Journal of Microbiological Methods 78 (2009) 59–65

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Journal of Microbiological Methods

j o u r n a l h o m e p a g e : w w w. e l s e v i e r. c o m / l o c a t e / j m i c m e t h

Multiplex real-time PCR for detection, identification and quantification of ‘Candidatus

Liberibacter solanacearum’ in potato plants with zebra chip
Wenbin Li a,⁎, Jorge A. Abad b, Ronald D. French-Monar c, John Rascoe d, Aimin Wen e, Neil C. Gudmestad e,
Gary A. Secor e, Ing-Ming Lee f, Yongping Duan g, Laurene Levy a
a
National Plant Germplasm and Biotechnology Laboratory, USDA-APHIS-PPQ-CPHST, Beltsville, MD 20705, United States
b
Plant Germplasm Quarantine Program, USDA-APHIS-PPQ-PHP-PSPI, Beltsville, MD 20705, United States
c
Plant Pathology and Microbiology, AgriLife Extension, Texas A&M, Amarillo, TX 79106, United States
d
Molecular Diagnostic Laboratory, USDA-APHIS-PPQ-PHP, Beltsville, MD 20705, United States
e
North Dakota State University, Department of Plant Pathology, Fargo, ND 58105, United States
f
Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD 20705, United States
g
U.S. Horticultural Research Laboratory, USDA-ARS, Fort Pierce, FL 34945, United States

a r t i c l e i n f o a b s t r a c t

Article history: The new Liberibacter species, ‘Candidatus Liberibacter solanacearum’ (Lso) recently associated with potato/
Received 30 January 2009 tomato psyllid-transmitted diseases in tomato and capsicum in New Zealand, was found to be consistently
Received in revised form 17 April 2009 associated with a newly emerging potato zebra chip (ZC) disease in Texas and other southwestern states in
Accepted 17 April 2009
the USA. A species-specific primer LsoF was developed for both quantitative real-time PCR (qPCR) and
Available online 3 May 2009
conventional PCR (cPCR) to detect and quantify Lso in infected samples. In multiplex qPCR, a plant
Keywords:
cytochrome oxidase (COX)-based probe-primer set was used as a positive internal control for host plants,
Bactericera cockerel which could be used to reliably access the DNA extraction quality and to normalize qPCR data for accurate
Phloem-limited bacterium quantification of the bacterial populations in environment samples. Neither the qPCR nor the cPCR using the
α-proteobacteria primer and/or probe sets with LsoF reacted with other Liberibacter species infecting citrus or other potato
pathogens. The low detection limit of the multiplex qPCR was about 20 copies of the target 16S rDNA
templates per reaction for field samples. Lso was readily detected and quantified in various tissues of ZC-
affected potato plants collected from fields in Texas. A thorough but uneven colonization of Lso was revealed
in various tissues of potato plants. The highest Lso populations were about 3 × 108 genomes/g tissue in the
root, which were 3-order higher than those in the above-ground tissues of potato plants. The Lso bacterial
populations were normally distributed across the ZC-affected potato plants collected from fields in Texas,
with 60% of ZC-affected potato plants harboring an average Lso population from 105 to 106 genomes/g tissue,
4% of plants hosting above 107 Lso genomes/g tissue, and 8% of plants holding below 103 Lso genomes/g
tissue. The rapid, sensitive, specific and reliable multiplex qPCR showed its potential to become a powerful
tool for early detection and quantification of the new Liberibacter species associated with potato ZC, and will
be very useful for the potato quarantine programs and seed potato certification programs to ensure the
availability of clean seed potato stocks and also for epidemiological studies on the disease.
Published by Elsevier B.V.

1. Introduction disease was found in the United States potatoes in 2000 near Pearsall,
Texas, and the Texas side of the Lower Rio Grande Valley, and currently
Zebra chip (ZC) of potato (Soanum tuberosum L.) was first observed has spread throughout Central America and southwestern U. S states
in Mexico in 1994 (Secor and Rivera, 2004; Munyaneza et al., 2007). A (Gudmestad and Secor, 2007). ZC drastically reduces quality and value
similar disease, potato purple top, was first recognized in Canada in of all market classes of potato. Outbreaks of the disease occurred from
1933 (Leyva-López et al., 2002). Potato ZC is defined by a streaking 2004 to 2006 in Mexico, and in Texas and other U. S. states costing
and dark striping in medullary ray tissue of affected potato tubers and growers and processors on both sides of the border millions of dollars
in fried, chipped potatoes from which arose its popular name. The in losses. In isolated instances, ZC has caused entire fields to be
abandoned (Gudmestad and Secor, 2007). The disease was recently
found in New Zealand (Liefting et al., 2008). ZC symptoms have been
⁎ Corresponding author. observed in many potato cultivars; none of them appears to be
E-mail address: Wenbin.Li@aphis.usda.gov (W. Li). resistant (Gudmestad and Secor, 2007).

0167-7012/$ – see front matter. Published by Elsevier B.V.

doi:10.1016/j.mimet.2009.04.009

This article is a U.S. government work, and is not subject to copyright in the United States.
60 W. Li et al. / Journal of Microbiological Methods 78 (2009) 59–65

Numerous symptoms have been observed in ZC affected plants ‘Ca. Liberibacter africanus’ (Laf) (Jagoueix et al., 1996). These two
including plant stunting, leaf scorch and chlorosis, swollen nodes, a species of Liberibacter are associated with two forms of citrus
‘zigzag’ appearance of the upper growth, proliferated auxiliary buds, Huanglongbing (HLB) (ex. citrus greening). In addition, the third
aerial tubers, browning of the vascular system in the below-ground form of HLB was found associated with ‘Ca. Liberibacter americanus’
portions of stalks, enlarged lenticels of the underground stalks, (Lam) in Brazil in 2004 (Teixeira et al., 2005). Real-time quantitative
collapsed stolons, brown discoloration of the vascular ring, necrotic PCR (qPCR) has become the most accurate and sensitive method for
flecking of internal tuber tissues, and occasionally streaking of the detection and quantification of plant pathogens since the first
medullary ray tissues (Gudmestad and Secor, 2007). Most of these commercial qPCR instrument was available (Heid et al., 1996). The
symptoms have been observed in plants exhibiting the purple top wilt higher detection sensitivity and quantitative power of qPCR was
syndrome associated with the clover proliferation phytoplasma clearly demonstrated for citrus Liberibacter species (Li et al., 2006,
recently found in Washington and Oregon states (Munyaneza et al., 2007, 2008a, 2009). The principle objective of this study was to
2007), and are similar to, but distinct from, those of net necrosis in develop a rapid, sensitive and specific TaqMan real-time PCR assay for
potato tubers caused by the phloem-limited potato leaf roll virus. detection, identification and quantification of ‘Ca. Liberibacter
Potato ZC was observed to be transmitted by the potato/tomato solanacearum’ in its host plants. The method can be used to
psyllid (Bactericera cockerelli Sulc) that is common and abundant in understand the pathway, epidemiology of the disease, for the
Southern U. S. and Mexico (Munyaneza et al., 2007). B. cockerelli was Germplasm Screening Programs and the Seed Potato Certification
first documented in Mexico in 1947, and has been a primary pest of program to ensure the availability of clean seed potato.
potato, chili pepper (Capsicum spp.), and tomato (Solanum lycoper-
icum) since 1960s (Garzón et al., 1992). It is unknown when the psyllid 2. Materials and methods
was introduced into the U. S. The severity of ZC can vary from year to
year and within a field, which might be a result of the differences in 2.1. Plant materials
weather conditions during winter and microclimates on the popula-
tions of the vector psyllids. The psyllid was found in greenhouses in Plant materials of 5-month old ZC suspect potato plants (Fig. 1)
Auckland, New Zealand, in May 2006, and soon found established were collected from Lubbock County, Texas and stored at 4 °C. Before
throughout most parts of the nation (Liefting et al., 2008). sampling, the plant materials were washed in tap water and then in
Graft transmission of potato ZC to healthy potato indicated that the distilled water. Materials of individual plants were divided into above-
cause of ZC is a graft transmissible pathogen and not attributed to an and below-ground sample groups. In the above-ground group, tissues
abiotic cause such as heat stress (heat necrosis), a psyllid toxin of leaf midribs and petioles, leaf blades, whole stalk, stalk epidermis,
(psyllid yellows) (Richard, 1928), a nutrient deficiency or toxicity, or a stalk cortices and aerial tubers were separately sampled. Samples of
combination of these factors (Gudmestad and Secor, 2007). The root epidermis, root cortices and tubers were separated from the
characteristic of the symptoms described above implies the involve- below-ground group. Lso-infected materials were also collected from
ment of a systemic or vascular pathogen, most likely a virus, viroid, potato and tomato plants that were experimentally inoculated with
prokaryote (bacterium or bacterial-like) or fungus as the causal agent the ZC disease by stalk grafting in a greenhouse (USDA-ARS, Beltsville,
of the disease. Extensive laboratory testing of ZC affected plants has Maryland). Similar samples from healthy materials of potato plants
already eliminated a number of potential candidate pathogens such as were collected as negative controls both from a ZC-free potato farm in
Ralstonia solanacearum, Serratia marcescens, and many viruses Texas and from greenhouse-grown plants of potato (USDA-APHIS-
including tomato spotted wilt, various strains of PVY strains, PPQ, Beltsville, Maryland).
geminiviruses, tobacco rattle, beet western yellows, potato leaf roll
and 10 other virus families (Gudmestad and Secor, 2007). ZC-affected
potato plants exhibited symptoms similar to those of potato purple
top wilt disease found in Washington and Oregon, USA, which was
associated by subgroup 16SrVI-A phytoplasma (Lee et al., 2004).
However, phytoplasmas were not consistently detected in potato
plants or tubers exhibiting ZC symptoms (Munyaneza et al., 2007),
suggesting some other pathogen(s) must be involved in ZC. In January
2008, a Liberibacter species designated as ‘Candidatus Liberibacter
solanacearum’ (Lso) (Liefting et al., 2009, in press) was associated
with diseases of tomato and capsicum plants in New Zealand (Liefting
et al., 2008). These diseases of tomato and capsicum showed very
similar symptoms to those reported as “psyllid yellows” (Richard,
1928) and to the foliar symptoms described for potato ZC (Liefting
et al., in press). In the U.S., the new Liberibacter species was
associated, on July 14, 2008, with potato ZC in Texas (Abad et al.,
2009; Bech, 2008). The solanaceous liberibacter species was also
detected in B. cockerelli collected on tomato plants in Texas and
transmitted empirically by the psyllids to induce “psyllid yellows” in
tomato and potato plants (Hansen et al., 2008). Although the
solanaceous liberibacter species is closely related with species of
liberibacter associated with citrus Huanglongbing (Lin et al., 2009),
the new Liberibacter species is not associated with the citrus disease
nor has it been found in Asian citrus psyllids (Diaphorina citri) (Li
et al., 2008b).
To detect the solanaceous Liberibacter species by conventional PCR
(cPCR), one forward primer, OA2, was developed (Liefting et al.,
2008). The specific primer was paired with the universal reverse Fig. 1. Typical symptoms of zebra chip on a potato plant collected in the field in Texas. This
primer OI2c that was designed for ‘Ca. Liberibacter asiaticus’ (Las) and plant was used in the trial on in-planta distribution of ‘Ca. Liberibacter solanacearum’.
 W. Li et al. / Journal of Microbiological Methods 78 (2009) 59–65 61

2.2. DNA extraction detection limit of real-time PCR for environmental samples using a
sample standard curve as described previously (Li et al., 2008a), 10-
Total DNA from field and greenhouse samples was isolated using the fold serial dilutions of the field DNA extract were prepared also using
DNeasy Plant Mini Kit (Qiagen, Valencia, CA), according to the the total DNA extract from midribs and petioles of healthy potato
manufacturer's instruction. For study on distribution of ‘Ca. Liberibacter plants.
solanacearum’, three sub-samples of 400 mg from each type of tissues
were collected for DNA extraction. For field or greenhouse samples, 2.6. PCR assays
100 mg of midribs and petioles was used per extraction. All samples
were cut into sections of about 1 mm wide and homogenized using a Conventional PCR assays were performed in the same standard
FastPrep (MP Biomedical, Solon, Ohio) bead mill as described conditions optimized previously (Li et al., 2007). In brief, the PCR
previously (Li et al., 2006). Sample DNA was eluted with 100 μl elution reaction mix contained 1× PCR buffer, 1 unit of Platinum Taq polymerase
buffer of the Qiagen kit. The concentration of total sample DNA (plant + (Invitrogen), 2.5 mM MgCl2, 200 μM each dNTPs, 200 μM each primer
pathogen) present in the extracts was estimated with a NanoDrop and 2 μl of DNA sample. The PCR amplification was carried out in 1 cycle
spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). at 94 °C for 2 min, 35 cycles at 94 °C for 30 s, 62 °C for 30 s and 72 °C for
1 min, and 1 cycle at 72 °C for 10 min, using a Biometra T3 thermocycler.
2.3. Primer and probe The PCR products were visualized in 1.0% agarose gel stained with
ethidium bromide. TaqMan real-time PCR assays with the Lso-specific
One species-specific forward primer LsoF, 5′-GTC GAG CGC TTA TTT primer-probe set Lso-HLBp-HLBr (Lsopr) and the positive internal
TTA ATA GGA-3′ was empirically designed at the signature region of control primer-probe set COXfpr (plant mitochondrial cytochrome
the 16S rRNA sequence of ‘Ca. Liberibacter solanacearum’ (NCBI oxidase) were performed as described previously (Li et al., 2006), using
GenBank accession number EU980389). The design of the forward a SmartCycler II (Cepheid, Sunnyvale, CA). The real-time PCR mix
primer was optimized to be compatible with the Liberibacter- contained 1x PCR buffer,1 unit of Platinum Taq polymerase (Invitrogen),
universal TaqMan probe (HLBp) and reverse primer (HLBr) used for 6.0 mM MgCl2, 240 μM each dNTPs, 240 μM each primer, 120 μM each
real-time PCR assays (Li et al., 2006), as well as with the reverse probe, and 2 μl of DNA sample. The real-time PCR program was 1 cycle at
primer OI2c employed in conventional PCR testing (Jagoueix et al., 95 °C for 20 s with optics off and 40 cycles at 95 °C for 1 s with optics off
1996). In silico PCR was performed for all the primer-probe and and at 58 °C for 40 s with optics on. Reactions for field diagnostic samples
primer-primer combinations by using BLASTn against the NCBI were performed in duplicate and those for experimental purposes were
GenBank database to ensure their specificity prior to primer and done in triplicate. Each diagnostic run contained one negative and one
probe synthesis by the Integrated DNA Technologies, Inc. positive control (Table 1).

2.4. 16S rRNA gene cloning and sequencing 2.7. Statistics analysis

To establish a standard curve for absolute quantification, a band of Real-time PCR data were exported from the SmartCycler software
1163 bp was amplified from 16S rDNA of Lso in a field sample from version 2.0D (Cepheid, Sunnyvale, CA) for calculation of mean
Texas with the newly-designed forward primer LsoF and the reverse crossing threshold (Ct) values and standard deviations (SDs).
primer OI2c (Jagoueix et al., 1996). To obtain the 16S rRNA gene Standard linear regressions (Y = a + bX) of the log concentration of
sequence of Lso, these two primers were paired with the 16S rRNA- the target DNA copies (Y) versus the mean Ct values (X) were
based universal primers, fD2, rP1 (Weisburg et al., 1991), XF04af and obtained. PCR amplification efficiency (AE) was calculated from the
XF04ar (Montero-Astua et al., 2007), in combinations of LsoR/rP1, slopes of the regressions using the equation AE = 10− slope − 1 (Li
fD1/OI2c, LsoF/XF04ar and XF04af/OI2c. PCR amplifications were et al., 2008a). Before the Ct values of real-time PCR were used for
performed using the validated conventional PCR protocol for detec- estimating the bacterial population, they were normalized by multi-
tion of Liberibacters (Li et al., 2007). The amplification products plying with a normalization coefficient (Nc) obtained from their
obtained were cloned into the TOPO TA pCRII vector (Invitrogen) and positive internal control reaction. Nc = 1-(inCt-MinCt)/MinCt: with
the plasmids were propagated in the strain Mach1-T1 of E. coli the ‘inCt’ being the Ct value of the internal control primer-probe set
(Invitrogen) and purified using a PureLink Quick Plasmid Miniprep kit COXfpr for a sample and the ‘MinCt’ being the mean inCt obtained
(Invitrogen). The 16S rDNA fragments were sequenced in both from all samples. For studies evaluating the bacterial population in
directions using the M13 forward and reverse primers at the Center various plant tissues, comparisons between types of tissues were
for Biosystems Research, DNA Sequencing Facility, University of made using one-way analysis of variance (ANOVA). When significant,
Maryland, College Park. the comparisons were evaluated by two-way ANOVA. Least significant
differences were calculated by a means comparison test (Tukey's)
2.5. Standard curves for quantification using a confidence level of P = 0.05.

The cloned plasmid with a fragment of 1163 bp from 16S rDNA 3. Results
obtained with the primer set LsoF/OI2c was named pTXZC18. The
number of copies of pTXZC18 was estimated using the number of base 3.1. Zebra chip syndrome
pairs (n = 5136) and the average molecular mass of a base pair in
double strand DNA (660 Da), resulting in one copy (molecule) of ZC affected potato plants collected from TX exhibited collapsed
pTXZC18 calculated to be 5.658 × 10− 6 pg. The initial concentration of stalks in addition to showing stunting and auxiliary bud proliferation
the pTXZC18 standard was adjusted in TE buffer to be 9.92 × 108 (Fig. 1). Young leaves were underdeveloped with symptoms such as
copies/μl (Fig. 3). To obtain an absolute standard curve (Fig. 4), 10-fold interveinal chlorosis and scorching. The stalks developed proliferated
serial dilutions from the initial concentration of pTXZC18 were auxiliary buds on the tips, aerial tubers on the stalks and swollen
prepared in a total DNA extract from midribs and petioles of healthy nodes on the upper growth causing a ‘zigzag’ appearance. The below-
potato plants. Based on the absolute standard curve determined ground portions of stalks had a brown vascular system, enlarged
above, the target DNA copy number of Lso in the DNA extract obtained lenticels, and collapsed stolons. The tubers were reduced in size and
from the root epidermis of the potato plant showing typical ZC developed necrotic flecking of internal tissues and streaking of the
symptoms (Fig. 1) was estimated to be 3.62 × 106. To evaluate the low medullary ray. ZC diseased potato plants generally developed very few
62 W. Li et al. / Journal of Microbiological Methods 78 (2009) 59–65

Table 1
Specificity of PCR assays for ‘Candidatus Liberibacter solanacearum’ in potato plants affected with zebra chip.

Pathogen Host Provider Origin Real-time PCR Conventional

HLBaspr HLBafpr HLBampr Lsopr PCR (LsoF/OI2c)

‘Ca. Liberibacter solanacearum’

Strain TX001 Potato French-Monar, R Texas 0 0 0 20.55 +
Strain TX002 Potato French-Monar, R Texas 0 0 0 27.42 +
Strain TX003 Potato French-Monar, R. Texas 0 0 0 30.05 +
Strain TX004 Potato French-Monar, R. Texas 0 0 0 31.22 +
Strain TX005 Potato French-Monar, R. Texas 0 0 0 31.24 +
Strain TX006 Potato French-Monar, R Texas 0 0 0 31.94 +
StrainTX007 Potato French-Monar, R Texas 0 0 0 32.18 +
StrainTX008 Potato French-Monar, R. Texas 0 0 0 32.46 +
Strain NTX2005 Potato Gudmestad, N. C. Texas 0 0 0 32.15 +
Strain NTX2006 Potato Gudmestad, N. C. Texas 0 0 0 34.26 +
Strain STX2007 Potato Gudmestad, N. C. Texas 0 0 0 35.20 −
Strain NTX2008 Potato Gudmestad, N. C. Texas 0 0 0 32.22 +
Strain NE2008a Potato Gudmestad, N. C. Nebraska 0 0 0 27.16 +
Strain CO2008 Potato Gudmestad, N. C. Colorado 0 0 0 31.39 +
Strain TXZC2p Potato Lee, I.-M. Greenhouse 0 0 0 29.17 +
Strain TXZC3p Potato Lee, I.-M. Greenhouse 0 0 0 29.55 +
Strain ZC8#1 Tomato Lee, I.-M. Greenhouse 0 0 0 30.74 +
Strain ZC8#2 Tomato Lee, I.-M. Greenhouse 0 0 0 25.25 +
‘Ca. Liberibacter asiaticus’
Strain FL136 Citrus Li, W. Florida 25.25 37.47 0 0 −
Strain KIN1 Citrus Iwanami, T. Japan 26.26 38.62 0 0 −
Strain Las 692 Citrus Teixeira, D. C. Brazil 25.21 37.25 0 0 −
‘Ca. Liberibacter africanus’
Strain Letaba Citrus Van Vurren, F. S. Africa 37.35 25.62 0 0 −
Strain Stellenbosch Citrus Van Vurren, F. S. Africa 38.12 26.08 0 0 −
Strain ITSC Citrus Van Vurren, F. S. Africa 38.04 24.24 0 0 −
‘Ca. Liberibacter americanus’
Lam 974 Citrus Teixeira, D. C. Brazil 0 0 22.26 0 −
Lam 975 Citrus Teixeira, D. C. Brazil 0 0 22.66 0 −
Lam 976 Citrus Teixeira, D. C. Brazil 0 0 24.62 0 −
Potato leaf roll virus Potato Gudmestad, N. C. Unknown 0 0 0 0 −
Clover proliferation phytoplasma Potato Gudmestad, N. C. Oregon 0 0 0 0 −
‘Candidatus Phytoplasma americanum’ Potato Gudmestad, N. C. Nebraska 0 0 0 0 −
Xyella fastidiosa PD strain Grapevine Hartung, J. S. Brazil 0 0 0 0 −
Xylella fastidiosa CVC strain Citrus Hartung, J. S. California 0 0 0 0 −

Based on USDA-APHIS' cutoff of real-time results, ‘0’ is negative; readings between ‘0 and 36.99’ are positive; readings above 36.99 are negative. Conventional PCR results: (+) yields
specific a band and (−) dose not yield a specific band.

rootlets. The symptoms observed in this study were nearly identical to of the affected plant. The sequences of all the amplicons of 1163 bp
those described previously for ZC (Gudmestad and Secor, 2007; Secor from various tissues above had a 99% homology with the solanaceous
et al., 2008). Liberibacter species (NCBI GenBank Accession number EU834130)
found associated with diseases of tomato and capsicum described in
3.2. Signature region of Lso 16S rRNA New Zealand (Liefting et al., 2008). The remainder of the 16S rRNA
sequence of Lso was obtained using the primer pairs LsoR/XF04ar and
PCR amplicons of 1163 bp (Fig. 2) were obtained by conventional XF04ar/OI2c. The 16S rRNA gene sequence (1503 bp) obtained from
PCR using the primer set Lso/OI2c, from DNA extracts obtained from the ZC-affected potato plant has been deposited in the GenBank
midribs/petioles, whole stalks, stalk epidermises, stalk cortices, root (accession EU980389). Comparative analysis of 16S rRNA gene
epidermises, root cortices and tubers of the potato plant affected with sequences revealed that the Lso from the ZC-affected potato collected
ZC in the field in Texas (Fig. 1), as well as from 10 fold dilutions of the in the field in Texas had a homology of 99%, 96%, 96%, and 94% with ‘Ca.
original DNA extracts obtained from the leaf blades and aerial tubers Liberibacter solanacearum’ found in New Zealand, Las, Laf and Lam,
respectively, and a homology of 99% with the bacterial symbiont ‘Ca.
Liberibacter psyllaurous’ detected in the potato/tomato psyllids
collected in Texas (Hansen et al., 2008). The primer sets fD1/rP1
and LsoF/rP1 failed to amplify 16S sequences from ZC-affected potato
plants collected from Texas. The primer set fD1/OI2c amplified a
fragment of about 1.4 kb from the field DNA sample.

3.3. Specificity of PCR assays for Lso

The specificity of the assays with the primer-probe set Lso-HLBp-

HLBr (Lsopr) was evaluated in single and multiplex real-time PCR
with the positive internal control primer-probe set COXfpr (Li et al.,
2006), using total DNA extracts from potato plants affected with ZC or
Fig. 2. Detection of ‘Ca. L. solanacearum’ by conventional PCR in DNA extracts of various other unrelated pathogens including potato leaf roll virus, clover
tissues: midribs and petioles, leaf blades, whole stalk, stalk epidermis, stalk cortices,
root epidermis, root cortices, aerial tubers, small tubers and medium tubers (lanes 1 to
proliferation Phytoplasma, ‘Candidatus Phytoplasma americanum’,
10) of potato plants affected by zebra chip in the field in Texas. Lanes 11 and 12 were no from citrus plants infected with ‘Ca. Liberibacter asiaticus’, ‘Ca.
template and positive controls. Marker (M) was the Extra ladder (Invitrogen). Liberibacter africanus’ and ‘Ca. Liberibacter americanus’, and genomic
 W. Li et al. / Journal of Microbiological Methods 78 (2009) 59–65 63

healthy potato plants (Fig. 3). Based on the absolute standard curve,
the template concentration of Lso 16s rDNA in a DNA extract obtained
from the root epidermis of the potato plant affected with ZC (Fig. 1)
was estimated to be 3.62 × 106. To obtain a sample standard curve to
be used for accurate quantification of the bacterium in plant materials,
10-fold serial dilutions of the environmental DNA sample were made
in the DNA extract complex from healthy potato plants (Fig. 4A and B).
According to the sample standard curve, the LDL of the real-time PCR
with the primer-probe set Lsopr multiplexed with COXfpr was about
20 copies of the 16S rDNA templates of the bacterium for environ-
mental samples. The amplification efficiency (AE) of the multiplex
real-time PCR was 90.99% for the bacterium in the affected plants of
potato.
As shown in Fig. 4B and C, the TaqMan real-time multiplex PCR was
about 10 fold more sensitive than the conventional PCR with the
primer set Lso/OI2c for Lso detection in plant materials. The
conventional PCR using the primer set Lso/OI2c developed in this
study was additionally 10 fold more sensitive than the conventional
PCR assays using OA2/OI2c (Liefting et al., 2008) for Lso detection in
plant materials in our optimized PCR conditions. Among 50 DNA
samples extracted from individual potato plants affected with ZC in
the field in Texas (Fig. 6), 46 (92%) tested positive for Lso using the
real-time multiplex PCR; 23 (46%) tested positive using the conven-
Fig. 3. Sensitivity of the primer-probe set LsoR/HLBp/HLBr specific to ‘Ca. L. tional PCR with the primer set Lso/OI2c; and 20 (40%) tested positive
solanacearum’ in multiplex real-time PCR with the positive internal control primer-
using the conventional PCR with the primer set OA2/OI2c. Samples
probe set COXfpr. The template plasmid pTXZC18 DNA diluted in a DNA extract from 5-
month old healthy potato plants was used to establish a linear regression for absolute
quantification: real-time PCR optics graph for ‘Ca. L. solanacearum’ (A) and standard
curve for absolute quantification of ‘Ca. L. solanacearum’ (B).

DNA from pure cultures of Xylella fastidiosa (Table 1). The assay with
Lsopr yielded positive results only from DNA samples infected with
Lso. Negative results were obtained for samples infected with other
potato pathogens or the three Liberibacter species in citrus evaluated.
None of the real-time PCR assays using HLBaspr, HLBafpr or HLBampr
specific to citrus Liberibacter species reacted with any DNA samples
infected with Lso. The specificity of Lsopr was retained in the
multiplex real-time PCR with the positive internal control primer-
probe set COXfpr. As expected, the conventional PCR primer set LsoF/
OI2c demonstrated the same specificity for Lso as the real-time PCR
primer-probe set Lsopr. Neither the multiplex real-time PCR assays
nor the conventional PCR tests for Lso gave any false positive results
for 14 DNA extracts obtained from uninfected greenhouse-grown
potato plants in Beltsville, Maryland and 50 DNA samples extracted
from putative healthy potato plants grown in the field in Texas. In
addition, Lso was detected in DNA extracts obtained from ZC-affected
potato plants collected in Texas in 2005, 2006 and 2007, in Nebraska in
2008, and Colorado in 2008 (Table 1). Unfortunately, DNA samples of
‘Ca. Liberibacter psyllaurous’ were not available to us for evaluation,
because only limited DNA extracts were obtained from potato/tomato
psyllids infected with this Liberibacter (Hansen et al., 2008) and DNA
extraction from psyllids is sample-destructive. However, ‘Ca. Liberi-
bacter psyllaurous’ should be detected by both real-time and
conventional PCR assays with the forward primer LsoF, because its
16S rRNA sequence (EU812557) has perfect priming sites not only for
LsoF but also for all the reverse primer OI2c, HLBr and the probe HLBp
evaluated in this study.

3.4. Sensitivity of PCR assays for Lso

The low detection limit (LDL) of the multiplex real-time PCR with Fig. 4. Low detection limit of primer-probe set LsoR/HLBp/HLBr specific to ‘Ca. L.
Lsopr and COXfpr was about 10 copies of pTXZC18 per reaction when solanacearum’ in multiplex real-time PCR with the positive internal control primer-
the plasmid DNA was diluted in water, consistent to those of the probe set COXfpr. Templates were serial dilutions of an environmental DNA sample
absolute standard curves based on plasmid DNA in water for other extracted from a ZC symptomatic potato plant grown in Texas: sample standard curve
for quantification of ‘Ca. L. solanacearum’ in real samples (A); real-time PCR optics
pathogens (Li et al., 2007; Palaniappan et al., 2005). However, the LDL graph (B) and conventional PCR gel (C) for ‘Ca. L. solanacearum’ in sample dilutions. The
of the assay with Lsopr was about 100 copies of pTXZC18 per reaction starting concentration in the original field sample was estimated to be 3.62 × 106 based
when the plasmid DNA was diluted in the DNA extract complex from on the absolute standard curve in Fig. 3.
64 W. Li et al. / Journal of Microbiological Methods 78 (2009) 59–65

with typical ZC symptoms tested always positive for Lso by qPCR. Lso
was also detected in asymptomatic materials of ZC-infected potato
plants collected in the field.

3.5. Uneven in planta distribution of Lso

Lso was detected and quantified by the real-time multiplex PCR

using Lsopr and COXfpr in all tissue types of the affected potato plants
examined (Fig. 5). The bacterium was also detected by conventional
PCR assays in all the tissues of potato plants, although there was
complete inhibition of the amplification in the conventional PCR in
Fig. 6. Population dynamics of ‘Ca. Liberibacter solanacearum’ in a potato plantation in
DNA extracts from leaf blades and aerial tubers (Fig. 2). Based on the
Texas. One group of 50 ZC suspect or symptomatic potato plants were collected for the
sample standard curve (Fig. 4) and three 16S rRNA operons per study in the field in Lubbock county of Texas. DNA was obtained from midribs and
genome (or per bacterial cell) (Duan et al., in press), the Lso petioles of each plant.
populations in ZC-affected potato plants were estimated in genome/
g tissue and no significant differences in the bacterial populations
among the aerial parts and tubers were observed. However, the tally inoculated by grafting. However, the titers of the bacterium were
bacterial population was significantly lower in stalks than other usually higher (above 106 genomes per gram of fresh midribs and
tissues above ground. The Lso populations in root epidermis and root petioles) in greenhouse-grown tomato plants inoculated with Lso by
cortices were approximately 3-order higher than in all other tissue grafting ZC-affected potato stalks.
types of potato plants evaluated. The highest bacterial population was
3 × 108 genome equivalents per gram of fresh tissues in potato root 4. Discussion
while the lowest Lso population was 1.2 × 104 genome equivalents per
gram of fresh ‘whole stalk’. On average, each type of other tissues The accurate detection of plant pathogens is of paramount
contained 1–5 × 105 genome equivalents per gram of tissues sampled. importance for the timely implementation of disease management
The mean populations of Lso varied over 3 orders of magnitude among and eradication strategies. ZC defied typical diagnostic technologies
the tissues of ZC infected potato plants used in this study. that would point to known plant pathogens, as the cause of the
disease had remained unknown until the disease it was recently
3.6. Distribution of Lso populations in the field associated with ‘Ca. Liberibacter solanacearum’. In this study, the Lso-
specific primer (LsoF) was designed at the species signature region of
To study the population dynamics of Lso associated with potato ZC, the bacterial 16S rRNA sequence. LsoF was compatible in the
one group of 50 ZC suspect or symptomatic potato plants collected in conventional PCR reaction with the reverse primer OI2c universal to
the field in Lubbock County of Texas were used. The COXfpr targeting ‘Ca. Liberibacter asiaticus’ and ‘Ca. Liberibacter africanus’ (Jagoueix et
at the host plant DNA of potato yielded stable Ct values of around al., 1996). The conventional PCR with LsoF/OI2c yielded a specific
22.00 for the DNA extracts from all the plant samples, indicating an band of 1163 bp from potato and tomato samples infected with Lso.
overall high quality of DNA extraction. As shown in Fig. 6, the Lso LsoF primer was successfully used together with the genus-universal
populations complied with a normal distribution cross the ZC-affected TaqMan probe HLBp and reverse primer HLBr in a real-time PCR assay
potato plants (Fig. 6). About 60% of plants had Lso populations from multiplexed with the positive internal control probe-primer set
105 to 106 genomes per gram of fresh midribs and petioles. Around COXfpr (Li et al., 2006). The low detection limit of the real-time
10% of plants had bacterial populations of 104 genomes per gram of multiplex PCR was about 20 copies of Lso 16S rDNA per reaction for
tissue. Approximate 8% of plants hosted no Lso or Lso populations less environmental samples. This low detection limit showed that the real-
than 104 genomes per gram of tissue. Only 18% of plants harbored Lso time multiplex PCR was at least 10- to 100-fold more sensitive than
populations higher than 106 genomes per gram of tissue. The Lso the conventional PCR assays, consistent to the previous comparison
populations were about 105 genomes per gram of fresh midribs and between real-time and conventional PCR assays for the citrus
petioles in most of the greenhouse-grown potato plants experimen- Liberibacters (Li et al., 2007). The real-time PCR assay also demon-
strated a high PCR amplification efficiency (over 90%) for environ-
mental DNA or plant samples of potato and tomato. In addition, the
positive internal control could be readily used to check the DNA
extraction quality from ZC-affected plant materials, and reliably
employed in normalization of real-time PCR data for accurate
quantification of the bacterial populations in a range of DNA or
plant samples from various environments. The real-time multiplex
PCR assay developed in this study showed potential to become a
valuable tool for early detection, identification and quantification of
‘Ca. Liberibacter solanacearum’ in ZC-affected plants. Additionally, the
specificity of this primer-probe set permits the differentiation of ZC
potatoes associated with ‘Ca. Liberibacter solanacearum’ from pota-
toes infected with ‘Ca. Phytoplasma americanum’ (Lee et al., 2006),
that should allow for better epidemiological studies to be conducted.
The populations of ‘Ca. Liberibacter solanacearum’ in potato plants
affected with ZC in the field were on average low at about 105
genomes per gram of tissues (Fig. 5), which was at least 1,000-factor
lower than that of ‘Ca. Libeirbacter asiaticus’ in leaf midribs of citrus
Fig. 5. Quantitative distribution of ‘Ca. Liberibacter solanacearum’ in various tissues of
an environmental DNA sample extracted from a ZC symptomatic potato plant grown in
(Li et al., 2009). This might be due to a short growing season of potato
Texas. Bacterial log populations with the same letter on their histogram bars are not plants, which is usually four months from planting to harvesting in
significantly different (P = 0.05). Texas. That may not be an ample time for the fastidious bacterium to
 W. Li et al. / Journal of Microbiological Methods 78 (2009) 59–65 65

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