Cleaner Sites, Cleaner Fuels: Microbial Valorization of Toxic Wastes

The field of bioprocess engineering is increasingly pivotal in addressing the twin global challenges of industrial waste management and sustainable energy production. As industries generate a growing volume of toxic and recalcitrant waste streams—including phenolic effluents, dye-laden solvents, refinery byproducts, crude glycerol, lignin-rich residues, landfill leachates, and plastic depolymerizates—the need for advanced remediation solutions has never been more acute. Recent research has explored the valorization of these wastes into renewable fuels such as ethanol, butanol, sustainable aviation fuel precursors, and biogas, with a particular focus on biological and bioelectrochemical pathways. However, despite advances in microbial engineering, enzymatic catalysis, and process integration, significant gaps remain in translating laboratory breakthroughs into scalable, real-world applications capable of simultaneously delivering environmental and energetic benefits.

This Research Topic aims to catalyze new insights and solutions at the intersection of bioremediation and sustainable fuel synthesis. Central questions include optimizing microbial and enzymatic systems for upcycling diverse and toxic waste streams; designing robust engineered consortia and biochassis; and intensifying processes through innovations in gas fermentation, syngas conversion, and co-culture management. Additionally, there is a need for systematic studies on toxicity mitigation, inhibitor tolerance, and life-cycle impacts, as well as demonstrations of field and pilot-scale viability with standardized performance evaluations. By fostering research that links contaminant removal with high-yield, cost-effective fuel production, this topic seeks to bridge environmental stewardship with energy innovation.

To gather further insights in the integration of waste remediation and fuel generation via biological processes, we welcome articles that address, but are not limited to, the following themes:

- Microbial and enzymatic upcycling of industrial and toxic waste streams

- Engineering consortia and microbial chassis for enhanced waste conversion

- Development and optimization of bioelectrochemical systems in waste-to-fuel applications

- Omics-guided strain design and process intensification strategies

- Toxicity mitigation and inhibitor tolerance mechanisms

- Techno-economic analysis and life cycle assessment (LCA) of integrated remediation-fuel processes

- Field and pilot-scale demonstrations with standardized metrics (e.g., contaminant removal, fuel yield, energy balance, production cost)

We encourage submissions of Original Research, Reviews, Methods, and Data Papers focused on both fundamental advances and applied demonstrations that enable the practical deployment of waste remediation coupled with renewable fuel production.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Classification
• Clinical Trial
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Classification
• Clinical Trial
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: waste-to-fuel, bioremediation, toxic effluents, engineered microbes, consortia, gas fermentation, lignin valorization, plastic upcycling, bioelectrochemical, circular economy

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.