Isolation and characterization of a highly efficient chlorpyrifos degrading strain of Cupriavidus taiwanensis from sludge

Microbial detoxification of bifenthrin insecticide by selected fungal strains and optimizing conditions using response surface methodology for agricultural sustainability

Bifenthrin is a type I broad spectrum pyrethroid insecticide widely employed in urban and agricultural settings with little knowledge about its biodegradation. Bifenthrin was subjected to a 35 days incubation period in which it was degraded by five fungal strains named as Aspergillus niger, Aspergillus flavus, Aspergillus fumigatus, Penicillium chrysogenum, and Lasiodiplodia theobromae. Penicillium chrysogenum was found to be extremely effective in degrading bifenthrin up to 85%. Furthermore, response surface methodology (RSM) with Box-Behnken design is applied to optimize the degradation conditions with varying pH, temperature (°C), and incubation time (days). The p value < 0.05 in the response surface design and analysis of variance showed the significance of the reaction parameters. The ideal conditions for Penicillium chrysogenum to break down bifenthrin (10 mgL-1) were found to be 30 °C, pH 7, and a 24 days incubation period. In eutrophic conditions and a glucose-rich media, this fungus co-metabolized bifenthrin. By hydrolytically cleaving the carboxyl ester bond, the Penicillium chrysogenum breaks down bifenthrin, as shown by the chromatogram of four metabolites from GCMS. The biodegradation of bifenthrin by strain Penicillium chrysogenum and its use in agronomic situations are now well understood as per the findings of this study.

Chlorpyrifos in environment and food: a critical review of detection methods and degradation pathways

Chlorpyrifos (CP) is a class of organophosphorus (OP) pesticides, which find extensive applications as acaricide, insecticide and termiticide. The use of CP has been indicated in environmental contamination and disturbance in the biogeochemical cycles. CP has been reported to be neurotoxic and has a detrimental effect on immunological and psychological health. Therefore, it is necessary to design and develop effective degradation methods for the removal of CP from the environment. In the past few years, physicochemical (advanced oxidation process) and biological treatment approaches have been widely employed for the pesticide removal. However, the byproducts of this process are more toxic than the parent compound and along with an incomplete degradation of CP. This review focuses on the toxicity of CP, the sources of contamination, degradation pathways, physicochemical, biological, and nano-technology based methods employed for the degradation of CP. In addition, consolidated information on various detection methods and materials used for the detection have been provided in this review.

Insights into the microbial degradation and catalytic mechanisms of chlorpyrifos

Chlorpyrifos is extensively used worldwide as an insecticide to control various insect pests. Long-term and irregular applications of chlorpyrifos have resulted in large-scale soil, groundwater, sediment, and air pollution. Numerous studies have shown that chlorpyrifos and its major intermediate metabolite 3,5,6-trichloropyridinol (TCP) accumulate in non-target organisms through biomagnification and have a strong toxic effect on non-target organisms, including human beings. Bioremediation based on microbial metabolism is considered an eco-friendly and efficient strategy to remove chlorpyrifos residues. To date, a variety of bacterial and fungal species have been isolated and characterized for the biodegradation of chlorpyrifos and TCP. The metabolites and degradation pathways of chlorpyrifos have been investigated. In addition, the chlorpyrifos-degrading enzymes and functional genes in microbes have been reported. Hydrolases can catalyze the first step in ester-bond hydrolysis, and this initial regulatory metabolic reaction plays a key role in the degradation of chlorpyrifos. Previous studies have shown that the active site of hydrolase contains serine residues, which can initiate a catalytic reaction by nucleophilic attack on the P-atom of chlorpyrifos. However, few reviews have focused on the microbial degradation and catalytic mechanisms of chlorpyrifos. Therefore, this review discusses the deep understanding of chlorpyrifos degradation mechanisms with microbial strains, metabolic pathways, catalytic mechanisms, and their genetic basis in bioremediation.

Metagenomic Analysis Reveals Bacterial and Fungal Diversity and Their Bioremediation Potential From Sediments of River Ganga and Yamuna in India

In this study, we report the presence of a microbial community of bioremediation potential in terms of relative abundance and taxonomic biodiversity in sediment samples of river Ganga and Yamuna, India at nine different sites. Metagenomic libraries were constructed using TruSeq Nano DNA Library Prep Kit and sequenced on NextSeq 500 by Illumina Next Generation Sequencing (NGS) technology. Bioremediation bacteria belong to 45 genera with 92 species and fungi belong to 13 genera with 24 species have been classified using Kaiju taxonomical classification. The study revealed that Proteobacteria was the most dominant bacterial flora, followed by Actinobacteria, Firmicutes, and Deinococcus-Thermus. PCA analysis revealed that bioremediation bacteria viz. Streptomyces bikiniensis, Rhodococcus qingshengii, Bacillus aerophilus, Pseudomonas veronii, etc., were more dominant in highly polluted river stretch as compared to less polluted river stretch. Similarly, the relative abundance of bioremediation fungi viz. Phanerochaete chrysosporium and Rhizopus oryzae, etc., were significantly correlated with the polluted Kanpur stretch of river Ganga. Several protein domains, which play a pivotal role in bioremediation in the polluted environments, including urea ABC transporter, UrtA, UrtD, UrtE, zinc/cadmium/mercury/lead-transporting ATPase, etc., were identified using protein domain analysis. The protein domains involved in pesticide biodegradation viz. P450, short-chain dehydrogenases/reductases (SDR), etc., were also discovered in river sediment metagenomics data. This is the first report on the richness of bioremediation microbial communities in the Ganga and Yamuna riverine ecosystems, highlighting their importance in aquatic pollution management.

Ortho and para oxydehalogenation of dihalophenols catalyzed by the monooxygenase TcpA and NAD(P)H:FAD reductase Fre

Dihalophenols such as dichlorophenols (DCPs) are important industrial chemical intermediates, but also persistent pollutants in the environment. Oxidative dehalogenation by microbes is an efficient biological method to degrade halophenols, but the mechanism is unclear yet. Cupriavidus nantongensis X1^T was a type strain of genus Cupriavidus, and could degrade 2,4-dichlorophenol of 50 mg/L within 12 h. The degradation rate constant was approximately 84 fold greater than that by Bacillus endophyticus CP1R43, a well-studied 2,4-DCP-degrading bacterial strain. The genes encoding 2,4,6-trichlorophenol monooxygenase (TcpA) and NAD(P)H:FAD reductase (Fre) from strain X1^T were cloned and expressed. The expressed TcpA Fre were purified. The molecular docking of TcpA with DCPs and point mutation experiments showed that the degradation activity of TcpA was associated with the length of the hydrogen bond between the substrates and the amino acids in the active pocket. DCPs were degraded via a stepwise oxidative dechlorination in a positive relationship between the oxidation ability and the electron-withdrawing potential of the p-position group. In addition, TcpA has dual dehalogenation and denitration functions. The results demonstrate that either strain X1^T or TcpA and Fre can effectively dehalogenate dihalophenols, which can be useful for the treatment of dihalophenols in wastewaters and remediation of DCP-contaminated environments.

Minute-Speed Biodegradation of Organophosphorus Insecticides by Cupriavidus nantongensis X1T

Organophosphorus insecticides (OPs) have been widely used to control agricultural pests, which has raised concerns about OP residues in crops and the environment. In this study, we investigated the degradation kinetics and pathways of 8 OPs by Cupriavidus nantongensis X1^T and identified the enzyme via gene cloning and in vitro assays. The degradation half-life of methyl parathion, triazophos, and phoxim was only 5, 9, and 43 min, respectively. It was 46 fold faster than that of triazophos by Bacillus sp. TAP-1, a well-studied triazophos-degrader. Strain X1^T completely degraded not only chlorpyrifos, methyl parathion, parathion, fenitrothion, triazophos, and phoxim at 50 mg/L within 48 h but also the phenolic metabolites. This was the fastest degradation of OPs by bacterial whole cells reported thus far. The OPs were first hydrolyzed by an OP hydrolase encoded by the opdB gene in strain X1^T, followed by further degradation of the metabolites. The crude enzyme maintained a full activity.

Kinetics and Catabolic Pathways of the Insecticide Chlorpyrifos, Annotation of the Degradation Genes, and Characterization of Enzymes TcpA and Fre in Cupriavidus nantongensis X1T

Chlorpyrifos is one of the most used organophosphorus insecticides. It is commonly degraded to 3,5,6-trichloro-2-pyridinol (TCP), which is water-soluble and toxic. Bacteria can degrade chlorpyrifos and TCP, but the biodegradation mechanism has not been well-characterized. Recently isolated Cupriavidus nantongensis X1^T can completely degrade 100 mg/L chlorpyrifos and 20 mg/L TCP with half-lives of 6 and 8 h, respectively. We annotated a complete gene cluster responsible for TCP degradation in recently sequenced strain X1^T. Two key genes, tcpA and fre, were cloned from X1^T and transferred and expressed in Escherichia coli BL21(DE3). Degradation of TCP by X1^T whole cell was compared with that by the enzymes 2,4,6-trichlorophenol monooxygenase and NAD(P)H:flavin reductase expressed and purified from E. coli BL21(DE3). Novel metabolites of TCP were isolated and characterized, indicating stepwise dechlorination of TCP, which was confirmed by TCP disappearance, mass balance, and detection and formation kinetics of chloride ion from TCP.

Simultaneous biodegradation of bifenthrin and chlorpyrifos by Pseudomonas sp. CB2

The degradation of bifenthrin (BF) and chlorpyrifos (CP), either together or individually, by a bacterial strain (CB2) isolated from activated sludge was investigated. Strain CB2 was identified as belonging to genus Pseudomonas based on the morphological, physiological, and biochemical characteristics and a homological analysis of the 16S rDNA sequence. Strain CB2 has the potential to degrade BF and CP, either individually or in a mixture. The optimum conditions for mixture degradation were as follows: OD_600nm = 0.5; incubation temperature = 30°C; pH = 7.0; BF-CP mixture (10 mg L^-1 of each). Under these optimal conditions, the degradation rate constants (and half-lives) were 0.4308 d^-1 (1.61 d) and 0.3377 d^-1 (2.05 d) for individual BF and CP samples, respectively, and 0.3463 d^-1 (2.00 d) and 0.2931 d^-1 (2.36 d) for the BF-CP mixture. Major metabolites of BF and CP were 2-methyl-3-biphenylyl methanol and 3,5,6-trichloro-2-pyridinol, respectively. No metabolite bioaccumulation was observed. The ability of CB2 to efficiently degrade BF and CP, particularly in a mixture, may be useful in bioremediation efforts.

Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge

A Gram-stain-negative, aerobic, coccoid to small rod-shaped bacterium, designated X1T, was isolated from sludge collected from the vicinity of a pesticide manufacturer in Nantong, Jiangsu Province, China. Based on 16S rRNA gene sequence analysis, strain X1T belonged to the genus Cupriavidus, and was most closely related to Cupriavidus taiwanensis LMG 19424T (99.1 % 16S rRNA gene sequence similarity) and Cupriavidus alkaliphilus LMG 26294T (98.9 %). Strain X1T showed 16S rRNA gene sequence similarities of 97.2-98.2 % with other species of the genus Cupriavidus. The major cellular fatty acids of strain X1T were C16 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3), C18 : 1ω7c and C17 : 0 cyclo, and the major respiratory quinone was ubiquinone Q-8. The major polar lipids of strain X1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phospholipid and hydroxyphosphatidylethanolamine. The DNA G+C content was 66.6 mol%. The DNA-DNA relatedness values of strain X1T with the five reference strains C. taiwanensis LMG 19424T, C. alkaliphilus LMG 26294T, Cupriavidus necator LMG 8453T, Cupriavidus gilardii LMG 5886T and 'Cupriavidus yeoncheonense' KCTC 42053 were lower than 70 %. The results obtained from phylogenetic analysis, phenotypic characterization and DNA-DNA hybridization indicated that strain X1T should be proposed to represent a novel species of the genus Cupriavidus, for which the name Cupriavidus nantongensis sp. nov. is proposed. The type strain is X1T (=KCTC 42909T=LMG 29218T).