Diversity of Endophytes in Tropical Forests

  • Sudipta Roy
  • Debdulal BanerjeeEmail author
Part of the Forestry Sciences book series (FOSC, volume 86)


The world of microorganisms is vast and spectacular, as they are found everywhere in nature. Endophytic microorganisms are discovered inside healthy plant tissues and resemble the normal microbiota of the animal intestinal system. Such microbes are thought to reside inter- or intracellular in almost all types of plant tissues. Endophytes are omnipresent and exist within all known plants in various ecosystems, but the geographic differences in endophyte diversity, community composition and host/tissue preference have not been well documented yet. Endophytic microorganisms can be biotrophic mutualists, benign commensals, decomposers, or latent pathogens. Studies have found that mutualistic microbes produce toxins including several classes of alkaloids that provide resistance to herbivores. In return, plants give microbes cellular or intracellular spaces as their shelter and nutrients for their growth. Endophytes that are normally unnoticed may play a significant role in plant diversity and ecological functioning. Endophyte-infected plants reduce the correlation between diversity and eco-functioning. For example, a plant harbouring endophytes often acquires more biomass than an uninfected one and contributes less productivity in that community. Tropical ecosystems are different in important ways from those of temperate regions. They are a major reservoir of plant biodiversity and play crucial roles in global climate regulation and biogeochemical cycling. However, limited information is available about the diversity of endophytic microbial communities in these forests. Earth has forest coverage of about 31% of total land. The tropics are regions of Earth found between 23.5°N and 23.5°S of the equator. The tropical rain forest biomes cover almost 12% of Earth’s ice-free land area, of which about 20% has been brought to human concern. There are still vast areas of undisturbed rain forests that draw the highest attention of endophyte researchers. Evidence indicates that changes in climatic conditions can profoundly alter the plant-microbe symbiosis, and some conflict of interest may arise there, leading into a natural competition for individual sustainability and reproduction of endophytes. In tropical countries, diseases such as malaria, tuberculosis and cholera are prevalent. As tropical forests are considered as the most diverse terrestrial ecosystem, having the largest number of endophytic microorganisms, it also can be considered as storage for a plethora of molecules with diverse bioactivity. Limiting resources of tropical rainforests always keep the selection pressure at peak. Therefore, a high opportunity exists to obtain novel molecules with added medicinal value from endophytic microorganisms of tropical rainforests. Proper strain identification by modern molecular polyphasic approach can disclose the true diversity of the endospheric ecosystem.







Clavicipitaceous endophytes


Non-clavicipatecious endophytes



Authors are thankful to UGC, New Delhi for financial assistance under innovative project.


  1. Adams AE, Kazenel MR, Rudgers JA (2017) Does a foliar endophyte improve plant fitness under flooding? Plant Ecol 218:711. Scholar
  2. Almeida TT, Orlandelli RC, Azevedo JL, Pamphile JA (2015) Molecular characterization of the endophytic fungal community associated with Eichhornia azurea (Kunth) and Eichhornia crassipes (Mart.) (Pontederiaceae) native to the Upper Paraná River floodplain. Brazil. Genet Mol Res 14:4920–4931CrossRefPubMedGoogle Scholar
  3. Arnold AE, Maynard Z, Gilbert G (2001) Fungal endophytes in dicotyledonous neotropical trees: patterns of abundance and diversity. Mycol Res 105:1502–1507CrossRefGoogle Scholar
  4. 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 95:388–398CrossRefPubMedGoogle Scholar
  5. Arnold AE, Lutzoni F (2007) Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88:541–549. Scholar
  6. Arnold AE, Maynard Z, Gilbert GS, Coley PD, Kursar TA (2000) Are tropical fungal endophytes hyperdiverse? Ecol Lett 3:267–274. Scholar
  7. Arnold AE, Mejía LC, Kyllo D, Rojas EI, Maynard Z, Robbins N, Herre EA (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci USA 100:15649–15654CrossRefPubMedGoogle Scholar
  8. Ashford RW (1997) What it takes to be a reservoir host. Belg J Zool 127:85–90Google Scholar
  9. Azevedo JL, Maccheroni JW, Pereira JO, Araújo WL (2000) Endophytic microrganisms: a review on insect control and recent advances on tropical plants. Elect J Biotechnol 3:40–65Google Scholar
  10. Baldassari R, Wickert E, de Goes A (2008) Pathogenicity, colony morphology and diversity of isolates of Guignardia citricarpa and G. mangiferae isolated from Citrus spp. Eur J Plant Pathol 120:103–110CrossRefGoogle Scholar
  11. Banerjee D (2011) Endophytic fungal diversity in tropical and subtropical plants. Res J Microbiol 6:54–62. Scholar
  12. Banerjee D, Jana M (2009) Production of exopolysaccharide by endophytic Stemphylium sp. Micología Aplicada Int 21:57–62Google Scholar
  13. Banerjee D, Mahapatra S, Manna S, Mukherjee R, Mukherjee S, Pati BR (2006) Occurrence of endophytic fungi in Vitexnegundo L. J Bot SocBeng 60:28–31Google Scholar
  14. Banerjee D, Manna S, Mahapatra S, Pati BR (2009) Fungal endophytes in three medicinal plants of Lamiaceae. Acta Microbiol et Immunol Hungarica 56:243–250CrossRefGoogle Scholar
  15. Banerjee D, Pandey A, Jana M, Strobel G (2014) Muscodor albus MOW12 an endophyte of Piper nigrum L. (Piperaceae) collected from North East India produces volatile antimicrobials. Ind J Microbio 54:27–32. Scholar
  16. Bejarano NV, Carrillo L (2016) Fungal endophytes in sweet orange Citrus sinensis (L.) Osbeck in Jujuy-Argentina. Asian J Agric Food Sci 4:54–59Google Scholar
  17. Brundrett MC (2006) Understanding the roles of multifunctional mycorrhizal and endophytic fungi. In: Schulz BJE, Boyle CJC, Sieber TN (eds) Microbial root endophytes. Springer, Berlin, Germany, pp 281–293CrossRefGoogle Scholar
  18. Carroll ID, Toovey S, Van Gompel A (2007) Dengue fever and pregnancy—A review and comment. Travel Med Infect Dis 5:183–188CrossRefPubMedGoogle Scholar
  19. Chareprasert S, Piapukiew J, Thienhirun S, Whalley AJS, Sihanonth P (2006) Endophytic fungi of teak leaves Tectona grandis L. and rain tree leaves Samanea saman Merr. W J Microbiol Biotechnol 22:481–486CrossRefGoogle Scholar
  20. Chowdhary K, Kaushik N (2015) Fungal endophyte diversity and bioactivity in the indian medicinal plant Ocimum sanctum Linn. PLoS ONE 10:e0141444. Scholar
  21. Clay K, Schardl CL (2002) Evolutionary origins and ecological consequences of endophyte symbiosis with grasses. Am Nat 160:S99–S127CrossRefPubMedGoogle Scholar
  22. Conn VM, Franco CMM (2004) Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones. Appl Environ Microbiol 70:1787–1794. Scholar
  23. Costa IPMW, Maia LC, Cavalcanti MA (2012) Diversity of leaf endophytic fungi in mangrove plants of northeast Brazil. Braz J Microbiol 43:1165–1173CrossRefGoogle Scholar
  24. David MO, Dinerstein E, Wikramanayake ED, Burgess ND, Underwood GVN, Emma C, Jennifer AA, Illanga I et al (2001) Terrestrial ecoregions of the world: a new map of life on earth. Bio Sci 51:933–938.[0933:TEOTWA]2.0.CO;2CrossRefGoogle Scholar
  25. Dreyfuss MM, Chapela IH (1994) Potential of fungi in discovery of novel low molecular weight pharmaceuticals. In: Gullo VP (ed) The discovery of natural products with therapeutic potential. Butterworth-Heinemann, London, UK, pp 49–80CrossRefGoogle Scholar
  26. Dreyfuss MM, Petrini O (1984) Further investigations on the occurrence and distribution of endophytic fungi in tropical plants. Bot Helv 94:33–40Google Scholar
  27. Fisher PJ, Petrini LE, Sutton BC, Petrini O (1995) A study of fungal endophytes in leaves, stems and roots of GynoxisoleifoliaMuchler (Compositae) from Ecuador. Nova Hedwigia 60:589–594Google Scholar
  28. Gibson L, Lee TM, Koh LP, Brook BW, Gardner TA, Barlow J et al (2011) Primary forests are irreplaceable for sustaining tropical biodiversity. Nature 478:378–381. Scholar
  29. Goebel NL, Edwards CA, Follows MJ, Zehr JP (2014) Modeled diversity effects on microbial ecosystem functions of primary production, nutrient uptake, and remineralization. Ecology 95:153–163CrossRefPubMedGoogle Scholar
  30. Haffer J (1969) Speciation in amazonian forest birds. Science 165:131. Scholar
  31. Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43:895–914. Scholar
  32. Hardoim PR, Nazir R, Sessitsch A, Elhottová D, Korenblum E, van Overbeek LS, van Elsas JD (2013) The new species Enterobacter oryziphilus sp. nov. and Enterobacter oryzendophyticus sp. nov. are key inhabitants of the endosphere of rice. BMC Microbiol 16:164CrossRefGoogle Scholar
  33. Hardoim PR, van Overbeek LS, Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16:463–471. Scholar
  34. Hardoim PR, van Overbeek LS, Ga Berg, Pirttilä AM, Compant S, Campisano A, DöringM Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol MolBiol Rev 79:293–320. Scholar
  35. Haruna E, Zin NM, Kerfahi D, Adams JM (2017) Extensive overlap of tropical rainforest bacterial endophytes between soil, plant parts, and plant species. MicrobEcol 22:1–16Google Scholar
  36. Hawksworth DL (1991) The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol Res 95:641–655CrossRefGoogle Scholar
  37. Heijden MGA, Martin FM, Selosse M, Sanders IR (2015) Mycorrhizal ecology and evolution: the past, the present, and the future. N Phytol 205:1406–1423. Scholar
  38. Hodgson S, Cates C, Hodgson J, Morley NJ, Sutton BC, Gange AC (2014) Vertical transmission of fungal endophytes is widespread in forbs. Ecol Evo 4:1199–1208. Scholar
  39. Hotez PJ, Brindley PJ, Bethony JM, King CH, Pearce EJ et al (2008) Helminth infections: the great neglected tropical diseases. J Clin Invest 118:1311–1321CrossRefPubMedPubMedCentralGoogle Scholar
  40. Janso JE, Carter GT (2010) Biosynthetic potential of phylogenetically unique endophytic actinomycetes from tropical plants. Appl Environ Microbiol 76:4377–4386. Scholar
  41. Jarvis BB, Mokhtari-Rejali N, Schenkel EP, Barros CS, Matzenbacher NI (1991) Tricothecene mycotoxins from Brazilian Baccharis species. Phytochem 30:789–797CrossRefGoogle Scholar
  42. Kazenel MR, Debban CL, Ranelli L, Hendricks WQ, Chung YA, Pendergast TH, Charlton ND, Young CA, Rudgers JA (2015) A mutualistic endophyte alters the niche dimensions of its host plant. AoB Plants. Scholar
  43. Knoth JL, Kim SH, Ettl GJ, Doty SL (2014) Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia. N Phytol 201:599–609. Scholar
  44. Mahapatra S, Banerjee D (2009) Extracellular tannase production by endophytic Hyalopus sp. J Gen Appl Microbiol 55:255–259CrossRefPubMedGoogle Scholar
  45. Mahapatra S, Banerjee D (2010) Diversity and screening for antimicrobial activity of endophytic fungi from Alstonia scholaris. Acta Microbiol et Immunol Hungarica 57:215–223CrossRefGoogle Scholar
  46. Mahapatra S, Banerjee D (2012) Structural elucidation and bioactivity of a novel exopolysaccharide from endophytic Fusarium solani SD5. Carbo Pol 90:683–689CrossRefGoogle Scholar
  47. Mahapatra S, Banerjee D (2016) Production and structural elucidation of exopolysaccharide from endophytic Pestalotiopsis sp. BC55. Int J Biol Macromol 82:182–191CrossRefGoogle Scholar
  48. McKloskey M (1993) Note on the fragmentation of primary rainforest. Ambio 22:250–51Google Scholar
  49. Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN (2014) Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Front Microbiol 5:479. Scholar
  50. Miguel PSB, Delvaux JC, Oliveira MNV, Moreira BC, Borges AC, Tótola MR, Neves JCL, Costa MD (2017) Diversity and distribution of the endophytic fungal community in eucalyptus leaves. Afr J Microbiol Res 11:92–105CrossRefGoogle Scholar
  51. Moricca S, Ragazzi A (2011) The holomorph Apiognomonia quercina/Discuta quercina as a pathogen/endophyte in Oak. In: Pirttila AM, Frank AC (eds) Endophytes of forest trees: biology and applications, forestry sciences, vol 80. Scholar
  52. Myers N, Mittermeier RA, Mittermeier CG et al (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858CrossRefGoogle Scholar
  53. Naik BS, Shashikala J, Krishnamurthy YL (2009) Study on the diversity of endophytic communities from rice (Oryzasativa L.) and their antagonistic activities in vitro. Microbiol Res 164:290–296CrossRefPubMedGoogle Scholar
  54. Nongkhlaw FMW, Joshi SR (2014) Epiphytic and endophytic bacteria that promote growth of ethnomedicinal plants in the subtropical forests of Meghalaya, India. Int J Trop Biol 62:1295–1308CrossRefGoogle Scholar
  55. Petrini O (1991) Fungal endophytes of tree leaves. In: Andrews JH, Hirano SS (eds) Microbial ecology of leaves. Springer, New York, USA, pp 179–197Google Scholar
  56. Petrini O, Dreyfuss MM (1981) Endophytische Pilze in epiphyischen Araceae, Bromeliaceae and Orchidaceae. Sydowia 34:135–148Google Scholar
  57. Qin S, Xing K, Jiang JH, Xu LH, Li WJ (2011) Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol 89:457–473CrossRefPubMedGoogle Scholar
  58. Ramankutty N, Evan AT, Monfreda C, Foley JA (2008) Farming the planet: 1. Geographic distribution of global agricultural lands in the year 2000. Global Biogeochem Cycles 22:1–19CrossRefGoogle Scholar
  59. Rodrigues KF, Samuels GJ (1992) Idriella species endophytic in palms. Mycotaxon 43:271–276Google Scholar
  60. Rodrigues KF, Leuchtmann A, Petrini O (1993) Endophytic species of Xylaria/; cultural and isozymic studies. Sydowia 45:116–138Google Scholar
  61. Rodrigues KF, Samuels GJ (1990) Preliminary study of endophytic fungi in a tropical palm. Mycol Res 94:827–830CrossRefGoogle Scholar
  62. Rodrigues KF, Samuels GJ (1994) Letendraeopsis palmarum, a new genus and species of loculoascomycetes. Mycologia 86:254–258CrossRefGoogle Scholar
  63. Rodriguez RJ, Henson J, Van Volkenburgh E, Hoy M, Wright L, Beckwith F, Kim YO, Redman RS (2008) Stress tolerance in plants via habitat-adapted symbiosis. ISME J 2(4):404–41CrossRefPubMedGoogle Scholar
  64. Rodriguez RJ, White JF Jr, Arnold AE, Redman RS (2009) Fungal endophytes: diversity and functional roles. N Phytol 182:314–330. Scholar
  65. Rondón VM, González MR (2006) Hongos endófitos en plantaciones de mango “Haden” de la Planicie de Maracaibo. Rev Fac Agronomía 23:273–284Google Scholar
  66. Roy S, Banerjee D (2014) Distribution of endophtyicactinomycetes of three medicinal plants and evaluation of their antibacterial potencies. J Adv Microbiol 1:218–226Google Scholar
  67. Roy S, Yasmin S, Ghosh S, Bhattacharya S, Banerjee D (2016) Anti-infective metabolites of a newly isolated Bacillus thuringiensis KL1 associated with kalmegh (Andrographis paniculata Nees.), a traditional medicinal herb. Microbiol Insights 9:1–7. Scholar
  68. Rudgers JA, Koslow JM, Clay K (2004) Endophytic fungi alter relationships between diversity and ecosystem properties. Ecol Lett 7:42–51CrossRefGoogle Scholar
  69. Rudgers JA, Mattingly WB, Koslow JM (2005) Mutualistic fungus promotes plant invasion into diverse communities. Oecologia 144:463CrossRefPubMedGoogle Scholar
  70. Sahney S, Benton MJ, Ferry PA (2010) Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land. Biol Lett 6:544–547. Scholar
  71. Saikkonen K, Faeth SH, Helander M, Sullivan TJ (1998) Fungal endophytes: Continuum of interactions with host plants. Ann Rev Ecol Syst 29:319–343CrossRefGoogle Scholar
  72. Santoyoa G, Hagelsiebb GM, Ma. del Carmen Orozco-Mosquedac, Glick BR (2016) Plant growth-promoting bacterial endophytes. Microbiol Res 183: 92–99.
  73. Seneviratne G., Weerasekara MLMAW, Kumaresan D, Zavahir JS (2017) Microbial signalling in plant- microbe interactions and its role on sustainability of agroecosystems. In: Singh JS, Seneviratne G (eds) Agro environmental sustainability, managing crop health. Springer, Switzerland, pp 1–16Google Scholar
  74. Sothcott KA, Johnson JA (1997) Isolation of endophytes from two species of palm from Bermuda. Can J Microbiol 43:789–792CrossRefGoogle Scholar
  75. Stammler G, Schutte GC, Speakman J, Miessner S, Crous PW (2013) Phyllosticta species on citrus: Risk estimation of resistance to QoI fungicides and identification of species with cytochrome b gene sequences. Crop Protection 48:6–12CrossRefGoogle Scholar
  76. Steenhoudt O, Vanderleyden J (2000) Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects. FEMS Microbiol Rev 24:487–506. Scholar
  77. Strobel G, Daisy B (2003) Bioprospecting for microbial endophytes and their natural products. Microbiol MolBol Rev 67:491–502CrossRefGoogle Scholar
  78. Strobel G, Daisy B, Castillo U et al (2004) Natural products from endophytic microorganisms. J Nat Prod 67:257–268CrossRefPubMedGoogle Scholar
  79. Strobel GA (2006) Harnessing endophytes for industrial microbiology. Curr Opin Microbiol 9:240–244CrossRefPubMedGoogle Scholar
  80. Strobel GA, Miller RV, Martinez-Miller C, Condron MM, Teplow DB, Hess WM (1999) Cryptocandin a potent and antimycotic from the endophytic fungus Cryptosporiopsis cf. Quercina Microbiol 145:1919–1926CrossRefGoogle Scholar
  81. Stone JK (1987) Initiation and development of latent infections by Rhabdocline parkeri on Douglas-fir. Can J Bot 65:2614–2621CrossRefGoogle Scholar
  82. Stone JK, Bacon CW, Jr White JF (2000) An overview of endophytic microbes: edophytism defined. In: Microbial endophytes, vol. 3. M Dekker, New York, p 29Google Scholar
  83. Suryanarayanan TS, Murali TS, Venkatesan G (2002) Occurrence and distribution of fungal endophytes in tropical forests across a rainfall gradient. Can J Bot 80:818–826CrossRefGoogle Scholar
  84. Thalavaipandian A, Ramesh V, Bagyalakshmi Muthuramkumar S, Rajendran A (2011) Diversity of fungal endophytes in medicinal plants of Courtallam hills, Western Ghats, India. Mycosphere 2:575–582CrossRefGoogle Scholar
  85. Thongsandee W, Matsuda Y, Ito S (2012) Temporal variations in endophytic fungal assemblages of Ginkgo biloba L. J For Res 17:213–218CrossRefGoogle Scholar
  86. Tilman D, Lehman CL, Thomsonn KT (1997) Plant diversity and ecosystem productivity: theoretical considerations. Proc Natl Acad Sci USA 4(94):1857–1861CrossRefGoogle Scholar
  87. Townsend AR, Cleveland CC, Houlton BZ, Alden CB, White JWC (2011) Multi-element regulation of the tropical forest carbon cycle. Front Ecol Environ 9:9–17CrossRefGoogle Scholar
  88. Webber J (1981) A natural biological-control of Dutch elm disease. Nature 292:449–451CrossRefGoogle Scholar
  89. Zhao K, Penttinen P, Guan T et al (2011) The diversity and anti-microbial activity of endophytic actinomycetes isolated from medicinal plants in Panxi Plateau China. Curr Microbiol 62:182–190CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Botany and ForestryVidyasagar UniversityMidnaporeIndia
  2. 2.Department of BiotechnologyOriental Institute of Science and TechnologyMidnaporeIndia

Personalised recommendations