Journal of Applied Microbiology ISSN 1364-5072
ORIGINAL ARTICLE
Greek indigenous streptomycetes as biocontrol agents
against the soil-borne fungal plant pathogen Rhizoctonia
solani
G.S. Kanini, E.A. Katsifas, A.L. Savvides, D.G. Hatzinikolaou and A.D. Karagouni
Department of Botany, Microbiology Group, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
Keywords
actinobacteria, antifungal activity, biocontrol,
phytopathogenic fungi, Rhizoctonia solani,
Streptomyces.
Correspondence
Amalia D. Karagouni, Department of Botany,
Microbiology Group, Faculty of Biology,
National and Kapodistrian University of
Athens, Panepistimioupolis, Zografou, 15781
Athens, Greece. E-mail: akar@biol.uoa.gr
2013/1342: received 26 July 2012, revised 31
December 2012 and accepted 6 January
2013
doi:10.1111/jam.12138
Abstract
Aims: To examine the biocontrol potential of multiactive Greek indigenous
Streptomyces isolates carrying antifungal activity against Rhizoctonia solani that
causes damping-off symptoms on beans.
Methods and Results: A total of 605 Streptomyces isolates originated from 12
diverse Greek habitats were screened for antifungal activity against R. solani
DSM843. Almost one-third of the isolates proved to be antagonistic against the
fungus. From the above isolates, six were selected due to their higher
antifungal activity, identified by analysing their 16S rRNA gene sequence and
studied further. The obtained data showed the following: firstly, the isolates
ACTA1383 and ACTA1557 exhibited the highest antagonistic activity, and
therefore, they were selected for in vivo experiments using bean seeds as target;
secondly, in solid and liquid culture experiments under optimum antagonistic
conditions, the medium extracts from the isolates OL80, ACTA1523,
ACTA1551 and ACTA1522 suppressed the growth of the fungal mycelium,
while extracts from ACTA 1383 and ACTA1557 did not show any activity.
Conclusions: These results corresponded important indications for the utility
of two Greek indigenous Streptomyces isolates (ACTA1557 and ACTA1383)
for the protection of the bean crops from R. solani damping-off symptoms,
while four of them (isolates OL80, ACTA1523, ACTA1551 and ACTA1522)
seem to be promising producers of antifungal metabolites.
Significance and Impact of the Study: This is the first study on the biocontrol
of R. solani using multiactive Streptomyces isolates originated from
ecophysiologically special Greek habitats. Our study provides basic information
to further explore managing strategies to control this critical disease.
Introduction
Among the most common phytopathogenic fungi,
Rhizoctonia solani K€
uhn [teleomorph: Thanatephorus
cucumeris (A.B. Frank) Donk; basidiomycetes] is an
important soil-borne pathogen responsible for the ‘damping-off’ of many widely cultured plants, such as potato
and tomato plant (De Curtis et al. 2010; Lahlali and Hijri
2010; Montealegre et al. 2010), bean plant (Balali and
Kowsari 2004; Godoy-Lutz et al. 2008; Nerey et al. 2010)
and cotton (Abd-Elsalam et al. 2010) thus constituting a
financial threat for farmers. The ‘damping-off’ symptom
1468
is characterized by the disability of seeds to shoot or by
the mortification of seedlings either before or after their
emergence. Especially for bean plants, ‘damping-off’
means the sudden decay of the young seedlings of the
plant, a few days after their emergence (Balali and
Kowsari 2004).
The pathogen is characterized by significant ecological
advantages such as an extremely broad host range and a
high survival rate of sclerotia, under various environmental conditions, and therefore, its control is difficult to
accomplish. Currently, Rhizoctonia diseases are not adequately controlled and their severity can only be limited
Journal of Applied Microbiology 114, 1468--1479 © 2013 The Society for Applied Microbiology
G.S. Kanini et al.
through a combination of cultural and crop protection
strategies. For instance, planting seeds in warm soils and
covering them with as little soil as possible speeds the
sprouting and development of the stem while reducing
the risk of stem canker. Farmers also use chemical control and several products like azoxystrobin (Amistar; Syngenta), chlorothalonil (Daconil 2787; Aventis), cymoxanil
(Curzate 50; Dupont), flutolanil (Monarch; Aventis),
pencycuron (Monceren; Bayer) and propamocarb (Previcur N; Aventis) (van den Boogert and Luttikholt 2004),
which have been developed for this purpose. They concern both seed treatment and soil application, although
they resulted in poor Rhizoctonia control (Wharton et al.
2007).
In Greece, Rhizoctonia solani harms tobacco plants
(northern Greece), tomato plants (northern and central
Greece) and bean plants (central and southern Greece).
The control of the soil-borne plant pathogens, including
R. solani, is based mainly on cultural practices like
decrease in soil moisture, soil coverage and the use of
phytopathogen-resistant hybrids. Greek farmers also use
chemical disinfectants with no significant effect, for
example, metham sodium (Vapam), quintozene + etridiazole as Terrachlor Super-X and methyl bromide
either prior to or after the infection, but their use is
limited because of their high cost and their strong toxicity (Marouli and Tzavella-Klonari 2002). Also, due to
the lack of coordination between the Greek Ministry of
Agriculture and the agricultural cooperatives, the flow of
information about treatment procedures is obscure and
inadequate.
The increasing concern for environmental protection
and demand for organic farming drives research towards
alternative control measures, such as the use of natural
antagonists to biologically control plant pathogens (De
Curtis et al. 2010; Hernandez-Suarez et al. 2011).
Actinobacteria and particularly members of the genus
Streptomyces are characterized by their complex morphological differentiation and the ability to produce a wide
variety of secondary metabolites (Challis and Hopwood
2003). These micro-organisms can be found in the rhizosphere of several plant species (Crawford et al. 1993;
Kortemaa et al. 1994; Tokala et al. 2002; Ramakrishnan
et al. 2009) behaving as endophytes that occur within the
roots of barley (Sadeghi et al. 2009; Kluth et al. 2010) or
the stems of potato (Sessitsch et al. 2002). Plant root
exudates stimulate rhizosphere growth of streptomycetes
that are strongly antagonistic to fungal pathogens (Yuan
and Crawford 1995).
Several Streptomyces species such as S. lydicus,
S. lividans, S. olivaceoviridis, S. scabies, S. plicatus, S. hydroscopicus, S. violaceusniger, S. humidus, S. avermitilis,
S. aurofaciens and S. roseoflavus are well-known
Streptomycetes as biocontrol agents against R. solani
producers of important compounds that are active
against a wide variety of fungal pathogens (Taechowisan
et al. 2009 ). These include a wide range of antibiotics as
well as a variety of enzymes (i.e., chitinases), which
degrade the fungal cell wall (Chamberlain and Crawford
1999; Gomes et al. 2000; Hwang et al. 2001; Getha and
Vikineswary 2002; Taechowisan et al. 2003; De Souza
et al. 2008). Metabolites from streptomycetes have been
used in agriculture as growth promoters (Igarashi et al.
2000; El-Tarabily 2008; Ichinose et al. 2008; Schrey and
Tarkka 2008) and selected strains of the genus also have
been used as direct biocontrol agents for other plant diseases (Yuan and Crawford 1995; Neeno-Eckwall et al.
2001; Shekhar et al. 2006; Godoy-Lutz et al. 2008; Bakker
et al. 2010).
The Greek territory, due to its geographical position
that is characterized by the Mediterranean climate conditions, has been proved to be a rich habitat for streptomycete populations with biotechnological interest (Katsifas
et al. 1999, 2000; Baur et al. 2006; Paululat et al. 2008,
2010).
In this study, we aimed to select Greek Streptomyces
isolates from the Athens University Microbiology Laboratory Culture Collection for their antifungal activity
against Rhizoctonia solani DSM843. Two of them were
used for in vivo studies to control the phytopathogenic
fungus R. solani DSM843 using the plant Phaseolus vulgaris L. (Fabaceae) as a model fungal target. In addition,
medium extracts from solid and liquid cultures of
selected isolates were investigated for their antifungal
activity. Gel filtration fractions of the above extracts were
also used for in vitro antifungal assays to provide initial
information on the molecular features of the possible
bioactive compounds.
Materials and methods
Microbial strains
A total of 605 bacterial isolates assigned to the genus
Streptomyces on the basis of their phenotypic characteristics (Herron and Wellington 1990) were screened in vitro
for antifungal activity against the phytopathogenic fungus
R. solani DSM843 (Table 1). These strains were derived
from the Athens University Microbiology Laboratory Culture Collection and have been isolated from 12 different
Greek habitats using selective media (Katsifas et al. 1999).
According to the 12 selected habitats, the samples are
grouped into soil samples from the rhizospheres of indigenous plants (Table 1A) and nonrhizosphere samples
(Table 1B). All isolates were maintained as spore suspensions in 30% (w/v) glycerol at 20°C (Herron and
Wellington 1990).
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Streptomycetes as biocontrol agents against R. solani
G.S. Kanini et al.
Table 1 Streptomyces strains and their antifungal activity from each of the 12 studied Greek habitats
Number of
isolates tested
Sampling area
(A) Rhizosphere samples
1. Rhizosphere of Ebenus sibthorpii
2. Rhizosphere of Ceratonia silicva
3. Rhizosphere of Olea europea
4. Rhizosphere of Abies cefalonica
5. Rhizosphere of Pinus brutia from Crete
6. Rhizosphere of evergreen woody
shrubs from an island of the Aegean Sea
7. Rhizosphere of evergreen woody
shrubs from an island of the Ionian Sea
8. Rhizosphere of coniferous trees (Arcadian forest)
Rhizosphere subtotals
(B) Nonrhizosphere samples
9. Hot spring water of thermopiles
thermal springs (Viotia District)
10. Sediment from a volcanic area
(Santorini Island – Aegean Sea)
11. Soil derived from cultivated area
(Marathon, Attica District)
12. Soil from protected natural
forest area (Kessariani, Attica District)
Nonrhizosphere subtotals
Total
39
47
75
20
24
22
30
100
357
5
Number (percentage) of isolates with
antifungal activity against Rhizoctonia solani
DSM843 {highest – lowest – average}*
10
9
25
0
12
13
(256%)
(191%)
(333%)
(00%)
(500%)
(591%)
{74; 13; 45}
{54;13; 28}
{90; 13; 41}
{97; 19; 45}
{115; 13; 50}
0 (00%)
26 (260%) {76; 14; 37}
95 (266%)
5 (1000%) {70; 22; 51}
30
1 (33%) {56; 56; 56}
186
100 (538%) {92; 13; 39}
27
12 (444%) {96; 25; 54}
248
605
118 (476%)
213 (352%)
*Antagonistic activity levels as expressed by the quotient of the inhibition zone area over streptomycete colony area (See In vitro antagonism bioassays).
Rhizoctonia solani DSM843 that was used as target
fungus for the antagonism bioassays belonged to the
anastomosis group 1 (AG-1) and was maintained on
potato dextrose agar (PDA) suggested by DSMZ,
Germany, at 4°C.
deionized sterile water. Three grams of wet mycelium (dry
weight, 15–18% w/w) was resuspended in 1000 ml deionized sterile water and was thoroughly mixed with 1 kg of
either sterile or nonsterile soil (Lu et al. 2004).
In vitro antagonism bioassays
Preparation of inoculum of biocontrol agents and fungi
Streptomycete aliquots (30 ll) from a spore suspension
in 30% (w/v) glycerol were used as inoculum for all in
vitro antagonism bioassays. For the same test, we used
two full loops of R. solani mycelium from a 5-day-old
culture on PDA.
For in vivo antagonism tests, a suspension of streptomycetes spores in Ringer ¼ salt solution (NaCl 215 g l 1,
KCl 015 g l 1, CaCl2 0075 g l 1, K2HPO4 05 g l 1
according to Wellington et al. 1990) (109 spores per ml)
was prepared from a 5-day-old culture on arginine–glycerol–salt agar (AGS), as described by Herron and Wellington (1990), and used for the bean seed treatments.
Rhizoctonia solani was cultured in nutrient broth (NB,
Biokar Diagnostics, Beauvais, France) for 5 days at 28°C
and 180 rpm. The mycelium was aseptically collected on
filter paper and washed with three culture volumes of
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Antifungal antagonism was determined using a modified
agar plate antagonism bioassay (Crawford et al. 1993).
All streptomycetes were spot inoculated in the centre of
NA agar plates (triplicate plates). Plates were incubated at
28°C for 2 days prior to fungal inoculation. The phytopathogenic fungus was inoculated in two antidiametrical
positions, 1 cm from the plate edge. Following fungal
inoculation, the plates were incubated at 28°C for 5 days.
Antagonistic activity of the streptomycetes was determined by measuring the inhibition zone, the presence of
which characterized the strain as positive.
Antagonism strength was determined by averaging
(triplicate plates per strain x three independent
experimental sets) the quotient of the area of the inhibition zone, which was formed around the streptomycetes
colony, over the area of the streptomycetes colony
itself [Antifungal activity = pR2z =pR2str (Rz = radius of
Journal of Applied Microbiology 114, 1468--1479 © 2013 The Society for Applied Microbiology
G.S. Kanini et al.
inhibition zone and Rstr = radius of streptomycetes
colony, modified from Seeley et al. 1990)].
Taxonomy of streptomycetes
The 22-mer BOX A1R oligonucleotide (5′-CTACGGCAA
GGCGACGCTGACG-3′) was used to generate BOX-PCR
profiles (Versalovic et al. 1991; Martin et al., 1992).
Amplification reactions were performed in volumes of
25 ll, containing 2 lmol l 1 of the single BOX primer,
200 lmol l 1 each of dATP, dCTP, dGTP and dTTP
(Bioprobe Systems/Quantum, Paris, France), PCR buffer
[10 mmol l 1 Tris–HCl (pH 90), 50 mmol l 1 KCl,
15 mmol l 1 MgCl2, 01% Triton X-100 and 02 mg
ml 1 bovine serum albumin], 15 units of Taq DNA
polymerase (Biotools, Surrey, UK) and 40 ng template
DNA. After initial denaturation for 7 min at 95°C, samples were cycled for 35 cycles using the following profile:
denaturation for 1 min at 94°C, primer annealing for
1 min at 53°C and primer extension for 8 min at 65°C,
with a final elongation step of 16 min at 65°C. The
BOX-PCR was repeated twice and yielded consisting
results. We analysed the BOX-PCR profile of the isolates
that showed the highest in vitro antifungal activity and
selected for further studies. The same isolates were further characterized through the amplification of their 16S
rRNA gene. The 16S rDNA fragment was amplified by
PCR using two universal primers (Edwards et al. 1989;
Lane 1991): pA (5′-AGA GTT TGA TCC TGG CTC AG3′) and R1492 (5′-TAC GGY TAC CTT GTT ACG ACT
T-3′). Amplification reactions were performed in volumes
of 50 ll containing 40 ng template DNA, 04 lmol l 1 of
each primer, 1X buffer with Mg2+, 1 unit of Taq DNA
Polymerase (Biotools) and 02 mmol l 1 dNTPs. Nucleases-free water was used to bring the reaction volume
to 50 ll. After initial denaturation at 95°C for 2 min,
samples were cycled for 30 PCR cycles using the following cycle profile: 95°C denaturation for 30 s, primer
annealing at 53°C for 30 s and primer extension at 72°C
for 2 min, plus a final 2-min elongation step at 72°C.
Amplified PCR products were separated by gel electrophoresis on 12% (w/v) agarose gel and then purified
using Nucleospinâ Extract PCR kit (Macherey-Nagel,
D€
uren, Germany). The 16S rDNA fragment (>1400 bp)
was fully sequenced (Macrogen, Seoul, Korea), and the
results were used for strain identification following comparison with existing sequences of Streptomyces type
strains (Altschul et al. 1997).
In vivo antagonism bioassays
Two Streptomyces isolates (ACTA1383 and ACTA1557)
were selected for in vivo experiments due to the strong
Streptomycetes as biocontrol agents against R. solani
suppression they caused to R. solani DSM843 growth in
vitro. A sandy silt loam soil (ASTM classification) with a
pH of 79 taken from an area under intense agricultural
exploitation in the Marathon area (42 km NE from the
centre of Athens) was used. Prior to its use, the soil was
air-dried in the dark at 22°C for at least 3 months,
passed through a 2-mm sieve and autoclaved twice
(121°C, 60 min) on two separate days.
Bean seeds were sterilized for 30 min in a 20% (w/v)
chlorine suspension and then dried under sterile conditions. A number of sterile seeds were immersed into a
suspension of streptomycetes spores in Ringer ¼ salt
solution (Wellington et al. 1990) (109 spores per ml)
for 30 min and then dried under sterile conditions.
Untreated sterile bean seeds and sterile bean seeds treated with the selected streptomycetes were planted in
pots containing sterile soil amended with Rhizoctonia
solani (3 g of wet washed mycelium per kg of soil) or
not (Lu et al. 2004). For every treatment, 24 seeds were
planted in each pot (three replicates for each pot were
prepared). Each full experiment was conducted in four
different occasions, over a time period of 8 months.
The pots were incubated at 28°C under fluorescent
light, and moisture was controlled daily at the level of
40% (w/w) for 25 days. The number of seeds that survived and/or germinated was evaluated to estimate the
ability of the examined streptomycetes to control the
fungi in vivo. In addition, the height and weight of the
emerged plants were measured for the estimation of
the in vivo antagonism strength. The same set of experiments was carried out using nonsterile soil of the same
origin.
Extraction and fractionation of streptomycetes
metabolites from solid and liquid cultures
In parallel, the Streptomyces isolates that showed the highest antifungal activity in vitro were grown on SAB [Streptomyces antibiotic broth (Atlas 1993)] because it was
selected as optimum medium for high antifungal activity
expression by the Streptomyces isolates. The cultures were
incubated at 28°C for 7 days in 1000-ml Erlenmeyer
flasks containing 500 ml of liquid medium on orbital
shaker S03, at 180 rpm. 500 ll of 108 spores ml 1 suspension was used as inoculum. Cultures were centrifuged
(Biofuge 28RS; Heraeus, Hanau, Germany) at 9000 g for
20 min. Supernatant was collected, concentrated by
lyophilization (1 : 100) and filtered (045 lm). For the
determination of antifungal activity, 200 ll from the concentrated culture supernatant was placed into wells on
SAA (Streptomyces antibiotic agar) plates (formed using
a cork borer – diameter 1 cm, depth 1 cm) that were
inoculated with the fungus.
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1471
Streptomycetes as biocontrol agents against R. solani
G.S. Kanini et al.
Additionally, the inhibition zones on SAA plates were
removed and blended for 3 min. The slurry was centrifuged at 40009g for 60 min and the supernatant was collected. After filtration, 200 ll was placed in a similar
manner into wells on SAA agar plates inoculated with the
fungus for the determination of the antifungal activity.
The extract from the solid culture of the four Streptomyces isolates (OL80, ACTA1523, ACTA1551 and
ACTA1522) was fractionated into a high molecular
weight (protein) and a low molecular weight (nonprotein) component on a PD-10 gel filtration column (GE
Healthcare, Athens, Greece) using de-ionized water for
elution, according to the manufacturer’s recommendation. Each fraction was concentrated by lyophilization
and examined for antifungal activity.
Data analysis
Statistical analysis of the various data sets was conducted
through one-way ANOVA (with post hoc pairwise multiple
comparisons by the Holm–Sidak method) and unpaired t
tests using SigmaStat/Plot software program (ver. 12.0;
Systat Software Inc., Chicago, IL, USA). In all runs, a
significance level of <005 was used.
Results
of them, encoded ACTA1383, was one among the 39
strains that were isolated from the rhizosphere of Ebenus
sibthorpii (Fabaceae), an endangered endemic plant
found in low numbers in the Kaisariani area, a preserved forest site, 4 km SE from the centre of Athens
(Katsifas et al. 1999). Two of the selected isolates,
encoded ACTA1557 and ACTA1551, were among the 24
isolates, found in large numbers, in the rhizosphere of
Pinus brutia, from a forest with coniferous trees on
Crete Island (Katsifas et al. 1999). The remaining three
isolates, encoded OL80, ACTA1522 and ACTA1523,
derived from the rhizosphere of Olea europa. All six isolates were among those that revealed the highest in vitro
antifungal activity (>7) against R. solani DSM843 (Table
3). The antagonistic activities among the six isolates
were statistically different as determined by one-way
ANOVA (F(5,12) = 82887, P = 00014). Post hoc paired
comparisons (Holm–Sidak method) revealed statistically
different antagonistic levels for all combinations of two
among the six isolates (P < 005), except for pairs that
included any two among the ACTA1551, ACTA1523 and
OL80 (P > 005).
Considering the BOX-PCR fingerprints of the six
selected micro-organisms, it was possible to group into
four different profiles according to their bar code; three
of these groups had only one representative (Fig. 1).
In vitro antifungal activity of the streptomycetes
A total of 213 strains of 605 (Athens University Microbiology Laboratory Culture Collection) showed in vitro
antagonistic activity against R. solani DSM843 (Table 1).
None of the isolates from Abies cefalonica rhizosphere
(sampling area 4) or from the rhizosphere of evergreen
shrubs of Ionian Sea Island (sampling area 7) were able
to suppress the phytopathogenic fungus, while only one
isolate from the area of Santorini Island (sampling area
10) showed antifungal activity.
Analysing the level of antifungal activity of the antagonistic isolates, they ranged from the minimum detectable
level of 13 to the maximum of 115. Comparing these
results (Table 1), it was found that Streptomyces isolates
with very high antagonistic activity against R. solani
DSM843 originated from the rhizosphere of the indigenous plants Olea europea, Pinus brutia and evergreen
shrubs spontaneous of the Aegean Sea Island (sampling
areas 3, 5 and 6).
Elaboration of the above findings and taking into
account the results from previous studies by our group
(Katsifas et al. 1999, 2000; Paululat et al. 2008; Baur
et al. 2006; Paululat et al. 2010; ACTAPHARM-Project,
Final Report, 2005, http://cordis.europa. eu/library) led
to the selection of six isolates, for further studies. One
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1
2
3
4
5
6
7
8
9
10
Figure 1 BOX-PCR-based fingerprinting analysis of the selected
Streptomyces isolates. Lane 1: 1000-bp ladder, Lane 2: water (negative control), Lane 3: ACTA1383, Lane 4: ACTA1557, Lane 5:
ACTA1551, Lane 6: ACTA1522, Lane 7: ACTA1523, Lane 8: OL80,
Lane 9: water (negative control), Lane 10: 1000-bp ladder.
Journal of Applied Microbiology 114, 1468--1479 © 2013 The Society for Applied Microbiology
G.S. Kanini et al.
Streptomycetes as biocontrol agents against R. solani
Three of the six isolates (ACTA1522, ACTA1523 and
OL80) shared the identical BOX-PCR bar code and
exhibited similar antifungal activity (Fig. 1). The rest of
the isolates showed very high antifungal activity and
revealed different BOX-PCR profiles, independently of
their habitat of origin. 16S rRNA gene sequence data
grouped the selected isolates to type strains of streptomycetes as shown in Table 2.
In vivo antifungal activity
Knowing that the culture medium is a crucial factor that
can affect the antagonistic character that microbes
express, we used the results from the in vitro antagonistic
assay to lead us to the selection of ACTA1383 (Streptomyces pseudovenezuelae) and ACTA1557 (Streptomyces fulvisimus) so as to use them for in vivo studies. This selection
was based on their very high antifungal activity expressed
in vitro (Table 3) and the observation from previous
work (Katsifas et al. 1999, 2000; Baur et al. 2006; Paululat et al. 2008, 2010) that they are multiproducers of bioactive substances. Thus, they characterized as promising
biocontrol agents in vivo.
Analysis of particle size of the soil that used for this
purpose indicated the presence (%, dry weight) of sand,
50; silt, 36; clay, 14. Mineralogy analysis showed the presence of (%, dry weight) illite, 65; chlorite, 7; kaolinite,
10; smectite, 12; talc, 6 and calcite <1. Phosphorus content was 124 mg l 1 dry soil and organic carbon was
123% (dry weight).
Macroscopic observation from these experiments indicated that, although the R. solani DSM843 mycelium
was developed in all cases, the extent of mycelial growth
was strongly dependent on the presence of the
streptomycetes.
In sterile soil experiments, germination of the streptomycete-treated seeds was markedly increased when compared to the untreated seeds (Table 4A), because
untreated seeds planted in sterile soil and infected with
the fungus (negative control A) showed very low levels
of germination (only the 27% of the planted seeds germinated) and very poor plant growth. Almost 40% of
Table 3 Antagonistic activity levels of the selected isolates as
expressed by the quotient of the inhibition zone area over streptomycete colony area (In vitro antagonism bioassays)
Streptomyces isolates
Antagonistic level
Streptomyces
Streptomyces
Streptomyces
Streptomyces
Streptomyces
Streptomyces
741
970
901
868
908
901
pseudovenezuelae ACTA1383
fulvissimus ACTA1557
rochei ACTA1551
longisporoflavus ACTA1522
longisporoflavus ACTA1523
longisporoflavus OL80
005
040
026
009
089
047
the streptomycete-treated seeds, planted in the same
R. solani DSM843-infected sterile soil, were able to germinate (Table 4A). Comparison of germination results
between the two streptomycete treatments did not yield
any statistically significant differences. The mean weights
of plants were very similar among the positive control
and the two streptomyces-treated seeds. In fact, the
plant weights between the positive control and
ACTA1557-treated seeds did not significantly differ,
while those of the ACTA1383-treated seeds were only
10% lower than the positive control. On the contrary,
the plant heights of the streptomycete-treated seeds
reached on average only the 15% the positive controls
heights. This weight/height pattern of plants in the sterile soil experiment reflects the difference in the morphology of the treated seed plants that were generally
‘shorter’ and ‘thicker’ (Fig. 2).
The in vivo results for the nonsterile soil were similar
to the sterile soil experiments as far as seed germination
is concerned (Table 4B). The only statistically significant
difference involved the reduced germination of the
ACTA1557-treated seeds in nonsterile soil (as compared
both against the same treatment in sterile soil and
against ACTA1383 in nonsterile soil). This was also
reflected in the plant weights where those of
ACTA1557-treated seeds were significantly lower than
those of the ACTA1383-treated seeds. Nonsterile soil
environment in general, though, had a significant positive effect on plant weight and height of the positive
controls and the streptomycete-treated seeds, when
Table 2 Taxonomy of the six selected streptomycetes by 16S rRNA gene sequence data
Streptomyces isolates
Closest phylogenetic relative (GeneBank Accession number)
% Identity*
GeneBank Accession number
ACTA1383
ACTA1557
ACTA1551
ACTA1522
ACTA1523
OL80
Streptomyces
Streptomyces
Streptomyces
Streptomyces
Streptomyces
Streptomyces
990
990
990
990
990
990
JN167527
JN167524
JN167525
JN167526
JN167528
JN167529
pseudovenezuelae (FR682807.1)
fulvissimus (AB184787.1)
rochei (HQ909756.1)
longisporoflavus (EF178687.1)
longisporoflavus (EF178687.1)
longisporoflavus (EF178687.1)
*The percentage identity with the 16 rDNA sequence of the closest phylogenetic relative.
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Streptomycetes as biocontrol agents against R. solani
G.S. Kanini et al.
Table 4 Germination data of bean seeds during in vivo antagonism bioassays. The total number of planted bean seeds was (24 per pot) 9
(three replicates for each pot) 9 (four independent experiments) = 288. Data from all experiments were combined for the analysis
Experimental set (abbreviation)
(A) Sterile soil
Positive control A (PcA)§
Streptomyces fulvissimus ACTA1557 (1557A)
S. pseudovenezuelae ACTA1383 (1383A)
Negative control A (NcA)¶
(B) Nonsterile soil
Positive control B (PcB)§
S. fulvissimus ACTA1557 (1557B)
S. pseudovenezuelae ACTA1383 (1383B)
Negative control B (NcB)¶
Total number (percentage
of germinated seeds)
Average of germinated
seeds per pot*
Mean weight
of plants (g)†
Mean height
of plants (cm)‡
232
116
100
8
(806)
(403)
(347)
(27)
1933
967
833
067
058
058
153
058
141
130
127
039
020
033
022
027
316 432
43 075
395 084
092 065
252
76
128
8
(875)
(264)
(444)
(27)
2100
633
1067
067
173
115
153
058
308
206
275
032
043
052
071
025
364
335
358
106
625
857
990
091
*One-way ANOVA on the number of germinated seeds per pot: Sterile soil (A) groups: Differences in the mean values among the treatment groups
[PcA, 1557A, 1383A and NcA] are statistically significant (P = <0001), and the corresponding pairwise multiple comparisons (Holm–Sidak
method) are all significantly different (P = <0001) except 1557A vs 1383A, which was not statistically significant (P = 0155). Nonsterile (B) soil
groups: the differences in the mean values among the treatment groups [PcB, 1557B, 1383B and NcB] are statistically significant (P = <0001)
and the corresponding pairwise multiple comparisons (Holm–Sidak method) are all significantly different (P = <0001). Pairwise comparisons
among sterile (A) and nonsterile (B) groups: PcA vs PcB and 1383A vs 1383B, not significantly different (P = 0189 and 0135, respectively).
1557B vs 1353B significantly different (P = 0011).
†Unpaired t-test on plant weights: PcA vs 1557A and 1557A vs 1383A not significantly different (P > 005). PcA vs 1383A significantly different
(P < 0001). PcB vs 1557B or 1383B and 1557B vs 1383B, all significantly different (P < 001). PcA vs PcB, 1557A vs 1557B and 1383A vs 1383B
all significantly different (P < 0001).
‡Unpaired t-test on plant heights: PcA vs 1557A or 1383A significantly different (P < 0001). 1557A vs 1383A, significantly different (P < 002).
PcB vs 1557B or 1383B and 1557B vs 1383B all not significantly different (P > 015). PcA vs PcB, 1557A vs 1557B and 1383A vs 1383B all
significantly different (P < 0001).
§Positive control: Noninfected sterile (A) or nonsterile (B) soil planted with sterilized seeds.
¶Negative control: Rhizoctonia solani-infected sterile (A) or nonsterile (B) soil planted with sterilized seeds.
controls and the treated seeds nor between the two
treatments (Table 4B and Fig. 3).
These results showed that Streptomyces pseudovenezuelae ACTA1383 proved more effective as a biocontrol
agent against Rhizoctonia solani in nonsterile processes
because seeds treated with its spore suspension promoted
better growth of the bean plants resulting in plants with
improved height and weight (Figs 2 and 3).
Streptomycetes metabolites from solid and liquid
cultures; fractionation of the extracts
(a)
(b)
(c)
(d)
Figure 2 In vivo antifungal ability of the selected Streptomyces isolates in sterile soil experiments – Growth of the bean plants (from left
to right). (a) Untreated seed planted in untreated sterile soil (positive
control), (b) seed treated with Streptomyces fulvisimus ACTA1557
and planted in Rhizoctonia solani DSM843-infected soil, (c) seed treated with Streptomyces pseudovenezuelae ACTA1383 and planted in
R. solani DSM843-infected soil and (d) untreated seed planted in
R. solani DSM843-infected soil (negative control).
compared to sterile soil results. This was especially true
for the heights of the plants that did not reveal any
significant differences neither between the positive
1474
The concentrated extracts from the liquid cultures did
nοt show any significant antifungal activity, while the
extracts taken from the agar inhibition zones of four of
the six isolates could strongly suppress the growth of
R. solani DSM843 (Fig. 4).
Following fractionation of the bioactive extracts in a
gel filtration column, the antifungal activity was observed
in the low molecular weight fractions.
Discussion
Selected Streptomyces sp. has been used in several studies
for the direct biocontrol of various plant diseases (Yuan
Journal of Applied Microbiology 114, 1468--1479 © 2013 The Society for Applied Microbiology
G.S. Kanini et al.
Streptomycetes as biocontrol agents against R. solani
(a)
(b)
(c)
(d)
Figure 3 In vivo antifungal ability of the selected Streptomyces isolates in nonsterile soil experiments – Growth of the bean plants (from left to
right). (a) Untreated seed planted in untreated sterile soil (positive control), (b) seed treated with Streptomyces fulvisimus ACTA1557 and planted
in Rhizoctonia solani DSM843-infected soil, (c) seed treated with Streptomyces pseudovenezuelae ACTA1383 and planted in R. solani DSM843infected soil and (d) Untreated seed planted in R. solani DSM843-infected soil (negative control).
(a)
(b)
(c)
(d)
(e)
Figure 4 Antifungal activity of the concentrated medium extracts derived from the solid cultures of four Streptomyces. Inhibition zone caused
from (a) S. longisporoflavus ACTA1522 extract, (b) S. longisporoflavus ACTA1523 extract, (c) S. longisporoflavus OL80 extract, (d) S. rochei
ACTA1551 extract and negative control (no streptomycete extract added) (e).
and Crawford 1995; Abd-Allah 2001; Neeno-Eckwall et al.
2001; Getha and Vikineswary 2002; Shekhar et al. 2006).
In addition, selected ecosystems such as tomato plant rhizosphere (Cao et al. 2004), banana roots (Cao et al.
2005) and wheat root tissues (Coombs and Franco 2003)
have been recently used as a source for the isolation of
streptomycetes with antifungal activity. However, studies
involving the evaluation and comparison of indigenous
streptomycete potential as biocontrol agents from a variety of different ecosystems are limited in the literature
(Gomes et al. 2000; Neeno-Eckwall et al. 2001; Shekhar
et al. 2006). The present work involved the screening of
605 Streptomyces isolates, originating from 12 different
and important habitats within the Greek territory, against
phytopathogenic fungus R. solani DSM843 and the evaluation of the in vitro and the in vivo antifungal activity of
selected streptomycetes. Previous work on Streptomyces
isolates of the Athens University Microbiology Laboratory
Culture Collection used in this study (Katsifas et al.
1999) grouped them into 19 different clusters according
to phenotypic identification with some species to be present in more than one habitat and some others to be
unique in some sites.
The data of this work, additionally to the above studies, suggested that sampling areas 1, 3 and 5 (Table 1)
were a rich pool of not only diverse species, but also
active species with high antagonistic activity, a suggestion
that may reflect the relation of their features with the
habitat of origin.
Particularly, the results from the in vitro antifungal
activity experiments showed that almost one-third of the
examined isolates could be antagonistic to R. solani
DSM843. Such a percentage (about 35%) justified that
the genus of Streptomyces could be the most appropriate
and promising target for biotechnological applications
and especially for biocontrol uses. In addition, it could
support a hypothesis that the Greek soil is a convenient
substrate for hosting such microbial communities’ biocontrol agents (Baur et al. 2006; Paululat et al. 2008,
2010). The latter is in agreement with the previous observations that the Greek Streptomyces isolates are multiactive compared to isolates from other countries
(ACTAPHARM, Final Report, 2005, http://cordis.europa.
eu/library).
The Aegean Sea climate, characterized by its high temperatures and low humidity, results in a soil poor in
Journal of Applied Microbiology 114, 1468--1479 © 2013 The Society for Applied Microbiology
1475
Streptomycetes as biocontrol agents against R. solani
G.S. Kanini et al.
nutrients. This fact creates conditions of environmental
stress on the indigenous populations of streptomycetes
and possibly leads to the prevalence of micro-organisms
with antagonistic properties. Furthermore, combined with
the high anthropogenic impact on the Aegean Sea
Islands, this could probably explain the high percentages
of isolates collected from the rhizosphere soil of the plant
Pinus brutia (indigenous plant of Crete) and of the evergreen shrubs that were antagonistic to R. solani in vitro.
On the contrary, both the rhizosphere of Abies cefalonica
and evergreen shrubs in the Ionian Sea Islands, which
were deliberately selected from areas less touristic and less
anthropogenically disturbed, did not yield any isolates
with antifungal activity obviously as a result of the very
different climatic conditions of the soil of origin (areas of
high humidity and low anthropogenic impact).
High percentages (538%) of isolates antagonistic to
the phytopathogenic fungi were also collected from a
nonrhizosphere sample of an agricultural area in Marathon (Attica District). This result again may be due to
the fact that the soil of origin was characterized by medium–high temperatures and human activity influence
(use of fertilizers and synthetic fungicides).
The results from the in vivo antagonism tests were
encouraging as they supported the possible systematic
use of the two selected Streptomyces strains for crop protection. It is known that the antagonistic profile of the
micro-organisms is strongly depended on the growth
conditions and there are differences between laboratory
cultures and in vivo processes. In addition, in vitro
assays are necessary for the screening of the potential
antagonistic strains. Therefore, laboratory cultures were
used as an original indication as it was the only way to
choose the strains for further research. It was shown
that the selected strains could express their antifungal
activity in vivo quite well. Interestingly, these results are
in agreement with those from previews studies on the
potential of Streptomyces isolates to be used as biocontrol agents. For instance, Mahadevan and Crawford
(1997) found that Streptomyces lydicus was identified as
a broad spectrum biocontrol agent while the results
from Farrag (2011) enhanced that finding. Moreover,
Reddi and Rao (1971) reported that isolates of Streptomyces ambofaciens were able to control Pythium damping-off in tomato plants and Fusarium wilt in cotton
plants, in an artificially infested soil. Rothrock and Gottlieb (1984) showed that S. hygroscopicus could effectively
control Rhizoctonia root rot in pea plants in growth
chambers, and Maldonado et al. (2010) proved that a
Streptomyces strain originated from Argentina reduced
damage caused by P. digitatum and Geotrichum candidum on citrus plants. These results correspond important indications for the utility of Streptomyces fulvisimus
1476
ACTA1557 and Streptomyces pseudovenezuelae ACTA1383
for the protection of the bean crops. Of additional
importance is that through our experimental approach,
the antifungal compounds excreted by the streptomycetes can provide their protective action to the plant just
by simple coating of the seeds with spore suspension
prior to sowing. This inoculation method has been
proved more effective as the biocontrol agent can rapidly and extensively cover the surface of the seeds (Lu
et al. 2004). Early colonization by a biocontrol agent
often is required to fill the critical niches and to effectively compete against pathogenic fungi (Mitchell 1992).
Thus, seed coating with bacterial and fungal biocontrol
agents often is utilized or required to control aggressive,
rapidly growing soil-borne pathogens, such as R. solani
(Mitchell 1992; Crawford et al. 1993; Nerey et al. 2010).
Additionally, this procedure is much easier to implement and more applicable for large scale cultivation,
compared to the classic one that includes enrichment of
the soil with the biocontrol agents, which is both
time-consuming and difficult to apply in real farming
conditions (Yuan and Crawford 1995; Whipps 2001).
Moreover, the data from the nonsterile soil experiments
enhanced the potential of the selected streptomycetes to
be used as biocontrol agents in real farming conditions
as it was shown that the coexistence of the examined
micro-organisms, especially Streptomyces pseudovenezuelae
ACTA1383, with the native microflora of the soil, made
the former more effective. The type of soil that reflects
on its microflora composition has been referred as an
important factor that affects the results of in vivo
biocontrol procedures. Suppressive soils contain microorganisms that are antagonistic to the pathogen or
promote the growth of the target plant (Whipps 2001).
The presence of these microbes, in combination with
the high populations of the introduced biocontrol
agents, can enhance the antimicrobial activity of the latter. Additionally, sterilization of soils by pasteurization,
fumigation or autoclaving usually allows the pathogen to
proliferate (Burgess et al. 1988), while in nonsterile soils,
the native microflora slows up the growth of the pathogen giving the opportunity to the biocontrol agent to
express its antimicrobial activity more effectively. This
observation may lead to the conclusion that not only
the germination of the seeds but also the growth of the
plants could be enhanced in situ by planting bean seeds
treated with Streptomyces pseudovenezuelae ACTA1383 in
the crop. Some questions could be raised for the application of the selected Streptomyces isolates (Streptomyces
fulvisimus ACTA1557 and Streptomyces pseudovenezuelae
ACTA1383) as biocontrol agents against Rhizoctonia
solani in real farming conditions, but the above results
could be characterized as a promising first step against
Journal of Applied Microbiology 114, 1468--1479 © 2013 The Society for Applied Microbiology
G.S. Kanini et al.
the agricultural–commercial exploitation of the selected
indigenous Streptomyces isolates, although the experiments were performed using only one type of soil and
one plant type as fungal target.
Considering that the mechanism of the antifungal
activity may vary among the production of antibiotic
compounds, the promotion of plant growth, the induction of systemic resistant to plants and the mycoparasitism (Haas and Defago 2005), we examined, in parallel,
the antifungal activity of both liquid culture concentrates
and solid culture extracts, in an effort to evaluate the biochemical characteristics of the antifungal metabolites. The
fact that antifungal activity was observed only in the solid
culture extracts and not in the liquid culture supernatants
may be attributed to the intrinsic differences between the
two growth conditions that may very well result in different excretion phenotypes. For instance, in liquid cultures,
the possible antifungal metabolites may be more susceptible to enzymatic breakdown, a phenomenon that is much
less intense in solid media where the antifungal/microbial
substances are continually diffusing into the agar (Buynitzky et al. 1979). The difference in oxygen availability,
which is higher for micro-organisms growing in solid
media, is another important factor that causes general
changes in the metabolism that probably results in differences in the expression levels of the various metabolites
by the streptomycete strains. In addition, the nutrient
limitation in the microenvironment around a growing
colony on solid agar media could induce the biosynthesis
of secondary metabolites (Buynitzky et al. 1979; Doelle
et al. 1992; Lahlali and Hijri 2010). Finally, the observation that the antifungal activity was present only in the
solid media extracts and not in the concentrates of the
streptomycete liquid cultures could also indicate a specific induction pattern that was caused by the simultaneous presence of a growing fungal mycelium on the
agar plates.
The fact that the antifungal activity was detected at the
low molecular weight fraction of the streptomycete solid
medium extracts suggested that the active compound(s)
was probably not a protein (hydrolytic enzyme) but
rather a smaller organic compound, such as a secondary
metabolite. Further biochemical analysis, using high-performance liquid chromatography fractionation coupled
with mass spectrometry and nuclear magnetic resonance
techniques, will allow us to refine its structure.
Acknowledgements
The study was supported by the National and Kapodistrian University of Athens’ Special Account for Research
Grants –’Kapodistrias’ Code No 70/4/4242.
Streptomycetes as biocontrol agents against R. solani
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