Open research questions in Microbial bioremediation and biosurfactants

What the literature leaves open

• FIGURE 15 Synthetic biology approaches for enhanced microbial bioremediation of environmental pollutants (Jiménez-Díaz et al., 2022). laboratory studies Recent advances in environmental biotechnology, microbial ecology, synthetic biology, data science, and materials engineering are opening new opportunities to enhance microbial systems for remediation. Future studies will look to increase remediation efficiency, increase the number of contaminants that can be degraded, and increase the monitoring capability, as well as combine biological processes with sustainable engineering solutions. Future research should move beyond proof-ofconcept toward hypothesis-driven field validation. Key research questions include whether engineered long-term stability and microbial consortia can maintain degradation performance under fluctuating environmental conditions, how microbial community composition changes during extended remediation periods, and whether multispecies systems consistently outperform indigenous microbial populations under field conditions. Future validation studies should include pilot-scale and field-scale trials with appropriate untreated controls, long-term monitoring programs, and standardized performance metrics. Monitoring should evaluate not only contaminant removal but also transformation products, mineralization, residual toxicity, contaminant bioavailability, geochemical stability, groundwater plume behavior, and microbial functional activity. The deployment of engineered microorganisms and synthetic biology approaches should be assessments accompanied addressing ecological transfer, persistence of introduced microorganisms, and potential consequences. Multi-omics unintended technologies should be further developed to identify functional genes, metabolic pathways, and microbial interactions that control contaminant degradation under field conditions. Artificial intelligence and machine learning tools may provide practical support for predictive modeling, process optimization, contaminant transport forecasting, and remediation decisionmaking when integrated with environmental monitoring datasets. These technologies are likely to be most effective in complex contaminated sites where multiple contaminants, heterogeneous environmental conditions, and long remediation periods challenge conventional remediation strategies. impacts, horizontal gene comprehensive environmental biosafety by 10.1 Synthetic biology to the (Sayler increase and Ripp, Synthetic biology has become an exciting new area with great promise in environmental remediation. Genetic engineering and metabolic pathway optimization techniques can be used to genetically engineer microorganisms to degrade pollutants that are naturally resistant to degradation. Synthetic biology can be used to introduce novel catabolic pathways, to increase the tolerance of production of enzymes, and microbial 2000). Engineered stress microorganisms can be created to remove specific contaminants, such as chlorinated compounds, pharmaceuticals, and PFAS. Synthetic gene circuits also have the potential to enhance environmental sensing and pollutant-responsive degradation systems. While significant advances have been made, practical use of engineered microorganisms for environmental applications also has to take into account biosafety issues and regulatory hurdles (Das et al., 2025). Figure 15 illustrates the role of synthetic biology in advancing microbial engineered remediation microorganisms, metabolic pathway optimization, and synthetic microbial consortia. These strategies improve pollutant detection, tolerance, providing degradation efficiency, and microbial promising recalcitrant environmental contaminants. remediation of solutions through the for 10.2 Engineered microbial consortia Complex microbial communities may be responsible for natural remediation processes instead of individual species. Thus, the design of engineered microbial consortia is currently under intense research. Engineered consortia are groupings of microorganisms that have complementary metabolic functions to provide for more complete degradation of many complex contaminant mixtures (Renganathan et al., 2025). These systems can help make the most of substrate oxidation, boost tolerance full mineralisation of pollutants by following metabolic pathways.

  Microbial remediation of recalcitrant pollutants in soil and geo-environmental engineering systems · 2026 · DOI

• remediation. The literature search was performed in Scopus, Web of Science, ScienceDirect, PubMed, and Google Scholar. Publications from 2000 to 2025 were considered, with older studies retained only when they established mechanisms that remain standard in the field, such as classical biodegradation pathways, reductive dehalogenation, biosorption, or biomineralization. The same core search structure was applied across databases, with minor syntax changes required by interfaces: (“microbial remediation” OR individual database “bioremediation”) AND (“recalcitrant pollutants” OR “persistent pollutants” OR “soil contamination”) AND (“PAHs” OR “petroleum hydrocarbons” OR “heavy metals” OR “metalloids” OR “PFAS” OR “pesticides” OR “microbial consortia” OR “geo- environmental engineering”). Additional pollutant-specific searches were performed for “microbially induced carbonate precipitation,” “bioelectrochemical remediation,” “microplastic soil remediation,” “PFAS biotransformation,” “omics monitoring,” and “synthetic biology bioremediation.” Records were screened first by title and abstract, and then by full text when the article addressed microbial processes, pollutant transformation or immobilization mechanisms, geo-environmental of microbes, sustainable toward for laboratory or field-scale soil or geoenvironmental matrices, remediation, monitoring endpoints, or emerging microbial technologies. Publications were excluded when they focused only on non-microbial treatment, did not address soil, sediment, groundwater, or geoenvironmental systems, or lacked sufficient methodological detail to support the claim for which they would be cited. This article is a narrative review rather than a systematic review. Therefore, record counts and PRISMA-style screening statistics were not used.

  Microbial remediation of recalcitrant pollutants in soil and geo-environmental engineering systems · 2026 · DOI

• Microbial fermentation is a promising strategy to eliminate PAH residues in food processing, but the underlying mechanisms remain poorly characterized.

  Benzo[a]pyrene degradation by Kefir-derived microbiota: medium optimization and metabolic pathways · 2026 · DOI

• Laboratory incubations have demonstrated that moderate heating of marine sediments can lead to the production of labile organic compounds such as acetate, however, it remains unclear whether heating alters the bioavailability of the remaining OM pool.

  The effects of thermal alteration on organic matter bioavailability in deeply buried marine sediments · 2026 · DOI

• This review distills remediation methods for hydrocarbon- contaminated soils into a life cycle framework, which reflects this strong interrelation between all three categories of outcomes. Life cycle impact assessment findings dem- onstrate that energy use and upstream production of energy sources and chemical reagents commonly account for sig- nificant impacts for which remediation methods and costs obviously also play a role in deciding feasibility and viabil- ity. This means that remediation methods do not rank best in all respects; rather, alternatives differ and depend upon contamination type and soil characteristics. One of the primary implications for practical applicabil- ity is that the LCIA process needs to function more as a decision-aiding process, rather than a simple ranking exer- cise. The best justifiable results are achieved by harmonized comparisons that provide clear definition of the functional unit, remediation target, system boundaries, background databases, and treatment of secondary waste and wastewa- ter. When these conditions are met, the analysis may use- fully track hotspots, help elucidate trade-offs for categories of impact, and facilitate the justification of technology choice for the purpose of sustainable remediation, such as achieved by the SuRF-UK process. Future research should be focused on improvements tar- geting the current limitations of LCAs in the remediation of hydrocarbon soil contamination: (1) Harmonization and reporting standards: Establish har- monized functional units and cleanup points, and enable cross-study comparability through diagrams of system boundaries and inventory transparency. (2) Uncertainty and sensitivity: the reporting of scenario and sensitivity analysis in future LCAs will be war- ranted, since uncertainty and sensitivity have been identified frequently within the literature as influential factors within LCIA. (3) Assessments of combined and coupled technologies based on consistent LCAs: Future research has to investigate treatment chains that integrate high mass removal with biological polishing and soil restoration Page 19 of 23 10 and examine directly if the dominant hotspot process could be diminished by coupling. (4) Integration of soil function and long-term outcomes: align the LCIA indicators with soil health and land reuse metrics so that "successful remediation" is measured by post-treatment function rather than simple contaminant removal. (5) Application of data-driven technology with a focus on data-driven LCA gap filling would cover developing algorithms that could estimate parameters of resource consumption, such as methane emission rates in ther- mal desorption, or dose-response algorithms associated with site-specific soil oxidant demand. These data tools would act as data-driven gap fillers in methodologies that were less frequently reported, such as transport dis- tances, which impact results of LCIA. Authors’ contributions Somayeh HonariMehr: Conceptualization, Methodology, Investigation, Writing—Original Draft, Data Curation. Fatemeh Mohammadzadehchali: Methodology, Formal Analysis, Data Curation, Writing—Review & Editing, Visualization. Abooali Gol- zary: Supervision, Project Administration, Resources, Writing—Re- view & Editing, Validation. All authors read and approved the final manuscript. Funding This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors. Data Availability Data are available on request from the correspond- ing author. Code Availability Not applicable.

  Review of Remediation Strategies for Hydrocarbon-Contaminated Soils: A Life Cycle Perspective on Technical, Environmental, and Economic Impacts · 2026 · DOI

• Effective bioremediation of PCDD/F-contaminated soils is constrained by three interconnected limitations that no single biological strategy has yet overcome in field settings. First, the bioaccessibility bottleneck imposed by strong sorption to aged organic matrices fundamentally limits contaminant availability to microbial cells and extracellu- lar enzymes, regardless of their intrinsic catalytic capac- ity. Second, the redox complexity of dioxin transformation — requiring sequential anaerobic dechlorination followed by aerobic oxidative processing — is difficult to control uniformly across heterogeneous field soils. Third, current monitoring frameworks frequently rely on bulk concentra- tion or TEQ metrics alone, which are insufficient to detect transient intermediates, non-monotonic toxicity trajectories, or redistribution artefacts that may obscure genuine detoxi- fication. These limitations collectively point to a necessary paradigm shift: the central challenge in PCDD/F biore- mediation is no longer the identification of more efficient degrading organisms, but the engineering of integrated, process-centric systems in which mass transfer, redox con- trol, biosafety, and analytical resolution are treated as pri- mary design variables. This reframing moves the field away from organism-centric optimisation toward the deliberate construction of treatment systems that are realistic, audit- able, and regulatorily defensible by design. The most cred- ible path forward is hybrid and modular. Successful future strategies will combine anaerobic dechlorination stages with controlled aerobic oxidative steps, integrate biologi- cal transformation with physicochemical leverage such as bioaccessibility enhancement or enzyme-assisted oxidation, and embed multi-tier monitoring — effect-based screen- ing coupled with congener-resolved HRGC–HRMS — as an integral component of system evaluation rather than an afterthought. Biosafety constraints, including the exclusive use of risk class 1, non-pathogenic, non-GMO organisms and systematic antibiotic resistance stewardship, must be incorporated from the outset. Progress in this field will ulti- mately be measured not by the expansion of the catalogue of active taxa, but by the capacity to deliver verifiable, durable, and regulatorily accepted environmental risk reduction at contaminated sites. World Journal of Microbiology and Biotechnology (2026) 42:208 1 3 Acknowledgements The authors sincerely thank Filip Josanovic for his meticulous work in verifying, cross-checking, and organizing the bibliography. Author contributions Rita Di Martino contributed to literature re- search and manuscript drafting, with a particular focus on the biotech- nology and microbiology sections. Fiorella Lucarini contributed to manuscript drafting and critical revision, with a specific focus on the chemistry-related sections, and was responsible for the preparation of the figures. Davide Staedler contributed to literature research, manu- script drafting, and overall coordination of the work. Data availability No datasets were generated or analysed during the current study.

  Bioremediation of dioxin-contaminated soils: Microbial approaches, field perspectives, and analytical challenges · 2026 · DOI

• Although the study employs culture-based isolation and molecular identification via 16S ribosomal DNA sequencing, it does not establish quantitative relationships between bacterial community diversity indices (Shannon, Simpson) or network complexity and crude oil degradation rates across the tested salinity range. Correlation analysis linking network topology metrics derived from co-occurrence analysis to hydrocarbon removal kinetics should be performed.

  Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation · 2026 · DOI

• The paper characterizes bacterial community succession during crude oil-degrading enrichment cultivation but does not investigate how co-occurring heavy metal contamination (common in oil field environments) modulates the composition and degradation capacity of the halotolerant bacterial consortia. The interaction between petroleum hydrocarbons, elevated salinity, and trace metals on community assembly should be examined in multi-stress microcosm experiments.

  Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation · 2026 · DOI

• The study integrates metagenomic analysis via Kraken2 and metaSPAdes assembly with culture-based isolation, but does not assess whether dominant unculturable taxa identified through metagenomics play functional roles in polycyclic aromatic hydrocarbon (PAH) or alkane degradation. Genomic-resolved metagenomics combined with metabolic reconstruction should be applied to determine the specific degradation pathways and substrate preferences of both culturable and unculturable community members across salinity conditions.

  Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation · 2026 · DOI

• The metagenomic and culture-based approaches are applied to enrichment cultivation systems, but the paper does not validate whether the identified bacterial consortia maintain their degradation efficiency and community structure stability when scaled to field-level bioremediation conditions in saline-alkaline oil-contaminated soils. Controlled pilot-scale experiments comparing laboratory enrichments to field-amended soil microcosms with natural salinity variation are needed.

  Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation · 2026 · DOI

• The paper examines bacterial community dynamics in crude oil-degrading enrichment cultivation across salinity gradients, but does not characterize the specific degradation genes (such as alkB, catA, or PAH-degradation pathways) that enable halotolerant bacteria to maintain hydrocarbon biodegradation capacity under elevated salinity conditions. Future work should map functional gene expression and enzyme activity profiles across the salinity gradient to identify salt-tolerance mechanisms coupled with oil degradation.

  Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation · 2026 · DOI

• A numerical pollutant fate model reproduced these experimental observations by considering sorption effects on the pollutant migration and bioavailability for growth of VPH degrading biomass, which is limited by a maximum soil biomass carrying capacity.

  Mechanisms of distinct activated carbon and biochar amendment effects on petroleum vapour biofiltration in soil · 2017 · DOI

• Future investigations are warranted into the potential of Cr-free chemicals for the leather indus- try, and the application of specialized microorganisms for leather biodegradation.

  Soil burial evaluation of finished leather biodegradability: microbial community dynamics and biogeochemical cycles · 2026 · DOI

• Our findings highlight biotransformation as an important but underexplored process governing the persistence, turnover, and ecological roles of microbial natural products.

  Beyond Antimicrobial Activity: Soil Bacteria Reveal a Biotransformation Fate for the Lanthipeptide Nisin · 2026 · DOI

• Petroleum pollution often involves mixtures of volatile monoaromatic compounds and recalcitrant PAHs, but the isolation and characterization of native hydrocarbon‑degrading microbes in Vietnam are still underexplored.

  <span><strong>Genome-supported identification and physiological characterization of </strong><i><strong>Rhodococcus ruber</strong></i><strong> KHA5.2, a hydrocarbon-</strong> <strong>oxidizing bacterium from Vietnamese coastal sands</strong></span> · 2026 · DOI

• IMPORTANCEMangrove ecosystems are highly vulnerable to petroleum contamination, yet the microorganisms responsible for hydrocarbon turnover in these environments remain poorly characterized.

  Genomic Decoding of Specialized Aromatic Hydrocarbon Degradation in Mangrove-Derived Gordonia sp. B7 2 · 2026 · DOI

• Although the remediation efficiency of various amendments has been investigated, the effectiveness of organic substrate in enhancing the microbiome in iron ore mine tailings remains unknown.

  Biological rehabilitation of iron ore mine tailings enhanced by organic substrate application · 2026 · DOI

• Bioaugmentation should be judged as a controlled intervention aimed at establishing a defined function under site conditions, not as the mere introduction of exogenous microorganisms. Its relevance depends on whether the target activity is expressed where it is needed, maintained for the period required to meet the remediation objective, and linked to a measurable improvement in environmental quality. The presence of the inoculum, taken alone, is not an adequate endpoint. The central analytical problem is attribution. A decline in parent- compound concentration may reflect true pathway execution, but it may also arise from partial conversion, altered bioavailability, dilution, or stimulation of resident populations. Future studies should therefore define success in operational terms before field application and align monitoring with that decision framework, so that functional expres- sion, persistence, and hazard reduction can be interpreted with suffi- cient confidence. Progress in the field will depend on tighter coupling between microbiology and process design. Performance is often limited less by the nominal catabolic capacity of the inoculum than by poor reten- tion, restricted access to the contaminant, unstable redox conditions, or loss of activity under field variability. In practice, inoculum selec- tion, delivery, retention, and maintenance of the metabolic niche should be treated as parts of the same design problem rather than as separate considerations. Safety must remain integral to evaluation, not secondary to removal efficiency. An intervention cannot be considered successful if it lowers concentration while worsening toxicity, disturbing treatment stability, or introducing unwanted ecological effects. The next phase of bioaugmentation research should therefore focus on clearer causal evi- dence, better transferability across field settings, and monitoring schemes scaled to the actual decision context. That is the basis on which bioaugmentation can support credible environmental management.

  Bioaugmentation as microbiome engineering: a framework for evaluating functional performance, persistence, and safety · 2026 · DOI

• The mechanisms underlying the initial adaptation phase (first week) and how A. oryzae and P. citrinum modify their metabolism in response to asphaltenes need deeper characterization.

  Asphaltene biodegradation and transcriptome responses of hydrocarbon degradation genes in soil by a novel tolerant fungal consortium · 2026 · DOI

• Field-scale application and bioremediation of heavily contaminated soils using this fungal consortium with biostimulation strategy requires validation beyond laboratory conditions.

  Asphaltene biodegradation and transcriptome responses of hydrocarbon degradation genes in soil by a novel tolerant fungal consortium · 2026 · DOI

• The role of biosurfactant and emulsifying activities reported for P. citrinum in potentiating synergistic degradation was not experimentally quantified.

  Asphaltene biodegradation and transcriptome responses of hydrocarbon degradation genes in soil by a novel tolerant fungal consortium · 2026 · DOI

• Other genes that encode oxidative extracellular enzymes, different from those evaluated in this study, could be induced during the first days of asphaltene degradation (e.g., other peroxidases, cellulases, or lipases).

  Asphaltene biodegradation and transcriptome responses of hydrocarbon degradation genes in soil by a novel tolerant fungal consortium · 2026 · DOI

• The studied microorganisms show promise for application to oil contamination cleanup of agricultural soils, but field-scale implementation and practical deployment remain to be explored.

  OIL-DESTRUCTOR BACTERIA WITH RESISTANCE TO THE PRESENCE OF ADDITIONAL POLLUTANTS · 2023 · DOI

Most-cited papers in Microbial bioremediation and biosurfactants

• A bacterium that degrades and assimilates poly(ethylene terephthalate) · Science · 2016 · 2,931 citations
• Fungal bioremediation: An overview of the mechanisms, applications and future perspectives · Environmental Chemistry and Ecotoxicology · 2024 · 183 citations
• Microbial consortium degrading of organic pollutants: Source, degradation efficiency, pathway, mechanism and application · Journal of Cleaner Production · 2024 · 135 citations
• THE DIFFERENT FACES OF BIOCHAR: CONTAMINATION RISK VERSUS REMEDIATION TOOL · Journal of Environmental Engineering and Landscape Management · 2017 · 91 citations
• Rice husk and its derived biochar assist phytoremediation of heavy metals and PAHs co-contaminated soils but differently affect bacterial community · Journal of Hazardous Materials · 2024 · 88 citations
• Microbial strategies driving low concentration substrate degradation for sustainable remediation solutions · npj Clean Water · 2024 · 71 citations
• Biolability of Fresh and Photodegraded Pyrogenic Dissolved Organic Matter From Laboratory‐Prepared Chars · Journal of Geophysical Research Biogeosciences · 2021 · 52 citations
• Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils · Environmental Science Processes & Impacts · 2020 · 42 citations
• Improved Biosurfactant Production by <i>Enterobacter cloacae</i> B14, Stability Studies, and its Antimicrobial Activity · Polish Journal of Microbiology · 2020 · 24 citations
• Aerobic BTEX biodegradation increases yield of perfluoroalkyl carboxylic acids from biotransformation of a polyfluoroalkyl surfactant, 6:2 FtTAoS · Environmental Science Processes & Impacts · 2022 · 21 citations

Most recent work

• Remediation of Petroleum Hydrocarbon-Contaminated Soils: Techniques, Mechanisms, and Future Perspectives · Water, Air, & Soil Pollution · 2026
• Microbial and multi-omics approaches for bioremediation of emerging contaminants: environmental impact and future engineering solutions · Biodegradation · 2026
• Advances in Dehalogenase Biocatalysis: Mechanisms, Engineering, and Industrial Perspectives · Journal of Agricultural and Food Chemistry · 2026
• Bioremediation of dioxin-contaminated soils: Microbial approaches, field perspectives, and analytical challenges · World Journal of Microbiology and Biotechnology · 2026
• Engineering Halomonas bluephagenesis TD01 as a Robust Chassis for the Sustainable Production of Hyaluronic Acid · Biomolecules · 2026
• Asphaltene biodegradation and transcriptome responses of hydrocarbon degradation genes in soil by a novel tolerant fungal consortium · Environmental Science and Pollution Research · 2026
• Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation · Journal of Microbiology and Biotechnology · 2026
• Beyond the freeze: unveiling the role of biosurfactant from polar regions in sustainable biotechnology applications—a review · Polar Biology · 2026
• Decoding Microbial Reductive Dechlorination of 209 Polychlorinated Biphenyl Congeners through Experiment-Aided Quantum Chemistry and Machine Learning · Environmental Science & Technology · 2026
• Bioaugmentation as microbiome engineering: a framework for evaluating functional performance, persistence, and safety · Frontiers in Microbiology · 2026

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