Bioprospecting of Endophytic Microbes from Higher Altitude Plants: Recent Advances and Their Biotechnological Applications

  • Vinay Kumar
  • Lata Jain
  • Ravindra Soni
  • Pankaj Kaushal
  • Reeta Goel
Part of the Rhizosphere Biology book series (RHBIO)


Endophytes are plant beneficial microbes that inhabit inside the plants and can enhance plant growth and development and tolerance to various biotic and abiotic stresses. Endophytes ubiquitously present in almost all the plant species grown worldwide and these microbes are known to provide direct benefits to the host plant by improving nutrient uptake by plant and controlling plant growth by synthesis of phytoharmones. In addition, they also produces wide range of natural compounds namely antibiotics, hydrolytic enzymes, peptides, alkaloids, etc. These novel compounds/metabolites can be prospective candidates for agriculture and pharmaceutical industries. In this chapter, efforts were made to comprehend the microbial diversity at high altitude plants and their functional traits in the plant hosts with regard to their significance and impacts on environment and humans.


Bioprospecting Endophytes Enzymes Secondary metabolites Himalayan region 


  1. Abdalla MA, Matasyoh JC (2014) Endophytes as producers of peptides: an overview about the recently discovered peptides from endophytic microbes. Nat Prod Bioprospect 4:257–270PubMedPubMedCentralCrossRefGoogle Scholar
  2. Afzal I, Chinaware ZK, Sikandar S, Shahzad S (2019) Plant beneficial endophytic bacteria: mechanisms, diversity, host range and genetic determinants. Microbiol Res 221:36–49PubMedCrossRefGoogle Scholar
  3. Alonso-Amelot ME (2008) High altitude plants, chemistry of acclimation and adaptation. Stud Nat Prod Chem 34:883–982CrossRefGoogle Scholar
  4. Alvin A, Kristin I, Miller B, Neilan A (2014) Exploring the potential of endophytes from medicinal plants as sources of antimycobacterial compounds. Microbiol Res 169:483–495PubMedCrossRefGoogle Scholar
  5. Bacon CW, White JF (2000) Microbial endophytes. Marcel Dekker Inc., New YorkGoogle Scholar
  6. Bagyalakshmi, Thalavaipandian A, Ramesh V, Rajendran A (2012) A novel endophytic fungus Pestalotiopsis sp inhabiting Pinus canerensis with antibacterial and antifungal potential. Int J Adv Life Sci 2012(1):1–7Google Scholar
  7. Berg G, Rybakova D, Grube M, Koberl M (2016) The plant microbiome explored: implications for experimental botany. J Exp Bot 67:995–1002. CrossRefPubMedGoogle Scholar
  8. Bhardwaj A, Sharma D, Jadon N, Agrawal PK (2015) Antimicrobial and phytochemical screening of endophytic fungi isolated from spikes of Pinus roxburghii. Arch Clin Microbiol 6(3):1–9Google Scholar
  9. Bischoff KM, Wicklow DT, Jordan DB et al (2009) Extracellular hemicellulolytic enzymes from the maize endophyte Acremonium zeae. Curr Microbiol 58(5):499–503PubMedCrossRefGoogle Scholar
  10. Cao X, Li J, Zhou L (2007) Determination of diosgenin content of the endophytic fungi from Paris polyphylla var. yunnanensis by using an optimum ELISA. Nat Prod Res Dev 19:1020–1023Google Scholar
  11. Chen X, Sang X, Li S, Zhang S, Bai L (2010) Studies on a chlorogenic acid-producing endophytic fungi isolated from Eucommia ulmoides Oliver. J Ind Microbiol Biotechnol 37:447–454PubMedCrossRefGoogle Scholar
  12. Chen B, Wang M, Hu Y, Lin Z, Yu R, Huang L (2011) Preliminary study on promoting effects of endophytic fungi to growth of Rehmannia glutinosa. Zhongguo Zhong Yao Za Zhi 36:1137–1140PubMedGoogle Scholar
  13. Chithra S, Jasim B, Sachidanandan P, Jyothis M, Radhakrishnan EK (2014) Piperine production by endophytic fungus Colletotrichum gloeosporioides isolated from Piper nigrum. Phytomedicine 21:534–540PubMedCrossRefGoogle Scholar
  14. Chowdhary K, Kaushik N (2015) Fungal endophyte diversity and bioactivity in the Indian medicinal plant Ocimum sanctum Linn. PLoS One 10(11):e0141444PubMedPubMedCentralCrossRefGoogle Scholar
  15. Christina A, Christapher V, Bhore SJ (2013) Endophytic bacteria as a source of novel antibiotics: an overview. Pharmacogn Rev 7(13):11–16PubMedPubMedCentralGoogle Scholar
  16. Cui Y, Yi D, Bai X, Sun B, Zhao Y, Zhang Y (2012) Ginkgolide B produced endophytic fungus (Fusarium oxysporum) isolated from Ginkgo biloba. Fitoterapia 83:913–920PubMedCrossRefGoogle Scholar
  17. Dash B, Soni R, Kumar V, Suyal DC, Dash D, Goel R (2019) Mycorrhizosphere: microbial interactions for sustainable agricultural production. In: Varma A, Choudhary DK (eds) Mycorrhizosphere and pedogenesis. Springer Nature, SingaporeGoogle Scholar
  18. Demain AL, Sanchez S (2009) Microbial drug discovery: 80 years of progress. J Antibiot 62:5–16PubMedCrossRefGoogle Scholar
  19. Deng BW, Liu KH, Chen WQ, Ding XW, Xie XC (2009) Fusarium solani, Tax-3, a new endophytic taxol-producing fungus from Taxus chinensis. World J Microbiol Biotechnol 25:139–143CrossRefGoogle Scholar
  20. Dhanya NN, Padmavathy S (2014) Impact of endophytic microorganisms on plants, environment and humans. Sci World J 2014:11. CrossRefGoogle Scholar
  21. Dunlap CA, Schisler DA, Bowman MJ, Rooney AP (2015) Genomic analysis of Bacillus subtilis OH 131.1 and coculturing with Cryptococcus flavescens for control of fusarium head blight. Plant Gene 2:1–9CrossRefGoogle Scholar
  22. Falardeau J, Wise C, Novitsky L, Avis TJ (2013) Ecological and mechanistic insights into the direct and indirect antimicrobial properties of Bacillus subtilis lipopeptides on plant pathogens. J Chem Ecol 39:869–878PubMedCrossRefGoogle Scholar
  23. Gherbawy YA, Elhariry HM (2014) Endophytic fungi associated with high-altitude Juniperus trees and their antimicrobial activities. Plant Biosyst 150:131. CrossRefGoogle Scholar
  24. Gherbawy YA, Elhariry HM (2016) Endophytic fungi associated with high-altitude Juniperus trees and their antimicrobial activities. Plant Biosyst Int J Dealing with all Aspects Plant Biolo 150(1):131–140CrossRefGoogle Scholar
  25. Godstime OC, Enwa FO, Augustina JO, Christopher EO (2014) Mechanisms of antimicrobial actions of phytochemicals against enteric pathogens—a review. J Pharm Chem Biol Sci 2:77–85Google Scholar
  26. Hallmann J, QuadtHallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43:895–914CrossRefGoogle Scholar
  27. Hanson T, Brooks TM, Da Fonseca GA, Hoffmann M, Lamoreux JF, Machlis G, Mittermeier CG, Mittermeier RA, Pilgrim JD (2009) Warfare in biodiversity hotspots. Conserv Biol 23:578–587PubMedCrossRefPubMedCentralGoogle Scholar
  28. Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16(10):463–471CrossRefGoogle Scholar
  29. Hardoim PR, Van Overbeek LS, Berg G, Maria A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320PubMedPubMedCentralCrossRefGoogle Scholar
  30. Jalgaonwala RE, Mohite BV, Mahajan RT (2011) Natural products from plant associated endophytic fungi. J Microbiol Biotechnol Res 1:21–32Google Scholar
  31. Kapoor N, Rajput P, Mushtaque MA, Gambhir L (2018) Bio-prospecting fungal endophytes of high altitude medicinal plants for commercially imperative enzymes. Biosci Biotech Res Comm 1(3):370–375Google Scholar
  32. Kaul S, Ahmed M, Zargar K, Sharma P, Dhar MK (2013) Prospecting endophytic fungal assemblage of Digitalis lanata Ehrh. (foxglove) as a novel source of digoxin: a cardiac glycoside. 3 Biotech 3(4):335–340PubMedCrossRefGoogle Scholar
  33. Kawaguchi M, Minamisawa K (2010) Plant–microbe communications for symbiosis. Plant Cell Physiol 51:1377–1380PubMedCrossRefGoogle Scholar
  34. Kim SU, Ford E (1999) Screening of taxol-producing endophytic fungi from Ginkgo biloba and Taxus cuspidata in Korea. Nat Prod Organic Chem 42:97–99Google Scholar
  35. Kloepper, J.W. and Ryu, C.M. (2006). Bacterial endophytes as elicitors of induced systemic resistance. Microbial root endophytes (Schulz BJE, Boyle CJC, Sieber TN, eds), pp. 33-52. Springer, BerlinCrossRefGoogle Scholar
  36. Knight CA, Bowman MJ, Fredericka L, Daye A, Leed C, Dunlapc CA (2018) The first report of antifungal lipopeptide production by a Bacillus subtilis subsp. inaquosorum strain. Microbiol Res 216:40–46PubMedCrossRefGoogle Scholar
  37. Kobayashi DY, Palumbo JD (2000) Bacterial endophytes and their effects on plants and uses in agriculture. In: Bacon CW, White JF (eds) Microbial endophytes. Marcel Dekker, Inc., New York, pp 199–233Google Scholar
  38. Kour A, Shawl AS, Rehman S, Sultan P, Qazi PH, Suden P et al (2008) Isolation and identification of an endophytic strain of Fusarium oxysporum producing podophyllotoxin from Juniperus recurva. World J Microbiol Biotech 24:115–1121CrossRefGoogle Scholar
  39. Kumar A, Verma JP (2018) Does plant—microbe interaction confer stress tolerance in plants: a review? Microbiol Res 207:41–52. CrossRefPubMedGoogle Scholar
  40. Kumar V, Soni R, Jain L, Dash B, Goel R (2019) Endophytic fungi: recent advances in identification and explorations. In: Singh BP (ed) Advances in endophytic fungal research, fungal biology. Springer Nature, Switzerland. CrossRefGoogle Scholar
  41. Kumaran RS, Muthumary J, Kim EK, Hur BK (2009) Production of taxol from Phyllosticta dioscoreae, a leaf spot fungus isolated from Hibiscus rosasinensis. Biotechnol Bioprocess Eng 14:76–83CrossRefGoogle Scholar
  42. Kusari S, Lamshöft M, Zühlke S, Spiteller M (2008) An endophytic fungus from Hypericum perforatum that produces hypericin. J Nat Prod 71:159–162PubMedCrossRefGoogle Scholar
  43. Kusari S, Hertweck C, Spiteller M (2012) Chemical ecology of endophytic fungi: origins of secondary metabolites. Chem Biol 19:792–798PubMedCrossRefGoogle Scholar
  44. Nagarajkumar M, Bhaskaran R, Velazhahan R (2004) Involvement of secondary metabolites and extracellular lytic enzymes produced by Pseudomonas fluorescens in inhibition of Rhizoctonia solani, the rice sheath blight pathogen. Microbiol Res 159:73–81PubMedCrossRefGoogle Scholar
  45. Ngumbi E, Kloepper J (2016) Bacterial-mediated drought tolerance: current and future prospects. Appl Soil Ecol 105:109–125CrossRefGoogle Scholar
  46. Nogales A, Nobre T, Valadas V, Ragonezi C, Goring M et al (2016) Can functional hologenomics aid tackling challenges in plant breeding? Brief Funct Genomics 15:288–197PubMedCrossRefGoogle Scholar
  47. Nongkhlaw FM, Joshi SR (2015) Investigation on the bioactivity of culturable endophytic and epiphytic bacteria associated with ethnomedicinal plants. J Infect Dev Ctries 9:954–961PubMedCrossRefGoogle Scholar
  48. Nter Brader G, Phane Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotechnol 27:30–37CrossRefGoogle Scholar
  49. Owen NL, Hundley N (2004) Endophytes e the chemical synthesizers inside plants. Sci Prog 87(2):79–99PubMedCrossRefPubMedCentralGoogle Scholar
  50. Pandey PK, Samanta R, Yadav RNS (2015) Plant beneficial endophytic bacteria from the ethnomedicinal Mussaenda roxburghii (Akshap) of eastern Himalayan Province, India. Adv Biol 2015:8. CrossRefGoogle Scholar
  51. Pandey A, Dhakar K, Jain R, Pandey N, Gupta VK, Kooliyottil R, Dhyani A, Malviya MK, Adhikari P (2018) Cold adapted fungi from Indian Himalaya: untapped source for bioprospecting. Proc Natl Acad Sci India Sect B Biol Sci 89:1125–1132. CrossRefGoogle Scholar
  52. Park JH, Choi GJ, Lee HB et al (2005) Griseofulvin from Xylaria sp. strain F0010, an endophytic fungus of Abies holophylla and its antifungal activity against plant pathogenic fungi. J Microbiol Biotechnol 15(1):112–117Google Scholar
  53. Petrini O (1991) Fungal endophytes of tree leaves. In: Andrews J, Hirano S (eds) Microbial ecology of leaves. Springer, New York, pp 179–197CrossRefGoogle Scholar
  54. Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SCM (2012) Hormonal modulation of plant immunity. Annu Rev Cell Dev Biol 28:489–521PubMedCrossRefPubMedCentralGoogle Scholar
  55. Porras-Alfaro A, Bayman P (2011) Hidden fungi, emergent properties: endophytes and microbiomes. Annu Rev Phytopathol 49:291–315PubMedCrossRefGoogle Scholar
  56. Powthong P, Jantrapanukorn B, Thongmee A, Suntornthiticharoen P (2012) Evaluation of endophytic fungi extract for their antimicrobial activity from Sesbania grandiflora (L.) Pers. Int J Biomed Pharma Res 3(2):132–136Google Scholar
  57. Qadri M, Johri S, Shah BA, Khajuria A, Sidiq T, Lattoo SK et al (2013) Identification and bioactive potential of endophytic fungi isolated from selected plants of the Western Himalayas. Springerplus 2:8PubMedPubMedCentralCrossRefGoogle Scholar
  58. Qiu M, Xie R, Shi Y, Zhang H, Chen H (2010) Isolation and identification of two flavonoid-producing endophytic fungi from Ginkgo biloba L. Ann Microbiol 60:143–115CrossRefGoogle Scholar
  59. Rai M, Rathod D, Agarkar G, Dar M, Brestic M, Pastore GM, Junior MRM (2014) Fungal growth promotor endophytes: a pragmatic approach towards sustainable food and agriculture. Symbiosis 62:63–79CrossRefGoogle Scholar
  60. Rehman S, Shawl A, Verma V, Kour A, Athar M, Andrabi R et al (2008) An endophytic Neurospora sp. from Nothapodytes foetida producing camptothecin. Prikl Biokhim Mikrobiol 44:225–231. CrossRefPubMedGoogle Scholar
  61. Riyaz-Ul-Hassan S, Strobel GA, Booth E, Knighton B, Floerchinger C, Sears J (2012) Modulation of volatile organic compound formation in the mycodiesel producing endophyte- Hypoxylon sp. C1-4. Microbiology 158:464–473Google Scholar
  62. Rodrigues AA, Araújo MVF, Soares Renan S, De Oliveira BFR, Ribeiro IG, Sibov ST, Vieira JDG (2018) Isolation and prospection of diazotrophic rhizobacteria associated with sugarcane under organic management. An Acad Bras Ciênc 90(4):3813–3829PubMedCrossRefGoogle Scholar
  63. Schulz B, Boyle C (2005) The endophytic continuum. Mycol Res 109:661–686PubMedCrossRefGoogle Scholar
  64. Schulz B, Boyle C, Draeger S, Rommert AK (2002) Endophytic fungi: a source of novel biologically active secondary metabolites. Mycol Res 106:996–1004CrossRefGoogle Scholar
  65. Shan W, Zhou Y, Liu H, Yu X (2018) Endophytic actinomycetes from tea plants (Camellia sinensis): isolation, abundance, antimicrobial, and plant-growth-promoting activities. Biomed Res Int 2018:1470305PubMedPubMedCentralGoogle Scholar
  66. Shweta S, Zuehlke S, Ramesha BT, Priti V, Kumar PM, Ravikanth G et al (2010) Endophytic fungal strains of Fusarium solani, from Apodytes dimidiata E. Mey. ex Arn (Lcacinaceae) produce camptothecin, 10-hydroxycamptothecin and 9-methoxycamptothecin. Phytochemistry 71:117–122PubMedCrossRefGoogle Scholar
  67. Singh D, Sharma A, Saini GK (2013) Biochemical and molecular characterisation of the bacterial endophytes from native sugarcane varieties of Himalayan region. 3 Biotech 3:205–212PubMedCrossRefGoogle Scholar
  68. Song YC, Huang WY, Sun C, Wang FW, Tan RX (2005) Characterization of graphislactone A as the antioxidant and free radical-scavenging substance from the culture of Cephalosporium sp. IFB-E001, an endophytic fungus in Trachelospermum jasminoides. Biol Pharm Bull 28(3):506–509PubMedCrossRefGoogle Scholar
  69. Stierle A, Strobel G, Stierle D (1993) Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew. Science 260:214–216PubMedCrossRefPubMedCentralGoogle Scholar
  70. Stierle A, Strobel G, Stierle D, Grothaus P, Bignami G (1995) The search for a taxol-producing microorganism among the endophytic fungi of the Pacific yew, Taxus brevifolia. J Nat Prod 58:1315–1324PubMedCrossRefPubMedCentralGoogle Scholar
  71. Strobel G (2006) Harnessing endophytes for industrial microbiology. Curr Opin Microbiol 9:240–244PubMedCrossRefPubMedCentralGoogle Scholar
  72. Strobel G, Daisy B (2003) Bioprospecting for microbial endophytes and their natural products. Microbiol Mol Biol Rev 67:491–502. CrossRefPubMedPubMedCentralGoogle Scholar
  73. Strobel GA, Daisy BH, Castillo U, Harper J (2004) Natural products from endophytic microorganisms. J Nat Prod 67:257–268PubMedCrossRefGoogle Scholar
  74. Tan XM, Zhou Y, Zhou X, Xia X, Wei Y, He L, Tang H, Yu L (2018) Diversity and bioactive potential of culturable fungal endophytes of Dysosma versipellis; a rare medicinal plant endemic to China. Sci Rep 8:5929PubMedPubMedCentralCrossRefGoogle Scholar
  75. Tenguria RK, Khan FN, Quereshi S (2011) Endophytes e-mines of pharmacological therapeutics. World J Sci Technol 1(5):127–149Google Scholar
  76. Theis KR, Dhelly NM, Klassen JL, Brucker RM, Baines JF, Bosch TCG, Cryan JF, Gilbert SF, Goodnight CJ, Lloyd EA, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein SR (2016) Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. mSystems 1(2):e00028–e00016PubMedPubMedCentralCrossRefGoogle Scholar
  77. Ulloa-Ogaz AL, Munoz-Castellanos LN, Nevarez-Moorillon GV (2015) Biocontrol of phytopathogens: antibiotic production as mechanism of control, the battle against microbial pathogens. In: Mendez Vilas A (ed) Basic science, technological advance and educational programs, vol 1. Formatex Research Center, pp 305–309Google Scholar
  78. Van Oosten VR, Bodenhausen N, Reymond P, Van Pelt JA, Van Loon LC, Dicke M, Pieterse CMJ (2008) Differential effectiveness of microbially induced resistance against herbivorous insects in Arabidopsis. Mol Plant Microbe Interact 21:919–930PubMedCrossRefGoogle Scholar
  79. van Opstal EJ, Bordenstein SR (2015) Rethinking heritability of the microbiome. Science 349:1172–1173PubMedCrossRefGoogle Scholar
  80. Vanittanakom N, Loeffler W, Koch U, Jung G (1986) Fengycin-a novel antifungal lipopeptide antibiotic produced by Bacillus subtilis F-29-3. J Antibiot 39:888–901PubMedCrossRefGoogle Scholar
  81. Verma P, Yadav AN, Kazy SK, Kumar S, Saxena A, Suman A (2015) Alleviation of cold stress in wheat seedlings by Bacillus amyloliquefaciens IARI-HHS2-30, an endophytic psychrotolerant K-solubilizing bacterium from NW Indian Himalayas. Natl J Life Sci 12(2):105–110Google Scholar
  82. Vimal SR, Singh JS, Arora NK, Singh S (2017) Soil-plant-microbe interactions in stressed agriculture management: a review. Pedosphere 27(2):177–192CrossRefGoogle Scholar
  83. Yadav M, Yadav A, Kumar S, Yadav JP (2016) Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains. BMC Microbiol 16:44PubMedPubMedCentralCrossRefGoogle Scholar
  84. Yang X, Guo S, Zhang L, Shao H (2003) Select of producing podophyllotoxin endophytic fungi from podophyllin plant. Nat Prod Res Dev 5:419–422Google Scholar
  85. Zeng S, Shao H, Zhang L (2004) An endophytic fungus producing a substance analogous to podophyllotoxin isolated from Diphylleia sinensis. J Microbiol 24:1–2Google Scholar
  86. Zhang P, Zhou PP, Yu LJ (2009) An endophytic taxol-producing fungus from Taxus media, Cladosporium cladosporioides MD2. Curr Microbiol 59:227–232PubMedCrossRefGoogle Scholar
  87. Zhao J, Fu Y, Luo M, Zu Y, Wang W, Zhao C et al (2012) Endophytic fungi from pigeon pea [Cajanus cajan (L.) Millsp.] produce antioxidant cajaninstilbene acid. J Agric Food Chem 60:4314–4319PubMedCrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  • Vinay Kumar
    • 1
  • Lata Jain
    • 1
  • Ravindra Soni
    • 2
  • Pankaj Kaushal
    • 1
  • Reeta Goel
    • 3
  1. 1.ICAR-National Institute of Biotic Stress Management, BarondaRaipurIndia
  2. 2.Department of Agril. MicrobiologyIndira Gandhi Krishi Vishwavidyalaya (IGKV)RaipurIndia
  3. 3.Department of MicrobiologyG. B. Pant University of Agriculture and TechnologyPantnagarIndia

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