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Sample records for nitrogen carbon assimilation

  1. Carbon and nitrogen assimilation in deep subseafloor microbial cells.

    PubMed

    Morono, Yuki; Terada, Takeshi; Nishizawa, Manabu; Ito, Motoo; Hillion, François; Takahata, Naoto; Sano, Yuji; Inagaki, Fumio

    2011-11-08

    Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individual microbial cells from 219-m-deep lower Pleistocene (460,000 y old) sediments from the northwestern Pacific off the Shimokita Peninsula of Japan. Sediment samples were incubated in vitro with (13)C- and/or (15)N-labeled glucose, pyruvate, acetate, bicarbonate, methane, ammonium, and amino acids. Significant incorporation of (13)C and/or (15)N and growth occurred in response to glucose, pyruvate, and amino acids (∼76% of total cells), whereas acetate and bicarbonate were incorporated without fostering growth. Among those substrates, a maximum substrate assimilation rate was observed at 67 × 10(-18) mol/cell per d with bicarbonate. Neither carbon assimilation nor growth was evident in response to methane. The atomic ratios between nitrogen incorporated from ammonium and the total cellular nitrogen consistently exceeded the ratios of carbon, suggesting that subseafloor microbes preferentially require nitrogen assimilation for the recovery in vitro. Our results showed that the most deeply buried subseafloor sedimentary microbes maintain potentials for metabolic activities and that growth is generally limited by energy but not by the availability of C and N compounds.

  2. Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions.

    PubMed

    Kurai, Tomohiro; Wakayama, Masataka; Abiko, Tomomi; Yanagisawa, Shuichi; Aoki, Naohiro; Ohsugi, Ryu

    2011-10-01

    The excessive application of nitrogen fertilizer to maximize crop yields causes negative environmental effects such as pollution and ecological imbalance. To overcome this problem, researchers have attempted to improve the nitrogen assimilation capacity of crops. Maize Dof1 (ZmDof1) is a plant-specific transcription factor shown to promote nitrogen assimilation in Arabidopsis thaliana (Arabidopsis) even under nitrogen-deficient conditions. The present study examines the effect of the introduction of the ZmDof1 gene on carbon and nitrogen assimilation in rice. ZmDof1 induced the expression of phosphoenolpyruvate carboxylase (PEPC) genes in transgenic rice plants and transactivated the PEPC promoters in protoplast transient assays, showing similar effects in rice as in Arabidopsis. Transgenic rice expressing ZmDof1 and grown in the presence of 360 μm (nitrogen-sufficient) or 90 μm (nitrogen-deficient) of nitrogen concentrations showed modulation of metabolite content and gene expression associated with the anaplerotic pathway for the TCA cycle, suggesting an increased carbon flow towards nitrogen assimilation. Furthermore, increases in carbon and nitrogen amounts per seedling were found in Dof1 rice grown under nitrogen-deficient conditions. Nitrogen deficiency also resulted in the predominant distribution of nitrogen to roots, accompanied by significant increases in root biomass and modification of the shoot-to-root ratio. Measurement of the CO₂ gas exchange rate showed a significant increase in the net photosynthesis rate in Dof1 rice under nitrogen-deficient conditions. Taken these together, the present study displayed that ZmDof1 expression in rice could induce gene expressions such as PEPC genes, modulate carbon and nitrogen metabolites, increase nitrogen assimilation and enhance growth under low-nitrogen conditions. © 2011 The Authors. Plant Biotechnology Journal © 2011 Society for Experimental Biology, Association of Applied Biologists and Blackwell

  3. Carbon dioxide level and form of soil nitrogen regulate assimilation of atmospheric ammonia in young trees.

    PubMed

    Silva, Lucas C R; Salamanca-Jimenez, Alveiro; Doane, Timothy A; Horwath, William R

    2015-08-21

    The influence of carbon dioxide (CO2) and soil fertility on the physiological performance of plants has been extensively studied, but their combined effect is notoriously difficult to predict. Using Coffea arabica as a model tree species, we observed an additive effect on growth, by which aboveground productivity was highest under elevated CO2 and ammonium fertilization, while nitrate fertilization favored greater belowground biomass allocation regardless of CO2 concentration. A pulse of labelled gases ((13)CO2 and (15)NH3) was administered to these trees as a means to determine the legacy effect of CO2 level and soil nitrogen form on foliar gas uptake and translocation. Surprisingly, trees with the largest aboveground biomass assimilated significantly less NH3 than the smaller trees. This was partly explained by declines in stomatal conductance in plants grown under elevated CO2. However, unlike the (13)CO2 pulse, assimilation and transport of the (15)NH3 pulse to shoots and roots varied as a function of interactions between stomatal conductance and direct plant response to the form of soil nitrogen, observed as differences in tissue nitrogen content and biomass allocation. Nitrogen form is therefore an intrinsic component of physiological responses to atmospheric change, including assimilation of gaseous nitrogen as influenced by plant growth history.

  4. Carbon dioxide level and form of soil nitrogen regulate assimilation of atmospheric ammonia in young trees

    PubMed Central

    Silva, Lucas C. R.; Salamanca-Jimenez, Alveiro; Doane, Timothy A.; Horwath, William R.

    2015-01-01

    The influence of carbon dioxide (CO2) and soil fertility on the physiological performance of plants has been extensively studied, but their combined effect is notoriously difficult to predict. Using Coffea arabica as a model tree species, we observed an additive effect on growth, by which aboveground productivity was highest under elevated CO2 and ammonium fertilization, while nitrate fertilization favored greater belowground biomass allocation regardless of CO2 concentration. A pulse of labelled gases (13CO2 and 15NH3) was administered to these trees as a means to determine the legacy effect of CO2 level and soil nitrogen form on foliar gas uptake and translocation. Surprisingly, trees with the largest aboveground biomass assimilated significantly less NH3 than the smaller trees. This was partly explained by declines in stomatal conductance in plants grown under elevated CO2. However, unlike the 13CO2 pulse, assimilation and transport of the 15NH3 pulse to shoots and roots varied as a function of interactions between stomatal conductance and direct plant response to the form of soil nitrogen, observed as differences in tissue nitrogen content and biomass allocation. Nitrogen form is therefore an intrinsic component of physiological responses to atmospheric change, including assimilation of gaseous nitrogen as influenced by plant growth history. PMID:26294035

  5. Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus

    PubMed Central

    Rineau, F; Shah, F; Smits, M M; Persson, P; Johansson, T; Carleer, R; Troein, C; Tunlid, A

    2013-01-01

    The majority of nitrogen in forest soils is found in organic matter–protein complexes. Ectomycorrhizal fungi (EMF) are thought to have a key role in decomposing and mobilizing nitrogen from such complexes. However, little is known about the mechanisms governing these processes, how they are regulated by the carbon in the host plant and the availability of more easily available forms of nitrogen sources. Here we used spectroscopic analyses and transcriptome profiling to examine how the presence or absence of glucose and/or ammonium regulates decomposition of litter material and nitrogen mobilization by the ectomycorrhizal fungus Paxillus involutus. We found that the assimilation of nitrogen and the decomposition of the litter material are triggered by the addition of glucose. Glucose addition also resulted in upregulation of the expression of genes encoding enzymes involved in oxidative degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism. In contrast, the addition of ammonium to organic matter had relatively minor effects on the expression of transcripts and the decomposition of litter material, occurring only when glucose was present. On the basis of spectroscopic analyses, three major types of chemical modifications of the litter material were observed, each correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggest that the expression of the decomposition and nitrogen assimilation processes of EMF can be tightly regulated by the host carbon supply and that the availability of inorganic nitrogen as such has limited effects on saprotrophic activities. PMID:23788332

  6. Improving representation of nitrogen uptake, allocation, and carbon assimilation in the Community Land Model

    NASA Astrophysics Data System (ADS)

    Ghimire, B.; Riley, W. J.; Koven, C.

    2013-12-01

    Nitrogen is the most important nutrient limiting plant carbon assimilation and growth, and is required for production of photosynthetic enzymes, growth and maintenance respiration, and maintaining cell structure. The forecasted rise in plant available nitrogen through atmospheric nitrogen deposition and the release of locked soil nitrogen by permafrost thaw in high latitude ecosystems is likely to result in an increase in plant productivity. However a mechanistic representation of plant nitrogen dynamics is lacking in earth system models. Most earth system models ignore the dynamic nature of plant nutrient uptake and allocation, and further lack tight coupling of below- and above-ground processes. In these models, the increase in nitrogen uptake does not translate to a corresponding increase in photosynthesis parameters, such as maximum Rubisco capacity and electron transfer rate. We present an improved modeling framework implemented in the Community Land Model version 4.5 (CLM4.5) for dynamic plant nutrient uptake, and allocation to different plant parts, including leaf enzymes. This modeling framework relies on imposing a more realistic flexible carbon to nitrogen stoichiometric ratio for different plant parts. The model mechanistically responds to plant nitrogen uptake and leaf allocation though changes in photosynthesis parameters. We produce global simulations, and examine the impacts of the improved nitrogen cycling. The improved model is evaluated against multiple observations including TRY database of global plant traits, nitrogen fertilization observations and 15N tracer studies. Global simulations with this new version of CLM4.5 showed better agreement with the observations than the default CLM4.5-CN model, and captured the underlying mechanisms associated with plant nitrogen cycle.

  7. Carbon and nitrogen assimilation activities of deep subseafloor microbes analyzed by NanoSIMS

    NASA Astrophysics Data System (ADS)

    Morono, Y.; Terada, T.; Inagaki, F.

    2009-12-01

    Deep subseafloor microbes play significant roles on biogeochemical cycles with extremely low metabolic activities. The subseafloor microbial community consists mainly of uncultured components; hence, their growth and metabolic characteristics remain almost completely unknown. Here, we presnet in vitro isotopic evidence that the deep subseafloor microbes actively incooporate multiple carbon and nitrogen compounds into their biomass using NanoSIMS. We incubated methane hydrate-bearing deep marine sediments with small 13C-labeled glucose, acetate, pyruvate, bicarbonate, amino-acids and methane in the presence of 15N-labeled ammonia as a nitrogen source for 2 and 6 monthes under the anaerobic condition. Using NanoSIMS, we observed the cells that incooprated 13C- or 15N-labeled substrates such as 13C-glucose, pyruvate, and 15N-ammonia up to 50% of their cellular carbon or nitrogen mass. Assimilation of 13C- and 15N-labeled amino acids as well as 13C-bicarbonates by autotrophs was also observed while 13C-methane was found to be difficult to be used for the carbon source, regardless of the presence of some additional electron acceptors for the energy respiration. These results indicate that the metabolic activities of deep subseafloor microbes can be stimulated in vitro by adding potential carbon and nitrogen sources, providing new insights into the biogeochemical functioning of the deep subseaflor microbes and its ecosystem.

  8. Photorespiration and nitrate assimilation: a major intersection between plant carbon and nitrogen.

    PubMed

    Bloom, Arnold J

    2015-02-01

    C3 carbon fixation has a bad reputation, primarily because it is associated with photorespiration, a biochemical pathway thought to waste a substantial amount of the carbohydrate produced in a plant. This review presents evidence collected over nearly a century that (1) Rubisco when associated with Mn(2+) generates additional reductant during photorespiration, (2) this reductant participates in the assimilation of nitrate into protein, and (3) this nitrate assimilation facilitates the use of a nitrogen source that other organisms tend to avoid. This phenomenon explains the continued dominance of C3 plants during the past 23 million years of low CO2 atmospheres as well as the decline in plant protein concentrations as atmospheric CO2 rises.

  9. Overexpression of Arabidopsis NLP7 improves plant growth under both nitrogen-limiting and -sufficient conditions by enhancing nitrogen and carbon assimilation.

    PubMed

    Yu, Lin-Hui; Wu, Jie; Tang, Hui; Yuan, Yang; Wang, Shi-Mei; Wang, Yu-Ping; Zhu, Qi-Sheng; Li, Shi-Gui; Xiang, Cheng-Bin

    2016-06-13

    Nitrogen is essential for plant survival and growth. Excessive application of nitrogenous fertilizer has generated serious environment pollution and increased production cost in agriculture. To deal with this problem, tremendous efforts have been invested worldwide to increase the nitrogen use ability of crops. However, only limited success has been achieved to date. Here we report that NLP7 (NIN-LIKE PROTEIN 7) is a potential candidate to improve plant nitrogen use ability. When overexpressed in Arabidopsis, NLP7 increases plant biomass under both nitrogen-poor and -rich conditions with better-developed root system and reduced shoot/root ratio. NLP7-overexpressing plants show a significant increase in key nitrogen metabolites, nitrogen uptake, total nitrogen content, and expression levels of genes involved in nitrogen assimilation and signalling. More importantly, overexpression of NLP7 also enhances photosynthesis rate and carbon assimilation, whereas knockout of NLP7 impaired both nitrogen and carbon assimilation. In addition, NLP7 improves plant growth and nitrogen use in transgenic tobacco (Nicotiana tabacum). Our results demonstrate that NLP7 significantly improves plant growth under both nitrogen-poor and -rich conditions by coordinately enhancing nitrogen and carbon assimilation and sheds light on crop improvement.

  10. Overexpression of Arabidopsis NLP7 improves plant growth under both nitrogen-limiting and -sufficient conditions by enhancing nitrogen and carbon assimilation

    PubMed Central

    Yu, Lin-Hui; Wu, Jie; Tang, Hui; Yuan, Yang; Wang, Shi-Mei; Wang, Yu-Ping; Zhu, Qi-Sheng; Li, Shi-Gui; Xiang, Cheng-Bin

    2016-01-01

    Nitrogen is essential for plant survival and growth. Excessive application of nitrogenous fertilizer has generated serious environment pollution and increased production cost in agriculture. To deal with this problem, tremendous efforts have been invested worldwide to increase the nitrogen use ability of crops. However, only limited success has been achieved to date. Here we report that NLP7 (NIN-LIKE PROTEIN 7) is a potential candidate to improve plant nitrogen use ability. When overexpressed in Arabidopsis, NLP7 increases plant biomass under both nitrogen-poor and -rich conditions with better-developed root system and reduced shoot/root ratio. NLP7–overexpressing plants show a significant increase in key nitrogen metabolites, nitrogen uptake, total nitrogen content, and expression levels of genes involved in nitrogen assimilation and signalling. More importantly, overexpression of NLP7 also enhances photosynthesis rate and carbon assimilation, whereas knockout of NLP7 impaired both nitrogen and carbon assimilation. In addition, NLP7 improves plant growth and nitrogen use in transgenic tobacco (Nicotiana tabacum). Our results demonstrate that NLP7 significantly improves plant growth under both nitrogen-poor and -rich conditions by coordinately enhancing nitrogen and carbon assimilation and sheds light on crop improvement. PMID:27293103

  11. Coordinated response of photosynthesis, carbon assimilation, and triacylglycerol accumulation to nitrogen starvation in the marine microalgae Isochrysis zhangjiangensis (Haptophyta).

    PubMed

    Wang, Hai-Tao; Meng, Ying-Ying; Cao, Xu-Peng; Ai, Jiang-Ning; Zhou, Jian-Nan; Xue, Song; Wang, Wei-liang

    2015-02-01

    The photosynthetic performance, carbon assimilation, and triacylglycerol accumulation of Isochrysis zhangjiangensis under nitrogen-deplete conditions were studied to understand the intrinsic correlations between them. The nitrogen-deplete period was divided into two stages based on the photosynthetic parameters. During the first stage, carbon assimilation was not reduced compared with that under favorable conditions. The marked increase in triacylglycerols and the variation in the fatty acid profile suggested that triacylglycerols were mainly derived from de novo synthesized acyl groups. In the second stage, the triacylglycerol content continued increasing while the carbohydrate content decreased from 44.0% to 26.3%. These results indicated that the intracellular conversion of carbohydrates to triacylglycerols occurred. Thus, we propose that sustainable carbon assimilation and incremental triacylglycerol production can be achieved by supplying appropriate amounts of nitrogen in medium to protect the photosynthetic process from severe damage using the photosynthetic parameters as indicators.

  12. Nitrogen and carbon assimilation by Saccharomyces cerevisiae during Sauvignon blanc juice fermentation.

    PubMed

    Pinu, Farhana R; Edwards, Patrick J B; Gardner, Richard C; Villas-Boas, Silas G

    2014-12-01

    To investigate the assimilation and production of juice metabolites by Saccharomyces cerevisiae during winemaking, we compared the metabolite profiles of 63 Sauvignon blanc (SB) grape juices collected over five harvesting seasons from different locations of New Zealand before and after fermentation by the commercial wine yeast strain EC1118 at 15 °C. Metabolite profiles were obtained using gas chromatography-mass spectrometry and nuclear magnetic resonance and the oenological parameters were determined by Fourier transform infrared spectroscopy. Our results revealed that the amino acids threonine and serine were the most consumed organic nitrogen sources, while proline and gamma-aminobutyric acid were the least consumed amino acids during SB juice fermentation. Saccharomyces cerevisiae metabolised some uncommon nitrogen sources (e.g. norleucine, norvaline and pyroglutamic acid) and several organic acids, including some fatty acids, most likely after fermenting the main juice sugars (glucose, fructose and mannose). However, consumption showed large variation between juices and in some cases between seasons. Our study clearly shows that preferred nitrogen and carbon sources were consumed by S. cerevisiae EC1118 independent of the juice fine composition, whilst the consumption of other nutrient sources mainly depended on the concentration of other juice metabolites, which explains the uniqueness of each barrel of wine. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  13. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

    SciTech Connect

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony Wayne; Song, Xia; Thornton, Peter E.; Zhang, Lihua

    2015-11-27

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, P and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg–1 dry soil, 0.1 mmol N Kg–1 dry soil, 0.1 mmol P Kg–1 dry soil, and 0.1 mmol S Kg–1 dry soil, respectively. Lastly, these findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models.

  14. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems.

    PubMed

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony W; Song, Xia; Thornton, Peter E; Zhang, Lihua

    2015-11-27

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, P and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg(-1) dry soil, 0.1 mmol N Kg(-1) dry soil, 0.1 mmol P Kg(-1) dry soil, and 0.1 mmol S Kg(-1) dry soil, respectively. These findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models.

  15. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

    PubMed Central

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony W.; Song, Xia; Thornton, Peter E.; Zhang, Lihua

    2015-01-01

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, P and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg−1 dry soil, 0.1 mmol N Kg−1 dry soil, 0.1 mmol P Kg−1 dry soil, and 0.1 mmol S Kg−1 dry soil, respectively. These findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models. PMID:26612423

  16. Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems

    DOE PAGES

    Xu, Xiaofeng; Hui, Dafeng; King, Anthony Wayne; ...

    2015-11-27

    How soil microbes assimilate carbon-C, nitrogen-N, phosphorus-P, and sulfur-S is fundamental for understanding nutrient cycling in terrestrial ecosystems. We compiled a global database of C, N, P, and S concentrations in soils and microbes and developed relationships between them by using a power function model. The C:N:P:S was estimated to be 287:17:1:0.8 for soils, and 42:6:1:0.4 for microbes. We found a convergence of the relationships between elements in soils and in soil microbial biomass across C, N, P, and S. The element concentrations in soil microbial biomass follow a homeostatic regulation curve with soil element concentrations across C, N, Pmore » and S, implying a unifying mechanism of microbial assimilating soil elements. This correlation explains the well-constrained C:N:P:S stoichiometry with a slightly larger variation in soils than in microbial biomass. Meanwhile, it is estimated that the minimum requirements of soil elements for soil microbes are 0.8 mmol C Kg–1 dry soil, 0.1 mmol N Kg–1 dry soil, 0.1 mmol P Kg–1 dry soil, and 0.1 mmol S Kg–1 dry soil, respectively. Lastly, these findings provide a mathematical explanation of element imbalance in soils and soil microbial biomass, and offer insights for incorporating microbial contribution to nutrient cycling into Earth system models.« less

  17. Stress-induced cytokinin synthesis increases drought tolerance through the coordinated regulation of carbon and nitrogen assimilation in rice.

    PubMed

    Reguera, Maria; Peleg, Zvi; Abdel-Tawab, Yasser M; Tumimbang, Ellen B; Delatorre, Carla A; Blumwald, Eduardo

    2013-12-01

    The effects of water deficit on carbon and nitrogen metabolism were investigated in flag leaves of wild-type and transgenic rice (Oryza sativa japonica 'Kitaake') plants expressing ISOPENTENYLTRANSFERASE (IPT; encoding the enzyme that mediates the rate-limiting step in cytokinin synthesis) under the control of P(SARK), a maturation- and stress-induced promoter. While the wild-type plants displayed inhibition of photosynthesis and nitrogen assimilation during water stress, neither carbon nor nitrogen assimilation was affected by stress in the transgenic P(SARK)::IPT plants. In the transgenic plants, photosynthesis was maintained at control levels during stress and the flag leaf showed increased sucrose (Suc) phosphate synthase activity and reduced Suc synthase and invertase activities, leading to increased Suc contents. The sustained carbon assimilation in the transgenic P(SARK)::IPT plants was well correlated with enhanced nitrate content, higher nitrate reductase activity, and sustained ammonium contents, indicating that the stress-induced cytokinin synthesis in the transgenic plants played a role in maintaining nitrate acquisition. Protein contents decreased and free amino acids increased in wild-type plants during stress, while protein content was preserved in the transgenic plants. Our results indicate that the stress-induced cytokinin synthesis in the transgenic plants promoted sink strengthening through a cytokinin-dependent coordinated regulation of carbon and nitrogen metabolism that facilitates an enhanced tolerance of the transgenic plants to water deficit.

  18. Salinity Effects on Photosynthesis, Carbon Allocation, and Nitrogen Assimilation in the Red Alga, Gelidium coulteri.

    PubMed

    Macler, B A

    1988-11-01

    The long-term effects of altered salinities on the physiology of the intertidal red alga Gelidium coulteri Harv. were assessed. Plants were transfered from 30 grams per liter salinity to media with salinities from 0 to 50 grams per liter. Growth rate, agar, photosynthesis, respiration, and various metabolites were quantified after 5 days and 5 weeks adaptation. After 5 days, growth rates were lower for plants at all altered salinities. Growth rates recovered from these values with 5 weeks adaptation, except for salinities of 10 grams per liter and below, where tissues bleached and died. Photosynthetic O(2) evolution was lower than control values at both higher and lower salinities after 5 days and did not change over time. Carbon fixation at the altered salinities was unchanged after 5 days, but decreased below 25 grams per liter and above 40 grams per liter after 5 weeks. Respiration increased at lower salinities. Phycobili-protein and chlorophyll were lower for all altered salinities after 5 days. These decreases continued at lower salinities, then were stable after 5 weeks. Chlorophyll recovered over time at higher salinities. Decreases in protein at lower salinities were quantitatively attributable to phycobili-protein loss. Total N levels and C:N ratios were nearly constant across all salinities tested. Carbon flow into glutamate and aspartate decreased with both decreasing and increasing salinities. Glycine, serine, and glycolate levels increased with both increasing and decreasing salinity, indicating a stimulation of photorespiration. The cell wall component agar increased with decreasing salinity, although biosynthesis was inhibited at both higher and lower salinities. The storage compound floridoside increased with increasing salinity. The evidence suggests stress responses to altered salinities that directly affected photosynthesis, respiration, and nitrogen assimilation and indirectly affected photosynthate flow. At low salinities, respiration and

  19. The allocation of assimilated carbon to shoot growth: in situ assessment in natural grasslands reveals nitrogen effects and interspecific differences.

    PubMed

    Gong, Xiao Ying; Berone, Germán Darío; Agnusdei, Mónica Graciela; Palma, Ricardo Manuel Rodríguez; Schäufele, Rudi; Lattanzi, Fernando Alfredo

    2014-04-01

    In grasslands, sustained nitrogen loading would increase the proportion of assimilated carbon allocated to shoot growth (A shoot), because it would decrease allocation to roots and also encourage the contribution of species with inherently high A shoot. However, in situ measurements of carbon allocation are scarce. Therefore, it is unclear to what extent species that coexist in grasslands actually differ in their allocation strategy or in their response to nitrogen. We used a mobile facility to perform steady-state (13)C-labeling of field stands to quantify, in winter and autumn, the daily relative photosynthesis rate (RPR~tracer assimilated over one light-period) and A shoot (~tracer remaining in shoots after a 100 degree days chase period) in four individual species with contrasting morpho-physiological characteristics coexisting in a temperate grassland of Argentina, either fertilized or not with nitrogen, and either cut intermittently or grazed continuously. Plasticity in response to nitrogen was substantial in most species, as indicated by positive correlations between A shoot and shoot nitrogen concentration. There was a notable interspecific difference: productive species with higher RPR, enhanced by fertilization and characterized by faster leaf turnover rate, allocated ~20% less of the assimilated carbon to shoot growth than species of lower productivity (and quality) characterized by longer leaf life spans and phyllochrons. These results imply that, opposite to the expected response, sustained nitrogen loading would change little the A shoot of grassland communities if increases at the species-level are offset by decreases associated with replacement of 'low RPR-high A shoot' species by 'high RPR-low A shoot' species.

  20. Process modeling of nitrogen effects on carbon assimilation and allocation-a review.

    PubMed

    Gillespie, A R; Chaney, W R

    1989-03-01

    Maximum forest productivity will only be realized through intensified management of mineral nutrition. This review examines selected individual tree and stand nutrition models. Nutrient supply is defined by mass flow and diffusion processes in a forest environment. Additionally, structures of biomass accumulation models are considered as well as nutritional limitations on assimilation functions and carbon allocation patterns.

  1. Antisense inhibition of NADH glutamate synthase impairs carbon/nitrogen assimilation in nodules of alfalfa (Medicago sativa L.).

    PubMed

    Cordoba, Elizabeth; Shishkova, Svetlana; Vance, Carroll P; Hernández, Georgina

    2003-03-01

    Legumes acquire significant amounts of nitrogen for growth from symbiotic nitrogen fixation. The glutamine synthetase (GS)/NADH-dependent glutamate synthase (NADH-GOGAT) cycle catalyzes initial nitrogen assimilation. This report describes the impact of specifically reducing nodule NADH-GOGAT activity on symbiotic performance of alfalfa (Medicago sativa L.). Four independent transgenic alfalfa lines, designated GA89, GA87, GA88, and GA82 (for GOGATantisense), containing an antisense NADH-GOGAT cDNA fragment under the control of the soybean leghemoglobin (lbc3) promoter were evaluated. The GA plants were fertile and showed normal growth in non-symbiotic conditions. The NADH-GOGAT antisense transgene was heritable and the T1 plants showed phenotypic alterations - similar to primary transformants. Clonally propagated plants were inoculated with Sinorhizobium meliloti after rooting and the symbiotic phenotype was analyzed 21 days post-inoculation. Nodules of each GA line had reduced NADH-GOGAT activity, ranging from 33 to 87% of control plants, that was accompanied by comparable decreases in RNA and protein. Plants from the GA89 line, with the lowest NADH-GOGAT activity (c. 30%), presented a strikingly altered symbiotic phenotype: concomitantly activities of key enzyme for carbon and nitrogen assimilation decreased; nodule amino acids and amides were reduced while sucrose accumulated. Antisense GOGAT plants were chlorotic, reduced in fresh weight, and had a lower N content than control plants. Photosynthesis was also impaired in antisense plants. Specifically, reducing NADH-GOGAT in nodules resulted in plants having impaired nitrogen assimilation and altered carbon/nitrogen metabolic flux.

  2. Effects of combined nitrogen on anapleurotic carbon assimilation and bleeding sap composition in Phaseolus vulgaris L.

    PubMed

    Cookson, C; Hughes, H; Coombs, J

    1980-04-01

    Dwarf french beans, Phaseolus vulgaris L., were grown with or without inoculation with rhizobia (strain 3644), and with or without a combined nitrogen source (nitrate or ammonium ions). The distribution of radioactivity into products of dark (14)CO2 assimilation was studied in roots or nodules from these plants. A detailed study was also made of the distribution and rates of excretion of nitrogen in xylem bleeding sap in 28 day old plants grown on the various sources of nitrogen. Whereas detached nodules accumulated radioactive glycine, serine and glutamate when incubated with (14)CO2, bleeding sap from plants root fed (14)CO2 contained low levels of radioactivity in these compounds but higher levels in allantoin. Chemical analysis showed allantoin to be the major compound transported in the xylem of nodulated plants, whether or not they were fed on combined nitrogen. In contrast uninoculated plants accumulated mainly amino acids in the bleeding sap, the amount and chemical composition of which depended on the combined nitrogen source.

  3. Carbon-nitrogen ratio and in vitro assimilate partitioning patterns in Cyrtanthus guthrieae L.

    PubMed

    Ncube, Bhekumthetho; Finnie, Jeffrey F; Van Staden, Johannes

    2014-01-01

    In response to variations in nutritional composition of the growth medium, plants often adjust their metabolism and progressively alter their growth patterns. Carbon (C) and nitrogen (N) constitute the major plant nutritional components influencing plant growth and development patterns. This study examined the growth dynamics and patterns of assimilate partitioning to primary and secondary metabolites in response to varying levels and combinations of C and N in the culture media of Cyrtanthus guthrieae. In vitro callus-derived C. guthrieae plantlets were cultured on solid Murashige and Skoog (MS) media with different concentrations and combinations of C and N. Relative growth rate (RGR) increased proportionally with an increase in C concentrations up to 88 mM sucrose (0.58 d(-1)) beyond which it was hardly influenced by further increases in C. Growth was also significantly favoured in media with high concentrations of N at all C concentrations tested. In C-limited media regimes with growth saturating N conditions, alkaloid accumulation became favoured while polyphenol content increased with an increase in C levels in the medium, a characteristic pattern that appeared to be less influenced by the amount of N. Of the primary metabolites, only proteins showed small significant variations across different media treatments, with starch and soluble sugars increasing proportionately with C levels. In the medium with a high sucrose concentration (175 mM), soluble sugars, amino acids and polyphenols increased markedly, possibly as an adaptive response to the reduced osmotic potential in the media and/or a storage mechanism for excess C and N reserves in the media. From a medicinal perspective, with regard to polyphenolic compounds in C. guthrieae, growth medium conditions that allow for high levels of C pools in the tissue would thus be favourable for the enhanced synthesis of this group of compounds. The medium conditions with 175 mM sucrose and 10.3 mM NH4NO3 gave the

  4. Assimilation and allocation of carbon and nitrogen of thermal and nonthermal Agrostis species in response to high soil temperature.

    PubMed

    Rachmilevitch, Shimon; Huang, Bingru; Lambers, Hans

    2006-01-01

    We studied whether changes in the assimilation and allocation of carbon and nitrogen are associated with plant tolerance to high soil temperatures. Two Agrostis species, thermal Agrostis scabra, a species adapted to high-temperature soils in geothermal areas in Yellowstone National Park (USA), and two cultivars of a cool-season species, Agrostis stolonifera, L-93 and Penncross, were exposed to soil temperatures of 37 or 20 degrees C, while shoots were exposed to 20 degrees C. Net photosynthesis rate, photochemical efficiency, NO(3) (-)-assimilation rate and root viability decreased with increasing soil temperatures in both species. However, the decreases were less pronounced for A. scabra than for both A. stolonifera cultivars. Carbon investment in growth of plants exposed to 37 degrees C decreased more dramatically in both A. stolonifera cultivars than in A. scabra. Nitrogen allocation to shoots was greater in A. scabra than in both creeping bentgrass cultivars at 37 degrees C soil temperature. Our results demonstrate that plant tolerance to high soil temperature is related to efficient expenditure and adjustment of C- and N-allocation patterns between growth and respiration.

  5. Regulation by cyanate of the genes involved in carbon and nitrogen assimilation in the cyanobacterium Synechococcus sp. strain PCC 7942.

    PubMed

    Suzuki, I; Sugiyami, T; Omata, T

    1996-05-01

    A mutant (M45) of the cyanobacterium Synechococcus sp. strain PCC 7942, which is defective in active transport of nitrate, was used for the studies of the nitrogen regulation of the genes involved in nitrate and CO2 assimilation. In a medium containing 30 mM nitrate as the nitrogen source, M45 grew under constant stress of nitrogen deficiency and accumulated a five-times-larger amount of the transcript of nirA, the gene for nitrite reductase, compared with nitrate-grown wild-type cells. By contrast, the level of the transcript of rbcL, the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, was 40% of the wild-type level. Addition of ammonium to the culture of M45 abolished the accumulation of the nirA transcript and stimulated the accumulation of the rbcL transcript, showing that ammonium repressed and activated the transcription of nirA and rbcL, respectively. Glutamine, the initial product of ammonium fixation, also showed negative and positive effects on nirA and rbcL, respectively. One of the metabolites of glutamine, carbamoylphosphate, and its decomposition product, cyanate, were found to repress nirA and also to markedly activate rbcL. Cyanate negatively regulated another ammonium-repressible gene, glnA, but had no effect on the psbAI and rps1 genes. The effects of cyanate were not ascribable to the ammonium and CO, resulting from its decomposition. These findings suggested that cyanate may act as a regulator of the ammonium-responsive genes involved in carbon and nitrogen assimilation in the cyanobacterium.

  6. Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains.

    PubMed

    Crauwels, S; Van Assche, A; de Jonge, R; Borneman, A R; Verreth, C; Troels, P; De Samblanx, G; Marchal, K; Van de Peer, Y; Willems, K A; Verstrepen, K J; Curtin, C D; Lievens, B

    2015-11-01

    Recent studies have suggested a correlation between genotype groups of Brettanomyces bruxellensis and their source of isolation. To further explore this relationship, the objective of this study was to assess metabolic differences in carbon and nitrogen assimilation between different B. bruxellensis strains from three beverages, including beer, wine, and soft drink, using Biolog Phenotype Microarrays. While some similarities of physiology were noted, many traits were variable among strains. Interestingly, some phenotypes were found that could be linked to strain origin, especially for the assimilation of particular α- and β-glycosides as well as α- and β-substituted monosaccharides. Based upon gene presence or absence, an α-glucosidase and β-glucosidase were found explaining the observed phenotypes. Further, using a PCR screen on a large number of isolates, we have been able to specifically link a genomic deletion to the beer strains, suggesting that this region may have a fitness cost for B. bruxellensis in certain fermentation systems such as brewing. More specifically, none of the beer strains were found to contain a β-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.

  7. Wheat ear carbon assimilation and nitrogen remobilization contribute significantly to grain yield.

    PubMed

    Zhou, Bangwei; Serret, Maria Dolores; Elazab, Abdelhalim; Bort Pie, Jordi; Araus, José Luis; Aranjuelo, Iker; Sanz-Sáez, Álvaro

    2016-11-01

    The role of wheat ears as a source of nitrogen (N) and carbon (C) in the grain filling process has barely been studied. To resolve this question, five wheat genotypes were labeled with (15) N-enriched nutrient solution. N remobilization and absorption were estimated via the nitrogen isotope composition of total organic matter and Rubisco. Gas exchange analyses showed that ear photosynthesis contributed substantially to grain filling in spite of the great loss of C due to respiration. Of the total kernel N, 64.7% was derived from the N acquired between sowing and anthesis, while the remaining 35.3% was derived from the N acquired between anthesis and maturity. In addition, 1.87 times more N was remobilized to the developing kernel from the ear than from the flag leaf. The higher yielding genotypes showed an increased N remobilization to the kernel compared to the lower yielding genotypes. In addition, the higher yielding genotypes remobilized more N from the ears to the kernel than the lower yielding genotypes, while the lower yielding genotypes remobilized more N from the flag leaf to the kernel. Therefore, the ears contribute significantly toward fulfilling C and N demands during grain filling.

  8. Stress-Induced Cytokinin Synthesis Increases Drought Tolerance through the Coordinated Regulation of Carbon and Nitrogen Assimilation in Rice1[C][W][OPEN

    PubMed Central

    Reguera, Maria; Peleg, Zvi; Abdel-Tawab, Yasser M.; Tumimbang, Ellen B.; Delatorre, Carla A.; Blumwald, Eduardo

    2013-01-01

    The effects of water deficit on carbon and nitrogen metabolism were investigated in flag leaves of wild-type and transgenic rice (Oryza sativa japonica ‘Kitaake’) plants expressing ISOPENTENYLTRANSFERASE (IPT; encoding the enzyme that mediates the rate-limiting step in cytokinin synthesis) under the control of PSARK, a maturation- and stress-induced promoter. While the wild-type plants displayed inhibition of photosynthesis and nitrogen assimilation during water stress, neither carbon nor nitrogen assimilation was affected by stress in the transgenic PSARK::IPT plants. In the transgenic plants, photosynthesis was maintained at control levels during stress and the flag leaf showed increased sucrose (Suc) phosphate synthase activity and reduced Suc synthase and invertase activities, leading to increased Suc contents. The sustained carbon assimilation in the transgenic PSARK::IPT plants was well correlated with enhanced nitrate content, higher nitrate reductase activity, and sustained ammonium contents, indicating that the stress-induced cytokinin synthesis in the transgenic plants played a role in maintaining nitrate acquisition. Protein contents decreased and free amino acids increased in wild-type plants during stress, while protein content was preserved in the transgenic plants. Our results indicate that the stress-induced cytokinin synthesis in the transgenic plants promoted sink strengthening through a cytokinin-dependent coordinated regulation of carbon and nitrogen metabolism that facilitates an enhanced tolerance of the transgenic plants to water deficit. PMID:24101772

  9. Tracer studies of nitrogen assimilation in yeast.

    PubMed

    ABRAMS, R; HAMMARSTEN, E

    1949-01-01

    By using N(15) as a tracer the assimilation of ammonia by the yeast, Torulopsis utilis, has been studied. It has been shown that: 1. There was no measurable incorporation of N in the protein or polynucleotide purine of carbon-starved yeast. 2. When ammonia is added to nitrogen-starved yeast there is a long lag period before division begins during which the yeast rapidly synthesizes protein, this process being accompanied by a turnover of polynucleotide purine. There was no significant dilution of the N(15)H(4) (+) of the medium by ordinary NH(4) (+). 3. When yeast containing N(15) is allowed to divide and grow in ordinary ammonia, the total amount of N(15) in the yeast remains constant. The dicarboxylic amino acids are most diluted, while arginine and nucleic acid guanine are not diluted at all.

  10. TRACER STUDIES OF NITROGEN ASSIMILATION IN YEAST

    PubMed Central

    Abrams, Richard; Hammarsten, E.; Reichard, P.; Sperber, E.

    1949-01-01

    By using N15 as a tracer the assimilation of ammonia by the yeast, Torulopsis utilis, has been studied. It has been shown that: 1. There was no measurable incorporation of N in the protein or polynucleotide purine of carbon-starved yeast. 2. When ammonia is added to nitrogen-starved yeast there is a long lag period before division begins during which the yeast rapidly synthesizes protein, this process being accompanied by a turnover of polynucleotide purine. There was no significant dilution of the N15H4+ of the medium by ordinary NH4+. 3. When yeast containing N15 is allowed to divide and grow in ordinary ammonia, the total amount of N15 in the yeast remains constant. The dicarboxylic amino acids are most diluted, while arginine and nucleic acid guanine are not diluted at all. PMID:18108495

  11. Assimilation of Unusual Carbon Compounds

    NASA Astrophysics Data System (ADS)

    Middelhoven, Wouter J.

    Yeast taxa traditionally are distinguished by growth tests on several sugars and organic acids. During the last decades it became apparent that many yeast species assimilate a much greater variety of naturally occurring carbon compounds as sole source of carbon and energy. These abilities are indicative of a greater role of yeasts in the carbon cycle than previously assumed. Especially in acidic soils and other habitats, yeasts may play a role in the degradation of carbon compounds. Such compounds include purines like uric acid and adenine, aliphatic amines, diamines and hydroxyamines, phenolics and other benzene compounds and polysaccharides. Assimilation of purines and amines is a feature of many ascomycetes and basidiomycetes. However, benzene compounds are degraded by only a few ascomycetous yeasts (e.g. the Stephanoascus/ Blastobotrys clade and black yeastlike fungi) but by many basidiomycetes, e.g. Filobasidiales, Trichosporonales, red yeasts producing ballistoconidia and related species, but not by Tremellales. Assimilation of polysaccharides is wide-spread among basidiomycetes

  12. Global Proteomics Reveal An Atypical Strategy for Carbon/Nitrogen Assimilation by a Cyanobacterium Under Diverse Environmental Perturbations

    SciTech Connect

    Wegener, Kimberly M.; Singh, Abhay K.; Jacobs, Jon M.; Elvitigala, Thanura R.; Welsh, Eric A.; Keren, Nir S.; Gritsenko, Marina A.; Ghosh, Bijoy K.; Camp, David G.; Smith, Richard D.; Pakrasi, Himadri B.

    2010-12-01

    Cyanobacteria, the only prokaryotes capable of oxygenic photosynthesis, are present in diverse ecological niches and play crucial roles in global carbon and nitrogen cycles. To proliferate in nature, cyanobacteria utilize a host of stress responses to accommodate periodic changes in environmental conditions. A detailed knowledge of the composition of, as well as the dynamic changes in, the proteome is necessary to gain fundamental insights into such stress responses. Toward this goal, we have performed a largescale proteomic analysis of the widely studied model cyanobacterium Synechocystis sp. PCC 6803 under 33 different environmental conditions. The resulting high-quality dataset consists of 22,318 unique peptides corresponding to 1,955 proteins, a coverage of 53% of the predicted proteome. Quantitative determination of protein abundances has led to the identification of 1,198 differentially regulated proteins. Notably, our analysis revealed that a common stress response under various environmental perturbations, irrespective of amplitude and duration, is the activation of atypical pathways for the acquisition of carbon and nitrogen from urea and arginine. In particular, arginine is catabolized via putrescine to produce succinate and glutamate, sources of carbon and nitrogen, respectively. This study provides the most comprehensive functional and quantitative analysis of the Synechocystis proteome to date, and shows that a significant stress response of cyanobacteria involves an uncommon mode of acquisition of carbon and nitrogen. Oxygenic phototrophic prokaryotes, the progenitors of the chloroplast, are crucial to global oxygen production and worldwide carbon and nitrogen cycles. These microalgae are robust organisms capable carbon neutral biofuel production. Synechocystis sp. PCC 6803 has historically been a model cyanobacterium for photosynthetic research and is emerging as a promising biofuel platform. Cellular responses are severely modified by environmental

  13. Canopy nitrogen, carbon assimilation, and albedo in temperate and boreal forests: Functional relations and potential climate feedbacks

    PubMed Central

    Ollinger, S. V.; Richardson, A. D.; Martin, M. E.; Hollinger, D. Y.; Frolking, S. E.; Reich, P. B.; Plourde, L. C.; Katul, G. G.; Munger, J. W.; Oren, R.; Smith, M.-L.; Paw U, K. T.; Bolstad, P. V.; Cook, B. D.; Day, M. C.; Martin, T. A.; Monson, R. K.; Schmid, H. P.

    2008-01-01

    The availability of nitrogen represents a key constraint on carbon cycling in terrestrial ecosystems, and it is largely in this capacity that the role of N in the Earth's climate system has been considered. Despite this, few studies have included continuous variation in plant N status as a driver of broad-scale carbon cycle analyses. This is partly because of uncertainties in how leaf-level physiological relationships scale to whole ecosystems and because methods for regional to continental detection of plant N concentrations have yet to be developed. Here, we show that ecosystem CO2 uptake capacity in temperate and boreal forests scales directly with whole-canopy N concentrations, mirroring a leaf-level trend that has been observed for woody plants worldwide. We further show that both CO2 uptake capacity and canopy N concentration are strongly and positively correlated with shortwave surface albedo. These results suggest that N plays an additional, and overlooked, role in the climate system via its influence on vegetation reflectivity and shortwave surface energy exchange. We also demonstrate that much of the spatial variation in canopy N can be detected by using broad-band satellite sensors, offering a means through which these findings can be applied toward improved application of coupled carbon cycle–climate models. PMID:19052233

  14. Canopy nitrogen, carbon assimilation, and albedo in temperate and boreal forests: Functional relations and potential climate feedbacks.

    PubMed

    Ollinger, S V; Richardson, A D; Martin, M E; Hollinger, D Y; Frolking, S E; Reich, P B; Plourde, L C; Katul, G G; Munger, J W; Oren, R; Smith, M-L; Paw U, K T; Bolstad, P V; Cook, B D; Day, M C; Martin, T A; Monson, R K; Schmid, H P

    2008-12-09

    The availability of nitrogen represents a key constraint on carbon cycling in terrestrial ecosystems, and it is largely in this capacity that the role of N in the Earth's climate system has been considered. Despite this, few studies have included continuous variation in plant N status as a driver of broad-scale carbon cycle analyses. This is partly because of uncertainties in how leaf-level physiological relationships scale to whole ecosystems and because methods for regional to continental detection of plant N concentrations have yet to be developed. Here, we show that ecosystem CO(2) uptake capacity in temperate and boreal forests scales directly with whole-canopy N concentrations, mirroring a leaf-level trend that has been observed for woody plants worldwide. We further show that both CO(2) uptake capacity and canopy N concentration are strongly and positively correlated with shortwave surface albedo. These results suggest that N plays an additional, and overlooked, role in the climate system via its influence on vegetation reflectivity and shortwave surface energy exchange. We also demonstrate that much of the spatial variation in canopy N can be detected by using broad-band satellite sensors, offering a means through which these findings can be applied toward improved application of coupled carbon cycle-climate models.

  15. Fine Mapping of Carbon Assimilation Rate 8, a Quantitative Trait Locus for Flag Leaf Nitrogen Content, Stomatal Conductance and Photosynthesis in Rice

    PubMed Central

    Adachi, Shunsuke; Yoshikawa, Kazuaki; Yamanouchi, Utako; Tanabata, Takanari; Sun, Jian; Ookawa, Taiichiro; Yamamoto, Toshio; Sage, Rowan F.; Hirasawa, Tadashi; Yonemaru, Junichi

    2017-01-01

    Increasing the rate of leaf photosynthesis is one important approach for increasing grain yield in rice (Oryza sativa). Exploiting the natural variation in CO2 assimilation rate (A) between rice cultivars using quantitative genetics is one promising means to identify genes contributing to higher photosynthesis. In this study, we determined precise location of Carbon Assimilation Rate 8 (CAR8) by crossing a high-yielding indica cultivar with a Japanese commercial cultivar. Fine mapping suggested that CAR8 encodes a putative Heme Activator Protein 3 (OsHAP3) subunit of a CCAAT-box-binding transcription factor called OsHAP3H. Sequencing analysis revealed that the indica allele of CAR8 has a 1-bp deletion at 322 bp from the start codon, resulting in a truncated protein of 125 amino acids. In addition, CAR8 is identical to DTH8/Ghd8/LHD1, which was reported to control rice flowering date. The increase of A is largely due to an increase of RuBP regeneration rate via increased leaf nitrogen content, and partially explained by reduced stomatal limitation via increased stomatal conductance relative to A. This allele also increases hydraulic conductivity, which would promote higher stomatal conductance. This indicates that CAR8 affects multiple physiological aspects relating to photosynthesis. The detailed analysis of molecular functions of CAR8 would help to understand the association between photosynthesis and flowering and demonstrate specific genetic mechanisms that can be exploited to improve photosynthesis in rice and potentially other crops. PMID:28197156

  16. Fine Mapping of Carbon Assimilation Rate 8, a Quantitative Trait Locus for Flag Leaf Nitrogen Content, Stomatal Conductance and Photosynthesis in Rice.

    PubMed

    Adachi, Shunsuke; Yoshikawa, Kazuaki; Yamanouchi, Utako; Tanabata, Takanari; Sun, Jian; Ookawa, Taiichiro; Yamamoto, Toshio; Sage, Rowan F; Hirasawa, Tadashi; Yonemaru, Junichi

    2017-01-01

    Increasing the rate of leaf photosynthesis is one important approach for increasing grain yield in rice (Oryza sativa). Exploiting the natural variation in CO2 assimilation rate (A) between rice cultivars using quantitative genetics is one promising means to identify genes contributing to higher photosynthesis. In this study, we determined precise location of Carbon Assimilation Rate 8 (CAR8) by crossing a high-yielding indica cultivar with a Japanese commercial cultivar. Fine mapping suggested that CAR8 encodes a putative Heme Activator Protein 3 (OsHAP3) subunit of a CCAAT-box-binding transcription factor called OsHAP3H. Sequencing analysis revealed that the indica allele of CAR8 has a 1-bp deletion at 322 bp from the start codon, resulting in a truncated protein of 125 amino acids. In addition, CAR8 is identical to DTH8/Ghd8/LHD1, which was reported to control rice flowering date. The increase of A is largely due to an increase of RuBP regeneration rate via increased leaf nitrogen content, and partially explained by reduced stomatal limitation via increased stomatal conductance relative to A. This allele also increases hydraulic conductivity, which would promote higher stomatal conductance. This indicates that CAR8 affects multiple physiological aspects relating to photosynthesis. The detailed analysis of molecular functions of CAR8 would help to understand the association between photosynthesis and flowering and demonstrate specific genetic mechanisms that can be exploited to improve photosynthesis in rice and potentially other crops.

  17. Clonal integration ameliorates the carbon accumulation capacity of a stoloniferous herb, Glechoma longituba, growing in heterogenous light conditions by facilitating nitrogen assimilation in the rhizosphere.

    PubMed

    Chen, Jin-Song; Li, Jun; Zhang, Yun; Zong, Hao; Lei, Ning-Fei

    2015-01-01

    Enhanced availability of photosynthates increases nitrogen (N) mineralization and nitrification in the rhizosphere via rhizodeposition from plant roots. Under heterogeneous light conditions, photosynthates supplied by exposed ramets may promote N assimilation in the rhizosphere of shaded, connected ramets. This study was conducted to test this hypothesis. Clonal fragments of the stoloniferous herb Glechoma longituba with two successive ramets were selected. Mother ramets were subjected to full sunlight and offspring ramets were subjected to 80 % shading, and the stolon between the two successive ramets was either severed or left intact. Measurements were taken of photosynthetic and growth parameters. The turnover of available soil N was determined together with the compostion of the rhizosphere microbial community. The microbial community composition in the rhizosphere of shaded offspring ramets was significantly altered by clonal integration. Positive effects of clonal integration were observed on NAGase activity, net soil N mineralization rate and net soil N nitrification rate. Increased leaf N and chlorophyll content as well as leaf N allocation to the photosynthetic machinery improved the photosynthetic capability of shaded offspring ramets when the stolon was left intact. Clonal integration improved the growth performance of shaded, connected offspring ramets and whole clonal fragments without any cost to the exposed mother ramets. Considerable differences in microbial community composition caused by clonal integration may facilitate N assimilation in the rhizosphere of shaded offspring ramets. Increased N content in the photosynthetic machinery may allow pre-acclimation to high light conditions for shaded offspring ramets, thus promoting opportunistic light capture. In accordance with the theory of the division of labour, it is suggested that clonal integration may ameliorate the carbon assimilation capacity of clonal plants, thus improving their fitness in

  18. Clonal integration ameliorates the carbon accumulation capacity of a stoloniferous herb, Glechoma longituba, growing in heterogenous light conditions by facilitating nitrogen assimilation in the rhizosphere

    PubMed Central

    Chen, Jin-Song; Li, Jun; Zhang, Yun; Zong, Hao; Lei, Ning-Fei

    2015-01-01

    Background and Aims Enhanced availability of photosynthates increases nitrogen (N) mineralization and nitrification in the rhizosphere via rhizodeposition from plant roots. Under heterogeneous light conditions, photosynthates supplied by exposed ramets may promote N assimilation in the rhizosphere of shaded, connected ramets. This study was conducted to test this hypothesis. Methods Clonal fragments of the stoloniferous herb Glechoma longituba with two successive ramets were selected. Mother ramets were subjected to full sunlight and offspring ramets were subjected to 80 % shading, and the stolon between the two successive ramets was either severed or left intact. Measurements were taken of photosynthetic and growth parameters. The turnover of available soil N was determined together with the compostion of the rhizosphere microbial community. Key Results The microbial community composition in the rhizosphere of shaded offspring ramets was significantly altered by clonal integration. Positive effects of clonal integration were observed on NAGase activity, net soil N mineralization rate and net soil N nitrification rate. Increased leaf N and chlorophyll content as well as leaf N allocation to the photosynthetic machinery improved the photosynthetic capability of shaded offspring ramets when the stolon was left intact. Clonal integration improved the growth performance of shaded, connected offspring ramets and whole clonal fragments without any cost to the exposed mother ramets. Conclusions Considerable differences in microbial community composition caused by clonal integration may facilitate N assimilation in the rhizosphere of shaded offspring ramets. Increased N content in the photosynthetic machinery may allow pre-acclimation to high light conditions for shaded offspring ramets, thus promoting opportunistic light capture. In accordance with the theory of the division of labour, it is suggested that clonal integration may ameliorate the carbon assimilation

  19. Transgenic plants that exhibit enhanced nitrogen assimilation

    DOEpatents

    Coruzzi, Gloria M.; Brears, Timothy

    2005-03-08

    The present invention relates to a method for producing plants with improved agronomic and nutritional traits. Such traits include enhanced nitrogen assimilatory and utilization capacities, faster and more vigorous growth, greater vegetative and reproductive yields, and enriched or altered nitrogen content in vegetative and reproductive parts. More particularly, the invention relates to the engineering of plants modified to have altered expression of key enzymes in the nitrogen assimilation and utilization pathways. In one embodiment of the present invention, the desired altered expression is accomplished by engineering the plant for ectopic overexpression of one of more the native or modified nitrogen assimilatory enzymes. The invention also has a number of other embodiments, all of which are disclosed herein.

  20. Transgenic plants that exhibit enhanced nitrogen assimilation

    DOEpatents

    Coruzzi, Gloria M.; Brears, Timothy

    2000-01-01

    The present invention relates to a method for producing plants with improved agronomic and nutritional traits. Such traits include enhanced nitrogen assimilatory and utilization capacities, faster and more vigorous growth, greater vegetative and reproductive yields, and enriched or altered nitrogen content in vegetative and reproductive parts. More particularly, the invention relates to the engineering of plants modified to have altered expression of key enzymes in the nitrogen assimilation and utilization pathways. In one embodiment of the present invention, the desired altered expression is accomplished by engineering the plant for ectopic overexpression of one of more the native or modified nitrogen assimilatory enzymes. The invention also has a number of other embodiments, all of which are disclosed herein.

  1. Transgenic plants that exhibit enhanced nitrogen assimilation

    DOEpatents

    Coruzzi, Gloria M.; Brears, Timothy

    1999-01-01

    The present invention relates to a method for producing plants with improved agronomic and nutritional traits. Such traits include enhanced nitrogen assimilatory and utilization capacities, faster and more vigorous growth, greater vegetative and reproductive yields, and enriched or altered nitrogen content in vegetative and reproductive parts. More particularly, the invention relates to the engineering of plants modified to have altered expression of key enzymes in the nitrogen assimilation and utilization pathways. In one embodiment of the present invention, the desired altered expression is accomplished by engineering the plant for ectopic overexpression of one of more the native or modified nitrogen assimilatory enzymes. The invention also has a number of other embodiments, all of which are disclosed herein.

  2. Insights into nutrient assimilation and export in naturally iron-fertilized waters of the Southern Ocean from nitrogen, carbon and oxygen isotopes

    NASA Astrophysics Data System (ADS)

    Trull, Thomas W.; Davies, Diana; Casciotti, Karen

    2008-03-01

    The KErguelen Ocean and Plateau compared Study (KEOPS) documented enhanced iron input and phytoplankton biomass over the deep Kerguelen plateau in comparison to surrounding high-nutrient low-chlorophyll (HNLC) waters in late summer 2005. We examined the influence of this iron on nitrogen and carbon metabolism by the microbial food-web, by comparing samples from on-plateau and off-plateau. Suspended particulate organic carbon (POC) was ˜5 times more abundant on-plateau and exhibited greater POC/PON (˜6.5 vs. ˜5.5), δ13C-POC (˜-21.5 vs. ˜-24.5‰) and δ15N-PON (˜+2 vs. ˜0‰) than off-plateau. These differences arose in part from changes in ecosystem structure as demonstrated by size-fractionation (1, 5, 20, 55, 210, and 335-μm filters in series), which revealed large isotopic variations with size ( δ13C-POC ranged from -28 to -19‰ and δ15N-PON from -3 to +5‰) and greater abundances of 13C- and 15N-enriched large phytoplankton over the plateau. The 13C enrichment in POC reflected faster growth rates and greater draw-down of dissolved inorganic carbon over the plateau. Quantitative comparison to the δ15N of dissolved nitrate indicates that the δ15N-PON enrichment derived from increased assimilation of nitrate, corresponding to new production f-ratios of 0.7-0.9 on-plateau vs. 0.4-0.6 off-plateau. Results from a sparse set of free-drifting sediment trap samples suggest control of export by zooplankton grazing. The 15N and 18O enrichments in dissolved nitrate exhibited a 1:1 correlation, indicating that phytoplankton assimilation controls nitrate availability and only a relatively small amount of nitrate was regenerated by nitrification. The δ15N-NO 3 values yield indistinguishable isotopic fractionation factors on and off the plateau ( 15ɛ of 4-5‰). This suggests that variations in iron availability may not bias the interpretation of paleo-environmental 15N records, and leaves intact the view that higher sedimentary δ15N-PON values during the

  3. Autotrophic nitrogen assimilation and carbon capture for microbial protein production by a novel enrichment of hydrogen-oxidizing bacteria.

    PubMed

    Matassa, Silvio; Verstraete, Willy; Pikaar, Ilje; Boon, Nico

    2016-09-15

    Domestic used water treatment systems are currently predominantly based on conventional resource inefficient treatment processes. While resource recovery is gaining momentum it lacks high value end-products which can be efficiently marketed. Microbial protein production offers a valid and promising alternative by upgrading low value recovered resources into high quality feed and also food. In the present study, we evaluated the potential of hydrogen-oxidizing bacteria to upgrade ammonium and carbon dioxide under autotrophic growth conditions. The enrichment of a generic microbial community and the implementation of different culture conditions (sequenced batch resp. continuous reactor) revealed surprising features. At low selection pressure (i.e. under sequenced batch culture at high solid retention time), a very diverse microbiome with an important presence of predatory Bdellovibrio spp. was observed. The microbial culture which evolved under high rate selection pressure (i.e. dilution rate D = 0.1 h(-1)) under continuous reactor conditions was dominated by Sulfuricurvum spp. and a highly stable and efficient process in terms of N and C uptake, biomass yield and volumetric productivity was attained. Under continuous culture conditions the maximum yield obtained was 0.29 g cell dry weight per gram chemical oxygen demand equivalent of hydrogen, whereas the maximum volumetric loading rate peaked 0.41 g cell dry weight per litre per hour at a protein content of 71%. Finally, the microbial protein produced was of high nutritive quality in terms of essential amino acids content and can be a suitable substitute for conventional feed sources such as fishmeal or soybean meal. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Nitrogen (N) assimilation and regeneration in hypoxic water column of Jinhae Bay, South Korea

    NASA Astrophysics Data System (ADS)

    Park, S.; An, S.; Lee, J.; Park, S.; Kim, Y.; Ryu, J.; Choe, S.

    2015-12-01

    Nitrogen generally controls the phytoplankton productivity in marine environment and detailed information regarding N cycling is necessary to understand extreme ecological processes such as hypoxic condition. Generally, primary production was measured using oxygen evolution or stable 13C isotope tracer experiment and nitrogen assimilation rate were estimated assuming certain carbon to nitrogen ratio. The regeneration of N is also estimated from the respiration rates although direct measurement method was applied in some experiments. We measured both photosynthetic and respiration rate using carbon and oxygen based methods, and at the same time, independent experiments for nitrogen assimilation and regeneration process measurement were conducted using stable isotope tracers. The differences of N assimilation and regeneration results between each method were analyzed in the context of hypoxic condition development.

  5. Plant nitrogen budget under elevated carbon dioxide level: Regulation by nitrogen absorption and assimilation. Progress report, October 1, 1995--July 31, 1996

    SciTech Connect

    BassiriRad, H.; Gutschick, V.

    1998-09-01

    The overall objective is to assess root physiological and morphological characteristics that may alter plant N acquisition capacity in response to rising atmospheric CO{sub 2} concentration. There is increasing evidence that plant and ecosystem responses to elevated levels of CO{sub 2} will ultimately depend on availability and acquisition rate of other resources such as N. Therefore, knowledge of any changes in root capacity to acquire N is crucial in predicting plant and ecosystem responses to high CO{sub 2}. Here the authors are testing two major hypotheses: (1) elevated CO{sub 2} will enhance root N uptake kinetics and (2) CO{sub 2} enrichment will increase root preference for NO{sub 3}{sup {minus}} as opposed to NH{sub 4}{sup +}. High CO{sub 2} enhances root energy status which should in turn favor energy-intensive processes such as NO{sub 3}{sup {minus}} uptake and assimilation. The above hypotheses are being tested on a range of species from native and agricultural ecosystems using a combination of field, lab and growth chamber studies. The authors have demonstrated a considerable interspecies variation in root N uptake responses to CO{sub 2} enrichment and attempts are now underway to evaluate if such variations are correlated with different functional groups. A comprehensive growth model, using physiological and allocation parameters, has been largely completed and will be used to analyze the completed experimental data.

  6. Carbon dioxide enrichment inhibits nitrate assimilation in wheat and Arabidopsis.

    PubMed

    Bloom, Arnold J; Burger, Martin; Rubio Asensio, Jose Salvador; Cousins, Asaph B

    2010-05-14

    The concentration of carbon dioxide in Earth's atmosphere may double by the end of the 21st century. The response of higher plants to a carbon dioxide doubling often includes a decline in their nitrogen status, but the reasons for this decline have been uncertain. We used five independent methods with wheat and Arabidopsis to show that atmospheric carbon dioxide enrichment inhibited the assimilation of nitrate into organic nitrogen compounds. This inhibition may be largely responsible for carbon dioxide acclimation, the decrease in photosynthesis and growth of plants conducting C(3) carbon fixation after long exposures (days to years) to carbon dioxide enrichment. These results suggest that the relative availability of soil ammonium and nitrate to most plants will become increasingly important in determining their productivity as well as their quality as food.

  7. Nitrogen assimilation in denitrifier Bacillus azotoformans LMG 9581(T).

    PubMed

    Sun, Yihua; De Vos, Paul; Willems, Anne

    2017-07-19

    Until recently, it has not been generally known that some bacteria can contain the gene inventory for both denitrification and dissimilatory nitrate (NO3(-))/nitrite (NO2(-)) reduction to ammonium (NH4(+)) (DNRA). Detailed studies of these microorganisms could shed light on the differentiating environmental drivers of both processes without interference of organism-specific variation. Genome analysis of Bacillus azotoformans LMG 9581(T) shows a remarkable redundancy of dissimilatory nitrogen reduction, with multiple copies of each denitrification gene as well as DNRA genes nrfAH, but a reduced capacity for nitrogen assimilation, with no nas operon nor amtB gene. Here, we explored nitrogen assimilation in detail using growth experiments in media with different organic and inorganic nitrogen sources at different concentrations. Monitoring of growth, NO3(-) NO2(-), NH4(+) concentration and N2O production revealed that B. azotoformans LMG 9581(T) could not grow with NH4(+) as sole nitrogen source and confirmed the hypothesis of reduced nitrogen assimilation pathways. However, NH4(+) could be assimilated and contributed up to 50% of biomass if yeast extract was also provided. NH4(+) also had a significant but concentration-dependent influence on growth rate. The mechanisms behind these observations remain to be resolved but hypotheses for this deficiency in nitrogen assimilation are discussed. In addition, in all growth conditions tested a denitrification phenotype was observed, with all supplied NO3(-) converted to nitrous oxide (N2O).

  8. The CCAAT box-binding factor stimulates ammonium assimilation in Saccharomyces cerevisiae, defining a new cross-pathway regulation between nitrogen and carbon metabolisms.

    PubMed

    Dang, V D; Bohn, C; Bolotin-Fukuhara, M; Daignan-Fornier, B

    1996-04-01

    In Saccharomyces cerevisiae, carbon and nitrogen metabolisms are connected via the incorporation of ammonia into glutamate; this reaction is catalyzed by the NADP-dependent glutamate dehydrogenase (NADP-GDH) encoded by the GDH1 gene. In this report, we show that the GDH1 gene requires the CCAAT box-binding activator (HAP complex) for optimal expression. This conclusion is based on several lines of evidence: (1) overexpression of GDH1 can correct the growth defect of hap2 and hap3 mutants on ammonium sulfate as a nitrogen source, (ii) Northern (RNA) blot analysis shows that the steady-state level of GDH1 mRNA is strongly lowered in a hap2 mutant, (iii) expression of a GDH1-lacZ fusion is drastically reduced in hap mutants, (iv) NADP-GDH activity is several times lower in the hap mutants compared with that in the isogenic wild-type strain, and finally, (v) site-directed mutagenesis of two consensual HAP binding sites in the GDH1 promoter strongly reduces expression of GDH1 and makes it HAP independent. Expression of GDH1 is also regulated by the carbon source, i.e., expression is higher on lactate than on ethanol, glycerol, or galactose, with the lowest expression being found on glucose. Finally, we show that a hap2 mutation does not affect expression of other genes involved in nitrogen metabolism (GDH2, GLN1, and GLN3 encoding, respectively, the NAD-GDH, glutamine synthetase, and a general activator of several nitrogen catabolic genes). The HAP complex is known to regulate expression of several genes involved in carbon metabolism; its role in the control of GDH1 gene expression, therefore, provides evidence for a cross-pathway regulation between carbon and nitrogen metabolisms.

  9. Nitrogen Mineralization and Assimilation at Millimeter Scales

    SciTech Connect

    Cliff, John B.; Bottomley, Peter J.; Gaspar, Dan J.; Myrold, David D.

    2006-11-15

    This study used inoculated, artificial soil microcosms containing sand, clay, cellulose, and localized hotspots of highly labile, organic-N containing dead bacteria to study N mineralization and assimilation at submillimeter and centimeter scales. Labeling with 15NH4+ along with measurement of label assimilated into microbial biomass at the bulk scale allowed estimation of gross rates of ammonification and N assimilation using isotope dilution. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) analyses of transects of organic-15N across Si wafers in contact with the microcosms indicated strong gradients of 15NH4+ assimilation as a function of proximity to the hotspots that were not apparent using bulk analyses. This combination of bulk and ToF-SIMS analyses represents a powerful approach to explore the physical and biochemical factors that affect N process heterogeneities in soils.

  10. Nitrogen dioxide assimilation as affected by light level

    SciTech Connect

    Srivastava, H. ); Ormond, D.; Marie, B. )

    1989-04-01

    The air pollutant NO{sub 2} is absorbed and assimilated by plants to serve as a source of nitrogen but only to a limited extent. The objective of this research was to identify the constraints on NO{sub 2} assimilation. Differential light levels were used to manipulate carbohydrate metabolites available for nitrogen assimilation. Bean plants were grown at four light levels with or without nutrient nitrate and exposed to 0.25 ppm NO{sub 2} for 6h each day. Growth of roots and shoots was inhibited by NO{sub 2} in both the presence and absence of nutrient nitrate. The inhibition was most pronounced at the lowest light level. Light level similarly influenced the effect of nitrate and of NO{sub 2} on soluble protein, nitrate nitrogen and Kjeldahl nitrogen in the root and shoot tissues. Two experiments demonstrated that the injurious effects of NO{sub 2} are more pronounced at low light than at high light and that more NO{sub 2} is assimilated into soluble shoot protein at higher light levels.

  11. Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation

    DOE PAGES

    Kurczy, Michael E.; Forsberg, Erica M.; Thorgersen, Michael P.; ...

    2016-04-05

    Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using 15NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containingmore » metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. In conclusion, the use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.« less

  12. Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation

    SciTech Connect

    Kurczy, Michael E.; Forsberg, Erica M.; Thorgersen, Michael P.; Poole, Farris L.; Benton, H. Paul; Ivanisevic, Julijana; Tran, Minerva L.; Wall, Judy D.; Elias, Dwayne A.; Adams, Michael W. W.; Siuzdak, Gary

    2016-04-05

    Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using 15NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. In conclusion, the use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.

  13. Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation.

    PubMed

    Kurczy, Michael E; Forsberg, Erica M; Thorgersen, Michael P; Poole, Farris L; Benton, H Paul; Ivanisevic, Julijana; Tran, Minerva L; Wall, Judy D; Elias, Dwayne A; Adams, Michael W W; Siuzdak, Gary

    2016-06-17

    Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using (15)NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. The use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.

  14. The biodiversity of carbon assimilation.

    PubMed

    Kroth, Peter G

    2015-01-01

    As all plastids that have been investigated so far can be traced back to endosymbiotic uptake of cyanobacteria by heterotrophic host cells, they accordingly show a high similarity regarding photosynthesis, which includes both the photosystems and the biochemical reactions around the CO2 fixation via the Calvin-Bassham cycle. Major differences between the different algal and plant groups may include the presence or absence of carbon concentrating mechanisms, pyrenoids, Rubisco activases, carbonic anhydrases as well as differences in the regulation of the Calvin-Bassham cycle. This review describes the diversity of primary carbon fixation steps in algae and plants and the respective regulatory mechanisms. Copyright © 2014 Elsevier GmbH. All rights reserved.

  15. Nitrogen assimilation from amorphous detritus by two coastal consumers

    NASA Astrophysics Data System (ADS)

    D'Avanzo, Charlene; Alber, Merryl; Valiela, Ivan

    1991-08-01

    The food value of recognizable pieces of dead vegetation, morphous detritus, has been the focus of many studies in coastal systems. In contrast, the nutritional quality and formation process of amorphous detritus, aggregates of dissolved organic matter (DOM), is poorly studied. We created 15N-labelled aggregates from the leachate of four macrophytes, a marsh grass and three macroalgae common in New England coastal waters. We fed the labelled aggregates to two coastal consumers, the grass shrimp Palaemonetes pugio and the sheepshead minnow Cyprinodon variegatus. Fish and shrimp fed each of the labelled aggregates became labelled with 15N. This study provides direct evidence for nitrogen assimilation from amorphous detritus by marine consumers. In addition, fish fed amorphous marsh grass detritus assimilated 10-40 times more nitrogen from this detritus than from morphous grass detritus. Therefore, amorphous aggregates may be higher-quality food than morphous detrital fragments for coastal consumers.

  16. Carbon assimilation and nitrogen in needles of fertilized and unfertilized field-grown Scots pine at natural and elevated concentrations of CO2.

    PubMed

    Laitinen, K; Luomala, E M; Kellomäki, S; Vapaavuori, E

    2000-07-01

    Effects of elevated CO2 concentration ([CO2]) on carbon assimilation and needle biochemistry of fertilized and unfertilized 25-30-year-old Scots pine (Pinus sylvestris L.) trees were studied in a branch bag experiment set up in a naturally regenerated stand. In each tree, one branch was enclosed in a bag supplied with ambient [CO2] (360 micromol mol(-1)), a second branch was enclosed in a bag supplied with elevated [CO2] (680 micromol(-1)) and a control branch was left unbagged. The CO2 treatments were applied from April 15 to September 15, starting in 1993 for unfertilized trees and in 1994 for fertilized trees, which were treated with N in June 1994. Net photosynthesis, amount and activity of Rubisco, N, starch, C:N ratio and SLA of needles were measured during the growing season of 1995. Light-saturated net photosynthetic rates of 1-year-old and current-year shoots measured at ambient [CO2] were not affected by growth [CO2] or N fertilization. Elevated [CO2] reduced the amount and activity of Rubisco, and the relative proportion of Rubisco to soluble proteins and N in needles of unfertilized trees. Elevated [CO2] also reduced the chlorophyll concentration (fresh weight basis) of needles of unfertilized trees. Soluble protein concentration of needles was not affected by growth [CO2]. Elevated [CO2] decreased the Rubisco:chlorophyll ratio in unfertilized and fertilized trees. Starch concentration was significantly increased at elevated [CO2] only in 1-year-old needles of fertilized trees. Elevated [CO2] reduced needle N concentration on a dry weight or structural basis (dry weight minus starch) in unfertilized trees, resulting in an increase in needle C:N ratio. Fertilization had no effect on soluble protein, chlorophyll, Rubisco or N concentration of needles. The decrease in the relative proportions of Rubisco and N concentration in needles of unfertilized trees at elevated [CO2] indicates reallocation of N resources away from Rubisco to nonphotosynthetic

  17. Improving carbon model phenology using data assimilation

    NASA Astrophysics Data System (ADS)

    Exrayat, Jean-François; Smallman, T. Luke; Bloom, A. Anthony; Williams, Mathew

    2015-04-01

    Carbon cycle dynamics is significantly impacted by ecosystem phenology, leading to substantial seasonal and inter-annual variation in the global carbon balance. Representing inter-annual variability is key for predicting the response of the terrestrial ecosystem to climate change and disturbance. Existing terrestrial ecosystem models (TEMs) often struggle to accurately simulate observed inter-annual variability. TEMs often use different phenological models based on plant functional type (PFT) assumptions. Moreover, due to a high level of computational overhead in TEMs they are unable to take advantage of globally available datasets to calibrate their models. Here we describe the novel CARbon DAta MOdel fraMework (CARDAMOM) for data assimilation. CARDAMOM is used to calibrate the Data Assimilation Linked Ecosystem Carbon version 2 (DALEC2) model using Bayes' Theorem within a Metropolis Hastings - Markov Chain Monte Carlo (MH-MCMC). CARDAMOM provides a framework which combines knowledge from observations, such as remotely sensed LAI, and heuristic information in the form of Ecological and Dynamical Constraints (EDCs). The EDCs are representative of real world processes and constrain parameter interdependencies and constrain carbon dynamics. We used CARDAMOM to bring together globally spanning datasets of LAI and the DALEC2 and DALEC2-GSI models. These analyses allow us to investigate the sensitivity ecosystem processes to the representation of phenology. DALEC2 uses an analytically solved model of phenology which is invariant between years. In contrast DALEC2-GSI uses a growing season index (GSI) calculated as a function of temperature, vapour pressure deficit (VPD) and photoperiod to calculate bud-burst and leaf senescence, allowing the model to simulate inter-annual variability in response to climate. Neither model makes any PFT assumptions about the phenological controls of a given ecosystem, allowing the data alone to determine the impact of the meteorological

  18. The assimilation of carbon by Chloropseudomonas ethylicum

    PubMed Central

    Callely, A. G.; Rigopoulos, N.; Fuller, R. C.

    1968-01-01

    1. The enzymes in ultrasonically prepared extracts of Chloropseudomonas ethylicum were studied to elucidate how this organism assimilates acetate and carbon dioxide and why it cannot grow with either of these two compounds alone. 2. Such extracts can (i) convert acetate and oxaloacetate into α-oxoglutarate, (ii) convert oxaloacetate into succinyl-CoA, (iii) convert phosphopyruvate into 3-phosphoglyceraldehyde and (iv) interconvert phosphopyruvate and pyruvate via oxaloacetate. 3. Pyruvate kinase, α-oxoglutarate dehydrogenase, ribulose diphosphate carboxylase, isocitrate lyase and malate synthase were not detected. 4. It is difficult to detect aconitate hydratase, fumarate hydratase and citrate synthase in extracts of the organism ultrasonically treated in tris buffer; to demonstrate these enzymes extracts should be prepared in phosphate buffer containing 2-mercaptoethanol. 5. Provided that this organism can synthesize pyruvate from acetate and carbon dioxide, the enzymes detected are sufficient to account for the nutritional requirements of this organism. PMID:5639917

  19. Dissecting the nitrogen assimilation system of E. coli: from molecules to physiology

    NASA Astrophysics Data System (ADS)

    Hwa, Terry

    2009-03-01

    Nitrogen assimilation is a major branch of cellular metabolism. For enteric bacteria such as E. coli, all of the nitrogen groups needed in biosynthesis are converted from ammonia by a relatively simple system comprised of 3 enzymes and 3 intermediate metabolites. This system is intricately regulated, at both the transcriptional and post-translational levels according to the nitrogen and carbon/energy status of the cell. While specific pieces of this regulation have been known for a long time, the strategy of regulation relating nitrogen influx to cellular demand is poorly understood. Clearly, the paradigm of end-product feedback inhibition well-established for the regulation of individual metabolic pathways is inadequate since there are too many products involving nitrogen. Through extensive experimental studies including quantitative characterization of the levels of key metabolites and enzymes for a carefully chosen spectrum of growth conditions and mutants, we obtain a dynamic picture of how the cell matches its rate of nitrogen assimilation with physiological needs through the intermediate metabolites.

  20. Assimilation of diazotrophic nitrogen into pelagic food webs.

    PubMed

    Woodland, Ryan J; Holland, Daryl P; Beardall, John; Smith, Jonathan; Scicluna, Todd; Cook, Perran L M

    2013-01-01

    The fate of diazotrophic nitrogen (N(D)) fixed by planktonic cyanobacteria in pelagic food webs remains unresolved, particularly for toxic cyanophytes that are selectively avoided by most herbivorous zooplankton. Current theory suggests that N(D) fixed during cyanobacterial blooms can enter planktonic food webs contemporaneously with peak bloom biomass via direct grazing of zooplankton on cyanobacteria or via the uptake of bioavailable N(D) (exuded from viable cyanobacterial cells) by palatable phytoplankton or microbial consortia. Alternatively, N(D) can enter planktonic food webs post-bloom following the remineralization of bloom detritus. Although the relative contribution of these processes to planktonic nutrient cycles is unknown, we hypothesized that assimilation of bioavailable N(D) (e.g., nitrate, ammonium) by palatable phytoplankton and subsequent grazing by zooplankton (either during or after the cyanobacterial bloom) would be the primary pathway by which N(D) was incorporated into the planktonic food web. Instead, in situ stable isotope measurements and grazing experiments clearly documented that the assimilation of N(D) by zooplankton outpaced assimilation by palatable phytoplankton during a bloom of toxic Nodularia spumigena Mertens. We identified two distinct temporal phases in the trophic transfer of N(D) from N. spumigena to the plankton community. The first phase was a highly dynamic transfer of N(D) to zooplankton with rates that covaried with bloom biomass while bypassing other phytoplankton taxa; a trophic transfer that we infer was routed through bloom-associated bacteria. The second phase was a slowly accelerating assimilation of the dissolved-N(D) pool by phytoplankton that was decoupled from contemporaneous variability in N. spumigena concentrations. These findings provide empirical evidence that N(D) can be assimilated and transferred rapidly throughout natural plankton communities and yield insights into the specific processes underlying

  1. Assimilation of Diazotrophic Nitrogen into Pelagic Food Webs

    PubMed Central

    Woodland, Ryan J.; Holland, Daryl P.; Beardall, John; Smith, Jonathan; Scicluna, Todd; Cook, Perran L. M.

    2013-01-01

    The fate of diazotrophic nitrogen (ND) fixed by planktonic cyanobacteria in pelagic food webs remains unresolved, particularly for toxic cyanophytes that are selectively avoided by most herbivorous zooplankton. Current theory suggests that ND fixed during cyanobacterial blooms can enter planktonic food webs contemporaneously with peak bloom biomass via direct grazing of zooplankton on cyanobacteria or via the uptake of bioavailable ND (exuded from viable cyanobacterial cells) by palatable phytoplankton or microbial consortia. Alternatively, ND can enter planktonic food webs post-bloom following the remineralization of bloom detritus. Although the relative contribution of these processes to planktonic nutrient cycles is unknown, we hypothesized that assimilation of bioavailable ND (e.g., nitrate, ammonium) by palatable phytoplankton and subsequent grazing by zooplankton (either during or after the cyanobacterial bloom) would be the primary pathway by which ND was incorporated into the planktonic food web. Instead, in situ stable isotope measurements and grazing experiments clearly documented that the assimilation of ND by zooplankton outpaced assimilation by palatable phytoplankton during a bloom of toxic Nodularia spumigena Mertens. We identified two distinct temporal phases in the trophic transfer of ND from N. spumigena to the plankton community. The first phase was a highly dynamic transfer of ND to zooplankton with rates that covaried with bloom biomass while bypassing other phytoplankton taxa; a trophic transfer that we infer was routed through bloom-associated bacteria. The second phase was a slowly accelerating assimilation of the dissolved-ND pool by phytoplankton that was decoupled from contemporaneous variability in N. spumigena concentrations. These findings provide empirical evidence that ND can be assimilated and transferred rapidly throughout natural plankton communities and yield insights into the specific processes underlying the propagation of ND

  2. The Assimilation of Diazotroph-Derived Nitrogen by Scleractinian Corals Depends on Their Metabolic Status

    PubMed Central

    Grover, Renaud; Maguer, Jean-François; Fine, Maoz; Ferrier-Pagès, Christine

    2017-01-01

    ABSTRACT Tropical corals are associated with a diverse community of dinitrogen (N2)-fixing prokaryotes (diazotrophs) providing the coral an additional source of bioavailable nitrogen (N) in oligotrophic waters. The overall activity of these diazotrophs changes depending on the current environmental conditions, but to what extent it affects the assimilation of diazotroph-derived N (DDN) by corals is still unknown. Here, in a series of 15N2 tracer experiments, we directly quantified DDN assimilation by scleractinian corals from the Red Sea exposed to different environmental conditions. We show that DDN assimilation strongly varied with the corals’ metabolic status or with phosphate availability in the water. The very autotrophic shallow-water (~5 m) corals showed low or no DDN assimilation, which significantly increased under elevated phosphate availability (3 µM). Corals that depended more on heterotrophy (i.e., bleached and deep-water [~45 m] corals) assimilated significantly more DDN, which contributed up to 15% of the corals’ N demand (compared to 1% in shallow corals). Furthermore, we demonstrate that a substantial part of the DDN assimilated by deep corals was likely obtained from heterotrophic feeding on fixed N compounds and/or diazotrophic cells in the mucus. Conversely, in shallow corals, the net release of mucus, rich in organic carbon compounds, likely enhanced diazotroph abundance and activity and thereby the release of fixed N to the pelagic and benthic reef community. Overall, our results suggest that DDN assimilation by corals varies according to the environmental conditions and is likely linked to the capacity of the coral to acquire nutrients from seawater. PMID:28074021

  3. The Assimilation of Diazotroph-Derived Nitrogen by Scleractinian Corals Depends on Their Metabolic Status.

    PubMed

    Bednarz, Vanessa N; Grover, Renaud; Maguer, Jean-François; Fine, Maoz; Ferrier-Pagès, Christine

    2017-01-10

    Tropical corals are associated with a diverse community of dinitrogen (N2)-fixing prokaryotes (diazotrophs) providing the coral an additional source of bioavailable nitrogen (N) in oligotrophic waters. The overall activity of these diazotrophs changes depending on the current environmental conditions, but to what extent it affects the assimilation of diazotroph-derived N (DDN) by corals is still unknown. Here, in a series of (15)N2 tracer experiments, we directly quantified DDN assimilation by scleractinian corals from the Red Sea exposed to different environmental conditions. We show that DDN assimilation strongly varied with the corals' metabolic status or with phosphate availability in the water. The very autotrophic shallow-water (~5 m) corals showed low or no DDN assimilation, which significantly increased under elevated phosphate availability (3 µM). Corals that depended more on heterotrophy (i.e., bleached and deep-water [~45 m] corals) assimilated significantly more DDN, which contributed up to 15% of the corals' N demand (compared to 1% in shallow corals). Furthermore, we demonstrate that a substantial part of the DDN assimilated by deep corals was likely obtained from heterotrophic feeding on fixed N compounds and/or diazotrophic cells in the mucus. Conversely, in shallow corals, the net release of mucus, rich in organic carbon compounds, likely enhanced diazotroph abundance and activity and thereby the release of fixed N to the pelagic and benthic reef community. Overall, our results suggest that DDN assimilation by corals varies according to the environmental conditions and is likely linked to the capacity of the coral to acquire nutrients from seawater.

  4. GlnK Facilitates the Dynamic Regulation of Bacterial Nitrogen Assimilation

    NASA Astrophysics Data System (ADS)

    Gosztolai, Adam; Schumacher, Jörg; Behrends, Volker; Bundy, Jacob G.; Heydenreich, Franziska; Bennett, Mark H.; Buck, Martin; Barahona, Mauricio

    2017-05-01

    Ammonium assimilation in E. coli is regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase (GS), the key enzyme for nitrogen assimilation, is poorly understood. We combine experiments and theory to study the dynamic roles of GlnB and GlnK during nitrogen starvation and upshift. We measure time-resolved in vivo concentrations of metabolites, total and post-translationally modified proteins, and develop a concise biochemical model of GlnB and GlnK that incorporates competition for active and allosteric sites, as well as functional sequestration of GlnK. The model predicts the responses of GS, GlnB and GlnK under time-varying external ammonium level in the wild type and two genetic knock-outs. Our results show that GlnK is tightly regulated under nitrogen-rich conditions, yet it is expressed during ammonium run-out and starvation. This suggests a role for GlnK as a buffer of nitrogen shock after starvation, and provides a further functional link between nitrogen and carbon metabolisms.

  5. GlnK Facilitates the Dynamic Regulation of Bacterial Nitrogen Assimilation.

    PubMed

    Gosztolai, Adam; Schumacher, Jörg; Behrends, Volker; Bundy, Jacob G; Heydenreich, Franziska; Bennett, Mark H; Buck, Martin; Barahona, Mauricio

    2017-05-23

    Ammonium assimilation in Escherichia coli is regulated by two paralogous proteins (GlnB and GlnK), which orchestrate interactions with regulators of gene expression, transport proteins, and metabolic pathways. Yet how they conjointly modulate the activity of glutamine synthetase, the key enzyme for nitrogen assimilation, is poorly understood. We combine experiments and theory to study the dynamic roles of GlnB and GlnK during nitrogen starvation and upshift. We measure time-resolved in vivo concentrations of metabolites, total and posttranslationally modified proteins, and develop a concise biochemical model of GlnB and GlnK that incorporates competition for active and allosteric sites, as well as functional sequestration of GlnK. The model predicts the responses of glutamine synthetase, GlnB, and GlnK under time-varying external ammonium level in the wild-type and two genetic knock-outs. Our results show that GlnK is tightly regulated under nitrogen-rich conditions, yet it is expressed during ammonium run-out and starvation. This suggests a role for GlnK as a buffer of nitrogen shock after starvation, and provides a further functional link between nitrogen and carbon metabolisms. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. Carbon and nitrogen partitioning in peach/plum grafts.

    PubMed

    Moing, A; Gaudillère, J P

    1992-01-01

    Modifications in root-shoot relationships induced by graft incompatibility were studied in peach/plum graft combinations by means of carbohydrate and nitrogen analyses and isotope labeling. Mobilization of stored carbon, phloem transport of carbon, and mobilization, assimilation and distribution of nitrogen were studied in one compatible peach/plum graft (Prunus persica L. Batsch cv. springtime grafted on Prunus cerasifera L. Ehrh cv. myrobalan P 2032) and one incompatible graft (Prunus persica L. Batsch cv. Springtime grafted on Prunus cerasifera L. Ehrh cv. myrobalan P 18) for 89 days after grafting. Carbon and nitrogen reserves were mobilized in the rootstock in both graft combinations during the first 78 days following grafting. After that, sorbitol concentration was lower in the roots of the incompatible graft than in the roots of the compatible graft, whereas soluble sugars and starch accumulated in the peach scion of the incompatible graft. In both graft types, carbon was allocated mainly to the scion. Labeling with (13)CO(2) from 78 to 81 days after grafting showed that carbon partitioning among the different plant organs was only slightly affected by graft incompatibility. Carbohydrate concentrations provided indirect evidence that carbon transfer to the roots was hindered in the incompatible graft. Labeling with (15)NO(3) showed that nitrogen distribution and the rate of nitrogen assimilation were similar in the two graft combinations from 57 to 78 days after grafting. Nitrogen assimilation in the incompatible graft ceased 78 days after grafting, whereas it continued in the compatible graft.

  7. Effect of foliar feeding on nitrogen assimilation in alfalfa plants at insufficient molybdenum supply.

    PubMed

    Hristozkova, Marieta; Geneva, Maria; Stancheva, Ira

    2009-06-01

    The influence of foliar feeding on the nitrogen assimilation in alfalfa plants under conditions of Mo shortage was studied. It was established that foliar fertilization with 0.3% solution of Agroleaf® resulted in increase of nitrogen fixation and nitrogen assimilation in the absence of Mo. Insufficient molybdenum supply leads to significant reduction of plant Mo content and nitrogen-fixing activity, while stress induced amino acids as alanine, GABA, threonine, proline and serine increased repeatedly. The negative effect of Mo deficiency on the enzyme activities related to the primary nitrogen assimilation (NR, GS, GOGAT) and plant growth diminished due to the foliar absorbed nutrients.

  8. A Joint Land-Atmosphere Carbon Data Assimilation System

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Zeng, N.; Kalnay, E.; Asrar, G.; Penny, S. G.

    2016-12-01

    After decades of effort, significant uncertainties remain in the global surface carbon fluxes. In recent years, observations of the global carbon cycle in the atmosphere and on land have all intensified dramatically. It is essential to use these data for quantifying the contribution of global surface carbon fluxes. A novel joint land-atmosphere carbon data assimilation system is developed to simultaneously handle multiple modeling components and multiple streams of data. This joint assimilation system consists of an atmosphere transport model - GEOSChem, a terrestrial model - VEGAS, and a 4D-LETKF data assimilation module. The GEOSChem model provides the 'top-down' atmosphere approach to estimate the surface carbon fluxes by assimilating atmospheric carbon observations, such as GlobalView surface flask observations, tower, aircraft and satellite observations including OCO-2 The VEGAS model provides the 'bottom-up' approach by constraining the model parameter uncertainty as well as the terrestrial carbon flux to atmosphere by assimilating land observations like satellite vegetation index, sun-induced fluorescence (SIF), and other surface-based observations for biosphere productivity. We estimate surface carbon fluxes in each of the above components separately in an OSSE framework to investigate the possibility and limitations of the 'top-down' versus the 'bottom-up' approaches. We then combine the two approaches together through both model coupling and data assimilation coupling to provide the best constraint for estimating the global surface carbon fluxes.

  9. Carbon Assimilation Profiles as a Tool for Identification of Zygomycetes▿

    PubMed Central

    Schwarz, Patrick; Lortholary, Olivier; Dromer, Françoise; Dannaoui, Eric

    2007-01-01

    Identification of Zygomycetes is difficult and time-consuming by standard microbiological procedures. Carbon assimilation profiles are commonly used for yeast-and bacterial-species identification but rarely for filamentous-fungus identification. Carbon assimilation profiles were evaluated using the commercialized kits ID32C and API 50 CH, which contain 31 and 49 tests, respectively, to serve as simple tools for species identification of Zygomycetes in clinical microbiology laboratories. Fifty-seven strains belonging to 15 species and varieties of Zygomycetes, including Rhizopus, Absidia, Mucor, and Rhizomucor species, were tested for intra- and interspecies variability based on their carbon assimilation profiles. Using ID32C strips, 6 tests were always positive, 7 were never positive, and 18 showed consistently different results between species. With API 50 CH strips, 15 tests were positive for all species, 13 were never positive, and 21 showed different results between species. Nevertheless, assimilation patterns were highly variable among Rhizopus oryzae isolates, and it was not possible to define a specific carbon assimilation profile. With both ID32C and API CH 50 strips, intraspecies variation was found to be low, while large differences were found between genera and species. The clustering of isolates based on their carbon assimilation profiles was in accordance with DNA-based phylogeny of Zygomycetes. In conclusion, carbon assimilation profiles allowed precise and accurate identification of most Zygomycetes to the species level. PMID:17329449

  10. Carbon assimilation profiles as a tool for identification of zygomycetes.

    PubMed

    Schwarz, Patrick; Lortholary, Olivier; Dromer, Françoise; Dannaoui, Eric

    2007-05-01

    Identification of Zygomycetes is difficult and time-consuming by standard microbiological procedures. Carbon assimilation profiles are commonly used for yeast-and bacterial-species identification but rarely for filamentous-fungus identification. Carbon assimilation profiles were evaluated using the commercialized kits ID32C and API 50 CH, which contain 31 and 49 tests, respectively, to serve as simple tools for species identification of Zygomycetes in clinical microbiology laboratories. Fifty-seven strains belonging to 15 species and varieties of Zygomycetes, including Rhizopus, Absidia, Mucor, and Rhizomucor species, were tested for intra- and interspecies variability based on their carbon assimilation profiles. Using ID32C strips, 6 tests were always positive, 7 were never positive, and 18 showed consistently different results between species. With API 50 CH strips, 15 tests were positive for all species, 13 were never positive, and 21 showed different results between species. Nevertheless, assimilation patterns were highly variable among Rhizopus oryzae isolates, and it was not possible to define a specific carbon assimilation profile. With both ID32C and API CH 50 strips, intraspecies variation was found to be low, while large differences were found between genera and species. The clustering of isolates based on their carbon assimilation profiles was in accordance with DNA-based phylogeny of Zygomycetes. In conclusion, carbon assimilation profiles allowed precise and accurate identification of most Zygomycetes to the species level.

  11. Remote sensing of leaf N to improve carbon assimilation prediction

    NASA Astrophysics Data System (ADS)

    Loozen, Yasmina; Rebel, Karin; Karssenberg, Derek; de Jong, Steven; Wassen, Martin

    2016-04-01

    Predicting and understanding carbon assimilation by terrestrial vegetation remains fundamental in the context of climate change. Carbon and nitrogen cycles are linked as nitrogen is an essential nutrient for plant growth. In this respect the N cycle is integrated into vegetation models predicting vegetation carbon uptake. However plant traits within the N cycle, such as leaf nitrogen, are lacking at large scales, which complicates the calibration and optimization of the N cycling modelling modules. Remote sensing techniques could offer the possibility to detect leaf N concentration at continental scales. In fact, it has already been used to sense leaf N at local, e.g. in agricultural oriented applications, as well as at regional scales. The objective of this study is to enhance the availability of leaf N estimates in forested ecosystems at European scale using remote sensing products. European forest leaf N data were obtained from the TRY database. The MERIS Terrestrial chlorophyll Index (MTCI) Level 3 product as well as two reflectance bands in the NIR region (band centers at 865 and 885nm) both from MERIS aboard ENVISAT (ESA) were used to study statistical relationship with leaf N data. In a first step, we analyzed 1892 Catalonian (NE Spain) forest plots using a linear regression method. The regressions results between leaf N and either MTCI or NIR bands were significant (p< 0.001). The R-square for the regression between leaf N and MTCI was equal to 0.13. The method performed better for broadleaves deciduous plots (R-square = 0.11) than for needleleaves or broadleaves evergreen plots. The relationship between leaf N and MTCI was also higher for the plots sampled during summer (R-square = 0.28 in July) than for the plots sampled during the rest of the year. In a second step the method will be applied on and will include more diverse forest types at the European level.

  12. Estimation of Global Surface Carbon Fluxes Using Advanced Data Assimilation

    NASA Astrophysics Data System (ADS)

    Kalnay, E.; Asrar, G.; Zeng, N.; Liu, Y.

    2016-12-01

    Kang et al., (JGR, 2011, 2012) developed an advanced data assimilation methodology able to recover (in a simulation mode) the surface carbon fluxes from the assimilation of realistic atmospheric CO2 measurements. After a spin-up of 3 months, the carbon fluxes were estimated accurately at a grid-size resolution and captured quite well the natural annual cycle and the anthropogenic sources without using any prior information. In our current research, led together with co-authors, we are assimilating both simulated and real observations into the GEOS-CHEM global model coupled with the VEGAS vegetation model, using strongly coupled LETKF Data Assimilation, with the ultimate goal of estimating global real carbon fluxes. The coupled GEOS-CHEM/VEGAS model reproduces very realistically the observed seasonal cycle of the CO2 flask data for April 2012-July 2014 at many Global View stations, after a spin-up of about 6 months. We confirmed that the LETKF Data Assimilation could also be used to estimate unmeasured parameters in VEGAS model, as long as their time scales are not longer than a few years. We are performing OSSE and OSE data assimilation experiments with this system, assimilating a) Global View observations, b) OCO-2 observations, and c) combining both set of observations in order to determine optimal data assimilation parameters for the estimation of surface carbon fluxes, and will present an overview of our results.

  13. Nitrogen doping in carbon nanotubes.

    PubMed

    Ewels, C P; Glerup, M

    2005-09-01

    Nitrogen doping of single and multi-walled carbon nanotubes is of great interest both fundamentally, to explore the effect of dopants on quasi-1D electrical conductors, and for applications such as field emission tips, lithium storage, composites and nanoelectronic devices. We present an extensive review of the current state of the art in nitrogen doping of carbon nanotubes, including synthesis techniques, and comparison with nitrogen doped carbon thin films and azofullerenes. Nitrogen doping significantly alters nanotube morphology, leading to compartmentalised 'bamboo' nanotube structures. We review spectroscopic studies of nitrogen dopants using techniques such as X-ray photoemission spectroscopy, electron energy loss spectroscopy and Raman studies, and associated theoretical models. We discuss the role of nanotube curvature and chirality (notably whether the nanotubes are metallic or semiconducting), and the effect of doping on nanotube surface chemistry. Finally we review the effect of nitrogen on the transport properties of carbon nanotubes, notably its ability to induce negative differential resistance in semiconducting tubes.

  14. Global change accelerates carbon assimilation by a wetland ecosystem engineer

    NASA Astrophysics Data System (ADS)

    Caplan, Joshua S.; Hager, Rachel N.; Megonigal, J. Patrick; Mozdzer, Thomas J.

    2015-11-01

    The primary productivity of coastal wetlands is changing dramatically in response to rising atmospheric carbon dioxide (CO2) concentrations, nitrogen (N) enrichment, and invasions by novel species, potentially altering their ecosystem services and resilience to sea level rise. In order to determine how these interacting global change factors will affect coastal wetland productivity, we quantified growing-season carbon assimilation (≈gross primary productivity, or GPP) and carbon retained in living plant biomass (≈net primary productivity, or NPP) of North American mid-Atlantic saltmarshes invaded by Phragmites australis (common reed) under four treatment conditions: two levels of CO2 (ambient and +300 ppm) crossed with two levels of N (0 and 25 g N added m-2 yr-1). For GPP, we combined descriptions of canopy structure and leaf-level photosynthesis in a simulation model, using empirical data from an open-top chamber field study. Under ambient CO2 and low N loading (i.e., the Control), we determined GPP to be 1.66 ± 0.05 kg C m-2 yr-1 at a typical Phragmites stand density. Individually, elevated CO2 and N enrichment increased GPP by 44 and 60%, respectively. Changes under N enrichment came largely from stimulation to carbon assimilation early and late in the growing season, while changes from CO2 came from stimulation during the early and mid-growing season. In combination, elevated CO2 and N enrichment increased GPP by 95% over the Control, yielding 3.24 ± 0.08 kg C m-2 yr-1. We used biomass data to calculate NPP, and determined that it represented 44%-60% of GPP, with global change conditions decreasing carbon retention compared to the Control. Our results indicate that Phragmites invasions in eutrophied saltmarshes are driven, in part, by extended phenology yielding 3.1× greater NPP than native marsh. Further, we can expect elevated CO2 to amplify Phragmites productivity throughout the growing season, with potential implications including accelerated spread

  15. Effects of nutritional history on nitrogen assimilation in congeneric temperate and tropical scleractinian corals

    USGS Publications Warehouse

    Piniak, G.A.; Lipschultz, F.

    2004-01-01

    The nutritional history of corals is known to affect metabolic processes such as inorganic nutrient uptake and photosynthesis, but little is known about how it affects assimilation efficiency of ingested prey items or the partitioning of prey nitrogen between the host and symbiont. The temperate scleractinian coral Oculina arbuscula and its tropical congener Oculina diffusa were acclimated to three nutritional regimes (fed twice weekly, starved, starved with an inorganic nutrient supplement), then fed Artemia nauplii labeled with the stable isotope tracer 15N. Fed corals of both species had the lowest assimilation efficiencies (36-51% for O. arbuscula, 38-57% for O. diffusa), but were not statistically different from the other nutritional regimes. Fed and starved corals also had similar NU4+ excretion rates. This is inconsistent with decreased nitrogen excretion and reduced amino acid catabolism predicted by both the nitrogen recycling and conservation paradigms. In coral host tissue, ???90% of the ingested 15N was in the TCA-insoluble (protein and nucleic acids) and ethanol-soluble (amino acids/low molecular weight compounds) within 4 h of feeding. The TCA-insoluble pool was also the dominant repository of the label in zooxanthellae of both species (40-53% in O. arbuscula, 50-60% in O. diffusa). However, nutritional history had no effect on the distribution of prey 15N within the biochemical pools of the host or the zooxanthellae for either species. This result is consistent with the nitrogen conservation hypothesis, as preferential carbon metabolism would minimize the effects of starvation on nitrogen-containing biochemical pools. ?? Springer-Verlag 2004.

  16. Impacts of data assimilation on the global ocean carbonate system

    NASA Astrophysics Data System (ADS)

    Visinelli, L.; Masina, S.; Vichi, M.; Storto, A.; Lovato, T.

    2016-06-01

    In an ocean reanalysis, historical observations are combined with ocean and biogeochemical general circulation models to produce a reconstruction of the oceanic properties in past decades. This is one possible method to better constrain the role of the ocean carbon cycle in the determination of the air-sea CO2 flux. In this work, we investigate how the assimilation of physical variables and subsequently the combined assimilation of physical data and inorganic carbon variables - namely dissolved inorganic carbon (DIC) and alkalinity - affect the modelling of the marine carbonate system and the related air-sea CO2 fluxes. The performance of the two assimilation exercises are quantitatively assessed against the assimilated DIC and alkalinity data and the independent ocean surface pCO2 observations from global datasets. We obtain that the assimilation of physical observations has contrasting effects in different ocean basins when compared with the DIC and alkalinity data: it reduces the root-mean square error against the observed pCO2 in the Atlantic and Southern oceans, while increases the model error in the North Pacific and Indian Oceans. In both cases the corrected evaporation rates are the major factor determining the changes in concentrations. The assimilation of inorganic carbon variables on top of the physical data gives a generalized improvement in the model error of inorganic carbon variables, also improving the annual mean and spatial distribution of air-sea fluxes in agreement with other published estimates. These results indicate that data assimilation of physical and inorganic carbon data does not guarantee the improvement of the simulated pCO2 in all the oceanic regions; nevertheless, errors in pCO2 are reduced by a factor corresponding to those associated with the air-sea flux formulations.

  17. Differing Daphnia magna assimilation efficiencies for terrestrial, bacterial, and algal carbon and fatty acids.

    PubMed

    Taipale, Sami J; Brett, Michael T; Hahn, Martin W; Martin-Creuzburg, Dominik; Yeung, Sean; Hiltunen, Minna; Strandberg, Ursula; Kankaala, Paula

    2014-02-01

    There is considerable interest in the pathways by which carbon and growth-limiting elemental and biochemical nutrients are supplied to upper trophic levels. Fatty acids and sterols are among the most important molecules transferred across the plant-animal interface of food webs. In lake ecosystems, in addition to phytoplankton, bacteria and terrestrial organic matter are potential trophic resources for zooplankton, especially in those receiving high terrestrial organic matter inputs. We therefore tested carbon, nitrogen, and fatty acid assimilation by the crustacean Daphnia magna when consuming these resources. We fed Daphnia with monospecific diets of high-quality (Cryptomonas marssonii) and intermediate-quality (Chlamydomonas sp. and Scenedesmus gracilis) phytoplankton species, two heterotrophic bacterial strains, and particles from the globally dispersed riparian grass, Phragmites australis, representing terrestrial particulate organic carbon (t-POC). We also fed Daphnia with various mixed diets, and compared Daphnia fatty acid, carbon, and nitrogen assimilation across treatments. Our results suggest that bacteria were nutritionally inadequate diets because they lacked sterols and polyunsaturated omega-3 and omega-6 (omega-3 and omega-6) fatty acids (PUFAs). However, Daphnia were able to effectively use carbon and nitrogen from Actinobacteria, if their basal needs for essential fatty acids and sterols were met by phytoplankton. In contrast to bacteria, t-POC contained sterols and omega-6 and omega-3 fatty acids, but only at 22%, 1.4%, and 0.2% of phytoplankton levels, respectively, which indicated that t-POC food quality was especially restricted with regard to omega-3 PUFAs. Our results also showed higher assimilation of carbon than fatty acids from t-POC and bacteria into Daphnia, based on stable-isotope and fatty acids analysis, respectively. A relatively high (>20%) assimilation of carbon and fatty acids from t-POC was observed only when the proportion of t

  18. Nitrogen fixation and carbon metabolism in legume nodules.

    PubMed

    Garg, Neera; Singla, Ranju; Geetanjali

    2004-02-01

    A large amount of energy is utilized by legume nodules for the fixation of nitrogen and assimilation of fixed nitrogen (ammonia) into organic compounds. The source of energy is provided in the form of photosynthates by the host plant. Phosphoenol pyruvate carboxylase (PEPC) enzyme, which is responsible for carbon dioxide fixation in C4 and crassulacean acid metabolism plants, has also been found to play an important role in carbon metabolism in legume root nodule. PEPC-mediated CO2 fixation in nodules results in the synthesis of C4 dicarboxylic acids, viz. aspartate, malate, fumarate etc. which can be transported into bacteroids with the intervention of dicarboxylate transporter (DCT) protein. PEPC has been purified from the root nodules of few legume species. Information on the relationship between nitrogen fixation and carbon metabolism through PEPC in leguminous plants is scanty and incoherent. This review summarizes the various aspects of carbon and nitrogen metabolism in legume root nodules.

  19. S-nitrosothiols regulate nitric oxide production and storage in plants through the nitrogen assimilation pathway

    PubMed Central

    Frungillo, Lucas; Skelly, Michael J.; Loake, Gary J.; Spoel, Steven H.; Salgado, Ione

    2014-01-01

    Nitrogen assimilation plays a vital role in plant metabolism. Assimilation of nitrate, the primary source of nitrogen in soil, is linked to generation of the redox signal nitric oxide (NO). An important mechanism by which NO regulates plant development and stress responses is through S-nitrosylation, i.e. covalent attachment of NO to cysteines to form S-nitrosothiols (SNO). Despite the importance of nitrogen assimilation and NO signalling, it remains largely unknown how these pathways are interconnected. Here we show that SNO signalling suppresses both nitrate uptake and reduction by transporters and reductases, respectively, to fine-tune nitrate homeostasis. Moreover, NO derived from nitrate assimilation suppresses the redox enzyme S-nitrosoglutathione Reductase 1 (GSNOR1) by S-nitrosylation, preventing scavenging of S-nitrosoglutathione, a major cellular bio-reservoir of NO. Hence, our data demonstrates that (S)NO controls its own generation and scavenging by modulating nitrate assimilation and GSNOR1 activity. PMID:25384398

  20. S-nitrosothiols regulate nitric oxide production and storage in plants through the nitrogen assimilation pathway.

    PubMed

    Frungillo, Lucas; Skelly, Michael J; Loake, Gary J; Spoel, Steven H; Salgado, Ione

    2014-11-11

    Nitrogen assimilation plays a vital role in plant metabolism. Assimilation of nitrate, the primary source of nitrogen in soil, is linked to the generation of the redox signal nitric oxide (NO). An important mechanism by which NO regulates plant development and stress responses is through S-nitrosylation, that is, covalent attachment of NO to cysteine residues to form S-nitrosothiols (SNO). Despite the importance of nitrogen assimilation and NO signalling, it remains largely unknown how these pathways are interconnected. Here we show that SNO signalling suppresses both nitrate uptake and reduction by transporters and reductases, respectively, to fine tune nitrate homeostasis. Moreover, NO derived from nitrate assimilation suppresses the redox enzyme S-nitrosoglutathione Reductase 1 (GSNOR1) by S-nitrosylation, preventing scavenging of S-nitrosoglutathione, a major cellular bio-reservoir of NO. Hence, our data demonstrates that (S)NO controls its own generation and scavenging by modulating nitrate assimilation and GSNOR1 activity.

  1. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.

    PubMed

    Hallam, Steven J; Mincer, Tracy J; Schleper, Christa; Preston, Christina M; Roberts, Katie; Richardson, Paul M; DeLong, Edward F

    2006-04-01

    Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.

  2. Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota

    PubMed Central

    Hallam, Steven J; Mincer, Tracy J; Schleper, Christa; Preston, Christina M; Roberts, Katie; Richardson, Paul M

    2006-01-01

    Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems. PMID:16533068

  3. In folio isotopic tracing demonstrates that nitrogen assimilation into glutamate is mostly independent from current CO2 assimilation in illuminated leaves of Brassica napus.

    PubMed

    Gauthier, Paul P G; Bligny, Richard; Gout, Elizabeth; Mahé, Aline; Nogués, Salvador; Hodges, Michael; Tcherkez, Guillaume G B

    2010-03-01

    *Nitrogen assimilation in leaves requires primary NH(2) acceptors that, in turn, originate from primary carbon metabolism. Respiratory metabolism is believed to provide such acceptors (such as 2-oxoglutarate), so that day respiration is commonly seen as a cornerstone for nitrogen assimilation into glutamate in illuminated leaves. However, both glycolysis and day respiratory CO(2) evolution are known to be inhibited by light, thereby compromising the input of recent photosynthetic carbon for glutamate production. *In this study, we carried out isotopic labelling experiments with (13)CO(2) and (15)N-ammonium nitrate on detached leaves of rapeseed (Brassica napus), and performed (13)C- and (15)N-nuclear magnetic resonance analyses. *Our results indicated that the production of (13)C-glutamate and (13)C-glutamine under a (13)CO(2) atmosphere was very weak, whereas (13)C-glutamate and (13)C-glutamine appeared in both the subsequent dark period and the next light period under a (12)CO(2) atmosphere. Consistently, the analysis of heteronuclear ((13)C-(15)N) interactions within molecules indicated that most (15)N-glutamate and (15)N-glutamine molecules were not (13)C labelled after (13)C/(15)N double labelling. That is, recent carbon atoms (i.e. (13)C) were hardly incorporated into glutamate, but new glutamate molecules were synthesized, as evidenced by (15)N incorporation. *We conclude that the remobilization of night-stored molecules plays a significant role in providing 2-oxoglutarate for glutamate synthesis in illuminated rapeseed leaves, and therefore the natural day : night cycle seems critical for nitrogen assimilation.

  4. Arabidopsis mutant analysis and gene regulation define a nonredundant role for glutamate dehydrogenase in nitrogen assimilation.

    PubMed

    Melo-Oliveira, R; Oliveira, I C; Coruzzi, G M

    1996-05-14

    Glutamate dehydrogenase (GDH) is ubiquitous to all organisms, yet its role in higher plants remains enigmatic. To better understand the role of GDH in plant nitrogen metabolism, we have characterized an Arabidopsis mutant (gdh1-1) defective in one of two GDH gene products and have studied GDH1 gene expression. GDH1 mRNA accumulates to highest levels in dark-adapted or sucrose-starved plants, and light or sucrose treatment each repress GDH1 mRNA accumulation. These results suggest that the GDH1 gene product functions in the direction of glutamate catabolism under carbon-limiting conditions. Low levels of GDH1 mRNA present in leaves of light-grown plants can be induced by exogenously supplied ammonia. Under such conditions of carbon and ammonia excess, GDH1 may function in the direction of glutamate biosynthesis. The Arabidopsis gdh-deficient mutant allele gdh1-1 cosegregates with the GDH1 gene and behaves as a recessive mutation. The gdh1-1 mutant displays a conditional phenotype in that seedling growth is specifically retarded on media containing exogenously supplied inorganic nitrogen. These results suggest that GDH1 plays a nonredundant role in ammonia assimilation under conditions of inorganic nitrogen excess. This notion is further supported by the fact that the levels of mRNA for GDH1 and chloroplastic glutamine synthetase (GS2) are reciprocally regulated by light.

  5. The carbon-assimilation experiment - The Viking Mars Lander.

    NASA Technical Reports Server (NTRS)

    Horowitz, N. H.; Hubbard, J. S.; Hobby, G. L.

    1972-01-01

    The carbon-assimilation experiment detects life in soils by measuring the incorporation of carbon from carbon-14 monoxide and carbon-14 dioxide into organic matter. It is based on the premise that Martian life, if it exists, is carbonaceous and exchanges carbon with the atmosphere, as do all terrestrial organisms. It is especially sensitive for photosynthesizing cells, but it detects heterotrophs also. The experiment has the particular advantage that it can be carried out under essentially Martian conditions of temperature, pressure, atmospheric composition, and water abundance.

  6. The carbon-assimilation experiment - The Viking Mars Lander.

    NASA Technical Reports Server (NTRS)

    Horowitz, N. H.; Hubbard, J. S.; Hobby, G. L.

    1972-01-01

    The carbon-assimilation experiment detects life in soils by measuring the incorporation of carbon from carbon-14 monoxide and carbon-14 dioxide into organic matter. It is based on the premise that Martian life, if it exists, is carbonaceous and exchanges carbon with the atmosphere, as do all terrestrial organisms. It is especially sensitive for photosynthesizing cells, but it detects heterotrophs also. The experiment has the particular advantage that it can be carried out under essentially Martian conditions of temperature, pressure, atmospheric composition, and water abundance.

  7. Consistent assimilation of multiple data streams in a carbon cycle data assimilation system

    NASA Astrophysics Data System (ADS)

    MacBean, Natasha; Peylin, Philippe; Chevallier, Frédéric; Scholze, Marko; Schürmann, Gregor

    2016-10-01

    Data assimilation methods provide a rigorous statistical framework for constraining parametric uncertainty in land surface models (LSMs), which in turn helps to improve their predictive capability and to identify areas in which the representation of physical processes is inadequate. The increase in the number of available datasets in recent years allows us to address different aspects of the model at a variety of spatial and temporal scales. However, combining data streams in a DA system is not a trivial task. In this study we highlight some of the challenges surrounding multiple data stream assimilation for the carbon cycle component of LSMs. We give particular consideration to the assumptions associated with the type of inversion algorithm that are typically used when optimising global LSMs - namely, Gaussian error distributions and linearity in the model dynamics. We explore the effect of biases and inconsistencies between the observations and the model (resulting in non-Gaussian error distributions), and we examine the difference between a simultaneous assimilation (in which all data streams are included in one optimisation) and a step-wise approach (in which each data stream is assimilated sequentially) in the presence of non-linear model dynamics. In addition, we perform a preliminary investigation into the impact of correlated errors between two data streams for two cases, both when the correlated observation errors are included in the prior observation error covariance matrix, and when the correlated errors are ignored. We demonstrate these challenges by assimilating synthetic observations into two simple models: the first a simplified version of the carbon cycle processes represented in many LSMs and the second a non-linear toy model. Finally, we provide some perspectives and advice to other land surface modellers wishing to use multiple data streams to constrain their model parameters.

  8. Online estimation of assimilable nitrogen by electrical conductivity measurement during alcoholic fermentation in enological conditions.

    PubMed

    Colombié, Sophie; Latrille, Eric; Sablayrolles, Jean-Marie

    2007-03-01

    The monitoring of alcoholic fermentation under enological conditions is currently poor due to the lack of sensors for online measurements. Such monitoring is currently limited to the measurement of CO(2) production or changes in density. In this study, we determined the potential value of measuring electrical conductivity. We showed that this measurement is related to the assimilation of nitrogen, which is typically the limiting nutrient, and directly correlated to ammoniacal nitrogen assimilation at any percentage of ammoniacal nitrogen in the medium. We also used electrical conductivity for the very precise monitoring of the kinetics of nitrogen assimilation after the addition of a pulse of diammonium hydrogen phosphate (DAP) during fermentation. The impact of initial conditions (e.g., must composition, grape variety, pH) remains unclear, but the robustness, precision and low price of the sensor used justify further studies of the potential value of measuring electrical conductivity on the pilot and industrial scales.

  9. The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling.

    PubMed

    Bernard, Stéphanie M; Habash, Dimah Z

    2009-01-01

    Glutamine synthetase assimilates ammonium into amino acids, thus it is a key enzyme for nitrogen metabolism. The cytosolic isoenzymes of glutamine synthetase assimilate ammonium derived from primary nitrogen uptake and from various internal nitrogen recycling pathways. In this way, cytosolic glutamine synthetase is crucial for the remobilization of protein-derived nitrogen. Cytosolic glutamine synthetase is encoded by a small family of genes that are well conserved across plant species. Members of the cytosolic glutamine synthetase gene family are regulated in response to plant nitrogen status, as well as to environmental cues, such as nitrogen availability and biotic/abiotic stresses. The complex regulation of cytosolic glutamine synthetase at the transcriptional to post-translational levels is key to the establishment of a specific physiological role for each isoenzyme. The diverse physiological roles of cytosolic glutamine synthetase isoenzymes are important in relation to current agricultural and ecological issues.

  10. The importance of cytosolic glutamine synthetase in nitrogen assimilation and recycling

    SciTech Connect

    Bernard, S.M.; Habash, D.Z.

    2009-07-02

    Glutamine synthetase assimilates ammonium into amino acids, thus it is a key enzyme for nitrogen metabolism. The cytosolic isoenzymes of glutamine synthetase assimilate ammonium derived from primary nitrogen uptake and from various internal nitrogen recycling pathways. In this way, cytosolic glutamine synthetase is crucial for the remobilization of protein-derived nitrogen. Cytosolic glutamine synthetase is encoded by a small family of genes that are well conserved across plant species. Members of the cytosolic glutamine synthetase gene family are regulated in response to plant nitrogen status, as well as to environmental cues, such as nitrogen availability and biotic/abiotic stresses. The complex regulation of cytosolic glutamine synthetase at the transcriptional to post-translational levels is key to the establishment of a specific physiological role for each isoenzyme. The diverse physiological roles of cytosolic glutamine synthetase isoenzymes are important in relation to current agricultural and ecological issues.

  11. Thermal responses of Symbiodinium photosynthetic carbon assimilation

    NASA Astrophysics Data System (ADS)

    Oakley, Clinton A.; Schmidt, Gregory W.; Hopkinson, Brian M.

    2014-06-01

    The symbiosis between hermatypic corals and their dinoflagellate endosymbionts, genus Symbiodinium, is based on carbon exchange. This symbiosis is disrupted by thermally induced coral bleaching, a stress response in which the coral host expels its algal symbionts as they become physiologically impaired. The disruption of the dissolved inorganic carbon (DIC) supply or the thermal inactivation of Rubisco have been proposed as sites of initial thermal damage that leads to the bleaching response. Symbiodinium possesses a highly unusual Form II ribulose bisphosphate carboxylase/oxygenase (Rubisco), which exhibits a lower CO2:O2 specificity and may be more thermally unstable than the Form I Rubiscos of other algae and land plants. Components of the CO2 concentrating mechanism (CCM), which supplies inorganic carbon for photosynthesis, may also be temperature sensitive. Here, we examine the ability of four cultured Symbiodinium strains to acquire and fix DIC across a temperature gradient. Surprisingly, the half-saturation constant of photosynthesis with respect to DIC concentration ( K P), an index of CCM function, declined with increasing temperature in three of the four strains, indicating a greater potential for photosynthetic carbon acquisition at elevated temperatures. In the fourth strain, there was no effect of temperature on K P. Finding no evidence for thermal inhibition of the CCM, we conclude that CCM components are not likely to be the primary sites of thermal damage. Reduced photosynthetic quantum yields, a hallmark of thermal bleaching, were observed at low DIC concentrations, leaving open the possibility that reduced inorganic carbon availability is involved in bleaching.

  12. Balance of assimilative and dissimilative nitrogen processes in a diatom-rich tidal flat sediment

    NASA Astrophysics Data System (ADS)

    Dähnke, K.; Moneta, A.; Veuger, B.; Soetaert, K.; Middelburg, J. J.

    2012-10-01

    Tidal flat sediments are subject to repetitive mixing and resuspension events. In a short-term (24 h) 15N-labelling experiment, we investigated reactive nitrogen cycling in a tidal flat sediment following an experimentally induced resuspension event. We focused on (a) the relative importance of assimilatory versus dissimilatory processes and (b) the role of benthic microalgae therein. 15N-labelled substrate was added to homogenized sediment, and 15N was subsequently traced into sediment and dissolved inorganic nitrogen (DIN) pools. Integration of results in a N-cycle model allowed us to quantify the proportion of major assimilatory and dissimilatory processes in the sediment. Upon sediment disturbance, rates of dissimilatory processes like nitrification and denitrification were very high, but declined rapidly towards a steady state. Once this was reached, the balance between assimilation and dissimilation in this tidal mudflat was mainly dependent on the nitrogen source: nitrate was utilized almost exclusively dissimilatory via denitrification, whereas ammonium was rapidly assimilated, with about a quarter of this assimilation due to benthic microalgae (BMA). Benthic microalgae significantly affected the nitrogen recycling balance in sediments, because in the absence of BMA activity the recovering sediment turned from a net ammonium sink to a net source. The driving mechanisms for assimilation or dissimilation accordingly appear to be ruled to a large extent by external physical forcing, with the entire system being capable of rapid shifts following environmental changes. Assimilatory pathways gain importance under stable conditions, with a substantial contribution of BMA to total assimilation.

  13. Efficient assimilation of cyanobacterial nitrogen by water hyacinth.

    PubMed

    Qin, Hongjie; Zhang, Zhiyong; Liu, Minhui; Wang, Yan; Wen, Xuezheng; Yan, Shaohua; Zhang, Yingying; Liu, Haiqin

    2017-10-01

    A (15)N labeling technique was used to study nitrogen transfer from cyanobacterium Microcystis aeruginosa to water hyacinth. (15)N atom abundance in M. aeruginosa peaked (15.52%) after cultivation in (15)N-labeled medium for 3weeks. Over 87% of algal nitrogen was transferred into water hyacinth after the 4-week co-cultivation period. The nitrogen quickly super-accumulated in the water hyacinth roots, and the labeled nitrogen was re-distributed to different organs (i.e., roots, stalks, and leaves). This study provides a new strategy for further research on cyanobacterial bloom control, nitrogen migration, and nitrogen cycle in eutrophic waters. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium

    PubMed Central

    Walworth, Nathan G.; Lee, Michael D.; Fu, Fei-Xue; Hutchins, David A.; Webb, Eric A.

    2016-01-01

    Most investigations of biogeochemically important microbes have focused on plastic (short-term) phenotypic responses in the absence of genetic change, whereas few have investigated adaptive (long-term) responses. However, no studies to date have investigated the molecular progression underlying the transition from plasticity to adaptation under elevated CO2 for a marine nitrogen-fixer. To address this gap, we cultured the globally important cyanobacterium Trichodesmium at both low and high CO2 for 4.5 y, followed by reciprocal transplantation experiments to test for adaptation. Intriguingly, fitness actually increased in all high-CO2 adapted cell lines in the ancestral environment upon reciprocal transplantation. By leveraging coordinated phenotypic and transcriptomic profiles, we identified expression changes and pathway enrichments that rapidly responded to elevated CO2 and were maintained upon adaptation, providing strong evidence for genetic assimilation. These candidate genes and pathways included those involved in photosystems, transcriptional regulation, cell signaling, carbon/nitrogen storage, and energy metabolism. Conversely, significant changes in specific sigma factor expression were only observed upon adaptation. These data reveal genetic assimilation as a potentially adaptive response of Trichodesmium and importantly elucidate underlying metabolic pathways paralleling the fixation of the plastic phenotype upon adaptation, thereby contributing to the few available data demonstrating genetic assimilation in microbial photoautotrophs. These molecular insights are thus critical for identifying pathways under selection as drivers in plasticity and adaptation. PMID:27830646

  15. Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium.

    PubMed

    Walworth, Nathan G; Lee, Michael D; Fu, Fei-Xue; Hutchins, David A; Webb, Eric A

    2016-11-22

    Most investigations of biogeochemically important microbes have focused on plastic (short-term) phenotypic responses in the absence of genetic change, whereas few have investigated adaptive (long-term) responses. However, no studies to date have investigated the molecular progression underlying the transition from plasticity to adaptation under elevated CO2 for a marine nitrogen-fixer. To address this gap, we cultured the globally important cyanobacterium Trichodesmium at both low and high CO2 for 4.5 y, followed by reciprocal transplantation experiments to test for adaptation. Intriguingly, fitness actually increased in all high-CO2 adapted cell lines in the ancestral environment upon reciprocal transplantation. By leveraging coordinated phenotypic and transcriptomic profiles, we identified expression changes and pathway enrichments that rapidly responded to elevated CO2 and were maintained upon adaptation, providing strong evidence for genetic assimilation. These candidate genes and pathways included those involved in photosystems, transcriptional regulation, cell signaling, carbon/nitrogen storage, and energy metabolism. Conversely, significant changes in specific sigma factor expression were only observed upon adaptation. These data reveal genetic assimilation as a potentially adaptive response of Trichodesmium and importantly elucidate underlying metabolic pathways paralleling the fixation of the plastic phenotype upon adaptation, thereby contributing to the few available data demonstrating genetic assimilation in microbial photoautotrophs. These molecular insights are thus critical for identifying pathways under selection as drivers in plasticity and adaptation.

  16. Nitrogen turnover in a tidal flat sediment: assimilation and dissimilation by bacteria and benthic microalgae

    NASA Astrophysics Data System (ADS)

    Dähnke, K.; Moneta, A.; Veuger, B.; Soetaert, K.; Middelburg, J. J.

    2012-06-01

    In a short-term (24 h) 15N-labeling experiment, we investigated reactive nitrogen cycling in a tidal flat sediment, focusing on the relative importance of assimilatory versus dissimilatory processes and the role of benthic microalgae therein. 15N-labeled ammonium and nitrate were added separately to homogenized sediment, and 15N was subsequently traced into sediment and dissolved inorganic nitrogen (DIN) pools. Integration of results in a N-cycle model allowed us to quantify rates for the major assimilatory and dissimilatory processes in the sediment. Overall, results indicate that the balance between assimilation and dissimilation in this tidal mudflat was mainly dependent on the nitrogen source. Nitrate was utilized almost exclusively dissimilatory via denitrification, whereas ammonium was rapidly assimilated, with about a quarter of this assimilation due to benthic microalgae (BMA). Benthic microalgae significantly affect assimilation of ammonium, because in the absence of BMA activity the sediments turns from a net ammonium sink to a net source. Nitrification rates were initially very high, but declined rapidly suggesting that nitrification rates are low in undisturbed sediments, and that in a dynamic environment like tidal flats, intense and fast nitrification/denitrification of ammonium is common. The driving mechanisms for assimilation or dissimilation accordingly appear to be ruled to a large extent by external physical forcing, with the entire system being capable of rapid shifts following environmental changes.

  17. Assimilation of Inorganic Nitrogen by Marine Invertebrates and Their Chemoautotrophic and Methanotrophic Symbionts

    PubMed Central

    Lee, Raymond W.; Childress, James J.

    1994-01-01

    Symbioses between marine invertebrates and their chemoautotrophic and methanotrophic symbionts are now known to exist in a variety of habitats where reduced chemical species are present. The utilization of chemical energy and reliance on C1 compounds by these symbioses are well documented. Much less is known about their metabolism of nitrogen. Earlier work has shown that the tissues of organisms in these associations are depleted of 15N compared with those of other marine organisms, indicating that local sources of nitrogen are assimilated and that novel mechanisms of nitrogen metabolism may be involved. Although these symbioses have access to rich sources of ammonium (NH4+ and NH3) and/or nitrate, several investigators have proposed that N2 fixation may account for some of these isotope values. Here we report that [15N]ammonium and, to a lesser degree, [15N]nitrate are assimilated into organic compounds by Solemya reidi, a gutless clam containing S-oxidizing bacteria, and seep mussel Ia, an undescribed mytilid containing methanotrophic bacteria. In contrast, Riftia pachyptila, the giant hydrothermal vent tube worm symbiotic with S-oxidizing bacteria, assimilated nitrate but not exogenous ammonium. The rates of assimilation of these sources are sufficient to at least partially support C1 compound metabolism. N2 assimilation was not exhibited by the symbionts tested. PMID:16349279

  18. Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

    PubMed Central

    van Heeswijk, Wally C.; Westerhoff, Hans V.

    2013-01-01

    SUMMARY We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now. PMID:24296575

  19. Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture

    PubMed Central

    Masclaux-Daubresse, Céline; Daniel-Vedele, Françoise; Dechorgnat, Julie; Chardon, Fabien; Gaufichon, Laure; Suzuki, Akira

    2010-01-01

    Background Productive agriculture needs a large amount of expensive nitrogenous fertilizers. Improving nitrogen use efficiency (NUE) of crop plants is thus of key importance. NUE definitions differ depending on whether plants are cultivated to produce biomass or grain yields. However, for most plant species, NUE mainly depends on how plants extract inorganic nitrogen from the soil, assimilate nitrate and ammonium, and recycle organic nitrogen. Efforts have been made to study the genetic basis as well as the biochemical and enzymatic mechanisms involved in nitrogen uptake, assimilation, and remobilization in crops and model plants. The detection of the limiting factors that could be manipulated to increase NUE is the major goal of such research. Scope An overall examination of the physiological, metabolic, and genetic aspects of nitrogen uptake, assimilation and remobilization is presented in this review. The enzymes and regulatory processes manipulated to improve NUE components are presented. Results obtained from natural variation and quantitative trait loci studies are also discussed. Conclusions This review presents the complexity of NUE and supports the idea that the integration of the numerous data coming from transcriptome studies, functional genomics, quantitative genetics, ecophysiology and soil science into explanatory models of whole-plant behaviour will be promising. PMID:20299346

  20. Inorganic nitrogen assimilation by the photosynthetic bacterium Rhodopseudomonas capsulata.

    PubMed Central

    Johansson, B C; Gest, H

    1976-01-01

    The photosynthetic bacterium Rhodopseudomonas capsulata lacks glutamate dehydrogenase and normally uses the glutamine synthetase/glutamate synthase sequence of reactions for assimilation of N2 and ammonia. The glutamine synthetase in cell-free extracts of the organism is completely sedimented by centrifugation at 140,000 X g for 2 h, is inhibited by L-alanine but not by adenosine 5'-monophosphate, and exhibits two apparent Km values for ammonia (ca. 13 muM and 1 mM). PMID:10281

  1. Gln3 is a main regulator of nitrogen assimilation in Candida glabrata.

    PubMed

    Pérez-Delos Santos, Francisco J; Riego-Ruiz, Lina

    2016-08-01

    After Candida albicans, the yeast Candida glabrata ranks second as an aetiological agent of candidaemia and is the most frequently encountered non-Candida albicans species in patients with invasive candidiasis. Transcriptome analysis in C. albicans, C. glabrata and Cryptoccocus neoformans has revealed that, when engulfed by macrophages, these yeasts upregulate genes involved in nutrient acquisition, including nitrogen transporters such as the general amino acid permease Gap1, the dicarboxylic amino acid permease Dip5, the basic amino acid permease Can1 and the ammonium permeases Mep1 and Mep2. Nitrogen assimilation has been well studied in model species of fungi, such as Aspergillus nidulans, Neurospora crassa and Saccharomyces cerevisiae. However, little is known about nitrogen assimilation in C. glabrata. In the present study, we report a major role for Gln3 in the assimilation of glutamine, ammonium and proline. Ure2 also has a role in nitrogen assimilation, but it is only observable in ammonium and glutamine. In addition, Gat1 has a minor role, which is only observable in the absence of Ure2 and Gln3. Gln3 is absolutely necessary for full ammonium uptake from media. We have also shown that MEP2 gene expression in C. glabrata is completely dependent on Gln3, whereas GAP1 regulation is mainly exerted by Gln3, with the exception of proline where Gat1 has a minor role. In addition, in C. glabrata Ure2 appears to be a negative regulator of these NCR-sensitive genes, similarly to what has been described in S. cerevisiae. Our data place Gln3 as a key regulator of nitrogen assimilation.

  2. Subcellular Investigation of Photosynthesis-Driven Carbon Assimilation in the Symbiotic Reef Coral Pocillopora damicornis

    PubMed Central

    Domart-Coulon, Isabelle; Escrig, Stephane; Humbel, Bruno M.; Hignette, Michel

    2015-01-01

    ABSTRACT  Reef-building corals form essential, mutualistic endosymbiotic associations with photosynthetic Symbiodinium dinoflagellates, providing their animal host partner with photosynthetically derived nutrients that allow the coral to thrive in oligotrophic waters. However, little is known about the dynamics of these nutritional interactions at the (sub)cellular level. Here, we visualize with submicrometer spatial resolution the carbon and nitrogen fluxes in the intact coral-dinoflagellate association from the reef coral Pocillopora damicornis by combining nanoscale secondary ion mass spectrometry (NanoSIMS) and transmission electron microscopy with pulse-chase isotopic labeling using [13C]bicarbonate and [15N]nitrate. This allows us to observe that (i) through light-driven photosynthesis, dinoflagellates rapidly assimilate inorganic bicarbonate and nitrate, temporarily storing carbon within lipid droplets and starch granules for remobilization in nighttime, along with carbon and nitrogen incorporation into other subcellular compartments for dinoflagellate growth and maintenance, (ii) carbon-containing photosynthates are translocated to all four coral tissue layers, where they accumulate after only 15 min in coral lipid droplets from the oral gastroderm and within 6 h in glycogen granules from the oral epiderm, and (iii) the translocation of nitrogen-containing photosynthates is delayed by 3 h. PMID:25670779

  3. A NAC for regulating metabolism: the nitrogen assimilation control protein (NAC) from Klebsiella pneumoniae.

    PubMed

    Bender, Robert A

    2010-10-01

    The nitrogen assimilation control protein (NAC) is a LysR-type transcriptional regulator (LTTR) that is made under conditions of nitrogen-limited growth. NAC's synthesis is entirely dependent on phosphorylated NtrC from the two-component Ntr system and requires the unusual sigma factor σ54 for transcription of the nac gene. NAC activates the transcription of σ70-dependent genes whose products provide the cell with ammonia or glutamate. NAC represses genes whose products use ammonia and also represses its own transcription. In addition, NAC also subtly adjusts other cellular functions to keep pace with the supply of biosynthetically available nitrogen.

  4. Subcellular investigation of photosynthesis-driven carbon assimilation in the symbiotic reef coral Pocillopora damicornis.

    PubMed

    Kopp, Christophe; Domart-Coulon, Isabelle; Escrig, Stephane; Humbel, Bruno M; Hignette, Michel; Meibom, Anders

    2015-02-10

    Reef-building corals form essential, mutualistic endosymbiotic associations with photosynthetic Symbiodinium dinoflagellates, providing their animal host partner with photosynthetically derived nutrients that allow the coral to thrive in oligotrophic waters. However, little is known about the dynamics of these nutritional interactions at the (sub)cellular level. Here, we visualize with submicrometer spatial resolution the carbon and nitrogen fluxes in the intact coral-dinoflagellate association from the reef coral Pocillopora damicornis by combining nanoscale secondary ion mass spectrometry (NanoSIMS) and transmission electron microscopy with pulse-chase isotopic labeling using [(13)C]bicarbonate and [(15)N]nitrate. This allows us to observe that (i) through light-driven photosynthesis, dinoflagellates rapidly assimilate inorganic bicarbonate and nitrate, temporarily storing carbon within lipid droplets and starch granules for remobilization in nighttime, along with carbon and nitrogen incorporation into other subcellular compartments for dinoflagellate growth and maintenance, (ii) carbon-containing photosynthates are translocated to all four coral tissue layers, where they accumulate after only 15 min in coral lipid droplets from the oral gastroderm and within 6 h in glycogen granules from the oral epiderm, and (iii) the translocation of nitrogen-containing photosynthates is delayed by 3 h. Our results provide detailed in situ subcellular visualization of the fate of photosynthesis-derived carbon and nitrogen in the coral-dinoflagellate endosymbiosis. We directly demonstrate that lipid droplets and glycogen granules in the coral tissue are sinks for translocated carbon photosynthates by dinoflagellates and confirm their key role in the trophic interactions within the coral-dinoflagellate association. Copyright © 2015 Kopp et al.

  5. Tidal influences on carbon assimilation by a salt marsh

    NASA Astrophysics Data System (ADS)

    Kathilankal, James C.; Mozdzer, Thomas J.; Fuentes, Jose D.; D'Odorico, Paolo; McGlathery, Karen J.; Zieman, Jay C.

    2008-10-01

    Salt marshes are among the most productive ecosystems on Earth, and play an important role in the global carbon cycle. Net carbon dioxide (CO2) ecosystem exchanges in coastal salt marshes remain poorly investigated. In Spartina alterniflora dominated North American Atlantic coast marshes, the lack of a clear understanding of how Spartina alterniflora responds to flooding limits our current ability to understand and predict salt marsh response to sea-level rise. Here we investigate the processes influencing ecosystem-level carbon exchanges between a S. alterniflora dominated salt marsh on the eastern shore of Virginia and the atmosphere. We examined the impacts of tidal inundation on the marsh-atmosphere carbon exchanges through a combination of eddy covariance measurements and in situ photosynthetic measurements. Maximum daytime carbon fluxes were observed during the middle of the growing season (July and August) and amounted to -10 μmol CO2 m-2 s-1, and the marsh assimilated 130 gC m-2 during the 2007 growing season. Our study is the first to quantify the effects of tidal inundation on marsh plants, which caused anywhere from 3% to 91% reductions in atmospheric carbon fluxes, with a mean reduction of 46 ± 26%, when compared to non-flooded conditions.

  6. The nac (nitrogen assimilation control) gene from Klebsiella aerogenes.

    PubMed Central

    Schwacha, A; Bender, R A

    1993-01-01

    The Klebsiella aerogenes nac gene, whose product is necessary for nitrogen regulation of a number of operons, was identified and its DNA sequence determined. The nac sequence predicted a protein a 305 amino acids with a strong similarity to members of the LysR family of regulatory proteins, especially OxyR from Escherichia coli. Analysis of proteins expressed in minicells showed that nac is a single-gene operon whose product has an apparent molecular weight of about 32 kDa as measured in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immediately downstream from nac is a two-gene operon, the first gene of which encodes another member of the LysR family. Upstream from nac is a tRNAAsn gene transcribed divergently from nac. About 60 bp upstream from the nac open reading frame lies a sequence nearly identical to the consensus for sigma 54-dependent promoters, with the conserved GG and GC nucleotides at -26 and -14 relative to the start of transcription. About 130 bp farther upstream (at -153 relative to the start of transcription) is a sequence nearly identical to the transcriptional activator NTRC-responsive enhancer consensus. Another weaker NTRC-binding site is located adjacent to this site (at -133 relative to the start of transcription). Thus, we propose that nac is transcribed by RNA polymerase carrying sigma 54 in response to the nitrogen regulatory (NTR) system. A transposon located between the promoter and the nac ORF prevented NTR-mediated expression of nac, supporting this identification of the promoter sequence. The insertion of over 5 kb of transposon DNA between the enhancer and its target promoter had only a weak effect on enhancer-mediated regulation, suggesting that enhancers may be able to act at a considerable distance on the bacterial chromosome. Images PMID:8458853

  7. An Improved Analysis of Forest Carbon Dynamics using Data Assimilation

    NASA Technical Reports Server (NTRS)

    Williams, Mathew; Schwarz, Paul A.; Law, Beverly E.; Kurpius, Meredith R.

    2005-01-01

    There are two broad approaches to quantifying landscape C dynamics - by measuring changes in C stocks over time, or by measuring fluxes of C directly. However, these data may be patchy, and have gaps or biases. An alternative approach to generating C budgets has been to use process-based models, constructed to simulate the key processes involved in C exchange. However, the process of model building is arguably subjective, and parameters may be poorly defined. This paper demonstrates why data assimilation (DA) techniques - which combine stock and flux observations with a dynamic model - improve estimates of, and provide insights into, ecosystem carbon (C) exchanges. We use an ensemble Kalman filter (EnKF) to link a series of measurements with a simple box model of C transformations. Measurements were collected at a young ponderosa pine stand in central Oregon over a 3-year period, and include eddy flux and soil C02 efflux data, litterfall collections, stem surveys, root and soil cores, and leaf area index data. The simple C model is a mass balance model with nine unknown parameters, tracking changes in C storage among five pools; foliar, wood and fine root pools in vegetation, and also fresh litter and soil organic matter (SOM) plus coarse woody debris pools. We nested the EnKF within an optimization routine to generate estimates from the data of the unknown parameters and the five initial conditions for the pools. The efficacy of the DA process can be judged by comparing the probability distributions of estimates produced with the EnKF analysis vs. those produced with reduced data or model alone. Using the model alone, estimated net ecosystem exchange of C (NEE)= -251 f 197g Cm-2 over the 3 years, compared with an estimate of -419 f 29gCm-2 when all observations were assimilated into the model. The uncertainty on daily measurements of NEE via eddy fluxes was estimated at 0.5gCm-2 day-1, but the uncertainty on assimilated estimates averaged 0.47 g Cm-2 day-1, and

  8. Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures.

    PubMed

    Glass, Jennifer B; Axler, Richard P; Chandra, Sudeep; Goldman, Charles R

    2012-01-01

    Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2-4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state.

  9. Molybdenum limitation of microbial nitrogen assimilation in aquatic ecosystems and pure cultures

    PubMed Central

    Glass, Jennifer B.; Axler, Richard P.; Chandra, Sudeep; Goldman, Charles R.

    2012-01-01

    Molybdenum (Mo) is an essential micronutrient for biological assimilation of nitrogen gas and nitrate because it is present in the cofactors of nitrogenase and nitrate reductase enzymes. Although Mo is the most abundant transition metal in seawater (107 nM), it is present in low concentrations in most freshwaters, typically <20 nM. In 1960, it was discovered that primary productivity was limited by Mo scarcity (2–4 nM) in Castle Lake, a small, meso-oligotrophic lake in northern California. Follow up studies demonstrated that Mo also limited primary productivity in lakes in New Zealand, Alaska, and the Sierra Nevada. Research in the 1970s and 1980s showed that Mo limited primary productivity and nitrate uptake in Castle Lake only during periods of the growing season when nitrate concentrations were relatively high because ammonium assimilation does not require Mo. In the years since, research has shifted to investigate whether Mo limitation also occurs in marine and soil environments. Here we review studies of Mo limitation of nitrogen assimilation in natural microbial communities and pure cultures. We also summarize new data showing that the simultaneous addition of Mo and nitrate causes increased activity of proteins involved in nitrogen assimilation in the hypolimnion of Castle Lake when ammonium is scarce. Furthermore, we suggest that meter-scale Mo and oxygen depth profiles from Castle Lake are consistent with the hypothesis that nitrogen-fixing cyanobacteria in freshwater periphyton communities have higher Mo requirements than other microbial communities. Finally, we present topics for future research related to Mo bioavailability through time and with changing oxidation state. PMID:22993512

  10. Carbon and nitrogen metabolism in ectomycorrhizal fungi and ectomycorrhizas.

    PubMed

    Martin, F; Ramstedt, M; Söderhäll, K

    1987-01-01

    The literature concerning the metabolism of carbon and nitrogen compounds in ectomycorrhizal associations of trees is reviewed. The absorption and translocation of mineral ions by the mycelia require an energy source and a reductant which are both supplied by respiratory catabolism of carbohydrates produced by the host plant. Photosynthates are also required to generate the carbon skeletons for amino acid and carbohydrate syntheses during the growth of the mycelia. Competition for photosynthates occurs between the fungal cells and the various vegetative sinks in the host tree. The nature of carbon compounds involved in these processes, their routes of metabolism, the mechanisms of control and the partitioning of metabolites between the various sites of utilization are only poorly understood. Both ascomycetous and basidiomycetous ectomycorrhizal fungi synthesize and some, if not all, accumulate mannitol, trehalose and triglycerides. The fungal strains employ the Embden--Meyerhof pathway of glucose catabolism and the key enzymes of the pentose phosphate pathway (6-phosphogluconate dehydrogenase, glucose-6-phosphate dehydrogenase, transaldolase and transketolase). Anaplerotic CO2 fixation, via pyruvate carboxylase and/or phosphoenolpyruvate carboxykinase, provides high pools of amino acids. This process could be important in the recapture and assimilation of respired CO2 in the rhizosphere. The ectomycorrhizas are thought to contain the Embden--Meyerhof pathway, the pentose phosphate pathway and the tricarboxylic acid cycle, which provide the carbon skeletons for the assimilation of ammonia into amino acids. The main route of assimilation of ammonia appears to be through the glutamine synthetase-glutamate synthase cycle in the ectomycorrhizas. Glutamate dehydrogenase plays a minor role in this process. Glutamate dehydrogenase and glutamine synthetase are present in free-living ectomycorrhizal fungi and they participate in the assimilation of ammonia and the synthesis

  11. Relationships between Carbon Assimilation, Partitioning, and Export in Leaves of Two Soybean Cultivars 1

    PubMed Central

    Fader, Gary M.; Koller, H. Ronald

    1983-01-01

    To evaluate leaf carbon balance during rapid pod-fill in soybean (Glycine max [L.] Merrill), measurements were made of CO2 assimilation at mid-day and changes in specific leaf weight, starch, and sucrose concentrations over a 9-hour interval. Assimilate export was estimated from CO2 assimilation and leaf dry matter accumulation. Chamber-grown `Amsoy 71' and `Wells' plants were subjected on the day of the measurements to one of six photosynthetic photon flux densities in order to vary CO2 assimilation rates. Rate of accumulation of leaf dry matter and rate of export both increased as CO2 assimilation rate increased in each cultivar. Starch concentrations were greater in Amsoy 71 than in Wells at all CO2 assimilation rates. At low CO2 assimilation rates, export rates in Amsoy 71 were maintained in excess of 1.0 milligram CH2O per square decimeter leaf area per hour at the expense of leaf reserves. In Wells, however, export rate continued to decline with decreasing CO2 assimilation rate. The low leaf starch concentration in Wells at low CO2 assimilation rates may have limited export by limiting carbon from starch remobilization. Both cultivars exhibited positive correlations between CO2 assimilation rate and sucrose concentration, and between sucrose concentration and export rate. Carbon fixation and carbon partitioning both influenced export rate via effects on sucrose concentration. PMID:16663211

  12. Differential accumulation of transcripts encoding sulfur assimilation enzymes upon sulfur and/or nitrogen deprivation in Arabidopsis thaliana.

    PubMed

    Yamaguchi, Y; Nakamura, T; Harada, E; Koizumi, N; Sano, H

    1999-04-01

    Expression of nine genes encoding enzymes involved in the sulfur assimilation pathway was examined by RNA blot hybridization. Significantly increased levels of transcripts encoding ATP sulfurylase and APS reductase were apparent under sulfur deprivation. However, in the absence of nitrogen, their responsiveness to sulfur deprivation was markedly reduced. Results suggest that the sulfur assimilation pathway is regulated at the transcriptional level by both nitrogen and sulfur sources.

  13. Quantifying the contribution of single microbial cells to nitrogen assimilation in aquatic environments

    NASA Astrophysics Data System (ADS)

    Musat, N.; Kuypers, M. M. M.

    2009-04-01

    Nitrogen is a primary productivity-limiting nutrient in the ocean. The nitrogen limitation of productivity may be overcome by organisms capable of converting dissolved N2 into fixed nitrogen available to the ecosystem. In many oceanic regions, growth of phytoplankton is nitrogen limited because fixation of N2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, NO3-) by anaerobic microbial processes. The amount of available fixed nitrogen in the ocean can be changed by the biological processes of heterotrophic denitrification, anaerobic ammonium oxidation and nitrogen fixation. For a complete understanding of nitrogen cycling in the ocean a link between the microbial and biogeochemical processes at the single cell level and their role in global biogeochemical cycles is essential. Here we report a recently developed method, Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS) and its potential application to study the nitrogen-cycle processes in the ocean. The method allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. It uses horseradish-peroxidase-labeled oligonucleotide probes and fluorine-containing tyramides for the identification of microorganisms in combination with stable-isotope-labeling experiments for analyzing the metabolic function of single microbial cells. HISH-SIMS was successfully used to study nitrogen assimilation and nitrogen fixation by anaerobic phototrophs in a meromictic alpine lake. The HISH-SIMS method enables studies of the ecophysiology of individual, phylogenetically identified microorganisms involved in the N-cycle and allows us to track the flow of nitrogen within microbial communities.

  14. Development of a rapid assimilable organic carbon method for water.

    PubMed

    Lechevallier, M W; Shaw, N E; Kaplan, L A; Bott, T L

    1993-05-01

    A rapid method for measurement of assimilable organic carbon (AOC) is proposed. The time needed to perform the assay is reduced by increasing the incubation temperature and increasing the inoculum density. The ATP luciferin-luciferase method quickly enumerates the test organisms without the need for plate count media or dilution bottles. There was no significant difference between AOC values determined with strain P17 for the ATP and plate count procedures. For strain NOX, the plate count procedure underestimated bacterial levels in some samples. Comparison of AOC values obtained by the Belleville laboratory (by the ATP technique) and the Stroud Water Research Center (by plate counts) showed that values were significantly correlated and not significantly different. The study concludes that the rapid AOC method can quickly determine the bacterial growth potential of water within 2 to 4 days.

  15. Assimilating Flask Sampling and OCO-2 Carbon Dioxide Measurements Using a Coupled Land-Atmosphere Data Assimilation System

    NASA Astrophysics Data System (ADS)

    Asrar, G.; Zeng, N.; Liu, Y.

    2016-12-01

    We apply a novel coupled land-atmosphere carbon data assimilation system to remote and in situ data to infer surface CO2 fluxes and terrestrial carbon model parameters. The system uses the Local-Ensemble-Transform-Kalman Filter (LETKF) that has been shown to be a powerful tool in a variety of atmosphere, ocean and carbon data assimilation settings. The LETKF system used here includes a number of advanced features, including variable localization, vertical localization, and short assimilation windows with temporal smoother to accommodate data streams of drastically different time scales. We will present results from the LETKF-GEOSChem system based on a combination of flask sampling and OCO-2 column CO2 measurements for the period of 2000-2016. Surface fluxes, including seasonal cycles, are obtained at model grid scale. Large Northern Hemispheric land carbon sink is clear, with foci in temperate and some boreal regions. With flask sampling data alone (2000-2014), the fluxes appear reasonable in many places including tropical rainforest regions. However, there are large biases in some subtropical regions such as India and the Sahel, where in-situ Data is sparse or do not exist. These biases appear to be minimized in 2015-2016 when OCO-2 data became available. We will also present some results demonstrating the impact of interannual variability in assimilated results, including the impact of OCO-2 on depicting the recent El Nino effect.

  16. Investigation of assimilable organic carbon (AOC) in flemish drinking water.

    PubMed

    Polanska, Monika; Huysman, Koen; van Keer, Chris

    2005-06-01

    The aim of the study was to investigate the drinking water supplied to majority of residents of Flanders in Belgium. Over 500 water samples were collected from different locations, after particular and complete treatment procedure to evaluate the efficiency of each treatment step in production of biologically stable drinking water. In this study assimilable organic carbon (AOC) was of our interest and was assumed as a parameter responsible for water biostability. The influence of seasons and temperature changes on AOC content was also taken into account. The AOC in most of the non-chlorinated product water of the studied treatment plants could not meet the biostability criteria of 10 mug/l, resulting in the mean AOC concentration of 50 microg/l. However, majority of the examined chlorinated water samples were consistent with proposed criteria of 50--100 microg/l for systems maintaining disinfectant residual. Here, mean AOC concentration of 72 microg/l was obtained. Granular activated carbon filtration was helpful in diminishing AOC content of drinking water; however, the nutrient removal was enhanced by biological process incorporated into water treatment (biological activated carbon filtration). Disinfection by means of chlorination and ozonation increased the water AOC concentration while the ultraviolet irradiation showed no impact on the AOC content. Examination of seasonal AOC variations showed similar fluctuations in six units with the highest values in summer and lowest in winter.

  17. Nitrogen, phosphorus, carbon and population.

    PubMed

    Gilland, Bernard

    2015-01-01

    Population growth makes food production increase necessary; economic growth increases demand for animal products and livestock feed. As further increase of the cropland area is ecologically undesirable, it is necessary to increase crop yields; this requires, inter alia, more nitrogen and phosphorus fertiliser despite the environmental problems which this will exacerbate. It is probable that a satisfactory food supply and an environmentally benign agriculture worldwide cannot be achieved without reducing population to approximately three billion. The reduction could be achieved by 2200 if the total fertility rate--currently 2.5--declined to 1.5 as a world average by 2050, and remained at that level until 2200, but the probability of such a global fertility trajectory is close to zero. It will also be necessary to replace fossil energy by nuclear and renewable energy in order to stabilise atmospheric carbon dioxide concentration, but the phase-out cannot be completed until the 22nd century, when the atmospheric concentration will be approximately 50% above the 2015 level of 400 ppm.

  18. Carbon and nitrogen balance of leaf-eating sesarmid crabs ( Neoepisesarma versicolor) offered different food sources

    NASA Astrophysics Data System (ADS)

    Thongtham, Nalinee; Kristensen, Erik

    2005-10-01

    Carbon and nitrogen budgets for the leaf-eating crab, Neoepisesarma versicolor, were established for individuals living on pure leaf diets. Crabs were fed fresh (green), senescent (yellow) and partly degraded (brown) leaves of the mangrove tree Rhizophora apiculata. Ingestion, egestion and metabolic loss of carbon and nitrogen were determined from laboratory experiments. In addition, bacterial abundance in various compartments of the crabs' digestive tract was enumerated after dissection of live individuals. Ingestion and egestion rates (in terms of dry weight) were highest, while the assimilation efficiency was poorest for crabs fed on brown leaves. The low assimilation efficiency was more than counteracted by the high ingestion rate providing more carbon for growth than for crabs fed green and yellow leaves. In any case, the results show that all types of leaves can provide adequate carbon while nitrogen was insufficient to support both maintenance (yellow leaves) and growth (green, yellow and brown leaves). Leaf-eating crabs must therefore obtain supplementary nitrogen by other means in order to meet their nitrogen requirement. Three hypotheses were evaluated: (1) crabs supplement their diet with bacteria and benthic microalgae by ingesting own faeces and/or selective grazing at the sediment surface; (2) assimilation of symbiotic nitrogen-fixing bacteria in the crabs' own intestinal system; and (3) nitrogen storage following occasional feeding on animal tissues (e.g. meiofauna and carcasses). It appears that hypothesis 1 is of limited importance for N. versicolor since faeces and sediment can only supply a minor fraction of the missing nitrogen due to physical constraints on the amount of material the crabs can consume. Hypothesis 2 can be ruled out because tests showed no nitrogen fixation activity in the intestinal system of N. versicolor. It is therefore likely that leaf-eating crabs provide most of their nitrogen requirement from intracellular deposits

  19. Ectomycorrhizal fungi enhance nitrogen and phosphorus nutrition of Nothofagus dombeyi under drought conditions by regulating assimilative enzyme activities.

    PubMed

    Alvarez, Maricel; Huygens, Dries; Olivares, Erick; Saavedra, Isabel; Alberdi, Miren; Valenzuela, Eduardo

    2009-08-01

    Drought stress conditions (DC) reduce plant growth and nutrition, restraining the sustainable reestablishment of Nothofagus dombeyi in temperate south Chilean forest ecosystems. Ectomycorrhizal symbioses have been documented to enhance plant nitrogen (N) and phosphorus (P) uptake under drought, but the regulation of involved assimilative enzymes remains unclear. We studied 1-year-old N. dombeyi (Mirb.) Oerst. plants in association with the ectomycorrhizal fungi Pisolithus tinctorius (Pers.) Coker & Couch. and Descolea antartica Sing. In greenhouse experiments, shoot and root dry weights, mycorrhizal colonization, foliar N and P concentrations, and root enzyme activities [glutamate synthase (glutamine oxoglutarate aminotransferase (GOGAT), EC 1.4.1.13-14), glutamine synthetase (GS, EC 6.3.1.2), glutamate dehydrogenase (GDH, EC 1.4.1.2-4), nitrate reductase (NR, EC 1.6.6.1), and acid phosphomonoesterase (PME, EC 3.1.3.1-2)] were determined as a function of soil-water content. Inoculation of N. dombeyi with P. tinctorius and D. antartica significantly stimulated plant growth and increased plant foliar N and P concentrations, especially under DC. Ectomycorrhizal inoculation increased the activity of all studied enzymes relative to non-mycorrhizal plants under drought. We speculate that GDH is a key enzyme involved in the enhancement of ectomycorrhizal carbon (C) availability by fuelling the tricarboxylic acid (TCA) cycle under conditions of drought-induced carbon deficit. All studied assimilative enzymes of the ectomycorrhizal associations, involved in C, N, and P transfers, are closely interlinked and interdependent. The up-regulation of assimilative enzyme activities by ectomycorrhizal fungal root colonizers acts as a functional mechanism to increase seedling endurance to drought. We insist upon incorporating ectomycorrhizal inoculation in existing Chilean afforestation programs.

  20. Nitrogen Assimilation, Abiotic Stress and Glucose 6-Phosphate Dehydrogenase: The Full Circle of Reductants

    PubMed Central

    Esposito, Sergio

    2016-01-01

    Glucose 6 phosphate dehydrogenase (G6PDH; EC 1.1.1.49) is well-known as the main regulatory enzyme of the oxidative pentose phosphate pathway (OPPP) in living organisms. Namely, in Planta, different G6PDH isoforms may occur, generally localized in cytosol and plastids/chloroplasts. These enzymes are differently regulated by distinct mechanisms, still far from being defined in detail. In the last decades, a pivotal function for plant G6PDHs during the assimilation of nitrogen, providing reductants for enzymes involved in nitrate reduction and ammonium assimilation, has been described. More recently, several studies have suggested a main role of G6PDH to counteract different stress conditions, among these salinity and drought, with the involvement of an ABA depending signal. In the last few years, this recognized vision has been greatly widened, due to studies clearly showing the non-conventional subcellular localization of the different G6PDHs, and the peculiar regulation of the different isoforms. The whole body of these considerations suggests a central question: how do the plant cells distribute the reductants coming from G6PDH and balance their equilibrium? This review explores the present knowledge about these mechanisms, in order to propose a scheme of distribution of reductants produced by G6PDH during nitrogen assimilation and stress. PMID:27187489

  1. Nitrogen Assimilation, Abiotic Stress and Glucose 6-Phosphate Dehydrogenase: The Full Circle of Reductants.

    PubMed

    Esposito, Sergio

    2016-05-11

    Glucose 6 phosphate dehydrogenase (G6PDH; EC 1.1.1.49) is well-known as the main regulatory enzyme of the oxidative pentose phosphate pathway (OPPP) in living organisms. Namely, in Planta, different G6PDH isoforms may occur, generally localized in cytosol and plastids/chloroplasts. These enzymes are differently regulated by distinct mechanisms, still far from being defined in detail. In the last decades, a pivotal function for plant G6PDHs during the assimilation of nitrogen, providing reductants for enzymes involved in nitrate reduction and ammonium assimilation, has been described. More recently, several studies have suggested a main role of G6PDH to counteract different stress conditions, among these salinity and drought, with the involvement of an ABA depending signal. In the last few years, this recognized vision has been greatly widened, due to studies clearly showing the non-conventional subcellular localization of the different G6PDHs, and the peculiar regulation of the different isoforms. The whole body of these considerations suggests a central question: how do the plant cells distribute the reductants coming from G6PDH and balance their equilibrium? This review explores the present knowledge about these mechanisms, in order to propose a scheme of distribution of reductants produced by G6PDH during nitrogen assimilation and stress.

  2. Reduced light and moderate water deficiency sustain nitrogen assimilation and sucrose degradation at low temperature in durum wheat.

    PubMed

    Majláth, Imre; Darko, Eva; Palla, Balázs; Nagy, Zoltán; Janda, Tibor; Szalai, Gabriella

    2016-02-01

    The rate of carbon and nitrogen assimilation is highly sensitive to stress factors, such as low temperature and drought. Little is known about the role of light in the simultaneous effect of cold and drought. The present study thus focused on the combined effect of mild water deficiency and different light intensities during the early cold hardening in durum wheat (Triticum turgidum ssp. durum L.) cultivars with different levels of cold sensitivity. The results showed that reduced illumination decreased the undesirable effects of photoinhibition in the case of net photosynthesis and nitrate reduction, which may help to sustain these processes at low temperature. Mild water deficiency also had a slight positive effect on the effective quantum efficiency of PSII and the nitrate reductase activity in the cold. Glutamine synthesis was affected by light rather than by water deprivation during cold stress. The invertase activity increased to a greater extent by water deprivation, but an increase in illumination also had a facilitating effect on this enzyme. This suggests that both moderate water deficiency and light have an influence on nitrogen metabolism and sucrose degradation during cold hardening. A possible rise in the soluble sugar content caused by the invertase may compensate for the decline in photosynthetic carbon assimilation indicated by the decrease in net photosynthesis. The changes in the osmotic potential can be also correlated to the enhanced level of invertase activity. Both of them were regulated by light at normal water supply, but not at water deprivation in the cold. However, changes in the metabolic enzyme activities and osmotic adjustment could not be directly contributed to the different levels of cold tolerance of the cultivars in the early acclimation period.

  3. Preparation of nitrogen-doped carbon tubes

    DOEpatents

    Chung, Hoon Taek; Zelenay, Piotr

    2015-12-22

    A method for synthesizing nitrogen-doped carbon tubes involves preparing a solution of cyanamide and a suitable transition metal-containing salt in a solvent, evaporating the solvent to form a solid, and pyrolyzing the solid under an inert atmosphere under conditions suitable for the production of nitrogen-doped carbon tubes from the solid. Pyrolyzing for a shorter period of time followed by rapid cooling resulted in a tubes with a narrower average diameter.

  4. Turbulence effects on the ratio of particulate carbon production to nutrient assimilation across nutrient gradients: An experimental approach.

    NASA Astrophysics Data System (ADS)

    Vidal, M.; Alcaraz, M.; Egge, J.; Jacobsen, A.; Marrasé, C.; Peters, F.; Roldán, C.; Thingstad, T. F.

    2003-04-01

    The uptake of inorganic carbon by the marine biota has been extensively studied in the context of the biological carbon pump. Carbon incorporation into biomass has been related to the availability of light and essential nutrients, such as dissolved inorganic nitrogen and phosphorus. Usually, it has been considered that nutrients are assimilated concurrently to inorganic carbon at constant Redfield proportions. Nevertheless, recent measurements have shown that, in some oceanic regions, the amount of inorganic carbon removed from the water significantly exceeded the amount expected from the removal of dissolved inorganic nutrients. This finding suggested that carbon incorporated into biomass per unit of consumed nitrogen or phosphorus might vary with time and across systems. The possible generalisation of this variability should have important consequences on the exportation of carbon and the role of the microbial plankton community on global carbon fluxes. Nutrient availability and light conditions have been invoked as the main factors influencing the ratio of particulate carbon production to nutrient assimilation. Despite the recognition of turbulence as a key factor influencing microbial dynamics, there is a lack of studies specifically relating the effect of turbulence on that ratio. Turbulence has been recently shown to increase the living carbon produced per phosphate consumed in microcosm experiments done with Mediterranean nutrient-starved plankton communities. According to this, we hypothesise that this effect may be found in other plankton communities and vary across gradients of nutrient concentration. We enclosed natural plankton communities from both Norwegian and Mediterranean coastal waters and subjected them to varying turbulence conditions and nutrient loads to monitor particulate and dissolved carbon and nutrient dynamics. We found that the effect of turbulence increased as nutrient concentration decreased. The magnitude of the response differed

  5. Disruption of the mitochondrial alternative oxidase (AOX) and uncoupling protein (UCP) alters rates of foliar nitrate and carbon assimilation in Arabidopsis thaliana.

    PubMed

    Gandin, Anthony; Denysyuk, Mykhaylo; Cousins, Asaph B

    2014-07-01

    Under high light, the rates of photosynthetic CO2 assimilation can be influenced by reductant consumed by both foliar nitrate assimilation and mitochondrial alternative electron transport (mAET). Additionally, nitrate assimilation is dependent on reductant and carbon skeletons generated from both the chloroplast and mitochondria. However, it remains unclear how nitrate assimilation and mAET coordinate and contribute to photosynthesis. Here, hydroponically grown Arabidopsis thaliana T-DNA insertional mutants for alternative oxidase (AOX1A) and uncoupling protein (UCP1) fed either NO3 (-) or NH4 (+) were used to determine (i) the response of NO3 (-) uptake and assimilation to the disruption of mAET, and (ii) the interaction of N source (NO3 (-) versus NH4 (+)) and mAET on photosynthetic CO2 assimilation and electron transport. The results showed that foliar NO3 (-) assimilation was enhanced in both aox1a and ucp1 compared with the wild-type, suggesting that foliar NO3 (-) assimilation is probably driven by a decreased capacity of mAET and an increase in reductant within the cytosol. Wild-type plants had also higher rates of net CO2 assimilation (A net) and quantum yield of PSII (ϕPSII) under NO3 (-) feeding compared with NH4 (+) feeding. Additionally, under NO3 (-) feeding, A net and ϕPSII were decreased in aox1a and ucp1 compared with the wild type; however, under NH4 (+) they were not significantly different between genotypes. This indicates that NO3 (-) assimilation and mAET are both important to maintain optimal rates of photosynthesis, probably in regulating reductant accumulation and over-reduction of the chloroplastic electron transport chain. These results highlight the importance of mAET in partitioning energy between foliar nitrogen and carbon assimilation.

  6. Disruption of the mitochondrial alternative oxidase (AOX) and uncoupling protein (UCP) alters rates of foliar nitrate and carbon assimilation in Arabidopsis thaliana

    PubMed Central

    Gandin, Anthony; Denysyuk, Mykhaylo; Cousins, Asaph B.

    2014-01-01

    Under high light, the rates of photosynthetic CO2 assimilation can be influenced by reductant consumed by both foliar nitrate assimilation and mitochondrial alternative electron transport (mAET). Additionally, nitrate assimilation is dependent on reductant and carbon skeletons generated from both the chloroplast and mitochondria. However, it remains unclear how nitrate assimilation and mAET coordinate and contribute to photosynthesis. Here, hydroponically grown Arabidopsis thaliana T-DNA insertional mutants for alternative oxidase (AOX1A) and uncoupling protein (UCP1) fed either NO3 – or NH4 + were used to determine (i) the response of NO3 – uptake and assimilation to the disruption of mAET, and (ii) the interaction of N source (NO3 – versus NH4 +) and mAET on photosynthetic CO2 assimilation and electron transport. The results showed that foliar NO3 – assimilation was enhanced in both aox1a and ucp1 compared with the wild-type, suggesting that foliar NO3 – assimilation is probably driven by a decreased capacity of mAET and an increase in reductant within the cytosol. Wild-type plants had also higher rates of net CO2 assimilation (A net) and quantum yield of PSII (ϕPSII) under NO3 – feeding compared with NH4 + feeding. Additionally, under NO3 – feeding, A net and ϕPSII were decreased in aox1a and ucp1 compared with the wild type; however, under NH4 + they were not significantly different between genotypes. This indicates that NO3 – assimilation and mAET are both important to maintain optimal rates of photosynthesis, probably in regulating reductant accumulation and over-reduction of the chloroplastic electron transport chain. These results highlight the importance of mAET in partitioning energy between foliar nitrogen and carbon assimilation. PMID:24799562

  7. Influence of nitrogen loading and plant nitrogen assimilation on nitrogen leaching and N₂O emission in forage rice paddy fields fertilized with liquid cattle waste.

    PubMed

    Riya, Shohei; Zhou, Sheng; Kobara, Yuso; Sagehashi, Masaki; Terada, Akihiko; Hosomi, Masaaki

    2015-04-01

    Livestock wastewater disposal onto rice paddy fields is a cost- and labor-effective way to treat wastewater and cultivate rice crops. We evaluated the influence of nitrogen loading rates on nitrogen assimilation by rice plants and on nitrogen losses (leaching and N2O emission) in forage rice fields receiving liquid cattle waste (LCW). Four forage rice fields were subjected to nitrogen loads of 107, 258, 522, and 786 kg N ha(-1) (N100, N250, N500, and N750, respectively) using basal fertilizer (chemical fertilizer) (50 kg N ha(-1)) and three LCW topdressings (each 57-284 kg N ha(-1)). Nitrogen assimilated by rice plants increased over time. However, after the third topdressing, the nitrogen content of the biomass did not increase in any treatment. Harvested aboveground biomass contained 93, 60, 33, and 31 % of applied nitrogen in N100, N250, N500, and N750, respectively. The NH4 (+) concentration in the pore water at a depth of 20 cm was less than 1 mg N L(-1) in N100, N250, and N500 throughout the cultivation period, while the NH4 (+) concentration in N750 increased to 3 mg N L(-1) after the third topdressing. Cumulative N2O emissions ranged from -0.042 to 2.39 kg N ha(-1); the highest value was observed in N750, followed by N500. In N750, N2O emitted during the final drainage accounted for 80 % of cumulative N2O emissions. This study suggested that 100-258 kg N ha(-1) is a recommended nitrogen loading rate for nitrogen recovery by rice plants without negative environmental impacts such as groundwater pollution and N2O emission.

  8. The carbon bonus of organic nitrogen enhances nitrogen use efficiency of plants

    PubMed Central

    Cambui, Camila Aguetoni; Gruffman, Linda; Palmroth, Sari; Oren, Ram; Näsholm, Torgny

    2016-01-01

    Abstract The importance of organic nitrogen (N) for plant nutrition and productivity is increasingly being recognized. Here we show that it is not only the availability in the soil that matters, but also the effects on plant growth. The chemical form of N taken up, whether inorganic (such as nitrate) or organic (such as amino acids), may significantly influence plant shoot and root growth, and nitrogen use efficiency (NUE). We analysed these effects by synthesizing results from multiple laboratory experiments on small seedlings (Arabidopsis, poplar, pine and spruce) based on a tractable plant growth model. A key point is that the carbon cost of assimilating organic N into proteins is lower than that of inorganic N, mainly because of its carbon content. This carbon bonus makes it more beneficial for plants to take up organic than inorganic N, even when its availability to the roots is much lower – up to 70% lower for Arabidopsis seedlings. At equal growth rate, root:shoot ratio was up to three times higher and nitrogen productivity up to 20% higher for organic than inorganic N, which both are factors that may contribute to higher NUE in crop production. PMID:27241731

  9. Nitrogen removal from aquaculture pond water by heterotrophic nitrogen assimilation in lab-scale sequencing batch reactors.

    PubMed

    De Schryver, Peter; Verstraete, Willy

    2009-02-01

    The potential use of sequencing batch reactors (SBRs) as an alternative bio-flocs technology (BFT) approach in aquaculture was explored. One SBR was dosed with glycerol and one with acetate for the decrease of the nitrogen concentration in simulated aquaculture water by microbial assimilation. At an optimal C/N ratio between 10 and 15, the nitrogen removal efficiency reached up to 98% (=110 mg N L(-1) reactor day(-1)) for both SBRs. The estimated biomass productivity reached 0.62-0.94 g C L(-1)r eactor day(-1) for the glycerol SBR and 0.54-0.82 g C L(-1) reactor day(-1) for the acetate SBR. The floc protein content, indicating biomass quality, reached up to 57% if grown on glycerol. With acetate, it attained a value of 61%. The highest average poly-beta-hydroxybutyrate (PHB) content was 16% on a dry weight basis for the acetate biomass.

  10. Differential contribution of the proline and glutamine pathways to glutamate biosynthesis and nitrogen assimilation in yeast lacking glutamate dehydrogenase

    PubMed Central

    Sieg, Alex G.; Trotter, Pamela J.

    2014-01-01

    In Saccharomyces cerevisiae, the glutamate dehydrogenase (GDH) enzymes play a pivotal role in glutamate biosynthesis and nitrogen assimilation. It has been proposed that, in GDH-deficient yeast, either the proline utilization (PUT) or the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway serves as the alternative pathway for glutamate production and nitrogen assimilation to the exclusion of the other. Using a gdh-null mutant (gdh1Δ2Δ3Δ), this ambiguity was addressed using a combination of growth studies and pathway-specific enzyme assays on a variety of nitrogen sources (ammonia, glutamine, proline and urea). The GDH-null mutant was viable on all nitrogen sources tested, confirming that alternate pathways for nitrogen assimilation exist in the gdh-null strain. Enzyme assays point to GS/GOGAT as the primary alternative pathway on the preferred nitrogen sources ammonia and glutamine, whereas growth on proline required both the PUT and GS/GOGAT pathways. In contrast, growth on glucose-urea media elicited a decrease in GOGAT activity along with an increase in activity of the PUT pathway specific enzyme Δ1-pyrroline-5-carboxylate dehydrogenase (P5CDH). Together, these results suggest the alternative pathway for nitrogen assimilation in strains lacking the preferred GDH-dependent route is nitrogen source dependent and that neither GS/GOGAT nor PUT serves as the sole compensatory pathway. PMID:24629525

  11. Differential contribution of the proline and glutamine pathways to glutamate biosynthesis and nitrogen assimilation in yeast lacking glutamate dehydrogenase.

    PubMed

    Sieg, Alex G; Trotter, Pamela J

    2014-01-01

    In Saccharomyces cerevisiae, the glutamate dehydrogenase (GDH) enzymes play a pivotal role in glutamate biosynthesis and nitrogen assimilation. It has been proposed that, in GDH-deficient yeast, either the proline utilization (PUT) or the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway serves as the alternative pathway for glutamate production and nitrogen assimilation to the exclusion of the other. Using a gdh-null mutant (gdh1Δ2Δ3Δ), this ambiguity was addressed using a combination of growth studies and pathway-specific enzyme assays on a variety of nitrogen sources (ammonia, glutamine, proline and urea). The GDH-null mutant was viable on all nitrogen sources tested, confirming that alternate pathways for nitrogen assimilation exist in the gdh-null strain. Enzyme assays point to GS/GOGAT as the primary alternative pathway on the preferred nitrogen sources ammonia and glutamine, whereas growth on proline required both the PUT and GS/GOGAT pathways. In contrast, growth on glucose-urea media elicited a decrease in GOGAT activity along with an increase in activity of the PUT pathway specific enzyme Δ(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH). Together, these results suggest the alternative pathway for nitrogen assimilation in strains lacking the preferred GDH-dependent route is nitrogen source dependent and that neither GS/GOGAT nor PUT serves as the sole compensatory pathway.

  12. Accumulation of nitrogen and changes in assimilation pigments of lichens transplanted in an agricultural area.

    PubMed

    Frati, Luisa; Brunialti, Giorgio; Gaudino, Stefania; Pati, Alessandra; Rosamilia, Silvia; Loppi, Stefano

    2011-07-01

    The results of a survey aimed at testing the hypothesis that the lichen Evernia prunastri, when transplanted in an agricultural area with high atmospheric NH(3) concentrations, would respond to NH(3) air pollution accumulating nitrogen in its thalli and showing changes in the concentration of assimilation pigments are presented. The results confirmed the hypothesis and showed that all lichen transplants accumulated nitrogen, suggesting that besides the release of atmospheric ammonia by animal stockfarms, the use of N-based fertilizers and the deposition of N-rich dust also may contribute to the high nitrogen availability to lichens in the study area. The result indicated that in the study area both the critical level of NH(3) and the critical load of N for lichens are exceeded and physiological damage is to be expected in sensitive species. The results of assimilation pigments in E. prunastri, with a decrease in the concentration of chlorophylls a and b and carotenoids, as well as chlorophyll degradation to phaeophytin, confirmed this hypothesis. However, owing to the limited data set and pending further studies, these conclusions should be considered as limited to the study area.

  13. Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution

    PubMed Central

    2011-01-01

    Background Besides being building blocks for proteins, amino acids are also key metabolic intermediates in living cells. Surprisingly a variety of organisms are incapable of synthesizing some of them, thus named Essential Amino Acids (EAAs). How certain ancestral organisms successfully competed for survival after losing key genes involved in amino acids anabolism remains an open question. Comparative genomics searches on current protein databases including sequences from both complete and incomplete genomes among diverse taxonomic groups help us to understand amino acids auxotrophy distribution. Results Here, we applied a methodology based on clustering of homologous genes to seed sequences from autotrophic organisms Saccharomyces cerevisiae (yeast) and Arabidopsis thaliana (plant). Thus we depict evidences of presence/absence of EAA biosynthetic and nitrogen assimilation enzymes at phyla level. Results show broad loss of the phenotype of EAAs biosynthesis in several groups of eukaryotes, followed by multiple secondary gene losses. A subsequent inability for nitrogen assimilation is observed in derived metazoans. Conclusions A Great Deletion model is proposed here as a broad phenomenon generating the phenotype of amino acids essentiality followed, in metazoans, by organic nitrogen dependency. This phenomenon is probably associated to a relaxed selective pressure conferred by heterotrophy and, taking advantage of available homologous clustering tools, a complete and updated picture of it is provided. PMID:22369087

  14. Assimilation and partitioning of prey nitrogen within two anthozoans and their endosymbiotic zooxanthellae

    USGS Publications Warehouse

    Piniak, G.A.; Lipschultz, F.; McClelland, J.

    2003-01-01

    The movement of nitrogen from zooplankton prey into the temperate scleractinian coral Oculina arbuscula and the anemone Aiptasia pallida was measured using 15N-labeled brine shrimp. The efficiency with which prey nitrogen was incorporated into cnidarian tissues was species-specific. O. arbuscula with a full complement of zooxanthellae had an assimilation efficiency of nearly 100%, compared to only 46% for corals containing few zooxanthellae. In A. pallida, symbiont density had no effect, and nitrogen assimilation was 23 to 29%. In both species, the host retained the bulk of the ingested label. Complete digestion was rapid (<4 h), as was the partitioning of the label between host amino acids and macromolecules. The label was primarily in the low-molecular weight-amino acid pool in O. arbuscula, where it remained for 30 h. A maximum of ca. 20% of the 15N appeared in the zooxanthellae, where it was rapidly converted into macromolecules. Individual amino acids in A. pallida tissues were highly labeled with 15N within 4 h and showed no subsequent enrichment with time; however, zooxanthellae amino acids became increasingly enriched over 30 h. Differences in 15N enrichment among amino acids were consistent with known synthesis and transformation pathways, but it was not possible to discriminate between host feeding and de novo synthesis.

  15. Primary productivity and nitrogen assimilation with identifying the contribution of urea in Funka Bay, Japan

    NASA Astrophysics Data System (ADS)

    Kudo, Isao; Hisatoku, Takatsugu; Yoshimura, Takeshi; Maita, Yoshiaki

    2015-06-01

    Primary production is supported by utilization of several forms of nitrogen (N), such as nitrate, ammonium, and urea. Nevertheless, only few studies have measured the concentration and uptake of urea despite its importance as a nitrogenous nutrient for phytoplankton. We measured primary productivity monthly at four depths within the euphotic zone using a clean technique and the 13C method by a 24 h in situ mooring incubation over a year in Funka Bay, a subarctic coastal area in Japan, to make better updated estimates (re-evaluation) of annual primary production. Nitrogenous (N) nutrient assimilation rates (nitrate, ammonium and urea) were also measured to elucidate the relative contributions of these nutrients to autotrophic production and to distinguish between new and regenerated production. The estimated annual primary production was 164 g C m-2, which was 40-60% higher than the previously reported values in the bay. Use of a clean technique and more frequent measurement during the spring bloom may have contributed to the higher rates. The production during the spring bloom was 56.5 g C m-2, accounting for 35% of the annual production. The maximum daily productivity occurred in the bloom at 1.4 g C m-2 d-1, which is one of the highest values among the world embayments. The annual primary production in the bay was classified as mesotrophic state based on the classification by Cloern et al. (2014). The assimilation rate of nitrate was maximal at 54 nmol N L-1 h-1 during the bloom. During the post-bloom periods with nitrate depleted conditions, assimilation rates of ammonium and urea increased and accounted for up to 85% of the total N assimilation. The assimilation rate of urea was almost comparable to that of ammonium throughout the year. Taking urea into account, the f-ratio ranged from 0.15 under the nitrate-depleted conditions to 0.8 under the spring bloom conditions. These ratios were overestimated by 50% and 10%, respectively, if urea uptake was eliminated

  16. Reviews and syntheses: Systematic Earth observations for use in terrestrial carbon cycle data assimilation systems

    NASA Astrophysics Data System (ADS)

    Scholze, Marko; Buchwitz, Michael; Dorigo, Wouter; Guanter, Luis; Quegan, Shaun

    2017-07-01

    The global carbon cycle is an important component of the Earth system and it interacts with the hydrology, energy and nutrient cycles as well as ecosystem dynamics. A better understanding of the global carbon cycle is required for improved projections of climate change including corresponding changes in water and food resources and for the verification of measures to reduce anthropogenic greenhouse gas emissions. An improved understanding of the carbon cycle can be achieved by data assimilation systems, which integrate observations relevant to the carbon cycle into coupled carbon, water, energy and nutrient models. Hence, the ingredients for such systems are a carbon cycle model, an algorithm for the assimilation and systematic and well error-characterised observations relevant to the carbon cycle. Relevant observations for assimilation include various in situ measurements in the atmosphere (e.g. concentrations of CO2 and other gases) and on land (e.g. fluxes of carbon water and energy, carbon stocks) as well as remote sensing observations (e.g. atmospheric composition, vegetation and surface properties).We briefly review the different existing data assimilation techniques and contrast them to model benchmarking and evaluation efforts (which also rely on observations). A common requirement for all assimilation techniques is a full description of the observational data properties. Uncertainty estimates of the observations are as important as the observations themselves because they similarly determine the outcome of such assimilation systems. Hence, this article reviews the requirements of data assimilation systems on observations and provides a non-exhaustive overview of current observations and their uncertainties for use in terrestrial carbon cycle data assimilation. We report on progress since the review of model-data synthesis in terrestrial carbon observations by Raupach et al.(2005), emphasising the rapid advance in relevant space-based observations.

  17. Ammonium nitrate and iron nutrition effects on some nitrogen assimilation enzymes and metabolites in Spirulina platensis.

    PubMed

    Esen, Merve; Ozturk Urek, Raziye

    2015-01-01

    The effect of various concentrations of ammonium nitrate (5-60 mM), an economical nitrogen source, on the growth, nitrate-ammonium uptake rates, production of some pigments and metabolites, and some nitrogen assimilation enzymes such as nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), and glutamate synthase (GOGAT) in Spirulina platensis (Gamont) Geitler was investigated. Ten millimolars of ammonium nitrate stimulated the growth, production of pigments and the other metabolites, and enzyme activities, whereas 30 and 60 mM ammonium nitrate caused inhibition. In the presence of 10 mM ammonium nitrate, different concentrations of iron were tried in the growth media of S. platensis. After achieving the best growth, levels of metabolite and pigment production, and enzyme activities in the presence of 10 mM ammonium nitrate as a nitrogen source, different iron concentrations (10-100 µM) were tried in the growth medium of S. platensis. The highest growth, pigment and metabolite levels, and enzyme activities were determined in the medium containing 50 µM iron and 10 mM ammonium nitrate. In this optimum condition, the highest dry biomass level, chlorophyll a, and pyruvate contents were obtained as 55.42 ± 3.8 mg mL(-1) , 93.114 ± 7.9 µg g(-1) , and 212.5 ± 18.7 µg g(-1) , respectively. The highest NR, NiR, GS, and GOGAT activities were 67.16 ± 5.1, 777.92 ± 52, 0.141 ± 0.01, and 44.45 ± 3.6, respectively. Additionally, 10 mM ammonium nitrate is an economical and efficient nitrogen source for nitrogen assimilation of S. platensis, and 50 µM iron is optimum for the growth of S. platensis. © 2014 International Union of Biochemistry and Molecular Biology, Inc.

  18. Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism

    PubMed Central

    Pérez-Delgado, Carmen M.; Moyano, Tomás C.; García-Calderón, Margarita; Canales, Javier; Gutiérrez, Rodrigo A.; Márquez, Antonio J.; Betti, Marco

    2016-01-01

    Nitrogen is one of the most important nutrients for plants and, in natural soils, its availability is often a major limiting factor for plant growth. Here we examine the effect of different forms of nitrogen nutrition and of photorespiration on gene expression in the model legume Lotus japonicus with the aim of identifying regulatory candidate genes co-ordinating primary nitrogen assimilation and photorespiration. The transcriptomic changes produced by the use of different nitrogen sources in leaves of L. japonicus plants combined with the transcriptomic changes produced in the same tissue by different photorespiratory conditions were examined. The results obtained provide novel information on the possible role of plastidic glutamine synthetase in the response to different nitrogen sources and in the C/N balance of L. japonicus plants. The use of gene co-expression networks establishes a clear relationship between photorespiration and primary nitrogen assimilation and identifies possible transcription factors connected to the genes of both routes. PMID:27117340

  19. Carbon Cost of Applying Nitrogen Fertilizer

    SciTech Connect

    Izaurralde, R Cesar C. ); Mcgill, William B.; Rosenberg, Norman J.

    2000-05-05

    When the addition of nitrogen (N) fertilizer leads to increased crop biomass, it also augments carbon (C)inputs to the soil and, hence often increases soil organic matter. Consequently, the efficient use of fertilizer N to increase crop production has also been found valuable for sequestering atmospheric carbon in soil.

  20. A Science Plan for Integrated Studies of Coupled Biosphere-Atmosphere Carbon and Nitrogen Cycles

    NASA Astrophysics Data System (ADS)

    Carroll, M.; Bertman, S. B.; Guenther, A.; Holland, E. A.; Shepson, P. B.; Sparks, J. P.

    2003-12-01

    Human activities, such as the burning of fossil fuels and the use of nitrogen fertilizers, have approximately doubled levels of reactive nitrogen in the biosphere. This perturbation has the potential to alter fundamental processes in terrestrial ecosystems where composition, diversity, and productivity are largely controlled by the availability of nitrogen. A variety of theoretical and experimental studies indicate that nitrogen inputs have a direct impact on fluxes of carbon into ecosystems controlling both CO2 assimilation and the exchange of carbon-based trace gases. In some systems, plant growth and carbon storage appear to be enhanced by nitrogen addition. In contrast, other systems exhibit stagnant or declining plant growth with nitrogen addition as the ecosystem becomes N-saturated and susceptible to stressors such as soil acidification and ozone damage. The magnitudes of the nitrogen and carbon responses appear to depend directly on the pathway and magnitude of nitrogen flux into ecosystems. However, the pathway of nitrogen entry into ecosystems, the chemical species of that nitrogen and its level of incorporation into plant and soil biomass pools are poorly understood in many, if not all, ecosystems. A workshop was held in Boulder, Colorado, in November 2003 to develop a science plan to address the critical need to integrate leaf-level plant physiology, ecosystem, and atmospheric chemistry perspectives to determine the fate of nitrogen and thus carbon in terrestrial systems. Participants brought expertise in plant physiological ecology, biochemistry, soil microbiology, biogeochemistry, atmospheric chemistry, biosphere/atmosphere fluxes, and integrated modeling. On behalf of all participants, we present here the prioritized results of the workshop; including gaps in understanding, technological challenges of integrating biological, ecosystem and atmospheric compartments of carbon and nitrogen cycling, feedbacks in carbon and nitrogen cycle coupling that are

  1. Nitrite Assimilation and Amino Nitrogen Synthesis in Isolated Spinach Chloroplasts 1

    PubMed Central

    Magalhaes, A. C.; Neyra, C. A.; Hageman, R. H.

    1974-01-01

    The assimilation of nitrite leading to de novo synthesis of amino nitrogen in a chloroplast-enriched fraction isolated from freshly harvested young spinach (Spinacia oleracea L.) leaves was demonstrated. The preparations showed approximately 55% intact chloroplasts as determined by light scattering properties and fixed CO2 at rates of approximately 100 μmoles hr−1 mg chlorophyll−1. The chloroplast-enriched fraction contained the enzymes, nitrite reductase and NADPH-glutamate dehydrogenase, needed for the reduction of nitrite and incorporation of ammonia into glutamate. Kinetic studies showed that the reduction of nitrite by the chloroplast-enriched fraction is light-dependent, and the process proceeds at rates of 6 to 12 μmoles hr−1 mg chlorophyll−1. The addition of nitrite to the chloroplast preparation caused a 3-fold increase in the production of α-amino nitrogen when compared with the control without nitrite. There was a stoichiometric relation between amino-nitrogen synthesis and nitrite disappearance from the medium. The ratio of amino-nitrogen: NO2− ranged from 0.6 to 0.9. The initial rate of amino-nitrogen production was faster when α-ketoglutarate was added to the nitrite reducing chloroplast medium than when it was omitted. However, these high rates were not sustained and the total amino-nitrogen production at the end of a 30-minute period was only slightly higher. These data show that chloroplasts are functionally able and contain the enzyme complement necessary to utilize light energy for the reduction of nitrite to amino nitrogen. Thus, chloroplasts should be considered as a major site for in vivo amino-nitrogen synthesis in green plants. PMID:16658715

  2. Characterization of Bioluminescent Derivatives of Assimilable Organic Carbon Test Bacteria

    PubMed Central

    Haddix, Pryce L.; Shaw, Nancy J.; LeChevallier, Mark W.

    2004-01-01

    The assimilable organic carbon (AOC) test is a standardized measure of the bacterial growth potential of treated water. We describe the design and initial development of an AOC assay that uses bioluminescent derivatives of AOC test bacteria. Our assay is based on the observation that bioluminescence peaks at full cell yield just prior to the onset of the stationary phase during growth in a water sample. Pseudomonas fluorescens P-17 and Spirillum sp. strain NOX bacteria were mutagenized with luxCDABE operon fusion and inducible transposons and were selected on minimal medium. Independent mutants were screened for high luminescence activity and predicted AOC assay sensitivity. All mutants tested were able to grow in tap water under AOC assay conditions. Strains P-17 I5 (with p-aminosalicylate inducer) and NOX I3 were chosen for use in the bioluminescence AOC test. Peak bioluminescence and plate count AOC were linearly related for both test bacteria, though data suggest that the P-17 bioluminescence assay requires more consistent luminescence monitoring. Bioluminescence results were obtained 2 or 3 days postinoculation, compared with 5 days for the ATP luminescence AOC assay and 8 days for the plate count assay. Plate count AOC assay results for nonmutant and bioluminescent bacteria from 36 water samples showed insignificant differences, indicating that the luminescent bacteria retained a full range of AOC measurement capability. This bioluminescence method is amenable to automation with a microplate format with programmable reagent injection. PMID:14766564

  3. Characterization of bioluminescent derivatives of assimilable organic carbon test bacteria.

    PubMed

    Haddix, Pryce L; Shaw, Nancy J; LeChevallier, Mark W

    2004-02-01

    The assimilable organic carbon (AOC) test is a standardized measure of the bacterial growth potential of treated water. We describe the design and initial development of an AOC assay that uses bioluminescent derivatives of AOC test bacteria. Our assay is based on the observation that bioluminescence peaks at full cell yield just prior to the onset of the stationary phase during growth in a water sample. Pseudomonas fluorescens P-17 and Spirillum sp. strain NOX bacteria were mutagenized with luxCDABE operon fusion and inducible transposons and were selected on minimal medium. Independent mutants were screened for high luminescence activity and predicted AOC assay sensitivity. All mutants tested were able to grow in tap water under AOC assay conditions. Strains P-17 I5 (with p-aminosalicylate inducer) and NOX I3 were chosen for use in the bioluminescence AOC test. Peak bioluminescence and plate count AOC were linearly related for both test bacteria, though data suggest that the P-17 bioluminescence assay requires more consistent luminescence monitoring. Bioluminescence results were obtained 2 or 3 days postinoculation, compared with 5 days for the ATP luminescence AOC assay and 8 days for the plate count assay. Plate count AOC assay results for nonmutant and bioluminescent bacteria from 36 water samples showed insignificant differences, indicating that the luminescent bacteria retained a full range of AOC measurement capability. This bioluminescence method is amenable to automation with a microplate format with programmable reagent injection.

  4. Relationship between photosynthetic capacity, nitrogen assimilation and nodule metabolism in alfalfa (Medicago sativa) grown with sewage sludge.

    PubMed

    Antolín, M Carmen; Fiasconaro, M Laura; Sánchez-Díaz, Manuel

    2010-10-15

    Sewage sludge has been used as N fertilizer because it contains some of inorganic N, principally as nitrate and ammonium ions. However, sewage sludge addition to legumes could result in impaired nodule metabolism due to the presence of inorganic N from sludge. A greenhouse experiment was conducted to examine the effects of sewage sludge on growth, photosynthesis, nitrogen assimilation and nodule metabolism in alfalfa (Medicago sativa L. cv. Aragón). Plants were grown in pots with a mixture of perlite and vermiculite (2:1, v/v). The experiment included three treatments: (1) plants inoculated with rhizobia and amended with sewage sludge at rate of 10% (w/w) (RS); (2) plants inoculated with rhizobia without any amendment (R); and (3) non-inoculated plants fed with ammonium nitrate (N). N(2)-fixing plants had lower growth and sucrose phosphate synthase activity but higher photosynthesis than nitrate-fed plants because they compensated the carbon cost of the rhizobia. However, sewage sludge-treated plants evidenced a loss of carbon sink strength due to N(2) fixation by means of decreased photosynthetic capacity, leaf chlorophylls and N concentration in comparison to untreated plants. Sewage sludge did no affect nodulation but decreased nodule enzyme activities involved in carbon and N metabolisms that may lead to accumulation of toxic N-compounds.

  5. Next Generation Carbon-Nitrogen Dynamics Model

    NASA Astrophysics Data System (ADS)

    Xu, C.; Fisher, R. A.; Vrugt, J. A.; Wullschleger, S. D.; McDowell, N. G.

    2012-12-01

    Nitrogen is a key regulator of vegetation dynamics, soil carbon release, and terrestrial carbon cycles. Thus, to assess energy impacts on the global carbon cycle and future climates, it is critical that we have a mechanism-based and data-calibrated nitrogen model that simulates nitrogen limitation upon both above and belowground carbon dynamics. In this study, we developed a next generation nitrogen-carbon dynamic model within the NCAR Community Earth System Model (CESM). This next generation nitrogen-carbon dynamic model utilized 1) a mechanistic model of nitrogen limitation on photosynthesis with nitrogen trade-offs among light absorption, electron transport, carboxylation, respiration and storage; 2) an optimal leaf nitrogen model that links soil nitrogen availability and leaf nitrogen content; and 3) an ecosystem demography (ED) model that simulates the growth and light competition of tree cohorts and is currently coupled to CLM. Our three test cases with changes in CO2 concentration, growing temperature and radiation demonstrate the model's ability to predict the impact of altered environmental conditions on nitrogen allocations. Currently, we are testing the model against different datasets including soil fertilization and Free Air CO2 enrichment (FACE) experiments across different forest types. We expect that our calibrated model will considerably improve our understanding and predictability of vegetation-climate interactions.itrogen allocation model evaluations. The figure shows the scatter plots of predicted and measured Vc,max and Jmax scaled to 25 oC (i.e.,Vc,max25 and Jmax25) at elevated CO2 (570 ppm, test case one), reduced radiation in canopy (0.1-0.9 of the radiation at the top of canopy, test case two) and reduced growing temperature (15oC, test case three). The model is first calibrated using control data under ambient CO2 (370 ppm), radiation at the top of the canopy (621 μmol photon/m2/s), the normal growing temperature (30oC). The fitted model

  6. Sulfoacetate released during the assimilation of taurine-nitrogen by Neptuniibacter caesariensis: purification of sulfoacetaldehyde dehydrogenase.

    PubMed

    Krejcík, Zdenĕk; Denger, Karin; Weinitschke, Sonja; Hollemeyer, Klaus; Paces, Václav; Cook, Alasdair M; Smits, Theo H M

    2008-08-01

    Taurine (2-aminoethanesulfonate) is a widespread natural product whose nitrogen moiety was recently shown to be assimilated by bacteria, usually with excretion of an organosulfonate via undefined novel pathways; other data involve transcriptional regulator TauR in taurine metabolism. A screen of genome sequences for TauR with the BLAST algorithm allowed the hypothesis that the marine gammaproteobacterium Neptuniibacter caesariensis MED92 would inducibly assimilate taurine-nitrogen and excrete sulfoacetate. The pathway involved an ABC transporter (TauABC), taurine:pyruvate aminotransferase (Tpa), a novel sulfoacetaldehyde dehydrogenase (SafD) and exporter(s) of sulfoacetate (SafE) (DUF81). Ten candidate genes in two clusters involved three sets of paralogues (for TauR, Tpa and SafE). Inducible Tpa and SafD were detected in cell extracts. SafD was purified 600-fold to homogeneity in two steps. The monomer had a molecular mass of 50 kDa (SDS-PAGE); data from gel filtration chromatography indicated a tetrameric native protein. SafD was specific for sulfoacetaldehyde with a K (m)-value of 0.12 mM. The N-terminal amino acid sequence of SafD confirmed the identity of the safD gene. The eight pathway genes were transcribed inducibly, which indicated expression of the whole hypothetical pathway. We presume that this pathway is one source of sulfoacetate in nature, where this compound is dissimilated by many bacteria.

  7. Effects of nitrogen stress on the photosynthetic CO2 assimilation, chlorophyll fluorescence, and sugar-nitrogen ratio in corn

    PubMed Central

    Jin, Xiuliang; Yang, Guijun; Tan, Changwei; Zhao, Chunjiang

    2015-01-01

    A field experiment was conducted using three corn cultivars (Jingyu7, Nongda80, and Tangyu10) and three nitrogen (N) application rates (0, 75, and 150 kg N ha−1). The objectives of this study were to investigate the responses of photosynthetic CO2 assimilation (Ph), the maximum quantum yield of photosystem II (Fv/Fm), leaf dry weight (LDW), leaf nitrogen concentration (LNC), leaf sugar concentration (LSC), and the sugar-to-nitrogen concentration ratio (S/N) to N levels in three different field-grown corn cultivars on three sampling dates. The results showed that the LDW, Fv/Fm, Ph, LNC, and LSC increased with increasing N levels, and the variation patterns of Fv/Fm, Ph, and LNC were “low-high-low”. In contrast, S/N decreased with increasing N levels, and its variation pattern was “high-low-high”. The values of LDW, Fv/Fm, Ph, LNC, LSC, and S/N were greatest under high N conditions, followed by medium N conditions, and finally low N conditions. Significant interactions occurred between Ph, Fv/Fm, LNC, LSC, LDW, and S/N, with the exception of the interaction between LSC and S/N and between LSC and LDW. The correlation coefficients between Ph and S/N and between Fv/Fm and S/N were −0.714 and −0.798, respectively. PMID:25831131

  8. Effects of nitrogen stress on the photosynthetic CO2 assimilation, chlorophyll fluorescence, and sugar-nitrogen ratio in corn

    NASA Astrophysics Data System (ADS)

    Jin, Xiuliang; Yang, Guijun; Tan, Changwei; Zhao, Chunjiang

    2015-04-01

    A field experiment was conducted using three corn cultivars (Jingyu7, Nongda80, and Tangyu10) and three nitrogen (N) application rates (0, 75, and 150 kg N ha-1). The objectives of this study were to investigate the responses of photosynthetic CO2 assimilation (Ph), the maximum quantum yield of photosystem II (Fv/Fm), leaf dry weight (LDW), leaf nitrogen concentration (LNC), leaf sugar concentration (LSC), and the sugar-to-nitrogen concentration ratio (S/N) to N levels in three different field-grown corn cultivars on three sampling dates. The results showed that the LDW, Fv/Fm, Ph, LNC, and LSC increased with increasing N levels, and the variation patterns of Fv/Fm, Ph, and LNC were ``low-high-low''. In contrast, S/N decreased with increasing N levels, and its variation pattern was ``high-low-high''. The values of LDW, Fv/Fm, Ph, LNC, LSC, and S/N were greatest under high N conditions, followed by medium N conditions, and finally low N conditions. Significant interactions occurred between Ph, Fv/Fm, LNC, LSC, LDW, and S/N, with the exception of the interaction between LSC and S/N and between LSC and LDW. The correlation coefficients between Ph and S/N and between Fv/Fm and S/N were -0.714 and -0.798, respectively.

  9. Effects of elevated atmospheric carbon dioxide on soil nitrogen cycling

    NASA Astrophysics Data System (ADS)

    Hofmockel, Kirsten S.

    Human activities including fossil fuel combustion, deforestation, and land conversion to agriculture have caused the concentration of atmospheric CO2 to increase since the Industrial Revolution. One approach to atmospheric CO2 reduction is sequestration in forest ecosystems. Presently little is known about the overall impact of elevated atmospheric CO2 on net ecosystem carbon storage, particularly in terms of nutrient limitations. In this dissertation I tested the hypothesis that elevated atmospheric CO2 will stimulate soil N availability, supporting long-term CO 2 sequestration in southeastern forests, examined asymbiotic N2 fixation, amino acid assimilation and ecosystem scale N cycling to understand changes in soil N cycling induced by elevated atmospheric CO 2. All research was conducted at the Duke Forest free Air CO2 Enrichment (FACE) experiment, where atmospheric CO2 concentrations have been maintained at 200 ul l-1 above ambient levels in the 30-m diameter treatment plots since 1996. This body of research indicates that elevated atmospheric CO2 does not stimulate soil N cycling at the decadal time scale. Field measurements of exogenous N inputs via asymbiotic N2 fixing bacteria reveal no CO2 stimulation. Soil moisture was the most important factor controlling field rates of N2 fixation. Changes in endogenous N cycling were evaluated using stable isotope tracer field experiments. Short-term experiments showed that more amino acid N was assimilated by both fine roots and microbes under ambient compared to elevated CO2. This significant treatment effect indicates that soil C limitation was a stronger driver of amino acid cycling than N limitation. Intact amino acid assimilation was comparable to NH4 assimilation and may make a small, but important contribution to plant N uptake in warm-temperate forest ecosystems. Inorganic N cycling was not affected by elevated atmospheric CO2. After two growing seasons, a 15N field tracer experiment showed no effects of

  10. Prediction of boron carbon nitrogen phase diagram

    NASA Astrophysics Data System (ADS)

    Yao, Sanxi; Zhang, Hantao; Widom, Michael

    We studied the phase diagram of boron, carbon and nitrogen, including the boron-carbon and boron-nitrogen binaries and the boron-carbon-nitrogen ternary. Based on the idea of electron counting and using a technique of mixing similar primitive cells, we constructed many ''electron precise'' structures. First principles calculation is performed on these structures, with either zero or high pressures. For the BN binary, our calculation confirms that a rhmobohedral phase can be stablized at high pressure, consistent with some experimental results. For the BCN ternary, a new ground state structure is discovered and an Ising-like phase transition is suggested. Moreover, we modeled BCN ternary phase diagram and show continuous solubility from boron carbide to the boron subnitride phase.

  11. Whole-plant and organ-level nitrogen isotope discrimination indicates modification of partitioning of assimilation, fluxes and allocation of nitrogen in knockout lines of Arabidopsis thaliana.

    PubMed

    Kalcsits, Lee A; Guy, Robert D

    2013-10-01

    The nitrogen isotope composition (δ¹⁵N) of plants has potential to provide time-integrated information on nitrogen uptake, assimilation and allocation. Here, we take advantage of existing T-DNA and γ-ray mutant lines of Arabidopsis thaliana to modify whole-plant and organ-level nitrogen isotope composition. Nitrate reductase 2 (nia2), nitrate reductase 1 (nia1) and nitrate transporter (nrt2) mutant lines and the Col-0 wild type were grown hydroponically under steady-state NO₃⁻ conditions at either 100 or 1000 μM NO₃⁻ for 35 days. There were no significant effects on whole-plant discrimination and growth in the assimilatory mutants (nia2 and nia1). Pronounced root vs leaf differences in δ¹⁵N, however, indicated that nia2 had an increased proportion of nitrogen assimilation of NO₃⁻ in leaves while nia1 had an increased proportion of assimilation in roots. These observations are consistent with reported ratios of nia1 and nia2 gene expression levels in leaves and roots. Greater whole-plant discrimination in nrt2 indicated an increase in efflux of unassimilated NO₃⁻ back to the rooting medium. This phenotype was associated with an overall reduction in NO₃⁻ uptake, assimilation and decreased partitioning of NO₃⁻ assimilation to the leaves, presumably because of decreased symplastic intercellular movement of NO₃⁻ in the root. Although the results were more varied than expected, they are interpretable within the context of expected mechanisms of whole-plant and organ-level nitrogen isotope discrimination that indicate variation in nitrogen fluxes, assimilation and allocation between lines. © 2013 Scandinavian Plant Physiology Society.

  12. The CarbonTracker Data Assimilation Shell (CTDAS) v1.0: implementation and global carbon balance 2001-2015

    NASA Astrophysics Data System (ADS)

    van der Laan-Luijkx, Ingrid T.; van der Velde, Ivar R.; van der Veen, Emma; Tsuruta, Aki; Stanislawska, Karolina; Babenhauserheide, Arne; Zhang, Hui Fang; Liu, Yu; He, Wei; Chen, Huilin; Masarie, Kenneth A.; Krol, Maarten C.; Peters, Wouter

    2017-07-01

    Data assimilation systems are used increasingly to constrain the budgets of reactive and long-lived gases measured in the atmosphere. Each trace gas has its own lifetime, dominant sources and sinks, and observational network (from flask sampling and in situ measurements to space-based remote sensing) and therefore comes with its own optimal configuration of the data assimilation. The CarbonTracker Europe data assimilation system for CO2 estimates global carbon sources and sinks, and updates are released annually and used in carbon cycle studies. CarbonTracker Europe simulations are performed using the new modular implementation of the data assimilation system: the CarbonTracker Data Assimilation Shell (CTDAS). Here, we present and document this redesign of the data assimilation code that forms the heart of CarbonTracker, specifically meant to enable easy extension and modification of the data assimilation system. This paper also presents the setup of the latest version of CarbonTracker Europe (CTE2016), including the use of the gridded state vector, and shows the resulting carbon flux estimates. We present the distribution of the carbon sinks over the hemispheres and between the land biosphere and the oceans. We show that with equal fossil fuel emissions, 2015 has a higher atmospheric CO2 growth rate compared to 2014, due to reduced net land carbon uptake in later year. The European carbon sink is especially present in the forests, and the average net uptake over 2001-2015 was 0. 17 ± 0. 11 PgC yr-1 with reductions to zero during drought years. Finally, we also demonstrate the versatility of CTDAS by presenting an overview of the wide range of applications for which it has been used so far.

  13. Role of GOGAT in carbon and nitrogen partitioning in Rhizobium etli.

    PubMed

    Castillo, A; Taboada, H; Mendoza, A; Valderrama, B; Encarnación, S; Mora, J

    2000-07-01

    The isolation and characterization of a Rhizobium etli glutamate auxotroph, TAD12, harbouring a single Tn5 insertion, is reported. This mutant produced no detectable glutamate synthase (GOGAT) activity. The cloning and physical characterization of a 7.2 kb fragment of R. etli DNA harbouring the structural genes gltB and gltD encoding the two GOGAT subunits GltB and GltD is also reported. In comparison with the wild-type strain (CFN42), the GOGAT mutant strain utilized less succinate and glutamate and grew less with this and other amino acids as nitrogen source. R. etli assimilates ammonium by the glutamine synthetase (GS)-GOGAT pathway and a GOGAT mutant prevents the cycling of glutamine by this pathway, something that impairs nitrogen and carbon metabolism and explains the decrease in the amino-nitrogen during exponential growth, with glutamate as nitrogen source. GOGAT activity also has a role in ammonium turnover and in the synthesis of amino acids and proteins, processes that are necessary to sustain cell viability in non-growing conditions. The assimilation of ammonium is important during symbiosis and glutamate constitutes 20-40% of the total amino-nitrogen. In symbiosis, the blockage of ammonium assimilation by a GOGAT mutation significantly decreases the amino-nitrogen pool of the bacteroids and may explain why more N(2) is fixed in ammonium, excreted to the plant cell, transported to the leaves and stored in the seeds.

  14. Worldwide organic soil carbon and nitrogen data

    SciTech Connect

    Zinke, P.J.; Stangenberger, A.G.; Post, W.M.; Emanual, W.R.; Olson, J.S.

    1986-09-01

    The objective of the research presented in this package was to identify data that could be used to estimate the size of the soil organic carbon pool under relatively undisturbed soil conditions. A subset of the data can be used to estimate amounts of soil carbon storage at equilibrium with natural soil-forming factors. The magnitude of soil properties so defined is a resulting nonequilibrium values for carbon storage. Variation in these values is due to differences in local and geographic soil-forming factors. Therefore, information is included on location, soil nitrogen content, climate, and vegetation along with carbon density and variation.

  15. Carbon and Nitrogen dynamics in deciduous and broad leaf trees under drought stress

    NASA Astrophysics Data System (ADS)

    Joseph, Jobin; Schaub, Marcus; Arend, Matthias; Saurer, Matthias; siegwolf, Rolf; Weiler, Markus; Gessler, Arthur

    2017-04-01

    Climate change is projected to lead to an increased frequency and duration of severe drought events in future. Already within the last twenty years, however, drought stress related forest mortality has been increasing across the globe. Tree and forest die off events have multiple adverse effects on ecosystem functioning and might convert previous carbon sinks to act as carbon sources instead and can thus intensify the effect of climate change and global warming. Current predictions of forest's functioning under drought and thus forest mortality under future climatic conditions are constrained by a still incomplete picture of the trees' physiological reactions that allows some trees to survive drought periods while others succumb. Concerning the effects of drought on the carbon balance and on tree hydraulics our picture is getting more complete, but still interactions between abiotic factors and pest and diseases as well as the interaction between carbon and nutrient balances as factors affecting drought induced mortality are not well understood. Reduced carbon allocation from shoots to roots might cause a lack of energy for root nutrient uptake and to a shortage of carbon skeletons for nitrogen assimilation and thus to an impaired nutrient status of trees. To tackle these points, we have performed a drought stress experiment with six different plant species, 3 broad leaf (maple, beech and oak) and 3 deciduous (pine, fir and spruce). Potted two-year-old seedlings were kept inside a greenhouse for 5 months and 3 levels of drought stress (no stress (control), intermediate and intensive drought stress) were applied by controlling water supply. Gas exchange measurements were performed periodically to monitor photosynthesis, transpiration, stomatal conductance. At the pinnacle of drought stress, we applied isotopic pulse labelling: On the one hand we exposed trees to 13CO2 to investigate on carbon dynamics and the allocation of new assimilates within the plant. Moreover

  16. Improvement of Nitrogen Assimilation and Fermentation Kinetics under Enological Conditions by Derepression of Alternative Nitrogen-Assimilatory Pathways in an Industrial Saccharomyces cerevisiae Strain

    PubMed Central

    Salmon, Jean-Michel; Barre, Pierre

    1998-01-01

    Metabolism of nitrogen compounds by yeasts affects the efficiency of wine fermentation. Ammonium ions, normally present in grape musts, reduce catabolic enzyme levels and transport activities for nonpreferred nitrogen sources. This nitrogen catabolite repression severely impairs the utilization of proline and arginine, both common nitrogen sources in grape juice that require the proline utilization pathway for their assimilation. We attempted to improve fermentation performance by genetic alteration of the regulation of nitrogen-assimilatory pathways in Saccharomyces cerevisiae. One mutant carrying a recessive allele of ure2 was isolated from an industrial S. cerevisiae strain. This mutation strongly deregulated the proline utilization pathway. Fermentation kinetics of this mutant were studied under enological conditions on simulated standard grape juices with various nitrogen levels. Mutant strains produced more biomass and exhibited a higher maximum CO2 production rate than the wild type. These differences were primarily due to the derepression of amino acid utilization pathways. When low amounts of dissolved oxygen were added, the mutants could assimilate proline. Biomass yield and fermentation rate were consequently increased, and the duration of the fermentation was substantially shortened. S. cerevisiae strains lacking URE2 function could improve alcoholic fermentation of natural media where proline and other poorly assimilated amino acids are the major potential nitrogen source, as is the case for most fruit juices and grape musts. PMID:9758807

  17. Improvement of nitrogen assimilation and fermentation kinetics under enological conditions by derepression of alternative nitrogen-assimilatory pathways in an industrial Saccharomyces cerevisiae strain.

    PubMed

    Salmon, J M; Barre, P

    1998-10-01

    Metabolism of nitrogen compounds by yeasts affects the efficiency of wine fermentation. Ammonium ions, normally present in grape musts, reduce catabolic enzyme levels and transport activities for nonpreferred nitrogen sources. This nitrogen catabolite repression severely impairs the utilization of proline and arginine, both common nitrogen sources in grape juice that require the proline utilization pathway for their assimilation. We attempted to improve fermentation performance by genetic alteration of the regulation of nitrogen-assimilatory pathways in Saccharomyces cerevisiae. One mutant carrying a recessive allele of ure2 was isolated from an industrial S. cerevisiae strain. This mutation strongly deregulated the proline utilization pathway. Fermentation kinetics of this mutant were studied under enological conditions on simulated standard grape juices with various nitrogen levels. Mutant strains produced more biomass and exhibited a higher maximum CO2 production rate than the wild type. These differences were primarily due to the derepression of amino acid utilization pathways. When low amounts of dissolved oxygen were added, the mutants could assimilate proline. Biomass yield and fermentation rate were consequently increased, and the duration of the fermentation was substantially shortened. S. cerevisiae strains lacking URE2 function could improve alcoholic fermentation of natural media where proline and other poorly assimilated amino acids are the major potential nitrogen source, as is the case for most fruit juices and grape musts.

  18. Transcriptome of Proteus mirabilis in the Murine Urinary Tract: Virulence and Nitrogen Assimilation Gene Expression▿†

    PubMed Central

    Pearson, Melanie M.; Yep, Alejandra; Smith, Sara N.; Mobley, Harry L. T.

    2011-01-01

    The enteric bacterium Proteus mirabilis is a common cause of complicated urinary tract infections. In this study, microarrays were used to analyze P. mirabilis gene expression in vivo from experimentally infected mice. Urine was collected at 1, 3, and 7 days postinfection, and RNA was isolated from bacteria in the urine for transcriptional analysis. Across nine microarrays, 471 genes were upregulated and 82 were downregulated in vivo compared to in vitro broth culture. Genes upregulated in vivo encoded mannose-resistant Proteus-like (MR/P) fimbriae, urease, iron uptake systems, amino acid and peptide transporters, pyruvate metabolism enzymes, and a portion of the tricarboxylic acid (TCA) cycle enzymes. Flagella were downregulated. Ammonia assimilation gene glnA (glutamine synthetase) was repressed in vivo, while gdhA (glutamate dehydrogenase) was upregulated in vivo. Contrary to our expectations, ammonia availability due to urease activity in P. mirabilis did not drive this gene expression. A gdhA mutant was growth deficient in minimal medium with citrate as the sole carbon source, and loss of gdhA resulted in a significant fitness defect in the mouse model of urinary tract infection. Unlike Escherichia coli, which represses gdhA and upregulates glnA in vivo and cannot utilize citrate, the data suggest that P. mirabilis uses glutamate dehydrogenase to monitor carbon-nitrogen balance, and this ability contributes to the pathogenic potential of P. mirabilis in the urinary tract. PMID:21505083

  19. Final Technical Report: Genetic Control of Nitrogen Assimilation in Klebsiella oxytoca.

    SciTech Connect

    Valley Stewart

    2007-03-07

    Klebsiella oxytoca, an enterobacterium closely related to Escherichia coli and amenable to molecular genetic analysis, is a long-established model organism for studies of bacterial nitrogen assimilation. Our work concerned utilization of purines, nitrogen-rich compounds that are widespread in the biosphere. This project began with our observation that molybdenum cofactor (chlorate-resistant) mutants can use (hypo)xanthine as sole nitrogen source (Garzón et al., J. Bacteriol. 174:6298, 1992). Since xanthine dehydrogenase is a molybdoenzyme, Klebsiella must use an alternate route for (hypo)xanthine catabolsim. We identified and characterized a cluster of 22 genes that encode the enzymes, permeases and regulators for utilizing hypoxanthine and xanthine as sole nitrogen source. (Hypoxanthine and xanthine arise from deamination of adenine and guanine, respectively.) Growth and complementation tests with insertion mutants, combined with protein sequence comparisons, allow us to assign probable functions for the products of these genes and to deduce the overall pathway. We present genetic evidence that the first two enzymes for the Klebsiella purine utilization pathway have been recruited from pathways involved in catabolism of aromatic compounds. The first, HxaAB enzyme catalyzing (hypo)xanthine oxidation, is related to well-studied aromatic ring hydroxylating oxygenases such as phthalate dioxygenase. The second, HxbA enzyme catalyzing urate hydroxylation, is related to single-component monooxygenases. Thus, the Klebsiella purine utilization pathway has likely experienced non-orthologous gene displacement, substituting these oxygenases for the conventional enzymes, xanthine dehydrogenase and uricase. We also present evidence that transcription of the hxaAB operon is subject to dual regulation: global general nitrogen regulation (Ntr) through an unknown mechanism, and (hypo)xanthine induction mediated by a LysR-type activator.

  20. What measurements are needed to capture coupled carbon and nitrogen cycles in arctic tundra?

    NASA Astrophysics Data System (ADS)

    Wright, K.; Rocha, A. V.

    2015-12-01

    Greening has been observed across the arctic, but the ecological processes that enable widespread increases in plant productivity have been difficult to understand with field measurements alone. Using the functional convergence of foliar nitrogen and leaf area index in arctic plants, we developed a simple coupled carbon and nitrogen cycling model (CCaN) to increase our understanding of warming induced vegetation changes and carbon and nitrogen coupling in the arctic. We used primary literature and data from long term ecological research sites at Toolik Field Station, Alaska to calculate prior ranges for CCaN parameters, and then we assimilated five years of eddy covariance data from a nearby field site using a batch data assimilation method based on Markov Chain Monte Carlo techniques. Variance decomposition analyses show that the majority of model variance in carbon and nitrogen stocks can be attributed to uncertainty in four parameters: proportion of nitrogen in foliage, proportion of nitrogen in roots, nitrogen uptake rate, and litter rate. These parameters associated with nitrogen cycling are widely used in biogeochemical cycling models and are difficult to constrain because they vary greatly across plant functional groups. The parameters responsible for variance in net ecosystem exchange vary seasonally; winter variance is controlled by parameters associated with the temperature sensitivity of heterotrophic respiration, and summer variance is controlled by the proportion of nitrogen in foliage. The widespread greening observed across the arctic over the last decade has been attributed to the direct effects of increased temperature, despite the inconsistency of the response of arctic plants to experimental warming indicating there must be other mechanisms at play. These mechanisms can be teased apart using models, but we must first improve model predictions by constraining widely-used processes and parameters, particularly those linked to nitrogen cycling.

  1. Nitrogen activated-carbon sorption compressor

    NASA Astrophysics Data System (ADS)

    Tzabar, Nir; Grossman, Gershon

    2012-06-01

    Joule-Thomson (JT) sorption cryocooling is the most mature technology for cooling from a normal Room-Temperature (RT) down to temperatures below 100 K in the absence of moving parts. Therefore, high reliability and no vibrations are attainable, in comparison with other cryocoolers. Nitrogen is usually used as the working fluid for cooling to temperatures between 80 and 100 K and activated carbons are the best adsorbent for this purpose. In this paper we present the development of a sorption compressor for nitrogen with a commercial Chemviron pelleted activated carbon. The development consists of sorption measurements that we performed for characterizing the adsorption of nitrogen on the selected adsorbent, and the compressor experimental results are compared with equilibrium condition analysis and numerical heat transfer analysis predictions

  2. Soil warming, carbon-nitrogen interactions, and forest carbon budgets.

    PubMed

    Melillo, Jerry M; Butler, Sarah; Johnson, Jennifer; Mohan, Jacqueline; Steudler, Paul; Lux, Heidi; Burrows, Elizabeth; Bowles, Francis; Smith, Rose; Scott, Lindsay; Vario, Chelsea; Hill, Troy; Burton, Andrew; Zhou, Yu-Mei; Tang, Jim

    2011-06-07

    Soil warming has the potential to alter both soil and plant processes that affect carbon storage in forest ecosystems. We have quantified these effects in a large, long-term (7-y) soil-warming study in a deciduous forest in New England. Soil warming has resulted in carbon losses from the soil and stimulated carbon gains in the woody tissue of trees. The warming-enhanced decay of soil organic matter also released enough additional inorganic nitrogen into the soil solution to support the observed increases in plant carbon storage. Although soil warming has resulted in a cumulative net loss of carbon from a New England forest relative to a control area over the 7-y study, the annual net losses generally decreased over time as plant carbon storage increased. In the seventh year, warming-induced soil carbon losses were almost totally compensated for by plant carbon gains in response to warming. We attribute the plant gains primarily to warming-induced increases in nitrogen availability. This study underscores the importance of incorporating carbon-nitrogen interactions in atmosphere-ocean-land earth system models to accurately simulate land feedbacks to the climate system.

  3. The re-assimilation of ammonia produced by photorespiration and the nitrogen economy of C3 higher plants.

    PubMed

    Keys, Alfred J

    2006-02-01

    Photorespiration involves the conversion of glycine to serine with the release of ammonia and CO(2). In C(3) terrestrial higher plants the flux through glycine and serine is so large that it results in the production of ammonia at a rate far exceeding that from reduction of new nitrogen entering the plant. The photorespiratory nitrogen cycle re-assimilates this ammonia using the enzymes glutamine synthetase and glutamine:2-oxoglutarateaminotransferase.

  4. Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce-Investigating the specific role of glutamine.

    PubMed

    Carlsson, Johanna; Svennerstam, Henrik; Moritz, Thomas; Egertsdotter, Ulrika; Ganeteg, Ulrika

    2017-01-01

    Somatic embryogenesis is an in vitro system employed for plant propagation and the study of embryo development. Nitrogen is essential for plant growth and development and, hence, the production of healthy embryos during somatic embryogenesis. Glutamine has been shown to increase plant biomass in many in vitro applications, including somatic embryogenesis. However, several aspects of nitrogen nutrition during somatic embryogenesis remain unclear. Therefore, we investigated the uptake and assimilation of nitrogen in Norway spruce pro-embryogenic masses to elucidate some of these aspects. In our study, addition of glutamine had a more positive effect on growth than inorganic nitrogen. The nitrogen uptake appeared to be regulated, with a strong preference for glutamine; 67% of the assimilated nitrogen in the free amino acid pool originated from glutamine-nitrogen. Glutamine addition also relieved the apparently limited metabolism (as evidenced by the low concentration of free amino acids) of pro-embryogenic masses grown on inorganic nitrogen only. The unusually high alanine concentration in the presence of glutamine, suggests that alanine biosynthesis was involved in alleviating these constraints. These findings inspire further studies of nitrogen nutrition during the somatic embryogenesis process; identifying the mechanism(s) that govern glutamine enhancement of pro-embryogenic masses growth is especially important in this regard.

  5. Implications of nitrogen phloem loading for carbon metabolism and transport during Arabidopsis development.

    PubMed

    Santiago, James P; Tegeder, Mechthild

    2017-03-14

    Metabolite transport processes and primary metabolism are highly interconnected. This study examined the importance of source-to-sink nitrogen partitioning, and associated nitrogen metabolism, for carbon capture, transport and usage. Specifically, Arabidopsis aap8 (AMINO ACID PERMEASE 8) mutant lines were analyzed to resolve the consequences of reduced amino acid phloem loading for source leaf carbon metabolism, sucrose phloem transport and sink development during vegetative and reproductive growth phase. Results showed that decreased amino acid transport had a negative effect on sink development of aap8 lines throughout the life cycle leading to an overall decrease in plant biomass. During vegetative stage, photosynthesis and carbohydrate levels were decreased in aap8 leaves, while expression of carbon metabolism and transport genes, as well as sucrose phloem transport were not affected despite reduced sink strength. However, when aap8 plants transitioned to reproductive phase, carbon fixation and assimilation as well as sucrose partitioning to siliques were strongly decreased. Overall, this work demonstrates that phloem loading of nitrogen has varying implication for carbon fixation, assimilation and source-to-sink allocation depending on plant growth stage. It further suggests alterations in source-sink relationships, and regulation of carbon metabolism and transport by sink strength in a development-dependent manner.

  6. Seed priming improves chilling tolerance in chickpea by modulating germination metabolism, trehalose accumulation and carbon assimilation.

    PubMed

    Farooq, Muhammad; Hussain, Mubshar; Nawaz, Ahmad; Lee, Dong-Jin; Alghamdi, Salem S; Siddique, Kadambot H M

    2017-02-01

    Chilling stress is one of the major abiotic stresses affecting chickpea productivity worldwide. This study evaluated the potential role of seed priming in improving resistance to chilling stress in chickpea (cv. Punjab, 2008). The priming treatments involved soaking seeds of chickpea cultivar Punjab 2008 in either water for 8 h (on-farm priming), aerated water (hydropriming) for 18 h, or CaCl2 solution (ψs -1.25 MPa; osmopriming) for 18 h. Primed and untreated seeds were grown either at 18/15 °C (control) or 13/10 °C (chilling stress). Chilling stress suppressed the growth of chickpea while seed priming mitigated the adverse effects of chilling stress by improving stand establishment, growth, water relations, photosynthesis, α-amylase activity, sugar metabolism, antioxidant enzyme activity, membrane stability, and leaf accumulation of proline, nitrogen, potassium and soluble phenolics. Seed priming also improved the performance of chickpea under optimal (control) conditions. The overall order of improvement in resistance to chilling by using seed priming was osmopriming > hydropriming > on-farm priming. Osmopriming improved seedling dry weight, specific leaf area, leaf CO2 net assimilation rate, maximal photochemical efficiency of PSII, α-amylase activity, trehalose content and leaf relative water content by 10, 22, 17, 20, 73, 48 and 7%, respectively, relative to the non-primed control under chilling stress. Under optimal temperature conditions, the corresponding values were 30, 32, 16, 10, 83, 75 and 5%, respectively. Sugar metabolism, especially trehalose content, was strongly linked with stand establishment, photosynthesis, antioxidant potential (under chilling stress) and plant biomass. Overall, seed priming improved chickpea performance under both optimal temperature conditions and chilling stress through better germination metabolism and the accumulation of trehalose, which protected from oxidative damage and helped to maintain carbon

  7. Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests

    Treesearch

    Fabien H. Wagner; Bruno Herault; Damien Bonal; Clement Stahl; Liana O. Anderson; Timothy R. Baker; Gabriel Sebastian Becker; Hans Beeckman; Danilo Boanerges Souza; Paulo Cesar Botosso; David M. J. S. Bowman; Achim Brauning; Benjamin Brede; Foster Irving Brown; Jesus Julio Camarero; Plinio Barbosa Camargo; Fernanda C. G. Cardoso; Fabricio Alvim Carvalho; Wendeson Castro; Rubens Koloski Chagas; Jerome Chave; Emmanuel N. Chidumayo; Deborah A. Clark; Flavia Regina Capellotto Costa; Camille Couralet; Paulo Henrique da Silva Mauricio; Helmut Dalitz; Vinicius Resende de Castro; Jacanan Eloisa de Freitas Milani; Edilson Consuelo de Oliveira; Luciano de Souza Arruda; Jean-Louis Devineau; David M. Drew; Oliver Dunisch; Giselda Durigan; Elisha Elifuraha; Marcio Fedele; Ligia Ferreira Fedele; Afonso Figueiredo Filho; Cesar Augusto Guimaraes Finger; Augusto Cesar Franco; Joao Lima Freitas Junior; Franklin Galvao; Aster Gebrekirstos; Robert Gliniars; Paulo Mauricio Lima de Alencastro Graca; Anthony D. Griffiths; James Grogan; Kaiyu Guan; Jurgen Homeier; Maria Raquel Kanieski; Lip Khoon Kho; Jennifer Koenig; Sintia Valerio Kohler; Julia Krepkowski; Jose Pires Lemos-Filho; Diana Lieberman; Milton Eugene Lieberman; Claudio Sergio Lisi; Tomaz Longhi Santos; Jose Luis Lopez Ayala; Eduardo Eijji Maeda; Yadvinder Malhi; Vivian R. B. Maria; Marcia C. M. Marques; Renato Marques; Hector Maza Chamba; Lawrence Mbwambo; Karina Liana Lisboa Melgaco; Hooz Angela Mendivelso; Brett P. Murphy; Joseph O' Brien; Steven F. Oberbauer; Naoki Okada; Raphael Pelissier; Lynda D. Prior; Fidel Alejandro Roig; Michael Ross; Davi Rodrigo Rossatto; Vivien Rossi; Lucy Rowland; Ervan Rutishauser; Hellen Santana; Mark Schulze; Diogo Selhorst; Williamar Rodrigues Silva; Marcos Silveira; Susanne Spannl; Michael D. Swaine; Jose Julio Toledo; Marcos Miranda Toledo; Marisol Toledo; Takeshi Toma; Mario Tomazello Filho; Juan Ignacio Valdez Hernandez; Jan Verbesselt; Simone Aparecida Vieira; Gregoire Vincent; Carolina Volkmer de Castilho; Franziska Volland; Martin Worbes; Magda Lea Bolzan Zanon; Luiz E. O. C. Aragao

    2016-01-01

    The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter...

  8. Carbon consequences of a nitrogen fixation feedback

    NASA Astrophysics Data System (ADS)

    Levy, J.; Medvigy, D.; Hedin, L.; Batterman, S. A.; Xu, X.

    2014-12-01

    Tropical forests constitute a globally important carbon sink but it is unclear how their productivity and carbon storage depend upon nutrients. There is increasing evidence of an ecosystem carbon-nitrogen feedback mechanism, by which symbiotic dinitrogen (N2) fixing trees can provide the nitrogen needed to maintain high rates of forest biomass growth following disturbance. Field-based evaluation of this feedback is difficult, however, as the expected effects on forest carbon stores would emerge very slowly, over decades to centuries of ecological succession. Moreover, there is no known way to inhibit the fixation process in trees without causing structural damage and perturbing the carbon cycle. Coupled land biogeochemistry-vegetation models offer a way to examine the role of feedbacks that unfold over successional time. However, it is unclear how the process of nitrogen fixation ought to be represented in models so that they can capture the potential effect of fixation on the long-term forest carbon sink. In this study, we integrate a newly developed individual-based model with field observations across Panamanian tropical forests to address: 1) whether N2 fixation enhances tropical forest carbon storage; 2) whether models must resolve fixation at the individual plant level to capture the fixation feedback; and 3) whether fixation interacts with plant functional types (i.e., early, mid, vs. late succession) to determine the carbon sink? We find that forests that have fixation recover faster and store more carbon in the long term than forests without fixation. This results in 94-118% more plant carbon stored by 30 years and an additional 13 tons C ha -1 stored over 300 years when compared to forests without fixation. Additionally, resolving fixation at the individual plant level is necessary to capture nitrogen dynamics over time and is particularly important for modeling succession and disturbance events. Finally, we find that the overall fixation effect is the

  9. Combined acid rain and lanthanum pollution and its potential ecological risk for nitrogen assimilation in soybean seedling roots.

    PubMed

    Zhang, Fan; Cheng, Mengzhu; Sun, Zhaoguo; Wang, Lihong; Zhou, Qing; Huang, Xiaohua

    2017-08-22

    Rare earth elements (REEs) are used in various fields, resulting in their accumulation in the environment. This accumulation has affected the survival and distribution of crops in various ways. Acid rain is a serious global environmental problem. The combined effects on crops from these two types of pollution have been reported, but the effects on crop root nitrogen assimilation are rarely known. To explore the impact of combined contamination from these two pollutants on crop nitrogen assimilation, the soybean seedlings were treated with simulated environmental pollution from acid rain and a representative rare earth ion, lanthanum ion (La(3+)), then the indexes related to plant nitrogen assimilation process in roots were determined. The results showed that combined treatment with pH 4.5 acid rain and 0.08 mM La(3+) promoted nitrogen assimilation synergistically, while the other combined treatments all showed inhibitory effects. Moreover, acid rain aggravated the inhibitory effect of 1.20 or 0.40 mM La(3+) on nitrogen assimilation in soybean seedling roots. Thus, the effects of acid rain and La(3+) on crops depended on the combination levels of acid rain intensity and La(3+) concentration. Acid rain increases the bioavailability of La(3+), and the combined effects of these two pollutants were more serious than that of either pollutant alone. These results provide new evidence in favor of limiting overuse of REEs in agriculture. This work also provides a new framework for ecological risk assessment of combined acid rain and REEs pollution on soybean crops. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Effects of available nitrogen on the uptake and assimilation of ferrocyanide and ferricyanide complexes in weeping willows.

    PubMed

    Yu, Xiao-Zhang; Gu, Ji-Dong

    2008-08-15

    The effects of different levels of external nitrogen on the uptake, distribution and assimilation of iron cyanide complexes were investigated. Pre-rooted weeping willows (Salix babylonica L.) were grown in a hydroponic solution with or without nitrogen and amended with potassium ferrocyanide or potassium ferricyanide at 25.0 +/- 0.5 degrees C for 144 h. Faster uptake of ferrocyanide than ferricyanide was observed in willows grown in the deionized water. Negligible difference in the removal rate between the two chemicals was detected for willows grown in nutrient solutions with or without amendment of nitrogen. The volatilization of ferro- and ferricyanide due to transpiration through plant aerial tissues was below detection level. Less then 20% of the ferrocyanide or ferricyanide taken up from the N-free nutrient solution was recovered in the biomass and majority was accumulated in the roots. In contrast, less than 9.0% of both iron cyanide complexes taken up was detected in the plant materials of willows grown in the N-containing nutrient solution and roots were the major sites for accumulation of both chemicals. A large fraction of the ferro- and ferricyanide taken up from the hydroponic solution was assimilated during the transport within plant materials. Willows grown in the N-containing nutrient solution showed a higher assimilation potential for both chemical forms than those grown in the N-free nutrient solution in general. The information collectively suggests that uptake and assimilation mechanisms for ferro- and ferricyanide are largely different in willows; the strength of external nitrogen had a negligible effect on the uptake of both chemicals, while assimilation of ferro- and ferricyanide in plant materials was strongly related to the presence of easily available nitrogen in the hydroponic solution.

  11. [Regulation of alkaline exoprotease and cephalosporin C synthesis in Acremonium chrysogenum by different carbon and nitrogen sources].

    PubMed

    Shuvalova, I A; Bartoshevich, Iu E

    1981-03-01

    The synthesis of exoproteases and cephalosporin C in Acremonium chrysogenum is repressed by easily assimilated forms of nitrogen and carbon according to the type of nitrogen metabolism repression and catabolism inhibition. Glucose and ammonium salts inhibited the mycelium fragmentation and prevented formation of conidia. Amino acids had a diverse effect on the synthesis of the proteases and antibiotic. Methionine played the role of an inductor of the synthesis of alkaline exoproteases, cephalosporin C and the mycelium fragmentation into arthrospores.

  12. Acrylonitrile, an advantageous precursor to synthesize nitrogen doped carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Aguilar-Elguézabal, A.; Román-Aguirre, M.; De la Torre, L.; Zaragoza, E. A.

    2017-05-01

    The nitrogen doped carbon nanotubes present specific characteristics that offer better performance than pure carbon nanotubes for application like biomedicine, hydrogen adsorption and electrocataytic devices. This work present a simple method to obtain well-aligned nitrogen doped multi wall carbon nanotubes, which present open channels with diameter around 50 nm. These carbon nanotubes are obtained using acrylonitrile as carbon and nitrogen source, which offers some advantages on the use of other precursors like ammonia, pyridine, benzylamine, acetonitrile or melamine.

  13. Does Ocean Color Data Assimilation Improve Estimates of Global Ocean Inorganic Carbon?

    NASA Technical Reports Server (NTRS)

    Gregg, Watson

    2012-01-01

    Ocean color data assimilation has been shown to dramatically improve chlorophyll abundances and distributions globally and regionally in the oceans. Chlorophyll is a proxy for phytoplankton biomass (which is explicitly defined in a model), and is related to the inorganic carbon cycle through the interactions of the organic carbon (particulate and dissolved) and through primary production where inorganic carbon is directly taken out of the system. Does ocean color data assimilation, whose effects on estimates of chlorophyll are demonstrable, trickle through the simulated ocean carbon system to produce improved estimates of inorganic carbon? Our emphasis here is dissolved inorganic carbon, pC02, and the air-sea flux. We use a sequential data assimilation method that assimilates chlorophyll directly and indirectly changes nutrient concentrations in a multi-variate approach. The results are decidedly mixed. Dissolved organic carbon estimates from the assimilation model are not meaningfully different from free-run, or unassimilated results, and comparisons with in situ data are similar. pC02 estimates are generally worse after data assimilation, with global estimates diverging 6.4% from in situ data, while free-run estimates are only 4.7% higher. Basin correlations are, however, slightly improved: r increase from 0.78 to 0.79, and slope closer to unity at 0.94 compared to 0.86. In contrast, air-sea flux of C02 is noticeably improved after data assimilation. Global differences decline from -0.635 mol/m2/y (stronger model sink from the atmosphere) to -0.202 mol/m2/y. Basin correlations are slightly improved from r=O.77 to r=0.78, with slope closer to unity (from 0.93 to 0.99). The Equatorial Atlantic appears as a slight sink in the free-run, but is correctly represented as a moderate source in the assimilation model. However, the assimilation model shows the Antarctic to be a source, rather than a modest sink and the North Indian basin is represented incorrectly as a sink

  14. Integration of Carbon, Nitrogen, and Oxygen Metabolism in Escherichia coli

    DTIC Science & Technology

    2012-10-22

    environmental fluctuations. As growth can be limited by the scarcity of any one nutrient, the rate at which each nutrient is assimilated must be...multiple nutrient systems. We discovered that the carbonaceous substrate of nitrogen assimilation , α-ketoglutarate, directly inhibits glucose uptake and...at which each nutrient is  assimilated  must be sensitive not only to  its own availability, but also to that of other nutrients. Remarkably, across

  15. Effect of carbon and nitrogen on the cannibalistic behavior of Bacillus subtilis.

    PubMed

    Nandy, Subir Kumar; Venkatesh, K V

    2008-12-01

    Bacillus subtilis is known to exhibit cannibalism under nutrient limitation to delay sporulation. Cells of B. subtilis in phosphate buffer solution (PBS) demonstrate an oscillatory behavior in cell number due to cannibalism. Since PBS did not contain any nutrients, the effect of carbon and nitrogen sources on the cannibalistic behavior is unclear. In this study, the effect of external carbon and nitrogen on the cannibalistic behavior of B. subtilis is presented. The studies demonstrated that when glucose as a carbon source was introduced into PBS in the absence of any other nutrients, the cannibalistic tendency was delayed. This delay increased with the increase in the amount of glucose present in the PBS. Thus, the cannibalism was observed to be very sensitive to the amount of carbon present in the medium. However, when the medium contained only ammonium sulfate as a nitrogen source and was devoid of any carbon, the effect on cannibalism was minimal. The study, therefore, demonstrated that cannibalism was more sensitive to carbon than nitrogen indicating that the phenomenon of cannibalism may be more dependent on the status of energy in the medium than on nitrogen assimilation.

  16. Temporary storage or permanent removal? The division of nitrogen between biotic assimilation and denitrification in stormwater biofiltration systems.

    PubMed

    Payne, Emily G I; Fletcher, Tim D; Russell, Douglas G; Grace, Michael R; Cavagnaro, Timothy R; Evrard, Victor; Deletic, Ana; Hatt, Belinda E; Cook, Perran L M

    2014-01-01

    The long-term efficacy of stormwater treatment systems requires continuous pollutant removal without substantial re-release. Hence, the division of incoming pollutants between temporary and permanent removal pathways is fundamental. This is pertinent to nitrogen, a critical water body pollutant, which on a broad level may be assimilated by plants or microbes and temporarily stored, or transformed by bacteria to gaseous forms and permanently lost via denitrification. Biofiltration systems have demonstrated effective removal of nitrogen from urban stormwater runoff, but to date studies have been limited to a 'black-box' approach. The lack of understanding on internal nitrogen processes constrains future design and threatens the reliability of long-term system performance. While nitrogen processes have been thoroughly studied in other environments, including wastewater treatment wetlands, biofiltration systems differ fundamentally in design and the composition and hydrology of stormwater inflows, with intermittent inundation and prolonged dry periods. Two mesocosm experiments were conducted to investigate biofilter nitrogen processes using the stable isotope tracer 15NO3(-) (nitrate) over the course of one inflow event. The immediate partitioning of 15NO3(-) between biotic assimilation and denitrification were investigated for a range of different inflow concentrations and plant species. Assimilation was the primary fate for NO3(-) under typical stormwater concentrations (∼1-2 mg N/L), contributing an average 89-99% of 15NO3(-) processing in biofilter columns containing the most effective plant species, while only 0-3% was denitrified and 0-8% remained in the pore water. Denitrification played a greater role for columns containing less effective species, processing up to 8% of 15NO3(-), and increased further with nitrate loading. This study uniquely applied isotope tracing to biofiltration systems and revealed the dominance of assimilation in stormwater biofilters

  17. Effects of nitrogen form on growth, CO2 assimilation, chlorophyll fluorescence, and photosynthetic electron allocation in cucumber and rice plants*

    PubMed Central

    Zhou, Yan-hong; Zhang, Yi-li; Wang, Xue-min; Cui, Jin-xia; Xia, Xiao-jian; Shi, Kai; Yu, Jing-quan

    2011-01-01

    Cucumber and rice plants with varying ammonium (NH4 +) sensitivities were used to examine the effects of different nitrogen (N) sources on gas exchange, chlorophyll (Chl) fluorescence quenching, and photosynthetic electron allocation. Compared to nitrate (NO3 −)-grown plants, cucumber plants grown under NH4 +-nutrition showed decreased plant growth, net photosynthetic rate, stomatal conductance, intercellular carbon dioxide (CO2) level, transpiration rate, maximum photochemical efficiency of photosystem II, and O2-independent alternative electron flux, and increased O2-dependent alternative electron flux. However, the N source had little effect on gas exchange, Chl a fluorescence parameters, and photosynthetic electron allocation in rice plants, except that NH4 +-grown plants had a higher O2-independent alternative electron flux than NO3 −-grown plants. NO3 − reduction activity was rarely detected in leaves of NH4 +-grown cucumber plants, but was high in NH4 +-grown rice plants. These results demonstrate that significant amounts of photosynthetic electron transport were coupled to NO3 − assimilation, an effect more significant in NO3 −-grown plants than in NH4 +-grown plants. Meanwhile, NH4 +-tolerant plants exhibited a higher demand for the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) for NO3 − reduction, regardless of the N form supplied, while NH4 +-sensitive plants had a high water-water cycle activity when NH4 + was supplied as the sole N source. PMID:21265044

  18. Effects of nitrogen form on growth, CO₂ assimilation, chlorophyll fluorescence, and photosynthetic electron allocation in cucumber and rice plants.

    PubMed

    Zhou, Yan-hong; Zhang, Yi-li; Wang, Xue-min; Cui, Jin-xia; Xia, Xiao-jian; Shi, Kai; Yu, Jing-quan

    2011-02-01

    Cucumber and rice plants with varying ammonium (NH(4)(+)) sensitivities were used to examine the effects of different nitrogen (N) sources on gas exchange, chlorophyll (Chl) fluorescence quenching, and photosynthetic electron allocation. Compared to nitrate (NO(3)(-))-grown plants, cucumber plants grown under NH(4)(+)-nutrition showed decreased plant growth, net photosynthetic rate, stomatal conductance, intercellular carbon dioxide (CO(2)) level, transpiration rate, maximum photochemical efficiency of photosystem II, and O(2)-independent alternative electron flux, and increased O(2)-dependent alternative electron flux. However, the N source had little effect on gas exchange, Chl a fluorescence parameters, and photosynthetic electron allocation in rice plants, except that NH(4)(+)-grown plants had a higher O(2)-independent alternative electron flux than NO(3)(-)-grown plants. NO(3)(-) reduction activity was rarely detected in leaves of NH(4)(+)-grown cucumber plants, but was high in NH(4)(+)-grown rice plants. These results demonstrate that significant amounts of photosynthetic electron transport were coupled to NO(3)(-) assimilation, an effect more significant in NO(3)(-)-grown plants than in NH(4)(+)-grown plants. Meanwhile, NH(4)(+)-tolerant plants exhibited a higher demand for the reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) for NO(3)(-) reduction, regardless of the N form supplied, while NH(4)(+)-sensitive plants had a high water-water cycle activity when NH(4)(+) was supplied as the sole N source.

  19. Improving the Modelled Global Terrestrial Carbon Cycle by Assimilating CO2 Mole Fractions and FAPAR with the MPI Carbon Cycle Data Assimilation System (MPI-CCDAS)

    NASA Astrophysics Data System (ADS)

    Schürmann, Gregor; Köstler, Christoph; Kaminski, Thomas; Giering, Ralf; Scholze, Marko; Kattge, Jens; Carvalhais, Nuno; Voßbeck, Michael; Rödenbeck, Christian; Reick, Christian; Zaehle, Sönke

    2015-04-01

    Long-term monitoring of ecosystem carbon fluxes and atmospheric CO2 concentrations provides independent observations of the land's carbon balance at different scales. However, the scale-gap between these observations makes a direct quantification of regional carbon balances based on these data impossible. Here, we describe first results of the MPI Carbon Cycle Data Assimilation System (MPI-CCDAS), designed to use multiple data streams at different scales to constrain parameters in the biosphere model JSBACH. We constrain the MPI-CCDAS with two complementary data-streams: CO2 mole fractions observed at a network of atmospheric monitoring stations, and remotely-sensed fraction of absorbed photosynthetically active radiation (TIP-FAPAR). The assimilation procedure greatly improves the representation of the seasonal cycle of atmospheric CO2, and reduces the global gross primary productivity (GPP) from 160 PgC/year to 118 PgC/year. Applying the MPI-CCDAS separately and jointly on both data streams allows to analyse the contribution of each data stream to the improved global carbon cycle model. Evaluation against independent carbon cycle estimates based on upscaled ecosystem flux measurements corroborates the adequacy of the model improvements, and demonstrates the utility of the CCDAS framework in consistently integrating carbon cycle data.

  20. Soil Carbon and Nitrogen Cycle Modeling

    NASA Astrophysics Data System (ADS)

    Woo, D.; Chaoka, S.; Kumar, P.; Quijano, J. C.

    2012-12-01

    Second generation bioenergy crops, such as miscanthus (Miscantus × giganteus) and switchgrass (Panicum virgatum), are regarded as clean energy sources, and are an attractive option to mitigate the human-induced climate change. However, the global climate change and the expansion of perennial grass bioenergy crops have the power to alter the biogeochemical cycles in soil, especially, soil carbon storages, over long time scales. In order to develop a predictive understanding, this study develops a coupled hydrological-soil nutrient model to simulate soil carbon responses under different climate scenarios such as: (i) current weather condition, (ii) decreased precipitation by -15%, and (iii) increased temperature up to +3C for four different crops, namely miscanthus, switchgrass, maize, and natural prairie. We use Precision Agricultural Landscape Modeling System (PALMS), version 5.4.0, to capture biophysical and hydrological components coupled with a multilayer carbon and ¬nitrogen cycle model. We apply the model at daily time scale to the Energy Biosciences Institute study site, located in the University of Illinois Research Farms, in Urbana, Illinois. The atmospheric forcing used to run the model was generated stochastically from parameters obtained using available data recorded in Bondville Ameriflux Site. The model simulations are validated with observations of drainage and nitrate and ammonium concentrations recorded in drain tiles during 2011. The results of this study show (1) total soil carbon storage of miscanthus accumulates most noticeably due to the significant amount of aboveground plant carbon, and a relatively high carbon to nitrogen ratio and lignin content, which reduce the litter decomposition rate. Also, (2) the decreased precipitation contributes to the enhancement of total soil carbon storage and soil nitrogen concentration because of the reduced microbial biomass pool. However, (3) an opposite effect on the cycle is introduced by the increased

  1. Radiochemistry of carbon, nitrogen and oxygen

    SciTech Connect

    Sajjad, M.; Lambrecht, R.M.

    1988-01-01

    The present monograph consists of two reviews. The first section deals with radiopharmaceutical and biomedical applications. The second section deals with analysis of carbon, nitrogen and oxygen in different materials by use of nuclear techniques. This monograph is published as part of our continuing effort to update, revise, and expand the previously published monographs to keep them current and relevant. 158 refs., 4 figs., 12 tabs.

  2. Leaf carbon assimilation and molecular phylogeny in Cattleya species (Orchidaceae).

    PubMed

    Andrade-Souza, V; Almeida, A-A F; Corrêa, R X; Costa, M A; Mielke, M S; Gomes, F P

    2009-08-11

    We examined leaf CO(2) assimilation and how it varied among species within the orchid genus Cattleya. Measurements of CO(2) assimilation and maximum quantum yield of PS II (Fv/Fm) were made for mature leaves of nine species using a portable system for photosynthesis measurement and a portable fluorometer. Leaf area was measured with an area meter, and the specific leaf mass was determined. DNA of nine Cattleya species and two species of Hadrolaelia was extracted using the CTAB protocol. Each sample was amplified and sequenced using primers for the trnL gene. The phylogenetic analyses, using neighbor-joining and maximum parsimony methods, retrieved a group that included Cattleya and Hadrolaelia species, in which the unifoliate species were separated from the bifoliates. The topologies of the two cladograms showed some similarities. However, C. guttata (bifoliate) was placed in the unifoliate clade in the neighbor-joining tree, while C. warneri (unifoliate) was not placed in this clade in the maximum parsimony tree. Most Cattleya species keep the leaf stomata closed from 6 am to 4 pm. We suggest that C. elongata, C. tigrina and C. tenuis have C(3)-crassulacean acid metabolism since they open their stomata around 12 am. The Fv/Fm values remained relatively constant during the measurements of CO(2) assimilation. The same was observed for the specific leaf mass values, although great variations were found in the leaf area values. When the species were grouped using molecular data in the neighbor-joining analysis, no relation was observed with CO(2) assimilation.

  3. Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone

    PubMed Central

    Astorga-Eló, Marcia; Ramírez-Flandes, Salvador; DeLong, Edward F; Ulloa, Osvaldo

    2015-01-01

    Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus. PMID:25700337

  4. Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone.

    PubMed

    Astorga-Eló, Marcia; Ramírez-Flandes, Salvador; DeLong, Edward F; Ulloa, Osvaldo

    2015-05-01

    Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus.

  5. Nonsteady state carbon sequestration in forest ecosystems of China estimated by data assimilation

    NASA Astrophysics Data System (ADS)

    Zhou, Tao; Shi, Peijun; Jia, Gensuo; Luo, Yiqi

    2013-12-01

    sequestration occurs only when terrestrial ecosystems are at nonsteady states. Despite of their ubiquity in the real world, the nonsteady states of ecosystems have not been well quantified, especially at regional and global scales. In this study, we developed a two-step data assimilation scheme to estimate carbon sink strength in China's forest ecosystems. Specifically, the two-step scheme consists of a steady state step and a nonsteady state step. In the steady state step, we constrained a process-based model (Terrestrial Ecosystem Regional (TECO-R) model) against biometric data (net primary production NPP, biomass, litter, and soil organic carbon) in mature forests. With a subset of the parameter values estimated from the steady state data assimilation being fixed, the nonsteady state data assimilation was performed to estimate carbon sequestration in China's forest ecosystems. Our results indicated that 17 out of the 22 total parameters in the TECO-R model were well constrained by the biometric data with the steady state data assimilation. When observations from both mature and developing forests were used, all the 10 parameters related to carbon sequestration in vegetation and soil carbon pools were well constrained at the nonsteady state step. The estimated mean vegetation carbon sink in China's forests is 89.7 ± 16.8 gC m-2 yr-1, comparable with the values estimated from the forest inventory and other process-based regional models. The estimated mean soil and litter carbon sinks in China's forests are 14.1 ± 20.7 and 4.7 ± 6.5 gC m-2 yr-1. This study demonstrated that a two-step data assimilation scheme can be a potent tool to estimate regional carbon sequestration in nonsteady state ecosystems.

  6. Carbon and nitrogen in ALH 84001

    NASA Astrophysics Data System (ADS)

    Grady, M. M.; Wright, I. P.; Douglas, C.; Pillinger, C. T.

    1994-07-01

    Reclassification of ALH 84001 as an orthopyroxenite related to SNCs brings the total number of martian meteorites to 10. Preliminary descriptions of ALH 84001 and the more detailed analysis that followed highlighted the presence of abundant Fe, Mg-carbonates distributed heterogeneously throughout the specimen. Previous studies of SNCs identified four discrete carbon-bearing components: materials that combusted at temperatures usually associated with organics, carbonates, magmatic carbon, and trapped martian atmospheric carbon dioxide. The isotopic compositions of these species are distinctive, and have been used to constrain the operation of martian surficial processes. Given the relatively high carbonate abundance in ALH 84001, detailed isotopic analyses of the specimen will undoubtedly provide further information on the formation mechanisms of these minerals. Nitrogen analysis could identify the presence of any N-bearing salts and trapped atmospheric species. This abstract reports the first results from analysis of carbon in ALH 84001. A high-resolution stepped combustion of 5.099 mg of powdered ALH 84001 was performed. The most outstanding feature of the analysis was the release of almost 50% of the total C across a narrow temperature range from 450-525 C, with (delta)C-13 is approximately +40%. The enrichment C-13 in carbonates from ALH 84001 indicates beyond any doubt that these salts are truly indigenous to the meteorite, rather than an Antarctic weathering product. Wright et al. defined a linear relationship between yield and C isotopic composition of carbonate in SNCs; the datum from ALH 84001 extends this association. For the carbonate to be formed by interaction of martian atmospheric CO2 with regolith material, reaction would need to have occurred at temperatures around 100 C. Such a high temperature is unlikely on the martian surface, and therefore the carbonates more probably formed in a hydrothermal environment.

  7. Integration of Carbon, Nitrogen, and Oxygen Metabolism in Escherichia coli--Final Report

    SciTech Connect

    Rabinowitz, Joshua D; Wingreen, Ned s; Rabitz, Herschel A; Xu, Yifan

    2012-10-22

    A key challenge for living systems is balancing utilization of multiple elemental nutrients, such as carbon, nitrogen, and oxygen, whose availability is subject to environmental fluctuations. As growth can be limited by the scarcity of any one nutrient, the rate at which each nutrient is assimilated must be sensitive not only to its own availability, but also to that of other nutrients. Remarkably, across diverse nutrient conditions, E. coli grows nearly optimally, balancing effectively the conversion of carbon into energy versus biomass. To investigate the link between the metabolism of different nutrients, we quantified metabolic responses to nutrient perturbations using LC-MS based metabolomics and built differential equation models that bridge multiple nutrient systems. We discovered that the carbonaceous substrate of nitrogen assimilation, -ketoglutarate, directly inhibits glucose uptake and that the upstream glycolytic metabolite, fructose-1,6-bisphosphate, ultrasensitively regulates anaplerosis to allow rapid adaptation to changing carbon availability. We also showed that NADH controls the metabolic response to changing oxygen levels. Our findings support a general mechanism for nutrient integration: limitation for a nutrient other than carbon leads to build-up of the most closely related product of carbon metabolism, which in turn feedback inhibits further carbon uptake.

  8. Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism.

    PubMed

    Pérez-Delgado, Carmen M; Moyano, Tomás C; García-Calderón, Margarita; Canales, Javier; Gutiérrez, Rodrigo A; Márquez, Antonio J; Betti, Marco

    2016-05-01

    Nitrogen is one of the most important nutrients for plants and, in natural soils, its availability is often a major limiting factor for plant growth. Here we examine the effect of different forms of nitrogen nutrition and of photorespiration on gene expression in the model legume Lotus japonicus with the aim of identifying regulatory candidate genes co-ordinating primary nitrogen assimilation and photorespiration. The transcriptomic changes produced by the use of different nitrogen sources in leaves of L. japonicus plants combined with the transcriptomic changes produced in the same tissue by different photorespiratory conditions were examined. The results obtained provide novel information on the possible role of plastidic glutamine synthetase in the response to different nitrogen sources and in the C/N balance of L. japonicus plants. The use of gene co-expression networks establishes a clear relationship between photorespiration and primary nitrogen assimilation and identifies possible transcription factors connected to the genes of both routes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  9. Cryogenic Adsorption of Nitrogen and Carbon Dioxide in Activated Carbon

    NASA Astrophysics Data System (ADS)

    Shen, Fuzhi; Liu, Huiming; Xu, Dong; Zhang, Hengcheng; Lu, Junfeng; Li, Laifeng

    2017-09-01

    Activated carbon have been used for a long time at low temperature for cryogenic applications. The knowledge of adsorption characteristics of activated carbon at cryogenic temperature is essential for some specific applications. However, such experimental data are very scare in the literature. In order to measure the adsorption characteristics of activated carbon under variable cryogenic temperatures, an adsorption measurement device was presented. The experiment system is based on the commercially available PCT-pro adsorption analyzer coupled to a two-stage Gifford McMahon refrigerator, which allows the sample to be cooled to 4.2K. Cryogenic environment can be maintained steadily without the cryogenic liquid through the cryocooler and temperature can be controlled precisely between 5K and 300K by the temperature controller. Adsorption measurements were performed in activated carbon for carbon dioxide and nitrogen and the adsorption isotherm were obtained.

  10. Nitrogen and Carbon Dynamics Across Trophic Levels Along an Atmospheric Nitrogen Deposition Gradient

    NASA Astrophysics Data System (ADS)

    Wissinger, B. D.; Bell, M. D.; Newingham, B. A.

    2011-12-01

    Atmospheric nitrogen deposition has altered soil biogeochemical processes and plant communities across the United States. Prior investigations have demonstrated these alterations; however, little is known about the effects of elevated nitrogen on higher trophic levels. Building upon previous research that revealed an atmospheric nitrogen deposition gradient from the San Bernardino Mountains through Joshua Tree National Park in California, we investigated atmospheric nitrogen and its effects on soils, plants, and harvester ants. We measured nitrogen and carbon concentrations, along with carbon and nitrogen stable isotopes, across trophic levels at eighteen urban and unpopulated sites along the deposition gradient. Carbon and nitrogen attributes were determined in atmospheric nitric acid, soil, Larrea tridentata and Ambrosia dumosa leaves, seeds from selected plant species, and ants. We predicted carbon and nitrogen ratios and isotopes to change in areas with higher nitrogen deposition and vary along the deposition gradient. Nitrogen (p=0.02) and carbon (p=0.05) concentrations, as well as C:N ratios (p=<0.001), significantly differed in Messor pergandei individuals among sites; however, no correlation was found between these carbon and nitrogen attributes and the nitrogen deposition gradient (%N r2=0.02, %C r2=0.007, C:N r2=0.02). The δ15N and δ13C values of the ants, leaf tissues, and seeds measured across the gradient follow similar patterns with r2 values all below 0.20. Our results suggest the current and previous rates of nitrogen deposition in this area are not enough to modify nitrogen and carbon concentrations and isotope values. Compensatory nitrogen cycling processes in the soil may reduce the effects of increased nitrogen on plants and thus higher trophic levels. Nitrogen and carbon dynamics across trophic levels might change after longer ecosystem exposure to elevated nitrogen; however, other abiotic and biotic factors are likely driving current

  11. Ruminal fermentation characteristics and microbial nitrogen assimilation in sheep fed differently composed grass silages.

    PubMed

    Seip, Katharina; Breves, Gerhard; Isselstein, Johannes; Daş, Gürbüz; Abel, Hansjörg

    2012-06-01

    The investigation aimed at examining if the composition of grassland silage affects the microbial nitrogen assimilation in the rumen of sheep. The silages were made of vegetative summer re-growths consisting of 48% grasses, 28% legumes and 24% other forbs (GCF) or of pure grass (G). Silage GCF contained more intermediately degradable non-structural and less slowly degradable carbohydrates, more crude protein (CP), a narrower ratio between slow and very slow degradable nitrogen (N), and exhibited higher in situ degradability of organic matter and CP than Silage G. Four adult wethers equipped with rumen fistulae were used in a two factorial trial. Feed was offered either as silage alone or as a mixture of silage and barley (60:40). Microbial N was estimated using continuous intraruminal 15N infusion and measurement of 15N-enrichment in microbes isolated from rumen liquor samples. With the exception of trends for ruminal butyrate concentrations, no interactions were detected between silage and barley feeding. Sheep receiving Silage GCF exhibited larger diurnal fluctuations of ammonia, and produced more microbial N (p < 0.05) than sheep on Silage G. Feeding the silages with barley decreased ruminal pH and elevated the concentrations of butyrate (p < 0.05). The 15N incorporation into microbial N was reduced by barley feeding (p < 0.05) along with a trend to accelerated rumen fluid turnover, resulting in similar microbial N yields as found in sheep receiving silage without barley. It is concluded that the larger and better balanced amounts of intermediately degradable carbohydrate- and N-containing fractions favoured the ruminal microbial protein synthesis in sheep consuming Silage GCF instead of Silage G.

  12. Metabolic plasticity of nitrogen assimilation by Porphyra umbilicalis (Linnaeus) Kützing

    NASA Astrophysics Data System (ADS)

    Kim, Jang K.; Kraemer, George P.; Yarish, Charles

    2012-12-01

    The physical stresses associated with emersion have long been considered major factors determining the vertical zonation of intertidal seaweeds. We examined Porphyra umbilicalis (Linnaeus) Kützing thalli from the vertical extremes in elevation of an intertidal population ( i.e. upper and lower intertidal zones) to determine whether Porphyra thalli acclimate to different vertical elevations on the shore with different patterns of nitrate uptake and nitrate reductase (NR) and glutamine synthetase (GS) activities in response to different degrees of emersion stress. We found that the nitrate uptake and NR recovery in the emersed tissues took longer in lower intertidal sub-population than in upper intertidal sub-population; and GS activity was also significantly affected by emersion and, interestingly, such an activity was enhanced by emersion of thalli from both upper and lower intertidal zones. These results suggested that intra-population variability in post-emersion recovery of physiological functions such as nutrient uptake and NR activity enables local adaptation and contributes to the wide vertical distribution of P. umbilicalis. The high GS activity during periodic emersion stress may be a protective mechanism enabling P. umbilicalis to assimilate nitrogen quickly when it again becomes available, and may also be an evidence of photorespiration during emersion.

  13. Mycobacterium tuberculosis Exploits Asparagine to Assimilate Nitrogen and Resist Acid Stress during Infection

    PubMed Central

    Gouzy, Alexandre; Larrouy-Maumus, Gérald; Bottai, Daria; Levillain, Florence; Dumas, Alexia; Wallach, Joshua B.; Caire-Brandli, Irène; de Chastellier, Chantal; Wu, Ting-Di; Poincloux, Renaud; Brosch, Roland; Guerquin-Kern, Jean-Luc; Schnappinger, Dirk; Sório de Carvalho, Luiz Pedro; Poquet, Yannick; Neyrolles, Olivier

    2014-01-01

    Mycobacterium tuberculosis is an intracellular pathogen. Within macrophages, M. tuberculosis thrives in a specialized membrane-bound vacuole, the phagosome, whose pH is slightly acidic, and where access to nutrients is limited. Understanding how the bacillus extracts and incorporates nutrients from its host may help develop novel strategies to combat tuberculosis. Here we show that M. tuberculosis employs the asparagine transporter AnsP2 and the secreted asparaginase AnsA to assimilate nitrogen and resist acid stress through asparagine hydrolysis and ammonia release. While the role of AnsP2 is partially spared by yet to be identified transporter(s), that of AnsA is crucial in both phagosome acidification arrest and intracellular replication, as an M. tuberculosis mutant lacking this asparaginase is ultimately attenuated in macrophages and in mice. Our study provides yet another example of the intimate link between physiology and virulence in the tubercle bacillus, and identifies a novel pathway to be targeted for therapeutic purposes. PMID:24586151

  14. Influence of shade on the growth and nitrogen assimilation of developing fruits on bell pepper

    SciTech Connect

    Achhireddy, N.R.; Fletcher, J.S.; Beevers, L.

    1982-08-01

    Accumulation of dry mass, total N, protein N, and soluble amino acid N in the developing fruit and seeds of bell pepper (Capsicum annuum L.) was determined at selected intervals following anthesis. The importance of photosynthesis to the growth and nitrogen (N) assimilation in the developing fruit wall plus placenta (FWP) and seeds was evaluated by comparing the growth and accumulation of reduced N in nonphotosynthetic and photosynthetic fruits (covered vs. uncovered). The growth rate of the FWP and seeds was similar under both conditions. After 65 days of growth, the fruits kept in the dark weighed about 15% less than those receiving illumination; seed weight was the same for both treatments. Total N content of the FWP or seed continued to increase up to 55 days after anthesis. The FWP accumulated over 90% of fruit's total N, and there were no significant differences between covered and uncovered fruits. Protein N accounted for about 50% of the total N present in both covered and uncovered fruits. 15 references, 2 figures, 2 tables.

  15. Effect of yeast assimilable nitrogen on the synthesis of phenolic aroma compounds by Hanseniaspora vineae strains.

    PubMed

    Martin, Valentina; Boido, Eduardo; Giorello, Facundo; Mas, Albert; Dellacassa, Eduardo; Carrau, Francisco

    2016-07-01

    In several grape varieties, the dominating aryl alkyl alcohols found are the volatile group of phenylpropanoid-related compounds, such as glycosylated benzyl and 2-phenylethyl alcohol, which contribute to wine with floral and fruity aromas after being hydrolysed during fermentation. Saccharomyces cerevisiae is largely recognized as the main agent in grape must fermentation, but yeast strains belonging to other genera, including Hanseniaspora, are known to predominate during the first stages of alcoholic fermentation. Although non-Saccharomyces yeast strains have a well-recognized genetic diversity, understanding of their impact on wine flavour richness is still emerging. In this study, 11 Hansenisapora vineae strains were used to ferment a chemically defined simil-grape fermentation medium, resembling the nutrient composition of grape juice but devoid of grape-derived secondary metabolites. GC-MS analysis was performed to determine volatile compounds in the produced wines. Our results showed that benzyl alcohol, benzyl acetate and 2-phenylethyl acetate are significantly synthesized by H. vineae strains. Levels of these compounds found in fermentations with 11 H. vineae different strains were one or two orders of magnitude higher than those measured in fermentations with a known S. cerevisiae wine strain. The implications for winemaking in response to the negative correlation of benzyl alcohol, benzyl acetate and 2-phenylethyl acetate production with yeast assimilable nitrogen concentrations are discussed. Copyright © 2016 John Wiley & Sons, Ltd.

  16. Chemical Data Assimilation Estimates of Continental US Ozone and Nitrogen Budgets during INTEX-A

    NASA Technical Reports Server (NTRS)

    Pierce, Robert B.; Schaack, Todd K.; Al-Saadi, Jassim A.; Fairlie, T. Duncan; Kittaka, Chieko; Lingenfelser, Gretchen; Natarajan, Murali; Olson, Jennifer; Soja, Amber; Zapotocny, Tom; hide

    2007-01-01

    Global ozone analyses, based on assimilation of stratospheric profile and ozone column measurements, and NOy predictions from the Real-time Air Quality Modeling System (RAQMS) are used to estimate the ozone and NOy budget over the Continental US during the July-August 2004 Intercontinental Chemical Transport Experiment-North America (INTEX-A). Comparison with aircraft, satellite, surface, and ozonesonde measurements collected during the INTEX-A show that RAQMS captures the main features of the global and Continental US distribution of tropospheric ozone, carbon monoxide, and NOy with reasonable fidelity. Assimilation of stratospheric profile and column ozone measurements is shown to have a positive impact on the RAQMS upper tropospheric/lower stratosphere ozone analyses, particularly during the period when SAGE III limb scattering measurements were available. Eulerian ozone and NOy budgets during INTEX-A show that the majority of the Continental US export occurs in the upper troposphere/lower stratosphere poleward of the tropopause break, a consequence of convergence of tropospheric and stratospheric air in this region. Continental US photochemically produced ozone was found to be a minor component of the total ozone export, which was dominated by stratospheric ozone during INTEX-A. The unusually low photochemical ozone export is attributed to anomalously cold surface temperatures during the latter half of the INTEX-A mission, which resulted in net ozone loss during the first 2 weeks of August. Eulerian NOy budgets are shown to be very consistent with previously published estimates. The NOy export efficiency was estimated to be 24 percent, with NOx+PAN accounting for 54 percent of the total NOy export during INTEX-A.

  17. Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth System Models

    SciTech Connect

    Xu, Xiaofeng; Schimel, Joshua; Thornton, Peter E; Song, Xia; Yuan, Fengming; Goswami, Santonu

    2014-01-01

    Microbial assimilation of soil organic carbon is one of the fundamental processes of global carbon cycling and it determines the magnitude of microbial biomass in soils. Mechanistic understanding of microbial assimilation of soil organic carbon and its controls is important for to improve Earth system models ability to simulate carbon-climate feedbacks. Although microbial assimilation of soil organic carbon is broadly considered to be an important parameter, it really comprises two separate physiological processes: one-time assimilation efficiency and time-dependent microbial maintenance energy. Representing of these two mechanisms is crucial to more accurately simulate carbon cycling in soils. In this study, a simple modeling framework was developed to evaluate the substrate and environmental controls on microbial assimilation of soil organic carbon using a new term: microbial annual active period (the length of microbes remaining active in one year). Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality (lower C:N ratio) leads to higher ratio of microbial carbon to soil organic carbon and vice versa. Increases in microbial annual active period from zero stimulate microbial assimilation of soil organic carbon; however, when microbial annual active period is longer than an optimal threshold, increasing this period decreases microbial biomass. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global dataset at the biome-level. The modeling framework of microbial assimilation of soil organic carbon and its controls developed in this study offers an applicable ways to incorporate microbial contributions to the carbon cycling into Earth system models for simulating carbon-climate feedbacks and to explain global patterns of microbial biomass.

  18. Marcell peatland carbon and nitrogen dynamics

    EPA Pesticide Factsheets

    This dataset include US Forest Service (contact Dr. Stephen Sebestyen at USFS) long-term precipitation, atmospheric deposition, and hydrologic data for the years 2010-2013. The dataset also includes unique (never before collected) data on ammonification, denitrification, microbial enzyme activity, and nitrification. These data will be useful for long-term trend analyses and for further investigations on carbon and nitrogen cycling in peatlands.This dataset is associated with the following publication:Hill , B., T. Jicha , L. Lehto, C. Elonen , S. Sebestyen , and R. Kolka. Comparisons of soil nitrogen mass balances for an ombrotrophic bog and a minerotrophic fen in northern Minnesota. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 550: 880-892, (2016).

  19. ACTIVITIES OF AMMONIA ASSIMILATION ENZYMES AS INDICATORS OF THE RELATIVE SUPPLY OF NITROGEN SUBSTRATES FOR MARINE BACTERIOPLANKTON IN SUB-TROPICAL COASTAL WATER

    EPA Science Inventory

    The supply of nitrogen substrates available for bacterial production in seawater was determined using the activities of ammonia assimilation enzymes, glutamine synthetase (GS) and glutamate dehydrogenase (GDH). Expression of GS and GDH by bacteria in pure culture is generally ind...

  20. ACTIVITIES OF AMMONIA ASSIMILATION ENZYMES AS INDICATORS OF THE RELATIVE SUPPLY OF NITROGEN SUBSTRATES FOR MARINE BACTERIOPLANKTON IN SUB-TROPICAL COASTAL WATER

    EPA Science Inventory

    The supply of nitrogen substrates available for bacterial production in seawater was determined using the activities of ammonia assimilation enzymes, glutamine synthetase (GS) and glutamate dehydrogenase (GDH). Expression of GS and GDH by bacteria in pure culture is generally ind...

  1. Aerobic-heterotrophic nitrogen removal through nitrate reduction and ammonium assimilation by marine bacterium Vibrio sp. Y1-5.

    PubMed

    Li, Yating; Wang, Yanru; Fu, Lin; Gao, Yizhan; Zhao, Haixia; Zhou, Weizhi

    2017-04-01

    An aerobic marine bacterium Vibrio sp. Y1-5 was screened to achieve efficient nitrate and ammonium removal simultaneously and fix nitrogen in cells without N loss. Approximately 98.0% of nitrate (100mg/L) was removed in 48h through assimilatory nitrate reduction and nitrate reductase was detected in the cytoplasm. Instead of nitrification, the strain assimilated ammonium directly, and it could tolerate as high as 1600mg/L ammonium concentration while removing 844.6mg/L. In addition, ammonium assimilation occurred preferentially in the medium containing nitrate and ammonium with a total nitrogen (TN) removal efficiency of 80.4%. The results of nitrogen balance and Fourier infrared spectra illustrated that the removed nitrogen was all transformed to protein or stored as organic nitrogen substances in cells and no N was lost in the process. Toxicological studies with the brine shrimp species Artemia naupliia indicated that Vibrio sp. Y1-5 can be applied in aquatic ecosystems safely. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Tropospheric ozone reduces carbon assimilation in trees: estimates from analysis of continuous flux measurements.

    PubMed

    Fares, Silvano; Vargas, Rodrigo; Detto, Matteo; Goldstein, Allen H; Karlik, John; Paoletti, Elena; Vitale, Marcello

    2013-08-01

    High ground-level ozone concentrations are typical of Mediterranean climates. Plant exposure to this oxidant is known to reduce carbon assimilation. Ozone damage has been traditionally measured through manipulative experiments that do not consider long-term exposure and propagate large uncertainty by up-scaling leaf-level observations to ecosystem-level interpretations. We analyzed long-term continuous measurements (>9 site-years at 30 min resolution) of environmental and eco-physiological parameters at three Mediterranean ecosystems: (i) forest site dominated by Pinus ponderosa in the Sierra Mountains in California, USA; (ii) forest site composed of a mixture of Quercus spp. and P. pinea in the Tyrrhenian sea coast near Rome, Italy; and (iii) orchard site of Citrus sinensis cultivated in the California Central Valley, USA. We hypothesized that higher levels of ozone concentration in the atmosphere result in a decrease in carbon assimilation by trees under field conditions. This hypothesis was tested using time series analysis such as wavelet coherence and spectral Granger causality, and complemented with multivariate linear and nonlinear statistical analyses. We found that reduction in carbon assimilation was more related to stomatal ozone deposition than to ozone concentration. The negative effects of ozone occurred within a day of exposure/uptake. Decoupling between carbon assimilation and stomatal aperture increased with the amount of ozone pollution. Up to 12-19% of the carbon assimilation reduction in P. ponderosa and in the Citrus plantation was explained by higher stomatal ozone deposition. In contrast, the Italian site did not show reductions in gross primary productivity either by ozone concentration or stomatal ozone deposition, mainly due to the lower ozone concentrations in the periurban site over the shorter period of investigation. These results highlight the importance of plant adaptation/sensitivity under field conditions, and the importance of

  3. The LysR-type transcription factor PacR is a global regulator of photosynthetic carbon assimilation in Anabaena.

    PubMed

    Picossi, Silvia; Flores, Enrique; Herrero, Antonia

    2015-09-01

    Cyanobacteria perform water-splitting photosynthesis and are important primary producers impacting the carbon and nitrogen cycles at global scale. They fix CO2 through ribulose-bisphosphate carboxylase/oxygenase (RuBisCo) and have evolved a distinct CO2 concentrating mechanism (CCM) that builds high CO2 concentrations in the vicinity of RuBisCo favouring its carboxylase activity. Filamentous cyanobacteria such as Anabaena fix CO2 in photosynthetic vegetative cells, which donate photosynthate to heterocysts that rely on a heterotrophic metabolism to fix N2 . CCM elements are induced in response to inorganic carbon limitation, a cue that exposes the photosynthetic apparatus to photodamage by over-reduction. An Anabaena mutant lacking the LysR-type transcription factor All3953 grew poorly and dies under high light. The rbcL operon encoding RuBisCo was induced upon carbon limitation in the wild type but not in the mutant. ChIP-Seq analysis was used to globally identify All3953 targets under carbon limitation. Targets include, besides rbcL, genes encoding CCM elements, photorespiratory pathway- photosystem- and electron transport-related components, and factors, including flavodiiron proteins, with a demonstrated or putative function in photoprotection. Quantitative reverse transcription polymerase chain reaction analysis of selected All3953 targets showed regulation in the wild type but not in the mutant. All3953 (PacR) is a global regulator of carbon assimilation in an oxygenic photoautotroph.

  4. Multicolor Nitrogen-Doped Carbon Dots for Live Cell Imaging.

    PubMed

    Du, Fengyi; Li, Jianan; Hua, Ye; Zhang, Miaomiao; Zhou, Zhou; Yuan, Jing; Wang, Jun; Peng, Wanxin; Zhang, Li; Xia, Sheng; Wang, Dongqing; Yang, Shiming; Xu, Wenrong; Gong, Aihua; Shao, Qixiang

    2015-05-01

    Doping carbon dots with nitrogen atoms considerably enhances their fluorescence properties. However, the mechanism by which the carbon dots are doped is not fully understood. We developed a facile bottom-up hydrothermal carbonization (HTC) process that uses glucose and glycine as precursors for the synthesis of photoluminescent nitrogen-doped carbon dots. The as-prepared nitrogen-doped carbon dots were mono-dispersed spherical particles with a diameter of -2.8 nm. The doped nitrogen atoms assumed pyridinic type and pyrrolic type configurations to participate in the nanocrystal structure of the carbon dots. It appeared that the nitrogen doping introduces a new internal structure. The aqueous solution of nitrogen-doped carbon dots showed excitation wavelength-dependent multicolor photoluminescence. Further, these nitrogen-doped carbon dots readily entered the cytoplasm of A549 cancer cells and showed no significant cytotoxicity. The internalized nitrogen-doped carbon dots were localized to the cell membrane and cytoplasm, particularly around the nucleus. Further, the as-prepared, biocompatible, nitrogen-doped carbon dots demonstrated the potential to be used as fluorescent probes for multicolor live cell labeling, tracking, and imaging.

  5. Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth system models.

    PubMed

    Xu, Xiaofeng; Schimel, Joshua P; Thornton, Peter E; Song, Xia; Yuan, Fengming; Goswami, Santonu

    2014-05-01

    A mechanistic understanding of microbial assimilation of soil organic carbon is important to improve Earth system models' ability to simulate carbon-climate feedbacks. A simple modelling framework was developed to investigate how substrate quality and environmental controls over microbial activity regulate microbial assimilation of soil organic carbon and on the size of the microbial biomass. Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality leads to higher ratio of microbial carbon to soil organic carbon. Microbial biomass carbon peaks and then declines as cumulative activity increases. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global data set at the biome level. The modelling framework developed in this study offers a simple approach to incorporate microbial contributions to the carbon cycling into Earth system models to simulate carbon-climate feedbacks and explain global patterns of microbial biomass.

  6. Carbon assimilation in Eucalyptus urophylla grown under high atmospheric CO2 concentrations: A proteomics perspective.

    PubMed

    Santos, Bruna Marques Dos; Balbuena, Tiago Santana

    2017-01-06

    Photosynthetic organisms may be drastically affected by the future climate projections of a considerable increase in CO2 concentrations. Growth under a high concentration of CO2 could stimulate carbon assimilation-especially in C3-type plants. We used a proteomics approach to test the hypothesis of an increase in the abundance of the enzymes involved in carbon assimilation in Eucalyptus urophylla plants grown under conditions of high atmospheric CO2. Our strategy allowed the profiling of all Calvin-Benson cycle enzymes and associated protein species. Among the 816 isolated proteins, those involved in carbon fixation were found to be the most abundant ones. An increase in the abundance of six key enzymes out of the eleven core enzymes involved in carbon fixation was detected in plants grown at a high CO2 concentration. Proteome changes were corroborated by the detection of a decrease in the stomatal aperture and in the vascular bundle area in Eucalyptus urophylla plantlets grown in an environment of high atmospheric CO2. Our proteomics approach indicates a positive metabolic response regarding carbon fixation in a CO2-enriched atmosphere. The slight but significant increase in the abundance of the Calvin enzymes suggests that stomatal closure did not prevent an increase in the carbon assimilation rates.

  7. Abiotic Stresses Downregulate Key Genes Involved in Nitrogen Uptake and Assimilation in Brassica juncea L.

    PubMed Central

    Goel, Parul; Singh, Anil Kumar

    2015-01-01

    Abiotic stresses such as salinity, drought and extreme temperatures affect nitrogen (N) uptake and assimilation in plants. However, little is known about the regulation of N pathway genes at transcriptional level under abiotic stress conditions in Brassica juncea. In the present work, genes encoding nitrate transporters (NRT), ammonium transporters (AMT), nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate dehydrogenase (GDH), asparagines synthetase (ASN) were cloned from Brassica juncea L. var. Varuna. The deduced protein sequences were analyzed to predict their subcellular localization, which confirmed localization of all the proteins in their respective cellular organelles. The protein sequences were also subjected to conserved domain identification, which confirmed presence of characteristic domains in all the proteins, indicating their putative functions. Moreover, expression of these genes was studied after 1h and 24h of salt (150 mM NaCl), osmotic (250 mM Mannitol), cold (4°C) and heat (42°C) stresses. Most of the genes encoding nitrate transporters and enzymes responsible for N assimilation and remobilization were found to be downregulated under abiotic stresses. The expression of BjAMT1.2, BjAMT2, BjGS1.1, BjGDH1 and BjASN2 was downregulated after 1hr, while expression of BjNRT1.1, BjNRT2.1, BjNiR1, BjAMT2, BjGDH1 and BjASN2 was downregulated after 24h of all the stress treatments. However, expression of BjNRT1.1, BjNRT1.5 and BjGDH2 was upregulated after 1h of all stress treatments, while no gene was found to be upregulated after 24h of stress treatments, commonly. These observations indicate that expression of most of the genes is adversely affected under abiotic stress conditions, particularly under prolonged stress exposure (24h), which may be one of the reasons of reduction in plant growth and development under abiotic stresses. PMID:26605918

  8. Abiotic Stresses Downregulate Key Genes Involved in Nitrogen Uptake and Assimilation in Brassica juncea L.

    PubMed

    Goel, Parul; Singh, Anil Kumar

    2015-01-01

    Abiotic stresses such as salinity, drought and extreme temperatures affect nitrogen (N) uptake and assimilation in plants. However, little is known about the regulation of N pathway genes at transcriptional level under abiotic stress conditions in Brassica juncea. In the present work, genes encoding nitrate transporters (NRT), ammonium transporters (AMT), nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate dehydrogenase (GDH), asparagines synthetase (ASN) were cloned from Brassica juncea L. var. Varuna. The deduced protein sequences were analyzed to predict their subcellular localization, which confirmed localization of all the proteins in their respective cellular organelles. The protein sequences were also subjected to conserved domain identification, which confirmed presence of characteristic domains in all the proteins, indicating their putative functions. Moreover, expression of these genes was studied after 1h and 24h of salt (150 mM NaCl), osmotic (250 mM Mannitol), cold (4°C) and heat (42°C) stresses. Most of the genes encoding nitrate transporters and enzymes responsible for N assimilation and remobilization were found to be downregulated under abiotic stresses. The expression of BjAMT1.2, BjAMT2, BjGS1.1, BjGDH1 and BjASN2 was downregulated after 1hr, while expression of BjNRT1.1, BjNRT2.1, BjNiR1, BjAMT2, BjGDH1 and BjASN2 was downregulated after 24h of all the stress treatments. However, expression of BjNRT1.1, BjNRT1.5 and BjGDH2 was upregulated after 1h of all stress treatments, while no gene was found to be upregulated after 24h of stress treatments, commonly. These observations indicate that expression of most of the genes is adversely affected under abiotic stress conditions, particularly under prolonged stress exposure (24h), which may be one of the reasons of reduction in plant growth and development under abiotic stresses.

  9. The Effects of Chlorophyll Assimilation on Carbon Fluxes in a Global Biogeochemical Model. [Technical Report Series on Global Modeling and Data Assimilation

    NASA Technical Reports Server (NTRS)

    Koster, Randal D. (Editor); Rousseaux, Cecile Severine; Gregg, Watson W.

    2014-01-01

    In this paper, we investigated whether the assimilation of remotely-sensed chlorophyll data can improve the estimates of air-sea carbon dioxide fluxes (FCO2). Using a global, established biogeochemical model (NASA Ocean Biogeochemical Model, NOBM) for the period 2003-2010, we found that the global FCO2 values produced in the free-run and after assimilation were within -0.6 mol C m(sup -2) y(sup -1) of the observations. The effect of satellite chlorophyll assimilation was assessed in 12 major oceanographic regions. The region with the highest bias was the North Atlantic. Here the model underestimated the fluxes by 1.4 mol C m(sup -2) y(sup -1) whereas all the other regions were within 1 mol C m(sup -2) y(sup -1) of the data. The FCO2 values were not strongly impacted by the assimilation, and the uncertainty in FCO2 was not decreased, despite the decrease in the uncertainty in chlorophyll concentration. Chlorophyll concentrations were within approximately 25% of the database in 7 out of the 12 regions, and the assimilation improved the chlorophyll concentration in the regions with the highest bias by 10-20%. These results suggest that the assimilation of chlorophyll data does not considerably improve FCO2 estimates and that other components of the carbon cycle play a role that could further improve our FCO2 estimates.

  10. Effect of shoot removal on remobilization of carbon and nitrogen during regrowth of nitrogen-fixing alfalfa.

    PubMed

    Aranjuelo, Iker; Molero, Gemma; Erice, Gorka; Aldasoro, Joseba; Arrese-Igor, Cesar; Nogués, Salvador

    2015-01-01

    The contribution of carbon and nitrogen reserves to regrowth following shoot removal has been studied in the past. However, important gaps remain in understanding the effect of shoot cutting on nodule performance and its relevance during regrowth. In this study, isotopic labelling was conducted at root and canopy levels with both (15) N2 and (13) C-depleted CO2 on exclusively nitrogen-fixing alfalfa plants. As expected, our results indicate that the roots were the main sink organs before shoots were removed. Seven days after regrowth the carbon and nitrogen stored in the roots was invested in shoot biomass formation and partitioned to the nodules. The large depletion in nodule carbohydrate availability suggests that root-derived carbon compounds were delivered towards nodules in order to sustain respiratory activity. In addition to the limited carbohydrate availability, the upregulation of nodule peroxidases showed that oxidative stress was also involved during poor nodule performance. Fourteen days after cutting, and as a consequence of the stimulated photosynthetic and N2 -fixing machinery, availability of Cnew and Nnew strongly diminished in the plants due to their replacement by C and N assimilated during the post-labelling period. In summary, our study indicated that during the first week of regrowth, root-derived C and N remobilization did not overcome C- and N-limitation in nodules and leaves. However, 14 days after cutting, leaf and nodule performance were re-established. © 2014 Scandinavian Plant Physiology Society.

  11. Relationship between carbon and nitrogen mineralization in a subtropical soil

    NASA Astrophysics Data System (ADS)

    Li, Qianru; Sun, Yue; Zhang, Xinyu; Xu, Xingliang; Kuzyakov, Yakov

    2014-05-01

    In most soils, more than 90% nitrogen is bonded with carbon in organic forms. This indicates that carbon mineralization should be closely coupled with nitrogen mineralization, showing a positive correlation between carbon and nitrogen mineralization. To test this hypothesis above, we conducted an incubation using a subtropical soil for 10 days at 15 °C and 25 °C. 13C-labeled glucose and 15N-labeled ammonium or nitrate was used to separate CO2 and mineral N released from mineralization of soil organic matter and added glucose or inorganic nitrogen. Phospholipid fatty acid (PLFA) and four exoenzymes (i.e. β-1,4- Glucosaminidase, chitinase, acid phosphatase, β-1,4-N- acetyl glucosamine glycosidase) were also analyzed to detect change in microbial activities during the incubation. Our results showed that CO2 release decreased with increasing nitrogen mineralization rates. Temperature did not change this relationship between carbon and nitrogen mineralization. Although some changes in PLFA and the four exoenzymes were observed, these changes did not contribute to changes in carbon and nitrogen mineralization. These findings indicates that carbon and nitrogen mineralization in soil are more complicated than as previously expected. Future investigation should focus on why carbon and nitrogen mineralization are coupled in a negative correlation not in a positive correlation in many soils for a better understanding of carbon and nitrogen transformation during their mineralization.

  12. The effects of Bacillus subtilis on nitrogen recycling from aquaculture solid waste using heterotrophic nitrogen assimilation in sequencing batch reactors.

    PubMed

    Lu, Lu; Tan, Hongxin; Luo, Guozhi; Liang, Wenyan

    2012-11-01

    A sequencing batch reactor (SBR) supplied with Bacillus subtilis (treatment group) was employed to treat the sludge from a re-circulating aquaculture system (RAS). The crude protein content of bio-flocs from the treatment group increased from 21.52%±1.5% to 29.65%±13.34%, which was 23.97%±11.62% greater than that of the SBRs without B. subtilis (control group). The removal rate of dissolved inorganic nitrogen (RR(DIN)) for the treatment group was 0.41±0.079 mg L(-1)d(-1), which was 1.17 times greater than that of the control group. The utility rate of total organic nitrogen (UR(TON)) for the treatment group was 1.42±0.33 mg L(-1)d(-1), which was 1.71 times greater than the control. The removal rate of dissolved organic carbon (RR(DOC)) for the treatment group was 138.39±7.77 mg L(-1)d(-1), which was 1.95 times greater than the control. The extra-cellular polymer substance (EPS) was primarily composed of polysaccharides. The flocs volume after 5 min (FV-5 min) reached 22.67%±2.08% at 19 days.

  13. [Effects of eutrophic nitrogen nutrition on carbon balance capacity of Liquidambar formosana seedlings under low light].

    PubMed

    Wang, Chuan-Hua; Li, Jun-Qing; Yang, Ying

    2011-12-01

    To investigate the effects of atmospheric nitrogen deposition on the seedlings regeneration of Liquidambar formosana, a greenhouse experiment was conducted, in which, the low light- and nitrogen supplies were controlled similar to those in typical L. formosana secondary forests, with the effects of different light- and nitrogen supply on the L. formosana seedlings survival, leaf functional traits, biomass allocation, and gas exchange studied. The whole plant light compensation point (LCP(whoIe-plant)) of the seedlings was estimated with a whole plant carbon balance model, and then compared with the understory photosynthetic active radiance (PAR) of the typical secondary forests. Under 3.0% and 6.0% of full sunlight, eutrophic nitrogen supply led to a decrease of seedlings survival (shade tolerance) and specific leaf area (SLA), but had no obvious effects on the seedlings biomass allocation. At eutrophic nitrogen supply, light intensity had significant effects on the leaf area based maximum assimilation rate, whereas increasing nitrogen supply under low light induced the increase of leaf mass based dark respiration rate. Both light intensity and nitrogen supply had significant effects on the mass based leaf respiration rate, and the interaction of light and nitrogen had significant effects on the mass based stem respiration rate. Increasing nitrogen supply increased the LCP(wholeplant), under 3.0%, 6.0%, and 12.0% of full sunlight, but decreased the LCP(whoIe-plant) under 25.0% of full sunlight. The decrease of the seedlings shade tolerance induced by the increasing nitrogen supply under low light was correlated with the variations of the seedlings carbon balance capacity. Under the background of elevated atmospheric nitrogen deposition, the maintenance of L. formosana populations in China would more depend on disturbances and gap regeneration, and the population dynamics would be deeply affected.

  14. Nitrogen assimilation and dissimilation by bacteria and benthic microalgae in tidal mudflat sediment in a 15N labeling study

    NASA Astrophysics Data System (ADS)

    Dähnke, K.; Moneta, A.; Veuger, B.; Soetaert, K.; Middelburg, J. J.

    2012-04-01

    In a short-term 15N-labeling experiment, we investigated the changes in relative utilization of reactive nitrogen in tidal flat sediment, focusing on the relative importance of assimilatory versus dissimilatory processes and the role of benthic microalgae therein. 15N-labeled ammonium and nitrate were added separately to homogenized tidal flat sediment, and 15N was subsequently traced into bulk sediment and inorganic nutrients in pore water. Integration of results in an N cycle model allowed us to quantify rates for the major assimilatory and dissimilatory processes in the sediment. Overall, the results indicate that the equilibrium between assimilation and dissimilation in this tidal mudflat is mainly dependent on the nitrogen source: Nitrate is utilized almost exclusively dissimilatory via denitrification, whereas ammonium is rapidly assimilated, with about a quarter of this assimilation due to BMA activity. The major influence of benthic microalgae is on assimilation of ammonium, ceasing BMA activity turns the sediments from a net ammonium sink to a net source. There is little evidence of dissimilative processes like nitrification in undisturbed sediments, but high initial nitrification rates suggest that in a dynamic environment like tidal flats, intense and fast nitrification/denitrification of ammonium is abundant. The driving mechanisms for assimilation or dissimilation accordingly appear to be ruled to a large extent by external physical forcing, with the entire system being capable of rapid shifts following environmental changes. Our combined experimental and model approach reveals that selective removal of labeled compounds takes place for both ammonium and nitrate. Mechanisms remain unclear, but this finding clearly challenges the traditional labeling approach and underscores the need to consider selective uptake in future labeling studies. Ignoring such selective uptake mechanisms will lead to misinterpretation of process rates when these are estimated

  15. [Simulation of water and carbon fluxes in harvard forest area based on data assimilation method].

    PubMed

    Zhang, Ting-Long; Sun, Rui; Zhang, Rong-Hua; Zhang, Lei

    2013-10-01

    Model simulation and in situ observation are the two most important means in studying the water and carbon cycles of terrestrial ecosystems, but have their own advantages and shortcomings. To combine these two means would help to reflect the dynamic changes of ecosystem water and carbon fluxes more accurately. Data assimilation provides an effective way to integrate the model simulation and in situ observation. Based on the observation data from the Harvard Forest Environmental Monitoring Site (EMS), and by using ensemble Kalman Filter algorithm, this paper assimilated the field measured LAI and remote sensing LAI into the Biome-BGC model to simulate the water and carbon fluxes in Harvard forest area. As compared with the original model simulated without data assimilation, the improved Biome-BGC model with the assimilation of the field measured LAI in 1998, 1999, and 2006 increased the coefficient of determination R2 between model simulation and flux observation for the net ecosystem exchange (NEE) and evapotranspiration by 8.4% and 10.6%, decreased the sum of absolute error (SAE) and root mean square error (RMSE) of NEE by 17.7% and 21.2%, and decreased the SAE and RMSE of the evapotranspiration by 26. 8% and 28.3%, respectively. After assimilated the MODIS LAI products of 2000-2004 into the improved Biome-BGC model, the R2 between simulated and observed results of NEE and evapotranspiration was increased by 7.8% and 4.7%, the SAE and RMSE of NEE were decreased by 21.9% and 26.3%, and the SAE and RMSE of evapotranspiration were decreased by 24.5% and 25.5%, respectively. It was suggested that the simulation accuracy of ecosystem water and carbon fluxes could be effectively improved if the field measured LAI or remote sensing LAI was integrated into the model.

  16. Physiology and gene expression profiles of Dekkera bruxellensis in response to carbon and nitrogen availability.

    PubMed

    de Barros Pita, Will; Silva, Denise Castro; Simões, Diogo Ardaillon; Passoth, Volkmar; de Morais, Marcos Antonio

    2013-11-01

    The assimilation of nitrate, a nitrogenous compound, was previously described as an important factor favoring Dekkera bruxellensis in the competition with Saccharomyces cerevisiae for the industrial sugarcane substrate. In this substrate, nitrogen sources are limited and diverse, and a recent report showed that amino acids enable D. bruxellensis to grow anaerobically. Thus, understanding the regulation of nitrogen metabolism is one fundamental aspect to comprehend the competiveness of D. bruxellensis in the fermentation environment. In the present study, we evaluated the physiological and transcriptional profiles of D. bruxellensis in response to different carbon and nitrogen supplies to determine their influence on growth, sugar consumption, and ethanol production. Besides, the expression of genes coding for nitrogen permeases and enzymes involved in the biosynthesis of glutamate and energetic metabolism were investigated under these conditions. Our data revealed that genes related to nitrogen uptake in D. bruxellensis are under the control of nitrogen catabolite repression. Moreover, we provide indications that glutamate dehydrogenase and glutamate synthase may switch roles as the major pathway for glutamate biosynthesis in D. bruxellensis. Finally, our data showed that in nonoptimal growth conditions, D. bruxellensis leans toward the respiratory metabolism. The results presented herein show that D. bruxellensis and S. cerevisiae share similar regulation of GDH–GOGAT pathway, while D. bruxellensis converts less glucose to ethanol than S. cerevisiae do when nitrogen is limited. The consequence of this particularity to the industrial process is discussed.

  17. Temporary Storage or Permanent Removal? The Division of Nitrogen between Biotic Assimilation and Denitrification in Stormwater Biofiltration Systems

    PubMed Central

    Payne, Emily G. I.; Fletcher, Tim D.; Russell, Douglas G.; Grace, Michael R.; Cavagnaro, Timothy R.; Evrard, Victor; Deletic, Ana; Hatt, Belinda E.; Cook, Perran L. M.

    2014-01-01

    The long-term efficacy of stormwater treatment systems requires continuous pollutant removal without substantial re-release. Hence, the division of incoming pollutants between temporary and permanent removal pathways is fundamental. This is pertinent to nitrogen, a critical water body pollutant, which on a broad level may be assimilated by plants or microbes and temporarily stored, or transformed by bacteria to gaseous forms and permanently lost via denitrification. Biofiltration systems have demonstrated effective removal of nitrogen from urban stormwater runoff, but to date studies have been limited to a ‘black-box’ approach. The lack of understanding on internal nitrogen processes constrains future design and threatens the reliability of long-term system performance. While nitrogen processes have been thoroughly studied in other environments, including wastewater treatment wetlands, biofiltration systems differ fundamentally in design and the composition and hydrology of stormwater inflows, with intermittent inundation and prolonged dry periods. Two mesocosm experiments were conducted to investigate biofilter nitrogen processes using the stable isotope tracer 15NO3− (nitrate) over the course of one inflow event. The immediate partitioning of 15NO3− between biotic assimilation and denitrification were investigated for a range of different inflow concentrations and plant species. Assimilation was the primary fate for NO3− under typical stormwater concentrations (∼1–2 mg N/L), contributing an average 89–99% of 15NO3− processing in biofilter columns containing the most effective plant species, while only 0–3% was denitrified and 0–8% remained in the pore water. Denitrification played a greater role for columns containing less effective species, processing up to 8% of 15NO3−, and increased further with nitrate loading. This study uniquely applied isotope tracing to biofiltration systems and revealed the dominance of assimilation in stormwater

  18. Isotope Fractionation in Photosynthetic Bacteria during Carbon Dioxide Assimilation 1

    PubMed Central

    Wong, William; Sackett, William M.; Benedict, C. Roy

    1975-01-01

    The δ PDB13C values have been determined for the cellular constituents and metabolic intermediates of autotrophically grown Chromatium vinosum. The isotopic composition of the HCO3- in the medium and the carbon isotopic composition of the bacterial cells change with the growth of the culture. The δ PDB13C value of the HCO3- in the media changes from an initial value of −6.6‰ to +8.1‰ after 10 days of bacterial growth and the δ PDB13C value of the bacterial cells change from −37.5‰ to −29.2‰ in the same period. The amount of carbon isotope fractionation during the synthesis of hexoses by the photoassimilation of CO2 has a range of −15.5‰ at time zero to −22.0‰ after 10 days. This range of fractionation compares to the range of carbon isotope fractionation for the synthesis of sugars from CO2 by ribulose 1,5-diphosphate carboxylase and the Calvin cycle. The amount of carbon isotope fractionation during the synthesis of aspartic acid from CO2 is −24.9‰ at time zero and −15.0‰ after 10 days of bacterial growth. This amount of fractionation is in the range of carbon isotope fractionation for the synthesis of C4 amino acids by a double carboxylation through ribulose 1,5-diphosphate and phosphoenolpyruvate carboxylase. PMID:16659105

  19. Desiccation of sediments affects assimilate transport within aquatic plants and carbon transfer to microorganisms.

    PubMed

    von Rein, I; Kayler, Z E; Premke, K; Gessler, A

    2016-11-01

    With the projected increase in drought duration and intensity in future, small water bodies, and especially the terrestrial-aquatic interfaces, will be subjected to longer dry periods with desiccation of the sediment. Drought effects on the plant-sediment microorganism carbon continuum may disrupt the tight linkage between plants and microbes which governs sediment carbon and nutrient cycling, thus having a potential negative impact on carbon sequestration of small freshwater ecosystems. However, research on drought effects on the plant-sediment carbon transfer in aquatic ecosystems is scarce. We therefore exposed two emergent aquatic macrophytes, Phragmites australis and Typha latifolia, to a month-long summer drought in a mesocosm experiment. We followed the fate of carbon from leaves to sediment microbial communities with (13) CO2 pulse labelling and microbial phospholipid-derived fatty acid (PLFA) analysis. We found that drought reduced the total amount of carbon allocated to stem tissues but did not delay the transport. We also observed an increase in accumulation of (13) C-labelled sugars in roots and found a reduced incorporation of (13) C into the PLFAs of sediment microorganisms. Drought induced a switch in plant carbon allocation priorities, where stems received less new assimilates leading to reduced starch reserves whilst roots were prioritised with new assimilates, suggesting their use for osmoregulation. There were indications that the reduced carbon transfer from roots to microorganisms was due to the reduction of microbial activity via direct drought effects rather than to a decrease in root exudation or exudate availability.

  20. Suppression of glutamate synthase genes significantly affects carbon and nitrogen metabolism in rice (Oryza sativa L.).

    PubMed

    Lu, YongEn; Luo, Feng; Yang, Meng; Li, XiangHua; Lian, XingMing

    2011-07-01

    Rice (Oryza sativa) glutamate synthase (GOGAT, EC 1.4.1.14) enzymes have been proposed to have great potential for improving nitrogen use efficiency, but their functions in vivo and their effects on carbon and nitrogen metabolism have not been systematically explored. In this research, we analyzed transcriptional profiles of rice GOGAT genes using a genome-wide microarray database, and investigated the effects of suppression of glutamate synthase genes on carbon and nitrogen metabolism using GOGAT co-suppressed rice plants. Transcriptional profiles showed that rice GOGAT genes were expressed differently in various tissues and organs, which suggested that they have different roles in vivo. Compared with the wild-type, tiller number, total shoot dry weight, and yield of GOGAT co-suppressed plants were significantly decreased. Physiological and biochemical studies showed that the contents of nitrate, several kinds of free amino acids, chlorophyll, sugars, sugar phosphates, and pyridine nucleotides were significantly decreased in leaves of GOGAT co-suppressed plants, but the contents of free ammonium, 2-oxoglutarate, and isocitrate in leaves were increased. We conclude that GOGATs play essential roles in carbon and nitrogen metabolism, and that they are indispensable for efficient nitrogen assimilation in rice.

  1. Exposure to an enriched CO2 atmosphere alters carbon assimilation and allocation in a pine forest ecosystem

    Treesearch

    Karina V.R. Schafer; Ram Oren; David S. Ellsworth; Chun-Ta Lai; Jeffrey D. Herricks; Adrien C. Finzi; Daniel D. Richter; Gabriel G. Katul

    2003-01-01

    We linked a leaf-level C02 assimilation model with a model that accounts for light attenuation in the canopy and measurements of sap-flux-based canopy conductance into a new canopy conductance-constrained carbon assimilation (4C-A) model. We estimated canopy C02 uptake (AnC) at...

  2. Effects of ammonium and nitrate on nutrient uptake and activity of nitrogen assimilating enzymes in western hemlock

    SciTech Connect

    Knoepp, J.D.; Turner, D.P.; Tingey, D.T.

    1993-01-01

    Western hemlock seedlings were grown in nutrient solutions with ammonium, nitrate or ammonium plus nitrate as nitrogen sources. The objectives were to examine (1) possible selectivity for ammonium or nitrate as an N source, (2) the maintenance of charge balance during ammonium and nitrate uptake, and (3) the activity of the nitrogen assimilating enzymes, nitrate reductase, glutamine synthetase, and glutamine dehydrogenase, in relation to the uptake of different nitrogen sources. The uptake studies revealed that western hemlock takes up ammonium faster than nitrate and that ammonium partially inhibits nitrate uptake. Nitrate reductase activity varied with nitrate availability in root tissue, but showed no response in needles, indicating that most nitrate is reduced in the roots. Results indicate that western hemlock may be adapted to sites where NH(4+) is the predominate N source.

  3. Computational protein design enables a novel one-carbon assimilation pathway.

    PubMed

    Siegel, Justin B; Smith, Amanda Lee; Poust, Sean; Wargacki, Adam J; Bar-Even, Arren; Louw, Catherine; Shen, Betty W; Eiben, Christopher B; Tran, Huu M; Noor, Elad; Gallaher, Jasmine L; Bale, Jacob; Yoshikuni, Yasuo; Gelb, Michael H; Keasling, Jay D; Stoddard, Barry L; Lidstrom, Mary E; Baker, David

    2015-03-24

    We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more efficiently and with less backward flux than any naturally occurring one-carbon assimilation pathway. When supplemented with enzymes carrying out the other steps in the pathway, FLS converts formate into dihydroxyacetone phosphate and other central metabolites in vitro. These results demonstrate how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway.

  4. Computational protein design enables a novel one-carbon assimilation pathway

    SciTech Connect

    Siegel, JB; Smith, AL; Poust, S; Wargacki, AJ; Bar-Even, A; Louw, C; Shen, BW; Eiben, CB; Tran, HM; Noor, E; Gallaher, JL; Bale, J; Yoshikuni, Y; Gelb, MH; Keasling, JD; Stoddard, BL; Lidstrom, ME; Baker, D

    2015-03-09

    We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more efficiently and with less backward flux than any naturally occurring one-carbon assimilation pathway. When supplemented with enzymes carrying out the other steps in the pathway, FLS converts formate into dihydroxyacetone phosphate and other central metabolites in vitro. These results demonstrate how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway.

  5. Computational protein design enables a novel one-carbon assimilation pathway

    PubMed Central

    Siegel, Justin B.; Smith, Amanda Lee; Poust, Sean; Wargacki, Adam J.; Bar-Even, Arren; Louw, Catherine; Shen, Betty W.; Eiben, Christopher B.; Tran, Huu M.; Noor, Elad; Gallaher, Jasmine L.; Bale, Jacob; Yoshikuni, Yasuo; Gelb, Michael H.; Keasling, Jay D.; Stoddard, Barry L.; Lidstrom, Mary E.; Baker, David

    2015-01-01

    We describe a computationally designed enzyme, formolase (FLS), which catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxyacetone molecule. The existence of FLS enables the design of a new carbon fixation pathway, the formolase pathway, consisting of a small number of thermodynamically favorable chemical transformations that convert formate into a three-carbon sugar in central metabolism. The formolase pathway is predicted to use carbon more efficiently and with less backward flux than any naturally occurring one-carbon assimilation pathway. When supplemented with enzymes carrying out the other steps in the pathway, FLS converts formate into dihydroxyacetone phosphate and other central metabolites in vitro. These results demonstrate how modern protein engineering and design tools can facilitate the construction of a completely new biosynthetic pathway. PMID:25775555

  6. Preparation of nitrogen-enriched activated carbons from brown coal

    SciTech Connect

    Robert Pietrzak; Helena Wachowska; Piotr Nowicki

    2006-05-15

    Nitrogen-enriched activated carbons were prepared from a Polish brown coal. Nitrogen was introduced from urea at 350{sup o}C in an oxidizing atmosphere both to carbonizates obtained at 500-700{sup o}C and to activated carbons prepared from them. The activation was performed at 800{sup o}C with KOH in argon. It has been observed that the carbonization temperature determines the amount of nitrogen that is incorporated (DC5U, 8.4 wt % N{sup daf}; DC6U, 6.3 wt % N{sup daf}; and DC7U, 5.4 wt % N{sup daf}). X-ray photoelectron spectroscopy (XPS) measurements have shown that nitrogen introduced both at the stage of carbonizates and at the stage of activated carbons occurs mainly as -6, -5, and imine, amine and amide groups. On the other hand, the activation of carbons enriched with nitrogen results in the formation of pyridonic nitrogen and N-Q. The introduction of nitrogen at the activated carbon stage leads to a slight decrease in surface area. It has been proven that the most effective way of preparing microporous activated carbons enriched with nitrogen to a considerable extent and having high surface area ({approximately} 3000 m{sup 2}/g) is the following: carbonization - activation - reaction with urea. 40 refs., 1 fig., 6 tabs.

  7. Phosphoenolpyruvate Carboxylase in Arabidopsis Leaves Plays a Crucial Role in Carbon and Nitrogen Metabolism.

    PubMed

    Shi, Jianghua; Yi, Keke; Liu, Yu; Xie, Li; Zhou, Zhongjing; Chen, Yue; Hu, Zhanghua; Zheng, Tao; Liu, Renhu; Chen, Yunlong; Chen, Jinqing

    2015-03-01

    Phosphoenolpyruvate carboxylase (PEPC) is a crucial enzyme that catalyzes an irreversible primary metabolic reaction in plants.Previous studies have used transgenic plants expressing ectopic PEPC forms with diminished feedback inhibition to examine the role of PEPC in carbon and nitrogen metabolism. To date, the in vivo role of PEPC in carbon and nitrogen metabolism has not been analyzed in plants. In this study, we examined the role of PEPC in plants, demonstrating that PPC1 and PPC2 were highly expressed genes encoding PEPC in Arabidopsis (Arabidopsis thaliana) leaves and that PPC1 and PPC2 accounted for approximately 93% of total PEPC activity in the leaves. A double mutant, ppc1/ppc2, was constructed that exhibited a severe growth-arrest phenotype. The ppc1/ppc2 mutant accumulated more starch and sucrose than wild-type plants when seedlings were grown under normal conditions. Physiological and metabolic analysis revealed that decreased PEPC activity in the ppc1/ppc2 mutant greatly reduced the synthesis of malate and citrate and severely suppressed ammonium assimilation. Furthermore, nitrate levels in the ppc1/ppc2 mutant were significantly lower than those in wild-type plants due to the suppression of ammonium assimilation. Interestingly, starch and sucrose accumulation could be prevented and nitrate levels could be maintained by supplying the ppc1/ppc2 mutant with exogenous malate and glutamate, suggesting that low nitrogen status resulted in the alteration of carbon metabolism and prompted the accumulation of starch and sucrose in the ppc1/ppc2 mutant. Our results demonstrate that PEPC in leaves plays a crucial role in modulating the balance of carbon and nitrogen metabolism in Arabidopsis.

  8. Carbon assimilation and export in sugar beet leaves. [Beta vulgaris

    SciTech Connect

    Tucci, M.A.; Geiger, D.K.; Servaites, J.C.

    1987-04-01

    Net carbon exchange rates (NCE), starch accumulation rates, gas exchange, and the maximum amount of carbon available for export were studied in Beta vulgaris L. following a 25% increase or a 25% decrease in ambient CO/sub 2/ (340 ..mu..l/L). Changing CO/sub 2/ by 25% above or below ambient had no effect on the ratio of internal CO/sub 2/ to ambient CO/sub 2/. Stomatal aperature adjusted in both cases to maintain the same relative stomatal limitation to NCE. Increasing CO/sub 2/ 25% increased NCE and water use efficiency, but slightly decreased stomatal conductance by 9% below leaves maintained at ambient. In contrast, a 25% reduction in CO/sub 2/ decreased NCE and water use efficiency. Decreasing CO/sub 2/ caused an increase in conductance also by 9%. Increasing CO/sub 2/ increased starch storage by 36%, but caused no change in the ratio of starch accumulation to NCE. A reduction in CO/sub 2/ caused a 60% decrease in the rate of starch storage and decreased the ratio of starch accumulation to NCE by one-half. The maximum amount of carbon available for export was increased 25% by increasing CO/sub 2/, but decreased by 5% following a reduction in CO2 level. These data are evidence that export rates are maintained at the expense of starch synthesis during periods of low NCE.

  9. Enzymes involved in the assimilation of one-carbon units by Pseudomonas MS.

    PubMed Central

    Wagner, C; Levitch, M E

    1975-01-01

    Pseudomonas MS can grow on methylamine and a number of other compounds containing C1 units as a sole source of carbon and energy. Assimilation of carbon into cell material occurs via the "serine pathway" since enzymes of this pathway are induced after growth on methylamine, but not malate or acetate. A mutant has been isolated which is unable to grow on methylamine or any other related substrate providing C1 units. This mutant is also unable to grow on acetate. Measurment of enzyme activities in cell-free extracts of wild-type cells showed that growth on methylamine caused induction of isocitrate lyase, a key enzyme in the glyoxylate cycle. The mutant organism lacks malate lyase, a key enzyme of the serine pathway, and isocitrate lyase as well. These results suggest that utilization of C1 units by Pseudomonas MS results in the net accumulation of acetate which is then assimilated into cell material via the glyoxylate cycle. PMID:238950

  10. Enzymes involved in the assimilation of one-carbon units by Pseudomonas MS.

    PubMed

    Wagner, C; Levitch, M E

    1975-06-01

    Pseudomonas MS can grow on methylamine and a number of other compounds containing C1 units as a sole source of carbon and energy. Assimilation of carbon into cell material occurs via the "serine pathway" since enzymes of this pathway are induced after growth on methylamine, but not malate or acetate. A mutant has been isolated which is unable to grow on methylamine or any other related substrate providing C1 units. This mutant is also unable to grow on acetate. Measurment of enzyme activities in cell-free extracts of wild-type cells showed that growth on methylamine caused induction of isocitrate lyase, a key enzyme in the glyoxylate cycle. The mutant organism lacks malate lyase, a key enzyme of the serine pathway, and isocitrate lyase as well. These results suggest that utilization of C1 units by Pseudomonas MS results in the net accumulation of acetate which is then assimilated into cell material via the glyoxylate cycle.

  11. Equilibration of the terrestrial water, nitrogen, and carbon cycles.

    PubMed

    Schimel, D S; Braswell, B H; Parton, W J

    1997-08-05

    Recent advances in biologically based ecosystem models of the coupled terrestrial, hydrological, carbon, and nutrient cycles have provided new perspectives on the terrestrial biosphere's behavior globally, over a range of time scales. We used the terrestrial ecosystem model Century to examine relationships between carbon, nitrogen, and water dynamics. The model, run to a quasi-steady-state, shows strong correlations between carbon, water, and nitrogen fluxes that lead to equilibration of water/energy and nitrogen limitation of net primary productivity. This occurs because as the water flux increases, the potentials for carbon uptake (photosynthesis), and inputs and losses of nitrogen, all increase. As the flux of carbon increases, the amount of nitrogen that can be captured into organic matter and then recycled also increases. Because most plant-available nitrogen is derived from internal recycling, this latter process is critical to sustaining high productivity in environments where water and energy are plentiful. At steady-state, water/energy and nitrogen limitation "equilibrate," but because the water, carbon, and nitrogen cycles have different response times, inclusion of nitrogen cycling into ecosystem models adds behavior at longer time scales than in purely biophysical models. The tight correlations among nitrogen fluxes with evapotranspiration implies that either climate change or changes to nitrogen inputs (from fertilization or air pollution) will have large and long-lived effects on both productivity and nitrogen losses through hydrological and trace gas pathways. Comprehensive analyses of the role of ecosystems in the carbon cycle must consider mechanisms that arise from the interaction of the hydrological, carbon, and nutrient cycles in ecosystems.

  12. Monitoring Carbon Assimilation of South American Tropical Forests

    NASA Astrophysics Data System (ADS)

    Costa, M. H.; Nunes, E. L.

    2009-12-01

    Net primary production (NPP) is a key variable for monitoring and understanding the impacts of environmental change on ecosystems and for generating realistic global and regional carbon budgets. However, although assessment of NPP over broad spatial scales has been made possible through the development of MODIS products such as MOD17A3, such global remotely sensed estimations are often inaccurate due to algorithm failure and parameterization issues. These inadequacies can be partly remedied by the development of biome-specific geographically localized algorithms. In this paper we develop a regional algorithm (RATE) for the automatic monitoring the rate of carbon fixation (as measured by NPP) of tropical forests in South America. The algorithm is based on a modification of the SITE model and uses data from the MODIS sensor (MOD12Q1 and MOD15A2 products) and meteorological data from the National Centers for Environmental Prediction (NCEP). The effectiveness of the algorithm was tested in eight field sites from two types of tropical forests in South America: the Amazon rainforest and the Atlantic forest. In the Amazonian sites, the RATE algorithm produced NPP values closer to the observed values than estimates from the MODIS NPP product, while in the Atlantic forest sites it generated NPP values similar to the MODIS sensor. In conclusion, RATE appears to be a reliable estimator of carbon fixation by tropical forests in South America, with an average error of only 4.7%, and is therefore a more precise way of monitoring regional environmental change in these globally important ecosystems.

  13. The Effects of Varying Crustal Carbonate Composition on Assimilation and CO2 Degassing at Arc Volcanoes

    NASA Astrophysics Data System (ADS)

    Carter, L. B.; Holmes, A. K.; Dasgupta, R.; Tumiati, S.

    2015-12-01

    Magma-crustal carbonate interaction and subsequent decarbonation can provide an additional source of CO2 release to the exogenic system superimposed on mantle-derived CO2. Carbonate assimilation at present day volcanoes is often modeled by limestone consumption experiments [1-4]. Eruptive products, however, do not clearly display the characteristic ultracalcic melt compositions produced during limestone-magma interaction [4]. Yet estimated CO2outflux [5] and composition of volcanics in many volcanic systems may allow ~3-17% limestone- or dolostone-assimilated melt contribution. Crystallization may retain ultracalcic melts in pyroxenite cumulates. To extend our completed study on limestone assimilation, here we explore the effect of varying composition from calcite to dolomite on chemical and thermal decarbonation efficiency of crustal carbonates. Piston cylinder experiments at 0.5 GPa and 900-1200 °C demonstrate that residual mineralogy during interaction with magma shifts from CaTs cpx and anorthite/scapolite in the presence of calcite to Di cpx and Fo-rich olivine with dolomite. Silica-undersaturated melts double in magnesium content, while maintaining high (>30 wt.%) CaO values. At high-T, partial thermal breakdown of dolomite into periclase and CO2 is minimal (<5%) suggesting that in the presence of magma, CO2 is primarily released due to assimilation. Assimilated melts at identical P-T conditions depict similarly high volatile contents (10-20 wt.% by EMPA deficit at 0.5 GPa, 1150 °C with hydrous basalt) with calcite or dolomite. Analysis of the coexisting fluid phase indicates the majority of water is dissolved in the melt, while CO2 released from the carbonate is preferentially partitioned into the vapor. This suggests that although assimilated melts have a higher CO2 solubility, most of the CO2can easily degas from the vapor phase at arc volcanoes, possibly more so at volcanic plumbing systems traversing dolomite [8]. [1]Conte et al 2009 EuJMin (21) 763

  14. Shoot-to-Root Mobile Transcription Factor HY5 Coordinates Plant Carbon and Nitrogen Acquisition.

    PubMed

    Chen, Xiangbin; Yao, Qinfang; Gao, Xiuhua; Jiang, Caifu; Harberd, Nicholas P; Fu, Xiangdong

    2016-03-07

    Coordination of shoot photosynthetic carbon fixation with root inorganic nitrogen uptake optimizes plant performance in a fluctuating environment [1]. However, the molecular basis of this long-distance shoot-root coordination is little understood. Here we show that Arabidopsis ELONGATED HYPOCOTYL5 (HY5), a bZIP transcription factor that regulates growth in response to light [2, 3], is a shoot-to-root mobile signal that mediates light promotion of root growth and nitrate uptake. Shoot-derived HY5 auto-activates root HY5 and also promotes root nitrate uptake by activating NRT2.1, a gene encoding a high-affinity nitrate transporter [4]. In the shoot, HY5 promotes carbon assimilation and translocation, whereas in the root, HY5 activation of NRT2.1 expression and nitrate uptake is potentiated by increased carbon photoassimilate (sucrose) levels. We further show that HY5 function is fluence-rate modulated and enables homeostatic maintenance of carbon-nitrogen balance in different light environments. Thus, mobile HY5 coordinates light-responsive carbon and nitrogen metabolism, and hence shoot and root growth, in a whole-organismal response to ambient light fluctuations.

  15. The identification of the nitrate assimilation related genes in the novel Bacillus megaterium NCT-2 accounts for its ability to use nitrate as its only source of nitrogen.

    PubMed

    Shi, Weiwei; Lu, Wei; Liu, Qunlu; Zhi, Yuee; Zhou, Pei

    2014-03-01

    Bacillus megaterium NCT-2 is a novel bacterium that can utilize nitrate as its only nitrogen source for growth.The nitrate assimilation related genes that are involved in this process would be expected to be crucial. However, little is known about the genomic background of this bacterium,let alone the sequences of the nitrate assimilation related genes. In order to further investigate the nitrate assimilation function of the NCT-2, genome sequencing was performed.After obtaining the fine map of the NCT-2 genome, which was submitted to the NCBI GenBank (AHTF00000000), the sequences of the nitrate assimilation related genes (the nitrate reductase electron transfer subunit nasB and the nitrate reductase catalytic subunit nasC, the nitrite reductase [NAD(P)H]large subunit nasD and the nitrite reductase [NAD(P)H] small subunit nasE, and the glutamine synthetase glnA) were identified.Multiple alignments were performed to find out the sequence identities of the nitrate assimilation related genes to that of their similar species. Through KEGG signaling mapping search, the nitrate assimilation related genes were revealed to be located in the nitrogen metabolism signaling pathway. The putative 3D protein structures of these genes were modeled by SWISS MODEL, and shown to be highly similar to the nitrate assimilation related genes in the PDB database. Finally, the sequence validity of the nitrate assimilation related genes was verified by PCR with specifically designed primers.

  16. Nitrogen and carbon storage in alpine plants.

    PubMed

    Monson, Russell K; Rosenstiel, Todd N; Forbis, Tara A; Lipson, David A; Jaeger, Charles H

    2006-02-01

    Alpine plants offer unique opportunities to study the processes and economics of nutrient storage. The short alpine growing season forces rapid completion of plant growth cycles, which in turn causes competition between vegetative and reproductive growth sinks during the early part of the growing season. Mobilization of stored nitrogen and carbon reserves facilitates competing sinks and permits successful completion of reproduction before the onset of winter stress. We discuss the theoretical framework for assessing the costs and benefits of nutrient storage in alpine plants in order to lay the foundation for interpretation of observations. A principal point that has emerged from past theoretical treatments is the distinction between reserve storage, defined as storage that occurs with a cost to growth, and resource accumulation, defined as storage that occurs when resource supply exceeds demand, and thus when there is no cost to growth. We then discuss two case studies, one already published and one not yet published, pertaining to the storage and utilization of nitrogen and carbon compounds in alpine plants from Niwot Ridge, Colorado. In the first case, we tested the hypothesis that the seasonal accumulation of amino acids in the rhizome of N-fertilized plants of Bistorta bistortoides provides an advantage to the plant by not imposing a cost to growth at the time of accumulation, but providing a benefit to growth when the accumulated N is remobilized. We show that, as predicted, there is no cost during N accumulation but, not as predicted, there is no benefit to future growth. In the presence of N accumulation, reliance on stored N for growth increases, but reliance on current-season, soil-derived N decreases; thus the utilization of available N in this species is a 'zero sum' process. Inherent meristematic constraints to growth cause negative feedback that limits the utilization of accumulated N and precludes long-term advantages to this form of storage. In the

  17. A new stepwise carbon cycle data assimilation system using multiple data streams to constrain the simulated land surface carbon cycle

    DOE PAGES

    Peylin, Philippe; Bacour, Cédric; MacBean, Natasha; ...

    2016-09-20

    Here, large uncertainties in land surface models (LSMs) simulations still arise from inaccurate forcing, poor description of land surface heterogeneity (soil and vegetation properties), incorrect model parameter values and incomplete representation of biogeochemical processes. The recent increase in the number and type of carbon cycle-related observations, including both in situ and remote sensing measurements, has opened a new road to optimize model parameters via robust statistical model–data integration techniques, in order to reduce the uncertainties of simulated carbon fluxes and stocks. In this study we present a carbon cycle data assimilation system that assimilates three major data streams, namely themore » Moderate Resolution Imaging Spectroradiometer (MODIS)-Normalized Difference Vegetation Index (NDVI) observations of vegetation activity, net ecosystem exchange (NEE) and latent heat (LE) flux measurements at more than 70 sites (FLUXNET), as well as atmospheric CO2 concentrations at 53 surface stations, in order to optimize the main parameters (around 180 parameters in total) of the Organizing Carbon and Hydrology in Dynamics Ecosystems (ORCHIDEE) LSM (version 1.9.5 used for the Coupled Model Intercomparison Project Phase 5 (CMIP5) simulations). The system relies on a stepwise approach that assimilates each data stream in turn, propagating the information gained on the parameters from one step to the next. Overall, the ORCHIDEE model is able to achieve a consistent fit to all three data streams, which suggests that current LSMs have reached the level of development to assimilate these observations. The assimilation of MODIS-NDVI (step 1) reduced the growing season length in ORCHIDEE for temperate and boreal ecosystems, thus decreasing the global mean annual gross primary production (GPP). Using FLUXNET data (step 2) led to large improvements in the seasonal cycle of the NEE and LE fluxes for all ecosystems (i.e., increased amplitude for

  18. A new stepwise carbon cycle data assimilation system using multiple data streams to constrain the simulated land surface carbon cycle

    SciTech Connect

    Peylin, Philippe; Bacour, Cédric; MacBean, Natasha; Leonard, Sébastien; Rayner, Peter; Kuppel, Sylvain; Kane, Abdou; Maignan, Fabienne; Chevallier, Frédéric; Ciais, Philippe; Prunet, Pascal

    2016-09-20

    Here, large uncertainties in land surface models (LSMs) simulations still arise from inaccurate forcing, poor description of land surface heterogeneity (soil and vegetation properties), incorrect model parameter values and incomplete representation of biogeochemical processes. The recent increase in the number and type of carbon cycle-related observations, including both in situ and remote sensing measurements, has opened a new road to optimize model parameters via robust statistical model–data integration techniques, in order to reduce the uncertainties of simulated carbon fluxes and stocks. In this study we present a carbon cycle data assimilation system that assimilates three major data streams, namely the Moderate Resolution Imaging Spectroradiometer (MODIS)-Normalized Difference Vegetation Index (NDVI) observations of vegetation activity, net ecosystem exchange (NEE) and latent heat (LE) flux measurements at more than 70 sites (FLUXNET), as well as atmospheric CO2 concentrations at 53 surface stations, in order to optimize the main parameters (around 180 parameters in total) of the Organizing Carbon and Hydrology in Dynamics Ecosystems (ORCHIDEE) LSM (version 1.9.5 used for the Coupled Model Intercomparison Project Phase 5 (CMIP5) simulations). The system relies on a stepwise approach that assimilates each data stream in turn, propagating the information gained on the parameters from one step to the next.

    Overall, the ORCHIDEE model is able to achieve a consistent fit to all three data streams, which suggests that current LSMs have reached the level of development to assimilate these observations. The assimilation of MODIS-NDVI (step 1) reduced the growing season length in ORCHIDEE for temperate and boreal ecosystems, thus decreasing the global mean annual gross primary production (GPP). Using FLUXNET data (step 2) led to large improvements in the seasonal cycle of the NEE and LE fluxes for all ecosystems (i.e., increased

  19. A new stepwise carbon cycle data assimilation system using multiple data streams to constrain the simulated land surface carbon cycle

    NASA Astrophysics Data System (ADS)

    Peylin, Philippe; Bacour, Cédric; MacBean, Natasha; Leonard, Sébastien; Rayner, Peter; Kuppel, Sylvain; Koffi, Ernest; Kane, Abdou; Maignan, Fabienne; Chevallier, Frédéric; Ciais, Philippe; Prunet, Pascal

    2016-09-01

    Large uncertainties in land surface models (LSMs) simulations still arise from inaccurate forcing, poor description of land surface heterogeneity (soil and vegetation properties), incorrect model parameter values and incomplete representation of biogeochemical processes. The recent increase in the number and type of carbon cycle-related observations, including both in situ and remote sensing measurements, has opened a new road to optimize model parameters via robust statistical model-data integration techniques, in order to reduce the uncertainties of simulated carbon fluxes and stocks. In this study we present a carbon cycle data assimilation system that assimilates three major data streams, namely the Moderate Resolution Imaging Spectroradiometer (MODIS)-Normalized Difference Vegetation Index (NDVI) observations of vegetation activity, net ecosystem exchange (NEE) and latent heat (LE) flux measurements at more than 70 sites (FLUXNET), as well as atmospheric CO2 concentrations at 53 surface stations, in order to optimize the main parameters (around 180 parameters in total) of the Organizing Carbon and Hydrology in Dynamics Ecosystems (ORCHIDEE) LSM (version 1.9.5 used for the Coupled Model Intercomparison Project Phase 5 (CMIP5) simulations). The system relies on a stepwise approach that assimilates each data stream in turn, propagating the information gained on the parameters from one step to the next. Overall, the ORCHIDEE model is able to achieve a consistent fit to all three data streams, which suggests that current LSMs have reached the level of development to assimilate these observations. The assimilation of MODIS-NDVI (step 1) reduced the growing season length in ORCHIDEE for temperate and boreal ecosystems, thus decreasing the global mean annual gross primary production (GPP). Using FLUXNET data (step 2) led to large improvements in the seasonal cycle of the NEE and LE fluxes for all ecosystems (i.e., increased amplitude for temperate ecosystems). The

  20. How Bedrock Nitrogen Influences Carbon Storage

    NASA Astrophysics Data System (ADS)

    Rios, C.; Mitchell, S. A.

    2016-12-01

    The purpose of this research is to examine how trees, specifically Douglas fir (Pseudotsuga menziesii) responds at sites with high amounts of nitrogen (N) from rocks. In forests where Douglas firs are found, their growth is usually limited by the amount of N available to them. By providing the trees with more N from the rocks, the trees can consume more carbon (C) from the atmosphere. This explores carbon sequestration, capturing C from the atmosphere in the biomass of the trees and reducing the amount of CO2 in the atmosphere. My hypothesis is that trees with access to more N from the rocks, which acts like a fertilizer, will be larger and capture more C from the atmosphere storing it as biomass. We will be collecting measurements from 12 sites in northern California. The sites range from 60 to 1000 parts per million (ppm) of N in the rocks. We will use the diameter at breast height (DBH) measurements to calculate the leaf area index (LAI), which tells us how much C the trees are holding per acre. Contributing to the research will also be the counting tree rings which indicate the age of trees, so we may also see if trees are able to see if trees with more N are growing more annually. The larger amount of N taken from the bedrock resulted in more CO2 taken from the atmosphere as biomass. This resulted in more photosynthetic vegetation per unit area which means the trees are more productive. Carbon stored at these sites helps to slow the effects of increasing atmospheric CO2.

  1. Production of fermentation aroma compounds by Saccharomyces cerevisiae wine yeasts: effects of yeast assimilable nitrogen on two model strains.

    PubMed

    Carrau, Francisco M; Medina, Karina; Farina, Laura; Boido, Eduardo; Henschke, Paul A; Dellacassa, Eduardo

    2008-11-01

    The contribution of yeast fermentation metabolites to the aromatic profile of wine is well documented; however, the biotechnological application of this knowledge, apart from strain selection, is still rather limited and often contradictory. Understanding and modeling the relationship between nutrient availability and the production of desirable aroma compounds by different strains must be one of the main objectives in the selection of industrial yeasts for the beverage and food industry. In order to overcome the variability in the composition of grape juices, we have used a chemically defined model medium for studying yeast physiological behavior and metabolite production in response to nitrogen supplementation so as to identify an appropriate yeast assimilable nitrogen level for strain differentiation. At low initial nitrogen concentrations, strain KU1 produced higher quantities of esters and fatty acids whereas M522 produced higher concentrations of isoacids, gamma-butyrolactone, higher alcohols and 3-methylthio-1-propanol. We propose that although strains KU1 and M522 have a similar nitrogen consumption profile, they represent useful models for the chemical characterization of wine strains in relation to wine quality. The differential production of aroma compounds by the two strains is discussed in relation to their capacity for nitrogen usage and their impact on winemaking. The results obtained here will help to develop targeted metabolic footprinting methods for the discrimination of industrial yeasts.

  2. Turnover of recently assimilated carbon in arctic bryophytes.

    PubMed

    Street, L E; Subke, J A; Sommerkorn, M; Heinemeyer, A; Williams, M

    2011-10-01

    Carbon (C) allocation and turnover in arctic bryophytes is largely unknown, but their response to climatic change has potentially significant impacts on arctic ecosystem C budgets. Using a combination of pulse-chase experiments and a newly developed model of C turnover in bryophytes, we show significant differences in C turnover between two contrasting arctic moss species (Polytrichum piliferum and Sphagnum fuscum). (13)C abundance in moss tissues (measured up to 1 year) and respired CO(2) (traced over 5 days) were used to parameterise the bryophyte C model with four pools representing labile and structural C in photosynthetic and stem tissue. The model was optimised using an Ensemble Kalman Filter to ensure a focus on estimating the confidence intervals (CI) on model parameters and outputs. The ratio of aboveground NPP:GPP in Polytrichum piliferum was 23% (CI 9-35%), with an average turnover time of 1.7 days (CI 1.1-2.5 days). The aboveground NPP:GPP ratio in Sphagnum fuscum was 43% (CI 19-65%) with an average turnover time of 3.1 days (CI 1.6-6.1 days). These results are the first to show differences in C partitioning between arctic bryophyte species in situ and highlight the importance of modelling C dynamics of this group separately from vascular plants for a realistic representation of vegetation in arctic C models.

  3. A dynamical systems analysis of the data assimilation linked ecosystem carbon (DALEC) models.

    PubMed

    Chuter, Anna M; Aston, Philip J; Skeldon, Anne C; Roulstone, Ian

    2015-03-01

    Changes in our climate and environment make it ever more important to understand the processes involved in Earth systems, such as the carbon cycle. There are many models that attempt to describe and predict the behaviour of carbon stocks and stores but, despite their complexity, significant uncertainties remain. We consider the qualitative behaviour of one of the simplest carbon cycle models, the Data Assimilation Linked Ecosystem Carbon (DALEC) model, which is a simple vegetation model of processes involved in the carbon cycle of forests, and consider in detail the dynamical structure of the model. Our analysis shows that the dynamics of both evergreen and deciduous forests in DALEC are dependent on a few key parameters and it is possible to find a limit point where there is stable sustainable behaviour on one side but unsustainable conditions on the other side. The fact that typical parameter values reside close to this limit point highlights the difficulty of predicting even the correct trend without sufficient data and has implications for the use of data assimilation methods.

  4. A dynamical systems analysis of the data assimilation linked ecosystem carbon (DALEC) models

    NASA Astrophysics Data System (ADS)

    Chuter, Anna M.; Aston, Philip J.; Skeldon, Anne C.; Roulstone, Ian

    2015-03-01

    Changes in our climate and environment make it ever more important to understand the processes involved in Earth systems, such as the carbon cycle. There are many models that attempt to describe and predict the behaviour of carbon stocks and stores but, despite their complexity, significant uncertainties remain. We consider the qualitative behaviour of one of the simplest carbon cycle models, the Data Assimilation Linked Ecosystem Carbon (DALEC) model, which is a simple vegetation model of processes involved in the carbon cycle of forests, and consider in detail the dynamical structure of the model. Our analysis shows that the dynamics of both evergreen and deciduous forests in DALEC are dependent on a few key parameters and it is possible to find a limit point where there is stable sustainable behaviour on one side but unsustainable conditions on the other side. The fact that typical parameter values reside close to this limit point highlights the difficulty of predicting even the correct trend without sufficient data and has implications for the use of data assimilation methods.

  5. Variation of summer phytoplankton community composition and its relationship to nitrate and regenerated nitrogen assimilation across the North Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Van Oostende, N.; Fawcett, S. E.; Marconi, D.; Lueders-Dumont, J.; Sabadel, A. J. M.; Woodward, E. M. S.; Jönsson, B. F.; Sigman, D. M.; Ward, B. B.

    2017-03-01

    The North Atlantic Ocean is considered a nitrogen (N) limited system once vernal stabilisation of the water column alleviates light limitation and allows phytoplankton growth to deplete surface nutrients to virtually undetectable levels. Ammonium and other regenerated N forms are then the main surface N source for phytoplankton production. The effort to determine which phytoplankton groups contribute to long-term biological export production would be greatly aided by information on which phytoplankton groups are responsible for the assimilation of nitrate, as opposed to those assimilating predominantly regenerated N. In this study, we used the natural abundance N isotopes to examine basin-scale patterns of nitrate and regenerated N assimilation and evaluated the relationships between these trends and phytoplankton community composition. Samples were collected during a summertime cruise transect (August-September 2013) from the subtropical (36°N 73°W) to the subarctic (54°N 20°W) North Atlantic and analysed for the N isotopic composition (δ15N vs. N2 in air) of particulate nitrogen (PN) and nitrate, size-fractionated chlorophyll a, and phytoplankton group biomass using flow cytometry. The depth of the 300 nmol l-1 nitrate isopleth shoaled from the subtropics (79 m), where phytoplankton stripped surface waters of nitrate, to the subarctic, where it intersected with the surface and the upward nutrient supply drove a summer phytoplankton bloom. The δ15N of PN above the nitracline increased from the subtropics (-0.3‰) to the subarctic (4.2‰), reflecting both a change in the δ15N of the subsurface nitrate source (from 2.4‰ to 5.1‰) and increased reliance by phytoplankton on nitrate relative to regenerated N. Throughout the transect, the phytoplankton community was mainly composed of pico- and nano-sized cells (>88% of chlorophyll a in the <20 μm size fraction). In the part of the transect southwest of the Grand Banks, Prochlorococcus and Synechococcus

  6. Carbon rhizodeposition by plants of contrasting strategies for resource acquisition: responses to various nitrogen fertility regimes

    NASA Astrophysics Data System (ADS)

    Baptist, Florence; Aranjuelo, I.; Lopez-Sangil, L.; Rovia, P.; Nogués, S.

    2010-05-01

    Rhizodeposition by plants is one of the most important physiological mechanisms related to carbon and nitrogen cycling which is also believed to vary along the acquisition-conservation continuum. However, owing to methodological difficulties (i.e. narrow zone of soil around roots and rapid assimilation by soil microbes), root exudation and variations between species are one of the most poorly understood belowground process. Although previous approaches such as hydroponic culture based system, permit the chemical analysis of exudates, the fact that this protocol is qualitative, conditions its utility (see review in Phillips et al. 2008). Others techniques based on pulse-labelling approach have been developed to quantify rhizodeposition but are rarely sufficient to uniformly label all plant inputs to soil. Consequently with this typical pulse chase methods, recent assimilates are labeled but the recalcitrant carbon will not be labeled and therefore the contribution of this carbon will not be considered. Hence, traditional pulse labelling is not a quantitative means of tracing carbon due to inhomogeneous labelling and so limits greatly comparative studies of rhizodeposition fluxes at the interspecific level. In this study we developped a new protocole based on a long-term (3 months) steady state 13C labelling in order (1) to quantify rhizodeposition fluxes for six graminoid species caracterized by contrasted nutrient acquisition strategies and (2) to investigate to what extent various level of nitrogen fertility regimes modulate rhizodeposition fluxes. This method will enable to quantify under natural soil conditions both the accumulation of 13C in the soil but also the quantity that has been respired by the microorganisms during a given time and so will give an integrated picture of rhizodeposition fluxes for each species under each nitrogen fertility level. Results are currently being processed and will be presented at the conference. References: Phillips RP, Erlitz

  7. The Mixed Lineage Nature of Nitrogen Transport and Assimilation in Marine Eukaryotic Phytoplankton: A Case Study of Micromonas

    PubMed Central

    McDonald, Sarah M.; Plant, Joshua N.; Worden, Alexandra Z.

    2010-01-01

    The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (≤2 μm diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer–probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of “mixed lineage gene affiliations” among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for

  8. Nitrogen controls the lability of Alaska Arctic soil carbon

    NASA Astrophysics Data System (ADS)

    Ziolkowski, L. A.; Li, H.

    2016-12-01

    Warming of Arctic soils is causing a large pool of once frozen carbon to become increasingly susceptible to microbial degradation and therefore additional atmospheric carbon dioxide emissions. The microbial degradation of soil carbon is typically studied by measuring carbon dioxide fluxes in laboratory-based incubations or in chambers at the soil surface, with each approach having its limitations. Hypotheses for the factors controlling the fate of soil carbon include temperature and the soil carbon to nitrogen content. However, the amount of soil carbon being used by microbes and what factors are controlling the depth dependent degradation remain unknown. Here we show that the amount of soil carbon being consumed by the microbes is a function of the relative soil nitrogen content rather than soil composition or age. By measuring the radiocarbon content of the soil organic carbon and the lipid membranes of the viable microbial community, we calculated the amount of soil carbon being consumed by the microbes along a transect of active layer soil cores from three tundra and one boreal sites in northern Alaska. We found that while the bulk organic carbon at all sites was progressively older with depth, the age of carbon in the microbes was more variable. Our results indicate that the nitrogen content was a major driver in the microbial usage of soil carbon, and was decoupled from both the soil carbon content and the microbial community composition. The greatest difference in radiocarbon content between soil organic carbon and microbes was observed at the depth of lowest nitrogen content, just below the organic-mineral soil boundary. These results suggest that the depth dependent nitrogen content may regulate the degradation of old, permafrost carbon and therefore potential limit climate feedbacks from Arctic soil degradation.

  9. Intercropping enhances soil carbon and nitrogen.

    PubMed

    Cong, Wen-Feng; Hoffland, Ellis; Li, Long; Six, Johan; Sun, Jian-Hao; Bao, Xing-Guo; Zhang, Fu-Suo; Van Der Werf, Wopke

    2015-04-01

    Intercropping, the simultaneous cultivation of multiple crop species in a single field, increases aboveground productivity due to species complementarity. We hypothesized that intercrops may have greater belowground productivity than sole crops, and sequester more soil carbon over time due to greater input of root litter. Here, we demonstrate a divergence in soil organic carbon (C) and nitrogen (N) content over 7 years in a field experiment that compared rotational strip intercrop systems and ordinary crop rotations. Soil organic C content in the top 20 cm was 4% ± 1% greater in intercrops than in sole crops, indicating a difference in C sequestration rate between intercrop and sole crop systems of 184 ± 86 kg C ha(-1) yr(-1). Soil organic N content in the top 20 cm was 11% ± 1% greater in intercrops than in sole crops, indicating a difference in N sequestration rate between intercrop and sole crop systems of 45 ± 10 kg N ha(-1) yr(-1). Total root biomass in intercrops was on average 23% greater than the average root biomass in sole crops, providing a possible mechanism for the observed divergence in soil C sequestration between sole crop and intercrop systems. A lowering of the soil δ(15) N signature suggested that increased biological N fixation and/or reduced gaseous N losses contributed to the increases in soil N in intercrop rotations with faba bean. Increases in soil N in wheat/maize intercrop pointed to contributions from a broader suite of mechanisms for N retention, e.g., complementary N uptake strategies of the intercropped plant species. Our results indicate that soil C sequestration potential of strip intercropping is similar in magnitude to that of currently recommended management practises to conserve organic matter in soil. Intercropping can contribute to multiple agroecosystem services by increased yield, better soil quality and soil C sequestration. © 2014 John Wiley & Sons Ltd.

  10. Terrestrial nitrogen-carbon cycle interactions at the global scale.

    PubMed

    Zaehle, S

    2013-07-05

    Interactions between the terrestrial nitrogen (N) and carbon (C) cycles shape the response of ecosystems to global change. However, the global distribution of nitrogen availability and its importance in global biogeochemistry and biogeochemical interactions with the climate system remain uncertain. Based on projections of a terrestrial biosphere model scaling ecological understanding of nitrogen-carbon cycle interactions to global scales, anthropogenic nitrogen additions since 1860 are estimated to have enriched the terrestrial biosphere by 1.3 Pg N, supporting the sequestration of 11.2 Pg C. Over the same time period, CO2 fertilization has increased terrestrial carbon storage by 134.0 Pg C, increasing the terrestrial nitrogen stock by 1.2 Pg N. In 2001-2010, terrestrial ecosystems sequestered an estimated total of 27 Tg N yr(-1) (1.9 Pg C yr(-1)), of which 10 Tg N yr(-1) (0.2 Pg C yr(-1)) are due to anthropogenic nitrogen deposition. Nitrogen availability already limits terrestrial carbon sequestration in the boreal and temperate zone, and will constrain future carbon sequestration in response to CO2 fertilization (regionally by up to 70% compared with an estimate without considering nitrogen-carbon interactions). This reduced terrestrial carbon uptake will probably dominate the role of the terrestrial nitrogen cycle in the climate system, as it accelerates the accumulation of anthropogenic CO2 in the atmosphere. However, increases of N2O emissions owing to anthropogenic nitrogen and climate change (at a rate of approx. 0.5 Tg N yr(-1) per 1°C degree climate warming) will add an important long-term climate forcing.

  11. Biochemical evaluation of sulfur and nitrogen assimilation potential of mustard (Brassica juncea L. Czern. & Coss.) under application of slow-release sulfur fertilizer.

    PubMed

    Ahmad, A; Abraham, G; Abdin, M Z

    2001-01-01

    Pot experiments were conducted to study the efficacy of a slow sulfur-releasing fertilizer, sulfur glass fritz (SGF 1), on growth, photosynthesis, and sulfur, and nitrogen assimilation potentials of brown mustard (Brassicajuncea L. Czern. & Coss. cv. Pusa Jaikisan). Growth as indicated by biomass accumulation slowed down in response to the application of sulfur glass fritz. A similar trend was observed in the case of photosynthesis rate. The activity of two marker enzymes, ATP-sulfurylase and nitrate reductase, showed very low levels of activity, indicating poor assimilation of sulfur and nitrogen by the plant under sulfur glass fritz. It is therefore concluded that the release of sulfur by sulfur glass fritz is too slow and that the initial nonavailability of sulfur to the plants could lead to suboptimization of both sulfur- and nitrogen-assimilating enzymes. These factors may contribute to low rates of photosynthesis and poor growth.

  12. Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests

    DOE PAGES

    Wagner, Fabien H.; Hérault, Bruno; Bonal, Damien; ...

    2016-04-28

    Here, the seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positivelymore » to precipitation when rainfall is < 2000 mm yr-1 (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall < 2000 mm yr-1.« less

  13. Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests

    SciTech Connect

    Wagner, Fabien H.; Hérault, Bruno; Bonal, Damien; Stahl, Clément; Anderson, Liana O.; Baker, Timothy R.; Becker, Gabriel Sebastian; Beeckman, Hans; Boanerges Souza, Danilo; Botosso, Paulo Cesar; Bowman, David M. J. S.; Bräuning, Achim; Brede, Benjamin; Brown, Foster Irving; Camarero, Jesus Julio; Camargo, Plínio Barbosa; Cardoso, Fernanda C. G.; Carvalho, Fabrício Alvim; Castro, Wendeson; Chagas, Rubens Koloski; Chave, Jérome; Chidumayo, Emmanuel N.; Clark, Deborah A.; Costa, Flavia Regina Capellotto; Couralet, Camille; da Silva Mauricio, Paulo Henrique; Dalitz, Helmut; de Castro, Vinicius Resende; de Freitas Milani, Jaçanan Eloisa; de Oliveira, Edilson Consuelo; de Souza Arruda, Luciano; Devineau, Jean-Louis; Drew, David M.; Dünisch, Oliver; Durigan, Giselda; Elifuraha, Elisha; Fedele, Marcio; Ferreira Fedele, Ligia; Figueiredo Filho, Afonso; Finger, César Augusto Guimarães; Franco, Augusto César; Freitas Júnior, João Lima; Galvão, Franklin; Gebrekirstos, Aster; Gliniars, Robert; Graça, Paulo Maurício Lima de Alencastro; Griffiths, Anthony D.; Grogan, James; Guan, Kaiyu; Homeier, Jürgen; Kanieski, Maria Raquel; Kho, Lip Khoon; Koenig, Jennifer; Kohler, Sintia Valerio; Krepkowski, Julia; Lemos-Filho, José Pires; Lieberman, Diana; Lieberman, Milton Eugene; Lisi, Claudio Sergio; Longhi Santos, Tomaz; López Ayala, José Luis; Maeda, Eduardo Eijji; Malhi, Yadvinder; Maria, Vivian R. B.; Marques, Marcia C. M.; Marques, Renato; Maza Chamba, Hector; Mbwambo, Lawrence; Melgaço, Karina Liana Lisboa; Mendivelso, Hooz Angela; Murphy, Brett P.; O'Brien, Joseph J.; Oberbauer, Steven F.; Okada, Naoki; Pélissier, Raphaël; Prior, Lynda D.; Roig, Fidel Alejandro; Ross, Michael; Rossatto, Davi Rodrigo; Rossi, Vivien; Rowland, Lucy; Rutishauser, Ervan; Santana, Hellen; Schulze, Mark; Selhorst, Diogo; Silva, Williamar Rodrigues; Silveira, Marcos; Spannl, Susanne; Swaine, Michael D.; Toledo, José Julio; Toledo, Marcos Miranda; Toledo, Marisol; Toma, Takeshi; Tomazello Filho, Mario; Valdez Hernández, Juan Ignacio; Verbesselt, Jan; Vieira, Simone Aparecida; Vincent, Grégoire; Volkmer de Castilho, Carolina; Volland, Franziska; Worbes, Martin; Zanon, Magda Lea Bolzan; Aragão, Luiz E. O. C.

    2016-04-28

    Here, the seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter productivity measurements), their associated canopy photosynthetic capacity (enhanced vegetation index, EVI) and climate, we ask how carbon assimilation and aboveground allocation are related to climate seasonality in tropical forests and how they interact in the seasonal carbon cycle. We found that canopy photosynthetic capacity seasonality responds positively to precipitation when rainfall is < 2000 mm yr-1 (water-limited forests) and to radiation otherwise (light-limited forests). On the other hand, independent of climate limitations, wood productivity and litterfall are driven by seasonal variation in precipitation and evapotranspiration, respectively. Consequently, light-limited forests present an asynchronism between canopy photosynthetic capacity and wood productivity. First-order control by precipitation likely indicates a decrease in tropical forest productivity in a drier climate in water-limited forest, and in current light-limited forest with future rainfall < 2000 mm yr-1.

  14. Contributions of Dissolved DMSP to Bacterial Carbon and Sulfur Assimilation Fluxes: Uncertainties and New Dimensions

    NASA Astrophysics Data System (ADS)

    Kiene, R. P.; Motard-Coté, J.

    2016-02-01

    Dimethylsulfoniopropionate (DMSP) is an organosulfur compound produced in large amounts by marine phytoplankton. Release of algal DMSP into the extracellular dissolved pool (DMSPd) makes it available for uptake by the microbial community. DMSPd concentrations are typically only 1-3 nM, but this pool is very dynamic with 1-5 turnovers per day in oligotrophic ocean waters and 10-100 turnovers per day in productive waters. Data from many different ocean regimes suggest that DMSPd contributes 3 to 15% of bacterial carbon requirements and from 50 to >100% of bacterial sulfur requirements in the euphotic zone, making DMSPd a globally-important substrate in the C & S cycles. Recent developments in DMSPd cycling research, however, raise some uncertainties about these estimates. Quantification of DMSPd cycling fluxes requires accurate measurements of the bioavailable DMSPd concentrations but these have proven difficult to obtain because conventional measurements include non-bioavailable DMSPd, and seawater processing can artificially elevate DMSPd concentrations. The conversion factors for estimating bacterial carbon and sulfur productions are also poorly constrained in DMSPd cycling studies leading to additional uncertainties. Typical low bacterial growth efficiencies used in calculating bacterial carbon demands may not apply to DMSP since DMSP-carbon use efficiency is high (50-60%) even in oligotrophic waters. Most of the estimates of DMSPd contributions to bacterial C and S fluxes have assumed that only heterotrophic bacteria participate in DMSP uptake and assimilation. We now know that prokaryotic and eukaryotic phytoplankton participate in DMSP uptake and sulfur assimilation and that light stimulates these activities, further complicating assessments of DMSPd contributions to heterotrophic metabolisms. DMSP-sulfur assimilation by diverse microbial players may help to explain why estimates of DMSPd contribution to bacterial sulfur production often exceed 100%.

  15. Report on carbon and nitrogen abundance studies

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, Erika

    1991-01-01

    The aim of the proposal was to determine the nitrogen to carbon abundance ratios from transition layer lines in stars with different T(sub eff) and luminosities. The equations which give the surface emission line fluxes and the measured ratio of the NV to CIV emission line fluxes are presented and explained. The abundance results are compared with those of photospheric abundance studies for stars in common with the photospheric investigations. The results show that the analyses are at least as accurate as the photospheric determinations. These studies can be extended to F and early G stars for which photospheric abundance determinations for giants are hard to do because molecular bands become too weak. The abundance determination in the context of stellar evolution is addressed. The N/C abundance ratio increases steeply at the point of evolution for which the convection zone reaches deepest. Looking at the evolution of the rotation velocities v sin i, a steep decrease in v sin i is related to the increasing depth of the convection zone. It is concluded that the decrease in v sin i for T(sub eff) less than or approximately = 5800 K is most probably due to the rearrangement of the angular momentum in the stars due to deep convective mixing. It appears that the convection zone is rotating with nearly depth independent angular momentum. Other research results and ongoing projects are discussed.

  16. Nitrogen Deposition Enhances Carbon Sequestration by Plantations in Northern China

    PubMed Central

    Du, Zhihong; Wang, Wei; Zeng, Wenjing; Zeng, Hui

    2014-01-01

    Nitrogen (N) deposition and its ecological effects on forest ecosystems have received global attention. Plantations play an important role in mitigating climate change through assimilating atmospheric CO2. However, the mechanisms by which increasing N additions affect net ecosystem production (NEP) of plantations remain poorly understood. A field experiment was initialized in May 2009, which incorporated additions of four rates of N (control (no N addition), low-N (5 g N m−2 yr−1), medium-N (10 g N m−2 yr−1), and high-N (15 g N m−2 yr−1)) at the Saihanba Forestry Center, Hebei Province, northern China, a locality that contains the largest area of plantations in China. Net primary production (NPP), soil respiration, and its autotrophic and heterotrophic components were measured. Plant tissue carbon (C) and N concentrations (including foliage, litter, and fine roots), microbial biomass, microbial community composition, extracellular enzyme activities, and soil pH were also measured. N addition significantly increased NPP, which was associated with increased litter N concentrations. Autotrophic respiration (AR) increased but heterotrophic respiration (HR) decreased in the high N compared with the medium N plots, although the HR in high and medium N plots did not significantly differ from that in the control. The increased AR may derive from mycorrhizal respiration and rhizospheric microbial respiration, not live root respiration, because fine root biomass and N concentrations showed no significant differences. Although the HR was significantly suppressed in the high-N plots, soil microbial biomass, composition, or activity of extracellular enzymes were not significantly changed. Reduced pH with fertilization also could not explain the pattern of HR. The reduction of HR may be related to altered microbial C use efficiency. NEP was significantly enhanced by N addition, from 149 to 426.6 g C m−2 yr−1. Short-term N addition may significantly enhance the

  17. Nitrogen deposition enhances carbon sequestration by plantations in northern China.

    PubMed

    Du, Zhihong; Wang, Wei; Zeng, Wenjing; Zeng, Hui

    2014-01-01

    Nitrogen (N) deposition and its ecological effects on forest ecosystems have received global attention. Plantations play an important role in mitigating climate change through assimilating atmospheric CO2. However, the mechanisms by which increasing N additions affect net ecosystem production (NEP) of plantations remain poorly understood. A field experiment was initialized in May 2009, which incorporated additions of four rates of N (control (no N addition), low-N (5 g N m⁻² yr⁻¹), medium-N (10 g N m⁻² yr⁻¹), and high-N (15 g N m⁻² yr⁻¹) at the Saihanba Forestry Center, Hebei Province, northern China, a locality that contains the largest area of plantations in China. Net primary production (NPP), soil respiration, and its autotrophic and heterotrophic components were measured. Plant tissue carbon (C) and N concentrations (including foliage, litter, and fine roots), microbial biomass, microbial community composition, extracellular enzyme activities, and soil pH were also measured. N addition significantly increased NPP, which was associated with increased litter N concentrations. Autotrophic respiration (AR) increased but heterotrophic respiration (HR) decreased in the high N compared with the medium N plots, although the HR in high and medium N plots did not significantly differ from that in the control. The increased AR may derive from mycorrhizal respiration and rhizospheric microbial respiration, not live root respiration, because fine root biomass and N concentrations showed no significant differences. Although the HR was significantly suppressed in the high-N plots, soil microbial biomass, composition, or activity of extracellular enzymes were not significantly changed. Reduced pH with fertilization also could not explain the pattern of HR. The reduction of HR may be related to altered microbial C use efficiency. NEP was significantly enhanced by N addition, from 149 to 426.6 g C m⁻² yr⁻¹. Short-term N addition may significantly enhance

  18. Proteomic analysis of Clostridium thermocellum ATCC 27405 reveals the upregulation of an alternative transhydrogenase-malate pathway and nitrogen assimilation in cells grown on cellulose.

    PubMed

    Burton, Euan; Martin, Vincent J J

    2012-12-01

    Clostridium thermocellum is a Gram-positive thermophilic anaerobic bacterium with the ability to directly convert cellulosic biomass into useful products such as ethanol and hydrogen. In this study, a quantitative comparative proteomic analysis of the organism was performed to identify proteins and biochemical pathways that are differentially utilized by the organism after growth on cellobiose or cellulose. The cytoplasmic and membrane proteomes of C. thermocellum grown on cellulose or cellobiose were quantitatively compared using a metabolic (15)N isotope labelling method in conjunction with nanoLC-ESI-MS/MS (liquid chromatography - electrospray ionization - tandem mass spectrometry). In total, 1255 proteins were identified in the study, and 129 of those were able to have their relative abundance per cell compared in at least one cellular compartment in response to the substrate provided. This study reveals that cells grown on cellulose increase their abundance of phosphoenolpyruvate carboxykinase while decreasing the abundance of pyruvate dikinase and oxaloacetate decarboxylase, suggesting that the organism diverts carbon flow into a transhydrogenase-malate pathway that can increase the production of the biosynthetic intermediates NADPH and GTP. Glutamate dehydrogenase was also found to have increased abundance in cellulose-grown cells, suggesting that the assimilation of ammonia is upregulated in cells grown on the cellulosic substrates. The results illustrate a mechanism by which C. thermocellum can divert carbon into alternative pathways for the purpose of producing biosynthetic intermediates necessary to respond to growth on cellulose, including transhydrogenation of NADH to NADPH and increased nitrogen assimilation.

  19. The fractionation of nitrogen and oxygen isotopes in macroalgae during the assimilation of nitrate

    NASA Astrophysics Data System (ADS)

    Swart, P. K.; Evans, S.; Capo, T.; Altabet, M. A.

    2014-05-01

    In order to determine and understand the stable isotope fractionation of 18O and 15N manifested during assimilation of NO3- in marine macro-benthic algae, two species (Ulva sp. and Agardhiella sp.) have been grown in a wide range of NO3- concentrations (2-500 μM). Two types of experiments were performed. The first was one in which the concentration of the NO3- was allowed to drift downward as it was assimilated by the algae, between 24 h replacements of media. These experiments proceeded for periods of between seven and ten days. A second set of experiments maintained the NO3- concentration at a low steady state value by means of a syringe pump. The effective fractionation during the assimilation of the NO3- was determined by measuring the δ15N of both the (i) new algal growth, and (ii) residual NO3- in the free drift experiments after 0, 12, 24, and 48 h. Fitting models to these data show that the fractionation during assimilation is dependent upon the concentration of NO3- and is effectively zero at concentrations of less than 1 μM. The change in the fractionation with respect to concentration is the greatest at lower concentrations (1-10 μM). The fractionation determined using the δ15N of the NO3- or the solid algal material provided statistically the same result. Therefore, at typical marine concentrations of NO3-, fractionation during assimilation can probably be considered to be negligible. Although the δ18O and δ15N of NO3- in the residual solution were correlated, the slope of the relationship varied with NO3- concentration, with slopes of greater than unity at low concentration. These results suggest shifts in the dominant fractionation mechanism between 1 and 10 μM NO3-. At typical marine concentrations of NO3-, fractionation during assimilation can be considered to be negligible. However, at higher concentrations, fractionation during assimilation will lead to both δ15N values for algal biomass lower than the NO3- source, but also 15N

  20. U.S. Eastern Continental Shelf Carbon Cycling (USECoS): Modeling, Data Assimilation, and Analysis

    NASA Technical Reports Server (NTRS)

    Mannino, Antonio

    2008-01-01

    Although the oceans play a major role in the uptake of fossil fuel CO2 from the atmosphere, there is much debate about the contribution from continental shelves, since many key shelf fluxes are not yet well quantified: the exchange of carbon across the land-ocean and shelf-slope interfaces, air-sea exchange of CO2, burial, and biological processes including productivity. Our goal is to quantify these carbon fluxes along the eastern U.S. coast using models quantitatively verified by comparison to observations, and to establish a framework for predicting how these fluxes may be modified as a result of climate and land use change. Our research questions build on those addressed with previous NASA funding for the USECoS (U.S. Eastern Continental Shelf Carbon Cycling) project. We have developed a coupled biogeochemical ocean circulation model configured for this study region and have extensively evaluated this model with both in situ and remotely-sensed data. Results indicate that to further reduce uncertainties in the shelf component of the global carbon cycle, future efforts must be directed towards 1) increasing the resolution of the physical model via nesting and 2) making refinements to the biogeochemical model and quantitatively evaluating these via the assimilation of biogeochemical data (in situ and remotely-sensed). These model improvements are essential for better understanding and reducing estimates of uncertainties in current and future carbon transformations and cycling in continental shelf systems. Our approach and science questions are particularly germane to the carbon cycle science goals of the NASA Earth Science Research Program as well as the U.S. Climate Change Research Program and the North American Carbon Program. Our interdisciplinary research team consists of scientists who have expertise in the physics and biogeochemistry of the U.S. eastern continental shelf, remote-sensing data analysis and data assimilative numerical models.

  1. U.S. Eastern Continental Shelf Carbon Cycling (USECoS): Modeling, Data Assimilation, and Analysis

    NASA Technical Reports Server (NTRS)

    Mannino, Antonio

    2008-01-01

    Although the oceans play a major role in the uptake of fossil fuel CO2 from the atmosphere, there is much debate about the contribution from continental shelves, since many key shelf fluxes are not yet well quantified: the exchange of carbon across the land-ocean and shelf-slope interfaces, air-sea exchange of CO2, burial, and biological processes including productivity. Our goal is to quantify these carbon fluxes along the eastern U.S. coast using models quantitatively verified by comparison to observations, and to establish a framework for predicting how these fluxes may be modified as a result of climate and land use change. Our research questions build on those addressed with previous NASA funding for the USECoS (U.S. Eastern Continental Shelf Carbon Cycling) project. We have developed a coupled biogeochemical ocean circulation model configured for this study region and have extensively evaluated this model with both in situ and remotely-sensed data. Results indicate that to further reduce uncertainties in the shelf component of the global carbon cycle, future efforts must be directed towards 1) increasing the resolution of the physical model via nesting and 2) making refinements to the biogeochemical model and quantitatively evaluating these via the assimilation of biogeochemical data (in situ and remotely-sensed). These model improvements are essential for better understanding and reducing estimates of uncertainties in current and future carbon transformations and cycling in continental shelf systems. Our approach and science questions are particularly germane to the carbon cycle science goals of the NASA Earth Science Research Program as well as the U.S. Climate Change Research Program and the North American Carbon Program. Our interdisciplinary research team consists of scientists who have expertise in the physics and biogeochemistry of the U.S. eastern continental shelf, remote-sensing data analysis and data assimilative numerical models.

  2. Nitrogen/Sulfur-Codoped Carbon Materials from Chitosan for Supercapacitors

    NASA Astrophysics Data System (ADS)

    Li, Mei; Han, Xianlong; Chang, Xiaoqing; Yin, Wenchao; Ma, Jingyun

    2016-08-01

    d-Methionine and chitosan have been used for fabrication of nitrogen/sulfur-codoped carbon materials by a hydrothermal process followed by carbonization at 750°C for 3 h. The as-prepared carbon materials showed enhanced electrochemical performance, combining electrical double-layer capacitance with pseudocapacitance owing to the doping with sulfur and nitrogen. The specific capacitance of the obtained carbon material reached 135 F g-1 at current density of 1 A g-1, which is much higher than undoped chitosan (67 F g-1). The capacitance retention of the carbon material was almost 97.2% after 5000 cycles at current density of 1 A g-1. With such improved electrochemical performance, the nitrogen/sulfur-codoped carbon material may have promising potential for use in energy-storage electrodes of supercapacitors.

  3. Carbonate assimilation during magma evolution at Nisyros (Greece), South Aegean Arc: Evidence from clinopyroxenite xenoliths

    NASA Astrophysics Data System (ADS)

    Spandler, Carl; Martin, Lukas H. J.; Pettke, Thomas

    2012-08-01

    To contribute to the understanding of magma evolution in arc settings we investigate the oldest volcanic unit (Kanafià Synthem) of Nisyros volcano, located in the eastern Aegean Sea (Greece). The unit consists of porphyritic pillow lavas of basaltic andesite composition with trace element signatures that are characteristic of island-arc magmas. Two lava types are distinguished on the basis of geochemistry and the presence or absence of xenoliths, with the xenolith-bearing lavas having distinctly elevated Sr, MREE/HREE and MgO/Fe2O3 compared to the xenolith-free lavas. Xenoliths include relatively rare quartzo-feldspathic fragments that represent continental-type material, and coarse clinopyroxenite xenoliths that consist largely of aluminous and calcic clinopyroxene, and accessory aluminous spinel. Anorthite-diopside reaction selvages preserved around the clinopyroxenite xenoliths demonstrate disequilibrium between the xenoliths and the host magma. The xenolith clinopyroxene is distinctly enriched in most lithophile trace elements compared to clinopyroxene phenocrysts in the host magmas. A notable exception is the Sr concentration, which is similar in both clinopyroxene types. The high Al and low Na contents of the clinopyroxenites preclude a cumulate, deep metamorphic, or mantle origin for these xenoliths. Instead, their composition and mineralogy are diagnostic of skarn rocks formed by magma-carbonate interaction in the mid/upper crust. The Kanafià lavas are interpreted to have undergone crystal fractionation, magma mixing/mingling and crustal assimilation while resident in the upper crust. We show that magma-carbonate reaction and associated skarn formation does not necessarily result in easily recognised modification of the melt composition, with the exception of increasing Sr contents. Carbonate assimilation also releases significant CO2, which will likely form a free vapour phase due to the low CO2 solubility of arc magmas. In the broader context, we stress

  4. Water Uptake and Carbon Assimilation in Maize at Elevated and ambient CO2: Modeling and Measurement.

    NASA Astrophysics Data System (ADS)

    Timlin, Dennis; Chun, Jong-Ahn; Kim, Soo-Hyung; Yang, Yang; Fleisher, David; Reddy, Vangimalla

    2013-04-01

    Potential transpiration in crops is dependent on both plant and environmental properties. Carbon dioxide content of the atmosphere is linked to potential transpiration because CO2 diffuses onto water saturated surfaces within plant stomata. At high CO2 concentrations, CO2 diffuses rapidly into stomata and therefore stomata do not have to remain open to the atmosphere for long periods of time. This results in lower transpiration rates per unit CO2 assimilated at elevated CO2 concentrations. The objective of this study was to measure CO2 assimilation and water uptake by maize under different irrigation regimes and two CO2 concentrations. The data were then used to evaluate the ability of the maize model MaizSim to simulate the effects of water stress and CO2 on water use and photosynthesis. MaizSim uses a Farquhar type photosynthesis model coupled a Ball-Berry stomatal control model. Non-linear beta functions are used to estimate the effects of temperature on growth and development processes. The experimental data come from experiments in outdoor, sunlit growth chambers at the USDA-ARS Beltsville Agricultural Research Center. The eight treatments comprised two levels of carbon dioxide concentrations (400 and 800 ppm) and four levels of water stress (well-watered control, mild, moderate, and severe). The water stress treatments were applied at both CO2 levels. Water contents were monitored hourly by a Time Domain Reflectometry (TDR) system. The model simulated higher water contents at the same time after applying water stress at the high CO2 treatment than for the low CO2 treatment as was found in the measured data. Measurement of water uptake by roots and carbon assimilation rates in the chambers will be addressed.

  5. Investigating spatial differentiation of model parameters in a carbon cycle data assimilation system

    NASA Astrophysics Data System (ADS)

    Ziehn, T.; Knorr, W.; Scholze, M.

    2011-06-01

    Better estimates of the net exchange of CO2 between the atmosphere and the terrestrial biosphere are urgently needed to improve predictions of future CO2 levels in the atmosphere. The carbon cycle data assimilation system (CCDAS) offers the capability of inversion, while it is at the same time based on a process model that can be used independent of observational data. CCDAS allows the assimilation of atmospheric CO2 concentrations into the terrestrial biosphere model BETHY, constraining its process parameters via an adjoint approach. Here, we investigate the effect of spatial differentiation of a universal carbon balance parameter of BETHY on posterior net CO2 fluxes and their uncertainties. The parameter, β, determines the characteristics of the slowly decomposing soil carbon pool and represents processes that are difficult to model explicitly. Two cases are studied with an assimilation period of 1979 to 2003. In the base case, there is a separate β for each plant functional type (PFT). In the regionalization case, β is differentiated not only by PFT, but also according to each of 11 large continental regions as used by the TransCom project. We find that the choice of spatial differentiation has a profound impact not only on the posterior (optimized) fluxes and their uncertainties, but even more so on the spatial covariance of the uncertainties. Differences are most pronounced in tropical regions, where observations are sparse. While regionalization leads to an improved fit to the observations by about 20% compared to the base case, we notice large spatial variations in the posterior net CO2 flux on a grid cell level. The results illustrate the need for universal process formulations in global-scale atmospheric CO2 inversion studies, at least as long as the observational network is too sparse to resolve spatial fluctuations at the regional scale.

  6. Provenance effect on carbon assimilation, photochemistry and leaf morphology in Mediterranean Cistus species under chilling stress.

    PubMed

    Puglielli, G; Cuevas Román, F J; Catoni, R; Moreno Rojas, J M; Gratani, L; Varone, L

    2017-07-01

    The potential resilience of shrub species to environmental change deserves attention in those areas threatened by climate change, such as the Mediterranean Basin. We asked if leaves produced under different climate conditions through the winter season to spring can highlight the leaf traits involved in determining potential resilience of three Cistus spp. to changing environmental conditions and to what extent intraspecific differences affect such a response. We analysed carbon assimilation, maximum quantum efficiency of PSII photochemistry (Fv /Fm ) and leaf morphological control of the photosynthetic process in leaves formed through the winter season into spring in C. creticus subsp. eriocephalus (CE), C. salvifolius (CS) and C. monspeliensis (CM) grown from seed of different provenances under common garden conditions. Intraspecific differences were found in Fv /Fm for CE and CS. Carbon assimilation-related parameters were not affected by provenance. Moreover, our analysis highlighted that the functional relationships investigated can follow seasonal changes and revealed patterns originating from species-specific differences in LMA arising during the favourable period. Cistus spp. have great ability to modify the structure and function of their leaves in the mid-term in order to cope with changing environmental conditions. The Fv /Fm response to chilling reveals that susceptibility to photoinhibition is a trait under selection in Cistus species. Concerning carbon assimilation, differing ability to control stomatal opening was highlighted between species. Moreover, seasonal changes of the functional relationships investigated can have predictable consequences on species leaf turnover strategies. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  7. Assimilation of Cellulose-Derived Carbon by Microeukaryotes in Oxic and Anoxic Slurries of an Aerated Soil

    PubMed Central

    Chatzinotas, Antonis; Schellenberger, Stefanie; Glaser, Karin

    2013-01-01

    Soil microeukaryotes may trophically benefit from plant biopolymers. However, carbon transfer from cellulose into soil microeukaryotes has not been demonstrated so far. Microeukaryotes assimilating cellulose-derived carbon in oxic and anoxic soil slurries were therefore examined by rRNA-based stable-isotope probing. Bacteriovorous flagellates and ciliates and, likely, mixotrophic algae and saprotrophic fungi incorporated carbon from supplemental [U-13C]cellulose under oxic conditions. A previous study using the same soil suggested that cellulolytic Bacteria assimilated 13C of supplemental cellulose. Thus, it can be assumed that ciliates, cercozoa, and chrysophytes assimilated carbon by grazing upon and utilizing metabolic products of Bacteria that hydrolyzed cellulose in the soil slurries. PMID:23851095

  8. Final report on "Carbon Data Assimilation with a Coupled Ensemble Kalman Filter"

    SciTech Connect

    Kalnay, Eugenia; Kang, Ji-Sun; Fung, Inez

    2014-07-23

    We proposed (and accomplished) the development of an Ensemble Kalman Filter (EnKF) approach for the estimation of surface carbon fluxes as if they were parameters, augmenting the model with them. Our system is quite different from previous approaches, such as carbon flux inversions, 4D-Var, and EnKF with approximate background error covariance (Peters et al., 2008). We showed (using observing system simulation experiments, OSSEs) that these differences lead to a more accurate estimation of the evolving surface carbon fluxes at model grid-scale resolution. The main properties of the LETKF-C are: a) The carbon cycle LETKF is coupled with the simultaneous assimilation of the standard atmospheric variables, so that the ensemble wind transport of the CO2 provides an estimation of the carbon transport uncertainty. b) The use of an assimilation window (6hr) much shorter than the months-long windows used in other methods. This avoids the inevitable “blurring” of the signal that takes place in long windows due to turbulent mixing since the CO2 does not have time to mix before the next window. In this development we introduced new, advanced techniques that have since been adopted by the EnKF community (Kang, 2009, Kang et al., 2011, Kang et al. 2012). These advances include “variable localization” that reduces sampling errors in the estimation of the forecast error covariance, more advanced adaptive multiplicative and additive inflations, and vertical localization based on the time scale of the processes. The main result has been obtained using the LETKF-C with all these advances, and assimilating simulated atmospheric CO2 observations from different observing systems (surface flask observations of CO2 but no surface carbon fluxes observations, total column CO2 from GoSAT/OCO-2, and upper troposphere AIRS retrievals). After a spin-up of about one month, the LETKF-C succeeded in reconstructing the true evolving surface fluxes of carbon at a model grid resolution. When

  9. Final Technical Report [Carbon Data Assimilation with a Coupled Ensemble Kalman Filter

    SciTech Connect

    Kalnay, Eugenia

    2013-08-30

    We proposed (and accomplished) the development of an Ensemble Kalman Filter (EnKF) approach for the estimation of surface carbon fluxes as if they were parameters, augmenting the model with them. Our system is quite different from previous approaches, such as carbon flux inversions, 4D-­Var, and EnKF with approximate background error covariance (Peters et al., 2008). We showed (using observing system simulation experiments, OSSEs) that these differences lead to a more accurate estimation of the evolving surface carbon fluxes at model grid-scale resolution. The main properties of the LETKF-­C are: a) The carbon cycle LETKF is coupled with the simultaneous assimilation of the standard atmospheric variables, so that the ensemble wind transport of the CO2 provides an estimation of the carbon transport uncertainty. b) The use of an assimilation window (6hr) much shorter than the months-long windows used in other methods. This avoids the inevitable “blurring” of the signal that takes place in long windows due to turbulent mixing since the CO2 does not have time to mix before the next window. In this development we introduced new, advanced techniques that have since been adopted by the EnKF community (Kang, 2009, Kang et al., 2011, Kang et al. 2012). These advances include “variable localization” that reduces sampling errors in the estimation of the forecast error covariance, more advanced adaptive multiplicative and additive inflations, and vertical localization based on the time scale of the processes. The main result has been obtained using the LETKF-­C with all these advances, and assimilating simulated atmospheric CO2 observations from different observing systems (surface flask observations of CO2 but no surface carbon fluxes observations, total column CO2 from GoSAT/OCO-­2, and upper troposphere AIRS retrievals). After a spin-­up of about one month, the LETKF-­C succeeded in reconstructing the true evolving surface fluxes of carbon at a model grid

  10. Differential Assimilation of Inorganic Carbon and Leucine by Prochlorococcus in the Oligotrophic North Pacific Subtropical Gyre

    PubMed Central

    Björkman, Karin M.; Church, Matthew J.; Doggett, Joseph K.; Karl, David M.

    2015-01-01

    The light effect on photoheterotrophic processes in Prochlorococcus, and primary and bacterial productivity in the oligotrophic North Pacific Subtropical Gyre was investigated using 14C-bicarbonate and 3H-leucine. Light and dark incubation experiments were conducted in situ throughout the euphotic zone (0–175 m) on nine expeditions to Station ALOHA over a 3-year period. Photosynthetrons were also used to elucidate rate responses in leucine and inorganic carbon assimilation as a function of light intensity. Taxonomic group and cell-specific rates were assessed using flow cytometric sorting. The light:dark assimilation rate ratios of leucine in the top 150 m were ∼7:1 for Prochlorococcus, whereas the light:dark ratios for the non-pigmented bacteria (NPB) were not significant different from 1:1. Prochlorococcus assimilated leucine in the dark at per cell rates similar to the NPB, with a contribution to the total community bacterial production, integrated over the euphotic zone, of approximately 20% in the dark and 60% in the light. Depth-resolved primary productivity and leucine incorporation showed that the ratio of Prochlorococcus leucine:primary production peaked at 100 m then declined steeply below the deep chlorophyll maximum (DCM). The photosynthetron experiments revealed that, for Prochlorococcus at the DCM, the saturating irradiance (Ek) for leucine incorporation was reached at approximately half the light intensity required for light saturation of 14C-bicarbonate assimilation. Additionally, high and low red fluorescing Prochlorococcus populations (HRF and LRF), co-occurring at the DCM, had similar Ek values for their respective substrates, however, maximum assimilation rates, for both leucine and inorganic carbon, were two times greater for HRF cells. Our results show that Prochlorococcus contributes significantly to bacterial production estimates using 3H-leucine, whether or not the incubations are conducted in the dark or light, and this should be

  11. Differential Assimilation of Inorganic Carbon and Leucine by Prochlorococcus in the Oligotrophic North Pacific Subtropical Gyre.

    PubMed

    Björkman, Karin M; Church, Matthew J; Doggett, Joseph K; Karl, David M

    2015-01-01

    The light effect on photoheterotrophic processes in Prochlorococcus, and primary and bacterial productivity in the oligotrophic North Pacific Subtropical Gyre was investigated using (14)C-bicarbonate and (3)H-leucine. Light and dark incubation experiments were conducted in situ throughout the euphotic zone (0-175 m) on nine expeditions to Station ALOHA over a 3-year period. Photosynthetrons were also used to elucidate rate responses in leucine and inorganic carbon assimilation as a function of light intensity. Taxonomic group and cell-specific rates were assessed using flow cytometric sorting. The light:dark assimilation rate ratios of leucine in the top 150 m were ∼7:1 for Prochlorococcus, whereas the light:dark ratios for the non-pigmented bacteria (NPB) were not significant different from 1:1. Prochlorococcus assimilated leucine in the dark at per cell rates similar to the NPB, with a contribution to the total community bacterial production, integrated over the euphotic zone, of approximately 20% in the dark and 60% in the light. Depth-resolved primary productivity and leucine incorporation showed that the ratio of Prochlorococcus leucine:primary production peaked at 100 m then declined steeply below the deep chlorophyll maximum (DCM). The photosynthetron experiments revealed that, for Prochlorococcus at the DCM, the saturating irradiance (E k) for leucine incorporation was reached at approximately half the light intensity required for light saturation of (14)C-bicarbonate assimilation. Additionally, high and low red fluorescing Prochlorococcus populations (HRF and LRF), co-occurring at the DCM, had similar E k values for their respective substrates, however, maximum assimilation rates, for both leucine and inorganic carbon, were two times greater for HRF cells. Our results show that Prochlorococcus contributes significantly to bacterial production estimates using (3)H-leucine, whether or not the incubations are conducted in the dark or light, and this should

  12. A data assimilation framework for constraining upscaled cropland carbon flux seasonality and biometry with MODIS

    NASA Astrophysics Data System (ADS)

    Sus, O.; Heuer, M. W.; Meyers, T. P.; Williams, M.

    2012-08-01

    Agroecosystem models are strongly dependent on information on land management patterns for regional applications. Land management practices play a major role in determining global yield variability, and add an anthropogenic signal to the observed seasonality of atmospheric CO2 concentrations. However, there is still little knowledge on spatial and temporal variability of important farmland activities such as crop sowing dates, and thus these remain rather crudely approximated within carbon cycle studies. In this study, we present a framework allowing for spatio-temporally resolved simulation of cropland carbon fluxes under observational constraints on land management and canopy greenness. We apply a data assimilation methodology in order to explicitly account for information on sowing dates and model leaf area index. MODIS 250 m vegetation index data were assimilated both variationally (for sowing date estimation) and sequentially (for improved model state estimation, using the Ensemble Kalman Filter) into a crop carbon mass balance model (SPAc). In doing so, we are able to accurately quantify the multiannual (2000-2006) regional carbon flux and biometry seasonality of maize-soybean crop rotations surrounding the Bondville Ameriflux eddy covariance site, averaged over 104 pixel locations within the wider area. (1) From Bondville site results we deduce that MODIS-derived sowing dates allow for accurate simulations of growing season carbon cycling at locations for which such ground-truth data are not available. Thus, this framework enables modellers to simulate current (i.e. last 10 yr) carbon cycling of major agricultural regions. Averaged over the 104 field patches analysed, relative spatial variability for biometry and net ecosystem exchange ranges from ~7 % to ~18 %. The annual sign of net biome productivity is not significantly different from carbon neutrality. (2) Moreover, observing carbon cycling at one single field with its individual sowing pattern is not

  13. Effect of methionine sulfoximine on nitrogen metabolism and externally supplied ammonium assimilation in kidney bean.

    PubMed

    Sadunishvili, T; Gvarliani, N; Nutsubidze, N; Kvesitadze, G

    1996-06-01

    L-Methionine sulfoximine (MSO) at concentration 1.25 mM in vivo causes the inhibition of glutamine synthetase (GS) in both roots and leaves of young seedlings of kidney bean following the accumulation of high levels of ammonia and decrease in amounts of free amino acids that is more pronounced in leaves. The inhibition of GS by MSO in leaves in the case of externally supplied 5 mM (15NH4)2SO4 assimilation leads to ammonia accumulation and the decrease in the amounts of glutamine and glutamic acid and the intensity of the incorporation of 15N into them. In roots the inhibition of GS is not followed by the decrease of 15N content into glutamate. It is concluded that the pathway of ammonia primary assimilation in leaves is via GS and glutamate synthase (GOGAT), while in roots glutamate dehydrogenase also plays an important role in this process.

  14. Patterns and variability in seedling carbon assimilation: implications for tree recruitment under climate change.

    PubMed

    Peltier, Drew M P; Ibáñez, Inés

    2015-01-01

    Predicting future forests' structure and functioning is a critical goal for ecologists, thus information on seedling recruitment will be crucial in determining the composition and structure of future forest ecosystems. In particular, seedlings' photosynthetic response to a changing environment will be a key component determining whether particular species establish enough individuals to maintain populations, as growth is a major determinant of survival. We quantified photosynthetic responses of sugar maple (Acer saccharum Marsh.), pignut hickory (Carya glabra Mill.), northern red oak (Quercus rubra L.) and eastern black oak (Quercus velutina Lam.) seedlings to environmental conditions including light habitat, temperature, soil moisture and vapor pressure deficit (VPD) using extensive in situ gas exchange measurements spanning an entire growing season. We estimated the parameters in a hierarchical Bayesian version of the Farquhar model of photosynthesis, additionally informed by soil moisture and VPD, and found that maximum Rubisco carboxylation (V(cmax)) and electron transport (J(max)) rates showed significant seasonal variation, but not the peaked patterns observed in studies of adult trees. Vapor pressure deficit and soil moisture limited J(max) and V(cmax) for all four species. Predictions indicate large declines in summer carbon assimilation rates under a 3 °C increase in mean annual temperature projected by climate models, while spring and fall assimilation rates may increase. Our model predicts decreases in summer assimilation rates in gap habitats with at least 90% probability, and with 20-99.9% probability in understory habitats depending on species. Predictions also show 70% probability of increases in fall and 52% probability in spring in understory habitats. All species were impacted, but our findings suggest that oak species may be favored in northeastern North America under projected increases in temperature due to superior assimilation rates under

  15. Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling

    PubMed Central

    Mooshammer, Maria; Wanek, Wolfgang; Hämmerle, Ieda; Fuchslueger, Lucia; Hofhansl, Florian; Knoltsch, Anna; Schnecker, Jörg; Takriti, Mounir; Watzka, Margarete; Wild, Birgit; Keiblinger, Katharina M; Zechmeister-Boltenstern, Sophie; Richter, Andreas

    2014-01-01

    Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empirical evidence that microbial decomposer communities in soil and plant litter regulate their NUE. We find that microbes retain most immobilized organic N (high NUE), when they are N limited, resulting in low N mineralization. However, when the metabolic control of microbial decomposers switches from N to C limitation, they release an increasing fraction of organic N as ammonium (low NUE). We conclude that the regulation of NUE is an essential strategy of microbial communities to cope with resource imbalances, independent of the regulation of microbial carbon use efficiency, with significant effects on terrestrial N cycling. PMID:24739236

  16. Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling.

    PubMed

    Mooshammer, Maria; Wanek, Wolfgang; Hämmerle, Ieda; Fuchslueger, Lucia; Hofhansl, Florian; Knoltsch, Anna; Schnecker, Jörg; Takriti, Mounir; Watzka, Margarete; Wild, Birgit; Keiblinger, Katharina M; Zechmeister-Boltenstern, Sophie; Richter, Andreas

    2014-04-16

    Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empirical evidence that microbial decomposer communities in soil and plant litter regulate their NUE. We find that microbes retain most immobilized organic N (high NUE), when they are N limited, resulting in low N mineralization. However, when the metabolic control of microbial decomposers switches from N to C limitation, they release an increasing fraction of organic N as ammonium (low NUE). We conclude that the regulation of NUE is an essential strategy of microbial communities to cope with resource imbalances, independent of the regulation of microbial carbon use efficiency, with significant effects on terrestrial N cycling.

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

    PubMed

    Vega-Mas, Izargi; Marino, Daniel; Sánchez-Zabala, Joseba; González-Murua, Carmen; Estavillo, Jose María; González-Moro, María Begoña

    2015-12-01

    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.

  18. Microcystin-tolerant Rhizobium protects plants and improves nitrogen assimilation in Vicia faba irrigated with microcystin-containing waters.

    PubMed

    Lahrouni, Majida; Oufdou, Khalid; El Khalloufi, Fatima; Benidire, Loubna; Albert, Susann; Göttfert, Michael; Caviedes, Miguel A; Rodriguez-Llorente, Ignacio D; Oudra, Brahim; Pajuelo, Eloísa

    2016-05-01

    Irrigation of crops with microcystins (MCs)-containing waters-due to cyanobacterial blooms-affects plant productivity and could be a way for these potent toxins entering the food chain. This study was performed to establish whether MC-tolerant rhizobia could benefit growth, nodulation, and nitrogen metabolism of faba bean plants irrigated with MC-containing waters. For that, three different rhizobial strains-with different sensitivity toward MCs-were used: RhOF96 (most MC-sensitive strain), RhOF125 (most MC-tolerant strain), or Vicz1.1 (reference strain). As a control, plants grown without rhizobia and fertilized by NH4NO3 were included in the study. MC exposure decreased roots (30-37 %) and shoots (up to 15 %) dry weights in un-inoculated plants, whereas inoculation with rhizobia protects plants toward the toxic effects of MCs. Nodulation and nitrogen content were significantly impaired by MCs, with the exception of plants inoculated with the most tolerant strain RhOF125. In order to deep into the effect of inoculation on nitrogen metabolism, the nitrogen assimilatory enzymes (glutamine synthetase (GS) and glutamate synthase (GOGAT)) were investigated: Fertilized plants showed decreased levels (15-30 %) of these enzymes, both in shoots and roots. By contrast, inoculated plants retained the levels of these enzymes in shoots and roots, as well as the levels of NADH-GOGAT activity in nodules. We conclude that the microcystin-tolerant Rhizobium protects faba bean plants and improves nitrogen assimilation when grown in the presence of MCs.

  19. Carbon isotopic composition of assimilated and respired CO2 in Southeastern US pine forests

    NASA Astrophysics Data System (ADS)

    Mortazavi, B.; Conte, M. H.; Chanton, J.; Martin, T.; Teklemerian, T.; Cropper, W.; Weber, J.

    2010-12-01

    We measured the 13C of assimilated carbon [foliage organic matter (δCOM), leaf soluble carbohydrates ((δCSC), and leaf waxes ((δCW)] and respiratory carbon [foliage (δCF), soil (δCS) and ecosystem respired CO2 (δCR)] over a two-year period at two sites in central Florida that are typical of Southeastern US coastal plain pine ecosystems. Our objective was to determine how climatic variables, operating by affecting plant physiology and photosynthetic discrimination (Δ), influence the isotopic composition of assimilated carbon pools and of ecosystem respired CO2. The first site was a naturally regenerated 32 m tall stand of mature longleaf pine (Pinus palustris Mill.) with mature slash pine (Pinus elliottii) subdominants, while the second was a planted, mid-rotation 13 m tall stand of slash pine (Pinus elliottii var. elliottii Engelm.). δCOM, δCSC, δCW, and δCF of P. palustris were 13C enriched by about 2‰ relative to that of P. elliottii in the mid-rotation plantation. Despite this enrichment, mean δCR of the P. palustris stand was similar to that at the P. elliottii plantation, reflecting additional respiratory inputs from the more isotopically depleted P. elliottii subdominant and understory. In both P. palustris and P. elliottii, a small decrease was observed in δCOM over the two year study, but not in δCSC, δCF, δCS or δCR. Intriguingly, a significant 2‰ decrease was also observed in the very long chain needlewaxes (C32-36 n-alkanoic acids), but not the more abundant C24-28 waxes. As the carbon in waxes is supplied by internal storage reserves, our data suggest there may be distinct carbon source pathways for waxes of differing chain lengths. The long-term decrease in the 13C of foliar carbon and waxes also suggests recovery from severe drought conditions prior to our study. δCF and δCR were consistently 13C enriched relative to assimilated C and were insensitive to variations in vapor pressure deficit (D). The small variability in δCA and

  20. Isotopic inferences of ancient biochemistries - Carbon, sulfur, hydrogen, and nitrogen

    NASA Technical Reports Server (NTRS)

    Schidlowski, M.; Hayes, J. M.; Kaplan, I. R.

    1983-01-01

    In processes of biological incorporation and subsequent biochemical processing sizable isotope effects occur as a result of both thermodynamic and kinetic fractionations which take place during metabolic and biosynthetic reactions. In this chapter a review is provided of earlier work and recent studies on isotope fractionations in the biogeochemical cycles of carbon, sulfur, hydrogen, and nitrogen. Attention is given to the biochemistry of carbon isotope fractionation, carbon isotope fractionation in extant plants and microorganisms, isotope fractionation in the terrestrial carbon cycle, the effects of diagenesis and metamorphism on the isotopic composition of sedimentary carbon, the isotopic composition of sedimentary carbon through time, implications of the sedimentary carbon isotope record, the biochemistry of sulfur isotope fractionation, pathways of the biogeochemical cycle of nitrogen, and the D/H ratio in naturally occurring materials.

  1. Isotopic inferences of ancient biochemistries - Carbon, sulfur, hydrogen, and nitrogen

    NASA Technical Reports Server (NTRS)

    Schidlowski, M.; Hayes, J. M.; Kaplan, I. R.

    1983-01-01

    In processes of biological incorporation and subsequent biochemical processing sizable isotope effects occur as a result of both thermodynamic and kinetic fractionations which take place during metabolic and biosynthetic reactions. In this chapter a review is provided of earlier work and recent studies on isotope fractionations in the biogeochemical cycles of carbon, sulfur, hydrogen, and nitrogen. Attention is given to the biochemistry of carbon isotope fractionation, carbon isotope fractionation in extant plants and microorganisms, isotope fractionation in the terrestrial carbon cycle, the effects of diagenesis and metamorphism on the isotopic composition of sedimentary carbon, the isotopic composition of sedimentary carbon through time, implications of the sedimentary carbon isotope record, the biochemistry of sulfur isotope fractionation, pathways of the biogeochemical cycle of nitrogen, and the D/H ratio in naturally occurring materials.

  2. The fractionation of nitrogen and oxygen isotopes in macroalgae during the assimilation of nitrate

    NASA Astrophysics Data System (ADS)

    Swart, P. K.; Evans, S.; Capo, T.; Altabet, M. A.

    2014-11-01

    In order to determine and understand the stable isotope fractionation of 18O and 15N manifested during assimilation of NO3- in marine macro-benthic algae, two species (Ulva sp. and Agardhiella sp.) have been grown in a wide range of NO3- concentrations (2-500 μM). Two types of experiments were performed. The first was one in which the concentration of the NO3- was allowed to drift downward as it was assimilated by the algae, between 24 hour replacements of media. These experiments proceeded for periods of between 7 and 10 days. A second set of experiments maintained the NO3- concentration at a low steady-state value by means of a syringe pump. The effective fractionation during the assimilation of the NO3- was determined by measuring the δ15N of both the (i) new algal growth and (ii) residual NO3- in the free-drift experiments after 0, 12, 24 and 48 h. Modelling these data show that the fractionation during assimilation is dependent upon the concentration of NO3- and is effectively 0 at concentrations of less than ~2 μM. The change in the fractionation with respect to concentration is the greatest at lower concentrations (2-10 μM). The fractionation stablizes between 4 and 6‰ at concentrations of between 50 and 500 μM. Although the δ18O and δ15N values of NO3- in the residual solution were correlated, the slope of relationship also varied with respect to NO3- concentration, with slopes of greater than unity at low concentration. These results suggest shifts in the dominant fractionation mechanism of 15N and 18O between concentrations of 1 and 10 μM NO3-. At higher NO3- concentrations (>10-50 μM), fractionation during assimilation will lead to δ15N values in algal biomass lower than the ambient NO3- and 15N enrichments in the residual NO3-.

  3. Nitrogen deposition: how important is it for global terrestrial carbon uptake?

    NASA Astrophysics Data System (ADS)

    Bala, G.; Devaraju, N.; Chaturvedi, R. K.; Caldeira, K.; Nemani, R.

    2013-07-01

    Global carbon budget studies indicate that the terrestrial ecosystems have remained a~large sink for carbon despite widespread deforestation activities. CO2-fertilization, N deposition and re-growth of mid-latitude forests are believed to be key drivers for land carbon uptake. In this study, we assess the importance of N deposition by performing idealized near-equilibrium simulations using the Community Land Model 4.0 (CLM4). In our equilibrium simulations, only 12-17% of the deposited Nitrogen is assimilated into the ecosystem and the corresponding carbon uptake can be inferred from a C : N ratio of 20:1. We calculate the sensitivity of the terrestrial biosphere for CO2-fertilization, climate warming and N deposition as changes in total ecosystem carbon for unit changes in global mean atmospheric CO2 concentration, global mean temperature and Tera grams of Nitrogen deposition per year, respectively. Based on these sensitivities, it is estimated that about 242 PgC could have been taken up by land due to the CO2 fertilization effect and an additional 175 PgC taken up as a result of the increased N deposition since the pre-industrial period. Because of climate warming, terrestrial ecosystem could have lost about 152 PgC during the same period. Therefore, since preindustrial times terrestrial carbon losses due to warming may have been approximately compensated by effects of increased N deposition, whereas the effect of CO2-fertilization is approximately indicative of the current increase in terrestrial carbon stock. Our simulations also suggest that the sensitivity of carbon storage to increased N deposition decreases beyond current levels, indicating climate warming effects on carbon storage may overwhelm N deposition effects in the future.

  4. Nitrogen deposition: how important is it for global terrestrial carbon uptake?

    NASA Astrophysics Data System (ADS)

    Bala, G.; Devaraju, N.; Chaturvedi, R. K.; Caldeira, K.; Nemani, R.

    2013-11-01

    Global carbon budget studies indicate that the terrestrial ecosystems have remained a large sink for carbon despite widespread deforestation activities. CO2 fertilization, N deposition and re-growth of mid-latitude forests are believed to be key drivers for land carbon uptake. In this study, we assess the importance of N deposition by performing idealized near-equilibrium simulations using the Community Land Model 4.0 (CLM4). In our equilibrium simulations, only 12-17% of the deposited nitrogen is assimilated into the ecosystem and the corresponding carbon uptake can be inferred from a C : N ratio of 20 : 1. We calculate the sensitivity of the terrestrial biosphere for CO2 fertilization, climate warming and N deposition as changes in total ecosystem carbon for unit changes in global mean atmospheric CO2 concentration, global mean temperature and Tera grams of nitrogen deposition per year, respectively. Based on these sensitivities, it is estimated that about 242 PgC could have been taken up by land due to the CO2 fertilization effect and an additional 175 PgC taken up as a result of the increased N deposition since the pre-industrial period. Because of climate warming, the terrestrial ecosystem could have lost about 152 PgC during the same period. Therefore, since pre-industrial times terrestrial carbon losses due to warming may have been more or less compensated by effects of increased N deposition, whereas the effect of CO2 fertilization is approximately indicative of the current increase in terrestrial carbon stock. Our simulations also suggest that the sensitivity of carbon storage to increased N deposition decreases beyond current levels, indicating that climate warming effects on carbon storage may overwhelm N deposition effects in the future.

  5. A data assimilation framework for constraining upscaled cropland carbon flux seasonality and biometry with MODIS

    NASA Astrophysics Data System (ADS)

    Sus, O.; Heuer, M. W.; Meyers, T. P.; Williams, M.

    2013-04-01

    Agroecosystem models are strongly dependent on information on land management patterns for regional applications. Land management practices play a major role in determining global yield variability, and add an anthropogenic signal to the observed seasonality of atmospheric CO2 concentrations. However, there is still little knowledge on spatial and temporal variability of important farmland activities such as crop sowing dates, and thus these remain rather crudely approximated within carbon cycle studies. In this study, we present a framework allowing for spatio-temporally resolved simulation of cropland carbon fluxes under observational constraints on land management and canopy greenness. We apply data assimilation methodology in order to explicitly account for information on sowing dates and model leaf area index. MODIS 250 m vegetation index data were assimilated both in batch-calibration for sowing date estimation and sequentially for improved model state estimation, using the ensemble Kalman filter (EnKF), into a crop carbon mass balance model (SPAc). In doing so, we are able to quantify the multiannual (2000-2006) regional carbon flux and biometry seasonality of maize-soybean crop rotations surrounding the Bondville Ameriflux eddy covariance site, averaged over 104 pixel locations within the wider area. (1) Validation at the Bondville site shows that growing season C cycling is simulated accurately with MODIS-derived sowing dates, and we expect that this framework allows for accurate simulations of C cycling at locations for which ground-truth data are not available. Thus, this framework enables modellers to simulate current (i.e. last 10 yr) carbon cycling of major agricultural regions. Averaged over the 104 field patches analysed, relative spatial variability for biometry and net ecosystem exchange ranges from ∼7% to ∼18%. The annual sign of net biome productivity is not significantly different from carbon neutrality. (2) Moreover, observing carbon

  6. Quantifying fire emissions and associated aerosols species using assimilation of satellite carbon monoxide retrievals.

    NASA Astrophysics Data System (ADS)

    Barre, J.; Edwards, D. P.; Worden, H. M.

    2016-12-01

    Wildfires tend to be more intense and hence costly and are predicted to increase in frequency under a warming climate. For example, the recent August 2015 Washington State fires were the largest in the state's history. Also in September and October 2015 very intense fires over Indonesia produced some of the highest concentration of carbon monoxide (CO) ever seen from space. Such larges fires impact not only the local environment but also affects air quality far downwind through the long-range transport of pollutants. Global to continental scale coverage showing the evolution of CO resulting from fire emission is available from satellite observations. Carbon monoxide is the only atmospheric trace gas for which satellite multispectral retrievals have demonstrated reliable independent profile information close to the surface and also higher in the free troposphere. The unique CO profile product from Terra/MOPITT clearly distinguishes near-surface CO from the free troposphere CO. Also previous studies have suggested strong correlations between primary emissions of fire organic and black carbon aerosols and CO. We will present results from the Ensemble Adjustement Kalman Filter (DART) system that has been developed to assimilate MOPITT CO in the global scale chemistry-climate model CAM-Chem. The ensemble technique allows inference on various fire model state variables such as CO emissions and also aerosol species resulting from fires such as organic and black carbon. The benefit of MOPITT CO assimilation on the Washington and Indonesian fire cases studies will be diagnosed regarding the CO fire emissions, black and organic carbon inference using the ensemble information.

  7. Quantifying Wildfire Emissions and associated Aerosol Species using Assimilation of Satellite Carbon Monoxide Retrievals

    NASA Astrophysics Data System (ADS)

    Edwards, David; Barre, Jerome; Worden, Helen; Gaubert, Benjamin

    2017-04-01

    Intense and costly wildfires tend are predicted to increase in frequency under a warming climate. For example, the recent August 2015 Washington State fires were the largest in the state's history. Also in September and October 2015 very intense fires over Indonesia produced some of the highest concentrations of carbon monoxide (CO) ever seen from satellite. Such larges fires impact not only the local environment but also affect air quality far downwind through the long-range transport of pollutants. Global to continental scale coverage showing the evolution of CO resulting from fire emission is available from satellite observations. Carbon monoxide is the only atmospheric trace gas for which satellite multispectral retrievals have demonstrated reliable independent profile information close to the surface and also higher in the free troposphere. The unique CO profile product from Terra/MOPITT clearly distinguishes near-surface CO from the free troposphere CO. Also previous studies have suggested strong correlations between primary emissions of fire organic and black carbon aerosols and CO. We will present results from the Ensemble Adjustement Kalman Filter (DART) system that has been developed to assimilate MOPITT CO in the global-scale chemistry-climate model CAM-Chem. The ensemble technique allows inference on various fire model state variables such as CO emissions, and also aerosol species resulting from fires such as organic and black carbon. The benefit of MOPITT CO profile assimilation for estimating the CO emissions from the Washington and Indonesian fire cases will be discussed, along with the ability of the ensemble approach to infer information on the black and organic carbon aerosol distribution. This study builds on capability to quantitatively integrate satellite observations and models developed in recent years through projects funded by the NASA ACMAP Program.

  8. Spectroscopic investigation of nitrogen-functionalized carbon materials

    SciTech Connect

    Wood, Kevin N.; Christensen, Steven T.; Nordlund, Dennis; Dameron, Arrelaine A.; Ngo, Chilan; Dinh, Huyen; Gennett, Thomas; O'Hayre, Ryan; Pylypenko, Svitlana

    2016-04-07

    Carbon materials are used in a diverse set of applications ranging from pharmaceuticals to catalysis. Nitrogen modification of carbon powders has shown to be an effective method for enhancing both surface and bulk properties of as-received material for a number of applications. Unfortunately, control of the nitrogen modification process is challenging and can limit the effectiveness and reproducibility of N-doped materials. Additionally, the assignment of functional groups to specific moieties on the surface of nitrogen-modified carbon materials is not straightforward. Herein, we complete an in-depth analysis of functional groups present at the surface of ion-implanted Vulcan and Graphitic Vulcan through the use of X-ray photoelectron spectroscopy (XPS) and near edge X-ray adsorption fine structure spectroscopy (NEXAFS). Our results show that regardless of the initial starting materials used, nitrogen ion implantation conditions can be tuned to increase the amount of nitrogen incorporation and to obtain both similar and reproducible final distributions of nitrogen functional groups. The development of a well-controlled/reproducible nitrogen implantation pathway opens the door for carbon supported catalyst architectures to have improved numbers of nucleation sites, decreased particle size, and enhanced catalyst-support interactions.

  9. [Effect of earthworm inoculation on soil carbon and nitrogen dynamics and on crop yield with application of corn residues].

    PubMed

    Li, Huixin; Hu, Feng; Shen, Qirong; Chen, Xiaoyun; Cang, Long; Wang, Xia

    2002-12-01

    This study was carried out in the Experimental Station of Nanjing Agricultural University, which is in a subtropical monsoon region characterized by a warm-wet spring and a hot-dry summer. The annual average temperature, precipitation and evaporation are 15.6 degrees C, 1010 mm and 1560 mm, respectively. In 1999, the experimental plots (2.8 m x 1.0 m x 0.6 m) were established by concrete frame. Soil in the plots was orthic aquisols collected from Rugao County, Jiangsu Province. Crop rotation was upland rice and winter wheat. At the beginning of the first crop (rice) season, earthworms (Pheretima sp.) were inoculated at a density of 10.m-2 and 20.m-2, respectively, in the plots with an application of corn residues at the rate of 1500 g.m-2(750 g.m-2 in the following seasons). The responses of soil carbon and nitrogen and crop yield to earthworm activity were investigated from 1999 to 2001. The results showed that earthworms had no significant influences on total soil carbon and nitrogen content, which implied that there was no depletion of soil carbon and nitrogen pools in the presence of earthworms. The maintenance of soil carbon might be explained by low assimilation efficiency of organic matter by earthworms, and by the compensation of carbon returning from plant production enhancement. Soil mineral nitrogen, soil microbial biomass carbon and microbial biomass nitrogen were increased, and nitrogen mineralization was strengthened by earthworm activities, which was more obvious at jointing/booting and heading stages. In comparison with no-worm treatments, the yield of rice wheat increased by 9.3% and 5.1%, respectively, in the treatments inoculated with earthworms. It was concluded that earthworm was very important in promoting nitrogen recycling of crop residues and plant productivity, and in keeping the balance of soil carbon pool as well.

  10. Ubiquitous dissolved inorganic carbon assimilation by marine bacteria in the Pacific Northwest coastal ocean as determined by stable isotope probing.

    PubMed

    DeLorenzo, Suzanne; Bräuer, Suzanna L; Edgmont, Chelsea A; Herfort, Lydie; Tebo, Bradley M; Zuber, Peter

    2012-01-01

    In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM (13)C-NaHCO(3), doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.

  11. Ubiquitous Dissolved Inorganic Carbon Assimilation by Marine Bacteria in the Pacific Northwest Coastal Ocean as Determined by Stable Isotope Probing

    PubMed Central

    DeLorenzo, Suzanne; Bräuer, Suzanna L.; Edgmont, Chelsea A.; Herfort, Lydie; Tebo, Bradley M.; Zuber, Peter

    2012-01-01

    In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM 13C-NaHCO3, doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process. PMID:23056406

  12. Carbon and nitrogen isotope variations in tree-rings as records of perturbations in regional carbon and nitrogen cycles.

    PubMed

    Bukata, Andrew R; Kyser, T Kurtis

    2007-02-15

    Increasing anthropogenic pollution from urban centers and fossil fuel combustion can impact the carbon and nitrogen cycles in forests. To assess the impact of twentieth century anthropogenic pollution on forested system carbon and nitrogen cycles, variations in the carbon and nitrogen isotopic compositions of tree-rings were measured. Individual annual growth rings in trees from six sites across Ontario and one in New Brunswick, Canada were used to develop site chronologies of tree-ring delta 15N and delta 13C values. Tree-ring 615N values were approximately 0.5% per hundred higher and correlated with contemporaneous foliar samples from the same tree, but not with delta 15N values of soil samples. Temporal trends in carbon and nitrogen isotopic compositions of these tree-rings are consistent with increasing anthropogenic influence on both the carbon and nitrogen cycles since 1945. Tree-ring delta 13C values and delta 15N values are correlated at both remote and urban-proximal sites, with delta 15N values decreasing since 1945 and converging on 1% per hundred at urban-proximal sites and decreasing but not converging on a single delta 15N value in remote sites. These results indicate that temporal trends in tree-ring nitrogen and carbon isotopic compositions record the regional extent of pollution.

  13. Modeling whole-tree carbon assimilation rate using observed transpiration rates and needle sugar carbon isotope ratios.

    PubMed

    Hu, Jia; Moore, David J P; Riveros-Iregui, Diego A; Burns, Sean P; Monson, Russell K

    2010-03-01

    *Understanding controls over plant-atmosphere CO(2) exchange is important for quantifying carbon budgets across a range of spatial and temporal scales. In this study, we used a simple approach to estimate whole-tree CO(2) assimilation rate (A(Tree)) in a subalpine forest ecosystem. *We analysed the carbon isotope ratio (delta(13)C) of extracted needle sugars and combined it with the daytime leaf-to-air vapor pressure deficit to estimate tree water-use efficiency (WUE). The estimated WUE was then combined with observations of tree transpiration rate (E) using sap flow techniques to estimate A(Tree). Estimates of A(Tree) for the three dominant tree species in the forest were combined with species distribution and tree size to estimate and gross primary productivity (GPP) using an ecosystem process model. *A sensitivity analysis showed that estimates of A(Tree) were more sensitive to dynamics in E than delta(13)C. At the ecosystem scale, the abundance of lodgepole pine trees influenced seasonal dynamics in GPP considerably more than Engelmann spruce and subalpine fir because of its greater sensitivity of E to seasonal climate variation. *The results provide the framework for a nondestructive method for estimating whole-tree carbon assimilation rate and ecosystem GPP over daily-to weekly time scales.

  14. Relationship of Nitrogen Use Efficiency with the Activities of Enzymes Involved in Nitrogen Uptake and Assimilation of Finger Millet Genotypes Grown under Different Nitrogen Inputs

    PubMed Central

    Gupta, Nidhi; Gupta, Atul K.; Gaur, Vikram S.; Kumar, Anil

    2012-01-01

    Nitrogen responsiveness of three-finger millet genotypes (differing in their seed coat colour) PRM-1 (brown), PRM-701 (golden), and PRM-801 (white) grown under different nitrogen doses was determined by analyzing the growth, yield parameters and activities of nitrate reductase (NR), glutamine synthetase (GS), glutamate synthase; GOGAT, and glutamate dehydrogenase (GDH) at different developmental stages. High nitrogen use efficiency and nitrogen utilization efficiency were observed in PRM-1 genotype, whereas high nitrogen uptake efficiency was observed in PRM-801 genotype. At grain filling nitrogen uptake efficiency in PRM-1 negatively correlated with NR, GS, GOGAT activities whereas it was positively correlated in PRM-701 and PRM-801, however, GDH showed a negative correlation. Growth and yield parameters indicated that PRM-1 responds well at high nitrogen conditions while PRM-701 and PRM-801 respond well at normal and low nitrogen conditions respectively. The study indicates that PRM-1 is high nitrogen responsive and has high nitrogen use efficiency, whereas golden PRM-701 and white PRM-801 are low nitrogen responsive genotypes and have low nitrogen use efficiency. However, the crude grain protein content was higher in PRM-801 genotype followed by PRM-701 and PRM-1, indicating negative correlation of nitrogen use efficiency with source to sink relationship in terms of seed protein content. PMID:22919342

  15. Sequestration of Carbon in Mycorrhizal Fungi Under Nitrogen Fertilization

    NASA Astrophysics Data System (ADS)

    Treseder, K. K.; Turner, K. M.

    2005-12-01

    Mycorrhizal fungi are root symbionts that facilitate plant uptake of soil nutrients in exchange for plant carbohydrates. They grow in almost every terrestrial ecosystem on earth, form relationships with about 80% of plant species, and receive 10 to 20% of the carbon fixed by their host plants. As such, they could potentially sequester a significant amount of carbon in ecosystems. We hypothesized that nitrogen fertilization would decrease carbon storage in mycorrhizal fungi, because plants should reduce investment of carbon in mycorrhizal fungi when nitrogen availability is high. We measured the abundance of two major groups of mycorrhizal fungi, arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi, in control and nitrogen-fertilized plots within three boreal ecosystems of inland Alaska. The ecosystems represented different recovery stages following severe fire, and comprised a young site dominated by AM fungi, an old site dominated by ECM fungi, and an intermediate site co-dominated by both groups. Pools of mycorrhizal carbon included root-associated AM and ECM structures, soil-associated AM hyphae, and soil-associated glomalin. Glomalin is a glycoprotein produced only by AM fungi. It is present in the cell walls of AM hyphae, and then is deposited in the soil as the hyphae senesce. Nitrogen significantly altered total mycorrhizal carbon pools, but its effect varied by site (site * N interaction, P = 0.05). Under nitrogen fertilization, mycorrhizal carbon was reduced from 99 to 50 g C m2 in the youngest site, was increased from 124 to 203 g C m2 in the intermediate-aged site, and remained at 35 g C m2 in the oldest site. The changes in total mycorrhizal carbon stocks were driven mostly by changes in glomalin (site * N interaction, P = 0.05), and glomalin stocks were strongly correlated with AM hyphal abundance (P < 0.01). Nevertheless, it is not clear why AM hyphae responded differently to nitrogen fertilization in the different sites. Carbon stocks within

  16. Nitrogen assimilation and short term retention in a nutrient-rich tidal freshwater marsh - a whole ecosystem 15N enrichment study

    NASA Astrophysics Data System (ADS)

    Gribsholt, B.; Struyf, E.; Tramper, A.; de Brabandere, L.; Brion, N.; van Damme, S.; Meire, P.; Dehairs, F.; Middelburg, J. J.; Boschker, H. T. S.

    2007-01-01

    An intact tidal freshwater marsh system (3477 m2) was labelled by adding 15N-ammonium as a tracer to the flood water inundating the ecosystem. The appearance and retention of 15N-label in different marsh components (leaves, roots, sediment, leaf litter and invertebrate fauna) was followed over 15 days. This allowed us to elucidate the direct assimilation and dependence on creek-water nitrogen on a relatively short term and provided an unbiased assessment of the relative importance of the various compartments within the ecosystem. Two separate experiments were conducted, one in spring/early summer (May 2002) when plants were young and building up biomass; the other in late summer (September 2003) when macrophytes were in a flowering or early senescent state. Nitrogen assimilation rate (per hour inundated) was >3 times faster in May compared to September. On both occasions, however, the results clearly revealed that the less conspicuous compartments such as leaf litter and ruderal vegetations are more important in nitrogen uptake and retention than the prominent reed (Phragmites australis) meadows. Moreover, short-term nitrogen retention in these nutrient rich marshes occurs mainly via microbial pathways associated with the litter and sediment. Rather than direct uptake by macrophytes, it is the large reactive surface area provided by the tidal freshwater marsh vegetation that is most crucial for nitrogen transformation, assimilation and short term retention in nutrient rich tidal freshwater marshes. Our results clearly revealed the dominant role of microbes in initial nitrogen retention in marsh ecosystems.

  17. Interactive state-parameter estimation of a crop carbon mass balance model through the assimilation of observed winter wheat carbon flux and stock data

    NASA Astrophysics Data System (ADS)

    Sus, O.; Williams, M. D.; Gruenwald, T.

    2010-12-01

    Next to the consideration of land management practises, modelling the carbon balance of croplands requires a crop carbon budget model that realistically simulates photosynthesis, ecosystem respiration, soil carbon dynamics, and phenology dependant on crop-specific parameters and carbon allocation patterns. A crop carbon mass balance model is a tool which can aid to answer questions related to cropland carbon sequestration potential, best-practise recommendations, seasonal patterns and amplitude of net carbon exchange (NEE), and prediction of biomass growth and crop yield. However, land management complicates modelling of cropland NEE by largely determining the onset and length of the growing season of agricultural areas. Human decision making on crop cultivars, sowing and harvest dates, and management practices is difficult to simulate, and corresponding reliable data for larger spatial and temporal scales is still sparse. Crop carbon budget models require a specific set of parameters, some of which are poorly understood and are thus of empirical rather than mechanistic nature. Here, we present a study that deals with the assimilation of observations of both carbon flux and stock data into a crop C budget model (SPAc). Our data assimilation procedure (the Ensemble Kalman Filter, EnKF) aims at updating both model states and parameters, so that we will gain insight into optimized parameter values and carbon stock/flux estimates within quantified confidence limits. We obtained measured data of NEE, LAI, and leaf, root, stem, and storage organ dry mass for a winter wheat season in 2005/2006 from the CarboEurope Fluxnet site at Klingenberg/Germany. We conducted several model experiments, for each of which we assimilated a unique combination of data sources. We find that the assimilation of NEE data leads to reduced model error (observed vs. modelled NEE) compared to a model run without data assimilation (a reduction of ~15-20% of RMSE). The assimilated dry mass data on

  18. Global sensitivity analysis, probabilistic calibration, and predictive assessment for the data assimilation linked ecosystem carbon model

    SciTech Connect

    Safta, C.; Ricciuto, Daniel M.; Sargsyan, Khachik; Debusschere, B.; Najm, H. N.; Williams, M.; Thornton, Peter E.

    2015-07-01

    In this paper we propose a probabilistic framework for an uncertainty quantification (UQ) study of a carbon cycle model and focus on the comparison between steady-state and transient simulation setups. A global sensitivity analysis (GSA) study indicates the parameters and parameter couplings that are important at different times of the year for quantities of interest (QoIs) obtained with the data assimilation linked ecosystem carbon (DALEC) model. We then employ a Bayesian approach and a statistical model error term to calibrate the parameters of DALEC using net ecosystem exchange (NEE) observations at the Harvard Forest site. The calibration results are employed in the second part of the paper to assess the predictive skill of the model via posterior predictive checks.

  19. Global sensitivity analysis, probabilistic calibration, and predictive assessment for the data assimilation linked ecosystem carbon model

    DOE PAGES

    Safta, C.; Ricciuto, Daniel M.; Sargsyan, Khachik; ...

    2015-07-01

    In this paper we propose a probabilistic framework for an uncertainty quantification (UQ) study of a carbon cycle model and focus on the comparison between steady-state and transient simulation setups. A global sensitivity analysis (GSA) study indicates the parameters and parameter couplings that are important at different times of the year for quantities of interest (QoIs) obtained with the data assimilation linked ecosystem carbon (DALEC) model. We then employ a Bayesian approach and a statistical model error term to calibrate the parameters of DALEC using net ecosystem exchange (NEE) observations at the Harvard Forest site. The calibration results are employedmore » in the second part of the paper to assess the predictive skill of the model via posterior predictive checks.« less

  20. Evidence for the assimilation of ancient glacier organic carbon in a proglacial stream food web

    USGS Publications Warehouse

    Fellman, Jason; Hood, Eran; Raymond, Peter A.; Hudson, J.H.; Bozeman, Maura; Arimitsu, Mayumi L.

    2015-01-01

    We used natural abundance δ13C, δ15N, and Δ14C to compare trophic linkages between potential carbon sources (leaf litter, epilithic biofilm, and particulate organic matter) and consumers (aquatic macroinvertebrates and fish) in a nonglacial stream and two reaches of the heavily glaciated Herbert River. We tested the hypothesis that proglacial stream food webs are sustained by organic carbon released from glacial ecosystems. Carbon sources and consumers in the nonglacial stream had carbon isotope values that ranged from -30‰ to -25‰ for δ13C and from -14‰ to 53‰ for Δ14C reflecting a food web sustained mainly on contemporary primary production. In contrast, biofilm in the two glacial stream sites was highly Δ14C-depleted (-215‰ to 175‰) relative to the nonglacial stream consistent with the assimilation of ancient glacier organic carbon. IsoSource modeling showed that in upper Herbert River, macroinvertebrates (Δ14C = -171‰ to 22‰) and juvenile salmonids (Δ14C = −102‰ to 17‰) reflected a feeding history of both biofilm (~ 56%) and leaf litter (~ 40%). We estimate that in upper Herbert River on average 36% of the carbon incorporated into consumer biomass is derived from the glacier ecosystem. Thus, 14C-depleted glacial organic carbon was likely transferred to higher trophic levels through a feeding history of bacterial uptake of dissolved organic carbon and subsequent consumption of 14C-depleted biofilm by invertebrates and ultimately fish. Our findings show that the metazoan food web is sustained in part by glacial organic carbon such that future changes in glacial runoff could influence the stability and trophic structure of proglacial aquatic ecosystems.

  1. Integrated operation of the photorespiratory cycle and cytosolic metabolism in the modulation of primary nitrogen assimilation and export of organic N-transport compounds from leaves: a hypothesis.

    PubMed

    Misra, Jitendra B

    2014-02-15

    Photorespiration is generally considered to be an essentially dissipative process, although it performs some protective and essential functions. A theoretical appraisal indicates that the loss of freshly assimilated CO2 due to photorespiration in well-watered plants may not be as high as generally believed. Even under moderately adverse conditions, these losses may not exceed 10%. The photorespiratory metabolism of the source leaves of well-watered and well-nourished crop plants ought to be different from that of other leaves because the fluxes of the export of both carbohydrates and organic N-transport compounds in source leaves is quite high. With a heuristic approach that involved the dovetailing of certain metabolic steps with the photorespiratory cycle (PR-cycle), a novel network is proposed to operate in the source-leaves of well-watered and well-nourished plants. This network allows for the diversion of metabolites from their cyclic-routes in sizeable quantities. With the removal of considerable quantities of glycine and serine from the cyclic route, the number of RuBP oxygenation events would be several times those of the formation of hydroxypyruvate. Thus, to an extreme extent, photorespiratory metabolism would become open-ended and involve much less futile recycling of glycine and serine. Conversion of glyoxylate to glycine has been proposed to be a crucial step in the determination of the relative rates of the futile (cyclic) and anabolic (open-ended) routes. Thus, in the source leaves of well-watered and well-nourished plants, the importance of the cyclic route is limited to the salvaging of photorespiratory intermediates for the regeneration of RuBP. The proposed network is resilient enough to coordinate the rates of the assimilation of carbon and nitrogen in accordance with the moisture and N-fertility statuses of the soil.

  2. Effects of nitrogen sources on the nitrate assimilation in Haloferax mediterranei: growth kinetics and transcriptomic analysis.

    PubMed

    Esclapez, Julia; Bravo-Barrales, Gloria; Bautista, Vanesa; Pire, Carmen; Camacho, Mónica; Bonete, María J

    2014-01-01

    The haloarchaeon Haloferax mediterranei is able to grow in a defined culture media not only in the presence of inorganic nitrogen salt but also with amino acid as the sole nitrogen source. Assimilatory nitrate and nitrite reductases, respectively, catalyze the first and second reactions. The genes involved in this process are nasA, which encodes nitrate reductase and is found within the operon nasABC, and nasD, which encodes nitrite reductase. These genes are subjected to transcriptional regulation, being repressed in the presence of ammonium and induced with either nitrate or nitrite. This type of regulation has also been described when the amino acids are used as nitrogen source in the minimal media. Furthermore, it has been observed that the microorganism growth depends on nitrogen source, obtaining the lowest growth rate in the presence of nitrate and aspartate. In this paper, we present the results of a comparative study of microorganism growth and transcriptomic analysis of the operon nasABC and gene nasD in different nitrogen sources. The results are the first ever produced in relation to amino acids as nitrogen sources within the Halobacteriaceae family. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  3. Rhizobium etli mutant modulates carbon and nitrogen metabolism in Phaseolus vulgaris nodules.

    PubMed

    Silvente, Sonia; Blanco, Lourdes; Camas, Alberto; Ortega, José-Luis; Ramírez, Mario; Lara-Flores, Miguel

    2002-07-01

    The aim of this study was to evaluate the biochemical events in root nodules which lead to increased yield when bean is inoculated with a Rhizobium etli mutant (CFN037) having increased respiratory capacity. CFN037-inoculated plants had 22% more nitrogen (N) than did wild-type (CE3)-inoculated plants. Root nodule enzymes involved in nodule carbon and nitrogen assimilation as well as in ureides and amides synthesis were assessed in plants inoculated with CFN037 and the CE3. Our results show that the xylem ureides content was lower while that of amino acids was higher in CFN037- compared with CE3-inoculated plants. Supporting these results, enzymes involved in ureide synthesis were reduced while activity of aspartate aminotransferase, glutamate synthase, sucrose synthase, and glucose-6-P dehydrogenase were increased in CFN037-induced nodules. Glutamate synthase and phosphoenolpyruvate carboxylase transcripts were detected early in the development of nodules induced by CFN037 compared with CE3. However, plants inoculated with strain CE3-vhb, which express the Vitreoscilla sp. hemoglobin and also displays increased respiratory capacity, did not have altered ureide transport in N2-fixing plants. The data suggest that inoculation with special selected mutant strains of R. etli can modulate nodule N assimilation and N transport compounds.

  4. The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7.

    PubMed

    Klähn, Stephan; Schaal, Christoph; Georg, Jens; Baumgartner, Desirée; Knippen, Gernot; Hagemann, Martin; Muro-Pastor, Alicia M; Hess, Wolfgang R

    2015-11-10

    Glutamine synthetase (GS), a key enzyme in biological nitrogen assimilation, is regulated in multiple ways in response to varying nitrogen sources and levels. Here we show a small regulatory RNA, NsiR4 (nitrogen stress-induced RNA 4), which plays an important role in the regulation of GS in cyanobacteria. NsiR4 expression in the unicellular Synechocystis sp. PCC 6803 and in the filamentous, nitrogen-fixing Anabaena sp. PCC 7120 is stimulated through nitrogen limitation via NtcA, the global transcriptional regulator of genes involved in nitrogen metabolism. NsiR4 is widely conserved throughout the cyanobacterial phylum, suggesting a conserved function. In silico target prediction, transcriptome profiling on pulse overexpression, and site-directed mutagenesis experiments using a heterologous reporter system showed that NsiR4 interacts with the 5'UTR of gifA mRNA, which encodes glutamine synthetase inactivating factor (IF)7. In Synechocystis, we observed an inverse relationship between the levels of NsiR4 and the accumulation of IF7 in vivo. This NsiR4-dependent modulation of gifA (IF7) mRNA accumulation influenced the glutamine pool and thus [Formula: see text] assimilation via GS. As a second target, we identified ssr1528, a hitherto uncharacterized nitrogen-regulated gene. Competition experiments between WT and an ΔnsiR4 KO mutant showed that the lack of NsiR4 led to decreased acclimation capabilities of Synechocystis toward oscillating nitrogen levels. These results suggest a role for NsiR4 in the regulation of nitrogen metabolism in cyanobacteria, especially for the adaptation to rapid changes in available nitrogen sources and concentrations. NsiR4 is, to our knowledge, the first identified bacterial sRNA regulating the primary assimilation of a macronutrient.

  5. Single-cell measurement of archaeal and bacterial carbon assimilation in dark Pacific Ocean waters

    NASA Astrophysics Data System (ADS)

    Dekas, A. E.; Mayali, X.; Parada, A. E.; Fuhrman, J. A.; Weber, P. K.; Pett-Ridge, J.

    2016-02-01

    Microbial activity in the dark ocean plays a critical role in nutrient and elemental cycling. Here, we investigated the activity of archaea and bacteria on the single-cell level during dark incubations of Pacific Ocean water, and specifically their capacity for chemoautotrophy. Samples were collected 19 km off the coast of Los Angeles, at a depth of 150 m, and off the coast of San Francisco, at the surface. Incubations were amended with isotopically-labeled organic or inorganic carbon (13C-bicarbonate, 15N-amino acids or dual-labeled 13C-15N-amino acids), and uptake was detected using nanoscale secondary ion mass spectrometry (NanoSIMS). We analyzed 4,968 individual cells using an automated NanoSIMS analysis with particle-recognition software. After 7 days, 95% and 89% of cells (deep and shallow, respectively) demonstrated anabolic activity, i.e., incorporation of at least one isotopically-labeled substrate. Chemoautotrophy was detected at both sites, with 36% and 9% of cells (deep and shallow, respectively) assimilating 13C-bicarbonate in the dark. Fluorescence in situ hybridization coupled to NanoSIMS analysis was performed to link 16S rRNA phylogeny to patterns of C-assimilation. Thaumarchaea were found to dominate chemoautotrophy at both sites, with 13C-bicarbonate assimilation in nearly all cells hybridized with the Cren537 probe, but none hybridized with a general bacterial probe (Eub338). Conversely, widespread assimilation of both 15N and 13C from 15N-13C-amino acids was observed in the bacterial assemblage, but not in the Thaumarchaea. Interestingly, Thaumarchaeal cells were enriched in 15N after incubation with 15N-13C-amino acids, but not 13C, suggesting selective N assimilation from amino acids or substrate recycling. Together, our results demonstrate the value of single-cell measurements in characterizing patterns of C metabolism in mixed microbial community, and underscore the importance of Thaumarchaea in marine chemoautotrophy.

  6. Preparation of carbon nanoparticles and carbon nitride from high nitrogen compound

    DOEpatents

    Huynh, My Hang V [Los Alamos, NM; Hiskey, Michael A [Los Alamos, NM

    2009-09-01

    The high-nitrogen compound 3,6-di(azido)-1,2,4,5-tetrazine (DiAT) was synthesized by a relatively simple method and used as a precursor for the preparation of carbon nanospheres and nanopolygons, and nitrogen-rich carbon nitrides.

  7. Carbon availability controls the growth of detritivores (Lumbricidae) and their effect on nitrogen mineralization.

    PubMed

    Tiunov, Alexei V; Scheu, Stefan

    2004-01-01

    Activity of soil decomposer microorganisms is generally limited by carbon availability, but factors controlling saprophagous soil animals remain largely unknown. In contrast to microorganisms, animals are unable to exploit mineral nutrient pools. Therefore, it has been suggested that soil animals, and earthworms in particular, are limited by the availability of nitrogen. In contrast to this view, a strong increase in density and biomass of endogeic earthworms in response to labile organic carbon addition has been documented in field experiments. The hypothesis that the growth of endogeic earthworms is primarily limited by carbon availability was tested in a laboratory experiment lasting for 10 weeks. In addition, it was investigated whether the effects of earthworms on microbial activity and nutrient mineralization depend on the availability of carbon resources. We manipulated food availability to the endogeic earthworm species Octolasion tyrtaeum by using two soils with different organic matter content, providing access to different amounts of soil, and adding labile organic carbon (glucose) enriched in (13)C. Glucose addition strongly increased the growth of O. tyrtaeum. From 8 to 17% of the total C in earthworm tissue was assimilated from the glucose added. Soil microbial biomass was not strongly affected by the addition of glucose, though basal respiration was significantly increased and up to 50% of the carbon added as glucose was incorporated into soil organic matter. The impact of earthworms on the mineralization and leaching of nitrogen depended on C availability. As expected, in C-limited soil, the presence of earthworms strongly increased nitrogen leaching. However, when C availability was increased by the addition of glucose, this pattern was reversed, i.e. the presence of O. tyrtaeum decreased nitrogen leaching and its availability to soil microflora. We conclude that irrespective of the total carbon content of soils, O. tyrtaeum was primarily limited

  8. Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast.

    PubMed

    Staschke, Kirk A; Dey, Souvik; Zaborske, John M; Palam, Lakshmi Reddy; McClintick, Jeanette N; Pan, Tao; Edenberg, Howard J; Wek, Ronald C

    2010-05-28

    Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as gamma-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.

  9. Coevolution Trumps Pleiotropy: Carbon Assimilation Traits Are Independent of Metabolic Network Structure in Budding Yeast

    PubMed Central

    Opulente, Dana A.; Morales, Christopher M.; Carey, Lucas B.; Rest, Joshua S.

    2013-01-01

    Phenotypic traits may be gained and lost together because of pleiotropy, the involvement of common genes and networks, or because of simultaneous selection for multiple traits across environments (multiple-trait coevolution). However, the extent to which network pleiotropy versus environmental coevolution shapes shared responses has not been addressed. To test these alternatives, we took advantage of the fact that the genus Saccharomyces has variation in habitat usage and diversity in the carbon sources that a given strain can metabolize. We examined patterns of gain and loss in carbon utilization traits across 488 strains of Saccharomyces to investigate whether the structure of metabolic pathways or selection pressure from common environments may have caused carbon utilization traits to be gained and lost together. While most carbon sources were gained and lost independently of each other, we found four clusters that exhibit non-random patterns of gain and loss across strains. Contrary to the network pleiotropy hypothesis, we did not find that these patterns are explained by the structure of metabolic pathways or shared enzymes. Consistent with the hypothesis that common environments shape suites of phenotypes, we found that the environment a strain was isolated from partially predicts the carbon sources it can assimilate. PMID:23326606

  10. Coevolution trumps pleiotropy: carbon assimilation traits are independent of metabolic network structure in budding yeast.

    PubMed

    Opulente, Dana A; Morales, Christopher M; Carey, Lucas B; Rest, Joshua S

    2013-01-01

    Phenotypic traits may be gained and lost together because of pleiotropy, the involvement of common genes and networks, or because of simultaneous selection for multiple traits across environments (multiple-trait coevolution). However, the extent to which network pleiotropy versus environmental coevolution shapes shared responses has not been addressed. To test these alternatives, we took advantage of the fact that the genus Saccharomyces has variation in habitat usage and diversity in the carbon sources that a given strain can metabolize. We examined patterns of gain and loss in carbon utilization traits across 488 strains of Saccharomyces to investigate whether the structure of metabolic pathways or selection pressure from common environments may have caused carbon utilization traits to be gained and lost together. While most carbon sources were gained and lost independently of each other, we found four clusters that exhibit non-random patterns of gain and loss across strains. Contrary to the network pleiotropy hypothesis, we did not find that these patterns are explained by the structure of metabolic pathways or shared enzymes. Consistent with the hypothesis that common environments shape suites of phenotypes, we found that the environment a strain was isolated from partially predicts the carbon sources it can assimilate.

  11. Equilibrium responses of global net primary production and carbon storage to doubled atmospheric carbon dioxide: Sensitivity to changes in vegetation nitrogen concentration

    USGS Publications Warehouse

    McGuire, David A.; Melillo, J.M.; Kicklighter, D.W.; Pan, Y.; Xiao, X.; Helfrich, J.; Moore, B.; Vorosmarty, C.J.; Schloss, A.L.

    1997-01-01

    insensitivity of NPP in the N+D simulations occurred because potential enhancements in NPP associated with reduced vegetation nitrogen concentration were approximately offset by lower nitrogen availability associated with the decomposition dynamics of reduced litter nitrogen concentration. For each 7.5% reduction in vegetation nitrogen concentration, soil carbon increased approximately an additional 60 Pg C, while vegetation carbon storage increased by only approximately 5 Pg C. As the reduction in vegetation nitrogen concentration gets greater in the lower N+D simulations, more of the additional carbon storage tends to become concentrated in the north temperateboreal region in comparison to the tropics. Other studies with TEM show that elevated CO2 more than offsets the effects of climate change to cause increased carbon storage. The results of this study indicate that carbon storage would be enhanced by the influence of changes in plant nitrogen concentration on carbon assimilation and decomposition rates. Thus changes in vegetation nitrogen concentration may have important implications for the ability of the terrestrial biosphere to mitigate increases in the atmospheric concentration of CO2 and climate changes associated with the increases.

  12. Nitrogen assimilation and transpiration: key processes conditioning responsiveness of wheat to elevated [CO2] and temperature.

    PubMed

    Jauregui, Iván; Aroca, Ricardo; Garnica, María; Zamarreño, Ángel M; García-Mina, José M; Serret, Maria D; Parry, Martin; Irigoyen, Juan J; Aranjuelo, Iker

    2015-11-01

    Although climate scenarios have predicted an increase in [CO(2)] and temperature conditions, to date few experiments have focused on the interaction of [CO(2)] and temperature effects in wheat development. Recent evidence suggests that photosynthetic acclimation is linked to the photorespiration and N assimilation inhibition of plants exposed to elevated CO(2). The main goal of this study was to analyze the effect of interacting [CO(2)] and temperature on leaf photorespiration, C/N metabolism and N transport in wheat plants exposed to elevated [CO(2)] and temperature conditions. For this purpose, wheat plants were exposed to elevated [CO(2)] (400 vs 700 µmol mol(-1)) and temperature (ambient vs ambient + 4°C) in CO(2) gradient greenhouses during the entire life cycle. Although at the agronomic level, elevated temperature had no effect on plant biomass, physiological analyses revealed that combined elevated [CO(2)] and temperature negatively affected photosynthetic performance. The limited energy levels resulting from the reduced respiratory and photorespiration rates of such plants were apparently inadequate to sustain nitrate reductase activity. Inhibited N assimilation was associated with a strong reduction in amino acid content, conditioned leaf soluble protein content and constrained leaf N status. Therefore, the plant response to elevated [CO(2)] and elevated temperature resulted in photosynthetic acclimation. The reduction in transpiration rates induced limitations in nutrient transport in leaves of plants exposed to elevated [CO(2)] and temperature, led to mineral depletion and therefore contributed to the inhibition of photosynthetic activity.

  13. Assimilation of multiple data sets with the ensemble Kalman filter to improve forecasts of forest carbon dynamics.

    PubMed

    Gao, Chao; Wang, Han; Weng, Ensheng; Lakshmivarahan, S; Zhang, Yanfen; Luo, Yiqi

    2011-07-01

    The ensemble Kalman filter (EnKF) has been used in weather forecasting to assimilate observations into weather models. In this study, we examine how effectively forecasts of a forest carbon cycle can be improved by assimilating observations with the EnKF. We used the EnKF to assimilate into the terrestrial ecosystem (TECO) model eight data sets collected at the Duke Forest between 1996 and 2004 (foliage biomass, fine root biomass, woody biomass, litterfall, microbial biomass, forest floor carbon, soil carbon, and soil respiration). We then used the trained model to forecast changes in carbon pools from 2004 to 2012. Our daily analysis of parameters indicated that all the exit rates were well constrained by the EnKF, with the exception of the exit rates controlling the loss of metabolic litter and passive soil organic matter. The poor constraint of these two parameters resulted from the low sensitivity of TECO predictions to their values and the poor correlation between these parameters and the observed variables. Using the estimated parameters, the model predictions and observations were in agreement. Model forecasts indicate 15 380-15 660 g C/ m2 stored in Duke Forest by 2012 (a 27% increase since 2004). Parameter uncertainties decreased as data were sequentially assimilated into the model using the EnKF. Uncertainties in forecast carbon sinks increased over time for the long-term carbon pools (woody biomass, structure litter, slow and passive SOM) but remained constant over time for the short-term carbon pools (foliage, fine root, metabolic litter, and microbial carbon). Overall, EnKF can effectively assimilate multiple data sets into an ecosystem model to constrain parameters, forecast dynamics of state variables, and evaluate uncertainty.

  14. Adaptation of maize source leaf metabolism to stress related disturbances in carbon, nitrogen and phosphorus balance

    PubMed Central

    2013-01-01

    Background Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses. Results To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C4 metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low P conditions indicated that only low P treated leaves suffered carbon starvation. Conclusions Maize employs very different strategies to manage N and P metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C4 maize leaves were particularly sensitive to P starvation. PMID:23822863

  15. Cyanobacterial blooms: carbon and nitrogen limitation have opposite effects on the buoyancy of oscillatoria.

    PubMed

    Klemer, A R; Feuillade, J; Feuillade, M

    1982-03-26

    Gas vacuolation in Oscillatoria rubescens decreased with increased nitrogen limitation and increased with transitions from nitrogen to inorganic carbon limitation. Gas vacuoles consist of protein vesicles that can accumulate in carbon- limited but not in unenriched nitrogen-limited cells. Nitrogen limitation is a factor in the formation of deep population maxima; carbon limitation can promote surface blooms.

  16. Influence of mitochondrial genome rearrangement on cucumber leaf carbon and nitrogen metabolism

    PubMed Central

    Jastrzębska, Agata; Kulka, Marek; Leśniak, Karolina; Podgórska, Anna; Pärnik, Tiit; Ivanova, Hiie; Keerberg, Olav; Gardeström, Per; Rychter, Anna M.

    2010-01-01

    The MSC16 cucumber (Cucumis sativus L.) mitochondrial mutant was used to study the effect of mitochondrial dysfunction and disturbed subcellular redox state on leaf day/night carbon and nitrogen metabolism. We have shown that the mitochondrial dysfunction in MSC16 plants had no effect on photosynthetic CO2 assimilation, but the concentration of soluble carbohydrates and starch was higher in leaves of MSC16 plants. Impaired mitochondrial respiratory chain activity was associated with the perturbation of mitochondrial TCA cycle manifested, e.g., by lowered decarboxylation rate. Mitochondrial dysfunction in MSC16 plants had different influence on leaf cell metabolism under dark or light conditions. In the dark, when the main mitochondrial function is the energy production, the altered activity of TCA cycle in mutated plants was connected with the accumulation of pyruvate and TCA cycle intermediates (citrate and 2-OG). In the light, when TCA activity is needed for synthesis of carbon skeletons required as the acceptors for NH4+ assimilation, the concentration of pyruvate and TCA intermediates was tightly coupled with nitrate metabolism. Enhanced incorporation of ammonium group into amino acids structures in mutated plants has resulted in decreased concentration of organic acids and accumulation of Glu. PMID:20830597

  17. Carbon and nitrogen isotope studies in an arctic ecosystem

    SciTech Connect

    Schell, D.M.

    1989-01-01

    This proposal requests funding for the completion of our current ecological studies at the MS-117 research site at Toolik Lake, Alaska. We have been using a mix of stable and radioisotope techniques to assess the fluxes of carbon and nitrogen within the ecosystem and the implications for long-term carbon storage or loss from the tundra. Several tentative conclusions have emerged from our study including: Tundra in the foothills is no longer accumulating carbon. Surficial radiocarbon abundances show little or no accumulation since 1000--2500 yrs BP. Coastal plain tundra is still accumulating carbon, but the rate of accumulation has dropped in the last few thousand years. Carbon export from watersheds in the Kuparuk and Imnavait Creek drainages are in excess of that expected from estimated primary productivity; and Nitrogen isotope abundances vary between species of plants and along hydrologic gradients.

  18. Carbon and nitrogen isotope studies in an arctic ecosystem

    SciTech Connect

    Schell, D.M.

    1989-12-31

    This proposal requests funding for the completion of our current ecological studies at the MS-117 research site at Toolik Lake, Alaska. We have been using a mix of stable and radioisotope techniques to assess the fluxes of carbon and nitrogen within the ecosystem and the implications for long-term carbon storage or loss from the tundra. Several tentative conclusions have emerged from our study including: Tundra in the foothills is no longer accumulating carbon. Surficial radiocarbon abundances show little or no accumulation since 1000--2500 yrs BP. Coastal plain tundra is still accumulating carbon, but the rate of accumulation has dropped in the last few thousand years. Carbon export from watersheds in the Kuparuk and Imnavait Creek drainages are in excess of that expected from estimated primary productivity; and Nitrogen isotope abundances vary between species of plants and along hydrologic gradients.

  19. Development and Application of a Bioluminescence-Based Test for Assimilable Organic Carbon in Reclaimed Waters▿

    PubMed Central

    Weinrich, Lauren A.; Giraldo, Eugenio; LeChevallier, Mark W.

    2009-01-01

    Assimilable organic carbon (AOC) is an important parameter governing the growth of heterotrophic bacteria in drinking water. Despite the recognition that variations in treatment practices (e.g., disinfection, coagulation, selection of filter media, and watershed protection) can have dramatic impacts on AOC levels in drinking water, few water utilities routinely measure AOC levels because of the difficulty of the method. To simplify the method, the Pseudomonas fluorescens P-17 and Spirillum sp. strain NOX test bacteria were mutagenized by using luxCDABE operon fusion and inducible transposons to produce bioluminescent strains. The growth of these strains can easily be monitored with a programmable luminometer to determine the maximum cell yield via luminescence readings, and these values can be fitted to the classical Monod growth curve to determine bacterial growth kinetics and the maximum growth rate. Standard curves using acetate carbon (at concentrations ranging from 0 to 1,000 μg/liter) resulted in coefficients of determination (r2) between luminescence units and acetate carbon levels of 0.95 for P-17 and 0.89 for NOX. The bioluminescence test was used to monitor reclaimed water, in which average AOC levels range between 150 and 1,400 μg/liter acetate carbon equivalents. Comparison of the conventional AOC assay and the bioluminescent assay produced an r2 of 0.92. PMID:19820156

  20. Improving the LPJ-GUESS modelled carbon balance with a particle filter data assimilation technique

    NASA Astrophysics Data System (ADS)

    McRobert, Andrew; Scholze, Marko; Kemp, Sarah; Smith, Ben

    2015-04-01

    The recent increases in anthropogenic carbon dioxide (CO_2) emissions have disrupted the equilibrium in the global carbon cycle pools with the ocean and terrestrial pools increasing their respective storages to accommodate roughly half of the anthropogenic increase. Dynamic global vegetation models (DGVM) have been developed to quantify the modern carbon cycle changes. In this study, a particle filter data assimilation technique has been used to calibrate the process parameters in the DGVM LPJ-GUESS (Lund-Potsdam-Jena General Ecosystem Simulator). LPJ-GUESS simulates individual plant function types (pft) as a competitive balance within high resolution forest patches. Thirty process parameters have been optimized twice, using both a sequential and iterative method of particle filter. The iterative method runs the model for the full time period of thirteen years and then evaluates the cost function from the mismatch of observations and model results before adjusting the parameters and repeating the full time period. The sequential method runs the model and particle filter for each year of the time series in order, adjusting the parameters between each year, then loops back to beginning of the series to repeat. For each particle, the model output of NEP (Net Ecosystem Productivity) is compared to eddy flux measurements from ICOS flux towers to minimize the cost function. A high-resolution regional carbon balance has been simulated for central Sweden using a network of several ICOS flux towers.

  1. Soil warming, carbon–nitrogen interactions, and forest carbon budgets

    PubMed Central

    Melillo, Jerry M.; Butler, Sarah; Johnson, Jennifer; Mohan, Jacqueline; Steudler, Paul; Lux, Heidi; Burrows, Elizabeth; Bowles, Francis; Smith, Rose; Scott, Lindsay; Vario, Chelsea; Hill, Troy; Burton, Andrew; Zhou, Yu-Mei; Tang, Jim

    2011-01-01

    Soil warming has the potential to alter both soil and plant processes that affect carbon storage in forest ecosystems. We have quantified these effects in a large, long-term (7-y) soil-warming study in a deciduous forest in New England. Soil warming has resulted in carbon losses from the soil and stimulated carbon gains in the woody tissue of trees. The warming-enhanced decay of soil organic matter also released enough additional inorganic nitrogen into the soil solution to support the observed increases in plant carbon storage. Although soil warming has resulted in a cumulative net loss of carbon from a New England forest relative to a control area over the 7-y study, the annual net losses generally decreased over time as plant carbon storage increased. In the seventh year, warming-induced soil carbon losses were almost totally compensated for by plant carbon gains in response to warming. We attribute the plant gains primarily to warming-induced increases in nitrogen availability. This study underscores the importance of incorporating carbon–nitrogen interactions in atmosphere–ocean–land earth system models to accurately simulate land feedbacks to the climate system. PMID:21606374

  2. Acetate Dissimilation and Assimilation in Mycobacterium tuberculosis Depend on Carbon Availability

    PubMed Central

    Rücker, Nadine; Billig, Sandra; Bücker, René; Jahn, Dieter

    2015-01-01

    ABSTRACT Mycobacterium tuberculosis persists inside granulomas in the human lung. Analysis of the metabolic composition of granulomas from guinea pigs revealed that one of the organic acids accumulating in the course of infection is acetate (B. S. Somashekar, A. G. Amin, C. D. Rithner, J. Troudt, R. Basaraba, A. Izzo, D. C. Crick, and D. Chatterjee, J Proteome Res 10:4186–4195, 2011, doi:http://dx.doi.org/10.1021/pr2003352), which might result either from metabolism of the pathogen or might be provided by the host itself. Our studies characterize a metabolic pathway by which M. tuberculosis generates acetate in the cause of fatty acid catabolism. The acetate formation depends on the enzymatic activities of Pta and AckA. Using actyl coenzyme A (acetyl-CoA) as a substrate, acetyl-phosphate is generated and finally dephosphorylated to acetate, which is secreted into the medium. Knockout mutants lacking either the pta or ackA gene showed significantly reduced acetate production when grown on fatty acids. This effect is even more pronounced when the glyoxylate shunt is blocked, resulting in higher acetate levels released to the medium. The secretion of acetate was followed by an assimilation of the metabolite when other carbon substrates became limiting. Our data indicate that during acetate assimilation, the Pta-AckA pathway acts in concert with another enzymatic reaction, namely, the acetyl-CoA synthetase (Acs) reaction. Thus, acetate metabolism might possess a dual function, mediating an overflow reaction to release excess carbon units and resumption of acetate as a carbon substrate. IMPORTANCE During infection, host-derived lipid components present the major carbon source at the infection site. β-Oxidation of fatty acids results in the formation of acetyl-CoA. In this study, we demonstrate that consumption of fatty acids by Mycobacterium tuberculosis activates an overflow mechanism, causing the pathogen to release excess carbon intermediates as acetate. The Pta

  3. CarbonTracker-CH4: an assimilation system for estimating emissions of atmospheric methane

    NASA Astrophysics Data System (ADS)

    Bruhwiler, L. M.; Dlugokencky, E.; Masarie, K.; Ishizawa, M.; Andrews, A.; Miller, J.; Sweeney, C.; Tans, P.; Worthy, D.

    2014-01-01

    We describe an assimilation system for atmospheric methane (CH4), CarbonTracker-CH4, and demonstrate the diagnostic value of global or zonally averaged CH4 abundances for evaluating the results. We show that CarbonTracker-CH4 is able to simulate the observed zonal average mole fractions and capture inter-annual variability in emissions quite well at high northern latitudes (53-90° N). CarbonTracker-CH4 estimates of total fluxes at high northern latitudes are about 81 Tg CH4 yr-1, about 12 Tg CH4 yr-1 (13%) lower than prior estimates, a result that is consistent with other atmospheric inversions. Emissions from European wetlands are decreased by 30%, a result consistent with previous; however, emissions from wetlands in Boreal Eurasia are increased relative to the prior estimate. Although CarbonTracker-CH4 does not estimate increases in emissions from high northern latitudes for 2000 through 2010, significant inter-annual variability in high northern latitude fluxes is recovered. During the exceptionally warm Arctic summer of 2007, estimated emissions were greater than the decadal average by 4.4 Tg CH4 yr-1. In 2008, temperatures returned to more normal values over Arctic North America while they stayed above normal over Arctic Eurasia. CarbonTracker-CH4 estimates were 2.4 Tg CH4 yr-1 higher than the decadal average, and the anomalous emissions occurred over Arctic Eurasia, suggesting that the data allow discrimination between these two source regions. Also, the emission estimates respond to climate variability without having the system constrained by climate parameters. CarbonTracker-CH4 estimates for temperate latitudes are only slightly increased over prior estimates, but about 10 Tg CH4 yr-1 is redistributed from Asia to North America. We used time invariant prior flux estimates, so for the period from 2000 to 2006, when the growth rate of global atmospheric CH4 was very small, the assimilation does not produce increases in natural or anthropogenic emissions in

  4. CarbonTracker-CH4: an assimilation system for estimating emissions of atmospheric methane

    NASA Astrophysics Data System (ADS)

    Bruhwiler, L.; Dlugokencky, E.; Masarie, K.; Ishizawa, M.; Andrews, A.; Miller, J.; Sweeney, C.; Tans, P.; Worthy, D.

    2014-08-01

    We describe an assimilation system for atmospheric methane (CH4), CarbonTracker-CH4, and demonstrate the diagnostic value of global or zonally averaged CH4 abundances for evaluating the results. We show that CarbonTracker-CH4 is able to simulate the observed zonal average mole fractions and capture inter-annual variability in emissions quite well at high northern latitudes (53-90° N). In contrast, CarbonTracker-CH4 is less successful in the tropics where there are few observations and therefore misses significant variability and is more influenced by prior flux estimates. CarbonTracker-CH4 estimates of total fluxes at high northern latitudes are about 81 ± 7 Tg CH4 yr-1, about 12 Tg CH4 yr-1 (13%) lower than prior estimates, a result that is consistent with other atmospheric inversions. Emissions from European wetlands are decreased by 30%, a result consistent with previous work by Bergamaschi et al. (2005); however, unlike their results, emissions from wetlands in boreal Eurasia are increased relative to the prior estimate. Although CarbonTracker-CH4 does not estimate an increasing trend in emissions from high northern latitudes for 2000 through 2010, significant inter-annual variability in high northern latitude fluxes is recovered. Exceptionally warm growing season temperatures in the Arctic occurred in 2007, a year that was also anonymously wet. Estimated emissions from natural sources were greater than the decadal average by 4.4 ± 3.8 Tg CH4 yr-1 in 2007. CarbonTracker-CH4 estimates for temperate latitudes are only slightly increased over prior estimates, but about 10 Tg CH4 yr-1 is redistributed from Asia to North America. This difference exceeds the estimated uncertainty for North America (±3.5 Tg CH4 yr-1). We used time invariant prior flux estimates, so for the period from 2000 to 2006, when the growth rate of global atmospheric CH4 was very small, the assimilation does not produce increases in natural or anthropogenic emissions in contrast to bottom

  5. Increased iron availability resulting from increased CO2 enhances carbon and nitrogen metabolism in the economical marine red macroalga Pyropia haitanensis (Rhodophyta).

    PubMed

    Chen, Binbin; Zou, Dinghui; Yang, Yufeng

    2017-04-01

    Ocean acidification caused by rising CO2 is predicted to increase the concentrations of dissolved species of Fe(II) and Fe(III), leading to the enhanced photosynthetic carbon sequestration in some algal species. In this study, the carbon and nitrogen metabolism in responses to increased iron availability under two CO2 levels (390 μL L(-1) and 1000 μL L(-1)), were investigated in the maricultivated macroalga Pyropia haitanensis (Rhodophyta). The results showed that, elevated CO2 increased soluble carbonhydrate (SC) contents, resulting from enhanced photosynthesis and photosynthetic pigment synthesis in this algae, but declined its soluble protein (SP) contents, resulting in increased ratio of SC/SP. This enhanced photosynthesis performance and carbon accumulation was more significant under iron enrichment condition in seawater, with higher iron uptake rate at high CO2 level. As a key essential biogenic element for algae, Fe-replete functionally contributed to P. haitanensis photosynthesis. Increased SC fundamentally provided carbon skeletons for nitrogen assimilation. The significant increase of carbon and nitrogen assimilation finally contributed to enhanced growth in this alga. This was also intuitively reflected by respiration that provided energy for cellular metabolism and algal growth. We propose that, in the predicted scenario of rising atmospheric CO2, P. haitanensis is capable to adjust its physiology by increasing its carbon and nitrogen metabolism to acclimate the acidified seawater, at the background of global climate change and simultaneously increased iron concentration due to decreased pH levels.

  6. The evolutionary rewiring of ubiquitination targets has reprogrammed the regulation of carbon assimilation in the pathogenic yeast Candida albicans.

    PubMed

    Sandai, Doblin; Yin, Zhikang; Selway, Laura; Stead, David; Walker, Janet; Leach, Michelle D; Bohovych, Iryna; Ene, Iuliana V; Kastora, Stavroula; Budge, Susan; Munro, Carol A; Odds, Frank C; Gow, Neil A R; Brown, Alistair J P

    2012-12-11

    Microbes must assimilate carbon to grow and colonize their niches. Transcript profiling has suggested that Candida albicans, a major pathogen of humans, regulates its carbon assimilation in an analogous fashion to the model yeast Saccharomyces cerevisiae, repressing metabolic pathways required for the use of alterative nonpreferred carbon sources when sugars are available. However, we show that there is significant dislocation between the proteome and transcriptome in C. albicans. Glucose triggers the degradation of the ICL1 and PCK1 transcripts in C. albicans, yet isocitrate lyase (Icl1) and phosphoenolpyruvate carboxykinase (Pck1) are stable and are retained. Indeed, numerous enzymes required for the assimilation of carboxylic and fatty acids are not degraded in response to glucose. However, when expressed in C. albicans, S. cerevisiae Icl1 (ScIcl1) is subjected to glucose-accelerated degradation, indicating that like S. cerevisiae, this pathogen has the molecular apparatus required to execute ubiquitin-dependent catabolite inactivation. C. albicans Icl1 (CaIcl1) lacks analogous ubiquitination sites and is stable under these conditions, but the addition of a ubiquitination site programs glucose-accelerated degradation of CaIcl1. Also, catabolite inactivation is slowed in C. albicans ubi4 cells. Ubiquitination sites are present in gluconeogenic and glyoxylate cycle enzymes from S. cerevisiae but absent from their C. albicans homologues. We conclude that evolutionary rewiring of ubiquitination targets has meant that following glucose exposure, C. albicans retains key metabolic functions, allowing it to continue to assimilate alternative carbon sources. This metabolic flexibility may be critical during infection, facilitating the rapid colonization of dynamic host niches containing complex arrays of nutrients. IMPORTANCE Pathogenic microbes must assimilate a range of carbon sources to grow and colonize their hosts. Current views about carbon assimilation in the

  7. Landscape level differences in soil carbon and nitrogen: Implications for soil carbon sequestration

    NASA Astrophysics Data System (ADS)

    Garten, Charles T.; Ashwood, Tom L.

    2002-12-01

    The objective of this research was to understand how land cover and topography act, independently or together, as determinants of soil carbon and nitrogen storage over a complex terrain. Such information could help to direct land management for the purpose of carbon sequestration. Soils were sampled under different land covers and at different topographic positions on the mostly forested 14,000 ha Oak Ridge Reservation in Tennessee, USA. Most of the soil carbon stock, to a 40-cm soil depth, was found to reside in the surface 20 cm of mineral soil. Surface soil carbon and nitrogen stocks were partitioned into particulate (≥53 μm) and mineral-associated organic matter (<53 μm). Generally, soils under pasture had greater nitrogen availability, greater carbon and nitrogen stocks, and lower C:N ratios than soils under transitional vegetation and forests. The effects of topography were usually secondary to those of land cover. Because of greater soil carbon stocks, and greater allocation of soil carbon to mineral-associated organic matter (a long-term pool), we conclude that soil carbon sequestration, but not necessarily total ecosystem carbon storage, is greater under pastures than under forests. The implications of landscape-level variation in soil carbon and nitrogen for carbon sequestration are discussed at several different levels: (1) nitrogen limitations to soil carbon storage; (2) controls on soil carbon turnover as a result of litter chemistry and soil carbon partitioning; (3) residual effects of past land use history; and (4) statistical limitations to the quantification of soil carbon stocks.

  8. Functions of autophagy in plant carbon and nitrogen metabolism.

    PubMed

    Ren, Chenxia; Liu, Jingfang; Gong, Qingqiu

    2014-01-01

    Carbon and nitrogen are essential components for plant growth. Although models of plant carbon and nitrogen metabolisms have long been established, certain gaps remain unfilled, such as how plants are able to maintain a flexible nocturnal starch turnover capacity over various light cycles, or how nitrogen remobilization is achieved during the reproductive growth stage. Recent advances in plant autophagy have shed light on such questions. Not only does autophagy contribute to starch degradation at night, but it participates in the degradation of chloroplast proteins and even chloroplasts after prolonged carbon starvation, thus help maintain the free amino acid pool and provide substrate for respiration. The induction of autophagy under these conditions may involve transcriptional regulation. Large-scale transcriptome analyses revealed that ATG8e belongs to a core carbon signaling response shared by Arabidopsis accessions, and the transcription of Arabidopsis ATG7 is tightly co-regulated with genes functioning in chlorophyll degradation and leaf senescence. In the reproductive phase, autophagy is essential for bulk degradation of leaf proteins, thus contributes to nitrogen use efficiency (NUE) both under normal and low-nitrogen conditions.

  9. Carbon and Nitrogen Cycling in a Shallow Coastal Tidal Basin

    NASA Astrophysics Data System (ADS)

    Hohn, S.; Voelker, C. D.; van Beusekom, J.; Schartau, M.

    2008-12-01

    The biogeochemical fluxes of carbon and nitrogen are tightly coupled via the production of biomass. The degree of this coupling is known to vary under different environmental conditions. Nitrogen limitation of phytoplankton organisms leads to increased C:N biomass ratios whereas light limitation at nutrient replete conditions causes a decrease in intracellular C:N ratios. The biogeochemical fluxes of carbon and nitrogen within and between a shallow coastal tidal basin in the danish-german Wadden Sea, the List tidal basin, and the adjacent North Sea are calculated with an ecosystem model that allows for variable C:N ratios in phytoplankton biomass. Differences in plankton C:N biomass ratios between both water boxes affect the net transport budgets of carbon and nitrogen between the North Sea and the List tidal basin and may also change the sign of the C:N ratio of biomass exchange, i.e. leading to net nitrogen export and net import of carbon into the tidal basin over an annual cycle. Benthic filterfeeding organisms consume phytoplankton biomass and release fresh nutrients to the water column. In the List tidal basin, the promoting effect on primary production due to nutrient release by benthic filterfeeders is found to outweigh the limiting effect due to grazing pressure on phytoplankton biomass.

  10. Effect of elevated carbon dioxide concentration on carbon assimilation under fluctuating light.

    PubMed

    Holišová, Petra; Zitová, Martina; Klem, Karel; Urban, Otmar

    2012-01-01

    Natural fluctuations in light intensity may significantly affect the amount of CO assimilated by plants and ecosystems. Little is known, however, about the interactive effect of dynamic light conditions and atmospheric CO concentrations. The hypothesis that elevated CO concentration (EC; 700 μmol CO mol) increases photosynthetic efficiency in dynamic light environments as compared to ambient CO concentration (AC; 385 μmol CO mol) was tested. Sun leaves of European beech ( L.) and current-year shoots of Norway spruce [ (L). Karst.] were exposed to five dynamic light regimes (LRs) occurring within forest canopies due to variable cloud cover or self-shading of leaves and to a steady-state LR. The LRs differed in the time course of incident irradiance, whereas the overall duration (600 s) and total amount of radiation (35.88 mmol photons m) were the same in all LRs. The EC treatment enhanced the amount of CO assimilated under all LRs tested. While the stimulation was only 37 to 50% in beech, it was 52 to 85% in spruce. The hypothesis that photosynthetic efficiency is stimulated by EC was confirmed in LRs when the leaves were pre-exposed to low light intensity and photosynthetic induction was required. By contrast, only a minor effect of EC treatment was found on the rate of induction loss and postillumination CO fixation in both species studied.

  11. Regulation of nitrogen uptake and assimilation: Effects of nitrogen source and root-zone and aerial environment on growth and productivity of soybean

    NASA Technical Reports Server (NTRS)

    Raper, C. David, Jr.

    1994-01-01

    The interdependence of root and shoot growth produces a functional equilibrium as described in quantitative terms by numerous authors. It was noted that bean seedlings grown in a constant environment tended to have a constant distribution pattern of dry matter between roots and leaves characteristic of the set of environmental conditions. Disturbing equilibrium resulted in a change in relative growth of roots and leaves until the original ratio was restored. To define a physiological basis for regulation of nitrogen uptake within the balance between root and shoot activities, the authors combined a partioning scheme and a utilization priority assumption in which: (1) all carbon enters the plant through photosynthesis in leaves and all nitrogen enters the plant through active uptake by roots, (2) nitrogen uptake by roots and secretion into the xylem for transport to the shoots are active processes, (3) availability of exogenous nitrogen determines concentration of soluble carbohydrates within the roots, (4) leaves are a source and a sink for carbohydrates, and (5) the requirement for nitrogen by leaf growth is proportionally greater during initiation and early expansion than during later expansion.

  12. Effects of Different Inorganic Nitrogen Sources on Photosynthetic Carbon Metabolism in Primary Leaves of Non-nodulated Phaseolus vulgaris L.

    PubMed

    Marques, I A; Oberholzer, M J; Erismann, K H

    1983-03-01

    Young bean plants (Phaseolus vulgaris L. var Saxa) were fed with three different types of inorganic nitrogen, after being grown on nitrogen-free nutrient solution for 8 days. The pattern of (14)CO(2) fixation was investigated in photosynthesizing primary leaf discs of 11-day-old plants (3 days with nitrogen source) and in a pulse-chase experiment in 13-day-old plants (5 days with nitrogen source).Ammonium caused, in contrast to nitrate nutrition, a higher level of (14)C incorporation into sugar phosphates but a lower incorporation of label into malate, glycolate, glycerate, aspartate, and alanine. The labeling kinetics of glycine and serine were little changed by the nitrogen source. Ammonium feeding also produced an increase in the ratio of extractable activities of ribulose-1,5-bisphosphate carboxylase to phosphoenolpyruvate carboxylase and an increase in dark respiration and the CO(2) compensation concentration. Net photosynthesis was higher in plants assimilating nitrate.The results point to stimulated turnover of the photosynthetic carbon reduction cycle metabolites, reduced phosphoenolpyruvate carboxylation, and altered turnover rates within the photosynthetic carbon oxidation cycle in ammonium-fed plants. Mechanisms of the regulation of primary carbon metabolism are proposed and discussed.

  13. A global carbon assimilation system based on a dual optimization method

    NASA Astrophysics Data System (ADS)

    Zheng, H.; Li, Y.; Chen, J. M.; Wang, T.; Huang, Q.; Huang, W. X.; Li, S. M.; Yuan, W. P.; Zheng, X.; Zhang, S. P.; Chen, Z. Q.; Jiang, F.

    2014-10-01

    Ecological models are effective tools to simulate the distribution of global carbon sources and sinks. However, these models often suffer from substantial biases due to inaccurate simulations of complex ecological processes. We introduce a set of scaling factors (parameters) to an ecological model on the basis of plant functional type (PFT) and latitudes. A global carbon assimilation system (GCAS-DOM) is developed by employing a Dual Optimization Method (DOM) to invert the time-dependent ecological model parameter state and the net carbon flux state simultaneously. We use GCAS-DOM to estimate the global distribution of the CO2 flux on 1° ×1° grid cells for the period from 2000 to 2007. Results show that land and ocean absorb -3.69 ± 0.49 Pg C year-1 and -1.91 ± 0.16 Pg C year-1, respectively. North America, Europe and China contribut -0.96 ± 0.15 Pg C year-1, -0.42 ± 0.08 Pg C year-1 and -0.21 ± 0.28 Pg C year-1, respectively. The uncertainties in the flux after optimization by GCAS-DOM have been remarkably reduced by more than 60%. Through parameter optimization, GCAS-DOM can provide improved estimates of the carbon flux for each PFT. Coniferous forest (-0.97 ± 0.27 Pg C year-1) is the largest contributor to the global carbon sink. Fluxes of once-dominant deciduous forest generated by BEPS is reduced to -0.79 ± 0.22 Pg C year-1, being the third largest carbon sink.

  14. A global carbon assimilation system based on a dual optimization method

    NASA Astrophysics Data System (ADS)

    Zheng, H.; Li, Y.; Chen, J. M.; Wang, T.; Huang, Q.; Huang, W. X.; Wang, L. H.; Li, S. M.; Yuan, W. P.; Zheng, X.; Zhang, S. P.; Chen, Z. Q.; Jiang, F.

    2015-02-01

    Ecological models are effective tools for simulating the distribution of global carbon sources and sinks. However, these models often suffer from substantial biases due to inaccurate simulations of complex ecological processes. We introduce a set of scaling factors (parameters) to an ecological model on the basis of plant functional type (PFT) and latitudes. A global carbon assimilation system (GCAS-DOM) is developed by employing a dual optimization method (DOM) to invert the time-dependent ecological model parameter state and the net carbon flux state simultaneously. We use GCAS-DOM to estimate the global distribution of the CO2 flux on 1° × 1° grid cells for the period from 2001 to 2007. Results show that land and ocean absorb -3.63 ± 0.50 and -1.82 ± 0.16 Pg C yr-1, respectively. North America, Europe and China contribute -0.98 ± 0.15, -0.42 ± 0.08 and -0.20 ± 0.29 Pg C yr-1, respectively. The uncertainties in the flux after optimization by GCAS-DOM have been remarkably reduced by more than 60%. Through parameter optimization, GCAS-DOM can provide improved estimates of the carbon flux for each PFT. Coniferous forest (-0.97 ± 0.27 Pg C yr-1) is the largest contributor to the global carbon sink. Fluxes of once-dominant deciduous forest generated by the Boreal Ecosystems Productivity Simulator (BEPS) are reduced to -0.78 ± 0.23 Pg C yr-1, the third largest carbon sink.

  15. Impact of assimilable nitrogen availability in glucose uptake kinetics in Saccharomyces cerevisiae during alcoholic fermentation.

    PubMed

    Palma, Margarida; Madeira, Sara Cordeiro; Mendes-Ferreira, Ana; Sá-Correia, Isabel

    2012-07-30

    The expression and activity of the different Saccharomyces cerevisiae hexose uptake systems (Hxt) and the kinetics of glucose uptake are considered essential to industrial alcoholic fermentation performance. However, the dynamics of glucose uptake kinetics during the different stages of fermentation, depending on glucose and nitrogen availability, is very poorly characterized. The objective of the present work was to examine thoroughly the alterations occurring in glucose uptake kinetics during alcoholic fermentation, by the wine strain S. cerevisiae PYCC 4072, of a synthetic grape juice basal medium with either a limiting or non-limiting initial nitrogen concentration and following nitrogen supplementation of the nitrogen-depleted sluggish fermentation. Independently of the initial concentration of the nitrogen source, glucose transport capacity is maximal during the early stages of fermentation and presumably sustained by the low-affinity and high-capacity glucose transporter Hxt1p. During nitrogen-limited sluggish fermentation, glucose uptake capacity was reduced to approximately 20% of its initial values (Vmax = 4.9 ± 0.8 compared to 21.9 ± 1.2 μmol h⁻¹ 10⁻⁸ cells), being presumably sustained by the low-affinity glucose transporter Hxt3p (considering the calculated Km = 39.2 ± 8.6 mM). The supplementation of the sluggish fermentation broth with ammonium led to the increase of glucose transport capacity associated to the expression of different glucose uptake systems with low and high affinities for glucose (Km = 58.2 ± 9.1 and 2.7 ± 0.4 mM). A biclustering analysis carried out using microarray data, previously obtained for this yeast strain transcriptional response to equivalent fermentation conditions, indicates that the activation of the expression of genes encoding the glucose transporters Hxt2p (during the transition period to active fermentation) and Hxt3p, Hxt4p, Hxt6p and Hxt7p (during the period of

  16. Impact of assimilable nitrogen availability in glucose uptake kinetics in Saccharomyces cerevisiae during alcoholic fermentation

    PubMed Central

    2012-01-01

    Background The expression and activity of the different Saccharomyces cerevisiae hexose uptake systems (Hxt) and the kinetics of glucose uptake are considered essential to industrial alcoholic fermentation performance. However, the dynamics of glucose uptake kinetics during the different stages of fermentation, depending on glucose and nitrogen availability, is very poorly characterized. The objective of the present work was to examine thoroughly the alterations occurring in glucose uptake kinetics during alcoholic fermentation, by the wine strain S. cerevisiae PYCC 4072, of a synthetic grape juice basal medium with either a limiting or non-limiting initial nitrogen concentration and following nitrogen supplementation of the nitrogen-depleted sluggish fermentation. Results Independently of the initial concentration of the nitrogen source, glucose transport capacity is maximal during the early stages of fermentation and presumably sustained by the low-affinity and high-capacity glucose transporter Hxt1p. During nitrogen-limited sluggish fermentation, glucose uptake capacity was reduced to approximately 20% of its initial values (Vmax = 4.9 ± 0.8 compared to 21.9 ± 1.2 μmol h-1 10-8 cells), being presumably sustained by the low-affinity glucose transporter Hxt3p (considering the calculated Km = 39.2 ± 8.6 mM). The supplementation of the sluggish fermentation broth with ammonium led to the increase of glucose transport capacity associated to the expression of different glucose uptake systems with low and high affinities for glucose (Km = 58.2 ± 9.1 and 2.7 ± 0.4 mM). A biclustering analysis carried out using microarray data, previously obtained for this yeast strain transcriptional response to equivalent fermentation conditions, indicates that the activation of the expression of genes encoding the glucose transporters Hxt2p (during the transition period to active fermentation) and Hxt3p, Hxt4p, Hxt6p and Hxt7p (during the

  17. [Influencing Factors of Assimilable Organic Carbon (AOC) Formation in Drinking Water During Ozonation Process].

    PubMed

    Dong, Bing-zhi; Zhang, Jia-li; He, Chang

    2016-05-15

    The influences of ozone dosage, pH and ionic strength on the formation of Assimilable Organic Carbon (AOC) during ozonation were investigated. The result demonstrated that within the range of 1-5 mg · L⁻¹ O₃, the formation of AOC increased with increasing ozone dosage, but higher ozone dosage (9 mg · L⁻¹) resulted in reduction of AOC formation. AOC formation increased with higher pH but decreased with increasing ionic strength. The result also showed that AOC formation with hydrophobic fraction (HPO) was the most, followed by transphilic fraction (TPI), and charged hydrophilic fraction (CHPI), while neutral hydrophilic fraction (NHPI) was the least. It was found that AOC formation related closely with SUVA of small molecular weight organics, and the lower SUVA produced more AOC.

  18. Variation in assimilable organic carbon formation during chlorination of Microcystis aeruginosa extracellular organic matter solutions.

    PubMed

    Sun, Xingbin; Yuan, Ting; Ni, Huishan; Li, Yanpeng; Hu, Yang

    2016-07-01

    This study investigated the chlorination of Microcystis aeruginosa extracellular organic matter (EOM) solutions under different conditions, to determine how the metabolites produced by these organisms affect water safety and the formation of assimilable organic carbon (AOC). The effects of chlorine dosages, coagulant dosage, reaction time and temperature on the formation of AOC were investigated during the disinfection of M.aeruginosa metabolite solutions. The concentration of AOC followed a decreasing and then increasing pattern with increasing temperature and reaction time. The concentration of AOC decreased and then increased with increasing chlorination dosage, followed by a slight decrease at the highest level of chlorination. However, the concentration of AOC decreased continuously with increasing coagulant dosage. The formation of AOC can be suppressed under appropriate conditions. In this study, chlorination at 4mg/L, combined with a coagulant dose of 40mg/L at 20°C over a reaction time of 12hr, produced the minimum AOC.

  19. Identification of groundwater microorganisms capable of assimilating RDX-derived nitrogen during in-situ bioremediation.

    PubMed

    Cho, Kun-Ching; Fuller, Mark E; Hatzinger, Paul B; Chu, Kung-Hui

    2016-11-01

    Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a nitroamine explosive, is commonly detected in groundwater at military testing and training sites. The objective of this study was to characterize the microbial community capable of using nitrogen derived from the RDX or RDX intermediates during in situ bioremediation. Active groundwater microorganisms capable of utilizing nitro-, ring- or fully-labeled (15)N-RDX as a nitrogen source were identified using stable isotope probing (SIP) in groundwater microcosms prepared from two wells in an aquifer previously amended with cheese whey to promote RDX biodegradation. A total of fifteen 16S rRNA gene sequences, clustered in Clostridia, β-Proteobacteria, and Spirochaetes, were derived from the (15)N-labeled DNA fractions, suggesting the presence of metabolically active bacteria capable of using RDX and/or RDX intermediates as a nitrogen source. None of the derived sequences matched RDX-degrading cultures commonly studied in the laboratory, but some of these genera have previously been linked to RDX degradation in site groundwater via (13)C-SIP. When additional cheese whey was added to the groundwater samples, 28 sequences grouped into Bacteroidia, Bacilli, and α-, β-, and γ-Proteobacteria were identified. The data suggest that numerous bacteria are capable of incorporating N from ring- and nitro-groups in RDX during anaerobic bioremediation, and that some genera may be involved in both C and N incorporation from RDX. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Bioluminescence-Based Method for Measuring Assimilable Organic Carbon in Pretreatment Water for Reverse Osmosis Membrane Desalination ▿

    PubMed Central

    Weinrich, Lauren A.; Schneider, Orren D.; LeChevallier, Mark W.

    2011-01-01

    A bioluminescence-based assimilable organic carbon (AOC) test was developed for determining the biological growth potential of seawater within the reverse osmosis desalination pretreatment process. The test uses Vibrio harveyi, a marine organism that exhibits constitutive luminescence and is nutritionally robust. AOC was measured in both a pilot plant and a full-scale desalination plant pretreatment. PMID:21148685

  1. Bioluminescence-based method for measuring assimilable organic carbon in pretreatment water for reverse osmosis membrane desalination.

    PubMed

    Weinrich, Lauren A; Schneider, Orren D; LeChevallier, Mark W

    2011-02-01

    A bioluminescence-based assimilable organic carbon (AOC) test was developed for determining the biological growth potential of seawater within the reverse osmosis desalination pretreatment process. The test uses Vibrio harveyi, a marine organism that exhibits constitutive luminescence and is nutritionally robust. AOC was measured in both a pilot plant and a full-scale desalination plant pretreatment.

  2. Assimilable organic carbon (AOC) in soil water extracts using Vibrio Harveyi BB721 and its implication for microbial biomass

    USDA-ARS?s Scientific Manuscript database

    Assimilable organic carbon (AOC) is commonly used to measure the growth potential of microorganisms in water, but has not yet been investigated for measuring microbial growth potential in soils. In this study, a simple, rapid, and non-growth based assay to determine AOC in soil was developed using a...

  3. EFFECT OF OZONATED WATER ON THE ASSIMILABLE ORGANIC CARBON AND COLIFORM GROWTH RESPONSE VALUES AND ON PATHOGENIC BACTERIA SURVIVAL

    EPA Science Inventory

    The assimilable organic carbon (AOC) and coliform growth response (CGR) are bioassays used to determine water quality. AOC and CGR are better indexes in determining whether water can support the growth of bacteria than biological oxygen demand (BOD). The AOC value of reconditione...

  4. EFFECT OF OZONATED WATER ON THE ASSIMILABLE ORGANIC CARBON AND COLIFORM GROWTH RESPONSE VALUES AND ON PATHOGENIC BACTERIA SURVIVAL

    EPA Science Inventory

    The assimilable organic carbon (AOC) and coliform growth response (CGR) are bioassays used to determine water quality. AOC and CGR are better indexes in determining whether water can support the growth of bacteria than biological oxygen demand (BOD). The AOC value of reconditione...

  5. [Quantifying soil autotrophic microbes-assimilated carbon input into soil organic carbon pools following continuous 14C labeling].

    PubMed

    Shi, Ran; Chen, Xiao-Juan; Wu, Xiao-Hong; Jian, Yan; Yuan, Hong-Zhao; Ge, Ti-Da; Sui, Fang-Gong; Tong, Cheng-Li; Wu, Jin-Shui

    2013-07-01

    Soil autotrophic microbe has been found numerous and widespread. However, roles of microbial autotrophic processes and the mechanisms of that in the soil carbon sequestration remain poorly understood. Here, we used soils incubated for 110 days in a closed, continuously labeled 14C-CO2 atmosphere to measure the amount of labeled C incorporated into the microbial biomass. The allocation of 14C-labeled assimilated carbon in variable soil C pools such as dissolved organic C (DOC) and microbial biomass C (MBC) were also examined over the 14C labeling span. The results showed that significant amounts of 14C-SOC were measured in paddy soils, which ranged from 69.06-133.81 mg x kg(-1), accounting for 0.58% to 0.92% of the total soil organic carbon (SOC). The amounts of 14C in the dissolved organic C (14C-DOC) and in the microbial biomass C (14C-MBC) were dependent on the soils, ranged from 2.54 to 8.10 mg x kg(-1), 19.50 to 49.16 mg x kg(-1), respectively. There was a significantly positive linear relationship between concentrations of 14C-SOC and 14C-MBC (R2 = 0.957**, P < 0.01). The 14C-DOC and 14C-MBC as proportions of total DOC, MBC, were 5.65%-24.91% and 4.23%-20.02%, respectively. Moreover, the distribution and transformation of microbes-assimilated-derived C had a greater influence on the dynamics of DOC and MBC than that on the dynamics of SOC. These data provide new insights into the importance of microorganisms in the fixation of atmospheric CO2 and of the potentially significant contributions made by microbial autotrophy to terrestrial C cycling.

  6. Inorganic nitrogen assimilation in yeasts: alteration in enzyme activities associated with changes in cultural conditions and growth phase.

    PubMed

    Thomulka, K W; Moat, A G

    1972-01-01

    Ammonia assimilation has been investigated in four strains of Saccharomyces cerevisiae by measuring, at intervals throughout the growth cycle, the activities of several enzymes concerned with inorganic ammonia assimilation. Enzyme activities in extracts of cells were compared after growth in complete and defined media. The effect of shift from growth in a complete to growth in a defined medium (and the reverse) was also determined. The absence of aspartase (EC 4.3.1.1, l-aspartate-ammonia lyase) activity, the low specific activities of alanine dehydrogenase, glutamine synthetase [EC 6.3.1.2, l-glutamate-ammonia ligase (ADP)], and the marked increase in activity of the nicotinamide adenine dinucleotide phosphate-linked glutamate dehydrogenase (NADP-GDH) [EC 1.4.1.4, l-glutamate:NADP-oxidoreductase (deaminating)] during the early stages of growth support the conclusion that yeasts assimilate ammonia primarily via glutamate. The NADP-GDH showed a rapid increase in activity just before the initiation of exponential growth, reached a maximum at the mid-exponential stage, and then gradually declined in activity in the stationary phase. The NADP-GDH reached a higher level of activity when the yeasts were grown on the defined medium as compared with complete medium. The nicotinamide adenine dinucleotide-linked glutamate dehydrogenase (NAD-GDH) [EC 1.4.1.2, l-glutamate:NAD-oxidoreductase (deaminating)] showed only slight increases in activity during the exponential phase of growth. There was an inverse relationship in that the NADP-GDH increased in activity as the NAD-GDH decreased. The NAD-GDH activity was higher after growth on the complete medium. The glutamate-oxaloacetate transaminase (EC 2.6.1.1. l-aspartate:2-oxoglutarate aminotransferase) activity rose and fell in parallel with the NADP-GDH, although its specific activity was somewhat lower. Although other ammonia-assimilatory enzymes were demonstrable, it seems unlikely that their combined activities could account

  7. Phylogenetic signal in phenotypic traits related to carbon source assimilation and chemical sensitivity in Acinetobacter species.

    PubMed

    Van Assche, Ado; Álvarez-Pérez, Sergio; de Breij, Anna; De Brabanter, Joseph; Willems, Kris A; Dijkshoorn, Lenie; Lievens, Bart

    2017-01-01

    A common belief is that the phylogeny of bacteria may reflect molecular functions and phenotypic characteristics, pointing towards phylogenetic conservatism of traits. Here, we tested this hypothesis for a large set of Acinetobacter strains. Members of the genus Acinetobacter are widespread in nature, demonstrate a high metabolic diversity and are resistant to several environmental stressors. Notably, some species are known to cause opportunistic human infections. A total of 133 strains belonging to 33 species with validly published names, two genomic species and species of an as-yet unknown taxonomic status were analyzed using the GENIII technology of Biolog, which allows high-throughput phenotyping. We estimated the strength and significance of the phylogenetic signal of each trait across phylogenetic reconstructions based on partial RNA polymerase subunit B (rpoB) and core genome sequences. Secondly, we tested whether phylogenetic distance was a good predictor of trait differentiation by Mantel test analysis. And finally, evolutionary model fitting was used to determine if the data for each phenotypic character was consistent with a phylogenetic or an essentially random model of trait distribution. Our data revealed that some key phenotypic traits related to substrate assimilation and chemical sensitivity are linked to the phylogenetic placement of Acinetobacter species. The strongest phylogenetic signals found were for utilization of different carbon sources such as some organic acids, amino acids and sugars, thus suggesting that in the diversification of Acinetobacter carbon source assimilation has had a relevant role. Future work should be aimed to clarify how such traits have shaped the remarkable ability of this bacterial group to dominate in a wide variety of habitats.

  8. Detection of potential leakage pathways from geological carbon storage by fluid pressure data assimilation

    NASA Astrophysics Data System (ADS)

    González-Nicolás, Ana; Baù, Domenico; Alzraiee, Ayman

    2015-12-01

    One of the main concerns of geological carbon storage (GCS) systems is the risk of leakage through "weak" permeable areas of the sealing formation or caprock. Since the fluid pressure pulse travels faster than the carbon dioxide (CO2) plume across the storage reservoir, the fluid overpressure transmitted into overlying permeable formations through caprock discontinuities is potentially detectable sooner than actual CO2 leakage occurs. In this work, an inverse modeling method based on fluid pressure measurements collected in strata above the target CO2 storage formation is proposed, which aims at identifying the presence, the location, and the extent of possible leakage pathways through the caprock. We combine a three-dimensional subsurface multiphase flow model with ensemble-based data assimilation algorithms to recognize potential caprock discontinuities that could undermine the long-term safety of GCS. The goal of this work is to examine and compare the capabilities of data assimilation algorithms such as the ensemble smoother (ES) and the restart ensemble Kalman filter (REnKF) to detect the presence of brine and/or CO2 leakage pathways, potentially in real-time during GCS operations. For the purpose of this study, changes in fluid pressure in the brine aquifer overlying to CO2 storage formation aquifer are hypothetically observed in monitoring boreholes, or provided by time-lapse seismic surveys. Caprock discontinuities are typically characterized locally by higher values of permeability, so that the permeability distribution tends to fit to a non-Gaussian bimodal process, which hardly complies with the requirements of the ES and REnKF algorithms. Here, issues related to the non-Gaussianity of the caprock permeability field are investigated by developing and applying a normal score transform procedure. Results suggest that the REnKF is more effective than the ES in characterizing caprock discontinuities.

  9. Carbon-nitrogen-water interactions: is model parsimony fruitful?

    NASA Astrophysics Data System (ADS)

    Puertes, Cristina; González-Sanchis, María; Lidón, Antonio; Bautista, Inmaculada; Lull, Cristina; Francés, Félix

    2017-04-01

    It is well known that carbon and nitrogen cycles are highly intertwined and both should be explained through the water balance. In fact, in water-controlled ecosystems nutrient deficit is related to this water scarcity. For this reason, the present study compares the capability of three models in reproducing the interaction between the carbon and nitrogen cycles and the water cycle. The models are BIOME-BGCMuSo, LEACHM and a simple carbon-nitrogen model coupled to the hydrological model TETIS. Biome-BGCMuSo and LEACHM are two widely used models that reproduce the carbon and nitrogen cycles adequately. However, their main limitation is that these models are quite complex and can be too detailed for watershed studies. On the contrary, the TETIS nutrient sub-model is a conceptual model with a vertical tank distribution over the active soil depth, dividing it in two layers. Only the input of the added litter and the losses due to soil respiration, denitrification, leaching and plant uptake are considered as external fluxes. Other fluxes have been neglected. The three models have been implemented in an experimental plot of a semi-arid catchment (La Hunde, East of Spain), mostly covered by holm oak (Quercus ilex). Plant transpiration, soil moisture and runoff have been monitored daily during nearly two years (26/10/2012 to 30/09/2014). For the same period, soil samples were collected every two months and taken to the lab in order to obtain the concentrations of dissolved organic carbon, microbial biomass carbon, ammonium and nitrate. In addition, between field trips soil samples were placed in PVC tubes with resin traps and were left incubating (in situ buried cores). Thus, mineralization and nitrification accumulated fluxes for two months, were obtained. The ammonium and nitrate leaching accumulated for two months were measured using ion-exchange resin cores. Soil respiration was also measured every field trip. Finally, water samples deriving from runoff, were collected

  10. Integration of carbon assimilation modes with photosynthetic light capture in the green alga Chlamydomonas reinhardtii.

    PubMed

    Berger, Hanna; Blifernez-Klassen, Olga; Ballottari, Matteo; Bassi, Roberto; Wobbe, Lutz; Kruse, Olaf

    2014-10-01

    The unicellular green alga Chlamydomonas reinhardtii is capable of using organic and inorganic carbon sources simultaneously, which requires the adjustment of photosynthetic activity to the prevailing mode of carbon assimilation. We obtained novel insights into the regulation of light-harvesting at photosystem II (PSII) following altered carbon source availability. In C. reinhardtii, synthesis of PSII-associated light-harvesting proteins (LHCBMs) is controlled by the cytosolic RNA-binding protein NAB1, which represses translation of particular LHCBM isoform transcripts. This mechanism is fine-tuned via regulation of the nuclear NAB1 promoter, which is activated when linear photosynthetic electron flow is restricted by CO(2)-limitation in a photoheterotrophic context. In the wild-type, accumulation of NAB1 reduces the functional PSII antenna size, thus preventing a harmful overexcited state of PSII, as observed in a NAB1-less mutant. We further demonstrate that translation control as a newly identified long-term response to prolonged CO(2)-limitation replaces LHCII state transitions as a fast response to PSII over-excitation. Intriguingly, activation of the long-term response is perturbed in state transition mutant stt7, suggesting a regulatory link between the long- and short-term response. We depict a regulatory circuit operating on distinct timescales and in different cellular compartments to fine-tune light-harvesting in photoheterotrophic eukaryotes.

  11. Temperature and carbon assimilation regulate the chlorosome biogenesis in green sulfur bacteria.

    PubMed

    Tang, Joseph Kuo-Hsiang; Saikin, Semion K; Pingali, Sai Venkatesh; Enriquez, Miriam M; Huh, Joonsuk; Frank, Harry A; Urban, Volker S; Aspuru-Guzik, Alán

    2013-09-17

    Green photosynthetic bacteria adjust the structure and functionality of the chlorosome-the light-absorbing antenna complex-in response to environmental stress factors. The chlorosome is a natural self-assembled aggregate of bacteriochlorophyll (BChl) molecules. In this study, we report the regulation of the biogenesis of the Chlorobaculum tepidum chlorosome by carbon assimilation in conjunction with temperature changes. Our studies indicate that the carbon source and thermal stress culture of C. tepidum grows slower and incorporates fewer BChl c in the chlorosome. Compared with the chlorosome from other cultural conditions we investigated, the chlorosome from the carbon source and thermal stress culture displays (a) smaller cross-sectional radius and overall size, (b) simplified BChl c homologs with smaller side chains, (c) blue-shifted Qy absorption maxima, and (d) a sigmoid-shaped circular dichroism spectra. Using a theoretical model, we analyze how the observed spectral modifications can be associated with structural changes of BChl aggregates inside the chlorosome. Our report suggests a mechanism of metabolic regulation for chlorosome biogenesis.

  12. sup 15 NO sub 3 assimilation and its inhibitory effect on symbiotic nitrogen fixation in peanut

    SciTech Connect

    Stanfill, S.B.; Wells, R.; Israel, D.W.; Rufty, T.W. )

    1990-05-01

    To assess the inhibitory effect of nitrate on the contribution of symbiotic N fixation to total plant N, cultivars of different nodulation capacity were monitored in a growth chamber study. Plants inoculated with Bradyrhizobium sp. (Arachis) strain NC 70.1 were grown in a nutrient solution containing 0, 2.5, 5 or 10 mM NO{sub 3} enriched with 2.5 atom % {sup 15}N. Plant harvests at 30 and 60 DAP provided tissue for measurement of growth, total N, NO{sub 3} and {sup 15}N partitioning. Nitrogenase activity was estimated via C{sub 2}H{sub 2} reduction. Data indicates that plant growth was associated to NO{sub 3} concentration. Average nodule weight and N plant{sup {minus}1} decreased in excess of 2.5mM NO{sub 3}. Specific nitrogenase activity diminished markedly with application of NO{sub 3} with a decline from 40.2 to 25.0 {mu}moles C{sub 2}H{sub 2} g hr{sup {minus}1} at 0 and 2.5mM NO{sub 3}, respectively. Nitrate and fixed N assimilation patterns will be elucidated by {sup 15}N analysis.

  13. Do elevation of CO(2) concentration and nitrogen fertilization alter storage and remobilization of carbon and nitrogen in pedunculate oak saplings?

    PubMed

    Vizoso, Seraphine; Gerant, Dominique; Guehl, Jean Marc; Joffre, Richard; Chalot, Michel; Gross, Patrick; Maillard, Pascale

    2008-11-01

    Soil nitrogen can alter storage and remobilization of carbon and nitrogen in forest trees and affect growth responses to elevated carbon dioxide concentration ([CO(2)]). We investigated these effects in oak saplings (Quercus robur L.) exposed for two years to ambient or twice ambient [CO(2)] in combination with low- (LN, 0.6 mmol N l(-1)) or high-nitrogen (HN, 6.1 mmol N l(-1)) fertilization. Autumn N retranslocation efficiency from senescing leaves was less in HN saplings than in LN saplings, but about 15% of sapling N was lost to the litter. During the dormant season, nonstructural carbohydrates made up 20 to 30% of the dry mass of perennial organs. Starch was stored mainly in large roots where it represented 35-46% of dry mass. Accumulation of starch increased in large roots in response to LN but was unaffected by elevated [CO(2)]. The HN treatment resulted in high concentrations of N-soluble compounds, and this effect was reduced by elevated [CO(2)], which decreased soluble protein N (-17%) and amino acid N (-37%) concentrations in the HN saplings. Carbon and N reserves were labeled with (13)C and (15)N, respectively, at the end of the first year. In the second year, about 20% of labeled C and 50% of labeled N was remobilized for spring growth in all treatments. At the end of leaf expansion, 50-60% of C in HN saplings originated from assimilation versus only 10-20% in LN saplings. In HN saplings only, N uptake occurred, and some newly assimilated N was allocated to new shoots. Through effects on the C and N content of perennial organs, elevated [CO(2)] and HN increased remobilization capacity, thereby supporting multiple shoot flushes, which increased leaf area and subsequent C acquisition in a positive feedback loop.

  14. Comparing the CarbonTracker and M5-4DVar data assimilation systems for CO2 surface flux inversions

    NASA Astrophysics Data System (ADS)

    Babenhauserheide, A.; Basu, S.; Houweling, S.; Peters, W.; Butz, A.

    2015-09-01

    Data assimilation systems allow for estimating surface fluxes of greenhouse gases from atmospheric concentration measurements. Good knowledge about fluxes is essential to understand how climate change affects ecosystems and to characterize feedback mechanisms. Based on the assimilation of more than 1 year of atmospheric in situ concentration measurements, we compare the performance of two established data assimilation models, CarbonTracker and TM5-4DVar (Transport Model 5 - Four-Dimensional Variational model), for CO2 flux estimation. CarbonTracker uses an ensemble Kalman filter method to optimize fluxes on ecoregions. TM5-4DVar employs a 4-D variational method and optimizes fluxes on a 6° × 4° longitude-latitude grid. Harmonizing the input data allows for analyzing the strengths and weaknesses of the two approaches by direct comparison of the modeled concentrations and the estimated fluxes. We further assess the sensitivity of the two approaches to the density of observations and operational parameters such as the length of the assimilation time window. Our results show that both models provide optimized CO2 concentration fields of similar quality. In Antarctica CarbonTracker underestimates the wintertime CO2 concentrations, since its 5-week assimilation window does not allow for adjusting the distant surface fluxes in response to the detected concentration mismatch. Flux estimates by CarbonTracker and TM5-4DVar are consistent and robust for regions with good observation coverage, regions with low observation coverage reveal significant differences. In South America, the fluxes estimated by TM5-4DVar suffer from limited representativeness of the few observations. For the North American continent, mimicking the historical increase of the measurement network density shows improving agreement between CarbonTracker and TM5-4DVar flux estimates for increasing observation density.

  15. Species-specific intrinsic water use efficiency and its mediation of carbon assimilation during the drought

    NASA Astrophysics Data System (ADS)

    Yi, K.; Wenzel, M. K.; Maxwell, J. T.; Novick, K. A.; Gray, A.; Roman, D. T.

    2015-12-01

    Drought is expected to occur more frequently and intensely in the future, and many studies have suggested frequent and intense droughts can significantly alter carbon and water cycling in forest ecosystems, consequently decreasing the ability of forests to assimilate carbon. Predicting the impact of drought on forest ecosystem processes requires an understanding of species-specific responses to drought, especially in eastern US where species composition is highly dynamic. An emerging approach for describing species-specific drought response is to classify the plant water use strategy into isohydric and anisohydric behaviors. Trees utilizing isohydric behavior regulate water potential by closing stomata to reduce water loss during drought conditions, while anisohydric trees allow water potential to drop by sustaining stomatal conductance, but with the risk of hydraulic failure caused by cavitation of xylem tissues. Since catastrophic cavitation occurs infrequently in the relatively wet eastern U.S., we hypothesize that 1) tree growth of isohydric trees will be more limited during the drought than the anisohydric trees due to decreased stomatal conductance, but 2) variation in intrinsic water use efficient (iWUE) during drought in isohydric trees will mediate the effects of drought on carbon assimilation. We will test these hypotheses by 1) analyzing tree-ring chronologies and dendrometer data on productivity, and 2) estimating intrinsic water use efficiency (iWUE) at multiple scales by analyzing gas exchange data for the leaf-level, inter-annual variability of d13C in tree stem cores for the tree-level, and eddy covariance technique for the stand-level. Our study site is the Morgan-Monroe State Forest (Indiana, USA). A 46 m flux tower has been continuously recording the carbon, water and energy fluxes, and tree diameter has been measured every 2 weeks using dendrometers, since 1998. Additional research, including gas exchange measurements performed during the

  16. Terrestrial carbon-nitrogen interactions across time-scales

    NASA Astrophysics Data System (ADS)

    Zaehle, Sönke; Sickel, Kerstin

    2017-04-01

    Through its role in forming amino acids, nitrogen (N) plays a fundamental role in terrestrial biogeochemistry, affecting for instance the photosynthetic rate of a leaf, and the amount of leaf area of a plant; with further consequences for quasi instantaneous terrestrial biophysical properties and fluxes. Because of the high energy requirements of transforming atmospheric N2 to biologically available form, N is generally thought to be limiting terrestrial productivity. Experimental evidence and modelling studies suggest that in temperate and boreal ecosystems, this N-"limitation" affects plant production at scales from days to decades, and potentially beyond. Whether these interactions play a role at longer timescales, such as during the transition from the last glacial maximum to the holocene, is currently unclear. To address this question, we present results from a 22000 years long simulation with dynamic global vegetation model including a comprehensive treatment of the terrestrial carbon and nitrogen balance and their interactions (using the OCN-DGVM) driven by monthly, transient climate forcing obtained from the CESM climate model (TRACE). OCN couples carbon and nitrogen processes at the time-scale of hours, but simulates a comprehensive nitrogen balance as well as vegetation dynamics with time-scales of centuries and beyond. We investigate in particular, whether (and at with time scale) carbon-nitrogen interactions cause important lags in the response of the terrestrial biosphere to changed climate, and which processes (such as altered N inputs from fixation or altered losses through leaching and denitrification) contribute to these lags.

  17. 14C-dead living biomass: evidence for microbial assimilation of ancient organic carbon during shale weathering.

    PubMed

    Petsch, S T; Eglington, T I; Edwards, K J

    2001-05-11

    Prokaryotes have been cultured from a modern weathering profile developed on a approximately 365-million-year-old black shale that use macromolecular shale organic matter as their sole organic carbon source. Using natural-abundance carbon-14 analysis of membrane lipids, we show that 74 to 94% of lipid carbon in these cultures derives from assimilation of carbon-14-free organic carbon from the shale. These results reveal that microorganisms enriched from shale weathering profiles are able to use a macromolecular and putatively refractory pool of ancient organic matter. This activity may facilitate the oxidation of sedimentary organic matter to inorganic carbon when sedimentary rocks are exposed by erosion. Thus, microorganisms may play a more active role in the geochemical carbon cycle than previously recognized, with profound implications for controls on the abundance of oxygen and carbon dioxide in Earth's atmosphere over geologic time.

  18. Rootstock and vineyard floor management influence on 'Cabernet Sauvignon' grape yeast assimilable nitrogen (YAN).

    PubMed

    Lee, Jungmin; Steenwerth, Kerri L

    2011-08-01

    This is a study on the influence that two rootstocks (110R, high vigour; 420A, low vigour) and three vineyard floor management regimes (tilled resident vegetation - usual practise in California, and barley cover crops that were either mowed or tilled) had upon grape nitrogen-containing compounds (mainly ammonia and free amino acids recalculated as YAN), sugars, and organic acids in 'Cabernet Sauvignon' clone 8. A significant difference was observed for some of the free amino acids between rootstocks. In both sample preparation methods (juiced or chemically extracted), 110R rootstock grapes were significantly higher in SER, GLN, THR, ARG, VAL, ILE, LEU, and YAN than were 420A rootstock grapes. Differences in individual free amino acid profiles and concentrations were observed between the two sample preparations, which indicate that care should be taken when comparing values from dissimilar methods. No significant differences among vineyard floor treatments were detected, which suggests that mowing offers vineyard managers a sustainable practise, alternative to tilling, without negatively affecting grape nitrogen compounds, sugars, or organic acids. Published by Elsevier Ltd.

  19. Optimization of carbon and nitrogen medium components for biomass production using non-Saccharomyces wine yeasts.

    PubMed

    Schnierda, T; Bauer, F F; Divol, B; van Rensburg, E; Görgens, J F

    2014-05-01

    The impact of different nitrogen and carbon sources on biomass production of the non-Saccharomyces wine yeast species Lachancea thermotolerans, Metschnikowia pulcherrima and Issatchenkia orientalis was assessed. Using a molasses-based medium, yeast extract and corn steep liquor as well as ammonium sulphate and di-ammonium phosphate (DAP) as nitrogen sources were compared in shake-flask cultures. A medium with 20 g l⁻¹ sugar (diluted molasses) and 500 mg l⁻¹ total yeast assimilable nitrogen, from yeast extract, gave the highest biomass concentrations and yields. Invertase pretreatment was required for cultures of M. pulcherrima and I. orientalis, and respective biomass yields of 0.7 and 0.8 g g⁻¹ were achieved in aerobic bioreactor cultures. The absence of ethanol production suggested Crabtree-negative behaviour by these yeasts, whereas Crabtree-positive behaviour by L. thermotolerans resulted in ethanol and biomass concentrations of 5.5 and 11.1 g l⁻¹, respectively. Recent studies demonstrate that non-Saccharomyces yeasts confer positive attributes to the final composition of wine. However, optimal process conditions for their biomass production have not been described, thereby limiting commercial application. In this study, industrial media and methods of yeast cultivation were investigated to develop protocols for biomass production of non-Saccharomyces yeast starter cultures for the wine industry. © 2014 The Society for Applied Microbiology.

  20. Transgenic tobacco plants that overexpress alfalfa NADH-glutamate synthase have higher carbon and nitrogen content.

    PubMed

    Chichkova, S; Arellano, J; Vance, C P; Hernández, G

    2001-11-01

    This work reports the characterization of transgenic tobacco (Nicotiana tabacum L.) plants that constitutively overexpress NADH-GOGAT. Three independent transformants, designated GOS10, GOS13 and GOS19 (for GOGAT sense), with stable integration of the chimeric alfalfa NADH-GOGAT gene fused to the CaMV 35S promoter were studied. The transgene was stably integrated and inherited by the progeny. In these GOS lines, the expression of NADH-GOGAT mRNA and protein was detected at low levels in roots and leaves, while the expression of the host tobacco NADH-GOGAT gene was nearly undetectable. The roots of GOS lines showed an elevated (15-40%) enzyme activity as compared to control plants. When GOS plants were grown under greenhouse conditions and fed with either nitrate or ammonium as the sole nitrogen source, they showed higher total carbon and nitrogen content in shoots and increased shoot dry weight when plants were entering into the flowering stage, as compared to control plants. The observed phenotype of GOS plants was interpreted as reflecting a higher capacity to assimilate nitrogen due to a higher NADH-GOGAT activity.

  1. A mobile light source for carbon/nitrogen cameras

    NASA Astrophysics Data System (ADS)

    Trower, W. P.; Karev, A. I.; Melekhin, V. N.; Shvedunov, V. I.; Sobenin, N. P.

    1995-05-01

    The pulsed light source for carbon/nitrogen cameras developed to image concealed narcotics/explosives is described. This race-track microtron will produce 40 mA pulses of 70 MeV electrons, have minimal size and weight, and maximal ruggedness and reliability, so that it can be transported on a truck.

  2. Angular distribution of photoelectrons from atomic oxygen, nitrogen, and carbon

    NASA Technical Reports Server (NTRS)

    Manson, S. T.; Kennedy, D. J.; Starace, A. F.; Dill, D.

    1974-01-01

    The angular distribution of photoelectrons from atomic oxygen is investigated using Hartree-Fock (HF) wave functions. The correct formulation is used to compare HS and HF results. Agreement between these results is good and the HS calculations have been extended to atomic nitrogen and carbon as well.

  3. Imaging carbon and nitrogen concentrations for narcotics and explosives screening

    SciTech Connect

    Trower, W.P.

    1993-12-31

    The author describes a nuclear technique for imaging carbon and nitrogen concentrations with surface densities characteristics of bulk narcotics and concealed explosives, the Carbon and the Nitrogen Camera. The physics is rooted in the tightly bound carbon-12 nucleus to which its neighboring isobars, nitrogen-12 and boron-12, decay rapidly (11 and 20 ms), mostly to its ground state, by emitting energetic beta particles (E{sub {beta}}{sup max} {approximately} 13 and 17 MeV) all of which produce bremsstrahlung and some yield annihilate radiation. The signal, photons detected in the multiscalar mode, results from the reactions {sup 13}C({gamma},p){sup 12}{Beta} for the bulk narcotics application and {sup 14}N({gamma},2n){sup 12}N and 14N({gamma},2p){sup 12}{Beta} for explosives detection and are initiated by a stepped pulsed electron beam with energy of {approximately} 30 and {approximately} 50 MeV, respectively. Images of 180 {approximately} 5 cm{sup 2} pixels taken in {approximately} 7 seconds will be presented of the carbon in a kilo of cocaine and the nitrogen in 125 grams of SEMTEX.

  4. Maize Source Leaf Adaptation to Nitrogen Deficiency Affects Not Only Nitrogen and Carbon Metabolism But Also Control of Phosphate Homeostasis1[W][OA

    PubMed Central

    Schlüter, Urte; Mascher, Martin; Colmsee, Christian; Scholz, Uwe; Bräutigam, Andrea; Fahnenstich, Holger; Sonnewald, Uwe

    2012-01-01

    Crop plant development is strongly dependent on the availability of nitrogen (N) in the soil and the efficiency of N utilization for biomass production and yield. However, knowledge about molecular responses to N deprivation derives mainly from the study of model species. In this article, the metabolic adaptation of source leaves to low N was analyzed in maize (Zea mays) seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under sufficient (15 mm) or limiting (0.15 mm) nitrate supply for up to 30 d. Limited availability of N caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the N stress but showed strong genotype- and age-dependent patterns. N starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation-related transcripts, on the other hand, were not influenced. Carbon assimilation-related transcripts were characterized by high transcriptional coordination and general down-regulation under low-N conditions. N deprivation caused a slight accumulation of starch but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions. PMID:22972706

  5. Nitrogen assimilation and short term retention in a nutrient-rich tidal freshwater marsh - a whole ecosystem 15N enrichment study

    NASA Astrophysics Data System (ADS)

    Gribsholt, B.; Struyf, E.; Tramper, A.; de Brabandere, L.; Brion, N.

    2006-07-01

    We conducted two (May 2002 and September 2003) pulse additions of 15NH4+ to the flood water inundating a tidal freshwater marsh fringing the nutrient-rich Scheldt River (Belgium) and traced the fate of ammonium in the intact ecosystem. Here we report in detail the 15N uptake into the various marsh components (leaves, roots, sediment, leaf litter and invertebrate fauna), and the 15N retention on a scale of 15 days. We particularly focus on the contributions of the rooted macrophytes and the microbial community in the sediment and on plant litter. Assimilation and short term retention of 15NH4+ was low on both occasions. Only 4-9% of the added 15N trace was assimilated, corresponding to 13-22% and 8-18% of the processed 15N (i.e. not exported as 15NH4+ in May and September, respectively. In May nitrogen assimilation rate (per hour inundated) was >3 times faster than in September. Macrophytes (above- and below ground) were of limited importance for short term 15N retention accounting for <6% of the total 15NH4+ processed by the marsh. The less dominant herbaceous species were more important (on an area basis) than the dominant reed (Phragmites australis). The microbial community colonizing the sediment and litter surfaces were responsible for most nitrogen assimilation and short-term retention in the marsh. The large reactive surface area available for microbial colonization together with direct plant uptake, are the crucial components for nitrogen assimilation, retention and transformation in nutrient-rich tidal freshwater marshes.

  6. Stable carbon, nitrogen and sulfur isotopes in non-carbonate fractions of cold-seep carbonates

    NASA Astrophysics Data System (ADS)

    Feng, Dong; Peng, Yongbo; Peckmann, Jörn; Roberts, Harry; Chen, Duofu

    2017-04-01

    Sulfate-driven anaerobic oxidation of methane (AOM) supports chemosynthesis-based communities and limits the release of methane from marine sediments. This process promotes the formation of carbonates close to the seafloor along continental margins. The geochemical characteristics of the carbonate minerals of these rocks are increasingly understood, questions remain about the geochemical characteristics of the non-carbonate fractions. Here, we report stable carbon, nitrogen and sulfur isotope patterns in non-carbonate fractions of seep carbonates. The authigenic carbonates were collected from three modern seep provinces (Black Sea, Gulf of Mexico, and South China Sea) and three ancient seep deposits (Marmorito, northern Italy, Miocene; SR4 deposit of the Lincoln Creek Formation and Whiskey Creek, western Washington, USA, Eocene to Oligocene). The δ13C values of non-carbonate fractions range from ˜-25‰ to -80‰ VPDB. These values indicate that fossil methane mixed with varying amounts of pelagic organic matter is the dominant source of carbon in these fractions. The relatively small offset between the δ34S signatures of the non-carbonate fractions and the respective sulfide minerals suggests that locally produced hydrogen sulfide is the main source of sulfur in seep environments. The δ15N values of the non-carbonate fractions are generally lower than the corresponding values of deep-sea sediments, suggesting that organic nitrogen is mostly of a local origin. This study reveals the potential of using δ13C, δ15N, δ34S values to discern seep and non-seep deposits. In cases where δ13Ccarbonate values are only moderately low due to mixing processes and lipid biomarkers have been erased in the course of burial, it is difficult to trace back AOM owing to the lack of other records. This problem is even more pronounced when authigenic carbonate is not available in ancient seep environments. Acknowledgments: The authors thank BOEM and NOAA for their years' support

  7. The interactive effect of fungicide residues and yeast assimilable nitrogen on fermentation kinetics and hydrogen sulfide production during cider fermentation.

    PubMed

    Boudreau, Thomas F; Peck, Gregory M; O'Keefe, Sean F; Stewart, Amanda C

    2017-01-01

    Fungicide residues on fruit may adversely affect yeast during cider fermentation, leading to sluggish or stuck fermentation or the production of hydrogen sulfide (H2 S), which is an undesirable aroma compound. This phenomenon has been studied in grape fermentation but not in apple fermentation. Low nitrogen availability, which is characteristic of apples, may further exacerbate the effects of fungicides on yeast during fermentation. The present study explored the effects of three fungicides: elemental sulfur (S(0) ) (known to result in increased H2 S in wine); fenbuconazole (used in orchards but not vineyards); and fludioxonil (used in post-harvest storage of apples). Only S(0) led to increased H2 S production. Fenbuconazole (≥0.2 mg L(-1) ) resulted in a decreased fermentation rate and increased residual sugar. An interactive effect of yeast assimilable nitrogen (YAN) concentration and fenbuconazole was observed such that increasing the YAN concentration alleviated the negative effects of fenbuconazole on fermentation kinetics. Cidermakers should be aware that residual fenbuconazole (as low as 0.2 mg L(-1) ) in apple juice may lead to stuck fermentation, especially when the YAN concentration is below 250 mg L(-1) . These results indicate that fermentation problems attributed to low YAN may be caused or exacerbated by additional factors such as fungicide residues, which have a greater impact on fermentation performance under low YAN conditions. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

  8. CarbonTracker-Lagrange: A model-data assimilation system for North American carbon flux estimates

    NASA Astrophysics Data System (ADS)

    He, Wei; Chen, Huilin; van der Velde, Ivar; Andrews, Arlyn; Sweeney, Colm; Baker, Ian; Ju, Weimin; van der Laan-Luijkx, Ingrid; Tans, Pieter; Peters, Wouter

    2016-04-01

    Understanding the regional carbon fluxes is of great importance for climate-related studies. To derive these carbon fluxes, atmospheric inverse modeling methods are often used. Different from global inverse modeling, regional studies need to deal with lateral boundary conditions (BCs) at the outer atmospheric domain studied. Also, regional inverse modeling systems typically use a higher spatial resolution and can be more computation-intensive. In this study, we implement a regional inverse modeling system for atmospheric CO₂ based on the CarbonTracker framework. We combine it with a high-resolution Lagrangian transport model, the Stochastic Time-Inverted Lagrangian Transport model driven by the Weather Forecast and Research meteorological fields (WRF-STILT). The new system uses independent information from aircraft CO₂ profiles to optimize lateral BCs, while simultaneously optimizing biosphere fluxes with near-surface CO₂ observations from tall towers. This Lagrangian transport model with precalculated footprints is computational more efficient than using an Eulerian model. We take SiBCASA biosphere model results as prior NEE from the terrestrial biosphere. Three different lateral BCs, derived from CarbonTracker North America mole fraction fields, CarbonTracker Europe mole fraction fields and an empirical BC from NOAA aircraft profiles, are employed to investigate the influence of BCs. To estimate the uncertainties of the optimized fluxes from the system and to determine the impacts of system setup on biosphere flux covariances, BC uncertainties and model-data mismatches, we tested various prior biosphere fluxes and BCs. To estimate the transport uncertainties, we also tested an alternative Lagrangian transport model Hybrid Single Particle Lagrangian Integrated Trajectory Model driven by the North American Mesoscale Forecast System meteorological fields (HYSPLIT-NAM12). Based on the above tests, we achieved an ensemble of inverse estimates from our system

  9. NaCl stress effects on enzymes involved in nitrogen assimilation pathway in tomato "Lycopersicon esculentum" seedlings.

    PubMed

    Debouba, Mohamed; Gouia, Houda; Suzuki, Akira; Ghorbel, Mohamed Habib

    2006-12-01

    Tomato plants (Lycopersicon esculentum Mill, cv. Chibli F1) grown for 10 days on control medium were exposed to differing concentrations of NaCl (0, 25, 50, and 100mM). Increasing salinity led to a decrease of dry weight (DW) production and protein contents in the leaves and roots. Conversely, the root to shoot (R/S) DW ratio was increased by salinity. Na(+) and Cl(-) accumulation were correlated with a decline of K(+) and NO(3)(-) in the leaves and roots. Under salinity, the activities of nitrate reductase (NR, EC 1.6.6.1) and glutamine synthetase (GS, EC 6.3.1.2) were repressed in the leaves, while they were enhanced in the roots. Nitrite reductase (NiR, EC 1.7.7.1) activity was decreased in both the leaves and roots. Deaminating activity of glutamate dehydrogenase (GDH, EC 1.4.1.2) was inhibited, whereas the aminating function was significantly stimulated by salinity in the leaves and roots. At a high salt concentration, the nicotinamide adenine dinucleotide reduced (NADH)-GDH activity was stimulated concomitantly with the increasing NH(4)(+) contents and proteolysis activity in the leaves and roots. With respect to salt stress, the distinct sensitivity of the enzymes involved in nitrogen assimilation is discussed.

  10. Increased proline loading to phloem and its effects on nitrogen uptake and assimilation in water-stressed white clover (Trifolium repens).

    PubMed

    Lee, Bok-Rye; Jin, Yu Lan; Avice, Jean-Christophe; Cliquet, Jean-Bernard; Ourry, Alain; Kim, Tae-Hwan

    2009-01-01

    The aim of this study was to investigate the physiological significance of increased proline loading to phloem caused by water-deficit stress in relation to nitrogen (N) uptake and assimilation. N uptake and N assimilation were quantified by 15N tracing in well-watered (control) and water deficit-stressed white clover (Trifolium repens). De novo proline synthesis and proline loading to the phloem were also compared between treatments. The relationships among proline concentrations in phloem exudates, N uptake, and assimilation of newly absorbed N were assessed. The newly synthesized proline in the phloem exudates increased rapidly after 3 d of water deficit. The water-deficit treatment significantly reduced the maximum nitrate reductase activity (NRA), and also attenuated de novo synthesis of amino acids and proteins in the roots. The increase in proline concentrations in phloem exudates was closely related to reductions in NRA in the roots, N uptake, and the assimilation of newly absorbed N. The accumulation of proline induced in roots by exogenous proline and NH4Cl treatments was closely associated with the decrease in NRA. These results indicate that increased proline transport to roots via phloem caused by water deficit has a significant influence on the down-regulation of N uptake and the assimilation of newly absorbed N.

  11. Investigation of assimilable organic carbon (AOC) and bacterial regrowth in drinking water distribution system.

    PubMed

    Liu, W; Wu, H; Wang, Z; Ong, S L; Hu, J Y; Ng, W J

    2002-02-01

    This paper investigated the variation of assimilable organic carbon (AOC) concentrations in water from several typical water treatment plants and distribution systems in a northern city of China. It is concluded from this study that: (1) The AOC in most of the product water of the studied water treatment plants and the water from the associated distribution systems could not meet the biostability criteria of 50-100 microg/L. (2) Only 4% of the measured AOC concentrations were less than 100 microg/L. However, about half of the measured AOC values were less than 200 microg/L. (3) Better source water quality resulted in lower AOC concentrations. (4) The variation of AOC concentrations in distribution systems was affected by chlorine oxidation and bacterial activity: the former resulted in an increase of AOC value while the latter led to a reduction in AOC. (5) The variation of AOC concentration followed different patterns in different distribution systems or different seasons due to their respective operational characteristics. (6) Less than 30% of AOC could be removed by a conventional treatment process, whereas 30-60% with a maximum of 50-60% could be removed by granular activated carbon (GAC). (7) The observation via scanning electron microscope (SEM) on distribution pipe tubercle samples demonstrated that the pipe inner wall was not smooth and bacteria multiplied in the crevice as well as in the interior wall of distribution pipes.

  12. Multigene manipulation of photosynthetic carbon assimilation increases CO2 fixation and biomass yield in tobacco

    PubMed Central

    Simkin, Andrew J.; McAusland, Lorna; Headland, Lauren R.; Lawson, Tracy; Raines, Christine A.

    2015-01-01

    Over the next 40 years it has been estimated that a 50% increase in the yield of grain crops such as wheat and rice will be required to meet the food and fuel demands of the increasing world population. Transgenic tobacco plants have been generated with altered combinations of sedoheptulose-1,7-bisphosphatase, fructose-1,6-bisphosphate aldolase, and the cyanobacterial putative-inorganic carbon transporter B, ictB, of which have all been identified as targets to improve photosynthesis based on empirical studies. It is shown here that increasing the levels of the three proteins individually significantly increases the rate of photosynthetic carbon assimilation, leaf area, and biomass yield. Furthermore, the daily integrated measurements of photosynthesis showed that mature plants fixed between 12–19% more CO2 than the equivalent wild-type plants. Further enhancement of photosynthesis and yield was observed when sedoheptulose-1,7-bisphosphatase, fructose-1,6-bisphosphate aldolase, and ictB were over-expressed together in the same plant. These results demonstrate the potential for the manipulation of photosynthesis, using multigene-stacking approaches, to increase crop yields. PMID:25956882

  13. Multigene manipulation of photosynthetic carbon assimilation increases CO2 fixation and biomass yield in tobacco.

    PubMed

    Simkin, Andrew J; McAusland, Lorna; Headland, Lauren R; Lawson, Tracy; Raines, Christine A

    2015-07-01

    Over the next 40 years it has been estimated that a 50% increase in the yield of grain crops such as wheat and rice will be required to meet the food and fuel demands of the increasing world population. Transgenic tobacco plants have been generated with altered combinations of sedoheptulose-1,7-bisphosphatase, fructose-1,6-bisphosphate aldolase, and the cyanobacterial putative-inorganic carbon transporter B, ictB, of which have all been identified as targets to improve photosynthesis based on empirical studies. It is shown here that increasing the levels of the three proteins individually significantly increases the rate of photosynthetic carbon assimilation, leaf area, and biomass yield. Furthermore, the daily integrated measurements of photosynthesis showed that mature plants fixed between 12-19% more CO2 than the equivalent wild-type plants. Further enhancement of photosynthesis and yield was observed when sedoheptulose-1,7-bisphosphatase, fructose-1,6-bisphosphate aldolase, and ictB were over-expressed together in the same plant. These results demonstrate the potential for the manipulation of photosynthesis, using multigene-stacking approaches, to increase crop yields. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  14. Unravelling nitrogen deposition effects on carbon cycling in forests

    NASA Astrophysics Data System (ADS)

    Luyssaert, S.; Inglima, I.; Ceulemans, R.; Ciais, P.; Dolman, H. A.; Grace, J.; Hollmén, J.; Law, B. E.; Matteucci, G.; Papale, D.; Piao, S. L.; Reichstein, M.; Schulze, E. D.; Sulkava, M.; Tang, J.; Janssens, I. A.

    2007-12-01

    Nitrogen (N) limitation constrains forest productivity over large areas. Where N is suboptimal, provision of N through fertilization or atmospheric deposition stimulates gross primary productivity (GPP) directly or by enabling forests to benefit from increased atmospheric CO2. Nitrogen deposition also enhances carbon sequestration, but the mechanisms via which this stimulation occurs have so far not been unravelled. Here we analyze observations from 133 forests to decipher how it influences the fate of the absorbed carbon. We find that N-deposition stimulate GPP which, in turn, results in an increase in biomass production (NPP). Whilst the increase in woody biomass production is proportional to the increase in GPP, a disproportional high amount of carbon is used for the production short-lived tissues such as roots and foliage, thereby increasing carbon-inputs to the soil. Nitrogen deposition also strongly retarded heterotrophic respiration and the associated carbon-losses from the soil. Thus, N-deposition strengthened the CO2 sink in the boreal and temperate regions, which are typically N-limited. A future shift in N-deposition towards tropical regions will not necessarily result in a similar increased sink-strength, because these regions are typically not N-limited but suffer from phosphorus, potassium and molybdenum deficiencies.

  15. Comparative Shotgun Proteomic Analysis of Wastewater-Cultured Microalgae: Nitrogen Sensing and Carbon Fixation for Growth and Nutrient Removal in Chlamydomonas reinhardtii.

    PubMed

    Patel, Anil K; Huang, Eric L; Low-Décarie, Etienne; Lefsrud, Mark G

    2015-08-07

    Chlamydomonas reinhardtii was batch-cultured for 12 days under continuous illumination to investigate nitrogen uptake and metabolic responses to wastewater processing. Our approach compared two conditions: (1) artificial wastewater containing nitrate and ammonia and (2) nutrient-sufficient control containing nitrate as sole form of nitrogen. Treatments did not differ in final biomass; however, comparison of group proteomes revealed significant differences. Label-free shotgun proteomic analysis identified 2358 proteins, of which 92 were significantly differentially abundant. Wastewater cells showed higher relative abundances of photosynthetic antenna proteins, enzymes related to carbon fixation, and biosynthesis of amino acids and secondary metabolites. Control cells showed higher abundances of enzymes and proteins related to nitrogen metabolism and assimilation, synthesis and utilization of starch, amino acid recycling, evidence of oxidative stress, and little lipid biosynthesis. This study of the eukaryotic microalgal proteome response to nitrogen source, availability, and switching highlights tightly controlled pathways essential to the maintenance of culture health and productivity in concert with light absorption and carbon assimilation. Enriched pathways in artificial wastewater, notably, photosynthetic carbon fixation and biosynthesis of plant hormones, and those in nitrate only control, most notably, nitrogen, amino acid, and starch metabolism, represent potential targets for genetic improvement requiring targeted elucidation.

  16. Carbon and nitrogen cycling in thermally heated sediments

    NASA Astrophysics Data System (ADS)

    Meyer-Dombard, D. R.; Burton, M.; Vennelakanti, S.; Havig, J. R.; Shock, E.

    2009-12-01

    Hydrothermally heated sediment environments, such as are found in abundance throughout Yellowstone National Park, host fully functional microbial ecosystems. As with any ecosystem, both sources and sinks of carbon, nitrogen, and a myriad of other nutrients and energy-driving factors must be supplied. While we know microbial communities in hydrothermal environments can be surprisingly diverse, we know little about basic ecological functions such as carbon and nitrogen cycling. Previous work has shown that carbon cycling in one hot spring in Yellowstone National Park [“Bison Pool”] and its associated runoff channel functions as a complex system. Analysis of carbon and nitrogen isotopes in sediments and biofilms across a temperature and chemical gradient at this location revealed that the four best studied carbon fixation pathways [Calvin, reverse tricarboxylic acid, acetyl-CoA, 3-hydroxypropionate cycles] may all be functioning in this system, and nitrogen fixation varies across the chemosynthetic/photosynthetic ecotone [1]. Microcosm experiments using biofilms from this hot spring as inoculae with 13C labeled carbon substrates indicate heterotrophic growth [2]. In addition, metagenomic analysis of environmental DNA has indicated the presence of genes involved in carbon fixation [both phototrophic and autotrophic], and heterotrophy, as well as nitrogen fixation [3]. Studies from other Yellowstone locations have also found genetic evidence for carbon and nitrogen fixation [4, 5]. Of particular interest is the role of individuals in carbon and nitrogen cycling as environmental conditions suitable for chemosynthetic and photosynthetic growth vary. This study explores the diversity of cbbM/cbbL [Calvin cycle], aclB/oor/porA [rTCA cycle], nifH [nitrogen fixation], nirK [nitrite reduction] and amoA [ammonia oxidation] genes across a variety of Yellowstone environments. The transition of genetic diversity within sediments and biofilms is focused on the chemosynthetic

  17. Flooding affects uptake and distribution of carbon and nitrogen in citrus seedlings.

    PubMed

    Martínez-Alcántara, Belén; Jover, Sara; Quiñones, Ana; Forner-Giner, María Ángeles; Rodríguez-Gamir, Juan; Legaz, Francisco; Primo-Millo, Eduardo; Iglesias, Domingo J

    2012-08-15

    Soil flooding has been widely reported to affect large areas of the world. In this work, we investigated the effect of waterlogging on citrus carbon and nitrogen pools and partitioning. Influence on their uptake and translocation was also studied through ¹⁵N and ¹³C labeling to provide insight into the physiological mechanisms underlying the responses. The data indicated that flooding severely reduced photosynthetic activity and affected growth and biomass partitioning. Total nitrogen content and concentration in the plant also progressively decreased throughout the course of the experiment. After 36 days of treatment, nitrogen content of flooded plants had decreased more than 2.3-fold compared to control seedlings, and reductions in nitrogen concentration ranged from 21 to 55% (in roots and leaves, respectively). Specific absorption rate and transport were also affected, leading to important changes in the distribution of this element inside the plant. Additionally, experiments involving labeled nitrogen revealed that ¹⁵N uptake rate and accumulation were drastically decreased at the end of the experiment (93% and 54%, respectively). ¹³CO₂ assimilation into the plant was strongly reduced by flooding, with δ¹³C reductions ranging from 22 to 37% in leaves and roots, respectively. After 36 days, the relative distribution of absorbed ¹³C was also altered. Thus, ¹³C recovery in flooded leaves increased compared to controls, whereas roots exhibited the opposite pattern. Interestingly, when carbohydrate partitioning was examined, the data revealed that sucrose concentration was augmented significantly in roots (37-56%), whereas starch was reduced. In leaves, a marked increase in sucrose was detected from the first sampling onwards (36-66%), and the same patter was observed for starch. Taken together, these results indicate that flooding altered carbon and nitrogen pools and partitioning in citrus. On one hand, reduced nitrogen concentration appears to

  18. Methods of detection and identificationoc carbon- and nitrogen-containing materials

    SciTech Connect

    Karev, Alexander Ivanovich; Raevsky, Valery Georgievich; Dzhalivyan, Leonid Zavenovich; Brothers, Louis Joseph; Wilhide, Larry K

    2013-11-12

    Methods for detecting and identifying carbon- and/or nitrogen-containing materials are disclosed. The methods may comprise detection of photo-nuclear reaction products of nitrogen and carbon to detect and identify the carbon- and/or nitrogen-containing materials.

  19. The Path of Carbon in Photosynthesis X. Carbon Dioxide Assimilation in Plants

    DOE R&D Accomplishments Database

    Calvin, M.; Bassham, J. A.; Benson, A. A.; Lynch, V.; Ouellet, C.; Schou, L.; Stepka, W.; Tolbert, N. E.

    1950-04-01

    The conclusions which have been drawn from the results of C{sup 14}O{sub 2} fixation experiments with a variety of plants are developed in this paper. The evidence for thermochemical reduction of carbon dioxide fixation intermediates is presented and the results are interpreted from such a viewpoint.

  20. Reduction of nitrogen- and carbon-based pollutants

    SciTech Connect

    Bowers, W.E.

    1990-05-22

    This patent describes a process for educing the concentration of nitrogen oxides in an oxygen-rich effluent from the combustion of a carbonaceous fuel. It comprises: injecting a solution comprising at least one additive compound selected from the group consisting of guanidine, guanidine carbonate, biguanide, guanylurea sulfate, melamine, dicyandiamide, biuret, 1,1{prime}-azobisformamide, methylol urea, methylol urea-urea condensation product, dimethylol urea, methyl urea, and dimethyl urea, at a concentration and a temperature effective to achieve reduction in nitrogen oxide levels in the effluent.

  1. Carbon and nitrogen source effects on basidiomycetes exopolysaccharide production.

    PubMed

    Elisashvili, V I; Kachlishvili, E T; Wasser, S P

    2009-01-01

    The capability to synthesize the extracellular polysaccharide (EPS) is widespread among eight mushroom species which accumulated 0.6-2.2 g/l of EPS in submerged cultivation. Glucose, maltose, and mannitol were the most appropriate carbon sources for biomass and EPS production. Organic nitrogen sources appeared to be the most suitable nitrogen sources for biomass and EPS accumulation. The cultivation process in shake flasks was successfully reproduced in a laboratory fermentor with enhanced EPS production. The highest yield of EPS (3.8-4.0 g/l) was achieved in cultivation of Agaricus nevoi and Inonotus levis.

  2. Comparing the CarbonTracker and TM5-4DVar data assimilation systems for CO2 surface flux inversions

    NASA Astrophysics Data System (ADS)

    Babenhauserheide, A.; Basu, S.; Houweling, S.; Peters, W.; Butz, A.

    2015-03-01

    Data assimilation systems allow for estimating surface fluxes of greenhouse gases from atmospheric concentration measurements. Good knowledge about fluxes is essential to understand how climate change affects ecosystems and to characterize feedback mechanisms. Based on assimilation of more than one year of atmospheric in-situ concentration measurements, we compare the performance of two established data assimilation models, CarbonTracker and TM5-4DVar, for CO2 flux estimation. CarbonTracker uses an Ensemble Kalman Filter method to optimize fluxes on ecoregions. TM5-4DVar employs a 4-D variational method and optimizes fluxes on a 6° × 4° longitude/latitude grid. Harmonizing the input data allows analyzing the strengths and weaknesses of the two approaches by direct comparison of the modelled concentrations and the estimated fluxes. We further assess the sensitivity of the two approaches to the density of observations and operational parameters such as temporal and spatial correlation lengths. Our results show that both models provide optimized CO2 concentration fields of similar quality. In Antarctica CarbonTracker underestimates the wintertime CO2 concentrations, since its 5-week assimilation window does not allow for adjusting the far-away surface fluxes in response to the detected concentration mismatch. Flux estimates by CarbonTracker and TM5-4DVar are consistent and robust for regions with good observation coverage, regions with low observation coverage reveal significant differences. In South America, the fluxes estimated by TM5-4DVar suffer from limited representativeness of the few observations. For the North American continent, mimicking the historical increase of measurement network density shows improving agreement between CarbonTracker and TM5-4DVar flux estimates for increasing observation density.

  3. Carbon and Nitrogen Chemistry of Lodranites: Relationship to Acapulco?

    NASA Astrophysics Data System (ADS)

    Grady, M. M.; Franchi, I. A.; Pillinger, C. T.

    1993-07-01

    Recent studies on the mineralogy, petrology, and oxygen isotopic composition of lodranites and acapulcoites indicate that these meteorites are probably derived from a common parent body, but experienced different degrees of partial melting [1,2]. Ar-Ar chronometry implies that lodranites were heated ca. 100 degrees C higher than acapulcoites, and cooled more slowly [3], however measurement of nitrogen and xenon in Acapulco [4,5] shows that volatiles are not equilibrated between different phases within the meteorite, hence its thermal history has been complex. The aim of this study is to determine the carbon and nitrogen chemistry of lodranites, for comparison with Acapulco, to indicate the effect that differing thermal histories might have had on the volatile inventories of these meteorites. The carbon chemistry of Acapulco has been described previously [6]. The meteorite contains ca. 400 ppm indigenous carbon, distributed between two major phases: graphite and carbides. Graphite has been identified petrographically in Acapulco [7], where it is intimately associated with metal. In contrast, both Lodran and MAC 88177 contain much lower quantities of indigenous carbon: approximately 100 ppm and 38 ppm respectively, released in decreasing amounts up to 1200 degrees C. In Lodran, delta^13C rises almost monotonically, from -25 per mil at 600 degrees C to -12 per mil at 1200 degrees C; total delta^13C is ca. -23 per mil. Neither meteorite shows evidence for the occurrence of graphite. Nitrogen released by pyrolysis of Acapulco totals ca. 2.8 ppm [4,5], and is resolvable into two components, with delta^15N ca. +10 per mil and -120 per mil [8]. The first component is, as yet, unidentified, but the second is believed to be associated with the metal fraction [8]. The procedure used herein, of several combustion steps below 500 degrees C to remove contaminants, followed by high resolution combustion up to 1200 degrees C, would also resolve discrete nitrogen-bearing components

  4. Controlled release of alendronate from nitrogen-doped mesoporous carbon

    DOE PAGES

    Saha, Dipendu; Spurri, Amanda; Chen, Jihua; ...

    2016-04-13

    With this study, we have synthesized a nitrogen doped mesoporous carbon with the BET surface area of 1066 m2/g, total pore volume 0.6 cm3/g and nitrogen content of 0.5%. Total alendronate adsorption in this carbon was ~5%. The release experiments were designed in four different media with sequential pH values of 1.2, 4.5, 6.8 and 7.4 for 3, 1, 3 and 5 h, respectively and at 37 °C to imitate the physiological conditions of stomach, duodenum, small intestine and colon, respectively. Release of the drug demonstrated a controlled fashion; only 20% of the drug was released in the media withmore » pH = 1.2, whereas 64% of the drug was released in pH = 7.4. This is in contrary to pure alendronate that was completely dissolved within 30 min in the first release media (pH = 1.2) only. The relatively larger uptake of alendronate in this carbon and its sustained fashion of release can be attributed to the hydrogen bonding between the drug and the nitrogen functionalities on carbon surface. Based on this result, it can be inferred that this formulation may lower the side effects of oral delivery of alendronate.« less

  5. Controlled release of alendronate from nitrogen-doped mesoporous carbon

    SciTech Connect

    Saha, Dipendu; Spurri, Amanda; Chen, Jihua; Hensley, Dale K.

    2016-04-13

    With this study, we have synthesized a nitrogen doped mesoporous carbon with the BET surface area of 1066 m2/g, total pore volume 0.6 cm3/g and nitrogen content of 0.5%. Total alendronate adsorption in this carbon was ~5%. The release experiments were designed in four different media with sequential pH values of 1.2, 4.5, 6.8 and 7.4 for 3, 1, 3 and 5 h, respectively and at 37 °C to imitate the physiological conditions of stomach, duodenum, small intestine and colon, respectively. Release of the drug demonstrated a controlled fashion; only 20% of the drug was released in the media with pH = 1.2, whereas 64% of the drug was released in pH = 7.4. This is in contrary to pure alendronate that was completely dissolved within 30 min in the first release media (pH = 1.2) only. The relatively larger uptake of alendronate in this carbon and its sustained fashion of release can be attributed to the hydrogen bonding between the drug and the nitrogen functionalities on carbon surface. Based on this result, it can be inferred that this formulation may lower the side effects of oral delivery of alendronate.

  6. Simultaneous tracing of carbon and nitrogen isotopes in human cells

    PubMed Central

    Nilsson, Roland; Jain, Mohit

    2016-01-01

    Stable isotope tracing is a powerful method for interrogating metabolic enzyme activities across the metabolic network of living cells. However, most studies of mammalian cells have used 13C-labeled tracers only and focused on reactions in central carbon metabolism. Cellular metabolism, however, involves other biologically important elements, including nitrogen, hydrogen, oxygen, phosphate and sulfur. Tracing stable isotopes of such elements may help shed light on poorly understood metabolic pathways. Here, we demonstrate the use of high-resolution mass spectrometry to simultaneously trace carbon and nitrogen metabolism in human cells cultured with 13C- and 15N-labeled glucose and glutamine. To facilitate interpretation of the complex isotopomer data generated, we extend current methods for metabolic flux analysis to handle multivariate mass isotopomer distributions (MMIDs). We find that observed MMIDs are broadly consistent with known biochemical pathways. Whereas measured 13C MIDs were informative for central carbon metabolism, 15N isotopes provided evidence for nitrogen-carrying reactions in amino acid and nucleotide metabolism. This computational and experimental methodology expands the scope of metabolic flux analysis beyond carbon metabolism, and may prove important to understanding metabolic phenotypes in health and disease. PMID:27098229

  7. Simultaneous tracing of carbon and nitrogen isotopes in human cells.

    PubMed

    Nilsson, Roland; Jain, Mohit

    2016-05-24

    Stable isotope tracing is a powerful method for interrogating metabolic enzyme activities across the metabolic network of living cells. However, most studies of mammalian cells have used (13)C-labeled tracers only and focused on reactions in central carbon metabolism. Cellular metabolism, however, involves other biologically important elements, including nitrogen, hydrogen, oxygen, phosphate and sulfur. Tracing stable isotopes of such elements may help shed light on poorly understood metabolic pathways. Here, we demonstrate the use of high-resolution mass spectrometry to simultaneously trace carbon and nitrogen metabolism in human cells cultured with (13)C- and (15)N-labeled glucose and glutamine. To facilitate interpretation of the complex isotopomer data generated, we extend current methods for metabolic flux analysis to handle multivariate mass isotopomer distributions (MMIDs). We find that observed MMIDs are broadly consistent with known biochemical pathways. Whereas measured (13)C MIDs were informative for central carbon metabolism, (15)N isotopes provided evidence for nitrogen-carrying reactions in amino acid and nucleotide metabolism. This computational and experimental methodology expands the scope of metabolic flux analysis beyond carbon metabolism, and may prove important to understanding metabolic phenotypes in health and disease.

  8. Zea3: a pleiotropic mutation affecting cotyledon development, cytokinin resistance and carbon-nitrogen metabolism.

    PubMed

    Faure, J D; Jullien, M; Caboche, M

    1994-04-01

    When photomorphogenesis takes place during early plant development, the cotyledons undergo a metabolic transition from heterotrophic sink metabolism to autotrophic source metabolism. A mutant screen was devised for seedlings affected in the regulation of nitrate assimilation during this early sink-source transition in Nicotiana plumbaginifolia. A mutant (EMS 203.6) was isolated for its inability to grow on low nitrate concentration. In contrast to wild-type (WT) plants, the mutant cotyledons remained tightly attached to each other throughout seedling development. It was found that a low carbon/nitrogen ratio (C/N ratio) in the medium was required for mutant growth. The higher the ratio was, the more the growth was inhibited. Mutant EMS 203.6 accumulated all amino acids in permissive conditions (low C/N ratio), and all amino acids and sugars also in selective (high C/N ratio) conditions. In addition, sucrose in the medium repressed light-regulated genes involved in nitrate assimilation and in photosynthesis in the mutant but not in the WT plants. The mutation was mapped to the Zea3 complementation group which confers resistance to zeatin. This zeatin resistance was associated with a hypertrophy of mutant cotyledons in response to cytokinin. Both cytokinin resistance and sensitivity to a high C/N ratio were not observed in etiolated mutant seedlings and were restricted to the jointed-cotyledon developmental stage. Previous physiological studies showed evidence for a role of cytokinins in the expression of nitrate reductase. Here, the first genetic evidence for a link between carbohydrate/nitrogen metabolism and cytokinin action during early development is provided.

  9. Integrating the nitrogen cycle in carbon and GHG observation systems

    NASA Astrophysics Data System (ADS)

    Kutsch, W. L.; Brummer, C.

    2013-12-01

    Nitrogen is an important factor for the regulation of carbon and GHG fluxes within ecosystems and between ecosystems and the atmosphere. Nitrogen fertilization is important for high agricultural yields but also increases N2O emissions. In Germany, e.g., N2O emissions from agriculture comprise about 6 % of the total GHG inventory. Nitrogen deposition may enhance productivity of ecosystems (e.g. forests, natural grasslands or wetlands) but may also change community structure - in particular in ecosystems that are adapted to low nitrogen availability. It also can lead to increased N2O emissions. Global nitrogen fluxes due to the trade of agricultural products may concentrate nitrogen in specific areas (e.g. in areas with high animal stock). In these areas increased N2O emissions are to be expected. The Thünen Institute of Climate-Smart Agriculture drives parts of the German ICOS consortium with a special focus on agricultural sites or indirect effects of agriculture on GHG emissions. We propose a concept to integrate nitrogen into research infrastructures for GHG monitoring. A conceptual frame will identify the most important parameters of the N cycle. Data from the CarboEurope and NitroEurope core site Gebesee (crop) will be presented to show first integrative results.Finally, first experiences with new technologies will be presented, comprising quantum cascade laser measurements of N2O and ammonia used with eddy covariance (EC) and chambers and EC measurements of total reactive nitrogen with the TRANC methodology (Marx et al. 2012).

  10. The link between assimilation and below-ground processes - stable isotopes as tools to assess carbon transfer

    NASA Astrophysics Data System (ADS)

    Gessler, A.; Wingate, L.; Ogeé, J.; Offermann, C.; Kodama, N.

    2011-12-01

    At present, there is lack of knowledge on how plant physiological processes, the transfer of carbon within the plant, carbon storage and remobilization in the plant tissues as well as the release of carbon from the roots to the soil interact with ecosystem-scale processes. On the background of global climate change, we need to mechanistically link plant physiology, CO2 net exchange between ecosystems and the atmosphere and plant biomass accumulation. This is the basis for predicting productivity of forests as well as their carbon sequestration potential in future. This paper will give an overview on how stable isotope studies can give insights into the fate of newly assimilated carbon transported within trees and transferred to the soil and atmosphere. The paper includes assessments characterizing temporal and spatial variation in the natural abundance of carbon and oxygen isotopes or applying isotopically enriched tracers. In addition, it highlights the fact that the stable isotope composition of assimilates transported within the plant contains important time integrated information on environmental conditions, leaf physiology, and post-photosynthetic metabolism. The paper on the one hand focuses on the fast turn over carbon pools, which fuel plant respiration and soil microbial activity and on the other hand explores the transfer of the isotope information to long-lived compounds in plant archives such as tree rings.

  11. Cadmium in white lupin nodules: impact on nitrogen and carbon metabolism.

    PubMed

    Sánchez-Pardo, Beatriz; Carpena, Ramón O; Zornoza, Pilar

    2013-02-15

    The aims of this work were to investigate the microlocalisation of cadmium (Cd) in Lupinus albus L. cv. Multolupa nodules, and to determine its effects on carbon and nitrogen metabolism. Nodulated white lupin plants were grown in a growth chamber with or without Cd (150 μM). Energy-dispersive X-ray microanalysis showed the walls of the outer nodule cortex cells to be the main area of Cd retention, helping to reduce the harmful effect Cd might have on the amount of N(2) fixed by the bacteroids. Sucrose synthase activity declined by 33% in the nodules of the Cd-treated plants, and smaller reductions were recorded in glutamine synthetase, aspartate aminotransferase, alkaline invertase and NADP-dependent isocitrate dehydrogenase activities. The Cd treatment also sharply reduced nodule concentrations of malate, succinate and citrate, while that of starch doubled, but that of sucrose experienced no significant change. In summary, the present results show that white lupins accumulate significant amounts of Cd in their root nodules. However, the activity of some enzymes involved in ammonium assimilation did decline, promoting a reduction in the plant N content. The downregulation of sucrose synthase limits the availability of carbon to the bacteroids, which might interfere with their respiration. Carbon metabolism therefore plays a primary role in the impaired function of the white lupin root nodule caused by Cd, while N metabolism appears to have a more secondary involvement. Copyright © 2012 Elsevier GmbH. All rights reserved.

  12. Integration of carbon and nitrogen metabolism with energy production is crucial to light acclimation in the cyanobacterium Synechocystis.

    PubMed

    Singh, Abhay K; Elvitigala, Thanura; Bhattacharyya-Pakrasi, Maitrayee; Aurora, Rajeev; Ghosh, Bijoy; Pakrasi, Himadri B

    2008-09-01

    Light drives the production of chemical energy and reducing equivalents in photosynthetic organisms required for the assimilation of essential nutrients. This process also generates strong oxidants and reductants that can be damaging to the cellular processes, especially during absorption of excess excitation energy. Cyanobacteria, like other oxygenic photosynthetic organisms, respond to increases in the excitation energy, such as during exposure of cells to high light (HL) by the reduction of antenna size and photosystem content. However, the mechanism of how Synechocystis sp. PCC 6803, a cyanobacterium, maintains redox homeostasis and coordinates various metabolic processes under HL stress remains poorly understood. In this study, we have utilized time series transcriptome data to elucidate the global responses of Synechocystis to HL. Identification of differentially regulated genes involved in the regulation, protection, and maintenance of redox homeostasis has offered important insights into the optimized response of Synechocystis to HL. Our results indicate a comprehensive integrated homeostatic interaction between energy production (photosynthesis) and energy consumption (assimilation of carbon and nitrogen). In addition, measurements of physiological parameters under different growth conditions showed that integration between the two processes is not a consequence of limitations in the external carbon and nitrogen levels available to the cells. We have also discovered the existence of a novel glycosylation pathway, to date known as an important nutrient sensor only in eukaryotes. Up-regulation of a gene encoding the rate-limiting enzyme in the hexosamine pathway suggests a regulatory role for protein glycosylation in Synechocystis under HL.

  13. Responses of Tree Seedlings to a Changing Atmosphere: Effects of Carbon Dioxide, Nitrogen Dioxide, and Ozone

    NASA Astrophysics Data System (ADS)

    Eller, A. S.; Sparks, J. P.

    2008-12-01

    Human activities have caused changes in the chemical composition of the atmosphere: the concentrations of carbon dioxide (CO2), nitrogen dioxide (NO2), and ozone (O3) have increased and are expected to continue increasing in the future. These gases have the potential to alter plant physiological processes, change growth rates, C:N, and carbon storage potential. The responses of tree seedlings to these changes will have a profound impact on the species composition and carbon storage potential of forests in the future. Others have found CO2 tends to increase plant growth and O3 to decrease it. NO2, if assimilated by plants, can be a source of nutrient nitrogen, but is also an oxidant with the potential to damage cell membranes and decrease growth. The objectives of this study were to determine the single and combined effects of CO2, NO2, and O3 on sugar maple, eastern hemlock, and two clones of trembling aspen. The trees were fumigated for two growing seasons with elevated (40ppb) or ambient NO2, elevated (560ppm) or ambient CO2, elevated (100 ppb 5 days/week) or ambient O3, and with or without additional soil nitrate (30 kg ha-1 yr-1) to simulate ecosystems with and without nitrogen limitation. We found that elevated CO2 increased total biomass of both maples and hemlocks. Further, the CO2 growth effect was most striking when combined with elevated O2; elevated CO2 eliminated the growth decrease induced by O3 especially when nitrogen was limited. Elevated NO2 had no effect on maple seedlings, but, similar to CO2, eliminated the decrease in growth under O3 on hemlock seedlings. The two aspen clones differed in their resistance to ozone. The non-resistant clone exhibited growth responses similar to maple. However, the resistant clone did not exhibit a growth response under any gas treatment regardless of soil nitrogen status. The variation in responses among species, within clones of the same species, and between fumigations was large in this study and suggests

  14. [Interactions of straw, nitrogen fertilizer and bacterivorous nematodes on soil labile carbon and nitrogen and greenhouse gas emissions].

    PubMed

    Zhang, Teng-Hao; Wang, Nan; Liu, Man-Qiang; Li, Fang-Hui; Zhu, Kang-Li; Li, Hui-Xin; Hu, Feng

    2014-11-01

    A 3 x 2 factorial design of microcosm experiment was conducted to investigate the interactive effects of straw, nitrogen fertilizer and bacterivorous nematodes on soil microbial biomass carbon (C(mic)) and nitrogen (N(mic)), dissolved organic carbon (DOC) and nitrogen (DON), mineral nitrogen (NH(4+)-N and NO(3-)-N), and greenhouse gas (CO2, N2O and CH4) emissions. Results showed that straw amendment remarkably increased the numbers of bacterivorous nematodes and the contents of Cmic and Nmic, but Cmic and Nmic decreased with the increasing dose of nitrogen fertilization. The effects of bacterivorous nematodes strongly depended on either straw or nitrogen fertilization. The interactions of straw, nitrogen fertilization and bacterivorous nematodes on soil DOC, DON and mineral nitrogen were strong. Straw and nitrogen fertilization increased DOC and mineral nitrogen contents, but their influences on DON depended on the bacterivorous nematodes. The DOC and mineral nitrogen were negatively and positively influenced by the bacterivorous nematodes, re- spectively. Straw significantly promoted CO2 and N2O emissions but inhibited CH4 emission, while interactions between nematodes and nitrogen fertilization on emissions of greenhouse gases were obvious. In the presence of straw, nematodes increased cumulative CO2 emissions with low nitrogen fertilization, but decreased CO2 and N2O emissions with high nitrogen fertilization on the 56th day after incubation. In summary, mechanical understanding the soil ecological process would inevitably needs to consider the roles of soil microfauna.

  15. Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs.

    PubMed

    Liseron-Monfils, Christophe; Bi, Yong-Mei; Downs, Gregory S; Wu, Wenqing; Signorelli, Tara; Lu, Guangwen; Chen, Xi; Bondo, Eddie; Zhu, Tong; Lukens, Lewis N; Colasanti, Joseph; Rothstein, Steven J; Raizada, Manish N

    2013-10-01

    Nitrogen is considered the most limiting nutrient for maize (Zea mays L.), but there is limited understanding of the regulation of nitrogen-related genes during maize development. An Affymetrix 82K maize array was used to analyze the expression of ≤ 46 unique nitrogen uptake and assimilation probes in 50 maize tissues from seedling emergence to 31 d after pollination. Four nitrogen-related expression clusters were identified in roots and shoots corresponding to, or overlapping, juvenile, adult, and reproductive phases of development. Quantitative real time PCR data was consistent with the existence of these distinct expression clusters. Promoters corresponding to each cluster were screened for over-represented cis-acting elements. The 8-bp distal motif of the Arabidopsis 43-bp nitrogen response element (NRE) was over-represented in nitrogen-related maize gene promoters. This conserved motif, referred to here as NRE43-d8, was previously shown to be critical for nitrate-activated transcription of nitrate reductase (NIA1) and nitrite reductase (NIR1) by the NIN-LIKE PROTEIN 6 (NLP6) in Arabidopsis. Here, NRE43-d8 was over-represented in the promoters of maize nitrate and ammonium transporter genes, specifically those that showed peak expression during early-stage vegetative development. This result predicts an expansion of the NRE-NLP6 regulon and suggests that it may have a developmental component in maize. We also report leaf expression of putative orthologs of nitrite transporters (NiTR1), a transporter not previously reported in maize. We conclude by discussing how each of the four transcriptional modules may be responsible for the different nitrogen uptake and assimilation requirements of leaves and roots at different stages of maize development.

  16. Carbon dioxide assimilation in cyanobacteria: regulation of ribulose, 1,5-bisphosphate carboxylase.

    PubMed Central

    Tabita, F R; Colletti, C

    1979-01-01

    Cyanobacteria assimilate carbon dioxide through the Calvin cycle and therefore must regulate the activity of ribulose 1,5-bisophosphate carboxylase. Using an in situ assay, as well as measuring the activity in crude, partially purified, and homogeneous preparations, we can show that a number of phosphorylated intermediates exert a regulatory role. Three diverse organisms, Agmenellum quadruplicatum, Aphanocapsa 6714, and Anabaena sp. CA, were studied, and it was found that the in situ and cell-free carboxylase activities were particularly affected by low levels of phosphogluconate and reduced nicotinamide adenine dinucleotide phosphate. There was a marked activation by these ligands when the inactive enzyme was assayed in the presence of low levels of bicarbonate, a result significantly different from a previous report. Moreover, the fully activated enzyme was inhibited by phosphogluconate. In situ Anabaena CA carboxylase activity exhibited a particular capacity for activation by phosphogluconate and reduced nicotinamide adenine dinucleotide phosphate. However, activation of the crude, partially purified, or homogeneous Anabaena CA carboxylase by phosphogluconate and reduced nicotinamide adenine dinucleotide phosphate was significantly decreased when compared with enzyme activity in permeabilized cells. It appears that the microenvironment or the conformation of the enzyme within the cell may be significantly different from that of the isolated enzyme. PMID:40958

  17. Carbon Assimilation and Leaf Water Status in Sugar Beet Leaves during a Simulated Natural Light Regimen.

    PubMed

    Geiger, D R; Shieh, W J; Lu, L S; Servaites, J C

    1991-11-01

    Carbon assimilation and leaf water status were studied in sugar beet (Beta vulgaris L., Klein E-type multigerm) leaves during a light period in which illumination either increased rapidly to full irradiance or changed gradually in a sinusoidal manner as generally occurs during a natural day. A light regimen that simulated the light of a natural day was produced by adjusting irradiance with a neutral-density filter under the control of a computer. Under this light regimen, photosynthesis, transpiration, and stomatal conductance followed the irradiance pattern very closely and ribulose bisphosphate carboxylase was nearly fully activated. When illumination was increased rapidly at the beginning of a light period, transpiration also increased quickly, causing leaves to wilt to some extent. The activation state of ribulose bisphosphate carboxylase increased to only 52%, but ribulose bisphosphate level was nearly twice as high as during the simulated natural day. In spite of the differences in activation state and ribulose bisphosphate levels, photosynthesis rates were very similar under both regimens. Nevertheless, differences in parameters between leaves under the two irradiance regimens can affect how a plant responds to internal or external factors, and therefore, the rate at which irradiance increases at the beginning of a light period is an important consideration when interpreting data.

  18. Microbial fuel cell biosensor for rapid assessment of assimilable organic carbon under marine conditions.

    PubMed

    Quek, Soon Bee; Cheng, Liang; Cord-Ruwisch, Ralf

    2015-06-15

    The development of an assimilable organic carbon (AOC) detecting marine microbial fuel cell (MFC) biosensor inoculated with microorganisms from marine sediment was successful within 36 days. This established marine MFC was tested as an AOC biosensor and reproducible microbiologically produced electrical signals in response to defined acetate concentration were achieved. The dependency of the biosensor sensitivity on the potential of the electron-accepting electrode (anode) was investigated. A linear correlation (R(2) > 0.98) between electrochemical signals (change in anodic potential and peak current) and acetate concentration ranging from 0 to 150 μM (0-3600 μg/L of AOC) was achieved. However, the present biosensor indicated a different-linear relation at somewhat elevated acetate concentration ranging from 150 to 450 μM (3600-10,800 μg/L of AOC). This high concentration of acetate addition could be measured by coulombic measurement (cumulative charges) with a linear correlation. For the acetate concentration detected in this study, the sensor recovery time could be controlled within 100 min. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Effect of carbon monoxide and nitrogen dioxide on ICR mice

    NASA Technical Reports Server (NTRS)

    Hilado, C. J.; Cumming, H. J.

    1977-01-01

    Times to incapacitation and death and LC(50) values were determined for male ICR mice exposed to different concentration of carbon monoxide for 30 min and of nitrogen dioxide for 10 min in a 4.2 liter hemispherical chamber. The data indicate that ICR mice are more resistant to these two toxicants than Swiss albino mice. The carbon monoxide LC(50) for a 30-min exposure was about 8,000 ppm for ICR mice compared to 3,570 ppm for Swiss albino mice. The nitrogen dioxide LC(50) for a 10-min exposure was above 2,000 ppm for ICR mice compared to about 1,000 ppm for Swiss albino mice.

  20. Transesterification of triglycerides using nitrogen-functionalized carbon nanotubes.

    PubMed

    Villa, Alberto; Tessonnier, Jean-Philippe; Majoulet, Olivier; Su, Dang Sheng; Schlögl, Robert

    2010-02-22

    Nitrogen-functionalized carbon nanotubes were synthesized by grafting amino groups to the surface of the nanotubes. The nanotubes exhibited promising results in the base-catalyzed liquid phase transesterification of glyceryl tributyrate with methanol, which is a model reaction for the production of biodiesel. The concentration of the active sites and the reaction parameters, such as temperature and glyceryl tributyrate to methanol ratio, were shown to significantly affect catalytic performance. The grafting technique employed allowed for design and control of the active sites. As a consequence, it was possible to design a nitrogen-functionalized carbon nanotube catalyst with a few strong, basic groups. This might be of interest for carbohydrate conversion reactions where strong basic sites are required but the pH of the solution should remain mild to avoid the degradation of the reactants and/or products.

  1. Effect of carbon monoxide and nitrogen dioxide on ICR mice

    NASA Technical Reports Server (NTRS)

    Hilado, C. J.; Cumming, H. J.

    1977-01-01

    Times to incapacitation and death and LC(50) values were determined for male ICR mice exposed to different concentration of carbon monoxide for 30 min and of nitrogen dioxide for 10 min in a 4.2 liter hemispherical chamber. The data indicate that ICR mice are more resistant to these two toxicants than Swiss albino mice. The carbon monoxide LC(50) for a 30-min exposure was about 8,000 ppm for ICR mice compared to 3,570 ppm for Swiss albino mice. The nitrogen dioxide LC(50) for a 10-min exposure was above 2,000 ppm for ICR mice compared to about 1,000 ppm for Swiss albino mice.

  2. Carbon and Nitrogen Content of Natural Planktonic Bacteria †

    PubMed Central

    Nagata, Toshi

    1986-01-01

    A method of estimating carbon and nitrogen content per unit of natural bacterial cell volume was developed. This method is based on the difference in the retentiveness of bacteria between two kinds of glass fiber filter, GF/C and GF/F (Whatman, Inc., Clifton, N.J.). Biovolume and biomass (carbon and nitrogen content) of bacteria which passed through the GF/C but not the GF/F filter were estimated with an epifluorescence microscopy and a CHN analyzer, respectively. From seasonal determinations of natural planktonic bacteria in epilimnetic waters of a mesotrophic lake, the conversion factors of 106 fg of C/μm3 and 25 fg of N/μm3 were derived as average values. By using these values, the contribution of bacteria to the biomass of lake plankton is discussed. PMID:16347114

  3. Worldwide Organic Soil Carbon and Nitrogen Data (1986) (NDP-018)

    DOE Data Explorer

    Zinke, P. J. [Univ. of California, Berkeley, CA (United States); Stangenberger, A. G. [Univ. of California, Berkeley, CA (United States); Post, W. M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Emanuel, W. R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Olson, J. S. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Millemann, R. E. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Boden, T. A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    1986-01-01

    This data base was begun with the collection and analysis of soil samples from California. Additional data came from soil surveys of Italy, Greece, Iran, Thailand, Vietnam, various tropical Amazonian areas, and U.S. forests and from the soil-survey literature. The analyzed samples were collected at uniform soil-depth increments and included bulk-density determinations. The data on each sample are soil profile number; soil profile carbon content; soil profile nitrogen content; sampling site latitude and longitude; site elevation; profile literature reference source; and soil profile codes for Holdridge life zone, Olson ecosystem type, and parent material. These data may be used to estimate the size of the soil organic carbon and nitrogen pools at equilibrium with natural soil-forming factors.

  4. The Evolutionary Rewiring of Ubiquitination Targets Has Reprogrammed the Regulation of Carbon Assimilation in the Pathogenic Yeast Candida albicans

    PubMed Central

    Sandai, Doblin; Yin, Zhikang; Selway, Laura; Stead, David; Walker, Janet; Leach, Michelle D.; Bohovych, Iryna; Ene, Iuliana V.; Kastora, Stavroula; Budge, Susan; Munro, Carol A.; Odds, Frank C.; Gow, Neil A. R.; Brown, Alistair J. P.

    2012-01-01

    ABSTRACT Microbes must assimilate carbon to grow and colonize their niches. Transcript profiling has suggested that Candida albicans, a major pathogen of humans, regulates its carbon assimilation in an analogous fashion to the model yeast Saccharomyces cerevisiae, repressing metabolic pathways required for the use of alterative nonpreferred carbon sources when sugars are available. However, we show that there is significant dislocation between the proteome and transcriptome in C. albicans. Glucose triggers the degradation of the ICL1 and PCK1 transcripts in C. albicans, yet isocitrate lyase (Icl1) and phosphoenolpyruvate carboxykinase (Pck1) are stable and are retained. Indeed, numerous enzymes required for the assimilation of carboxylic and fatty acids are not degraded in response to glucose. However, when expressed in C. albicans, S. cerevisiae Icl1 (ScIcl1) is subjected to glucose-accelerated degradation, indicating that like S. cerevisiae, this pathogen has the molecular apparatus required to execute ubiquitin-dependent catabolite inactivation. C. albicans Icl1 (CaIcl1) lacks analogous ubiquitination sites and is stable under these conditions, but the addition of a ubiquitination site programs glucose-accelerated degradation of CaIcl1. Also, catabolite inactivation is slowed in C. albicans ubi4 cells. Ubiquitination sites are present in gluconeogenic and glyoxylate cycle enzymes from S. cerevisiae but absent from their C. albicans homologues. We conclude that evolutionary rewiring of ubiquitination targets has meant that following glucose exposure, C. albicans retains key metabolic functions, allowing it to continue to assimilate alternative carbon sources. This metabolic flexibility may be critical during infection, facilitating the rapid colonization of dynamic host niches containing complex arrays of nutrients. PMID:23232717

  5. Vacancy Mediated Mechanism of Nitrogen Substitution in Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Menon, Madhu; Sadanadan, Bindu; Rao, Apparao M.

    2003-01-01

    Nitrogen substitution reaction in a graphene sheet and carbon nanotubes of different diameter are investigated using the generalized tight-binding molecular dynamics method. The formation of a vacancy in curved graphene sheet or a carbon nanotube is found to cause a curvature dependent local reconstruction of the surface. Our simulations and analysis show that vacancy mediated N substitution (rather than N chemisorption) is favored on the surface of nanotubes with diameter larger than 8 nm. This predicted value of the critical minimum diameter for N incorporation is confirmed by experimental results presented.

  6. Nitrogen-doped carbon dots as multifunctional fluorescent probes

    NASA Astrophysics Data System (ADS)

    Du, Fengyi; Jin, Xin; Chen, Junhui; Hua, Ye; Cao, Mulan; Zhang, Lirong; Li, Jianan; Zhang, Li; Jin, Jie; Wu, Chaoyang; Gong, Aihua; Xu, Wenrong; Shao, Qixiang; Zhang, Miaomiao

    2014-11-01

    Highly fluorescent nitrogen-doped carbon dots (NCDs) were prepared through the hydrothermal carbonization of citric acid and ammonium acetate. The resulting NCDs were quasi-spherical particles with an average diameter of approximately 2.1 nm. They exhibited excellent photoluminescent properties and had favorable solubility in water. Furthermore, the NCDs had low cytotoxicity and were readily integrated with cytoplasm. This makes them particularly suitable for multicolor bioimaging. Most importantly, NCDs internalized by cancer cells can be detected at four channels simultaneously with flow cytometry, which further demonstrates that the NCDs can be used as multifunctional fluorescent probes for biomedical applications.

  7. Effects of assimilable organic carbon and free chlorine on bacterial growth in drinking water.

    PubMed

    Liu, Xiaolu; Wang, Jingqi; Liu, Tingting; Kong, Weiwen; He, Xiaoqing; Jin, Yi; Zhang, Bolin

    2015-01-01

    Assimilable organic carbon (AOC) is one of the most important factors affecting the re-growth of microorganisms in drinking water. High AOC concentrations result in biological instability, but disinfection kills microbes to ensure the safety of drinking water. Free chlorine is an important oxidizing agent used during the disinfection process. Therefore, we explored the combined effects of AOC and free chlorine on bacterial growth in drinking water using flow cytometry (FCM). The initial AOC concentration was 168 μg.L(-1) in all water samples. Without free chlorine, the concentrations of intact bacteria increased but the level of AOC decreased. The addition of sodium hypochlorite caused an increase and fluctuation in AOC due to the oxidation of organic carbon. The concentrations of intact bacteria decreased from 1.1 × 10(5) cells.mL(-1) to 2.6 × 10(4) cells.mL(-1) at an initial free chlorine dose of 0.6 mg.L(-1) to 4.8 × 10(4) cells.mL(-1) at an initial free chlorine dose of 0.3 mg.L(-1) due to free chlorine originating from sodium hypochlorite. Additionally, free chlorine might be more obviously affected AOC concentrations than microbial growth did. These results suggested that AOC and free chlorine might have combined effects on microbial growth. In this study, our results showed concentrations determined by FCM were higher than those by HPC, which indicated that some E. coli detected by FCM might not be detected using HPC in drinking water. The level of free chlorine might restrain the consumption of AOC by inhibiting the growth of E. coli; on the other hand, chlorination might increase the level of AOC, thereby increase the potential for microbial growth in the drinking water network.

  8. Actual and potential transpiration and carbon assimilation in an irrigated poplar plantation.

    PubMed

    Kim, Hyun-Seok; Oren, Ram; Hinckley, Thomas M

    2008-04-01

    We examined the tradeoffs between stand-level water use and carbon uptake that result when biomass production of trees in plantations is maximized by removing nutrient and water limitations. A Populus trichocarpa Torr. x P. deltoides Bartr. & Marsh. plantation was irrigated and received frequent additions of nutrients to optimize biomass production. Sap flux density was measured continuously over four of the six growing-season months, supplemented with periodic measurements of leaf gas exchange and water potential. Measurements of tree diameter and height were used to estimate leaf area and biomass production based on allometric relationships. Sap flux was converted to canopy conductance and analyzed with an empirical model to isolate the effects of water limitation. Actual and soil-water-unlimited potential CO(2) uptakes were estimated with a canopy conductance constrained carbon assimilation (4C-A) scheme, which couples actual or potential canopy conductance with vertical gradients of light distribution, leaf-level conductance, maximum Rubisco capacity and maximum electron transport. Net primary production (NPP) was about 43% of gross primary production (GPP); when estimated for individual trees, this ratio was independent of tree size. Based on the NPP/GPP ratio, we found that current irrigation reduced growth by about 18% compared with growth with no water limitation. To achieve maximum growth, however, would require 70% more water for transpiration, and would reduce water-use efficiency by 27%, from 1.57 to 1.15 g stem wood C kg(-1) water. Given the economic and social values of water, plantation managers appear to have optimized water use.

  9. Effects of Assimilable Organic Carbon and Free Chlorine on Bacterial Growth in Drinking Water

    PubMed Central

    Liu, Tingting; Kong, Weiwen; He, Xiaoqing; Jin, Yi; Zhang, Bolin

    2015-01-01

    Assimilable organic carbon (AOC) is one of the most important factors affecting the re-growth of microorganisms in drinking water. High AOC concentrations result in biological instability, but disinfection kills microbes to ensure the safety of drinking water. Free chlorine is an important oxidizing agent used during the disinfection process. Therefore, we explored the combined effects of AOC and free chlorine on bacterial growth in drinking water using flow cytometry (FCM). The initial AOC concentration was 168 μg.L-1 in all water samples. Without free chlorine, the concentrations of intact bacteria increased but the level of AOC decreased. The addition of sodium hypochlorite caused an increase and fluctuation in AOC due to the oxidation of organic carbon. The concentrations of intact bacteria decreased from 1.1×105 cells.mL-1 to 2.6×104 cells.mL-1 at an initial free chlorine dose of 0.6 mg.L-1 to 4.8×104 cells.mL-1 at an initial free chlorine dose of 0.3 mg.L-1 due to free chlorine originating from sodium hypochlorite. Additionally, free chlorine might be more obviously affected AOC concentrations than microbial growth did. These results suggested that AOC and free chlorine might have combined effects on microbial growth. In this study, our results showed concentrations determined by FCM were higher than those by HPC, which indicated that some E. coli detected by FCM might not be detected using HPC in drinking water. The level of free chlorine might restrain the consumption of AOC by inhibiting the growth of E. coli; on the other hand, chlorination might increase the level of AOC, thereby increase the potential for microbial growth in the drinking water network. PMID:26034988

  10. Forest defoliator pests alter carbon and nitrogen cycles

    PubMed Central

    Grüning, Maren; Simon, Judy; Reinhardt, Annett-Barbara; Lamersdorf, Norbert; Thies, Carsten

    2016-01-01

    Climate change may foster pest epidemics in forests, and thereby the fluxes of elements that are indicators of ecosystem functioning. We examined compounds of carbon (C) and nitrogen (N) in insect faeces, leaf litter, throughfall and analysed the soils of deciduous oak forests (Quercus petraea L.) that were heavily infested by the leaf herbivores winter moth (Operophtera brumata L.) and mottled umber (Erannis defoliaria L.). In infested forests, total net canopy-to-soil fluxes of C and N deriving from insect faeces, leaf litter and throughfall were 30- and 18-fold higher compared with uninfested oak forests, with 4333 kg C ha−1 and 319 kg N ha−1, respectively, during a pest outbreak over 3 years. In infested forests, C and N levels in soil solutions were enhanced and C/N ratios in humus layers were reduced indicating an extended canopy-to-soil element pathway compared with the non-infested forests. In a microcosm incubation experiment, soil treatments with insect faeces showed 16-fold higher fluxes of carbon dioxide and 10-fold higher fluxes of dissolved organic carbon compared with soil treatments without added insect faeces (control). Thus, the deposition of high rates of nitrogen and rapidly decomposable carbon compounds in the course of forest pest epidemics appears to stimulate soil microbial activity (i.e. heterotrophic respiration), and therefore, may represent an important mechanism by which climate change can initiate a carbon cycle feedback. PMID:27853551

  11. Forest defoliator pests alter carbon and nitrogen cycles.

    PubMed

    L-M-Arnold, Anne; Grüning, Maren; Simon, Judy; Reinhardt, Annett-Barbara; Lamersdorf, Norbert; Thies, Carsten

    2016-10-01

    Climate change may foster pest epidemics in forests, and thereby the fluxes of elements that are indicators of ecosystem functioning. We examined compounds of carbon (C) and nitrogen (N) in insect faeces, leaf litter, throughfall and analysed the soils of deciduous oak forests (Quercus petraea L.) that were heavily infested by the leaf herbivores winter moth (Operophtera brumata L.) and mottled umber (Erannis defoliaria L.). In infested forests, total net canopy-to-soil fluxes of C and N deriving from insect faeces, leaf litter and throughfall were 30- and 18-fold higher compared with uninfested oak forests, with 4333 kg C ha(-1) and 319 kg N ha(-1), respectively, during a pest outbreak over 3 years. In infested forests, C and N levels in soil solutions were enhanced and C/N ratios in humus layers were reduced indicating an extended canopy-to-soil element pathway compared with the non-infested forests. In a microcosm incubation experiment, soil treatments with insect faeces showed 16-fold higher fluxes of carbon dioxide and 10-fold higher fluxes of dissolved organic carbon compared with soil treatments without added insect faeces (control). Thus, the deposition of high rates of nitrogen and rapidly decomposable carbon compounds in the course of forest pest epidemics appears to stimulate soil microbial activity (i.e. heterotrophic respiration), and therefore, may represent an important mechanism by which climate change can initiate a carbon cycle feedback.

  12. Boron/Carbon/Silicon/Nitrogen Ceramics And Precursors

    NASA Technical Reports Server (NTRS)

    Riccitiello, Salvatore; Hsu, Ming TA; Chen, Timothy S.

    1996-01-01

    Ceramics containing various amounts of boron, carbon, silicon, and nitrogen made from variety of polymeric precursors. Synthesized in high yield from readily available and relatively inexpensive starting materials. Stable at room temperature; when polymerized, converted to ceramics in high yield. Ceramics resist oxidation and other forms of degradation at high temperatures; used in bulk to form objects or to infiltrate other ceramics to obtain composites having greater resistance to oxidation and high temperatures.

  13. Boron/Carbon/Silicon/Nitrogen Ceramics And Precursors

    NASA Technical Reports Server (NTRS)

    Riccitiello, Salvatore; Hsu, Ming TA; Chen, Timothy S.

    1996-01-01

    Ceramics containing various amounts of boron, carbon, silicon, and nitrogen made from variety of polymeric precursors. Synthesized in high yield from readily available and relatively inexpensive starting materials. Stable at room temperature; when polymerized, converted to ceramics in high yield. Ceramics resist oxidation and other forms of degradation at high temperatures; used in bulk to form objects or to infiltrate other ceramics to obtain composites having greater resistance to oxidation and high temperatures.

  14. Nitrogen uptake and utilization by intact plants

    NASA Technical Reports Server (NTRS)

    Raper, C. D., Jr.; Tolley-Henry, L. C.

    1986-01-01

    The results of experiments support the proposed conceptual model that relates nitrogen uptake activity by plants as a balanced interdependence between the carbon-supplying function of the shoot and the nitrogen-supplying function of the roots. The data are being used to modify a dynamic simulation of plant growth, which presently describes carbon flows through the plant, to describe nitrogen uptake and assimilation within the plant system. Although several models have been proposed to predict nitrogen uptake and partitioning, they emphasize root characteristics affecting nutrient uptake and relay on empirical methods to describe the relationship between nitrogen and carbon flows within the plant. Researchers, on the other hand, propose to continue to attempt a mechanistic solution in which the effects of environment on nitrogen (as well as carbon) assimilation are incorporated through their direct effects on photosynthesis, respiration, and aging processes.

  15. Water deficit stress-induced changes in carbon and nitrogen partitioning in Chenopodium quinoa Willd.

    PubMed

    Bascuñán-Godoy, Luisa; Reguera, Maria; Abdel-Tawab, Yasser M; Blumwald, Eduardo

    2016-03-01

    Water deficit stress followed by re-watering during grain filling resulted in the induction of the ornithine pathway and in changes in Quinoa grain quality. The genetic diversity of Chenopodium quinoa Willd. (Quinoa) is accompanied by an outstanding environmental adaptability and high nutritional properties of the grains. However, little is known about the biochemical and physiological mechanisms associated with the abiotic stress tolerance of Quinoa. Here, we characterized carbon and nitrogen metabolic changes in Quinoa leaves and grains in response to water deficit stress analyzing their impact on the grain quality of two lowland ecotypes (Faro and BO78). Differences in the stress recovery response were found between genotypes including changes in the activity of nitrogen assimilation-associated enzymes that resulted in differences in grain quality. Both genotypes showed a common strategy to overcome water stress including the stress-induced synthesis of reactive oxygen species scavengers and osmolytes. Particularly, water deficit stress induced the stimulation of the ornithine and raffinose pathways. Our results would suggest that the regulation of C- and N partitioning in Quinoa during grain filling could be used for the improvement of the grain quality without altering grain yields.

  16. A data assimilation framework for constraining upscaled cropland carbon flux seasonality with MODIS

    NASA Astrophysics Data System (ADS)

    Sus, O.; Williams, M.

    2012-04-01

    Agroecosystem models are strongly dependent on information on land management patterns for regional applications. Land management practices play a major role in determining global yield variability, and add an anthropogenic signal to the observed seasonality of atmospheric CO2 concentrations. However, there is still little knowledge on spatial and temporal variability of important farmland activities such as crop sowing dates, cultivar selection, and fertilisation application, and thus these remain rather crudely approximated within carbon (C) cycle studies. In this study, we present a data assimilation framework allowing for spatiotemporally resolved simulation of cropland C fluxes under observational constraints on sowing dates and canopy greenness. MODIS 250 m vegetation index data were assimilated both variationally (for sowing date estimation) and sequentially (for improved model state estimation, using the EnKF) into a crop C mass balance model (SPAc). In doing so, we are able to accurately quantify the multiannual (2000-2006) regional C flux seasonality of maize-soybean crop rotations surrounding the Bondville (IL, US) Ameriflux EC site, averaged over 104 pixel locations within the wider area (32 km - 25 km). We find that MODIS-derived sowing dates allow for highly accurate simulations of growing season C cycling at locations for which ground-truth sowing dates are not available. Resulting simulations provide an envelope on upscaled cropland phenology, with significant deviations from plot-scale observations at Bondville: study area average growing season length is ~20 days longer than observed, primarily because of an earlier estimated start of season. Relative spatial variability of net ecosystem exchange (NEE) of C ranges from ~7% to ~10%, but variability in net biome productivity is considerably larger (~24% to ~32%). Differences between Bondville and upscaled NEE are especially large in years with non-optimal weather conditions for sowing. This shows

  17. Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants

    PubMed Central

    Palenchar, Peter M; Kouranov, Andrei; Lejay, Laurence V; Coruzzi, Gloria M

    2004-01-01

    Background Carbon and nitrogen are two signals that influence plant growth and development. It is known that carbon- and nitrogen-signaling pathways influence one another to affect gene expression, but little is known about which genes are regulated by interactions between carbon and nitrogen signaling or the mechanisms by which the different pathways interact. Results Microarray analysis was used to study global changes in mRNA levels due to carbon and nitrogen in Arabidopsis thaliana. An informatic analysis using InterAct Class enabled us to classify genes on the basis of their responses to carbon or nitrogen treatments. This analysis provides in vivo evidence supporting the hypothesis that plants have a carbon/nitrogen (CN)-sensing/regulatory mechanism, as we have identified over 300 genes whose response to combined CN treatment is different from that expected from expression values due to carbon and nitrogen treatments separately. Metabolism, energy and protein synthesis were found to be significantly affected by interactions between carbon and nitrogen signaling. Identified putative cis-acting regulatory elements involved in mediating CN-responsive gene expression suggest multiple mechanisms for CN responsiveness. One mechanism invokes the existence of a single CN-responsive cis element, while another invokes the existence of cis elements that promote nitrogen-responsive gene expression only when present in combination with a carbon-responsive cis element. Conclusion This study has allowed us to identify genes and processes regulated by interactions between carbon and nitrogen signaling and take a first step in uncovering how carbon- and nitrogen-signaling pathways interact to regulate transcription. PMID:15535867

  18. Effects of reduced carbonic anhydrase activity on CO2 assimilation rates in Setaria viridis: a transgenic analysis.

    PubMed

    Osborn, Hannah L; Alonso-Cantabrana, Hugo; Sharwood, Robert E; Covshoff, Sarah; Evans, John R; Furbank, Robert T; von Caemmerer, Susanne

    2017-01-01

    In C4 species, the major β-carbonic anhydrase (β-CA) localized in the mesophyll cytosol catalyses the hydration of CO2 to HCO3(-), which phosphoenolpyruvate carboxylase uses in the first step of C4 photosynthesis. To address the role of CA in C4 photosynthesis, we generated transgenic Setaria viridis depleted in β-CA. Independent lines were identified with as little as 13% of wild-type CA. No photosynthetic defect was observed in the transformed lines at ambient CO2 partial pressure (pCO2). At low pCO2, a strong correlation between CO2 assimilation rates and CA hydration rates was observed. C(18)O(16)O isotope discrimination was used to estimate the mesophyll conductance to CO2 diffusion from the intercellular air space to the mesophyll cytosol (gm) in control plants, which allowed us to calculate CA activities in the mesophyll cytosol (Cm). This revealed a strong relationship between the initial slope of the response of the CO2 assimilation rate to cytosolic pCO2 (ACm) and cytosolic CA activity. However, the relationship between the initial slope of the response of CO2 assimilation to intercellular pCO2 (ACi) and cytosolic CA activity was curvilinear. This indicated that in S. viridis, mesophyll conductance may be a contributing limiting factor alongside CA activity to CO2 assimilation rates at low pCO2. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  19. Carbon and Nitrogen Accumulation Rates in Salt Marshes in Oregon, USA

    EPA Science Inventory

    Two important ecosystem services of wetlands are carbon sequestration and filtration of nutrients and particulates. We quantified the carbon and nitrogen accumulation rates in salt marshes at 135 plots distributed across eight estuaries located in Oregon, USA. Net carbon and ...

  20. Carbon and Nitrogen Accumulation Rates in Salt Marshes in Oregon, USA

    EPA Science Inventory

    Two important ecosystem services of wetlands are carbon sequestration and filtration of nutrients and particulates. We quantified the carbon and nitrogen accumulation rates in salt marshes at 135 plots distributed across eight estuaries located in Oregon, USA. Net carbon and ...

  1. A critical review on the improvement of photosynthetic carbon assimilation in C3 plants using genetic engineering.

    PubMed

    Ruan, Cheng-Jiang; Shao, Hong-Bo; Teixeira da Silva, Jaime A

    2012-03-01

    Global warming is one of the most serious challenges facing us today. It may be linked to the increase in atmospheric CO2 and other greenhouse gases (GHGs), leading to a rise in sea level, notable shifts in ecosystems, and in the frequency and intensity of wild fires. There is a strong interest in stabilizing the atmospheric concentration of CO2 and other GHGs by decreasing carbon emission and/or increasing carbon sequestration. Biotic sequestration is an important and effective strategy to mitigate the effects of rising atmospheric CO2 concentrations by increasing carbon sequestration and storage capacity of ecosystems using plant photosynthesis and by decreasing carbon emission using biofuel rather than fossil fuel. Improvement of photosynthetic carbon assimilation, using transgenic engineering, potentially provides a set of available and effective tools for enhancing plant carbon sequestration. In this review, firstly different biological methods of CO2 assimilation in C3, C4 and CAM plants are introduced and three types of C4 pathways which have high photosynthetic performance and have evolved as CO2 pumps are briefly summarized. Then (i) the improvement of photosynthetic carbon assimilation of C3 plants by transgenic engineering using non-C4 genes, and (ii) the overexpression of individual or multiple C4 cycle photosynthetic genes (PEPC, PPDK, PCK, NADP-ME and NADP-MDH) in transgenic C3 plants (e.g. tobacco, potato, rice and Arabidopsis) are highlighted. Some transgenic C3 plants (e.g. tobacco, rice and Arabidopsis) overexpressing the FBP/SBPase, ictB and cytochrome c6 genes showed positive effects on photosynthetic efficiency and growth characteristics. However, over the last 28 years, efforts to overexpress individual, double or multiple C4 enzymes in C3 plants like tobacco, potato, rice, and Arabidopsis have produced mixed results that do not confirm or eliminate the possibility of improving photosynthesis of C3 plants by this approach. Finally, a prospect

  2. [Effects of chlorimuron-ethyl and urea on soil microbial biomass carbon and nitrogen and soil inorganic nitrogen].

    PubMed

    Tan, Huan-Bo; Li, Xin-Yu; Zhang, Hui-Wen; Li, Xu; Xu, Ming-Kai

    2012-08-01

    A microcosm experiment was conducted to study the effects of different concentration chlorimuron-ethyl (20, 200, and 2000 microg x kg(-1) soil) and its combination with urea (120 mg x kg(-1) soil) on the dynamic changes of soil microbial biomass carbon and nitrogen and soil nitrate nitrogen and ammonium nitrogen. Applying chlorimuron-ethyl alone decreased the soil microbial biomass carbon and nitrogen throughout the experiment period (60 days), and the decrement increased with increasing chlorimuron-ethyl concentration. Chlorimuron-ethyl had little effects on the soil ammonium nitrogen and nitrite nitrogen in the early period of the experiment, but increased the soil ammonium nitrogen in the mid-period (15 d) and the soil nitrate nitrogen in the late period (after 30 days) significantly. Both urea addition and its combination with chlorimuron-ethyl increased the soil microbial biomass carbon and nitrogen obviously in a short time, but the effect of combined addition of urea and chlorimuron-ethyl weakened then. Applying urea and its combination with chlorimuron-ethyl resulted in a lasting increase of soil nitrate nitrogen and ammonium nitrogen.

  3. Properties of nitrogen-doped amorphous hydrogenated carbon films

    SciTech Connect

    Amir, O.; Kalish, R. )

    1991-11-01

    Nitrogen-containing hydrogenated amorphous carbon (a-C:H(N)) films are grown from a dc plasma of a N{sub 2}+C{sub 6}H{sub 6} gas mixture. By varying the N{sub 2} fraction in this mixture films with different amounts of N are produced. The actual amount of nitrogen in the {ital a}-C:H(N) films is determined by nuclear reaction analysis and by Auger electron spectroscopy profiling. The nitrogen concentration in the films grows exponentially with nitrogen content in the gas mixture reaching concentrations as high as 10 at.% for the films grown from a N{sub 2}-rich gas mixture (N{sub 2}/(N{sub 2}+C{sub 6}H{sub 6})=0.75). The electrical and structural properties of the N{sub 2}-doped films are studied by performing electrical conductivity, thermopower (TP), optical absorption, and electron-paramagnetic resonance measurements. Films with low ({lt}1 at.%) nitrogen content exhibit fairly high resistivities, have an optical gap of 1 eV, are rich with dangling bonds (5{times}10{sup 20} cm{sup {minus}3}) and their thermopower is positive and in the mV/K regime, indicating conductivity in the valence band tail. However, with increased N doping, the resistivity decreases and the optical band gap shrinks and reached zero for the highest doped film. The TPs for films containing more than 1 at.% are in the {mu}V/K range, indicating hopping conductivity around the Fermi level. The results of all measurements are consistent with the model of Robertson for the electrical structure of amorphous hydrogenated carbon and for the proposed doping mechanism in this material.

  4. Effects of cryptogamic covers on the global carbon and nitrogen balance as investigated by different approaches

    NASA Astrophysics Data System (ADS)

    Weber, Bettina; Porada, Philipp; Elbert, Wolfgang; Burrows, Susannah; Caesar, Jennifer; Steinkamp, Jörg; Tamm, Alexandra; Andreae, Meinrat O.; Büdel, Burkhard; Kleidon, Axel; Pöschl, Ulrich

    2014-05-01

    Cryptogamic covers are composed of cyanobacteria, green algae, lichens, bryophytes, fungi and bacteria in varying proportions. As cryptogamic ground covers, comprising biological soil and rock crusts they occur on many terrestrial ground surfaces. Cryptogamic plant covers, containing epiphytic and epiphyllic crusts as well as foliose or fruticose lichens and bryophytes spread over large portions of terrestrial plant surfaces. Photoautotrophic organisms within these crusts sequester atmosphe