Comparative proteome analysis of butachlor-degrading bacteria

Insights into the metabolic pathways and biodegradation mechanisms of chloroacetamide herbicides

Chloroacetamide herbicides are widely used around the world due to their high efficiency, resulting in increasing levels of their residues in the environment. Residual chloroacetamides and their metabolites have been frequently detected in soil, water and organisms and shown to have toxic effects on non-target organisms, posing a serious threat to the ecosystem. As such, rapid and efficient techniques that eliminate chloroacetamide residues from the ecosystem are urgently needed. Degradation of these herbicides in the environment mainly occurs through microbial metabolism. Microbial strains such as Acinetobacter baumannii DT, Bacillus altitudinis A16, Pseudomonas aeruginosa JD115, Sphingobium baderi DE-13, Catellibacterium caeni DCA-1, Stenotrophomonas acidaminiphila JS-1, Klebsiella variicola B2, and Paecilomyces marquandii can effectively degrade chloroacetamide herbicides. The degradation pathway of chloroacetamide herbicides in aerobic bacteria is mainly initiated by an N/C-dealkylation reaction, followed by aromatic ring hydroxylation and cleavage processes, whereas dechlorination is the initial reaction in anaerobic bacteria. The molecular mechanisms associated with bacterial degradation of chloroacetamide herbicides have been explored, with amidase, hydrolase, reductase, ferredoxin and cytochrome P450 oxygenase currently known to play a pivotal role in the catabolic pathways of chloroacetamides. The fungal pathway for the degradation of these herbicides is more complex with more diversified products, and the degradation enzymes and genes involved remain to be discovered. However, there are few reviews specifically summarizing the microbial degrading species and biochemical mechanisms of chloroacetamide herbicides. Here, we briefly summarize the latest progress resulting from research on microbial strain resources and enzymes involved in degradation of these herbicides and their corresponding genes. Furthermore, we explore the biochemical pathways and molecular mechanisms for biodegradation of chloroacetamide herbicides in depth, thereby providing a reference for further research on the bioremediation of such herbicides.

Biotechnological tools to elucidate the mechanism of pesticide degradation in the environment

Pesticides are widely used in agriculture, households, and industries; however, they have caused severe negative effects on the environment and human health. To clean up pesticide contaminated sites, various technological strategies, i.e. physicochemical and biological, are currently being used throughout the world. Biological approaches have proven to be a viable method for decontaminating pesticide-contaminated soils and water environments. The biological process eliminates contaminants by utilizing microorganisms' catabolic ability. Pesticide degradation rates are influenced by a variety of factors, including the pesticide's structure, concentration, solubility in water, soil type, land use pattern, and microbial activity in the soil. There is currently a knowledge gap in this field of study because researchers are unable to gather collective information on the factors affecting microbial growth, metabolic pathways, optimal conditions for degradation, and genomic, transcriptomic, and proteomic changes caused by pesticide stress on the microbial communities. The use of advanced tools and omics technology in research can bridge the existing gap in our knowledge regarding the bioremediation of pesticides. This review provides new insights on the research gaps and offers potential solutions for pesticide removal from the environment through the use of various microbe-mediated technologies.

Atlas of the microbial degradation of fluorinated pesticides

Fluorine-based agrochemicals have been benchmarked as the golden standard in pesticide development, prompting their widespread use in agriculture. As a result, fluorinated pesticides can now be found in the environment, entailing serious ecological implications due to their harmfulness and persistence. Microbial degradation might be an option to mitigate these impacts, though environmental microorganisms are not expected to easily cope with these fluoroaromatics due to their recalcitrance. Here, we provide an outlook on the microbial metabolism of fluorinated pesticides by analyzing the degradation pathways and biochemical processes involved, while also highlighting the central role of enzymatic defluorination in their productive metabolism. Finally, the potential contribution of these microbial processes for the dissipation of fluorinated pesticides from the environment is also discussed.

Degradation of butachlor and propanil by Pseudomonas sp. strain But2 and Acinetobacter baumannii strain DT

Herbicides have been extensively used globally, resulting in severe environmental pollution. Novel butachlor-degrading Pseudomonas sp. strain But2 isolated from soil can degrade butachlor regardless of the concentration and grows without a lag phase. Specific degradation was increased at 0.01-0.1 mM, and did not change significantly at higher concentrations. During degradation, 2-chloro-N-(2,6-diethylphenyl) acetamide, 2,6-diethylaniline, and 1,3-diethylbenzene were formed, which indicated that deamination occurred. Moreover, Pseudomonas sp. strains could tolerate propanil at up to 0.8 mM. The mixed bacterial culture of Pseudomonas sp. But2 and Acinetobacter baumannii DT (a propanil-degrading bacterial strain) showed highly effective biodegradation of both butachlor and propanil in liquid media and soil. For example, under treatment with the mixed culture, the half-lives of propanil and butachlor were 1 and 5 days, respectively, whereas those for the control were 3 and 15 days. The adjuvants present in herbicides reduced degradation in liquid media, but did not influence herbicide removal from the soil. The results showed that the mixed bacteria culture is a good candidate for the removal of butachlor and propanil from contaminated soils.

Current insights into the microbial degradation for butachlor: strains, metabolic pathways, and molecular mechanisms

The herbicide butachlor has been used in huge quantities worldwide, affecting various environmental systems. Butachlor residues have been detected in soil, water, and organisms, and have been shown to be toxic to these non-target organisms. This paper briefly summarizes the toxic effects of butachlor on aquatic and terrestrial animals, including humans, and proposes the necessity of its removal from the environment. Due to long-term exposure, some animals, plants, and microorganisms have developed resistance toward butachlor, indicating that the toxicity of this herbicide can be reduced. Furthermore, we can consider removing butachlor residues from the environment by using such butachlor-resistant organisms. In particular, microbial degradation methods have attracted much attention, with about 30 kinds of butachlor-degrading microorganisms have been found, such as Fusarium solani, Novosphingobium chloroacetimidivorans, Chaetomium globosum, Pseudomonas putida, Sphingomonas chloroacetimidivorans, and Rhodococcus sp. The metabolites and degradation pathways of butachlor have been investigated. In addition, enzymes associated with butachlor degradation have been identified, including CndC1 (ferredoxin), Red1 (reductase), FdX1 (ferredoxin), FdX2 (ferredoxin), Dbo (debutoxylase), and catechol 1,2 dioxygenase. However, few reviews have focused on the microbial degradation and molecular mechanisms of butachlor. This review explores the biochemical pathways and molecular mechanisms of butachlor biodegradation in depth in order to provide new ideas for repairing butachlor-contaminated environments. KEY POINTS: • Biodegradation is a powerful tool for the removal of butachlor. • Dechlorination plays a key role in the degradation of butachlor. • Possible biochemical pathways of butachlor in the environment are described.

Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes

Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.

Characterization of a Novel Butachlor Biodegradation Pathway and Cloning of the Debutoxylase (Dbo) Gene Responsible for Debutoxylation of Butachlor in Bacillus sp. hys-1

Bacillus sp. strain hys-1, which was isolated from active sludge, could degrade >90% butachlor at a concentration of 100 mg/L within 7 days. The present work revealed that strain hys-1 could mineralize butachlor via the following pathway: butachlor was initially metabolized to 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide by debutoxylation and then transformed to form 2-chloro-N-(2,6-diethylphenyl)acetamide by N-demethylation. Subsequently, it was converted to 2,6-diethylaniline and further mineralized into CO2 and H2O. In addition, the catalytic efficiency of crude cell extracts descended as follows: alachlor > acetochlor > butachlor. Furthermore, a novel 744 bp gene responsible for transforming butachlor into 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide was cloned from strain hys-1 and the encoding debutoxylase was designated Dbo. Then Dbo was expressed in Escherichia coli BL21 (DE3) and purified using Ni-nitrilotriacetic acid affinity chromatography. Dbo displayed the highest activity against butachlor at pH 6.5 and 30 °C. Metal ions played an important role in Dbo activity. To the best of the authors' knowledge, this is the first report that strain hys-1 can mineralize butachlor by a novel metabolic mechanism and the first identification of a gene encoding butachlor debutoxylase.

Syntrophic biodegradation of butachlor by Mycobacterium sp. J7A and Sphingobium sp. J7B isolated from rice paddy soil

Two bacterial strains involved in syntrophic degradation of chloroacetamide herbicide butachlor were isolated from a rice paddy soil. Analysis of 16S rRNA gene sequences indicated that the two isolates were related to members of the genera Mycobacterium and Sphingobium, respectively. Thus, a pair consisted of Mycobacterium sp. J7A and Sphingobium sp. J7B could rapidly degrade butachlor (100 mg L(-1)) at 28 °C within 24 h, while each isolate alone was not able to completely degrade butachlor. The isolate Mycobacterium sp. J7A was observed to grow slightly on butachlor, possibly utilizing the alkyl side chain of butachlor as its carbon and energy source, but the isolate Sphingobium sp. J7B alone could not grow on butachlor at all. Gas chromatography-mass spectrometry on catabolic intermediates revealed that the strain J7A produced and accumulated 2-chloro-N-(2,6-diethylphenyl) acetamide (CDEPA) during growth on butachlor. This intermediate was not further degraded by strain J7A, but strain J7B was observed to be able to completely degrade and grow on it through 2,6-diethylaniline (DEA). The results showed that butachlor was completely degraded by the two isolates by syntrophic metabolism, in which strain Mycobacterium sp. J7A degraded butachlor to CDEPA, which was subsequently degraded by strain Sphingobium sp. J7B through DEA.

Biodegradation of chloroacetamide herbicides by Paracoccus sp. FLY-8 in vitro

A butachlor-degrading strain, designated FLY-8, was isolated from rice field soil and was identified as Paracoccus sp. Strain FLY-8 could degrade and utilize six chloroacetamide herbicides as carbon sources for growth, and the degradation rates followed the order alachlor > acetochlor > propisochlor > butachlor > pretilachlor > metolachlor. The influence of molecular structure of the chloroacetamide herbicides on the microbial degradation rate was first analyzed; the results indicated that the substitutions of alkoxymethyl side chain with alkoxyethyl side chain greatly reduced the degradation efficiencies; the length of amide nitrogen's alkoxymethyl significantly affected the biodegradability of these herbicides: the longer the alkyl was, the slower the degradation efficiencies occurred. The phenyl alkyl substituents have no obvious influence on the degradation efficiency. The pathway of butachlor complete mineralization was elucidated on the basis of the results of metabolite identification and enzyme assays. Butachlor was degraded to alachlor by partial C-dealkylation and then converted to 2-chloro-N-(2,6-dimethylphenyl)acetamide by N-dealkylation, which subsequently transformed to 2,6-diethylaniline, which was further degraded via the metabolites aniline and catechol, and catechol was oxidized through an ortho-cleavage pathway. This study highlights an important potential use of strain FLY-8 for the in situ bioremediation of chloroacetamide herbicides and their metabolite-contaminated environment.