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Do plant microbiomes shape adaptive potential of their hosts? A hologenomic approach to distribution and adaptation.

Carlsberg Foundation Reintegration Fellowships


Explaining why related species have very different abilities to spread, adapt and survive is a central question in evolutionary biology. Plants host a broad range of microorganisms in e.g. their roots and leaves, and these microorganisms are recognized as key to the ability of plants to explore resources in its environment. The hologenome theory states that microorganisms should be considered an integral part of their host, and suggest that adaptive genomic changes in a host also can include changes in its microbiome. I will investigate if a plant's individual genome determines the range and diversity of microorganisms it is able to associate with, and whether any differences in microbiomes between plant species are related to different abilities to spread and adapt.


Describing the correlation between individual plant genotypes and their microbiomes within and among habitats is the first step towards understanding which role microbionts play in plant distribution patterns and adaptation to different habitats. If range and variability of microbiont associations is an expression of adaptability of species, it could provide an alternative explanation to what determines species distribution in plants in addition to already acknowledged biotic and abiotic factors.


I will use orchids and their associated microbiomes as a model system to study the association between wild plant genomes, their microbiont communities and their habitat. Orchid microbiont communities profiles will be generated from bacterial and fungal metagenomic analysis of tissue samples from individual orchids and coupled with host genomic variation using individual level sampling of two orchid species. This will allow me to explore the link between individual plant genotype and microbiont community profiles. To investigate if microbiont community diversity is correlated with ability to spread and adapt, I will generate microbiont community profiles for 20 congeneric orchid species and correlate it with the extent of their distribution areas and the diversity of habitats they use.


Wild plant populations need to rapidly respond and adapt to the accelerating climatic and landscape changes in order to survive and reproduce. This project will enhance our knowledge on the role microorganisms play for a plants' ability to exploit and adapt to its environment, of significance for predicting effects of global change of plants species. The results could also offer an alternative explanation as to why some orchid species are rare and/or threatened and provide specific habitat usage knowledge relevant for conservation of the orchid species included in the project.