bands in the proper size. The PCR process and detection of each antibiotic repeat 3 times. (b)
The dendrogram constructed based on gene phlD. The dendrograms is generated by the
neighbor-joining method. The bars indicate sequence divergence. Present bootstrap values of
more than 50% (from 1,000 replicates) are indicated at nodes.
10
Figure S9 Transparent zones formed by ALEB 7B in cell wall degradation enzyme-producing
and siderophore-production ability detecting mediums. Transparent zones can be observed on
detecting medium of starch (a), xylan (b), carboxymethyl cellulose (c), and pectin (d). A
yellow-orange halo around the colony of ALEB 7B indicates its siderophore production ability
(e).
11
References
Raaijmakers, J.M., Weller, D.M., Thomashow, L.S. (1997) Frequency of antibiotic-producing
Pseudomonas spp. in natural environments. Appl Environ Microb 63, 881-887.
Souza, J.T., Raaijmakers, J.M. (2003) Polymorphisms within the prnD and pltC genes from
pyrrolnitrin and pyoluteorin-producing Pseudomonas and Burkholderia spp. FEMS
Microbiol Ecol 43, 21-34.
12