Temperate tree microbiomes: Divergent soil and phyllosphere microbial communities share few but dominant taxa

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Aims: The phyllosphere and soil are crucial and distinct microbial spheres in forests, connected through trees that interact with both. As part of the tree's holobiont, these communities are vital to the fitness and evolution of the host. Differences between the spheres may be particularly evident at the two extreme ends of tall and long-lived trees of natural temperate forest; the top-canopy and the soil. Here, we evaluated the connectivity between the top-canopy and soil microbial communities of European beech and Norway spruce trees to determine the significance of tree-sphere and host-species identity, and to assess the contribution of taxa inhabiting both spheres.

Methods: Bacterial and fungal community composition was determined through metabarcoding analysis of linked top-canopy leaf and bulk soil samples collected from tall (old) trees in the natural forest of Bavarian Forest National Park.

Results: This study shows sphere-specific communities in European temperate forests, characterized by low connectivity. Results highlight that spheres exert stronger influence than host identity. Only a few taxa inhabited both spheres, yet they accounted for the bulk of the (relative) abundance in each sphere.

Conclusion: Analysing the divergence and shared characteristics of these interlinked communities redefines the tree holobiont concept and enhances our understanding of the evolution of plant-associated microbial communities in a sphere-specific manner. This study emphasizes the importance of examining multiple microbiome components for a thorough understanding of temperate forest ecology, while also highlighting the existence of a small group of overlapping taxa that may play a bigger role than previously anticipated.

Original languageEnglish
JournalPlant and Soil
Early online date3 Nov 2023
Publication statusE-pub ahead of print/First online - 3 Nov 2023


  • 16S rRNA gene
  • Bulk soil
  • ITS rRNA region
  • Phyllosphere
  • Temperate forest microbiome
  • eDNA


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