Microbial Adaptation and Metabolic Reprogramming under Emerging Contaminants Stress in Engineered Water/Wastewater Treatment Ecosystems

Emerging contaminants (ECs), including pharmaceuticals, microplastics, per- and polyfluoroalkyl substances (PFAS), antibiotic resistance genes (ARGs), and endocrine disruptors, are increasingly detected in global water cycles at concentrations that challenge conventional treatment technologies. Engineered ecosystems (e.g., activated sludge, anaerobic membrane bioreactors, microbial electrochemical cells) harness microbial consortia for pollution mitigation, yet their functional stability is compromised by EC-induced stress. While microbes deploy sophisticated adaptation strategies from stress-signal sensing to metabolic reprogramming, the decoding of resistance mechanisms and trade-offs between detoxification and ecosystem function remains fragmented. This knowledge gap impedes the design of resilient, next-generation water treatment infrastructures.

While microbial communities are central to bioremediation, nutrient removal, and contaminant degradation, their synergistic/antagonistic relationships and metabolic networks remain underexplored, especially facing the stress of emerging contaminants. This knowledge gap limits the optimization of engineered ecosystems (e.g., activated sludge, biofilms, anaerobic digesters) and natural aquatic remediation approaches. This Research Topic seeks to decode microbial stress response networks and metabolic trade-offs under EC exposure. We aim to 1) Reveal how ECs disrupt microbial community structure, signaling pathways, and functional gene expression; 2) Identify key metabolic adaptations (e.g., energy reallocation, co-metabolism, stress enzyme induction) enabling contaminant detoxification; 3) Bridge molecular-scale mechanisms to ecosystem-level performance in engineered environments.

We invite contributions addressing (but not limited to) the following themes:

1. Microbial Stress Response Networks:
1) ECs (pharmaceuticals, PFAS, microplastics, heavy metals, and potential pathogens) biotransformation and antibiotic resistome networks
2)EC-triggered gene regulation (e.g., oxidative stress genes, efflux pumps, SOS response)
3)Quorum sensing interference and biofilm dysbiosis
4)Horizontal gene transfer facilitates ARG dissemination
5)Single-cell heterogeneity in stress tolerance (e.g., persister cell formation)

2. Metabolic Reprogramming for Contaminant Detoxification:
1) Novel biodegradation pathways for priority ECs:
—PFAS defluorination enzymes
—Plastisphere-associated plasticizer metabolism
—Co-metabolism of pharmaceuticals
2) Energy trade-offs: Catabolic redirection vs. anabolic collapse
3) Stress-induced secondary metabolite production

3. System-Level Resilience Engineering:
1) Omics-guided consortia design: Metagenomics-proteomics integration for stress-primed communities
2) Bioaugmentation strategies: EC-degrading strains vs. functional guild transplantation
3) Hybrid systems: Coupling microbial processes with advanced oxidation or electrochemistry
4) Real-time resilience monitoring: Biosensors for stress biomarkers (e.g., chaperones, antioxidants)

4. Ecotoxicological Implications:
1) Trophic transfer of ECs and ARGs in treatment microbiomes
2) Chronic low-dose EC effects on microbial evolutionary trajectories
3) Climate change multipliers (e.g., temperature shocks on EC toxicity)

Article types and fees

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

• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• ... View all formats

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Article types

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

• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Emerging contaminants, Antibiotic resistance genes, PFAS biodegradation, Metabolic trade-offs, Heavy metal biotransformation, Synthetic microbial consortia, Multi-omics integration, Engineered microbiome

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.