The metabolic flux phenotype of heterotrophic Arabidopsis cells reveals a flexible balance between the cytosolic and plastidic contributions to carbohydrate oxidation in response to phosphate limitation

Understanding the mechanisms that allow plants to respond to variable and reduced availability of inorganic phosphate is of increasing agricultural importance because of the continuing depletion of the rock phosphate reserves that are used to combat inadequate phosphate levels in the soil. Changes in gene expression, protein levels, enzyme activities and metabolite levels all point to a reconfiguration of the central metabolic network in response to reduced availability of inorganic phosphate, but the metabolic significance of these changes can only be assessed in terms of the fluxes supported by the network. Steady‐state metabolic flux analysis was used to define the metabolic phenotype of a heterotrophic Arabidopsis thaliana cell culture grown on a Murashige and Skoog medium containing 0, 1.25 or 5 mm inorganic phosphate. Fluxes through the central metabolic network were deduced from the redistribution of ¹³C into metabolic intermediates and end products when cells were labelled with [1‐¹³C], [2‐¹³C], or [¹³C₆]glucose, in combination with ¹⁴C measurements of the rates of biomass accumulation. Analysis of the flux maps showed that reduced levels of phosphate in the growth medium stimulated flux through phosphoenolpyruvate carboxylase and malic enzyme, altered the balance between cytosolic and plastidic carbohydrate oxidation in favour of the plastid, and increased cell maintenance costs. We argue that plant cells respond to phosphate deprivation by reconfiguring the flux distribution through the pathways of carbohydrate oxidation to take advantage of better phosphate homeostasis in the plastid.     

Nitrogen flux into metabolites and microcystins changes in response to different nitrogen sources in Microcystis aeruginosa NIES-843

The over-enrichment of nitrogen (N) in the environment has contributed to severe and recurring harmful cyanobacterial blooms, especially by the non-N₂-fixing Microcystis spp. N chemical speciation influences cyanobacterial growth, persistence and the production of the hepatotoxin microcystin, but the physiological mechanisms to explain these observations remain unresolved. Stable-labelled isotopes and metabolomics were employed to address the influence of nitrate, ammonium, and urea on cellular physiology and production of microcystins in Microcystis aeruginosa NIES-843. Global metabolic changes were driven by both N speciation and diel cycling. Tracing ¹⁵N-labelled nitrate, ammonium, and urea through the metabolome revealed N uptake, regardless of species, was linked to C assimilation. The production of amino acids, like arginine, and other N-rich compounds corresponded with greater turnover of microcystins in cells grown on urea compared to nitrate and ammonium. However, ¹⁵N was incorporated into microcystins from all N sources. The differences in N flux were attributed to the energetic efficiency of growth on each N source. While N in general plays an important role in sustaining biomass, these data show that N-speciation induces physiological changes that culminate in differences in global metabolism, cellular microcystin quotas and congener composition.     

Photobioreactor design for isotopic non‐stationary 13C‐metabolic flux analysis (INST 13C‐MFA) under photoautotrophic conditions

Adaptive metabolic behavior of photoautotrophic microorganisms toward genetic and environmental perturbations can be interpreted in a quantitative depiction of carbon flow through a biochemical reaction network using isotopic non‐stationary ¹³C‐metabolic flux analysis (INST ¹³C‐MFA). To evaluate ¹³C‐metabolic flux maps for Chlamydomonas reinhardtii, an original experimental framework was designed allowing rapid, reliable collection of high‐quality isotopomer data against time. It involved (i) a short‐time ¹³C labeling injection device based on mixing control in a torus‐shaped photobioreactor with plug‐flow hydrodynamics allowing a sudden step‐change in the ¹³C proportion in the substrate feed and (ii) a rapid sampling procedure using an automatic fast filtration method coupled to a manual rapid liquid nitrogen quenching step. ¹³C‐substrate labeling enrichment was controlled through the total dissolved inorganic carbon concentration in the pulsed solution. First results were obtained from steady‐state continuous culture measurements allowing the characterization of the kinetics of label incorporation into light‐limited growing cells cultivated in a photobioreactor operating at the maximal biomass productivity for an incident photon flux density of 200 µmol m^?2 s^?1. ¹³C label incorporation was measured for 21 intracellular metabolites using IC‐MS/MS in 58 samples collected across a labeling experiment duration of 7 min. The fastest labeling rate was observed for 2/3‐phosphoglycerate with an apparent isotopic stationary state reached after 300 s. The labeling rate was consistent with the optimized mixing time of about 4.9 s inside the reactor and the shortest reliable sampling period assessed at 5 s. Biotechnol. Bioeng. 2012; 109: 3030–3040. © 2012 Wiley Periodicals, Inc.     

Metabolic network reconstruction,growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8

Thermus thermophilus is an extremely thermophilic bacterium with significant biotechnological potential. In this work, we have characterized aerobic growth characteristics of T. thermophilus HB8 at temperatures between 50 and 85 °C, constructed a metabolic network model of its central carbon metabolism and validated the model using ¹³C-metabolic flux analysis (¹³C–MFA). First, cells were grown in batch cultures in custom constructed mini-bioreactors at different temperatures to determine optimal growth conditions. The optimal temperature for T. thermophilus grown on defined medium with glucose was 81 °C. The maximum growth rate was 0.25 h⁻¹. Between 50 and 81 °C the growth rate increased by 7-fold and the temperature dependence was described well by an Arrhenius model with an activation energy of 47 kJ/mol. Next, we performed a ¹³C-labeling experiment with [1,2-¹³C] glucose as the tracer and calculated intracellular metabolic fluxes using ¹³C–MFA. The results provided support for the constructed network model and highlighted several interesting characteristics of T. thermophilus metabolism. We found that T. thermophilus largely uses glycolysis and TCA cycle to produce biosynthetic precursors, ATP and reducing equivalents needed for cells growth. Consistent with its proposed metabolic network model, we did not detect any oxidative pentose phosphate pathway flux or Entner-Doudoroff pathway activity. The biomass precursors erythrose-4-phosphate and ribose-5-phosphate were produced via the non-oxidative pentose phosphate pathway, and largely via transketolase, with little contribution from transaldolase. The high biomass yield on glucose that was measured experimentally was also confirmed independently by ¹³C–MFA. The results presented here provide a solid foundation for future studies of T. thermophilus and its metabolic engineering applications.     

Nitrate regulation of nitrate uptake and nitrate reductase expression in barley grown at different nitrate:ammonium ratios at constant relative nitrogen addition rate

Barley (Hordeum vulgare L. cv. Golf) was cultured using the relative addition rate technique, where nitrogen is added in a fixed relation to the nitrogen already bound in biomass. The relative rate of total nitrogen addition was 0.09 day^?1 (growth limiting by 35%), while the nitrate addition was varied by means of different nitrate: ammonium ratios. In 3- to 4-week-old plants, these ratios of nitrate to ammonium supported nitrate fluxes ranging from 0 to 22 μmol g^?1 root dry weight h^?1, whereas the total N flux was 21.8 ± 0.25 μmol g^?1 root dry weight h^?1 for all treatments. The external nitrate concentrations varied between 0.18 and 1.5 μM. The relative growth rate, root to total biomass dry weight ratios, as well as Kjeldahl nitrogen in roots and shoots were unaffected by the nitrate:ammonium ratio. Tissue nitrate concentration in roots were comparable in all treatments. Shoot nitrate concentration increased with increasing nitrate supply, indicating increased translocation of nitrate to the shoot. The apparent V_max for net nitrate uptake increased with increased nitrate fluxes. Uptake activity was recorded also after growth at zero nitrate addition. This activity may have been induced by the small, but detectable, nitrate concentration in the medium under these conditions. In contrast, nitrate reductase (NR) activity in roots was unaffected by different nitrate fluxes, whereas NR activity in the shoot increased with increased nitrate supply. NR-mRNA was detected in roots from all cultures and showed no significant response to the nitrate flux, corroborating the data for NR activity. The data show that an extremely low amount of nitrate is required to elicit expression of NR and uptake activity. However, the uptake system and root NR respond differentially to increased nitrate flux at constant total N nutrition. It appears that root NR expression under these conditions is additionally controlled by factors related to the total N flux or the internal N status of the root and/or plant. The method used in this study may facilitate separation of nitrate-specific responses from the nutritional effect of nitrate.     

Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis

Glucose and xylose are the two most abundant sugars derived from the breakdown of lignocellulosic biomass. While aerobic glucose metabolism is relatively well understood in E. coli, until now there have been only a handful of studies focused on anaerobic glucose metabolism and no ¹³C-flux studies on xylose metabolism. In the absence of experimentally validated flux maps, constraint-based approaches such as MOMA and RELATCH cannot be used to guide new metabolic engineering designs. In this work, we have addressed this critical gap in current understanding by performing comprehensive characterizations of glucose and xylose metabolism under aerobic and anaerobic conditions, using recent state-of-the-art techniques in ¹³C metabolic flux analysis (¹³C-MFA). Specifically, we quantified precise metabolic fluxes for each condition by performing parallel labeling experiments and analyzing the data through integrated ¹³C-MFA using the optimal tracers [1,2-¹³C]glucose, [1,6-¹³C]glucose, [1,2-¹³C]xylose and [5-¹³C]xylose. We also quantified changes in biomass composition and confirmed turnover of macromolecules by applying [U-¹³C]glucose and [U-¹³C]xylose tracers. We demonstrated that under anaerobic growth conditions there is significant turnover of lipids and that a significant portion of CO₂ originates from biomass turnover. Using knockout strains, we also demonstrated that β-oxidation is critical for anaerobic growth on xylose. Quantitative analysis of co-factor balances (NADH/FADH₂, NADPH, and ATP) for different growth conditions provided new insights regarding the interplay of energy and redox metabolism and the impact on E. coli cell physiology.     

DIFFERENCES IN GROWTH AND PHYSIOLOGY OF MARINE SYNECHOCOCCUS (CYANOBACTERIA) ON NITRATE VERSUS AMMONIUM ARE NOT DETERMINED SOLELY BY NITROGEN SOURCE REDOX STATE1

The preference of phytoplankton for ammonium over nitrate has traditionally been explained by the greater metabolic cost of reducing oxidized forms of nitrogen. This “metabolic cost hypothesis” implies that there should be a growth disadvantage on nitrate compared to ammonium or other forms of reduced nitrogen such as urea, especially when light limits growth, but in a variety of phytoplankton taxa, this predicted difference has not been observed. Our experiments with three strains of marine Synechococcus (WH7803, WH7805, and WH8112) did not reveal consistently faster growth (cell division) on ammonium or urea as compared to nitrate. Urease and glutamine synthetase (GS) activities varied with nitrogen source in a manner consistent with regulation by cellular nitrogen status via NtcA (rather than by external availability of nitrogen) in all three strains and indicated that each strain experienced some degree of nitrogen insufficiency during growth on nitrate. At light intensities that strongly limited growth, the composition (carbon, nitrogen, and pigment quotas) of WH7805 cells using nitrate was indistinguishable from that of cells using ammonium, but at saturating light intensities, cellular carbon, nitrogen, and pigment quotas were significantly lower in cells using nitrate than ammonium. These and similar results from other phytoplankton taxa suggest that a limitation in some step of nitrate uptake or assimilation, rather than the extra cost of reducing nitrate per se, may be the cause of differences in growth and physiology between cells using nitrate and ammonium.     

Robust biological nitrogen fixation in a model grass–bacterial association

Nitrogen‐fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C₄ grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen‐13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen‐limiting conditions when inoculated with an ammonium‐excreting strain of Azospirillum brasilense. ¹¹C‐labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen‐starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen‐sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production.     

The effects of nitrogen addition on the growth of two exotic and two native forest understory plants

Many studies have linked the spread of exotic, invasive species to high nitrogen supply, but most of this work does not distinguish between various inorganic forms and different concentrations of available nitrogen. Previous research has suggested that exotic, invasive species common in eastern deciduous forests may preferentially utilize nitrate in contrast to native species that preferentially make use of ammonium. We tested this hypothesis by comparing the growth response of two common forest invaders, Berberis thunbergii and Microstegium vimineum, and two co-occurring native species (Vaccinium pallidum and Hamamelis virginiana) to different forms of nitrogen under varying concentrations in a greenhouse experiment. Two forms of nitrogen (nitrate or ammonium) were added at different concentrations (22, 106, and 212 mg N l⁻¹) to all species. Growth response variables included survival, stem length, stem diameter, above and belowground biomass, and estimated seed production (Microstegium only). Unexpectedly the exotic species did not respond preferentially to nitrate addition. Microstegium responded most strongly to both nitrogen forms depending on the response variable. Berberis and Hamamelis surprisingly reacted similarly to nitrogen additions. As expected, Vaccinium fared poorly under most treatment conditions, but did show some growth in NH₄ ⁺ treatments. Our findings suggest species response to nitrogen addition is complex, and that exotic species do not all respond similarly to nitrogen inputs. In this study, the response of exotic and native species to available nutrients does not provide a general mechanism of invasion success.     

Differential effects of ammonium and nitrate deposition on fen phanerogams and bryophytes

Question: High atmospheric nitrogen (N) deposition has been shown to affect productivity and species composition of terrestrial ecosystems. This study focused on the differential effects of the two inorganic N forms in atmospheric deposition (i.e. ammonium and nitrate). Methods and location: Nutrient addition experiments were carried out during 4 years in a mesotrophic fen in a low‐deposition area in Ireland. In a factorial design, plots were fertilized with ammonium and/or nitrate, in two doses comparable with 35 and 70 kg N ha^?1 y^?1 and compared with an unfertilized control. Results: Vascular plant biomass as well as bryophyte biomass were not affected by N dose but showed significantly different responses to the N form. In the ammonium‐fertilized plots, vascular plant biomass was higher and moss biomass was lower than the control, while nitrate additions had no effect. Vascular plant species density was high (16 species per 0.49 m²) and was not affected by any of the treatments; bryophyte species density was also high (seven species per 0.04 m²) but showed a significant decrease upon ammonium fertilization. Conclusion: The vulnerability of the mesotrophic vegetation to enhanced atmospheric N deposition depends strongly on the N form. If N would be mainly deposited as NO_x, no detrimental effects on the vegetation will occur. If, however, the deposition is mainly in the form of NH_y, the bryophyte vegetation will be seriously damaged, while the vascular plant vegetation will show an increased biomass production with possible shifts in dominance from Carex and herb species to grasses and shrubs.     

Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: flux variability analysis in relation to ¹³C metabolic flux analysis

Plant oils are an important renewable resource, and seed oil content is a key agronomical trait that is in part controlled by the metabolic processes within developing seeds. A large‐scale model of cellular metabolism in developing embryos of Brassica napus (bna572) was used to predict biomass formation and to analyze metabolic steady states by flux variability analysis under different physiological conditions. Predicted flux patterns are highly correlated with results from prior ¹³C metabolic flux analysis of B. napus developing embryos. Minor differences from the experimental results arose because bna572 always selected only one sugar and one nitrogen source from the available alternatives, and failed to predict the use of the oxidative pentose phosphate pathway. Flux variability, indicative of alternative optimal solutions, revealed alternative pathways that can provide pyruvate and NADPH to plastidic fatty acid synthesis. The nutritional values of different medium substrates were compared based on the overall carbon conversion efficiency (CCE) for the biosynthesis of biomass. Although bna572 has a functional nitrogen assimilation pathway via glutamate synthase, the simulations predict an unexpected role of glycine decarboxylase operating in the direction of NH₄⁺ assimilation. Analysis of the light‐dependent improvement of carbon economy predicted two metabolic phases. At very low light levels small reductions in CO₂ efflux can be attributed to enzymes of the tricarboxylic acid cycle (oxoglutarate dehydrogenase, isocitrate dehydrogenase) and glycine decarboxylase. At higher light levels relevant to the ¹³C flux studies, ribulose‐1,5‐bisphosphate carboxylase activity is predicted to account fully for the light‐dependent changes in carbon balance.     

The use of different soil nitrogen sources by young Norway spruce plants

 Three-year-old Norway spruce trees were planted into a low-nitrogen mineral forest soil and supplied either with two different levels of mineral nitrogen (NH₄NO₃) or with a slow-release form of organic nitrogen (keratin). Supply of mineral nitrogen increased the concentrations of ammonium and nitrate in the soil solution and in CaCl₂-extracts of the rhizosphere and bulk soil. In the soil solution, in all treatments nitrate concentrations were higher than ammonium concentrations, while in the soil extracts ammonium concentrations were often higher than nitrate concentrations. After 7 months of growth, ¹⁵N labelled ammonium or nitrate was added to the soil. Plants were harvested 2 weeks later. Keratin supply to the soil did not affect growth and nitrogen accumulation of the trees. In contrast, supply of mineral nitrogen increased shoot growth and increased the ratio of above-ground to below-ground growth. The proportion of needle biomass to total above-ground biomass was not increased by mineral N supply. The atom-% ¹⁵N was higher in younger needles than in older needles, and in younger needles higher in plants supplied with ¹⁵N-nitrate than in plants supplied with ¹⁵N-ammonium. The present data show that young Norway spruce plants take up nitrate even under conditions of high plant internal N levels. Received: 1 April 1998 / Accepted: 9 October 1998     

Kinetic flux profiling dissects nitrogen utilization pathways in the oleaginous green alga Chlorella protothecoides

As a promising candidate for biodiesel production, the green alga Chlorella protothecoides can efficiently produce oleaginous biomass and the lipid biosynthesis is greatly influenced by the availability of nitrogen source and corresponding nitrogen assimilation pathways. Based on isotope‐assisted kinetic flux profiling (KFP), the fluxes through the nitrogen utilization pathway were quantitatively analyzed. We found that autotrophic C. protothecoides cells absorbed ammonium mainly through glutamate dehydrogenase (GDH), and partially through glutamine synthetase (GS), which was the rate‐limiting enzyme of nitrogen assimilation process with rare metabolic activity of glutamine oxoglutarate aminotransferase (GOGAT, also known as glutamate synthase); whereas under heterotrophic conditions, the cells adapted to GS‐GOGAT cycle for nitrogen assimilation in which GS reaction rate was associated with GOGAT activity. The fact that C. protothecoides chooses the adenosine triphosphate‐free and less ammonium‐affinity GDH pathway, or alternatively the energy‐consuming GS‐GOGAT cycle with high ammonium affinity for nitrogen assimilation, highlights the metabolic adaptability of C. protothecoides exposed to altered nitrogen conditions.     

Restricted use of nitrate and a strong preference for ammonium reflects the nitrogen ecophysiology of a light‐limited red alga

Ammonium and nitrate are important sources of inorganic nitrogen for coastal primary producers. Nitrate has higher energy requirement for uptake and assimilation, compared with ammonium, suggesting that it might be a more efficient nitrogen source for slow‐growing, light‐limited macroalgae. To address this hypothesis, we examined the nitrogen ecophysiology of Anotrichium crinitum, a rhodophyte macroalgae common in low‐light habitats in New Zealand. We measured seasonal changes in seawater nitrate and ammonium concentrations and the concentration of nitrate and ammonium stored internally by A. crinitum. We determined the maximal uptake rates of nitrate and ammonium seasonally and grew A. crinitum in the laboratory with these nitrogen sources under two ecologically relevant saturating light levels. Our results show that field‐harvested A. crinitum has a high affinity for ammonium and although it will grow when supplied exclusively with nitrate, internal nitrate pools are low and it is unable to take up nitrate without several days of acclimation to saturating light. Our data predict that A. crinitum would be able to sustain growth with ammonium as the sole source of nitrogen, a strategy that would help it survive under low‐light conditions that prevail in the field.     

Nitrogen form, availability, and mycorrhizal colonization affect biomass and nitrogen isotope patterns in Pinus sylvestris

Nitrogen (N) isotope patterns are useful for understanding carbon and nitrogen dynamics in mycorrhizal systems but questions remain about how different N forms, fungal symbionts, and N availabilities influence δ¹⁵N signatures. Here, we studied how biomass allocation and δ¹⁵N patterns in Pinus sylvestris L. cultures were affected by nitrogen supply rate (3% per day or 4% per day relative to the nitrogen already present), nitrogen form (ammonium versus nitrate), and mycorrhizal colonization by fungi with a greater (Laccaria laccata) or lesser (Suillus bovinus) ability to assimilate nitrate. Mycorrhizal (fungal) biomass was greater with ammonium than with nitrate nutrition for Suillus cultures but similar for Laccaria cultures. Total biomass was less with nitrate nutrition than with ammonium nutrition for nonmycorrhizal cultures and was less in mycorrhizal cultures than in nonmycorrhizal cultures. The sequestration of available N by mycorrhizal fungi limited plant N supply. This limitation and the higher energetic cost of nitrate reduction than ammonium assimilation appeared to control plant biomass accumulation. Colonization decreased foliar δ¹⁵N by 0.5 to 2.2‰ (nitrate) or 1.7 to 3.5‰ (ammonium) and increased root tip δ¹⁵N by 0 to 1‰ (nitrate) or 0.6 to 2.3‰ (ammonium). Root tip δ¹⁵N and fungal biomass on root tips were positively correlated in ammonium treatments (r ²?=?0.52) but not in nitrate treatments (r ²?=?0.00). Fungal biomass on root tips was enriched in ¹⁵N an estimated 6–8‰ relative to plant biomass in ammonium treatments. At high nitrate availability, Suillus colonization did not reduce plant δ¹⁵N. We conclude that: (1) transfer of ¹⁵N-depleted N from mycorrhizal fungi to plants produces low plant δ¹⁵N signatures and high root tip and fungal δ¹⁵N signatures; (2) limited nitrate reduction in fungi restricted transfer of ¹⁵N-depleted N to plants when nitrate is supplied and may account for many field observations of high plant δ¹⁵N under such conditions; (3) plants could transfer assimilated nitrogen to fungi at high nitrate supply but such transfer was without ¹⁵N fractionation. These factors probably control plant δ¹⁵N patterns across N availability gradients and were here incorporated into analytical equations for interpreting nitrogen isotope patterns in mycorrhizal fungi and plants.     

Do cyanobacteria dominate in eutrophic lakes because they fix atmospheric nitrogen?

1. The sources of nitrogen for phytoplankton were determined for a bloom‐prone lake as a means of assessing the hypothesis that cyanobacteria dominate in eutrophic lakes because of their ability to fix nitrogen when the nitrogen : phosphorous (N : P) supply ratio is low and nitrogen a limiting resource. 2. Nitrogen fixation rates, estimated through acetylene reduction with ¹⁵N calibration, were compared with ¹⁵N‐tracer estimates of ammonium and nitrate uptake monthly during the ice‐free season of 1999. In addition, the natural N stable isotope composition of phytoplankton, nitrate and ammonium were measured biweekly and the contribution of N₂ to the phytoplankton signature estimated with a mixing model. 3. Although cyanobacteria made up 81–98% of phytoplankton biomass during summer and autumn, both assays suggested minimal N acquisition through fixation (<9% for the in‐situ incubations; <2% for stable isotope analysis). Phytoplankton acquired N primarily as ammonium (82–98%), and secondarily as nitrate (15–18% in spring and autumn, but <5% in summer). Heterocyst densities of <3 per 100 fixer cells confirmed low reliance on fixation. 4. The lake showed symptoms of both light and nitrogen limitation. Cyanobacteria may have dominated by monopolizing benthic sources of ammonium, or by forming surface scums that shaded other algae.