Endophytic Fungi: Diversity, Abundance, and Plant Growth-Promoting Attributes

  • Shimaa Mohsen El Mansy
  • Fatma Ahmed Abo Nouh
  • Mariam Khaled Mousa
  • Ahmed M. Abdel-Azeem
Part of the Fungal Biology book series (FUNGBIO)


Endophytes are ubiquitous in the plant world; no report of a plant species not associated with them is known; all plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 years of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups, Clavicipitaceous C and nonclavicipitaceous NC have been discriminated based on phylogeny and life history traits. The NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts, and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology. Fungal endophytes recovered from plants in terrestrial (agroecosystems and natural) ecosystems ranking from tropical and subtropical, grasslands and savannahs,croplands, hot desert, temperate boreal, tundra, Arctic/Antarctic biomes, alpine, xeric environments, aquatic ecosystems and mangroves.


Diversity Fungal endophyte Clavicipitaceous Nonclavicipitaceous Plant growth promoting 


  1. Abd-El-Khair H, Khalifa R, Haggag KHE (2010) Effect of Trichoderma species on damping off diseases incidence, some plant enzymes activity and nutritional status of bean plants. J Am Sci 6:147–159Google Scholar
  2. Abdel-Azeem AM (2020) Recent developments on genus Chaetomium. Springer, SwitzerlandGoogle Scholar
  3. Abdel-Azeem AM, Zaki SM, Khalil WF, Makhlouf NA, Farghaly LM (2016) Anti-rheumatoid activity of secondary metabolites produced by endophytic Chaetomium globosum. Front Microbiol 7(1477):1–11Google Scholar
  4. Abdel-Azeem AM, Omran MA, Mohamed RA (2018) Evaluation of the curative probability of bioactive metabolites from endophytic fungi isolated from some medicinal plants against paracetamol-induced liver injury in mice. LAP LAMBERT Academic PublishingGoogle Scholar
  5. Abdel-Azeem AM, Abdel-Azeem MA, Khalil WF (2019) Endophytic fungi as a new source of antirheumatoid metabolites. In Watson RR, Preedy VR (eds) Bioactive food as dietary interventions for arthritis and related inflammatory diseases. Elsevier, Amsterdam, pp 355–384.
  6. Abo Nahas HH (2019) Endophytic fungi: A gold mine of antioxidants. Microbiol Biosyst 4(1):58–79Google Scholar
  7. Abo Nouh FA (2019) Endophytic fungi for sustainable agriculture. Microbiol Biosyst 4:31–44Google Scholar
  8. Ali AH, Radwan U, El-Zayat S, El-Sayed MA (2018) Desert plant-fungal endophytic association: the beneficial aspects to their hosts. Biol Forum 10:138–145Google Scholar
  9. Allegrucci N, Velazquez MS, Russo ML, Perez E, Scorsetti AC (2017) Endophytic colonisation of tomato by the entomopathogenic fungus Beauveria bassiana: the use of different inoculation techniques and their effects on the tomato leaf miner Tuta absoluta (Lepidoptera: Gelechiidae). J Plant Prot Res 57:205–211Google Scholar
  10. Anitha D, Vijaya T, Pragathi D, Reddy NV, Mouli KC, Venkateswarulu N, Bhargav DS (2013) Isolation and characterization of endophytic fungi from endemic medicinal plants of Tirumala Hills. Int J Life Sci Biotechn Pharm 2:367–373Google Scholar
  11. Anuar EN, Nulit R, Idris AS (2015) Growth promoting effects of endophytic fungus Phlebia GanoEF3 on oil palm (Elaeis guineensis) seedlings. Int J Agric Biol 17:135–141Google Scholar
  12. Arnold AE (2008) Endophytic fungi: hidden components of tropical community ecology. In: Schnitzer S, Carson W (eds) Tropical forest community ecology. Malden, MA, USA: Blackwell Scientific, Inc., pp 254–271Google Scholar
  13. Arnold AE, Herre EA (2003) Canopy cover and leaf age affect colonization by tropical fungal endophytes: ecological pattern and process in Theobroma cacao (Malvaceae). Mycologia 95:388–398PubMedGoogle Scholar
  14. Arnold AE, Lutzoni F (2007) Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88:541–549PubMedGoogle Scholar
  15. Arnold AE, Maynard Z, Gilbert GS, Coley PD, Kursar TA (2000) Are tropical fungal endophytes hyperdiverse? Ecol Lett 3:267–274Google Scholar
  16. Arnold EA, Mejia LC, Kyllo D, Rojas E, Maynard Z, Robbins N, Herre EA (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci U S A 100:15649–15654PubMedPubMedCentralGoogle Scholar
  17. Arnold AE, Henk DA, Eells RL, Lutzoni F, Vilgalys R (2007) Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99:185–206PubMedGoogle Scholar
  18. Arnold AE, Miadlikowska J, Higgins KL, Sarvate SD, Gugger P, Way A, Hofstetter V, Kauff F, Lutzoni F (2009) A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Syst Biol 58:283–297PubMedGoogle Scholar
  19. Arora J, Ramawat KG (2017) An introduction to endophytes. In: Maheshwari DK (ed) Endophytes: biology and biotechnology, sustainable development and biodiversity 15. Springer, Cham, pp 1–16. Scholar
  20. Bacon CW, Hill NS (1996) Symptomless grass endophytes: products of coevolutionary symbioses and their role in the ecological adaptations of grasses. In: Redkin SC, Carris LM (eds) Endophytic fungi in grasses and woody plants. APS Press, St Paul, pp 155–178Google Scholar
  21. Bacon CW, White JFJ (2000) Physiological adaptations in the evolution of endophytism in the Clavicipitaceae. In: Bacon CW, White JFJ (eds) Microbial endophytes. Marcel Dekker Inc, New York, pp 237–263Google Scholar
  22. Bacon CW, Porter JK, Robbins JD, Luttrell ES (1977) Epichloë typhina from toxic tall fescue grasses. Appl Environ Microbiol 34:576–581PubMedPubMedCentralGoogle Scholar
  23. Barazani O, Benderoth M, Groten K, Kuhlemeier C, Baldwin IT (2005) Piriformospora indica and Sebacina vermifera increase growth performance at the expense of herbivore resistance in Nicotiana attenuata. Oecologia 146:234–243PubMedGoogle Scholar
  24. Berardo C, Bulai IM, Baptista P, Gomes T, Venturino E (2018) Modeling the endophytic fungus Epicoccum nigrum action to fight the “olive knot” disease caused by Pseudomonas savastanoi pv. savastanoi (Psv) bacteriain Olea europaea L. trees. In: Mondaini RP (ed) Trends in biomathematics: modeling, optimization and computational problems. Springer International Publishing AG, Cham, pp 189–207Google Scholar
  25. Bischoff JF, White JR (2005) Evolutionary development of the clavicipitaceae. In: Dighton J, White JF, Oudemans P (eds) The fungal community: its organization and role in the ecosystem. Taylor and Francis, Boca Raton, pp 505–518Google Scholar
  26. Bultman TL, White JF (1988) “Pollination” of a fungus by a fly. Oecologia 75:317–319Google Scholar
  27. Campanile G, Ruscelli A, Luisi N (2007) Antagonistic activity of endophytic fungi towards Diplodia corticola assessed by in vitro and in planta tests. Eur J Plant Pathol 117:237–246Google Scholar
  28. Carroll G (1988) Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology 69:2–9Google Scholar
  29. Chadha N, Mishra M, Prasad R (2014) Root endophytic fungi: research update. J Biol Life Sci 5:135–158Google Scholar
  30. Chadha N, Prasad R, Varma A (2015) Plant promoting activities of fungal endophytes associated with tomato roots from central Himalaya, India and their interaction with Piriformospora indica. Int J Pharm Bio Sci 6:333–343Google Scholar
  31. Chhipa H, Deshmukh SK (2019) Fungal endophytes: rising tools in sustainable agriculture production. In: Jha S (ed) Endophytes and secondary metabolites. Springer International Publishing AG, Cham, pp 1–24Google Scholar
  32. Chung KR, Schardl CL (1997) Sexual cycle and horizontal transmission of the grass symbiont, Epichloe typhina. Mycol Res 101:295–301Google Scholar
  33. Clay K (1988) Fungal endophytes of grasses: a defensive mutualism between plants and fungi. Ecology 69:10–16Google Scholar
  34. Clay K (1990) Fungal endophytes of grasses. Annu Rev Ecol Syst 21:275–297Google Scholar
  35. Clay K, Schardl CL (2002) Evolutionary origins and ecological consequences of endophyte symbiosis with grasses. Am Nat 160:S99–S127PubMedGoogle Scholar
  36. Currah RS, Van Dyk M (1986) A survey of some perennial vascular plant species native to Alberta for occurrence of mycorrhizal fungi. Can Field-Nat 100:330–342Google Scholar
  37. Dai CC, Yu BY, Li X (2008) Screening of endophytic fungi that promote the growth of Euphorbia pekinensis. Afr J Biotechnol 7:3505–3510Google Scholar
  38. Danielsen S, Jensen DF (1999) Fungal endophytes from stalks of tropical maize and grasses: isolation, identification, and screening for antagonism against Fusarium verticillioides in maize stalks. Biocontrol Sci Tech 9:545–553Google Scholar
  39. De Bary A (1879) Die Erscheinung der Symbiose. In: Trubner KJ (ed) Vortrag auf der Versammlung der Naturforscher und Ärtze zu Cassel. Verlag von K. J. Trubner, Strassburg, pp 1–30Google Scholar
  40. De Battista JP, Bacon CW, Severson R, Plattner RD, Bouton JH (1990) Indole acetic acid production by the fungal endophyte of tall fescue. Agron J 82:878–880Google Scholar
  41. De Cal A, Larena I, Linan M, Torres R, Lamarca N et al (2009) Population dynamics of Epicoccum nigrum, a biocontrol agent against brown rot in stone fruit. J Appl Microbiol 106:592–605PubMedGoogle Scholar
  42. de Paula TJ, Rotter C, Han B (2001) Effect of soil moisture and panting date on Rhizoctonia root rot of beans and its control by Trichoderma harzianum. Bull OILB/SROP 24:99–10Google Scholar
  43. Doley P, Jha DK (2010) Endophytic fungal assemblages from ethnomedicinal plant Rauwolfia serpentina (L) Benth. J Plant Pathol Microbiol 40:44–48Google Scholar
  44. Dong S, Tian Z, Chen PJ, Kumar RS, Shen CH, Cai D, Oelmüller R, Yeh KW (2013) The maturation zone is an important target of Piriformospora indica in Chinese cabbage roots. J Exp Bot 64:4529–4540PubMedPubMedCentralGoogle Scholar
  45. El-Kafrawy AA (2002) Biological control of bean damping-off caused by Rhizoctonia solani. Egypt J Agric Res 80:57–70Google Scholar
  46. Ernst M, Mendgen KW, Wirsel SGR (2003) Endophytic fungal mutualists: seed-borne Stagonospora spp. enhance reed biomass production in axenic microcosms. Mol Plant-Microbe Interact 16:580–587PubMedGoogle Scholar
  47. Evans HC, Holmes KA, Thomas SE (2003) Endophytes and mycoparasites associated with an indigenous forest tree, Theobroma gileri, in Ecuador and a preliminary assessment of their potential as biocontrol agents of cocoa diseases. Mycol Prog 2:149–160Google Scholar
  48. Fakhro A, Andrade-Linares DR, von Bargen S, Bandte M, Büttner C, Grosch R, Schwarz D, Franken P (2010) Impact of Piriformospora indica on tomato growth and on interaction with fungal and viral pathogens. Mycorrhiza 20:191–200PubMedGoogle Scholar
  49. Fávaro LCDL, Sebastianes FLDS, Araujo WL (2012) Epicoccum nigrum P16, a sugarcane endophyte, produces antifungal compounds and induces root growth. PLoS One 7:1–10Google Scholar
  50. Feldman TS, O’Brien H, Arnold AE (2008) Moth dispersal of mycoparasites and endophytes associated with Claviceps paspali and the grass Paspalum (Poaceae). Microb Ecol 56: 742–750Google Scholar
  51. Fisher PJ, Petrini O (1992) Fungal saprobes and pathogens as endophytes of rice (Oryza sativa L). New Phytol 120:137–143Google Scholar
  52. Fouda AH, El-Din Hassan S, Eid AM, El-Din Ewais E (2015) Biotechnological applications of fungal endophytes associated with medicinal plant Asclepias sinaica (Bioss). Ann Agric Sci 60:95–104Google Scholar
  53. Franken P (2012) The plant strengthening root endophyte Piriformospora indica: potential application and biology behind. Appl Microbiol Biotechnol 96:1455–1464PubMedPubMedCentralGoogle Scholar
  54. Fröhlich J, Hyde KD (1999) Biodiversity of palm fungi in the tropics: are global fungal diversity estimates realistic? Biodivers Conserv 8:977–1004Google Scholar
  55. Funk CR, White JFJ (1997) Use of natural and transformed endophytes for turf improvement. In: Hill N, Bacon CW (eds) Endophyte/grass interactions. Plenum, New York, pp 229–239Google Scholar
  56. Gamboa MA, Bayman P (2001) Communities of endophytic fungi in leaves of a tropical timber tree (Guarea guidonia: Meliaceae). Biotropica 33:352–360Google Scholar
  57. Ganley RJ, Brunsfeld SJ, Newcombe G (2004) A community of unknown, endophytic fungi in western white pine. Proc Natl Acad Sci U S A 101:10107–10112PubMedPubMedCentralGoogle Scholar
  58. Gao KX, Mendgen K (2006) Seed-transmitted beneficial endophytic Stagonospora sp. can penetrate the walls of the root epidermis, but does not proliferate in the cortex, of Phragmites australis. Can J Bot 84:981–988Google Scholar
  59. Garbary DJ, Macdonald KA (1995) The Ascophyllum polysiphonia Mycosphaerella symbiosis. Mutualism in the Ascophyllum mycosphaerella interaction. Bot Mar 38:221–225Google Scholar
  60. Gasoni L, deGurfinkel BS (1997) The endophyte Cladorrhinum foecundissimum in cotton roots: phosphorus uptake and host growth. Mycol Res 101:867–870Google Scholar
  61. Gautam AK, Kant M, Thakur Y (2013) Isolation of endophytic fungi from Cannabis sativa and study their antifungal potential. Arch Phytopathol Plant Protect 46:627–635Google Scholar
  62. Girlanda M, Perotto S, Luppi AM (2006) Molecular diversity and ecological roles of mycorrrhiza-associated sterile fungal endophytes in Mediterranean ecosysems. In: Boyle CJC, Sieber TN (eds) Microbial root endophytes. Springer-Verlag, Berlin, pp 207–226Google Scholar
  63. Griffith GW, Hedger JN (1994) The breeding biology of biotypes of the witches’ broom pathogen of cacao, Crinipellis perniciosa. Heredity 72:278–289Google Scholar
  64. Guerin D (1898) Sur la presence d’un champignon dans l’lvraie. J Bot 12:230–238Google Scholar
  65. Gundel PE, Pérez LI, Helander M, Saikkonen K (2013a) Symbiotically modified organisms: non-toxic fungal endophytes in grasses. Trends Plant Sci 18:420–427PubMedGoogle Scholar
  66. Gundel PE, Helander M, Casas C, Hamilton CE, Faeth SH, Saikkonen K (2013b) Neotyphodium fungal endophyte in tall fescue (Schedonorus phoenix): a comparison of three northern European wild populations and the cultivar Kentucky-31. Fungal Divers 60:15–24Google Scholar
  67. Guo LD, Hyde KD, Liew ECY (2000) Identification of endophytic fungi from Livistona chinensis based on morphology and rDNA sequences. New Phytol 147:617630Google Scholar
  68. Guyot J, Omanda EM, Pinard F (2005) Some epidemiological investigations on Colletotrichum leaf disease on rubber tree. Crop Prot 24:65–77Google Scholar
  69. Halmschlager E, Butin H, Donaubauer E (1993) Endophytic fungi in leaves and twigs of Quercus petraea. Eur J Plant Pathol 23:51–63Google Scholar
  70. Hamayun M, Khan SA, Ahmad N, Khan AL, Rehman G, Sohn EY, Kim SK, Joo GJ, Lee I-J (2009a) Phoma herbarum as a new gibberellin producing and plant growth-promoting fungus. J Microbiol Biotechnol 19:1244–1249Google Scholar
  71. Hamayun M, Khan SA, Ahmad N, Tang DS, Kang SM, Sohn E-Y, Hwang YH, Shin DH, Lee BH, Kim JG, Lee I-J (2009b) Cladosporium sphaerospermum as a new plant growth promoting endophyte from the roots of Glycine max (L.) Merr. World J Microbiol Biotechnol 25:627–632Google Scholar
  72. Hamayun M, Khan SA, Khan MA, Khan AL, Kang SM, Kim SK, Joo GJ, Lee IJ (2009c) Gibberellin production by pure cultures of a new strain of Aspergillus fumigatus. World J Microbiol Biotechnol 25:1785–1792Google Scholar
  73. Hamayun M, Khan SA, Khan AL, Rehman G, Kim Y-H, Iqbal I, Hussain J, Sohn E-Y, Lee I-J (2010) Gibberllin production and plant growth promotion from pure cultures of Cladosporium sp.MH-6 isolated from cucumber (Cucumis sativus L.). Mycologia 102:989–995PubMedGoogle Scholar
  74. Hanausek TF (1898) Vorlaufige mittheilung uber den von a vogl in der frucht von lolium temulentum entdeckten pilz. Berichte der Deutschen Botanischen Gesellschaft 16:203Google Scholar
  75. Haran S, Schickler H, Chet I (1996) Molecular mechanisms of lytic enzymes involved in the biocontrol activity of Trichoderma harzianum. Microbiology 142:2321–2331Google Scholar
  76. Harper JL (1990) In: Burdon JJ, Leather SR (eds) Pests, pathogens and plant communities. Blackwell, Oxford, pp. 3Ð14Google Scholar
  77. Hasan HAH (2002) Gibberellin and auxin production by plant root fungi and their biosynthesis under salinity-calcium interaction. Rost Vyroba 48:101–106Google Scholar
  78. Hashem M, Ali E (2004) Epicoccum nigrum as biocontrol agent of Pythium damping-off and root-rot of cotton seedlings. Arch Phytopathol Plant Protect 37:283–297Google Scholar
  79. Hermosa R, Viterbo A, Chet I, Monte E, Monte E (2012) Plant-beneficial effects of Trichoderma and of its genes. Microbiology 158:17–25PubMedGoogle Scholar
  80. Herre EA, Bael SAV, Maynard Z, Robbins N, Bischoff J, Arnold AE, Rojas E, Mejía LC, Cordero RA, Woodward C, Kyllo DA (2005) Tropical plants as chimera: some implications of foliar endophytic fungi for the study of host plant defense, physiology, and genetics. In: Burslem DFRP, Pinard MA, Hartley SE (eds) Biotic interactions in the tropics. Cambridge University Press, Cambridge, pp 226–240Google Scholar
  81. Higgins KL, Arnold AE, Miadlikowska J, Sarvate SD, Lutzoni F (2007) Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages. Mol Phylogenet Evol 42:543–555PubMedGoogle Scholar
  82. Hilszczańska D (2016) Endophytes – characteristics and possibilities of application in forest management. Leśne Prace Badawcze 77:276–282Google Scholar
  83. Hirsch G, Braun U (1992) Communities of parasitic microfungi. In: Winterhoff W (ed) Handbook of vegetative science, Fungi in vegetation science. Kluwer Academic Publishers, Dordrecht, pp 225–250Google Scholar
  84. Hoffman MT, Arnold AE (2008) Geographic locality and host identity shape fungal endophyte communities in cupressaceous trees. Mycol Res 112:331–344PubMedGoogle Scholar
  85. Holliday PA (1998) Dictionary of plant pathology. Cambridge University Press, CambridgeGoogle Scholar
  86. Holmes KA, Schroers H-J, Thomas SE, Evans HC, Samuels GJ (2004) Taxonomy and biocontrol potential of a new species of Trichoderma from the Amazon basin of South America. Mycol Prog 3:199–210Google Scholar
  87. Iannone LJ, Novas MV, Young CA, Battista JDE, Schardl CL (2012) Endophytes of native grasses from South America: biodiversity and ecology. Fungal Ecol 5:357–363Google Scholar
  88. Jain P, Pundir RK (2017) Potential role of endophytes in sustainable agriculture-recent developments and future prospects. In: Maheshwari DK (ed) Endophytes: biology and biotechnology, sustainable development and biodiversity 15. Springer International Publishing AG, Cham, pp 145–160Google Scholar
  89. James TY, Kauff F, Schoch C, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J et al (2006) Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443:818–822PubMedGoogle Scholar
  90. Jiménez-Romero C, Ortega-Barria E, Arnold AE, Cubilla-Rios L (2008) Activity against Plasmodium falciparum of lactones isolated from the endophytic fungus Xylaria sp. Pharm Biol 46:1–4Google Scholar
  91. Johansson JF, Paul LR, Finlay RD (2004) Interactions in the mycorrhizosphere and their significance. for sustainable agriculture. FEMS Microbiol Ecol 48:1–13Google Scholar
  92. Johnson JM, Alex T, Oelmüller R (2014) Piriformospora indica: the versatile and multifunctional root endophytic fungus for enhanced yield and tolerance to biotic and abiotic stress in crop plants. J Trop Agric 52:103–122Google Scholar
  93. Jumpponen A (2001) Dark septate endophytes – are they mycorrhizal? Mycorrhiza 11:207–211Google Scholar
  94. Jumpponen A, Trappe JM (1998) Dark septate endophytes: a review of facultative biotrophic root colonizing fungi. New Phytol 140:295–310Google Scholar
  95. Kandar M, Suhandono S, Aryantha INP (2018) Growth promotion of rice plant by endophytic fungi. J Pure Appl Microbiol 12:1569–1577Google Scholar
  96. Kawaide H (2006) Biochemical and molecular analysis of gibberellins biosynthesis in fungi. Biosci Biotechnol Biochem 70:583–590PubMedGoogle Scholar
  97. Khan AL, Lee IJ (2013) Endophytic Penicillium funiculosum LHL06 secretes gibberellin that reprograms Glycine max L. growth during copper stress. BMC Plant Biol 13:86PubMedPubMedCentralGoogle Scholar
  98. Khan SA, Hamayun M, Yoon HJ, Kim H-Y, Suh SJ, Hwang SK, Kim JM, Lee I-J, Choo YS, Yoon UH, Kong WS, Lee BM, Kim JG (2008) Plant growth promotion and Penicillium citrinum. BMC Microbiol 8:231PubMedPubMedCentralGoogle Scholar
  99. Khan SA, Hamayun M, Kim HY, Yoon HJ, Lee IJ, Kim JG (2009b) Gibberellin production and plant growth promotion by a newly isolated strain of Gliomastix murorum. World J Microbiol Biotechnol 25:829–833Google Scholar
  100. Khan SA, Hamayun M, Kim HY, Yoon HJ, Seo JC, Choo YS, Lee I-J, Kim SD, Rhee IK, Kim JG (2009c) A new strain of Arthrinium phaeospermum isolated from Carex kobomugi Ohwi is capable of gibberellin production. Biotechnol Lett 31:283–287PubMedGoogle Scholar
  101. Khan AL, Hamayun M, Ahmad N, Waqas M, Kang SM, Kim YH, Lee IJ (2011) Exophiala sp. LHL08 reprograms Cucumis sativus to higher growth under abiotic stresses. Physiol Plant 143:329–343PubMedGoogle Scholar
  102. Khan AL, Hamayun M, Kim YH, Kang SM, Lee IJ (2011a) Ameliorative symbiosis of endophyte (Penicillium funiculosum LHL06) under salt stress elevated plant growth of Glycine max L. Plant Physiol Biochem 49:852–861PubMedGoogle Scholar
  103. Khan AL, Hamayun M, Kim YH, Kang SM, Lee JH, Lee IJ (2011b) Gibberellins producing endophytic Aspergillus fumigatus sp. LH02 influenced endogenous phytohormonal levels, isoflavonoids production and plant growth in salinity stress. Process Biochem 46:440–447Google Scholar
  104. Khan SA, Hamayun M, Khan AL, Lee IJ, Shinwari ZK, Kim JG (2012) Isolation of plant growth promoting endophytic fungi from dicots inhabiting coastals and dunes of Korea. Pak J Bot 44:1453–1460Google Scholar
  105. Khan AR, Ullah I, Waqas M, Shahzad R, Hong SJ, Park GS, Jung BK, Lee IJ, Shin JH (2015a) Plant growth-promoting potential of endophytic fungi isolated from Solanumnigrum leaves. World J Microbiol Biotechnol 31:1461–1466PubMedGoogle Scholar
  106. Khan AL, Hussain J, Al-Harrasi A, Al-Rawahi A, Lee IJ (2015b) Endophytic fungi: resource for gibberellins and crop abiotic stress resistance. Crit Rev Biotechnol 35:62–74PubMedGoogle Scholar
  107. Khare E, Mishra J, Arora NK (2018) Multifaceted interactions between endophytes and plant: developments and prospects. Front Microbiol 9:1–12Google Scholar
  108. Khiralla A, Spina R, Yagi S, Mohamed L, Laurain-Mattar D (2016) Endophytic fungi: occurrence, classification, function and natural products. In: Hughes E (ed) Endophytic fungi: diversity, characterization and biocontrol. Nova Science, New York, pp 1–19Google Scholar
  109. Kirk PM, Cannon PF, David JC, Stalpers JA (2001) Dictionary of the fungi. CABI Publishing, WallingfordGoogle Scholar
  110. Kithsiri Wijeratne EM, Paranagama PA, Marron MT, Gunatilaka MK, Arnold AE, Gunatilaka AAL (2008) Sesquiterpene quinines and related metabolites from Phyllosticta spinarum, a fungal strain endophytic in Platycladus orientalis in the Sonoran Desert. J Nat Prod 71:218–222Google Scholar
  111. Koroch A, Juliani H, Bischoff J, Lewis E, Bills G, Simon J, White JFJ (2004) Examination of plant biotrophy in the scale insect parasitizing fungus dussiella tuberiformis. Symbiosis 37:267–280Google Scholar
  112. Kour D, Rana KL, Yadav N, Yadav AN, Singh J, Rastegari AA, Saxena AK (2019) Agriculturally and industrially important fungi: current developments and potential biotechnological applications. In: Yadav AN, Singh S, Mishra S, Gupta A (eds) Recent advancement in white biotechnology through fungi. vol 2: Perspective for value-added products and environments, Springer International Publishing, Cham, pp 1–64. Scholar
  113. Kumar M, Yadav V, Tuteja N, Johri AK (2009) Antioxidant enzyme activities in maize plants colonized with Piriformospora indica. Microbiology 155:780–790PubMedGoogle Scholar
  114. Kumar M, Sharma R, Jogawat A, Singh P, Dua M, Gill SS, Trivedi DK, Tuteja N, Verma AK, Oelmuller R, Johri AK (2012) Piriformospora indica, a root endophytic fungus, enhances abiotic stress tolerance of the host plant. In: Tuteja N, Gill SS, Tiburcio AF, Tuteja R (eds) Improving crop resistance to abiotic stress. Wiley-Blackwell, Weinheim, pp 543–558Google Scholar
  115. 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 International Publishing AG, Cham, pp 267–281Google Scholar
  116. Kusari S, Spiteller M (2012) Metabolomics of endophytic fungi producing associated plant secondary metabolites: progress, challenges and opportunities. In: Roessner U (ed) Metabolomics. InTech, Rijeka, pp 241–266Google Scholar
  117. Lana TG, Azevedo JL, Pomella AWV, Monteiro RTR, Silva CB, Araujo WL (2011) Endophytic and pathogenic isolates of the cacao fungal pathogen Moniliophthora perniciosa (Tricholomataceae) are indistinguishable based on genetic and physiological analysis. Genet Mol Res 10:326–334Google Scholar
  118. Lata R, Chowdhury S, Gond S, White JF (2018) Induction of abiotic stress tolerance in plants by endophytic microbes. Appl Microbiol 66:268–276Google Scholar
  119. Lewis DH (1985) Symbiosis and mutualism: crisp concepts and soggy semantics. In: Boucher DH (ed) The biology of mutualism. Croom Helm Ltd, London, pp 29–39Google Scholar
  120. Li JY, StrobelGA SR, Hess WM, Ford E (1996) Endophytic taxol producing fungi from bald cypress Taxodium distichum. Microbiology 142:2223–2226PubMedGoogle Scholar
  121. Li JY, Strobel GA, Harper JK, Lobkovsky E, Clardy J (2000) Cryptocin, a potent tetramic acid antimycotic from the endophytic fungus Cryptosporiopsis quercina. Org Lett 2:767–770PubMedGoogle Scholar
  122. Li WC, Zhou J, Guo SY, Guo LD (2007) Endophytic fungi associated with lichens in Baihua mountain of Beijing, China. Fungal Divers 25:69–80Google Scholar
  123. Li X, Ren A, Han R, Yin L, Wei M, Gao Y (2012) Endophyte mediated effects on the growth and physiology of Achnatherum sibiricum are conditional on both N and P availability. PLoS One 7:e48010Google Scholar
  124. Lodge DJ, Fisher PJ, Sutton BC (1996) Endophytic fungi of Manilkara bidentata leaves in Puerto Rico. Mycologia 88:733–738Google Scholar
  125. Lopez-Llorca LV, Jansson H-B, Vicente JGM, Salinas J (2006) Nematophagous fungi as root endophytes. In: Schulz B, Boyle C, Sieber T (eds) Microbial root endophytes. Springer-Verlag, Berlin, pp 191–206Google Scholar
  126. Lugtenberg BJJ, Caradus JR, Johnson LJ (2016) Fungal endophytes for sustainable crop production. FEMS Microbiol Ecol 92:1–17Google Scholar
  127. Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E et al (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot 91:1446–1480PubMedGoogle Scholar
  128. Machungo C, Losenge T, Kahangi E, Coyne D, Dubois T, Kimenju J (2009) Effect of endophytic Fusarium oxysporum on growth of tissue-cultured Banana plants. Afr J Hort Sci 2:160–167Google Scholar
  129. Macia’-Vicente JG, Jansson HB, Samir K, Abdullah SK, Descals E, Salinas J, Lopez-Llorca LV (2008) Fungal root endophytes from natural vegetation in Mediterranean environments with special reference to Fusarium spp. FEMS Microbiol Ecol 64:90–105Google Scholar
  130. Mahmoud RS, Narisawa K (2013) A new fungal endophyte, Scolecobasidium humicola, promotes tomato growth under organic nitrogen conditions. PLoS One 8:e78746PubMedPubMedCentralGoogle Scholar
  131. Malla R, Prasad R, Kumari R, Giang PH, Pokharel U, Oelmüller R, Varma A (2004) Phosphorus solubilizing symbiotic fungus: Piriformospora indica. Endocytobiosis Cell Res 15:579–600Google Scholar
  132. Mandyam K, Jumpponen A (2005) Seeking the elusive function of the root-colonising dark septate endophyte. Stud Mycol 53:173–189Google Scholar
  133. Márquez LM, Redman RS, Rodriguez RJ, Roossinck MJ (2007) A virus in a fungus in a plant – three way symbiosis required for thermal tolerance. Science 315:513–515PubMedGoogle Scholar
  134. Merlin E (1922) On the mycorrhizas of Pinus sylvestris L. and Picea abies Karst. A preliminary note. J Ecol 9:254–257Google Scholar
  135. Monk KA, Samuels GJ (1990) Mycophagy in grasshoppers (Orthoptera, Acrididae) in Indo-Malayan rain forest. Biotropica 22:16–21Google Scholar
  136. Moon C, Miles C, Jarlfors U, Schardl CL (2002) The evolutionary origins of three new Neotyphodium endophyte species in grasses indigenous to the southern hemisphere. Mycologia 94:694–711PubMedGoogle Scholar
  137. Moy M, Belanger F, Duncan R, Freehof A, Leary C, Meyer W, Sullivan R, White JFJ (2000) Identification of epiphyllous mycelial nets on leaves of grasses infected by Clavicipitaceous endophytes. Symbiosis 28:291–302Google Scholar
  138. Mucciarelli M, Scannerini S, Bertea C, Maffei M (2003) In vitro and in vivo peppermint (Mentha piperita) growth promotion by nonmycorrhizal fungal colonization. New Phytol 158:579–591Google Scholar
  139. Mukherjee M, Mukherjee PK, Horwitz BA, Zachow C, Berg G, Zeilinger S (2012) Trichoderma-plant-pathogen interactions: advances in genetics of biological control. Indian J Microbiol 52:522–529PubMedPubMedCentralGoogle Scholar
  140. Murphy BR, Doohan FM, Hodkinson TR (2015) Fungal root endophytes of a wild barley species increase yield in a nutrient-stressed barley cultivar. Symbiosis 65:1–7Google Scholar
  141. Musetti R, Grisan S, Polizzotto R, Martini M, Paduano C et al (2011) Interactions between ‘Candidatus Phytoplasma mali’ and the apple endophyte Epicoccum nigrum in Catharanthus roseus plants. J Appl Microbiol 110:746–756PubMedGoogle Scholar
  142. Nadeem A, Hamayun M, Khan SA, Khan AL, Lee IJ, Shin DH (2010) Gibberellin-producing endophytic fungi isolated from Monochoria vaginalis. J Microbiol Biotechnol 20:1744–1749Google Scholar
  143. Narisawa K, Kawamata H, Currah RS, Hashiba T (2002) Suppression of Verticillium wilt in eggplant by some fungal root endophytes. Eur J Plant Pathol 108:103–109Google Scholar
  144. Nath R, Sharma GD, Barooah M (2012a) Efficiency of tricalcium phosphate solubilization by two different endophytic Penicillium sp. isolated from tea (Camelia sinensis L.) Er. J Exp Biol 2:1354–1358Google Scholar
  145. Nath R, Sharma GD, Barooah M (2012b) Plant growth promoting endophytic fungi isolated from tea (Camellia sinensis L.) shrubs of Assam, India. Appl Ecol Environ Res 13:877–891Google Scholar
  146. Newsham KK (1994) First record of intracellular sporulation by a coelomycete fungus. Mycol Res 98:1390–1392Google Scholar
  147. O’Dell TE, Massicotte HB, Trappe JM (1993) Root colonization of Lupinus latifolius Agardh and Pinus contorta Dougl. by Phialocephala fortinii Wang and Wilcox. New Phytol 124:93–100Google Scholar
  148. Oelmüller R, Shahollari B, Peškan-Berghöfer T, Trebicka A, Giong PH, Sherameti I, Oudhoff M, Venus Y, Altschmied L, Varma A (2004) Molecular analyses of the interaction between Arabidopsis roots and the growth-promoting fungus Piriformospora indica. Endocytobiosis Cell Res 15:504–517Google Scholar
  149. Oelmüller R, Peškan-Berghöfer T, Shahollari B, Sherameti I, Varma A (2005) MATH-domain containing proteins represent a novel gene family in Arabidopsis thaliana and are involved in plant/microbe interactions. Physiol Plant 124:152–166Google Scholar
  150. Oelmüller R, Sherameti I, Tripathi S, Varma A, Jena F, Botanik A, Str D (2009) Piriformospora indica, a cultivable root endophyte with multiple biotechnological applications. Symbiosis 49:1–17Google Scholar
  151. Pan JJ, Baumgarten AM, May G (2008) Effects of host plant environment and Ustilago maydis infection on the fungal endophyte community of maize (Zea mays). New Phytol 178:147–156PubMedGoogle Scholar
  152. Park Y, Mishra RC, Yoon S, Kim H, Park C, Seo S, Bae H (2018) Endophytic Trichoderma citrinoviride isolated from mountain-cultivated ginseng (Panax ginseng) has great potential as a biocontrol agent against ginseng pathogens. J Ginseng Res 43:408–420PubMedPubMedCentralGoogle Scholar
  153. Peškan-Berghöfer T, Shahollari B, Giong PH, Hehl S, Markert C, Blanke V, Kost G, Varma AK, Oelmüller R (2004) Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant-microbe interactions and involves early plant protein modifications in the endoplasmatic reticulum and at the plasma membrane. Physiol Plant 122:465–477Google Scholar
  154. Petrini O (1986) Taxonomy of endophytic fungi of aerial plant tissues. In: Fokkema NJ, van den Huevel J (eds) Microbiology of the phyllosphere. Cambridge University Press, Cambridge, pp 175–187Google Scholar
  155. Petrini O, Fisher PJ (1990) Occurrence of fungal endophytes in twigs of Salix fragilis and Quercus robur. Mycol Res 94:1077–1080Google Scholar
  156. Petrini O, Müller E (1979) Pilzliche Endophyten, am Beispiel von Juniperus communis L. Sydowia 32:224–225Google Scholar
  157. Peyronel B (1924) Prime ricerche sulla micorizae endotrofiche e sulla microflora radicola normalle della fanerograme. Rev Biol 6:17–53Google Scholar
  158. Philipson MN, Christey MC (1986) The relationship of host and endophyte during flowering seed formation and germination of Lolium perenne. N Z J Bot 24:125–134Google Scholar
  159. Pineda A, Zheng SJ, van Loon JJA, Pieterse CMJ, Dicke M (2010) Helping plants to deal with insects: the role of beneficial soilborne microbes. Trend Plant Sci 15:507–514Google Scholar
  160. Promputtha I, Lumyong S, Dhanasekaran V, McKenzie E, Hyde K, Jeewan R (2007) A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence. Microb Ecol 53:579–590PubMedGoogle Scholar
  161. Rabha AJ, Naglot A, Sharma GD, Gogoi HK (2014) In vitro evaluation of antagonism of endophytic Colletotrichum gloeosporioides against potent fungal pathogens of Camellia sinensis. Indian J Microbiol 54:302–309PubMedPubMedCentralGoogle Scholar
  162. Rai MK, Varma A, Pandey AK (2004) Antifungal potential of Spilanthes calva after inoculation of Piriformospora indica. Mycoses 47:479–481PubMedGoogle Scholar
  163. Rana KL, Kour D, Sheikh I, Dhiman A, Yadav N, Yadav AN, et al. (2019a) Endophytic fungi: biodiversity, ecological significance, and potential industrial applications. In: Yadav AN, Mishra S, Singh S, Gupta A (eds) Recent advancement in white biotechnology through fungi. vol 1: Diversity and enzymes perspectives, Springer, Cham, pp 1–62Google Scholar
  164. Rana KL, Kour D, Sheikh I, Yadav N, Yadav AN, Kumar V, Singh BP, Dhaliwal HS, Saxena AK (2019b) Biodiversity of endophytic fungi from diverse niches and their biotechnological applications. In: Singh BP (ed) Advances in endophytic fungal research: present status and future challenges. Springer International Publishing, Cham, pp 105–144. Scholar
  165. Rana KL, Kour D, Yadav AN (2019c) Endophytic microbiomes: biodiversity, ecological significance and biotechnological applications. Res J Biotechnol 14:142–162Google Scholar
  166. Rana KL, Kour D, Kaur T, Sheikh I, Yadav AN, Kumar V, Suman A, Dhaliwal HS (2020) Endophytic microbes from diverse wheat genotypes and their potential biotechnological applications in plant growth promotion and nutrient uptake. Proc Natl Acad Sci India Sec B Biol Sci.
  167. Rayner MC (1915) Obligate symbiosis in Calluna vulgaris. Ann Bot 29:97–133Google Scholar
  168. Read DJ (1999) Mycorrhiza—the state of the art. In: Varma A, Hock B (eds) Mycorrhiza. Springer-Verlag, Berlin, pp 3–34Google Scholar
  169. Redman RS, Dunigan DD, Rodriguez RJ (2001) Fungal symbiosis: from mutualism to parasitism, who controls the outcome, host or invader? New Phytol 151:705–716Google Scholar
  170. Redman RS, Sheehan KB, Stout RG, Rodriguez RJ, Henson JM (2002) Thermotolerance conferred to plant host and fungal endophyte during mutualistic symbiosis. Science 298:1581–1581PubMedGoogle Scholar
  171. Rehner SA, Samuels GJ (1995) Molecular systematics of the hypocreales: a teleomorph gene phylogeny and the status of their anamorphs. Can J Bot 73:816–823Google Scholar
  172. Ren AZ, Li X, Han R, Yin LJ, Wei MY, Gao YB (2011) Benefits of a symbiotic association with endophytic fungi are subject to water and nutrient availability in Achnatherum sibiricum. Plant Soil 346:363–373Google Scholar
  173. Ren A, Wei M, Yin L, Wu L, Zhou Y, Li X et al (2014) Benefits of a fungal endophyte in Leymus chinensis depend more onwater than on nutrient availability. Environ Exp Bot 108:71–78Google Scholar
  174. Reza Sabzalian M, Mirlohi A (2010) Neotyphodium endophytes trigger salt resistance in tall and meadow fescues. J Plant Nutr Soil Sci 173:952–957Google Scholar
  175. Richard C, Fortin JA (1974) Distribution geographique, ecologie, physiologie, pathogenicite et sporulation du mycelium radicus atrovirens. Phytoprotection 55:67–88Google Scholar
  176. Rim SO, Lee JH, Choi WY, Hwang SK, Suh SJ, Lee IJ, Rhee IK, Kim JG (2005) Fusarium proliferatum KGL0401 as a new gibberellin-producing fungus. J Microbiol Biotechnol 15:809–814Google Scholar
  177. Rodriguez R, Redman R (2008) More than 400 million years of evolution and some plants still can’t make it on their own: plant stress tolerance via fungal symbiosis. J Exp Bot 59:1109–1114PubMedGoogle Scholar
  178. Rodriguez RJ, Redman RS, Henson JM (2004) The role of fungal symbioses in the adaptation of plants to high stress environments. Mitig Adapt Strateg Glob Chang 9:261–272Google Scholar
  179. Rodriguez RJ, Henson J, Van Volkenburgh E, Hoy M, Wright L, Beckwith F, Kim Y, Redman RS (2008) Stress tolerance in plants via habitat-adapted symbiosis. Int Soc Microb Ecol 2:404–416Google Scholar
  180. Rodriguez RJ, White JF, Arnold AE, Redman RS (2009) Fungal endophytes: diversity and functional roles. New Phytol 182:314–330PubMedGoogle Scholar
  181. Rodriguez-Galvez E, Mendgen K (1995) The infection process of Fusarium oxysporum in cotton root tips. Protoplasma 189:61–72Google Scholar
  182. Rubini MR, Silva-Ribeiro RT, Pomella AWV, Maki CS, Araujo WL, dos Santos DR, Azevedo JL (2005) Diversity of endophytic fungal community of cacao (Theobroma cacao L.) and biological control of Crinipellis perniciosa, causal agent of Witches’ broom disease. Int J Biol Sci 1:24–33PubMedPubMedCentralGoogle Scholar
  183. Saba H, Vibhash D, Manisha M, Prashant KS, Farhan H, Tauseef A (2012) Trichoderma- a promising plant growth stimulator and biocontrol agent. Mycosphere 3:524–531Google Scholar
  184. Sahay NS, Varma A (1999) Piriformospora indica: a new biological hardening tool for micropropagated plants. FEMS Microbiol Lett 181:297–302PubMedGoogle Scholar
  185. Santamaría J, Bayman P (2005) Fungal epiphytes and endophytes of coffee leaves (Coffea arabica). Microb Ecol 50:1–8PubMedGoogle Scholar
  186. Schardl CL, Moon CD (2003) Processes of species evolution in Epichloë/Neotyphodium endophytes of grasses. In: White JFJ, Bacon CW, Hywel-Jones NL, Spatafora JW (eds) Clavicipitalean fungi: evolutionary biology, chemistry, biocontrol and cultural impacts. Marcel-Dekker, New York, pp 273–310Google Scholar
  187. Schulz BJE (2006) Mutualistic interactions with fungal root endophytes. In: Schulz BJE, Boyle CJC, Sieber TN (eds) Microbial root endophytes. Springer-Verlag, Berlin, pp 261–280Google Scholar
  188. Schulz B, Boyle C (2005) The endophytic continuum. Mycology Res 109:661–686Google Scholar
  189. Selosse MA, Baudoin E, Vandenkoornhuyse P (2004) Symbiotic microorganisms, a key for ecological success and protection of plants. C R Biol 327:639–648PubMedGoogle Scholar
  190. Selosse MA, Vohník M, Chauvet E (2008) Out of the rivers: are some aquatic hyphomycetes plant endophytes? New Phytol 178:3–7PubMedGoogle Scholar
  191. Sharma S, Kour D, Rana KL, Dhiman A, Thakur S, Thakur P, et al. (2019) Trichoderma: biodiversity, ecological significances, and industrial applications. In: Yadav AN, Mishra S, Singh S, Gupta A (eds) Recent advancement in white biotechnology through fungi. vol 1: Diversity and enzymes perspectives, Springer International Publishing, Cham, pp 85–120.
  192. Sherameti I, Shahollari B, Venus Y, Altschmied L, Varma A, Oelmüller R (2005) The endophytic fungus Piriformospora indica stimulates the expression of nitrate reductase and the starch-degrading enzyme glucan-water dikinase in tobacco and Arabidopsis roots through a homeodomain transcription factor that binds to a conserved motif in their promoters. J Biol Chem 280:26241–26247PubMedGoogle Scholar
  193. Shweta S, Zuehlke S, Ramesha BT, Priti V, Mohana Kumar P, Ravikant G, Spiteller M, Vasudeva R, Uma SR (2010) Endophytic fungal strains of Fusarium solani, from Apodytes dimidiata E.Mey. ex Arn (Icacinaceae) produce camptothecin, 10-hydroxycamptothecin and 9-methoxycamptothecin. Phytochemistry 71:117–122PubMedGoogle Scholar
  194. Silva DDDE, Crous PW, Ades PK, Hyde KD, Taylor PWJ (2017) Life styles of Colletotrichum species and implications for plant biosecurity. Fungal Biol Rev 31:155–168Google Scholar
  195. Singh A, Sharma J, Rexer KH, Varma A (2000) Plant productivity determinants beyond minerals, water and light: Piriformospora indica—a revolutionary plant growth promoting fungus. Curr Sci 79:1548–1554Google Scholar
  196. Sirrenberg A, Göbel C, Grond S, Czempinski N, Ratzinger A, Karlovsky P, Santos P, Feussner I, Pawlowski K (2007) Piriformospora indica affects plant growth by auxin production. Physiol Plant 131:581–589PubMedGoogle Scholar
  197. Song M, Chai Q, Li X, Yao X, Li C, Christensen MJ et al (2015a) An asexual Epichloë endophyte modifies the nutrient stoichiometry of wild barley (Hordeum brevisubulatum) under salt stress. Plant Soil 387:153–165Google Scholar
  198. Song M, Li X, Saikkonen K, Li C, Nan Z (2015b) An asexual Epichloë endophyte enhances waterlogging tolerance of Hordeum brevisubulatum. Fungal Ecol 13:44–52Google Scholar
  199. Song H, Nan Z, Song Q, Xia C, Li X, Yao X, Xu W, Kuang Y, Tian P, Zhang Q (2016) Advances in research on Epichloë endophytes in Chinese native grasses. Front Microbiol 7:1399PubMedPubMedCentralGoogle Scholar
  200. Spatafora JW, Blackwell M (1993) Molecular systematics of unitunicate perithecial ascomycetes: the Clavicipitales-Hypocreales connection. Mycologia 85:912–922Google Scholar
  201. Spatafora JW, Sung G-H, Sung J-M, Hywel-Jones NL, White JFJ (2007) Phylogenetic evidence for an animal pathogen origin of ergot and the grass endophytes. Mol Ecol 16:1701–1711PubMedGoogle Scholar
  202. Srivastava R, Mehta CM, Sharma AK (2011) Fusarium pallidoroseum—a new biofertilizer responsible for enhancing plant growth in different crops. Int Res J Microbiol 2:192–199Google Scholar
  203. Steinebrunner F, Twele R, Francke W, Leuchtmann A, Schiestl FP (2008) Role of odour compounds in the attraction of gamete vectors in endophytic Epichloe fungi. New Phytol 178:401–411PubMedGoogle Scholar
  204. Stone JK, Bacon CW, White JF (2000) An overview of endophytic microbes: endophytism defined. In: Bacon CW, White JF (eds) Microbial endophytes. Marcel Dekker Inc, New York, pp 3–30Google Scholar
  205. Stone JK, Polishook JD, White JF Jr (2004) Endophytic fungi. In: Mueller GM, Bills GF, Foster MS (eds) Biodiversity of fungi: inventory and monitoring methods. Elsevier Academic Press, New York, pp 241–270Google Scholar
  206. Strobel G, Daisy B (2003) Bioprospecting for microbial endophytes and their natural products. Microbiol Mol Biol Rev 67:491–502PubMedPubMedCentralGoogle Scholar
  207. Stuart RM, Romao AS, Pizzirani-Kleiner AA, Azevedo JL, Araujo WL (2010) Culturable endophytic filamentous fungi from leaves of transgenic imidazolinone-tolerant sugarcane and its non-transgenic isolines. Arch Microbiol 192:307–313PubMedGoogle Scholar
  208. Suman A, Yadav AN, Verma P (2016) Endophytic microbes in crops: diversity and beneficial impact for sustainable agriculture. In: Singh D, Abhilash P, Prabha R (eds) Microbial inoculants in sustainable agricultural productivity, research perspectives. Springer-Verlag, New Delhi, pp 117–143. Scholar
  209. Sun X, Guo L-D, Hyde KD (2011) Community composition of endophytic fungi in Acer truncatum and their role in decomposition. Fungal Divers 47:85–95Google Scholar
  210. Tadych M, Bergen M, Dugan FM, White JF (2007) Evaluation of the potential role of water in the spread of conidia of the Neotyphodium endophyte of Poa ampla. Mycol Res 111:466–472PubMedGoogle Scholar
  211. Tadych M, Bergen MS, White JF Jr (2014) Epichloë spp. associated with grasses: new insights on life cycles, dissemination and evolution. Mycologia 106:181–201PubMedGoogle Scholar
  212. Talapatra K, Das AR, Saha AK, Das P (2017) In vitro antagonistic activity of a root endophytic fungus towards plant pathogenic fung. J Appl Biol Biotechnol 5:68–71Google Scholar
  213. Tejesvi MV, Kajula M, Mattila S, Pirttilä AM (2011) Bioactivity and genetic diversity of endophytic fungi in Rhododendron tomentosum Harmaja. Fungal Divers 47:97–107Google Scholar
  214. Torres MS, White JFJ, Bischoff JF (2007) Hypocrella panamensis sp. nov (Clavicipitaceae Hypocreales): evaluation on the basis of morphological and molecular characters. Mycol Res 111:317–323PubMedGoogle Scholar
  215. Torres M, Tadych M, White JF, Bills GF (2011) Isolation and identification of fungal endophytes. In: Pirttila AM, Sorvari SI (eds) Prospects and applications for plant associated microbes: a laboratory manual, part B: fungi. BBI (Biobien Innovations), Turku, pp 153–164Google Scholar
  216. U’Ren JM, Lutzoni F, Miadlikowska J, Arnold AE (2008) Evolutionary relationships of endophytic, endolichenic, and saprotrophic fungi in the Chiricahua Mountains. Inoculum 54:60–61Google Scholar
  217. Unterseher M, Schnittler M (2009) Dilution-to-extinction cultivation of leaf-inhabiting endophytic fungi in beech (Fagus sylvatica L.) different cultivation techniques influence fungal biodiversity assessment. Mycol Res 113:645–654PubMedGoogle Scholar
  218. Usuki F, Narisawa K (2007) A mutualistic symbiosis between a dark, septate endophytic fungus, Heteroconium chaetospira and a nonmycorrhizal plant, Chinese cabbage. Mycology 99:175–184Google Scholar
  219. Van Der Wouder BJ, Pegtel DM, Bakker JP (1994) Nutrient limitation after longterm nitrogen-fertilizer application in cut grasslands. J Appl Ecol 31:405–412Google Scholar
  220. Vandenkoornhuyse P, Mahé S, Ineson P, Staddon P, Ostle N, Cliquet JB, Francez AJ, Fitter AH, Young JPW (2007) Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA. Proceedings of the National Academy of Sciences, USA 104: 16970–16975Google Scholar
  221. Varma A, Verma S, Sudha Sahay N, Bütehorn B, Franken P (1999) Piriformospora indica, a cultivable plant growth promoting root endophyte. Appl Environ Microbiol 65:2741–2744PubMedPubMedCentralGoogle Scholar
  222. Vasiliauskas R, Menkis A, Finlay RD, Stenlid J (2007) Wood-decay fungi in fine living roots of conifer seedlings. New Phytol 174:441–446PubMedGoogle Scholar
  223. Vega FE, Posada F, Aime MC, Pavaripoll M, Infante F, Rehner SA (2008) Entomopathogenic fungal endophytes. Biol Control 46:72–82Google Scholar
  224. Vega FE, Simpkins A, Aime MC, Posada F, Peterson SW, Rehner SA, Infante F, Castillo A, Arnold AE (2010) Fungal endophyte diversity in coffee plants from Colombia, Hawai’i, Mexico and Puerto Rico. Fungal Ecol 3:122–138Google Scholar
  225. Verma S, Varma A, Rexer K-H, Hassel A, Kost G, Sarbhoy A, Bisen P, Bütehorn B, Franken P (1998) Piriformospora indica, gen. et sp. nov., a new root-colonizing fungus. Mycologia 90:896–903Google Scholar
  226. Verma P, Yadav AN, Kumar V, Singh DP, Saxena AK (2017) Beneficial plant-microbes interactions: biodiversity of microbes from diverse extreme environments and its impact for crop improvement. In: Singh DP, Singh HB, Prabha R (eds) Plant-microbe interactions in agro-ecological perspectives, Microbial interactions and agro-ecological impacts, vol 2. Springer, Singapore, pp 543–580. Scholar
  227. Vidal S (2015) Entomopathogenic fungi as endophytes: plant–endophyte–herbivore interactions and prospects for use in biological control. Curr Sci 109:46–54Google Scholar
  228. Vignale MV, Astiz-Gasso MM, Novas MV, Iannone LJ (2013) Epichloid endophytes confer resistance to the smut Ustilago bullata in the wild grass Bromus auleticus (Trin.). Biol Control 67:1–7Google Scholar
  229. Vitousek PM, Walker LR (1989) Biological invasion by Myrica faya in Hawaii: Plant demography, nitrogen fixation, ecosystem effects. Ecoll Monogr 59:247–265Google Scholar
  230. Vogl A (1898) Mehl und die anderen mehlprodukte der cerealien und leguminosen. Z Nahrungsm Unters Hyg Warenk 12:25–29Google Scholar
  231. Waller F, Achatz B, Baltruschat H, Fodor J, Becker K, Fischer M, Heier T, Ralph Hückelhoven H, Neumann C, Wettstein DV, Franken P, Kogel K-H (2005) The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield. Proc Natl Acad Sci U S A 102:13386–13391PubMedPubMedCentralGoogle Scholar
  232. Waller DM, Dole J, Bersch AJ (2008) Effects of stress and phenotypic variation on inbreeding depression in Brassica rapa. Evolution 62:917–931PubMedGoogle Scholar
  233. Wang CJK, Wilcox HE (1985) New species of ecendomycorrhizal and psuedomycorrhizal fungi: Phialophora findlandia, Chloridium paucisporum and Phialocephala fortinii. Mycologia 77:951–958Google Scholar
  234. Waqas M, Khan AL, Kamran M, Hamayun M, Kang SM, Kim YH, Lee IJ (2012) Endophytic fungi produce gibberellins and indole-acetic acid and promotes host-plant growth during stress. Molecules 17:10754–10773PubMedPubMedCentralGoogle Scholar
  235. Waqas M, Khan AL, Lee IJ (2014a) Bioactive chemical constituents produced by endophytes and effects on rice plant growth. J Plant Interact 9:478–487Google Scholar
  236. Waqas M, Khan AL, Kang SM, Kim YH, Lee IJ (2014b) Phytohormone-producing fungal endophytes and hardwood-derived biochar interact to ameliorate heavy metal stress in soybeans. Biol Fertil Soils 50:1155–1167Google Scholar
  237. Waqas M, Khan AL, Hamayun M, Shahzad R, Kang SM, Kim JG, Lee IJ (2015) Endophytic fungi promote plant growth and mitigate the adverse effects of stem rot: an example of Penicillium citrinum and Aspergillus terreus. J Plant Interact 10:280–287Google Scholar
  238. Weber RWS, Stenger E, Meffert A, Hahn M (2004) Brefeldin a production by Phoma medicaginis in dead pre-colonized plant tissue: a strategy for habitat conquest? Mycol Res 108:662–671PubMedGoogle Scholar
  239. Western JH, Cavett JJ (1959) The choke disease of cocksfoot (Dactylis glomerata) caused by Epichloë typhina (Fr) Tul. Trans Brit Mycol Soc 42:298–307Google Scholar
  240. White JFJ (1988) Endophyte-host associations in forage grasses. I. A proposal concerning origin and evolution. Mycologia 80:442–446Google Scholar
  241. White JFJ, Bultman TL (1987) Endophyte-host associations in forage grasses. VIII. Heterothallism in Epichloë typhina. Am J Bot 74:1716–1721Google Scholar
  242. White JFJ, Morrow AC, Morgan-Jones G, Chambless DA (1991) Endophyte-host associations in forage grasses. IV. Primary stromata formation and seed transmission in Epichloë typhina: developmental and regulatory aspects. Mycologia 83:72–81Google Scholar
  243. White JFJ, Martin TI, Cabral D (1996) Endophyte-host associations in grasses. III. Conidia formation by Acremonium endophytes in the phylloplanes of Agrostis hiemalis and Poarigidifolia. Mycologia 88:174–178Google Scholar
  244. Wille PA, Aeschbacher RA, Boller T (1999) Distribution of fungal endophyte genotypes in douptly infected host grasses. Plant J 18:349–358PubMedGoogle Scholar
  245. Wilson D (1995) Endophyte—the evolution of a term, and clarification of its use and definition. Oikos 73:274–276Google Scholar
  246. Yadav AN (2017) Beneficial role of extremophilic microbes for plant health and soil fertility. J Agric Sci 1:1–4Google Scholar
  247. Yadav AN (2018) Biodiversity and biotechnological applications of host-specific endophytic fungi for sustainable agriculture and allied sectors. Acta Sci Microbiol 1:1–5Google Scholar
  248. Yadav AN (2019) Endophytic fungi for plant growth promotion and adaptation under abiotic stress conditions. Acta Sci Agric 3:91–93Google Scholar
  249. Yadav AN, Kumar R, Kumar S, Kumar V, Sugitha T, Singh B, Chauhan V, Dhaliwal HS, Saxena AK (2017) Beneficial microbiomes: biodiversity and potential biotechnological applications for sustainable agriculture and human health. J Appl Biol Biotechnol 5:45–57Google Scholar
  250. Yadav AN, Kumar V, Prasad R, Saxena AK, Dhaliwal HS (2018a) Microbiome in crops: diversity, distribution and potential role in crops improvements. In: Prasad R, Gill SS, Tuteja N (eds) Crop improvement through microbial biotechnology. Elsevier, Amsterdam, pp 305–332Google Scholar
  251. Yadav AN, Verma P, Kumar V, Sangwan P, Mishra S, Panjiar N, et al. (2018b) Biodiversity of the genus Penicillium in different habitats. In: Gupta VK, Rodriguez-Couto S (eds) New and future developments in microbial biotechnology and bioengineering, Penicillium system properties and applications. Elsevier, Amsterdam, pp 3–18.
  252. Yadav AN, Kour D, Rana KL, Yadav N, Singh B, Chauhan VS, Rastegari AA, Hesham AE-L, Gupta VK (2019a) Metabolic engineering to synthetic biology of secondary metabolites production. In: Gupta VK, Pandey A (eds) New and future developments in microbial biotechnology and bioengineering. Elsevier, Amsterdam, pp 279–320. Scholar
  253. Yadav AN, Mishra S, Singh S, Gupta A (2019b) Recent advancement in white biotechnology through fungi. Vol 1: Diversity and enzymes perspectives. Springer International Publishing, ChamGoogle Scholar
  254. Yadav AN, Singh S, Mishra S, Gupta A (2019c) Recent advancement in white biotechnology through fungi. Vol 2: Perspective for value-added products and environments. Springer International Publishing, ChamGoogle Scholar
  255. Yadav AN, Singh S, Mishra S, Gupta A (2019d) Recent advancement in white biotechnology through fungi. Vol 3: Perspective for sustainable environments. Springer International Publishing, ChamGoogle Scholar
  256. Yadav AN, Singh J, Rastegari AA, Yadav N (2020) Plant microbiomes for sustainable agriculture. Springer International Publishing, ChamGoogle Scholar
  257. You YH, Yoon H, Kang SM, Shin JH, Choo YS, Lee IJ, Lee JM, Kim JG (2012) Fungal diversity and plant growth promotion of endophytic fungi from six halophytes in Suncheon Bay. J Microbiol Biotechnol 22:1549–1556PubMedGoogle Scholar
  258. Zabalgogeazcoa I (2008) Fungal endophytes and their interaction with plant pathogens. Spanish J Agri Res 6:138–146Google Scholar
  259. Zabalgogeazcoa I, Ciudad AG, Vázquez de Aldana BR, Criado BG (2006) Effects of the infection by the fungal endophyte Epichloë festucae in the growth and nutrient content of Festuca rubra. Eur J Agron 24:374–384Google Scholar
  260. Zhang YP, Nan ZB (2007) Growth and anti-oxidative systems changes in Elymus dahuricus is affected by Neotyphodium endophyte under contrasting water availability. J Agron Crop Sci 193:377–386Google Scholar
  261. Zhang YP, Nan ZB (2010) Germination and seedling anti-oxidative enzymes of endophyte-infected populations of Elymus dahuricus under osmotic stress. Seed Sci Technol 38:522–527Google Scholar
  262. Zhang X, Fan X, Li C, Nan Z (2010a) Effects of cadmium stress on seed germination, seedling growth and antioxidative enzymes in Achnatherum inebrians plants infected with a Neotyphodium endophyte. Plant Growth Regul 60:91–97Google Scholar
  263. Zhang X, Li C, Nan Z (2010b) Effects of cadmium stress on growth and anti-oxidative systemsin Achnatherumine brians symbiotic with Neotyphodium gansuense. J Hazard Mater 175:703–709PubMedGoogle Scholar
  264. Zhang XX, Li CJ, Nan ZB (2012a) Effects of cadmium stress on seed germination and seedling growth of Elymus dahuricus infected with the Neotyphodiumendophyte. Sci China Life Sci 55:793–799PubMedGoogle Scholar
  265. Zhang XX, Li CJ, Nan ZB, Matthew C (2012b) Neotyphodium endophyte increases Achnatherum inebrians (drunken horse grass) resistance to herbivores and seed predators. Weed Res 52:70–78Google Scholar
  266. Zhang X, Lin L, Zhu Z, Yang X, Wang Y, An Q (2013) Colonization and modulation of host growth and metal uptake by endophytic bacteria of Sedum alfredii. Int J Phytoremediation 15:51–64PubMedGoogle Scholar
  267. Zhou Z, Zhang C, Zhou W, Li W, Chu L, Yan J (2014) Diversity and plant growthpromoting ability of endophytic fungi from the five flower plant species collected from Yunnan, Southwest China. J Plant Interact 9:585–591Google Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Shimaa Mohsen El Mansy
    • 1
  • Fatma Ahmed Abo Nouh
    • 2
  • Mariam Khaled Mousa
    • 2
  • Ahmed M. Abdel-Azeem
    • 2
  1. 1.Zoology Department, Faculty of ScienceUniversity of Suez CanalIsmailiaEgypt
  2. 2.Systematic Mycology Laboratory, Botany Department, Faculty of ScienceUniversity of Suez CanalIsmailiaEgypt

Personalised recommendations