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

Andrea Manzotti*, Alessandro Bergna, Meike Burow, Hans J L Jørgensen, Tomislav Cernava, Gabriele Berg, David B Collinge, Birgit Jensen

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article numberfiaa052
JournalFEMS Microbiology Ecology
Issue number5
Publication statusPublished - 1 May 2020


  • amplicon sequencing
  • fungal endophytes
  • fungal lifestyle
  • host genotype
  • microbiome
  • phytohormones

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Microbiology
  • Ecology

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