Effects of Manure and Biochar on Community Assembly and Co-Occurrence Patterns of Abundant and Rare Microbial Taxa in Border-Row Rhizosphere

Although biochar and manure have been shown in many studies to influence abundant microbial communities, their differential effects on the rare and abundant microbial communities in soybean–corn intercropping systems remain poorly understood. Understanding how biochar and manure differentially shape these unique communities is critical to optimizing the sustainability and productivity of intercropping systems. Therefore, this study employed ITS and 16S rRNA sequencing to obtain the relative ASV abundance and thereby investigated how partial substitution of inorganic fertilizer with pig manure and corn stalk biochar influences the diversity, structure, assembly, and co-occurrence patterns of abundant and rare microbiota in border-row rhizospheres. Diversity analysis revealed that biochar and manure significantly increased the richness and evenness of rare fungal communities compared with conventional fertilization. In contrast, the richness and evenness of rare bacterial communities and abundant fungal communities remained stable. Null model analysis revealed that assembly processes shifted toward determinism for rare bacterial communities and toward stochasticity for rare fungal, abundant bacterial, and abundant fungal communities. Co-occurrence network analysis revealed that biochar and manure synergistically reduced the complexity and interaction strength of the rare bacterial network, whereas increasing the complexity and connectivity of the rare fungal network. These results demonstrate that biochar and manure promote distinct community assembly processes in border rows, thereby reshaping the ecological networks of rare and abundant taxa.