Detoxification of polycyclic aromatic hydrocarbons (PAHs) in Arabidopsis thaliana involves a putative flavonol synthase

Phenanthrene-Induced Cytochrome P450 Genes and Phenanthrene Tolerance Associated with Arabidopsis thaliana CYP75B1 Gene

Polycyclic aromatic hydrocarbons (PAHs) form an important group of organic pollutants due to their distribution in the environment and their carcinogenic and/or mutagenic effects. In order to identify at the molecular level some of the players in the biodegradation and tolerance response to PAHs in plants, we have phenotyped 32 Arabidopsis thaliana T-DNA mutant lines corresponding to 16 cytochrome P450 (CYP) genes that showed to be differentially expressed under contrasted stress conditions induced by phenanthrene, a 3-ring PAH. This screening has allowed us to identify CYP75B1 (At5g07990) T-DNA mutants as the only ones being sensitive to phenanthrene-induced stress, supporting that CYP75B1 protein is necessary for PAH tolerance. CYP75B1 codes for a 3'flavonol hydroxylase. CYP75B1 gene was heterologously expressed on yeast in order to investigate whether it affects the A. thaliana response to phenanthrene by participating in its metabolization. Heterologously-produced CYP75B1 enzyme shows to be catalytically efficient against its physiological substrates (e.g., naringenin) but unable to metabolize phenanthrene or 9-phenanthrenol. In contrast, CYP75B1 seems rather involved in phenanthrene tolerance as a crucial element by regulating concentration of antioxidants through the production of 3'-hydroxylated flavonoids such as quercetin and cyanidin. In particular, we report a highly increased generation of reactive oxygen species (H2O2 and singlet oxygen) in cyp75b1 mutants compared to control plants in response to phenanthrene treatment. Overall, CYP75B1 shows to play an important role in the response to the deleterious effects of phenanthrene exposure and this is related to oxidative stress sensitivity rather than metabolization.

Co-pyrolysis of chicken manure with tree bark for reduced biochar toxicity and enhanced plant growth in Arabidopsis thaliana

Co-pyrolysis of chicken manure with tree bark was investigated to mitigate salinity and potentially toxic element (PTE) concentrations of chicken manure-derived biochar. The effect of tree bark addition (0, 25, 50, 75 and 100 wt%) on the biochar composition, surface functional groups, PTEs and polycyclic aromatic hydrocarbons (PAH) concentration in the biochar was evaluated. Biochar-induced toxicity was assessed using an in-house plant growth assay with Arabidopsis thaliana. This study shows that PTE concentrations can be controlled through co-pyrolysis. More than 50 wt% of tree bark must be added to chicken manure to reduce the concentrations below the European Biochar Certificate-AGRO (EBC-AGRO) threshold. However, the amount of PAH does not show a trend with tree bark addition. Furthermore, co-pyrolysis biochar promotes plant growth at different application concentrations, whereas pure application of 100 wt% tree bark or chicken manure biochar results in decreased growth compared to the reference. In addition, increased plant stress was observed for 100 wt% chicken manure biochar. These data indicate that co-pyrolysis of chicken manure and tree bark produces EBC-AGRO-compliant biochar with the potential to stimulate plant growth. Further studies need to assess the effect of these biochars in long-term growth experiments.

Ectopic expression of an Old Yellow Enzyme (OYE3) gene from Saccharomyces cerevisiae increases the tolerance and phytoremediation of 2-nitroaniline in rice

2-nitroaniline (2-NA) is an environmental pollutant and has been extensively used as intermediates in organic synthesis. The presence of 2-NA in the environment is not only harmful for aquatic life but also mutagenic for human beings. In this study, we constructed transgenic rice expressing an Old Yellow Enzyme gene, ScOYE3, from Saccharomyces cerevisiae. The ScOYE3 transgenic plants were comprehensively investigated for their biochemical responses to 2-NA treatment and their 2-NA phytoremediation capabilities. Our results showed that the rice seedlings exposed to 2-NA stress, showed growth inhibition and biomass reduction. However, the transgenic plants exhibited strong tolerance to 2-NA stress compared to wild-type plants. Ectopic expression of ScOYE3 could effectively protect transgenic plants against 2-NA damage, which resulted in less reactive oxygen species accumulation in transgenic plants than that in wild-type plants. Our phytoremediation assay revealed that transgenic plants could eliminate more 2-NA from the medium than wild-type plants. Moreover, omics analysis was performed in order to get a deeper insight into the mechanism of ScOYE3-mediated 2-NA transformation in rice. Altogether, the function of ScOYE3 during 2-NA detoxification was characterized for the first time, which serves as strong theoretical support for the phytoremediation potential of 2-NA by Old Yellow Enzyme genes.

Phenanthrene metabolism in Panicum miliaceum: anatomical adaptations, degradation pathway, and computational analysis of a dioxygenase enzyme

Polycyclic aromatic compounds (PAHs) are persistent organic pollutants of environmental concern due to their potential impacts on food chain, with plants being particularly vulnerable. While plants can uptake, transport, and transform PAHs, the precise mechanisms underlying their localization and degradation are not fully understood. Here, a cultivation experiment conducted with Panicum miliaceum exposed different concentrations of phenanthrene (PHE). Intermediate PHE degradation compounds were identified via GC-MS analysis, leading to the proposal of a phytodegradation pathway featuring three significant benzene ring cleavage steps. Our results showed that P. miliaceum exhibited the ability to effectively degrade high levels of PHE, resulting in the production of various intermediate products through several chemical changes. Examination of the localization and anatomical characteristics revealed structural alterations linked to PHE stress, with an observed enhancement in PHE accumulation density in both roots and shoots as treatment levels increased. Following a 2-week aging period, a decrease in the amount of PHE accumulation was observed, along with a change in its localization. Bioinformatics analysis of the P. miliaceum 2-oxoglutarate-dependent dioxygenase (2-ODD) DAO-like protein revealed a 299 amino acid structure with two highly conserved domains, namely 2OG-FeII_Oxy and DIOX_N. Molecular docking analysis aligned with experimental results, strongly affirming the potential link and direct action of 2-ODD DAO-like protein with PHE. Our study highlights P. miliaceum capacity for PAHs degradation and elucidates the mechanisms behind enhanced degradation efficiency. By integrating experimental evidence with bioinformatics analysis, we offer valuable insights into the potential applications of plant-based remediation strategies for PAHs-contaminated environments.

Nitro-PAHs: Occurrences, ecological consequences, and remediation strategies for environmental restoration

Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) are persistent pollutants that have been introduced into the environment as a result of human activities. They are produced when PAHs undergo oxidation and are highly resistant to degradation, resulting in prolonged exposure and significant health risks for wildlife and humans. Nitro-PAHs' potential to induce cancer and mutations has raised concerns about their harmful effects. Furthermore, their ability to accumulate in the food chain seriously threatens the ecosystem and human health. Moreover, nitro-PAHs can disrupt the normal functioning of the endocrine system, leading to reproductive and developmental problems in humans and other organisms. Reducing nitro-PAHs in the environment through source management, physical removal, and chemical treatment is essential to mitigate the associated environmental and human health risks. Recent studies have focused on improving nitro-PAHs' phytoremediation by incorporating microorganisms and biostimulants. Microbes can break down nitro-PAHs into less harmful substances, while biostimulants can enhance plant growth and metabolic activity. By combining these elements, the effectiveness of phytoremediation for nitro-PAHs can be increased. This study aimed to investigate the impact of introducing microbial and biostimulant agents on the phytoremediation process for nitro-PAHs and identify potential solutions for addressing the environmental risks associated with these pollutants.

Polycyclic aromatic hydrocarbon (PAH) accumulation in selected medicinal plants: a mini review

The use of plant-based products in healthcare systems has experienced a tremendous rise leading to a substantial increase in global demand. However, the quality and effectiveness of such plant-based treatments are often affected due to contamination of various pollutants including polycyclic aromatic hydrocarbons (PAHs). Like other plants, medicinal plants also uptake and accumulate PAHs when exposed to a contaminated environment. The consumption of such medicinal plants and/or plant-based products causes negative effects on health rather than providing any therapeutic advantages. Unfortunately, research focusing on PAH accumulation in medicinal plants has received very limited attention. This review discusses a sizable number of literature regarding the concentration of sixteen priority PAH pollutants as recognised by the US Environmental Protection Agency (USEPA) in different medicinal plants. The review also highlights the risk assessment of cancer associated with some medicinal plants in terms of benzo[a]pyrene (BaP) equivalent concentrations.

Mechanism of synergistic remediation of soil phenanthrene contamination in paddy fields by rice-crab coculture and bioaugmentation with Pseudomonas sp

Polycyclic aromatic hydrocarbons (PAHs) are persistent and harmful pollutants with high priority concern in agricultural fields. This work constructed a rice-crab coculture and bioaugmentation (RCM) system to remediate phenanthrene (a model PAH) contamination in rice fields. The results showed that RCM had a higher remediation performance of phenanthrene in rice paddy compared with rice cultivation alone, microbial addition alone, and crab-rice coculture, reaching a remediation efficiency of 88.92 % in 42 d. The concentration of phenanthrene in the rice plants decreased to 6.58 mg/kg, and its bioconcentration effect was efficiently inhibited in the RCM system. In addition, some low molecular weight organic acids of rice root increased by 12.87 %∼73.87 %, and some amino acids increased by 140 %∼1150 % in RCM. Bioturbation of crabs improves soil aeration structure and microbial migration, and adding Pseudomonas promoted the proliferation of some plant growth-promoting rhizobacteria (PGPRs), which facilitated the degradation of phenanthrene. This coupling rice-crab coculture with bioaugmentation had favorable effects on soil enzyme activity, microbial community structure, and PAH degradation genes in paddy fields, enhancing the removal of and resistance to PAH contamination in paddy fields and providing new strategies for achieving a balance between production and remediation in contaminated paddy fields.

Microbiome based approaches for the degradation of polycyclic aromatic hydrocarbons (PAHs): A current perception

Globally, polycyclic aromatic hydrocarbons (PAHs) pollution is primarily driven by their release into the air through various combustion processes, including burning fossil fuels such as coal, oil, and gas in motor vehicles, power plants, and industries, as well as burning organic matter like wood, tobacco, and food in fireplaces, cigarettes, and grills. Apart from anthropogenic pollution sources, PAHs also occur naturally in crude oil, and their potential release during oil extraction, refining processes, and combustion further contributes to contamination and pollution concerns. PAHs are resistant and persistent in the environment because of their inherent features, viz., heterocyclic aromatic ring configurations, hydrophobicity, and thermostability. A wide range of microorganisms have been found to be effective degraders of these recalcitrant contaminants. The presence of hydrocarbons as a result of numerous anthropogenic activities is one of the primary environmental concerns. PAHs are found in soil, water, and the air, making them ubiquitous in nature. The presence of PAHs in the environment creates a problem, as their presence has a detrimental effect on humans and animals. For a variety of life forms, PAH pollutants are reported to be toxic, carcinogenic, mutation-inducing, teratogenic, and immune toxicogenics. Degradation of PAHs via biological activity is an extensively used approach in which diverse microorganisms (fungal, algal, clitellate, and protozoan) and plant species and their derived composites are utilized as biocatalysts and biosurfactants. Some microbes have the ability to transform and degrade these PAHs, allowing them to be removed from the environment. The goal of this review is to provide a critical overview of the existing understanding of PAH biodegradation. It also examines current advances in diverse methodologies for PAH degradation in order to shed light on fundamental challenges and future potential.

Molecular Defensive Mechanism of Echinacea purpurea (L.) Moench against PAH Contaminations

The understanding of the molecular defensive mechanism of Echinacea purpurea (L.) Moench against polycyclic aromatic hydrocarbon (PAH) contamination plays a key role in the further improvement of phytoremediation efficiency. Here, the responses of E. purpurea to a defined mixture of phenanthrene (PHE) and pyrene (PYR) at different concentrations or a natural mixture from an oilfield site with a history of several decades were studied based on transcriptomics sequencing and widely targeted metabolomics approaches. The results showed that upon 60-day PAH exposure, the growth of E. purpurea in terms of biomass (p < 0.01) and leaf area per plant (p < 0.05) was negatively correlated with total PAH concentration and significantly reduced at high PAH level. The majority of genes were switched on and metabolites were accumulated after exposure to PHE + PYR, but a larger set of genes (3964) or metabolites (208) showed a response to a natural PAH mixture in E. purpurea. The expression of genes involved in the pathways, such as chlorophyll cycle and degradation, circadian rhythm, jasmonic acid signaling, and starch and sucrose metabolism, was remarkably regulated, enhancing the ability of E. purpurea to adapt to PAH exposure. Tightly associated with transcriptional regulation, metabolites mainly including sugars and secondary metabolites, especially those produced via the phenylpropanoid pathway, such as coumarins, flavonoids, and their derivatives, were increased to fortify the adaptation of E. purpurea to PAH contamination. These results suggest that E. purpurea has a positive defense mechanism against PAHs, which opens new avenues for the research of phytoremediation mechanism and improvement of phytoremediation efficiency via a mechanism-based strategy.

Physiological and Biochemical Responses of Solanum lycopersicum L. to Benzo[a]pyrene Contaminated Soils

Benzo[a]pyrene (BaP) is noted as one of the main cancer-causing pollutants in human beings and may damage the development of crop plants. The present work was designed to explore more insights into the toxic effects of BaP on Solanum lycopersicum L. at various doses (20, 40, and 60 MPC) spiked in Haplic Chernozem. A dose-dependent response in phytotoxicity were noted, especially in the biomass of the roots and shoots, at doses of 40 and 60 MPC BaP and the accumulation of BaP in S. lycopersicum tissues. Physiological and biochemical response indices were severely damaged based on applied doses of BaP. During the histochemical analysis of the localization of superoxide in the leaves of S. lycopersicum, formazan spots were detected in the area near the leaf's veins. The results of a significant increase in malondialdehyde (MDA) from 2.7 to 5.1 times, proline 1.12- to 2.62-folds, however, a decrease in catalase (CAT) activity was recorded by 1.8 to 1.1 times. The activity of superoxide dismutase (SOD) increased from 1.4 to 2, peroxidase (PRX) from 2.3 to 5.25, ascorbate peroxidase (APOX) by 5.8 to 11.5, glutathione peroxidase (GP) from 3.8 to 7 times, respectively. The structure of the tissues of the roots and leaves of S. lycopersicum in the variants with BaP changed depending on the dose: it increased the intercellular space, cortical layer, and the epidermis, and the structure of the leaf tissues became looser.

Transcription Factor AtOFP1 Involved in ABA-Mediated Seed Germination and Root Growth through Modulation of ROS Homeostasis in Arabidopsis

Ovate family proteins (OFPs) are valued as a family of transcription factors that are unique to plants, and they play a pluripotent regulatory role in plant growth and development, including secondary-cell-wall synthesis, DNA repair, gibberellin synthesis, and other biological processes, via their interaction with TALE family proteins. In this study, CHIP-SEQ was used to detect the potential target genes of AtOFP1 and its signal-regulation pathways. On the other hand, Y2H and BIFC were employed to prove that AtOFP1 can participate in ABA signal transduction by interacting with one of the TALE family protein called AtKNAT3. ABA response genes are not only significantly upregulated in the 35S::HAOFP1 OE line, but they also show hypersensitivity to ABA in terms of seed germination and early seedling root elongation. In addition, the AtOFP1-regulated target genes are mainly mitochondrial membranes that are involved in the oxidative–phosphorylation pathway. Further qRT-PCR results showed that the inefficient splicing of the respiratory complex I subunit genes NAD4 and NAD7 may lead to ROS accumulation in 35S::HA-AtOFP1 OE lines. In conclusion, we speculated that the overexpression of AtOFP1 may cause the ABA hypersensitivity response by increasing the intracellular ROS content generated from damage to the intima systems of mitochondria.

Pyrene remediation by Trametes maxima: an insight into secretome response and degradation pathway

The rapid pace of economic development has resulted in the release of several polycyclic aromatic hydrocarbons (PAHs) into the environment. Microbial degradation using white-rot fungi is a promising method for the removal of PAHs from the environment. In the present study, biodegradation of recalcitrant PAH by a white-rot fungus, Trametes maxima IIPLC-32, was investigated using pyrene. The pyrene concentration decreased by 79.80%, 65.37%, and 56.37% within 16 days from the initial levels of 10 mg L^-1, 25 mg L^-1, and 50 mg L^-1, respectively. Gas chromatographic-mass spectrometric identification of prominent metabolites 1-hydroxypyrene, 2-methyl-1-naphthyl acetic acid, di-n-butyl phthalate, and diethyl phthalate helped in determining the pyrene degradation pathway. The presence of 81 extracellular proteins was revealed by secretome analysis. The identified proteins up-regulated in response to pyrene degradation were classified into detoxification proteins (6.12%), redox proteins (6.12%), stress proteins (4.08%), metabolic-related proteins (26.53%), translation and transcriptional proteins (49%), catalytic proteins (49%), and other proteins (8.16%). Knowledge of secretome analysis in pyrene degradation helped to understand the degradation mechanism of pyrene. Also, the study suggests that T. maxima IIPLC-32 has the potential to be used in the bioremediation of PAH contaminated aquatic environment.

Heat stress leads to rapid lipid remodeling and transcriptional adaptations in Nicotiana tabacum pollen tubes

After reaching the stigma, pollen grains germinate and form a pollen tube that transports the sperm cells to the ovule. Due to selection pressure between pollen tubes, pollen grains likely evolved mechanisms to quickly adapt to temperature changes to sustain elongation at the highest possible rate. We investigated these adaptions in tobacco (Nicotiana tabacum) pollen tubes grown in vitro under 22°C and 37°C by a multi-omics approach including lipidomic, metabolomic, and transcriptomic analysis. Both glycerophospholipids and galactoglycerolipids increased in saturated acyl chains under heat stress (HS), while triacylglycerols (TGs) changed less in respect to desaturation but increased in abundance. Free sterol composition was altered, and sterol ester levels decreased. The levels of sterylglycosides and several sphingolipid classes and species were augmented. Most amino acid levels increased during HS, including the noncodogenic amino acids γ-amino butyrate and pipecolate. Furthermore, the sugars sedoheptulose and sucrose showed higher levels. Also, the transcriptome underwent pronounced changes with 1,570 of 24,013 genes being differentially upregulated and 813 being downregulated. Transcripts coding for heat shock proteins and many transcriptional regulators were most strongly upregulated but also transcripts that have so far not been linked to HS. Transcripts involved in TG synthesis increased, while the modulation of acyl chain desaturation seemed not to be transcriptionally controlled, indicating other means of regulation. In conclusion, we show that tobacco pollen tubes are able to rapidly remodel their lipidome under HS likely by post-transcriptional and/or post-translational regulation.

Transcriptomic analyses reveal increased expression of dioxygenases, monooxygenases, and other metabolizing enzymes involved in anthracene degradation in the marine alga Ulva lactuca

To analyze the mechanisms involved in anthracene (ANT) degradation in the marine alga Ulva lactuca, total RNA was obtained from the alga cultivated without ANT and with 5 μM of ANT for 24 h, and transcriptomic analyses were performed. A de novo transcriptome was assembled, transcripts differentially expressed were selected, and those overexpressed were identified. Overexpressed transcripts potentially involved in ANT degradation were: one aromatic ring dioxygenase, three 2-oxoglutarate Fe (II) dioxygenases (2-OGDOs), and three dienelactone hydrolases that may account for anthraquinone, phthalic anhydride, salicylic acid, and phthalic acid production (pathway 1). In addition, two flavin adenine dinucleotide (FAD)-dependent monooxygenases, four cytP450 monooxygenases, two epoxide hydrolase, one hydroxyphenylpyruvic acid dioxygenase (HPPDO), and two homogentisic acid dioxygenases (HGDOs) were identified that may also participate in ANT degradation (pathway 2). Moreover, an alkane monooxygenase (alkB), two alcohol dehydrogenases, and three aldehyde dehydrogenases were identified, which may participate in linear hydrocarbon degradation (pathway 3). Furthermore, the level of transcripts encoding some of mentioned enzymes were quantified by qRT-PCR are in the alga cultivated with 5 μM of ANT for 0-48 h, and those more increased were 2-OGDO, HGDO, and alkB monooxygenase. Thus, at least three pathways for ANT and linear hydrocarbons degradation may be existed in U. lactuca. In addition, ANT metabolites were analyzed by gas chromatography and mass spectrometry (GC-MS), allowing the identification of anthraquinone, phthalic anhydride, salicylic acid, and phthalic acid, thus validating the pathway 1.

Detoxification of phenanthrene in Arabidopsis thaliana involves a Dioxygenase For Auxin Oxidation 1 (AtDAO1)

Polycyclic aromatic hydrocarbon (PAH) contamination has a negative impact on ecosystems. PAHs are a large group of toxins with two or more benzene rings that are persistent in the environment. Some PAHs can be cytotoxic, teratogenic, and/or carcinogenic. In the bacterium Pseudomonas, PAHs can be modified by dioxygenases, which increase the reactivity of PAHs. We hypothesize that some plant dioxygenases are capable of PAH biodegradation. Herein, we investigate the involvement of Arabidopsis thaliana At1g14130 in the degradation of phenanthrene, our model PAH. The At1g14130 gene encodes Dioxygenase For Auxin Oxidation 1 (AtDAO1), an enzyme involved in the oxidative inactivation of the hormone auxin. Expression analysis using a β-glucuronidase (GUS) reporter revealed that At1g14130 is prominently expressed in new leaves of plants exposed to media with phenanthrene. Analysis of the oxidative state of gain-of-function mutants showed elevated levels of H₂O₂ after phenanthrene treatments, probably due to an increase in the oxidation of phenanthrene by AtDAO1. Biochemical assays with purified AtDAO1 and phenanthrene suggest an enzymatic activity towards the PAH. Thus, data presented in this study support the hypothesis that an auxin dioxygenase, AtDAO1, from Arabidopsis thaliana contributes to the degradation of phenanthrene and that there is possible toxic metabolite accumulation after PAH exposure.

A 110 Year Sediment Record of Polycyclic Aromatic Hydrocarbons Related to Economic Development and Energy Consumption in Dongping Lake, North China

A sedimentary record of the 16 polycyclic aromatic hydrocarbon (PAH) pollutants from Dongping Lake, north China, is presented in this study. The influence of regional energy structure changes for 2–6-ring PAHs was investigated, in order to assess their sources and the impact of socioeconomic developments on the observed changes in concentration over time. The concentration of the ΣPAH₁₆ ranged from 77.6 to 628.0 ng/g. Prior to the 1970s, the relatively low concentration of ΣPAH₁₆ and the average presence of 44.4% 2,3-ring PAHs indicated that pyrogenic combustion from grass, wood, and coal was the main source of PAHs. The rapid increase in the concentration of 2,3-ring PAHs between the 1970s and 2006 was attributed to the growth of the urban population and the coal consumption, following the implementation of the Reform and Open Policy in 1978. The source apportionment, which was assessed using a positive matrix factorization model, revealed that coal combustion was the most important regional source of PAHs pollution (>51.0%). The PAHs were mainly transported to the site from the surrounding regions by atmospheric deposition rather than direct discharge.

Biochemical and Metabolic Plant Responses toward Polycyclic Aromatic Hydrocarbons and Heavy Metals Present in Atmospheric Pollution

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) are toxic components of atmospheric particles. These pollutants induce a wide variety of responses in plants, leading to tolerance or toxicity. Their effects on plants depend on many different environmental conditions, not only the type and concentration of contaminant, temperature or soil pH, but also on the physiological or genetic status of the plant. The main detoxification process in plants is the accumulation of the contaminant in vacuoles or cell walls. PAHs are normally transformed by enzymatic plant machinery prior to conjugation and immobilization; heavy metals are frequently chelated by some molecules, with glutathione, phytochelatins and metallothioneins being the main players in heavy metal detoxification. Besides these detoxification mechanisms, the presence of contaminants leads to the production of the reactive oxygen species (ROS) and the dynamic of ROS production and detoxification renders different outcomes in different scenarios, from cellular death to the induction of stress resistances. ROS responses have been extensively studied; the complexity of the ROS response and the subsequent cascade of effects on phytohormones and metabolic changes, which depend on local concentrations in different organelles and on the lifetime of each ROS species, allow the plant to modulate its responses to different environmental clues. Basic knowledge of plant responses toward pollutants is key to improving phytoremediation technologies.

Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome-wide association study, QTL-seq and transcriptome sequencing in cotton

Combining GWAS, QTL-seq and transcriptome sequencing detected basal defense-related genes showing gDNA sequence variation and expression difference in diverse cotton lines, which might be the molecular mechanisms of VW resistance in G. hirsutum. Verticillium wilt (VW), which is caused by the soil-borne fungus Verticillium dahliae, is a major disease in cotton (Gossypim hirsutum) worldwide. To facilitate the understanding of the genetic basis for VW resistance in cotton, a genome-wide association study (GWAS), QTL-seq and transcriptome sequencing were performed. The GWAS of VW resistance in a panel of 120 core elite cotton accessions using the Cotton 63K Illumina Infinium SNP array identified 5 QTL from 18 significant SNPs meeting the 5% false discovery rate threshold on 5 chromosomes. All QTL identified through GWAS were found to be overlapped with previously reported QTL. By combining GWAS, QTL-seq and transcriptome sequencing, we identified eight candidate genes showing both gDNA sequence variation and expression difference between resistant and susceptible lines, most related to transcription factors (TFs), flavonoid biosynthesis and those involving in the plant basal defense and broad-spectrum disease resistance. Ten KASP markers were successfully validated in diverse cotton lines and could be deployed in marker-assisted breeding to enhance VW resistance. These results supported our inference that the gDNA sequence variation or expression difference of those genes involving in the basal defense in diverse cotton lines might be the molecular mechanisms of VW resistance in G. hirsutum.

Assessment of oxidative stress response genes in Avicennia marina exposed to oil contamination - Polyphenol oxidase (PPOA) as a biomarker

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Avicennia marina plants tolerate exposure to mild oil contamination in soil and they can survive at higher concentrations.

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Oil contaminated soil induced stronger transcriptional responses in leaves than in roots of A. marina.

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Our suggested biomarker PPOA showed a significant up-regulation in leaves under all tested oil concentrations

Mangrove plants, which inhabit and form sensitive ecosystems in the intertidal zones of tropical and subtropical coastlines, though vulnerable to petroleum pollution, still maintain their growth under oil contamination. To elucidate the molecular response of mangrove plants to crude oil–sediment mixture, seeds of Avicennia marina were planted and grown on 0, 2.5, 5.0, 7.5 and10 % (w/w) oil-contaminated soil. Plant biomass was highly affected from 3.05 ± 0.28 (Control) to 0.50 ± .07 (10 %) and from 3.47 ± 0.12 to 1.88 ± 0.08 in 2 and 4 months old plants respectively. The expression analysis of 11genes belonging to detoxification pathways in the roots and leaves of 2 and 4 month-old plants was evaluated by qRT-PCR. Our results showed changes in expression levels of Fe-SOD, Mn-SOD, CAT, PRX, PPOs, GSTs, and NAP2 whose products are involved in reactive oxygen species (ROS) and xenobiotic detoxification. PPOA showed the highest expression induction of 43 ± 1.15, followed by CAT (12.61 ± 3.25) and PPOB (6.38 ± 1.34) in leaves of 2 months old seedlings grown on 7.5, 10 and 7.5 % oil contaminated soil respectively. PPOA (39.23 ± 2.1), PRX (32.13 ± 1.2) as well as PPOB (26.11 ± 1.3) showed the highest expression induction in leaves of 4 months old plants grown in 2.5 % oil contaminated soil. Our data indicated that PPOA can be a good biomarker candidate gene for long term exposure to oil contamination in A. marina.

Benzopyrene induces oxidative stress and increases expression and activities of antioxidant enzymes, and CYP450 and GST metabolizing enzymes in Ulva lactuca (Chlorophyta)

Benzopyrene is rapidly incorporated and metabolized, and induces oxidative stress and activation of antioxidant enzymes, and CYP450 and GST metabolizing enzymes in Ulva lactuca. To analyze absorption and metabolism of benzo[a]pyrene (BaP) in Ulva lactuca, the alga was cultivated with 5 µM of BaP for 72 h. In the culture medium, BaP level rapidly decreased reaching a minimal level at 12 h and, in the alga, BaP level increased until 6 h, remained stable until 24 h, and decreased until 72 h indicating that BaP is being metabolized in U. lactuca. In addition, BaP induced an initial increase in hydrogen peroxide decreasing until 24 h, superoxide anions level that remained high until 72 h, and lipoperoxides that initially increased and decreased until 72 h, showing that BaP induced oxidative stress. Activities of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (AP), glutathione reductase (GR) and glutathione peroxidase (GP) were increased, whereas dehydroascorbate reductase (DHAR) activity was unchanged. The level of transcripts encoding these antioxidant enzymes was increased, but transcripts encoding DHAR remained unchanged. Interestingly, the activity of glutathione-S-transferase (GST) was also increased, and inhibitors of cytochrome P450 (CYP450) and GST activities enhanced the level of BaP in algal tissue, suggesting that these enzymes participate in BaP metabolism.

Effects of cellulose on polycyclic aromatic hydrocarbons removal and microbial community structure variation during anaerobic digestion of sewage sludge

Waste-activated sludge (WAS) with trace organic pollutants, e.g., polycyclic aromatic hydrocarbons (PAHs), has become an environmental concern. Anaerobic technology is a feasible option for WAS treatment due to its advantages of low-energy consumption and high-energy recovery compared to aerobic technology, but it still has many shortcomings, such as low biogas production and a low organic pollutant removal efficiency. Thus, this study investigated the effects of cellulose on PAHs degradation and microbial community structure variation during anaerobic digestion of sewage sludge. Four semicontinuous experiments were set by adding cellulose to sewage sludge based on the volatile solids (VS) concentration. The proportions of sludge VS to cellulose VS were 1:0 (CK), 1:0.2, 1:0.5 and 1:1. The results showed the following: (1) The biodegradation of 2-ring, 3-ring and 4-ring PAHs was enhanced by cellulose addition, with total PAHs removal efficiencies of 14.82%, 20.75% and 19.35%, respectively. (2) The abundance of bacteria that could degrade PAHs, such as Chloroflexi, Bacteroidetes, Aminicenantes, Planctomycetes and Spirochaeta, was obviously increased by cellulose addition. (3) The abundance of Methanosaeta during sludge anaerobic digestion was apparently increased by cellulose addition. Methanobacterium and Methanolinea appeared after cellulose addition, while they were not observed in the blank experiment.

Molecular mechanisms in phytoremediation of environmental contaminants and prospects of engineered transgenic plants/microbes

Concerns about emerging environmental contaminants have been growing along with industrialization and urbanization around the globe. Among various options for remediating these contaminants, phytotechnology is suggested as a feasible option to maintain the environmental sustainability. The recent advances in phytoremediation, genetic/molecular/omics/metabolic engineering, and nanotechnology are opening new paths for efficient treatment of emerging organic/inorganic contaminants. In this respect, elucidation of molecular mechanisms and genetic engineering of hyperaccumulator plants is expected to enhance remediation of environmental contaminants. This review was organized to offer valuable insights into the molecular mechanisms of phytoremediation and the prospects of transgenic hyperaccumulators with enhanced stress tolerance to diverse contaminants such as heavy metals and metalloids, xenobiotics, explosives, poly aromatic hydrocarbons (PAHs), petroleum hydrocarbons, pesticides, and nanoparticles. The roles of genoremediation and nanoparticles in augmenting the phytoremediation technology are also described in an interrelated framework with biotechnological prospects (e.g., plant molecular nano-farming). Finally, political debate on the preferential use of crops versus non-crop hyperaccumulators in genoremediation, limitations of transgenics in phytotechnologies, and their public acceptance issues are discussed in the policy framework.

The Contribution of Plant Dioxygenases to Hypoxia Signaling

Dioxygenases catalyze the incorporation of one or two oxygen atoms into target organic substrates. Besides their metabolic role, these enzymes are involved in plant signaling pathways as this reaction is in several instances required for hormone metabolism, to control proteostasis and regulate chromatin accessibility. For these reasons, alteration of dioxygenase expression or activity can affect plant growth, development, and adaptation to abiotic and biotic stresses. Moreover, the requirement of co-substrates and co-factors, such as oxygen, 2-oxoglutarate, and iron (Fe²⁺), invests dioxygenases with a potential role as cellular sensors for these molecules. For example, inhibition of cysteine deoxygenation under hypoxia elicits adaptive responses to cope with oxygen shortage. However, biochemical and molecular evidence regarding the role of other dioxygenases under low oxygen stresses is still limited, and thus further investigation is needed to identify additional sensing roles for oxygen or other co-substrates and co-factors. Here, we summarize the main signaling roles of dioxygenases in plants and discuss how they control plant growth, development and metabolism, with a focus on the adaptive responses to low oxygen conditions.

Glutaredoxin S25 and its interacting TGACG motif-binding factor TGA2 mediate brassinosteroid-induced chlorothalonil metabolism in tomato plants

The presence of pesticide residues in fresh fruits and vegetables poses a serious threat to human health. Brassinosteroids (BRs) can reduce pesticide residues in plants, but the underlying mechanisms still remain unclear. Here, we identified a tomato glutaredoxin gene GRXS25 which was induced by 24-epibrassinolide (EBR) and chlorothalonil (CHT) in a way dependent on apoplastic reactive oxygen species (ROS). Silencing of GRXS25 in tomato abolished EBR-induced glutathione S-transferases (GSTs) gene expression and activity, leading to an increased CHT residue. Yeast two-hybrid and bimolecular fluorescence complementation assays showed protein-protein interaction between GRXS25 and a transcription factor TGA2. Electrophoretic mobility shift and chromatin immunoprecipitation assays indicated that TGA2 factor bound to the TGACG-motif in the GST3 promoter. While silencing of TGA2 strongly compromised, overexpression of TGA2 enhanced expression of GST genes and CHT residue metabolism. Our results suggest that BR-induced apoplastic ROS trigger metabolism of pesticide residue in tomato plants through activating TGA2 factor via GRXS25-dependent posttranslational redox modification. Activation of plant detoxification through physiological approaches has potential implication in improving the food safety of agricultural products.

Bio-based remediation of petroleum-contaminated saline soils: Challenges, the current state-of-the-art and future prospects

Exploiting synergism between plants and microbes offers a potential means of remediating soils contaminated with petroleum hydrocarbons (PHCs). Salinity alters the physicochemical characteristics of soils and suppresses the growth of both plants and soil microbes, so the bioremediation of saline soils requires the use of plants and in microbes which can tolerate salinity. This review focuses on the management of PHC-contaminated saline soils, surveying what is currently known with respect to the potential of halophytes (plants adapted to saline environments) acting in concert with synergistic microbes to degrade PHCs. The priority is to identify optimal combinations of halophyte(s) and the bacteria present as endophytes and/or associated with the rhizosphere, and to determine what are the factors which most strongly affect their viability.

Combination of rhamnolipid and biochar in assisting phytoremediation of petroleum hydrocarbon contaminated soil using Spartina anglica

Biochar (BC) and rhamnolipid (RL) is used in bioremediation of petroleum hydrocarbons, however, the combined effect of BC and RL in phytoremediation has not been studied until now. In this paper, the phytoremediation of petroleum hydrocarbon-contaminated soil using novel plant Spartina anglica was enhanced by the combination of biochar (BC) and rhamnolipid (RL). Samples of petroleum-contaminated soil (10, 30 and 50 g/kg) were amended by BC, BC+ RL and rhamnolipid modified biochar (RMB), respectively. After 60 day's cultivation, the removal rate of total petroleum hydrocarbons (TPHs) for unplanted soil (UP), planted soil (P), planted soil with BC addition (P-BC), planted soil with BC and RL addition (P-BC + RL) and planted soil with addition of RMB (P-RMB) were 8.6%, 19.1%, 27.7%, 32.4% and 35.1% in soil with TPHs concentration of 30 g/kg, respectively. Compared with UP, the plantation of Spartina anglica significantly decreased the concentration of C_8-14 and tricyclic PAHs. Furthermore, the application of BC and RMB alleviated the toxicity of petroleum hydrocarbons to Spartina anglica via improving plant growth with increasing plant height, root vitality and total chlorophyll content. High-throughput sequencing result indicated that rhizosphere microbial community of Spartina anglica was regulated by the application of BC and RMB, with increase of bacteria and plant mycorrhizal symbiotic fungus in biochar and RMB amended soil.

Regulation of endogenous phytohormones alters the fluoranthene content in Arabidopsis thaliana

Phytohormones are crucial endogenous modulators that regulate and integrate plant growth and responses to various environmental pollutants, including the uptake of pollutants into the plant. However, possible links between endogenous phytohormone pathways and pollutant accumulation are unclear. Here we describe the fluoranthene uptake, plant growth, and superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and glutathione S-transferase (GST) activities in relation to different endogenous phytohormones and different levels in Arabidopsis thaliana. Three phytohormone inhibitors-N-1-naphthyl-phthalamic acid (NPA), daminozide (DZ), and silver nitrate (SN)-were used to regulate endogenous auxin, gibberellin, and ethylene levels, respectively. Fluoranthene inhibited plant growth and root proliferation while increasing GST and SOD activity. The three inhibitors reduced fluoranthene levels in Arabidopsis by either affecting plant growth or modulating antioxidant enzyme activity. NPA reduced plant growth and increased CAT activity. SN promoted plant growth and increased POD and CAT activity, whereas DZ increased POD activity.

MtBZR1 Plays an Important Role in Nodule Development in Medicago truncatula

Brassinosteroid (BR) is an essential hormone in plant growth and development. The BR signaling pathway was extensively studied, in which BRASSINAZOLE RESISTANT 1 (BZR1) functions as a key regulator. Here, we carried out a functional study of the homolog of BZR1 in Medicago truncatula R108, whose expression was induced in nodules upon Sinorhizobium meliloti 1021 inoculation. We identified a loss-of-function mutant mtbzr1-1 and generated 35S:MtBZR1 transgenic lines for further analysis at the genetic level. Both the mutant and the overexpression lines of MtBZR1 showed no obvious phenotypic changes under normal growth conditions. After S. meliloti 1021 inoculation, however, the shoot and root dry mass was reduced in mtbzr1-1 compared with the wild type, caused by partially impaired nodule development. The transcriptomic analysis identified 1319 differentially expressed genes in mtbzr1-1 compared with wild type, many of which are involved in nodule development and secondary metabolite biosynthesis. Our results demonstrate the role of MtBZR1 in nodule development in M. truncatula, shedding light on the potential role of BR in legume–rhizobium symbiosis.

Selenium alleviates phytotoxicity of phenanthrene and pyrene in Alternanthera Philoxeroides

To investigate if selenium can alleviate phytotoxicity of phenanthrene and pyrene, two high molecular weight (HMW) PAHs (polycyclic aromatic hydrocarbons) in Alternanthera philoxeroides are considered. A 60-day pot-culture experiment was carried out to assess the effects of selenium (0.5 mg Se·kg^-1 soil) on A. philoxeroides exposed to two PAH pollutants, pyrene (PYR) and phenanthrene (PHE), at levels of 10, 100, and 1000 mg·kg^-1. The test index included growth, chlorophyl, gas exchange and chlorophyl fluorescence parameters, and indicators of oxidative stress (H₂O₂ and malondialdehyde MDA). The response of plants to PAH exposure was concentration dependent; indicators of plant health declined, while indicators of plant stress rose. The maximum values of H₂O₂ and MDA were recorded at 1000 mg·kg^-1 PYR, followed by 1000 mg·kg^-1 PHE. However, application of Se (0.5 mg·kg^-1) to the soil significantly decreased the phytotoxic response to PAH exposure. This study demonstrated that Se increases the tolerance of A. philoxeroides to PYR and PHE, improving the feasibility of phytoremediating high level PAH contamination and expediting ecological restoration.

Surfactant-enhanced bioremediation of DDTs and PAHs in contaminated farmland soil

Field-scale bioremediation of dichlorodiphenyl trichloroethanes (DDTs) and polycyclic aromatic hydrocarbons (PAHs) contaminated farmland soil from the Shenyang North New Area of China was studied using the bacteria Arthrobacter globiformis. The additive effects of different concentrations of biosurfactant rhamnolipids (RLs) and anionic-nonionic mixed surfactant (SDBS-Tween 80) were evaluated. DDT and PAH removal rates by A. globiformis after 150 days of remediation were 52.1% and 21.9%, respectively. At the optimum RL concentration of 5 mg kg^-1, DDTs and PAHs had removal rates of 64.3% and 35.6%, respectively, at 150 days. This was 60.7% and 29.3% higher than the control; 36.9% and 19.8% higher than soil with RL-5 alone; and 12.2% and 13.8% higher than the A. globiformis treatment alone. RL-5 can enhance soil enzyme activity and A. globiformis reproduction during the DDT and PAH biodegradation processes. This study illustrates a highly efficient, low-cost in situ soil bioremediation technology that could have practical utility.

Chemiluminescence assay for detection of 2-hydroxyfluorene using the G-quadruplex DNAzyme-H2O2-luminol system

A chemiluminescence (CL) based assay is described for the determination of the environmental pollutant 2-hydroxyfluorene (2-HOFlu) which is found to inhibit the CL of a system composed of the G-quadruplex/hemin complex (a DNAzyme), H₂O₂, and luminol. The G-rich aptamer PW17 is transformed to a potassium(I)-stabilized G-quadruplex-hemin complex which displays peroxidase-like activity to catalyze the oxidation of luminol by H₂O₂ which is accompanied by strong blue CL emission. On addition of 2-HOFlu, it will participate in the G-quadruplex DNAzyme-mediated oxidation by H₂O₂. As a result, CL intensity is decreased. The difference in CL intensity (ΔI) before and after addition of 2-HOFlu serves as the signal for its quantitation. In water of pH 9.0, a linear relationship is found for the 1 nM to 1 μM concentration range, with a 0.2 nM detection limit. The assay is highly selective over other fluorene derivatives. It was successfully applied to the determination of 2-HOFlu in spiked lake water samples. The method is rapid, cost-effective and convenient. Conceivably, it has a wide scope in that it may be applied to other target pollutants for which G-quadruplexes are available. Graphical abstract A chemiluminescence (CL) assay is described for the determination of the environmental pollutant 2-hydroxyfluorene (2-HOFlu) based on the inhibition of the CL system composed of the G-quadruplex/hemin complex (a DNAzyme), H₂O₂, and luminol.

Historical records and sources of polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) in sediment from a representative plateau lake, China

The PAH and OCP concentrations in sediment cores collected from a deep lake were measured and evaluated chronologically. The results indicated that the PAH and OCP concentrations significantly increased from the 1950s to the 1990s and subsequently decreased to recent years. Integrated molecular diagnostic ratios indicated that the predominant petrogenic sources occurred from the 1950s-1980s. Petroleum and fuel combustion dominated the source of contamination more recently as a result of energy structure changes in this region. Additionally, HCHs and DDTs were the dominant OCP compounds, making up a majority of the total OCPs present (>85%). HCHs accounted for a larger ratio of the OCPs between the 1950s and 1980s, suggesting that HCHs were the dominant POPs in this period. DDTs then became dominant in the 1980s and later. High α/γ-HCH ratios suggested that the emission and conversion of local technical HCHs were the predominant HCHs source. The ratios of (DDE + p,p'-DDD)/DDTs and p,p'-DDT/DDTs indicated that the DDTs mainly originated from historical input. In addition, the dramatic decrease since the 1980s may be the result of China's banning of DDTs. However, DDTs were still present in the 1990s, suggesting DDTs were still used in this region and beyond.