Phenanthrene-triggered tricarboxylic acid cycle response in wheat leaf

Influence mechanisms underlying the degradation of petroleum hydrocarbons in response to various nitrogen dosages supplementation through metatranscriptomics analysis

Exogenous nitrogen supplementation for the bioremediation of petroleum-contaminated soils is a widely adopted and effective environmentally friendly strategy. However, the mechanism by which varying nitrogen dosages affect hydrocarbon degradation pathways remains unclear. This study conducted bioremediation on soil with a total petroleum hydrocarbon (TPH) content of 17,090 mg/kg over 210 days. The results indicated that low-dosage nitrogen supplementation (136 mg N/kg, LN) achieved a 24.8 % TPH removal, significantly outperforming high-dosage nitrogen treatment (1360 mg N/kg, HN), which achieved only 12.8 % TPH removal. The LN treatment demonstrated nitrogen availability efficiency (NAVE) and nitrogen partial factor availability (NPFA) values of 6.03 mg/mg and 31.11 mg/mg, respectively, compared to -0.90 mg/mg and 1.60 mg/mg for the HN treatment. The metatranscriptomic data were employed to investigate differential gene expression across individual samples and for GO and KEGG functional annotation. The annotation results revealed a significant increase in the number of differentially expressed genes (DEGs) associated with each functional category as the nitrogen dose increased. Notably, the LN treatment upregulated genes such as bbsE, bbsF, golA, and badH, which are crucial for encoding aromatic hydrocarbon degradation. Additionally, pyruvate metabolism genes including aceE, acdA, and atoB were enriched due to the LN treatment. In contrast, the HN treatment promoted soil nitrogen metabolism through enhanced expression of nitrogen cycling-related genes such as narK, narG, narH, nirA, and nirK, contributing to competitive interactions with carbon metabolism and impeding hydrocarbon degradation by soil microorganisms. These results suggest that the regulation of nitrogen application is crucial for enhancing hydrocarbon biodegradation efficiency in petroleum-contaminated soils.

Response of wheat (Triticum aestivum L. cv.) to the coexistence of micro-/nanoplastics and phthalate esters alters its growth environment

Micro- and nano-plastics (MPs/NPs) have emerged as a global pollutant, yet their impact on the root environment of plants remains scarcely explored. Given the widespread pollution of phthalate esters (PAEs) in the environment due to the application of plastic products, the co-occurrence of MPs/NPs and PAEs could potentially threaten the growth medium of plants. This study examined the combined effects of polystyrene (PS) MPs/NPs and PAEs, specifically dibutyl phthalate and di-(2-ethylhexyl) phthalate, on the chemical properties and microbial communities in a wheat growth medium. It was observed that the co-pollution with MPs/NPs and PAEs significantly increased the levels of oxalic acid, formic acid, and total organic carbon (TOC), enhanced microbial activity, and promoted the indigenous input and humification of dissolved organic matter, while slightly reducing the pH of the medium solution. Although changes in chemical indices were primarily attributed to the addition of PAEs, no interaction between PS MPs/NPs and PAEs was detected. High-throughput sequencing revealed no significant change in microbial diversity within the media containing both PS MPs/NPs and PAEs compared to the media with PS MPs/NPs alone. However, alterations in energy and carbohydrate metabolism were noted. Proteobacteria dominated the bacterial communities in the medium solution across all treatment groups, followed by Bacteroidetes and Verrucomicrobia. The composition and structure of these microbial communities varied with the particle size of the PS in both single and combined treatments. Moreover, variations in TOC, oxalic acid, and formic acid significantly influenced the bacterial community composition in the medium, suggesting they could modulate the abundance of dominant bacteria to counteract the stress from exogenous pollutants. This research provides new insights into the combined effects of different sizes of PS particles and another abiotic stressor in the wheat root environment, providing a critical foundation for understanding plant adaptation in complex environmental conditions.

Metabolic and oxidative stress response of sea cucumber Apostichopus japonicus exposed to acute high concentration of bisphenol AF

Bisphenols are known as endocrine disruptor that affect the development, and growth of marine creatures, including human. There were plenty of manuscripts evaluated the toxicology of bisphenol A (BPA) and its analogues such as bisphenol F (BPF), bisphenol AF (BPAF), and bisphenol S (BPS), but limits of them studied the effects of bisphenol analogues on echinoderms. In this study, we used metabolomics to investigate the metabolic response of sea cucumber (Apostichopus japonicus) exposed to BPAF, and the activities of glutathione (GSH), catalase (CAT), and superoxide dismutase (SOD) were determined. The results demonstrated alterations in lipid metabolism, glycerophospholipid metabolism, and biosynthesis of amino acids following BPAF treatment. Sea cucumbers upregulated the glycerophospholipid metabolism to repair the destruction of intestine cellular homeostasis. Six metabolites were selected as the potential biomarkers for the exposure of BPAF. This study revealed the metabolic response and oxidative response of sea cucumber arising from BPAF exposure, and provided theoretical support for the risk assessment of bisphenol analogues on economically important echinoderms, such as A. japonicus.

Enhanced crude oil degradation by remodeling of crude oil-contaminated soil microbial community structure using sodium alginate/graphene oxide/Bacillus C5 immobilized pellets

Bioaugmentation (BA) of oil-contaminated soil by immobilized microorganisms is considered to be a promising technology. However, available high-efficiency microbial agents remain very limited. Therefore, we prepared a SA/GO/C5 immobilized gel pellets by embedding the highly efficient crude oil degrading bacteria Bacillus C5 in the SA/GO composite material. The optimum preparation conditions of SA/GO/C5 immobilized gel pellets were: SA 3.0%, GO 25.0 μg/mL, embedding amount of C5 6%, water bath temperature of 50°C, CaCl₂ solution concentration 3% and cross-linking time 20 h. BA experiments were carried out on crude oil contaminated soil to explore the removal effect of SA/GO/C5 immobilized pellets. The results showed that the SA/GO/C5 pellets exhibited excellent mechanical strength and specific surface area, which facilitated the attachment and growth of the Bacillus C5. Compared with free bacteria C5, the addition of SA/GO/C5 significantly promoted the removal of crude oil in soil, reaching 64.92% after 30 d, which was 2.1 times the removal rate of C5. The addition of SA/GO/C5 promoted the abundance of soil exogenous Bacillus C5 and indigenous crude oil degrading bacteria Alcanivorax and Marinobacter. In addition, the enrichment of hydrocarbon degradation-related functional abundance was predicted by PICRUSt2 in the SA/GO/C5 treatment group. This study demonstrated that SA/GO/C5 is an effective method for remediating crude oil-contaminated soil, providing a basis and option for immobilized microorganisms bioaugmentation to remediate organic contaminated soil.

Comparative analysis of remediation efficiency and ultrastructural translocalization of polycyclic aromatic hydrocarbons in Medicago sativa, Helianthus annuus, and Tagetes erecta

Polycyclic aromatic hydrocarbons (PAHs) are semi-volatile anthropogenic contaminants that can damage soil fertility and threaten the environment due to their hazardous effects on various ecological parameters. The experimental objective was divided into two parts because PAHs are always present in mixtures. The toxicity of anthracene, phenanthrene, pyrene, and fluoranthene was examined and investigated the potential of three phytoremediator plants species viz Tagetes erecta, Helianthus annuus, and Medicago sativa for remediation and translocation of individual PAH. PAHs were shown to have inhibitory or stimulating effects on growth, antioxidant properties, and impact on the structure of plant cells. The result showed that M. sativa significantly enhances the removal rate of PAHs in the soil. The dissipation rate reached 96.2% in M. sativa planted soil, followed by H. annuus and T. erecta. Among the plant species, M. sativa exhibited the highest root and shoot concentrations (314.37 and 169.55 mg kg-1), while the lowest concentration was 187.56 and 76.60 mg kg-1 in T. erecta. SEM-EDX and fluorescence micrographs confirmed that pyrene altered plant tissue's ultrastructure and cell viability and was found to be the most toxic and resistant. M. sativa was proven to be the most effective plant for the mitigation of PAHs.

Proteomic and Biochemical Evidence Involving Root Cell Wall Biosynthesis and Modification, Tricarboxylic Acid Cycle, and Glutathione Metabolism in Cultivar-Dependent Cd Accumulation of Water Spinach (Ipomoea aquatica)

Proteomic analysis and biochemical tests were employed to investigate the critical biological processes responsible for the different cadmium (Cd) accumulations between two water spinach (Ipomoea aquatica) cultivars, QLQ and T308. QLQ, with lower shoot Cd accumulation and translocation factor than T308, possessed higher expression of cell wall biosynthesis and modification proteins in roots, together with higher lignin and pectin contents, higher pectin methylesterase activity, and lower pectin methylation. The results demonstrated that QLQ could more effectively restrict root-to-shoot Cd translocation by compartmentalizing more Cd in root cell walls. In contrast, T308 showed higher expression of the tricarboxylic acid (TCA) cycle, glutathione (GSH) metabolism, and heavy metal transporter proteins, accompanied by higher GSH content and glutathione S-transferase (GST) and glutathione reductase (GR) activity, which accelerated Cd uptake and translocation in T308. These findings revealed several critical biological processes responsible for cultivar-dependent Cd accumulation in water spinach, which are important for elucidating Cd accumulation and transport mechanisms in different cultivars.

Combined transcriptome and metabolome analyses reveal the mechanisms of ultrasonication improvement of brown rice germination

This study investigated the effects of ultrasonication treatment on the germination rate of brown rice. Brown rice grains were subjected to ultrasound (40 kHz/30 min) and then incubated for 36 h at 37 °C to germinate the seeds. Ultrasonic treatment increased the germination rate of brown rice by up to ∼28 % at 30 h. Transcriptomic and metabolomic analyses were performed to explore the mechanisms underlying the effect of ultrasonic treatment on the brown rice germination rate. Comparing the treated and control check samples, 867 differentially expressed genes (DEGs) were identified, including 638 upregulated and 229 downregulated), as well as 498 differentially accumulated metabolites (DAMs), including 422 up accumulated and 76 down accumulated. Multi-omics analysis revealed that the germination rate of brown rice was promoted by increased concentrations of low-molecular metabolites (carbohydrates and carbohydrate conjugates, fatty acids, amino acids, peptides, and analogues), and transcription factors (ARR-B, NAC, bHLH and AP2/EREBP families) as well as increased carbon metabolism. These findings provide new insights into the mechanisms of action of ultrasound in improving the brown rice germination rate and candidate DEGs and DAMs responsible for germination have been identified.

Nanoscale Iron trioxide catalyzes the synthesis of auxins analogs in artificial humic acids to enhance rice growth

Humic acids (HAs), kinds of valuable active carbon, are critical for improving soil fertility. However, the majority of soils are poor in HAs, arousing the development of artificial HAs. In this study, two iron-based catalysts (nanoscale iron trioxide (nFe₂O₃) and FeCl₃) were used to catalyze the hydrothermal humification of waste corn straw. With the help of ultra-performance liquid chromatography-mass spectrometry, we proposed the specific humification process with the action of catalysis for the first time, which is of great significance for the design, synthesis and application of artificial HAs in the future. Moreover, the growth-promoting effect and mechanisms of the artificial HAs were determined by rice planting in a greenhouse. Results showed that compared to no catalyst treatment, the FeCl₃ and nFe₂O₃ catalysts increased the decomposition rate of macromolecular biomass by 39 and 14 %, respectively, increasing the yield of artificial HAs. During the humification process, nFe₂O₃ catalysts benefit the formation of many aromatic structure monomers including furfural and hydroxycaproic acids. These monomers were condensed into growth hormone analogs such as vanillin and methionine sulfoxide and were further built in the artificial HAs. Therefore, the artificial HAs from nFe₂O₃ catalytic treatment promoted the rice growth the best, showing that the resultant germination rate, root activity, and photosynthetic rate of rice increased by 50, 167, and 72 %, respectively; moreover, the uptake and accumulation of water and nutrient by roots as well as the contents of soluble protein and sugar of rice are also significantly increased. This could be ascribed to the upregulated expression of functional genes including OsRHL1, OsZPT5-07, OsSHR2 and OsDCL. Considering both the economic and environmental benefits, we suggested that the artificial HAs, especially that produced with the action of nFe₂O₃ catalysis, are promising in alleviating environmental stress from waste biomass and sustainably improving agricultural production.

Integrated eco-physiological, biochemical, and molecular biological analyses of selenium fortification mechanism in alfalfa

Foliar Se (IV) application at 100 mg/kg can act as a positive bio-stimulator of redox, photosynthesis, and nutrient metabolism in alfalfa via phenotypes, nutritional compositions, biochemistry, combined with transcriptome analysis. Selenium (Se) is an essential element for mammals, and plants are the primary source of dietary Se. However, Se usually has dual (beneficial/toxic) effects on the plant itself. Alfalfa (Medicago sativa L.) is one of the most important forage resources in the world due to its high nutritive value. In this study, we have investigated the effects of sodium selenite (Se (IV)) (0, 100, 200, 300, and 500 mg/kg) on eco-physiological, biochemical, and transcriptional mechanisms in alfalfa. The phenotypic and nutritional composition alterations revealed that lower Se (IV) (100 mg/kg) levels positively affected alfalfa; it enhanced the antioxidant activity, which may contribute to redox homeostasis and chloroplast function. At 100 mg/kg Se (IV) concentration, the H₂O_2, and malondialdehyde (MDA) contents decreased by 36.72% and 22.62%, respectively, whereas the activity of glutathione peroxidase (GPX) increased by 31.10%. Se supplementation at 100 mg/kg increased the plant pigments contents, the light-harvesting capacity of PSII (Fv/Fm) and PSI (ΔP700max), and the carbon fixation efficiency, which was demonstrated by enhanced photosynthesis (37.6%). Furthermore, alfalfa shifted carbon flux to protein synthesis to improve quality at 100 mg/kg of Se (IV) by upregulating carbohydrate and amino acid metabolic genes. On the contrary, at 500 mg/kg, Se (IV) became toxic. Higher Se (IV) disordered the plant antioxidant system, increasing H₂O₂ and MDA by 14.2 and 4.3%, respectively. Moreover, photosynthesis was inhibited by 20.2%, and more structural substances, such as lignin, were synthesized. These results strongly suggest that Se (IV) at a concentration of 100 mg/kg act as the positive bio-stimulator of redox metabolism, photosynthesis, and nutrient in alfalfa.

Nitric oxide promotes energy metabolism and protects mitochondrial DNA in peaches during cold storage

The mitochondria are important organelles related to energy metabolism and are susceptible to oxidative damage. In this experiment, peaches (Prunus persica) were treated with distilled water (as the control), 15 μmol L-1 of nitric oxide (NO), and 20 μmol L-1 of carboxy-PTIO (NO scavenger). The changes in mitochondrial physiological indicators, energy metabolism process, and mitochondrial DNA (mtDNA) damage and repair were quantified. Compared with the control, NO treatment reduced mitochondrial oxygen consumption and the reactive oxygen species content, increased mitochondrial respiration control rate, and promoted energy metabolism by influencing the activities of citrate synthase, aconitase, isocitrate dehydrogenase, and α-ketoglutarate dehydrogenase in the tricarboxylic acid cycle and ATPase activity in peach mitochondria. NO treatment also maintained the relative copy number of mtDNA and the relative amplification of long PCR in peaches, decreased the level of 8-hydroxy-2 deoxyguanosine, and upregulated the expression of PpOGG1, PpAPE1, and PpLIG1. These results indicated that exogenous NO treatment (15 μmol L-1) could reduce mtDNA oxidative damage, maintain mtDNA molecular integrity, and inhibit mtDNA copy number reduction by reducing the reactive oxygen species content, thereby promoting mitochondrial energy metabolism and prolonging the storage life of peaches at low temperatures.

Transcriptome analysis revealed accumulation-assimilation of selenium and physio-biochemical changes in alfalfa (Medicago sativa L.) leaves

BACKGROUND

Selenium (Se) is an increasing concern for investigators predominantly because of its consumption in the human body mainly from crops. As the fourth largest plant crop globally, alfalfa is one of the most important forages. Alfalfa was fertilized with selenium(IV) (Se(IV)) under field conditions to study the accumulation and assimilation of Se(IV) and to assess the impact of Se fertilization.

RESULTS

It was analyzed that the physio-biochemistry, Se species, combined with transcriptome after spraying Se(IV) at different times (0, 12, and 48 h). 9402 and 12 607 differentially expressed genes (DEGs) were identified at 12 h (versus 0 h) and 48 h (versus 12 h). DEG functional enrichments proposed two time-specific biological processes: Se(IV) accumulation was the primary process at 0-12 h, and its assimilation mainly occurred during 12-48 h. This was further proved by the separation of various Se speciation at different times. It showed that Se-supplementation also affected the soluble protein, soluble sugar, pigment contents and antioxidant capacity. Selenium-biofortification could improve the stress resistance of alfalfa by enhancing antioxidant system to scavenge reactive oxygen species (e.g. hydrogen peroxide) and boosting carbohydrate metabolism.

CONCLUSION

By integrating physio-biochemistry, Se-related metabolites, and transcriptome under Se(IV) treatment, this study provides data to guide further work on Se-fortification in alfalfa. © 2022 Society of Chemical Industry.

Metabolic Profiling of Sugars and Organic Acids, and Expression Analyses of Metabolism-Associated Genes in Two Yellow-Peel Pitaya Species

Sugar and organic acids are important factors determining pitaya fruit quality. However, changes in sugars and acids, and expressions of metabolism-associated genes during fruit maturation of yellow-peel pitayas are not well-documented. In this study, metabolic and expression analyses in pulps of different fruit developmental stages of ‘Wucihuanglong’ (‘WCHL’, Hylocereus undatus) and ‘Youcihuanglong’ pitaya (‘YCHL’, Hylocereus megalanthus) were used to explore the sugar and organic acid metabolic process. Total phenols and flavonoids were mainly accumulated at S1 in pitaya pulps. Ascorbic acid contents of ‘WCHL’ pitaya were higher than that of ‘YCHL’ pitaya during fruit maturation. Starch was mainly accumulated at early fruit development stages while soluble sugars were rich in late stages. Sucrose, fructose, and glucose were the main sugar components of ‘YCHL’ pitaya while glucose was dominant in ‘WCHL’ pitaya. Malic and citric acids were the main organic acids in ‘WCHL’ and ‘YCHL’ pitayas, respectively. Based on the transcriptome analyses, 118 genes involved in pitaya sugar and organic acid metabolism were obtained. Results from the correlation analyses between the expression profiling of candidate genes and the contents of sugar and organic acid showed that 51 genes had a significant correlation relationship and probably perform key role in pitaya sugar and organic acid metabolism processes. The finding of the present study provides new information for quality regulation of pitayas.

LpNOL-knockdown suppression of heat-induced leaf senescence in perennial ryegrass involving regulation of amino acid and organic acid metabolism

The nonyellow COLORING 1-like gene (NOL) is known for its roles in accelerating leaf senescence, but the underlying metabolic mechanisms for heat-induced leaf senescence remain unclear. The objectives of this study were to identify metabolites and associated metabolic pathways regulated by knockdown of NOL in perennial ryegrass (Lolium perenne) and to determine the metabolic mechanisms of NOL controlling heat-induced leaf senescence. Wild-type (WT; cv. "Pinnacle") and two lines (Noli-1 and Noli-2) of perennial ryegrass with LpNOL knockdown were exposed to heat stress at 35/33°C (day/night) or nonstress control temperatures at 25/22°C (day/night) for 30 days in growth chambers. Leaf electrolyte leakage, chlorophyll (Chl) content, photochemical efficiency (F_v /F_m ), and net photosynthetic rate (Pn) were measured as physiological indicators of leaf senescence, while gas chromatography-mass spectrometry was performed to identify metabolites regulated by LpNOL. Knockdown of LpNOL suppressed heat-induced leaf senescence and produced a stay-green phenotype in perennial ryegrass, as manifested by increased Chl content, photochemical efficiency, net photosynthetic rate, and cell membrane stability in Noli-1 and Noli-2. Five metabolites (valine, malic acid, threonic acid, shikimic acid, chlorogenic acid) were uniquely upregulated in LpNOL plants exposed to heat stress, and six metabolites (aspartic acid, glutamic acid, 5-oxoproline, phenylalanine, proline, tartaric acid) exhibited more pronounced increases in their content in LpNOL plants than the WT. LpNOL could regulate heat-induced leaf senescence in perennial ryegrass through metabolic reprogramming in the pathways of respiration, secondary metabolism, antioxidant metabolism, and protein synthesis.

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.

Transcriptome and metabolome profiling to elucidate mechanisms underlying the blue discoloration of radish roots during storage

The internal blue discoloration of radish roots (Raphanus sativus) during storage affects their quality. We here performed transcriptome and metabolome profiling to investigate the mechanisms underlying the bluing of radish roots during storage. On comparing white radish (WR) and blue radish (BR), we identified 14,171 differentially expressed genes (upregulated: 7,383, downregulated: 6,788) and 145 differentially accumulated metabolites (upregulated: 117, downregulated: 28). Functional annotation analysis and metabolome profiling revealed that the blue discoloration of radish roots was promoted by high content of glucosinolates, oxidation system (ROS, CAT, POD) or low reduction system (GSH, GPX, APX, GST, ASA). Our results provide new insights into the underlying metabolic causes of the blue discoloration of radish roots and report candidate genes and metabolites involved in blue compound biosynthesis.

Influence of organic carbon fractions of freshwater biofilms on the sorption for phenanthrene and ofloxacin: The important role of aliphatic carbons

Sorption to biofilms is thought to be a crucial process controlling the fate of trace organic contaminants in aquatic systems. The organic composition of biofilms is regarded as the determining factor in the sorption mechanism of biofilm organic carbon fractions; however, its role is not well known. Here, the sorption of phenanthrene and ofloxacin was modeled with classic and emerging organic contaminants, respectively, by comparatively investigating nine type of freshwater biofilms cultured in a river, lake, and reservoir in spring, summer, and autumn. The chemical features of the nine biofilms were analyzed using elemental analysis, infrared spectroscopy, X-ray photoelectron spectroscopy, and carbon-13 nuclear magnetic resonance. Results showed that the freshwater biofilms were aliphatic-rich natural amorphous solid substances with O-containing functional groups, and their surface polarity was significantly lower than their bulk polarity. All the isotherms of phenanthrene and ofloxacin sorption by the biofilms were linear. The organic carbon-normalized partition coefficient values for phenanthrene and ofloxacin on the nine biofilms ranged from 91.9 to 364.2 L g^-1 and 3.2 to 43.2 L g^-1, respectively. The van der Waals interaction between a majority of aliphatic carbon (73.4%-83.9%) in biofilms and the two sorbates was much stronger than π-π interactions between a minority of aromatic carbon (12.7%-21.7%) and sorbates. The surface polarity of the biofilms regulated polar interactions including the hydrogen bonding and electron donor-acceptor interactions. Both the aliphatic carbon and surface polarity in the biofilms enhanced the sorption of phenanthrene and ofloxacin. The sorption characteristics and mechanisms of polycyclic aromatic hydrocarbons and antibiotics on biofilms shown in our present and previous studies are different from those of other ubiquitous natural solid materials such as soils and sediments. This study provides insight into the importance of aliphatic carbon fractions of freshwater biofilms for the sorption of classic and emerging organic contaminants.