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Development of a real-time PCR assay for Pseudomonas cichorii, the causal agent of midrib rot in greenhouse-grown lettuce, and its detection in irrigating water

Bart Cottyn, Steve Baeyen, Ellen Pauwelyn, Ines Verbaendert, Paul De Vos UGent, Peter Bleyaert, Monica Höfte UGent and Martine Maes (2011) PLANT PATHOLOGY. 60(3). p.453-461
abstract
Midrib rot is an emerging disease in greenhouse production of lettuce caused by Pseudomonas cichorii, and probably introduced through contaminated irrigation water. Concentrations of 100 CFU mL(-1) are enough to induce the typical midrib rot symptoms. A sensitive real-time PCR assay was developed, based on a 90-bp amplicon from the pathogenicity gene cluster hrcRST and a Taqman Minor Groove Binding probe. Specificity of the assay was tested with 39 P. cichorii strains, including the type strain, and 89 strains from 83 other Pseudomonas species. The relationship between detection signals and P. cichorii DNA concentrations was linear over 6-logs. Detection threshold with excellent reproducibility was 500 fg of DNA or about 70 genome copies. Sample preparation and DNA isolation were optimized to allow detection in 1 L water samples. The assay was first evaluated with greenhouse irrigation water spiked with serial dilutions of P. cichorii. The calculated cell numbers obtained with real-time PCR were 10-fold lower than plate counts of actual spiked cells. However, the assay consistently detected 100 CFU per reaction, corresponding to the detection of 1 CFU mL(-1) of irrigation water, which is well below the concentration needed for midrib rot infection. Finally, the assay proved to be valuable for detecting infective P. cichorii concentrations in the irrigation water of a commercial lettuce production greenhouse.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
SYRINGAE, DNA, Pseudomonas cichorii, midrib rot, capitata, Lactuca sativa var, irrigation water, hrcRST genes, GENES, PLANTS, VIRIDIFLAVA, PROTEIN, ARABIDOPSIS, IDENTIFICATION, PATHOGENICITY, AMPLIFICATION
journal title
PLANT PATHOLOGY
Plant Pathol.
volume
60
issue
3
pages
453 - 461
Web of Science type
Article
Web of Science id
000290175300007
JCR category
AGRONOMY
JCR impact factor
2.125 (2011)
JCR rank
15/79 (2011)
JCR quartile
1 (2011)
ISSN
0032-0862
DOI
10.1111/j.1365-3059.2010.02388.x
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1251505
handle
http://hdl.handle.net/1854/LU-1251505
date created
2011-06-01 15:29:41
date last changed
2016-12-19 15:42:48
@article{1251505,
  abstract     = {Midrib rot is an emerging disease in greenhouse production of lettuce caused by Pseudomonas cichorii, and probably introduced through contaminated irrigation water. Concentrations of 100 CFU mL(-1) are enough to induce the typical midrib rot symptoms. A sensitive real-time PCR assay was developed, based on a 90-bp amplicon from the pathogenicity gene cluster hrcRST and a Taqman Minor Groove Binding probe. Specificity of the assay was tested with 39 P. cichorii strains, including the type strain, and 89 strains from 83 other Pseudomonas species. The relationship between detection signals and P. cichorii DNA concentrations was linear over 6-logs. Detection threshold with excellent reproducibility was 500 fg of DNA or about 70 genome copies. Sample preparation and DNA isolation were optimized to allow detection in 1 L water samples. The assay was first evaluated with greenhouse irrigation water spiked with serial dilutions of P. cichorii. The calculated cell numbers obtained with real-time PCR were 10-fold lower than plate counts of actual spiked cells. However, the assay consistently detected 100 CFU per reaction, corresponding to the detection of 1 CFU mL(-1) of irrigation water, which is well below the concentration needed for midrib rot infection. Finally, the assay proved to be valuable for detecting infective P. cichorii concentrations in the irrigation water of a commercial lettuce production greenhouse.},
  author       = {Cottyn, Bart and Baeyen, Steve and Pauwelyn, Ellen and Verbaendert, Ines and De Vos, Paul and Bleyaert, Peter and H{\"o}fte, Monica and Maes, Martine},
  issn         = {0032-0862},
  journal      = {PLANT PATHOLOGY},
  keyword      = {SYRINGAE,DNA,Pseudomonas cichorii,midrib rot,capitata,Lactuca sativa var,irrigation water,hrcRST genes,GENES,PLANTS,VIRIDIFLAVA,PROTEIN,ARABIDOPSIS,IDENTIFICATION,PATHOGENICITY,AMPLIFICATION},
  language     = {eng},
  number       = {3},
  pages        = {453--461},
  title        = {Development of a real-time PCR assay for Pseudomonas cichorii, the causal agent of midrib rot in greenhouse-grown lettuce, and its detection in irrigating water},
  url          = {http://dx.doi.org/10.1111/j.1365-3059.2010.02388.x},
  volume       = {60},
  year         = {2011},
}

Chicago
Cottyn, Bart, Steve Baeyen, Ellen Pauwelyn, Ines Verbaendert, Paul De Vos, Peter Bleyaert, Monica Höfte, and Martine Maes. 2011. “Development of a Real-time PCR Assay for Pseudomonas Cichorii, the Causal Agent of Midrib Rot in Greenhouse-grown Lettuce, and Its Detection in Irrigating Water.” Plant Pathology 60 (3): 453–461.
APA
Cottyn, Bart, Baeyen, S., Pauwelyn, E., Verbaendert, I., De Vos, P., Bleyaert, P., Höfte, M., et al. (2011). Development of a real-time PCR assay for Pseudomonas cichorii, the causal agent of midrib rot in greenhouse-grown lettuce, and its detection in irrigating water. PLANT PATHOLOGY, 60(3), 453–461.
Vancouver
1.
Cottyn B, Baeyen S, Pauwelyn E, Verbaendert I, De Vos P, Bleyaert P, et al. Development of a real-time PCR assay for Pseudomonas cichorii, the causal agent of midrib rot in greenhouse-grown lettuce, and its detection in irrigating water. PLANT PATHOLOGY. 2011;60(3):453–61.
MLA
Cottyn, Bart, Steve Baeyen, Ellen Pauwelyn, et al. “Development of a Real-time PCR Assay for Pseudomonas Cichorii, the Causal Agent of Midrib Rot in Greenhouse-grown Lettuce, and Its Detection in Irrigating Water.” PLANT PATHOLOGY 60.3 (2011): 453–461. Print.