Soil microbiomes reveal different strategies for nitrogen acquisition in aspen-dominated stands from Mexico and Canada

Plant species shape soil microbiome composition through species-specific interactions. However, it is less clear how these host-microbe interactions vary across populations of genetically structured species, particularly those spanning diverse climatic and soil gradients. In this study, we explore the influence of host genetic composition and edaphic factors on the soil microbiome of Populus tremuloides Michx., one of North America’s most widespread tree species. Using 16S, ITS, and 18S metabarcoding on soils from natural stands and soil, rhizosphere, and root samples from a greenhouse common garden setup, we examined microbiome diversity and community structure in two genetically distinct aspen genetic groups: one from Eastern Canada (Quebec), spanning boreal and cold temperate forests, and the other from Northwestern Mexico, representing warm temperate forests. While the soil microbial communities were distinguishable between the two genetic groups, we also observed significant differences among the three ecological regions. Variation in soil properties contributed to differences both between and within genetic groups, whereas under indoor and uniform soil conditions, genetic diversity within and between groups significantly impacted microbial communities. Despite taxonomic similarities, soil microbiomes associated with the Canadian and Mexican groups diverged functionally, reflecting distinct strategies for nitrogen acquisition. Boreal Canadian aspen stands and seedlings showed stronger associations with ectomycorrhizal fungi, while Mexican stands harbored a greater abundance and diversity of nitrogen-fixing bacteria. Our findings highlight how local adaptations to climate and soil conditions in aspen extend to their microbial partners, emphasizing the potential role of host-microbe interactions in shaping tree resilience and susceptibility to future climate changes.