Novel insights into the metabolic pathway of iprodione by soil bacteria

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.

Biodegradation of Iprodione and Chlorpyrifos Using an Immobilized Bacterial Consortium in a Packed-Bed Bioreactor

This work provides the basis for implementing a continuous treatment system using a bacterial consortium for wastewater containing a pesticide mixture of iprodione (IPR) and chlorpyrifos (CHL). Two bacterial strains (Achromobacter spanius C1 and Pseudomonas rhodesiae C4) isolated from the biomixture of a biopurification system were able to efficiently remove pesticides IPR and CHL at different concentrations (10 to 100 mg L^-1) from the liquid medium as individual strains and free consortium. The half-life time (T_1/2) for IPR and CHL was determined for individual strains and a free bacterial consortium. However, when the free bacterial consortium was used, a lower T_1/2 was obtained, especially for CHL. Based on these results, an immobilized bacterial consortium was formulated with each bacterial strain encapsulated individually in alginate beads. Then, different inoculum concentrations (5, 10, and 15% w/v) of the immobilized consortium were evaluated in batch experiments for IPR and CHL removal. The inoculum concentration of 15% w/v demonstrated the highest pesticide removal. Using this inoculum concentration, the packed-bed bioreactor with an immobilized bacterial consortium was operated in continuous mode at different flow rates (30, 60, and 90 mL h^-1) at a pesticide concentration of 50 mg L^-1 each. The performance in the bioreactor demonstrated that it is possible to efficiently remove a pesticide mixture of IPR and CHL in a continuous system. The metabolites 3,5-dichloroaniline (3,5-DCA) and 3,5,6-trichloro-2-pyridinol (TCP) were produced, and a slight accumulation of TCP was observed. The bioreactor was influenced by TCP accumulation but was able to recover performance quickly. Finally, after 60 days of operation, the removal efficiency was 96% for IPR and 82% for CHL. The findings of this study demonstrate that it is possible to remove IPR and CHL from pesticide-containing wastewater in a continuous system.

Degradation of iprodione by a novel strain Azospirillum sp. A1-3 isolated from Tibet

A bacterial strain A1-3 with iprodione-degrading capabilities was isolated from the soil for vegetable growing under greenhouses at Lhasa, Tibet. Based on phenotypic, phylogenetic, and genotypic data, strain A1-3 was considered to represent a novel species of genus Azospirillum. It was able to use iprodione as the sole source of carbon and energy for growth, 27.96 mg/L (50.80%) iprodione was reduced within 108 h at 25°C. During the degradation of iprodione by Azospirillum sp. A1-3, iprodione was firstly degraded to N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine, and then to (3,5-dichlorophenylurea) acetic acid. However, (3,5-dichlorophenylurea) acetic acid cannot be degraded to 3,5-dichloroaniline by Azospirillum sp. A1-3. A ipaH gene which has a highly similarity (98.72-99.92%) with other previously reported ipaH genes, was presented in Azospirillum sp. A1-3. Azospirillum novel strain with the ability of iprodione degradation associated with nitrogen fixation has never been reported to date, and Azospirillum sp. A1-3 might be a promising candidate for application in the bioremediation of iprodione-contaminated environments.

Isolation, characterization and industrial application of a Cladosporium herbarum fungal strain able to degrade the fungicide imazalil

Imazalil (IMZ) is an imidazole fungicide commonly used by fruit-packaging plants (FPPs) to control fungal infections during storage. Its application leads to the production of pesticide-contaminated wastewaters, which, according to the European Commission, need to be treated on site. Considering the lack of efficient treatment methods, biodepuration systems inoculated with tailored-made inocula specialized on the removal of such persistent fungicides appear as an appropriate solution. However, nothing is known about the biodegradation of IMZ. We aimed to isolate and characterize microorganisms able to degrade the recalcitrant fungicide IMZ and eventually to test their removal efficiency under near practical bioengineering conditions. Enrichment cultures from a soil receiving regular discharges of effluents from a FPP, led to the isolation of a Cladosporium herbarum strain, which showed no pathogenicity on fruits, a trait essential for its biotechnological exploitation in FPPs. The fungus was able to degrade up to 100 mg L^-1 of IMZ. However, its degrading capacity and growth was reduced at increasing IMZ concentrations in a dose-dependent manner, suggesting the involvement of a detoxification rather than an energy-gain mechanism in the dissipation of IMZ. The isolate could tolerate and gradually degrade the fungicides fludioxonil (FLD) and thiabendazole (TBZ), also used in FPPs and expected to coincide alongside IMZ in FPP effluents. The capacity of the isolate to remove IMZ in a practical context was evaluated in a benchtop immobilized-cell bioreactor fed with artificial IMZ-contaminated wastewater (200 mg L^-1). The fungal strain established in the reactor, completely dominated the fungal community and effectively removed >96% of IMZ. The bioreactor also supported a diverse bacterial community composed of Sphingomonadales, Burkholderiales and Pseudomonadales. Our study reports the isolation of the first IMZ-degrading microorganism with high efficiency to remove IMZ from agro-industrial effluents under bioengineering conditions.

Microbial adaptation and impact into the pesticide's degradation

The imprudent use of agrochemicals to control agriculture and household pests is unsafe for the environment. Hence, to protect the environment and diversity of living organisms, the degradation of pesticides has received widespread attention. There are different physical, chemical, and biological methods used to remediate pesticides in contaminated sites. Compared to other methods, biological approaches and their associated techniques are more effective, less expensive and eco-friendly. Microbes secrete several enzymes that can attach pesticides, break down organic compounds, and then convert toxic substances into carbon and water. Thus, there is a lack of knowledge regarding the functional genes and genomic potential of microbial species for the removal of emerging pollutants. Here we address the knowledge gaps by highlighting systematic biology and their role in adaptation of microbial species from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Moreover, by co-metabolism, the microbial species fulfill their nutritional requirements and perform more efficiently than single microbial-free cells. But in an open environment, free cells of microbes are not much prominent in the degradation process due to environmental conditions, incompatibilities with mechanical equipment and difficulties associated with evenly distributing inoculum through the agroecosystem. This review highlights emerging techniques involving the removal of pesticides in a field-scale environment like immobilization, biobed, biocomposites, biochar, biofilms, and bioreactors. In these techniques, different microbial cells, enzymes, natural fibers, and strains are used for the effective biodegradation of xenobiotic pesticides.

Development toxicity and cardiotoxicity in zebrafish from exposure to iprodione

Iprodione is a highly effective broad-spectrum fungicide commonly used for early disease control in fruit trees and vegetables. Pesticides often flow into watercourses due to rainfall, causing toxicity in non-target organisms, eventually entering the food chain. However, little information is available in the current literature about the toxicity of iprodione to cardiac development. The present study aimed to investigate the effect of iprodione on early embryonic development and its cardiotoxicity in aquatic animals, using zebrafish as a model. At 6-72 h post-fertilization (hpf), zebrafish were exposed to concentrations of 15 mg/L, 20 mg/L, and 25 mg/L (72 h-LC₅₀ = 21.15 mg/L). We found that exposure to iprodione resulted in yolk edema, increased mortality, and shortened body length in zebrafish embryos. In addition, iprodione was also found to induce edema in the pericardium of zebrafish, decrease heart rate, and cause the failure of cardiac cyclization. Exposure to iprodione significantly increased the accumulation of ROS and altered the activity of antioxidant enzymes (MDA, CAT) in zebrafish embryos. Moreover, iprodione induced changes in the transcription levels of heart developmental-related genes and apoptosis-related genes. In addition, Astaxanthin (antioxidant) can partially rescue the toxic phenotype caused by iprodione. Apoptosis-related genes and heart developmental-related genes were rescued after astaxanazin treatment. The results suggest that iprodione induces developmental and cardiac toxicity in zebrafish embryos, which provides new evidence of the toxicity of iprodione to organisms in aquatic ecosystems and assessing human health risks.

The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity?

Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant-soil system and agricultural production.

Pesticide-tolerant bacteria isolated from a biopurification system to remove commonly used pesticides to protect water resources

In this study, we selected and characterized different pesticide-tolerant bacteria isolated from a biomixture of a biopurification system that had received continuous applications of a pesticides mixture. The amplicon analysis of biomixture reported that the phyla Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were predominant. Six strains grew in the presence of chlorpyrifos and iprodione. Biochemical characterization showed that all isolates were positive for esterase, acid phosphatase, among others, and they were identified as Pseudomonas, Rhodococcus and Achromobacter based on molecular and proteomic analysis. Bacterial growth decreased as both pesticide concentrations increased from 10 to 100 mg L^-1 in liquid culture. The Achromobacter sp. strain C1 showed the best chlorpyrifos removal rate of 0.072–0.147 d^-1 a half-life of 4.7–9.7 d and a maximum metabolite concentration of 2.10 mg L^-1 at 120 h. On the other hand, Pseudomonas sp. strain C9 showed the highest iprodione removal rate of 0.100–0.193 d^-1 a half-life of 4–7 d and maximum metabolite concentration of 0.95 mg L^-1 at 48 h. The Achromobacter and Pseudomonas strains showed a good potential as chlorpyrifos and iprodione-degrading bacteria.

Biodegradation of Malathion Using Pseudomonas stutzeri(MTCC 2643)

Pesticides are applied in agricultural fields for controlling pest population to achieve crop protection. But they cause damage to nontarget organisms and affect the quality of environment including water, air and soil. The present study has been designed to test the efficiency of Pseudomonas stutzerion the degradation of malathion. The bacterial strain was subjected to 50, 100, 150 and 200 ppm of malathion in minimal broth for 30 hours and changes in orthophosphate levels, pH and turbidity were monitored for every six hours. Efficiency of free and immobilized cells were compared for orthophosphate release. Influence of different sugars on degradation was also compared. Degradation of 150 ppm of malathion was confirmed with UV-Visible spectrophotometric analysis and HPLC analysis. The data were subjected to two way analysis of variance and the results are discussed.

An Amidase Gene, ipaH, Is Responsible for the Initial Step in the Iprodione Degradation Pathway of Paenarthrobacter sp. Strain YJN-5

Iprodione [3-(3,5-dichlorophenyl) N-isopropyl-2,4-dioxoimidazolidine-1-carboxamide] is a highly effective broad-spectrum dicarboxamide fungicide. Several bacteria with iprodione-degrading capabilities have been reported; however, the enzymes and genes involved in this process have not been characterized. In this study, an iprodione-degrading strain, Paenarthrobacter sp. strain YJN-5, was isolated and characterized. Strain YJN-5 degraded iprodione through the typical pathway, with hydrolysis of its N-1 amide bond to N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine as the initial step. The ipaH gene, encoding a novel amidase responsible for this step, was cloned from strain YJN-5 by the shotgun method. IpaH shares the highest similarity (40%) with an indoleacetamide hydrolase (IAHH) from Bradyrhizobium diazoefficiens USDA 110. IpaH displayed maximal enzymatic activity at 35°C and pH 7.5, and it was not a metalloamidase. The k_cat and K_m of IpaH against iprodione were 22.42 s^-1 and 7.33 μM, respectively, and the catalytic efficiency value (k_cat/K_m ) was 3.09 μM^-1 s^-1 IpaH has a Ser-Ser-Lys motif, which is conserved among members of the amidase signature family. The replacement of Lys82, Ser157, and Ser181 with alanine in IpaH led to the complete loss of enzymatic activity. Furthermore, strain YJN-5M lost the ability to degrade iprodione, suggesting that ipaH is the only gene responsible for the initial iprodione degradation step. The ipaH gene could also be amplified from another previously reported iprodione-degrading strain, Microbacterium sp. strain YJN-G. The sequence similarity between the two IpaHs at the amino acid level was 98%, indicating that conservation of IpaH exists in different strains.IMPORTANCE Iprodione is a widely used dicarboxamide fungicide, and its residue has been frequently detected in the environment. The U.S. Environmental Protection Agency has classified iprodione as moderately toxic to small animals and a probable carcinogen to humans. Bacterial degradation of iprodione has been widely investigated. Previous studies demonstrate that hydrolysis of its N-1 amide bond is the initial step in the typical bacterial degradation pathway of iprodione; however, enzymes or genes involved in iprodione degradation have yet to be reported. In this study, a novel ipaH gene encoding an amidase responsible for the initial degradation step of iprodione in Paenarthrobacter sp. strain YJN-5 was cloned. In addition, the characteristics and key amino acid sites of IpaH were investigated. These findings enhance our understanding of the microbial degradation mechanism of iprodione.

Isolation and characterization of a bacterium able to degrade high concentrations of iprodione

A bacterial strain CQH-1 capable of mineralizing iprodione was isolated and characterized. On the basis of its morphological, physiological, and biochemical characteristics combined with phylogenetic analysis of its 16S rRNA gene sequence, strain CQH-1 was identified as a Microbacterium sp. CQH-1. It was able to use iprodione and 3,5-dichloroaniline as the sole source of carbon and energy for its growth. It completely degraded 100 mg·L^-1 iprodione within 96 h at 30 °C. During the degradation of iprodione by strain CQH-1, 2 compounds were detected in GC-MS analysis and were recognized as N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine and 3,5-dichloroaniline. So, the biodegradation pathway of iprodione by strain CQH-1 was proposed. This is the first report of an iprodione-mineralizing strain from the genus Microbacterium, and strain CQH-1 might be a promising candidate for application in the bioremediation of iprodione-contaminated environments.

Dynamics of biochemical properties associated with soil nitrogen mineralization following nitrification inhibitor and fungicide applications

Agrochemical applications may have side effects on soil biochemical properties related to soil nitrogen (N) mineralization and thus affect N cycling. The present study aimed to evaluate the effects of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) and fungicide iprodione on soil neutral protease (NPR), alkaline protease (APR), chitinase (CHI), and their functional genes (nprA, aprA, and chiA) related to soil N mineralization. The following four treatments were included: blank control (CK), single DMPP application (DAA), weekly iprodione applications (IPR), and the combined applications of DMPP and iprodione (DI). Compared with the CK treatment, DMPP application significantly inhibited the CHI activity in the first 14 days of incubation, and iprodione applications, particularly when applied alone, decreased the NPR, APR, and CHI activities. Relative to the IPR treatment, extra DMPP application had the potential to alleviate the inhibitory effects of iprodione on the activities of these enzymes. DMPP application significantly increased aprA gene abundances after 14 days of incubation. However, repeated iprodione applications, alone or with the DMPP, decreased nprA and chiA gene abundances. Relative to the CK treatment, DMPP application generated negligible effects on the positive/negative correlations between soil enzyme activities and the corresponding functional gene abundances. However, the positive correlation between the CHI activity and chiA gene abundance was changed to negative correlation by repeated iprodione applications, alone or together with the DMPP. Our results demonstrated that agrochemical applications, particularly repeated fungicide applications, can have inadvertent effects on enzyme activities and functional gene abundances associated with soil N mineralization.