Annals of Microbiology

, Volume 65, Issue 2, pp 785–797 | Cite as

Molecular profiling of fungal assemblages in the healthy and infected roots of Decalepis arayalpathra (J. Joseph & V. Chandras) Venter, an endemic and endangered ethnomedicinal plant from Western Ghats, India

  • Kandasamy Premalatha
  • Sivaraman Gokul
  • Amit Kumar
  • Priyanka Mishra
  • Pooja Mishra
  • Kaliamoorthy Ravikumar
  • Alok Kalra
Original Article
First Online:
Received:
Accepted:

Abstract

Decalepis arayalpathra, an endangered, endemic ethnomedicinal plant from southern Western Ghats, India, is targeted for its aromatic and medicinal properties. This study aimed at to identify fungal endophyte populations associated with healthy and diseased roots of this perennial shrub. Healthy and rotted root samples of D. arayalpathra were collected, fungal endophytes assemblages were identified both by culture-dependent and culture-independent approaches, further sequenced and the retrieved sequences were analysed with the reference sequences in GenBank to know their phylogenetic relationships. Analysis of the ITS rDNA region generated 24 different Ascomycota and three Basidiomycota taxa. Trichoderma sp. was most abundant in healthy and diseased root samples, while Penicillium and Aspergillus were confined to healthy roots. Furthermore, Fusarium solani, Fusarium oxysporum and Mucor velutinosus were found to be the most frequent fungi identified from the rotted root samples, thus substantiated to be the cause for D. arayalpathra decline in the wild. Interestingly, the strains assigned to Fusarium sp. were isolated from diseased roots showing typical clearly visible symptoms, such as a severe brown discolouration on the taproot. Molecular profiling of all the pure fungal isolates, viz., Trichoderma, Penicillium, Aspergillus, Fusarium and Mucor, revealed high sequence similarities (≥ 98 %) to corresponding reference sequences. Sequencing of Trichoderma pure cultures isolated from healthy and diseased roots revealed sequence similarities to Trichoderma harzianum, T. hamatum, T. koningiopsis, T. asperellum, T. pubescens and Hypocrea sp. This confirms the morphological examinations, as Hypocrea is the teleomorph stage of Trichoderma sp. This study signifies the first work pertaining to the taxonomy of the fungal endophytic community of D. arayalpathra, and the results reported in this work may help to ascertain the cause of root rot disease often perceived in D. arayalpathra. Also, it could be useful to identify the promising endophytic communities against the root rot diseases occurring in D. arayalpathra.

Keywords

Decalepis arayalpathra Endophytes Root rot rDNA Phylogenetic analysis 
This is a preview of subscription content, log in to check access.

Notes

Acknowledgments

K. Premalatha gives thanks to the Director of CSIR-CIMAP, India for awarding the Quick Hire Scientist fellowship. The financial support from the Council of Scientific and Industrial Research (CSIR), New Delhi, India through the projects PMSI (BSC-0117) and ChemBiO (BSC-0203) is gratefully acknowledged. SG and KR thanks the Department of Science and Technology, Government of India and Tamil Nadu State Biodiversity authority/Principal Chief Conservator of Forests, Tamil Nadu Forest Department for permission to carry out research work in the wildlife sanctuary.

References

  1. Altschul SF, Gish W, Miller W, Myers E, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  2. Alvarez C, Barbosa GG, de Oliveira RVC, Morales BP, Wanke B, Lazéra MS (2013) Techniques for the detection of pathogenic Cryptococcus species in wood decay substrata and the evaluation of viability in stored samples. Mem Inst Oswaldo Cruz, Rio de Janeiro 108:126–129CrossRefGoogle Scholar
  3. Anonymous (2011) Tamil Nadu State Biodiversity Notification, Ministry of Environment and Forests, New Delhi, India. REGD. No. D.L-33004/99Google Scholar
  4. Ben Chobba I, Elleuch A, Ayadi I, Khannous L, Namsi A, Cerqueira F, Drira N, Gharsasllah N, Vallaeys T (2013) Fungal diversity in adult date palm (Phoenix dactylifera L.) revealed by culture-dependent and culture-independent approaches. J Zhejiang Univ Sci B (Biomed Biotechnol) in pressGoogle Scholar
  5. Cai L, Hyde KD, Taylor PWJ, Weir BS, Waller J, Abang MM, Zhang JZ, Yang YL, Phoulivong S, Liu ZY, Prihastuti H, Shivas RG, McKenzie EHC, Johnston PR (2009) A polyphasic approach for studying Colletotrichum. Fungal Divers 39:183–204Google Scholar
  6. Duong LM, Jeewon R, Lumyong S, Hyde KD (2006) DGGE coupled with ribosomal DNA phylogeneis reveal uncharacterized fungal phylotypes on living leaves of Magnolia lilifera. Fungal Divers 23:121–138Google Scholar
  7. Filion M, Hamelin RC, Bernier L, St-Arnaud M (2004) Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery. Appl Environ Microbiol 70:3541–3551CrossRefPubMedCentralPubMedGoogle Scholar
  8. Fitton M, Holliday P (1970) “Myrothecium roridum,” In: Commonwealth Mycological Institute. Descriptions of Pathogenic Fungi and Bacteria, No. 253, Commonwealth Agricultural Bureau, Kew, pp 1–2Google Scholar
  9. Gao XX, Zhou H, Xu DY, Yu CH, Chen YQ, Qu LH (2005) High diversity of endophytic fungi from the pharmaceutical plant, Heterosmilax japonica Kunth revealed by cultivation-independent approach. FEMS Microbiol Lett 249:255–266CrossRefPubMedGoogle Scholar
  10. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118CrossRefPubMedGoogle Scholar
  11. Gong LJ, Guo SX (2009) Endophytic fungi from Dracaena cambodiana and Aquilaria sinensis and their antimicrobial activity. Afr J Biotechnol 8:731–736Google Scholar
  12. Halleen F, Mostert L, Crous PW (2007) Pathogenicity testing of lesser-known vascular fungi of grapevines. Australas Plant Pathol 36:277–285CrossRefGoogle Scholar
  13. Hofstetter V, Bart B, Daniel C, Olivier V, Arnaud C, Katia G (2012) What if esca disease of grapevine were not a fungal disease? Fungal Divers 54:51–67CrossRefGoogle Scholar
  14. Jebaraj CS, Raghukumar C, Behnke A, Stoeck T (2010) Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiol Ecol 71:399–412CrossRefPubMedGoogle Scholar
  15. Joseph J, Chandrasekaran V (1978) Janakia arayalpathra—a new genus and species of Periplocaceae from Kerala, South India. J Indian Bot Soc 57:308–312Google Scholar
  16. Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56:211–236CrossRefPubMedGoogle Scholar
  17. Lazéra MS, Cavalcanti MAS, Londero AT, Trilles L, Nishikawa MM, Wanke B (2000) Possible primary ecological niche of Cryptococcus neoformans. Med Mycol 38:379–383CrossRefPubMedGoogle Scholar
  18. Lutz MP, Feichtinger G, Defago G, Duffy B (2003) Mycotoxigenic Fusarium and deoxynivalenol production repress chitinase gene expression in the biocontrol agent Trichoderma atroviride P1. Appl Environ Microbiol 69:3077–3084CrossRefPubMedCentralPubMedGoogle Scholar
  19. Molur S, Walker (1997) Report on Conservation Assessment and Management Plan (CAMP) workshop for selected species of medicinal plants of southern India, Bangalore, 16–18, pp 108Google Scholar
  20. Naik BS, Shashikala J, Krishnamurthy YL (2008) Diversity of fungal endophytes in shrubby medicinal plants of Malnad region, Western Ghats, Southern India. Fungal Ecol 1:89–93CrossRefGoogle Scholar
  21. O’Donnell K, Cigelnik E, Nirenberg HI (1998) Molecular systematic and phylogeography of the Gibberella fujikuroi species complex. Mycologia 90:465–493CrossRefGoogle Scholar
  22. Prabakaran V, Ravikumar K (2003) Revisiting Janakia arayalpathra. Newsl MPCA MAPPA 3(1)Google Scholar
  23. Prabakaran V, Ravikumar K, Vijayasankar R (2001) Janakia arayalpathra–the quest. Amruth 5(5)Google Scholar
  24. Premalatha K, Kalra A (2013) Molecular phylogenetic identification of endophytic fungi isolated from resinous and healthy wood of Aquilaria malaccensis, a red listed and highly exploited medicinal tree. Fungal Ecol 6:205–211CrossRefGoogle Scholar
  25. Pushpangadan P, Rajasekaran S, Ratheesh Kumar PK, Jawahar CR, Radhakrishnan K, Nair CPR, Sarada Amma L, Bhat AV (1990) ‘AMRITHAPALA’ (Janakia arayalpathra, Joseph, Chandrasekaran), a new drug from the Kani Tribe of Kerala. Anc Sci Life 9:121Google Scholar
  26. Ravikumar K, Ved DK (2000) Illustrated field guide to 100 red listed medicinal plants of conservation concern in southern India. FRLHT, Bangalore, pp 383–386Google Scholar
  27. Rivera-Orduña FN, Roberto SA, Zoila FR, Jorge GN, Luis FB (2011) Diversity of endophytic fungi of Taxus globosa (Mexican yew). Fungal Divers 47:65–74CrossRefGoogle Scholar
  28. Sharma P (2011) Complexity of Trichoderma-Fusarium interaction and manifestation of biological control. Aust J Crop Sci 5:1027–1038Google Scholar
  29. Shine VJ, Shyamal S, Latha PG, Rajasekharan S (2007) Gastric antisecretory and antiulcer activities of Decalepis arayalpathra. Pharm Biol 45:210–216CrossRefGoogle Scholar
  30. Sudha CG, Seeni S (2001) Establishment and analysis of fast-growing normal root culture of Decalepis arayalpathra, a rare endemic medicinal plant. Curr Sci 81:371–374Google Scholar
  31. Summerell BA, Leslie JF (2011) Fifty years of Fusa-rium: how could nine species have ever been enough? Fungal Divers 50:135–144CrossRefGoogle Scholar
  32. Suryanarayanan TS, Vijaykrishna D (2001) Fungal endophytes of aerial roots of Ficus. Fungal Divers 8:155–161Google Scholar
  33. Venter HJT, Verhoeven RL (1997) A tribal classification of the Periplocoideae (Asclepiadaceae). Taxon 46:705–720CrossRefGoogle Scholar
  34. Wang Y, Guo LD, Hyde KD (2005) Taxonomic placement of sterile morphotypes of endophytic fungi from Pinus tabulaeformis (Pinaceae) in northeast China based on rDNA sequences. Fungal Divers 20:235–260Google Scholar
  35. Wiyakrutta S, Sriubolmas N, Panphut W, Thongon N, Danwisetkanjana K, Ruangrungsi N, Meevootisom V (2004) Endophytic fungi with anti-microbial, anti-cancer and anti- malarial activities isolated from Thai medicinal plants. World J Microbiol Biotechnol 20:265–272CrossRefGoogle Scholar
  36. Worapong J, Sun J, Newcombe G (2009) First report of Myrothecium roridum from a Gymnosperm. N Am Fungi 4:1–6CrossRefGoogle Scholar
  37. Xu L, Zhou L, Zhao J, Li J, Li X, Wang J (2008) Fungal endophytes from Dioscorea zingiberensis rhizomes and their antibacterial activity. Lett Appl Microbiol 46:68–72CrossRefPubMedGoogle Scholar
  38. Yang CH, Crowley DE, Menge JA (2001) 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots. FEMS Microbiol Ecol 35:129–136CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg and the University of Milan 2014

Authors and Affiliations

  • Kandasamy Premalatha
    • 1
  • Sivaraman Gokul
    • 3
  • Amit Kumar
    • 2
  • Priyanka Mishra
    • 2
  • Pooja Mishra
    • 1
  • Kaliamoorthy Ravikumar
    • 3
  • Alok Kalra
    • 1
  1. 1.Department of Microbial Technology and EntomologyCSIR–Central Institute of Medicinal and Aromatic PlantsLucknowIndia
  2. 2.Department of Plant Biology and SystematicsCSIR–Central Institute of Medicinal and Aromatic Plants Research CentreBangaloreIndia
  3. 3.School for Conservation of Natural ResourcesRepository for Medicinal Resources I-AIM (FRLHT)BangaloreIndia

Personalised recommendations