Skip to main content
SpringerLink
Log in

Detection and Identification of Phytophthora Pathogens that Are Threatening Forest Ecosystems Worldwide

  • Chapter
  • First Online:
River Basin Environment: Evaluation, Management and Conservation

Abstract

Introduced Phytophthora species are a serious threat to forest trees and nursery plants. These pathogens have spread rapidly and widely due to human activities such as international plant trading, and have caused negative impacts on forest ecosystems. Imported plants should be carefully inspected for the presence of pathogens using molecular detection methods. Since large numbers of specimens are tested in quarantine, the detection method must be simple, rapid and accurate. A loop-mediated isothermal amplification (LAMP) method has the advantage of high tolerance to amplification inhibitors, and thus, simple DNA extraction methods can be used. In this chapter, we will discuss processes for LAMP detection including LAMP primer design; methods for DNA extraction from environmental samples such as plants, soil and water; the applicability various instruments for LAMP assays; and experimental settings for accurate detection with regard to sampling and potential contamination sources. This information will be very useful for researchers in creating detection procedures involving LAMP. LAMP-based detection is expected to have various applications in the future, and is one of the most promising options for pathogen detection, which is needed for disease control.

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

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 59.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 59.99
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

Similar content being viewed by others

References

  • Abad, ZG, Burgess T, Bienapfl JC, Redford AJ, Coffey M, Knight L (2019) IDphy: molecular and morphological identification of Phytophthora based on the types. USDA APHIS PPQ S&T Beltsville Lab, USDA APHIS PPQ S&T ITP, Centre for Phytophthora Science and Management, and World Phytophthora Collection

    Google Scholar 

  • Almasi MA, Ojaghkandi MA, Hemmatabadi A, Hamidi F, Aghaei S (2013) Development of colorimetric loop-mediated isothermal amplification assay for rapid detection of the tomato yellow leaf curl virus. J Plant Pathol Microbiol 04:153

    Google Scholar 

  • Becherer L, Borst N, Bakheit M, Frischmann S, Zengerle R, von Stetten F (2020) Loop-mediated isothermal amplification (LAMP) – review and classification of methods for sequence-specific detection. Anal Methods 12(6):717–746

    Article  Google Scholar 

  • Bilodeau GJ, Martin FN, Coffey MD, Blomquist CL (2014) Development of a multiplex assay for genus- and species-specific detection of Phytophthora based on differences in mitochondrial gene order. Phytopathology 104(7):733–748

    Article  CAS  PubMed  Google Scholar 

  • Brasier CM (2008) The biosecurity threat to the UK and global environment from international trade in plants. Plant Pathol 57:792–808

    Article  Google Scholar 

  • Brasier C (2009) Phytophthora biodiversity: how many Phytophthora species are there? In: Goheen EM, Frankel SJ (tech. coords.) Proceedings of the fourth meeting of the International Union of Forest Research Organizations (IUFRO) working party S07.02.09: Phytophthoras in forests and natural ecosystems. Gen. Tech. Rep. PSW-GTR-221. U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station, Albany, pp 101–115

    Google Scholar 

  • Brasier CM, Beales PA, Kirk SA, Denman S, Rose J (2005) Phytophthora kernoviae sp. nov., an invasive pathogen causing bleeding stem lesions on forest trees and foliar necrosis of ornamentals in the UK. Mycol Res 109(8):853–859

    Article  PubMed  Google Scholar 

  • Burgess TI, Simamora AV, White D, Wiliams B, Schwager M, Stukely MJC, Hardy G (2018) New species from Phytophthora clade 6a: evidence for recent radiation. Persoonia 41:1–17

    Article  CAS  PubMed  Google Scholar 

  • Dell B, Hardy G, Vear K (2005) History of Phytophthora cinnamomi management in Western Australia. In: Calver M et al (ed) Proceedings 6th National Conference of the Australian Forest History Society, pp 391–406

    Google Scholar 

  • Fichtner EJ, Rizzo DM, Kirk SA, Webber JF (2012) Infectivity and sporulation potential of Phytophthora kernoviae to select North American native plants. Plant Pathol 61(2):224–233

    Article  Google Scholar 

  • Garkaklis MJ, Calver MC, Wilson BA, Hardy GESJ (2004) Habitat alteration caused by an introduced plant disease, Phytophthora cinnamomi: a potential threat to the conservation of Australian forest fauna. In: Lunney D (ed) The conservation of Australia’s forest fauna, 2nd edn. Royal Zoological Society of New South Wales, Mosman, pp 899–913

    Chapter  Google Scholar 

  • Genebank Project, National Agriculture and Food Research Organization (NARO): database of plant diseases in Japan, based on “common names of plant diseases in Japan” compiled by Phytopathological Society of Japan. URL https://www.gene.affrc.go.jp/databases-micro_pl_diseases_en.php

  • Goto M, Honda E, Ogura A, Nomoto A, Hanaki K (2009) Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue. BioTechniques 46(3):167–172

    Article  CAS  PubMed  Google Scholar 

  • Grünwald NJ, Goss EM, Press CM (2008) Phytophthora ramorum: a pathogen with a remarkably wide host range causing sudden oak death on oaks and ramorum blight on woody ornamentals. Mol Plant Pathol 9(6):729–740

    Article  PubMed  PubMed Central  Google Scholar 

  • Hansen EM, Goheen DJ, Jules ES, Ullian B (2000) Managing Port-Orford-Cedar and the Introduced Pathogen Phytophthora lateralis. Plant Dis 84(1):4–14

    Article  PubMed  Google Scholar 

  • Hieno A, Li M, Afandi A, Otsubo K, Suga H, Kageyama K (2019) Rapid detection of Phytophthora nicotianae by simple DNA extraction and real-time loop-mediated isothermal amplification assay. J Phytopathol 167(3):174–184

    Article  CAS  Google Scholar 

  • Hieno A, Li M, Afandi A, Otsubo K, Suga H, Kageyama K (2020) Detection of the genus Phytophthora and the species Phytophthora nicotianae by LAMP with a QProbe. Plant Dis 104(9):2469–2480

    Article  CAS  PubMed  Google Scholar 

  • Hieno A, Li M, Otsubo K, Suga H, Kageyama K (2021) Multiplex LAMP detection of the genus Phytophthora and four Phytophthora species P. ramorum, P. lateralis, P. kernoviae, and P. nicotianae, with a plant internal control. Microbes Environ 36(2):ME21019

    Article  PubMed Central  Google Scholar 

  • Hill J, Beriwal S, Chandra I, Paul VK, Kapil A, Singh T, Wadowsky RM, Singh V, Goyal A, Jahnukainen T, Johnson JR, Tarr PI, Vats A (2008) Loop-mediated isothermal amplification assay for rapid detection of common strains of Escherichia coli. J Clin Microbiol 46(8):2800–2804

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hong CX, Moorman GW (2005) Plant pathogens in irrigation water: challenges and opportunities. Crit Rev Plant Sci 24:189–208

    Article  Google Scholar 

  • Invasive Species Compendium, CABI URL https://www.cabi.org/isc/

  • Jung T, Orlikowski L, Henricot B, Abad-Campos P, Aday AG, Aguín Casal O, Bakonyi J, Cacciola SO, Cech T, Chavarriaga D, Corcobado T, Cravador A, Decourcelle T, Denton G, Diamandis S, Doğmuş-Lehtijärvi HT, Franceschini A, Ginetti B, Green S, Glavendekić M, Hantula J, Hartmann G, Herrero M, Ivic D, Jung MH, Lilja A, Keca N, Kramarets V, Lyubenova A, Machado H, di San M, Lio G, Mansilla Vázquez PJ, Marçais B, Matsiakh I, Milenkovic I, Moricca S, Nagy ZÁ, Nechwatal J, Olsson C, Oszako T, Pane A, Paplomatas EJ, Pintos Varela C, Prospero S, Rial Martínez C, Rigling D, Robin C, Rytkönen A, Sánchez ME, Sanz Ros AV, Scanu B, Schlenzig A, Schumacher J, Slavov S, Solla A, Sousa E, Stenlid J, Talgø V, Tomic Z, Tsopelas P, Vannini A, Vettraino AM, Wenneker M, Woodward S, Peréz-Sierra A, Deprez-Loustau ML (2016) Widespread Phytophthora infestations in European nurseries put forest, semi-natural and horticultural ecosystems at high risk of Phytophthora diseases. For Pathol 46(2):134–163

    Article  Google Scholar 

  • Jung T, Jung MH, Cacciola SO, Cech T, Bakonyi J, Seress D, Mosca S, Schena L, Seddaiu S, Pane A, di San M, Lio G, Maia C, Cravador A, Franceschini A, Scanu B (2017a) Multiple new cryptic pathogenic Phytophthora species from Fagaceae forests in Austria, Italy and Portugal. IMA Fungus 8(2):219–244

    Article  PubMed  PubMed Central  Google Scholar 

  • Jung T, Jung MH, Scanu B, Seress D, Kovacs GM, Maia C, Perez-Sierra A, Chang TT, Chandelier A, Heungens K, van Poucke K, Abad-Campos P, Leon M, Cacciola SO, Bakonyi J (2017b) Six new Phytophthora species from ITS Clade 7a including two sexually functional heterothallic hybrid species detected in natural ecosystems in Taiwan. Persoonia 38:100–135

    Article  CAS  PubMed  Google Scholar 

  • Jung T, Perez-Sierra A, Duran A, Jung MH, Balci Y, Scanu B (2018) Canker and decline diseases caused by soil- and airborne Phytophthora species in forests and woodlands. Persoonia 40:182–220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jung T, Jung MH, Webber JF, Kageyama K, Hieno A, Masuya H, Uematsu S, Pérez-Sierra A, Harris AR, Forster J, Rees H, Scanu B, Patra S, Kudláček T, Janoušek J, Corcobado T, Milenković I, Nagy Z, Csorba I, Bakonyi J, Brasier CM (2021) The destructive tree pathogen Phytophthora ramorum originates from the laurosilva forests of East Asia. J Fungi 7(3):226

    Article  CAS  Google Scholar 

  • Kaneko H, Kawana T, Fukushima E, Suzutani T (2007) Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances. J Biochem Biophys Methods 70(3):499–501

    Article  CAS  PubMed  Google Scholar 

  • Li M, Ishiguro Y, Kageyama K, Zhu Z (2015) A simple method for normalization of DNA extraction to improve the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR. Lett Appl Microbiol 61(2):179–185

    Article  PubMed  CAS  Google Scholar 

  • Li M, Guo Q, Liang M, Zhao Q, Lin T, Gao H, Hieno A, Kageyama K, Zhang X, Cui L, Yan Y, Qiang Y (2022) Population dynamics, effective soil factors, and LAMP detection systems for Phytophthora species associated with kiwifruit diseases in China. Plant Dis 106(3):846–853

    Article  PubMed  Google Scholar 

  • Lin X, Huang X, Urmann K, Xie X, Hoffmann MR (2019) Digital loop-mediated isothermal amplification on a commercial membrane. ACS Sens 4(1):242–249

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin FN, Tooley PW, Blomquist CL (2004) Molecular detection of Phytophthora ramorum, the causal agent of sudden oak death in California, and two additional species commonly recovered from diseased plant material. Phytopathology 94(6):621–631

    Article  CAS  PubMed  Google Scholar 

  • Miles TD, Martin FN, Coffey MD (2015) Development of rapid isothermal amplification assays for detection of Phytophthora spp. in plant tissue. Phytopathology 105(2):265–278

    Article  CAS  PubMed  Google Scholar 

  • Mori Y, Notomi T (2009) Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases. J Infect Chemother 15(2):62–69

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mori Y, Nagamine K, Tomita N, Notomi T (2001) Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun 289(1):150–154

    Article  CAS  PubMed  Google Scholar 

  • Nagamine K, Hase T, Notomi T (2002) Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol Cell Probes 16(3):223–229

    Article  CAS  PubMed  Google Scholar 

  • Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28(12):E63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parke JL, Grünwald NJ (2012) A systems approach for management of pests and pathogens of nursery crops. Plant Dis 96(9):1236–1244

    Article  PubMed  Google Scholar 

  • Pham HM, Nakajima C, Ohashi K, Onuma M (2005) Loop-mediated isothermal amplification for rapid detection of Newcastle disease virus. J Clin Microbiol 43(4):1646–1650

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rizzo DM, Garbelotto M, Hansen EM (2005) Phytophthora ramorum: integrative research and management of an emerging pathogen in California and Oregon forests. Annu Rev Phytopathol 43:309–335

    Article  PubMed  CAS  Google Scholar 

  • Robideau GP, De Cock AW, Coffey MD, Voglmayr H, Brouwer H, Bala K, Chitty DW, Desaulniers N, Eggertson QA, Gachon CM, Hu CH, Kupper FC, Rintoul TL, Sarhan E, Verstappen EC, Zhang Y, Bonants PJ, Ristaino JB, Levesque CA (2011) DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Mol Ecol Resour 11(6):1002–1011

    Article  CAS  PubMed  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

    Article  Google Scholar 

  • Rolando JC, Jue E, Schoepp NG, Ismagilov RF (2019) Real-time, digital LAMP with commercial microfluidic chips reveals the interplay of efficiency, speed, and background amplification as a function of reaction temperature and time. Anal Chem 91(1):1034–1042

    Article  CAS  PubMed  Google Scholar 

  • Roy BA, Alexander HM, Davidson J, Campbell FT, Burdon JJ, Sniezko R, Brasier C (2014) Increasing forest loss worldwide from invasive pests requires new trade regulations. Front Ecol Environ 12(8):457–465

    Article  Google Scholar 

  • Schena L, Hughes KJ, Cooke DE (2006) Detection and quantification of Phytophthora ramorum, P. kernoviae, P. citricola and P. quercina in symptomatic leaves by multiplex real-time PCR. Mol. Plant Pathol 7(5):365–379

    CAS  Google Scholar 

  • Schena L, Duncan JM, Cooke DEL (2008) Development and application of a PCR-based molecular tool box for the identification of Phytophthora species damaging forests and natural ecosystems. Plant Pathol 57(1):64–75

    CAS  Google Scholar 

  • Scibetta S, Schena L, Chimento A, Cacciola SO, Cooke DE (2012) A molecular method to assess Phytophthora diversity in environmental samples. J Microbiol Methods 88(3):356–368

    Article  CAS  PubMed  Google Scholar 

  • Suwannin P, Polpanich D, Leelayoova S, Mungthin M, Tangboriboonrat P, Elaissari A, Jangpatarapongsa K, Ruang-Areerate T, Tangchaikeeree T (2021) Heat-enhancing aggregation of gold nanoparticles combined with loop-mediated isothermal amplification (HAG-LAMP) for Plasmodium falciparum detection. J Pharm Biomed Anal 203:114178

    Article  CAS  PubMed  Google Scholar 

  • Tanner NA, Zhang Y, Evans TC Jr (2015) Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes. BioTechniques 58(2):59–68

    Article  CAS  PubMed  Google Scholar 

  • Tomita N, Mori Y, Kanda H, Notomi T (2008) Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc 3(5):877–882

    Article  CAS  PubMed  Google Scholar 

  • Tomlinson JA, Barker I, Boonham N (2007) Faster, simpler, more-specific methods for improved molecular detection of Phytophthora ramorum in the field. Appl Environ Microbiol 73(12):4040–4047

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tomlinson JA, Dickinson MJ, Boonham N (2010) Rapid detection of Phytophthora ramorum and P. kernoviae by two-minute DNA extraction followed by isothermal amplification and amplicon detection by generic lateral flow device. Phytopathology 100:143–149

    Article  CAS  PubMed  Google Scholar 

  • USDA Agricultural Research Service URL https://nt.ars-grin.gov/fungaldatabases/fungushost/fungushost.cfm

  • Watanabe H (2014) The detection methods for high-temperature-Pythium species in hydroponic culture by bait and membrane filter. Plant Protect (written in Japanese) 68(6):309–313

    Google Scholar 

  • Watanabe H, Muramoto Y, Adachi M, Fukuta S, Takahashi R, Kageyama K (2013) Reducing clogging by using a filter aid for the detection of plant pathogen using a membrane filter method. Ann Rept Kansai Pl Prot (written in Japanese) 55:65–66

    Article  Google Scholar 

  • Webber JF (2009) Management of Phytophthora kernoviae and P. ramorum in Southwest England. In: Goheen EM, Frankel SJ (eds) Phytophthoras in forests and natural ecosystems. General Technical Report PSW-GTR-221. USDA Forest Service, Albany, pp 177–183

    Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninskey JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, San Diego, pp 315–322

    Google Scholar 

  • Yang X, Hong C (2018) Differential usefulness of nine commonly used genetic markers for identifying Phytophthora species. Front Microbiol 9:2334

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang X, Tyler BM, Hong C (2017) An expanded phylogeny for the genus Phytophthora. IMA Fungus 8(2):355–384

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang ZP, Zhang Y, Liu JP, Zhang JT, An ZX, Quan FS, Zhang L, Cai X, Pu SW (2009) Codeposition of dNTPs detection for rapid LAMP-based sexing of bovine embryos. Reprod Domest Anim 44(1):116–121

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Xu Y, Fohlerova Z, Chang H, Iliescu C, Neuzil P (2019) LAMP-on-a-chip: revising microfluidic platforms for loop-mediated DNA amplification. Trends Anal Chem 113:44–53

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Research for this review was supported by a Grant-in Aid for “Development of detection and identification techniques of pests” in “Research and development of adaptation measures for global warming and abnormal weather” from the Ministry of Agriculture, Forestry, and Fisheries of Japan. We thank Emeritus Prof. E. M. Hansen, Prof. M. D. Coffey, Dr. P. W. Tooley, Prof. C. Hong, Dr. B. S. Weir, Dr. T. I. Burgess, Dr. T. Jung, Mr. S. Uematsu and Dr. H. Watanabe for providing isolates of many important Phytophthora spp., and Dr. S. Subandiyah and Dr. A. Wibowo for providing plant DNA samples. We also thank Mr. T. Sakoda, Mr. K. Ueda for technical assistance.

Author information

Authors and Affiliations

  1. River Basin Research Center, Gifu University, Gifu, Japan

    Ayaka Hieno, Kayoko Otsubo & Koji Kageyama

  2. College of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi, China

    Mingzhu Li

  3. College of Agriculture, Guizhou University, Guiyang, Guizhou, China

    Wenzhuo Feng

  4. Department of Plant Protection, Faculty of Agriculture, Universitas Lampung, Bandar Lampung, Lampung, Indonesia

    Auliana Afandi

  5. Institute for Glyco-core Research, Gifu University, Gifu, Japan

    Haruhisa Suga

Authors
  1. Ayaka Hieno
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mingzhu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenzhuo Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Auliana Afandi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kayoko Otsubo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Haruhisa Suga
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Koji Kageyama
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ayaka Hieno .

Editor information

Editors and Affiliations

  1. River Basin Research Center, Gifu University, Gifu, Gifu, Japan

    Fusheng Li

  2. River Basin Research Center, Gifu University, Gifu, Gifu, Japan

    Yoshio Awaya

  3. River Basin Research Center, Gifu University, Gifu, Gifu, Japan

    Koji Kageyama

  4. River Basin Research Center, Gifu University, Gifu, Gifu, Japan

    Yongfen Wei

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Hieno, A. et al. (2022). Detection and Identification of Phytophthora Pathogens that Are Threatening Forest Ecosystems Worldwide. In: Li, F., Awaya, Y., Kageyama, K., Wei, Y. (eds) River Basin Environment: Evaluation, Management and Conservation. Springer, Singapore. https://doi.org/10.1007/978-981-19-4070-5_6

Download citation

Publish with us

Policies and ethics

Search

Navigation