Extraction of DNA from orange juice, and detection of bacterium Candidatus liberibacter asiaticus by real-time PCR

Journal of Agricultural and Food Chemistry

Volumn 61, Issue 39, 2013, Pages 9339-9346

  Bai, Jinhe ^a   Baldwin, Elizabeth ^a   Liao, Hui Ling ^b   Zhao, Wei ^a   Kostenyuk, Igor ^b   Burns, Jacqueline ^b   Irey, Mike ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c US Sugar Corporation   (United States)

Author keywords

16S rDNA; Amplification inhibitor; Candidatus Liberibacter asiaticus; Greening disease; Huanglongbing; Orange juice; qPCR

Indexed keywords

16S RDNA; CANDIDATUS LIBERIBACTER ASIATICUS; HUANGLONGBING; ORANGE JUICE; QPCR;

BACTERIA; DNA; EXTRACTION; FRUIT JUICES; FRUITS; PH EFFECTS;

POLYMERASE CHAIN REACTION;

BACTERIAL DNA; FUNGAL PROTEIN; POLYGALACTURONASE; RIBOSOME DNA;

ANALYSIS; ARTICLE; ASPERGILLUS NIGER; BEVERAGE; CHEMISTRY; COMPARATIVE STUDY; ENZYMOLOGY; FOOD CONTROL; FRUIT; HYDROLYSIS; ISOLATION AND PURIFICATION; METABOLISM; METHODOLOGY; MICROBIOLOGY; MULTIPLEX POLYMERASE CHAIN REACTION; PH; PLANT LEAF; REAL TIME POLYMERASE CHAIN REACTION; RHIZOBIACEAE; SWEET ORANGE; ULTRASOUND;

ANALYTIC SAMPLE PREPARATION METHODS; ASPERGILLUS NIGER; BEVERAGES; CITRUS SINENSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FOOD INSPECTION; FRUIT; FUNGAL PROTEINS; HYDROGEN-ION CONCENTRATION; HYDROLYSIS; MULTIPLEX POLYMERASE CHAIN REACTION; PLANT LEAVES; POLYGALACTURONASE; REAL-TIME POLYMERASE CHAIN REACTION; RHIZOBIACEAE; SONICATION;

EID: 84892984999     PISSN: 00218561     EISSN: 15205118     Source Type: Journal    
DOI: 10.1021/jf402364y     Document Type: Article

References (54)

1. Baldwin, E.; Plotto, A.; Manthey, J.; McCollum, G.; Bai, J.; Irey, M.; Cameron, R.; Luzio, G. Effect of Liberibacter infection (Huanglongbing disease) of citrus on orange fruit physiology and fruit/fruit juice quality: chemical and physical analyses. J. Agric. Food Chem. 2010, 58, 1247-1262.
2. Plotto, A.; Baldwin, E.; McCollum, G.; Manthey, J.; Narciso, J.; Irey, M. Effect of Liberibacter infection (Huanglongbing or "Greening" disease) of citrus on orange juice flavor quality by sensory evaluation. J. Food Sci. 2010, 75, S220-S230.
3. Gottwald, T. R.; Graham, J. H.; Irey, M. S.; McCollum, T. G.; Wood, B. W. Inconsequential effect of nutritional treatments on huanglongbing control, fruit quality, bacterial titer and disease progress. Crop Protect. 2012, 36, 73-82.
4. Trivedi, P.; Sagaram, U. S.; Kim, J. S.; Brlansky, R. H.; Rogers, M. E.; Stelinski, L. L.; Oswalt, C.; Wang, N. Quantification of viable Candidatus Liberibacter asiaticus in hosts using quantitative PCR with the aid of ethidium monoazide (EMA). Eur. J. Plant Pathol. 2009, 124, 553-563.
5. Stover, E.; McCollum, G. Incidence and severity of huanglongbing and Candidatus Liberibacter asiaticus titer among field-infected citrus cultivars. HortScience 2011, 46, 1344-1348.
6. Li, W.; Hartung, J. S.; Levy, L. Quantitative real-time PCR for detection and identification of Candidatus Liberibacter species associated with citrus huanglongbing. J. Microbiol. Methods 2006, 66, 104-115.
7. Li, W.; Li, D.; Twieg, E.; Hartung, J. S.; Levy, L. Optimized quantification of unculturable Candidatus Liberibacter Spp. in host plants using real-time PCR. Plant Dis. 2008, 92, 854-861. (Pubitemid 351954906)
8. Liao, H. L.; Burns, J. K. Gene expression in Citrus sinensis fruit tissues harvested from huanglongbing-infected trees: Comparison with girdled fruit. J. Exp. Bot. 2012, 63, 3307-3319.
9. Liu, Y.; Cai, X.; Zhang, X.; Gao, Q.; Yang, X.; Zheng, Z.; Luo, M.; Huang, X. Real time PCR using TaqMan and SYBR Green for detection of Enterobacter sakazakii in infant formula. J. Microbiol. Method. 2006, 65, 21-31.
10. Deng, M. Q.; Cliver, D. O. Comparative detection of Cryptosporidium parvum oocysts from apple juice. Int. J. Food Microbiol. 2000, 54, 155-162. (Pubitemid 30125797)
11. Kim, H.-J.; Cho, J.-C. Simple and rapid detection of Listeria monocytogenes in fruit juice by real-time PCR without enrichment culture. Food Control 2010, 21, 1419-1423.
12. Ogunjimi, A. A.; Choudary, P. V. Adsorption of endogenous polyphenols relieves the inhibition by fruit juices and fresh produce of immuno-PCR detection of Escherichia coli 0157:H7. FEMS Immunol. Med. Microbiol. 1999, 23, 213-220. (Pubitemid 29132807)
13. Tsai, Y. L.; Olson, B. H. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol. 1992, 58, 2292-2295.
14. Wilson, I. G. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 1997, 63, 3741-3751. (Pubitemid 27411322)
15. Justesen, U.; Knuthsen, P.; Leth, T. Quantitative analysis of flavonols, flavones, and flavanones in fruits, vegetables and beverages by high-performance liquid chromatography with photo-diode array and mass spectrometric detection. J. Chromatogr. A 1998, 799, 101-110. (Pubitemid 28161212)
16. Hartung, J. S.; Daniel, J. F.; Pruvost, O. P. Detection of Xanthomonas campestris pv. citri by the polymerase chain reaction method. Appl. Environ. Microbiol. 1993, 59, 1143-1148. (Pubitemid 23096657)
17. Hocquellet, A.; Toorawa, P.; Bové, J. M.; Garnier, M. Detection and identification of the two Candidatus Liberobacter species associated with citrus huanglongbing by PCR amplification of ribosomal protein genes of the beta operon. Mol. Cell. Probes 1999, 13, 373-379. (Pubitemid 29488062)
18. Jagoueix, S.; Bové, J. M.; Garnier, M. PCR detection of the two 'Candidatus' liberobacter species associated with greening disease of citrus. Mol. Cell. Probes 1996, 10, 43-50. (Pubitemid 26098563)
19. Saunders, G. C. DNA Extraction. In Analytical Molecular Biology: Quality and Validation, Saunders, G. C.; Parkes, H. C., Eds.; The Royal Society of Chemistry: Cambridge, 1999; pp 29-46.
20. Mackay, I. M.; Arden, K. E.; Nitsche, A. Real-time PCR in virology. Nucleic Acids Res. 2002, 30, 1292-1305. (Pubitemid 34679706)
21. Ros-Chumillas, M.; Egea-Cortines, M.; Lopez-Gomez, A.; Weiss, J. Evaluation of a rapid DNA extraction method to detect yeast cells by PCR in orange juice. Food Control 2007, 18, 33-39. (Pubitemid 43942247)
22. Kim, J. S.; Wang, N. Characterization of copy numbers of 16S rDNA and 16S rRNA of Candidatus Liberibacter asiaticus and the implication in detection in planta using quantitative PCR. BMC Res. Notes 2009, 2, 37.
23. Fan, J.; Chen, C.; Brlansky, R. H.; Gmitter, F. G.; Li, Z. G. Changes in carbohydrate metabolism in Citrus sinensis infected with 'Candidatus Liberibacter asiaticus'. Plant Pathol. 2010, 59, 1037-1043.
24. Bové, J. M. Huanglongbing: A destructive, newly-emerging, century-old disease of citrus. J. Plant Pathol. 2006, 88, 7-37.
25. Weisburg, W. G.; Barns, S. M.; Pelletier, D. A.; Lane, D. J. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 1991, 173, 697-703.
26. Tatineni, S.; Sagaram, U. S.; Gowda, S.; Robertson, C. J.; Dawson, W. O.; Iwanami, T.; Wang, N. In planta distribution of 'Candidatus Liberibacter asiaticus' as revealed by polymerase chain reaction (PCR) and real-time PCR. Phytopathology 2008, 98, 592-599. (Pubitemid 351731864)
27. de Lipthay, J. R.; Enzinger, C.; Johnsen, K.; Aamand, J.; Serensen, S. J. Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis. Soil Biol. Biochem. 2004, 36, 1607-1614.
28. Picard, C.; Ponsonnet, C.; Paget, E.; Nesme, X.; Simonet, P. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 1992, 58, 2717-2722.
29. van Burik, J. A. H.; Schreckhise, R. W.; White, T. C.; Bowden, R. A.; Myerson, D. Comparison of six extraction techniques for isolation of DNA from filamentous fungi. Med. Mycol. 1998, 36, 299-303. (Pubitemid 28564428)
30. Scott, K.; Playford, J. DNA Extraction technique for PCR in rain forest species. Biotechnology 1996, 20, 974-978. (Pubitemid 126509226)
31. Pessina, D.; Gentili, R.; Barcaccia, G.; Nicolas, S.; Rossi, G.; Barbesti, S.; Sgorbati, S. DNA content, morphometric and molecular marker analyses of Citrus limonimedica, C. limon and C. medica for the determination of their variability and genetic relationships within the genus Citrus. Sci. Hort. 2011, 129, 663-673.
32. Seker, M.; Tuzcu, O.; Ollitrault, P. Comparison of nuclear DNA content of citrus rootstock populations by flow cytometry analysis. Plant Breeding 2003, 122, 169-172. (Pubitemid 36557591)
33. Bain, J. M. Morphological, anatomical, and physiological changes in the developing fruit of the Valencia orange, Citrus sinensis (L.) Osbeck. Aust. J. Bot. 1958, 6, 1-24.
34. Tisserat, B.; Jones, D.; Galletta, P. D. Juice vesicle populations in citrus fruit.****Bot. Gaz. 1990, 151, 64-72.
35. Okada, M.; Whitkus, R.; Lowrey, T. Genetics of adaptive radiation in Hawaiian and Cook Islands species ofTetramolopium (Asteraceae; Astereae). I. Nuclear RFLP marker diversity. Am. J. Bot. 1997, 84, 1236-1246. (Pubitemid 27409067)
36. Rether, B.; Delmas, G.; Laouedj, A. Isolation of polysaccharide-free DNA from plants. Plant Mol. Biol. Rep. 1993, 11, 333-337.
37. Shepherd, L. D.; McLay, T. G. B. Two micro-scale protocols for the isolation of DNA from polysaccharide-rich plant tissue. J. Plant Res. 2011, 124, 311-314.
38. Varma, A.; Padh, H.; Shrivastava, N. Plant genomic DNA isolation: An art or a science. Biotechnol. J. 2007, 2, 386-392. (Pubitemid 46738865)
39. Rogstad, S.; Keane, B.; Keiffer, C.; Hebard, F.; Sisco, P. DNA extraction from plants: The use of pectinase. Plant Mol. Biol. Rep. 2001, 19, 353-359. (Pubitemid 33695190)
40. Renard, A.; Gómez di Marco, P.; Egea-Cortines, M.; Weiss, J. Application of whole genome amplification and quantitative PCR for detection and quantification of spoilage yeasts in orange juice. Int. J. Food Microbiol. 2008, 126, 195-201.
41. Scott, M.; Knight, A. Quantitative PCR analysis for fruit juice authentication using PCR and laboratory-on-a-chip capillary electrophoresis according to the Hardy-Weinberg Law. J. Agric. Food Chem. 2009, 57, 4545-4551.
42. Wan, K.; Yousef, A. E.; Schwartz, S. J.; Wang, H. H. Rapid, specific, and sensitive detection of spoilage molds in orange juice using a real-time taqman PCR assay. J. Food Protect. 2006, 69, 385-390. (Pubitemid 43276039)
43. Klerks, M. M.; Zijlstra, C.; van Bruggen, A. H. C. Comparison of real-time PCR methods for detection of Salmonella enterica and Escherichia coli O157:H7, and introduction of a general internal amplification control. J. Microbiol. Methods 2004, 59, 337-349.
44. Rousselon, N.; Delgenes, J.-P.; Godon, J.-J. A new real time PCR (TaqMan PCR) system for detection of the16S rDNA gene associated with fecal bacteria. J. Microbiol. Methods 2004, 59, 15-22. (Pubitemid 39119909)
45. Loftin, K. A.; Adams, C. D.; Meyer, M. T.; Surampalli, R. Effects of ionic strength, temperature, and pH on degradation of selected antibiotics all rights reserved. J. Environ. Qual. 2008, 37, 378-386. (Pubitemid 351399257)
46. Wilfinger, W. W.; Mackey, K.; Chomczynski, P. Effect of pH and ionic strength on the spectrophotometric assessment of nucleic acid purity. Biotechnology 1997, 22, 474-481. (Pubitemid 27131043)
47. Henegariu, O.; Heerema, N. A.; Dlouhy, S. R.; Vance, G. H.; Vogt, P. H. Multiplex PCR: critical parameters and step-by-step protocol. Biotechnology 1997, 21, 504-511. (Pubitemid 27398202)
48. Elnifro, E. M.; Ashshi, A. M.; Cooper, R. J.; Klapper, P. E. Multiplex PCR: Optimization and application in diagnostic virology. Clin. Microbiol. Rev. 2000, 13, 559-570.
49. Martin, R. R.; James, D.; Levesque, C. A. Impacts of molecular technologies on plant disease management. Ann. Rev. Phytopathol. 2000, 38, 207-239.
50. Schaad, N. W.; Fredric, R. D. Real-time PCR and its application for rapid plant disease diagnostics. Can. J. Plant Pathol. 2002, 24, 250-258.
51. Jannine, B.; Shawcross, S.; Theaker, J.; Whitcombe, D.; Ferrie, R.; Newton, C.; Little, S. The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res. 1997, 25, 3235-3241. (Pubitemid 27338681)
52. De Lomas, J. G.; Sunzeri, F. J.; Busch, M. P. False negative results by polymerase chain reaction due to contamination by glove powder. Transfusion 1992, 32, 83-85.
53. Farag, N. S.; Gomah, A. A.; Balabel, N. M. A. False negative multiplex PCR results with certain groups of antibiotics. Plant Pathol. J. 2010, 9, 73-78.
54. Duan, Y.; Zhou, L.; Hall, D. G.; Li, W.; Doddapaneni, H.; Lin, H.; Liu, L.; Vahling, C. M.; Gabriel, D. W.; Williams, K. P.; Dickerman, A.; Sun, Y.; Gottwald, T. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics. Mol. Plant-Microbe Interact. 2009, 22, 1011-1020.