In This Article Expand or collapse the "in this article" section Fungal Endophytes

  • Introduction
  • General Overviews
  • Books
  • Classification and Evolutionary Relationships
  • Diversity and Incidence
  • Nature of the Plant–Endophyte Symbiosis
  • Host-Population Biology
  • Coevolution of Endophytes and Hosts
  • Community and Ecosystem-Level Effects
  • Applied Uses

Ecology Fungal Endophytes
Gregory P. Cheplick
  • LAST REVIEWED: 29 April 2015
  • LAST MODIFIED: 29 April 2015
  • DOI: 10.1093/obo/9780199830060-0049


Symbiotic interactions between diverse species are widespread in nature. Endophytes are microbes, such as fungi and bacteria, that live symbiotically within plant species. Although fungal hyphae can be readily observed with a microscope in the roots, stems, and leaves of their plant hosts, only in the past several decades have ecologists recognized their potential to alter host growth and physiology, internal biochemistry, reproduction, and population dynamics. The symbiosis between plant host and endophyte is often viewed as a mutualism, but extensive studies have revealed that the symbioses can range from parasitism, to commensalism, to mutualism. This is partly because whether the effects of endophytes on their hosts are positive or negative depends greatly on environmental conditions and the genotype of host and endophyte. In the grass family, endophytic fungi often produce alkaloids, secondary compounds that can defend the host plants from insect and vertebrate herbivores. However, the concept of defensive mutualism has been the subject of considerable debate and has not yet been accepted by all researchers. The effects of endophytes have the potential to cascade upward to higher trophic levels, such as primary and secondary consumers. In addition to the alterations they potentially cause in the evolutionary ecology of host populations, endophytic fungi can cause changes in community and ecosystem properties. This article will provide an introduction to the diverse literature on the ecology and coevolutionary biology of fungal endophytes and their host-plant populations.

General Overviews

A sampling of the diversity of associations that occur between microbes and plants is provided in the Bacon and White 2000 collection of edited papers. The taxonomic diversity and life histories of two major groups of endophytic fungi, based on whether they are in the family Clavicipitaceae or not, have been categorized and described in Rodriguez, et al. 2009. Isaac 1992 provides an overview of a variety of plant–fungus interactions (e.g., pathogenic, mutualistic) at the cellular and biochemical levels from the perspective of fungal and plant-based physiology. The papers compiled in Redlin and Carres 1996 offer insights into the systematics, ecology, and evolution of fungal endophytes of trees and grasses. Many overviews have described the symbiotic continuum of plant–fungal interactions as ranging from antagonistic to mutualistic (e.g., Saikkonen, et al. 1998). By far, the fungal endophytes that have been most extensively investigated are those that inhabit the leaf, stem, and seed tissues of many grass species (Clay and Schardl 2002; also see Cheplick and Faeth 2009, cited under Books). These fungi are obligate biotrophs (Isaac 1992), and their hyphae grow in the intercellular spaces of the host tissues, as illustrated in Christensen and Voisey 2007. A much-cited overview of the evolutionary history of clavicipitaceous endophytes and the ecological consequences of their symbiosis with grasses is provided in Clay and Schardl 2002. Saikkonen, et al. 2004 considers the conflicting selective forces that influence the coevolution of the endophyte–plant symbiosis. A collection of eleven papers from an international symposium on fungal endophytes provides further information on endophyte diversity worldwide, biochemistry, and ecological interactions (White and Bacon 2012).

  • Bacon, Charles W., and James F. White Jr., eds. 2000. Microbial endophytes. New York: Dekker.

    Employing a broad definition of endophyte to include any microbial inhabitant of the living, internal tissues of a host plant, this collection of seventeen papers includes articles on bacterial symbionts, mycorrhizal fungi, and endophytic fungi of stems and leaves. Examines morphology, physiology, ecology, genetic-molecular biology, and evolution of endophytic microbes.

  • Christensen, M. J., and C. R. Voisey. 2007. The biology of the endophyte/grass partnership. In Proceedings of the Sixth International Symposium on Fungal Endophytes of Grasses: Christchurch, New Zealand, March 25–28, 2006. Edited by A. J. Popay and Errol Ross Thom, 123–133. Dunedin, New Zealand: New Zealand Grassland Association.

    Important for its many excellent micrographs that show endophytic hyphae by using a variety of microscopic techniques. Also provides an overview of fungal growth and development within the host-plant tissues.

  • Clay, Keith, and Christopher Schardl. 2002. Evolutionary origins and ecological consequences of endophyte symbiosis with grasses. American Naturalist 160.S4: S99–S127.

    DOI: 10.1086/342161

    A highly cited, useful overview of the life history and phylogeny of fungal endophytes, alkaloid biochemistry, and consequences of endophyte infection to plant populations, communities, and ecosystems. Appropriate for the beginning graduate student or researcher new to the field. Available online for purchase or by subscription.

  • Isaac, Susan. 1992. Fungal-plant interactions. London: Chapman & Hall.

    A general introduction to the diversity of fungal interactions with plants, mostly from a physiological and biochemical perspective. Covers phytohormones, carbohydrate metabolism and transport, and fungal life histories. Suitable for advanced undergraduate or graduate students and botanists or mycologists researching symbiosis.

  • Redlin, Scott C., and Lori M. Carris, eds. 1996. Endophytic fungi in grasses and woody plants: Systematics, ecology, and evolution. St. Paul, MN: American Phytopathological Society.

    A collection of eleven chapters that explore the ecological and evolutionary aspects of fungal endophytes in trees (including palms) and grasses.

  • Rodriguez, R. J., J. F. White Jr., A. E. Arnold, and R. S. Redman. 2009. Fungal endophytes: Diversity and functional roles. New Phytologist 182.2: 314–330.

    DOI: 10.1111/j.1469-8137.2009.02773.x

    Based on phylogeny and life history, fungal endophytes are categorized as clavicipitceous or not and separated into distinct functional groups. Includes much information on the potential benefits and costs to plants infected by endophytes and summarizes much pertinent literature.

  • Saikkonen, Kari, Stanley H. Faeth, Marjo Helander, and T. J. Sullivan. 1998. Fungal endophytes: A continuum of interactions with host plants. Annual Review of Ecology and Systematics 29:319–343.

    DOI: 10.1146/annurev.ecolsys.29.1.319

    A highly cited review article that focuses on the wide range of endophyte–host interactions that occur in nature, from antagonistic, to neutral, to mutualistic. Available online for purchase or by subscription.

  • Saikkonen, Kari, Piippa Wäli, Marjo Helander, and Stanley H. Faeth. 2004. Evolution of endophyte-plant symbioses. Trends in Plant Science 9.6: 275–280.

    DOI: 10.1016/j.tplants.2004.04.005

    Discusses the relevant selection pressures that impact the coevolutionary interactions of endophytes with their hosts, including the genetic consequences of horizontal versus vertical transmission. Available online for purchase or by subscription.

  • White, James F., Jr., and Charles W. Bacon, eds. 2012. Special issue: The secret world of endophytes. Fungal Ecology 5.3.

    DOI: 10.1016/j.funeco.2012.03.003

    Special journal issue with eleven papers on the diversity of fungal endophytes in select geographical regions, biochemistry, and ecological interactions of hosts and insects.

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