Systematic Identification of Native <i>Bacillus</i> spp. as a Sustainable Approach to Mitigate Cadmium in Cocoa

ABSTRACT One of the most pressing challenges for the cocoa industry is cadmium (Cd) accumulation, which poses serious health risks and limits access to international markets. Notably, Cd concentrations in many cocoa products exceed the European Union's maximum permissible threshold of 0.60 mg kg −1 in finished chocolate, threatening exports and farmer livelihoods. Previous studies have explored different methods for Cd remediation; however, they have been found to be costly and inefficient at the Cd concentrations typical of cocoa. Microorganisms, such as Bacillus spp., offer a promising alternative for Cd bioremediation during cocoa processing. In this study, we present a systematic screening of natural Bacillus isolates from cocoa fermentations as a sustainable approach for Cd remediation. Our multidisciplinary approach, integrating metagenomics, in vitro functional assays, microscopic imaging, genome sequencing, phylogenetic analysis, and functional annotation underscores the potential of Bacillus spp. as an effective, scalable, and natural solution for Cd mitigation. Bacillus , a dominant genus in industrial cocoa fermentations, exhibited diverse Cd tolerance profiles across 69 natural isolates. Notably, we identified two isolates— Bacillus subtilis Luk29 and Bacillus paranthracis Luk27—with demonstrated Cd removal capabilities in synthetic media under fermentation‐relevant conditions. Growth kinetics were assessed under varying Cd concentrations, pH, and temperature conditions for Cd removal. Genome annotation revealed that both strains possess strong Cd resistance mechanisms, including efflux systems, ATPases, and MerR‐family regulators. This work contributes to our understanding of microbial impacts on cocoa safety while providing a scalable strategy for enhancing the sustainability and marketability of cocoa products worldwide.