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Alpine meadow degradation causes a notable decrease in palatable grasses and an increase in forbs and toxic plants in recent decades. Stellera chamaejasme is one of the most serious toxic weeds, which exerts an increasing threat on alpine meadow in Qinghai–Tibetan Plateau. Combined DNA sequencing with geostatistics was applied to analyze a typical degraded meadow invaded by S. chamaejasme in Qinghai Province, China. The study aimed to determine the spatial variation of soil fungi and its interrelationship with the plant–soil environment. Alpha diversity and relative abundance of fungal phyla and classes showed moderate or strong spatial dependency and were structured in patches of 19–318 m, and taxonomic composition exhibited much higher spatial variability than alpha diversity. Compared to plant cover, the matching of patch size showed a closer spatial link between soil properties and fungal community. Community coverage, SOM, TN, TP, and TK positively correlated to fungal diversity and taxonomic composition; no direct correlation was found between S. chamaejasme coverage and fungal community. The result suggested significant but weak association between plant–soil properties and soil fungal community at local scale. Patchy pattern of S. chamaejasme may disturb spatial variations of soil properties and fungal community, since S. chamaejasme in higher coverage corresponded to lower TK content, which contributed to a decrease in fungal diversity indirectly.

Spatial Distribution and Influencing Factors of Soil Fungi in a Degraded Alpine Meadow Invaded by Stellera chamaejasme