Skip to main content
SpringerLink
Log in

Sympatric occurrence of sibling Phytophthora species associated with foot rot disease of black pepper in India

  • Environmental Microbiology - Research Paper
  • Published:
Brazilian Journal of Microbiology Aims and scope Submit manuscript

Abstract

Foot rot disease caused by Phytophthora capsici is a serious threat to black pepper cultivation in India and globally. High diversity exists among the Phytophthora isolates of black pepper and hence detailed investigations of their morphology and phylogenetic taxonomy were carried out in the present study. In order to resolve the diversity, 182 isolates of Phytophthora, collected from different black pepper-growing tracts of South India during 1998–2013 and maintained in the National Repository of Phytophthora at ICAR-Indian Institute of Spices Research, Kozhikode, were subjected to morphological, molecular and phylogenetic characterization. Morphologically all the isolates were long pedicellate with umbellate/simple sympodial sporangiophores and papillate sporangia with l/b ranging from 1.63 to 2.55 µm. Maximum temperature for the growth was ~ 34 °C. Chlamydospores were observed in “tropicalis” group, whereas they were absent in “capsici” group. Initial molecular studies using internal transcribed spacer (ITS) marker gene showed two clear cut lineages—“capsici-like” and “tropicalis-like” groups among them. Representative isolates from each group were subjected to host differential test, multilocus sequence typing (MLST) and phylogeny studies. MLST analysis of seven nuclear genes (60S ribosomal protein L10, beta-tubulin, elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA and TigA gene fusion protein) clearly delineated black pepper Phytophthora isolates into two distinct species—P. capsici and P. tropicalis. On comparing with type strains from ATCC, it was found that the type strains of P. capsici and P. tropicalis differed from black pepper isolates in their infectivity on black pepper. The high degree of genetic polymorphism observed in black pepper Phytophthora isolates is an indication of the selection pressure they are subjected to in the complex habitat which ultimately may lead to speciation. So based on the extensive analysis, it is unambiguously proved that the foot rot disease of black pepper in India is predominantly caused by two species of Phytophthora, viz. P. capsici and P. tropicalis. Presence of multiple species of Phytophthora in the black pepper agro-ecosystem warrants a revisit to the control strategy being adopted for managing this serious disease. The silent molecular evolution taking place in such an ecological niche needs to be critically studied for the sustainable management of foot rot disease.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

All nucleotide sequence data were submitted to GenBank public nucleic acid sequence repository (https://www.ncbi.nlm.nih.gov/genbank/) and their accession numbers are listed as Supplementary Tables 3–5. The multiple sequence alignment of datasets are submitted to the TreeBASE.

Code availability

Not applicable.

References

  1. Pratibha VH, Hegde V, Sharadraj KM, Rajesh MK, Rachana KE, Chowdappa P (2018) Differentiation of Phytophthora species associated with plantation crops using PCR and high-resolution melting curve analysis. J Plant Pathol 100:233–240. https://doi.org/10.1007/s42161-018-0065-3

    Article  Google Scholar 

  2. Donahoo RS, Lamour KH (2008) Interspecific hybridization and apomixis between Phytophthora capsici and Phytophthora tropicalis. Mycologia 100(6):911–920. https://doi.org/10.3852/08-028

    Article  CAS  PubMed  Google Scholar 

  3. Bowers JH, Martin FN, Tooley PW, Luz EDMN (2007) Genetic and morphological diversity of temperate and tropical isolates of Phytophthora capsici. Phytopathology 97:492–503. https://doi.org/10.1094/PHYTO-97-4-0492

    Article  CAS  PubMed  Google Scholar 

  4. Leonian LH (1922) Stem and fruit blight of peppers caused by Phytophthora capsici sp. nov. Phytopathology 12(9):401–408

    Google Scholar 

  5. Holliday P (2001) A dictionary of plant pathology. Cambridge University Press, Cambridge

    Google Scholar 

  6. Gevens AJ, Donahoo RS, Lamour KH, Hausbeck MK (2007) Characterization of Phytophthora capsici from Michigan surface irrigation water. Phytopathology 97:421–428. https://doi.org/10.1094/PHYTO-97-4-0421

    Article  CAS  PubMed  Google Scholar 

  7. Lamour KH, Hausbeck MK (2000) Mefenoxam insensitivity and the sexual stage of Phytophthora capsici in Michigan cucurbit fields. Phytopathology 90:396–400. https://doi.org/10.1094/PHYTO.2000.90.4.396

    Article  CAS  PubMed  Google Scholar 

  8. Ristaino JB, Johnston SA (1999) Ecologically based approaches to management of Phytophthora blight on bell pepper. Plant Dis 83:1080–1089. https://doi.org/10.1094/PDIS.1999.83.12.1080

    Article  PubMed  Google Scholar 

  9. Alizadeh A, Tsao PH (1985) Effect of light on sporangium formation, morphology, ontogeny, and caducity of Phytophthora capsici and “P. palmivora” MF4 isolates from black pepper and other hosts. Trans Br Mycol Soc 85:47–69. https://doi.org/10.1016/S0007-1536(85)80155-8

    Article  Google Scholar 

  10. Oudemans P, Coffey MD (1991) A revised systematics of twelve papillate Phytophthora species based on isozyme analysis. Mycol Res 95:1025–1046. https://doi.org/10.1016/S0953-7562(09)80543-1

    Article  CAS  Google Scholar 

  11. Uchida JY, Aragaki M (1985) Occurrence of chlamydospores in Phytophthora capsici. Mycologia 77:832–835. https://doi.org/10.1080/00275514.1985.12025170

    Article  Google Scholar 

  12. Tsao PH, Alizadeh A (1988) Recent advances in the taxonomy and nomenclature of the so-called “Phytophthora palmivora” MF-4 occurring on cocoa and other tropical crops. In: Proceedings of 10th International Cocoa Research Conference, Santo Domingo, Dominican Republic, pp. 441–445

  13. Mchau GRA, Coffey MD (1994) An integrated study of morphological and isozyme patterns found within a worldwide collection of Phytophthora citrophthora and a redescription of the species. Mycol Res 98:1291–1299. https://doi.org/10.1016/S0953-7562(09)80301-8

    Article  Google Scholar 

  14. Cissin J, Bhai RS, Vinitha KB, Babu KN, Anandaraj M (2016) Cross species amplification of microsatellite loci from Phytophthora spp. to assess genetic diversity among the Phytophthora isolates from black pepper. J Spices Aromatic Crops 25(2):104–112. https://updatepublishing.com/journal/index.php/josac/article/view/5172

  15. Vinitha KB, Ananadaraj M, Bhai RS (2016) Virulence of Phytophthora isolates from Piper nigrum L. and their sensitivity to metalaxyl-mancozeb. J Plant Crops 44(2):67–76. https://doi.org/10.19071/jpc.2016.v44.i2.3100

    Article  Google Scholar 

  16. Chen QH, Weng QY, Wang YC, Zheng XB (2004) Identification and sequencing of ribosomal DNA-ITS of Phytophthora sojae in Fujian. Acta Phytopathologica 34(2):112–116

    Google Scholar 

  17. Blair JE, Coffey MD, Park SY, Geiser DM, Kang S (2008) A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genet Biol 45(3):266–277. https://doi.org/10.1016/j.fgb.2007.10.010

    Article  CAS  PubMed  Google Scholar 

  18. Martin FN, Blair JE, Coffey MD (2014) A combined mitochondrial and nuclear multilocus phylogeny of the genus Phytophthora. Fungal Genet Biol 66:19–32. https://doi.org/10.1016/j.fgb.2014.02.006

    Article  CAS  PubMed  Google Scholar 

  19. Yang X, Tyler BM, Hong C (2017) An expanded phylogeny for the genus Phytophthora. IMA Fungus 8(2):355–384. https://doi.org/10.5598/imafungus.2017.08.02.09

    Article  PubMed  PubMed Central  Google Scholar 

  20. Tsao PH, Guy S (1977) Inhibition of Mortierella and Pythium in a Phytophthora isolation medium containing Hymexazol. Phytopathol 67:798–801

    Google Scholar 

  21. Bhai RS, Anandaraj M, Sarma YR, Veena SS, Saji KV (2007) Screening of black pepper (Piper nigrum L.) germplasm for resistance to foot rot disease caused by Phytophthora capsici Leonian. J Spices Aromatic Crops 16(2):115–117. https://updatepublishing.com/journal/index.php/josac/article/view/4876

  22. Prakash KM, Bhai RS, Jiji J, Saji KV, Sujatha VS, Santhoshkumar AV (2019) Exploitation of resistant sources to Phytophthora capsici Leon. from genetic stocks of black pepper (Piper nigrum L.). Int J Curr Microbiol Appl Sci 8(5):1487–1496. https://doi.org/10.20546/ijcmas.2019.805.171

    Article  Google Scholar 

  23. Erwin DC, Ribeiro OK (1996) Phytophthora diseases worldwide. American Phytopathological Society, St. Paul, Minnesota

    Google Scholar 

  24. Sheji C, Renu SG, Balaji S, Anandaraj M (2009) Ribosomal DNA analysis of three Phytophthora species occurring in India. Indian Phytopathol 62(2):155–162

    CAS  Google Scholar 

  25. Cooke DE, Drenth A, Duncan JM, Wagels G, Brasier CM (2000) A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genet Biol 30:17–32. https://doi.org/10.1006/fgbi.2000.1202

    Article  CAS  PubMed  Google Scholar 

  26. White TJ, Bruns T, Lee S, Taylor J (1990) Analysis of phylogenetic relationships by amplification and direct sequencing of ribosomal RNA genes. In: Innis MA et al (eds) PCR protocols: a guide to methods and applications. Academic, New York, pp 315–322

    Google Scholar 

  27. 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. https://idtools.org/id/phytophthora/ index.php. Accessed 31August 2021

  28. Kong P, Hong CX, Tooley PW, Ivors K, Garbelotto M, Richardson PA (2004) Rapid identification of Phytophthora ramorum using PCR-SSCP analysis of ribosomal DNA ITS-1. Lett Appl Microbiol 38:433–439. https://doi.org/10.1111/j.1472-765X.2004.01510.x

    Article  CAS  PubMed  Google Scholar 

  29. Rubio L, Ayllón MA, Guerri J, Pappu H, Niblett C, Moreno P (1996) Differentiation of citrus tristeza closterovirus (CTV) isolates by single-strand conformation polymorphism analysis of the coat protein gene. Ann Appl Biol 129:479–489. https://doi.org/10.1111/j.1744-7348.1996.tb05770.x

    Article  CAS  Google Scholar 

  30. Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948. https://doi.org/10.1093/bioinformatics/btm404

    Article  CAS  PubMed  Google Scholar 

  31. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  32. Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25(7):1253–1256. https://doi.org/10.1093/molbev/msn083

    Article  CAS  PubMed  Google Scholar 

  33. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3):539–542. https://doi.org/10.1093/sysbio/sys029

    Article  PubMed  PubMed Central  Google Scholar 

  34. Silvar C, Merino F, Díaz J (2006) Diversity of Phytophthora capsici in Northwest Spain: analysis of virulence, metalaxyl response, and molecular characterization. Plant Dis 90(9):1135–1142. https://doi.org/10.1094/PD-90-1135

    Article  CAS  PubMed  Google Scholar 

  35. Hulvey J, Hurtado-Gonzalez O, Aragón-Caballero L, Gobena D, Storey D, Finley L, Lamour K (2011) Genetic diversity of the pepper pathogen Phytophthora capsici on farms in the Amazonian high jungle of Peru. American J Plant Sci 2:461–466. https://doi.org/10.4236/ajps.2011.23054

    Article  CAS  Google Scholar 

  36. Gobena D, Roig J, Galmarini C, Hulvey J, Lamour K (2012) Genetic diversity of Phytophthora capsici isolates from pepper and pumpkin in Argentina. Mycologia 104(1):102–107. https://doi.org/10.3852/11-147

    Article  CAS  PubMed  Google Scholar 

  37. Castro-Rocha A, Shrestha S, Lyon B et al (2016) An initial assessment of genetic diversity for Phytophthora capsici in northern and central Mexico. Mycol Progress 15:15. https://doi.org/10.1007/s11557-016-1157-0

    Article  Google Scholar 

  38. Castro-Rocha A, Hulvey JP, Wick R, Shrestha SK, Lamour K (2017) Genetic diversity of Phytophthora capsici recovered from Massachusetts between 1997 and 2014. Mycol Progress 16:999–1006. https://doi.org/10.1007/s11557-017-1334-9

    Article  Google Scholar 

  39. Chen XR, Zhang Y, Huang SX, Liu TT, Qiao GH (2018) Investigation of the genetic diversity of Phytophthora capsici in China using a universal fluorescent labelling method. J Phytopathol 167:111–122. https://doi.org/10.1111/jph.12779

    Article  CAS  Google Scholar 

  40. Sun WX, Jia YJ, O’Neill NR, Feng BZH, Zhang XG (2008) Genetic diversity in Phytophthora capsici from eastern China. Can J Plant Pathol 30(3):414–424. https://doi.org/10.1080/07060660809507539

    Article  Google Scholar 

  41. Waterhouse GM (1963) Key to the species of Phytophthora de Barry. Mycological Papers No. 92, Commonwealth Mycological Institute, Kew, UK

  42. Vijaya P (2008) Studies on characterization and variability of Phytophthora species pathogenic to black pepper (Piper nigrum). Ph. D. Thesis, University of Calicut, Kerala, India

  43. Kroon LPNM, Brouwer H, de Cock AWAM, Govers F (2012) The genus Phytophthora anno 2012. Phytopathology 102:348–364. https://doi.org/10.1094/PHYTO-01-11-0025

    Article  PubMed  Google Scholar 

  44. Martin FN, Abad ZG, Balci Y, Ivors K (2012) Identification and detection of Phytophthora: reviewing our progress, identifying our needs. Plant Dis 96:1080–1103. https://doi.org/10.1094/PDIS-12-11-1036-FE

    Article  PubMed  Google Scholar 

  45. Mchau GRA, Coffey MD (1995) Evidence for the existence of two subpopulations in Phytophthora capsici and a redescription of the species. Mycol Res 99:89–102. https://doi.org/10.1016/S0953-7562(09)80321-3

    Article  Google Scholar 

  46. Aragaki M, Uchida JY (2001) Morphological distinctions between Phytophthora capsici and P. tropicalis sp. nov. Mycologia 93:137–145

    Article  Google Scholar 

  47. Hong CX, Gallegly ME, Browne GT, Bhat RG, Richardson PA, Kong P (2009) The avocado subgroup of Phytophthora citricola constitutes a distinct species, Phytophthora mengei sp nov. Mycologia 101:833–840. https://doi.org/10.3852/08-214

    Article  CAS  PubMed  Google Scholar 

  48. Farhana MDSN, Rahamah Bivi M, Khairulmazmi A, Wong SK, Sariah M (2013) Morphological and molecular characterization of Phytophthora capsici, the causal agent of foot rot disease of black pepper in Sarawak, Malaysia. Int J Agric Biol 15:1083–1090

    Google Scholar 

  49. Yang X, Hong C (2018) Differential usefulness of nine commonly used genetic markers for identifying Phytophthora species. Front Microbiol 9:2334. https://doi.org/10.3389/fmicb.2018.02334

    Article  PubMed  PubMed Central  Google Scholar 

  50. Nieto Feliner G, Rosselló JA (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol 44(2):911–919. https://doi.org/10.1016/j.ympev.2007.01.013

    Article  CAS  PubMed  Google Scholar 

  51. Abad ZG, Ivors KL, Gallup CA, Abad JA, Shew HD (2011) Morphological and molecular characterization of Phytophthora glovera sp. nov. from tobacco in Brazil. Mycologia 103(2):341–350. https://doi.org/10.3852/09-157

    Article  PubMed  Google Scholar 

  52. Robideau GP, de Cock AWAM, Coffey MD et al (2011) DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Mol Ecol Resour 11:1002–1011. https://doi.org/10.1111/j.1755-0998.2011.03041.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Rahman MZ, Uematsu S, Coffey MD, Uzuhashi S, Suga H, Kageyama K (2014) Re-evaluation of Japanese Phytophthora isolates based on molecular phylogenetic analyses. Mycoscience 55:314–327. https://doi.org/10.1016/j.myc.2013.11.005

    Article  CAS  Google Scholar 

  54. Ye W, Wang Y, Shen D, Li D, Pu T et al (2016) Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics. Mol Plant-Microbe Int 29:573–583. https://doi.org/10.1094/MPMI-03-16-0056-R

    Article  CAS  Google Scholar 

  55. Stamps DJ, Waterhouse GM, Newhook FJ, Hall GS (1990) Revised tabular key to the species of Phytophthora. Mycological papers No. 162, CAB International, Wallingford Oxon, UK

  56. Jeevalatha A, Biju CN, Bhai RS (2021) Ypt1 gene-based recombinase polymerase amplification assay for Phytophthora capsici and P. tropicalis detection in black pepper. Eur J Plant Pathol 159:863–875. https://doi.org/10.1007/s10658-021-02211-0

    Article  CAS  Google Scholar 

  57. Dung PN, Cuong HV, Tuat NV, Matsumoto M (2014) Analysis of internal transcribed spacer (ITS) region of Phytophthora tropicalis causing quick wilt disease of black pepper in Vietnam. Arch Phytopathol Plant Prot 47(7):842–851. https://doi.org/10.1080/03235408.2013.823713

    Article  Google Scholar 

  58. Storey DB (2014) World wide diversity of Phytophthora capsici. PhD dissertation, University of Tennessee, USA. https://trace.tennessee.edu/utk_graddiss/2862

Download references

Funding

The authors received funding from ICAR, New Delhi through an outreach project—PHYTOFURA (F. No.16–2/08/outreach-PP).

Author information

Authors and Affiliations

  1. Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, Kerala, 673012, India

    R. Suseela Bhai, A. Jeevalatha, C. N. Biju, K. B. Vinitha, Jose Cissin, O. B. Rosana, A. Fayad, R. Praveena, M. Anandaraj & Santhosh J. Eapen

Authors
  1. R. Suseela Bhai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. Jeevalatha
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. C. N. Biju
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. K. B. Vinitha
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jose Cissin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. O. B. Rosana
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. A. Fayad
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. R. Praveena
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. M. Anandaraj
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Santhosh J. Eapen
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization: M. Anandaraj, Santhosh J. Eapen; methodology: R. Suseela Bhai, Santhosh J. Eapen; formal analysis and investigation: A. Jeevalatha, C. N. Biju, K. B. Vinitha, Cissin Jose, O. B. Rosana, A. Fayad; writing—original draft preparation: R. Suseela Bhai; writing—review and editing: A. Jeevalatha, Santhosh J. Eapen; funding acquisition: M. Anandaraj; resources: R. Praveena, Santhosh J. Eapen; supervision: M. Anandaraj, Santhosh J. Eapen.

Corresponding author

Correspondence to Santhosh J. Eapen.

Ethics declarations

Ethics approval

This article does not contain any experiments with human participants or animals.

Consent to participate

All authors agreed with the content and that all gave explicit consent to submit and obtained consent from the institute/organization where the work has been carried out.

Consent for publication

All authors have read very carefully and approved the current version of this manuscript.

Competing interests

The authors declare no competing interests.

Additional information

Responsible Editor: Luiz Henrique Rosa

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 46 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bhai, R.S., Jeevalatha, A., Biju, C.N. et al. Sympatric occurrence of sibling Phytophthora species associated with foot rot disease of black pepper in India. Braz J Microbiol 53, 801–818 (2022). https://doi.org/10.1007/s42770-022-00716-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s42770-022-00716-2

Keywords

Search

Navigation