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Unravelling the factors shaping microbial community structure across plant holobiont is required to promote plant health and crop productivity. 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. 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). The revealed distinct drives in determining the community assembly in quinoa-associated microbes are thought to be essential for underpinning plant–microbe interactions.

Our understandings on the patterns and mechanisms of plant community assembly during succession, especially the primary succession in glacier retreat areas, remain limited. The Hailuogou Glacier Chronosequence provides a distinctive place to disentangle the biotic interactions and abiotic filtering effects on community successional trajectories. Through community-weighted approaches, we quantified elements allocation and regulation in leaves and roots, N:P stoichiometry, and the biotic and abiotic controls guiding community dynamics along the 120-year chronosequence. Across seven primary successional stages, plant leaves featured higher concentrations of macro-elements with lower coefficients of variation (CV) with increasing succession; whereas, fine roots contained more micro-elements with higher CV. From the early to late stages, foliar N:P increased linearly from 8.2 to 20.1. These findings highlighted that the limiting factor for plant growth shifted from N to P over one century of deglaciation. Edaphic factors (pH, bulk density, N and P concentrations) acted as deterministic filtering for trait convergence in the early stages, while biotic factors (species richness and plant litter biomass) for competitive exclusion dominated the late stages hosting species with stronger homoeostatic regulation and more conservative nutrient use.