Biodegradation Pathway and Detoxification of β-cyfluthrin by the Bacterial Consortium and Its Bacterial Community Structure

Bacterial Cytochrome P450 Involvement in the Biodegradation of Fluorinated Pyrethroids

Fluorinated pyrethroids, such as cyfluthrin and cyhalothrin, are more effective insecticides due to their enhanced stability and lipophilicity. However, they pose greater risks to non-target organisms. Their persistence in the environment and accumulation in tissues can lead to increased toxicity and ecological concerns. This study investigates the biodegradation of the fluorinated pyrethroids β-cyfluthrin (BCF) and λ-cyhalothrin (LCH) using a newly isolated Bacillus sp. MFK14 from a garden soil microbial consortium. Initial screening using 19F NMR analysis showed that the microbial consortium degraded both pyrethroids, leading to the isolation of Bacillus sp. MFK14. Subsequent GC-MS analysis revealed various degradation intermediates in both pyrethroids after incubation with Bacillus sp. MFK14. Notably, Bacillus sp. MFK14 completely degraded β-cyfluthrin and λ-cyhalothrin within 48 h at 30 °C. Fluoride ions from β-cyfluthrin and trifluoroacetic acid (TFA) from λ-cyhalothrin were detected as the end-products by 19F NMR analysis of the aqueous fraction. The pathway of the degradation was proposed for both the pyrethroids indicating shared biodegradation pathways despite different fluorinations. Inhibition studies with 1-ABT suggested the involvement of bacterial cytochrome P450 (CYP) enzymes in their biodegradation. The CYPome of Bacillus sp. MFK14 includes 23 CYP variants that showed significant sequence similarity to known bacterial CYPs, suggesting potential roles in pyrethroid biodegradation and environmental persistence. These findings highlight the potential for bioremediation of fluorinated pesticides, offering an environmentally sustainable approach to mitigate their ecological impact.

Degradation Kinetics and Mechanism of β-Cypermethrin and 3-Phenoxybenzoic Acid by Lysinibacillus pakistanensis VF-2 in Soil Remediation

Pyrethroid pesticide residues have detrimental effects on soil ecology and crop growth during insecticidal operations in agriculture. In this study, a novel strain Lysinibacillus pakistanensis VF-2 was isolated from long-term pesticide-treated cropland and had a maximum degradation efficiency of 81.66% for synthetic pyrethroid β-cypermethrin (β-CY) under optimized conditions. The analysis of intermediate products revealed that the degradation pathway of β-CY mainly involves ester bond hydrolysis, diphenyl ether decomposition, and phthalate ester degradation. Whole-genome sequencing and RT-qPCR analysis revealed the involvement of carboxylesterases, dioxygenases, and aromatic compound degrading enzymes in the degradation of β-CY. In the soil bioaugmentation experiment, the strain VF-2 can synergistically interact with indigenous microorganisms, significantly enhancing the degradation efficiency of β-CY and its metabolite 3-phenoxybenzoic acid (3-PBA) from 17.08% and 7.62% to 73.46% and 62.29%, respectively. This study suggests that strain VF-2 is a promising candidate for in situ coremediation of pyrethroid and intermediate metabolite residues in soil.

Comparative study of fenpropathrin and its main metabolite in soil-earthworm microcosms: Toxicity, degradation, transcriptome, and oxidative stress

This study comprehensively investigated the comparative acute toxicities, degradation, transcriptome, and oxidative stress induction of fenpropathrin (FEN) and its main metabolite 3-phenoxybenzoic acid (3-PBA)in soil-earthworm microcosms. FEN degradation half-life ranged from 19.09 to 28.52 days, and the peak-shaped trends of 3-PBA were also observed in different soil types. The LC50 values of FEN and 3-PBA were 12.75 and 7.49 μg/cm2, respectively, suggesting that 3-PBA was more toxic to earthworms. Furthermore, the sub-lethal toxicities indicated that 3-PBA exerted more prominent alterations in protein content, enzyme activity, lipid peroxidation, and oxidative stress in earthworms. Additionally, integrated biomarker response evaluations indicated that 3-PBA induced more prominent sub-lethal toxicity in earthworms than FEN. Finally, exposure to FEN and 3-PBA resulted in distinct differentially expressed genes (DEGs) in earthworms. Enrichment analysis revealed that these DEGs were predominantly enriched in purine metabolism and bile secretion pathways in earthworms. Moreover, the p53 signaling pathway, cell cycle, DNA replication, drug metabolism, and pyrimidine metabolism were also enriched in earthworms after exposure to FEN and 3-PBA. These results suggested that FEN and 3-PBA induced varying toxicities in earthworms. This study highlighted the systemic differences in the toxicities, degradation, transcriptome, and oxidative stress induction between FEN and 3-PBA in soil-earthworm microcosms. Our findings could be used for a comprehensive risk assessment of FEN and 3-PBA in the soil ecosystem.

Degradation of a novel herbicide fluchloraminopyr in soil: Dissipation kinetics, degradation pathways, transformation products identification and ecotoxicity assessment

With the continuous application of new agricultural chemicals in agricultural systems, it is imperative to study the environmental fate and potential transformation products (TPs) of these chemicals to better assess their ecological and health risks, as well as guide scientific application. The dissipation of fluchloraminopyr was firstly evaluated under aerobic/anaerobic condition in four representative soils, with Dissipation Time 50 (DT50) values ranging from 0.107 to 4.76 days. Eight TPs generated by soil degradation were identified via Ultra-High Performance Liquid Chromatography coupled with Quadrupole Time-of-Flight Mass Spectrometry (UHPLC-QTOF/MS) and Density Functional Theory (DFT) calculations. The predominant transformation reactions of fluchloraminopyr in soil include oxidation, dechlorination, hydroxylation, and acetylation. The predictions from toxicological software indicated that the acute and chronic toxicity of TPs to aquatic organisms was significantly lower than that of fluchloraminopyr. Moreover, both M267 and M221 exhibited higher acute oral toxicity to terrestrial organisms compared to the parent compound. Consequently, these findings offer essential ecological risk evaluation data for the judicious application of fluchloraminopyr.

Preparation of white rot fungal inoculum and its application to bioremediation of chlorimuron-ethyl-contaminated soil

Chlorimuron-ethyl is currently the primary herbicide used for chemical weed control in a soybean field. In this study, a solid microbial inoculum (corn stalk-white rot fungus (W-1)) was prepared for the remediation of farmland soil contaminated by chlorimuron-ethyl. Firstly, the preparation method of the microbial inoculum was studied. Secondly, the degradation rate of the chlorimuron-ethyl in the ground by the solid microbial inoculum is improved by optimizing the proportion of the protective agent. Then the effects of applying solid microbial inoculum, free bacteria and corn straw on the degradation rate of chlorimuron-ethyl in soil were weighed. Finally, Illumina MiSeq sequencing was used to measure the composition and diversity of bacterial and fungal communities in the ground before and after using microbial inoculum. The degradation rate of chlorimuron-ethyl in soil by solid microbial inoculum was 84.87% after 20 d using corn straw as the support, room temperature drying, 4% Ca3(PO4)2 as the protective drying agent, and 1%(w) dextrin as the ultraviolet protective agent. Inoculation of white rot fungi could significantly affect the community structure of bacteria and fungi in the soil, making the chlorimuron-ethyl degrading communities become the dominant communities and playing an essential role in the degradation of chlorimuron-ethyl. The results showed that using solid microbial inoculum was an effective way to repair farmland soil polluted by chlorimuron-ethyl.

Efficacy of novel bacterial consortia in degrading fipronil and thiobencarb in paddy soil: a survey for community structure and metabolic pathways

Introduction

Fipronil (FIP) and thiobencarb (THIO) represent widely utilized pesticides in paddy fields, presenting environmental challenges that necessitate effective remediation approaches. Despite the recognized need, exploring bacterial consortia efficiently degrading FIP and THIO remains limited.

Methods

This study isolated three unique bacterial consortia-FD, TD, and MD-demonstrating the capability to degrade FIP, THIO, and an FIP + THIO mixture within a 10-day timeframe. Furthermore, the bioaugmentation abilities of the selected consortia were evaluated in paddy soils under various conditions.

Results

Sequencing results shed light on the consortia's composition, revealing a diverse bacterial population prominently featuring Azospirillum, Ochrobactrum, Sphingobium, and Sphingomonas genera. All consortia efficiently degraded pesticides at 800 µg/mL concentrations, primarily through oxidative and hydrolytic processes. This metabolic activity yields more hydrophilic metabolites, including 4-(Trifluoromethyl)-phenol and 1,4-Benzenediol, 2-methyl-, for FIP, and carbamothioic acid, diethyl-, S-ethyl ester, and Benzenecarbothioic acid, S-methyl ester for THIO. Soil bioaugmentation tests highlight the consortia's effectiveness, showcasing accelerated degradation of FIP and THIO-individually or in a mixture-by 1.3 to 13-fold. These assessments encompass diverse soil moisture levels (20 and 100% v/v), pesticide concentrations (15 and 150 µg/g), and sterile conditions (sterile and non-sterile soils).

Discussion

This study offers an understanding of bacterial communities adept at degrading FIP and THIO, introducing FD, TD, and MD consortia as promising contenders for bioremediation endeavors.

Quantitative proteomic analysis reveals the mechanism and key esterase of β-cypermethrin degradation in a bacterial strain from fermented food

Beta-cypermethrin (β-CY) residues in food are an important threat to human health. Microorganisms can degrade β-CY residues during fermentation of fruits and vegetables, while the mechanism is not clear. In this study, a comprehensively investigate of the degradation mechanism of β-CY in a food microorganism was conducted based on proteomics analysis. The β-CY degradation bacteria Gordonia alkanivorans GH-1 was derived from fermented Pixian Doubanjiang. Its crude enzyme extract could degrade 77.11% of β-CY at a concentration of 45 mg/L within 24 h. Proteomics analysis revealed that the ester bond of β-CY is broken under the action of esterase to produce 3-phenoxy benzoic acid, which was further degraded by oxidoreductase and aromatic degrading enzyme. The up-regulation expression of oxidoreductase and esterase was confirmed by transcriptome and quantitative reverse transcription PCR. Meanwhile, the expression of esterase Est280 in Escherichia coli BL21 (DE3) resulted in a 48.43% enhancement in the degradation efficiency of β-CY, which confirmed that this enzyme was the key enzyme in the process of β-CY degradation. This study reveals the degradation mechanism of β-CY by microorganisms during food fermentation, providing a theoretical basis for the application of food microorganisms in β-CY residues.

Microbial Fermentation as an Efficient Method for Eliminating Pyrethroid Pesticide Residues in Food: A Case Study on Cyfluthrin and Aneurinibacillus aneurinilyticus D-21

The microbial fermentation of food has emerged as an efficient means to eliminate pesticide residues in agricultural products; however, the specific degradation characteristics and mechanisms remain unclear. In this study, a Gram-positive bacterium, Aneurinibacillus aneurinilyticus D-21, isolated from fermented Pixian Douban samples exhibited the capability to degrade 45 mg/L of cyfluthrin with an efficiency of 90.37%. Product analysis unveiled a novel cyfluthrin degradation pathway, involving the removal of the cyanide group and ammoniation of the ester bond into an amide. Whole genome analysis discovered the enzymes linked to cyfluthrin degradation, including nitrilase, esterase, carbon-nitrogen ligases, and enzymes associated with aromatic degradation. Additionally, metabolome analysis identified 140 benzenoids distributed across various aromatic metabolic pathways, further substantiating D-21's catabolic capability toward aromatics. This study underscores the exceptional pyrethroid degradation prowess of A. aneurinilyticus D-21, positioning it as a promising candidate for the biotreatment of pesticide residues in food systems.

Heavy metal-tolerant bacteria Bacillus cereus BCS1 degrades pyrethroid in a soil-plant system

The heightened concern about the environmental impacts of pollutants drives interest in reducing their threats to humans and the environment. Bioremediating polluted sites under environmental stresses like biotic and abiotic poses significant challenges. This study aimed to isolate a bacterium that effectively degrades pyrethroids even under abiotic stresses involving heavy metals and biotic stresses with autochthonous factors. Here, a bacterial strain, Bacillus cereus BCS1 was isolated. The response surface methodology was established to quantify the environmental impacts on pyrethroid degradation. BCS1 effectively degraded pyrethroids across conditions at 21-36 °C, pH 6.5-8.0 and inoculum sizes 1.9-4.1 mg·L-1, exceeding 90% degradation. Notably, over 84% of β-cypermethrin (β-CP) was degraded even when exposed to various concentrations of lead (10-1000 mg·L-1), chromium (10-1000 mg·L-1), or cadmium (0.5-50 mg·L-1). Moreover, BCS1 significantly accelerated β-CP degradation in soil-plant systems, displaying biotic stress tolerance, with lower half-life values (10.1 and 9.5 d) in soil and higher removal (92.1% and 60.9%) in plants compared to controls (27.7 and 25.7 d), and (18.2% and 24.3%). This study presents a novel strain capable of efficiently degrading pyrethroids and displaying remarkable environmental stress resistance. Findings shed light on bioremediating organic pollutants in complex soil ecosystems.

Linking Carbendazim Accumulation with Soil and Endophytic Microbial Community Diversities, Compositions, Functions, and Assemblies: Effects of Urea-hydrogen Peroxide and Nitrification Inhibitors

Fungicide carbendazim accumulation in soils and plants is a wide concern. Nitrogen (N) is a substantial nutrient limiting crop growth and affecting soil microbial activity and the community in degrading fungicides. We investigated the effects of urea-hydrogen peroxide (UHP) and nitrification inhibitors Dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) on carbendazim accumulation and soil and endophytic microbial communities. The UHP application had negligible influences on soil and plant carbendazim accumulation, but the combined UHP and DCD decreased soil carbendazim accumulation by 5.31% and the combined UHP and DMPP decreased plant carbendazim accumulation by 44.36%. The combined UHP and nitrification inhibitor significantly decreased the ratios of soil Firmicutes and endophytic Ascomycota. Soil microbial community assembly was governed by the stochastic process, while the stochastic and deterministic processes governed the endophyte. Our findings could provide considerable methods to reduce fungicide accumulation in soil-plant systems with agricultural N management strategies.

High-efficiency degradation of methomyl by the novel bacterial consortium MF0904: Performance, structural analysis, metabolic pathways, and environmental bioremediation

Methomyl is a widely used carbamate pesticide, which has adverse biological effects and poses a serious threat to ecological environments and human health. Several bacterial isolates have been investigated for removing methomyl from environment. However, low degradation efficiency and poor environmental adaptability of pure cultures severely limits their potential for bioremediation of methomyl-contaminated environment. Here, a novel microbial consortium, MF0904, can degrade 100% of 25 mg/L methomyl within 96 h, an efficiency higher than that of any other consortia or pure microbes reported so far. The sequencing analysis revealed that Pandoraea, Stenotrophomonas and Paracoccus were the predominant members of MF0904 in the degradation process, suggesting that these genera might play pivotal roles in methomyl biodegradation. Moreover, five new metabolites including ethanamine, 1,2-dimethyldisulfane, 2-hydroxyacetonitrile, N-hydroxyacetamide, and acetaldehyde were identified using gas chromatography-mass spectrometry, indicating that methomyl could be degraded firstly by hydrolysis of its ester bond, followed by cleavage of the C-S ring and subsequent metabolism. Furthermore, MF0904 can successfully colonize and substantially enhance methomyl degradation in different soils, with complete degradation of 25 mg/L methomyl within 96 and 72 h in sterile and nonsterile soil, respectively. Together, the discovery of microbial consortium MF0904 fills a gap in the synergistic metabolism of methomyl at the community level and provides a potential candidate for bioremediation applications.

Cellular Response and Molecular Mechanism of Glyphosate Degradation by Chryseobacterium sp. Y16C

Glyphosate is one of the most widely used herbicides worldwide. Unfortunately, the continuous use of glyphosate has resulted in serious environmental contamination and raised public concern about its impact on human health. In our previous study, Chryseobacterium sp. Y16C was isolated and characterized as an efficient degrader that can completely degrade glyphosate. However, the biochemical and molecular mechanisms underlying its glyphosate biodegradation ability remain unclear. In this study, the physiological response of Y16C to glyphosate stimulation was characterized at the cellular level. The results indicated that, in the process of glyphosate degradation, Y16C induced a series of physiological responses in the membrane potential, reactive oxygen species levels, and apoptosis. The antioxidant system of Y16C was activated to alleviate the oxidative damage caused by glyphosate. Furthermore, a novel gene, goW, was expressed in response to glyphosate. The gene product, GOW, is an enzyme that catalyzes glyphosate degradation, with putative structural similarities to glycine oxidase. GOW encodes 508 amino acids, with an isoelectric point of 5.33 and a molecular weight of 57.2 kDa, which indicates that it is a glycine oxidase. GOW displays maximum enzyme activity at 30 °C and pH 7.0. Additionally, most of the metal ions exhibited little influence on the enzyme activity except for Cu²⁺. Finally, with glyphosate as the substrate, the catalytic efficiency of GOW was higher than that of glycine, although opposite results were observed for the affinity. Taken together, the current study provides new insights to deeply understand and reveal the mechanisms of glyphosate degradation in bacteria.

Rapid Biodegradation of the Organophosphorus Insecticide Acephate by a Novel Strain Burkholderia sp. A11 and Its Impact on the Structure of the Indigenous Microbial Community

The acephate-degrading microbes that are currently available are not optimal. In this study, Burkholderia sp. A11, an efficient degrader of acephate, presented an acephate-removal efficiency of 83.36% within 56 h (100 mg·L^-1). The A11 strain has a broad substrate tolerance and presents a good removal effect in the concentration range 10-1600 mg·L^-1. Six metabolites from the degradation of acephate were identified, among which the main products were methamidophos, acetamide, acetic acid, methanethiol, and dimethyl disulfide. The main degradation pathways involved include amide bond breaking and phosphate bond hydrolysis. Moreover, strain A11 successfully colonized and substantially accelerated acephate degradation in different soils, degrading over 90% of acephate (50-200 mg·kg^-1) within 120 h. 16S rDNA sequencing results further confirmed that the strain A11 gradually occupied a dominant position in the soil microbial communities, causing slight changes in the diversity and composition of the indigenous soil microbial community structure.

Biodegradation of the Pesticides Bifenthrin and Fipronil by Bacillus Isolated from Orange Leaves

The pyrethroid bifenthrin and the phenylpyrazole fipronil are widely employed insecticides, and their extensive use became an environmental issue. Therefore, this study evaluated their biodegradation employing bacterial strains of Bacillus species isolated from leaves of orange trees, aiming at new biocatalysts with high efficiency for use singly and in consortium. Experiments were performed in liquid culture medium at controlled temperature and stirring (32 °C, 130 rpm). After 5 days, residual quantification by HPLC-UV/Vis showed that Bacillus amyloliquefaciens RFD1C presented 93% biodegradation of fipronil (10.0 mg.L^-1 initial concentration) and UPLC-HRMS analyses identified the metabolite fipronil sulfone. Moreover, Bacillus pseudomycoides 3RF2C showed a biodegradation of 88% bifenthrin (30.0 mg.L^-1 initial concentration). A consortium composed of the 8 isolated strains biodegraded 81% fipronil and 51% bifenthrin, showing that this approach did not promote better results than the most efficient strains employed singly, although high rates of biodegradation were observed. In conclusion, bacteria of the Bacillus genus isolated from leaves of citrus biodegraded these pesticides widely applied to crops, showing the importance of the plant microbiome for degradation of toxic xenobiotics.

Effects of Free or Immobilized Bacterium Stenotrophomonas acidaminiphila Y4B on Glyphosate Degradation Performance and Indigenous Microbial Community Structure

The overuse of glyphosate has resulted in serious environmental contamination. Thus, effective techniques to remove glyphosate from the environment are required. Herein, we isolated a novel strain Stenotrophomonas acidaminiphila Y4B, which completely degraded glyphosate and its major metabolite aminomethylphosphonic acid (AMPA). Y4B degraded glyphosate over a broad concentration range (50-800 mg L^-1), with a degradation efficiency of over 98% within 72 h (50 mg L^-1). Y4B degraded glyphosate via the AMPA pathway by cleaving the C-N bond, followed by degradation of AMPA and subsequent metabolism. Y4B demonstrated strong competitiveness and substantially accelerated the degradation of glyphosate in different soils, degrading 71.93 and 89.81% of glyphosate (400 mg kg^-1) within 5 days in sterile and nonsterile soils, respectively. The immobilized cells of Y4B were more efficient than their free cells and they displayed excellent biodegradation efficiency in a sediment-water system. Taken together, Y4B is an ideal degrader for the bioremediation of glyphosate-contaminated sites.

Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach

The ability of microorganisms to detoxify xenobiotic compounds allows them to thrive in a toxic environment using carbon, phosphorus, sulfur, and nitrogen from the available sources. Biotransformation is the most effective and useful metabolic process to degrade xenobiotic compounds. Microorganisms have an exceptional ability due to particular genes, enzymes, and degradative mechanisms. Microorganisms such as bacteria and fungi have unique properties that enable them to partially or completely metabolize the xenobiotic substances in various ecosystems.There are many cutting-edge approaches available to understand the molecular mechanism of degradative processes and pathways to decontaminate or change the core structure of xenobiotics in nature. These methods examine microorganisms, their metabolic machinery, novel proteins, and catabolic genes. This article addresses recent advances and current trends to characterize the catabolic genes, enzymes and the techniques involved in combating the threat of xenobiotic compounds using an eco-friendly approach.