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Microbial-driven nature-based solutions for environmental antimicrobial resistance and emerging contaminants: mechanisms, platform trade-offs, and decision framework

Frontiers in Microbiology 2026
Atin Kumar, Nilotpal Das, Sandeep Gawdiya, Rohit Kumar, Pradeepto Pal, Sharad Sachan, Pritam Ghosh, Hanuman Singh Jatav, Caleb Ayomide Babatunde

Summary

This review pulls together years of research on using natural systems — like wetland plants and helpful microbes — to clean up drug residues, microplastics, and other pollutants from water and soil, while also fighting antibiotic-resistant "superbugs." The catch: these microbial cleanup systems can sometimes backfire, accidentally becoming breeding grounds for resistance genes if not carefully designed. The takeaway is that nature-based cleanup methods are promising and eco-friendly, but need smarter design and monitoring to actually protect human health rather than create new risks.

Body Systems
Study Type Environmental

Introduction: Antimicrobial resistance (AMR) and emerging contaminants (ECs), including pharmaceuticals, personal care products, microplastics, and endocrine-disrupting chemicals, pose interconnected threats to environmental and human health. Nature-based solutions (NbS) have emerged as sustainable and cost-effective approaches for mitigating these challenges through ecosystem-driven processes. Methods: This review follows a PRISMA-guided narrative-systematic synthesis of literature published between 2000 and 2024, using data sources including Scopus, Web of Science, and PubMed. The analysis integrates evidence on microbial mechanisms, NbS platform performance, and environmental AMR-EC interactions. Results: The synthesis highlights that microbial-driven NbS exploit metabolic diversity, functional plasticity, and plant-microbe interactions to degrade, transform, immobilize, or eliminate contaminants in soil, water, and wastewater systems. Advances in microbial ecology, synthetic biology, and omics approaches have enabled the design of functional microbial consortia capable of targeting antibiotic residues, resistance genes, and recalcitrant pollutants. NbS platforms such as constructed wetlands, rhizosphere-based systems, biofilters, and microbial electrochemical technologies demonstrate variable performance influenced by microbial diversity, redox processes, and system design. However, trade-offs exist, including the potential for microbial biofilms to act as reservoirs of antibiotic resistance genes. Discussion: Despite their potential, microbial-driven NbS face challenges related to scalability, long-term performance, ecological risks, and regulatory acceptance. This review proposes a microbial NbS decision framework linking environmental sources, microbial mechanisms, platform design, and monitoring indicators to support sustainable and risk-aware implementation. Overall, the effectiveness of NbS depends on optimizing microbial functional diversity, system design, and resistance suppression strategies to ensure long-term environmental and public health benefits.

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