Omics-Guided Enzyme Engineering and Microbial Biotechnologies for Soil Remediation: Advances in the Degradation of PFAS, Microplastics, and Emerging Pollutants

Soil contamination by per- and polyfluoroalkyl substances (PFAS), microplastics, and emerging persistent pollutants poses a critical threat to environmental and human health. While biological remediation using enzymes and microbial consortia offers sustainable alternatives to physicochemical methods, translation from laboratory to field remains challenging. This review critically examines recent advances in omics-guided enzyme engineering and microbial biotechnologies for soil remediation. We systematically evaluate microbial diversity as a resource, key enzyme classes (hydrolases, oxidoreductases, and dehalogenases), and factors modulating enzymatic performance in complex soil matrices. Special emphasis is placed on omics technologies metagenomics, metatranscriptomics, and metaproteomics that have accelerated enzyme discovery, alongside emerging artificial intelligence applications for enzyme mining and engineering. Dedicated sections address enzymatic degradation of microplastics, particularly PETase and related enzymes, and the persistent challenge of PFAS bioremediation, highlighting recent progress in reductive defluorination. We identify critical knowledge gaps, including enzyme stability in soil, scalability, and regulatory barriers. Finally, we propose an integrated framework combining synthetic microbial communities, CRISPR-assisted strain improvement, and AI-enabled monitoring systems as a roadmap toward effective, field-deployable remediation solutions.