Plant Endophytes


Endophytes are defined as microorganisms colonising the interior of plants without causing disease. They comprise mainly fungi and bacteria, and their lifestyle range from merely receiving shelter and nutrients from the host to interactions benefitting both themselves and the host plant. In recent years, there has been an increased interest in understanding the communities of organisms inside plants; how they influence the host and how they can be utilised to benefit plants and humans. Therefore, the transmission and recruitment of endophytes, as well as methods to study the composition of endophytic communities, are important issues for successful exploitation. Beneficial effects include protection against biotic stress caused by pests and pathogens as well as against abiotic stress, for instance, drought, salinity and temperature. Furthermore, endophytes can promote growth by production of plant hormones and nutrient acquisition and some endophytes can be used for bioremediation and production of pharmaceuticals and nutraceuticals.

Key Concepts

  • Endophytes are organisms living inside plants without causing disease.
  • Most endophytes are commensalistic, but some are mutualistic.
  • Most endophytes are bacteria and fungi.
  • Endophyte communities can be studied by cultureā€dependent and cultureā€independent methods.
  • Recruitment of endophytes can be from environment or from mother plants.
  • Endophytes can protect plants from biotic and abiotic stress.
  • Endophytes can help in nutrient acquisition for the plant and cause growth promotion.
  • Endophytes can help in bioremediation and participate in the production of specialised metabolites with industrial application.

Keywords: endophyte; fungi; bacteria; transmission; biotic stress; abiotic stress; growth promotion; nutrient acquisition; bioremediation; specialised metabolites

Figure 1. Spectrum of interactions between plant and plant‐associated microbes. Lifestyle strategy of plant‐associated microorganisms can range from mutualism, where both organisms benefit from the interaction to situations in which the microorganism harms the host, described as parasitism. Blue squares and lines illustrate endophytic colonisation of the plant and the black colour illustrates the damage caused by plant pathogens.
Figure 2. Methods for characterisation of the endophyte communities in plants using culture‐independent and culture‐dependent approaches.
Figure 3. Where endophytes come from and how they are transmitted. (a) Horizontal transmission of microorganisms originating from soil, air and seeds. (b) Vertical transmission of systemic microorganisms from plant to plant by seed, pollen or vegetative propagation material. Yellow squares illustrate microorganisms that can be transmitted to the plant from the environment. Blue squares and lines illustrate endophytic colonization of the plant.
Figure 4. Endophytes interact with the host plant and other microorganisms. Some of the mechanisms used by the endophytes in these interactions have the potential for use in plant growth promotion and abiotic stress alleviation as well as biological control of pathogenic microorganisms. Blue squares and lines illustrate endophytic colonization of the plant.


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Further Reading

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Sessitsch A, Hardoim P, Döring J, et al. (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Molecular Plant‐Microbe Interactions 25: 28–36.

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Jørgensen, Hans J Lyngs, Collinge, David B, Rojas, Edward C, Latz, Meike A C, Manzotti, Andrea, Ntana, Fani, and Jensen, Birgit(Mar 2020) Plant Endophytes. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0028893]