Distinct factors drive the assembly of quinoa-associated microbiomes along elevation

Background and aims Unravelling the factors shaping microbial community structure across plant holobiont is required to promote plant health and crop productivity. Methods We compared microbial communities in soils and plant compartments of two contrasting quinoa cultivars, grown in low-input cropping systems along an elevation gradient in northwest Yunnan plateau, China. Results With a compartment-dependent effect, alpha-diversity (Shannon and Chao1 indices) of both bacterial and fungal communities generally increased with increasing elevation. Both bacterial and fungal diversities decreased in the order of rhizosphere> root > leaf, but no significant difference was found between two plant genotypes or between bulk soil and rhizosphere. Representing a unique niche for microbial communities, leaf had a much stronger selection effect than root. With insignificant effect of plant genotype, local environmental filtering (i.e. climate, edaphic and plant traits) could have played an important role in structuring soil microbial communities, but they were weak for root and leaf endophytes, except for root fungi. The relative importance of stochastic and deterministic processes in bacterial or fungal communities varied with the elevational scale, showing contrasting patterns within each plant-associated compartment, except for leaf (determinism). Conclusions The revealed distinct drives in determining the community assembly in quinoa-associated microbes are thought to be essential for underpinning plant–microbe interactions.