The aim of this study was to conduct transcriptomic, proteomic, and metabolomic analysis to provide a comprehensive view of plant response to tetracycline stress. Pumpkin seeds were cultured for 7 days without or with tetracycline at 10 mg/L. Pumpkin roots showed excessive growth inhibition, but not yet strong growth restraining in cotyledons. Tetracycline affected the abundance of metabolites related to flavonoid biosynthesis and amino acid metabolism. Main changes of metabolites in flavonoid biosynthesis were consistent with mRNA changes. Amino acid changes are mainly mediated by proteins or mRNAs. To be specific, tetracycline treatment increased the levels of rutin, caffeate, cinnamaldehyde, 4-hydroxycinnamic acid, ferulic acid, naringenin, apigenin, luteolin, (-)-epigallocatechin, astragalin, L-serine, and glutathione and the transcript levels related to these compounds; and decreased the levels of indole pyruvate, indole acetaldehyde, L-arginine, S-adenosylhomocysteine, L-glutamine, and gamma-glutamylcysteine and the transcript levels related to these compounds. Tetracycline treatment also increased the levels of oxoglutaric acid, L-glutamic acid, gamma-aminobutyric acid, and gamma-glutamylalanine and enzymes involved in their production; and decreased the levels of L-isoleucine, L-valine, and L-leucine and enzymes involved in their production. We elucidated several biological processes (e.g. phenylpropanoid/flavonoid biosynthesis pathways, amino acid metabolic pathways) that were altered by tetracycline, and provided a multi-omic perspective on the mechanisms underlying the response to tetracycline stress in pumpkin roots. We provide a useful reference for the development of environmental quality management methods.

The relationship between metabolite changes and biological endpoints in response to cadmium (Cd) stress remains unclear. Fountain grass has good Cd enrichment and tolerance abilities and is widely used in agriculture and landscaping. We analyzed the metabolic responses by detecting the metabolites through UPLC-MS and examined the relationships between metabolite changes and the characteristics of morphology and physiology to different Cd stress in fountain grass. Our results showed that under Cd stress, 102 differential metabolites in roots and 48 differential metabolites in leaves were detected, with 20 shared metabolites. Under Cd stress, most of the carbohydrates in leaves and roots decreased, which contributed to the lowered leaf/root length and fresh weight. In comparison, most of the differential amino acids and lipids decreased in the leaves but increased in the roots. Almost all the differential amino acids in the roots were negatively correlated with root length and root fresh weight, while they were positively correlated with malondialdehyde content. However, most of the differential amino acids in the leaves were positively correlated with leaf length and leaf fresh weight but negatively correlated with malondialdehyde content. Metabolic pathway analysis showed that Cd significantly affects seven and eight metabolic pathways in the leaves and roots, respectively, with only purine metabolism co-existing in the roots and leaves. Our study is the first statement on metabolic responses to Cd stress and the relationships between differential metabolites and biological endpoints in fountain grass. The coordination between various metabolic pathways in fountain grass enables plants to adapt to Cd stress. This study provides a comprehensive framework by explaining the metabolic plasticity and Cd tolerance mechanisms of plants.

Environmental factors, including antibiotics such as tetracycline, can alter biological processes in plants. To ascertain how cell/tissue response to tetracycline, a multi-omic analysis was implemented to explore the molecular mechanism of tetracycline influencing the growth of ryegrass root. Tetracycline induced extensive changes in the root metabolome in plants, particularly impacting metabolites of flavonoid metabolic pathways, which were supported through consistent differences between transcriptome and proteome. Cross-comparison between mRNA and protein contents considered the authentication of congruence with related metabolites and revealed changes of several biological processes under tetracycline stress. Overall, we present an undemanding multi-omic strategy to survey the significant influence on the root under tetracycline stress.

Metabolomics is an effective tool to test the response of plants to environmental stress; however, the relationships between metabolites and biological endpoints remained obscure in response to drought stress. Carex breviculmis is widely used in forage production, turf management, and landscape application and it is particularly resistant to drought stress. We investigated the metabolomic responses of C. breviculmis to drought stress by imposing a 22-day natural soil water loss. The results showed that water-deficit restrained plant growth, reducing plant height, leaf fresh weight, and total weight, however, increasing soluble protein content and malondialdehyde content. In total, 129 differential metabolites in the leaves were detected between drought and control using the Ultrahigh Performance Liquid Chromatography-Mass Spectrometer (UPLC-MS) method. Drought enhanced most of the primary and secondary metabolites in the differential metabolites. Almost all the sugars, amino acids, organic acids, phytohormones, nucleotides, phenylpropanoids and polyketides in the differential metabolites were negatively correlated with plant height and leaf fresh weight, while they were positively correlated with soluble protein content and malondialdehyde content. Metabolic pathway analysis showed that drought stress significantly affected aminoacyl-tRNA biosynthesis, TCA cycling, starch and sucrose metabolism. Our study is the first statement on metabolomic responses to drought stress in the drought-enduring plant C. breviculmis. According to the result, the coordination between diverse metabolic pathways in C. breviculmis enables the plant to adapt to a drought environment. This study will provide a systematic framework for explaining the metabolic plasticity and drought tolerance mechanisms of C. breviculmis under drought stress.

In this study, pumpkin seedlings were subjected to cadmium stress (100 mg/L cadmium ion solution, 10 days) without or with wheat straw biochar at different concentrations (0%, 0.5%, 1%, and 2% w/v). As the biochar concentration increased, the amount of cadmium accumulated in the root and stem of pumpkin seedlings decreased and the fresh weight of root, stem and leaf increased. The highest cadmium concentration was in the root, followed by the stem and then the leaf. 1% and 2% biochar treatments reduced the oxidative stress of cadmium to seedlings, and added the contents of fatty acid, carbohydrate, amino acid and indoleacetic acid in the root. With the increase of biochar concentration, the metabolites promoting root growth increased. These results provide new information about how biochar alleviates cadmium stress by affecting the metabolic response.

Changes in the types and contents of metabolites in plants can occur in response to environmental stress. In this study, pumpkin seeds were cultivated in a cadmium ion solution (cadmium sulfate) for 7 days, and growth parameters, antioxidant enzyme activities, and metabolites in the root, stem, and leaf were analyzed. The results showed that cadmium accumulation characteristics were in the order of root > stem > leaf. Cadmium restrained root growth and promoted superoxide dismutase, peroxidase, catalase activities in the root, but inhibited their activities in the leaf. Cadmium did not change the total biomass of pumpkin seedlings. Orthogonal partial least squares (OPLS) analyses were conducted to detect the relationships between fresh weight and metabolites. These analyses revealed that maltose had significantly positive relationships with the fresh weight of the root, stem, and leaf. Cadmium influenced glyoxylate and dicarboxylate metabolism, aminoacyl-tRNA biosynthesis, sulfur metabolism, butanoate metabolism, alanine, aspartate and glutamate metabolism, glutathione metabolism, glycine, serine and threonine metabolism in the root; glycolysis/gluconeogenesis in the stem; and biosynthesis of unsaturated fatty acids, galactose metabolism, cutin, suberine and wax biosynthesis in the leaf. It is important that cadmium inhibited root growth by inhibiting carbohydrate transport from the leaf to the root and promoted leaf growth by the accumulation of carbohydrates in the leaf. Furthermore, cadmium also restrained amino acid metabolism in the root of pumpkin seedlings. These results provide new information about how pumpkin seedlings respond to cadmium stress.

Metabolomics is an implement for testing the toxicity of antibiotics, and provides a comprehensive view of the overall response to stress; however, the connections between metabolites and biologic endpoints keep unclear in response to antibiotics. In this study, wheat seeds were exposed to tetracycline for 5 days. The results proved that tetracycline restrained growth, reduced chlorophyl and carotinoid contents and cell permeability, and increased reactive oxygen species (ROS) levels and malondialdehyde (MDA) content. Orthogonal partial least squares (OPLS) was used to analyze the connections between metabolites and biologic endpoints, which discovered that 11 metabolic pathways were significantly affected by tetracycline, and amino acid metabolism could largely apply to root growth and ROS accumulation, while carbohydrate metabolism could have a ruling effect on tetracycline-induced cell permeability. 13 metabolites all played active roles in mediating tetracycline’s effects on root length, root fresh weight and cell permeability but had no significant effects on ROS levels. The majority of metabolites with passive effects on root length, root fresh weight and cell permeability had active effects on ROS levels. These results offer a view about stress reaction of wheat to tetracycline.

Metalaxyl is one of the main fungicides used to control pepper blight caused by Phytophthora capsici. Metalaxyl resistance of P. capsici, caused by the long-term intense use of this fungicide, has become one of the most serious challenges facing pest management. To reveal the potential resistance mechanism of P. capsici to fungicide metalaxyl, a metalaxyl-resistant mutant strain SD1-9 was obtained under laboratory conditions. The pathogenicity test showed that mutant strain SD1-9 had different pathogenicity to different host plants with or without the treatment of metalaxyl compared with that of the wild type SD1. Comparative transcriptome sequencing of mutant strain SD1-9 and wild type SD1 led to the identification of 3845 differentially expressed genes, among them, 517 genes were upregulated, while 3328 genes were down-regulated in SD1-9 compared to that in the SD1. The expression levels of 10 genes were further verified by real-time RT-PCR. KEGG analysis showed that the differentially expressed genes were enriched in the peroxisome, endocytosis, alanine and tyrosine metabolism. The expression of the candidate gene XLOC_020226 during 10 life history stages was further studied, the results showed that expression level reached a maximum at the zoospores stage and basically showed a gradually increasing trend with increasing infection time in pepper leaves in SD1-9 strain, while its expression gradually increased in the SD1 strain throughout the 10 stages, indicated that XLOC_020226 may be related to the growth and pathogenicity of P. capsici. In summary, transcriptome analysis of plant pathogen P. capsici strains with different metalaxyl resistance not only provided database of the genes involved in the metalaxyl resistance of P. capsici, but also allowed us to gain novel insights into the potential resistance mechanism of P. capsici to metalaxyl in peppers.

Tetracycline is an antibiotic that frequently contaminates the environment. In this study, the growth and metabolites of ryegrass seedlings treated with tetracycline (0, 1, 10 or 100 mg/L) for 5 days were investigated. The results showed that the growth of ryegrass and the concentrations of carotenoid and chlorophyll decreased as the tetracycline concentration increased. Tetracycline increased the production of reactive oxygen species (ROS) and cell permeability and triggered mitochondrial membrane potential loss in the roots of ryegrass. The metabolic profiles of ryegrass differed between the control and tetracycline-treated groups. The contents of glucose, shikimic acid, aconitic acid, serine, lactose, phenylalanine, mannitol, galactose, gluconic acid, asparagine, and glucopyranose were positively correlated with root length and had high variable importance projection values. These compounds may have crucial functions in root extension. Tetracycline also affected aminoacyl-tRNA biosynthesis, nitrogen metabolism, and alanine, aspartate and glutamate metabolism in the roots. Tetracycline may affect root extension by regulating the synthesis/degradation of these metabolites or the activity of their biosynthetic pathways. These results provide an insight into the stress response of ryegrass to tetracycline.