Microbial and Enzymatic Degradation of Pollutants: From Pathways to Scalable Bioprocesses

Persistent and emerging pollutants, including petroleum hydrocarbons, halogenated and aromatic compounds, synthetic dyes, pesticides, pharmaceuticals, per- and polyfluoroalkyl substances (PFAS), and plastics, accumulate in industrial effluents, soils, sediments, and water systems and pose growing environmental and regulatory challenges. Microorganisms and their enzymes offer a sustainable route to break these compounds down, often converting complex, toxic molecules into simpler, less harmful products. Bacteria, fungi, microalgae, and engineered consortia carry diverse catabolic pathways and biocatalysts, such as oxygenases, laccases, peroxidases, dehalogenases, hydrolases, and plastic-degrading enzymes, that act on a wide range of pollutants under both aerobic and anaerobic conditions.Despite decades of progress, translating pollutant biodegradation from the laboratory to robust bioprocesses remains difficult. Recalcitrant pollutants resist complete mineralization, degradation intermediates can be as toxic as the parent compound, and microbial activity is sensitive to pollutant concentration, bioavailability, and process conditions. Bottlenecks in enzyme stability, pathway efficiency, strain robustness, and reproducibility at scale continue to limit deployment. Advances in microbial genetics, enzyme engineering, synthetic biology, omics, microbiome engineering, and bioreactor design are opening new opportunities, while artificial intelligence and machine learning accelerate enzyme discovery, pathway prediction, process optimization, and biodegradation modeling, and advanced monitoring tools track pathways and intermediates in real time. Even so, a gap persists between mechanistic insight and scalable, reliable technologies.GoalThis Research Topic gathers cutting-edge research and reviews that connect the mechanisms of pollutant degradation to scalable, real-world bioprocesses. By uniting pathway, biocatalyst, strain, and process-level perspectives, and by harnessing AI and machine learning, microbiome engineering, and advanced analytical monitoring, the collection seeks to strengthen the efficiency, robustness, and reproducibility of biodegradation technologies. We aim to bridge the recurring gap between mechanistic understanding and dependable deployment, whether in engineered reactors or at contaminated sites, and to support integration into industrial effluent treatment, bioremediation, plastic waste management, and a cleaner, more circular bioeconomy. We hope to foster dialogue among researchers in microbiology, industrial microbiology, enzymology, bioprocess engineering, data science, and environmental biotechnology to advance more sustainable approaches to pollutant removal.The collection also contributes to several United Nations Sustainable Development Goals (SDGs): SDG 6 (Clean Water and Sanitation) through improved effluent and water treatment; SDG 9 (Industry, Innovation and Infrastructure) through scalable bioprocesses; SDG 12 (Responsible Consumption and Production) through circular strategies; SDG 13 (Climate Action) through low-impact alternatives to conventional treatment; and SDG 14 (Life Below Water) and SDG 15 (Life on Land) through the protection of aquatic and terrestrial ecosystems from persistent and emerging pollutants.ScopeWe welcome Original Research, Reviews, Mini Reviews, Methods, Hypothesis and Theory, Brief Research Reports, Perspectives, and Opinion articles. A non-exhaustive list of subjects includes:o Microbial degradation pathways, aerobic and anaerobic, including anoxic activation mechanisms, for hydrocarbons, aromatics, halogenated compounds, dyes, pesticides, pharmaceuticals, PFAS, and plasticso Discovery, characterization, and engineering of pollutant-degrading enzymes (oxygenases, laccases, peroxidases, dehalogenases, hydrolases, and others)o Strain engineering and synthetic biology for degradation efficiency, substrate range, and robustnesso Microbial consortia, co-cultures, and community-level and microbiome-engineering approaches as sources of novel pathways and enzymeso AI and machine learning for enzyme discovery, pathway prediction, and process optimization, including digital twin frameworks for modeling and monitoring biodegradationo Omics, systems biology, and bioinformatics to elucidate catabolic pathways and regulationo Bioavailability, biosurfactants, and strategies to enhance pollutant accessibilityo Advanced monitoring tools (biosensors, metabolomics, isotope tracing, real-time analytics)o Identification, fate, and toxicity of intermediates and pathways to complete mineralizationo Bioreactor design, immobilization, and process optimizationo Scale-up, process intensification, and reproducibility across engineered reactors and in situ or field-scale treatmento Techno-economic and sustainability assessment of degradation processeso Case studies linking pathway or enzyme design to treatment performance and outcomes Topic editors: Chirayu Desai, Giovanni Pilloni, Nazneen Hussain, Boonfei Tan, Anwar Usman Source: https://www.frontiersin.org/research-topics/83060/microbial-and-enzymatic-degradation-of-pollutants-from-pathways-to-scalable-bioprocesses