Soil microorganisms play a pivotal role in the biogeochemical cycles of alpine meadow ecosystems, especially in the context of permafrost thaw. However, the mechanisms driving microbial community responses to environmental changes, such as variations in active layer thickness (ALT) of permafrost, remain poorly understood. This study utilized next-generation sequencing to explore the composition and co-occur rence patterns of soil microbial communities, focusing on bacteria and micro-eukaryotes along a permafrost thaw gradient. The results showed a decline in bacterial alpha diversity with increasing permafrost thaw, whereas micro-eukaryotic diversity exhibi ted an opposite trend. Although changes in microbial community composition were observed in permafrost and seasonally frozen soils, these shifts were not statistically significant. Bacterial communities exhibited a greater differentiation between frozen and seasonally frozen soils, a pattern not mirrored in eukaryotic communities. Linear discriminant analysis effect size analysis revealed a higher number of potential biomark ers in bacterial communities compared with micro-eukaryotes. Bacterial co-occurrence networks were more complex, with more nodes, edges, and positive linkages than those of micro-eukaryotes. Key factors such as soil texture, ALT, and bulk density significantly influenced bacterial community structures, particularly affecting the relative abundan ces of the Acidobacteria, Proteobacteria, and Actinobacteria phyla. In contrast, fungal communities (e.g., Nucletmycea, Rhizaria, Chloroplastida, and Discosea groups) were more affected by electrical conductivity, vegetation coverage, and ALT. This study highlights the distinct responses of soil bacteria and micro-eukaryotes to permafrost thaw, offering insights into microbial community stability under global climate change.

Yam is an important medicinal and edible dual-purpose plant with high economic value. However, nematode damage severely affects its yield and quality. One of the major effects of nematode infestations is the secondary infection of pathogenic bacteria or fungi through entry wounds made by the nematodes. Understanding the response of the symbiotic microbial community of yam plants to nematodes is crucial for controlling such a disease. In this study, we investigated the rhizosphere and how endophytic microbiomes shift after nematode infection during the tuber expansion stage in the Dioscorea opposita Thunb. cultivar Tiegun. Our results revealed that soil depth affected the abundance of nematodes, and the relative number of Meloidogyne incognita was higher in the diseased soil at a depth of 16 to 40 cm than those at a depth of 0 to 15 and 41 to 70 cm. The abundance of and interactions among soil microbiota members were significantly correlated with root-knot nematode (RKN) parasitism at various soil depths. However, the comparison of the microbial alpha-diversity and composition between healthy and diseased rhizosphere soil showed no difference. Compared with healthy soils, the co-occurrence networks of M. incognita-infested soils included a higher ratio of positive correlations linked to plant health. In addition, we detected a higher abundance of certain taxonomic groups belonging to Chitinophagaceae and Xanthobacteraceae in the rhizosphere of RKN-infested plants. The nematodes, besides causing direct damage to plants, also possess the ability to act synergistically with other pathogens, especially Ramicandelaber and Fusarium, leading to the development of disease complexes. In contrast to soil samples, RKN parasitism specifically had a significant effect on the composition and assembly of the root endophytic microbiota. The RKN colonization impacted a wide variety of endophytic microbiomes, including Pseudomonas, Sphingomonas, Rhizobium, Neocosmospora, and Fusarium. This study revealed the relationship between RKN disease and changes in the rhizosphere and endophytic microbial community, which may provide novel insights that help improve biological management of yam RKNs.