"Promoting resistance through microbiome and epigenetic changes"

Background and Objective

Climate change and globalization lead to the spread of new, non-native pests in the EU, which can cause greater damage than in their countries of origin due to a lack of co-evolution. This threatens individual forest ecosystems economically and in their sustainability, as well as the biodiversity of trees. The project idea is based on the observation that within some tree genera, certain species, subspecies, or varieties possess resistance to pathogenic fungi. Examples include Asian elm species that are often resistant to the causative agent of Dutch elm disease, and differences in susceptibility of various Douglas fir varieties to Swiss needle cast. Instead of identifying genetically determined resistances and transferring them through crossbreeding, which would lead to the loss of original species, the project focuses on the microbiome - the community of fungi and bacteria living in or on plants. The microbiome has a significant influence on resistance to pathogens. The aim is to establish an effective method for transferring microbiomes from resistant species to susceptible tree species. Various transfer methods will be tested, with the goal of transferring the complete microbiome of resistant trees. The effect will be evaluated through resistance tests. In addition to phenotypic assessment, DNA studies will provide insight into whether microbiome transfer triggers epigenetic changes that lead to resistance (priming). The project utilizes new insights into the importance of the microbiome, epigenome, and priming for resistance development. These factors can influence resistance without altering the DNA sequence. Various methods for transferring microorganisms have already been tested on woody plants, e.g., stem inoculation, direct injection, leaf inoculation, and root inoculation. The planned project aims to transfer complete microbiomes instead of just individual isolates or consortia. If successful, "microbiome therapy" could be adapted to other host-pathogen systems and represent an efficient method for developing resistance against rapidly spreading tree diseases.

Approach

The project includes various work packages:

WP1. Comparative microbiome analysis of seedlings, seeds, and in vitro plants of resistant (Chinese elm, coastal Douglas fir) and susceptible (mountain elm, interior Douglas fir) species or varieties

WP2. Microbiome transfer through incubation of seedlings/plants with microbiome extract

WP3. Microbiome transfer through graftings

WP4. Establishment and implementation of resistance tests

WP5. Investigation of epigenetic changes after microbiome transfer