The plant hologenome – is plant adaptative potential shaped by its microbionts?

Project Information

PLANTHOLOGENOME

Grant agreement ID: 101067963

DOI

10.3030/101067963

Project closed

EC signature date 14 November 2022

Start date 1 September 2023

End date 31 December 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 230 774,40

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 1 - PLANTHOLOGENOME (The plant hologenome – is plant adaptative potential shaped by its microbionts?)

Reporting period: 2023-09-01 to 2025-12-31

Summary of the context and overall objectives of the project

Explaining why related species have very different abilities to spread, adapt and survive is a central question in evolutionary biology. The hologenome theory can offer a novel perspective on this, hypothesizing that any plant species’ ability to adapt to its environment is affected by the range of microbial symbionts it is able to associate with, and as this ability differs among hosts, it must be determined by variation encoded in the host genomes. This project explored this hypothesis using orchids and their microbiome as a model system for plant hologenomic studies. Orchids constitute the world’s largest groups of flowering plants, are obligate dependent on symbiotic relationships with specific mycorrhizal fungi for germination, and many species are rare and/or threatened . Orchid hologenomic studies are hence useful for both exploring general macro-ecological patterns of plant microbiomes, as well as generating specific knowledge on habitat exploration ability relevant for conservation. The objectives were to 1) Explore the correlation between individual wild orchid host genomes and the diversity and composition of their microbiome at intraspecific level, 2) Measure the range and variability of microbiome composition in congeneric wild orchid species across their range, and 3) Correlate species level microbiome composition and variability with distribution, habitat use and relatedness among species.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The project explored correlation between wild orchid host genomics and the diversity and composition of their fungal microbiome, at individual, population level and species level. This was conducted by generating both host genomic data and root mycobiome data for 1) app. 250 individuals of two species in the genus Platanthera across 22 populations in Denmark, and 2) for 28 Platanthera species across eastern US from New Hampshire to Texas, yielding genomic data for 1000+ individuals and identifying more than 600 orchid-fungus associations. These datasets were supplemented with data on habitat characteristics, including soil parameters for the Danish populations.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The data revealed a strong overall correlation between Platanthera orchid host genomic profiles and their root mycobiomes across populations in Denmark, indicating that genetically more similar individuals harbour more similar microbionts than more distantly related, in support of the hologenome theory. Further, the project found significant correlation between orchid mycobiomes and specific soil variables in their habitats, especially between certain fungal strains and highly calcareous soils, indicating a role of the mycobiome in adaptation to local conditions by the host plant.
The assessment of microbiome range and variability of microbiome in 28 Platanthera species in eastern US demonstrated that composition and variability in microbiome differ among orchid species, confirming an effect of the host plant species on its microbiome. Both generalist and specialists Platanthera orchids were characterised, with specialists associating with 1-few mycobionts across their distribution area, while generalists associated with a broader range of mycorrhizal fungi. Closely related species had more similar mycobiont profiles, whereas more distantly related taxa were less likely to have an overlap in mycobionts. For most Platanthera taxa, we did not find any correlation between geographic distance between populations within taxa, and their mycobionts. However, in several species, mycobiont composition was correlated with intraspecific genetic clustering and biome type. These taxa exhibited substantial intraspecific genetic differentiation, with distinct coastal, mountain, and inland populations, which were associated with different mycobiont partners. This pattern indicates that plant mycobiont composition varies across habitat types and could be involved in local adaptation.

Study organisms for plant hologenomics, Platanthera orchids