Insights into the community structure and lifestyle of the fungal root endophytes of tomato by combining amplicon sequencing and isolation approaches with phytohormone profiling

Abstract

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.

Microbiome Modulation—Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants

“…Interestingly, all healthy plant microbiomes naturally also contain potential pathogens in seeds as well as in the rhizosphere ( Berg et al, 2005 ; Wassermann et al, 2019 ). Manzotti et al (2020) showed that after isolation and re-inoculation, they could exert their pathogenicity on the same host plant ( Manzotti et al, 2020 ). This is an interesting observation underlying the conclusion that the balance and evenness within the plant microbiome is crucial for plant health.…”

Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars

“…With only a few rare exceptions, plants are generally associated with highly diversified microbial communities ( Heil, 2015 ; Manzotti et al, 2020 ). These microorganisms are closely associated with ecosystem functions, which can be either beneficial or harmful ( Graham et al, 2016 ).…”

Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato

“…Scanning electron micrographs of leaves and isolation studies already indicated trichome surfaces as preferential microbial niche [23,24] but currently there are no microbiome data to evidence that. Recently, it was shown for the tomato rhizosphere how plants shape their endophytic microbiome due to the biosynthesis of phytohormones [25]. We therefore hypothesized that due to their specific chemical composition, glandular trichomes may form a specific microbiome distinct from that of the leaf.…”