Characterization of a novel oxyfluorfen-degrading bacterial strain Chryseobacterium aquifrigidense and its biochemical degradation pathway

In vitro assays reveal inherently insecticide-tolerant termite symbionts

Introduction: Termite symbionts are well known for conferring a myriad of benefits to their hosts. Bacterial symbionts are repeatedly associated with increased fitness, nutritional supplementation, pathogen protection, and proper development across insect taxa. In addition, several recent studies link bacterial symbionts to reduced insecticide efficacy. This has important implications both in pest control management and environmental bioremediation efforts. Insects' guts may be a valuable resource for microbes with broad application given their unique niches and metabolic diversity. Though insecticide resistance in termites is considered unlikely due to their life history, the close association of termites with a multitude of bacteria raises the question: is there potential for symbiont-mediated pesticide tolerance in termites? Methods and results: We identified a candidate that could grow in minimal medium containing formulated pesticide. This bacterial isolate was then subjected to continuous culture and subsequently demonstrated improved performance in the presence of pesticide. Isolates subjected to continuous culture were then grown at a range of concentrations from 1-10X the formulation rate. After constant exposure for several generations, isolates grew significantly better. Conclusion: Here we demonstrate that naïve insect hosts can harbor symbionts with inherent insecticide tolerance capable of rapid adaptation to increasing insecticide concentrations overtime. This has broad implications for both pest control and environmental cleanup of residual pesticides.

A nitroreductase DnrA catalyzes the biotransformation of several diphenyl ether herbicides in Bacillus sp. Za

Diphenyl ether herbicides, typical globally used herbicides, threaten the agricultural environment and the sensitive crops. The microbial degradation pathways of diphenyl ether herbicides are well studied, but the nitroreduction of diphenyl ether herbicides by purified enzymes is still unclear. Here, the gene dnrA, encoding a nitroreductase DnrA responsible for the reduction of nitro to amino groups, was identified from the strain Bacillus sp. Za. DnrA had a broad substrate spectrum, and the K_m values of DnrA for different diphenyl ether herbicides were 20.67 μM (fomesafen), 23.64 μM (bifenox), 26.19 μM (fluoroglycofen), 28.24 μM (acifluorfen), and 36.32 μM (lactofen). DnrA also mitigated the growth inhibition effect on cucumber and sorghum through nitroreduction. Molecular docking revealed the mechanisms of the compounds fomesafen, bifenox, fluoroglycofen, lactofen, and acifluorfen with DnrA. Fomesafen showed higher affinities and lower binding energy values for DnrA, and residue Arg244 affected the affinity between diphenyl ether herbicides and DnrA. This research provides new genetic resources and insights into the microbial remediation of diphenyl ether herbicide-contaminated environments. KEY POINTS: • Nitroreductase DnrA transforms the nitro group of diphenyl ether herbicides. • Nitroreductase DnrA reduces the toxicity of diphenyl ether herbicides. • The distance between Arg244 and the herbicides is related to catalytic efficiency.

Oxyfluorfen induces cell cycle arrest by regulating MAPK, PI3K and autophagy in ruminant immortalized mammary epithelial cells

Oxyfluorfen, a phenoxy phenyl-type herbicide, causes significant damage to ecosystems through chronically effecting invertebrates, fish, and mammals. Considering its adverse effect on ecosystem conservation, it is necessary to investigate its toxic effects on animals. However, the mechanisms of oxyfluorfen toxicity on bovines are not well established. This study investigated the cytotoxic effect of oxyfluorfen on bovine mammary epithelial cells (MAC-T). We conducted several functional experiments to examine the response of MAC-T to oxyfluorfen under various concentrations (0, 1, 2, 5, and 10 ppm). Oxyfluorfen decreased cell viability and increased apoptotic cells by regulating the expression of apoptotic genes and proteins in MAC-T. In addition, oxyfluorfen-treated cells exhibited reduced PCNA expression with a low 3D spheroid formation as compared to that of control cells. Furthermore, oxyfluorfen treatment suppressed cell cycle progression with a decrease in cyclin D1 and cyclin A2 in MAC-T. Next, we performed western blot analysis to verify intercellular signaling changes in oxyfluorfen-treated MAC-T. The phosphor-AKT protein was increased, whereas MAPK signal pathways were decreased. Particularly, the combination of oxyfluorfen with U0126 or SP600125 completely blocked the ERK1/2 and JNK pathways leading to cell viability in MAC-T. Moreover, oxyfluorfen induced inflammatory gene expression and autophagy by increasing phosphorylation of P62 and LC3B in MAC-T. These results demonstrated that oxyfluorfen has cytotoxic effect on MAC-T, implying that the milk production capacity in cows may eventually harm humans.

Enrichment of tetracycline-degrading bacterial consortia: Microbial community succession and degradation characteristics and mechanism

Tetracycline (TC) is an antibiotic that is recently found as an emerging pollutant with low biodegradability. Biodegradation shows great potential for TC dissipation. In this study, two TC-degrading microbial consortia (named SL and SI) were respectively enriched from activated sludge and soil. Bacterial diversity decreased in these finally enriched consortia compared with the original microbiota. Moreover, most ARGs quantified during the acclimation process became less abundant in the finally enriched microbial consortia. Microbial compositions of the two consortia as revealed by 16 S rRNA sequencing were similar to some extent, and the dominant genera Pseudomonas, Sphingobacterium, and Achromobacter were identified as the potential TC degraders. In addition, consortia SL and SI were capable of biodegrading TC (initial 50 mg/L) by 82.92% and 86.83% within 7 days, respectively. They could retain high degradation capabilities under a wide pH range (4-10) and at moderate/high temperatures (25-40 °C). Peptone with concentrations of 4-10 g/L could serve as a desirable primary growth substrate for consortia to remove TC through co-metabolism. A total of 16 possible intermediates including a novel biodegradation product TP245 were detected during TC degradation. Peroxidase genes, tetX-like genes and the enriched genes related to aromatic compound degradation as revealed by metagenomic sequencing were likely responsible for TC biodegradation.

Acetyltransferase OsACE2 acts as a regulator to reduce the environmental risk of oxyfluorfen to rice production

The constant use of the pesticide oxyfluorfen (OFF) in farmland contaminates the soil, posing threats to crop growth and human health. To avoid the contamination of food crops with OFF, it is critically important to understand its absorption and degradation mechanisms. In this study, we characterized a new functional locus encoding an acetyltransferase (OsACE2) that can facilitate OFF degradation in rice. OsACE2 was drastically induced by OFF at 0.04-0.2 mg L^-1 for 6 days and the rice growth was significantly inhibited. To demonstrate the regulatory role of OsACE2 in resistance to OFF toxicity, we generated OsACE2 overexpression (OE) and knockout mutant using genetic transformation and gene-editing technologies (CRISPR/Cas9). The OE plants grown in the hydroponic medium showed improved growth (plant elongation and biomass), increased chlorophyll content, and reduced OFF-induced oxidative stress. The OsACE2-improved growth phenotypes of rice were attributed to the significantly lower OFF accumulation in OE plants. Conversely, knocking out OsACE2 resulted in compromised growth phenotypes compared to the wild-type (WT). Using LC-LTQ-HRMS/MS, five mono-metabolites and eleven conjugates of OFF were characterized through various canonical pathways, such as hydrolysis, oxidation, reduction, glycosylation, acetylation, malonylation, and interaction with amino acids. These metabolites increased in the OE plants, and five acetylated conjugates were reported for the first time. Collectively, OsACE2 plays a primary role in catabolizing OFF residues in rice through multiple degradation pathways and reducing OFF in its growth environment.

The Lethal and Sub-Lethal Effects of Fluorinated and Copper-Based Pesticides-A Review

In recent decades, pollution levels have increased, mainly as a result of the intensive anthropogenic activities such industrial development, intensive agricultural practices, among others. The impact of metals and organic contaminants is, nowadays, a great concern to the scientific and political communities. Copper compounds are the main sold pesticides in Europe, as well as herbicides, including glyphosate. Diphenyl ethers are the second ones most sold. Glyphosate and copper compounds are intensively studied, but the opposite is seen in the case of diphenyl ethers, including fluorinated pesticides (e.g., oxyfluorfen). Some research has been performed to increase the knowledge about these contaminants, daily inputted on the aquatic systems and with dangerous effects at physical and biochemical levels on the organisms. A wide range of biomarkers (e.g., growth, survival, reproductive success, enzymatic activity, lipid metabolism) has been applied to determine the potential effects in many species. This review intends to: (a) perform a compilation of the knowledge in previous research about the action mode of organic (fluorinated-based herbicide) and inorganic (copper-based pesticides) contaminants; (b) carry out an information survey about the lethal and sub-lethal effects of the fluorinated-based pesticides, namely the oxyfluorfen and the copper-based pesticides, on aquatic species from different trophic levels, according to in vitro and in vivo studies; (c) understand the impact of oxyfluorfen and copper-based pesticides, considering their effects reported in in vitro studies and, simultaneously, the authorized concentrations by legal organizations and the effective concentrations of each pollutant found in the environment. The literature analyzed revealed noxious effects of Cu and oxyfluorfen to aquatic organisms, including freshwater and marine species, even when exposed to the reference as well as to environmental concentrations, thus highlighting the importance of more monitoring and ecotoxicological studies, to chemical pollutants and different species from different ecological niches, to sustain and improve the legislation.

Effects of different colored polyethylene mulching films on bacterial communities from soil during enrichment incubation

Studies have shown that mulching agricultural fields with plastic residues can influence microbial communities in the environment, but few studies have investigated the differences in the soil microbial communities in distinct areas under mulching with different colored plastic products. Thus, in this study, we explored how different colored polyethylene mulching films (PMFs) might affect soil bacterial communities during enrichment incubation. We found significant differences in the bacterial communities under different colored PMFs after incubation. Treatment with the same colored PMF obtained more similar bacterial community compositions. For instance, at the class level, Gammaproteobacteria and Bacteroidia were most abundant with black PMF, whereas Actinobacteria and Bacteroidia were most abundant with white PMF. The most abundant genera were Acinetobacter and Chryseobacterium with black PMF but Rhodanobacter and Paenarthrobacter with white PMF. Polyethylene- and hydrocarbon-degrading bacteria were the core members detected under both treatments, and the bacterial communities were predicted to have the potential for the biodegradation and metabolism of xenobiotics after enrichment culture according to the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) tool. In addition, the bacterial communities in soil from Xinjiang treated with white PMF and in soil from Yangling treated with black PMF were strongly correlated and stable. Our results suggest that the color of the PMF applied affected the soil bacterial communities, where plastics with the same color may have recruited similar species of microorganisms, although the origins of these microorganisms were not the same.

Characterization of a novel glyphosate-degrading bacterial species, Chryseobacterium sp. Y16C, and evaluation of its effects on microbial communities in glyphosate-contaminated soil

Widespread use of the herbicide glyphosate in agriculture has resulted in serious environmental problems. Thus, environment-friendly technological solutions are urgently needed for the removal of residual glyphosate from soil. Here, we successfully isolated a novel bacterial strain, Chryseobacterium sp. Y16C, which efficiently degrades glyphosate and its main metabolite aminomethylphosphonic acid (AMPA). Strain Y16C was found to completely degrade glyphosate at 400 mg·L-1 concentration within four days. Kinetics analysis indicated that glyphosate biodegradation was concentration-dependent, with a maximum specific degradation rate, half-saturation constant, and inhibition constant of 0.91459 d-1, 15.79796 mg·L-1, and 290.28133 mg·L-1, respectively. AMPA was identified as the major degradation product of glyphosate degradation, suggesting that glyphosate was first degraded via cleavage of its C-N bond prior to subsequent metabolic degradation. Strain Y16C was also found to tolerate and degrade AMPA at concentrations up to 800 mg·L-1. Moreover, strain Y16C accelerated glyphosate degradation in soil indirectly by inducing a slight alteration in the diversity and composition of soil microbial community. Taken together, our results suggest that strain Y16C may be a potential microbial agent for bioremediation of glyphosate-contaminated soil.

Screening of Carbofuran-Degrading Bacteria Chryseobacterium sp. BSC2-3 and Unveiling the Change in Metabolome during Carbofuran Degradation

Carbofuran is one of the most commonly used N-methylcarbamate-based pesticides and is excellent for controlling pests; however, carbofuran also causes soil and water pollution. Although various studies have been conducted on the bioremediation of pesticide-contaminated soil, the changes occurring in the metabolome during the bioremediation of carbofuran are not fully understood. In this study, the intracellular and extracellular metabolites of the Chryseobacterium sp. BSC2-3 strain were analysed during carbofuran degradation by using a liquid chromatography–mass spectrometry-based metabolomics approach. We found that the BSC2-3 strain extracellularly transformed carbofuran into 3-hydroxycarbofuran. Intracellular metabolite analysis revealed that carbofuran mainly affected aminobenzoate degradation, ubiquinone and terpenoid-quinone biosynthesis, and arginine and proline metabolism. Carbofuran especially affected the metabolic pathway for the degradation of naphthalene and aminobenzoate. Metabolomics additionally revealed that the strain produces disease resistance inducers and plant growth regulators. We also identified the genes involved in the production of indole-3-acetic acid, which is one of the most active auxins. Overall, we identified the metabolic changes induced in carbofuran-degrading bacteria and the genes predicted to be responsible for the degradation of carbofuran.

Biochemical Effects of Two Pesticides in Three Different Temperature Scenarios on the Diatom Thalassiosira weissflogii

The exponential increase of the human population demands the overuse of fertilizers and pesticides in agriculture practices to suppress food production needs. The excessive use of these chemicals (fertilizers and pesticides) can comport deleterious effects to the ecosystems, including aquatic systems and communities. Oxyfluorfen is a fluorine-based herbicide, and its application has increased, since it is seen as an alternative to control glyphosate-resistant weeds. Copper sulfate is an inorganic pesticide based on copper which is being used in several chemical formulations, and it is the second main constituent of fungicides. Besides the known effects of such products in organisms, climatic changes pose an additional issue, being a main concern among scientists and politicians worldwide, since these alterations may worsen ecosystems’ and organisms’ sensitivity to stress conditions, such as the exposure to pollutants. Thalassiosira weissflogii (Grunow) G. A. Fryxell & Hasle, 1977 plays an important role in aquatic food webs as a primary producer and an essential food source to zooplankton. Thus, alterations on the diatom’s abundance and nutritional value may lead to consequences along the trophic chain. However, few studies have evaluated the biochemical impacts of oxyfluorfen and copper sulfate exposure on diatoms. This study intends to (1) evaluate the effects on the growth rate of both contaminants on T. weissfloggi at three temperatures, considering the actual scenario of climatic changes, and (2) assess biochemical changes on the diatom when exposed to the chemicals at different temperatures. To achieve these aims, the marine diatom was exposed to the two chemicals individually at different temperatures. The results showed an increase in the growth rate with increasing temperatures. Oxyfluorfen exhibited higher toxicity than copper sulfate. At the biochemical level, the microalgae were greatly affected when exposed to oxyfluorfen at 20 °C and 25 °C and when exposed to copper sulfate at 15 °C. Moreover, a general increase was observed for the polysaccharide content along the copper sulfate and oxyfluorfen concentrations. Therefore, the contaminants show the ability to interfere with the diatom growth and the nutritive value, with their effects dependent on the temperature.

Facilitated bio-mineralization of N,N-dimethylformamide in anoxic denitrification system: Long-term performance and biological mechanism

Due to highly recalcitrant and toxicological nature of N,N-dimethylformamide (DMF), efficient removal of DMF is challenging for biological wastewater treatment. In this study, an anoxic denitrification system was developed and continuously operated for 220 days in order to verify the enhanced DMF biodegradation mechanism. As high as 41.05 mM DMF could be thoroughly removed in the anoxic denitrification reactor at hydraulic residence time (HRT) of 24 h, while the total organic carbon (TOC) and nitrate removal efficiencies were as high as 95.7 ± 2.5% and 98.4 ± 1.1%, respectively. Microbial community analyses indicated that the species related to DMF hydrolysis (Paracoccus, Brevundimonas and Chryseobacterium) and denitrification (Paracoccus, Arenimonas, Hyphomicrobium, Aquamicrobium and Bosea) were effectively enriched in the anoxic denitrification system. Transcriptional analysis coupled with enzymatic activity assay indicated that both hydrolysis and mineralization of DMF were largely enhanced in the anoxic denitrification system. Moreover, the occurrence of microbial denitrification distinctly facilitated carbon source utilization to produce electron and energy, which was rather beneficial for better reactor performance. This study demonstrated that the anoxic denitrification system would be a potential alternative for efficient treatment of wastewater polluted by recalcitrant pollutants such as DMF.

Characterization of hexaconazole-degrading strain Sphingobacterium multivorum and analysis of transcriptome for biodegradation mechanism

Hexaconazole is a triazole fungicide, which is stable and difficult to degrade in the environment. The existence of hexaconazole could pose a certain risk to the environment and the health of living organisms. In this study, an efficient degradation strain B-3 (Sphingobacterium multivorum) of hexaconazole was isolated from sewage, activated sludge, and soil. The degradation efficiency of hexaconazole can reach 85.6% in 6 days at a temperature of 32.5 °C, pH of 6.31, initial inoculum of 0.4 g L^-1 and initial concentration of hexaconazole of 50 mg L^-1. During degradation, three metabolites (M1: 2-(2, 4-dichlorophenyl)-1-(1H-1, 2, 4-triazol-1-yl) hexane-2, 5-diol; M2: 2-(2, 4-dichlorophenyl) hexane-1, 2-diol; M3: 1H-1, 2, 4-triazole) were identified. Moreover, 45.6% hexaconazole can be degraded in 60 days in natural soil containing B-3. The results of the transcriptome sequencing indicated the presence of 864 differential genes, in which aldehyde dehydrogenase, monooxygenase, RND transporters, and ABC transporters were up-regulated. The generation of 2-(2, 4-dichlorophenyl)-1-(1H-1, 2, 4-triazol-1-yl) hexane-2, 5-diol may be due to the participation of monooxygenase.

Removal of oxyfluorfen from polluted effluents by combined bio-electro processes

In this work, the combination of biological and electrochemical processes to mineralize oxyfluorfen has been studied. First, an acclimatized mixed-culture biological treatment was used to degrade the biodegradable fraction of the pesticide, reaching up to 90% removal. After that, the non-biodegraded fraction was oxidised by electrolysis using boron-doped diamond as the anode. The results showed that the electrochemical technique was able to completely mineralize the residual pollutants. The study of the influence of the supporting electrolyte on the electrochemical process showed that the trace mineral solution used in the biological treatment was enough to completely mineralize the oxyfluorfen, resulting in total organic carbon removal rates that were well-fitted by a first-order model with a kinetic constant of 0.91 h^-1. However, the first-order degradation rate increased approximately 20% when Na₂SO₄ was added as supporting electrolyte, reaching a degradation rate of 1.16 h^-1 with a power consumption that was approximately 70% lower.

Biological treatment of wastewater polluted with an oxyfluorfen-based commercial herbicide

Fluoxil-24 is a commercial herbicide based on oxyfluorfen (a hazardous non-soluble organochlorinated compound) and additional compounds used as solvents. The aim of this work is to study the biotreatability of this commercial herbicide in water through batch experiments performed at different temperatures (15, 20, 25 and 30 °C) and initial concentrations (85, 150, 300 and 500 mg L^-1 of oxyfluorfen). Activated sludge from an oil refinery wastewater treatment plant was acclimated and used for biodegradation experiments. Two main mechanisms, volatilization and biodegradation, were observed to be responsible of the herbicide removal. Fluoxil-24 removal efficiencies between approximately 40% and 80% were reached after 70 h, depending on the conditions used, and oxyfluorfen was not completely removed. Regarding the influence of the temperature, thermal inhibition problems appeared at 30 °C, and the volatilization rate of solvents increased, causing oxyfluorfen to become unavailable for microorganisms. An increase of herbicide initial concentration did not clearly affect the herbicide removal efficiency, whereas it negatively affected the biological mechanism. The experimental results were fitted to a mathematical model that included both simultaneous mechanisms of volatilization and Monod biodegradation kinetics. The model was able to predict the experimental results, and the calculated model parameters confirmed the effect of the variables under study.

Simultaneous efficient removal of oxyfluorfen with electricity generation in a microbial fuel cell and its microbial community analysis

The performance of a microbial fuel cell (MFC) to degrade oxyfluorfen was investigated. Approximately 77% of 50 mg/L oxyfluorfen was degraded within 24 h by anodic biofilm. The temperature, pH, and initial oxyfluorfen concentration had a significant effect on oxyfluorfen degrading, and a maximum degradation rate of 94.95% could theoretically be achieved at 31.96 °C, a pH of 7.65, and an initial oxyfluorfen concentration of 120.05 mg/L. Oxyfluorfen was further catabolized through various microbial metabolism pathways. Moreover, the anodic biofilm exhibited multiple catabolic capacities to 4-nitrophenol, chloramphenicol, pyraclostrobin, and sulfamethoxazole. Microbial community analysis indicated that functional bacteria Arcobacter, Acinetobacter, Azospirillum, Azonexus, and Comamonas were the predominant genera in the anodic biofilm. In terms of the efficient removal of various organic compounds and energy recovery, the MFC seemed to be a promising approach for the treatment of environmental contaminants.

Detoxification of diphenyl ether herbicide lactofen by Bacillus sp. Za and enantioselective characteristics of an esterase gene lacE

A bacterial strain Za capable of degrading diphenyl ether herbicide lactofen was isolated and identified as Bacillus sp. This strain could degrade 94.8% of 50mgL^-1 lactofen after 4days of inoculation in flasks. It was revealed that lactofen was initially hydrolyzed to desethyl lactofen, which was further transformed to acifluorfen, followed by the reduction of the nitro group to yield aminoacifluorfen. The phytotoxicity of the transformed product aminoacifluorfen to maize was decreased significantly compared with the lactofen. A gene lacE, encoding an esterase responsible for lactofen hydrolysis to desethyl lactofen and acifluorfen continuously, was cloned from Bacillus sp. Za. The deduced amino acid belonging to the esterase family VII contained a typical Ser-His-Asp/Glu catalytic triad and the conserved motifs GXSXG. The purified recombinant protein LacE displayed maximal esterase activity at 40°C and pH 7.0. Additionally, LacE had broad substrate specificity and was capable of hydrolyzing p-nitrophenyl esters. The enantioselectivity of LacE during lactofen degradation was further studied, and the results indicated that the (S)-(+)-lactofen was degraded faster than the (R)-(-)-lactofen, which could illustrate the reported phenomenon that (S)-(+)-lactofen was preferentially degraded in soil and sediment.