Vol. 12, No. 11, 1999 / 951
MPMI Vol. 12, No. 11, 1999, pp. 951–959. Publication no. M-1999-0830-01R. © 1999 The American Phytopathological Society
The Plant-Growth-Promoting Rhizobacterium
Paenibacillus polymyxa Induces Changes in Arabidopsis
thaliana Gene Expression: A Possible Connection
Between Biotic and Abiotic Stress Responses
Salme Timmusk and E. Gerhart H. Wagner
Department of Microbiology, SLU (Swedish University of Agricultural Sciences), Box 7025, S-75007
Accepted 15 July 1999.
This paper addresses changes in plant gene expression in-
duced by inoculation with plant-growth-promoting rhizo-
bacteria (PGPR). A gnotobiotic system was established
with Arabidopsis thaliana as model plant, and isolates of
Paenibacillus polymyxa as PGPR. Subsequent challenge by
either the pathogen Erwinia carotovora (biotic stress) or
induction of drought (abiotic stress) indicated that inocu-
lated plants were more resistant than control plants. With
RNA differential display on parallel RNA preparations
from P. polymyxa-treated or untreated plants, changes in
gene expression were investigated. From a small number
of candidate sequences obtained by this approach, one
mRNA segment showed a strong inoculation-dependent
increase in abundance. The corresponding gene was iden-
tified as ERD15, previously identified to be drought stress
responsive. Quantification of mRNA levels of several
stress-responsive genes indicated that P. polymyxa induced
mild biotic stress. This suggests that genes and/or gene
classes associated with plant defenses against abiotic and
biotic stress may be co-regulated. Implications of the ef-
fects of PGPR on the induction of plant defense pathways
Additional keywords: dehydration, RT-PCR.
It is evident from a great number of reports that certain
bacterial strains are beneficial for the growth of plants. A
group of bacteria that display such effects are called plant
growth-promoting rhizobacteria (PGPR). Paenibacillus poly-
myxa (previously Bacillus polymyxa; Ash et al. 1993), a
common soil bacterium, belongs to this group. A range of ac-
tivities has been found to be associated with P. polymyxa
treatment, some of which might be involved in plant growth
promotion (Timmusk et al. 1999, and references therein). The
mechanism by which P. polymyxa exerts its beneficial effect is
not understood: e.g., in certain P. polymyxa strains (Lindberg
and Granhall 1984), atmospheric nitrogen fixation ability does
not correlate with the observed growth-promoting effect
(Lindberg et al. 1985).
PGPR can affect plant growth directly or indirectly. Indirect
promotion of plant growth occurs when PGPR antagonize or
prevent the effects of phytopathogens or deleterious microor-
ganisms (Glick 1994). The fact that no significant growth
promotion was found in response to P. polymyxa inoculation
under gnotobiotic conditions (Lindberg et al 1985), in the ab-
sence of pathogens or deleterious microorganisms, supports
the idea that indirect growth-promoting mechanisms might be
Most mechanisms proposed to explain indirect growth pro-
motion suggest that the active principle may be a secondary
bacterial metabolite that antagonizes pathogens. Metabolites
include HCN, siderophores, and antibiotics. P. polymyxa is
known to produce antibiotic compounds, and inoculation with
P. polymyxa suppresses several plant pathogens (Yuen et al.
1991; Oedjijono et al. 1993). Alternatively, direct competition
for nutrients is a plausible scenario.
Recently, induced resistance to diseases, or plant “immuni-
zation,” has received increasing attention (Uknes et al. 1992).
This refers to a process in which plants exhibit an increased
level of resistance to infection by a pathogen after appropriate
stimulation (Ross 1961). Induced resistance can be triggered
by, e.g., infection with a necrotizing pathogen (Kuc 1982;
Ross 1961), or by treatment with certain chemicals, e.g., sali-
cylic acid (SA) (White 1979). This response is referred to as
systemic acquired resistance (SAR). Induced resistance can
also be a result of root colonization by PGPR (Alström 1991;
Wei et al. 1991). The latter response is called induced sys-
temic resistance (ISR), and has been shown to protect against
disease in several plant species (Thomashow and Weller 1995,
and references therein; van Wees et al. 1997), but has so far
been demonstrated only in pseudomonads. Mechanisms of
induced resistance are, with some exceptions, still elusive.
Maurhofer et al. (1994) have shown that ISR induced by the
Pseudomonas fluorescens strain CHA0 is associated with
pathogenesis-related (PR) protein accumulation. Later reports
suggested that ISR may be controlled by an SA-independent
pathway (van Wees et al. 1997; Pieterse et al. 1998).
Lipopolysaccharides from bacterial outer membranes (van
Peer and Schippers 1992), siderophores (Leeman et al. 1996),
jasmonic acid (JA), and ethylene (ET) (Pieterse et al. 1998)
have all been proposed to be involved in the induction of ISR.
Corresponding author: Salme Timmusk
952 / Molecular Plant-Microbe Interactions
The present paper reports on a study that addresses changes
of plant gene expression following inoculation by the root-
invading PGPR P. polymyxa. A gnotobiotic system was used
to show that P. polymyxa isolates confer resistance to biotic
(Erwinia carotovora challenge) and abiotic (drought) stress.
With RNA differential display (RNA-DD) and reverse tran-
scription-polymerase chain reaction (RT-PCR), genes were
identified whose expression level was altered upon treatment
with the PGPR.
A gnotobiotic system for studies of PGPR effects on plants.
Since the present study addresses changes in plant gene ex-
pression conferred, directly or indirectly, by treatment with
PGPR, the choice of suitable model organisms was of impor-
tance. The PGPR used here, P. polymyxa, has a relatively wide
host range. In addition to cereals, several dicots are suscepti-
ble to infection, including Arabidopsis thaliana (data not
shown). A. thaliana was chosen as the model plant because it
provides a good experimental system for genetic studies, and a
great number of sequence entries in data bases are available,
thus facilitating the identification of genes whose expression
might be altered by the PGPR.
To evaluate putative plant-growth-promoting effects of pre-
viously isolated P. polymyxa strains, a gnotobiotic system was
established. Defined and controlled plant growth medium and
growth conditions were used in which effects of P. polymyxa
on the target plant A. thaliana could be evaluated. The choice
of a gnotobiotic system for this study was motivated by the
need to exclude the uncontrolled variations in experimental
conditions associated with studies carried out on plants grown
in soil. It would also facilitate follow-up studies on metabo-
lites produced by the PGPR that could be candidate media-
tors/elicitors of the effects observed.
As a test of putative protecting effects, PGPR-treated and
control plants were challenged under biotic or abiotic stress
conditions, respectively. E. carotovora subsp. carotovora
(strain Scc 3193) was chosen as the biotic stress factor since it
is a pathogen of very wide host range and therefore provides a
system for the study of nonspecific plant-pathogen interac-
tions. Drought was chosen as the abiotic stress factor.
P. polymyxa isolates mediate protection of A. thaliana
from pathogen attack and drought stress.
Different strains of P. polymyxa had previously been iso-
lated by Lindberg and Granhall (1984) and were shown to be
effective as PGPR on cereals. Some of these isolates, denoted
P. polymyxa B2, B3, and B4, were tested in this study. In
brief, plants were inoculated with a defined number of the
PGPR. After a period of 24 h, an antibiotic was added to both
the inoculated and the control plants in order to reduce the
Fig. 1. Inhibition of soft rot symptom development by prior Paenibacillus polymyxa inoculation. Axenic seedlings of Arabidopsis. thaliana C24 were
grown and inoculated with P. polymyxa (see Materials and Methods). Subsequently, plants were locally inoculated by Erwinia carotovora and cultured
for 12 h. The (A) P. polymyxa-treated plant shows signaticantly less severe characteristic symptoms than (B) a control plant that shows almost complete
maceration at the same time point.
Vol. 12, No. 11, 1999 / 953
number of free bacteria that had failed to enter plant roots. In
pilot experiments, we observed that Arabidopsis plants treated
with P. polymyxa showed mild stress symptoms: they were
reproducibly smaller than mock-treated control plants, and
their root system was clearly stunted. This effect was associ-
ated with PGPR infection and not antibiotic treatment, and
was obtained, with similar efficiencies, in several P. polymyxa
strains tested (B2, B3, and B4; data not shown).
The two types of stress were applied 1 week after PGPR
treatment. For biotic stress treatment, one leaf per plantlet was
inoculated by E. carotovora (5 × 108 CFU per ml) and plants
were further grown for 24 h before analysis. Pre-treatment
with P. polymyxa induced significant resistance: limited mac-
eration was generally observed around the infection site (Fig.
1A), but the plants were still vital after 2 subsequent days of
growth. In contrast, the leaves of control plants were already
almost completely macerated at this time point (Fig. 1B). Vi-
able count tests of E. carotovora extracted from leaves of
PGPR-treated plants, at half-day intervals after infection, indi-
cated decreasing numbers of the pathogen, compared with
those in control plants (data not shown).
To study induced drought tolerance, a second set of plants
was exposed to drought stress. Again, PGPR-treated plants
were more resistant and tolerated drought stress significantly
better than control plants. The latter showed severe wilting
symptoms after 3 days of exposure to drought stress (Fig. 2).
P. polymyxa treatment induces changes
in plant gene expression.
The observations reported above show that inoculation of A.
thaliana by P. polymyxa B2 confers significant resistance to at
least one plant pathogen and to drought treatment. Since this
effect most likely is associated with changes in plant gene ex-
pression, we employed RNA-DD (Liang and Pardee 1992) to
monitor changes in mRNA levels in plants associated with
PGPR treatment. Total RNA was isolated, 1 week after inocula-
tion (prior to stress treatment), in parallel from P. polymyxa-
treated and control plants. The mRNA was converted into
cDNA and subsequently amplified by PCR to yield a number of
radioactively labeled DNA fragments. The conversion of
mRNA into first-strand cDNA was accomplished by RT with
(separately) four anchored primers complementary to the poly-A
tail. These primers, and the set of five arbitrary primers used to
generate the DNA fragments in combination with the former,
are shown in Table 1 (see Materials and Methods for details of
the procedure). All PCRs with different primer combinations
were performed in duplicate. PCR amplifications of P. po-
lymyxa-treated and control samples were subjected to gel
electrophoresis in parallel to permit easy comparison and to
identify bands of altered intensity, depending on the treatment.
A typical example of such an experiment is shown in Figure 3.
From this gel and others (data not shown) containing frag-
ments generated with a total of 20 primer combinations, frag-
Fig. 2. Enhancement of drought stress tolerance by Paenibacillus polymyxa inoculation. Plants grown and inoculated as described in Figure 1 caption.
Subsequently, exposure to drought stress was induced (Materials and Methods). The (A) P. polymyxa-treated plant shows less severe characteristic wilt-
ing symptoms than (B) an untreated control plant.
954 / Molecular Plant-Microbe Interactions
ments of interest were eluted, re-amplified by PCR with the
same set of primers, and subsequently cloned into the pCR-2
vector plasmid. To minimize the number of false positives, a
hybridization screen method was employed (Consalez et al.
1996). Six insert sequences scored positive. The sequences of
these inserts were determined and compared with entries
available in genomic and cDNA data bases. One of these se-
quences was identified as a segment of the previously known
gene ERD15 of A. thaliana (Kiyosue et al. 1994a).
P. polymyxa treatment strongly increases expression
of the drought-stress-induced gene Erd15.
As a confirmatory experiment, semi-quantitative RT-PCR
was performed to test for differential expression of the se-
quences obtained. Primers derived from sequences internal to
the inserts—thus different from the ones used to isolate the
fragments—were used to amplify nested PCR fragments di-
rectly from the original first-strand cDNA obtained from
treated and untreated plants. As an independent control for
mRNA/cDNA content in samples, ACT2 (gene encoding Ac-
tin 2; An et al. 1996) was used. In this analysis, only one of
the candidate sequences scored clearly positive in the RT-PCR
test. Figure 4A shows that the gene segment of the ERD15
gene was differentially expressed: a fragment of correct size
was obtained when cDNA was derived from P. polymyxa B2-
treated plants, whereas the samples from untreated plants
yielded no visible PCR product. In contrast to this striking
difference, the control sequence of the ACT2 gene was ampli-
fied to equal intensity when cDNA dilutions from both treated
and untreated plants were used (Fig. 4B). Analysis of the
other five insert sequences did not support significant differ-
ences in mRNA levels between the two treatments. Only one
such example is shown in Figure 4C (clone 682).
The ERD15 gene sequence identified by the above protocol
represented the 3′-terminal mRNA segment, as expected from
the primer sets used. Its sequence (217 bp) was compared with
the published sequence (DDBG accession no. D30719). Of six
independently obtained insert sequences, five were identical to
the published sequence, whereas the remaining one carried
both an insertion of 1 bp and a 1-bp substitution. The 3′-
terminal 22 codons of the ERD15 reading frame were con-
tained in the inserts, and the site of poly(A) addition was
identical to the previously published sequence.
P. polymyxa causes mild biotic stress.
Since the differential expression of the ERD15 gene was
unexpected, we decided to test two other known drought-
responsive genes. The genes RAB18 (Lång and Palva 1992)
and LTI78 (Nordin et al. 1993) display elevated expression
levels upon drought stress. The RT-PCR experiment summa-
rized in Figure 5 shows that expression of the abscisic acid
(ABA)-responsive gene RAB18 was fourfold higher in P. po-
lymyxa-treated plants than in control plants, whereas the
LTI78 gene was not differentially expressed.
Since we considered the possibility that P. polymyxa
treatment might represent a mild biotic stress, other genes of
interest were tested for differential expression. It has been
shown that ET, JA, and SA have central roles in regulating
defense gene expression (Vidal 1998). Hence, we analyzed
the expression of marker genes for each of these pathways:
HEL (hevein, ET pathway; Potter et al. 1993), ATVSP
(vegetative storage protein acid phosphatase, JA pathway;
Berger et al. 1995), and PR-1 (SA pathway; Uknes et al.
1992) were chosen. The RT-PCR experiments summarized
in Figure 5 show that all three marker genes were overex-
pressed in plants previously treated with P. polymyxa, the
induction levels varying from twofold to sixfold. We infer
that this relatively small, but significant, increase is indica-
tive of a “mild” biotic stress.
We report here on an investigation of changes in gene ex-
pression in the model plant A. thaliana induced by the PGPR
Table 1. Primers used
Primer nameUse in experimenta
RNA-DD + first-strand cDNA
RNA-DD + first-strand cDNA
RNA-DD + first-strand cDNA
RNA-DD + first-strand cDNA
RNA-DD / second primer
RNA-DD / second primer
RNA-DD / second primer
RNA-DD / second primer
RNA-DD / second primer
RT-PCR / RAB18 primer 1
RT-PCR / RAB18 primer 2
RT-PCR / PR-1 primer 1
RT-PCR / PR-1 primer 2
RT-PCR / HEL primer 1
RT-PCR / HEL primer 2
RT-PCR / ATVSP primer 1
RT-PCR / ATVSP primer 2
RT-PCR / ERD-15 primer 1
RT-PCR / ERD-15 primer 2
RT-PCR / LTI-78 primer 1
RT-PCR / LTI-78 primer 2
Sequencing / PCR
Sequencing / PCR
See Materials and Methods
See Materials and Methods
See Materials and Methods
See Materials and Methods
aRNA-DD = RNA differential display; RT-PCR = reverse transcription-polymerase chain reaction.
Vol. 12, No. 11, 1999 / 955
P. polymyxa. Inoculation with this root-invading bacterium
conferred partial resistance to biotic (E. carotovora; Fig. 1)
and abiotic (drought; Fig. 2) stress. From a number of gene
segments detected by RNA-DD, only one scored positive: the
ERD15 gene sequence was identified as a segment of its
mRNA, abundantly present in PGPR-treated, but not un-
treated, A. thaliana (Fig. 4). This gene has previously been
shown to be drought stress responsive (Kiyosue et al.
1994a). It was therefore surprising that induction of ERD15
could be induced prior to abiotic stress, i.e., merely by in-
oculation with P. polymyxa. The induction level of the
ERD15 mRNA was high and estimated to be more than 50
times higher in samples from treated than from untreated
plants (Fig. 4). This may suggest that the ERD15 protein car-
ries out a second function in a defense against biotic stress,
although no biochemical data are available to account for its
putative role. A further possibility is that as P. polymyxa
treatment results in stunted roots (see Results), intracellular
water availability might be affected, thus inducing the dehy-
dration-responsive ERD15 gene.
Since RNA-DD only yielded one differentially expressed
gene, further characterization of the effect of inoculation was
done by additional RT-PCR experiments performed on mRNA
segments of stress-related genes. The twofold to sixfold in-
duction of the JA-responsive ATVSP, the ET-responsive HEL,
and the SA-responsive PR-1 genes bears the signature of a
mild biotic stress induced by P. polymyxa inoculation. This
effect is not unexpected, since these endophytic bacteria pro-
duce polygalacturonase and cellulase (S. Timmusk, unpub-
lished) as well as pectate lyase (Forrest and Lyon 1990). Exo-
Fig. 3. Autoradiogram obtained from RNA differential display (RNA-DD) analysis of RNA isolated from Paenibacillus polymyxa-treated and untreated
plants with five primer combinations (Materials and Methods). Primers used are indicated. U or T denote template RNA from untreated or treated plants,
respectively. Two independent (duplicate) reactions were analyzed in parallel. Some bands of altered intensity, in comparison between T and U lanes, are
indicated by arrows. Only bands that reproducibly showed up in repeated experiments were chosen for further analysis.
956 / Molecular Plant-Microbe Interactions
Fig. 4. ERD15 is differentially expressed in Paenibacillus polymyxa-treated plant tissue. Reverse transcription-polymerase chain reactions (RT-PCRs)
were performed as described in Materials and Methods. Reaction mixtures were electrophoresed on 2% agarose gels, stained with ethidium bromide, and
photographed. A, Primers complementary to sites within the insert sequence (internal primers) were used for RT-PCR to amplify a fragment from either
cloned insert DNA used as a size control (C) or from RNA extracted from plants treated with P. polymyxa (T). U denotes RT-PCRs carried out on RNA
isolated from untreated plants. B, As controls for equal RNA content in the samples, RNA preparations were subjected to RT-PCR with a set of ACTIN2-
specific primers. C, One example of an analysis performed on one of the inserts (clone 682) that had scored positive in the pre-screening test (see Results
for details). Primers sets were again derived from insert-internal sequences. Serial dilutions of template were used to ensure that results were not ob-
scured by saturation of the PCR. Arrows indicate positions of expected fragments.
Fig. 5. Differential expression of additional stress-associated genes. Reverse transcription-polymerase chain reactions (RT-PCRs) were performed with
sets of primers specific for biotic stress-associated genes (ATVSP, HEL, PR-1), abiotic stress-associated genes (RAB18, LTI78), and, as a control, ACT2.
Template RNA was from Paenibacillus polymyxa-treated (T) or untreated (U) plants. Serial dilutions were used, and [35S]dATP was included in the PCRs
for labeling of fragments. An autoradiogram is shown. Approximate values for ratio of intensities between bands found in T and U samples, determined
by PhosphorImager analysis, are indicated below.
Vol. 12, No. 11, 1999 / 957
enzyme preparations produced by E. carotovora have been
implicated in triggering a defense response against the patho-
gen (Vidal et al. 1998), most likely via release of pectic frag-
ments from the plant cell wall (Palva et al. 1993). Similarly,
Maurhofer et al. (1994) showed that inoculation of plants by
the root-invading Pseudomonas fluorescens strain CHA0 in-
duced the synthesis of PR proteins. As P. polymyxa also in-
duces gene expression of PR-1 (Fig. 5), this suggests that (i)
the PGPR induce a mild biotic stress and (ii) this effect initi-
ated a systemic response that resulted in partial protection
from the pathogen upon subsequent challenge. Whether or not
hydrolytic/pectinolytic enzymes are the main factor in the
generation of elicitors in these cases and may represent a
common denominator in induction of the systemic response is
not yet established.
To assess the significance of the unexpected induction of
ERD15, two additional abiotic stress-related genes were tested
for changes in mRNA levels. The RAB18 gene (also: LEA/
DHN; Welin et al. 1994) is induced by drought and ABA,
whereas LTI78 (previously: LTI140) is strongly induced by
low temperature, but only weakly by ABA and drought
(Nordin et al. 1993). The RT-PCR experiments shown in Fig-
ure 5 indicate that P. polymyxa induced RAB18 four- to six-
fold, whereas LTI78 was unresponsive. So far, this suggests
that the unexpected induction of the ERD15 gene is not
unique, since a second drought-responsive gene also showed
an inoculation-dependent increase in expression level, albeit
less pronounced. Since the present study did not include de-
terminations of the levels of the various defense-related plant
hormones, we cannot rule out that ABA is a key mediator in
the induction of the ERD15 and RAB18 genes. We note, how-
ever, that the ERD15 gene was previously isolated in a screen
for dehydration-induced genes at a time point prior to the on-
set of ABA accumulation in the plant (Kiyosue et al. 1994b).
Hence, the most significant result obtained in this study
suggests that application of a mild biotic stress can affect
genes that hitherto have been associated with abiotic (here:
drought) stress. This is strengthened by the protective effect of
P. polymyxa inoculation upon plants when subjected to subse-
quent drought stress treatment (Fig. 2). It is not unexpected
that different plant stress response pathways could be acti-
vated in concert: e.g., abiotic stress conditions, such as freez-
ing and drought, may result in physical damage to plant tissue,
which in turn should facilitate access of pathogens. Earlier
work has indicated that abiotic stress can activate defenses
against pathogens (biotic stress), whereas the reverse has
rarely been found. So far, most stress-related proteins have not
been analyzed for their biochemical activities, although some
of them may carry out functions that are of importance in both
types of stress situations. Moreover, some biotic and abiotic
stress situations may result in similar physiological effects,
and hence co-regulation of certain defense genes may be evo-
lutionarily selected. For instance, several soil bacteria (e.g.,
Bacillus subtilis) produce osmolytes such as glycine betaine
because they are subjected to frequent fluctuations in osmotic
conditions (Lucht and Bremer 1994). Such compounds, if re-
leased within plant cells, could cause a mild osmotic stress by
lowering the water potential outside the cell membrane. A
wide variety of genes are induced by dehydration in order to
protect plant cells from water deficit (Shinozaki and Yama-
guchi-Shinozaki 1996, and references therein). Thus, bacterial
root invasion could be perceived as a local dehydration
through effects on the root system, which then might result in
the induction of drought stress genes.
In conclusion, the results shown here indicate that inocula-
tion by the PGPR P. polymyxa can protect A. thaliana against
a bacterial pathogen and drought stress in a gnotobiotic sys-
tem. This effect correlates with an increase in the expression
not only of genes associated with biotic stress (PR-1, HEL,
ATVSP) but also of those associated with drought stress
(ERD15, RAB18). Even though more trivial explanations are
possible (see above), these results may suggest that this bacte-
rium can trigger both biotic and abiotic stress-related defense
pathways, or that pathways are overlapping. The observed
protection is consistent with a mild pathogenic effect. It is
conceivable that plant growth promotion represents a trade-
off between maximal growth rate and an increased resis-
tance toward pathogens. Whether the simultaneous induction
of known drought response genes and pathogenesis-related
genes is co-incidental or a beneficial selected trait is as yet
This study can only be considered a starting point in de-
tailed investigations of PGPR effects on plants. Clearly, the
identification of only one gene whose altered expression level
was detectable by RNA-DD asks for additional examples.
Furthermore, it will be of interest to test whether the striking
increase in ERD15 expression is mediated by changes in the
level of one (or several) of the key plant hormones.
MATERIALS AND METHODS
Plant material and growth conditions.
Seeds of A. thaliana ecotype C24 were surface sterilized by
incubation in saturated and filtered aqueous calcium chlorate
solution for 30 min, followed by repeated washes in sterile,
distilled water. Seeds were then sown on MS-2 medium
(Murashige and Skoog 1962). Plants were replanted after
germination and subsequently grown for 2 weeks in a growth
chamber at 22°C with a 16-h light regime.
Plant inoculation by P. polymyxa.
The P. polymyxa strains B2, B3, and B4, isolated from the
rhizosphere of wheat (Lindberg and Granhall 1984), were
grown in L medium (Miller 1972) at 30°C to late log phase.
Sequence analysis of a segment of 16S rDNA confirmed the
classification of the bacteria as P. polymyxa (data not shown).
After 2 weeks of growth, plants were inoculated by soaking
their roots in overnight cultures of P. polymyxa in L medium
(approximately 108 bacteria per ml) for 24 h; control plants
were soaked in L medium. Both P. polymyxa-treated and un-
treated plantlets were then treated with Cefotaxim at 100 µg/
ml to reduce the number of bacteria around the roots. Plantlets
were further grown for 1 week in Cefotaxim-containing me-
dium. Bacterial growth in stems and leaves was evaluated by
homogenizing four inoculated plants in 10 ml of 10 mM
MgSO4 and plating of serial dilutions on L agar plates.
Test of induced resistance to pathogen.
One week after inoculation with P. polymyxa, six plants
were locally inoculated by the E. carotovora strain Scc 3193
(Pirhonen et al. 1988). Bacterial growth and inoculation of
plants were performed as described (Palva et al. 1994). In-
958 / Molecular Plant-Microbe Interactions
oculated plantlets were further incubated, and E. carotovora
growth in planta was evaluated at 12-h intervals as described
Test of drought stress tolerance.
Axenic seedlings of A. thaliana C24 were propagated and
inoculated by P. polymyxa as described above. Plants were
exposed to drought stress by opening the lids of the culture
dishes for a period of 3 days.
Plant material (approximately 300 mg per plant; combined
from six plants) was ground in liquid nitrogen. RNA was ex-
tracted by a method based on LiCl-precipitation (Verwoerd et
al. 1989). RNA samples were treated with DNase I as de-
scribed in Sambrook et al. (1989) with RQ1 DNase (Promega,
Madison, WI). Aliquots of total RNA (approximately 0.2 µg)
were used for first-strand cDNA synthesis reactions that in-
cluded MMLV reverse transciptase (Promega), dNTPs (20
µM), and, separately, primers dT12MG, dT12MC, T12MA, and
dT12MT (all at 1 µM; Table 1). All primers were included in
the differential display kit (Genhunter, Brookline, MA). “M”
denotes a mixture of dA, dC, and dG, thus rendering the an-
chored primers degenerate. Subsequently, five 10-mer primers
were used, separately, in combination with the dT12MN prim-
ers in a total of 20 different reactions. Taq DNA polymerase
(Perkin-Elmer, Foster City, CA) was used for amplifications,
and PCR was performed in a Rapid Cycler (Idaho Technolo-
gies, Idaho Falls, ID). Labeling of the PCR fragments gener-
ated was done by inclusion of [35S]dATP (Amersham Pharma-
cia Biotech, Uppsala, Sweden). Reaction conditions were
according to the manufacturer’s manual. Aliquots of the reac-
tions were run on 8% sequencing gels, followed by drying and
exposure to X-ray film (Kodak, Rochester, NY). Bands of in-
terest were excised from the gel, and the DNA fragments
eluted. For re-amplification of the eluate, we used the same
set of primers that had generated the band in question. This
yielded DNA fragments for direct cloning into the pCR-2
vector plasmid (Invitrogen, San Diego, CA). Pre-screening of
candidate inserts before RT-PCR analysis (see below) was
done as published (Consalez et al. 1996).
DNA sequence analysis.
DNA sequences of inserts were obtained with a PCR cycle-
sequencing kit (Amersham Life Science, Cleveland, OH) on
an ABI377 Sequenator (Perkin Elmer). Sequences were com-
pared with available genomic and cDNA entries by BLAST
To determine relative increases/decreases of mRNA abun-
dance in parallel samples (treated/untreated), aliquots of initial
RNA preparations were first reverse transcribed with gene-
specific primers (Table 1). Subsequently, serial dilutions of the
cDNA were made and used for PCRs with pairs of gene se-
quence-specific primers. Serial dilutions were employed,
since PCR amplification is exponential and thus band inten-
sity differences must be measured before saturation of the
amplification reaction is reached. Labeling of the fragments
during PCR was done by inclusion of [35S]-dATP, and frag-
ments were separated on 2% agarose gels. Dried gels were
exposed to X-ray film, and band intensities quantified by a
PhosphorImager (Molecular Dynamics, Sunnyvale, CA).
We are grateful to U. Granhall for strains of P. polymyxa used in this
study and for advice during the initial stages of this work. We are in-
debted to S. Vidal and B. Welin for RT-PCR primers and critical reading
of the manuscript, R. Grönros for help with preparation of photographs,
and D. Clapham for valuable discussions. We are grateful to P. Eng-
ström, U. Granhall, J. Schnürer, and J. Valkonen for critical reading of
the manuscript. This work was performed with financial support from
Stiftelsen Lantbruksforskning (SLF).
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