Soil Metagenome Sequencing involves sequencing the collective DNA from soil microbial communities without the need to isolate and culture individual organisms. It captures the genetic material of bacteria, archaea, fungi, viruses and other microorganisms in soil. The key techniques followed are shotgun metagenomics, amplicon sequencing, metatranscriptomics and Single-Cell Genomics. Among these shotgun metagenomics randomly sequences all DNA in a sample, providing comprehensive data on microbial diversity and functional genes. Thus AI driven microbial diversity profiling identified rhizosphere soil microbes of mandarin orange and cataloging were carried out. AI-driven analysis and interpretation of massive, complex datasets generated by metagenomics reveals the lead role of beneficial microbes that can enhance crop yields or reduce dependency on chemical fertilizers. Understanding the diversity patterns of potentially beneficial bacteria in mandarin orange rhizosphere soil provides a unified framework for improving the mandarin orange ecosystem in lower Pulney hills of Tamilnadu, India. The dominant phyla in soil samples were Firmicutes (31%) and Proteobacteria (25%) and key genera include Bacillus (11%), Clostridium (8%), and Pseudomonas (6%), highlighting their significant roles in the soil ecosystem. Other notable observation was from Actinobacteria (15%) and Bacteroidota (9%), which further emphasize the richness and complexity of the microbial community. It provided the valuable insight about the signature beneficial bacterial community viz., Bacillus, Pseudomonas, Actinobacteria and Burkholderia that were synergistically involved in nutrient cycling, disease suppression, and maintaining the overall crop vigor. This data provided the portrait of the available potentially beneficial bacteria in the mandarin orange ecosystem and will certainly pave the way for their use in the conservation of citrus ecosystem. By integrating soil metagenome sequencing with Artificial Intelligence (AI), the hidden potential of microbial ecosystems, can be further unlocked for fostering sustainable agriculture.