Skip to main content
SpringerLink
Log in

Diagnosis of Plant Pathogens and Implications for Plant Quarantine: A Risk Assessment Perspective

  • Chapter
  • First Online:
Detection and Diagnostics of Plant Pathogens

Part of the book series: Plant Pathology in the 21st Century ((ICPP,volume 5))

Abstract

The Scientific Panel on Plant Health (PLH) of the European Food Safety Authority was established in 2006 as the reference EU body for risk assessment in the plant health area in the frame of phytosanitary measures to prevent the introduction and further spread of organisms harmful (pests) to plants or plants products. Proper diagnosis and detection are critical for the categorization and assessment of pests that are or may qualify as quarantine pests, and for appropriate application of phytosanitary measures. In carrying out its responsibilities, the PLH Panel is frequently faced by the changes in taxonomy and nomenclature: these may often lead to a re-evaluation of previous pest records, concerns with published literature, and in some cases with the increased use of molecular taxonomic and identification tools. Pathogens that were previously considered strains/varieties of a single species, in some cases have now been elevated to specific status. In other cases pathogens previously recognised as species complexes have now been partitioned into named species, using molecular criteria rather than traditional methods. The problems that can arise are illustrated in this Chapter by examples representative of the main pathogen taxa.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Ah-You N, Gagnevin L, Grimont PAD, Brisse S, Nesme X, Chiroleu F, Bui Thi Ngoc L, Jouen E, Lefeuvre P, Vernière C, Pruvost O (2009) Polyphasic characterization of Xanthomonas pathogenic to Anacardiaceae and their relatedness to different Xanthomonas species. Int J Syst Evol 59(2):306–318

    CAS  Google Scholar 

  • Almeida NF, Yan S, Cai R, Clarke CR, Morris CE, Schaad NW, Schuenzel EL, Lacy GH, Sun X, Jones JB, Castillo JA, Bull CT, Leman S, Guttman DS, Setubal JC, Vinatzer BA (2010) PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology 100:208–215

    PubMed  CAS  Google Scholar 

  • Aveskamp MM, de Gruyter J, Crous PW (2008) Biology and recent developments in the systematics of Phoma, a complex genus of major quarantine significance. Fungal Divers 31:1–18

    Google Scholar 

  • Aveskamp MM, Verkley GJM, De Gruyter J, Murace MA, Perelló A, Woudenberg JH, Groenwald JZ, Crous PW (2009) DNA phylogeny reveals polyphyly of Phoma section Peyronellaea and multiple taxonomic novelties. Mycologia 101(3):363–382

    PubMed  CAS  Google Scholar 

  • Aveskamp MM, De Gruyter J, Woudenberg JHC, Verkley GJM, Crous PW (2010) Highlights of the Didymellaceae: a polyphasic approach to characterise Phoma and related pleosporalean genera. Stud Mycol 65(1):1–60

    PubMed  CAS  PubMed Central  Google Scholar 

  • Baker KF, Dimock A, Davis LH (1949) Life history and control of the ascochyta ray blight of chrysanthemum. Phytopathology 39:789–805

    Google Scholar 

  • Barnes I, Crous PW, Wingfield BD, Wingfield MJ (2004) Multigene phylogenies reveal that red band needle blight of Pinus is caused by two distinct species of Dothistroma, D. septosporum and D. pini. Stud Mycol 50:551–565

    Google Scholar 

  • Barnes I, Kirisits T, Akulov A, Chhetri DB, Wingfield BD, Bulgakov TS, Wingfield MJ (2008) New host and country records of the Dothistroma needle blight pathogens from Europe and Asia. For Pathol 38:178–195

    Google Scholar 

  • Barnes I, Kirisits T, Wingfield MJ, Wingfield BD (2011) Needle blight of pine caused by two species of Dothistroma in Hungary. For Pathol 41:361–369

    Google Scholar 

  • Blok VC (2005) Achievements in and future prospects for molecular diagnostics of plant-parasitic nematodes. Can J Plant Pathol 27:176–185

    CAS  Google Scholar 

  • Bonants PMJ, Van Gent-Pelzer MPE, Hooftman R, Cooke DEL, Guy DC, Duncan JM (2004) A combination of baiting and different PCR formats, including measurement of real-time quantitative fluorescence, for detection of Phytophthora fragariae in strawberry plants. Eur J Plant Pathol 110:689–702

    CAS  Google Scholar 

  • Boutet X, Vercauteren A, Heungens K, Laurent F, Chandelier A (2010) Oospores progenies from Phytophthora ramorum. Fungal Biol 114:369–378

    Google Scholar 

  • Brady C, Cleenwerck I, Denman S, Venter S, Rodríguez-Palenzuela P, Couthino TA, Vos P (2011) Proposal to reclassify. Brenneria quercina, (Hildebrand & Schroth 1967) Hauben et al. 1999 into a novel genus, Lonsdalea gen. nov., as Lonsdalea quercina comb. nov., descriptions of Lonsdalea quercina subsp. quercina comb. nov., Lonsdalea quercina subsp. iberica subsp. nov. and Lonsdalea quercina subsp. britannica subsp. nov., emendation of the description of the genus Brenneria, reclassification of Dickeya dieffenbachiaeas Dickeya dadantii subsp. dieffenbachiae comb. nov., and emendation of the description of Dickeya dadantii. Int J Syst Evol Microbiol 62:1592–1602

    PubMed  Google Scholar 

  • Brasier CM (2003) Sudden oak death exhibits transatlantic differences. Mycol Res 107:258–259

    PubMed  Google Scholar 

  • Brasier CM, Kirk S (2004) Production of gametangia by Phytophthora ramorum in vitro. Mycol Res 108:823–827

    PubMed  Google Scholar 

  • Brasier CM, Vettraino AM, Chang TT, Vannini A (2010) Phytophthora lateralis discovered in an old growth Chamaecyparis forest in Taiwan. Plant Pathol 59:595–603

    CAS  Google Scholar 

  • Bui Thi Ngoc L, Vernière C, Jarne P, Brisse S, Guérin F, Boutry S, Gagnevin L, Pruvost O (2009) From local surveys to global surveillance: three high throughput genotyping methods for the epidemiological monitoring of Xanthomonas citri pv. Citri pathotypes. Appl Environ Microbiol 75:1173–1184

    PubMed  PubMed Central  Google Scholar 

  • Bui Thi Ngoc L, Vernière C, Jouen E, Ah-You N, Lefeuvre P, Chiroleu F, Gagnevin L, Pruvost O (2010) Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants of Xanthomonas citri pv. citri and Xanthomonas campestris pv. bilvae. Int J Syst Evol Microbiol 60:515–525

    PubMed  Google Scholar 

  • Burkholder WH, McFadden LA, Dimock AW (1953) A bacterial blight of chrysanthemums. Phytopathology 43:522–526

    Google Scholar 

  • Cooke DEL, Drenth A, Duncan JM, Wagels G, Brasier CM (2000) A molecular phylogeny of Phytophthora and related Oomycetes. Fungal Genet Biol 30:17–32

    PubMed  CAS  Google Scholar 

  • Coomans A, Huys R, Heyns J, Luc M (2001) Character analysis, phylogeny, and biogeography of the genus Xiphinema Cobb, 1913 (Nematoda: Longidoridae). Annales Musée Royal de L’Afrique Centrale (Zoologie) 287:1–289

    Google Scholar 

  • De Gruyter JD, Boerema GH, Aa HA (2002) Contributions towards a monograph of Phoma (Coelomycetes). VI-2. Section Phyllostictoides: outline of its taxa. Persoonia 18(1):1–53

    Google Scholar 

  • De Gruyter J, Aveskamp MM, Woudenberg JHC, Verkley GJM, Groenewald JZ, Crous PW (2009) Molecular phylogeny of Phoma and allied anamorph genera: towards a reclassification of the Phoma complex. Mycol Res 113:508–519

    PubMed  Google Scholar 

  • De Gruyter J, Woudenberg JHC, Aveskamp MM, Verkley GJM, Groenewald JZ, Crous PW (2010) Systematic reappraisal of species in Phoma section Paraphoma, Pyrenochaeta and Pleurophoma. Mycologia 102:1066–1081

    PubMed  Google Scholar 

  • De Gruyter J, Woudenberg JHC, Aveskamp MM, Verkley GJM, Groenewald JZ, Crous PW (2013) Redisposition of Phoma-like anamorphs in Pleosporales. Stud Mycol 75:1–36

    PubMed  PubMed Central  Google Scholar 

  • Decraemer W, Robbins RT (2007) The who, what and where of Longidoridae and Trichodoridae. J Nematol 39:295–297

    PubMed  PubMed Central  Google Scholar 

  • Dickey RS (1979) Erwinia chrysanthemi: a comparative study of phenotypic properties of strains from several hosts and other Erwinia species. Phytopathology 69:324–329

    Google Scholar 

  • DOE JGI (DOE Joint Genome Institute) (2012) Dothideomycete sequencing and comparative analysis. US Department of Energy, Office of Science. University of California, USA. Available online at: http://genome.jgi.doe.gov/programs/fungi/fungal-projects.jsf

  • Duncan JM (2001) Redcore. Third and final year progress report to EU DGXII (SMT4-CT97-2162) 1–42

    Google Scholar 

  • Duncan JM, Kennedy DM, Scott PH (1991) Relationships between non-papillate, soilborne species of Phytophthora I: root rot of raspberry. In Phytophthora eds Publi. Cambridge, University Press for British Mycological Society, pp 139–147

    Google Scholar 

  • Dye DW, Lelliott RA (1974) Genus II. Xanthomonas Dowson 1939, 187. In: Bergey’s manual of determinative bacteriology. Williams and Wilkins, Baltimore, pp 243–249

    Google Scholar 

  • EFSA Panel on Plant Health (2011a) Scientific opinion on the assessment of the risk of solanaceous pospiviroids for the EU territory and the identification and evaluation of risk management options. EFSA J 9:133 (2330)

    Google Scholar 

  • EFSA Panel on Plant Health (2011b) Scientific opinion on the pest risk analysis on Phytophthora ramorum prepared by the FP6 project RAPRA. EFSA J 9:107 (2186)

    Google Scholar 

  • EFSA Panel on Plant Health (2012a) Scientific opinion on the pest categorisation of the tospoviruses. EFSA J 10:101 (2772)

    Google Scholar 

  • EFSA Panel on Plant Health (2012b) Scientific opinion on the risks to plant health posed by European versus non-European populations of the potato cyst nematodes Globodera pallida and Globodera rostochiensis. EFSA J 10:71 (2644)

    Google Scholar 

  • EFSA Panel on Plant Health (2013a) Scientific opinion on the risks to plant health posed by Stagonosporopsis chrysanthemi (Stevens) Crous, Vaghefi and Taylor [Didymella ligulicola (Baker, Dimock and Davis) Arx var. ligulicola; syn. Didymella ligulicola (Baker, Dimock and Davis) Arx] in the EU territory, with identification and evaluation of risk reduction options. EFSA J 11:72 (3376)

    Google Scholar 

  • EFSA Panel on Plant Health (2013b) Scientific opinion on the risk to plant health posed by Dothistroma septosporum (Dorog.) M. Morelet (Mycosphaerella pini E. Rostrup, syn. Scirrhia pini) and Dothistroma pini Hulbary to the EU territory with the identification and evaluation of risk reduction options. EFSA J 11:173 (3026)

    Google Scholar 

  • EFSA Panel on Plant Health (2013c) Scientific opinion on the risks to plant health posed by Bemisia tabaci species complex and viruses it transmits for the EU territory. EFSA J 11:302 (3162)

    Google Scholar 

  • EFSA Panel on Plant Health (2014) Scientific opinion on the risks to plant health posed by Phytophthora fragariae Hickman var. fragariae in the EU territory, with the identification and evaluation of risk reduction options. EFSA J 12(1):63 (3539)

    Google Scholar 

  • Egel DS, Graham JH, Stall RE (1991) Genomic relatedness of Xanthomonas campestris strains causing diseases of citrus. Appl Environ Microbiol 57:2724–2730

    PubMed  CAS  PubMed Central  Google Scholar 

  • Elliott M, Sumampong G, Varga A, Shamoun SF, James D, Masri S, Briere SC, Grünwald NJ (2009) PCR-RFLP markers identify three lineages of the North American and European populations of Phytophthora ramorum. For Pathol 39:266–278

    Google Scholar 

  • EPPO (2009) Xiphinema americanum sensu lato. Bulletin OEPP/EPPO Bulletin 39:382–392

    Google Scholar 

  • Evans K, Franco J, De Scurrah MM (1975) Distribution of species of potato cyst nematodes in South America. Nematologica 21:365–369

    Google Scholar 

  • Fleming CC, Powers TO (1998) Potato cyst nematodes: species, pathotypes and virulence concepts. In: Marks RJ, Brodie BB (eds) Potato cyst nematodes: biology, distribution and control. CABI Publishing, Wallingford, pp 51–57

    Google Scholar 

  • Franco J, Evans K (1978) Multiplication of some South American and European populations of potato cyst Nematodes on potatoes possessing the resistance genes H1, H2 and H3. Plant Pathol 27:1–6

    Google Scholar 

  • Garbelotto M, Rizzo DM (2005) A California-based chronological review (1995–2004) of research on Phytophthora ramorum, the causal agent of sudden oak death. Phytopathol Mediterr 44(2):127–143

    Google Scholar 

  • Gasser RB (2001) Identification of parasitic Nematodes and study of genetic variability using PCR approaches. In: Kennedy MW, Harnett W (eds) Parasitic nematodes, molecular biology, biochemistry and Immunology. CABI Pub, New York, pp 53–82

    Google Scholar 

  • Goss EM, Carbone I, Gruenwald NJ (2009) Ancient isolation and independent evolution of the three clonal lineages of the exotic sudden oak death pathogen Phytophthora ramorum. Mol Ecol 18:1161–1174

    PubMed  CAS  Google Scholar 

  • Graham JH, Gottwald TR (1991) Research perspectives on eradication of citrus bacterial diseases in Florida. Plant Dis 75:1193–1200

    Google Scholar 

  • Grenier E, Fournet S, Petit E, Anthoine G (2010) A cyst nematode “species factory” called the Andes. Nematology 12:163–169

    Google Scholar 

  • Groenewald M, Barnes I, Bradshaw RE, Brown AV, Dale A, Groenewald JZ, Lewis KJ, Wingfield BD, Wingfield MJ, Crous PW (2007) Characterization and distribution of mating type genes in the Dothistroma needle blight pathogens. Phytopathology 97:825–834

    PubMed  CAS  Google Scholar 

  • Gutiérrez-Gutiérrez C, Castillo P, Cantalapiedra-Navarrete C, Landa BB, Derycke S, Palomares-Rius JE (2011) Genetic structure of Xiphinema pachtaicum and X. index populations based on mitochondrial DNA variation. Phytopathology 101:1168–1175

    PubMed  Google Scholar 

  • Gutiérrez-Gutiérrez C, Cantalapiedra-Navarrete C, Decraemer W, Vovlas N, Prior T, Palomares Rius JE, Castillo P (2012) Phylogeny, diversity, and species delimitation in some species of the Xiphinema americanum-group complex (Nematoda: Longidoridae), as inferred from nuclear and mitochondrial DNA sequences and morphology. Eur J Plant Pathol 134:561–597

    Google Scholar 

  • Hansen EM (2010) Some challenges of recognizing invasive Phytophthoras and finding their origins. In: Proceedings of the 4th Sudden Oak Death Symposium, USDA Forest Service, Albany, CA, USA, pp 17–21

    Google Scholar 

  • Hauben L, Moore ERB, Vauterin L, Steenackers M, Mergaert J, Verdonck L, Swings J (1998) Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol 21:384–397

    PubMed  CAS  Google Scholar 

  • He Y, Subbotin S, Rubtsova TV, Lamberti F, Brown DJF, Moens M (2005) A molecular phylogenetic approach to Longidoridae (Nematoda: Dorylaimida). Nematology 7:111–124

    CAS  Google Scholar 

  • Hellmers E (1955) Bacterial wilt of carnations. Gardeners’. Chronicle 137(3567):194–195

    Google Scholar 

  • Hellmers E (1958) Four wilt diseases of perpetual-flowering carnations in Denmark. Dansk Botanisk Arkiv 18:1–200

    Google Scholar 

  • Hickman C (1940) The red core root disease of the strawberry caused by Phytophthora fragariae n. sp. J Pomol 18:89–118

    Google Scholar 

  • Hockland S, Niere B, Grenier E, Blok V, Phillips M, Den Nijs L, Anthoine G, Pickup G, Viaene N (2012) An evaluation of the implications of virulence in non-European populations of Globodera pallida and G. rostochiensis for potato cultivation in Europe. Nematology 14(1):1–13

    Google Scholar 

  • Ioos R, Fabre B, Saurat C, Fourrier C, Frey P, Marçais B (2010) Development, comparison, and validation of real-time and conventional PCR tools for the detection of the fungal pathogens causing brown spot and red band needle blights of pine. Phytopathology 100:105–114

    PubMed  CAS  Google Scholar 

  • Ivors KL, Hayden K, Bonants PJM, Rizzo DM, Garbelotto M (2004) AFLP and phylogenetic analyses of North American and European populations of Phytophthora ramorum. Mycol Res 108:378–392

    PubMed  CAS  Google Scholar 

  • Ivors KL, Garbelotto M, Vries IDE, Ruyter-Spira C, Hekkert BT, Rosenzweig N, Bonants P (2006) Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations. Mol Ecol 15:1493–1505

    PubMed  CAS  Google Scholar 

  • Janse JD, Ruissen MA (1988) Characterisation and classification of Erwinia chrysanthemi strains from several hosts in the Netherlands. Phytopathology 78:800–808

    Google Scholar 

  • Janssen P, Coopman R, Huys G, Swings J, Bleeker M, Vos P, Zabeau M, Kersters K (1996) Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology 142:1881–1893

    PubMed  CAS  Google Scholar 

  • Jeger M, Schans J, Lövei GL, Van Lenteren J, Navajas M, Makowski D, Stancanelli G, Tramontini S, Ceglarska EB (2012) Special issue: risk assessment in support of plant health. EFSA J 10(10):8 (s1012)

    Google Scholar 

  • Jones JT, Haegeman A, Danchin EGJ, Gaur HS, Helder J, Jones MGK, Kikuchi T, Manzanilla-López R, Palomares-Rius JE, Wesemael WML, Perry RN (2013) Top 10 plant-parasitic nematodes in molecular plant pathology. Mol Plant Pathol 14:946–961

    PubMed  Google Scholar 

  • Kliejunas JT (2010) Sudden oak death and Phytophthora ramorum: a summary of the literature. Gen Tech Rep PSW-GTR-234. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station

    Google Scholar 

  • Lamberti F, Bleve-Zacheo T (1979) Studies on Xiphinema americanum sensu lato with descriptions of fifteen new species (Nematoda, Longidoridae). Nematol Mediterr 7:51–106

    Google Scholar 

  • Lamberti F, Carone M (1991) A dichotomous key for the identification of species of Xiphinema (Nematoda: Dorylaimida) within the X. americanum group. Nematol Mediterr 19:341–348

    Google Scholar 

  • Lamberti F, Molinari S, Moens M, Brown DJF (2000) The Xiphinema americanum-group. I. Putative species, their geographical occurrence and distribution, and regional polytomous identification keys for the group. Russian J Nematol 8:65–84

    Google Scholar 

  • Lamberti F, Hockland S, Agostinelli A, Moens M, Brown DJF (2004) The Xiphinema americanum group. III. Keys to species identification. Nematol Mediterr 32:53–56

    Google Scholar 

  • Laurila J, Hannukkala A, Nykyri J, Pasanen M, Helias V, Garlant L, Pirhonen M (2010) Symptoms and yield reduction caused by Dickeya spp. strains isolated from potato and river water in Finland. Eur J Plant Pathol 126:249–262

    Google Scholar 

  • Lelliot RA, Dickey RS (1984) Genus VII. Erwinia Winslow, Broadhurst, Buchanan, Krumwiede, Rogers and Smith 1920, Bergey’s manual of systematic bacteriology. The Williams & Wilkins 1, Baltimore, p 469–476

    Google Scholar 

  • Lima MB (1965) Studies on species of the genus Xiphinema and other nematodes. Ph.D. Thesis, University of London, pp 165

    Google Scholar 

  • Luc M, Baujard P (2001) On specific determination within the Xiphinema americanum group (Nematoda: Longidoridae). Nematology 3:727–728

    Google Scholar 

  • Luc M, Coomans A, Loof PAA, Baujard P (1998) The Xiphinema americanum group (Nematoda: Longidoridae). Observations on Xiphinema brevicollum Lordello & Da Costa, 1961 and comments on the group. Fundam Appl Nematol 21:475–490

    Google Scholar 

  • Man in’t Veld WA (2007) Gene flow analysis demonstrates that Phytophthora fragariae var. rubi constitutes a distinct species, Phytophthora rubi comb.nov. Mycopathologia 99:222–226

    Google Scholar 

  • Mascheretti S, Croucher P, Vettraino A, Prospero S, Garbelotto M (2008) Reconstruction of the sudden oak death epidemic in California through microsatellite analysis of the pathogen Phytophthora ramorum. Mol Ecol 17:2755–2768

    PubMed  CAS  Google Scholar 

  • Mascheretti S, Croucher P, Kozanitas M, Baker L, Garbelotto M (2009) Genetic epidemiology of the sudden oak death pathogen Phytophthora ramorum in California. Mol Ecol 18:4577–4590

    PubMed  CAS  Google Scholar 

  • McGrath PF, Harrison BD (1995) Transmission of tomato leaf curl geminiviruses by Bemisia tabaci: effects of virus isolate and vector biotype. Ann Appl Biol 126:307–316

    Google Scholar 

  • Mound LA (1996) The Thysanoptera vector species of tospoviruses. Acta Horticulturae 431:298–306

    Google Scholar 

  • Newton AC, Duncan JM, Augustin NH, Guy DC, Cooke DEL (2010) Survival, distribution and genetic variability of inoculum of the strawberry red core pathogen, Phytophthora fragariae var. fragariae, in soil. Plant Pathol 59:472–479

    Google Scholar 

  • Nicol JM, Turner SJ, Coyne DL, Den Nijs L, Hockland S, Maafi ZT (2011) Current nematode threats to world agriculture. In: Jones JT, Gheysen G, Fenoll C (eds) Genomics and molecular genetics of plant–nematode interactions. Springer, Heidelberg, pp 21–44

    Google Scholar 

  • Parkinson NM, Stead D, Bew J, Heeney J, Tsor (Lahkim) L, Elphinstone J (2009) Dickeya species relatedness and clade structure determined by comparison of recA sequences. Int J Syst Evol Microbiol 59:2388–2393

    PubMed  CAS  Google Scholar 

  • Patel MK, Allayyanavaramath SB, Kulkarni YS (1953) Bacterial shot-hole and fruit canker of Aegle marmelos Correa. Curr Sci 22:216–217

    Google Scholar 

  • Pethybridge SJ, Scott JB, Hay FS (2004) Genetic relationships among isolates of Phoma ligulicola from pyrethrum and chrysanthemum based on ITS sequences and its detection by PCR. Aust Plant Pathol 33:173–181

    CAS  Google Scholar 

  • Pethybridge SJ, Hay FS, Clarkson RA, Groom T, Wilson CR (2008) Host range of Australian Phoma ligulicola var. inoxydablis isolates from Pyrethrum. J Phytopathol 156:506–508

    Google Scholar 

  • Plantard O, Picard D, Valette S, Scurrah M, Grenier E, Mugniery D (2008) Origin and genetic diversity of Western European populations of the potato cyst nematode (Globodera pallida) inferred from mitochondrial sequences and microsatellite loci. Mol Ecol 17:2208–2218

    PubMed  CAS  Google Scholar 

  • Plyusnin AMQ, Beaty BJ, Elliott RM, Goldbach R, Kormelink R, Lundkvist Å, Schmaljohn CS, Tesh RB (2012) Bunyaviridae. In: King MJA, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy, ninth report of the international committee on taxonomy of viruses. Elsevier Academic Press, London, pp 725–741

    Google Scholar 

  • Prospero S, Hansen EM, Grünwald NJ, Winton LM (2007) Population dynamics of the sudden oak death pathogen Phytophthora ramorum in Oregon from 2001 to 2004. Mol Ecol 16:2958–2973

    PubMed  CAS  Google Scholar 

  • Prospero S, Grünwald NJ, Winton LM, Hansen EM (2009) Migration patterns of the emerging plant pathogen Phytophthora ramorum on the West Coast of the United States of America. Phytopathology 99:739–749

    PubMed  CAS  Google Scholar 

  • Rademaker JLW, Hoste B, Louws FJ, Kersters K, Swings J, Vauterin L, Vauterin P, De Bruijn FJ (2000) Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model system. Int J Syst Evol Microbiol 50:665–677

    PubMed  CAS  Google Scholar 

  • Rademaker JLW, Louws FJ, Schultz MH, Rossbach U, Vauterin L, Swings J, De Bruijn FJ (2005) A comprehensive species to strain taxonomic framework for Xanthomonas. Phytopathology 95:1098–1111

    PubMed  CAS  Google Scholar 

  • Rizzo DM, Garbelotto M, Davidson JM, Slaughter GW (2002) Phytophthora ramorum as the cause of extensive mortality of Quercus spp. and Lithocarpus densiflorus in California. Plant Dis 86:205–214

    Google Scholar 

  • Robideau GP, De Cock AWAM, Coffey MD, Voglmayr H, Brouwer H, Bala K, Chitty DW, Désaulniers N, Eggertson QA, Gachon CMM, Hu C-H, Kupper FC, Rintoul TL, Sarhan E, Verstappen ECP, Zhang Y, Bonants PJM, Ristaino JB, Lévesque CA (2011) DNA barcoding of oomycetes with cytochrome oxidase subunit I and internal transcribed spacer. Mol Ecol Resour 11:1002–1911

    PubMed  CAS  PubMed Central  Google Scholar 

  • Robin C, Piou D, Feau N, Douzon G, Schenck N, Hansen EM (2011) Root and aerial infections of Chamaecyparis lawsoniana by Phytophthora lateralis: a new threat for European countries. For Pathol 41(5):417–424

    Google Scholar 

  • Rodriguez LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A (2012) Genomes-based phylogeny of the genus Xanthomonas. BMC Microbiol 12:43

    Google Scholar 

  • Samson R, Nassan-Agha N (1978) Biovars and serovars among 129 strains of Erwinia chrysanthemi. Sta Path Veg Phytobact, INRA, Angers, pp 547–553

    Google Scholar 

  • Samson R, Legendre JB, Christen R, Fischer-le-Le Saux M, Achouak W, Gardan L (2005) Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int J Syst Evol Microbiol 55:1415–1427

    PubMed  CAS  Google Scholar 

  • Sanfaçon H, Iwanami T, Karasev AV, Van der Vlugt R, Wellink J, Wetzel T, Yoshikawa N (2012) Secoviridae. In: King MJA, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy, ninth report of the international committee on taxonomy of viruses. Elsevier Academic Press, London, pp 881–899

    Google Scholar 

  • Schaad NW, Postnikova E, Lacy GH, Sechler A, Agarkova I, Stromberg PE, Stromberg VK, Vidaver AK (2006) Amended classification of Xanthomonad pathogens on citrus. Syst Appl Microbiol 29:690–695

    PubMed  Google Scholar 

  • Schans J, Ceglarska EB, Cheek S, Stancanelli G (2008) The EFSA panel on plant health: accomplishments and challenges for the EU pest risk assessment. J Plant Pathol 90 (2, Supplement), S2:40

    Google Scholar 

  • Seinhorst JW (1982) The relationship in field experiments between population density of Globodera rostochiensis before planting potatoes and yield of potato tubers. Nematologica 28:277–284

    Google Scholar 

  • Širca S, Stare BG, Plesko IM, Marn MV, Urek G, Javornik B (2007) Xiphinema rivesi from Slovenia transmit Tobacco ringspot virus and Tomato ringspot virus to cucumber bait plants. Plant Dis 91:770–770

    Google Scholar 

  • Slawiak M, Beckhoven JRCMV, Speksnijder AGCL, Czajkowski R, Grabe G, Wolf JMVD (2009) Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe. Eur J Plant Pathol 125(2):245–261

    Google Scholar 

  • Stevens FL (1907) List of New York fungi. J Mycol 13:67–72

    Google Scholar 

  • Sun XA, Stall RE, Jones JB, Cubero J, Gottwald TR, Graham JH, Dixon WN, Schubert TS, Chaloux PH, Stromberg VK, Lacy GH, Sutton BD (2004) Detection and characterization of a new strain of citrus canker bacteria from key Mexican lime and Alemow in South Florida. Plant Dis 88:1179–1188

    CAS  Google Scholar 

  • Tarjan AC (1969) Variation within the Xiphinema americanum group (Nematoda: Longidoridae). Nematologica 15:241–252

    Google Scholar 

  • Tassi F (1900) Novae Micromycetum species descriptae et iconibus illustratae. Bullettino del Laboratorio ed Orto Botanico, Siena, Vol. III, Fasc. III/IV, 116–132

    Google Scholar 

  • Taylor CE, Brown DJF (1997) Nematode vectors of plant viruses. CAB International, Wallingford, p 286

    Google Scholar 

  • Tomilin BA (1979) Key to fungi of the genus Mycosphaerella Johans. Nanka, Leningrad, pp 200–201

    Google Scholar 

  • Torchetti EM, Navarro B, Di Serio F (2012) A single polyprobe for detecting simultaneously eight pospiviroids infecting ornamentals and vegetables. J Virol Methods 186(1–2):141–6

    PubMed  CAS  Google Scholar 

  • Toth IK, Van der Wolf JM, Saddler G, Lojkowska E, Helias V, Pirhonen M, Tsror L, Elphinstone JG (2011) Dickeya species: an emerging problem for potato production in Europe. Plant Pathol 60:385–399

    Google Scholar 

  • Vaghefi N, Pethybridge SJ, Ford R, Nicolas ME, Crous PW, Taylor PWJ (2012) Stagonosporopsis spp. associated with ray blight disease of Asteraceae. Aust Plant Pathol 41:675–686

    Google Scholar 

  • Van der Aa HA, Noordeloos ME, Gruyter J (1990) Species concept in some larger general coelomycetes. Stud Mycol 32:3–19

    Google Scholar 

  • Van der Helm F (2009) Bacterierot in Sedum: hoe te handelen? Vakblad voor de Bloemisterij, pp 33–43

    Google Scholar 

  • Van Doorn J, Vreeburg P, Van Leeuwen P, Dees R (2008) The presence and survival of soft rot (Erwinia) in flower bulb production systems. In: X International Symposium on Flower Bulbs and Herbaceous Perennials 886:365–379.

    Google Scholar 

  • Van Leeuwen P, Dees R, Vreeburg P, En van Doorn J (2012) Oorzaak Erwinia problemen dahlia vooral Dickeya dianthicola. BloembollenVisie 246:22–23

    Google Scholar 

  • Vauterin L, Swings J (1997) Are classification and phytopathological diversity compatible in Xanthomonas ? J Ind Microbiol Biotechnol 19:77–82

    CAS  Google Scholar 

  • Vauterin L, Hoste B, Kersters K, Swings J (1995) Reclassification of Xanthomonas. Int J Syst Bacteriol 45:472–489

    CAS  Google Scholar 

  • Vercauteren A, De Dobbelaere I, Grünwald NJ, Bonants P, Van Bockstaele E, Maes M, Heungens K (2010) Clonal expansion of the Belgian Phytophthora ramorum populations based on new microsatellite markers. Mol Ecol 19:92–107

    PubMed  CAS  Google Scholar 

  • Vercauteren A, Boutet X, D’hondt L, Van Bockstaele E, Maes M, Leus L, Chandelier A, Heungens K (2011) Aberrant genome size and instability of Phytophthora ramorum oospore progenies. Fungal Genet Biol 48:537–543

    PubMed  CAS  Google Scholar 

  • Vernière C, Hartung JS, Pruvost OP, Civerolo EL, Alvarez AM, Maestri P, Luisetti J (1998) Characterization of phenotypically distinct strains of Xanthomonas axonopodis pv. citri from Southwest Asia. Eur J Plant Pathol 104:477–487

    Google Scholar 

  • Vives MC, Velázquez K, Pina JA, Moreno P, Guerri J, Navarro L (2013) Identification of a new Enamovirus associated with Citrus Vein Enation disease by deep sequencing of small RNAs. Phytopathology 103(10):1077–1086

    PubMed  CAS  Google Scholar 

  • Walker J, Baker K (1983) The correct binomial for the chrysanthemum ray blight pathogen in relation to its geographical distribution. Trans Br Mycol Soc 80:31–38

    Google Scholar 

  • Webster CG, Reitz SR, Perry KL, Adkins S (2011) A natural M RNA reassortant arising from two species of plant- and insect-infecting bunyaviruses and comparison of its sequence and biological properties to parental species. Virology 413:216–225

    PubMed  CAS  Google Scholar 

  • Werres S, Marwitz R, Man In T, Veld WA, De Cock AWAM, Bonants PJM, De Weerdt M, Themann K, Ilieva E, Baayen RP (2001) Phytophthora ramorum sp. nov., a new pathogen on Rhododendron and Viburnum. Mycol Res 105:1155–1165

    CAS  Google Scholar 

  • Whitfield AE, Ullman DE, German TL (2005) Tospovirus-thrips interactions. Annu Rev Phytopathol 43:459–489

    PubMed  CAS  Google Scholar 

  • Wilcox WF, Scott PH, Hamm PB, Kennedy DM, Duncan JM, Brasier CM, Hansen EM (1993) Identity of a Phytophthora species attacking raspberry in Europe and North America. Mycol Res 97(7):817–831, 33

    Google Scholar 

  • Young JM, Bradbury JF, Gardan L, Gvozdyak RI, Stead DE, Takikawa Y, Vidaver AK (1991) Comment on the reinstatement of Xanthomonas citri (ex Hasse 1915) Gabriel et al. 1989 and X. phaseoli (ex Smith 1897) Gabriel et al. 1989: Indication of the need for minimal standards for the genus Xanthomonas. Int J Syst Evol Microbiol 41:172–177

    Google Scholar 

  • Young JM, Bull CT, De Boer SH, Firrao G, Gardan L, Saddler GE, Stead DE, Takikawa Y (2001) Classification, nomenclature and plant pathogenic bacteria-A clarification. Phytopathology 91:617–620

    PubMed  CAS  Google Scholar 

  • Young JM, Park DC, Shearman HM, Fargier E (2008) A multilocus sequence analysis of the genus Xanthomonas. Syst Appl Microbiol 31:366–377

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Authors thank the following working group members, hearing experts and EFSA staff involved in the scientific opinions mentioned in this Chapter: R. Baker, T. Been, P. Bielza, P. Bonants, C. Brasier, A. Brown, P.J. De Barro, H. De Gruyter, F. Di Serio, E. Dormannsne Simon, J. Duncan, R. Flores, A. Fox, M. Garbelotto, N. Gauthier, G. Gilioli, T. Goumperis, J. Gregoire, E. Grenier, I, Holb, S. Hockland, G. Hollo, M. Ioannou, D. Janssen, J. Jones, O.E. Karadjova, V. Kertesz, S. Kozelska, O. Mosbach-Schulz, M. Navajas, S. Pasquali, M. Pautasso, D. Peters, A. Porta Puglia, T. Rafoss, A. Rortais, M. Ruffini, J. Schans, R. Singh, A. Sletten, S. Tramontini, A. Urbaneja, E. van de Weg, J.C. Van Lenteren, J.T.J. Verhoeven, I. Vloutoglou, S. Vos, S. Winter

The present paper is published under the sole responsibility of the authors and may not be considered as a scientific output by the European Food Safety Authority (EFSA). The position and opinions presented in this publication are those of the authors alone and do not necessarily represent the views of EFSA.

Author information

Authors and Affiliations

  1. Università Cattolica del Sacro Cuore, Via E. Parmense 84, 29100, Piacenza, Italy

    Vittorio Rossi

  2. INRA and University of Bordeaux Virology Team, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d’Ornon Cedex, France

    Thierry Candresse

  3. Centre for Environmental Policy, Imperial College London, Silwood Park campus, Ascot, SL5 7PY, UK

    Michael J. Jeger

  4. Anses, French Agency for Food, Environmental and Occupational Health and Safety, 7 rue Jean Dixméras, 49044, Angers, France

    Charles Manceau

  5. Kmetijski inštitut Slovenije, Hacquetova ulica 17, 1000, Ljubljana, Slovenia

    Gregor Urek

  6. European Food Safety Authority, Animal and Plant Health Unit, Via Carlo Magno 1A, 43126, Parma, Italy

    Giuseppe Stancanelli

Authors
  1. Vittorio Rossi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thierry Candresse
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michael J. Jeger
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Charles Manceau
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gregor Urek
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Giuseppe Stancanelli
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Vittorio Rossi .

Editor information

Editors and Affiliations

  1. AGROINNOVA, University of Torino, Grugliasco, Torino, Italy

    Maria Lodovica Gullino

  2. Plant Research International, Wageningen UR, Wageningen, Utrecht, The Netherlands

    Peter J. M. Bonants

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Rossi, V., Candresse, T., Jeger, M.J., Manceau, C., Urek, G., Stancanelli, G. (2014). Diagnosis of Plant Pathogens and Implications for Plant Quarantine: A Risk Assessment Perspective. In: Gullino, M., Bonants, P. (eds) Detection and Diagnostics of Plant Pathogens. Plant Pathology in the 21st Century, vol 5. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9020-8_12

Download citation

Publish with us

Policies and ethics

Search

Navigation