Little is known about the influence of host genotype and phytohormones on the composition of fungal endophytic communities. We investigated the influence of host genotype and phytohormones on the structure of the fungal endophytic communities of tomato roots by amplicon sequencing of the ITS1 region and combined this approach with isolation and functional characterization of the isolates. A significant effect of the host genotype on the dominant fungal species was found by comparing the cultivars Castlemart and UC82B and, surprisingly, root pathogens were among the most abundant taxa. In contrast, smaller changes in the relative abundance of the dominant species were found in mutants impaired in jasmonic acid biosynthesis (def1) and ethylene biosynthesis (8338) compared to the respective wild types. However, def1 showed significantly higher species richness compared to the wild type. Analysis of the phytohormone profiles of these genotypes indicates that changes in the phytohormone balance may contribute to this difference in species richness. Assessing the lifestyle of isolated fungi on tomato seedlings revealed the presence of both beneficial endophytes and latent pathogens in roots of asymptomatic plants, suggesting that the interactions between members of the microbiome maintain the equilibrium in the community preventing pathogens from causing disease.
There are increasing efforts aiming to utilise endophytes as biological control agents (BCAs) to improve crop production. However, reliability remains a major practical constraint for the development of novel BCAs. Many organisms are adapted to their specific habitat; it is optimistic to expect that a new organism added can find a niche or even out-compete those adapted and already present. Our approach for isolating novel BCAs for specific plant diseases is therefore to look in healthy plants in a habitat where disease is a problem, since we predict that it is more likely to find competitive strains among those present and adapted. In vitro inhibitory activities often do not correlate with in planta efficacy, especially since endophytes rely on intimate plant contact. They can, however, be useful to indicate modes of action. We therefore screen for in planta biological activity as early as possible in the process in order to minimise the risk of discarding valuable strains. Finally, some fungi are endophytic in one situation and pathogenic in another (the mutualism-parasitism continuum). This depends on their biology, environmental conditions, the formulation of inoculum, the health, developmental stage and cultivar of the host plant, and the structure of the plant microbiome .
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 culture‐dependent and culture‐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.
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