Novel degradation pathways for Chlorpyrifos and 3, 5, 6-Trichloro-2-pyridinol degradation by bacterial strain Bacillus thuringiensis MB497 isolated from agricultural fields of Mianwali, Pakistan

Microbial detoxification of chlorpyrifos, profenofos, monocrotophos, and dimethoate by a multifaceted rhizospheric Bacillus cereus strain PM38 and its potential for the growth promotion in cotton

Bacillus genera, especially among rhizobacteria, are known for their ability to promote plant growth and their effectiveness in alleviating several stress conditions. This study aimed to utilize indigenous Bacillus cereus PM38 to degrade four organophosphate pesticides (OPs) such as chlorpyrifos (CP), profenofos (PF), monocrotophos (MCP), and dimethoate (DMT) to mitigate the adverse effects of these pesticides on cotton crop growth. Strain PM38 exhibited distinct characteristics that set it apart from other Bacillus species. These include the production of extracellular enzymes, hydrogen cyanide, exopolysaccharides, Indol-3-acetic acid (166.8 μg/mL), siderophores (47.3 μg/mL), 1-aminocyclopropane-1-carboxylate deaminase activity (32.4 μg/mL), and phosphorus solubilization (162.9 μg/mL), all observed at higher concentrations. This strain has also shown tolerance to salinity (1200 mM), drought (20% PEG-6000), and copper and cadmium (1200 mg/L). The amplification of multi-stress-responsive genes, such as acdS, ituC, czcD, nifH, sfp, and pqqE, further confirmed the plant growth regulation and abiotic stress tolerance capability in strain PM38. Following the high-performance liquid chromatography (HPLC) analysis, the results showed striking compatibility with the first kinetic model. Strain PM38 efficiently degraded CP (98.4%), PF (99.7%), MCP (100%), and DMT (95.5%) at a concentration of 300 ppm over 48 h at 35 °C under optimum pH conditions, showing high coefficients of determination (R2) of 0.974, 0.967, 0.992, and 0.972, respectively. The Fourier transform infrared spectroscopy (FTIR) analysis and the presence of opd, mpd, and opdA genes in the strain PM38 further supported the potential to degrade OPs. In addition, inoculating cotton seedlings with PM38 improved root length under stressful conditions. Inoculation of strain PM38 reduces stress by minimizing proline, thiobarbituric acid-reactive compounds, and electrolyte leakage. The strain PM38 has the potential to be a good multi-stress-tolerant option for a biological pest control agent capable of improving global food security and managing contaminated sites.

Synergistic insights into pesticide persistence and microbial dynamics for bioremediation

Rampant use of fertilizers and pesticides for boosting agricultural crop productivity has proven detrimental impact on land, water, and air quality globally. Although fertilizers and pesticides ensure greater food security, their unscientific management negatively impacts soil fertility, structure of soil microbiome and ultimately human health and hygiene. Pesticides exert varying impacts on soil properties and microbial community functions, contingent on factors such as their chemical structure, mode of action, toxicity, and dose-response characteristics. The diversity of bacterial responses to different pesticides presents a valuable opportunity for pesticide remediation. In this context, OMICS technologies are currently under development, and notable advancements in gene editing, including CRISPR technologies, have facilitated bacterial engineering, opening promising avenues for reducing toxicity and enhancing biological remediation. This paper provides a holistic overview of pesticide dynamics, with a specific focus on organophosphate, organochlorine, and pyrethroids. It covers their occurrence, activity, and potential mitigation strategies, with an emphasis on the microbial degradation route. Subsequently, the pesticide degradation pathways, associated genes and regulatory mechanisms, associated OMICS approaches in soil microbes with a special emphasis on CRISPR/Cas9 are also being discussed. Here, we analyze key environmental factors that significantly impact pesticide degradation mechanisms and underscore the urgency of developing alternative strategies to diminish our reliance on synthetic chemicals.

Emerging technologies for the removal of pesticides from contaminated soils and their reuse in agriculture

Pesticides are becoming more prevalent in agriculture to protect crops and increase crop yields. However, nearly all pesticides used for this purpose reach non-target crops and remain as residues for extended periods. Contamination of soil by widespread pesticide use, as well as its toxicity to humans and other living organisms, is a global concern. This has prompted us to find solutions and develop alternative remediation technologies for sustainable management. This article reviews recent technological developments for remediating pesticides from contaminated soil, focusing on the following major points: (1) The application of various pesticide types and their properties, the sources of pesticides related to soil pollution, their transport and distribution, their fate, the impact on soil and human health, and the extrinsic and intrinsic factors that affect the remediation process are the main points of focus. (2) Sustainable pesticide degradation mechanisms and various emerging nano- and bioelectrochemical soil remediation technologies. (3) The feasible and long-term sustainable research and development approaches that are required for on-site pesticide removal from soils, as well as prospects for applying them directly in agricultural fields. In this critical analysis, we found that bioremediation technology has the potential for up to 90% pesticide removal from the soil. The complete removal of pesticides through a single biological treatment approach is still a challenging task; however, the combination of electrochemical oxidation and bioelectrochemical system approaches can achieve the complete removal of pesticides from soil. Further research is required to remove pesticides directly from soils in agricultural fields on a large scale.

Biodegradation of chlorpyrifos pollution from contaminated environment - A review on operating variables and mechanism

Chlorpyrifos (CPF) is a highly toxic phosphate-rich organic pesticide (OP), identified as an emerging contaminant and used extensively in agricultural production. CPF persistence in the environment and its potential health hazards has become increasingly concerning worldwide in recent years due to exponential rise in food demand. Biodegradation of chlorpyrifos by microbial cultures is a promising approach to reclaiming contaminated soil and aquatic environments. The purpose of this review is to summarize the current understanding of microbiological aspects of xenobiotic chlorpyrifos biodegradation, including microbial diversity, metabolic pathways, and factors that modulate it. In both aerobic and anaerobic environments, CPF is biochemically broken down by a broad spectrum of bacteria and fungi. Hydrolysis, dehalogenation, and oxidation of chlorpyrifos are all enzymatic reactions that lead to its degradation. Biodegradation rate and efficiency are strongly influenced by parametric variables such as co-substrates abundance, pH, temperature, and initial chlorpyrifos concentration. The review provides evidence that microbial biodegradation is a viable method for remediating chlorpyrifos-contaminated sites in a sustainable and safe manner.

Biodegradation strategies of veterinary medicines in the environment: Enzymatic degradation

One Health closely integrates healthy farming, human medicine, and environmental ecology. Due to the ecotoxicity and risk of transmission of drug resistance, veterinary medicines (VMs) are regarded as emerging environmental pollutants. To reduce or mitigate the environmental risk of VMs, developing friendly, safe, and effective removal technologies is an important means of environmental remediation for VMs. Many previous studies have proved that biodegradation has significant advantages in removing VMs, and biodegradation based on enzyme catalysis presents higher operability and specificity. This review focused on biodegradation strategies of environmental pollutants and reviewed the enzymatic degradation of VMs including antimicrobial drugs, insecticides, and disinfectants. We reviewed the sources and catalytic mechanisms of peroxidase, laccase, and organophosphorus hydrolases, and summarized the latest research status of immobilization methods and bioengineering techniques in improving the performance of degrading enzymes. The mechanism of enzymatic degradation for VMs was elucidated in the current research. Suggestions and prospects for researching and developing enzymatic degradation of VMs were also put forward. This review will offer new ideas for the biodegradation of VMs and have a guide significance for the risk mitigation and detoxification of VMs in the environment.

New roles for Bacillus thuringiensis in the removal of environmental pollutants

For a long time, the well-known Gram-positive bacterium Bacillus thuringiensis (Bt) has been extensively studied and developed as a biological insecticide for Lepidoptera and Coleoptera pests due to its ability to secrete a large number of specific insecticidal proteins. In recent years, studies have found that Bt strains can also potentially biodegrade residual pollutants in the environment. Many researchers have isolated Bt strains from multiple sites polluted by exogenous compounds and characterized and identified their xenobiotic-degrading potential. Furthermore, its pathway for degradation was also investigated at molecular level, and a number of major genes/enzymes responsible for degradation have been explored. At present, a variety of xenobiotics involved in degradation in Bt have been reported, including inorganic pollutants (used in the field of heavy metal biosorption and recovery and precious metal recovery and regeneration), pesticides (chlorpyrifos, cypermethrin, 2,2-dichloropropionic acid, etc.), organic tin, petroleum and polycyclic aromatic hydrocarbons, reactive dyes (congo red, methyl orange, methyl blue, etc.), and ibuprofen, among others. In this paper, the biodegrading ability of Bt is reviewed according to the categories of related pollutants, so as to emphasize that Bt is a powerful agent for removing environmental pollutants.

Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations

Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.

Identification of two possible metabolic pathways responsible for the biodegradation of 3, 5, 6-trichloro-2-pyridinol in Micrococcus luteus ML

3, 5, 6-Trichloro-2-pyridinol (TCP) is a metabolite of the insecticide chlorpyrifos and the herbicide triclopyr, and it is higher toxic than the parent compounds. Microbially-mediated mineralization appears to be the primary degradative pathway and the important biological process of detoxification. However, little information is available on TCP complete metabolic pathways and mechanisms. In this study, the degradation of TCP was studied with a novel strain Micrococcus luteus ML isolated from a stable TCP degrading microbiota. Strain ML was capable of degrading 61.6% of TCP (50 mg/L) and 35.4% of chlorpyrifos (50 mg/L) at 24 h and 48 h under the optimal conditions (temperature: 35 °C; pH: 7.0), respectively. It could also degrade 3, 5-dichloro-2-pyridone, 6-chloropyridin-2-ol, 2-hydroxypyridine and phoxim when provided as sole carbon and energy sources. Seven TCP intermediate metabolites were detected in strain ML and two possible degradation pathways of TCP were proposed on the basis of LC-MS analysis. Both the hydrolytic-oxidative dechlorination pathway and the denitrification pathway might be involved in TCP biodegradation by strain ML. To the best of our knowledge, this is the first report on two different pathways responsible for TCP degradation in one strain, and this finding also provides novel information for studying the metabolic mechanism of TCP in pure culture.

Latest eco-friendly approaches for pesticides decontamination using microorganisms and consortia microalgae: A comprehensive insights, challenges, and perspectives

Pesticides are chemical compounds that are considered toxic to many organisms, including humans. Their elimination from polluted sites attracted the attention of Scientifics in the last decade; Among the various methods used to decontaminate pesticides from the environment, the microbial-algae consortium is a promising bioremediation technology, which implies several advantages as an eco-friendly process that generate biomass produced that could be valorized in the form of bioenergy, In this review, we will discuss the latest eco-friendly approaches using microorganisms to remediate sites contaminated by pesticides, and shows the ability of microbial, algae and their consortium to remove pesticides and the role of different enzymes in degradation processes.

Recent advances in assessment methods and mechanism of microbe-mediated chlorpyrifos remediation

Chlorpyrifos (CP) is one of the Organophosphorus pesticides (OPs) primarily used in agriculture to safeguard crops from pests and diseases. The pervasive use of chlorpyrifos is hazardous to humans and the environment as it inhibits the receptor for acetylcholinesterase activity, leading to abnormalities linked to the central nervous system. Hence, there is an ardent need to develop an effective and sustainable approach to the on-site degradation of chlorpyrifos. The role of microbes in the remediation of pesticides is considered the most effective and eco-friendly approach, as they have strong degradative potential due to their gene and enzymes naturally adapted to these sites. Several reports have previously been published on exploring the role of microbes in the degradation of CP. However, detection of CP as an environmental contaminant is an essential prerequisite for developing an efficient microbial-mediated biodegradation method with less harmful intermediates. Most of the articles published to date discuss the fate and impact of CP in the environment along with its degradation mechanism but still fail to discuss the analytical portion. This review is focused on the latest developments in the field of bioremediation of CP along with its physicochemical properties, toxicity, fate, and conventional (UV-Visible spectrophotometer, FTIR, NMR, GC-MS, etc) and advanced detection methods (Biosensors and immunochromatography-based methods) from different environmental samples. Apart from it, this review explores the role of metagenomics, system biology, in-silico tools, and genetic engineering in facilitating the bioremediation of CP. One of the objectives of this review is to educate policymakers with scientific data that will enable the development of appropriate strategies to reduce pesticide exposure and the harmful health impacts on both Human and other environmental components. Moreover, this review provides up-to-date developments related to the sustainable remediation of CP.

Mechanism and kinetics of chlorpyrifos co-metabolism by using environment restoring microbes isolated from rhizosphere of horticultural crops under subtropics

The indiscriminate use of organophosphate insecticide chlorpyrifos in agricultural crops causes significant soil and water pollution and poses a serious threat to the global community. In this study, a microbial consortium ERM C-1 containing bacterial strains Pseudomonas putida T7, Pseudomonas aeruginosa M2, Klebsiella pneumoniae M6, and a fungal strain Aspergillus terreus TF1 was developed for the effective degradation of chlorpyrifos. Results revealed that microbial strains were not only utilizing chlorpyrifos (500 mg L^–1) but also coupled with plant growth-promoting characteristics and laccase production. PGP traits, that is, IAA (35.53, 45.53, 25.19, and 25.53 μg mL^–1), HCN (19.85, 17.85, 12.18, and 9.85 μg mL^–1), and ammonium (14.73, 16.73, 8.05, and 10.87 μg mL^–1) production, and potassium (49.53, 66.72, 46.14, and 52.72 μg mL^–1), phosphate (52.37, 63.89, 33.33, and 71.89 μg mL^–1), and zinc (29.75, 49.75, 49.12, and 57.75 μg mL^–1) solubilization tests were positive for microbial strains T7, M2, M6, and TF1, respectively. The laccase activity by ERM C-1 was estimated as 37.53, 57.16, and 87.57 enzyme U mL^–1 after 5, 10, and 15 days of incubation, respectively. Chlorpyrifos degradation was associated with ERM C-1 and laccase activity, and the degree of enzyme activity was higher in the consortium than in individual strains. The biodegradation study with developed consortium ERM C-1 showed a decreased chlorpyrifos concentration from the 7th day of incubation (65.77% degradation) followed by complete disappearance (100% degradation) after the 30th day of incubation in the MS medium. First-order degradation kinetics with a linear model revealed a high k ^–day value and low t_1/2 value in ERM C-1. The results of HPLC and GC-MS analysis proved that consortium ERM C-1 was capable of completely removing chlorpyrifos by co-metabolism mechanism.

Molecular characterization of chlorpyrifos degrading bacteria isolated from contaminated dairy farm soils in Nakuru County, Kenya

Chlorpyrifos (CP) is an organophosphate widely used as an insecticide and acaricide. Extensive application of CP contaminates ecosystems, polluting the environment and food products, creating health complications to humans due to its neurotoxicity. The study evaluated CP bioremediation by bacteria isolated from dairy farm soils in Nakuru County, Kenya, through enrichment culture technique. The growth response of the bacteria and degradation of chlorpyrifos was monitored every five days using UV-VIS Spectrophotometer (600nm). Enrichment culture technique led to the isolation of eighteen (MA1-MA18) potential CP degraders belonging to the genera Pseudomonas, Stenotrophomonas, Bacillus, Alicaligenes, and Achromobacter. The efficacy of four (4) strains was further investigated using Gas Chromatography-Mass Spectrometry (GC-MS) analysis. The results showed that all four strains significantly degraded chlorpyrifos in Minimum Salt Medium (MSM): Lysinibacillus sp.HBUM206408 (87.16 %), Stenotrophomonas maltophilia (82.04 %), Pseudomonas putida (89.52 %), and Achromobacter insuavis (91.08 %) within 16 days, producing 2-Hydroxy-3, 5, 6-trichloropyridine (TCP) as the main metabolite. Therefore, these strains can be used to degrade chlorpyrifos in contaminated soil. There is a need for further studies to determine the possible mechanisms and other metabolites of chlorpyrifos degradation by the isolates obtained in the study. Besides, future studies should explore the efficacy and survival of the organisms in the contaminated environment.

Biotransformation of dimethoate into novel metabolites by bacterial isolate Pseudomonas kilonensis MB490

Bacterial strain (Pseudomonas kilonensis MB490) isolated from agricultural fields of Mianwali, was selected to check its potential to degrade Organophosphate insecticide dimethoate (DM). Strain MB490 was able to degrade dimethoate equally well at given pH range (6.0, 7.0 and 8.0), thus showing its pH independence for dimethoate degradation. Optimum temperature for dimethoate degradation varied from 25-30 °C. There was more dimethoate degradation under shaking conditions with optimum growth. Strain MB490 showed 90% dimethoate degradation in M-9 broth and 90.6% in soil slurry, while exhibited 81.5% dimethoate degradation in soil microcosm within 9 days, based on HPLC analysis of bacterial samples supplemented with 200 mg/L dimethoate. The average half-life (t _1/2) of dimethoate after bacterial degradation ranged from 1.95 days in 1st phase to 5 days in 2nd phase in M-9 broth, soil slurry and soil microcosm, while in control media without bacteria, it ranged from 30 to 64.3 days. GCMS investigation revealed the transformation of dimethoate into 5 metabolic products namely Methyl diethanol amine, Aspartylglycine ethyl ester, Phosphonothioic acid propyl-O, S-dimethyl ester, O, O, O-Trimethyl thiophosphate and omethoate which were ultimately mineralized by the strain MB490, providing energy for its growth.

A review on catalytic-enzyme degradation of toxic environmental pollutants: Microbial enzymes

Industrialization and other human anthropogenic activities cause serious threats to the environment. The toxic pollutants can cause detrimental diseases on diverse living beings in their respective ecosystems. Bioremediation is one of the efficient remediation methods in which the toxic pollutants are removed from the environment by the application of microorganisms or their biologically active products (enzymes). Typically, the microorganisms in the environment produce various enzymes to immobilize and degrade the toxic environmental pollutants by utilizing them as a substrate for their growth and development. Both the bacterial and fungal enzymes can degrade the toxic pollutants present in the environment and convert them into non-toxic forms through their catalytic reaction mechanism. Hydrolases, oxidoreductases, dehalogenases, oxygenases and transferases are the major classes of microbial enzymes responsible for the degradation of most of the toxic pollutants in the environment. Recently, there are different immobilizations and genetic engineering techniques have been developed to enhance enzyme efficiency and diminish the process cost for pollutant removal. This review focused on enzymatic removal of toxic pollutants such as heavy metals, dyes, plastics and pesticides in the environment. Current trends and further expansion for efficient removal of toxic pollutants through enzymatic degradation are also reviewed in detail.