Deciphering Soil Keystone Microbial Taxa: Structural Diversity and Co-Occurrence Patterns from Peri-Urban to Urban Landscapes

Assessing microbial community stability and soil quality requires understanding the role of keystone microbial taxa in maintaining diversity and functionality. This study collected soil samples from four major habitats in the urban and peri-urban areas of 20 highly urbanized provinces in China using both the five-point method and the S-shape method and explored their microbiota through high-throughput sequencing techniques. The data was used to investigate changes in the structural diversity and co-occurrence patterns of keystone microbial communities from peri-urban (agricultural land) to urban environments (hospitals, wastewater treatment plants, and zoos) across different regions. Using network analysis, we examined the structure and symbiosis of soil keystone taxa and their association with environmental factors during urbanization. Results revealed that some urban soils exhibited higher microbial diversity, network complexity, and community stability compared to peri-urban soil. Significant differences were observed in the composition, structure, and potential function of keystone microbial taxa between these environments. Correlation analysis showed a significant negative relationship between keystone taxa and mean annual precipitation (<i>p</i> < 0.05), and a strong positive correlation with soil nutrients, microbial diversity, and community stability (<i>p</i> < 0.05). These findings suggest that diverse keystone taxa are vital for sustaining microbial community stability and that urbanization-induced environmental changes modulate their composition. Shifts in keystone taxa composition reflect alterations in soil health and ecosystem functioning, emphasizing their role as indicators of soil quality during urban development. This study highlights the ecological importance of keystone taxa in shaping microbial resilience under urbanization pressure.