Synthetic microbial communities derived from native niches enhance the high-temperature adaptability of Pinus yunnanensis seedlings.

The microbiome rewilding hypothesis suggests that understanding and reconstructing the microbial communities lost through domestication is vital for enhancing seedling quality and adaptability. Therefore, we investigated the structure and assembly of symbiotic microbial communities associated with Pinus yunnanensis, the most significant conifer species in southwestern China, and its dwarf variant, P. yunnanensis var. pygmaea. Subsequently, the functions of these microbes were characterized by inoculating dominant microbes and constructing synthetic communities, and examined their colonization status post-inoculation using amplicon sequencing. The results indicate that: (a) microbial communities are primarily differentiated by niche (soil, roots, needles), followed by geographical location, while trunk form variation has a minimal impact; (b) fungi are influenced by both chemistry and geographical factors, showing dispersion limitation, while bacteria are mainly affected by chemistry, exhibiting homogeneous diffusion; (c) single endophyte inoculation has a neutral to slightly negative impact on seedling growth but enhances resistance to high temperatures; (d) synthetic microbial communities (SynComs), constructed based on the strains' origin and initial functional screening, enhanced seedling growth and provided better protection against high-temperature stress than single strains. (e) one SynCom (SC5), composed of the dominant root isolates Phialocephala sp. (Fun6) and Paraburkholderia sp. (Bac7), significantly increased total seedling biomass by 62% and improved thermotolerance. These findings enhance our understanding of the symbiotic microbial communities of P. yunnanensis and demonstrate the potential of using specific SynComs, such as SC5, as bio-inoculants to improve seedling quality and stress tolerance in nursery production.