Enantioselective Catabolism of the Two Enantiomers of the Phenoxyalkanoic Acid Herbicide Dichlorprop by Sphingopyxis sp. DBS4

SFC-MS/MS enantioseparation, stereoselective behavior and risk assessment of the chiral pesticide bitertanol in four vegetables and soil

The stereoselective behavior and dietary risk of bitertanol in four vegetables and soil were studied. Firstly, the method for measuring bitertanol stereoisomers by SFC-MS/MS was established and optimized, and the analysis time was 5 min. In addition, cis-(+)-(1R,2S)-bitertanol and trans-(+)-(1R,2R)-bitertanol were preferentially dissipated in cabbage and pakchoi, while trans-(+)-(1S,2S)-bitertanol had a preferential dissipation in lettuce. For diastereoisomers, cis-bitertanol was dissipated with preference in the vegetables under test. The dissipation halflives of rac-bitertanol were as follows: pakchoi (0.57-0.74 days) < cabbage (0.87-1.07 days) < celery (1.32-1.63 days) < lettuce (1.75-2.37 days) < soil (22.5-24.7 days). Finally, the final residual concentrations of rac-bitertanol in lettuce (0.0128 mg/kg) and celery (0.0289 mg/kg) were higher than the maximum residue limit (MRL, 0.01 mg/kg), which should raise concern. The results of dietary risk assessment showed that both the chronic dietary risk and the acute dietary risk of rac-bitertanol in these test vegetables were negligible.

Enantioselective Metabolism of Chiral Fungicide Prothioconazole by Mycobacterium sp. Y-3 and Its Bioaugmentation

Prothioconazole (PTC) is a kind of chiral triazole fungicide widely used in agricultural production, which can easily cause residual contamination and chiral selective toxicity. Microorganisms are the main participants involved in pollutant degradation in the environment. However, studies on the microbial enantioselective degradation of PTC and bioaugmentation of PTC-contaminated soil are still scarce. Herein, we isolated an efficient PTC-degrading strain, Mycobacterium sp. Y-3. Strain Y-3 preferentially metabolized (R)-PTC over (S)-PTC; the degradation rate of (R)-PTC was 2.5 times that of (S)-PTC. The T1/2 values of 20-80 μM (Rac)-/(S)-/(R)-PTC after treatment with strain Y-3 were 4.1-7.1 h at 37 °C and pH 5.0. The addition of glutamine could significantly enhance the PTC degradation ability of strain Y-3. Strain Y-3 metabolized PTC via methylation to form prothioconazole-S-methyl, the detoxification pathway for PTC. In bioaugmentation experiments, strain Y-3 eliminated PTC residues in the soil within 12 days. High-throughput sequencing analysis indicated that strain Y-3 colonized well in the soil. Inoculation with strain Y-3 reduced soil microbial community diversity and richness, while the bioaugmentation treatment enhanced the soil microbial community associations. These findings provide new insights into the enantioselective microbial metabolism of chiral PTC and in situ bioaugmentation of PTC-contaminated soils.

Earthworms-enhanced bacterial degradation of the chiral fungicide penflufen R-enantiomer

The widespread application of chiral fungicides as seed-coating agents in agriculture has led to serious residue accumulation in soil, increasingly drawing attention to soil pollution remediation strategies for chiral pesticides. This study explored the role of earthworms and soil microorganisms in selectively accelerating the degradation of penflufen in soil. The results showed that soil microorganisms significantly accelerated penflufen enantiomer degradation, particularly the R-enantiomer. Nocardioides, Variovorax, Arthrobacter, and Pseudomonas were identified as key degrading microorganisms associated with the preferential degradation of the R-enantiomer. The addition of earthworms further significantly enhanced the preferential degradation of the R-enantiomer. Importantly, earthworms markedly promoted the growth and reproduction of the four aforementioned degrading microorganisms in soil treated with enantiomers. Notably, the relative abundance of these degrading microorganisms was significantly higher in R-enantiomer-treated soil with earthworms than in soil treated with the S-enantiomer. Additionally, earthworms significantly increased the relative abundance of degradation genes p450, bphA1, and benA in the soil, especially in the R-enantiomer treated soil. Nocardioides, Variovorax, Arthrobacter, and Pseudomonas were identified as potential hosts for the degradation gene benA. More importantly, twelve strains of penflufen-degrading bacteria were isolated from the treated soil, of which eight belonged to the aforementioned four microorganisms and exhibited a remarkable ability to preferentially degrade the R-enantiomer. This finding highlights the potential of adding earthworms to soil, in conjunction with key degrading microorganisms, which preferentially accelerates penflufen R-enantiomer degradation.

Assessing the impact of soil microbial fuel cells on atrazine removal in soil

Widespread pesticide use in agriculture is a major source of soil pollution, driving biodiversity loss and posing serious threads to human health. The recalcitrant nature of most of these pesticides demands for effective remediation strategies. In this study, we assess the ability of soil microbial fuel cell (SMFC) technology to bioremediate soil polluted by the model pesticide atrazine. To elucidate the degradation mechanism and consequently define effective implementation strategies, we provide the first comprehensive investigation of the SMFC performance, in which the monitoring of the electrochemical performance of the system is combined with Quadrupole Time-of-Flight (QTOF) mass spectrometry and microbial analyses. Our results show that, while both SMFC and natural attenuation lead to a reduction on atrazine levels, the SMFC modulates the activity of different microbial pathways. As a result, atrazine degradation by natural attenuation leads to high levels of deisoproylatrazine (DIPA), a very toxic degradation metabolite, while DIPA levels in soil treated by SMFC remain comparatively low. The beta diversity and differential abundance analyses revealed how the microbial community evolves over time in the SMFCs degrading atrazine, demonstrating the enrichment of electroactive taxa on the anode, and the enrichment of a mixture of electroactive and atrazine-degrading taxa at the cathode. The detection and taxonomic classification of peripheral atrazine degrading genes, atzA, atzB and atzC, was carried out in combination with the differential abundance analysis. Results revealed that these genes are likely harboured by members of the order Rhizobiales enriched at the cathode, thus promoting atrazine degradation via the conversion of hydroxyatrazine (HA) into N-isopropylammelide (NIPA), as confirmed by mass spectrometry data. Overall, the comprehensive approach adopted in this work, provides fundamental insights into the degradation pathways of atrazine in soil by SMFC technology, which is critical for practical applications, thus suggesting an effective approach to advance research in the field.

Novel 4-chlorophenoxyacetate dioxygenase-mediated phenoxyalkanoic acid herbicides initial catabolism in Cupriavidus sp. DL-D2

Microbial metabolism is an important driving force for the elimination of 4-chlorophenoxyacetic acid residues in the environment. The α-Ketoglutarate-dependent dioxygenase (TfdA) or 2,4-D oxygenase (CadAB) catalyzes the cleavage of the aryl ether bond of 4-chlorophenoxyacetic acid to 4-chlorophenol, which is one of the important pathways for the initial metabolism of 4-chlorophenoxyacetic acid by microorganisms. However, strain Cupriavidus sp. DL-D2 could utilize 4-chlorophenoxyacetic acid but not 4-chlorophenol for growth. This scarcely studied degradation pathway may involve novel enzymes that has not yet been characterized. Here, a gene cluster (designated cpd) responsible for the catabolism of 4-chlorophenoxyacetic acid in strain DL-D2 was cloned and identified, and the dioxygenase CpdA/CpdB responsible for the initial degradation of 4-chlorophenoxyacetic acid was successfully expressed, which could catalyze the conversion of 4-chlorphenoxyacetic acid to 4-chlorocatechol. Then, an aromatic cleavage enzyme CpdC further converts 4-chlorocatechol into 3-chloromuconate. The results of substrate degradation experiments showed that CpdA/CpdB could also degrade 3-chlorophenoxyacetic acid and phenoxyacetic acid, and homologous cpd gene clusters were widely discovered in microbial genomes. Our findings revealed a novel degradation mechanism of 4-chlorophenoxyacetic acid at the molecular level.

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.

Enantioselective Behaviors of Chiral Pesticides and Enantiomeric Signatures in Foods and the Environment

Unreasonable application of pesticides may result in residues in the environment and foods. Chiral pesticides consist of two or more enantiomers, which may exhibit different behaviors. This Review intends to provide progress on the enantioselective residues of chiral pesticides in foods. Among the main chiral analytical methods, high performance liquid chromatography (HPLC) is the most frequently utilized. Most chiral pesticides are utilized as racemates; however, due to enantioselective dissipation, bioaccumulation, biodegradation, and chiral conversion, enantiospecific residues have been found in the environment and foods. Some chiral pesticides exhibit strong enantioselectivity, highlighting the importance of evaluation on an enantiomeric level. However, the occurrence characteristics of chiral pesticides in foods and specific enzymes or transport proteins involved in enantioselectivity needs to be further investigated. This Review could help the production of some chiral pesticides to single-enantiomer formulations, thereby reducing pesticide consumption as well as increasing food production and finally reducing human health risks.

Versatile Biocatalytic C(sp3 )-H Oxyfunctionalization for the Site- Selective and Stereodivergent Synthesis of α- and β-Hydroxy Acids

C(sp3 )-H oxyfunctionalization, the insertion of an O-atom into C(sp3 )-H bonds, streamlines the synthesis of complex molecules from easily accessible precursors and represents one of the most challenging tasks in organic chemistry with regard to site and stereoselectivity. Biocatalytic C(sp3 )-H oxyfunctionalization has the potential to overcome limitations inherent to small-molecule-mediated approaches by delivering catalyst-controlled selectivity. Through enzyme repurposing and activity profiling of natural variants, we have developed a subfamily of α-ketoglutarate-dependent iron dioxygenases that catalyze the site- and stereodivergent oxyfunctionalization of secondary and tertiary C(sp3 )-H bonds, providing concise synthetic routes towards four types of 92 α- and β-hydroxy acids with high efficiency and selectivity. This method provides a biocatalytic approach for the production of valuable but synthetically challenging chiral hydroxy acid building blocks.

Insights on the isolation, identification, and degradation characteristics of three bacterial strains against mandipropamid and their application potential for polluted soil remediation

Bacteria-induced biodegradation techniques have become an effective approach for removing pesticide residues from polluted soils. However, their effect on chiral fungicides must be systematically evaluated and the efficiency and risk of each chiral enantiomer must be better understood. In this study, we isolated and enriched seven bacterial strains that are able to degrade mandipropamid from contaminated soil samples. Three bacterial strains with high degradation efficiency (63.6%-73.4%) were screened and identified as Pseudomonas sp. (M01), Mycolicibacterium parafortuitum (MW05), and Stenotrophomonas maltophilia (MW09) by morphological and 16S rRNA gene sequencing analyses. The degradation characteristics of three strains (M01, MW05, and MW09) was investigated and it was revealed that pH, temperature, and initial concentration of mandipropamid significantly impacted their degradation efficiency. The optimal conditions for degradation were a nutrient source of mandipropamid and an inoculation amount of 5%. We used a Box-Behnken model experiment and an analysis of variance to determine the most suitable conditions for degrading mandipropamid at various pH, temperature, and initial concentration levels. A response surface methodology analysis showed that the three strains had the highest mandipropamid degradation efficiency (> 96%) under various conditions (pH: 7.15-7.71, temperature: 28.61-30.76 °C, initial concentration: 5.524-5.934 mg/L). Mycelial, intracellular, and extracellular enzymes also had an impact on the degradation of mandipropamid enantiomers by the three strains. In soil remediation trials, the three bacterial strains could effectively enantioselectively degrade rac-mandipropamid residues in polluted sterilized and natural soil samples (R-enantiomer was degraded faster) and influence the activity of urease and β-glucosidase in the soil. The results revealed several candidate bacterial strains for mandipropamid biodegradation and provide information on mandipropamid biological detoxification in soil environments.

Isolation of Sphingomonas sp. AJ-1 and its enantioselective S-methylation of the triazole fungicide prothioconazole

Prothioconazole is a widely used chiral triazole fungicide, and its residue pollution has attracted wide attention in recent years. However, little is known about microbial metabolic processes of prothioconazole enantiomers. In this study, a prothioconazole-degrading strain, Sphingomonas sp. AJ-1, was isolated from activated sludge. The optimal temperature and pH for prothioconazole degradation by strain AJ-1 were 30 °C and 6.0, respectively, and the degradation rate of prothioconazole by strain AJ-1 was negatively correlated with the initial concentration. When supplemented with additional carbon source, the degradation rates of 10 mg/L (Rac)-/(S)-/(R)-prothioconazole by strain AJ-1 were 76.0 %, 100.0 % and 64.8 % within 6 d, respectively. The CS bond of prothioconazole was methylated to produce (S)-/(R)-prothioconazole-S-methyl by strain AJ-1, but the degradation rate of prothioconazole by strain AJ-1 with (S)-enantiomer was 2.54-fold of that with (R)-enantiomer. Moreover, the toxicity of (Rac)-prothioconazole-S-methyl was 5.57 times lower than that of (Rac)-prothioconazole to Pseudokirchneriella subcapitata. The results showed that strain AJ-1 had obvious enantioselective metabolism for prothioconazole, and this metabolism was a detoxification process. This study provides new insights into the enantioselective metabolism of the chiral fungicide prothioconazole in microorganisms.

Agriterribacter soli sp. nov., isolated from herbicide-contaminated soil

A Gram-stain-negative, non-spore-forming and rod-shaped bacterium, designated strain NS-102T, was isolated from herbicide-contaminated soil sampled in Nanjing, PR China, and its taxonomic status was investigated by a polyphasic approach. Cell growth of strain NS-102T occurred at 16–42 °C (optimum, 30 °C), at pH 5.0–8.0 (optimum, pH 6.0) and in the presence of 0–3.5 % (w/v) NaCl (optimum, without addition of NaCl). The 16S rRNA gene sequence of strain NS-102T shows high similarity to that of Agriterribacter humi YJ03T (96.9 % similarity), followed by Terrimonas terrae T16R-129T (93.8 %) and Terrimonas pekingensis QHT (93.6 %). Average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the draft genomes of strain NS-102T and A. humi YJ03T were 72.5, 69.4 and 18.6%, respectively. The only respiratory quinone was MK-7, and phosphatidylethanolamine and unidentified lipids were the major polar lipids. The major cellular fatty acids of strain NS-102T contained high amounts of iso-C15 : 0 (24.6 %), iso-C17 : 03-OH (24.1 %), iso-C15 : 0 G (16.6 %) and summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) (15.6 %). The G+C content of the total DNA was determined to be 40.0 mol%. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain NS-102T represents a novel species of the genus Agriterribacter , for which the name Agriterribacter soli sp. nov. is proposed. The type strain is NS-102T (=CCTCC AB 2017249T=KCTC 62322T).

A Synergistic Consortium Involved in rac-Dichlorprop Degradation as Revealed by DNA Stable Isotope Probing and Metagenomic Analysis

rac-Dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in rac-dichlorprop degradation. However, the compositions of the microbial consortia involved in rac-dichlorprop degradation remain largely unknown. In this study, DNA stable isotope probing (SIP) and metagenomic analysis were integrated to reveal the key microbial consortium responsible for rac-dichlorprop degradation in a rac-dichlorprop-degrading enrichment. OTU340 (Sphingobium sp.) and OTU348 (Sphingopyxis sp.) were significantly enriched in the rac-[¹³C]dichlorprop-labeled heavy DNA fractions. A rac-dichlorprop degrader, Sphingobium sp. strain L3, was isolated from the enrichment by a traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomic analysis of the associations between rac-dichlorprop degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA, involved in the initial degradation of the (R)- and (S)-enantiomers of dichlorprop, respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop-degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella, Sphingomonas, Pseudomonas, and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. IMPORTANCE Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide rac-dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of the microbial consortium and the interactions between community members during the biodegradation of rac-dichlorprop are unclear. In this study, DNA-SIP and metagenomic analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella, Sphingomonas, Pseudomonas, and Achromobacter synergistically cooperated with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. Our study provides new insights into the synergistic degradation of rac-dichlorprop at the community level and implies the existence of novel degrading genes for rac-dichlorprop in nature.

Enantioselective degradation of the organophosphorus insecticide isocarbophos in Cupriavidus nantongensis X1T: Characteristics, enantioselective regulation, degradation pathways, and toxicity assessment

The chiral pesticide enantiomers often show selective efficacy and non-target toxicity. In this study, the enantioselective degradation characteristics of the chiral organophosphorus insecticide isocarbophos (ICP) by Cupriavidus nantongensis X1^T were investigated systematically. Strain X1^T preferentially degraded the ICP R isomer (R-ICP) over the S isomer (S-ICP). The degradation rate constant of R-ICP was 42-fold greater than S-ICP, while the former is less bioactive against pest insects but more toxic to humans than the latter. The concentration ratio of S-ICP to R-ICP determines whether S-ICP can be degraded by strain X1^T. S-ICP started to degrade only when the ratio (C_S-ICP/C_R-ICP) was greater than 62. Divalent metal cations could improve the degradation ability of strain X1^T. The detected metabolites that were identified suggested a novel hydrolysis pathway, while the hydrolytic metabolites were less toxic to fish and green algae than those from P-O bond breakage. The crude enzyme degraded both R-ICP and S-ICP in a similar rate, indicating that enantioselective degradation was due to the transportation of strain X1^T. The strain X1^T also enantioselectively degraded the chiral organophosphorus insecticides isofenphos-methyl and profenofos. The enantioselective degradation characteristics of strain X1^T make it suitable for remediation of chiral organophosphorus insecticide contaminated soil and water.