Endophytic Fungi


Endophytic fungi are those that colonise the tissues of virtually all terrestrial plants species. Endophytism has evolved multiple times among disparate lineages of fungi. Thus, there are currently no natural systems for classifying endophytic fungi. Not surprisingly, their impacts on host plants may be negative, neutral or positive depending on both fungus–host combination and environmental conditions. From an ecological point of view, endophytic fungi may function nonexclusively as weak pathogens, saprotrophs or mutualists, depending on circumstances. Because some interactions between endophytic fungi and plants are highly beneficial to plants, particularly under stressful conditions, there is an interest in inoculating agricultural crops with particular fungal strains to improve yield. However, care must be exercised because a fungus that is beneficial to one plant species under particular circumstances may be less so under other circumstances or to other plant species.

Key Concepts

  • Endophytic fungi colonise living tissues of virtually all terrestrial plants.
  • Multiple lineages of fungi have evolved to engage in this symbiosis.
  • Transmission of fungal propagules may be either vertical or horizontal.
  • When the transmission is horizontal, colonisation may be limited by distance to inoculum source.
  • Endophytic fungi benefit from the symbiosis, but the net effect on the plant may be positive, neutral or negative.
  • Some endophytic fungi may function as plant pathogens under certain circumstances.
  • Some endophytic fungi may function as decomposers of plant litter.
  • Some endophytic fungi may confer a substantial benefit to their host plants.
  • Because endophytic fungi influence traits that determine plant fitness, it is useful to consider the symbiosis a holobiont.
  • Endophytic fungal inoculants are being considered in agricultural systems, but their impacts on nontarget plant species need to be carefully considered.

Keywords: biotrophic; decomposer; endophytic; holobiont; mutualistic; pathogenic; saprotrophic fungi


Abbott LK, Robson A and Hall I (1983) Introduction of vesicular arbuscular mycorrhizal fungi into agricultural soils. Australian Journal of Agricultural Research 34: 741–749.

Afkhami ME and Rudgers JA (2008) Symbiosis lost: imperfect vertical transmission of fungal endophytes in grasses. The American Naturalist 172: 405–416. DOI: 10.1086/589893.

Arnold AE, Mejía LC, Kyllo D, et al. (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proceedings of the National Academy of Sciences 100: 15649–15654. DOI: 10.1073/pnas.2533483100.

Arnold A and Lutzoni F (2007) Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots? Ecology 88: 541–549.

Bordenstein SR and Theis KR (2015) Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLoS Biology 13: 1–23. DOI: 10.1371/journal.pbio.1002226.

Busby PE, Ridout M and Newcombe G (2016) Fungal endophytes: modifiers of plant disease. Plant Molecular Biology 90: 645–655. DOI: 10.1007/s11103‐015‐0412‐0.

Carroll G (1988) Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology 69: 2–9.

Cheplick GP and Clay K (1988) Acquired chemical defenses in grasses: the role of fungal endophytes. Oikos 52: 309–318. DOI: 10.2307/3565204.

Clay K (1988) Fungal endophytes of grass: a defensive mutualism between plants and fungi. Ecology 69: 10–16. DOI: 10.2307/1943155.

Cowan M (1999) Plant products as antimicrobial agents. Clinical Microbiology Reviews 12: 564–582. DOI: 10.1016/j.tibtech.2009.09.002.

Doebeli M and Knowlton N (1998) The evolution of interspecific mutualisms. Proceedings of the National Academy of Sciences 95: 8676–8680.

Engel P and Moran NA (2013) The gut microbiota of insects ‐ diversity in structure and function. FEMS Microbiology Reviews 37: 699–735. DOI: 10.1111/1574‐6976.12025.

Foster KR and Wenseleers T (2006) A general model for the evolution of mutualisms. Journal of Evolutionary Biology 19: 1283–1293. DOI: 10.1111/j.1420‐9101.2005.01073.x.

Gange AC, Dey S, Currie AF and Sutton BC (2007) Site‐ and species‐specific differences in endophyte occurrence in two herbaceous plants. Journal of Ecology 95: 614–622.

Gleason H (1926) The individualistic concept of the plant association. Bulletin of the Torrey Botanical Club 53: 7–26.

Gould S and Lewontin R (1979) The spandrels of San Marco and the panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society B: Biological Sciences 205: 581–598.

Hjeljord LG and Tronsmo A (2003) Effect of germination initiation on competitive capacity of Trichoderma atroviride P1 conidia. Phytopathology 93: 1593–1598. DOI: 10.1094/PHYTO.2003.93.12.1593.

Hubbard M, Germida J and Vujanovic V (2012) Fungal endophytes improve wheat seed germination under heat and drought stress. Botany 90: 137–149. DOI: 10.1139/b11‐091.

Johnson LJ, De Bonth ACM, Briggs LR, et al. (2013) The exploitation of epichloae endophytes for agricultural benefit. Fungal Diversity. DOI: 10.1007/s13225‐013‐0239‐4.

Koide RT, Sharda JN, Herr JR and Malcolm GM (2006) Ectomycorrhizal fungi and the biotrophy – saprotrophy continuum. The New Phytologist 178: 230–233.

Koide RT, Ricks KD and Davis ER (2017) Climate and dispersal influence the structure of leaf fungal endophyte communities of Quercus gambelii in the eastern Great Basin, USA. Fungal Ecology 30: 19–28. DOI: 10.1016/j.funeco.2017.08.002.

Latch G and Christensen M (1985) Artificial infection of grasses with endophytes. The Annals of Applied Biology 107: 17–24. DOI: 10.1111/j.1744‐7348.1985.tb01543.x.

López‐Bucio J, Pelagio‐Flores R and Herrera‐Estrella A (2015) Trichoderma as biostimulant: exploiting the multilevel properties of a plant beneficial fungus. Scientia Horticulturae 196: 109–123. DOI: 10.1016/j.scienta.2015.08.043.

Mithöfer A and Boland W (2012) Plant defense against herbivores: chemical aspects. Annual Review of Plant Biology 63: 431–450. DOI: 10.1146/annurev‐arplant‐042110‐103854.

Moubasher A, Abdel‐Sater M and Zeinab S (2017) Yeasts and filamentous fungi inhabiting guts of three insect species in Assiut, Egypt. Mycosphere 8: 1297–1316. DOI: 10.5943/mycosphere/8/9/4.

Müller MM, Valjakka R, Suokko A and Hantula J (2001) Diversity of endophytic fungi of single Norway spruce needles and their role as pioneer decomposers. Molecular Ecology 10: 1801–1810. DOI: 10.1046/j.1365‐294X.2001.01304.x.

Orole OO and Adejumo TO (2009) Activity of fungal endophytes against four maize wilt pathogens. African Journal of Microbiology Research 3: 969–973.

Pan JJ and May G (2009) Fungal‐fungal associations affect the assembly of endophyte communities in maize (Zea mays). Microbial Ecology 58: 668–678. DOI: 10.1007/s00248‐009‐9543‐7.

Redman RS, Dunigan DD and Rodriguez RJ (2001) Fungal symbiosis from mutualism to parasitism: who controls the outcome, host or invader? The New Phytologist 151: 705–716. DOI: 10.1046/j.0028‐646x.2001.00210.x.

Redman RS, Kim YO, Woodward CJDADA, et al. (2011) Increased fitness of rice plants to abiotic stress via habitat adapted symbiosis: a strategy for mitigating impacts of climate change. PLoS One 6: 1–10. DOI: 10.1371/journal.pone.0014823.

Ricks KD and Koide RT (2019) Biotic filtering of endophytic fungal communities in Bromus tectorum. Oecologia 189: 993–1003. DOI: 10.1007/s00442‐019‐04388‐y.

Rodriguez RJ, Redman RS and Henson JM (2004) The role of fungal symbioses in the adaptation of plants to high stress environments. Mitigation and Adaptation Strategies for Global Change 9: 261–272. DOI: 10.1023/B:MITI.0000029922.31110.97.

Rodriguez RJ and Redman RS (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. Journal of Experimental Botany 59: 1109–1114. DOI: 10.1093/jxb/erm342.

Rodriguez RJ, Henson J, Van Volkenburgh E, et al. (2008) Stress tolerance in plants via habitat‐adapted symbiosis. The ISME Journal 2: 404–416. DOI: 10.1038/ismej.2007.106.

Rodriguez R, White J, Arnold A and Redman R (2009) Fungal endophytes: diversity and functional roles. The New Phytologist 182: 314–330. DOI: 10.1111/j.1469‐8137.2009.02773.x.

Saikkonen K, Wali P, Helander M and Faeth SH (2004) Evolution of endophyte‐plant symbioses. Trends in Plant Science 9: 275–280. DOI: 10.1016/j.tplants.2004.04.005.

Schreiner R and Koide R (1993) Antifungal compounds from the roots of mycotrophic and non‐mycotrophic plant species. The New Phytologist 123: 99–105.

Schwartz MW, Hoeksema JD, Gehring CA, et al. (2006) The promise and the potential consequences of the global transport of mycorrhizal fungal inoculum. Ecology Letters 9: 501–515. DOI: 10.1111/j.1461‐0248.2006.00910.x.

Shah NH and Paulsen GM (2003) Interaction of drought and high temperature on photosynthesis and grain‐filling of wheat. Plant and Soil 257: 219–226. DOI: 10.1023/A:1026237816578.

Sherwood‐Pike M, Stone JK and Carroll GC (1986) Rhabdocline parkeri a ubiquitous foliar endophyte of Douglas fir. Canadian Journal of Botany 64 (64): 1849–1855.

Sieber TN (2007) Endophytic fungi in forest trees: are they mutualists? Fungal Biology Reviews 21: 75–89. DOI: 10.1016/j.fbr.2007.05.004.

Stacey G and Upchurch RG (1984) Rhizobium inoculation of legumes. Trends in Biotechnology 2: 65–70. DOI: 10.1016/0167‐7799(84)90012‐X.

Streeter JG (1994) Failure of inoculant rhizobia to overcome the dominance of indigenous strains for nodule formation. Canadian Journal of Microbiology 40: 513–522. DOI: 10.1139/m94‐084.

Szink I, Davis E, Ricks KD and Koide R (2016) New evidence for broad trophic status of leaf endophytic fungi of Quercus gambelii. Fungal Ecology 22: 2–9. DOI: 10.1016/j.bmcl.2008.01.042.

Van Oppen MJH, Palstra FP, Piquet AMT and Miller DJ (2001) Patterns of coral‐dinoflagellate associations in Acropora: significance of local availability and physiology of Symbiodinium strains and host‐symbiont selectivity. Proceedings of the Royal Society B: Biological Sciences 268: 1759–1767. DOI: 10.1098/rspb.2001.1733.

Vincent JB, Weiblen GD and May G (2016) Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees. Molecular Ecology 25: 825–841. DOI: 10.1111/mec.13510.

Waqas M, Khan AL, Hamayun M, et al. (2015) Endophytic infection alleviates biotic stress in sunflower through regulation of defence hormones, antioxidants and functional amino acids. European Journal of Plant Pathology 141: 803–824. DOI: 10.1007/s10658‐014‐0581‐8.

Weir T, Huff D, Christ B and Romaine CP (2017) RAPD‐PCR analysis of genetic variation among isolates of Alternaria solani and Alternaria alternata from potato and tomato. Mycologia 90: 813–821.

Welte CU, de Graaf RM, van den Bosch TJM, et al. (2016) Plasmids from the gut microbiome of cabbage root fly larvae encode SaxA that catalyses the conversion of the plant toxin 2‐phenylethyl isothiocyanate. Environmental Microbiology 18: 1379–1390. DOI: 10.1111/1462‐2920.12997.

Zhou J, Yang H, Tang F, et al. (2017) Relative roles of competition, environmental selection and spatial processes in structuring soil bacterial communities in the Qinghai‐Tibetan Plateau. Applied Soil Ecology 117: 223–232. DOI: 10.1016/j.apsoil.2017.05.012.

Further Reading

Eberl F, Uhe C and Unsicker SB (2018) Friend or foe? The role of leaf‐inhabiting fungal pathogens and endophytes in tree‐insect interactions. Fungal Ecology 38: 1–9.

Hardoim PR, van Overbeek LS and van EJD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends in Microbiology 16: 463–471.

Hardoim PR, van Overbeek LS, Berg G, et al. (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiology and Molecular Biology Reviews 79: 293–320.

Rho H, Hsieh M, Kandel SL, et al. (2018) Do endophytes promote growth of host plants under stress? A meta‐analysis on plant stress mitigation by endophytes. Microbial Ecology 75: 407–418.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Koide, Roger T(Nov 2019) Endophytic Fungi. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0027206]