Functional stratification of core and variable microbial taxa in the Codonopsis pilosula rhizosphere: Links to soil enzyme activity, nutrient cycling, and spatiotemporal dynamics

Soil microbial communities are crucial drivers of soil ecological functions, yet the distinct functional roles of core (consistently present), intermediate, and variable (conditionally present) microbial taxa remain largely unelucidated. This study investigated rhizosphere and endophytic microbial communities, soil multi-nutrient cycling (MNC), soil enzyme activity (SEA), and pH associated with the economically important crop Codonopsis pilosula across six diverse geographical sites and four seasons. We categorized microbial taxa by prevalence (core, intermediate, variable), and analyzed their co-occurrence networks. Results demonstrated that spatial variation primarily shaped fungal communities, while seasonal changes predominantly impacted bacterial communities. Rhizosphere networks were also more complex than endophytic networks. Our results revealed a clear functional stratification of these prevalence groups: core microbes, particularly in the rhizosphere, were strongly associated with foundational soil processes like enzyme activity and organic matter transformation, suggesting their role as a stable backbone for ecosystem functions. Conversely, intermediate and variable groups were more closely associated with specific physicochemical conditions, including pH and mineral nutrient status, highlighting their potential roles in environmental adaptation and specialized niche functions. These findings confirm a functional stratification within the root microbiome and offer a refined framework for developing targeted soil management strategies to enhance the sustainable cultivation of economically important perennial crops.