Microbial innovation reduces chemical pollution

During biodegradation, organic substances are completely broken down into inorganic components by microorganisms. Microorganisms are the most abundant in nature. Their diversity, catalytic processes, and capacity to function without oxygen make them efficient and economically viable for the degradation of pesticides and other complex organic pollutants 93. Bacteria, fungi, and actinomycetes are the main pesticide degraders and transformants. They can make structural modifications to the pesticide molecule to reduce its toxicity. In addition, fungi typically biotransform insecticides and other xenobiotics, which bacteria can further degrade and make harmless before being released into the environment 186.

Fungi and bacteria produce several extracellular enzymes that act on various organic chemicals, making them ideal bioremediation agents. Microbial extracellular enzymes, particularly oxidases, laccases, and manganese peroxidases, play essential roles in the degradation process. Cytochrome P450, glutathione S-transferases (GSTs), and esterases have been reported as the primary enzyme families associated with pesticide degradation. Several pesticide-degrading microorganisms have been identified 187. For instance, recent studies by Ambreen and Yasmin 188 using Bacillus thuringiensis strain MB497 showed complete chlorpyrifos degradation (up to 99.9% in nine days). The results of this study also revealed the production of a novel metabolite, di-isopropyl methane phosphonate, which was obtained through alkylation/desulfurization reactions and then mineralized to produce carbon and phosphorus to support bacterial growth 188.

Enzyme-based pesticide degradation is a new treatment method for removing pesticides from polluted environments. Fungi and bacteria, particularly white rot fungi, are considered extracellular enzyme-producing microorganisms for this process. Environmental effects can produce and secrete these enzymes, which are involved in lignin degradation. Several microbial strains, including Transferases, isomerases, hydrolases, and ligases enzymes, are responsible for the biodegradation of pesticides, making them a promising bioremediation agent.189,190. In addition, enzymes are responsible for various metabolic reactions, such as hydrolysis, oxidation, oxygen addition, amino group oxidation, benzene ring hydroxyl group addition, dehalogenation, nitro group reduction, sulfur replacement, side chain metabolism, and ring cleavage, all of which are catalyzed by these enzymes. The metabolic ability of microbes to detoxify or modify pollutant molecules, which is based on accessibility and bioavailability, drives biodegradation191.

In general, three steps are involved in pesticide metabolism. Step I involves reduction, oxidation, or hydrolysis to create a more water-soluble and less poisonous compound. Step II involves the conjugation of a pesticide or pesticide metabolite to a sugar or amino acid, which boosts its water solubility and lowers its toxicity. Step III involves the conversion of step II metabolites into non-toxic secondary conjugates. Bacteria and fungi produce intracellular and extracellular enzymes 192. Although microbial biodegradation is an efficient, cost-effective, and environmentally beneficial method, some challenges remain. One of the biggest challenges is the inability to cultivate some microbial species, which makes it difficult to identify the environmental pollutants that cause the most damage. In addition, temperature, pH, and humidity influence the performance of microbes in the field, and rivalry between the target microorganism and other native microorganisms may restrict their growth.

Microbial consortiums can create an efficient system for pesticide bioremediation; however, selecting a partner bacterium that works well together is essential for constructing a strong system. Hence, to further evaluate this symbiotic association, a thorough investigation of the molecular dynamics, metabolic transitions and shifts, and small-molecule interactions between the microorganism and the surrounding conditions and environmental factors is required 193. Microbial catabolism is diverse and capable of breaking down a wide range of chemical substances; filling all the knowledge gaps is challenging. However, potential metabolic pathways and toxicity endpoints can be predicted using in silico investigations, system modeling, and molecular dynamics, as shown in Figure 11. The development of genetic bioaugmentation, which involves introducing donor bacteria into polluted soil to increase the capacity of native bacteria to break down pesticides, is a successful strategy 194. A general overview of the intricate biodegradation processes is provided by multi-OMICS techniques (genomics, transcriptome, and metabolomics), making it feasible to identify and characterize various molecular mechanisms, metabolic pathways, their control, and potential interconnections, as shown in Figure 11.

Currently, most research is focused on the application of molecular docking in environmental remediation for the intermolecular investigation of microbial biodegradation of pesticides, as shown in Figure 12, which has enabled the discovery of new genes and enzymes involved in remediation mechanisms, bridging research gaps and expanding our understanding of the remediation of xenobiotics 192.