Plasmid as a measure of microbial degradation capacity for 2,4-dichlorophenoxyacetic acid

Microorganism-Driven 2,4-D Biodegradation: Current Status and Emerging Opportunities

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely used around the world in both agricultural and non-agricultural fields due to its high activity. However, the heavy use of 2,4-D has resulted in serious environmental contamination, posing a significant risk to non-target organisms, including human beings. This has raised substantial concerns regarding its impact. In addition to agricultural use, accidental spills of 2,4-D can pose serious threats to human health and the ecosystem, emphasizing the importance of prompt pollution remediation. A variety of technologies have been developed to remove 2,4-D residues from the environment, such as incineration, adsorption, ozonation, photodegradation, the photo-Fenton process, and microbial degradation. Compared with traditional physical and chemical remediation methods, microorganisms are the most effective way to remediate 2,4-D pollution because of their rich species, wide distribution, and diverse metabolic pathways. Numerous studies demonstrate that the degradation of 2,4-D in the environment is primarily driven by enzymatic processes carried out by soil microorganisms. To date, a number of bacterial and fungal strains associated with 2,4-D biodegradation have been isolated, such as Sphingomonas, Pseudomonas, Cupriavidus, Achromobacter, Ochrobactrum, Mortierella, and Umbelopsis. Moreover, several key enzymes and genes responsible for 2,4-D biodegradation are also being identified. However, further in-depth research based on multi-omics is needed to elaborate their role in the evolution of novel catabolic pathways and the microbial degradation of 2,4-D. Here, this review provides a comprehensive analysis of recent progress on elucidating the degradation mechanisms of the herbicide 2,4-D, including the microbial strains responsible for its degradation, the enzymes participating in its degradation, and the associated genetic components. Furthermore, it explores the complex biochemical pathways and molecular mechanisms involved in the biodegradation of 2,4-D. In addition, molecular docking techniques are employed to identify crucial amino acids within an alpha-ketoglutarate-dependent 2,4-D dioxygenase that interacts with 2,4-D, thereby offering valuable insights that can inform the development of effective strategies for the biological remediation of this herbicide.

Rapid Biodegradation of the Herbicide 2,4-Dichlorophenoxyacetic Acid by Cupriavidus gilardii T-1

Phytotoxicity and environmental pollution of residual herbicides have caused much public concern during the past several decades. An indigenous bacterial strain capable of degrading 2,4-dichlorophenoxyacetic acid (2,4-D), designated T-1, was isolated from soybean field soil and identified as Cupriavidus gilardii. Strain T-1 degraded 2,4-D 3.39 times more rapidly than the model strain Cupriavidus necator JMP134. T-1 could also efficiently degrade 2-methyl-4-chlorophenoxyacetic acid (MCPA), MCPA isooctyl ester, and 2-(2,4-dichlorophenoxy)propionic acid (2,4-DP). Suitable conditions for 2,4-D degradation were pH 7.0-9.0, 37-42 °C, and 4.0 mL of inoculums. Degradation of 2,4-D was concentration-dependent. 2,4-D was degraded to 2,4-dichlorophenol (2,4-DCP) by cleavage of the ether bond and then to 3,5-dichlorocatechol (3,5-DCC) via hydroxylation, followed by ortho-cleavage to cis-2-dichlorodiene lactone (CDL). The metabolites 2,4-DCP or 3,5-DCC at 10 mg L^-1 were completely degraded within 16 h. Fast degradation of 2,4-D and its analogues highlights the potential for use of C. gilardii T-1 in bioremediation of phenoxyalkanoic acid herbicides.

Degradation of Swainsonine by the NADP-Dependent Alcohol Dehydrogenase A1R6C3 in Arthrobacter sp. HW08

Swainsonine is an indolizidine alkaloid that has been found in locoweeds and some fungi. Our previous study demonstrated that Arthrobacter sp. HW08 or its crude enzyme extract could degrade swainsonie efficiently. However, the mechanism of swainsonine degradation in bacteria remains unclear. In this study, we used label-free quantitative proteomics method based on liquid chromatography-electrospray ionization-tandem mass spectrometry to dissect the mechanism of swainsonine biodegradation by Arthrobacter sp. HW08. The results showed that 129 differentially expressed proteins were relevant to swainsonine degradation. These differentially expressed proteins were mostly related to the biological process of metabolism and the molecular function of catalytic activity. Among the 129 differentially expressed proteins, putative sugar phosphate isomerase/epimerase A1R5X7, Acetyl-CoA acetyltransferase A0JZ95, and nicotinamide adenine dinucleotide phosphate (NADP)-dependent alcohol dehydrogenase A1R6C3 were found to contribute to the swainsonine degradation. Notably, NADP-dependent alcohol dehyrodgenase A1R6C3 appeared to play a major role in degrading swainsonine, but not as much as Arthrobacter sp. HW08 did. Collectively, our findings here provide insights to understand the mechanism of swainsonine degradation in bacteria.

Model development with defined biological mechanisms for xenobiotic treatment activated sludge at steady state

Activated sludge treatment of a xenobiotic organic compound, much different from treatment of biogenic organics, must be modeled with interactions involving a two-part biomass of degrader and nondegrader, which selectively or competitively grow on a two-part substrate of input xenobiotic and its biogenic metabolites. A xenobiotic treatment model was developed which incorporates kinetics of the growth of degrader and nondegrader, the line dividing metabolites into xenobiotic and biogenic, yields of degrader and nondegrader from utilization of their parts of substrates, and kinetics of degrader reversion to nondegrader due to instability of the degradative element degraders carry. Experimental activated sludge operated for treatment of a xenobiotic generated data for calibration of the model. With the input of influent xenobiotic concentration, mean cell and hydraulic residence times, and calibrated parameters, the model readily outputs concentrations of degrader, nondegrader, and effluent biogenic residue that closely match the results obtained from experiments.

Microbial degradation of herbicides

Herbicides remain the most effective, efficient and economical way to control weeds; and its market continues to grow even with the plethora of generic products. With the development of herbicide-tolerant crops, use of herbicides is increasing around the world that has resulted in severe contamination of the environment. The strategies are now being developed to clean these substances in an economical and eco-friendly manner. In this review, an attempt has been made to pool all the available literature on the biodegradation of key herbicides, clodinafop propargyl, 2,4-dichlorophenoxyacetic acid, atrazine, metolachlor, diuron, glyphosate, imazapyr, pendimethalin and paraquat under the following objectives: (1) to highlight the general characteristic and mode of action, (2) to enlist toxicity in animals, (3) to pool microorganisms capable of degrading herbicides, (4) to discuss the assessment of herbicides degradation by efficient microbes, (5) to highlight biodegradation pathways, (6) to discuss the molecular basis of degradation, (7) to enlist the products of herbicides under degradation process, (8) to highlight the factors effecting biodegradation of herbicides and (9) to discuss the future aspects of herbicides degradation. This review may be useful in developing safer and economic microbiological methods for cleanup of soil and water contaminated with such compounds.

Evolutions of microbial degradation pathways for parent xenobiotic and for its metabolites follow different schemes

BACKGROUND AND PURPOSES

The pathways used by microorganisms for the metabolism of every xenobiotic substrate are specific. The catabolism of a xenobiotic goes through a series of intermediate steps and lower intermediates (metabolites) appear in sequence. The structure of the metabolites can be similar to the parents due to kinship. The purposes of this study were to examine if the degradation pathways that were developed for a parent xenobiotic are effective to degrade the parent's lower metabolites, and if the reverse is true.

MATERIALS AND METHODS

The xenobiotic substrates, 2,4-dichlorophenoxyacetic acid (2,4-D, the parent xenobiotic) and its metabolite 2,4-dichlorophenol (2,4-DCP), were independently subjected to acclimation and degradation tests by the biomasses of mixed-culture activated sludge and a pure culture of Arthrobacter sp.

RESULTS

Activated sludge and Arthrobacter sp. that were acclimated to 2,4-D effectively degraded 2,4-D and the lower metabolites of 2,4-D, typically 2,4-DCP. During the degradation of 2,4-D, accumulations of the lower metabolites of 2,4-D were not found. The degradation pathways acquired from acclimation to 2,4-D are effective for all the metabolites of 2,4-D. However, pathways acquired from acclimation to 2,4-DCP are not effective in the degradation of the parent 2,4-D.

CONCLUSIONS

Microorganisms acclimated to 2,4-D evolve their degradation pathways by a scheme that is different from the scheme the microorganisms employ when they are acclimated to the metabolites of 2,4-D.

Biodegradation kinetics of 2,4-D by bacterial strains isolated from soil

The aim of the study was to characterize the 2,4-dichlorophenoxyacetic acid (2,4-D) degradative potential of three bacterial strains identified by MIDI-FAME profiling as Burkholderia cepacia (DS-1), Pseudomonas sp. (DS-2) and Sphingomonas paucimobilis (DS-3) isolated from soil with herbicide treatment history. All strains were capable of using herbicide as the only source of carbon and energy when grown in mineral salt medium (MSM) containing 2,4-D (50 mg/l). Over a 10 day incubation period, 69%, 73% and 54% of the initial dose of 2,4-D were degraded by strains DS-1, DS-2 and DS-3, respectively. Analysis of 2,4-dichlorophenol (2,4-DCP) concentration, the main metabolite of 2,4-D degradation, revealed that strains DS-1 and DS-2 may also have the potential to metabolize this compound. The percentage of 2,4-DCP removal was 67% and 77% in relation to maximum values of 9.5 and 9.2 mg/l determined after 4 and 2 days for MSM+DS-1 and MSM+DS-2, respectively. The degradation kinetics of 2,4-D (50 mg/kg) in sterile soil (SS) showed different potential of tested strains to degrade 2,4-D. The times within which the initial 2,4-D concentration was reduced by 50% (DT50) were 6.3, 5.0 and 9.4 days for SS+DS-1, SS+DS-2 and SS+DS-3, respectively.

The biomass yielding process of xenobiotic degradation

Yields of activated sludge and an Arthrobacter sp. biomass on organic xenobiotic 2,4-dichlorophenoxyacetic acid (2,4-D) and on the intermediates of selected 2,4-D metabolism pathways were measured. Activated sludge yield on 2,4-D was lower by approximately 24-45% compared to the combined yields produced separately by the lower intermediates. For activated sludge, cell synthesis only consumed 33% of the electrons generated from 2,4-D oxidation, while the other 67% were used for energy. The high energy consumption, which was the primary cause of low activated sludge yield from 2,4-D degradation, occurred mainly in the catabolism of 2,4-D. The degrader sludge supplied this catabolism energy demand with the ATP contained in the biomass. As a result, the sludge's ATP contents suffered a deficit that was not fully remunerated after 2,4-D was degraded. Metabolism of the lower intermediates provided materials for further biomass growth and refilled part of the energy initially consumed.

Modeling the acclimation of activated sludge to a xenobiotic

This work established a mathematical model that formulated degrader formation by conversion of indigenous microbial cells. Degrader conversion is attributed to genetic induction whose force is dependent on the strength of acclimating xenobiotic and the amount of indigenous cells. After successful conversion, which requires an amount of time proportionate to the lag, degraders grow on the xenobiotic substrate. This model formulated the lag and degrader formation with the sigmoid function and degrader growth with the Haldane kinetics. The model so completed accurately simulates the degradation and biomass courses during acclimation and degradation of a xenobiotic by indigenous activated sludge, wherein the factors relating to the acclimation process are given values. The model serves the need for a rational representation of microbial acclimation to a xenobiotic.