Mining exploration programmes are being expensive and risky due to the limitations of conventional prospecting methods in identifying desired mineralisation. Worldwide, mining exploration programmes have a success rate of approximately 0.7%. Bio-geochemical methods, a sub-branch of geochemical prospecting, are used to identify potential mineralisation areas by studying the distribution of plants containing certain metals. Turkey's leading position in the world in terms of boron reserves increases the strategic importance of boron. On the other hand, metagenome analysis is an important tool in scientific research for detecting microorganisms. Our study aims to develop a cost-effective and efficient biological alternative method for detecting boron mines. Metagenome analysis output showed correlation with the presence of Calothrix sp. NIES-3974, Snodgrassella alvi, Xanthomonas citri, X. citri pv. Fuscans, Pseudomonas viciae, and Aphanothecaceae bacteria and detecting of the potential boron traces in soil. Modelling studies were also conducted on aquaporin z protein, related to the boron uptake, that can be used for utilising from boron detection.