The composition and complex interaction of microorganisms in forest trees is still not very well understood. However, current studies on cultivated plants indicate that the microbiome can have a significant influence on plant development, vitality and susceptibility to pathogens.
In the project “TreeLAMP”, the composition of the microbial community of ten adult trees and nine seedlings of Douglas fir was characterised in an exploratory study using sequence-based methods. Approximately 9.5 million fungal sequences (ITS1) and approx. 4.3 million bacterial sequences (16S rRNA gene) were generated over all samples by Illumina MiSeq sequencing. In a first step the quality of the sequence data was checked and sequences with low quality were filtered with dada2. The taxonomic classification was carried out with the program kaiju (database NCBI nr+euk).
For the characterisation of the fungal community, between 13,817 and 410,464 sequences per tree sample were analysed. In total 83 fungal species were identified. However, on average 0.5 % of the sequences could not be classified and 48.1 % could not be determined up to species level. The DNA of the bacterial community shows with 899 to 11,807 significantly less sequences per sample. But in comparison 79.4 % of the sequences could be determined up to species level, 15.2 % of the sequences were assigned to at most a genus, and 5.3 % could not be classified. In total 142 bacterial species were identified. In summary, the composition of the fungal and bacterial species community differs, as expected, between adult trees and seedlings. Differences in species composition were also observed within adult trees and seedlings, whereby the bacterial community was generally more heterogeneous than the fungal community.