Biodegradation of the pyridinecarboxamide insecticide flonicamid by Microvirga flocculans and characterization of two novel amidases involved

Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit-like amidase mediates the degradation of insecticide flonicamid by Variovorax boronicumulans CGMCC 4969

The main metabolic product of the pyridinecarboxamide insecticide flonicamid, N-(4-trifluoromethylnicotinyl)glycinamide (TFNG-AM), has been shown to have very high mobility in soil, leading to its accumulation in the environment. Catabolic pathways of flonicamid have been widely reported, but few studies have focused on the metabolism of TFNG-AM. Here, the rapid transformation of TFNG-AM and production of the corresponding acid product N-(4-trifluoromethylnicotinoyl) glycine (TFNG) by the plant growth-promoting bacterium Variovorax boronicumulans CGMCC 4969 were investigated. With TFNG-AM at an initial concentration of 0.86 mmol/L, 90.70 % was transformed by V. boronicumulans CGMCC 4969 resting cells within 20 d, with a degradation half-life of 4.82 d. A novel amidase that potentially mediated this transformation process, called AmiD, was identified by bioinformatic analyses. The gene encoding amiD was cloned and expressed recombinantly in Escherichia coli, and the enzyme AmiD was characterized. Key amino acid residue Val154, which is associated with the catalytic activity and substrate specificity of signature family amidases, was identified for the first time by homology modeling, structural alignment, and site-directed mutagenesis analyses. When compared to wild-type recombinant AmiD, the mutant AmiD V154G demonstrated a 3.08-fold increase in activity toward TFNG-AM. The activity of AmiD V154G was greatly increased toward aromatic L-phenylalanine amides, heterocyclic TFNG-AM and IAM, and aliphatic asparagine, whereas it was dramatically lowered toward benzamide, phenylacetamide, nicotinamide, acetamide, acrylamide, and hexanamid. Quantitative PCR analysis revealed that AmiD may be a substrate-inducible enzyme in V. boronicumulans CGMCC 4969. The mechanism of transcriptional regulation of AmiD by a member of the AraC family of regulators encoded upstream of the amiD gene was preliminarily investigated. This study deepens our understanding of the mechanisms of metabolism of toxic amides in the environment, providing new ideas for microbial bioremediation.

Efficient Biodegradation of the Neonicotinoid Insecticide Flonicamid by Pseudaminobacter salicylatoxidans CGMCC 1.17248: Kinetics, Pathways, and Enzyme Properties

Nitrile-containing insecticides can be converted into their amide derivatives by Pseudaminobacter salicylatoxidans. N-(4-trifluoromethylnicotinoyl) glycinamide (TFNG-AM) is converted to 4-(trifluoromethyl) nicotinoyl glycine (TFNG) using nitrile hydratase/amidase. However, the amidase that catalyzes this bioconversion has not yet been fully elucidated. In this study, it was discovered that flonicamid (FLO) is degraded by P. salicylatoxidans into the acid metabolite TFNG via the intermediate TFNG-AM. A half-life of 18.7 h was observed for P. salicylatoxidans resting cells, which transformed 82.8% of the available FLO in 48 h. The resulting amide metabolite, TFNG-AM, was almost all converted to TFNG within 19 d. A novel amidase-encoding gene was cloned and overexpressed in Escherichia coli. The enzyme, PmsiA, hydrolyzed TFNG-AM to TFNG. Despite being categorized as a member of the amidase signature enzyme superfamily, PsmiA only shares 20-30% identity with the 14 previously identified members of this family, indicating that PsmiA represents a novel class of enzyme. Homology structural modeling and molecular docking analyses suggested that key residues Glu247 and Met242 may significantly impact the catalytic activity of PsmiA. This study contributes to our understanding of the biodegradation process of nitrile-containing insecticides and the relationship between the structure and function of metabolic enzymes.

Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action

The cereal leaf beetle (CLB, Oulema melanopus) is one of the major cereal pests. The effect of insecticides belonging to different chemical classes, with different mechanisms of action and the active substances' concentrations on the CLB bacterial microbiome, was investigated. Targeted metagenomic analysis of the V3-V4 regions of the 16S ribosomal gene was used to determine the composition of the CLB bacterial microbiome. Each of the insecticides caused a decrease in the abundance of bacteria of the genus Pantoea, and an increase in the abundance of bacteria of the genus Stenotrophomonas, Acinetobacter, compared to untreated insects. After cypermethrin application, a decrease in the relative abundance of bacteria of the genus Pseudomonas was noted. The dominant bacterial genera in cypermethrin-treated larvae were Lactococcus, Pantoea, while in insects exposed to chlorpyrifos or flonicamid it was Pseudomonas. Insecticide-treated larvae were characterized, on average, by higher biodiversity and richness of bacterial genera, compared to untreated insects. The depletion of CLB-associated bacteria resulted in a decrease in larval survival, especially after cypermethrin and chlorpyrifos treatments. The use of a metagenome-based functional prediction approach revealed a higher predicted function of bacterial acetyl-CoA C-acetyltransferase in flonicamid and chlorpyrifos-treated larvae and tRNA dimethyltransferase in cypermethrin-treated insects than in untreated insects.

Rapid Degradation of Hazardous Amides by Immobilized Engineered Pseudomonas putida KT2440 Based on a Novel Gene Expression Vector

The amides 4-trifluoromethylnicotinamide, acrylamide, and benzamide are widely used in agriculture and industry, posing hazards to the environment and animals. Immobilized bacteria are preferred in wastewater treatment, but degradation of these amides by immobilized engineered bacteria has not been explored. Here, engineered Pseudomonas putida KT2440 pLSJ15-amiA was constructed by introducing a new amidase gene expression vector into environmentally safe P. putida KT2440. P. putida KT2440 pLSJ15-amiA had high amidase activity, even at 80 °C. P. putida KT2440 pLSJ15-amiA immobilized with calcium alginate exhibited a greater environmental tolerance than free cells. The amides were rapidly degraded by the immobilized cells, but the activity was inhibited by high concentrations of substrates. The substrate inhibition model revealed that the optimum initial concentrations of 4-trifluoromethylnicotinamide, acrylamide, and benzamide for degradation by immobilized cells were 197.65, 350.76, and 249.40 μmol/L, respectively. This study develops a novel and excellent immobilized biocatalyst for remediation of wastewater containing hazardous amides.

Metabolic Profiling and Comparative Proteomic Insight in Respect of Amidases during Iprodione Biodegradation

The fungicide iprodione (IPR) (3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide) is a highly toxic compound. Although IPR has been restricted, it is still being applied in many places around the world, constituting an environmental risk. The biodegradation of IPR is an attractive option for reducing its residues. In this study, we isolated thirteen IPR-tolerant bacteria from a biopurification system designed to treat pesticides. A study of biodegradation using different strains was comparatively evaluated, and the best degradation rate of IPR was presented by Achromobacter sp. C1 with a half-life (T1/2) of 9 days. Based on a nano-LC-MS/MS analysis for the strains, proteins solely expressed in the IPR treatment were identified by highlighting the strain Achromobacter sp. C1, with 445 proteins primarily involved in the biosynthesis of secondary metabolites and microbial metabolism in diverse environments. Differentially expressed protein amidases were involved in six metabolic pathways. Interestingly, formamidase was inhibited while other cyclases, i.e., amidase and mandelamide hydrolase, were overexpressed, thereby minimizing the effect of IPR on the metabolism of strain C1. The dynamic changes in the protein profiles of bacteria that degrade IPR have been poorly studied; therefore, our results offer new insight into the metabolism of IPR-degrading microorganisms, with special attention paid to amidases.

New mechanisms of biochar-assisted vermicomposting by recognizing different active di-(2-ethylhexyl) phthalate (DEHP) degraders across pedosphere, charosphere and intestinal sphere

Biochar-assisted vermicomposting can significantly accelerate soil DEHP degradation, but little information is known about the underlying mechanisms as different microspheres exist in soil ecosystem. In this study, we identified the active DEHP degraders in biochar-assisted vermicomposting by DNA stable isotope probing (DNA-SIP) and surprisingly found their different compositions in pedosphere, charosphere and intestinal sphere. Thirteen bacterial lineages (Laceyella, Microvirga, Sphingomonas, Ensifer, Skermanella, Lysobacter, Archangium, Intrasporangiaceae, Pseudarthrobacter, Blastococcus, Streptomyces, Nocardioides and Gemmatimonadetes) were responsible for in situ DEHP degradation in pedosphere, whereas their abundance significantly changed in biochar or earthworm treatments. Instead, some other active DEHP degraders were identified in charosphere (Serratia marcescens and Micromonospora) and intestinal sphere (Clostridiaceae, Oceanobacillus, Acidobacteria, Serratia marcescens and Acinetobacter) with high abundance. In biochar-assisted vermicomposting, the majority of active DEHP degraders were found in charosphere, followed by intestinal sphere and pedosphere. Our findings for the first time unraveled the spatial distribution of active DEHP degraders in different microspheres in soil matrices, explained by DEHP dynamic adsorption on biochar and desorption in earthworm gut. Our work highlighted that charosphere and intestinal sphere exhibited more contribution to the accelerated DEHP biodegradation than pedosphere, providing novel insight into the mechanisms of biochar and earthworm in improving contaminant degradation.

Characterization of 17β-estradiol-degrading enzyme from Microbacterium sp. MZT7 and its function on E2 biodegradation in wastewater

BACKGROUND

17β-estradiol (E2) residues exhibit harmful effects both for human and animals and have got global attention of the scientific community. Microbial enzymes are considered as one of the effective strategies having great potential for removal E2 residues from the environment. However, limited literature is available on the removal of E2 from wastewater using short-chain dehydrogenase.

RESULTS

In this study, 17β-estradiol degrading enzyme (17β-HSD-0095) was expressed and purified from Microbacterium sp. MZT7. The optimal pH and temperature for reaction was 7 and 40 °C, respectively. Molecular docking studies have shown that the ARG215 residue form a hydrogen bond with oxygen atom of the substrate E2. Likewise, the point mutation results have revealed that the ARG215 residue play an important role in the E2 degradation by 17β-HSD-0095. In addition, 17β-HSD-0095 could remediate E2 contamination in synthetic livestock wastewater.

CONCLUSIONS

These findings offer some fresh perspectives on the molecular process of E2 degradation and the creation of enzyme preparations that can degrade E2.

Cloning and expression of the phenazine-1-carboxamide hydrolysis gene pzcH and the identification of the key amino acids necessary for its activity

Phenazine-1-carboxamide (PCN), a phenazine derivative, can cause toxicity risks to non target organisms. In this study, the Gram-positive bacteria Rhodococcus equi WH99 was found to have the ability to degrade PCN. PzcH, a novel amidase belonging to amidase signature (AS) family, responsible for hydrolyzing PCN to PCA was identified from strain WH99. PzcH shared no similarity with amidase PcnH which can also hydrolyze PCN and belong to the isochorismatase superfamily from Gram-negative bacteria Sphingomonas histidinilytica DS-9. PzcH also showed low similarity (˂ 39%) with other reported amidases. The optimal catalysis temperature and pH of PzcH was 30 °C and 9.0, respectively. The K_m and k_cat values of PzcH for PCN were 43.52 ± 4.82 μM and 17.028 ± 0.57 s^-1, respectively. The molecular docking and point mutation experiment demonstrated that catalytic triad Lys80-Ser155-Ser179 are essential for PzcH to hydrolyze PCN. Strain WH99 can degrade PCN and PCA to reduce their toxicity against the sensitive organisms. This study enhances our understanding of the molecular mechanism of PCN degradation, presents the first report on the key amino acids in PzcH from the Gram-positive bacteria and provides an effective strain in the bioremediation PCN and PCA contaminated environments.

Photocatalytic Removal of Thiamethoxam and Flonicamid Pesticides Present in Agro-Industrial Water Effluents

Pesticide residues, when present in agricultural wastewater, constitute a potential risk for the environment and human health. Hence, focused actions for their abatement are of high priority for both the industrial sectors and national authorities. This work evaluates the effectiveness of the photocatalytic process to decompose two frequently detected pesticides in the water effluents of the fruit industry: thiamethoxam-a neonicotinoid compound and flonicamid-a pyridine derivative. Their photocatalytic degradation and mineralization were evaluated in a lab-scale photocatalytic batch reactor under UV-A illumination with the commercial photocatalyst Evonik P25 TiO2 by employing different experimental conditions. The complete degradation of thiamethoxam was achieved after 90 min, when the medium was adjusted to natural or alkaline pH. Flonicamid was proven to be a more recalcitrant substance and the removal efficiency reached ~50% at the same conditions, although the degradation overpassed 75% in the acidic pH medium. Overall, the pesticides’ degradation follows the photocatalytic reduction pathways, where positive charged holes and hydroxyl radicals dominate as reactive species, with complete mineralization taking place after 4 h, regardless of the pH medium. Moreover, it was deduced that the pesticides’ degradation kinetics followed the Langmuir-Hinshelwood (L-H) model, and the apparent rate constant, the initial degradation rate, as well as the L-H model parameters, were determined for both pesticides.

Biodegradation of sulfoxaflor and photolysis of sulfoxaflor by ultraviolet radiation

Sulfoxaflor (SUL, [N-[methyloxido[1-[6-(trifluoromethyl)-3-pyridinyl] ethyl]-λ⁴-sulfanylidene] cyanamide]) is a widely used systemic insecticide, and its residue has frequently been detected in the environment, posing a potential threat to the environment. In this study, Pseudaminobacter salicylatoxidans CGMCC 1.17248 rapidly converted SUL into X11719474 via a hydration pathway mediated by two nitrile hydratases (AnhA and AnhB). Extensive (96.4%) degradation of 0.83 mmol/L SUL was achieved by P. salicylatoxidans CGMCC 1.17248 resting cells within 30 min (half-life of SUL 6.4 min). Cell immobilization by entrapment into calcium alginate remediated 82.8% of the SUL in 90 min, and almost no SUL was observed in surface water after incubation for 3 h. P. salicylatoxidans NHases AnhA and AnhB both hydrolyzed SUL to X11719474, although AnhA exhibited much better catalytic performance. The genome sequence of P. salicylatoxidans CGMCC 1.17248 revealed that this strain could efficiently eliminate nitrile-containing insecticides and adapt to harsh environments. We firstly found that UV irradiation transforms SUL to the derivatives X11719474 and X11721061, and the potential reaction pathways were proposed. These results further deepen our understanding of the mechanisms of SUL degradation as well as the environmental fate of SUL.

Novel biodegradation pathway of insecticide flonicamid mediated by an amidase and its unusual substrate spectrum

The insecticide flonicamid (FLO) and its main degradation intermediate 4-trifluoromethylnicotinamide (TFNA-AM) are hazardous to the environment and animals. Microbial transformation of FLO has been well studied, but no study has yet reported on TFNA-AM degradation by a microorganism. Here, Pseudomonas stutzeri CGMCC 22915 effectively degraded TFNA-AM to 5-trifluoromethylnicotinic acid (TFNA). P. stutzeri CGMCC 22915 degraded 60.0% of TFNA-AM (1154.44 μmol/L) within 6 h with a half-life of just 4.5 h. Moreover, P. stutzeri CGMCC 22915 significantly promoted TFNA-AM decomposition in surface water. The reaction was catalyzed by an amidase, PsAmiA. PsAmiA is encoded in a novel nitrile-converting enzyme gene cluster. The enzyme shared only 20-44% identities with previously characterized signature amidases. PsAmiA was successfully expressed in Escherichia coli and its enzymatic properties were investigated using TFNA-AM as the substrate. PsAmiA was more active toward amides without hydrophilic groups, and did not hydrolyze another amide metabolite of FLO, N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM), which is structurally very similar to TFNA-AM. Molecular docking of PsAmiA and TFNA-AM indicated that hydrophobic residues Leu148, Ala150, Ala195, Ile225, Trp341, Leu460, and Ile463 may affect its substrate spectrum. This study provides new insights of the environmental fate of FLO at the molecular level and the structure-function relationships of amidases.

Removal of sulfamethoxazole and antibiotic resistance genes in paddy soil by earthworms (Pheretima guillelmi): Intestinal detoxification and stimulation of indigenous soil bacteria

Vermiremediation, which use earthworms to remove contaminants from soil, has been proven to be an alternative, low-cost technology. However, the effects of earthworm activity, especially the degraders in earthworm intestines, on the fate of sulfamethoxazole (SMX), and the effects of intestinal bacteria on degrading bacteria in soil are unclear. In this study, the effects of earthworms on the fate of SMX and related antibiotic resistance genes (ARGs) were investigated. Special attention was paid to the impact of earthworms on SMX degradation efficiency, degradation products, related ARGs, and degraders in both soil and earthworm intestines; the effect of intestinal bacteria on soil bacteria associated with SMX was also studied. Earthworms significantly accelerated SMX degradation by both intestinal detoxification and the stimulation of indigenous soil bacteria. Compared with the treatment without earthworms, the treatment with earthworms reduced SMX residues by 25.1 %, 49.2 %, 35.7 %, 34.2 %, and 35.7 % on the 10th, 20th, 30th, 60th, and 90th days, respectively. Compared with those in soil (treated with earthworms), the SMX residues in wormcasts were further reduced by 12.2-29.0 % from the 2nd to the 20th day, producing some unique anaerobic degradation products that were distinct from those in the soil. In earthworm intestines, SMX degradation was enhanced by bacteria of the genera Microvirga, Sphingomonas, Methylobacterium, Bacillus, and Tumebacillus. All of these bacteria (except Bacillus spp.) entered and colonised the soil with wormcasts, further promoting SMX degradation. Additionally, earthworms removed a significant number of ARGs by increasing the fraction of potential SMX degraders and inhibiting the potential hosts of ARGs and int1. This study demonstrated that earthworms could remediate SMX-contaminated soil by enhancing the removal of SMX and ARGs.

Taxonomic response of bacterial and fungal populations to biofertilizers applied to soil or substrate in greenhouse-grown cucumber

Reductions in the quality and yield of crops continuously produced in the same location for many years due to annual increases in soil-borne pathogens. Environmentally-friendly methods are needed to produce vegetables sustainably and cost effectively under protective cover. We investigated the impact of biofertilizers on cucumber growth and yield, and changes to populations of soil microorganisms in response to biofertilizer treatments applied to substrate or soil. We observed that some biofertilizers significantly increased cucumber growth and decreased soil-borne pathogens in soil and substrate. Rhizosphere microbial communities in soil and substrate responded differently to different biofertilizers, which also led to significant differences in microbial diversity and taxonomic structure at different times in the growing season. Biofertilizers increase the prospects of re-using substrate for continuously producing high-quality crops cost-effectively from the same soil each year while at the same time controlling soil-borne disease.

Microvirga roseola sp. nov. and Microvirga lenta sp. nov., isolated from Taklamakan Desert soil

Two Gram-negative, rod-shaped, non-spore-forming bacteria, designated SM9T and SM2T, were isolated from Taklamakan Desert soil samples. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains SM9T and SM2T had the highest sequence similarity to the type strains Microvirga indica BCRC 80972T and Microvirga soli NBRC 112417T with similarity values of 98.2 and 97.7 %, respectively, and Microvirga was among the predominant genera in the desert soil. The draft genomes of these two strains were 4.56 Mbp (SM9T) and 5.08 Mbp (SM2T) long with 65.1 mol% (SM9T) and 63.5 mol% (SM2T) G+C content. To adapt to the desert environment, these two strains possessed pathways for the synthesis of stress metabolite trehalose. The major fatty acids (>5 %) included C18 : 1 ω9c in SM2T, but C16 : 0, C18 : 0 and C19 : 0 cyclo ω8c in SM9T, while the major menaquinone was ubiquinone 10 in both strains. The major polar lipids of SM9T and SM2T were phosphatidylglycerol, phosphatidylethanolamine and phospholipid. The average nucleotide identity and digital DNA–DNA hybridization results further indicated that strains SM9T and SM2T were distinguished from phylogenetically related species and represented two novel species within the genus Microvirga , for which the names Microvirga roseola sp. nov. (type strain SM2T=KCTC 72792T=CGMCC 1.17776T) and Microvirga lenta sp. nov. (type strain SM9T=KCTC 82729T=CCTCC AB 2021131T) are proposed.

Characterization of nitrilases from Variovorax boronicumulans that functions in insecticide flonicamid degradation and β-cyano-L-alanine detoxification

AIMS

To characterize the functions of nitrilases of Variovorax boronicumulans CGMCC 4969 and evaluate flonicamid (FLO) degradation and β-cyano-L-alanine (Ala(CN)) detoxification by this bacterium.

METHODS AND RESULTS

V. boronicumulans CGMCC 4969 nitrilases (NitA and NitB) were purified and substrate specificity assay indicated that both of them degraded insecticide FLO to N-(4-trifluoromethylnicotinoyl)glycinamide (TFNG-AM) and 4-(trifluoromethyl)nicotinol glycine (TFNG). Ala(CN), a plant detoxification intermediate, was hydrolyzed by NitB. Escherichia coli overexpressing NitA and NitB degraded 41.2 and 93.8% of FLO (0.87 mmol·L^-1 ) within 1 h, with half-lives of 1.30 and 0.25 h, respectively. NitB exhibited the highest nitrilase activity toward FLO. FLO was used as a substrate to compare their enzymatic properties. NitB was more tolerant to acidic conditions and organic solvents than NitA. Conversely, NitA was more tolerant to metal ions than NitB. CGMCC 4969 facilitated FLO degradation in soil and surface water and utilized Ala(CN) as a sole nitrogen source for growth.

CONCLUSIONS

CGMCC 4969 efficiently degraded FLO mediated by NitA and NitB; NitB was involved in Ala(CN) detoxification.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study promotes our understanding of versatile functions of nitrilases from CGMCC 4969 that is promising for environmental remediation.