A novel amidohydrolase (DmhA) from Sphingomonas sp. that can hydrolyze the organophosphorus pesticide dimethoate to dimethoate carboxylic acid and methylamine

Unveiling the analgesic and antipyretic drug acetaminophen catabolic mechanism in Pseudomonas taiwanensis AP-1

Acetaminophen (APAP), an analgesic and antipyretic drug, is commonly detected in wastewater treatment plant (WWTP) effluents, surface water, and soil, indicating its status as an emerging environmental contaminant. In this study, we isolated a bacterium, Pseudomonas taiwanensis AP-1, capable of completely mineralizing APAP and utilizing it as the sole carbon source for growth. A newly identified metabolite, γ-glutamyl-4-aminophenol (γ-G4AP), was reported for the first time in the degradation of APAP by strain AP-1. Two amidases (ApaH1 and ApaH2), responsible for the conversion of APAP to 4-aminophenol (4-AP), were identified through a combination of genomic comparison, heterologous expression, and gene knockout. Notably, ApaH1 played a pivotal role in the degradation of APAP by strain AP-1. The catalytic triad of ApaH1 (K82-S161-S185) and ApaH2 (K85-S160-S184) were identified as by molecular docking and site-directed mutagenesis. Additionally, a gene cluster apd for the metabolism of 4-AP was also successfully identified in strain AP-1, consisting of the aniline dioxygenase gene cluster apdBCD1D2EF and the BT catabolic gene apdGH. Interestingly, the 4-AP metabolic gene cluster apd was highly conserved among other Pseudomonas strains capable of APAP degradation. Our results provide new insights into the mechanism of APAP biodegradation and strain AP-1 may be a promising bacterium for the bioremediation of APAP pollutions.

Bacterial bioaugmentation for paracetamol removal from water and sewage sludge. Genomic approaches to elucidate biodegradation pathway

Wastewater treatment plants (WWTPs) are recognized as significant contributors of paracetamol (APAP) into the environment due to their limited ability to degrade it. This study used a bioaugmentation strategy with Pseudomonas extremaustralis CSW01 and Stutzerimonas stutzeri CSW02 to achieve APAP biodegradation in solution in wide ranges of temperature (10-40 °C) and pH (5-9), reaching DT50 values < 1.5 h to degrade 500 mg L-1 APAP. Bacterial strains also mineralized APAP in solution (<30 %), but when forming consortia with Mycolicibacterium aubagnense HPB1.1, mineralization significantly increased (up to 74 % and 58 % for CSW01 +HPB1.1 and CSW02 +HPB1.1, respectively), decreasing DT50 values to only 1 and 9 days. Despite the complete degradation of APAP and its high mineralization, residual toxicity throughout the process was observed. Three APAP metabolites were identified (4-aminophenol, hydroquinone and trans-2-hexenoic acid) that quickly disappeared, but residual toxicity remained, indicating the presence of other non-detected intermediates. CSW01 and CSW02 degraded also 100 % APAP (50 mg kg-1) adsorbed on sewage sludge, with DT50 values of only 0.7 and 0.3 days, respectively, but < 15 % APAP was mineralized. A genome-based analysis of CSW01 and CSW02 revealed that amidases, deaminases, hydroxylases, and dioxygenases enzymes were involved in APAP biodegradation, and a possible metabolic pathway was proposed.

Characterization of a novel amidohydrolase with promiscuous esterase activity from a soil metagenomic library and its application in degradation of amide herbicides

Amide herbicides have been extensively used worldwide and have received substantial attention due to their adverse environmental effects. Here, a novel amidohydrolase gene was identified from a soil metagenomic library using diethyl terephthalate (DET) as a screening substrate. The recombinant enzyme, AmiH52, was heterologously expressed in Escherichia coli and later purified and characterized, with the highest activity occurring at 40 ℃ and pH 8.0. AmiH52 was demonstrated to have both esterase and amidohydrolase activities, which exhibited highly specific activity for p-nitrophenyl butyrate (2669 U/mg) and degrading activity against several amide herbicides. In particular, it displayed the strongest activity against propanil, with a high degradation rate of 84% at 8 h. A GC-MS analysis revealed that propanil was transformed into 3,4-dichloroaniline (3,4-DCA) during this degradation. The molecular interactions and binding stability were then analyzed by molecular docking and molecular dynamics simulation, which revealed that several key amino acid residues, including Tyr164, Trp66, Ala59, Val283, Arg58, His33, His191, and His226, are involved in the specific interactions with propanil. This study provides a function-driven screening method for amide herbicide hydrolase from the metagenomic libraries and a promising propanil-degrading enzyme (AmiH52) for potential applications in environmental remediation.

Complete biodegradation of fungicide carboxin and its metabolite aniline by Delftia sp. HFL-1

Fungicide carboxin was commonly used in the form of seed coating for the prevention of smut, wheat rust and cotton damping-off, leading carboxin and its probable carcinogenic metabolite aniline to directly enter the soil with the seeds, causing residual pollution. In this study, a novel carboxin degrading strain, Delftia sp. HFL-1, was isolated. Strain HFL-1 could use carboxin as the carbon source for growth and completely degrade 50 mg/L carboxin and its metabolite aniline within 24 h. The optimal temperatures and pH for carboxin degrading by strain HFL-1 were 30 to 42 °C and 5 to 9, respectively. Furthermore, the complete mineralization pathway of carboxin by strain HFL-1 was revealed by High Resolution Mass Spectrometer (HRMS). Carboxin was firstly hydrolyzed into aniline and further metabolized into catechol through multiple oxidation processes, and finally converted into 4-hydroxy-2-oxopentanoate, a precursor of the tricarboxylic acid cycle. Genome sequencing revealed the corresponding degradation genes and cluster of carboxin. Among them, amidohydrolase and dioxygenase were key enzymes involved in the degradation of carboxin and aniline. The discovery of transposons indicated that the aniline degradation gene cluster in strain HFL-1 was obtained via horizontal transfer. Furthermore, the degradation genes were cloned and overexpressed. The in vitro test showed that the expressed degrading enzyme could efficiently degrade aniline. This study provides an efficient strain resource for the bioremediation of carboxin and aniline in contaminated soil, and further revealing the molecular mechanism of biodegradation of carboxin and aniline.

Microbiology and Biochemistry of Pesticides Biodegradation

Pesticides are chemicals used in agriculture, forestry, and, to some extent, public health. As effective as they can be, due to the limited biodegradability and toxicity of some of them, they can also have negative environmental and health impacts. Pesticide biodegradation is important because it can help mitigate the negative effects of pesticides. Many types of microorganisms, including bacteria, fungi, and algae, can degrade pesticides; microorganisms are able to bioremediate pesticides using diverse metabolic pathways where enzymatic degradation plays a crucial role in achieving chemical transformation of the pesticides. The growing concern about the environmental and health impacts of pesticides is pushing the industry of these products to develop more sustainable alternatives, such as high biodegradable chemicals. The degradative properties of microorganisms could be fully exploited using the advances in genetic engineering and biotechnology, paving the way for more effective bioremediation strategies, new technologies, and novel applications. The purpose of the current review is to discuss the microorganisms that have demonstrated their capacity to degrade pesticides and those categorized by the World Health Organization as important for the impact they may have on human health. A comprehensive list of microorganisms is presented, and some metabolic pathways and enzymes for pesticide degradation and the genetics behind this process are discussed. Due to the high number of microorganisms known to be capable of degrading pesticides and the low number of metabolic pathways that are fully described for this purpose, more research must be conducted in this field, and more enzymes and genes are yet to be discovered with the possibility of finding more efficient metabolic pathways for pesticide biodegradation.

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.

Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5

The herbicide propanil and its major metabolite 3,4-dichloroaniline (3,4-DCA) are difficult to biodegrade and pose great health and environmental risks. However, studies on the sole or synergistic mineralization of propanil by pure cultured strains are limited. A two-strain consortium (Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34), obtained from a swep-mineralizing enrichment culture that can synergistically mineralize propanil, has been previously reported. Here, another propanil degradation strain, Bosea sp. P5, was successfully isolated from the same enrichment culture. A novel amidase, PsaA, responsible for initial propanil degradation, was identified from strain P5. PsaA shared low sequence identity (24.0-39.7 %) with other biochemically characterized amidases. PsaA exhibited optimal activity at 30 °C and pH 7.5 and had k_cat and K_m values of 5.7 s^-1 and 125 μM, respectively. PsaA could convert the herbicide propanil to 3,4-DCA but exhibited no activity toward other herbicide structural analogs. This catalytic specificity was explained by using propanil and swep as substrates and then analyzed by molecular docking, molecular dynamics simulation and thermodynamic calculations, which revealed that Tyr138 is the key residue that affects the substrate spectrum of PsaA. This is the first propanil amidase with a narrow substrate spectrum identified, providing new insights into the catalytic mechanism of amidase in propanil hydrolysis.

The gut symbiont Sphingomonas mediates imidacloprid resistance in the important agricultural insect pest Aphis gossypii Glover

BACKGROUND

Neonicotinoid insecticides are applied worldwide for the control of agricultural insect pests. The evolution of neonicotinoid resistance has led to the failure of pest control in the field. The enhanced detoxifying enzyme activity and target mutations play important roles in the resistance of insects to neonicotinoid resistance. Emerging evidence indicates a central role of the gut symbiont in insect pest resistance to pesticides. Existing reports suggest that symbiotic microorganisms could mediate pesticide resistance by degrading pesticides in insect pests.

RESULTS

The 16S rDNA sequencing results showed that the richness and diversity of the gut community between the imidacloprid-resistant (IMI-R) and imidacloprid-susceptible (IMI-S) strains of the cotton aphid Aphis gossypii showed no significant difference, while the abundance of the gut symbiont Sphingomonas was significantly higher in the IMI-R strain. Antibiotic treatment deprived Sphingomonas of the gut, followed by an increase in susceptibility to imidacloprid in the IMI-R strain. The susceptibility of the IMI-S strain to imidacloprid was significantly decreased as expected after supplementation with Sphingomonas. In addition, the imidacloprid susceptibility in nine field populations, which were all infected with Sphingomonas, increased to different degrees after treatment with antibiotics. Then, we demonstrated that Sphingomonas isolated from the gut of the IMI-R strain could subsist only with imidacloprid as a carbon source. The metabolic efficiency of imidacloprid by Sphingomonas reached 56% by HPLC detection. This further proved that Sphingomonas could mediate A. gossypii resistance to imidacloprid by hydroxylation and nitroreduction.

CONCLUSIONS

Our findings suggest that the gut symbiont Sphingomonas, with detoxification properties, could offer an opportunity for insect pests to metabolize imidacloprid. These findings enriched our knowledge of mechanisms of insecticide resistance and provided new symbiont-based strategies for control of insecticide-resistant insect pests with high Sphingomonas abundance.

Wide substrate range for a candidate bioremediation enzyme isolated from Nocardioides sp. strain SG-4 G

Narrow substrate ranges can impact heavily on the range of applications and hence commercial viability of candidate bioremediation enzymes. Here we show that an ester hydrolase from Nocardioides strain SG-4 G has potential as a bioremediation agent against various pollutants that can be detoxified by hydrolytic cleavage of some carboxylester, carbamate, or amide linkages. Previously we showed that a radiation-killed, freeze-dried preparation (ZimA) of this strain can rapidly degrade the benzimidazole fungicide carbendazim due to the activity of a specific ester hydrolase, MheI. Here, we report that ZimA also has substantial hydrolytic activity against phthalate diesters (dimethyl, dibutyl, and dioctyl phthalate), anilide (propanil and monalide), and carbamate ester (chlorpropham) herbicides under laboratory conditions. The reaction products are substantially less toxic, or inactive as herbicides, than the parent compounds. Tests of strain SG-4 G and Escherichia coli expressing MheI found they were also able to hydrolyse dimethyl phthalate, propanil, and chlorpropham, indicating that MheI is principally responsible for the above activities.

Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates

Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 h while excreting 4-aminophenol, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.

Dimethoate residues in Pakistan and mitigation strategies through microbial degradation: a review

Organophosphate pesticides (OPs) are used extensively for crop protection worldwide due to their high water solubility and relatively low persistence in the environment compared to other pesticides, such as organochlorines. Dimethoate is a broad-spectrum insecticide that belongs to the thio-organophosphate group of OPs. It is applied to cash crops, animal farms, and houses. It has been used in Pakistan since the 1960s, either alone or in a mixture with other OPs or pyrethroids. However, the uncontrolled use of this pesticide has resulted in residual accumulation in water, soil, and tissues of plants via the food chain, causing toxic effects. This review article has compiled and analyzed data reported in the literature between 1998 and 2021 regarding dimethoate residues and their microbial bioremediation. Different microorganisms such as bacteria, fungi, and algae have shown potential for bioremediation. However, an extensive role of bacteria has been observed compared to other microorganisms. Twenty bacterial, three fungal, and one algal genus with potential for the remediation of dimethoate have been assessed. Active bacterial biodegraders belong to four classes (i) alpha-proteobacteria, (ii) gamma-proteobacteria, (iii) beta-proteobacteria, and (iv) actinobacteria and flavobacteria. Microorganisms, especially bacterial species, are a sustainable technology for dimethoate bioremediation from environmental samples. Yet, new microbial species or consortia should be explored.

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.

Microbial detoxification of dimethoate through mediated hydrolysis by Brucella sp. PS4: molecular profiling and plant growth-promoting traits

High toxicity of dimethoate requires efficient ways for detoxification and removal of its residues in contaminated environments. Microbial remediation is a process that utilizes the degradation potential of microbes to provide a cost-effective and reliable approach for pesticide abatement. For this purpose, a dimethoate-degrading bacterium Brucella sp. was isolated from a contaminated agricultural soil sample in Multan, Pakistan. This isolate was found to tolerate up to 100 ppm of dimethoate in minimal salt medium and was further evaluated for plant growth-promoting traits. The strain gave positive results for amylase, ammonia, and catalase production, while other traits such as indole acetic acid production and potassium solubilization were also confirmed. Thus, the strain could play an important role for plant nutrient transmission in the plant rhizosphere. Optimization of growth parameters (i.e., pH and temperature) depicted the potential of PS4 to be best tolerating dimethoate, with maximum cell density at λ 600 nm. Optimum pH and temperature for growth were found to be 6 and 35 °C, respectively. Based on optimization results as well as different attributes, the rhizospheric bacterial isolate PS4 was further subjected to a batch degradation experiment under different concentrations of dimethoate (25, 50, 75, and 100 ppm). This promising dimethoate-degrading isolate was found to degrade 83% of dimethoate (at 100 ppm) within a period of 7 days. In addition, it degraded 88% of dimethoate at 50 ppm, indicating that the bacterial isolate utilized dimethoate solely as a source of energy. The strain followed the first order reaction kinetics, depicting its dependence on dimethoate as energy and carbon source. Molecular profiling further supported its role in plant growth promotion and multi-stress tolerance. This research showed that Brucella sp. is capable of degrading dimethoate, and therefore, it would be useful in the investigation of novel bioremediation techniques at pesticide-polluted sites.

Mineralization of the herbicide swep by a two-strain consortium and characterization of a new amidase for hydrolyzing swep

BACKGROUND

Swep is an excellent carbamate herbicide that kills weeds by interfering with metabolic processes and inhibiting cell division at the growth point. Due to the large amount of use, swep residues in soil and water not only cause environmental pollution but also accumulate through the food chain, ultimately pose a threat to human health. This herbicide is degraded in soil mainly by microbial activity, but no studies on the biotransformation of swep have been reported.

RESULTS

In this study, a consortium consisting of two bacterial strains, Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34, was enriched from a contaminated soil sample and shown to be capable of mineralizing swep. Swep was first transformed by Comamonas sp. SWP-3 to the intermediate 3,4-dichloroaniline (3,4-DCA), after which 3,4-DCA was mineralized by Alicycliphilus sp. PH-34. An amidase gene, designated as ppa, responsible for the transformation of swep into 3,4-DCA was cloned from strain SWP-3. The expressed Ppa protein efficiently hydrolyzed swep and a number of other structural analogues, such as propanil, chlorpropham and propham. Ppa shared less than 50% identity with previously reported arylamidases and displayed maximal activity at 30 °C and pH 8.6. Gly449 and Val266 were confirmed by sequential error prone PCR to be the key catalytic sites for Ppa in the conversion of swep.

CONCLUSIONS

These results provide additional microbial resources for the potential remediation of swep-contaminated sites and add new insights into the catalytic mechanism of amidase in the hydrolysis of swep.

Characterization of an arylamidase from a newly isolated propanil-transforming strain of Ochrobactrum sp. PP-2

Propanil, one of the most extensively used post-emergent contact herbicides, has also been reported to have adverse effect on environmental safety. A bacterial strain of Ochrobactrum sp. PP-2, which was capable of transforming propanil, was isolated from a propanil-contaminated soil collected from a chemical factory. An arylamidase gene mah responsible for transforming propanil to 3,4-dichloroaniline (3,4-DCA) was cloned from strain PP-2 by shotgun method and subsequently confirmed by function expression. The arylamidase Mah shares low amino acid sequence identity (27-50%) with other biochemically characterized amidases and shows less than 30% identities to other reported propanil hydrolytic enzymes. Mah was most active at pH 8 and 35 °C. Mah had a remarkable activity toward propanil (K_m = 6.3 ± 1.2 µM), showing the highest affinity efficiency for propanil as compared with other reported propanil hydrolytic enzymes. Our study also provides a new arylamidase for the hydrolysis of propanil.

Identification and characterization of a novel carboxylesterase (FpbH) that hydrolyzes aryloxyphenoxypropionate herbicides

OBJECTIVE

To identify and characterize a novel aryloxyphenoxypropionate (AOPP) herbicide-hydrolyzing carboxylesterase from Aquamicrobium sp. FPB-1.

RESULTS

A carboxylesterase gene, fpbH, was cloned from Aquamicrobium sp. FPB-1. The gene is 798 bp long and encodes a protein of 265 amino acids. FpbH is smaller than previously reported AOPP herbicide-hydrolyzing carboxylesterases and shares only 21-35% sequence identity with them. FpbH was expressed in Escherichia coli BL21(DE3) and the product was purified by Ni-NTA affinity chromatography. The purified FpbH hydrolyzed a wide range of AOPP herbicides with catalytic efficiency in the order: haloxyfop-P-methyl > diclofop-methyl > fenoxaprop-P-ethyl > quizalofop-P-ethyl > fluazifop-P-butyl > cyhalofop-butyl. The optimal temperature and pH for FpbH activity were 37 °C and 7, respectively.

CONCLUSIONS

FpbH is a novel AOPP herbicide-hydrolyzing carboxylesterase; it is a good candidate for mechanistic study of AOPP herbicide-hydrolyzing carboxylesterases and for bioremediation of AOPP herbicide-contaminated environments.