Multi-omics insights into bacterial and fungal bioremediation of Potentially Toxic Elements (PTEs): a critical overview of their applications

Potentially toxic elements (PTEs) are persistent contaminants of terrestrial and aquatic ecosystems and heavy metals and metalloids represent a major environmental and health concern. Microbial bioremediation exploits the ability of bacteria, fungi, and microbial communities to modulate PTE fate through processes including biosorption, bioaccumulation, redox transformation, biomineralization, precipitation, chelation, and extracellular sequestration. This review examines the major advances of the last decade in the application of genomics, transcriptomics, proteomics, and metabolomics and their integration, to investigate molecular mechanisms of microbial adaptation to PTE contamination, supporting the selection of suitable microorganisms or microbial communities and the development of more effective bioremediation strategies. Genomic and metagenomic analyses enable the identification of genes and gene families associated with PTE resistance and adaptation, revealing both metal-specific and more general responses according to the presence of operons and/or cluster genes. Transcriptomic and proteomic approaches are applied to validate genetic potentialities, identifying mechanisms and protein mediators for transport, detoxification, redox homeostasis, and metal interactions. Metabolomics complements these approaches by characterizing metabolites involved in microbial responses, including organic acids, siderophores, biosurfactants, and extracellular polymeric substance-associated compounds. The review also discusses the advantages, limitations, and complementarity of the different omics approaches, emphasizing their impact in feasibility to move from ex situ to in situ applications. Finally, the review also addresses how omics layers could be combined across the phases of a real bioremediation project (screening, implementation, monitoring), highlighting integrated multi-omics approaches as powerful tools for developing and optimizing effective bioremediation strategies.