2026· Dutse Journal of Pure and Applied Sciences· Vol 12, pp. 55-64· 0 citations
TL;DR
Past prior and ongoing knowledge about microbial biodegradation is discussed using peer-reviewed literature from 2012–2026 to provide a framework for converting laboratory discoveries into field-level deployments to enable precision bioremediation approach for polluted ecosystem rehabilitation and public health safety.
Abstract
Activities from several Industrial, agricultural, and urban settings have led to alarming environmental pollution, with about 2.3 billion tonnes of chemicals being produced annually. In this review, we discuss the use of microbial degradation as an eco-friendly and cost-effective option for the cleanup of the environment. We examine the core mechanisms of pollutant degradation, featuring principal microbes such as bacteria (Bacillus spp, Pseudomonas spp, Rhodococcus spp, Alcanivorax spp), fungi (Phanerochaete spp, Chrysosporium spp.), and their enzyme repertoire (oxygenases, dehalogenases, reductases). This review also considers how multi-omics technologies (proteomics, metagenomics, transcriptomics, and metabolomics) have led to a better understanding of microbial consortia interactions in polluted environments by allowing culture-free approaches. We also discuss the roles of biotechnological innovations such as CRISPR-based environmental engineering, synthetic biology, cell-free systems, engineered microbial consortia and artificial intelligence-driven predictive modelling in addressing the issues facing natural attenuation. However, in spite of the significant achievement that have been made using several clean up procedures to prevent or minimize environmental pollution there are still some challenges such as the effect of environmental complexity, microbial competition, and regulations for the use of genetically engineered organisms. This review discuss past prior and ongoing knowledge about microbial biodegradation using peer-reviewed literature from 2012–2026 to provide a framework for converting laboratory discoveries into field-level deployments to enable precision bioremediation approach for polluted ecosystem rehabilitation and public health safety.
Pollution by emerging contaminants like microplastic is one of the major environmental concerns. Microplastics have become ubiquitous anthropogenic pollutants of aquatic, terrestrial and atmospheric ecosystems, and can generate considerable ecological and health-related risks. Conventional remediation regimes are widely ineffective, due to the physicochemical recalcitrance of polymer matrices. Recent advances in microbial biotechnology have revealed several contrasting microbial taxa and enzyme systems, which can convert or mineralize synthetic polymers through a variety of pathways of complex biochemistry. This review summarizes the current understanding of microbial–polymer interactions, including surface colonization, biofilm-mediated depolymerization, and intracellular uptake of degradation intermediates. It also discusses recent developments in enzyme engineering, strain optimization employing the CRISPR method, and synthetic biology approaches improving catabolic efficiency. The advent of a variety of multi-omics technologies of metagenomics, transcriptomics, and metabolomics has enabled the characterization of novel hydrolases and oxidoreductases with a high potential catalytic efficiency. Advances in nanobiocatalysis, enzyme immobilization, and bioreactor technology improve the scale-up of these processes. Related molecular developments and environmental applications will promote the application of microbial biotechnology as a selective and sustainable tool for the mitigation of microplastic accumulation and the development of a circular bioeconomy that interacts positively with ecosystem resilience.
The roles of bacteria, fungi, archaea, algae and cyanobacteria in nutrient cycling, soil fertility improvement, plant growth promotion, biological nitrogen fixation, disease suppression and pollutant degradation are examined.
Sarita Dubey, Vaishalee Thakur, Akanksha Sharma· Journal of Advances in Biolo...· 0 citations
1,4-Dithiane, a degradation product of abandoned Japanese chemical weapons, is a persistent organic pollutant with ecological risks. A synthetic microbiome (SM) was constructed through pollution stress screening and ratio optimization, consisting of Shinella sp., Alcaligenes faecalis, Sphingomonas sp., and Stenotrophomonas sp. at an optimal ratio of 1: 1: 2: 2. The SM achieved a 1,4-dithiane degradation rate of 95.2% and reduced intermediate accumulation. Soil remediation experiments showed complete pollutant removal within 60 days, along with improved soil health: reduced bioavailability of heavy metals (Cu, Zn, Cd), increased pH (6.47-6.95), elevated organic matter and enzyme activities, and decreased salinity and redox potential. Integration of ionomics, 16S sequencing, metagenomics, metabolomics, and HT-qPCR revealed that SM colonization reshaped microbial community structure, suppressed ARG-harboring bacteria (e.g., Pseudomonas), and activated core pathways (oxidative phosphorylation and glutathione metabolism), enhancing metabolic activity and oxidative stress tolerance. Consequently, the diversity, abundance, and diffusion potential of soil ARGs and mobile genetic elements were significantly reduced. These findings provide microbial solutions and a theoretical basis for concurrent organic pollution control and soil ecological risk management.
Xu Yang, Xiao-hui Ji, Chen Li et al.· Journal of Hazardous Materia...· 0 citations
Biodegradation research historically followed a reductionist approach focused on axenic (pure) cultures capable of catabolizing the specific contaminant(s) of interest. While this approach has substantially advanced our understanding of the microbiology, physiology, biochemistry, and genetics of contaminant degradation under laboratory conditions, it does not capture the complexity of natural and engineered environments. During in situ bioremediation, microbiomes are exposed to mixtures of contaminants, and microbial interactions profoundly influence contaminant transformation and fate. In anoxic environments, degradation of chlorinated compounds is often sustained by metabolic cooperation among taxonomically and physiologically distinct microorganisms. Through the exchange of metabolites such as hydrogen, formate, acetate, and other nutrients, microbial populations establish interdependent networks that overcome thermodynamic and physiological constraints, enabling self-sustaining systems of contaminant transformations that would be inefficient or impossible with individual organisms. We highlight examples of microbial interactions that underpin anaerobic catabolism of chlorinated contaminants, including systems resulting in self-sustained anaerobic bioremediation.
Gao Chen, F. Loffler· Current Opinion in Microbiol...· 0 citations
Microbial biostimulants and microbial plant protection products overlap in biological function, creating both R&D opportunities and regulatory challenges. In particular, multi-strain bacterial consortia may simultaneously affect nutrient mobilisation and abiotic stress tolerance, induce resistance, and demonstrate direct antagonism against phytopathogens. This multifunctionality complicates early product development because strain identity alone is sometimes insufficient in predicting product function, efficacy, or the most appropriate regulatory and claims strategy. Here, we used non-targeted LC-MS metabolomics as a hypothesis-generating tool to support formulation decisions for microbial consortia. Three bacterial consortia were compared: a full soil-oriented consortium C1 containing Bacillus spp., Rhodopseudomonas palustris, Nitrosomonas europaea, and Nitrobacter winogradskyi; a Bacillus-only consortium C2 intended for foliar stress-resilience applications; and a Bacillus-only consortium C3 grown with a chitin-related inducer to promote biocontrol-associated metabolism. Metabolomic profiling revealed clear differences between formulations. The full consortium C1 showed higher relative abundances of features putatively associated with biofertilising and growth support, whereas the Bacillus-only consortium C2 contained features putatively associated with biocontrol and induced resistance that were not detected in C1 under the applied criteria. The addition of the chitin-related inducer (C3) did not yield a completely distinct metabolite profile but increased the relative abundance of selected features putatively associated with biocontrol, while decreasing features putatively annotated as auxin-related or associated with abiotic stress responses. These results suggest that non-targeted metabolomics can help differentiate metabolic profiles putatively associated with biostimulant- and plant-protection-oriented formulations and thereby support prioritisation before extensive greenhouse or field testing. By linking formulation, medium composition, and microbial interactions to measurable metabolic signatures, metabolomics provides an evidence-based, hypothesis-generating framework for formulation development and the prioritisation of subsequent efficacy trials.
Polina Volkova, John M. Wong, Jacqueline Wong· Metabolites· 0 citations
This work provides a critical evaluation of the functional gaps between genomic potential and in situ microbial activity and offers a novel synthesis of how multiomics integration and predictive modeling can move beyond species cataloging toward a more robust, evidence‐based framework for environmental sustainability.