The global rise of antimicrobial resistance (AMR) and the spread of contaminants of emerging concern (CECs)—such as pharmaceuticals, pesticides, and microplastics—pose growing threats to environmental and public health. Traditional treatment technologies often fall short in effectively removing these pollutants, especially in decentralised or resource-limited settings. Nature-based solutions (NbS), including constructed wetlands, biofilters, soil-based systems, and microalgae-based approaches, have emerged as promising, cost-effective sustainable alternatives. These systems rely on complex microbial communities to degrade, transform, or immobilise contaminants. However, the underlying microbial processes, resistance mechanisms, and system-level interactions are not yet fully understood. Integrating advanced tools like systems biology, synthetic biology, and sensor technologies with NbS could enhance their efficiency and predictability. A deeper understanding of microbial innovation within NbS frameworks is urgently needed to combat the spread of AMR and CECs across various ecosystems.

This Research Topic aims to advance scientific understanding of how microbial communities contribute to NbS for mitigating AMR and CECs in the environment. We seek interdisciplinary contributions that explore microbial dynamics, resistance gene attenuation, and biotransformation pathways within NbS systems such as wetlands, biofilters, microalgae-based platforms, plant-based systems, etc. Special emphasis will be placed on studies integrating systems biology, functional genomics, or emerging technologies (e.g., nanotech, biosensors, modelling) to enhance the design, monitoring, and scalability of NbS. Submissions addressing both natural and engineered environments—including agricultural soils and runoff, hospital and urban streams, wastewater, and surface waters—are welcome. By bringing together microbiology, environmental biotechnology, and systems ecology, this Topic aims to promote sustainable and science-based approaches to pollutant control, ultimately supporting public health, ecosystem resilience, and the One Health vision.

This Research Topic aims to explore microbial innovations within NbS frameworks to address AMR and CECs across various environmental settings (e.g., urban, agricultural, aquatic). We welcome submissions focusing on:

• Microbial ecology and functional dynamics in NbS Note; amplicon based (16S rRNA, 18S rRNA, etc profiles) are not within the scope of this RT and will be desk rejected, more details below.

• Constructed wetlands, soil biofiltration, plant-base technology or microalgae-based treatment systems

• Mechanisms of antimicrobial resistance attenuation and horizontal gene transfer

• Systems biology approaches to optimize microbial performance

• Monitoring tools and biosensors for CECs and AMR tracking

• Integration of nature-based and technological solutions (e.g., nanotechnology, AI-driven design)

• Multi-scale modeling of NbS for contaminant removal

This topic encourages interdisciplinary contributions from microbiology, environmental science, biotechnology, systems biology, and public health to advance understanding and application of NbS in mitigating the global threat of AMR and CECs.

Amplicon-based studies (e.g., 16S rRNA, 18S rRNA, ITS profiling) that are purely taxonomic or descriptive in nature are outside the scope of this Research Topic and will be desk rejected. Submissions should go beyond community composition analyses and provide functional insights or experimental validation of microbial roles. This may include studies that integrate amplicon data with environmental parameters, metabolic pathway inference, or other experimental evidence of function.

Are you interested in contributing a manuscript to this Research Topic?

Microbial Innovations in Nature-Based Solutions: Tackling Antimicrobial Resistance and Emerging Contaminants