How to safeguard soil health against silver nanoparticles through a microbial functional gene-based approach?

Silver nanoparticles (AgNPs), a major anthropogenic stressor, can threaten soil health by disrupting vital microbial processes critical to maintaining key soil functions such as nutrient cycling, organic matter decomposition, and soil structure formation. Their safe use demands proactive strategies to preserve soils, a globally essential and non-renewable resource that acts as the ultimate sink for nanoparticles released into ecosystems. As functionally critical components of soil ecosystems, microorganisms warrant central consideration in developing nanotoxicity mitigation strategies. This review establishes a framework for soil health protection through systematic examination of (a) AgNPs-mediated ecotoxicological impacts on soil ecosystems, (b) microbial community tolerance thresholds, and (c) ecosystem functions most vulnerable to AgNPs exposure. Through bibliometric analysis of 61 studies, we synthesized comprehensive data on AgNPs-tolerant/sensitive microbial taxa and functional genes, while highlighting critical research gaps and priority research area. Our assessment identifies the following key challenges in predicting AgNPs ecotoxicity in soil systems: (1) a wide toxicity dose–response range, with significant effects observed even at environmentally relevant concentrations (≤1.0 mg/kg), (2) high microbial taxonomic heterogeneity complicating targeted identification, as most taxa remain unculturable, uncharacterized, or classifiable only at higher taxonomic ranks, and (3) limited knowledge of soil-AgNPs-environment interactions hindering identification of critical factors controlling AgNPs toxicity in soils. We then demonstrate how functional gene analysis can improve toxicity prediction accuracy and identify compromised soil processes. This functional genomics approach outperforms taxonomic characterization in predicting AgNPs impacts on soil health by directly quantifying disturbances to critical ecosystem processes. This framework will guide future research in predicting AgNPs’ impacts on soil microbial functionality and overall soil health, while offering a broadly applicable approach to assess toxicity for other emerging anthropogenic stressors, including engineered nanomaterials, pesticides, microplastics, and other soil contaminants.