Recent insights into the microbial catabolism of aryloxyphenoxy-propionate herbicides: microbial resources, metabolic pathways and catabolic enzymes

Efficient Biodegradation of Multiple Aryloxyphenoxypropionate Herbicides by Corynebacterium sp. Z-1 and the Proposed Degradation Mechanism

Esterases are crucial for aryloxyphenoxypropionate herbicide (AOPP) biodegradation. However, the underlying molecular mechanisms of AOPP biodegradation by esterases are poorly understood. In the current work, Corynebacterium sp. Z-1 was isolated and found to degrade multiple AOPPs, including quizalofop-p-ethyl (QPE), haloxyfop-p-methyl (HPM), fenoxaprop-p-ethyl (FPE), cyhalofop-butyl (CYB), and clodinafop-propargyl (CFP). A novel esterase, QfeH, which catalyzes the cleavage of ester bonds in AOPPs to form AOPP acids, was identified from strain Z-1. The catalytic activities of QfeH toward AOPPs decreased in the following order: CFP > FPE > CYB > QPE > HPM. Molecular docking, computational analyses, and site-directed mutagenesis indicated the catalytic mechanisms of QfeH-mediated degradation of different AOPPs. Notably, the key residue S159 is essential for the activity of QfeH. Moreover, V222Y, T227M, T227A, A271R, and M275K mutants, exhibiting 2.9-5.0 times greater activity than QfeH, were constructed. This study facilitates the mechanistic understanding of AOPPs bioremediation by esterases.

Characterization of two novel hydrolases from Sphingopyxis sp. DBS4 for enantioselective degradation of chiral herbicide diclofop-methyl

Diclofop-methyl, an aryloxyphenoxypropionate (AOPP) herbicide, is a chiral compound with two enantiomers. Microbial detoxification and degradation of various enantiomers is garnering immense research attention. However, enantioselective catabolism of diclofop-methyl has been rarely explored, especially at the molecular level. This study cloned two novel hydrolase genes (dcmA and dcmH) in Sphingopyxis sp. DBS4, and characterized them for diclofop-methyl degradation. DcmA, a member of the amidase superfamily, exhibits 26.1-45.9% identity with functional amidases. Conversely, DcmH corresponded to the DUF3089 domain-containing protein family (a family with unknown function), sharing no significant similarity with other biochemically characterized proteins. DcmA exhibited a broad spectrum of substrates, with preferential hydrolyzation of (R)-(+)-diclofop-methyl, (R)-(+)-quizalofop-ethyl, and (R)-(+)-haloxyfop-methyl. DcmH also preferred (R)-(+)-quizalofop-ethyl and (R)-(+)-haloxyfop-methyl degradation while displaying no apparent enantioselective activity towards diclofop-methyl. Using site-directed mutagenesis and molecular docking, it was determined that Ser175 was the fundamental residue influencing DcmA's activity against the two enantiomers of diclofop-methyl. For the degradation of AOPP herbicides, DcmA is an enantioselective amidase that has never been reported in research. This study provided novel hydrolyzing enzyme resources for the remediation of diclofop-methyl in the environment and deepened the understanding of enantioselective degradation of chiral AOPP herbicides mediated by microbes.

Efficient production of R-2-(4-hydroxyphenoxy) propionic acid by Beauveria bassiana using biofilm-based two-stage fermentation

In this work, a novel biofilm-based fermentation of Beauveria bassiana was employed to convert R-2- phenoxypropionic acid (R-PPA) to R-2-(4-hydroxyphenoxy) propionic acid (R-HPPA). The biofilm culture model of Beauveria bassiana produced a significantly higher R-HPPA titer than the traditional submerged fermentation method. Mannitol dosage, tryptone dosage, and initial pH were the factors that played a significant role in biofilm formation and R-HPPA synthesis. Under the optimal conditions, the maximum R-HPPA titer and productivity approached 22.2 g/L and 3.2 g/(L·d), respectively. A two-stage bioreactor combining agitation and static incubation was developed to further increase R-HPPA production. The process was optimized to achieve 100 % conversion of R-PPA, with a maximum R-HPPA titer of 50 g/L and productivity of 3.8 g/(L·d). This newly developed biofilm-based two-stage fermentation process provides a promising strategy for the industrial production of R-HPPA and related hydroxylated aromatic compounds.

Efficiency and ecological safety of herbicide haloxyfop-R-methyl on removal of coastal invasive plant Spartina alterniflora

Spartina alterniflora is a global invasive plant and has caused considerable damage to coastal wetland ecosystem. This study evaluated the efficiency and ecological safety of herbicide haloxyfop-R-methyl (HPME) in removing S alterniflora in Laizhou Bay. The results showed that the density of regenerated S. alterniflora after 10 months of application of 0.01, 0.02 and 0.03 g/m2 HPME decreased by 86.67 %, 99.16 % and 99.31 %, respectively. Moreover, seed abortion rates were 62.25 %, 92.24 % and 94.82 %, and weight of roots in HPME groups were 56.63 %, 59.99 %, and 40.10 % of those in the control group. After 4 days of application, HPME could not be detected in S. alterniflora and sediments. In addition, HPME did not change sediment physicochemical properties, macrozoobenthos community and microbial community structure during 16 days, but increased the density of native macrozoobenthos after 1 year. Therefore, HPME might be an effective and ecologically safe chemical for the eradication of S. alterniflora.

Determination of quizalofop-p-ethyl in onion: residual dissipation pattern, weed control efficiency, and food safety assessment under field conditions

Monitoring pesticide residue levels becomes crucial to maintain quality and guarantee food safety as the consumption of onion green leaves and immature and mature bulbs (either raw or processed) rises. A field experiment was conducted for two consecutive seasons with quizalofop-p-ethyl (5% EC) at 50 and 100 g a.i. ha-1 to evaluate weed control efficiency and to determine terminal residues. Post-emergence application of fop herbicide at 100 g a.i. ha-1 kept the weed density and dry weight reasonably at a lower level and enhanced the productivity of onion with higher economic returns. A rapid, sensitive, and analytical method was developed using high-performance liquid chromatography (HPLC) with excellent linearity (r2 > 0.99). The limit of quantification for quizalofop-p-ethyl was established at 0.04 mg kg-1 with signal to noise (S/N) ratio ≥ 10. The method was successfully applied and initial quantified residues were in the range of 2.5-4.4 mg kg-1 irrespective of seasons and doses. Finally, the presence of targeted herbicide residues in harvested samples was confirmed by liquid chromatography tandem mass spectrometry (LC-MS/MS) under optimized operating conditions. Dietary risk assessment assured harvested onions were safe for consumption at the recommended dose. It also can be concluded that quizalofop ethyl did not adversely influence soil micro-organisms at standard rates of application.

Research Progress of Benzothiazole and Benzoxazole Derivatives in the Discovery of Agricultural Chemicals

Benzoxazole and benzothiazole have a broad spectrum of agricultural biological activities, such as antibacterial, antiviral, and herbicidal activities, which are important fused heterocyclic scaffold structures in agrochemical discovery. In recent years, great progress has been made in the research of benzoxazoles and benzothiazoles, especially in the development of herbicides and insecticides. With the widespread use of benzoxazoles and benzothiazoles, there may be more new products containing benzoxazoles and benzothiazoles in the future. We systematically reviewed the application of benzoxazoles and benzothiazoles in discovering new agrochemicals in the past two decades and summarized the antibacterial, fungicidal, antiviral, herbicidal, and insecticidal activities of the active compounds. We also discussed the structural-activity relationship and mechanism of the active compounds. This work aims to provide inspiration and ideas for the discovery of new agrochemicals based on benzoxazole and benzothiazole.

Magnetic metal-organic frameworks immobilized enzyme-based nano-biocatalytic systems for sustainable biotechnology

Nanobiocatalysts, in which enzyme molecules are integrated into/onto multifunctional materials, such as metal-organic frameworks (MOFs), have been fascinating and appeared as a new interface of nanobiocatalysis with multi-oriented applications. Among various nano-support matrices, functionalized MOFs with magnetic attributes have gained supreme interest as versatile nano-biocatalytic systems for organic bio-transformations. From the design (fabrication) to deployment (application), magnetic MOFs have manifested notable efficacy in manipulating the enzyme microenvironment for robust biocatalysis and thus assure requisite applications in several areas of enzyme engineering at large and nano-biocatalytic transformations, in particular. Magnetic MOFs-linked enzyme-based nano-biocatalytic systems offer chemo-regio- and stereo-selectivities, specificities, and resistivities under fine-tuned enzyme microenvironments. Considering the current sustainable bioprocesses demands and green chemistry needs, we reviewed synthesis chemistry and application prospects of magnetic MOFs-immobilized enzyme-based nano-biocatalytic systems for exploitability in different industrial and biotechnological sectors. More specifically, following a thorough introductory background, the first half of the review discusses various approaches to effectively developed magnetic MOFs. The second half mainly focuses on MOFs-assisted biocatalytic transformation applications, including biodegradation of phenolic compounds, removal of endocrine disrupting compounds, dye decolorization, green biosynthesis of sweeteners, biodiesel production, detection of herbicides and screening of ligands and inhibitors.

Effects of haloxyfop-p-methyl on the developmental toxicity, neurotoxicity, and immunotoxicity in zebrafish

Pesticides are extensively used in agricultural production, and their residues in soil, water, and agricultural products have become a threat to aquatic ecosystem. In this study, the toxicity of haloxyfop-p-methyl, an aryloxyphenoxypropionate herbicide was studied using the model animal zebrafish. The development of zebrafish larvae was affected by haloxyfop-p-methyl including spinal deformities, decreased body length, slow heart rate, and large yolk sac area. Behavior analysis revealed that behavior activity of larvae was weakened significantly including shortened displacement distance, reduced swimming speed, increased angular speed winding degrees, in accordance with higher AChE activity. Besides, exposure to haloxyfop-p-methyl could induce oxidative stress companied by the increased intents of ROS, MDA and increased activities of CAT and SOD. In immunotoxicity, haloxyfop-p-methyl not only reduced the innate immune cells such as neutrophils and macrophages, but also affected T cells mature in thymus. Furthermore, haloxyfop-p-methyl could induce neutrophils apoptosis, accompanied with the upregulation of the expression of proapoptotic protein such as Bax and P53 and the downregulation of the expression of antiapoptotic protein Bcl-2. In addition, haloxyfop-p-methyl could induce the expression of Jak, STAT and proinflammatory cytokine genes (IFN-γ, TNF-α, and IL-8). These results indicate that haloxyfop-p-methyl induces developmental toxicity, neurotoxicity, and immunotoxicity in zebrafish, providing a perspective on the toxicological mechanism of haloxyfop-p-methyl in teleosts.

Insights of microbial community evolution under benzisothiazolinone exposure in different soil environments

Benzisothiazolinones (1, 2-benzisothiazoline-3-one; BIT) is widely used to control bacterial and fungal diseases of various crops, and their residues in soil may play an important role in the interaction between soil microorganisms. We studied microbial remediation in five representative soils under different soil conditions (unsterilized, sterilized and flooded) using 16S rRNA gene sequencing to investigate the effect of microorganisms on the degradation of BIT residues in soils to minimize the potentially toxic effects of BIT. High-throughput sequencing data showed that the structure and abundance of bacterial communities in BIT soils changed greatly, which might affect their degradation pathways, while Principal Coordinates Analysis (PCoA) results showed that there was no significant difference in the fungal community in different treatments of the five soils, but the degradation rate of BIT was more influenced by anaerobic microorganisms. Furthermore, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria were the predominant bacterial phyla, accounting for 93.74% of all OTUs, which played an important role in the degradation of BIT. Lysinibacillus had a high relative abundance (21.10%) under flooded treatment conditions in Jilin soil, and its bioremediation may be a reason for the rapid degradation of BIT in flooded treatment. Besides, only soil organic matter (SOM) and pH among the soil properties had significant effects on the microbial community. Based on the further analysis of bacterial phenotype, some microorganisms related to the biodegradation of BIT were found, mainly belonging to Proteobacteria, Bacteroidetes and Firmicutes. This study provides a useful theoretical basis for the biodegradation of BIT using isolated microorganisms.

Transcriptome analysis reveals hepatotoxicity in zebrafish induced by cyhalofop‑butyl

Cyhalofop‑butyl is a highly effective aryloxyphenoxypropionate herbicide and widely used for weed control in paddy fields. With the increasing residue of cyhalofop‑butyl, it poses a threat to the survival of aquatic organisms. Here, we investigated the effect of cyhalofop‑butyl on zebrafish to explore its potential hepatotoxic mechanism. The results showed that cyhalofop‑butyl induced hepatocyte degeneration, vacuolation and necrosis of larvae after embryonic exposure for 4 days and caused liver atrophy after 5 days. Meanwhile, the activities of enzymes related to liver function were significantly increased by 0.2 mg/L cyhalofop‑butyl and higher, such as alanine transaminase (ALT) and aspartate transaminase (AST). And the contents of triglyceride (TG) involved in lipid metabolism were significantly decreased by 0.4 mg/L cyhalofop-buty. The expression of genes related to liver development was also significantly down-regulated. Furthermore, transcriptome results showed that the pathways involved in metabolism, immune system and endocrine system were significantly impacted, which may be related to hepatoxicity. To sum up, the present study demonstrated the hepatoxicity caused by cyhalofop-buty and its underlying mechanism. The results may provide new insights for the risk of cyhalofop‑butyl to aquatic organisms and new horizons for the pathogenesis of hepatotoxicity.

Biodegradation of herbicides by a plant nonheme iron dioxygenase: mechanism and selectivity of substrate analogues

Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogs by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C 2 -hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R - and S -methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R -isomer give high rebound barriers.

Magnetic ZIF-8-Based Mimic Multi-enzyme System as a Colorimetric Biosensor for Detection of Aryloxyphenoxypropionate Herbicides

In the present study, a magnetic mimic multi-enzyme system was developed by encapsulating the aryloxyphenoxypropionate (AOPP) herbicide hydrolase QpeH and alcohol oxidase (AOx) in zeolitic imidazolate framework (ZIF-8) nanocrystals with magnetic Fe₃O₄ nanoparticles (MNPs) to detect AOPP herbicides. The structural, protein loading capacity and loading ratio, porosity, and magnetic properties of QpeH/AOx@mZIF-8 were characterized by scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy, thermogravimetric analysis, nitrogen sorption, and vibrating sample magnetometry. An AOPP herbicide colorimetric biosensor made with QpeH/AOx@mZIF-8 had the highest sensitivity toward quizalofop-P-ethyl (QpE) with a limit of detection of 8.2 μM. This system was suitable to detect two other AOPP herbicides, including fenoxaprop-P-ethyl (FpE) and haloxyfop-P-methyl (HpE). The practical application of the biosensor was verified through quantitative analysis of QpE residues in industrial wastewater and field soils. Furthermore, QpeH/AOx@mZIF-8 exhibited excellent long-term storage stability (at least 50 days), easy separation by magnet, and reusability (at least 10 cycles), supporting its promising role in simple and low-cost detection of AOPP herbicides in real environmental samples.

Influence of the herbicide haloxyfop-R-methyl on bacterial diversity in rhizosphere soil of Spartina alterniflora

Haloxyfop-R-methyl (haloxyfop) can efficiently control Spartina alterniflora in coastal ecosystems, but its effect on soil microbial communities is not known. In the present study, the impact of the haloxyfop on rhizosphere soil bacterial communities of S. alterniflora over the dissipation process of the herbicide has been studied in a coastal wetland. The response of the bacterial community in the rhizoplane (iron plaque) of S. alterniflora subjected to haloxyfop treatment was also investigated. Results showed that the persistence of haloxyfop in the rhizosphere soil followed an exponential decay with a half-life of 2.6-4.9 days, and almost all of the haloxyfop dissipated on Day 30. The diversity of rhizosphere soil bacteria was decreased at the early stages (Days 1, 3 & 7) and recovered at late stages (Days 15 & 30) of the haloxyfop treatment. Application of haloxyfop treatment increased the relative abundance of the genera Pseudomonas, Acinetobacter, Pontibacter, Shewanella and Aeromonas. Strains isolated from these genera can degrade herbicides efficiently, which possibly played a role in the degradation of haloxyfop. The rhizoplane bacterial diversity was reduced on Day 15 while being vastly enhanced on Day 30. Soil variables, including the electric conductivity, redox potential, and soil moisture, along with the soil haloxyfop residue, jointly shape the bacterial community in rhizosphere soil.

Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil

Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same inoculation level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil.