Molecular Monitoring in Soil Bioremediation: From Genetic Potential to Verified Pathway Operation

Sequence-based tools have greatly improved the molecular description of soil bioremediation, but detection alone cannot confirm that a contaminant is being degraded by a defined pathway. In soils, bioavailability limitations, redox microsites, relic DNA, gene mobility, and community restructuring can decouple gene presence from reaction flux. This review synthesizes an operational framework that separates three inferential levels: pathway potential, in situ activity, and verified pathway operation. The framework links inoculant fate, functional gene abundance, gene expression, pathway reconstruction, stable isotope probing, and targeted chemical analysis under explicit quality assurance, quality control, and decision rules. Particular attention is given to distinguishing parent compound loss from mineralization and detoxification and to using isotopic attribution when functional redundancy or inoculant-native overlap obscures agency. Instead of being presented as conceptually new, these principles are organized into a practical workflow for soil systems. This structure clarifies what can be discerned from genes, transcripts, proteins, metabolites, and transformation products at each evidentiary tier and provides a conservative basis for integrating multi-omics with mechanistic and quantitative interpretation.