Bridging metabolome and microbiome diversification

The plant microbiome has been extensively studied in recent years, whereby a variety of plant-microbe interactions that are essential for growth and health of the host plant were discovered. However, the majority of these interactions and functions, such as the impact of the microbiome on the metabolome, are poorly understood. Plants use metabolites to shape and direct their associated microbial communities; however, there is some evidence that, vice versa, the plant-associated microorganisms influence the metabolic fingerprint of their host plant, leading to different metabolic phenotypes. The overall objective of the project is to experimentally investigate the possibility to direct the plants chemical profile via plant-associated microorganisms. Studies concerning correlations between microbial communities and plant metabolites will be conducted on two Asteraceae medicinal plants, the German chamomile (Matricaria chamomilla L.) and the pot marigold (Calendula officinalis L.). These plant species were selected as suitable model plants for these studies because of their rich secondary metabolism with particularly high levels of flavonoids, sesquiterpenes, and triterpenes, their known diversification in chemical profiles, and their cultivation and medicinal utilization all over the world. An interconnected experimental design enables (i) to analyze the effect of the soil microbiome on the plant metabolome, (ii) the development of a model for predicting metabolite production, (iii) targeted inoculation experiments to verify correlations, and (iv) to elucidate the functional linkage of the rhizosphere microbiome by a metagenomic study. A multi-phasic approach exploiting novel meta-omics technologies will be used to deeply analyze plants grown in natural ecosystems as well as in specifically developed in vitro systems. Promising correlations will be evaluated in detail under strictly controlled conditions. We aim to elucidate the linkage of the plant microbiome and metabolome in order to improve the plants usability as bioresource for compounds with therapeutic and biotechnological relevancy.

The co-evolved and specifically composed plant microbiota represents an enormous biodiversity on Earth. However, less is known about functional diversity and whether it correlates with structural diversity. In the present study, both were analyzed by disentangling the microbiota of three medicinal plants at the root-soil interface grown in desert ecosystems under organic farming. Significant differences were observed for structural diversity between all investigated microhabitats (soil, rhizosphere, endorhiza) and plant species (chamomile, marigold, nightshade). Unique genera were identified for each plant species. To explore this plant-driven effect for functional understanding, deepening metagenomics analyses were implemented for rhizosphere samples, which showed the most different composition. However, all rhizosphere microbiomes were characterized by similar functions comprising mainly i) plant nutrition and metabolic interplay (e.g. ion, amino acid, vitamin, lipid, and carbohydrate transport and metabolism, secondary metabolites biosynthesis, transport, and catabolism), ii) plant health (e.g. defense mechanisms, chaperones), and iii) biogeochemical cycling. A lot of signatures support the high activity, which is well known for the root-soil interface. Binning resulted in 298 metagenome-assembled genomes (MAGs); their taxonomy confirmed plant-specific bacteria. Three selected plant-specific MAGs for each plant underlined the metagenome-mined rhizosphere functions, showed multifunctionality and, despite taxonomic differences, functional similarity. Sphingobium, Pseudomonas, and Gemmatirosa multifunctionally contributed to the overall functioning of the rhizosphere; the highest number of 79 encoded rhizospheric core functions was observed for the multifunctionally equipped Sphingobium MAG. The study uncovered functional similarity in structurally different rhizosphere microbiomes and underlines the importance of rhizosphere functioning and diversity for plant and ecosystem health.