Transient and vertically transmitted microbiome of Quercus robur Raw amplicon sequencing reads

Here we tested the hypothesis that the plant microbiome is at least partially inherited through vertical transmission. We also investigated where microbes reside within a seed, and how microbes are subsequently transmitted from the seed to belowground and aboveground plant parts. To this aim, an experimental culturing device was constructed to grow oak seedlings in a microbe-free environment and keep belowground and aboveground tissues separated.Amplicon sequencing of fungal ITS2 and bacterial 16S rDNA revealed that the seed microbiome is diverse and non-randomly distributed within an acorn. The large majority (>95%) of fungi and bacteria present in the acorn were transmitted to developing seedling. The microbial composition of the phyllosphere strongly resembled the composition found in the embryo, in contrast to the roots and pericarp contained distinct communities. Similar relationships were observed for both fungi and bacteria. Collectively, the obtained data demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within a seed and the plant developed from that seed, indicating inheritance, niche differentiation, and divergent transmission routes for the establishment of root and phyllosphere communities in oak seedlings. Data from the conducted study provides new information on the importance of the maternal environment as a source of the seedling microbiome. These findings have significant implications on our understanding of the continuity of the plant microbiome across generations.