RESEARCH ARTICLE

In vitro antagonists of Rhizoctonia solani tested on lettuce:

rhizosphere competence, biocontrol e⁄ciency and rhizosphere
microbial community response
Modupe F. Adesina1, Rita Grosch2, Antje Lembke1, Tzenko D. Vatchev3 & Kornelia Smalla1
1
Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany; 2Institute for Vegetables and Ornamental Crops
(IGZ), Großbeeren, Germany; and 3Department of Plant Pathology and Immunology, Plant Protection Institute, Sofia, Bulgaria

Correspondence: Kornelia Smalla, Julius Abstract

Kühn-Institut – Federal Research Centre for
Cultivated Plants (JKI), Messeweg 11/12,
D-38104 Braunschweig, Germany. Tel.: 149
531 299 3814; fax: 149 531 299 3006;
e-mail: kornelia.smalla@jki.bund.de
Received 30 July 2008; revised 18 March 2009;
accepted 24 March 2009.
Final version published online June 2009.
DOI:10.1111/j.1574-6941.2009.00685.x
Editor: Jim Prosser
Keywords
Rhizoctonia solani; antagonists; lettuce;
rhizosphere competence; biocontrol; microbial
communities.
The rhizosphere competence of 15 in vitro antagonists of Rhizoctonia solani was
determined 4 weeks after sowing inoculated lettuce seeds into nonsterile soil.
Based on the colonization ability determined by selective plating, eight strains were
selected for growth chamber experiments to determine their efficacy in controlling
bottom rot caused by R. solani on lettuce. Although in the first experiment all
antagonists colonized the rhizosphere of lettuce with CFU counts above 2  106 g 1
of root fresh weight, only four isolates significantly reduced disease severity. In
subsequent experiments involving these four antagonists, only Pseudomonas
jessenii RU47 showed effective and consistent disease suppression. Plate counts
and denaturing gradient gel electrophoresis (DGGE) fingerprints of Pseudomonas-
specific gacA genes amplified from total community DNA confirmed that RU47
established as the dominant Pseudomonas population in the rhizosphere of
inoculated lettuce plants. Furthermore, the DGGE fingerprint revealed that
R. solani AG1-IB inoculation severely affected the bacterial and fungal community
structure in the rhizosphere of lettuce and that these effects were much less
pronounced in the presence of RU47. Although the exact mechanism of antag-
onistic activity and the ecology of RU47 remain to be further explored, our results
suggest that RU47 is a promising agent to control bottom rot of lettuce.

stitute or a supplement to reduce the use of chemical

Introduction
Rhizoctonia solani Kühn, the anamorph of Thanatephorus
cucumeris (Frank) Donk, is a widespread soil-borne fungus
comprising plant parasitic or saprophytic strains (Ogoshi,
1987; González Garcı́a et al., 2006). The species affects many
important agricultural and horticultural crops worldwide,
causing diseases such as black scurf, crown rot and bottom
rot (Ogoshi, 1996). The control of the pathogen is difficult
because of its wide host range and its ability to survive as
sclerotia under adverse environmental conditions. In prac-
tice, the control of diseases caused by R. solani relies mainly
on fungicides (Kataria & Gisi, 1996). However, increasing
concern about the health and environmental hazards asso-
ciated with the use of agrochemicals has resulted in the
search for viable alternatives. Hence, biological control
involving the use of microorganisms that can suppress or
antagonize plant pathogens is being considered as a sub-
pesticides (Sweetingham, 1996; Compant et al., 2005). Over
the last decades, bacteria with the ability to suppress
R. solani have been isolated from different soils (Weller
et al., 2002; Faltin et al., 2004; Garbeva et al., 2004; Berg
et al., 2005; Adesina et al., 2007). However, many studies
have reported variabilities in the performance of biological
control agents (BCA) and lack of a correlation between in
vitro inhibition tests and the field performance of BCA
(Milus & Rothrock, 1997; Schottel et al., 2001). It is assumed
that the major contributors to this inconsistency in planta
are the inherent characteristics of the BCA such as poor root
colonization or insufficient production of antifungal meta-
bolites at the pathogen infection sites due to variable
expression of genes involved in disease suppression (Raaij-
makers & Weller, 2001; Haas & Défago, 2005; Raaijmakers
et al., 2008). Recently, the application of molecular
DNA-based methods contributed toward an improved

c 2009 Federation of European Microbiological Societies FEMS Microbiol Ecol 69 (2009) 62–74
Published by Blackwell Publishing Ltd. All rights reserved
Biocontrol of Rhizoctonia solani and rhizosphere competence
understanding of the ecology of BCA in the rhizosphere
where the BCA interact not only with the plant and the
pathogen but also with the indigenous microbial commu-
nity (Götz et al., 2006; Scherwinski et al., 2008).
In this study, 15 strains were selected from a collection of
bacterial isolates with in vitro antagonistic activity towards
R. solani AG3 (the causal agent of black scurf on potato) and/
or Fusarium oxysporum (which causes wilting disease in
diverse crops), which were previously isolated and character-
ized (Adesina et al., 2007). The in vitro antagonists that
originated from four disease-suppressive soils located in
France, the Netherlands, Sweden and the United Kingdom
were first screened for their ability to colonize the rhizosphere
of lettuce in nonsterile soil. Based on their colonization ability,
eight strains were selected for growth chamber experiments.
The work presented here aimed to investigate the potential of
the in vitro antagonists to suppress bottom rot disease caused
by R. solani AG1-IB on lettuce plants in vivo (growth chamber
experiments) and to study the survival and root colonization
efficiency of the antagonists by means of selective plating. The
abundance of the most promising antagonist and the response
of the indigenous fungal and bacterial communities in the
rhizosphere to plant inoculation were evaluated by cultiva-
tion-independent molecular fingerprints. This is one of the
few studies assessing not only biocontrol efficiency but also
the survival of the bacterial inoculants and effects on the
indigenous microbial communities.
Materials and methods
Bacterial and fungal strains
Fifteen out of 248 antagonists isolated from four suppressive
soils (Adesina et al., 2007) were selected on the basis of
either their (1) strong in vitro activity against R. solani AG3
(isolate Ben3; host plant, potato) or (2) activity towards
both R. solani AG3 and F. oxysporum (isolate Foln3; host
plant, flax). All bacterial antagonists used in this study were
maintained on R2A agar (Difco, Detroit, MI). Rhizoctonia
solani AG1-IB (isolate 7/3; host plant, lettuce) and AG2
(isolate W4; host plant cabbage) were obtained from the
strain collection of the Institute for Vegetables and Orna-
mental Crops, Großbeeren, Germany) and maintained on
Waksman agar containing 5 g of proteose-peptone (Merck,
Darmstadt, Germany), 10 g of glucose (Merck), 3 g of meat
extract (Chemex, München, Germany), 5 g of NaCl (Merck),
20 g of agar (Difco), and distilled water (to 1 L) (pH 6.8).
Generation of antibiotic-resistant mutants
To facilitate reisolation of the bacterial inoculants from the
rhizosphere, spontaneous rifampicin-resistant mutants of the
bacterial antagonists were generated by plating overnight
cultures onto R2A agar supplemented with rifampicin
FEMS Microbiol Ecol 69 (2009) 62–74
63
(75 mg mL 1). The 15 rifampicin-resistant mutant strains were
tested for inhibitory activity against two highly pathogenic
isolates belonging to the R. solani anastomosis groups AG1-IB
and AG2 (Faltin et al., 2004; Grosch et al., 2004). In vitro
inhibitory activity against R. solani AG1-IB and AG2 was
determined essentially as described by Adesina et al. (2007).
The mutant strains were stored at 80 1C in Luria–
Bertani broth (ROTH, Germany) containing 20% glycerol
supplemented with rifampicin (75 mg mL 1).
Lettuce rhizosphere colonization assays
To determine the rhizosphere competence of the 15 rifam-
picin-resistant strains, rhizosphere colonization assays were
performed in nonsterile soil under greenhouse conditions.
Lettuce seeds (cultivar ‘Tizian’, Syngenta, Bad Salzuflen,
Germany) were surface sterilized in 2% sodium hypochlor-
ite (NaOCl) for 5 min, followed by three subsequent wash-
ing steps with sterile distilled water. The seeds were
pregerminated on sterile moistened filter papers in sterile
Petri dishes for 2 days at room temperature. Pregerminated
lettuce seeds were soaked in a cell suspension (cell concen-
tration adjusted to c. 109 cells mL 1) of each bacterial
antagonist for 1 h. Four pregerminated and inoculated seeds
per pot were sown into nonsterile potting soil [turf sub-
strate/clay granulate No. 4230, Klasmann-Deilmann GmbH,
Geeste, Germany, sieved (2-mm mesh width) and mixed
with 80% (w/w) sand]. The pots were kept in the greenhouse
at 20 1C and 30% humidity. Each treatment was replicated
three times. Four weeks after sowing, the plants were care-
fully removed from the soil and vigorously shaken. The
roots with adhering soil were placed in a Stomacher plastic
bag and processed after adding sterile saline mechanically by
Stomacher blending for 3 min at high speed. CFU of the
inoculant per gram of root fresh weight (rfw) were deter-
mined by plating serial dilutions of the rhizosphere suspen-
sions on R2A supplemented with rifampicin (75 mg mL 1)
and cycloheximide (100 mg mL 1). The CFU were counted
after 2 days of incubation at 28 1C.
Growth chamber experiments
Based on the results of the rhizosphere colonization assays,
eight antagonistic isolates with the ability to colonize lettuce
roots at cell densities of approximately log CFU 4 4 g 1 of
rfw or more were selected for the growth chamber experi-
ments. The efficacy of eight antagonistic isolates in control-
ling bottom rot disease caused by R. solani AG1-IB on
lettuce plants (cultivar ‘Tizian’) was assessed under favor-
able conditions for the pathogen in the growth chamber
(York, Mannheim, Germany; 16 h/8 h day/night cycle,
500 mmol m 2 s 1, 20/15 1C and 60%/80% relative humid-
ity). In experiment 1, all eight in vitro antagonists were
evaluated. Four isolates with the best disease suppression
c2009 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
64
were included in experiments 2 and 3, while only two
isolates with the best results in experiments 1 and 2 were
assessed in experiment 4. In experiment 3, the effect on plant
growth was determined based on lettuce shoot and root dry
weight, in treatments without pathogen inoculation.
Seeds were treated with bacterial antagonists directly before
sowing. Each antagonist was grown overnight on nutrient agar
supplemented with rifampicin at 75 mg mL 1. Overnight-
grown colonies were resuspended in a sterile 0.3% NaCl
solution and shaken to obtain a homogeneous cell suspension.
The concentration was adjusted in a spectrophotometer to a
density corresponding to c. 109 CFU mL 1. Lettuce seeds were
soaked in the bacterial suspension for 1 h at room temperature.
Seeds that were incubated in sterile saline for the same time
served as a control. Seeds were germinated in a seedling tray
containing 92 holes filled with a nonsterile mixture of quartz
sand and substrate [Fruhsdorfer Einheitserde Typ P, Germany;
chemical analysis (mg per 100 g): N = 75, P = 75, K = 125;
pH 5.9] at a 1 : 1 ratio (v/v). Lettuce plantlets were transferred
at the two- to three-leaf stage to pots filled with the same soil
mixture with one plant per pot. Drenching of lettuce plants
with bacterial antagonists was carried out 24 h after transplant-
ing. Each plant of the treatment inoculated with RU47 and
R. solani (RU471Rs) was drenched with 20 mL of the bacterial
suspension (107 CFU mL 1) and the noninoculated healthy
control (Ctrl) and inoculated with R. solani (Ctrl1Rs) treat-
ments received 20 mL of sterile saline. The pathogen was added
on barley kernels infested with the R. solani AG1-IB (isolate 7/3;
Schneider et al., 1997) 1 day after drenching the plants with
bacterial antagonists. Five kernels per lettuce seedling were
placed 1 cm deep at a distance of 2 cm from the lettuce plant.
Noninfested barley kernels were added to the control treat-
ments accordingly. The pots were watered daily to maintain the
substrate moisture. Each treatment consisted of six replicates
(four pots per replicate) arranged in a randomized design. Nine
additional pots (three plants per time point and treatment)
were included for microbial analysis.
Suppression of bottom rot disease by bacterial
inoculants
Seven weeks after sowing (4 weeks after pathogen inocula-
tion), the experiments were terminated and a total of 24
plants were evaluated for suppression of bottom rot disease
of R. solani AG1-IB based on (1) the disease incidence and
on (2) the effect on the shoot dry weight (SDW). The disease
incidence was assessed by recording the number of plants
with visual symptoms or the number of dead plants. The
shoot dry weight of each lettuce plant was measured.
Root colonization by bacterial inoculants
To determine the survival and root colonization efficiency
of the inoculated antagonists, rhizosphere samples were
collected at three time points: 3, 5 and 7 weeks after sowing.
c 2009 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
M.F. Adesina et al.
For each treatment and sampling time three symptomless
plants were used. Loosely adhering soil was removed from
the roots by shaking the plants. Five grams of roots with
adhering soil were suspended in 20 mL of sterile saline and
shaken vigorously in sterile flask containing six glass beads
(0.6 mm in diameter) on a rotary shaker for 1 h at 307 r.p.m.
Aliquots of the rhizosphere suspension were immediately
processed for enumeration of the inoculated strains. Serially
diluted rhizosphere suspensions were plated on R2A med-
ium (Difco) supplemented with rifampicin (75 mg mL 1)
and cycloheximide (100 mg mL 1). The remaining rhizo-
sphere suspension was centrifuged at 13 000 g for 5 min.
After discarding the supernatants, the cell pellets were stored
frozen at 20 1C.
The ability of the most promising antagonist RU47 to
colonize the vascular tissue of lettuce roots and leaves was
determined at 7 weeks after sowing in experiment 3. Roots
from the inoculated plants were shaken to remove loosely
adhering soils and washed in running water. One gram of
the washed roots or leaves were soaked in 1% sodium
hypochlorite for 1 min. Surface-sterilized root or leaf sam-
ples were rinsed four times with sterile distilled water and
macerated using a sterile mortal and pestle. The suspensions
of the macerated roots or leaves were serially diluted and
plated as mentioned above.
DNA extraction from rhizosphere samples
Total community (TC)-DNA was obtained from the rhizo-
sphere pellets by means of the Bio101 extraction kit
(Q.BIOgene, Carlsbad, CA) after a harsh lysis step. The TC-
DNA was purified using the GENECLEAN Spin kit (Q.BIO-
gene). DNA yields were estimated after electrophoresis in
1% agarose gel stained with ethidium bromide under UV
light in comparison with the 1-kb gene-rulerTM DNA
ladder (Fermentas, St Leon-Rot, Germany) run on the same
agarose gel. Depending on the yield of the extracted TC-
DNA, dilutions were made with sterile milliQ water between
1 : 50 and 1 : 100 (c. 1–5 ng) and were used as a template for
PCR amplification of bacterial 16S rRNA gene fragments.
Undiluted TC-DNA, or 1 : 10 dilutions (c. 20 ng DNA)
served as a template for PCR of fungal 18S rRNA gene
fragments.
PCR amplification of 16S and 18S rRNA and gacA
gene fragments for denaturing gradient gel
electrophoresis (DGGE) analysis
To amplify the 16S rRNA gene fragments of Pseudomonas
from TC-DNA the nested PCR system described by Milling
et al. (2004) was used. Diluted amplicons obtained from the
first PCR served as templates for a second PCR using the
bacterial primers F984-GC/R1378 and PCR conditions
described by Heuer et al. (1997). To generate bacterial
FEMS Microbiol Ecol 69 (2009) 62–74
Biocontrol of Rhizoctonia solani and rhizosphere competence
community fingerprints, the latter primer system and
conditions were used to directly amplify 16S rRNA gene
fragments from TC-DNA. Amplification of the Pseudomonas-
specific gacA gene fragment (575 bp) was performed
using the nested PCR approach described by Costa et al.
(2007). Amplification of 18S rRNA gene fragments
(1650 bp) was done using the primer pair NS0/EF3
(Messner & Prillinger, 1995; Smit et al., 1999) in a first PCR
assay, followed by a second PCR step with the primer pair
NS1/FR1GC (White et al., 1990; Vainio & Hantula, 2000).
The PCR conditions used were described by Costa et al.
(2006).
DGGE
DGGE analysis was performed using the Dcode System
apparatus (Bio-Rad Inc., Hercules, CA). The polyacrylamide
gel was a gradient gel containing 9% (fungi) or a double
gradient gel of 6–9% (bacteria, Pseudomonas and gacA)
acrylamide with a denaturant gradient of 18–38%
(fungi) or 26–58% (bacteria, Pseudomonas and gacA) of
denaturants according to Gomes et al. (2005) (where 100%
denaturants contain 7 M urea and 40% formamide). Ali-
quots of PCR samples (2–4 mL) were applied to the DGGE
gels, and the run was performed in 1  Tris-acetate-EDTA
buffer at 58 1C with a constant voltage of 220 V for 6 h
(bacteria, Pseudomonas, gacA) or 180 V for 18 h (fungi). The
DGGE gels were silver stained, according to Heuer et al.
(2001).
Cluster analysis of DGGE fingerprints
Fungal, bacterial, Pseudomonas and gacA-based Pseudomonas
DGGE community fingerprints were analyzed using the
software package GELCOMPAR II version 5.6 (Applied Maths,
Kortrijk, Belgium). Background was subtracted using a
rolling disk method with an intensity of 10 (relative units),
and the lanes were normalized.
A dendrogram was constructed by the Pearson correlation
index for each pair of lanes within a gel and cluster analysis
by the unweighted pair group method using arithmetic
averages (UPGMA).
Statistical analysis
The STATISTICA program (StatSoft Inc., Tulsa, OK) was used
for the statistical analysis. The CFU data of bacterial counts
per gram rfw were logarithmically (log10) transformed
before statistical analysis. The data on inoculants’ densities,
plant shoot and root dry weight were analyzed after ANOVA
using Tukey’s test procedure (HSD) with P = 0.05.
FEMS Microbiol Ecol 69 (2009) 62–74
65
Results
In vitro activity of antagonists and colonization
of lettuce root
To facilitate monitoring of the 15 in vitro antagonistic
strains by selective plating, rifampicin-resistant mutants
were generated for all antagonists. The ability of the 15
in vitro antagonists to colonize the roots of lettuce plants
was determined 4 weeks after sowing inoculated pregermi-
nated lettuce seeds into nonsterile soil. Eight strains with
CFU counts 4 4  103 g 1 rfw were selected for subsequent
growth chamber experiments. The in vitro antagonistic
activities of these eight strains towards representatives of
the R. solani anastomosis groups AG1-IB (host plant,
lettuce), AG2 (host plant, sugar beet) and AG3 (host plant:
potato) are given in Table 1. Five antagonists (KS16, KS90,
KS70, KS74 and KF36) showed strong in vitro inhibitory
activity against R. solani AG1-IB (the model pathogen used
in this study for the growth chamber experiments) with
inhibition zones larger than 6 mm while strain RN86
expressed a moderate inhibitory activity of o 6 mm zone
of inhibition. Only Serratia marcescens AFNS31 and Pseudo-
monas jessenii RU47 displayed weak activity against R. solani
AG1-IB with inhibition zones o 3 mm after 5 days of
incubation. Information on the identity of the strains
selected for the growth chamber experiment, their in vitro
antagonistic activity and their secondary metabolite pro-
duction is given in Table 1.
Survival of the antagonists in the rhizosphere
of lettuce plants under growth chamber
conditions
Although similar cell densities of bacterial suspension were
used for seed inoculation (c. 109 mL 1), the cell densities of
antagonists on the seed surfaces showed remarkable differ-
ences and were in the range of 8  104– 8  107 CFU per seed
(data not shown). However, the bacterial inoculants actively
colonized the lettuce roots. The CFU counts of the inoculant
strains determined 3 weeks after sowing ranged between
2  106 and 6  107 CFU g 1 rfw (Table 2) and decreased
for all antagonists during the time course of the experiment
about one order of magnitude, except for KS16, which
slightly increased in experiment 1 (Table 2).
At the end of experiment 1, the CFU counts per gram of
lettuce rfw were not significantly different for the antago-
nists RU47, KF36, KS16, KS74 and KS90 (Table 2). Compar-
able results were obtained in experiment 2, which was
performed only with four of these isolates (RU47, KF36,
KS16 and KS74). Despite their good ability to colonize the
rhizosphere, the in vitro antagonists KS70, AFNS31 and
RN86 failed to control the pathogen in experiment 1.
c 2009 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
66 M.F. Adesina et al.

R. solani AG1-IB R. solani AG2 R. solani AG3 F. oxysporum Protease Glucanase Cellulase Chitinase Siderophore 2,4-DAPG fresh root weight

Strain code, KS and KF strains isolated on Kings’B from Swedish and French soil; AFNS strain isolated on AGS from French soil; RN and RU strains isolated on R2A from the Netherlands and the United
Almost all plants died due to high disease severity by

Kingdom, respectively (Adesina et al., 2007). Inhibition zones: 1, mycelia die back and inhibition zone of 1.0–2.9 mm; 11, inhibition zone of 3.0–5.9 mm; 111, inhibition zone of 6.0 mm and more;
Log10CFU g 1 of
R. solani infection and thus the colonization density could

4.94  0.36
4.29  0.30
3.65  1.03
4.14  0.05
4.63  0.42
4.17  0.75
3.43  0.71
4.07  0.25

–, tests conducted in this study (otherwise: Adesina et al., 2007); DAPG, detection of the phlD gene by PCR-Southern blot hybridization (M.F. Adesina et al. in preparation); ND, not determined.
not be followed until the end of experiment 1 for these
isolates.
In experiment 3, the ability of isolate RU47 to colonize
the vascular tissue of lettuce leaves and roots was deter-
mined 7 weeks after sowing by dilution plating of the

ND
suspension of surface-sterilized macerated roots and leaves
1
1

1
1
from lettuce plants inoculated with RU47. We observed no
Prescreening
Table 1. In vitro characterization of eight selected antagonists and rhizosphere competence (CFU per gram fresh root weight) in prescreening greenhouse experiment

colony growth on the plates, suggesting that the strain did

111
111
111
111
111

not grow endophytically.

11
1
1

Suppression of bottom rot disease by

introduced bacterial antagonists
1

At the end of each experiment, a total of 24 plants per

treatment (six replicates per treatment and four plants
per replicate) were used to evaluate the ability of the
inoculated antagonists to suppress bottom rot disease
Hydrolytic enzymes

caused by R. solani AG1-IB on lettuce plants. Evaluation

of the pathogen effect on lettuce was based on the number
of surviving plants and the SDW compared with the Ctrl
treatment.
1
1
1
1
1
1
1
1

In experiment 1, disease severity and pathogen pressure

were high as evidenced by the high numbers of dead plants
(23 of 24 plants) and a high reduction in the shoot biomass
in the Ctrl1Rs treatment only (Table 3). However, also in
11

1
1

1
1
1

the treatments inoculated with the strong in vitro antago-

nists KS90 and KS70, as well as treatments inoculated with
the medium and weak antagonists RN86 and AFNS31,
111
111

111
111

respectively (Table 1), none or low numbers of surviving

11

1
1
1

plants and significantly reduced dry shoot biomass were

found (Table 3). This indicates a high disease pressure of the
R. solani AG1-IB strain used in this study on lettuce plants
under the given cultivation conditions. In experiment 1,
11
11
11
11
1

high numbers of surviving plants and a shoot biomass

Antifungal activity

comparable to those from healthy Ctrl plants were obtained

for plants inoculated with isolates RU47, KF36, KS16
and KS74 (Table 3). Based on these findings, experiments 2
111
111
111
111
111

11

and 3 were repeated only with these strains. Despite the

1

high level of disease severity caused by the pathogen,

16S rRNA gene partial sequencing

the highest number of surviving plants was found in

100
100

100

100
98

99

99
99
%

treatments inoculated with RU47 in all experiments

(Table 3), indicating a consistent and strong antagonistic
Pseudomonas fluorescens

activity of this bacterium towards R. solani AG1-IB.

Serratia marcescens

Although KF36 had a similar disease-suppressive effect as

RU47 in experiments 1 and 2, its suppression of the
P. fluorescens

P. fluorescens
P. fluorescens

P. cannabina

pathogen was inconsistent in the four experiments per-

Closest hit

P. jessenii
P. fulgida

formed. In fact, none or one surviving plant was recovered

, no activity.

from treatments inoculated with KF36 in experiments 3 and

4 (Table 3). In comparison with RU47 and KF36, strains
AFNS31
Codes

KS16 and KS74 were less efficient in controlling R. solani

RN86
RU47
KS16
KS90
KS70
KS74
KF36

AG1-IB in experiments 1 and 2.

c 2009 Federation of European Microbiological Societies FEMS Microbiol Ecol 69 (2009) 62–74
Published by Blackwell Publishing Ltd. All rights reserved
Biocontrol of Rhizoctonia solani and rhizosphere competence 67

Effects of bacterial antagonist on the growth of the pathogen. The shoot and root dry weight obtained for
lettuce plants plants inoculated was similar to the healthy Ctrl plants.
The effects of RU47, KF36, KS16 and KS74 (which showed
significant disease suppression in experiment 1) on lettuce Treatment effects on indigenous microbial
growth were evaluated in experiment 3. The effects of the communities
inoculants on plant growth were determined in treatments
inoculated with each bacterial antagonist without adding The effect of the pathogen R. solani1-IB and of the inoculant
strain P. jessenii RU47 on the relative abundance of domi-
nant bacterial, fungal and Pseudomonas populations in the
rhizosphere of lettuce plants was investigated using DGGE
Table 2. Colonization density of bacterial antagonists on lettuce ‘Tizian’ analysis of 16S rRNA, 18S rRNA or gacA gene fragments
(log10 CFU g 1 of fresh root weight) cultivated in growth chamber at amplified from TC-DNA. DGGE profiles were compared
20/15 1C 3, 5 and 7 weeks after sowing (WAS) in three independent
between three replicate rhizosphere samples from the non-
experiments (1, 2 and 3)
inoculated healthy control plants (Ctrl), plants grown with
Experiments 3 WAS 5 WAS 7 WAS R. solani (Ctrl1Rs) and plants with a combined inoculation
Experiment 1 of RU47 and R. solani (RU471Rs) at three sampling times
RU471Rs 7.17  0.04 cb 6.72  0.15 a 5.92  0.12 cb (3, 5 and 7 weeks after sowing). Although DGGE analyses
KF361Rs 7.57  0.27 c 6.55  0.22 a 6.63  0.12 c were performed for experiments 1, 2 and 3, only the data for
KS161Rs 6.39  0.37 ab 6.40  0.55 a 6.58  0.19 c
experiment 3 are presented here.
KS741Rs 6.57  0.26 ab 6.46  0.13 a 5.82  0.23 cb
KS901Rs 6.52  0.08 ab 6.81  0.66 a 5.95  0.39 cb
The bacterial DGGE profiles showed complex patterns
KS701Rs 6.20  0.53 a 6.21  0.58 a 4.75  0.39 a indicating many equally abundant bacterial populations.
AFNS311Rs 6.85  0.38 ab 6.15  0.33 a 5.53  0.42 ab Detection of strain RU47 in the bacterial rhizosphere
RN861Rs 6.68  0.02 ND ND patterns of inoculated plants was impossible due to the
Experiment 2 presence of a band with identical electrophoretic mobility as
RU471Rs 6.19  0.38 a 5.00  0.33 a 4.88  0.49 a the 16S rRNA gene fragment amplified from RU47 in the
KF361Rs 6.55  0.30 a 5.93  0.21 b 5.54  0.44 a
replicates of Ctrl and Ctrl1Rs treatments (Fig. 1a and b).
KS161Rs 6.53  0.07 a 5.48  0.35 ab 5.45  0.24 a
KS741Rs 5.86  0.47 a 4.96  0.38 a 4.92  0.33 a
Seven weeks after sowing, this band was much less intense in
Experiment 3 the replicates of RU471Rs (Fig. 1b). Three weeks after
RU471Rs 5.82  0.06 a 5.24  0.27 5.62  0.22 sowing, a clear effect of the seed inoculation could be
KF361Rs 5.92  0.06 a ND ND detected (data not shown). Cluster analysis (UPGMA of
KS161Rs 5.22  0.22 a ND ND Pearson’s correlation indices) of the bacterial DGGE profiles
KS741Rs 6.09  0.28 a ND ND showed that the bacterial patterns of rhizosphere samples
CFU of the same experiment followed by the same letter are not taken 5 weeks after sowing (2 weeks after transplanting)
significantly different according to Tukey’s test (P = 0.05). displayed a higher degree of variability between replicates,
ND, parameter not determined due to the death of nearly all plants, thus and the clustering of the treatments was less pronounced
no surviving plants for sampling. (Fig. 1a). Seven weeks after sowing, the separation of the

Table 3. Biological control effect of bacterial antagonists toward Rhizoctonia solani after seed and plant inoculation of lettuce ‘Tizian’ cultivated in
growth chamber at 20/15 1C for 7 weeks on number of dead plants (DP, from 24 plants) and shoot dry weight (SDW)
Experiment 1 Experiment 2 Experiment 3 Experiment 4

Treatments DP SDW (g per plant) SD DP SDW (g per plant) SD DP SDW (g per plant) SD DP SDW (g per plant) SD
Ctrl 0 5.2 a 0.4 0 3.9 a 0.2 0 2.8 a 0.1 0 1.6 a 0.05
Ctrl1Rs 23 0.9 bc 0.5 13 2.2 b 0.9 24 0.6 b 0.1 24 0.2 b 0.03
RU471Rs 0 4.7 a 0.2 0 3.5 ac 0.1 7 1.9 c 0.5 3 1.3 c 0.14
KF361Rs 0 4.9 a 0.6 0 3.4 ac 0.2 23 0.6 b 0.1 24 0.2 b 0.03
KS161Rs 1 4.1 a 0.5 5 2.8 bc 0.6 22 0.6 b 0.3
KS741Rs 4 3.9 a 0.7 3 3.0 ab 0.5 23 0.7 b 0.3
KS901Rs 11 2.2 c 1.2
KS701Rs 21 1.4 bc 1.0
AFNS311Rs 21 1.6 bc 0.8
RN861Rs 24 0.6 b 0.1

Dry weight followed by the same letter is not significantly different according to Tukey’s test (P = 0.05). DP, dead plant; SD, standard deviation.

FEMS Microbiol Ecol 69 (2009) 62–74

c 2009 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
68 M.F. Adesina et al.

Fig. 1. Comparison among DGGE fingerprints of bacterial 16S rRNA gene fragments amplified from community DNA extracts obtained from the
rhizosphere of lettuce plants without inoculation (Ctrl), with Rhizoctonia solani inoculation alone (Ctrl1Rs) and with combined inoculation of RU47
(seed and young plant inoculation) and R. solani (RU471Rs) at (a) 5 weeks after sowing and (b) 7 weeks after sowing. Beside each gel, the
corresponding UPGMA dendrogram based on Pearson’s correlation indices is given. A, B and C are the three independent replicates per treatment.

cluster formed by the fingerprints of the Ctrl1Rs replicates
was more pronounced [ o 30% similarity to the Ctrl and
RU471Rs treatments (Fig. 1b)]. The replicates of the
RU471Rs and Ctrl treatments formed a joint cluster.
Analysis of the Pseudomonas community pattern in the
rhizosphere of lettuce plants showed a band with the same
mobility as RU47 only in treatments inoculated with
the antagonist 3 and 5 weeks after sowing (data not shown),
whereas 7 weeks after sowing, the detection of RU47 was
not possible because a band with similar electrophoretic
mobility as the 16S rRNA gene fragment amplified from
RU47 was detected in all treatments (data not shown). In
contrast to the bacterial community profiles, Pseudomonas
rhizosphere patterns of lettuce plants were less complex,

c 2009 Federation of European Microbiological Societies FEMS Microbiol Ecol 69 (2009) 62–74
Published by Blackwell Publishing Ltd. All rights reserved
Biocontrol of Rhizoctonia solani and rhizosphere competence
Fig. 2. Comparison among DGGE fingerprints
of Pseudomonas-specific gacA gene fragments
amplified from community DNA extracts
obtained from the rhizosphere of lettuce plants
without inoculation (Ctrl), with Rhizoctonia
solani inoculation alone (Ctrl1Rs) and with
combined inoculation of RU47 (seed and young
plant inoculation) and R. solani (RU471Rs) at
(a) 5 weeks after sowing and (b) 7 weeks after
sowing. Beside each gel, the corresponding
UPGMA dendrogram based on Pearson’s
correlation indices is given. A, B and C are the
three independent replicates per treatment.
with fewer numbers of bands. Aside from a band that was
pronounced in the fingerprints of the Ctrl and RU471Rs
samples taken 7 weeks after sowing, the banding patterns
did not markedly differ at each sampling time for all
treatments. UPGMA analysis of the Pseudomonas DGGE
banding patterns confirmed that replicates of all treatments
shared a high similarity (4 80%) at all sampling times.
Overall, a rather low degree of variability was observed
among treatments, and the diversity of this group was
almost not affected by inoculation with RU47 (data not
shown).
The DGGE profiles of the Pseudomonas-specific gacA
gene fragments displayed a higher number of bands, indi-
cating a better separation of Pseudomonas populations
(Fig. 2a and b) as compared with Pseudomonas 16S rRNA
DGGE profiles. A band with the mobility of RU47 was
detected only in the RU471Rs treatments, and this band
was clearly separated from a dominant band that was
observed in the fingerprints of all treatments (Fig. 2a and
b). Although this dominant band was less well separated
from the RU47 band in the gacA fingerprints of rhizosphere
communities sampled 7 weeks after sowing, the inoculant
strain was still detectable at that time point for all replicates
of RU471Rs (Fig. 2a). Also, the gacA fingerprints of samples
taken 5 weeks after sowing shared a high similarity (4 60%)
FEMS Microbiol Ecol 69 (2009) 62–74
69
among all treatments. However, the fingerprints of the
RU471Rs treatment clearly clustered separately from the
replicates of the Ctrl1Rs and Ctrl treatments most likely
due to the presence of a strong band with the same
electrophoretic mobility as RU47. All gacA fingerprints of
the samples taken 7 weeks after sowing displayed a high
similarity, although treatment-dependent clustering was
observed.
The fungal fingerprints for rhizosphere samples taken 5
weeks after sowing (Fig. 3a) revealed a high similarity of the
Ctrl and RU471Rs treatments with treatment-dependent
separate clusters. In contrast, the samples of the Ctrl1Rs
treatments were variable and two of the three replicates of
Ctrl1Rs shared o 25% with the fingerprints of all other
samples. This trend became even more pronounced 7 weeks
after sowing. All replicates of Ctrl1Rs treatment formed a
separate cluster with o 20% similarity to the fingerprints of
the RU471Rs and Ctrl treatment. Several bands (Fig. 3b,
bands a, b, c d) were detected in the fingerprints of these
treatments that were not found in the patterns of the
Ctrl1Rs treatments. Obviously, the inoculation with
R. solani AG1-IB had a major impact on the fungal
fingerprints. In contrast, the fingerprints of the RU471Rs
treatment displayed a high similarity to the noninoculated
control, indicating no major effect in this treatment on the
c 2009 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
70 M.F. Adesina et al.

Fig. 3. Comparison among DGGE fingerprints of fungal 18S rRNA gene fragments amplified from community DNA extracts obtained from the
rhizosphere of lettuce plants without inoculation (Ctrl), with Rhizoctonia solani inoculation alone (Ctrl1Rs) and with combined inoculation of RU47
(seed and young plant inoculation) and R. solani (RU471Rs) at (a) 5 weeks after sowing and (b) 7 weeks after sowing. Beside each gel, the
corresponding UPGMA dendrogram based on Pearson’s correlation indices is given. A, B and C are the three independent replicates per treatment. The
bands indicated as circled a, b, c and d are bands that are common to the replicates of the Ctrl and the RU47+Rs plants.

c 2009 Federation of European Microbiological Societies FEMS Microbiol Ecol 69 (2009) 62–74
Published by Blackwell Publishing Ltd. All rights reserved
Biocontrol of Rhizoctonia solani and rhizosphere competence
relative abundance of dominant fungal ribotypes. The
DGGE profiles of fungal communities revealed that a band
with electrophoretic mobility corresponding to that of the
18S rRNA gene fragment amplified from R. solani was much
stronger in the Ctrl1Rs treatment than in the RU471Rs
treatment (Fig. 3a and b), indicating an increased relative
abundance of R. solani in the lettuce rhizosphere of the
Ctrl1Rs treatment.
Discussion
In this study, in vitro antagonists were tested in growth
chamber experiments with lettuce artificially inoculated
with R. solani AG1-IB in order to assess their potential to
colonize lettuce roots and to suppress R. solani AG1-IB-
based disease symptoms and effect on plant growth. Inter-
estingly, only one strain (P. jessenii RU47) with weak in vitro
antagonistic activity against R. solani AG1-1B (Table 1)
displayed efficient and consistent disease suppression
throughout the four independent growth chamber experi-
ments. These findings confirm previous observations that in
vitro inhibition does not necessarily correlate with in vivo
performance (Milus & Rothrock, 1997; Schottel et al., 2001;
Faltin et al., 2004; Gravel et al., 2005).
Seven of the eight strains selected were previously as-
signed to Pseudomonas by 16S rRNA gene sequencing
(Adesina et al., 2007), and for all of them proteolytic activity
and siderophore production was detected on plates. Four
Pseudomonas fluorescens strains (KF36, KS16, KS74 and
KS90), which displayed strong in vitro antagonistic activity
towards R. solani AG1-IB, carried the phlD gene involved in
2,4-diacetylphloroglucinol (2,4-DAPG) biosynthesis (M.F.
Adesina et al., unpublished data), suggesting that the strains
might produce 2,4-DAPG. The important role of 2,4-DAPG
production in efficient biocontrol was demonstrated re-
cently (Haas & Défago, 2005; Rezzonico et al., 2007). In
growth chamber experiment 1 all potentially 2,4-DAPG-
producing P. fluorescens strains, except for KS90, showed
good disease suppression. Although the strong in vitro
antagonist P. fluorescens KS90 carried the phlD gene and its
CFU counts per gram of rfw were not significantly different
from the P. fluorescens strains KS16 and KS74, the disease
control by this strain was much less efficient. However, all
three other phlD-carrying P. fluorescens strains inoculated in
experiment 3 failed to control the disease. The reasons for
the variability observed are not clear. Differences in the
expression of genes involved in antibiotic production due to
lower cell densities in experiment 3 in comparison with
experiment 1 (Table 2) in combination with high pathogen
pressure might be discussed. Four out of the eight in vitro
antagonists of R. solani AG1-IB selected in our study failed
to efficiently control the pathogen in the growth chamber
experiment 1 (Table 3), although two of these four isolates
FEMS Microbiol Ecol 69 (2009) 62–74
71
displayed strong in vitro antagonistic activity against
R. solani AG1-IB.
In the growth chamber experiments, the bacterial antago-
nists were applied by seed inoculation and plant drenching.
Drenching of young lettuce plants with a bacterial cell
suspension can easily be carried out before transplanting
lettuce seedlings into the field. The CFU counts of the
inoculant strains per gram of rfw determined 3 weeks after
sowing in three independent growth chamber experiments
were much higher than the counts obtained in the pre-
screening greenhouse experiment. The reasons for this
difference might be that the soil composition and availabil-
ity of nutrients were different in the soils used. The ratio of
sand to substrate of the soil used for the greenhouse
prescreening experiment was 80 : 20 in contrast to the soil
used for the growth chamber experiments, where the ratio
was 50 : 50. This observation might point to an influence of
the soil on the ability of the inoculant strains to colonize the
rhizosphere of lettuce. Maloney et al. (1997) found that the
availability of carbon and nitrogen affected the rhizobacter-
ial population. The ability of inoculant strains to colonize
the root system after seed inoculation or root inoculation
has been pinpointed as a key factor for successful biocontrol
by many authors (Bloemberg & Lugtenberg, 2001; Haas &
Défago, 2005). All strains showed rather good seed and root
colonization as most inoculants established at cell densities
4 106 g 1 rfw 3 weeks after sowing. In the case of P. fulgida
KS70, which displayed strong in vitro antagonistic activity
towards a range of fungi and bacteria, less efficient coloniza-
tion might have contributed to the failure to control the
pathogen AG1-IB in the growth chamber experiment. How-
ever, P. fluorescens KS90 and S. marcescens AFNS31 also
failed to suppress bottom rot of R. solani, but nevertheless
they colonized lettuce roots at the same or similar popula-
tion densities as the biocontrol-efficient strain RU47. This
implies that the inability of these isolates to suppress disease
was not due to insufficient root colonization, but may have
resulted from insufficient production of antifungal metabo-
lites, different colonization patterns, for example the colo-
nization of the strains at locations different from the
infectious site of the pathogen or insufficient cell density of
the antagonists at the infectious site or differences in the
plant response. However, because the colonization patterns
were not investigated in this study, it cannot be excluded
that differences in colonization patterns between the strains
existed. Using gfp-tagged inoculant strains, several studies
reported heterogeneous colonization patterns and the ques-
tion of what triggers the colonization of some sites and not
of others was raised (Gamalero et al., 2003; Götz et al.,
2006). In contrast to studies performed under field condi-
tions on the control of R. solani by means of bacterial
antagonists (Grosch et al., 2005; Scherwinski et al., 2008),
the growth chamber experiments were performed under
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Published by Blackwell Publishing Ltd. All rights reserved
72
well-controlled conditions and with an extremely high
pathogen pressure. A variation still existed between the
experiments (Tables 2 and 3). The major variable factor
was the growth of lettuce (Ctrl). In each of the independent
growth chamber experiments, the Ctrl1Rs and RU471Rs
treatments were compared with the control. The variability
in the lettuce growth might be due to different factors. The
experiments were performed in the time period of c. 1 year
in the same chamber and thus it cannot be excluded that
aging of the lamps resulted in less plant growth. The
cultivation in the growth chamber started only after trans-
planting at the two- to three-leaf stage, and slightly varying
conditions in the greenhouse might have also contributed to
the decreased lettuce growth in experiment 2 and even more
pronounced in experiment 3. The reduced SDW determined
paralleled a tendency toward decreased CFU per rfw 3 weeks
after seed inoculation. Despite the variability in the growth
of lettuce plants and CFU per rfw determined 3 weeks after
seed inoculation, the biocontrol efficiency of strain RU47
was consistent. However, these factors might have contrib-
uted to the variable control by the phlD carrying P. fluor-
escens strains KF36, KS16 and KS74.
Plant inoculation with bacterial antagonists has been
reported to influence microbial community structure as
determined by culture-independent methods that rely on
amplification of rRNA gene fragments from rhizosphere
DNA extracts such as PCR-based DGGE (Götz et al., 2006).
In other studies, no or only transient changes were observed
(Lottmann et al., 2000; Scherwinski et al., 2008). In the
present study, PCR-DGGE analysis enabled us to compare
the bacterial and fungal community profiles of the three
different treatments and thus to evaluate the effect of the
pathogen R. solani AG1-IB in the presence or absence of
P. jessenii RU47 on the rhizosphere microbiota. We could
demonstrate that the pathogen R. solani AG1-IB influenced
not only the fungal but also the bacterial community
patterns. The effects of R. solani AG1-IB became more
pronounced during the experiment for both fungi and
bacteria. In the presence of RU47, this effect was less strong
and the fingerprints of the RU471Rs and Ctrl treatment
formed a joint cluster for bacterial and fungal fingerprints.
However, the detection of RU47 was hampered in the
bacterial community patterns due to the complexity of these
patterns and the presence of ribotypes, which have similar
electrophoretic mobility as RU47. The complexity of the
DGGE patterns was reduced with the use of group-specific
primers, thus enhancing the resolution for the Pseudomonas
group analyzed by DGGE. The gacA-based Pseudomonas
DGGE profiles revealed that RU47 successfully established,
as a band corresponding to the electrophoretic mobility to
RU47 was found only in the rhizosphere patterns of lettuce
of the RU471Rs treatment in the gacA-based Pseudomonas
community patterns. Furthermore, we observed that the
c 2009 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
M.F. Adesina et al.
presence of R. solani AG1-IB and the inoculation with RU47
had almost no effect on the Pseudomonas group and that the
gacA DGGE fingerprints of all treatments, despite a treat-
ment-dependent clustering, had high similarity among the
treatments. This observation contradicts the hypothesis that
organisms that are closely related to the BCA itself are most
likely to be affected by the BCA due to competition for the
same niches and resources (Winding et al., 2004; Götz et al.,
2006). Moreover, the band patterns of the gacA-based
Pseudomonas community revealed remarkable diversity of
the gacA gene in the rhizosphere of lettuce plant originating
from all treatments. As found in this study, a better resolu-
tion of gacA-based Pseudomonas community fingerprints
than of 16S-based Pseudomonas community fingerprints
was of reported by Costa et al. (2007).
In conclusion, out of the eight in vitro antagonists
investigated in this study, we found only one promising
strain: P. jessenii RU47. For this strain, in vitro proteolytic
activity and siderophore production were observed, while
chitinolytic, glucanolytic and cellulolytic activities, and
genes encoding antibiotics such as 2,4-diacetylphloroglucinol
(2,4-DAPG), phenazine, pyrrolnitrin and pyoluteorin were
not detected. In vitro production of salicylic acid as side-
rophores by several resistance-inducing bacteria under low-
iron conditions has been reported, and its role in the
induced-systemic resistance (ISR) elicitation process was
demonstrated in the case of Pseudomonas aeruginosa
KMPCH (de Meyer et al., 1999). Hence, siderophore pro-
duction has been suggested to trigger the ISR signal pathway
in plants (Audenaert et al., 2002; van Loon & Bakker, 2005).
Considering the strong and consistent suppression of the
pathogen at very high disease severity by strain RU47 in vivo
on lettuce, which is contrary to the weak and rather
insignificant direct inhibition of R. solani AG1-IB by this
strain in vitro and the in vitro production of siderophores by
strain RU47, it is assumed that induction of systemic
resistance in lettuce is the possible mechanism by which
strain RU47 could protect lettuce plants against R. solani
AG1-IB. Nonetheless, its exact mechanism still remains
unclear and its explanation needs future investigation.
Strain RU47 did not promote shoot or root biomass of
lettuce compared with the noninoculated healthy plant in
the absence of the pathogen. On the basis of this observa-
tion, we suggest that for biological application under the
conditions where the strain was tested, it can only be used to
control bottom rot disease in a soil infested with the
pathogen and not for a growth-promoting purpose under
noninfested conditions. However, future experiments under
field conditions and in different soil types have to show
whether the RU47 conferred control effect is specific for R.
solani AG1-IB and specific for lettuce plants or whether
strain RU47 can also provide protection of lettuce plants
against other pathogens.
FEMS Microbiol Ecol 69 (2009) 62–74
Biocontrol of Rhizoctonia solani and rhizosphere competence
Acknowledgements
This work was supported by grants from DAAD and Gisela
und Hermann Stegemann-Stiftung to M.F.A., by the
EU BIOTECH project METACONTROL and the project
BRA05/021. Furthermore, the support of Angelika Fandrey,
Guo-Chun Ding and Ilse-Marie Jungkurth is acknowledged.
References
Adesina MF, Lembke A, Costa R, Speksnijder A & Smalla K
(2007) Screening of bacterial isolates from various European
soils for in vitro antagonistic activity towards Rhizoctonia
solani and Fusarium oxysporum: site-dependent composition
and diversity revealed. Soil Biol Biochem 39: 2818–2828.
Audenaert K, Pattery T, Cornelis P & Höfte M (2002) Induction
of systemic resistance to Botrytis cinerea in tomato by
Pseudomonas aeruginosa 7NSK2: role of salicylic acid,
pyochelin, and pyocyanin. Mol Plant Microbe In 15:
1147–1156.
Berg G, Krechel A, Ditz M, Faupel A, Ulrich A & Hallmann J
(2005) Endophytic and ectophytic potato-associated bacterial
communities differ in structure and antagonistic function
against plant pathogenic fungi. FEMS Microbiol Ecol 51:
215–229.
Bloemberg GV & Lugtenberg BJJ (2001) Molecular basis of plant
growth promotion and biocontrol by rhizobacteria. Curr Opin
Plant Biol 4: 343–350.
Compant S, Duffy B, Nowak J, Clement C & Barka E (2005) Use
of plant growth-promoting bacteria for biocontrol of plant
diseases: principles, mechanisms of action and future
prospects. Appl Environ Microb 71: 4951–4959.
Costa R, Götz M, Mrotzek N, Lottmann J, Berg G & Smalla K
(2006) Effects of site and plant species on rhizosphere
community structure as revealed by molecular analysis of
microbial guilds. FEMS Microbiol Ecol 56: 236–249.
Costa R, Gomes N, Krögerrecklenfort E, Opelt K, Berg G &
Smalla K (2007) Pseudomonas community structure and
antagonistic potential in the rhizosphere: insights gained by
combining phylogenetic and functional gene-based analyses.
Environ Microbiol 9: 2260–2273.
de Meyer G, Capieau K, Audenaert K, Buchala A, Métraux J &
Höfte M (1999) Nanogram amounts of salicylic acid produced
by the Rhizobacterium Pseudomonas aeruginosa 7NSK2
activate the systemic acquired resistance pathway in Bean. Mol
Plant Microbe In 12: 450–458.
Faltin F, Lottmann J, Grosch R & Berg G (2004) Strategy to select
and assess antagonistic bacteria for biological control of
Rhizoctonia solani Kühn. Can J Microbiol 50: 811–820.
Gamalero E, Lingua G, Berta G & Lemanceau P (2003) Methods
for studying root colonization by introduced beneficial
bacteria. Agronomie 23: 407–418.
Garbeva P, van Veen JA & van Elsas JD (2004) Assessment of the
diversity, and antagonism towards Rhizoctonia solani AG3, of
Pseudomonas species in soil from different agricultural
regimes. FEMS Microbiol Ecol 47: 51–64.
FEMS Microbiol Ecol 69 (2009) 62–74
73
Gomes NCM, Kosheleva IA, Abraham WR & Smalla K (2005)
Effects of the inoculant strain Pseudomonas putida KT2442
(pNF142) and of naphthalene contamination on the soil
bacterial community. FEMS Microbiol Ecol 54: 21–33.
González Garcı́a V, Portal Onco MA & Rubio Susan V (2006)
Review. Biology and systematics of the form genus
Rhizoctonia. Span J Agric Res 4: 55–79.
Götz M, Gomes NCM, Dratwinski A, Costa R, Berg G, Peixoto R,
Mendonça-Hagler L & Smalla K (2006) Survival of gfp-tagged
antagonistic bacteria in the rhizosphere of tomato plants and
their effects on the indigenous bacterial community. FEMS
Microbiol Ecol 56: 207–218.
Gravel V, Martinez C, Antoun H & Tweddell RJ (2005)
Antagonist microorganisms with the ability to control
Pythium damping-off tomato seeds in rockwool. BioControl
50: 771–786.
Grosch R, Schneider JHM & Kofoet A (2004) Characterisation of
Rhizoctonia solani anastomosis groups causing bottom rot in
field-grown lettuce in Germany. Eur J Plant Pathol 110: 53–62.
Grosch R, Faltin F, Lottmann J, Kofoet A & Berg G (2005)
Effectiveness of 3 antagonistic bacterial isolates to control
Rhizoctonia solani Kühn on lettuce and potato. Can J Microbiol
51: 345–353.
Haas D & Défago G (2005) Biological control of soil-borne
pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3:
307–319.
Heuer H, Krsek M, Baker P, Smalla K & Wellington EMH (1997)
Analysis of actinomycete communities by specific
amplification of genes encoding 16S rRNA and gel
electrophoretic separation in denaturing gradients. Appl
Environ Microb 63: 3233–3241.
Heuer H, Wieland G, Schönfeld J, Schönwälder A, Gomes NCM
& Smalla K (2001) Bacterial community profiling using DGGE
or TGGE analysis. Environmental Molecular Microbiology:
Protocols and Applications (Rouchelle P, ed), pp. 177–190.
Horizon Scientific Press, Wymondham, UK.
Kataria HR & Gisi U (1996) Chemical control of Rhizoctonia
species. Rhizoctonia Species: Taxonomy, Molecular Biology,
Ecology, Pathology and Disease Control (Sneh B, Jabaji-Hare S,
Neate S & Dijst G, eds), pp. 537–547. Kluwer Academic
Publishers, Dordrecht, the Netherlands.
Lottmann J, Heuer H, de Vries J, Mahn A, Düring K, Wackernagel
W, Smalla K & Berg G (2000) Establishment of introduced
antagonistic bacteria in the rhizosphere of transgenic potatoes
and their effect on the bacterial community. FEMS Microbiol
Ecol 33: 41–49.
Maloney PE, van Bruggen AHC & Hu S (1997) Bacterial
community structure in relation to the carbon environments
in lettuce and tomato rhizosphere and in bulk soil. Microbiol
Ecol 34: 109–117.
Messner R & Prillinger H (1995) Saccharomyces species
assignment by long range ribotyping. Antonie van
Leeuwenhoek 67: 363–370.
Milling A, Smalla K, Maidl FX, Schloter M & Munch JC (2004)
Effects of transgenic potatoes with altered starch composition
c2009 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
74
on the diversity of soil and rhizosphere bacteria and fungi.
Plant Soil 266: 23–29.
Milus EA & Rothrock CS (1997) Efficacy of bacterial seed
treatments for controlling Pythium root rot of winter wheat.
Plant Dis 81: 180–184.
Ogoshi A (1987) Ecology and pathogenicity of anastomosis and
intraspecific groups of Rhizoctonia solani Kühn. Annu Rev
Phytopathol 25: 125–143.
Ogoshi A (1996) The genus Rhizoctonia. Rhizoctonia Species:
Taxonomy, Molecular Biology, Ecology, Pathology and Disease
Control (Sneh B, Jabaji-Hare S, Neate S & Dijst G, eds),
pp. 1–9. Kluwer Academic Publishers, Dordrecht, the
Netherlands.
Raaijmakers JM & Weller DM (2001) Exploiting genotypic
diversity of 2,4-diacetylphloroglucinol-producing Pseudomonas
spp.: characterization of superior root-colonizing P. fluorescens
strain Q8r1-96. Appl Environ Microb 67: 2545–2554.
Raaijmakers JM, Paulitz CT, Steinberg C, Alabouvette C &
Moenne-Loccoz Y (2008) The rhizosphere: a playground and
battlefield for soilborne pathogens and beneficial
microorganisms. Plant Soil DOI: 10.1007/s11104-008-9568-6.
Rezzonico F, Zala M, Keel C, Duffy B, Moënne-Loccoz Y &
Défago G (2007) Is the ability of biocontrol fluorescent
pseudomonads to produce the antifungal metabolite
2,4-diacetylphloroglucinol really synonymous with higher
plant protection? New Phytol 173: 861–872.
Scherwinski K, Grosch R & Berg G (2008) Effect of bacterial
antagonists on lettuce: active biocontrol of Rhizoctonia
solani and negligible, short-term effects on nontarget
microorganism. FEMS Microbiol Ecol 64: 106–116.
Schneider JHM, Schilder MT & Dijst G (1997) Characterization
of Rhizoctonia solani AG-2 isolates causing bare patch in field-
grown tulips in the Netherlands. Eur J Plant Pathol 103:
265–279.
c 2009 Federation of European Microbiological Societies
Published by Blackwell Publishing Ltd. All rights reserved
M.F. Adesina et al.
Schottel JL, Shimizu K & Kinkel LL (2001) Relationship of in vitro
pathogen inhibition and soil colonization to potato scab
biocontrol by antagonistic Streptomyces spp. Biol Control 20:
102–112.
Smit E, Leeflang P, Glandorf B, van Elsas JD & Wernars K (1999)
Analysis of fungal diversity in the wheat rhizosphere by
sequencing of cloned PCR-amplified genes encoding 18S
rRNA and temperature gradient gel electrophoresis. Appl
Environ Microb 65: 2614–2621.
Sweetingham MW (1996) Integrated control of Rhizoctonia
species. Rhizoctonia Species: Taxonomy, Molecular Biology,
Ecology, Pathology and Disease Control (Sneh B, Jabaji-Hare S,
Neate S & Dijst G, eds), pp. 549–558. Kluwer Academic
Publishers, Dordrecht, the Netherlands.
Vainio EJ & Hantula J (2000) Direct analysis of wood-inhabiting
fungi using denaturing gradient gel electrophoresis of
amplified ribosomal DNA. Mycol Res 104: 927–936.
van Loon LC & Bakker PAHM (2005) Induced systemic resistance
as a mechanism of disease suppression by rhizobacteria. PGPR:
Biocontrol and Biofertilization (Siddiqui ZA, ed), pp. 39–66.
Springer, Dordrecht, the Netherlands.
Weller DM, Raaijmakers JM, McSpadden Gardener BB &
Thomashow LS (2002) Microbial population responsible for
specific soil suppressiveness to plant pathogens. Annu Rev
Phytopathol 40: 309–348.
White TJ, Bruns TD, Lee S & Taylor J (1990) Analysis of
phylogenetic relationships by amplification and direct
sequencing of ribosomal RNA genes. PCR Protocols: A Guide to
Methods and Applications (Innis MA, Gelfand DH, Sninsky JJ
& White TJ, eds), pp. 315–322. New York Academic Press,
New York.
Winding A, Binnerup SJ & Pritchard H (2004) Non-target effects
of bacterial biological control agents suppressing root
pathogenic fungi. FEMS Microbiol Ecol 47: 129–141.
FEMS Microbiol Ecol 69 (2009) 62–74