The use of proteomic analysis for exploring the phytoremediation mechanism of Scirpus triqueter to pyrene

Functionally coherent transcriptional responses of Jatropha curcas and Pseudomonas fragi for rhizosphere mediated degradation of pyrene

Pyrene is an extremely hazardous, carcinogenic polycyclic aromatic hydrocarbon (PAH). The plant-microbe interaction between Pseudomonas fragi DBC and Jatropha curcas was employed for biodegradation of pyrene and their transcriptional responses were compared. The genome of P. fragi DBC had genes for PAH degrading enzymes i.e. dioxygenases and dehydrogenases, along with root colonization (trpD, trpG, trpE and trpF), chemotaxis (flhF and flgD), stress adaptation (gshA, nuoHBEKNMG), and detoxification (algU and yfc). The transcriptional expression of catA and yfc that respectively code for catabolic enzyme (catechol-1, 2-dioxygnase) and glutathione-s-transferase for detoxification functions were quantitatively measured by qPCR. The catA was expressed in presence of artificial root exudate with or without pyrene, and glucose confirming the non-selective approach of bacteria, as desired. Pyrene induced 100-fold increase of yfc expression than catA, while there was no expression of yfc in absence of pyrene. The transcriptome of plant roots, in presence of pyrene, with or without P. fragi DBC inoculation was analysed. The P. fragi DBC could upregulate the genes for plant growth, induced the systemic acquired resistance and also ameliorated the stress response in Jatropha roots.

Interactions between pyrene and heavy metals and their fates in a soil-maize (Zea mays L.) system: Perspectives from the root physiological functions and rhizosphere microbial community

The co-occurrence of polycyclic aromatic hydrocarbons (PAHs) and heavy metals in agricultural soils has become a worldwide food crop security concern. Pot experiments, rhizosphere microbial metagenomic sequencing, and root metatranscriptomic sequencing were performed to investigate the interactions among pyrene, Cu, and Cd in a soil-maize (Zea mays L.) system. This study provided direct evidence that the co-presence of PAHs and heavy metals changed the root physiological functions and the rhizosphere microbial community, which subsequently influenced the fate of the contaminants. Co-contamination at low levels tended to enhance the uptake potential and biodegradation performance of the plant, whereas increased contaminant concentrations produced opposite effects. The co-presence of 1000 mg/kg Cu decreased the abundance of Mycobacterium in the rhizosphere and reduced pyrene degradation by 12%-16%. The presence of 400-750 mg/kg pyrene altered the metabolic processes, molecular binding functions, and catalytic activity of enzymes in the maize roots, thus impeding the phytoextraction of Cu and Cd. Competitive absorption between Cu and Cd was observed for the 800-1000 mg/kg Cu and 50-100 mg/kg Cd co-treatment, in which Cu showed a competitive advantage, enhancing its root-to-shoot translocation. These findings provide important information for the production of safe crops and for the development of phytoremediation technologies.

The influence of polycyclic aromatic hydrocarbons in protein profile of Medicago sativa L

Medicago sativa L. (alfalfa) are studied as potential phytoremediation agents of priority pollutants like polycyclic aromatic hydrocarbons (PAH). However, elucidation of the biochemical mechanisms involved in phytoremediation is a topic to be explored with knowledge gaps. This study aims to identify and classify proteins expressed in the aerial parts of laboratory-cultivated alfalfa in the presence and absence of pyrene, anthracene, and phenanthrene. Soil samples were amended with 100 mg.kg^-1 of each PAH (total concentration of 300 ppm) and cultivated with alfalfa plants for 20 days. After this, aerial parts of cultivated plants from each condition were collected for qualitative proteomic analysis (ESI-Q/TOF). The results showed a significant increase (Student's t-test p < 0.05) of 41.7% in the concentration of proteins from plants grown in PAH-amended substrates, changes in the protein profile, with intense protein bands observed at 40-55, 34, 28, and 15 kDa when compared to the control. A total of 504 proteins were identified and classified into 12 functional categories, highlighting the identification of 11 phytoremediation-related proteins candidates in plants grown in the presence of PAH, with biological functions related to diverse metabolisms involved in the xenobiotics biodegradation (included PAH), glutathione and response to stress.

The mechanism of chelator improved the tolerance and accumulation of poplar to Cd explored through differential expression protein based on iTRAQ

Appropriate chelator may increase plant tolerance and accumulation for Cd in soil, but its molecular mechanism is unclear. In this experiment, the technology of isobaric tags for relative and absolute quantitation (iTRAQ) was used to compare the differential expression proteins (DEPs) and differential expression genes (DEGs) characteristics of poplar accumulating Cd combined with EDTA and/or EGTA. The results showed that the Cd concentrations, biomasses and activities of antioxidant enzymes of poplar were significantly increased in the treatments of chelator addition compared to the T_Cd. The number of co-intersecting specific proteins of T_Cd/CK, T_Cd+EDTA/T_Cd, T_Cd+EGTA/T_Cd and T_Cd+EDTA+EGTA/T_Cd was 49. Using the GO function and KEGG analysis, it was found that EDTA and EGTA might improve some main metabolic pathways of poplar leaves, which were involved in the enhancement of the expression of carbohydrate and energy metabolism-related proteins, regulation of cell energy metabolism, complementing and cooperating with each other in various ways, and dynamic regulation of energy metabolism. Particularly, chelator might induce the regulation of protein synthesis, folding and transport, and degradation of abnormal proteins in response to Cd toxicity. These results provided a theoretical basis for further elucidation of molecular mechanisms of poplar response to Cd stress.

Characterization of Di-n-Butyl Phthalate Phytoremediation by Garden Lettuce (Lactuca sativa L. var. longifolia) through Kinetics and Proteome Analysis

Di-n-dutyl phthalate (DBP), an endocrine disruptor, is one of the most widely used phthalate esters (PAEs) in the world. It can be accumulated in seafood or agricultural products and represents a substantial risk to human health via the food chain. Thus, finding a plant which can remediate DBP but have no effects on growth is the main topic of the development of DBP phytoremediation. This study used garden lettuce (Lactuca sativa L. var. longifolia), which has a significant DBP absorption capability, as a test plant to measure phytoremediation kinetics and proteome changes after being exposed to DBP. The results show that DBP accumulated in different parts of the garden lettuce but the physiological status and morphology showed no significant changes following DBP phytoremediation. The optimal condition for the DBP phytoremediation of garden lettuce is one critical micelle concentration (CMC) of non-ionic surfactant Tween 80 and the half-life (t1/2, days), which calculated by first-order kinetics, was 2.686 days for 5 mg L−1 of DBP. This result indicated that the addition of 1 CMC of Tween 80 could enhance the efficiency of DBP phytoremediation. In addition, the results of biotoxicity showed that the median effective concentration (EC50) of DBP for Chlorella vulgaris is 4.9 mg L−1. In this case, the overall toxicity markedly decreased following phytoremediation. In the end, the result of proteome analysis showed six protein spots, revealing significant alterations. According to the information of these proteomes, DBP potentially causes osmotic and oxidative stress in garden lettuce. In addition, since DBP had no significant effects on the morphology and physiological status of garden lettuce, garden lettuce can be recommended for use in the plant anti-DBP toxicity test, and also as the candidate plant for DBP phytoremediation. We hope these findings could provide valuable information for DBP-contaminated water treatment in ecological engineering applications or constructed wetlands.

Elevated temperature and CO2 affect responses of European aspen (Populus tremula) to soil pyrene contamination

High northern latitudes are climatic sensitive areas, and are also regions to which polycyclic aromatic hydrocarbons (PAHs) easily transport and accumulate with potential risk to natural ecosystems. However, the effect of PAHs on northern woody plant growth and defense under climate change is very little studied. Here, we conducted a unique experiment in greenhouses to investigate sex-related responses of the dioecious Populus tremula to pyrene (50mgkg^-1) and residue of pyrene in soils under ambient and elevated temperature (+1.8°C on average) and CO₂ (740ppm). Pyrene decreased stem biomass and leaf area by 9% and 6%, respectively under ambient conditions, and the reduction of leaf area was more severe under elevated temperature (38%), elevated CO₂ (37%), and combined T+CO₂ (42%). Other growth parameters were unchanged by pyrene. Pyrene did not affect the concentration of leaf total phenolics under ambient conditions, but increased it by 16%, 1%, and 20% compared to controls under elevated temperature, elevated CO₂, and T+CO₂, respectively. Pyrene had only minor sex-specific effects on plant growth and phenolics. The concentration of residual pyrene in pyrene-spiked soils was higher under elevated CO₂ than under ambient, elevated temperature, and combined T+CO₂. The results suggest that both sexes of P. tremula have the capacity to regulate growth and metabolism to adjust to the stress of the tested pyrene contamination under elevated temperature and CO₂, but potential risk of pyrene to plants still exists in the future changing climate.

Effects of soil pyrene contamination on growth and phenolics in Norway spruce (Picea abies) are modified by elevated temperature and CO2

With the constant accumulation of polycyclic aromatic hydrocarbons (PAHs) in soil and increasing temperature and CO₂ levels, plants will inevitably be exposed to combined stress. Studies on the effects of such combined stresses are needed to develop mitigation and adaptation measures. Here, we investigated the effects of soil pyrene contamination (50 mg kg^-1) on growth and phenolics of 1-year-old Norway spruce seedlings from five different origins in Finland at elevated temperature (+ 2 °C) and CO₂ (+ 360 ppm). Pyrene significantly decreased spruce height growth (0-48%), needle biomass (0-44%), stem biomass (0-43%), and total phenolic concentrations in needles (2-13%) and stems (1-19%) compared to control plants. Elevated temperature alone did not affect growth but led to lower concentrations of total phenolics in needles (5-29%) and stems (5-18%) in both soil treatments. By contrast, elevated CO₂ led to higher needle biomass (0-39%) in pyrene-spiked soils and higher concentrations of stem phenolics (0-18%) in pyrene-spiked and control soils compared to ambient treatments. The decrease in height growth and phenolic concentrations caused by pyrene was greater at elevated temperature, while elevated CO₂ only marginally modified the response. Seedlings from different origins showed different responses to the combined environmental stressors. The changes in growth and in the quantity and quality of phenolics in this study suggest that future climate changes will aggravate the negative influence of soil pyrene pollution on northern conifer forest ecosystems.

Insights into the molecular mechanism of the responses for Cyperus alternifolius to PhACs stress in constructed wetlands

Cyperus alternifolius has been widely reported to be an effective phytoremediation plant in constructed wetland systems (CWs). In this context, an integrated biochemical and proteomic analysis of C. alternifolius leaves exposed to pharmaceutically active compounds (PhACs) in CWs was conducted to understand the mechanism of phytoremediation. The obtained results showed the antioxidant enzyme activities were induced throughout the experiment; however over time, the malondialdehyde content is not significantly different from the control and the photosynthetic pigment contents in plant were subsequently slowly recovered. Therefore, we concluded that reactive oxygen species could be effectively counteracted by the enhanced antioxidant enzyme activities, and therefore the photosynthetic pigments were ultimately restored. Leaf extract proteome maps were obtained through 2-DE, and an average of 55, 49, and 24 spots were significantly altered by 30, 100, and 500 μg/L of PhACs over the control, respectively. Protein expression patterns showed that proteins in C. alternifolius leaves are associated with photosynthesis, energy metabolism, defense, and protein synthesis. Moreover, the most relevant pathways modulated by PhACs were photosynthesis and energy metabolism. The protein expression involved in antioxidant defense and stress response generally increased in all the PhAC treatments. The regulated proteins may favor PhAC degradation in CWs; however, the role of these proteins in degrading PhACs remains unknown; further biochemical studies should be conducted. This study indicated that C. alternifolius can tolerate multiple PhACs.

Mechanism study of alachlor biodegradation by Paecilomyces marquandii with proteomic and metabolomic methods

Alachlor is an herbicide that is widely used worldwide to protect plant crops against broadleaf weeds and annual grasses. However, due to its endocrine-disrupting activity, its application had been banned in the European Union. As described in our earlier work, Paecilomyces marquandii is a microscopic fungus capable of alachlor removal by N-acetyl oxidation. Our current work uses proteomics and metabolomics to gain a better understanding of alachlor biodegradation by the microscopic fungus P. marquandii. The data revealed that the addition of alachlor reduced the culture growth and glucose consumption rates. Moreover, the rates of glycolysis and the tricarboxylic acids (TCA) cycle increased during the initial stage of growth, and there was a shift toward the formation of supplementary materials (UDP-glucose/galactose) and reactive oxygen species (ROS) scavengers (ascorbate). Proteomic analysis revealed that the presence of xenobiotics resulted in a strong upregulation of enzymes related to energy, sugar metabolism and ROS production. However, the unique overexpression of cyanide hydratase in alachlor-containing cultures may implicate this enzyme as the key protein involved in the alachlor biodegradation pathway. The characterization of P. marquandii-mediated alachlor removal in terms of cell structure and function provides a deeper insight into the strategies of microorganisms toward xenobiotic biodegradation.