336 / Molecular Plant-Microbe Interactions
MPMI Vol. 24, No. 3, 2011, pp. 336–351. doi:10.1094/MPMI-09-10-0221.
Endophytic Trichoderma Isolates
from Tropical Environments Delay Disease Onset
and Induce Resistance Against Phytophthora capsici
in Hot Pepper Using Multiple Mechanisms
Hanhong Bae,1,2 Daniel P. Roberts,1 Hyoun-Sub Lim,1,3 Mary D. Strem,1 Soo-Chul Park,4 Choong-Min Ryu,5
Rachel L. Melnick,1 and Bryan A. Bailey1
1U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705,
U.S.A.; 2School of Biotechnology, Yeungnam University, 214-1 Daedong, Gyeongsan-si, Gyeongbuk-do 712-749, Korea;
3Department of Applied Biology, Chungnam National University, Daejeon, 305-764, Korea; 4Molecular
Genetics Division, National Institute of Agricultural Science and Technology, RDA, Suweon 441-707, Korea; 5Systems
Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-600, Korea
Submitted 29 September 2010. Accepted 17 November 2010.
Endophytic Trichoderma isolates collected in tropical envi-
ronments were evaluated for biocontrol activity against
Phytophthora capsici in hot pepper (Capsicum annuum).
Six isolates were tested for parasitic and antimicrobial ac-
tivity against P. capsici and for endophytic and induced
resistance capabilities in pepper. Isolates DIS 70a, DIS
219b, and DIS 376f were P. capsici parasites, while DIS
70a, DIS 259j, DIS 320c, and DIS 376f metabolites inhib-
ited P. capsici. All six isolates colonized roots but were inef-
ficient stem colonizers. DIS 259j, DIS 320c, and DIS 376f
induced defense-related expressed sequence tags (EST) in
32-day-old peppers. DIS 70a, DIS 259j, and DIS 376f de-
layed disease development. Initial colonization of roots by
DIS 259j or DIS 376f induced EST with potential to impact
Trichoderma endophytic colonization and disease develop-
ment, including multiple lipid transferase protein (LTP)-
like family members. The timing and intensity of induction
varied between isolates. Expression of CaLTP-N, encoding
a LTP-like protein in pepper, in N. benthamiana leaves re-
duced disease development in response to P. nicotianae
inoculation, suggesting LTP are functional components of
resistance induced by Trichoderma species. Trichoderma
isolates were endophytic on pepper roots in which, de-
pending on the isolate, they delayed disease development
by P. capsici and induced strong and divergent defense
Genus Trichoderma species have been described as “oppor-
tunistic avirulent plant symbionts” due to their abilities to bene-
fit from and provide benefit in direct interactions with plants
(Harman et al. 2004). Most of this discussion centered on
Trichoderma spp. as soil inhabitants and root colonizers. The
biocontrol capabilities of several Trichoderma species have
been extensively documented (Harman et al. 2004). Tricho-
derma isolates employ several mechanisms in providing bio-
control of disease, including antibiosis, parasitism, and induced
resistance. In the context of Trichoderma species limiting dis-
ease, antibiosis results from the production of antimicrobial
metabolites by Trichoderma spp. (Harman et al. 2004; Howell
1998, 2003), while parasitism is evidenced by the direct pene-
tration and parasitism of pathogens by Trichoderma spp. (Chet
et al. 1998; Harman et al. 2004). Induced resistance results
when plant defense is activated in response to Trichoderma
colonization (Alfano et al. 2007; Djonovic et al. 2006; Harman
et al. 2004; Korolev et al. 2007; Meyer et al. 1998; Segarra et
al. 2009; Shoresh and Harman 2008a; Shoresh et al. 2005). A
Trichoderma isolate may use more than one of these mecha-
nisms in providing biocontrol of plant diseases.
We have been studying a group of Trichoderma isolates col-
lected from highly competitive tropical environments (Bailey et
al. 2006, 2008). They are unique because they were isolated as
endophytes not of roots but of aerial plant tissues, including tree
trunks, stems, and fruit (Bailey et al. 2006, 2008). In developing
this collection, many new Trichoderma species have been de-
scribed. Examples include T. ovalisporum (Holmes et al. 2004),
T. martiale (Hanada et al. 2008), T. stromaticum (Samuels et al.
2000), T. theobromicola, and T. paucisporum (Samuels et al.
2006b), T. koningiopsis (Samuels et al. 2006a), and T. evansii
(Samuels and Ismaiel 2009). The biocontrol potentials of these
newly described species are being studied, but details on their
activities are lacking. Primarily, they have been studied in the
tropical crop Theobroma cacao (Bailey et al. 2006; Hanada et al.
2008; Holmes et al. 2004; Samuels et al. 2000).
Although collected from plants in tropical climates, we see
no a priori reason why the biocontrol potential of these Tricho-
derma isolates should be limited to tropical cropping systems.
Specificity may exist between microbes and their host plants
through coevolution (Burdon and Thrall 2009). The possibility
that plant host specificity has contributed to the development
Current address for Hanhong Bae: School of Biotechnology, Yeungnam
University, 214-1 Daedong, Gyeongsan-si, Gyeongbuk-do 712-749, Korea.
Current address for Hyun-Sub Lim: Department of Applied Biology, Chung-
nam National Univ., Daejeon, 305-764, Korea.
Corresponding author: B. A. Bailey; E-mail: firstname.lastname@example.org
*The e-Xtra logo stands for “electronic extra” and indicates that two supple-
mentary tables and supplementary results information are published online.
Figure 1 also appears in color online.
This article is in the public domain and not copyrightable. It may be freely
reprinted with customary crediting of the source. The American Phyto-
pathological Society, 2011.
Vol. 24, No. 3, 2011 / 337
of new Trichoderma species capable of colonizing plant cano-
pies in a tropical environment is intriguing but yet unproven.
One of the diseases being targeted for biocontrol in cacao is
black pod, caused by several Phytophthora species including
P. capsici, P. citrophthora, P. palmivora, and P. megakarya
(Guest 2007). Phytophthora species cause disease in many dif-
ferent plant species (Birch et al. 2006). P. capsici has a broad
host range but isolates can show specificity (Tian and Babadoost
2004). For example, although some isolates of P. capsici cause
disease on cacao, others cause a devastating disease on hot
pepper (Capsicum annuum), causing severe yield losses (Kim
and Hwang 1992).
In this study, the first objective was to determine if Tricho-
derma isolates collected as endophytes of plants in tropical cli-
mates can establish endophytic relationships with hot pepper
and can provide control of disease in the P. capsici–pepper
pathosystem. The second objective was to characterize the dif-
ferent biocontrol activities possessed by the Trichoderma iso-
lates and the consequences of their endophytic associations
with pepper. The third objective was to determine whether
transient expression of Trichoderma-induced pepper expressed
sequence tags (EST) related to resistance could reduce disease
development in N. benthamiana leaves infected by P. nicotia-
The six Trichoderma isolates (Table 1) were evaluated for
their abilities to parasitize P. capsici mycelia. Five of the six
isolates (all but DIS 320c) completely colonized the P. capsici
precolonized plates within 7 days (Table 2). Only three of the
isolates, DIS 70a, DIS 219b, and DIS 376f, prevented P. cap-
sici from being reisolated from the P. capsici side of the pre-
colonized plates (Table 2). P. capsici was not reisolated, while
DIS 320c was reisolated. Water agar slides were coinoculated
with P. capsici and individual Trichoderma isolates. Intense
coiling of DIS 259j mycelia on and around the P. capsici my-
celia was observed but without penetration (Fig. 1H). DIS 70a
(Fig. 1F) and DIS 376f (Fig. 1E) directly penetrated the P. cap-
sici mycelia but without significant coiling. DIS 219b (Fig.
1C) and DIS 85f (Fig. 1G) were observed to form parallel
associations with P. capsici mycelia, but penetration was not
observed. DIS 320c repressed normal growth of P. capsici, re-
sulting in densely stained mycelium tips (Fig. 1D), but neither
coiling nor penetration was observed.
Antibiosis and phytotoxicity.
Extracellular metabolites were harvested from Trichoderma
culture filtrates and were evaluated for their antibiosis activi-
ties against P. capsici and their phytotoxic activities against
pepper. In the antibiosis study, DIS 320c completely prevented
growth of P. capsici (Table 2). DIS 259j, DIS 70a, and DIS
376f produced metabolites that inhibited growth of P. capsici
56.5, 30.7, and 19.2%, respectively (Table 2). Metabolites pro-
duced by DIS 320c also damaged pepper roots, causing the
tips to brown (data not shown). The metabolites produced by
the other isolates did not damage pepper roots.
Trichoderma endophytic growth in hot pepper.
The six Trichoderma isolates (Table 1), DIS 70A, DIS 85f,
DIS 219b, DIS 259j, DIS 320c, and DIS 376f, were 100% effi-
Table 2. Endophytic growth, parasitism, and antibiosis activities of six selected endophytic Trichoderma isolatesw
Phytophthora capsici side
Trichoderma side Growth inhibitionz
Isolate Root Stem T P T P Colony diameter Inhibition
– 100 – 100 2.6 ± 0.04
1.80 ± 0.04
3.08 ± 0.04
3.65 ± 0.06
1.13 ± 0.05
2.10 ± 0.07
w Endophytic growth was determined by the ability of Trichoderma isolates to internally colonize pepper roots or stems and survive surface sterilization.
Parasitism was determined by the ability of Trichoderma isolates to colonize P. capsici precolonized plates from the Trichoderma-inoculated side to the
opposite edge where the P. capsici was originally inoculated and to prevent P. capsici regrowth from subsamples. Antibiosis was determined by the ability
of Trichoderma metabolites from culture filtrate to inhibit growth of P. capsici when incorporated into agar media.
x Seedlings grown for 35 days in Trichoderma-precolonized soil were dissected and surface-sterilized, and approximately 1-cm of surface-sterilized tissue
sections of roots and stems were plated on cornmeal dextrose agar. For each seedling, four lower stem sections and one root section were plated and were
observed for Trichoderma growth (percentage of sections showing growth).
y At 7 days after inoculation of P. capsici-precolonized plates with Trichoderma isolates, agar plugs were removed from the P. capsici- and Trichoderma-
inoculated sides. Each plug was plated and observed for growth of Trichoderma (T) or P. capsici (P). Data are presented as percentage of plugs showing
growth of P. capsici or Trichoderma.
z A 5-mm-diameter plug of P. capsici R198 was added to agar plates containing heat-treated Trichoderma culture filtrates in minimal salts broth agar media.
The mean radial growth of P. capsici was observed after 5 days of incubation. Data are presented as colony diameter ± standard error and percent inhibition
of growth relative to growth on control plates.
Table 1. Trichoderma isolates used, their species, host plant, country of origin, and reference to isolate or species description
Isolate Species Host Origin Reference
T. caribbaeum var. aequatoriale
Holmes et al. 2004
Samuels et al. 2006b
Bae at al. 2009
Lu and Samuels 2003
Samuels et al. 2006a
Samuels and Ismaiel 2009
z Isolate DIS 259j has only recently been described. All of the strains were provided by G. J. Samuels, who identified them by sequencing a 0.65-kb region
of the translation-elongation factor 1-alpha (tef1) gene. The GenBank number for isolate DIS 259j tef1 is GQ862819.
338 / Molecular Plant-Microbe Interactions
cient in colonizing pepper roots (Table 2). In contrast, the maxi-
mum endophytic colonization of pepper stems by any isolate
Late-stage systemic induced resistance.
Depending on the isolate, Trichoderma colonization altered
expression of candidate stress responsive genes and EST in 32-
day-old pepper seedlings. Data for 12 genes and EST (Table 3)
are presented for roots (Fig. 2) and leaves (Fig. 3). Genes
CaLTP1, CaCH21, CaPO1, CaPR4, CaSC1, and CaPEAS1
showed altered expression in pepper roots 32 days after Tricho-
derma colonization in an isolate-dependent manner (Fig. 2).
DIS 259j, DIS 320c, and DIS 376f were the most consistent
inducers of gene and EST expression in root. Inoculation of
pepper roots with Trichoderma spp. altered the expression of
genes and EST in leaves encoding pathogenesis-related (PR)
proteins (CaLTP1, CaPR1, CaCHI2, CaPR4), enzymes involved
in secondary metabolism (CaSC1, CaHMG2), hormone biosyn-
thesis or action (CaJA2, CaNPR1, CaGA2ox), and gene regu-
lation (CaMAPK4, CaMK1). The Trichoderma isolates altering
gene and EST expression in leaves most consistently were DIS
259j, DIS 320c, and DIS 376f (Fig. 3).
Biocontrol of disease.
Pepper seedlings (42-day-old) precolonized by individual
Trichoderma isolates were transplanted into P. capsici–in-
fested soil and were observed for disease symptom develop-
ment for 14 days (Fig. 4). Symptoms typically were expressed
as a rapidly expanding black lesion at the stem base, emanat-
ing from below the soil line, followed by wilting within 24 h.
The most consistent isolate in delaying symptom expression
was DIS 376f, which delayed symptom expression by more
than three days when averaged over the three independent dis-
ease assays (Table 4). At the end of the three disease assays
(Fig. 4), 50, 60, and 25% of the pepper seedlings precolonized
by DIS 376f remained asymptomatic while 0, 10, and 0% of
control plants remained asymptomatic. DIS 259j and DIS 70a
were next in efficiency at delaying symptom expression when
considered over all three disease assays (Table 4).
Early induced responses
to Trichoderma colonization in hot pepper.
In order to study the early interactions between the Tricho-
derma spp. and hot pepper, seedlings were grown on artificial
media for 14 days and were then inoculated with individual
Trichoderma isolates. Initially, a study was carried out using
all six Trichoderma isolates and 24-day-old seedlings. The
roots were harvested after 72 h of exposure to Trichoderma
Table 3. Pepper genes and expressed sequence tags (EST) used in evaluating the response of pepper seedlings to Trichoderma colonization
EST Putative function GenBank ID Citation
Pathogenesis related (PR1)
Lipid tranferase-like protein (LTP)-like (LTPI/PR2)
Chitinase class II
3-hydroxy-3-methyl-glutaryl-coenzyme A reductase
Cell wall peroxidase
Gibberellic acid 2-oxidase
Mitogen-activated protein kinase 1 (MK1)
Kim and Hwang 2000
Jung et al. 2003
Shin et al. 2001
Hong et al. 2000
Back et al. 1998
Ha et al. 2003
Do et al. 2003
Choi et al. 2007
Zavala-Paramo et al. 2000
Shin et al. 2001
Shin et al. 2001
Fig. 1. Interactions between Trichoderma isolates and Phytophthora cap-
sici on water agar slides. Glass slides covered with water agar were inocu-
lated at opposite ends with agar plugs of P. capsici R198 and individual
Trichoderma isolates. After 5 days of incubation, the slides were stained
with lacto phenol cotton blue and were observed under the microscope
(600× magnification) in areas at which the Trichoderma isolates had
overgrown the P. capsici. A, P. capsici mycelium, B, P. capsici germi-
nating sporangia, P. capsici in the presence of Trichoderma, C, DIS 219b,
D, DIS 320c, E, DIS 376f, F, DIS 70a, G, DIS 85f , H, DIS 259j. P = P.
capsici, T = Trichoderma, TIP = Trichoderma mycelium in Phytophthora
mycelium, TOP = Trichoderma mycelium on Phytophthora mycelium.
The size bar for the figure (H) represents 16.7 µm.
Vol. 24, No. 3, 2011 / 339
spp., and gene and EST expression was evaluated by quantita-
tive polymerase chain reaction (qPCR). In these same samples,
expression of the Trichoderma actin gene (TriACT) was deter-
mined. The data are presented in two ways: i) for fungal actin
(TriACT) and hot pepper genes and EST, EST expression as a
percent of hot pepper actin expression, and ii) for hot pepper
genes and EST, the fold increase in EST expression relative to
TriACT expression (FI/%Tact) as described below. All six Tricho-
derma isolates altered expression of one or more pepper genes
and EST relative to plant actin expression, but the strongest
inducers were DIS 219b and DIS 259j (Fig. 5, left panel).
When pepper gene and EST fold induction is calculated in
terms relative to TriACT expression, which proposes Tricho-
derma colonization, a different picture emerges. DIS 85f, DIS
259j, and DIS 376f were stronger inducers of pepper gene ex-
pression when the level of Trichoderma colonization was con-
sidered (Fig. 5, right panel). The expression levels for TriACT
were 12.2, 2.7, 15.9, 1.5, 7.1, and 4.4% of pepper actin
(CaACT) expression for DIS 70a, DIS 85f, DIS 219b, DIS
259j, DIS 320c, and DIS 376f, respectively. Based on the ex-
pression level of TriACT in root tissues 72 h after Trichoderma
inoculation, DIS 219b and DIS 70a heavily colonized pepper
Fig. 2. Gene expression in pepper roots 32 days after inoculation with Trichoderma isolates. Pepper seeds were planted in Pro-Mix PGX inoculated with
Trichoderma isolates. Seedlings were grown in a controlled environment chamber with a 12-h-light and 12-h-dark photoperiod at 25°C. After 32 days, roots
were harvested for quantitative polymerase chain reaction. Genes and expressed sequence tags (Table 3) include CaLTP1, CaCHI2, CaPO1, CaPR4, CaSC1,
CaPEAS1, CaHMG2, CaMK1, CaGA2ox, CaMAPK4, CaJA2, and CaPR1.
340 / Molecular Plant-Microbe Interactions
roots followed by DIS 320c and DIS 376f, followed by DIS
85f, and then DIS 259j.
Microarray analysis using a single biological replication was
carried out (Supplementary Results) to identify candidate EST
for further analysis of DIS 259j- and DIS 376f-induced sam-
ples by qPCR, using a 36- to 72-h timecourse fully replicated
six times. The universal TriACT primer set (Supplementary Ta-
ble S1) was used to assess the relative level of colonization of
the pepper roots by DIS 259j and DIS 376f (Fig. 6). Visual ob-
servations of plate colonization indicate the two Trichoderma
isolates completely colonized the plates the pepper seedlings
were growing on, with less than a 12-h difference between the
two isolates (Fig. 6A). The levels of TriACT transcript detected
for each isolate were different from levels detected in the con-
trol samples but were not different between isolates regardless
of the time sampled (Fig. 6B).
The expression levels of 12 EST highly induced in the mi-
croarray results were analyzed (Table 5, Supplementary Table
S2 for statistical analysis). EST CaAEC (an auxin efflux car-
rier component) was similarly induced by DIS 259j and DIS
376f at 48 h, six EST were preferentially induced by DIS 259j,
and seven EST were preferentially induced by DIS 376f (Fig.
7). All 12 EST studied to verify the microarray were induced
by one or both of the Trichoderma isolates during the time-
Fig. 3. Gene expression in pepper leaves 32 days after inoculation with Trichoderma isolates. Pepper seeds were planted in Pro-Mix PGX mix inoculated
with Trichoderma. Seedlings were grown in a controlled environment chamber with a 12-h-light and 12-h-dark photoperiod at 25°C. After 32 days, leaves
above the fifth node were harvested for quantitative polymerase chain reaction. Gene/expressed sequence tags include CaHMG2, CaGA2ox, CaMAPK4,
CaNPR1, CaMK1, CaPO2, CaLTP1, CaPR1, CaCHI2, CaPR4, CaJA2, and CaSC1.
Vol. 24, No. 3, 2011 / 341
course, and all 12 of the EST followed the pattern of isolate-
specific induction at 48 h indicated by the microarray analysis.
DIS 259j induced CaPOR (porin/voltage-dependent anion
channels), CaPER (a peroxidase), CaTR (a tropinone reduc-
tase), CaZFP (zinc finger protein), and CaBKC (beta-ketoacyl-
CoA synthase/FIDDLEHEAD-like). DIS 376f induced
CaMLO (seven transmembrane proteins), CaCYP (cytochrome
P450), CaGT (1,6-glucosyltransferase), CaACS (1-aminocy-
clopropane-1-carboxylate [ACC] synthase), and CaGAD (glu-
An additional 12-member subset (Table 6) of lipid tranferase
protein (LTP)-like family members was studied by qPCR analy-
sis over the 36- to 72-h postinoculation timecourse (Fig. 8).
The subset was assembled based on sequence similarity to
Arabidopsis EST and differential expression in response to the
two Trichoderma isolates in the microarray results. DIS 376f
preferentially induced CaLTP-I, and CaLTP-L. DIS 259j pref-
erentially induced CaLTP-C, CaLTP-N, CaLTP-B, CaLTP-A,
CaLTP-J, and CaLTP-E. CaLTP-M, CaLTP-F, and CaLTP-K
were induced by both DIS 259j and DIS 376f.
Expressing Trichoderma-induced pepper genes
in N. benthamiana leaves.
Expression of CaLTP-N, CaPOR, and CaMLO 3 days after
agroinfiltration of N. benthamiana leaves was detected at an
average 3.7, 6.2, and 22.6% of N. benthamiana actin expres-
sion, respectively. The area under the disease progress curve
(AUDPC) for leaves infiltrated with pGD-CaLTP-N was re-
duced by 42% in comparison with the pGD-empty vector con-
trol (Table 7). The results for the pGD-CaPOR and pGD-
CaMLO were inconsistent between experiments, even though
their mean AUDPC were lower than the empty vector controls.
Isolates DIS 70a, DIS 219b, and DIS 376f completely elimi-
nated P. capsici growth when cocultured. DIS 70a and DIS
376f penetrated P. capsici without coiling. Coiling, a common
recognition response of parasitic Trichoderma (Chet et al. 1998;
Harman et al. 2004), is not a requirement for parasitism. DIS
70a is also a parasite of the basidiomycete Moniliophthora
roreri, causal agent of frosty pod rot on Theobroma cacao,
demonstrating a broad host range across kingdoms and plant
hosts (Bailey et al. 2008). Trichoderma species produce many
metabolites with antimicrobial activity (Howell 1998) and also
produce metabolites that inhibit plant growth (Bailey and
Lumsden 1998). DIS 320c produced metabolites that strongly
inhibited growth of P. capsici. The DIS 320c metabolites inhibit-
ing P. capsici growth may be related to the metabolites in
those same samples, causing damage to pepper roots. Phytoph-
thora species are globally spread and cause disease on many
different plant species (Birch et al. 2006), including species
from which some of the Trichoderma isolates were collected
(Bowers et al. 2001; Guest 2007). The Trichoderma isolates
have been exposed to many pathogenic and beneficial mi-
crobes during their evolution into unique species, and antibio-
sis and parasitism capabilities against Phytophthora and other
plant pathogens may have proven advantageous.
Trichoderma isolates collected from aerial plant tissues in
the tropics were inefficient colonizers of hot pepper stems, al-
though they efficiently internally colonized hot pepper roots.
Five of the isolates studied can be considered endophytes, since
they penetrated and survived in pepper roots without causing
observable damage (Stone et al. 2000). Isolate DIS320c is a
Fig. 4. Impact of Trichoderma spp. on disease development in pepper
caused by Phytophthora capsici. Individual 42-day-old pepper plants
(Trichoderma-inoculated or uninoculated controls) were transplanted into
soil infested with P. capsici. Three experiments were carried out consisting
of 10, 20, and 20 replicate pots per treatment, with one plant per pot,
arranged in a completely randomized design. The percentage of diseased
plants receiving each treatment was determined daily for 14 days after
Table 4. Increase in the average number of days without symptoms
(DWS) in response to Trichoderma treatmenty
Treatment DWS Means separation
yThree experiments were carried out. Trichoderma-colonized seedlings and
controls were transplanted into Phytophthora capsici–infested soil and
were monitored daily for symptom development for 14 days. Symptoms
were sunken necrotic lesions on the stem at the soil line, followed by wilt-
ing of the plant. DWS values represent the average over three experiments.
zMeans not followed by the same letters are significantly different (P ≤
342 / Molecular Plant-Microbe Interactions
Fig. 5. The early response of pepper root gene expression after inoculation with Trichoderma isolates. Pepper seedlings were grown for 14 days and were
inoculated with Trichoderma isolates on agar plates to determine the early responses in the pepper-Trichoderma interaction. Pepper roots were harvested 72 h
after inoculation, and RNA was extracted for quantitative polymerase chain reaction analysis. The expression of eight pepper expressed sequence tags (EST)
responsive to stress were analyzed, i.e., CaPR1, CaPR5, CaMK1, CaPEAS1, CaCHI2, CaPR10, CaPR4, and CaHMG2. The data are expressed as a
percentage of pepper actin expression for each sample (graphs on the left) and the increase in EST expression (fold induction) relative to Trichoderma actin
expression (graphs on the right).
Vol. 24, No. 3, 2011 / 343
possible exception, since it produced compounds that damaged
roots. The endophytic nature of two of the isolates, DIS 70a
and DIS 219b, has been studied in detail on cacao (Bae et al.
2009; Bailey et al. 2006, 2008). They are aggressive endo-
phytes of cacao, being reisolated at high frequencies from the
xylem of stems in addition to roots, cotyledons, and plumules
(Bailey et al. 2008). Both isolates intensely colonized hot pepper
roots but were poor colonizers of pepper stems, when grown
under conditions similar to those used in the cacao studies
(Bailey et al. 2008). The observations demonstrate that some
aspects of specificity in regards to endophytic capability are
due to tissue type and general host suitability rather than host
identity. Roots are more easily colonized by Trichoderma spp.
than stems, seemingly regardless of the plant species (Harman
et al. 2004). In terms of host suitability, the developing woody
stem of cacao (Bailey et al. 2006, 2008) is a more suitable
niche for Trichoderma growth than the stem of pepper. Tricho-
derma spp. can actively influence their own ability to colonize
plant tissues, as demonstrated by the discovery that the T. as-
perellum class 1 hydrophobin TasHyd1 supports colonization
of plant roots, possibly by protecting the hyphal tips from
plant defense compounds (Viterbo and Chet 2006).
In 32-day-old seedlings, the Trichoderma isolates altered ex-
pression of gene and EST, some with known functions in
pepper (Table 3) and others with strong sequence similarity to
other disease resistance and stress-response genes. This in-
cludes genes and EST previously demonstrated to be induced
by P. capsici (CaLTP1, CaCHI2, CaHMG2, CaPEAS1), viruses
(CaPR4, CaPR10), and bacteria (CaPR1, CaCHI2, CaPO2,
CaPO1, CaGA2ox). Genes involved in the hypersensitive re-
sponse (CaPR4, CaPO2, CaPO1, CaPR10), responsive to UV
exposure (CaMK1, CaSC1), and sesquiterpene phytoalexins
biosynthesis (CaSC1, CaHMG2, and CaPEAS1) were induced.
Genes involved in hormone metabolism and action were also
induced, i.e., ethylene (CaPR1, CaCHI2), salicylic acid
(CaNPR1), jasmonic acid (CaNPR1, CaJA2), and gibberellic
acid (CaGA2ox). There is significant overlap in the local
(roots) and systemic (leaves) responses to Trichoderma spp. at
this late stage of colonization despite the diversity of isolates
studied. DIS 259j, DIS 320c, and DIS 376f were the most con-
sistent in altering gene expression (Figs. 2 and 3).
The potential for Trichoderma spp. providing protection
against disease caused by Phytophthora spp. has been demon-
strated in many cropping systems, although with isolates of
relatively few Trichoderma species (Ahmed et al. 2000;
Etebarian et al. 2000; Ezziyyani et al. 2005; Hoitink et al.
2006; Khan et al. 2004; Orlikowski 1995; Porras et al. 2007;
Smith et al. 1990). Our disease assay included five Tricho-
derma species (Table 1), four recently identified as new spe-
cies (Trichoderma caribbaeum var. aequatoriale, T. theobro-
micola, T. ovalisporum, and T. stilbohypoxyli) from three
countries (Cameroon, Ecuador, and Peru), isolated from the
canopy of four tropical plant species (Cola praecuta, Theo-
broma cacao, Theobroma gileri, and Banisteriopsis caapi). T.
theobromicola isolate DIS 376f, provided a consistent delay in
Table 5. Expressed sequence tags (EST) used to verify the microarray results and evaluate the early response of pepper seedlings to Trichoderma colonization
EST Putative function GenBank ID tBLASTX Species Relatednessy
Auxin efflux carrier component
Voltage-dependent anion channel
C3HC4-type Zinc ring finger
y Relatedness values represent expected value to percent identity for each EST.
z CaUNK is an EST included in the microarray (caKS13046E01.ab1_rev) with no equivalent sequence in GenBank.
Fig. 6. Initial colonization of pepper roots by Trichoderma isolates DIS
259j and DIS 376f as measured by relative amounts of Trichoderma actin
(TriACT). Pepper seedlings were grown 14 days and were inoculated with
Trichoderma isolates on agar plates. Top, The percentage of the agar plates
colonized by Trichoderma isolates was estimated. Bottom, A universal
actin primer pair was used to monitor relative Trichoderma activity in the
pepper root zone. Pepper roots were harvested 36, 48, 60, and 72 h after
inoculation, and RNA was extracted for quantitative polymerase chain
reaction analysis. The data are expressed as TriACT as a percentage of
pepper actin (CaACT).
344 / Molecular Plant-Microbe Interactions
disease development (Table 4). T. stilbohypoxyli isolate DIS
259j and T. ovalisporum isolate DIS 70a also significantly de-
layed disease development (Table 4). DIS 70a is an endophyte
of T. cacao and a parasite of M. perniciosa and M. roreri
(Holmes et al. 2004, 2006). Isolates of T. stilbohypoxyli (but
not isolate DIS 259j) were shown to be endophytes of cacao
and produced metabolites that inhibited M. roreri in vitro and
on cacao pods but were not parasites of M. roreri (Lu and
Although DIS 259j, DIS 320c, and DIS 376f were the most
consistent in altering gene expression, only DIS 259j and DIS
376f consistently delayed disease development. DIS 320c
failed to protect against P. capsici, despite the ability to sys-
temically induce defense responses in pepper. The root dam-
age caused by DIS 320c metabolites may have provided a
point of entry for P. capsici, negating the benefit of defense-
gene induction. DIS 70a significantly delayed disease develop-
ment but induced very few defense-related genes and EST
among of the gene repertoire selected here. As DIS 70a and
DIS 376f are both parasites of P. capsici, it is possible that
parasitism contributes to their abilities to delay disease.
In the two volume book series “Trichoderma & Gliocladium”
(Harman and Kubicek 1998), induced resistance by Tricho-
derma was cited as a needed future work without reference to
diseases caused by Phytophthora spp. A review by Harman and
associates (2004) discusses Trichoderma-induced resistance to
disease in detail but cited only one reference to induced resis-
tance to Phytophthora species (Ahmed et al. 2000). The impor-
tance of induced resistance in some Phytophthora-plant patho-
systems has been demonstrated (Ahmed et al. 2000; Ezziyyani
et al. 2005; Hoitink et al. 2006; Khan et al. 2004) but detailed
molecular studies are lacking. The recent detailed molecular
studies of resistance induced by Trichoderma species do not
address induced resistance in Phytophthora-plant pathosystems
(Alfano et al. 2007; Korolev et al. 2007; Segarra et al. 2009;
Shoresh and Harman 2008a; Shoresh et al. 2005).
Fig. 7. Expressed sequence tags (EST) encoding stress-related proteins are differentially induced by Trichoderma isolates DIS 259j and DIS 376f. quantita-
tive polymerase chain reaction (qPCR) was carried out, using primers for 12 EST that were indicated to be highly induced, by microarray analysis of RNA
samples collected 48 h after Trichoderma inoculation. Pepper seedlings were grown 14 days and were inoculated with Trichoderma isolates on agar plates.
Pepper roots were harvested 36, 48, 60, and 72 hours after inoculation, and RNA was extracted for qPCR analysis. EST include CaCYP, CaMLO, CaGT,
CaACS, CaUNK, CaGAD, CaAEC, CaBKC, CaZFP, CaTR, CaPER, and CaPOR.
Vol. 24, No. 3, 2011 / 345
In the cases in which detailed molecular analysis of the
interaction has taken place, ethylene- and jasmonic acid–de-
pendent induced systemic resistance (ISR) has been implicated
(Korolev et al. 2007; Segarra et al. 2009; Shoresh et al. 2005)
as opposed to salicylic acid–associated systemic acquired re-
sistance (SAR). It is unclear if this is true in all cases in which
Trichoderma spp. induce systemic effects in plants. Alfano and
associates (2007) found that, although many aspects of the
response of tomato to Trichoderma hamatum isolate 382 were
similar to those previously reported in other Trichoderma-
plant interactions, expression of genes involved in the jasmo-
nate and ethylene signaling pathways of ISR (Lox1, Pal1,
ETR1, and CTR1) was not altered. Trichoderma spp. also alter
expression of genes involved in plant cell metabolism (Alfano
et al. 2007), and in the case of T. harzianum isolate T22, pro-
teins involved in carbohydrate metabolism and photosynthesis
are up-regulated in association with enhanced plant growth
(Shoresh and Harman 2008b).
Depending on the Trichoderma isolate, many different pep-
tides have been identified as elicitors of plant defense. The
Trichoderma virens hydrophobin-like (cerato-platanin protein
family) elicitor SM1 induces resistance in plants, and its action
has been extensively studied in cotton and maize (Djonovic et
al. 2006, 2007). SM1-related EST were expressed at high lev-
els by all the Trichoderma isolates studied (data not shown),
but when cloned and sequenced, the SM1-related EST lacked
the glycosylation site critical to maintaining Trichoderma
SM1-related peptides in active form (Vargas et al. 2008). This
would suggest that SM1-related peptide elicitors are not in-
volved in the resistance induced by DIS 259j or DIS 376f.
Additional Trichoderma elicitors include the 10-kDa class II
hydrophobin Hytra1 (Ruocco et al. 2004, 2007), the 22-kDa
xylanase EIX (Bailey et al. 1990; Lotan and Fluhr 1990), the
short-chain peptide peptaibols (Viterbo et al. 2007), and the
protein Swollenin (Brotman et al. 2008).
DIS 259j and DIS 376f delayed disease development and
demonstrated divergent induction patterns for many EST when
examined by qPCR analysis (Figs. 7 and 8). Some of these
EST have putative functions with potential importance to the
P. capsici–pepper pathosystem and Trichoderma-induced plant
defense. For example, CaMLO is related to a class of seven
transmembrane proteins, the most relevant member of which,
in recessive form, confers resistance to powdery mildew
(Miklis et al. 2007). The gene product appears to delay cell
death in response to powdery mildew, which allows infection-
allowing colonization to take place. An obvious question is
whether CaMLO impacts the ability of Trichoderma spp. to
colonize plant tissues. TcACS putatively encodes an ACC syn-
thase. ACC synthase is a primary control point in ethylene bio-
synthesis (Fluhr and Mattoo 1996), and ethylene induces many
plant defense genes, including PR proteins, as has been dem-
onstrated for PR1 in pepper (Kim and Hwang 2000). CaPOR
encodes a protein related to mitochondrial porin and voltage-
dependent anion channels (VDAC). In Nicotiana tabacum,
VDAC are being studied for their importance in programmed
cell death (Tateda et al. 2009). CaGAD putatively encodes a
glutamate decarboxylase, a primary enzyme leading to the pro-
duction of γ-amino-n-butyric acid (GABA) in plants (Bouché
and Fromm 2004). DIS 219b confers drought tolerance in
Theobroma cacao through enhanced root growth (Bae et al.
2009). In that study, GABA was shown to accumulate in re-
sponse to Trichoderma colonization (Bae et al. 2009).
DIS 376f and DIS 259j also differentially induced EST-en-
coding members of a lipid transfer protein (LTP)-like family of
proteins (Fig. 8). LTP play a role in plant responses to biotic and
abiotic stress. Plant LTP are a class of small, soluble, and mostly
basic proteins found in large gene families in plants (Yeats and
Rose 2008). Although the nucleotide and amino-acid sequences
diverge, several features are conserved, including eight cysteine
residues to form four disulphide bonds, an N-terminus signal
peptide that likely directs the proteins to the endoplasmic reticu-
lum, and a retention signal at the C-terminus allowing entry into
the secretory pathway. Several functions have been proposed for
LTP-like proteins in plants, including facilitating the transfer of
lipids between membranes, involvement in cuticle biosynthesis,
and fatty acid and acyl coenzyme A carrier proteins. They are
generally secreted and associated with the plant cell wall. LTP
share a number of structural similarities with oomycetous elicit-
ins. Elicitins are thought to be a class of hydrophobins specific
to the oomycetes, including Phytophthora spp. (Yu 1995). The
elicitins and tobacco LTP1 compete for the same plasma mem-
brane receptors (Buhot et al. 2004). Additionally, LTP1 binds
jasmonic acid and, together, they compete with stronger affinity
for the elicitin-binding site and are capable of inducing resis-
tance at a distance from the point of application. The LTP se-
quences in pepper are diverse, with the most closely related EST
to LTP1 in pepper being CaLTP-M, which was induced by both
isolates. Jung and associates (2003) found LTP1 to be induced in
the incompatible interaction between P. capsici and pepper but
not the compatible interaction. Of the LTP studied, CaLTP-N is
most closely related to DIR1 (Lascombe et al. 2008; Maldonado
et al. 2002). When DIR1 is mutated, long-distance induction of
SAR-derived resistance is lost. CaLTP-N has a distinct pattern
of induction, depending on the isolate being studied. DIS 259j
causes a bimodal induction, with a peak at 48 h after inoculation
and a second rise in expression 72 h after inoculation. DIS 376f
Table 6. Lipid tranferase protein (LTP)-like related expressed sequence tags (EST) used to verify microarray results and evaluate the early response of
pepper seedlings to Trichoderma colonization
EST GenBank ID tBLASTX Species Relatednessz
z Relatedness values represent expected value to percent identity for each EST.
346 / Molecular Plant-Microbe Interactions
does not induce CaLTP-N expression until 72 h after inocula-
tion. When CaLTP-N is expressed in N. benthamiana leaves, it
provides protection against P. nicotianae, reducing AUDPC by
42% over 5 days (Table 7). The reduction in disease caused by
CaLTP-N expression in N. benthamiana, taken together with
early and systemic induction of CaLTP1/CaLTP-M in pepper
seedlings responding to Trichoderma isolates DIS 259j and DIS
376f, provides evidence for the function of LTP in resistance
induced by Trichoderma spp. in pepper.
When isolates DIS 259j and DIS 376f were applied to cacao
seedlings using previously published methods (Bailey et al.
2006), the molecular responses observed were similar to those
observed with isolate DIS 70a (Bailey et al. 2006) and much
less intense than those observed in pepper (unpublished data).
Although induced resistance to Phytophthora spp. has been
demonstrated in cacao (Arnold et al. 2003; Melnick et al.
2008), only muted molecular responses have been observed.
Strong induction of classical plant defense genes, such as
genes encoding PR-related proteins, has not yet been observed
in cacao. Cacao is heavily colonized by a divergent endophytic
fungal community in above- and below-ground tissues (Arnold
et al. 2003; Evans et al. 2003; Rubini et al. 2005), and we sug-
gest cacao may promote endophytic colonization by suppress-
ing its induced-resistance responses. On the other hand, annual
plant species have been shown to respond to root colonization
by specific Trichoderma isolates with a strong defense response
(Harman et al. 2004), which limits colonization of plant tissues
(Metcalf and Wilson 2001; Yedidia et al. 1999, 2000). The di-
vergent responses of cacao and pepper to colonization by the
same endophytic Trichoderma species leads us to suggest the
two species may have taken different paths in response to
endophytic microbial species.
A complex picture emerges when, under the same conditions,
the impact of multiple endophytic Trichoderma isolates on the
P. capsici–pepper pathosystem are considered. Direct interac-
tions between Trichoderma spp. and pathogens through metabo-
Fig. 8. Expressed sequence tags (EST) encoding members of the lipid tranferase protein (LTP)-like protein family are differentially induced by Trichoderma
isolates DIS 259j and DIS 376f. Quantitative polymerase chain reaction (qPCR) was carried out, using primers for LTP-like protein EST that were indicated
as being induced, by microarray analysis of RNA samples collected 48 h after Trichoderma inoculation. Pepper seedlings were grown 14 days and were inocu-
lated with Trichoderma isolates on agar plates. Pepper roots were harvested 36, 48, 60, and 72 h after inoculation, and RNA was extracted for qPCR analysis.
Vol. 24, No. 3, 2011 / 347
lite production and parasitism require the active metabolism of
Trichoderma isolates and may benefit from aggressive coloni-
zation of plant tissues by endophytic Trichoderma isolates.
Endophytic colonization by Trichoderma spp. is dependent on
both the tissue and the plant species being colonized.
Of the six Trichoderma isolates studied, DIS 70a, DIS 259j,
and DIS 376f delayed disease development. Isolate 70a, an
aggressive root colonizer, was a poor inducer of pepper gene
expression both early and late in the Trichoderma-pepper
interaction. DIS 259j and DIS 376f were not highly aggressive
colonizers of pepper roots, but they strongly induced defense-
response genes as early as 36 h after inoculation and as late as
32 days after inoculation. The altered gene expression occurred
both in the roots at the site of colonization and systemically in
pepper leaves. A unique isolate-dependent pattern of pepper
EST induction was observed during initial root colonization,
but the systemic pattern of induction tended to converge after
32 days. Transient expression of CaLTP-N, a LTP-like protein
encoding pepper EST, in N. benthamiana leaves reduced dis-
ease development in response to P. nicotianae inoculation, pro-
viding evidence LTP function in Trichoderma-induced resis-
tance to infection by Phytophthora spp.
MATERIALS AND METHODS
Trichoderma and P. capsici isolates and growth.
Six isolates of Trichoderma spp. were used in this study (Ta-
ble 1). The Trichoderma isolates were maintained on potato
dextrose agar (PDA) (Difco, Sparks, MD, U.S.A.) at 25°C. P.
capsici isolates R198, RA4, 223, and R8 (Bowers et al. 2007)
were maintained in clarified V8 agar (cV8) at 25°C.
P. capsici parasite screening.
Trichoderma isolates were screened for parasitic ability
against P. capsici as previously described (Evans et al. 2003;
Holmes et al. 2004). P. capsici R198 was inoculated on the
edge of 9-cm-diameter plates of cV8, and the plates were
maintained at 25°C in the dark for 12 days. A strip of Tricho-
derma inoculum (2.5 × 0.5 cm) was excised from a growing
edge of a 5-day-old culture on PDA and was placed at the
opposite edge of a 9-cm-diameter cV8 plate precolonized with
P. capsici. Three replicate plates were used for each Tricho-
derma isolate. After 7 days in the dark at 25°C, samples were
removed with a 5-mm-diameter cork borer, starting at the P.
capsici inoculum side moving to the Trichoderma inoculum
side. Each sample was plated on a minimal salts broth agar
plate (MIN) (5-cm diameter) (Srinivasan et al. 1992), and the
plates were observed over a period of 10 days for growth of
the Trichoderma spp., P. capsici, or both.
A water-agar microscope slide assay was also performed to
screen the Trichoderma isolates for parasitic ability against P.
capsici. Glass slides were covered with water agar (1.5%). The
slides were inoculated 3 cm apart with 5-mm-diameter plugs
of P. capsici R198 and Trichoderma spp. from the growing
edge of a 5- to 7-day-old cV8 plate and PDA, respectively.
Three replicate slides were used for each Trichoderma isolate.
The slides were maintained at room temperature, and the inter-
action between the two organisms was observed in the area of
contact after 5 days. The slides were stained with lacto phenol
cotton blue and were photographed with a Nikon Eclipse E600
compound scope (Nikon, Inc., Melville, NY, U.S.A.) equipped
with a Nikon digital camera DXM1200 at 600× magnification.
Metabolite production and their impact
on P. capsici and hot pepper growth.
The conidia of Trichoderma isolates were harvested from 2-
week-old cultures grown on PDA at 25°C, as previously de-
scribed (Samuels et al. 2006b). Sterile distilled water (4 ml)
was added to the PDA plate, and the plate was scrubbed gently
with a bent glass rod. The conidia suspension was filtered
through four layers of sterile cheese cloth. Samples of MIN
media (50 ml) in 125-ml flasks were inoculated with 1 ml of a
1 × 106 conidia suspension and were incubated in a shaker at
25°C and 110 rpm for 7 days. Mycelia were removed using
four layers of sterile cheese cloth, and the filtrates were steril-
ized using a 0.22-μm membrane disposable 30-ml syringe fil-
ter system (Millipore, Billerica, MA, U.S.A) and were stored
at –20°C until used. The filtrates were placed in a 90°C water
bath for 2 h to inactivate enzyme activity. An equal volume of
the heat-treated filtrate was added to strengthened agar, 3%
MIN. Controls were prepared by replacing the filtrate with the
corresponding uninoculated MIN broth. The plates were
inoculated centrally with a 5-mm-diameter plug of P. capsici
R198 and were incubated at 25°C. Three replicate plates were
used for each isolate. The mean radial growth of P. capsici was
observed after 5 days.
The effect of Trichoderma metabolites on pepper seedlings
was also studied. Metabolites in MIN broth were mixed with
an equal volume of 2× strength Murashige-Skoog (MS) basal
salts medium supplemented with 2× vitamin B5, 0.4% phy-
tagel, and 0.2 mM morpholineethanesulfonic acid (MES)-
KOH (pH 5.7). Fourteen-day-old pepper seedlings grown from
surface-sterilized seed on 1× MS basal salts medium supple-
mented with 1× vitamin B5, 0.2% phytagel, and 0.1 mM
MES-KOH (pH 5.7) were transferred to the solidified agar
plates containing Trichoderma culture filtrates. The plates
were sealed with parafilm, were incubated under fluorescent
lights (16-h-light period) at 23°C for 4 days, and were ob-
served for root damage. Roots were photographed under a
Nikon SMZ1500 dissecting scope (Nikon, Inc.) equipped with
a Nikon digital camera (DXM1200) at 50 and 100× magnifica-
tion. Cross sections of the roots were made and photographed
with a Nikon Eclipse E600 compound scope (Nikon) equipped
with a Nikon digital camera DXM1200 at 200× magnification.
Endophytic growth–Magenta box study.
Two agar plugs (0.5 cm in diameter) of each Trichoderma
isolate were added to a sterilized soil-less mix (Pro-Mix PGX
mix; Premier Horticulture Inc., Quakertown, PA, U.S.A.) in
double Magenta boxes (77 × 77 × 194 mm; Magenta, Chi-
cago). The Magenta boxes contained 9 cm of sterile soil-less
mix and had four holes (0.5 cm diameter) sealed with tape on
the bottom. Sterile water (25 ml) was added to the soil-less
mix at the time of inoculation. The Magenta boxes were main-
tained in growth chambers as described below for 14 days be-
fore being planted with pepper seed (Capsicum annuum L. cv.
Table 7. Area under the disease progress curve (AUDPC) for Phytophthora
nicotiana–challenged Nicotiana benthamiana leaves after infiltration with
Agrobacterium tumefaciens EH105 carrying Trichoderma-induced pepper
Plasmid construct AUDPC Means separation
yThree days after infiltration, detached leaves were inoculated with zoo-
spores (approximately 5 × 104zoospores/ml). Necrosis measurements
(% under droplet) were made for 5 days or until the empty vector control
reached a rating of 400%. AUDPC was determined as described by
Shanner and Finney (1977), and the data were analyzed by PROC
MIXED followed by Tukey’s analysis (P ≤ 0.05).
z Means not followed by the same letters are significantly different (P ≤
348 / Molecular Plant-Microbe Interactions
Bugang). Seeds were surface-sterilized in 30% sodium hypo-
chlorite for 5 min, followed by five washes in sterile distilled
water. Sterilized seeds were germinated on 1.5% water-agar
plates under fluorescent lights for 4 days at 25°C. Three ger-
minated seeds were planted in each Magenta box 3 cm deep
into the sterile soil-less mix with or without Trichoderma spp.
Seedlings were grown with a 12-h-light and 12-h-dark cycle at
25°C. The irradiance was 50 μmol m–2 s–1 photosynthetically
active radiation. After 35 days, the pepper seedlings (two per
Magenta box) were dissected, and approximately 1-cm tissue
sections of roots and stems were plated on 1× corn meal dex-
trose agar (Becton Dickinson and Company, Sparks, MD,
U.S.A.). For each seedling the lower stem was cut into four
sections and one root section was plated for each seedling.
Treatments consisted of six replications. The plated plant sec-
tions were incubated on the lab bench for 5 to 7 days, until the
Trichoderma isolates grew out of the pepper-tissue sections
and were assessed as positive or negative for colonization.
Induced resistance and disease suppression assay.
Preparation of Trichoderma inoculum. Hot pepper (Capsicum
annuum L. cv. Bugang) seeds were sown into Trichoderma-
amended Pro-Mix PGX mix. The Trichoderma inocula were
prepared using Biodac granular carrier (20/50; Kadant Gran
Tek, Inc., Green Bay, WI, U.S.A.). Biodac (50 g) was aliquoted
into mycobags (Unicorm Imp. & Mfg. Corp., Commerce, TX,
U.S.A.) with 50 ml of diluted V8 juice (10%). The bags were
sealed and were autoclaved for 60 min twice over 2 days. Four
plugs (0.5-cm diameter) of each Trichoderma isolate, grown
on PDA agar plates for 3 to 5 days, were added to the bags.
The bags were resealed and were incubated at room tempera-
ture for 3 weeks.
Preparation of P. capsici inoculum. Petri dishes containing
cV8 juice agar (Bowers and Mitchell 1990) were inoculated
with P. capsici isolates R1198, RA4, 223, and R899 (Bowers
et al. 2007). The plates were incubated at room temperature for
2 days in the dark and an additional 3 days under light. Biodac
(100 g) was mixed with 100 ml of cV8 and added to a myco-
bag, and the mycobag was autoclaved for 60 min on two con-
secutive days. For each P. capsici isolate, four 1-cm2 agar
plugs were added to the mycobag and the mycobag was incu-
bated at room temperature for 2 to 4 weeks.
Inoculation of hot pepper with Trichoderma spp. Tricho-
derma-inoculated Biodac was added into Pro-Mix PGX mix
(0.1%, vol/vol), and seeds were sown in square pots (5 × 5 × 6
cm). Tap water was applied until the seeds germinated, after
which the seedlings were watered with Miracle-Gro (Scotts
Miracle-Gro Co., Marysville, OH, U.S.A.) twice a week.
Seedlings were grown in a controlled environment chamber
(model M-2; EGC Corp., Chagrin Falls, OH, U.S.A.) with a
12-h-light and 12-h-dark photoperiod at 25°C. The irradiance
was 100 µmol m–2 s–1 photosynthetically active radiation. Rela-
tive humidity was not controlled in this experiment, but rela-
tive humidity was always above 50%. After 32 days of growth,
leaves above the fifth node and roots were harvested for qPCR.
Real-time reverse transcriptase qPCR. Induced resistance
was also observed by real-time reverse transcriptase qPCR. To-
tal RNA and cDNA synthesis, qPCR conditions, and data
analysis were performed as described by Bailey and associates
(2006). Relative transcript levels of each gene were normal-
ized with respect to pepper actin transcript levels (%CaACT).
Mean values were obtained from six biological replications.
Transplanting Trichoderma-colonized hot pepper into P.
capsici–inoculated soils. P. capsici in Biodac was added to
moistened soil at a rate of 0.15 g per liter of soil 2 days prior
to transplanting pepper. Individual pepper plants (42-day-old
Trichoderma-inoculated or uninoculated controls) were trans-
planted into empty 7.62-cm pots and the remaining volume of
the pot was filled with soil infested with P. capsici. Three ex-
periments were carried out consisting of 10, 20, and 20 repli-
cate pots per treatment, with one plant per pot, arranged in a
completely randomized design. Days to symptom expression
was determined for each plant for the 14 days after transplant-
ing. The number of days without symptoms was calculated for
each seedling as the number of days until symptoms appeared
minus one, with the minimum being zero and the maximum
being 13. The data for days without symptoms was combined
over the three experiments for analysis. The data were ana-
lyzed as a two-way factorial with treatment (control plus six
Trichoderma isolates) and experiment (experiments one, two
and three) as factors, using the PROC MIXED procedure of
SAS 9.1 (SAS Institute Inc., Raleigh, NC, U.S.A.), and means
were separated using Tukey's studentized range test.
The early responses
in the hot pepper–Trichoderma interaction.
Seedling growth and inoculation on artificial media. Pepper
seedlings were grown and inoculated with Trichoderma spp.
on agar plates to determine the early responses in the pepper-
Trichoderma interaction. Pepper seeds were surface-sterilized
in 30% sodium hypochlorite for 10 min, followed by three
washes in sterile distilled water. Sterile seeds were placed on
plates containing 1× strength MS basal salts medium supple-
mented with 1× vitamin B5, 0.2% phytagel, and 0.1 mM
MES-KOH (pH 5.7), and the plates were sealed with parafilm.
The plates were incubated under fluorescent lights (16-h light
period) at 23°C for 14 or 24 days, depending on the study. The
plates were inoculated with PDA plugs (0.5-cm diameter) of
the Trichoderma isolates, and the Trichoderma isolates were
allowed to colonize the pepper seedlings. Four PDA plugs
were applied per plate. PDA plugs without Trichoderma were
used on control plates. Pepper roots were harvested 36, 48, 60,
or 72 h after inoculation, depending on the study. Total RNA
was extracted as described above.
Pepper gene expression in response to initial Trichoderma
colonization. Eight EST listed in Table 3 were studied by
qPCR analysis of pepper root RNA harvested from plate-
grown seedlings 72 h after inoculation with all six Tricho-
derma isolates. Each treatment combination included six inde-
pendent replications. Expression of TriACT was also determined
using consensus primers generated from sequences available in
GenBank. The data are presented in two ways: i) for fungal
actin (TriACT) and hot pepper genes and EST, EST expression
as a percentage of hot pepper actin expression and ii) for hot
pepper genes and EST, the fold increase in EST expression
relative to TriACT expression (FI/%Tact). This was accomplished
by subtracting the mean expression level relative to plant actin
for each EST in the controls (Expct) from each EST expression
level relative to plant actin in individual treated samples
(Exptrt) and then dividing the increase in expression level in
individual Trichoderma treated samples (Exptrt – Expct) by the
mean expression level relative to plant actin in the control
samples (Expct), yielding the fold induction for each sample
relative to plant actin. The fold induction for each sample rela-
tive to plant actin was divided by the percentage of TriACT
relative to plant actin (%ExpTact) in each sample, yielding the
fold increase relative to the percent TriACT (FI/%Tact):
(FI/%Tact) = [(Exptrt – Expct)/(Expct)]/(%ExpTact).
In order to identify new candidate EST for study of early
gene expression in the pepper-Trichoderma interaction, experi-
ments were performed with
a single replication pepper mi-
croarray. EST identified in the microarray results were studied
by qPCR analysis of pepper root RNA harvested from plate-
Vol. 24, No. 3, 2011 / 349
grown seedlings 36, 48, 60, and 72 h after inoculation with
Trichoderma isolates DIS259j and DIS376f. Each treatment
combination included six independent replications. A total of
24 EST (Tables 5 and 6) were evaluated over the full time-
course, including 12 members of the pepper LTP-like gene
family. Expression of TriACT was determined by qPCR analy-
sis, as described above. Analysis of variance was conducted on
the data for TriACT, and each pepper EST was expressed as
percent plant actin, using PROC GLM followed by a Tukey
test using SAS 9.2 (SAS Institute Inc.).
Cloning of CaLTP-N, CaPOR,
and CaMLO and the impact of their
on the N. benthamiana–P. nicotianae interaction.
The full-length mRNAs for CaLTP-N and CaPOR were avail-
able in GenBank. In order to clone the full-length of CaMLO, 5′
rapid amplification of cDNA ends (RACE) was performed,
using the RACE system according to manufacturer’s recommen-
dation (Invitrogen, Carlsbad, CA, U.S.A.). The RACE products
were cloned into pCR2.1-TOPO vector (Invitrogen) for se-
quencing. DNA sequences were determined by COSMO
Genetech (Seoul, Korea). A full length of CaMLO (1,745 bp),
consisting of a 1,236-bp open reading frame encoding 411
amino acids, was obtained. The sequence of CaMLO was
deposited in GenBank (HQ324112). The deduced amino-acid
sequences of CaMLO showed highest identity (67%) with the
MLO-like protein 6 of Vitis vinifera (E-value = 2e-140).
The pGD binary vector system was used for expressing
CaLTP-N, CaPOR, and CaMLO in N. benthamiana leaves as
described by Goodin and associates (2002). CaLTP-N,
CaPOR, and CaMLO were amplified from pepper cDNA and
were cloned into TOPO vector (Invitrogen). After sequence
confirmation, the correct size fragments from XhoI/BamHI
(CaLTP-N, CaPOR) and XhoI/HindIII (CaMLO) digests were
inserted into the XhoI/BamHI and XhoI/HindIII sites of pGD
vector, respectively. pGD-CaLTP-N, pGD-CaPOR, and pGD-
CaMLO were transformed into Agrobacterium tumefaciens
EH105 and were infiltrated into the abaxial side of N. bentha-
miana leaves, as described by Lim and associates (2009). A fi-
nal EH105 concentration of 0.4 optical density at 600 nm was
applied in this experiment. Three to four leaves were infiltrated
on each plant, and two plants were infiltrated with each of two
independent isolates of each construct.
After 3 days, zoospores were liberated from 7- to 10-day-
old cultures of P. nicotianae, following modification from
Lawrence (1978) and two to four 20-µl drops (approximately 5
× 104 zoospores/ml) were applied to the abaxial side of freshly
detached previously infiltrated leaves maintained on wetted
Whatman paper in petri dishes. Percent necrosis measurements
were made for each drop on each leaf over the next 5 days or
until the empty vector control reached a necrosis rating of
400% of the original drop area. AUDPC was determined as de-
scribed by Shanner and Finney (1977). The experiment was
repeated four times, and the combined data were analyzed by
PROC MIXED followed by Tukey analysis using SAS 9.2 and
a significance level of P ≤ 0.05. The expression of the pepper
genes in N. benthamiana leaves was monitored by qPCR,
using the methods described above. Total RNA was isolated
from N. benthamiana leaves 3 days after agroinfiltration, using
the Qiagen RNeasy plant mini kit with the optional on-column
DNase step (Qiagen Inc., Valencia, CA, U.S.A.).
This work was partially supported by the grant from the BioGreen 21
program of Rural Development and Administration, Republic of Korea.
The United States Department of Agriculture is an equal opportunity pro-
vider and employer.
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