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Transcriptomic and metabolomic profiling of Zea mays fed with urea and ammonium

ABSTRACT: Plant nutrition takes advantage by the simultaneous presence of more N forms in the rhizosphere. In the last decades the interplay between ammonium and nitrate acquisition systems in roots has been deeply investigated. Although widely used as fertilizers, the occurrence of cross connection between urea and ammonium nutrition has been scarcely studied in plants, especially at molecular level. In a recent paper we provided evidence that maize plants fed with urea and ammonium mix showed a better N-uptake efficiency than plants fed with ammonium or urea alone. To elucidate the molecular mechanism underlying this response, transcriptomic and metabolomic changes occurring in maize plants were investigated. Transcriptomic analyses indicated that several transporters and enzymes involved in N-nutrition were found upregulated by all three N-treatments (AMT1.3, NRT1.1, NRT2.1, GS1, GOGAT, GDH), confirming that urea is a direct source of N for plants. Depending on N-form available in nutrient solution a peculiar response at transcriptomic and metabolomic level was observed, especially after 24 hours of treatment. In comparison to one single N-form, urea and ammonium mix induced a prompt assimilation of N, characterized by an overaccumulation of main amino acids in shoots, and an upregulation of ZmAMT1.1. Moreover even a peculiar modulation of aquaporins, carbonic anydrases, glutamine synthetase, amino aspartate, as well as the glycolysis-TCA cycle was induced in roots by urea and ammonium mix. Depending on N-form available in the external media, even changes in phytohormone’s composition were observed in maize (CKs, ABA, JA); in particular, already after 24 hours of treatment, urea induced the accumulation of trans-zeatin in shoots. Through a multiomics approach, we provide for the first time molecular characterization of maize response to urea and ammonium nutrition. This study paves the way to formulate guidelines for the optimization of N fertilization of crops to improve the N use efficiency in plants and therefore limit N losses in the environment.

ORGANISM(S): Zea mays

PROVIDER: GSE167027 | GEO | 2021/11/24

REPOSITORIES: GEO

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Project description:In comparison with provision of either ammonium or nitrate alone, simultaneously supplying both forms of N results in superior growth and yield for the majority of plants including rice. Using a rice 22K oligo-array, we performed transcriptome analysis to identify genes of rice (Oryza sativa L. ssp. japonica) responsive to change of N-supply forms and N-starvation. Using the supply of ammonium nitrate (one to one molar ratio) as control, the total number of root genes that were equal or more than two fold up- or down- regulated was 445, 324, and 781 by upon supply of either ammonium or nitrate or continuous N starvation, respectively for 96 h. In the shoot the equivalent numbers were much smaller only 32, 58, and 165, respectively. Clustering of the rice genes associated with different environmental stresses revealed substantial organ specificity of the root and shoot to N starvation, and also to the N supply form. Genes encoding transporters for ammonium and nitrate, nitrate reductase, glutamate dehydrogenase, and aspartate amino transferase, showed great response to change of the N supply form, especially to N starvation. Some of the genes involved in chlorophyll metabolism, carbon fixation and assimilation, were enhanced by ammonium supply only, but significantly suppressed by N-starvation. In the shoot there was increased expression of more general stress genes under nitrate when compared to ammonium nutrition. In the root the reverse situation was true with more apparent stress under ammonium nutrition. The microarray approach has revealed new levels of complexity in the response of rice to the form of N supply. Experiment Overall Design: Rice seedlings were grown in a hydroponic system in a growth chamber with control of both temperature and light. After normal growth for two weeks and for one week with completely avoiding any N source, the plants at four and a half leaf stage were re-supplied with ammonium nitrate (equal amount of either form of N), or only ammonium (ammonium sulphate and ammonium chloride), or only nitrate (calcium nitrate and magnesium nitrate), and continuing at zero N (N starvation). All the other essential nutrients were the same for all four treatments, except for sulfate and chloride which ranged between 1.1 â 2.6 mM and 0.5 â 2.5 mM, respectively. In Arabidopsis, addition of 3 mM Cl to âcontrolsâ did not produce any changes in the expression of genes in an experiment investigating the re-supply of 3 mM nitrate (Scheible et al., 2004). In other microarray experiments, extra addition of 5 mM Cl for Arabidopsis (Wang et al., 2000; Wang et al., 2004) and 1.4 mM sulphate for tomato (Wang et al., 2001) were used to replace nitrate for identifying the N deprivation responsive genes. Therefore, we assume that the relative smaller difference in sulfate and chloride concentrations among the four treatments in the normal supply range for plants would not significantly affect the expression profile of genes responsible for changes in N supply form and starvation in our experiments. Experiment Overall Design: For identifying the genes responding to the various N conditions by micro-array analysis, we extracted total RNA respectively from the roots and shoots at the 96 h after initiation of the four respective treatments. We used amplified and labeled cRNA from ammonium nitrate treatment as control, we performed array-hybridization for the cRNA from the treatment of single ammonium form, single nitrate form, or continuous N depletion, respectively. Agilent 60-mer oligonucleotide arrays containing 21,938 unique transcription units (Agilent Technologies, Tokyo, Japan) were used. Two biological replicates of each treatment were performed for microarray analyses.

Project description:As maize seedlings germinate into the soil, they encounter an environment teeming with insects seeking rich sources of nutrition. Maize presumably has developed a number of molecular mechanisms to ensure survival at the beginning of its life cycle. Bioassays indicated maize seedlings were more toxic to caterpillars than shoots from 3 or 4 leafed plants. Microarray technology was utilized to document the expression of a number of genes with potential defensive functions in seedling tissue. In addition to elevated levels of the genes involved in the biosynthesis of DIMBOA (2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one), an anti-insect resistance molecule, other highly expressed genes in the seedling encode the following putative proteins: defensin, hydroxyproline and proline-rich protein, thaumatin-like protein, lipase, cystatin, protease inhibitor, and a variety of proteases. Changes in the levels of gene expression by the microarray technology were well correlated to results using quantitative RT-PCR. The potential resistance genes identified occurred mainly on chromosomes 1 and 5 in the B73 genome. Analysis of promoters of four DIMBOA biosynthetic genes determined that a Dof transcription factor, two of which were differentially expressed in three vegetative stages, is possibly involved in regulation of the DIMBOA biosynthetic pathway. The results indicate that maize employs a wide variety of potential resistance mechanisms in seedling tissue to resist a possible insect attack. Three different Zea mays plant (B73) life stages were sampled: a) seedlings, which had grown just above the soil line, which also served as reference tissue (reference tissue was always labeled Cy5 and consisted of leaf shoots pooled from 12 plants); b) leaf shoots from plants with four leaves; and c) leaf shoots from plants with six leaves. There were 3 samples (biological replications) of each treatment (6 plants per sample) and the samples were labeled Cy3 and which were combined with a reference chip for a total of 9 chips: (3 biological replicates of seedling, 4 leaf stage and 6 leaf stage).

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Transcriptomic and metabolomic profiling of Zea mays fed with urea and ammonium

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