CRISPR-genome editing: Revolutionizing beneficial Bacteria and Fungi for sustainable agriculture

The manipulation of beneficial microorganisms transcends conventional biotechnology to become the biogenic infrastructure of a resilient agriculture. Although the CRISPR/Cas9 system has established itself as a superior genome editing tool, mainly due to its precision, simplicity, and cost-effectiveness, its full translation into agromicrobial ecosystems faces critical biological and technical bottlenecks. This review rigorously evaluates the implementation of CRISPR systems in fundamental taxa, such as Trichoderma , Bacillus , and diazotrophic bacteria, confronting systemic challenges that include the cytotoxicity of Cas9 overexpression, the frequency of off-target mutations, and structural instability in organisms. Additionally, Brazilian bioinnovation has subverted these limitations through the development of marker-free genomic architectures and the optimization of virulence factors in biocontrol agents, establishing a new paradigm of microbial engineering. The evolution of these tools requires not only the improvement of delivery methods, currently inefficient in several species, but also a radical modernization of regulatory frameworks. This paper discusses how the legal classification of these organisms under Brazilian biosafety will shape the future of intellectual property (IP) and the commercial viability of next-generation inoculants. Ultimately, it proposes that overcoming these technical obstacles and changing public perception are imperative for genome editing to catalyze a sustainable revolution in global agricultural productivity.