Composition and Diversity of Soil Microbial Communities in Walnut Orchards at Different Altitudes in Southeastern Tibet

To understand the distribution of the soil microbial community in natural walnut orchards at different altitude gradients (3000–3500 m) and to reveal the mechanism of the soil microbial activity in natural walnut orchards adapting to high-altitude environments, soil samples from four groups of natural walnut orchards in Gyaca County, southeast Tibet, were studied. Illumina MiSeq sequencing technology was used to analyze the community composition and diversity of soil bacteria and fungi and their responses to the altitudes. The alpha diversity results showed that the vertical distribution pattern of the fungal community was more obvious than that of the bacterial community and the bacterial community diversity first increased (~3364 m) and then decreased with altitude. The number of amplicon sequence variants (ASVs) in the soil bacterial community was significantly higher than that in the fungal community, but soil bacterial and fungal communities in walnut orchards at different altitudes exhibited both inheritance and uniqueness. At the phylum level, the dominant bacterial phyla at different altitudes were Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi (relative abundances > 10.0% in each treatment). With the increase in altitude, the relative abundance of Actinobacteria increased gradually while that of Acidobacteria and Proteobacteria decreased gradually. The dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota (relative abundances >5.0% in each treatment). With the increase in altitude, the relative abundance of Ascomycota increased significantly. At the genus level, the number of dominant bacteria and fungi in the soil decreased gradually with increased altitude and showed anisotropic distribution characteristics. The relative abundances of Actinobacteria among the bacterial phyla—and Olpidiomycota and Zoopagomycota among the fungal phyla—were positively correlated with the altitude ( p < 0.05). Most dominant bacterial and fungal phyla were highly significantly ( p < 0.01) or significantly ( p < 0.05) negatively correlated with the altitude. Soil nitrogen and phosphorus availabilities are the main limiting factors of microbial community diversity. Therefore, altitude caused changes in soil physicochemical properties which directly or indirectly affected the composition and diversity of soil bacterial and fungal communities, and our study provides a theoretical basis for the altitudinal pattern and succession changes in soil microbial communities in the natural walnut orchards of southeast Tibet.