Microbiome of medicinal plants. Phyllosphere

During the recent past many studies have investigated the microbiome of plants including several medicinal plants (MP). Microbial communities of the associated soil, rhizosphere and the above-ground organs have been included but there is still scarce information on their seasonal development and in particular considering simultaneously different plant organs. Studies addressed predominantly either the prokaryotic or fungal microbiome. Further, a distinction of epi- and endophytic communities of the above-ground plant organs has been made relatively rarely. Therefore we made a comprehensive investigation of the bacterial and fungal microbiome of the MP Achillea millefolium and studied the epi- and endophytic microbial communities of leaves, buds and flower between spring and summer together with the microbiome of the associated soil at one location. Further we assessed the core microbiome of Achillea of four different locations at distances up to 250 km in southern Germany and Switzerland. In addition the bacterial and fungal epi- and endophytic leaf microbiome of the arborescent shrub Hamamelis virginiana and the associated soil was investigated. The results show a generally decreasing diversity of both microbial communities from soil to flower of Achillea. The diversity of both endophytic leaf communities of Achillea increased from April to July whereas that of the epiphytic leaf communities decreased. In contrast, the diversity of the fungal communities of both leaf compartments and that of epiphytic bacteria of Hamamelis increased over time indicating plant-specific differences in the temporal development of the microbial communities. Both MPs exhibited distinct microbial communities with plant-specific but also overlapping taxa. The core taxa of Achillea constituted a lower fraction of the number of total taxa than of the total abundance of all taxa. The results of our study provide a basis to relate interactions of the microbiome with their host plant to the production of bioactive compounds.