Comparison of Actinobacterial Rhizosphere Communities in Agricultural Soil of Beni-Suef, Egypt, using Cultural and Non-Cultural Methods

The agricultural soil microbiome in Beni-Suef, Egypt, plays a crucial role in crop health and adaptation. However, the diversity and function of its microbial communities, particularly Actinobacteria, key contributors to soil health and nutrient cycling, remain largely underexplored. To investigate microbial diversity, ten rhizosphere soil samples were collected from wheat plants across five distinct regions of Beni-Suef. Both culture-dependent and culture-independent (metagenomic) methods were employed. The culture-independent analysis (metagenomic analysis) focused on identifying dominant Actinobacterial orders, while cultured isolates were identified by 16S rRNA gene sequencing. Metagenomic analysis revealed that Acidimicrobiales dominated the Actinobacterial community (60.0% to 88.0%), followed by Actinomycetales (32.7%-75.6%), Nitriliruptorales (1.5%-4.0%), and Solirubrobacterales (2.0%-6.0%). Ten Actinobacterial isolates obtained through culturing were identified as members of the genera Streptomyces, Saccharothrix, Saccharopolyspora, Nocardiopsis, and Actinocorallia. Data obtained from this study demonstrates that Actinobacterial community structure varies significantly across agricultural sites in Beni-Suef, reflecting the influence of local environmental conditions. Our findings underscore the ecological importance of Actinobacteria in maintaining soil functionality and highlight the value of integrating culture-dependent and -independent methods for comprehensive microbial community analysis.