Dark matter of an orchid: metagenome of the microbiome associated with the rhizosphere of Dactylorhiza traunsteineri

Plant microbiota forms complex co-associations with its host, promoting health in natural environments. Root-associated bacteria (RAB) colonize root compartments and can modulate plant functions by producing bioactive compounds as part of their secondary metabolism. We present an in-depth analysis of the rhizosphere-associated microbiome of the endangered marsh orchid Dactylorhiza traunsteineri. Using deep sequencing of 16S rRNA genes, we identified Proteobacteria, Actinobacteria, Myxococcota, Bacteroidota, and Acidobacteria as predominant phyla associated with the rhizosphere of D. traunsteineri. Using deep shotgun metagenomics and de novo assembly, we extracted high-quality metagenome-assembled genomes (MAGs), revealing significant metabolic and biosynthetic potentials of the D. traunsteineri’s RABs. Our study offers a comprehensive investigation into the microbial community of the D. traunsteineri rhizosphere, highlighting a potential novel source of critical bioactive substances. Our study offers novel insights and a robust platform for future investigations into D. traunsteineri's rhizosphere, crucial for understanding plant-microbe interactions and aiding conservation efforts for endangered orchids.