From forests to microbiomes : The mediation of plant-soil systems by root-symbiotic fungi

Plant-microbial symbioses play crucial roles in ecological and biogeochemical processes such as carbon and nutrient cycling, plant-soil feedback, and evolutionary dynamics. However, less is known about how these symbioses influence the broader soil microbial communities (microbiomes) that they interact with, which is essential to understanding the ecosystem processes they facilitate. In this thesis, I investigate the effect of mycorrhizal type and other root symbioses on the structure and potential function of belowground microbiomes, as well as leaf microbiomes and leaf element concentrations. To accomplish this, I used a variety of techniques, including metabarcoding and metagenomic analysis of microbial communities and their functional genes from field studies at various scales, from single vegetation communities to a European latitudinal gradient. Regionally, I found that sites dominated by arbuscular mycorrhizal (AM) vegetation had relatively more AM fungi, bacteria, fungal saprotrophs, and pathogens in their soils compared to ectomycorrhizal (EcM) vegetation, and that coniferous EcM vegetation was a particularly important determinant of soil conditions and microbiome features. I also found that root colonization by dark septate endophytic (DSE) fungi was strongly associated with the composition of microbial communities and functional genes, including a negative relationship with the relative abundance of fungal pathogens and bacteria across Europe. Lastly, I found that tree species with different root symbioses and levels of colonization and their leaf element profiles were a key factor shaping leaf microbial communities and diversity compared to climate, with contrasting relative abundances of bacterial and fungal guilds and taxa between and within tree species. Overall, my findings suggest that the biotic interactions between plants and their root symbionts are important factors determining the structure and function of microbiomes across vegetation communities and tree species, with implications for wider ecosystem processes.