Variation in soil microbial communities associated with critically endangered Wollemi pine affects fungal, but not bacterial, assembly within seedling roots

•Limited information exists regarding the microbial communities associated with the roots of critically endangered Wollemi pine.•Soil-associated fungal and bacterial communities under Wollemi pine are highly variable but, to a certain extent, divergent from soils under the surrounding vegetation.•Environmental variation in the field contributed to subsequent assembly of fungal, but not bacterial, communities within the roots of Wollemi pine seedlings•Fungal communities under the surrounding vegetation may contain greater richness of genera associated with plant pathogens.

The critically endangered Wollemi pine (Wollemia nobilis W. Jones, K. Hill & J. Allen) has very low levels of recruitment in the wild. Wollemi pine grows on shallow soils of poor nutrient status and high acidity and is likely to be highly dependent on microorganisms such as mycorrhizal fungi and other microorganisms that contribute to nutrient cycling in soils. The microbial communities present in soil around wild Wollemi pine and the specificity of subsequent assembly in seedling roots has never been assessed. We analysed soil fungal and bacterial communities associated with wild Wollemi pine and neighbouring co-dominant, coachwood. Root-associated assemblages in seedlings were evaluated in the presence of inoculum collected from under Wollemi pine or coachwood (Ceratopetalum apetalum) in the field. Variation partitioning revealed that fungal and bacterial community assembly in soil were associated with different processes, with fungi more strongly influenced by spatial factors and bacteria influence equally by spatial and edaphic factors. Variation in soil microbial communities in the wild affected fungal, but not bacterial assembly in roots of Wollemi pine seedlings. Wollemi pine recruited a distinct bacterial community in its roots regardless of soil origin.