Characterization of metabolic states of Arabidopsis thaliana under diverse carbon and nitrogen nutrient conditions via targeted metabolomic analysis

Chemical imaging reveals diverse functions of tricarboxylic acid metabolites in root growth and development

Understanding how plants grow is critical for agriculture and fundamental for illuminating principles of multicellular development. Here, we apply desorption electrospray ionization mass spectrometry imaging (DESI-MSI) to the chemical mapping of the developing maize root. This technique reveals a range of small molecule distribution patterns across the gradient of stem cell differentiation in the root. To understand the developmental logic of these patterns, we examine tricarboxylic acid (TCA) cycle metabolites. In both Arabidopsis and maize, we find evidence that elements of the TCA cycle are enriched in developmentally opposing regions. We find that these metabolites, particularly succinate, aconitate, citrate, and α-ketoglutarate, control root development in diverse and distinct ways. Critically, the developmental effects of certain TCA metabolites on stem cell behavior do not correlate with changes in ATP production. These results present insights into development and suggest practical means for controlling plant growth.

Leaf cytokinin accumulation promotes potato growth in mixed nitrogen supply by coordination of nitrogen and carbon metabolism

The source and sink balance determines crop growth, which is largely modulated by nitrogen (N) supplies. The use of mixed ammonium and nitrate as N supply can improve plant growth, however mechanisms involving the coordination of carbon and N metabolism are not well understood. Here, we investigated potato plants responding to N forms and confirmed that, compared with sole nitrate supply, mixed N (75 %/25 % nitrate/ammonium) enhanced leaf area, photosynthetic activity and N metabolism and accordingly resulted in outgrowth of stolons and shoot axillary buds. Cytokinin transportation in xylem sap and local cytokinin synthesis in leaves were up-regulated in mixed-N-treated potato plants relative to sole nitrate provision; and exogenous application of 6-benzylaminopurine in addition to sole nitrate restored leaf area, photosynthetic capacity and N content in leaves to the similar as those under mixed-N treatment. Partial defoliation, an effective method to enhance the sink strength, induced more cytokinin content in leaflets under two treatments relative to their respective controls and ultimately resulted in larger photosynthesis capacity and leaf area. These results suggest that mixed-N-enhanced plant growth through the coordination of carbon and N metabolism largely depends on the signal molecule cytokinin modulated by N supplies.

Loss of a pyridoxal-phosphate phosphatase rescues Arabidopsis lacking an endoplasmic reticulum ATP carrier

The endoplasmic reticulum (ER)-located ATP/ADP-antiporter (ER-ANT1) occurs specifically in vascular plants. Structurally different transporters mediate energy provision to the ER, but the cellular function of ER-ANT1 is still unknown. Arabidopsis (Arabidopsis thaliana) mutants lacking ER-ANT1 (er-ant1 plants) exhibit a photorespiratory phenotype accompanied by high glycine levels and stunted growth, pointing to an inhibition of glycine decarboxylase (GDC). To reveal whether it is possible to suppress this marked phenotype, we exploited the power of a forward genetic screen. Absence of a so far uncharacterized member of the HaloAcid Dehalogenase (HAD)-like hydrolase family strongly suppressed the dwarf phenotype of er-ant1 plants. Localization studies suggested that the corresponding protein locates to chloroplasts, and activity assays showed that the enzyme dephosphorylates, with high substrate affinity, the B6 vitamer pyridoxal 5'-phosphate (PLP). Additional physiological experiments identified imbalances in vitamin B6 homeostasis in er-ant1 mutants. Our data suggest that impaired chloroplast metabolism, but not decreased GDC activity, causes the er-ant1 mutant dwarf phenotype. We present a hypothesis, setting transport of PLP by ER-ANT1 and chloroplastic PLP dephosphorylation in the cellular context. With the identification of this HAD-type PLP phosphatase, we also provide insight into B6 vitamer homeostasis.

Excessive ammonium assimilation by plastidic glutamine synthetase causes ammonium toxicity in Arabidopsis thaliana

Plants use nitrate, ammonium, and organic nitrogen in the soil as nitrogen sources. Since the elevated CO₂ environment predicted for the near future will reduce nitrate utilization by C₃ species, ammonium is attracting great interest. However, abundant ammonium nutrition impairs growth, i.e., ammonium toxicity, the primary cause of which remains to be determined. Here, we show that ammonium assimilation by GLUTAMINE SYNTHETASE 2 (GLN2) localized in the plastid rather than ammonium accumulation is a primary cause for toxicity, which challenges the textbook knowledge. With exposure to toxic levels of ammonium, the shoot GLN2 reaction produced an abundance of protons within cells, thereby elevating shoot acidity and stimulating expression of acidic stress-responsive genes. Application of an alkaline ammonia solution to the ammonium medium efficiently alleviated the ammonium toxicity with a concomitant reduction in shoot acidity. Consequently, we conclude that a primary cause of ammonium toxicity is acidic stress.

Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters

In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.

Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters

In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.

QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F₂ and F₂-derived F₃ families) and late (F₆ and F₇, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F₂ and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F₂ mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

How does nitrate regulate plant senescence?

Nitrogen is an essential macronutrient for plant growth and development and plays an important role in the whole life process of plants. Nitrogen is an important component of amino acids, chlorophyll, plant hormones and secondary metabolites. Nitrogen deficiency leads to early senescence in plants, which is accompanied by changes in gene expression, metabolism, growth, development, and physiological and biochemical traits, which ensures efficient nitrogen recycling and enhances the plant's tolerance to low nitrogen. Therefore, it is very important to understand the adaptation mechanisms of plants under nitrogen deficiency for the efficient utilization of nitrogen and gene regulation. With the popularization of molecular biology, bioinformatics and transgenic technology, the metabolic pathways of nitrogen-deficient plants have been verified, and important progress has been made. However, how the responses of plants to nitrogen deficiency affect the biological processes of the plants is not well understood. The current research also cannot completely explain how the metabolic pathways identified show other reactions or phenotypes through interactions or cascades after nitrogen inhibition. Nitrate is the main form of nitrogen absorption. In this review, we discuss the role of nitrate in plant senescence. Understanding how nitrate inhibition affects nitrate absorption, transport, and assimilation; chlorophyll synthesis; photosynthesis; anthocyanin synthesis; and plant hormone synthesis is key to sustainable agriculture.

Quantitative proteomics analysis of tomato growth inhibition by ammonium nitrogen

As a single nitrogen source, ammonium (NH₄⁺) can inhibit the growth of plants, especially when applied in excess. Tandem mass tag (TMT) quantitative proteomics technology was employed in the current study to explore and analyze the mechanisms of ammonium-induced inhibition. F₁ tomato (Lycopersicon esculentum Mill) was used in this study. Seedlings at the four leaf-stages grown in a greenhouse were irrigated using nutrient solution with NH₄⁺-N as single nitrogen source (15 mmol L^-1, single NO₃^--N as control) for 5 weeks. Compared to the control, the root biomass of NH₄⁺-N-treated seedlings decreased by 50%. In addition, NH₄⁺ content in roots was 2.83-fold increased and soluble sugar and protein contents were increased. However, the starch content did not change significantly. The activities of glutamine synthetase (GS), glutamate synthetase (GOGAT) and glutamate dehydrogenase (GDH), which are involved in ammonium assimilation, were increased, and glutamine (Gln) content was also increased. However, glutamate (Glu) content, which is important for amino transfer, did not significantly increase. Ammonium assimilation was inhibited. Root quantitative proteomics showed that carbonic anhydrase Q5NE21 was significantly downregulated. Although K4BPV5 and K4D9J3 proteins, which improve ammonium assimilation, were upregulated, ammonium assimilation was limited. In addition, NH₄⁺ accumulated, which is likely due to Q5NE21 downregulation. Meanwhile, cell wall metabolism related to phenylpropanoid biosynthesis was altered due to the accumulation of NH₄⁺ levels. Subsequently, tomato root growth was inhibited.

Repeated fed-batch strategy and metabolomic analysis to achieve high docosahexaenoic acid productivity in Crypthecodinium cohnii

Background

Docosahexaenoic acid (DHA) is essential for human diet. However, high production cost of DHA using C. cohnii makes it currently less competitive commercially, which is mainly caused by low DHA productivity. In recent years, repeated fed-batch strategies have been evaluated for increasing the production of many fermentation products. The reduction in terms of stability of culture system was one of the major challenges for repeated fed-batch fermentation. However, the possible mechanisms responsible for the decreased stability of the culture system in the repeated fed-batch fermentation are so far less investigated, restricting the efforts to further improve the productivity. In this study, a repeated fed-batch strategy for DHA production using C. cohnii M-1-2 was evaluated to improve DHA productivity and reduce production cost, and then the underlying mechanisms related to the gradually decreased stability of the culture system in repeated fed-batch culture were explored through LC– and GC–MS metabolomic analyses.

Results

It was discovered that glucose concentration at 15–27 g/L and 80% medium replacement ratio were suitable for the growth of C. cohnii M-1-2 during the repeated fed-batch culture. A four-cycle repeated fed-batch culture was successfully developed and assessed at the optimum cultivation parameters, resulting in increasing the total DHA productivity by 26.28% compared with the highest DHA productivity of 57.08 mg/L/h reported using C. cohnii, including the time required for preparing seed culture and fermentor. In addition, LC– and GC–MS metabolomics analyses showed that the gradually decreased nitrogen utilization capacity, and down-regulated glycolysis and TCA cycle were correlated with the decreased stability of the culture system during the long-time repeated fed-batch culture. At last, some biomarkers, such as Pyr, Cit, OXA, FUM, l-tryptophan, l-threonine, l-leucine, serotonin, and 4-guanidinobutyric acid, correlated with the stability of culture system of C. cohnii M-1-2 were identified.

Conclusions

The study proved that repeated fed-batch cultivation was an efficient and energy-saving strategy for industrial production of DHA using C. cohnii, which could also be useful for cultivation of other microbes to improve productivity and reduce production cost. In addition, the mechanisms study at metabolite level can also be useful to further optimize production processes for C. cohnii and other microbes.

Overexpression of OsMYB305 in Rice Enhances the Nitrogen Uptake Under Low-Nitrogen Condition

Excessive nitrogen fertilizer application causes severe environmental degradation and drives up agricultural production costs. Thus, improving crop nitrogen use efficiency (NUE) is essential for the development of sustainable agriculture. Here, we characterized the roles of the MYB transcription factor OsMYB305 in nitrogen uptake and assimilation in rice. OsMYB305 encoded a transcriptional activator and its expression was induced by N deficiency in rice root. Under low-N condition, OsMYB305 overexpression significantly increased the tiller number, shoot dry weight and total N concentration. In the roots of OsMYB305-OE rice lines, the expression of OsNRT2.1, OsNRT2.2, OsNAR2.1, and OsNiR2 was up-regulated and 15NO3 - influx was significantly increased. In contrast, the expression of lignocellulose biosynthesis-related genes was repressed so that cellulose content decreased, and soluble sugar concentration increased. Certain intermediates in the glycolytic pathway and the tricarboxylic acid cycle were significantly altered and NADH-GOGAT, Pyr-K, and G6PDH were markedly elevated in the roots of OsMYB305-OE rice lines grown under low-N condition. Our results revealed that OsMYB305 overexpression suppressed cellulose biosynthesis under low-nitrogen condition, thereby freeing up carbohydrate for nitrate uptake and assimilation and enhancing rice growth. OsMYB305 is a potential molecular target for increasing NUE in rice.

Exogenous Treatment with Glutamate Induces Immune Responses in Arabidopsis

Plant resistance inducers (PRIs) are compounds that protect plants from diseases by activating immunity responses. Exogenous treatment with glutamate (Glu), an important amino acid for all living organisms, induces resistance against fungal pathogens in rice and tomato. To understand the molecular mechanisms of Glu-induced immunity, we used the Arabidopsis model system. We found that exogenous treatment with Glu induces resistance against pathogens in Arabidopsis. Consistent with this, transcriptome analyses of Arabidopsis seedlings showed that Glu significantly induces the expression of wound-, defense-, and stress-related genes. Interestingly, Glu activates the expression of genes induced by pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns at much later time points than the flg22 peptide, which is a bacterial-derived PAMP. The Glu receptor-like (GLR) proteins GLR3.3 and GLR3.6 are involved in the early expression of Glu-inducible genes; however, the sustained expression of these genes does not require the GLR proteins. Glu-inducible gene expression is also not affected by mutations in genes that encode PAMP receptors (EFR, FLS2, and CERK1), regulators of pattern-triggered immunity (BAK1, BKK1, BIK1, and PBL1), or a salicylic acid biosynthesis enzyme (SID2). The treatment of roots with Glu activates the expression of PAMP-, salicylic acid-, and jasmonic acid-inducible genes in leaves. Moreover, the treatment of roots with Glu primes chitin-induced responses in leaves, possibly through transcriptional activation of LYSIN-MOTIF RECEPTOR-LIKE KINASE 5 (LYK5), which encodes a chitin receptor. Because Glu treatment does not cause discernible growth retardation, Glu can be used as an effective PRI.

Potential biomonitoring of atmospheric carbon dioxide in Coffea arabica leaves using near-infrared spectroscopy and partial least squares discriminant analysis

The potencial of Coffea arabica leaves as bioindicators of atmospheric carbon dioxide (CO₂) was evaluated in a free-air carbon dioxide enrichment (FACE) experiment by using near-infrared reflectance (NIR) spectroscopy for direct analysis and partial least squares discriminant analysis (PLS-DA). A supervised classification model was built and validated from the spectra of coffee leaves grown under elevated and current CO₂ levels. PLS-DA allowed correct test set classification of 92% of the elevated-CO₂ level leaves and 100% of the current-CO₂ level leaves. The spectral bands accounting for the discrimination of the elevated-CO₂ leaves were at 1657 and 1698 nm, as indicated by the variable importance in the projection (VIP) score together with the regression coefficients. Seven months after suspension of enriched CO₂, returning to current-CO₂ levels, new spectral measurements were made and subjected to PLS-DA analysis. The predictive model correctly classified all leaves as grown under current-CO₂ levels. The fingerprints suggest that after suspension of elevated-CO₂, the spectral changes observed previously disappeared. The recovery could be triggered by two reasons: the relief of the stress stimulus or the perception of a return of favorable conditions. In addition, the results demonstrate that NIR spectroscopy can provide a rapid, nondestructive, and environmentally friendly method for biomonitoring leaves suffering environmental modification. Finally, C. arabica leaves associated with NIR and mathematical models have the potential to become a good biomonitoring system.

Association analysis of phenotypic and metabolomic changes in Arabidopsis accessions and their F1 hybrids affected by different photoperiod and sucrose supply

Photoperiod and sucrose (Suc) assimilation play important roles in the regulation of plant growth and development. However, it remains unclear how natural variation of plants could contribute to metabolic changes under various growth conditions. Here, we investigated the developmental and metabolomic responses of two natural accessions of Arabidopsis thaliana, Columbia (Col) and C24, and their reciprocal F₁ hybrids grown under four carbon source regimens, i.e., two different photoperiods and the presence or absence of exogenous Suc supply. The effect of exogenous Suc clearly appeared in the growth of Col and the F₁ hybrid but not in C24, whereas long-day conditions had significant positive effects on the growth of all lines. Comparative metabolite profiling of Col, C24, and the F₁ hybrid revealed that changes in metabolite levels, particularly sugars, were highly dependent on genotype-specific responses rather than growth conditions. The presence of Suc led to over-accumulation of seven metabolites, including four sugars, a polyamine, and two amino acids in C24, whereas no such accumulation was observed in the profiles of Col and the F₁ hybrid. Thus, the comparative metabolite profiling revealed that the two parental lines of the hybrid show a distinct difference in sugar metabolism.

Sugar-induced de novo cytokinin biosynthesis contributes to Arabidopsis growth under elevated CO2

Carbon availability is a major regulatory factor in plant growth and development. Cytokinins, plant hormones that play important roles in various aspects of growth and development, have been implicated in the carbon-dependent regulation of plant growth; however, the details of their involvement remain to be elucidated. Here, we report that sugar-induced cytokinin biosynthesis plays a role in growth enhancement under elevated CO₂ in Arabidopsis thaliana. Growing Arabidopsis seedlings under elevated CO₂ resulted in an accumulation of cytokinin precursors that preceded growth enhancement. In roots, elevated CO₂ induced two genes involved in de novo cytokinin biosynthesis: an adenosine phosphate-isopentenyltransferase gene, AtIPT3, and a cytochrome P450 monooxygenase gene, CYP735A2. The expression of these genes was inhibited by a photosynthesis inhibitor, DCMU, under elevated CO₂, and was enhanced by sugar supplements, indicating that photosynthetically generated sugars are responsible for the induction. Consistently, cytokinin precursor accumulation was enhanced by sugar supplements. Cytokinin biosynthetic mutants were impaired in growth enhancement under elevated CO₂, demonstrating the involvement of de novo cytokinin biosynthesis for a robust growth response. We propose that plants employ a system to regulate growth in response to elevated CO₂ in which photosynthetically generated sugars induce de novo cytokinin biosynthesis for growth regulation.

Confirmation of mesophyll signals controlling stomatal responses by a newly devised transplanting method

There are opposing views on whether the responses of stomata to environmental stimuli are all autonomous reactions of stomatal guard cells or whether mesophyll is involved in these responses. Transplanting isolated epidermis onto mesophyll is a potent methodology for examining the roles of mesophyll-derived signals in stomatal responses. Here we report on development of a new transplanting method. Leaf segments of Commelina communis L. were pretreated in the light or dark at 10, 39 or 70Pa ambient CO2 for 1h. Then the abaxial epidermises were removed and the epidermal strips prepared from the other leaves kept in the dark at 39Pa CO2, were transplanted onto the mesophyll. After illumination of the transplants for 1h at 39Pa CO2, stomatal apertures were measured. We also examined the molecular sizes of the mesophyll signals by inserting the dialysis membrane permeable to molecules smaller than 100-500Da or 500-1000Da between the epidermis and mesophyll. Mesophyll pretreatments in the light at low CO2 partial pressures accelerated stomatal opening in the transplanted epidermal strips, whereas pretreatments at 70Pa CO2 suppressed stomatal opening. Insertion of these dialysis membranes did not suppress stomatal opening significantly at 10Pa CO2 in the light, whereas insertion of the 100-500Da membrane decelerated stomatal closure at high CO2. It is probable that the mesophyll signals inducing stomatal opening at low CO2 in the light would permeate both membranes, and that those inducing stomatal closure at high CO2 would not permeate the 100-500Da membrane. Possible signal compounds are discussed.

Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum

Massively input and accumulated ammonium is one of the main causes of eutrophication in aquatic ecosystems, which severely deteriorates water quality. Previous studies showed that one of the commonly used macrophytes, Myriophyllum aquaticum, was capable of not only withstanding ammonium of high concentration, but also efficiently assimilating extracellular ammonium to constitutive amino acids and proteins. However, the genetic mechanism regulating such efficient nitrogen metabolism in M. aquaticum is still poorly understood. Therefore, RNA-based analysis was performed in this study to understand the ammonium regulatory mechanism in M. aquaticum in response to various concentrations of ammonium. A total of 7721 genes were differentially expressed, of which those related to nitrogen-transport, assimilation, and remobilization were highly-regulated in response to various concentrations of ammonium. We have also identified transcription factors and protein kinases that were rapidly induced in response to ammonium, which suggests their involvement in ammonium-mediated signalling. Meanwhile, secondary metabolism including phenolics and anthocyanins biosynthesis was also activated in response to various concentrations of ammonium, especially at high ammonium concentrations. These results proposed a complex physiological and genetic regulation network related to nitrogen, carbohydrate, transcription factors, and secondary metabolism for nitrogen use efficiency in M. aquaticum.

Increased biomass accumulation in maize grown in mixed nitrogen supply is mediated by auxin synthesis

The use of mixed nitrate and ammonium as a nitrogen source can improve plant growth. Here, we used metabolomics and transcriptomics to study the underlying mechanisms. Maize plants were grown hydroponically in the presence of three forms of nitrogen (nitrate alone, 75%/25% nitrate/ammonium, and ammonium alone). Plants grown with mixed nitrogen had a higher photosynthetic rate than those supplied only with nitrate, and had the highest leaf area and shoot and root biomass among the three nitrogen treatments. In shoot and root, the concentration of nitrogenous compounds (ammonium, glutamine, and asparagine) and carbohydrates (sucrose, glucose, and fructose) in plants with a mixed nitrogen supply was higher than that with nitrate supply, but lower than that with ammonium supply. The activity of the related enzymes (glutamate synthase, asparagine synthase, phosphoenolpyruvate carboxylase, invertase, and ADP-glucose pyrophosphorylase) changed accordingly. Specifically, the mixed nitrogen source enhanced auxin synthesis via the shikimic acid pathway, as indicated by the higher levels of phosphoenolpyruvate and tryptophan compared with the other two treatments. The expression of corresponding genes involving auxin synthesis and response was up-regulated. Supply of only ammonium resulted in high levels of glutamine and asparagine, starch, and trehalose hexaphosphate. We conclude that, in addition to increased photosynthesis, mixed nitrogen supply enhances leaf growth via increasing auxin synthesis to build a large sink for carbon and nitrogen utilization, which, in turn, facilitates further carbon assimilation and nitrogen uptake.

Complex regulatory network allows Myriophyllum aquaticum to thrive under high-concentration ammonia toxicity

Plants easily experience ammonia (NH₄⁺) toxicity, especially aquatic plants. However, a unique wetland plant species, Myriophyllum aquaticum, can survive in livestock wastewater with more than 26 mM NH₄⁺. In this study, the mechanisms of the M. aquaticum response to NH₄⁺ toxicity were analysed with RNA-seq. Preliminary analysis of enzyme activities indicated that key enzymes involved in nitrogen metabolism were activated to assimilate toxic NH₄⁺ into amino acids and proteins. In response to photosystem damage, M. aquaticum seemed to remobilize starch and cellulose for greater carbon and energy supplies to resist NH₄⁺ toxicity. Antioxidative enzyme activity and the secondary metabolite content were significantly elevated for reactive oxygen species removal. Transcriptomic analyses also revealed that genes involved in diverse functions (e.g., nitrogen, carbon and secondary metabolisms) were highly responsive to NH₄⁺ stress. These results suggested that a complex physiological and genetic regulatory network in M. aquaticum contributes to its NH₄⁺ tolerance.

Nitrogen Feeding Strategies and Metabolomic Analysis To Alleviate High-Nitrogen Inhibition on Docosahexaenoic Acid Production in Crypthecodinium cohnii

It is well-known that high-nitrogen content inhibits cell growth and docosahexaenoic acid (DHA) biosynthesis in heterotrophic microalgae Crypthecodinium cohnii. In this study, two nitrogen feeding strategies, pulse-feeding and continuous-feeding, were evaluated to alleviate high-nitrogen inhibition effects on C. cohnii. The results showed that continuous-feeding with a medium solution containing 50% ( w/v) yeast extract at 2.1 mL/h during 12-96 h was the optimal nitrogen feeding strategy for the fermentation process, when glucose concentration was maintained at 15-27 g/L during the same period. With the optimized strategy, 71.2 g/L of dry cell weight and DHA productivity of 57.1 mg/L/h were achieved. In addition, metabolomic analysis was applied to determine the metabolic changes during different nitrogen feeding conditions, and the changes in amino acids, polysaccharides, purines, and pentose phosphate pathway were observed, providing valuable metabolite-level information for exploring the mechanism of the high-nitrogen inhibition effect and further improving DHA productivity in C. cohnii.

Effects of Elevated Atmospheric CO2 on Respiratory Rates in Mature Leaves of Two Rice Cultivars Grown at a Free-Air CO2 Enrichment Site and Analyses of the Underlying Mechanisms

Respiratory CO2 efflux and O2 uptake rates in leaves change in response to the growth CO2 concentration ([CO2]). The degrees of change vary depending on the responses of cellular processes such as nitrogen (N) assimilation and accumulation of organic acids to growth [CO2]. However, the underlying mechanisms remain unclear. Here, we examined the respiratory characteristics of mature leaves of two rice varieties with different yield capacities at different growth stages under ambient and elevated [CO2] conditions at a free-air CO2 enrichment site. We also examined the effect of increased water temperature on leaf respiration. We measured the rates of CO2 efflux and O2 uptake, and determined N contents, primary metabolite contents and maximal activities of respiratory enzymes. The leaf CO2 efflux rates decreased in plants grown at elevated [CO2] in both varieties, and were higher in high-yielding Takanari than in Koshihikari. The leaf O2 uptake rates showed little change with respect to growth [CO2] and variety. The increased water temperature did not significantly affect the CO2 efflux and O2 uptake rates. The N and amino acid contents were significantly higher in Takanari than in Koshihikari. The enhanced N assimilation in Takanari may have consumed more respiratory NADH, leading to higher CO2 efflux rates. In Koshihikari, the ratio of tricarboxylic acid (TCA) cycle intermediates changed and maximal activities of enzymes in the TCA cycle decreased at elevated [CO2]. Therefore, the decreased rates of CO2 efflux in Koshihikari may be due to the decreased activities of TCA cycle enzymes at elevated [CO2].

Nitrification in agricultural soils: impact, actors and mitigation

Nitrogen is one of the most important nutrients for plant growth and hence heavily applied in agricultural systems via fertilization. Nitrification, that is, the conversion of ammonium via nitrite to nitrate by soil microorganisms, however, leads to nitrate leaching and gaseous nitrous oxide production and as such to an up to 50% loss of nitrogen availability for the plant. Nitrate leaching also results in eutrophication of groundwater, drinking water and recreational waters, toxic algal blooms and biodiversity loss, while nitrous oxide is a greenhouse gas with a global warming potential 300× greater than carbon dioxide. Logically, inhibition of nitrification is an important strategy used in agriculture to reduce nitrogen losses, and contributes to a more environmental-friendly practice. However, recently identified and crucial players in nitrification, that is, ammonia-oxidizing archaea and comammox bacteria, seem to be under-investigated in this respect. In this review, we give an update on the different pathways in ammonia oxidation, the relevance for agriculture and the interaction with nitrification inhibitors. As such, we hope to pinpoint possible strategies to optimize the efficiency of nitrification inhibition.

Elevated CO2 Induces Root Defensive Mechanisms in Tomato Plants When Dealing with Ammonium Toxicity

An adequate carbon supply is fundamental for plants to thrive under ammonium stress. In this work, we studied the mechanisms involved in tomato (Solanum lycopersicum L.) response to ammonium toxicity when grown under ambient or elevated CO2 conditions (400 or 800 p.p.m. CO2). Tomato roots were observed to be the primary organ dealing with ammonium nutrition. We therefore analyzed nitrogen (N) and carbon (C) metabolism in the roots, integrating the physiological response with transcriptomic regulation. Elevated levels of CO2 preferentially stimulated root growth despite the high ammonium content. The induction of anaplerotic enzymes from the tricarboxylic acid (TCA) cycle led to enhanced amino acid synthesis under ammonium nutrition. Furthermore, the root transcriptional response to ammonium toxicity was improved by CO2-enriched conditions, leading to higher expression of stress-related genes, as well as enhanced modulation of genes related to signaling, transcription, transport and hormone metabolism. Tomato roots exposed to ammonium stress also showed a defense-like transcriptional response according to the modulation of genes related to detoxification and secondary metabolism, involving principally terpenoid and phenolic compounds. These results indicate that increasing C supply allowed the co-ordinated regulation of root defense mechanisms when dealing with ammonium toxicity.

Starch as a source, starch as a sink: the bifunctional role of starch in carbon allocation

Starch commands a central role in the carbon budget of the majority of plants on earth, and its biological role changes during development and in response to the environment. Throughout the life of a plant, starch plays a dual role in carbon allocation, acting as both a source, releasing carbon reserves in leaves for growth and development, and as a sink, either as a dedicated starch store in its own right (in seeds and tubers), or as a temporary reserve of carbon contributing to sink strength, in organs such as flowers, fruits, and developing non-starchy seeds. The presence of starch in tissues and organs thus has a profound impact on the physiology of the growing plant as its synthesis and degradation governs the availability of free sugars, which in turn control various growth and developmental processes. This review attempts to summarize the large body of information currently available on starch metabolism and its relationship to wider aspects of carbon metabolism and plant nutrition. It highlights gaps in our knowledge and points to research areas that show promise for bioengineering and manipulation of starch metabolism in order to achieve more desirable phenotypes such as increased yield or plant biomass.

Interactions between nitrate and ammonium in their uptake, allocation, assimilation, and signaling in plants

Nitrogen (N) availability is a major factor determining plant growth and productivity. Plants acquire inorganic N from the soil, mainly in the form of nitrate and ammonium. To date, researchers have focused on these N sources, and demonstrated that plants exhibit elaborate responses at both physiological and morphological levels. Mixtures of nitrate and ammonium are beneficial in terms of plant growth, as compared to nitrate or ammonium alone, and therefore synergistic responses to both N sources are predicted at different steps ranging from acquisition to assimilation. In this review, we summarize interactions between nitrate and ammonium with respect to uptake, allocation, assimilation, and signaling. Given that cultivated land often contains both nitrate and ammonium, a better understanding of the synergism between these N sources should help to identify targets with the potential to improve crop productivity.

CO2 enrichment modulates ammonium nutrition in tomato adjusting carbon and nitrogen metabolism to stomatal conductance

Ammonium (NH4(+)) toxicity typically occurs in plants exposed to high environmental NH4(+) concentration. NH4(+) assimilating capacity may act as a biochemical mechanism avoiding its toxic accumulation but requires a fine tuning between nitrogen assimilating enzymes and carbon anaplerotic routes. In this work, we hypothesized that extra C supply, exposing tomato plants cv. Agora Hybrid F1 to elevated atmospheric CO2, could improve photosynthetic process and thus ameliorate NH4(+) assimilation and tolerance. Plants were grown under nitrate (NO3(-)) or NH4(+) as N source (5-15mM), under two atmospheric CO2 levels, 400 and 800ppm. Growth and gas exchange parameters, (15)N isotopic signature, C and N metabolites and enzymatic activities were determined. Plants under 7.5mM N equally grew independently of the N source, while higher ammonium supply resulted toxic for growth. However, specific stomatal closure occurred in 7.5mM NH4(+)-fed plants under elevated CO2 improving water use efficiency (WUE) but compromising plant N status. Elevated CO2 annulled the induction of TCA anaplerotic enzymes observed at non-toxic NH4(+) nutrition under ambient CO2. Finally, CO2 enrichment benefited tomato growth under both nutritions, and although it did not alleviate tomato NH4(+) tolerance it did differentially regulate plant metabolism in N-source and -dose dependent manner.

Effects of Elevated Atmospheric CO2 on Primary Metabolite Levels in Arabidopsis thaliana Col-0 Leaves: An Examination of Metabolome Data

Elevated atmospheric CO(2) concentrations ([CO(2)]) affect primary metabolite levels because CO(2) is a direct substrate for photosynthesis. In several studies, the responses of primary metabolite levels have been examined using Arabidopsis thaliana leaves, but these results have not been comprehensively discussed. Here, we examined metabolome data for A. thaliana accession Col-0 leaves that were grown at elevated [CO(2)] with sufficient nitrogen (N) nutrition. At elevated [CO(2)], starch, monosaccharides and several major amino acids accumulated in leaves. The degree of accumulation depended on whether the rooting medium contained NH(4) (+) or only NO(3) (-). Because low N conditions induce an increase in carbohydrates similar to that of elevated [CO(2)], we compared the responses of primary metabolite levels between elevated [CO(2)] and low N conditions. Levels of the tricarboxylic acid (TCA) cycle-associated organic acids and major amino acids decreased with low N, but not with elevated [CO(2)]. Even at elevated [CO(2)], the low N induced the decreases in the levels of organic acids and major amino acids. A small sink size also affects the primary metabolite response patterns in leaves under elevated [CO(2)] conditions. Thus, care is necessary when interpreting primary metabolite changes in leaves of field-grown plants.

Emergence of a new step towards understanding the molecular mechanisms underlying nitrate-regulated gene expression

Nitrogen is one of the primary macronutrients of plants, and nitrate is the most abundant inorganic form of nitrogen in soils. Plants take up nitrate in soils and utilize it both for nitrogen assimilation and as a signalling molecule. Thus, an essential role for nitrate in plants is triggering changes in gene expression patterns, including immediate induction of the expression of genes involved in nitrate transport and assimilation, as well as several transcription factor genes and genes related to carbon metabolism and cytokinin biosynthesis and response. Significant progress has been made in recent years towards understanding the molecular mechanisms underlying nitrate-regulated gene expression in higher plants; a new stage in our understanding of this process is emerging. A key finding is the identification of NIN-like proteins (NLPs) as transcription factors governing nitrate-inducible gene expression. NLPs bind to nitrate-responsive DNA elements (NREs) located at nitrate-inducible gene loci and activate their NRE-dependent expression. Importantly, post-translational regulation of NLP activity by nitrate signalling was strongly suggested to be a vital process in NLP-mediated transcriptional activation and subsequent nitrate responses. We present an overview of the current knowledge of the molecular mechanisms underlying nitrate-regulated gene expression in higher plants.

A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches

Nitrogen (N), as an essential element in amino acids, nucleotides, and proteins, is a key factor in plant growth and development. Omics approaches such as metabolomics and transcriptomics have become a promising way to inspect complex network interactions in N metabolism and can be used for monitoring the uptake and regulation, translocation, and remobilization of N. In this review, the authors highlight recent progress in omics approaches, including transcript profiling using microarrays and deep sequencing, and show recent technical developments in metabolite profiling for N studies. Further, network analysis studies including network inference methods with correlations, information-theoretic measures, and a network concept to examine gene expression clusters in relation to N regulatory systems in plants are introduced, and integrating network inference methods and integrated networks using multiple omics data are discussed. Finally, this review summarizes recent omics application examples using metabolite and/or transcript profiling analysis to elucidate the regulation of N metabolism and signalling and the coordination of N and carbon metabolism in model plants (Arabidopsis and rice), crops (tomato, maize, and legumes), and trees (Populus).

Regulation of senescence under elevated atmospheric CO₂ via ubiquitin modification

Elevated atmospheric CO₂ concentration is a serious global environmental problem. Elevated CO₂ affects plant growth by changing primary metabolism, closely related to carbon (C) and nitrogen (N) availability. Under sufficient N conditions, plant growth is dramatically promoted by elevated CO₂. When N availability is limited, however, elevated CO₂ disrupts the balance between cellular C and N (C/N). Disruption of the C/N balance is regarded as an important factor in plant growth defects. Here we highlight the regulation of senescence in higher plants by atmospheric CO₂ and N, and the physiological function of C/N-related ubiquitin ligase ATL31 under condition of elevated CO₂. We also provide an overview of the ubiquitin ligases and related enzymes involved in regulating senescence in plants.