Abstract
Seeds and propagating materials of plants are the primary source of pathogen inoculum to cause diseases. These materials also transmit the pathogen from one place to other places and establish the disease in a new area. Hence, it is an utmost requirement to detect the pathogen of a particular crop before transportation and sowing to ensure that no potentially damaging pathogens are introduced in the field through seeds and planting materials. This can be most effectively accomplished by keeping out pathogens from seed lots by either discarding or treating seeds with chemicals. Various conventional methods for the detection of pathogens such as visual examination, selective growth media, serological methods, and bioassay have been used commonly. But these methods have disadvantages like inefficiency, less specificity, less sensitivity, and more time-consuming. Now-a-days, polymerase chain reaction (PCR) has more potential to improve bacterial pathogen detection in seeds as well as planting materials. There are advanced techniques like BIO-PCR, immunomagnetic separation-PCR (IMS-PCR), and magnetic capture hybridization-PCR (MCH-PCR) which reduce inhibitory compounds during PCR, which further improve the detection level of bacterial pathogens from seeds and planting materials. IMS-PCR and MCH-PCR are more attractive due to their simple and universally applicable methods to test seeds for different culturable and non-culturable bacterial pathogens. However, it is difficult to adapt their applicability for routine testing of seed under the laboratory. It should be ensured that these methods should work and these methods must be validated in multi-laboratory tests thoroughly and these tests should be reproducible and repeatable before their commercialization.
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Adachi N, Oku T (2000) PCR-mediated detection of Xanthomonas oryzae pv. oryzae by amplification of the 16S-23S rDNA spacer region sequence. J Gen Plant Pathol 66:303–309
Alvarez AM (2004) Integrated approaches for detection of plant pathogenic bacteria and diagnosis of bacterial diseases. Annu Rev Phytopathol 42:339–366
Anonymous (2007) EPPO standards PM 7/80 (1) diagnostics Xanthomonas oryzae. Bull OEPP/EPPO Bull 37:543–553
Audy P, Braat CE, Saindon G et al (1996) A rapid and sensitive PCR-based assay for concurrent detection of bacteria causing common and halo blight in bean seed. Phytopathology 86:361–366
Berg T, Tesoriero L, Hailstones DL (2005) PCR-based detection of Xanthomonas campestris in Brassica seed. Plant Pathol 54:416–427
Berg T, Tesoriero L, Hailstones DL (2006) A multiplex realtime PCR assay for detection of Xanthomonas campestris from brassicas. Lett Appl Microbiol 42: 624–630
Bertolini E, Penyalver R, Garcı’a A et al (2003) Highly sensitive detection of Pseudomonas savastanoi pv. savastanoi in asymptomatic olive plants by nested-PCR in a single closed tube. J Microbiol Methods 52:261–266
Braun-Kiewnick A, Sands DC (2001) Gram negative bacteria. In: Schaad NW, Jones JB, Chun W (eds) Laboratory guide for identification of plant pathogenic bacteria, 3rd edn. APS Press, St. Paul, pp 84–120
Chakrabarty PK, Sable S, Monga D et al (2005) Polymerase chain reaction based detection of Xanthomonas axonopodis pv. malvacearum and Cotton leaf curl virus. Indian J Agric Sci 75(8):524–527
Chen J, Griffiths MW (2001) Detection of Salmonella and simultaneous detection of Salmonella and Shiga-like toxin producing Escherichia coli using the magnetic capture hybridization polymerase chain reaction. Lett Appl Microbiol 32:7–11
Chen JR, Johnson R, Griffiths M (1998) Detection of verotoxigenic Escherichia coli by magnetic capture hybridization PCR. Appl Environ Microbiol 64:147–152
Chitarra LG, van den Bulk RW (2003) The application of flow cytometry and fluorescent probe technology for detection and assessment of viability of plant pathogenic bacteria. Eur J Plant Pathol 109:407–417
Cho MS, Kang MJ, Kim CK et al (2011) Sensitive and specific detection of Xanthomonas oryzae pv. oryzae by real-time bio-PCR using pathovar-specific primers based on an rhs family gene. Plant Dis 95(5):589–594
Choi HK, Silva FG, da Lim HJ et al (2010) Diagnosis of pierce’s disease using biomarkers specific to Xylella fastidiosa rRNA and Vitis vinifera gene expression. Phytopathology 100(10):1089–1099
Chun WWC, Alvarez AM (1983) A starch-methionine medium for isolation of Xanthomonas campestris pv. campestris from plant debris in soil. Plant Dis 67:632–635
Civerolo EL, Sasser M, Helkie C et al (1982) Selective medium for Xanthomonas campestris pv. pruni. Plant Dis 66:39–43
Cockerill FR, Smith TF (2002) Rapid-cycle real-time PCR: a revolution for clinical microbiology. Am Soc Microbiol News 88:77–83
Cuppels DA, Elmhirst J (1999) Disease development and changes in the natural Pseudomonas syringae pv. tomato populations on field tomato plants. Plant Dis 83:759–764
Cuppels DA, Moore RA, Morris VL (1990) Construction and use of a nonradioactive DNA hybridization probe for detection of Pseudomonas syringae pv. tomato on tomato plants. Appl Environ Microbiol 56:1743–1749
de Moraes RR, Maruniak JE, Funderburk JE (1999) Methods for detection of Anticarsia gemmatalis nucleopolyhedrovirus DNA in soil. Appl Environ Microbiol 65:2307–2311
Dreier J, Bermpohl A, Eichenlaub R (1995) Southern hybridization and PCR for specific detection of Clavibacter michiganensis subsp. michiganensis. Mol Plant Microbe Interact 10:195–206
Elphinstone JG, Hennessy J, Wilson JK et al (1996) Sensitivity of different methods for the detection of Pseudomonas solanacearum in potato tuber extracts. Bull EPPO/OEPP Bull 26:663–678
Franken AAJM, van Vuurde JWL (1990) Problems and new approaches in the use of serology for seed-borne bacteria. Seed Sci Technol 18:415–426
Gitaitis R, Walcott R (2007) The epidemiology and management of seed-borne bacterial diseases. Annu Rev Phytopathol 45:71–97
Gitaitis RD, Walcott RR, Sanders FH et al (2004) A lognormal distribution of phytopathogenic bacteria in corn, cowpea, tomato and watermelon seeds. Phytopathology 94:S34
Goszczynska T, Serfontein JJ (1998) Milk-tween agar, a semi-selective medium for isolation and differentiation of Pseudomonas syringae, Pseudomonas syringae pv. phaseolicola and Xanthomonas axonopodis pv. phaseoli. J Microbiol Methods 32:65–72
Goszczynska T, Venter SN, Coutinho TA (2006) PA 20, a semi-selective medium for isolation and enumeration of Pantoea ananatis. J Microbiol Methods 64:225–231
Gould WD, Hagedorn C, Bardinelli TR et al (1985) New selective media for enumeration and recovery of fluorescent pseudomonads from various habitats. Appl Environ Microbiol 49:28–32
Gund SV, Moger N, Krishnaraj PU et al (2011) Development of race specific SCAR marker for detection of Ralstonia solanacearum (race 2). J Appl Biosc 37:91–96
Isabelle RS, Delphine L, Lionel G et al (2010) Multiplex nested PCR for detection of Xanthomonas axonopodis pv. allii from onion seeds. Appl Environ Microbiol 76(9):2697–2703
Jacobsen CS (1995) Microscale detection of specific bacterial DNA in soil with a magnetic capture-hybridization and PCR amplification assay. Appl Environ Microbiol 61(9):3347–3352
Jock S, Jacob T, Kim WS et al (2003) Instability of short sequence DNA repeats of pear pathogenic Erwinia strains from Japan and Erwinia amylovora fruit tree and raspberry strains. Mol Gen Genomics 268:739–749
Kado CI, Heskett MG (1970) Selective media for isolation of Agrobacterium, Corynebacterium, Erwinia, Pseudomonas and Xanthomonas. Phytopathology 60:969–976
Kaluzna M, Janse JD, Young JM (2012) Detection and identification methods and new tests as used and developed in the framework of COST 873 for bacteria pathogenic to stone fruits and nuts Pseudomonas syringae pathovars. (Special Issue: Advances from the European Research and Training Network COST Action 873 (2006–2012). J Plant Pathol 94 (1):Supplement, S1.117–S1.126
Kang MJ, Kim MH, Hwang DJ et al (2012) Quantitative in planta PCR assay for specific detection of Xanthomonas oryzae pv. oryzicola using putative membrane protein based primer set. Crop Prot 40:22–27
Kawaradani M, Okada K, Kusakari S (2000) New selective medium for isolation of Burkholderia glumae from rice seeds. J Gen Plant Pathol 66:234–237
Kim BK, Cho MS, Kim MH et al (2012) Rapid and specific detection of Burkholderia glumae in rice seed by real-time bio-PCR using species-Specific primers based on an rhs family gene. Plant Dis 96(4):577–580
Kim HM, Song WY (1996) Characterization of ribosomal RNA intergenic spacer region of several seedborne bacterial pathogens of rice. Seed Sci Technol 24:571–580
Koike ST, Barak JD, Henderson DM et al (1999) Bacterial blight of leek: a new disease in California caused by Pseudomonas syringae. Plant Dis 83:165–170
Kubota R, Vine BG, Alvarez AM et al (2008) Detection of Ralstonia solanacearum by loop-mediated isothermal amplification. Phytopathology 98:1045–1051
Kurian KM, Watson CJ, Wyllie AH (1999) DNA chip technology. J Pathol 187:267–271
Lamka GL, Hill JH, McGee DC et al (1991) Development of an immunosorbent assay for seedborne Erwinia stewartii in corn seeds. Phytopathology 81:839–846
Langrell SRH, Barbara DJ (2001) Magnetic capture hybridisation for improved PCR detection of Nectria galligena from lignified apple extracts. Plant Mol Biol Rpt 19:5–11
Leach JE, White FF (1991) Molecular probes for disease diagnosis and monitoring. In: Khush GS, Toenniessen GH (eds) Rice biotechnology. CAB Inter, Oxon, pp 281–307
Leite RP Jr, Minsavage GV, Bonas U et al (1994) Detection and identification of phytopathogenic Xanthomonas strains by amplification of DNA sequences related to the hrp genes of Xanthomonas campestris pv. vesicatoria. Appl Environ Microbiol 60:1068–1077
Li P, Lin B, Shen H et al (2011) Species-specific detection of Dickeya sp. (Pectobacterium chrysanthemi) in infected banana, tissues, soil and water. Afr J Biotechnol 10:16774–16780
Lin CH, Hsu ST, Tzeng KC et al (2009) Detection of race 1 strains of Ralstonia solanacearum in field samples in Taiwan using a BIO-PCR method. Eur J Plant Pathol 124:75–85
Lin H, Chen CW, Doddapaneni H et al (2010) A new diagnostic system for ultra-sensitive and specific detection and quantification of Candidatus Liberibacter asiaticus, the bacterium associated with citrus Huanglongbing. J Microbiol Methods 81(1):17–25
Lopez MM, Penalver J, Morente MC et al (2012) Evaluation of the efficiency of a conventional PCR protocol for the diagnosis of bacterial spot disease caused by Xanthomonas arboricola pv. pruni in stone fruits and almond (Special Issue: Advances from the European Research and Training Network COST Action 873 (2006-2012). J Plant Pathol 94(1):Supplement S1.75–S1.82
Louws FJ, Rademaker JLW, de Bruijn FJ (1999) The three Ds of PCR-based genomic analysis of phytobacteria: diversity, detection, and disease diagnosis. Annu Rev Phytopathol 37:81–125
Maeda Y, Shinohara H, Kiba A et al (2006) Phylogenetic study and multiplex PCR-based detection of Burkholderia plantarii, Burkholderia glumae and Burkholderia gladioli using gyrB and rpoD sequences. Int J Syst Evol Microbiol 56:1031–1038
Maes M (1993) Fast classification of plant associated bacteria in the Xanthomonas genus. FEMS Microbiol Lett 113:161–165
Maes M, Garbeva P, Kamoen O (1996) Recognition and detection in seed of the Xanthomonas pathogens that cause cereal leaf streak using rDNA spacer sequences and polymerase chain reaction. Phytopathology 86:63–69
McGuire RG, Jones JB, Sasser M (1986) Tween media for semiselective isolation of Xanthomonas campestris pv. vesicatoria from soil and plant material. Plant Dis 70:887–891
Mehta YR, Bomfeti C, Bolognini V (2005) A semiselective agar medium to detect the presence of Xanthomonas axonopodis pv. malvacearum in naturally infected cotton seed. Fitopatol Bras 30:489–496
Menelas B, Block CC, Esker PD et al (2006) Quantifying the feeding periods required by corn flea beetles to acquire and transmit Pantoea stewartii. Plant Dis 90:319–324
Meng XQ, Umesh KC, Davis RM et al (2004) Development of PCR based assays for detecting Xanthomonas campestris pv. carotae, the carrot bacterial leaf blight pathogen, from different substrates. Plant Dis 88:1226–1234
Mew TW (1993) Xanthomonas oryzae pathovars on rice: cause of bacterial blight and bacterial leaf streak. In: Swings JG, Civerolo EL (eds) Xanthomonas. Chapman and Hall, London, pp 30–39
Mohan SK, Schaad NW (1987) An improved agar plating assay for detecting Pseudomonas syringae pv. syringae and P.s. pv. phaseolicola in contaminated bean seed. Phytopathology 77:1390–1395
Mondal KK, Rajendran TP, Phaneendra C et al (2012) The reliable and rapid polymerase chain reaction (PCR) diagnosis for Xanthomonas axonopodis pv. punicae in pomegranate. African J Microbiol Res 6(30):5950–5956
Mulrean EN, Schroth MN (1981) A semiselective medium for the isolation of Xanthomonas campestris pv. juglandis from walnut buds and catkins. Phytopathology 71:336–339
Munhoz CF, Weiss B, Hanai LR et al (2011) Genetic diversity and a PCR-based method for Xanthomonas axonopodis detection in passion fruit. Phytopathology 101(4):416–424
Nielsen SS, Gronbaek C, Agger JF et al (2002) Maximum-likelihood estimation of sensitivity and specificity of ELISAs and faecal culture for diagnosis of paratuberculosis. Prev Vet Med 53:191–204
Ojeda S, Verdier V (2000) Detecting Xanthomonas axonopodis pv. manihotis in cassava true seeds by nested polymerase chain reaction assay. Can J Plant Pathol 22:241–247
Olsvik O, Popovic T, Skjerve E et al (1994) Magnetic separation techniques in diagnostic microbiology. Clin Microbiol Rev 7:43–54
Pagani MC (2004) An ABC transporter protein and molecular diagnoses of Xanthomonas arboricola pv. pruni causing bacterial spot of stone fruits Ph. D. thesis. University of North Carolina, Raleigh
Pan YB, Grisham MP, Burner DM et al (1998) A polymerase chain reaction protocol for the detection of Clavibacter xyli subsp. xyli, the causal agent of sugarcane ratoon stunting disease. Plant Dis 82:285–290
Poussier S, Cheron JJ, Couteau A et al (2002) Evaluation of procedures for reliable PCR detection of Ralstonia solanacearum in common natural substrates. J Microbiol Methods 51:349–359
Pradhanang PM, Elphinstone JG, Fox RTV (2000) Specific detection of Ralstonia solanacearum in soil: a comparison of different techniques. Plant Pathol 49:414–422
Prosen D, Hatziloukas E, Schaad NW et al (1993) Specific detection of Pseudomonas syringae pv. phaseolicola DNA in bean seed by polymerase chain reaction-based amplification of a phaseolotoxin gene region. Phytopathology 83:965–970
Ranjan RK, Singh D, Baranwal VK (2016) Simultaneous detection of brown rot- and soft rot-causing bacterial pathogens from potato tubers through multiplex PCR. Curr Microbiol 73:652. https://doi.org/10.1007/s00284-016-1110-0
Rico A, Erdozáin M, Ortiz-Barredo A et al (2006) Detection by multiplex PCR and characterization of non-toxigenic strains of Pseudomonas syringae pv. phaseolicola from different places in Spain. Spanish J Agril Res 4:261–267
Rico A, Lopez R, Asensio C et al (2003) Non-toxigenic strains of Pseudomonas syringae pv. phaseolicola are a main cause of halo blight of beans in Spain and escape current detection methods. Phytopathology 93:1553–1559
Roumagnac P, Gagnevin L, Pruvost O (2000) Detection of Xanthomonas sp., the causal agent of onion bacterial blight, in onion seeds using a newly developed semi-selective isolation medium. Eur J Plant Pathol 106:867–877
Saettler AW, Schaad NW, Roth DF (1989) Detection of bacteria in seed and other planting material. American Phytopathological Society, St. Paul
Sakthivel N, Mortensen NC, Mathur SB (2001) Detection of Xanthomonas oryzae pv. oryzae in artificially inoculated and naturally infected rice seeds and plants by molecular techniques. Appl Microbiol Biotechnol 56:435–441
Santos MS, Cruz L, Norskov P et al (1997) A rapid and sensitive detection of Clavibacter michiganensis subsp. michiganensis in tomato seeds by polymerase chain reaction. Seed Sci Technol 25:581–584
Sayler RJ, Cartwright RD, Yang Y (2006) Genetic characterization and real-time PCR detection of Burkholderia glumae, a new emerging bacterial pathogen of rice in the United States. Plant Dis 90:603–610
Schaad NW (1978) Use of direct and indirect immunofluorescence tests for identification of Xanthomonas campestris. Phytopathology 68:249–252
Schaad NW, Berthier-Schaad Y, Knorr D (2007) A high through put membrane BIO-PCR technique for ultra-sensitive detection of Pseudomonas syringae pv. phaseolicola. Plant Pathol 56:1–8. https://doi.org/10.1111/j.1365-3059.2006.01488.x
Schaad NW, Cheong SS, Tamaki S et al (1995) A combined biological and enzymatic amplification (BIO-PCR) technique to detect Pseudomonas syringae pv. phaseolicola in bean seed extracts. Phytopathology 85:243–248
Schaad NW, Frederick RD, Shaw J et al (2003) Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. Annu Rev Phytopathol 41:305–324
Schaad NW, Opgenorth D, Gaush P (2002) Real-time polymerase chain reaction for one-hour on-site diagnosis of pierce’s disease of grape in early season asymptomatic vines. Phytopathology 92:721–728
Schaad NW, White WC (1974) Survival of Xanthomonas campestris pv. campestris in soil. Phytopathology 64:1518–1520
Serdani M, Curtis M, Miller ML et al (2013) Loop-mediated isothermal amplification and polymerase chain reaction methods for specific and rapid detection of Rhodococcus fascians. Plant Dis 97:517–529
Shepherd M, Block CC, Mcgee DC (1997) A new seed health assay for Clavibacter michiganensis subsp. nebraskensis. Phytopathology Abstr 87(6):S89
Singh D, Dhar S (2011) Bio-PCR based diagnosis of Xanthomonas campestris pathovars in black rot infected leaves of crucifers. Indian Phytopath 64(1):7–11
Singh D, Raghavendra BT, Singh Rathaur P et al (2014a) Detection of black rot disease causing pathogen Xanthomonas campestris pv. campestris by bio-PCR from seeds and plant parts of cole crops. Seed Sci Technol 42:36–46
Singh D, Sinha S, Yadav DK et al (2014b) Detection of Ralstonia solanacearum from asymptomatic tomato plants, irrigation water, and soil through non-selective enrichment medium with hrp gene-based bio-PCR. Curr Microbiol 69(2):127–134
Singh D, Sinha S, Singh RP (2015) Detection of Xanthomonas oryzae pv. oryzae from seeds and leaves of rice (Oryza sativa) using hrp gene based BIO-PCR marker. Indian J Agric Sci 85(4):519–524
Song WY, Kim HM, Hwang CY et al (2004) Detection of Acidovorax avenae ssp. avenae in rice seeds using BIO-PCR. J Phytopathol 152:667–676
Sutton MD, Katznelson H (1953) Isolation of bacteriophages for the detection and identification of some seed-borne pathogenic bacteria. Can J Bot 31(2):201–205
Toussaint V, Morris CE, Carisse O (2001) A new semi-selective medium for Xanthomonas campestris pv. vitians, the causal agent of bacterial leaf spot of lettuce. Plant Dis 85:131–136
Tran TM, Jacobs JM, Huerta A et al (2016) Sensitive, secure detection of race 3 biovar 2 and native U.S. strains of Ralstonia solanacearum. Plant Dis 100(3):630–639
Umesha S, Avinash P (2015) Multiplex PCR for simultaneous identification of Ralstonia solanacearum and Xanthomonas perforans. 3 Biotech 5(3):245–252
Umesha S, Chandan S, Swamy LN (2012) Colony PCR-single strand confirmation polymorphism for the detection of Ralstonia solanacearum in tomato. Inter J Integ Biol 13:45–51
Walcott RR, Gitaitis RD (2000) Detection of Acidovorax avenae subsp. citrulli in watermelon seed using immunomagnetic separation and the polymerase chain reaction. Plant Dis 84:470–474
Walcott RR, Gitaitis RD, Castro AC et al (2002) Natural infestation of onion seeds by Pantoea ananatis, causal agent of center rot. Plant Dis 86:106–111
Waters CM, Bolkan HA (1992) An improved semi-selective medium and method of extraction for detecting Clavibacter michiganensis subsp. michiganensis in tomato seeds. Phytopathology 82:1072
Wensing A, Zimmermann S, Geider K (2010) Identification of the corn pathogen Pantoea stewartii by mass spectrometry of whole-cell extracts and its detection with novel PCR primers. Appl Environ Microbiol 76(18):6248–6256
Wensing A, Gernold M, Geider K (2012) Detection of Erwinia species from the apple and pear flora by mass spectroscopy of whole cells and with novel PCR primers. J Appl Microbiol 112(1):147–158
Williams PH (1980) Black rot: a continuing threat to world crucifers. Plant Dis 64:736–742
Wittwer CT, Herrmann MG, Gundry CN et al (2001) Real-time multiplex PCR assays. Methods 25(4):430–442
Wullings BA, van Beuningen AR, Janse JD et al (1998) Detection of Ralstonia solanacearum which causes brown rot of potato, by fluorescent in situ hybridization with 23S rRNA-targeted probes. Appl Environ Microbiol 64:4546–4554
Wydra K, Khatri-chhetri G, Mavridis A et al (2004) A diagnostic medium for the semi-selective isolation and enumeration of Xanthomonas axonopodis pv. vignicola. Eur J Plant Pathol 110(10):991–1001
Yashitola J, Krishnaveni D, Reddy APK et al (1997) Genetic diversity within the population of Xanthomonas oryzae pv. oryzae in India. Phytopathology 87:760–765
Yuan WQ (1990) Culture medium for Xanthomonas campestris pv. oryzae. J Appl Bacteriol 69:798–805
Yuanbo D, Zheng CJ, Rong CS et al (1983) A technique for the detection of Xanthomonas campestris pv. oryzae using bacteriophage. Seed Sci Technol 11:579–582
Zaccardelli M, Campanile F, Spasiano A et al (2007) Detection and identification of the crucifer pathogen, Xanthomonas campestris pv. campestris, by PCR amplification of the conserved Hrp/type III secretion system gene hrc C. Eur J Plant Pathol 118:299–306
Zhao T, Feng J, Sechler A et al (2009) An improved assay for detection of Acidovorax citrulli in watermelon and melon seed. Seed Sci Technol 37:78616–13321
Zhao WJ, Zhu S, Liao XL et al (2007) Detection of Xanthomonas oryzae pv. oryzae in seeds using a specific TaqMan probe. Mol Biotechnol 35:119–127
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Singh, D., Rathaur, P.S. (2020). Detection of Seed and Propagating Material-Borne Bacterial Diseases of Economically Important Crops. In: Kumar, R., Gupta, A. (eds) Seed-Borne Diseases of Agricultural Crops: Detection, Diagnosis & Management. Springer, Singapore. https://doi.org/10.1007/978-981-32-9046-4_6
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