Transcriptome analysis of Plantago major as a phytoremediator to identify some genes related to cypermethrin detoxification

Pesticide pollution: toxicity, sources and advanced remediation approaches

The Food and Agricultural Organization of the United Nations (FAO) estimates that food production must rise by 70% to meet the demands of an additional 2.3 billion people by 2050. This forecast underscores the persistent reliance on pesticides, making it essential to assess their toxicity and develop effective remediation strategies. Given the widespread utilisation of pesticides, it requires an urgent need to evaluate their toxicity and explore feasible remediation approaches for their removal. Hence, this review provides an overview of the latest information on the presence, distribution, sources, fate, and trends of pesticides in global environmental matrices, emphasizing the ecological and health risks posed by pesticide pollution. Currently, the dominant remediation techniques encompass physical, chemical, and biological methods, yet studies focusing on advanced remediation techniques remain limited. This review critically evaluates both newer and traditional approaches to pesticide removal, offering a descriptive and analytical comparison of various methods. The selection of the appropriate treatment method depends largely on the nature of the pesticide and the effectiveness of the chosen technique. In many cases, technologies such as membrane bioreactors and the fenton process could be integrated with biological technologies to enhance performance and overcome limitations. The study concludes that a hybrid approach combining various remediation strategies offers the most effective and sustainable solution for pesticide removal. Finally, the review underscores the need for further scientific investigation into the most viable technologies while discussing the challenges and prospects of developing safe, reliable, cost-effective, and eco-friendly methods for removing pesticides from the environment.

Decontamination of Chlorpyrifos Residue in Soil by Using Mentha piperita (Lamiales: Lamiaceae) for Phytoremediation and Two Bacterial Strains

This study utilizes Mentha piperita (MI) for the first time to investigate the uptake and translocation of chlorpyrifos (CPF; 10 µg g-1) from soil, introducing a new approach to improve the efficacy of this technique, which includes using biosurfactants (Bacillus subtilis and Pseudomonas aeruginosa) at 107 CFU/mL to degrade CPF under greenhouse conditions. Moreover, antioxidant enzymes, including superoxide dismutase (SOD) and peroxidase (Prx), and oxidative stress due to hydrogen peroxide (H2O2) and malondialdehyde (MDA) in MI roots and leaves were evaluated under CPF stress. Our results demonstrated that amending soil with MI and B. subtilis followed by P. aeruginosa significantly reduced CPF levels in the soil (p > 0.05) and enhanced CPF concentrations in MI roots and leaves after 1, 3, 7, 10, and 14 days of the experiment. Furthermore, CPF showed its longest half-life (t1/2) in soil contaminated solely with CPF, lasting 15.36 days. Conversely, its shortest half-life occurred in soil contaminated with CPF and treated with MI along with B. subtilis, lasting 4.65 days. Soil contaminated with CPF and treated with MI and P. aeruginosa showed a half-life of 7.98 days. The half-life (t1/2) of CPF-contaminated soil with MI alone was 11.41 days. A batch equilibrium technique showed that B. subtilis is better than P. aeruginosa for eliminating CPF from soil in In vitro experiments. Notably, CPF-polluted soil treated with coadministration of MI and the tested bacteria improved the activities of SOD and Prx and reduced H2O2 and MDA compared with CPF-polluted soil treated with MI alone. Our findings demonstrated that using B. subtilis and P. aeruginosa as biosurfactants to augment phytoremediation represents a commendable strategy for enhancing the remediation of CPF contamination in affected sites while reducing the existence of harmful pesticide remnants in crop plants.

Transcriptome analysis shows that Glomus versiforme decrease the accumulation and toxicity of cadmium in Ipomoea aquatic Forsk

So far, the physiological and molecular mechanisms of the impact of arbuscular mycorrhizal fungus (AMF) on Cd absorption, transport and detoxification in Ipomoea aquatica (water spinach) are still unclear. In the present study, a pot experiment was performed to investigate the impact of AMF-Glomus versiforme (Gv) on the photosynthetic characteristics, Cd uptake, antioxidative system and transcriptome in water spinach in the soils supplemented with 5 mg Cd kg-1. Gv inoculation improved significantly the photosynthetic characteristics and growth of water spinach. Furthermore, Gv colonization significantly promoted the activities of catalase (CAT), peroxidase (POD) and glutathione reductase (GR), contents of glutathione (GSH) and ascorbic acid (AsA), and the total antioxidant capacity (TCA), but decreased malondialdehyde (MDA) content in water spinach. In addition, Gv inoculation significantly increased pH in rhizosphere soils and decreased the Cd concentrations and uptakes in water spinach. Importantly, 2670 differentially expressed genes (DEGs) were screened in water spinach root colonized with Gv in 5 mg Cd kg-1 soil, of which 2008 DEGs were upregulated and 662 DEGs were downregulated. Especially, the expression levels of POD, CAT, GR, dehydroascorbate reductase 2 (DHAR2), glutathione S-transferase U8 (GSTU8) and glutathione synthetase (GSHS) and cytochrome P450 (Cyt P450) genes were significantly up-regulated in water spinach inoculated with Gv. Meanwhile, the plant cadmium resistance protein 2 (PCR2), metal tolerance protein 4 (MTP4), ATP-binding cassette transporter C family member (ABCC), ABC-yeast cadmium factor 1 (ABC-YCF1) and metallothionein (MT) genes were also up-regulated in mycorrhizal water spinach. Our results firstly elucidated the mechanism by which AMF reduced the uptake and phytotoxicity of Cd in water spinach through a transcriptome analysis.

Detoxification mechanism of herbicide in Polypogon fugax and its influence on rhizosphere enzyme activities

The excessive use of chemical herbicides has resulted in evolution of herbicide-resistant weeds. Cytochrome P450 monooxygenases (P450s) are vital detoxification enzymes for herbicide-resistant weeds. Herein, we confirmed a resistant (R) Polypogon fugax population showing resistance to quizalofop-p-ethyl, acetolactate synthase (ALS)-inhibiting herbicide pyroxsulam, and several other ACCase (acetyl-CoA carboxylase)-inhibiting herbicides. Molecular analysis revealed no target-site gene mutations in the R population. Foliar spraying with malathion clearly reversed the quizalofop-p-ethyl phytotoxicity. Higher level of quizalofop-p-ethyl degradation was confirmed in the R population using HPLC analysis. Subsequently, RNA-Seq transcriptome analysis indicated that the overexpression of CYP89A2 gene appeared to be responsible for reducing quizalofop-p-ethyl phytotoxicity. The molecular docking results supported a metabolic effect of CYP89A2 protein on most herbicides tested. Furthermore, we found that low doses of herbicides stimulated the rhizosphere enzyme activities in P. fugax and the increase of rhizosphere dehydrogenase of R population may be related to its resistance mechanism. In summary, our research has shown that metabolic herbicide resistance mediated by CYP89A2, contributes to quizalofop-p-ethyl resistance in P. fugax.

Differential effects of arsenite and arsenate on rice (Oryza sativa) plants differing in glutathione S-transferase gene expression

Contamination of paddy soils with arsenic (As) can cause phytotoxicity in rice and increase the accumulation of arsenic in grains. The uptake and accumulation of As in rice depends on the different As species present in the soil. Plants detoxify As by conjugating and sequestering xenobiotic compounds into vacuoles using various enzymes. However, the severity of damage induced by arsenite (As(III)) and arsenate (As(V)), as well as the roles of glutathione S-transferase in detoxifying these As species in rice, are not fully understood. In this study, we developed plant materials overexpressing a glutathione S-transferase gene OsGSTU40 under the control of the maize UBIL promoter. Through systematic investigations of both wild-type Nipponbare (Oryza sativa L., ssp. japonica) and OsGSTU40 overexpression lines under chronic or acute stress of As, we aimed to understand the toxic effects of both As(III) and As(V) on rice plants at the vegetative growth stage. We hypothesized that (i) As(III) and As(V) have different toxic effects on rice plants and (ii) OsGSTU40 played positive roles in As toxicity tolerance. Our results showed that As(III) was more detrimental to plant growth than As(V) in terms of plant growth, biomass, and lipid peroxidation in both chronic and acute exposure. Furthermore, overexpression of OsGSTU40 led to better plant growth even though uptake of As(V), but not As(III), into shoots was enhanced in transgenic plants. In acute As(III) stress, transgenic plants exhibited a lower level of lipid peroxidation than wild-type plants. The element composition of plants was dominated by the different As stress treatments rather than by the genotype, while the As concentration was negatively correlated with phosphorus and silicon. Overall, our findings suggest that As(III) is more toxic to plants than As(V) and that glutathione S-transferase OsGSTU40 differentially affects plant reactions and tolerance to different species of arsenic.

Clean-Up of Heavy Metals from Contaminated Soil by Phytoremediation: A Multidisciplinary and Eco-Friendly Approach

Pollution from heavy metals is one of the significant environmental concerns facing the world today. Human activities, such as mining, farming, and manufacturing plant operations, can allow them access to the environment. Heavy metals polluting soil can harm crops, change the food chain, and endanger human health. Thus, the overarching goal for humans and the environment should be the avoidance of soil contamination by heavy metals. Heavy metals persistently present in the soil can be absorbed by plant tissues, enter the biosphere, and accumulate in the trophic levels of the food chain. The removal of heavy metals from contaminated soil can be accomplished using various physical, synthetic, and natural remediation techniques (both in situ and ex situ). The most controllable (affordable and eco-friendly) method among these is phytoremediation. The removal of heavy metal defilements can be accomplished using phytoremediation techniques, including phytoextraction, phytovolatilization, phytostabilization, and phytofiltration. The bioavailability of heavy metals in soil and the biomass of plants are the two main factors affecting how effectively phytoremediation works. The focus in phytoremediation and phytomining is on new metal hyperaccumulators with high efficiency. Subsequently, this study comprehensively examines different frameworks and biotechnological techniques available for eliminating heavy metals according to environmental guidelines, underscoring the difficulties and limitations of phytoremediation and its potential application in the clean-up of other harmful pollutants. Additionally, we share in-depth experience of safe removing the plants used in phytoremediation-a factor frequently overlooked when choosing plants to remove heavy metals in contaminated conditions.

Transcriptome analysis reveals insight into the protective effect of N-acetylcysteine against cadmium toxicity in Ganoderma lucidum (Polyporales: Polyporaceae)

Ganoderma lucidum is widely cultivated and used as traditional medicine in China and other Asian countries. As a member of macrofungi, Ganoderma lucidum is also prone to bioaccumulation of cadmium and other heavy metals in a polluted environment, which affects the growth and production of Ganoderma lucidum, as well as human health. N-Acetyl-L-cysteine (NAC) is considered a general antioxidant and free radical scavenger that is involved in the regulation of various stress responses in plants and animals. However, whether NAC could regulate cadmium stress responses in macrofungi, particularly edible fungi, is still unknown. In this work, we found that the exogenous NAC could alleviate Cd-induced growth inhibition and reduce the cadmium accumulation in Ganoderma lucidum. The application of the NAC cloud also inhibit cadmium-induced H₂O₂ production in the mycelia. By using transcriptome analysis, 2920 and 1046 differentially expressed unigenes were identified in "Cd100 vs CK" and "NAC_Cd100 vs Cd100," respectively. These differential unigenes were classified into a set of functional categories and pathways, which indicated that various biological pathways may play critical roles in the protective effect of NAC against Cd‑induced toxicity in Ganoderma lucidum. Furthermore, it suggested that the ATP-binding cassette transporter, ZIP transporter, heat shock protein, glutathione transferases, and Cytochrome P450 genes contributed to the increased tolerance to cadmium stress after NAC application in Ganoderma lucidum. These results provide new insight into the physiological and molecular response of Ganoderma lucidum to cadmium stress and the protective role of NAC against cadmium toxicity.

Transcriptome analysis of the toxicity response of green macroalga Caulerpa lentillifera J. Agardh to high dissolved arsenite

Arsenic (As) is a hazardous pollutant that negatively impacts the physiological functions of alga. So far, a detailed understanding of algal response to As stress is still lacking. In this study, a transcriptome analysis was performed to illustrate the toxicity response of Caulerpa lentillifera J. Agardh, an edible algae with rich nutrition, to arsenite [As(III)], a toxic form of As. Totally, 1913 differentially expressed genes (DEGs) were screened, of which 642 were up- and 1271 were downregulated in C. lentillifera under As(III) stress (30 mg·L^-1) compared with control. As(III) stress promoted the growth of C. lentillifera at low concentration (0.1 mg·L^-1) and inhibited the growth at high concentration (≥ 0.5 mg·L^-1). Multiple DEGs involved in oxidoreductase activities were significantly affected by As(III), and several DEGs related to antioxidant enzyme activity were downregulated, resulting in suffering from oxidative stress in C. lentillifera. Results also showed that As(III) stress inhibited chlorophyll and carotenoid synthesis, destroyed the integrity of chloroplasts, and interfered with the absorption of light energy, thereby inhibiting photosynthesis in C. lentillifera. The highly enriched ABC transporter-related genes involved in the detoxification process were upregulated under As(III) stress, indicating their critical role in the resistance to As stress in C. lentillifera. The gene expressions for 10 selected DEGs were confirmed by qRT-PCR, showing the reliability of the data revealed by RNA sequencing. Our novel work illustrated the toxicity of C. lentillifera under As(III) stress at the molecular level, serving as a basis for future investigations on the prevention and treatment of such pollutants.

A Novel Reference for Bt-Resistance Mechanism in Plutella xylostella Based on Analysis of the Midgut Transcriptomes

Simple Summary

Plutella xylostella is a very serious pest to cruciferous vegetables. At present, the control methods used are mainly traditional insecticides and the cultivation of Bt crops. However, with the long-term and large-scale use of insecticides, the diamondback moth has developed strong resistance to many kinds of insecticides and Bt crops. The Cry1S1000 strain of P. xylostella used here is a strain with more than 8000 times resistance to Bt Cry1Ac protoxin. In this paper, we used transcriptome sequencing to determine the midgut transcriptome of the G88-susceptible strain, Cry1S1000-resistant strain and its corresponding toxin-induced strains to find more genes related to Bt resistance. Our results will provide a reference for optimizing the control strategy of diamondback moth resistance and improving the control efficiency of biopesticides and Bt crops.

Abstract

The diamondback moth, Plutella xylostella, is a lepidopteran insect that mainly harms cruciferous vegetables, with strong resistance to a variety of agrochemicals, including Bacillus thuringiensis (Bt) toxins. This study intended to screen genes associated with Bt resistance in P. xylostella by comparing the midgut transcriptome of Cry1Ac-susceptible and -resistant strains together with two toxin-treated strains 24 h before sampling. A total of 12 samples were analyzed by BGISEQ-500, and each sample obtained an average of 6.35 Gb data. Additionally, 3284 differentially expressed genes (DEGs) were identified in susceptible and resistant strains. Among them, five DEGs for cadherin, 14 for aminopeptidase, zero for alkaline phosphatase, 14 for ATP binding cassette transport, and five heat shock proteins were potentially involved in resistance to Cry1Ac in P. xylostella. Furthermore, DEGs associated with “binding”, “catalytic activity”, “cellular process”, “metabolic process”, and “cellular anatomical entity” were more likely to be responsible for resistance to Bt toxin. Thus, together with other omics data, our results will offer prospective genes for the development of Bt resistance, thereby providing a brand new reference for revealing the resistance mechanism to Bt of P. xylostella.

Do the herbicides pinoxaden, tribenuron-methyl, and pyroxsulam influence wheat (Triticum aestivum L.) physiological parameters?

Herbicides reduce the unsafe effects of weeds, but they are likely to have negative impact on essential and secondary metabolism in crops. However, the combined effect of different herbicides on chemical constituents of different varieties of wheat is still not fully obvious. The current investigation was carried out to determine the effects of three post-emergence herbicides (pinoxaden, tribenuron-methyl, and pyroxsulam) on total protein, lipid, and carbohydrate concentrations of three bread wheat cultivars (Misr 1, Giza 171, and Gemmiza 11). These herbicides were added individually and in combinations at recommended and/or half recommended doses. Our findings revealed that the individual application of herbicides decreased total protein and total lipid concentrations in fresh shoots of the three studied wheat cultivars, but increased total carbohydrate concentration. Combined addition of herbicides at recommended and half recommended doses generally decreased the concentrations of total proteins, total lipids, and total carbohydrates. However, the combined addition of tribenuron-methyl and pinoxaden at recommended dose enhanced total protein and total lipid concentrations under Misr1 and Gemmiza 11 cultivars compared to control treatment. Furthermore, the combined addition of tribenuron-methyl and pyroxsulam at half recommended dose enhanced total protein concentration in Giza 171 up to 15.05% and Gemmiza 11 up to 15.09% cultivars, and total lipid concentration in Misr 1 (7.53%) and Giza 171 (9.81%) cultivars against control treatment, where it was the lowest. Total carbohydrate concentration was enhanced by the sole application of pinoxaden by 53.55%, 52.40%, and 51.79% for Misr 1, Giza 171, and Gemmiza 11 cultivars, respectively. Moreover, individual or combined additions of the studied pesticides at recommended and half recommended doses negatively affected wheat grains under all cultivars via decreasing their concentration of nutrients (nitrogen, phosphorus, and potassium) as well as total protein and total carbohydrates. The highest reduction of nitrogen, phosphorus, and potassium concentrations compared to control was observed when tribenuron-methyl+pyroxsulam was applied at the half recommended dose under the three studied cultivars. However, the combined application of tribenuron-methyl+pyroxsulam at the half recommended dose caused the great depression in total proteins and total carbohydrates of wheat grains. Under the stress effect of herbicides, individual application of pinoxaden gave the best results for nitrogen and potassium content as well as total protein and total carbohydrate concentrations in the three studied wheat grain cultivars.

Biochemical and phytoremediation of Plantago major L. to protect tomato plants from the contamination of cypermethrin pesticide

Phytoremediation is an environmentally friendly therapy to minimize soil pollution. Cypermethrin (CYP) is one of the most frequently used pyrethroid insecticides against a variety of pests. We aimed at evaluating the potential of using an economic plant like tomato (Solanum lycopersicum L.) as a control alone and together with Plantago major L. (PM) for the uptake of CYP residue from contaminated soil, also, investigating the antioxidant enzymes such as (SOD, POD, and CAT) in roots of PM and tomato. For the first time, we studied the intercropping between PM on tomato plants for the uptake of CYP residue from contaminated soil and phytoremediation of PM as a curative plant to save tomato plants from CYP residue. In a pot experiment, we have cultivated PM and tomato in soil polluted with CYP (10 μg g-1). Data showed that PM and tomato accumulated significant amounts of CYP in their tissues. However, PM is better than tomato in uptake CYP from the soil. The longest half-life value (t1/2) of CYP was in PM + tomato together treatment (12.7 days), and the shortest was in the soil with tomato alone (6.81 days). Moreover, the activity of SOD, POD, and CAT in treated tomato and PM roots significantly (p > 0.05) exceeded control plants after 8 days from exposure. In this study, a good strategy was recommended to uptake CYP residue from soil by PM and protect tomato plants from CYP residue as well as safe for human and non-target organisms.

Electrophoretic banding patterns of protein induced by pinoxaden, tribenuron-methyl, and pyroxsulam herbicides in wheat leaves (Triticum aestivum L.)

Herbicides are the most effective tool against weed flora in cereal crops that help to maintain and increase crop yields. This investigation was conducted in the winter season of 2018 to study the stress effect of three post-emergence herbicides including pinoxaden, tribenuron-methyl, and pyroxsulam on the biochemical changes at the molecular cell level of wheat. These herbicides were applied either lonely with a rate of 0.45 L.ha^-1, 22.5 gm.ha^-1, and 0.16 Ib a.i/A, respectively, or in combinations together on three Egyptian varieties of bread wheat known as Misr 1, Giza17 1, and Gemmiza 11. Firstly, the abovementioned herbicides were used at the recommended and half recommended doses with their combinations for these varieties to investigate DNA-protein linkage as a signal effect of herbicides at the molecular cell level.Our data showed that the treatment of wheat varieties with the tested herbicides induced new bands with low and high molecular weights of 37.49, 40.08, 146.55, and 147.23 KDa with relative mobility of 0.1574, 0.1603, 0.2166, and 0.2168, respectively. These bands were not presented in the control treatment, suggesting that it might be used as a biochemical marker for plant defense genes. Meanwhile, the control treatment exhibited only five or six bands in the three varieties. However, the tested varieties showed that the same number of bands, the molecular weights of bands, and their relative mobility were significantly varied between the single and the combinations treatment of herbicides. The best treatment was achieved by the combination between pinoxaden and tribenuron-methyl at a recommended dose which induced a large number of protein bands compared to the control treatment on the wheat variety cv. Misr 1, which gave one band with low molecular weight 71.44 KDa at R_f 0.1854 and other with the highest molecular weight 147.23 KDa at R_f 0.2168, compared to the control treatment.

Novel Transcriptome Study and Detection of Metabolic Variations in UV-B-Treated Date Palm (Phoenix dactylifera cv. Khalas)

Date palm (Phoenix dactylifera) is one of the most widespread fruit crop species and can tolerate drastic environmental conditions that may not be suitable for other fruit species. Excess UV-B stress is one of the greatest concerns for date palm trees and can cause genotoxic effects. Date palm responds to UV-B irradiation through increased DEG expression levels and elaborates upon regulatory metabolic mechanisms that assist the plants in adjusting to this exertion. Sixty-day-old Khalas date palm seedlings (first true-leaf stage) were treated with UV-B (wavelength, 253.7 nm; intensity, 75 μW cm-2 for 72 h (16 h of UV light and 8 h of darkness). Transcriptome analysis revealed 10,249 and 12,426 genes whose expressions were upregulated and downregulated, respectively, compared to the genes in the control. Furthermore, the differentially expressed genes included transcription factor-encoding genes and chloroplast- and photosystem-related genes. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to detect metabolite variations. Fifty metabolites, including amino acids and flavonoids, showed changes in levels after UV-B excess. Amino acid metabolism was changed by UV-B irradiation, and some amino acids interacted with precursors of different pathways that were used to synthesize secondary metabolites, i.e., flavonoids and phenylpropanoids. The metabolite content response to UV-B irradiation according to hierarchical clustering analysis showed changes in amino acids and flavonoids compared with those of the control. Amino acids might increase the function of scavengers of reactive oxygen species by synthesizing flavonoids that increase in response to UV-B treatment. This study enriches the annotated date palm unigene sequences and enhances the understanding of the mechanisms underlying UV-B stress through genetic manipulation. Moreover, this study provides a sequence resource for genetic, genomic and metabolic studies of date palm.

Plantago media L.-Explored and Potential Applications of an Underutilized Plant

The search of valuable natural compounds should be directed towards alternative vegetal resources, and to the re-discovery of underutilized plants. Belonging to the Plantaginaceae family, the hoary plantain (Plantago media L.) represents one of the lesser studied species from the Plantago genus. The literature study revealed the under-utilization of the hoary plantain, a surprising aspect, considering its widespread. If the composition of Plantago media L. is rather well established, its applications are not nearly studied as for other Plantago species. The goal of the present paper is to summarize the findings regarding the applications of P. media, and, having as starting point the applications of related species, to propose new emerging areas of research, such as the biomedical applications validation through in vivo assays, and the evaluation of its potential towards industrial applications (i.e., development of food or personal care products), pisciculture or zootechny, phytoremediation and other environmental protection applications, or in the nanotechnology area (materials phytosynthesis). The present work constitutes not only a brief presentation of this plant's present and potential applications, but also an invitation to research groups world-wide to explore the available vegetal resources.