Molecular Mechanisms Governing Microbial Bioremediation Performance in Environmental Matrices

Dear Colleagues,

Microbial communities remove, transform, or immobilise contaminants in soils, sediments, groundwater, and wastewater, yet remediation performance in these complex matrices remains difficult to predict from laboratory characterisation alone. The determining factors are molecular: which catabolic or resistance genes are present and actively transcribed, whether the corresponding enzymes are expressed and catalytically competent under in situ conditions, which intermediates accumulate, and how contaminant speciation and bioavailability constrain the reaction that microorganisms can actually perform. This Special Issue is built around that specific question. We seek studies that identify the molecular determinants of bioremediation performance and demonstrate, with functional evidence, how those determinants govern measurable remediation outcomes in environmental matrices.

Accordingly, this Special Issue sets an explicit molecular threshold for inclusion. Submissions must provide functional evidence, obtained through one or more of the following: quantification or expression analysis of catabolic, resistance, or biotransformation genes; metatranscriptomic or proteomic measurement of the active fraction of the community; metabolite and intermediate profiling; enzyme assays including kinetics, inhibition, and stability under matrix-relevant conditions; stable isotope probing or isotope fractionation; targeted genetic experiments such as knockout, complementation, heterologous expression, or reporter systems; and direct chemical measurement of the contaminant and its products. Studies restricted to 16S rRNA amplicon profiling, phylogenetic reconstruction, or descriptive shifts in community composition are outside the scope of this collection unless such data are used in support of, and interpreted alongside, functional measurements that establish activity.

Organic contaminants: For hydrocarbons, halogenated solvents, pesticides, pharmaceuticals, and other organic pollutants, the collection should focus on biodegradation and mineralisation. Contributions are expected to resolve the degradation pathway rather than infer it, reporting transformation products and intermediates, the enzymes and genes catalysing the individual steps, the extent of mineralisation where relevant, and the residual toxicity of the resulting mixture. Studies of incomplete degradation, dead-end metabolites, and toxic intermediates are welcome, as these outcomes carry direct consequences for remediation practice.

Metals and metalloids: Metals are not degraded. The relevant processes are redox transformation, precipitation, biosorption, sequestration, and immobilisation, and the collection treats them as a distinct class with distinct evidentiary requirements. Contributions could characterise the molecular basis of the transformation, including efflux and resistance determinants, metal-binding proteins and siderophores, metalloreductases, sulfate- and iron-reducing activity, ureolytic and other biomineralisation pathways, and the composition of extracellular polymeric substances where these mediate binding. Performance claims should be supported by contaminant speciation, evidence on the mineralogical or chemical form of the immobilised metal, residual bioavailability and toxicity, and the stability of immobilisation under environmentally realistic conditions such as pH change, redox cycling, competing ions, or leaching over time.

Applied and field-scale studies: Applied contributions are strongly encouraged, provided they connect a defined molecular mechanism to remediation performance rather than reporting removal efficiencies alone. Bioaugmentation studies should confirm that the introduced inoculum persists and remains metabolically active, using strain-resolved or marker-based tracking together with expression or activity data, and should distinguish the contribution of the inoculum from that of the resident microbial community, for example through appropriate uninoculated and biostimulation-only controls. Biostimulation, bioreactor, permeable barrier, and biomineralisation-based treatment studies are similarly welcome where the reported performance is interpreted against gene, transcript, protein, metabolite, or enzyme activity data collected from the same system.

Environmental context and adaptation: This Special Issue retains an interest in tropical and industrialising regions, but only where geography is the entry point to a molecular question. Relevant contributions link defined local conditions, such as sustained high temperature, intense precipitation and leaching, laterite and peat matrices, or chronic mixed industrial and agricultural contaminant loading, to specific molecular functions and adaptations in the resident microbiota, and then to remediation outcomes. Comparative work on thermally adapted catabolic enzymes, resistance determinants under chronic co-exposure, and the performance of indigenous versus non-native inocula in the same matrix is particularly welcome. Studies whose only distinguishing feature is sampling location are not within the scope of this Special Issue.

Original research articles, systematic and mechanistically framed reviews, and short communications reporting well-supported functional findings will be considered. Together, the collection aims to establish which molecular determinants actually govern bioremediation performance in environmental matrices, and to make that evidence usable in the design of treatment strategies.

Dr. Armstrong Omoregie
Guest Editor

Manuscript Submission Information

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