Microbial bioherbicides: Integrating bioprocessing, mechanisms of action and protein engineering for sustainable weed management

The widespread use of synthetic herbicides in agriculture has intensified concerns regarding environmental sustainability and human health, while the evolution of herbicide resistance has outpaced the discovery of new modes of action. Bioherbicides have consequently emerged as a viable alternative, comprising biologically derived compounds capable of suppressing weed growth. This review adopts an integrated perspective on microbially derived bioherbicides, following the active biomolecules from the producing strain and its fermentation conditions to their physiological targets in the plant and to the molecular strategies available for their optimization. Unlike previous reviews, which address these dimensions separately and focus mainly on secondary metabolites, particular emphasis is placed here on enzymes with herbicidal activity and on protein engineering approaches. Based on a structured literature search, 39 original studies were analyzed. Phytopathogenic fungi, mainly Fusarium, Diaporthe, Phoma, Alternaria and Trichoderma, predominate as producing organisms, followed by bacteria of the genera Streptomyces, Pseudomonas and Bacillus, and submerged fermentation using low-cost agro-industrial substrates is the prevailing production strategy. Enzymatic classes such as cutinases, lipases, cellulases, pectinases and proteases act primarily by degrading the cuticle and the cell wall, whereas secondary metabolites frequently target the photosynthetic apparatus, particularly photosystem II; most of these compounds, however, still lack a defined mode of action within established herbicide classification systems. Molecular approaches, including heterologous expression, molecular docking and metabolic engineering, remain comparatively underexplored despite their potential to enhance activity, stability and specificity. Advances in formulation stability, bioprocess scalability, mechanistic characterization and regulatory harmonization are identified as the key requirements to translate these biomolecules into commercially viable products for sustainable weed management. Graphical abstract