Genetic diversity, distribution, and molecular diagnosis...
Transcript of Genetic diversity, distribution, and molecular diagnosis...
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Historical Diversity and Molecular Diagnosis of Bacterial Pathogens on
Tomato in Pennsylvania
Ekaterina (Katya) Nikolaeva
Pennsylvania Department of AgricultureBureau of Plant Industry
Division of Plant Health
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PDA historical collection of bacterial strains from tomato.
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Xanthomonas Clavibacter Pseudomonas
266 strains from more than 5,000 clinical tomato samples.
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Pseudomonas spp. on tomato in PA
“Pith necrosis”
(Pseudomonas spp.)
Bacterial speck
(P. syringae pv. tomato)
38 strains (1987 – 2015)
• Positive by specific PCR (Bereswill et al., 1994; Zaccardelli, 2005)
K. Nikolaeva, PDA
K. Nikolaeva, PDA
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Bacterial canker on tomato in PA
Clavibacter michiganensis
subs. michiganensis
67 strains (1990 – 2015)
Positive by specific real-time PCR (Luo et al., 2008)
K. Nikolaeva, PDA
T. Olson, PDA
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Bacterial Spot Xanthomonads (BSX) on tomato in PA
X. perforans (100%, XV938)
1994-2012, 90 strains
X. gardneri (99-100%, XCGA2)
1995-2015, 32 strains
X. vesicatoria (100%, XV1111)
1996, 1 strain
X. euvesicatoria (100%, XV155)
not found on tomato but present on pepper (53 strains, 1987-2015)
Based on sequencing of 16S rRNA and BOX PCR.
T. Olson, PDA
S. Kim, PDA
S. Kim, PDA
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Bacterial Spot Xanthomonads (BSX) on pepper and tomato in PA.
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X. euvesicatoria X. vesicatoria X. perforans X. gardneri
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Box PCR (rep-PCR) with PA BSX strains (Versalovic et al., 1991).
Representatives of PA BSX strains: lanes 2 -10 - X. gardneri; lanes 11-17, 19, 21, 22 -X. perforans; lanes 20 and 23 X. euvesicatoria; lane 24 - X. vesicatoria; non-BSX strains: lanes 25-27 X. vitians; lane 28 and 29 – X. campestris pv. campestris
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Specificity of conventional PCR primers to PA BSX strains.
a 133 PDA BSX strains isolated from tomato and pepper were tested with published PCR primer pairs specific for BSX (Obradovic et
al., 2004; Cuppels et al., 2006; Park et al., 2009; Moretti et al., 2009; Koenraadt et al., 2009). Results are based on three replications.
Number of positive samples/Total tested samples.
Primers (target)a X. gardneri X. perforansX.
euvesicatoriaX.
vesicatoriaNon-BSX
RST65/RST69 (HrpB gene, vesicatoria group)
1/28a 73/74 15/15 0/1 8/17
BSX1/2 (KK1750 sequence, vesicatoria
group)18/23 36/74 4/13 1/1 5/17
XCVF/XCVR (Hrs protein, X. euvesicatoria)
0/28 0/89 15/15 0/1 0/17
Xeu2.4/Xeu2.5 (Rep PCR fragment, X.
euvesicatoria)0/28 0/89 15/15 0/1 0/17
Bs-XeF/ Bs-XeR (AFLP product, X.
euvesicatoria)0/28 0/77 15/15 0/1 0/17
Bs-XvF/ Bs-XvR (AFLP product, X. vesicatoria)
0/28 0/77 0/15 1/1 0/17
Bs-XgF/ Bs-XgR (AFLP product, X. gardneri)
27/28 0/76 0/15 0/1 0/17
Bs-XpF/ Bs-XpR (AFLP product, X. perforans)
0(2)/28 69/77 0/15 0/1 0/17
a
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Specific Multiplex real-time PCR for detection of X. gardneri from plant samples.
1)Specific for X. gardneri
Primers: Xg263F/Xg438RProbe: Xg360P
Target: arvBs1 effector gene
2)Specific for plant DNA(internal control)
Primers: COX-F/COX-RProbe: COX-P
Target: COX gene(Weller et al., 2000)
Two primer and probe sets:
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Multiplex real-time PCR for detection of X. gardneri
Multiplex real-time PCR for detection of X. gardneri from plant samples. Total DNA extracted with Qiagen kit.
Simplex real-time PCR for detection of X. gardneri from bacterial cultures without DNA extraction.
Cepheid real-time PCR machine Time: >1 h
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100 mg healthy tissues of tomato were mixed with 0.1 ml bacterial suspension of X. gardneri strain Rf-1. DNAs from plant/ bacterial mixtures were extracted using Qiagen kit. b The Ct values c No fluorescence was detected after 40 cycles of PCR amplification.d Healthy tomato tissues.
Detection of X. gardneri in tomato tissue samples.
Bacterial CFU
Tomato/ X. gardneri Tomato/ X. perforans
Xg, Cta Cox, Cta Xg, Cta Cox, Cta
107 16.95b ± 0.43 20.3 ± 1.30 >40c 22.29 ± 0.24
106 20.21 ± 0.87 20.47 ± 0.08 >40 22.43 ± 0.76
105 23.38 ± 1.12 21.53 ± 0.23 >40 22.48 ± 0.44
104 27.45 ± 1.23 21.71 ± 1.08 >40 22.85 ± 0.67
103 34.21 ± 1.87 21.01 ± 1.70 >40 21.98 ± 0.23
102 >40 22.65 ± 0.46 >40 23.15 ± 0.34
101 >40 23.12 ± 0.58 >40 21.97 ± 0.87
100 >40 21.80 ± 0.07 >40 22.56 ± 0.86
Controld >40 22.47 ± 0.29 >40 22.60 ± 0.28
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Effectiveness of real-time PCR for detection of X. gardneri from PDA clinical samples
a Samples expressing Bacterial Spot symptoms (PDA: Harrisburg, PA). DNA from plant tissues was extracted and purified using Qiagen kit.b Identification based on culture characteristics and conventional and/or BOX PCR.
PDA Clinical # Host Plant parts
Purified DNAa
Culture IdentificationbXg, Ct Cox, Ct
2013-99-99-0054
Tomato Leaves 19.23 20.39 Yes X. gardneri
Stems 25.94 20.84 Yes X. gardneri
Fruits 18.35 21.5 Yes X. gardneri
Flowers 21.48 19.62 Yes X. gardneri
2011-02-35-0028 Tomato Leaves 26.18 22.68 Yes X. gardneri
2011-99-99-0063 Tomato Leaves 21.26 20.77 Yes X. gardneri
2012-99-99-0094 Tomato Leaves 24.73 27.52 Yes X. gardneri
2012-07-41-0035 Tomato Leaves 17.06 20.93 Yes X. gardneri
2015-99-99-0107
Tomato Leaves 21.87 23.09 Yes X. gardneri
Tomato Fruits 23.56 22.04 Yes X. gardneri
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Effectiveness of real-time PCR for detection of X. gardneri from PDA clinical samples
PDA Clinical Host Plant parts
Purified DNAa
Culture IdentificationbXg, Ct Cox, Ct
2010-99-99-0113
Tomato Leaves >40.00c 21.56 Yes X. perforansStem >40.00 22.58 Yes X. perforans
Fruits >40.00 20.99 Yes X. perforans
2012-99-99-0108 Tomato Leaves >40.00 21.83 Yes X. perforans
2013-07-31-0067 Pepper Leaves >40.00 21.18 Yes X. euvesicatoria
2012-03-13-0029 Pepper Leaves >40.00 21.44 Yes X. euvesicatoria
2012-99-99-0089 Tomato Leaves >40.00 19.87 YesClavibacter michiganensis
2012-99-99-0109 Tomato Leaves >40.00 20.72 YesClavibacter michiganensis
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Multiplex real-time PCR for detection of X. gardneri. Conclusions:
Xg263F/Xg438R real-time PCR is fast and specific for X. gardneri detection.
Sensitivity of detection of X. gardneri
30 fg of target DNA from extracted DNA;
4 CFU from bacterial culture without DNA extraction;
103 CFU per 100 mg of plant samples.
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PDA exotic disease survey on Solanaceous (Farm Bill 2015)
Ralstonia solanaceous bv2Phytoplasma
Phytoplasma diseases Bacterial wilt (Ralstonia solanacearum)
Photo Source: Phil Hamm, Oregon State University
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PDA Phytoplasmas survey targets (2015)
Exotic Phytoplasmas
(not present in US):
• Australian Grapevine Yellows (Ca.Phytoplasma australiense)
• Bois noir/StolburPhytoplasma (Ca. Phytoplasma solani)
General Phytoplasmas:
• Tomato Big Bud Disease
(found in CA, AR, NY) Granett, 1974;
Shaw et al., 1993; Dale et al., 1975
• “Brote Grande” on pepper (found in NM, AR) Randall et al., 2009
• American Potato Purple Top Wilt (found in TX, NE) Lee et al., 2006;
• Potato Aster Yellows, Potato Purple Top Wilt (found in CA, AK, OR, WA, ID) Lee et al., 2004; Lee et
al., 2006
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Phytoplasma symptoms on Tomato:
B.
• Witches' brooms• Enlarged buds form like a cyst • Leaves become yellow-green or
purplish and roll along their margins. • Flower distortion. • Fruit development is arrested following
infection.
aciar.gov.au
Persley D. & Cooke T. AU
www.apsnet.org
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Phytoplasma
Very small bacteria.
37 species described. All of them plant pathogens.
Cause diseases in hundreds of plants.
Reside inside plant phloem.
Do not have cell walls.
Symptoms can be unevenly distributed on the plants.
Insect-transmitted (mainly by Leafhoppers) or seed born.
Cannot be cultured in a lab.
Identification can be done only at USDA approved Lab!
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PDA Phytoplasma 2015 survey on Solanaceous
Diagnostics:
• Visual symptoms
• Molecular:
PDA Lab –USDA approved for Phytoplasma detection
Modified Phytoplasma-USDA approved specific real-time PCR
COX primers/probe as internal control (Weller et al., 2000)
Our Results:
>100 symptomatic samples
• Tomato – 13 PA counties
• Potato – 6 PA counties
• Pepper – 4 PA counties
No Phytoplasma positive found.
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Bacterial wilt survey(Ralstonia solanacearum)
• Affects potato, tomato, pepper, and eggplant.
• Symptoms: wilting, leaf chlorosis (yellowing), necrosis (browning) of vascular tissue, stunting, vascular rings, and rotting of tubers.
• R. solanacearum bv2 is on USDA PPQ Select Agent list!
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PDA Ralstonia solanacearum survey (2015)
Diagnostics:
• Visual symptoms
• ImmunoStrips (Agdia, Inc.) - species level
USDA work instruction
Our Results:
35 symptomatic samples
• Tomato – 7 PA counties
• Potato – 4 PA counties
• No Ralstonia positive found.
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Contributors:
Ekaterina (Katya) Nikolaeva1, PhD
Seong Hwan Kim1, PhD
Ruth Welliver1, PhD
Tracey Olson1
Tucker Piergallini1
Seogchan Kang2, PhD
1- Pennsylvania Department of Agriculture, Harrisburg, PA
2- Department of Plant Pathology & Environmental Microbiology, Penn State University, University Park, PA
Acknowledgments:
Specialty Crop Grants from PDA (ME442316 and ME445580)
Farm Bill 2015