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Sample records for nitrogen carbon assimilation

  1. The influence of root assimilated inorganic carbon on nitrogen acquisition/assimilation and carbon partitioning.

    PubMed

    Viktor, A; Cramer, M D

    2005-01-01

    Understanding of the influences of root-zone CO2 concentration on nitrogen (N) metabolism is limited. The influences of root-zone CO2 concentration on growth, N uptake, N metabolism and the partitioning of root assimilated 14C were determined in tomato (Lycopersicon esculentum). Root, but not leaf, nitrate reductase activity was increased in plants supplied with increased root-zone CO2. Root phosphoenolpyruvate carboxylase activity was lower with NO3(-)- than with NH4(+)-nutrition, and in the latter, was also suppressed by increased root-zone CO2. Increased growth rate in NO3(-)-fed plants with elevated root-zone CO2 concentrations was associated with transfer of root-derived organic acids to the shoot and conversion to carbohydrates. With NH4(+)-fed plants, growth and total N were not altered by elevated root-zone CO2 concentrations, although 14C partitioning to amino acid synthesis was increased. Effects of root-zone CO2 concentration on N uptake and metabolism over longer periods (> 1 d) were probably limited by feedback inhibition. Root-derived organic acids contributed to the carbon budget of the leaves through decarboxylation of the organic acids and photosynthetic refixation of released CO2. PMID:15720630

  2. Leaf nitrogen dioxide uptake coupling apoplastic chemistry, carbon/sulfur assimilation, and plant nitrogen status.

    PubMed

    Hu, Yanbo; Sun, Guangyu

    2010-10-01

    Emission and plant uptake of atmospheric nitrogen oxides (NO + NO(2)) significantly influence regional climate change by regulating the oxidative chemistry of the lower atmosphere, species composition and the recycling of carbon and nutrients, etc. Plant uptake of nitrogen dioxide (NO(2)) is concentration-dependent and species-specific, and covaries with environmental factors. An important factor determining NO(2) influx into leaves is the replenishment of the substomatal cavity. The apoplastic chemistry of the substomatal cavity plays crucial roles in NO(2) deposition rates and the tolerance to NO(2), involving the reactions between NO(2) and apoplastic antioxidants, NO(2)-responsive germin-like proteins, apoplastic acidification, and nitrite-dependent NO synthesis, etc. Moreover, leaf apoplast is a favorable site for the colonization by microbes, which disturbs nitrogen metabolism of host plants. For most plant species, NO(2) assimilation in a leaf primarily depends on the nitrate (NO(3) (-)) assimilation pathway. NO(2)-N assimilation is coupled with carbon and sulfur (sulfate and SO(2)) assimilation as indicated by the mutual needs for metabolic intermediates (or metabolites) and the NO(2)-caused changes of key metabolic enzymes such as phosphoenolpyruvate carboxylase (PEPc) and adenosine 5'-phosphosulfate sulfotransferase, organic acids, and photorespiration. Moreover, arbuscular mycorrhizal (AM) colonization improves the tolerance of host plants to NO(2) by enhancing the efficiency of nutrient absorption and translocation and influencing foliar chemistry. Further progress is proposed to gain a better understanding of the coordination between NO(2)-N, S and C assimilation, especially the investigation of metabolic checkpoints, and the effects of photorespiratory nitrogen cycle, diverse PEPc and the metabolites such as cysteine, O-acetylserine (OAS) and glutathione. PMID:20628880

  3. 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

  4. 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

    2015-01-01

    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 ((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. 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. Interaction of Sulfate Assimilation with Carbon and Nitrogen Metabolism in Lemna minor1

    PubMed Central

    Kopriva, Stanislav; Suter, Marianne; von Ballmoos, Peter; Hesse, Holger; Krähenbühl, Urs; Rennenberg, Heinz; Brunold, Christian

    2002-01-01

    Cysteine synthesis from sulfide and O-acetyl-l-serine (OAS) is a reaction interconnecting sulfate, nitrogen, and carbon assimilation. Using Lemna minor, we analyzed the effects of omission of CO2 from the atmosphere and simultaneous application of alternative carbon sources on adenosine 5′-phosphosulfate reductase (APR) and nitrate reductase (NR), the key enzymes of sulfate and nitrate assimilation, respectively. Incubation in air without CO2 led to severe decrease in APR and NR activities and mRNA levels, but ribulose-1,5-bisphosphate carboxylase/oxygenase was not considerably affected. Simultaneous addition of sucrose (Suc) prevented the reduction in enzyme activities, but not in mRNA levels. OAS, a known regulator of sulfate assimilation, could also attenuate the effect of missing CO2 on APR, but did not affect NR. When the plants were subjected to normal air after a 24-h pretreatment in air without CO2, APR and NR activities and mRNA levels recovered within the next 24 h. The addition of Suc and glucose in air without CO2 also recovered both enzyme activities, with OAS again influenced only APR. 35SO42− feeding showed that treatment in air without CO2 severely inhibited sulfate uptake and the flux through sulfate assimilation. After a resupply of normal air or the addition of Suc, incorporation of 35S into proteins and glutathione greatly increased. OAS treatment resulted in high labeling of cysteine; the incorporation of 35S in proteins and glutathione was much less increased compared with treatment with normal air or Suc. These results corroborate the tight interconnection of sulfate, nitrate, and carbon assimilation. PMID:12428005

  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. 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

    2016-01-01

    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

  9. 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

  10. 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.

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

    DOE PAGESBeta

    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, 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

  12. 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

  13. Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations

    PubMed Central

    Levicán, Gloria; Ugalde, Juan A; Ehrenfeld, Nicole; Maass, Alejandro; Parada, Pilar

    2008-01-01

    Background Carbon and nitrogen fixation are essential pathways for autotrophic bacteria living in extreme environments. These bacteria can use carbon dioxide directly from the air as their sole carbon source and can use different sources of nitrogen such as ammonia, nitrate, nitrite, or even nitrogen from the air. To have a better understanding of how these processes occur and to determine how we can make them more efficient, a comparative genomic analysis of three bioleaching bacteria isolated from mine sites in Chile was performed. This study demonstrated that there are important differences in the carbon dioxide and nitrogen fixation mechanisms among bioleaching bacteria that coexist in mining environments. Results In this study, we probed that both Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans incorporate CO2 via the Calvin-Benson-Bassham cycle; however, the former bacterium has two copies of the Rubisco type I gene whereas the latter has only one copy. In contrast, we demonstrated that Leptospirillum ferriphilum utilizes the reductive tricarboxylic acid cycle for carbon fixation. Although all the species analyzed in our study can incorporate ammonia by an ammonia transporter, we demonstrated that Acidithiobacillus thiooxidans could also assimilate nitrate and nitrite but only Acidithiobacillus ferrooxidans could fix nitrogen directly from the air. Conclusion The current study utilized genomic and molecular evidence to verify carbon and nitrogen fixation mechanisms for three bioleaching bacteria and provided an analysis of the potential regulatory pathways and functional networks that control carbon and nitrogen fixation in these microorganisms. PMID:19055775

  14. 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. PMID:16626470

  15. ANTISENSE INHIBITION OF NADH-GLUTAMATE SYNTHASE IMPAIRS CARBON/NITROGEN ASSIMILATION IN NODULES OF ALFALFA (MEDICAGO SATIVA)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Legumes acquire significant amounts of nitrogen for growth from symbiotic nitrogen fixation in root nodules. The glutamine synthetase (GS)/NADH-dependent glutamate synthase (NADH-GOGAT) cycle catalyzes initial nitrogen assimilation. This report describes the impacts of specific reduction on nodule N...

  16. Nitrogen Assimilation in Mycorrhizas 1

    PubMed Central

    Genetet, Isabelle; Martin, Francis; Stewart, George R.

    1984-01-01

    Ammonium assimilation was followed in N-starved mycelia from the ectomycorrhizal Ascomycete Cenococcum graniforme. The evaluation of free amino acid pool levels after the addition of 5 millimolar NH4+ indicated that the absorbed ammonium was assimilated rapidly. Post-feeding nitrogen content of amino acids was very different from the initial values. After 8 hours of NH4+ feeding, glutamine accounted for the largest percentage of free amino acid nitrogen (43%). The addition of 5 millimolar methionine sulfoximine (MSX) to NH4+-fed mycelia caused an inhibition of glutamine accumulation with a corresponding increase in glutamate and alanine levels. Using 15N as a tracer, it was found that the greatest initial labeling was into glutamine and glutamate followed by aspartate, alanine, and ornithine. On inhibiting glutamine synthetase using MSX, 15N enrichment of glutamate, alanine, aspartate, and ornithine continued although labeling of glutamine was quite low. Moreover, the incorporation of 15N label in insoluble nitrogenous compounds was lower in the presence of MSX. From the composition of free amino acid pools, the 15N labeling pattern and effects of MSX, NH4+ assimilation in C. graniforme mycelia appears to proceed via glutamate dehydrogenase pathway. This study also demonstrates that glutamine synthesis is an important reaction of ammonia utilization. PMID:16663852

  17. 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. PMID:26135985

  18. 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

  19. Inhibition of nitrogen and photosynthetic carbon assimilation of maize seedlings by exposure to a combination of salt stress and potassium-deficient stress.

    PubMed

    Qu, Chunxiang; Liu, Chao; Ze, Yuguan; Gong, Xiaolan; Hong, Mengmeng; Wang, Ling; Hong, Fashui

    2011-12-01

    The main aim of this work is to identify how the combined stresses affect the interdependent nitrogen and photosynthetic carbon assimilations in maize. Maize plants were cultivated in Meider's solution. They were subjected to salt stress and potassium deficiency in the K-present Meider's media and K-deficient Meider's media. After 5 weeks, we measured chlorophyll a fluorescence and the activities of several enzymes in metabolic checkpoints coordinating primary nitrogen and carbon assimilation in the leaves of maize. The study showed that the combination of salt stress and potassium-deficient stress more significantly decreased nitrate uptake, plant growth, the activities of nitrate reductase, glutamate dehydrogenase, glutamate synthase, urease, glutamic-pyruvic transaminase, glutamic-oxaloace transaminase, sucrose-phosphate synthase, phosphoenolpyruvate carboxylase, and the synthesis of free amino acids, chlorophyll, and protein than those of each individual stress, respectively. However, the combined stresses significantly increased the accumulation of ammonium and carbohydrate products. The combined stresses also significantly decreased the oxygen evolution, the electron transport, and the efficiency of photochemical energy conversion by photosystem II in maize seedlings. Taken together, a combination of salt stress and potassium-deficient stress impaired the assimilations of both nitrogen and carbon and decreased the photosystem II activity in maize. PMID:21455705

  20. Carbon and Nitrogen Assimilation and Partitioning in Soybeans Exposed to Low Root Temperatures 1

    PubMed Central

    Walsh, Kerry B.; Layzell, David B.

    1986-01-01

    Low root temperature effects on vegetative growth of soybean (Harosoy 63 × Rhizobium japonicum USDA 16) were examined in 35 day old plants exposed to temperatures of 15°C (shoots at 25°C) for an 11 day period. Duing this period various aspects of C and N assimilation and partitioning were monitored including shoot night and nodulated root respiration, C and N partitioning to six plant parts, C2H2 reduction, H2 evolution, leaf area, transpiration, net photosynthesis, and N2 fixation. The low temperature treatment resulted in a decrease in the net rate of N2 fixation but nitrogenase relative efficiency increased. In response, the plant retained N in the tissues of the nodulated root and decreased N partitioning to young shoot tissues, thereby inducing the remobilization of N from older leaves, and reducing leaf area development. The leaf area specific rate of net photosynthesis was not affected over the study period; however, shoot and nodulated root respiration declined. Consequently, C accumulated in mature leaves and stems, partly in the form of increased starch reserves. Three possibilities were considered for increasing low temperature tolerance in nodulated soybeans: (a) decrease in temperature optima for nitrogenase, (b) increased development of nodules and N2 fixation capacity at low temperature, and (c) alterations in the pattern of C and N partitioning in response to low temperature conditions. PMID:16664592

  1. Nitrogen mineralization and assimilation at millimeter scales.

    PubMed

    Myrold, David D; Pett-Ridge, Jennifer; Bottomley, Peter J

    2011-01-01

    The assimilation (uptake or immobilization) of inorganic nitrogen (N) and the production of ammonium (NH(4)(+)) from organic N compounds are universal functions of microorganisms, and the balance between these two processes is tightly regulated by the relative demands of microbes for N and carbon (C). In a heterogeneous environment, such as soils, bulk measurements of N mineralization or immobilization do not reflect the variation of these two processes in different microhabitats (1μm-1mm). Our purpose is to review the approaches that can be applied to measure N mineralization and immobilization within soil microhabitats, at scales of millimeter (using adaptations of (15)N isotope pool dilution and IRMS-isotope ratio mass spectrometry) to micrometer (using SIMS-secondary ion mass spectrometry). PMID:21514461

  2. 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

  3. 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

  4. Assimilating AmeriFlux Site Data into the Community Land Model with Carbon-Nitrogen Coupling via the Ensemble Kalman Filter

    NASA Astrophysics Data System (ADS)

    Pettijohn, J. C.; Law, B. E.; Williams, M. D.; Stoeckli, R.; Thornton, P. E.; Hudiburg, T. M.; Thomas, C. K.; Martin, J.; Hill, T. C.

    2009-12-01

    The assimilation of terrestrial carbon, water and nutrient cycle measurements into land surface models of these processes is fundamental to improving our ability to predict how these ecosystems may respond to climate change. A combination of measurements and models, each with their own systematic biases, must be considered when constraining the nonlinear behavior of these coupled dynamics. As such, we use the sequential Ensemble Kalman Filter (EnKF) to assimilate eddy covariance (EC) and other site-level AmeriFlux measurements into the NCAR Community Land Model with Carbon-Nitrogen coupling (CLM-CN v3.5), run in single-column mode at a 30-minute time step, to improve estimates of relatively unconstrained model state variables and parameters. Specifically, we focus on a semi-arid ponderosa pine site (US-ME2) in the Pacific Northwest to identify the mechanisms by which this ecosystem responds to severe late summer drought. Our EnKF analysis includes water, carbon, energy and nitrogen state variables (e.g., 10 volumetric soil moisture levels (0-3.43 m), ponderosa pine and shrub evapotranspiration and net ecosystem exchange of carbon dioxide stocks and flux components, snow depth, etc.) and associated parameters (e.g., PFT-level rooting distribution parameters, maximum subsurface runoff coefficient, soil hydraulic conductivity decay factor, snow aging parameters, maximum canopy conductance, C:N ratios, etc.). The effectiveness of the EnKF in constraining state variables and associated parameters is sensitive to their relative frequencies, in that C-N state variables and parameters with long time constants require similarly long time series in the analysis. We apply the EnKF kernel perturbation routine to disrupt preliminary convergence of covariances, which has been found in recent studies to be a problem more characteristic of low frequency vegetation state variables and parameters than high frequency ones more heavily coupled with highly varying climate (e

  5. 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

  6. Transgenic plants that exhibit enhanced nitrogen assimilation

    SciTech Connect

    Coruzzi, G.M.; Brears, T.

    1999-09-21

    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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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. PMID:27262118

  12. 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.

  13. 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.

  14. 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.

  15. 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. PMID:27045776

  16. 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

  17. Fluxes of Reserve-Derived and Currently Assimilated Carbon and Nitrogen in Perennial Ryegrass Recovering from Defoliation. The Regrowing Tiller and Its Component Functionally Distinct Zones1

    PubMed Central

    Schnyder, Hans; de Visser, Ries

    1999-01-01

    The quantitative significance of reserves and current assimilates in regrowing tillers of severely defoliated plants of perennial ryegrass (Lolium perenne L.) was assessed by a new approach, comprising 13C/12C and 15N/14N steady-state labeling and separation of sink and source zones. The functionally distinct zones showed large differences in the kinetics of currently assimilated C and N. These are interpreted in terms of ”substrate” and ”tissue” flux among zones and C and N turnover within zones. Tillers refoliated rapidly, although C and N supply was initially decreased. Rapid refoliation was associated with (a) transient depletion of water-soluble carbohydrates and dilution of structural biomass in the immature zone of expanding leaves, (b) rapid transition to current assimilation-derived growth, and (c) rapid reestablishment of a balanced C:N ratio in growth substrate. This balance (C:N, approximately 8.9 [w/w] in new biomass) indicated coregulation of growth by C and N supply and resulted from complementary fluxes of reserve- and current assimilation-derived C and N. Reserves were the dominant N source until approximately 3 d after defoliation. Amino-C constituted approximately 60% of the net influx of reserve C during the first 2 d. Carbohydrate reserves were an insignificant source of C for tiller growth after d 1. We discuss the physiological mechanisms contributing to defoliation tolerance. PMID:10198102

  18. Diversity of nitrogen assimilation pathways among microbial photosynthetic eukaryotes.

    PubMed

    Terrado, Ramon; Monier, Adam; Edgar, Robyn; Lovejoy, Connie

    2015-06-01

    In an effort to better understand the diversity of genes coding for nitrogen (N) uptake and assimilation pathways among microalgae, we analyzed the transcriptomes of five phylogenetically diverse single celled algae originally isolated from the same high arctic marine region. The five photosynthetic flagellates (a pelagophyte, dictyochophyte, chrysoph-yte, cryptophyte and haptophyte) were grown on standard media and media with only urea or nitrate as a nitrogen source; cells were harvested during late exponential growth. Based on homolog protein sequences, transcriptomes of each alga were interrogated to retrieve genes potentially associated with nitrogen uptake and utilization pathways. We further investigated the phylogeny of poorly characterized genes and gene families that were identified. While the phylogeny of the active urea transporter (DUR3) was taxonomically coherent, those for the urea transporter superfamily, putative nitrilases and amidases indicated complex evolutionary histories, and preliminary evidence for horizontal gene transfers. All five algae expressed genes for ammonium assimilation and all but the chrysophyte expressed genes involved in nitrate utilization and the urea cycle. Among the four algae with nitrate transporter transcripts, we detected lower expression levels in three of these (the dictyochophyte, pelagophyte, and cryptophyte) grown in the urea only medium compared with cultures from the nitrate only media. The diversity of N pathway genes in the five algae, and their ability to grow using urea as a nitrogen source, suggest that these flagellates are able to use a variety of organic nitrogen sources, which would be an advantage in an inorganic nitrogen - limited environment, such as the Arctic Ocean. PMID:26986665

  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 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

  1. Ammonia assimilation pathways in nitrogen-fixing Clostridium kluyverii and Clostridium butyricum.

    PubMed Central

    Kanamori, K; Weiss, R L; Roberts, J D

    1989-01-01

    Pathways of ammonia assimilation into glutamic acid were investigated in ammonia-grown and N2-fixing Clostridium kluyverii and Clostridium butyricum by measuring the specific activities of glutamate dehydrogenase, glutamine synthetase, and glutamate synthase. C. kluyverii had NADPH-glutamate dehydrogenase with a Km of 12.0 mM for NH4+. The glutamate dehydrogenase pathway played an important role in ammonia assimilation in ammonia-grown cells but was found to play a minor role relative to that of the glutamine synthetase/NADPH-glutamate synthase pathway in nitrogen-fixing cells when the intracellular NH4+ concentration and the low affinity of the enzyme for NH4+ were taken into account. In C. butyricum grown on glucose-salt medium with ammonia or N2 as the nitrogen source, glutamate dehydrogenase activity was undetectable, and the glutamine synthetase/NADH-glutamate synthase pathway was the predominant pathway of ammonia assimilation. Under these growth conditions, C. butyricum also lacked the activity of glucose-6-phosphate dehydrogenase, which catalyzes the regeneration of NADPH from NADP+. However, high activities of glucose-6-phosphate dehydrogenase as well as of NADPH-glutamate dehydrogenase with a Km of 2.8 mM for NH4+ were present in C. butyricum after growth on complex nitrogen and carbon sources. The ammonia-assimilating pathway of N2-fixing C. butyricum, which differs from that of the previously studied Bacillus polymyxa and Bacillus macerans, is discussed in relation to possible effects of the availability of ATP and of NADPH on ammonia-assimilating pathways. PMID:2564848

  2. 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.

  3. 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

  4. Nitrogen assimilation by single cells in hot springs

    NASA Astrophysics Data System (ADS)

    Poret-peterson, A. T.; Romaniello, S. J.; Bose, M.; Williams, P.; Elser, J. J.; Shock, E.; Anbar, A. D.; Hartnett, H. E.

    2012-12-01

    Microorganisms drive biogeochemical cycles and require nutrients, such as ammonium and nitrate, to function. As a result, following nutrient flows provides opportunities to study how microbial activity influences ecosystem-level processes. Most past measurements of microbial nutrient uptake rely on bulk measurements, which are informative but provide little information about heterogeneity among community members involved in elemental transformations, nor about possible effects of physiological state or taxonomic identity. Since microbial communities tend to be phylogenetically and physiologically diverse, it is reasonable to expect that community members will respond differently to nutrient addition. Here, we examine nitrogen assimilation (via addition of 15N-labeled ammonium or nitrate) in Yellowstone hot spring microbial communities. Using the NanoSIMS, we imaged cells at a very high spatial resolution (nanometer scale) necessary to determine 15N enrichments in single micron-sized cells. We compare the N isotopic enrichments observed in single cells to that determined in bulk sediments by standard isotope ratio mass spectrometry. NanoSIMS imaging of 56 individual cells from sediments of an acidic hot spring (pH 4.7, T=67oC) incubated with 15N-ammonium shows that about two-thirds of the cells (38) exhibited 15N-enrichment. Most cells had 15N enrichments from 0.39 to 0.91 atom %, while some cells were much more significantly enriched. Bulk analyses of sediments show that ammonium assimilation and nitrate assimilation readily occurred at this spring. These findings show that microbes in this hot spring may differentially take up ammonium, which may arise from a number of factors including differences in cellular N requirements, growth rates, and the ability to transport ammonium. This work represents some of the first single-cell isotopic measurements from an extreme environment. Efforts are underway to image sediment samples from other hot springs and to pair Nano

  5. 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.

  6. 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.

  7. Nitrogen Application Rate and Carbon Asssimilation in Potato: What can this tell us about nitrogen demand and uptake?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The interaction between nitrogen application rate and carbon assimilation in potato strongly affects growth and developmental rates. Two consecutive experiments were carried out in the summer of 2005 in six sunlit, controlled environment plant growth chambers with six nitrogen application rates and ...

  8. 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. PMID:16533068

  9. Mineralizable phosphorus, nitrogen, and carbon relationships in dairy manure at various carbon-to-phosphorus ratios

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Animal manure contains all major elements required for plant and microorganisms’ uptake and assimilation for growth, namely, phosphorus (P), nitrogen, and carbon. Information about interactions between transformations of nutrients and the turnover of P forms in dairy manure, is essential to accurat...

  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. Rhizobium sp. strain ORS571 ammonium assimilation and nitrogen fixation.

    PubMed Central

    Donald, R G; Ludwig, R A

    1984-01-01

    Among rhizobia studied, Rhizobium sp. strain ORS571 alone grew unambiguously on N2 as sole N source. In ORS571 , only the glutamine synthetase (GS)-glutamate synthase ( GOGAT ) pathway assimilated ammonium. However, ORS571 exhibited two unique physiological aspects of this pathway: ORS571 had only GS I, whereas all other Rhizobiaceae studied had both GS I and GS II, and both NADPH- and NADH-dependent GOGAT activities were present. ORS571 GS-affected and NADPH- GOGAT -affected mutant strains were defective in both ammonium assimilation (Asm-) and N2 fixation (Nif-) in culture and in planta ; NADH- GOGAT mutants were Asm- but Nif+. "Bacteroid" GS activity was essentially nil, suggesting symbiotic ammonium export. Physiological studies on effects of glutamine, ammonium, methionine sulfoximine, and diazo-oxo-norleucine on nitrogenase induction in culture implied a regulatory role for the intracellular glutamine pool. Images PMID:6144666

  13. 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

  14. Transcriptome of Proteus mirabilis in the murine urinary tract: virulence and nitrogen assimilation gene expression.

    PubMed

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

    2011-07-01

    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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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. PMID:22993512

  20. 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.

  1. 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

  2. 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

  3. Regulation of hydrogen sulfide liberation in wine-producing Saccharomyces cerevisiae strains by assimilable nitrogen.

    PubMed

    Jiranek, V; Langridge, P; Henschke, P A

    1995-02-01

    Saccharomyces cerevisiae wine-producing yeast cultures grown under model winemaking conditions could be induced to liberate hydrogen sulfide (H2S) by starvation for assimilable nitrogen. The amount of H2S produced was dependent on the yeast strain, the sulfur precursor compound, the culture growth rate, and the activity of the sulfite reductase enzyme (EC 1.8.1.2) immediately before nitrogen depletion. Increased H2S formation relative to its utilization by metabolism was not a consequence of a de novo synthesis of sulfite reductase. The greatest amount of H2S was produced when nitrogen became depleted during the exponential phase of growth or during growth on amino acids capable of supporting short doubling times. Both sulfate and sulfite were able to act as substrates for the generation of H2S in the absence of assimilable nitrogen; however, sulfate reduction was tightly regulated, leading to limited H2S liberation, whereas sulfite reduction appeared to be uncontrolled. In addition to ammonium, most amino acids were able to suppress the liberation of excess H2S when added as sole sources of nitrogen, particularly for one of the strains studied. Cysteine was the most notable exception, inducing the liberation of H2S at levels exceeding that of the nitrogen-depleted control. Threonine and proline also proved to be poor substitutes for ammonium. These data suggest that any compound that can efficiently generate sulfide-binding nitrogenous precursors of organic sulfur compounds will prevent the liberation of excess H2S. PMID:7574581

  4. Regulation of hydrogen sulfide liberation in wine-producing Saccharomyces cerevisiae strains by assimilable nitrogen.

    PubMed Central

    Jiranek, V; Langridge, P; Henschke, P A

    1995-01-01

    Saccharomyces cerevisiae wine-producing yeast cultures grown under model winemaking conditions could be induced to liberate hydrogen sulfide (H2S) by starvation for assimilable nitrogen. The amount of H2S produced was dependent on the yeast strain, the sulfur precursor compound, the culture growth rate, and the activity of the sulfite reductase enzyme (EC 1.8.1.2) immediately before nitrogen depletion. Increased H2S formation relative to its utilization by metabolism was not a consequence of a de novo synthesis of sulfite reductase. The greatest amount of H2S was produced when nitrogen became depleted during the exponential phase of growth or during growth on amino acids capable of supporting short doubling times. Both sulfate and sulfite were able to act as substrates for the generation of H2S in the absence of assimilable nitrogen; however, sulfate reduction was tightly regulated, leading to limited H2S liberation, whereas sulfite reduction appeared to be uncontrolled. In addition to ammonium, most amino acids were able to suppress the liberation of excess H2S when added as sole sources of nitrogen, particularly for one of the strains studied. Cysteine was the most notable exception, inducing the liberation of H2S at levels exceeding that of the nitrogen-depleted control. Threonine and proline also proved to be poor substitutes for ammonium. These data suggest that any compound that can efficiently generate sulfide-binding nitrogenous precursors of organic sulfur compounds will prevent the liberation of excess H2S. PMID:7574581

  5. 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. PMID:19470091

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

    PubMed

    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

  7. 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

  8. 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. PMID:16348936

  9. 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. PMID:26788956

  10. 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. PMID:25388561

  11. 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

  12. 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.

  13. 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. PMID:26790176

  14. 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

  15. Lanthanum (III) regulates the nitrogen assimilation in soybean seedlings under ultraviolet-B radiation.

    PubMed

    Huang, Guangrong; Wang, Lihong; Zhou, Qing

    2013-01-01

    Ultraviolet-B (UV-B, 280-320 nm) radiation has seriously affected the growth of plants. Finding the technology/method to alleviate the damage of UV-B radiation has become a frontal topic in the field of environmental science. The pretreatment with rare earth elements (REEs) is an effective method, but the regulation mechanism of REEs is unknown. Here, the regulation effects of lanthanum (La(III)) on nitrogen assimilation in soybean seedlings (Glycine max L.) under ultraviolet-B radiation were investigated to elucidate the regulation mechanism of REEs on plants under UV-B radiation. UV-B radiation led to the inhibition in the activities of the key enzymes (nitrate reductase, glutamine synthetase, glutamate synthase) in the nitrogen assimilation, the decrease in the contents of nitrate and soluble proteins, as well as the increase in the content of amino acid in soybean seedlings. The change degree of UV-B radiation at the high level (0.45 W m(-2)) was higher than that of UV-B radiation at the low level (0.15 W m(-2)). The pretreatment with 20 mg L(-1) La(III) could alleviate the effects of UV-B radiation on the activities of nitrate reductase, glutamine synthetase, glutamate synthase, and glutamate dehydrogenase, promoting amino acid conversion and protein synthesis in soybean seedlings. The regulation effect of La(III) under UV-B radiation at the low level was better than that of UV-B radiation at the high level. The results indicated that the pretreatment with 20 mg L(-1) La(III) could alleviate the inhibition of UV-B radiation on nitrogen assimilation in soybean seedlings. PMID:23090712

  16. 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. PMID:25425155

  17. 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

  18. 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. PMID:27117340

  19. 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

  20. Inorganic Carbon-Stimulated O2 Photoreduction Is Suppressed by NO2- Assimilation in Air-Grown Cells of Synechococcus UTEX 625.

    PubMed

    Mir, N. A.; Salon, C.; Canvin, D. T.

    1995-12-01

    The effect of NO2- assimilation on O2 exchange and CO2 fixation of the cyanobacterium, Synechococcus UTEX 625, was studied mass spectrometrically. Upon addition of 1 mM inorganic carbon to the medium, inorganic carbon pools developed and accelerated O2 photoreduction 5-fold when CO2 fixation was inhibited. During steady-state photosynthesis at saturating light, O2 uptake represented 32% of O2 evolution and balanced that portion of O2 evolution that could not be accounted for by CO2 fixation. Under these conditions, NO2- assimilation reduced O2 uptake by 59% but had no influence on CO2 fixation. NO2- assimilation decreased both CO2 fixation and O2 photoreduction at low light and and increased net O2 evolution at all light intensities. The increase in net O2 evolution observed during simultaneous assimilation of carbon and nitrogen over carbon alone was due to a suppression of O2 photoreduction by NO2- assimilation. When CO2 fixation was precluded, NO2- assimilation inhibited O2 photoreduction and stimulated O2 evolution. When the electron supply was limiting (low light), competition among O2, CO2, and NO2- for electrons could be observed, but when the electron supply was not limiting (saturating light), O2 photoreduction and/or NO2- reduction caused electron transport that was additive to that for maximum CO2 fixation. PMID:12228670

  1. Preparation of nitrogen-doped carbon tubes

    SciTech Connect

    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.

  2. Culture Studies of Nitrogen and Oxygen Isotope Effects Associated with Nitrate Assimilation and Denitrification

    NASA Astrophysics Data System (ADS)

    Sigman, D. M.; Granger, J.; Lehmann, M. F.; Difiore, P. J.; Tortell, P. D.

    2007-12-01

    The isotope effects of nitrate-consuming reactions such as nitrate assimilation and denitrification are potential indicators of the physiological state of the organisms carrying out these reactions. Moreover, an understanding of these isotope effects is needed to use the stable isotopes to investigate the fluxes associated with these reactions in modern and ancient environments. We have used batch cultures to investigate the nitrogen (N) and oxygen (O) isotope effects of (1) nitrate assimilation by eukaryotic and prokaryotic algae and by heterotrophic bacteria, and (2) nitrate reduction by denitrifying bacteria. We observe intra- and inter-specific variation in isotope effect amplitudes and, in the case of denitrifiers, indications of isotope effect decreases during individual nitrate drawdown experiments. However, the measured N and O isotope effect ratio is close to 1 for all studied organisms, with the exception of an unusual denitrifier (Rhodobacter sphaeroides) that possesses only periplasmic (non-respiratory) nitrate reductase. This observation and other findings are consistent with nitrate reductase being the predominant source of isotope fractionation and with most isotope effect amplitude variability arising from variable degrees to which nitrate imported into the cell is reduced versus effluxed back into the environment; the more efflux, the more complete the expression of the fractionation imparted by nitrate reduction. If this is the case, then isotope effect amplitudes in the field should be related to physiological conditions in the environment, a prediction that, we argue, is supported by recent studies of (1) nitrate assimilation in the polar ocean and (2) denitrification in sediment porewaters.

  3. Foliar nitrate reductase: A marker for assimilation of atmospheric nitrogen oxides

    SciTech Connect

    Norby, R.J.

    1988-01-01

    Atmospheric deposition of nitrates to forest canopies has been implicated as predisposing trees to environmental stresses. A first step in the evaluation of this hypothesis is the determination of whether atmospheric nitrates are absorbed and metabolized by tree foliage. The enzyme nitrate reductase (NR) is an appropriate marker for nitrate metabolism because it is the rate-limiting step in the assimilation of nitrate into organic compounds and it is substrate-inducible. In laboratory studies, NR was not induced in red spruce foliage exposed to NO/sub 3//sup /minus// in acid mist, but NR activity increased dramatically in spruce seedlings exposed to NO/sub 2/ or HNO/sub 3/ vapor, suggesting that gaseous nitrogen oxides can be assimilated by spruce foliage. Nitrate reductase activity also can be measured in the field and may be a useful marker for trees that are impacted by nitrogen pollution, but extensive characterization of diurnal and seasonal variation in foliar NR activity is an important prerequisite. 24 refs.

  4. Worldwide organic soil carbon and nitrogen data

    SciTech Connect

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

    1984-05-01

    A compilation of soil carbon and nitrogen storage data for more than 3500 soil profiles from under natural vegetation or relatively undisturbed sites is presented in this report. A summary table of the carbon and nitrogen storage in a pedon of surface cubic meter for each soil profile, as well as location, elevation, climate, parent material, and vegetation information, are presented. The data were used to determine average carbon and nitrogen storage on land surfaces of the world. Calculations were also made of storage related to climatic classifications, ecosystem clasifications, and latitudinal increments from the equator to 75/sup 0/. Carbon (kg.m/sup -3/) varies from 2 in hot dry climates, through 10 in many cold dry or seasonally moist (warm or hot) climates, to more than 30 in wet alpine or subpolar climates. Nitrogen storage, an order of magnitude smaller than carbon storage in soils, shows broad parallels but exceeds 1600 g.m/sup -3/ for subtropical/tropical premontane or lower montane soils, as well as alpine or subpolar wet soils. Such limiting conditions, defined by a balance of income and loss rates for mature soil profiles, also explain much of the variation among major ecosystem complexes whose soils are partly disturbed, incompletely recovered, or imperfectly known regarding their maturity and stability. Classifying profiles into Holdridge life zones and using appropriate life zone areas, we estimate 1309 x 10/sup 15/ g carbon and 92 x 10/sup 15/ g nitrogen in the world's soils. Alternatively, using average organic carbon and nitrogen densities from one degree latitude bands multiplied by the earth's surface area in the respective bands, we arrive at 1728 x 10/sup 15/ g of carbon and 117 x 10/sup 15/ g of nitrogen. Inadequacies that lead to the disparate estimates are discussed. 123 references, 5 figures, 7 tables.

  5. 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. PMID:20591568

  6. A global two component signal transduction system that integrates the control of photosynthesis, carbon dioxide assimilation, and nitrogen fixation

    PubMed Central

    Joshi, Hemalata M.; Tabita, F. Robert

    1996-01-01

    Photosynthesis, biological nitrogen fixation, and carbon dioxide assimilation are three fundamental biological processes catalyzed by photosynthetic bacteria. In the present study, it is shown that mutant strains of the nonsulfur purple photosynthetic bacteria Rhodospirillum rubrum and Rhodobacter sphaeroides, containing a blockage in the primary CO2 assimilatory pathway, derepress the synthesis of components of the nitrogen fixation enzyme complex and abrogate normal control mechanisms. The absence of the Calvin–Benson–Bassham (CBB) reductive pentose phosphate CO2 fixation pathway removes an important route for the dissipation of excess reducing power. Thus, the mutant strains develop alternative means to remove these reducing equivalents, resulting in the synthesis of large amounts of nitrogenase even in the presence of ammonia. This response is under the control of a global two-component signal transduction system previously found to regulate photosystem biosynthesis and the transcription of genes required for CO2 fixation through the CBB pathway and alternative routes. In addition, this two-component system directly controls the ability of these bacteria to grow under nitrogen-fixing conditions. These results indicate that there is a molecular link between the CBB and nitrogen fixation process, allowing the cell to overcome powerful control mechanisms to remove excess reducing power generated by photosynthesis and carbon metabolism. Furthermore, these results suggest that the two-component system integrates the expression of genes required for the three processes of photosynthesis, nitrogen fixation, and carbon dioxide fixation. PMID:8962083

  7. 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.

  8. 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.

  9. Insights into Nitrogen Isotopic Fractionation During Algal Assimilation of Nitrate and Ammonium

    NASA Astrophysics Data System (ADS)

    Evans, S. L.; Swart, P. K.; Capo, T. R.

    2008-12-01

    Nitrogen availability is an important factor controlling algal growth in marine environments, representing a limiting nutrient throughout much of the global ocean. Anthropogenic inputs to the coastal zone may shift the nutrient regime, leading to questions regarding the extent of anthropogenic nutrient impacts in near-shore environments. A large body of work has been completed relating the δ15N of algae, seagrasses, and other benthic organisms to anthropogenic nutrient sources. However, previous work by our research group characterizing the δ15N of organic material associated with waste water discharge points, and in reef and embayment environments of the south Florida coastal zone, has suggested that δ15N values alone do not provide unequivocal evidence of anthropogenic nitrogen loading. Greater understanding of nitrogen processing and isotopic fractionation in coastal benthic organisms is necessary before blanket assumptions regarding nutrient uptake and source association can be universally accepted. Closed system mesocosm incubations examining fractionation associated with assimilation of nitrate and ammonium in cultured red algae, Gracilaria sp. and Agardhiella sp., were completed under varied nitrate and ammonium concentrations from 10 to 500 μM with initial nitrogen isotopic compositions of 2.7-3 ‰. Following 8-day incubations, the isotopic composition of new algal growth ranged between +2.43 and -5.77 ‰, with more depleted values coincident with higher N-availability. Rayleigh fractionation calculations yield fractionation factors of 4-9 ‰ (α values of 1.0045 to 1.008), which represent significantly larger values than those previously reported in the literature for macroalgae. 15N-tracer experiments (initial δ15N = 1000 ‰) were also conducted to assess nutrient preferences in the cultured algae. Isotopic composition of new algal growth varied from -1.3 to +495.0 ‰ with only Agardhiella exhibiting an obvious preference for ammonium

  10. 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.

  11. 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.

  12. 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.

  13. Carbon assimilation and loss in early bioenrgy systems

    NASA Astrophysics Data System (ADS)

    Zenone, T.; Chen, J.; Robertson, G. P.

    2011-12-01

    In this study we established a field experiment and deployed a cluster of eddy-covariance towers to quantify the magnitude and changes of ecosystem carbon assimilation, loss, and balance (i.e, Net Ecosystem Production) in three permanent grasslands and different types of candidate biofuel crop production systems (Switchgrass, mixed prairie, soybean and corn) that were converted from agricultural crops or CRP land. The six fields were converted to soybean in 2009 before establishing the biofuel cropping systems in 2010. Our field observations made between January 2009 (i.e., pre-conversion) through December 2010 showed that conversion of CRP to soybean induced net C emissions during the first year of bioenergy crops cultivation (2009) resulting in a NEP that ranging from 288.6 g C m-2 , 189.7 g C m-2 to 173.9 g C m-2 .During the second growth season (2010), the C balance and loss via respiration were mostly related to previous land use: in scenario 1 corn cultivation induced a net C accumulation of 310 and 220 g C m-2 year-1, resulting in a C balance of -42 g C m-2 over the 2 years at the sites previously cultivated as CRP , and -340 g C m-2 at the site under corn-soybean rotation. The two corn sites with different land use history showed a remarkable difference in the ecosystem respiration (Reco): overall Reco was greater of about 56% at the site converted from permanent grassland. In scenario 2 (switchgrass cultivation), regardless the previous land use history, both sites were C source over the 2 years of cultivation: scenario with a cumulative NEP varying from 153.9 g C m-2 while to 281.8 g C m-2; this site was characterized by the lowest SOC content (Zenone et al 2010) in comparison to the others. In scenario 3, site converted back to a permanent mixed prairie , even with the presence of oat as cover crop has resulted in a significative C emission over the 2 year with a cumulative NEP of 303.7 g C m-2. At the grassland reference site annual NEP in 2009 was -42

  14. Diet-animal fractionation of nitrogen stable isotopes reflects the efficiency of nitrogen assimilation in ruminants.

    PubMed

    Cantalapiedra-Hijar, G; Ortigues-Marty, I; Sepchat, B; Agabriel, J; Huneau, J F; Fouillet, H

    2015-04-14

    The natural abundance of ¹⁵N in animal proteins (δ¹⁵Nanimal) is greater than that in the diet consumed by the animals (δ¹⁵Ndiet), with a discrimination factor (Δ¹⁵N = δ¹⁵Nanimal - δ¹⁵Ndiet) that is known to vary according to nutritional conditions. The objectives of the present study were to test the hypothesis that Δ¹⁵N variations depend on the efficiency of nitrogen utilisation (ENU) in growing beef cattle, and to identify some of the physiological mechanisms responsible for this N isotopic fractionation in ruminants. Thus, we performed the regression of the Δ¹⁵N of plasma proteins obtained from thirty-five finishing beef cattle fed standard and non-conventional diets against different feed efficiency indices, including ENU. We also performed the regression of the Δ¹⁵N of different ruminant N pools (plasma and milk proteins, urine and faeces) against different splanchnic N fluxes obtained from multi-catheterised lactating dairy cows. The Δ¹⁵N of plasma proteins was negatively correlated with feed efficiency indices in beef cattle, especially ENU (body protein gain/N intake) and efficiency of metabolisable protein (MP) utilisation (body protein gain/MP intake). Although Δ¹⁵N obtained from different N pools in dairy cows were all negatively correlated with ENU, the highest correlation was found when Δ¹⁵N was calculated from plasma proteins. Δ¹⁵N showed no correlation with urea-N recycling or rumen NH₃ absorption, but exhibited a strong correlation with liver urea synthesis and splanchnic amino acid metabolism, which points to a dominant role of splanchnic tissues in the present N isotopic fractionation study. PMID:25716533

  15. 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

    2011-06-01

    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

  16. 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

  17. 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. PMID:25700337

  18. 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

  19. Essentiality of mitochondrial oxidative metabolism for photosynthesis: optimization of carbon assimilation and protection against photoinhibition.

    PubMed

    Padmasree, K; Padmavathi, L; Raghavendra, A S

    2002-01-01

    The review emphasizes the essentiality of mitochondrial oxidative metabolism for photosynthetic carbon assimilation. Photosynthetic activity in chloroplasts and oxidative metabolism in mitochondria interact with each other and stimulate their activities. During light, the partially modified TCA cycle supplies oxoglutarate to cytosol and chloroplasts. The marked stimulation of O2 uptake after few minutes of photosynthetic activity, termed as light enhanced dark respiration (LEDR), is now a well-known phenomenon. Both the cytochrome and alternative pathways of mitochondrial electron transport are important in such interactions. The function of chloroplast is optimized by the complementary nature of mitochondrial metabolism in multiple ways: facilitation of export of excess reduced equivalents from chloroplasts, shortening of photosynthetic induction, maintenance of photorespiratory activity, and supply of ATP for sucrose biosynthesis as well as other cytosolic needs. Further, the mitochondrial oxidative electron transport and phosphorylation also protects chloroplasts against photoinhibition. Besides mitochondrial respiration, reducing equivalents (and ATP) are used for other metabolic phenomena, such as sulfur or nitrogen metabolism and photorespiration. These reactions often involve peroxisomes and cytosol. The beneficial interaction between chloroplasts and mitochondria therefore extends invariably to also peroxisomes and cytosol. While the interorganelle exchange of metabolites is the known basis of such interaction, further experiments are warranted to identify other biochemical signals between them. The uses of techniques such as on-line mass spectrometric measurement, novel mutants/transgenics, and variability in metabolism by growth conditions hold a high promise to help the plant biologist to understand this PMID:12027265

  20. Preliminary studies on the evolution of carbon assimilation abilities within Mucorales.

    PubMed

    Pawłowska, Julia; Aleksandrzak-Piekarczyk, Tamara; Banach, Agnieszka; Kiersztyn, Bartosz; Muszewska, Anna; Serewa, Lidia; Szatraj, Katarzyna; Wrzosek, Marta

    2016-05-01

    Representatives of Mucorales belong to one of the oldest lineages of terrestrial fungi. Although carbon is of fundamental importance for fungal growth and functioning, relatively little is known about enzymatic capacities of Mucorales. The evolutionary history and the variability of the capacity to metabolize different carbon sources among representatives of the order Mucorales was studied using Phenotypic Microarray Plates. The ability of 26 strains belonging to 23 nonpathogenic species of Mucorales to use 95 different carbon sources was tested. Intraspecies variability of carbon assimilation profiles was lower than interspecies variation for some selected strains. Although similarities between the phylogenetic tree and the dendrogram created from carbon source utilization data were observed, the ability of the various strains to use the analyzed substrates did not show a clear correlation with the evolutionary history of the group. Instead, carbon assimilation profiles are probably shaped by environmental conditions. PMID:27109371

  1. CUMULATE ROCKS ASSOCIATED WITH CARBONATE ASSIMILATION, HORTAVÆR COMPLEX, NORTH-CENTRAL NORWAY

    NASA Astrophysics Data System (ADS)

    Barnes, C. G.; Prestvik, T.; Li, Y.

    2009-12-01

    The Hortavær igneous complex intruded high-grade metamorphic rocks of the Caledonian Helgeland Nappe Complex at ca. 466 Ma. The complex is an unusual mafic-silicic layered intrusion (MASLI) because the principal felsic rock type is syenite and because the syenite formed in situ rather than by deep-seated partial melting of crustal rocks. Magma differentiation in the complex was by assimilation, primarily of calc-silicate rocks and melts with contributions from marble and semi-pelites, plus fractional crystallization. The effect of assimilation of calcite-rich rocks was to enhance stability of fassaitic clinopyroxene at the expense of olivine, which resulted in alkali-rich residual melts and lowering of silica activity. This combination of MASLI-style emplacement and carbonate assimilation produced three types of cumulate rocks: (1) Syenitic cumulates formed by liquid-crystal separation. As sheets of mafic magma were loaded on crystal-rich syenitic magma, residual liquid was expelled, penetrating the overlying mafic sheets in flame structures, and leaving a cumulate syenite. (2) Reaction cumulates. Carbonate assimilation, illustrated by a simple assimilation reaction: olivine + calcite + melt = clinopyroxene + CO2 resulted in cpx-rich cumulates such as clinopyroxenite, gabbro, and mela-monzodiorite, many of which contain igneous calcite. (3) Magmatic skarns. Calc-silicate host rocks underwent partial melting during assimilation, yielding a Ca-rich melt as the principal assimilated material and permitting extensive reaction with surrounding magma to form Kspar + cpx + garnet-rich ‘cumulate’ rocks. Cumulate types (2) and (3) do not reflect traditional views of cumulate rocks but instead result from a series of melt-present discontinuous (peritectic) reactions and partial melting of calc-silicate xenoliths. In the Hortavær complex, such cumulates are evident because of the distinctive peritectic cumulate assemblages. It is unclear whether assimilation of

  2. 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.

  3. Regulation of Sulfate Assimilation by Nitrogen Nutrition in the Duckweed Lemna minor L. 1

    PubMed Central

    Brunold, Christian; Suter, Marianne

    1984-01-01

    The effect of nitrate and ammonium on the extractable activity of two enzymes of assimilatory sulfate reduction, ATP sulfurylase (EC 2.7.7.4) and adenosine 5′-phosphosulfate sulfotransferase (APSSTase), was examined in Lemna minor L. cultivated under steady state conditions. Nitrate reductase (EC 1.6.6.1) was measured for comparison. Low nitrate concentrations (0.2 and 0.04 millimolar) caused a decrease in the specific activity of all three enzymes measured. Twenty-four hours after transfer to medium without a nitrogen source, the specific activity of APSSTase and nitrate reductase was at less than 30% of the original level, whereas ATP sulfurylase was still at about 80%. NH4+ added to the nutrient solution caused a 50 to 100% increase in the specific activity of APSSTase within 24 hours, followed by a slow decrease. After 72 hours with NH4+, the specific activity was still 25% higher than originally. During the same period, the extractable protein increased by 30% on a fresh weight basis, and total protein by 55 to 60%. Nitrate reductase activity decreased to less than 5%. After omission of NH4+ from the nutrient solution extractable APSSTase activity rapidly decreased to the level of cultures with NO3− as a nitrogen source. Using [35S]SO42− as a sulfur source, an increased incorporation of label into the protein fraction could be detected when NH4+ was added to the nutrient solution. This indicated that more sulfate was assimilated and used for protein synthesis. The higher extractable activity of APSSTase with NH4+ may be a regulatory mechanism involved in the formation of sufficient sulfur amino acids during a period of increased protein synthesis. PMID:16663886

  4. 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

  5. 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.

  6. 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.

  7. 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. PMID:26945700

  8. 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; Lenzen, Allen; Stobie, James; Johnson, Donald; Avery, Melody A.; Sachse, Glen W.; Thompson, Anne; Cohen, Ron; Dibb, Jack E.; Crawford, James H.; Rault, Didier F.; Martin, Randall; Szykman, James J.; Fishman, Jack

    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.

  9. 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...

  10. 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.

  11. 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

  12. Carbon and nitrogen dynamics in the rhizosphere of Pinus ponderosa seedlings

    SciTech Connect

    Norton, J.M.

    1991-01-01

    The rhizosphere is a dynamic soil region characterized by dense microbial populations and enhanced rates of microbial processes. The rhizosphere may be especially important in determinign the spatial distribution of carbon and nitrogen cycling in forest soils. The author has investigated the flow of carbon from roots to the soil, the quantity and metabolic status of bacteria and fungi, and the production and consumption of inorganic nitrogen in the rhizosphere of Pinus ponderosa seedlings. The role of plant/microbial competition for inorganic nitrogen in determining the availability of nitrogen to plant assimilation was assessed. The author examined the flow of recently fixed photosynthate from roots to the soil using a [sup 14]C pulse-labelling technique. The highest concentration of recently fixed photosynthate carbon in the soil was adjacent to the young root tip region. Fine mycorrhizal roots had the highest rate of carbon loss to the soil per unit carbon assimilated by the root. Mycorrhizal hyphae played an important role in the redistribution of recently fixed photosynthate throughout the soil. The input of plant carbon to the soil by rhizodeposition was an important energy source for the microbial community even in soil not directly adjacent to the root. In short-term [sup 15]N experiments, the author observed that rates of mineralization and NH[sub 4][sup +] immobilization were higher in soils harvested from adjacent to roots than in soils harvested from greater than 5 mm from any root. Results from intact microcosms suggest that NH[sub 4][sup +] supply and competition between roots, heterotrophs and nitrifiers for NH[sub 4][sup +] were the direct controls on NH[sub 4][sup +] immobilization rates rather than the supply of, recently fixed carbon by rhizodeposition. Plants were more successful competitors for NH[sub 3][sup [minus

  13. 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.

  14. Differentiation of Corynebacterium amycolatum, C. minutissimum, and C. striatum by carbon substrate assimilation tests.

    PubMed

    Renaud, F N; Dutaur, M; Daoud, S; Aubel, D; Riegel, P; Monget, D; Freney, J

    1998-12-01

    We tested the carbon substrate assimilation patterns of 40 Corynebacterium amycolatum strains, 19 C. minutissimum strains, 50 C. striatum strains, and 1 C. xerosis strain with the Biotype 100 system (bioMérieux, Marcy-l'Etoile, France). Twelve carbon substrates of 99 allowed discrimination among the species tested. Additionally, assimilation of 3 of these 12 carbon substrates (maltose, N-acetyl-D-glucosamine, and phenylacetate) was tested with the API 20 NE identification system (bioMérieux). Since concordant results were observed with the two systems for these three carbon substrates, either identification system can be used as a supplementary tool to achieve phenotypic differential identification of C. amycolatum, C. minutissimum, and C. striatum in the clinical microbiology laboratory. PMID:9817901

  15. 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

  16. 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.

  17. 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. PMID:25684321

  18. 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

  19. 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.

  20. 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. PMID:23959165

  1. Controls of Climate Anomalies on Terrestrial Carbon Assimilation in East Asia

    NASA Astrophysics Data System (ADS)

    Choi, G.; Kang, S.

    2010-12-01

    Understanding of feedback between climate system and terrestrial ecosystems is of importance to an accurate estimation of global carbon partitioning and cycles in the warmer climate with more anthropogenic carbon in the atmosphere. In this study, a method to improve terrestrial carbon assimilation data, estimated from cloud-contaminated Moderate-Resolution Imaging Spectroradiometer (MODIS) imagery, is suggested and potential associations between inter-annual or intra-annual climate anomalies and carbon assimilation by terrestrial ecosystems in East Asia are examined based on the improved MODIS data. The negative anomalies of Net Primary Productivity (NPP) in 2004 are attributable to reduced solar radiation in northern East Asia, while droughts are responsible for the similar reduction in the NPP in subtropical East Asia. The impacts of seasonal climate anomalies and extreme climatic events on intra-annual variations of terrestrial carbon assimilation in monsoonal East Asia will also be discussed. Acknowledgement: This work was funded by the Korea Meteorological Administration Research and Development Program under Grant RACS 2010-4014.

  2. 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.

  3. Long-term ferrocyanide application via deicing salts promotes the establishment of Actinomycetales assimilating ferrocyanide-derived carbon in soil.

    PubMed

    Gschwendtner, Silvia; Mansfeldt, Tim; Kublik, Susanne; Touliari, Evangelia; Buegger, Franz; Schloter, Michael

    2016-07-01

    Cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. As degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. However, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. The question remains if biodegradation in soils can occur without previous photolysis. By conducting a microcosm experiment using soils with/without pre-exposition to road salts spiked with (13) C-labelled ferrocyanide, we were able to confirm biodegradation and in parallel to identify bacteria using ferrocyanide as C source via DNA stable isotope probing (DNA-SIP), TRFLP fingerprinting and pyrosequencing. Bacteria assimilating (13) C were highly similar in the pre-exposed soils, belonging mostly to Actinomycetales (Kineosporia, Mycobacterium, Micromonosporaceae). In the soil without pre-exposition, bacteria belonging to Acidobacteria (Gp3, Gp4, Gp6), Gemmatimonadetes (Gemmatimonas) and Gammaproteobacteria (Thermomonas, Xanthomonadaceae) used ferrocyanide as C source but not the present Actinomycetales. This indicated that (i) various bacteria are able to assimilate ferrocyanide-derived C and (ii) long-term exposition to ferrocyanide applied with deicing salts leads to Actinomycetales outcompeting other microorganisms for the use of ferrocyanide as C source. PMID:27194597

  4. CARBON AND NITROGEN METABOLISM IN LEGUME NODULES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Symbiotic root nodules are in essence highly integrated factories for C utilization and N assimilation. Significant progress has been made in physical, biochemical, and molecular characterization of the primary enzymes involved in C utilization and amide N assimilation. Recent advances in genomic me...

  5. 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. PMID:24122235

  6. RuBP limitation of photosynthetic carbon fixation during NH sub 3 assimilation: Interactions between photosynthesis, respiration, and ammonium assimilation in N-limited green algae

    SciTech Connect

    Elrifi, I.R.; Holmes, J.J.; Weger, H.G.; Mayo, W.P.; Turpin, D.H. )

    1988-06-01

    The effects of ammonium assimilation on photosynthetic carbon fixation and O{sub 2} exchange were examined in two species of N-limited green algae, Chlorella pyrenoidosa and Selenastrum minutum. Under light-saturating conditions, ammonium assimilation resulted in a suppression of photosynthetic carbon fixation by S. minutum but not by C. pyrenoidosa. These different responses are due to different relationships between cellular ribulose bisphosphate (RuBP) concentration and the RuBP binding site density of ribulose bisphosphate carboxylase/oxygenase (Rubisco). In both species, ammonium assimilation resulted in a decrease in RuBP concentration. In S. minutum the concentration fell below the RuBP binding site density of Rubisco, indicating RuBP limitation of carboxylation. In contrast, RuBP concentration remained above the binding site density in C. pyrenoidosa. Compromising RuBP regeneration in C. pyrenoidosa with low light resulted in an ammonium-induced decrease in RuBP concentration below the RuBP binding site density of Rubisco. This resulted in a decrease in photosynthetic carbon fixation. In both species, ammonium assimilation resulted in a larger decrease in net O{sub 2} evolution than in carbon fixation. Mass spectrometric analysis shows this to be a result of an increase in the rate of mitochondrial respiration in the light.

  7. 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. PMID:25775555

  8. 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

  9. 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.

  10. Phosphoenolpyruvate Carboxylase in Arabidopsis Leaves Plays a Crucial Role in Carbon and Nitrogen Metabolism1

    PubMed Central

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

    2015-01-01

    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. PMID:25588735

  11. 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.

  12. 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

  13. Genetic variation in circadian regulation of nocturnal stomatal conductance enhances carbon assimilation and growth.

    PubMed

    Resco de Dios, Víctor; Loik, Michael E; Smith, Renee; Aspinwall, Michael J; Tissue, David T

    2016-01-01

    Circadian resonance, whereby a plant's endogenous rhythms are tuned to match environmental cues, has been repeatedly shown to be adaptive, although the underlying mechanisms remain elusive. Concomitantly, the adaptive value of nocturnal transpiration in C3 plants remains unknown because it occurs without carbon assimilation. These seemingly unrelated processes are interconnected because circadian regulation drives temporal patterns in nocturnal stomatal conductance, with maximum values occurring immediately before dawn for many species. We grew individuals of six Eucalyptus camaldulensis genotypes in naturally lit glasshouses and measured sunset, predawn and midday leaf gas exchange and whole-plant biomass production. We tested whether sunrise anticipation by the circadian clock and subsequent increases in genotype predawn stomatal conductance led to rapid stomatal opening upon illumination, ultimately affecting genotype differences in carbon assimilation and growth. We observed faster stomatal responses to light inputs at sunrise in genotypes with higher predawn stomatal conductance. Moreover, early morning and midday stomatal conductance and carbon assimilation, leaf area and total plant biomass were all positively correlated with predawn stomatal conductance across genotypes. Our results lead to the novel hypothesis that genotypic variation in the circadian-regulated capacity to anticipate sunrise could be an important factor underlying intraspecific variation in tree growth. PMID:26147129

  14. Multi-model terrestrial and oceanic carbon exchange estimates from data assimilation in GEOCARBON

    NASA Astrophysics Data System (ADS)

    van der Laan-Luijkx, I.; Peters, W.; Peylin, P.; Dolman, A. J.; Gerbig, C.; Zaehle, S.; Rödenbeck, C.; Schürmann, G. J.; Scholze, M.; Kaminski, T.; Williams, M. D.; Bloom, A. A.; Toque, N.; Dobricic, S.; Vichi, M.; Masina, S.; Bertino, L.; Heinze, C.; Gloor, E.

    2012-12-01

    The European Union FP7 project GEOCARBON aims to synthesize existing observations, data products, and models that inform on the recent carbon balance of the oceans and terrestrial biosphere. One of its components specifically employs data assimilation techniques to optimally combine observations and process models. To capture the large range of carbon exchange estimates that is often possible within the limited observational constraints, a wide variety of methods and models is included in GEOCARBON. A significant effort is made to quantitatively assess the outcome of each data assimilation system, to identify robust features across methods, and to synthesize multi-model results into a final estimate of land and ocean carbon exchange, and its uncertainty. We will present the first results from data assimilation of a variety of observations (atmospheric CO2 mole fractions, surface ocean pCO2, ocean chlorophyll, biomass surveys, and eddy-covariance CO2 fluxes) in a variety of systems (atmospheric inversions, biosphere model optimizations, ocean CCDAS) using a variety of techniques (4dVar, ensemble kalman filtering). Our first analyses will focus on independent evaluation of the results and quantification of the uncertainties on our estimates.

  15. 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.

  16. Interactive effects of nitrogen deposition and insect herbivory on carbon and nitrogen dynamics: Results from CENTURY

    NASA Astrophysics Data System (ADS)

    Throop, H. L.; Holland, E. A.; Parton, W. J.; Ojima, D. S.; Keough, C.

    2002-12-01

    The direct effects of nitrogen deposition on nutrient availability in ecosystems have been well studied, however, little is known about the indirect effects of nitrogen deposition on insect herbivory and subsequent changes to ecosystem processes. Numerous empirical studies have demonstrated that host plant nitrogen concentration can strongly affect individual insect consumption rates and population dynamics. We used the CENTURY ecosystem model to explore how interactions between nitrogen deposition and insect herbivory might affect plant production and the pools and fluxes of carbon and nitrogen in an old field community. We modified the preexisting CENTURY mammalian grazing functions to reflect patterns of insect herbivory. Vegetative tissue loss to herbivores was modeled as a dynamic function based on the carbon to nitrogen ratio of aboveground vegetation. Parameterization of the plant response to nitrogen and herbivory was based on field data collected on Ambrosia artemisiifolia (common ragweed, Asteraceae). The modeled response to nitrogen deposition included a strong increase in plant production, decreased plant C:N ratios, and increased soil organic carbon pools. Insect herbivory alone generally caused depressed aboveground production, decreased soil organic carbon pools, and decreased nitrogen mineralization rates. These relationships broke down, however, under moderate nitrogen deposition loads (over 30 kg N ha-1 yr-1) in simulations where insect herbivory increased in response to declining plant C:N. In these cases, herbivory acted to depress the positive influence of nitrogen deposition on carbon storage in soil and vegetative pools and caused strong increases in nitrogen mineralization rates. The results of these simulations suggest that herbivory may play an increasingly important role in affecting ecosystem processes under conditions of high nitrogen deposition. Including effects of herbivory in ecosystem analyses, particularly in systems where rates

  17. 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

    2016-03-01

    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. PMID:26877080

  18. Movement of carbon among estuarine habitats and its assimilation by invertebrates.

    PubMed

    Connolly, Rod M; Gorman, Daniel; Guest, Michaela A

    2005-08-01

    We measured the extent of movement of carbon and its assimilation by invertebrates among estuarine habitats by analysing carbon stable isotopes of invertebrates collected along transects crossing the boundary of two habitats. The habitats were dominated by autotrophs with distinct isotope values: (1) mudflats containing benthic microalgae (mean -22.6, SE 0.6 per thousand) and (2) seagrass and its associated epiphytic algae (similar values, pooled mean -9.8, 0.5 per thousand). Three species of invertebrates were analysed: a palaemonid shrimp, Macrobrachium intermedium, and two polychaete worms, Nephtys australiensis and Australonereis ehlersi. All species had a similar narrow range of isotope values (-9 to -14 per thousand), and showed no statistically significant relationship between position along transect and isotope values. Animals were relying on carbon from seagrass meadows whether they were in seagrass or on mudflats hundreds of metres away. Particulate organic matter collected from superficial sediments along the transects had similar values to animals (mean -11.1, SE 1.3 per thousand) and also showed no significant relationship with position. The isotope values of these relatively immobile invertebrates and the particulate detritus suggest that carbon moves from subtidal seagrass meadows to mudflats as particulate matter and is assimilated by invertebrates. This assimilation might be direct in the case of the detritivorous worm, A. ehlersi, but must be via invertebrate prey in the case of the carnivorous worm, N. australiensis and the scavenging shrimp, M. intermedium. The extent of movement of carbon among habitats, especially towards shallower habitats, is surprising since in theory, carbon is more likely to move offshore in situations such as the current study where habitats are in relatively open, unprotected waters. PMID:16001216

  19. Coevolution of metal availability and nitrogen assimilation in cyanobacteria and algae.

    PubMed

    Glass, J B; Wolfe-Simon, F; Anbar, A D

    2009-03-01

    Marine primary producers adapted over eons to the changing chemistry of the oceans. Because a number of metalloenzymes are necessary for N assimilation, changes in the availability of transition metals posed a particular challenge to the supply of this critical nutrient that regulates marine biomass and productivity. Integrating recently developed geochemical, biochemical, and genetic evidence, we infer that the use of metals in N assimilation - particularly Fe and Mo - can be understood in terms of the history of metal availability through time. Anoxic, Fe-rich Archean oceans were conducive to the evolution of Fe-using enzymes that assimilate abiogenic NH(4)(+) and NO(2)(-). The N demands of an expanding biosphere were satisfied by the evolution of biological N(2) fixation, possibly utilizing only Fe. Trace O(2) in late Archean environments, and the eventual 'Great Oxidation Event' c. 2.3 Ga, mobilized metals such as Mo, enabling the evolution of Mo (or V)-based N(2) fixation and the Mo-dependent enzymes for NO(3)(-) assimilation and denitrification by prokaryotes. However, the subsequent onset of deep-sea euxinia, an increasingly-accepted idea, may have kept ocean Mo inventories low and depressed Fe, limiting the rate of N(2) fixation and the supply of fixed N. Eukaryotic ecosystems may have been particularly disadvantaged by N scarcity and the high Mo requirement of eukaryotic NO(3)(-) assimilation. Thorough ocean oxygenation in the Neoproterozoic led to Mo-rich oceans, possibly contributing to the proliferation of eukaryotes and thus the Cambrian explosion of metazoan life. These ideas can be tested by more intensive study of the metal requirements in N assimilation and the biological strategies for metal uptake, regulation, and storage. PMID:19320747

  20. Photosynthetic electron transport controls nitrogen assimilation in cyanobacteria by means of posttranslational modification of the glnB gene product.

    PubMed Central

    Tsinoremas, N F; Castets, A M; Harrison, M A; Allen, J F; Tandeau de Marsac, N

    1991-01-01

    A glnB gene is identified in the cyanobacterium Synechococcus sp. PCC 7942, and its gene product is found to be covalently modified as a result of imbalance in electron transfer in photosynthesis, where photosystem II is favored over photosystem I. The gene was cloned and sequenced and found to encode a polypeptide of 112 amino acid residues, whose sequence shows a high degree of similarity to the Escherichia coli regulatory protein, PII. In E. coli, PII is involved in signal transduction in transcriptional and post-translational regulation of nitrogen assimilation. Increase in ammonium ion concentration is shown to decrease covalent modification of the Synechococcus PII protein, as in enteric bacteria. We therefore propose that the photosynthetic electron transport chain may regulate the pathway of nitrogen assimilation in cyanobacteria by means of posttranslational, covalent modification of the glnB gene product. The existence of the glnB gene in different strains of cyanobacteria is demonstrated and its implications are discussed. Images PMID:1905010

  1. Multi-Sensor Model-Data Assimilation for Improved Modeling of Savanna Carbon and Water Budgets

    NASA Astrophysics Data System (ADS)

    Barrett, D. J.; Renzullo, L. J.; Guerschman, J.; Hill, M. J.

    2007-12-01

    Model-data assimilation methods are increasingly being used to improve model predictions of carbon pools and fluxes, soil profile moisture contents, and evapotranspiration at catchment to regional scales. In this talk, I will discuss the development of model-data assimilation methods for application to parameter and state estimation problems in the context of savanna carbon and water cycles. A particular focus of this talk will be on the integration of in situ datasets and multiple types of satellite observations with radiative transfer, surface energy balance, and carbon budget models. An example will be drawn from existing work demonstrating regional estimation of soil profile moisture content based on multiple satellite sensors. The data assimilation scheme comprised a forward model, observation operators, multiple observation datasets and an optimization scheme. The forward model propagates model state variables in time based on climate forcing, initial conditions and model parameters and includes processes governing evapotranspiration, water budget and carbon cycle processes. The observation operators calculate modeled land surface temperature and microwave brightness temperatures based on the state variables of profile soil moisture and soil surface layer soil moisture at less than 2.5 cm depth. Satellite observations used in the assimilation scheme are surface brightness temperatures from AMSR-E (passive microwave at 6.9GHz at horizontal polarization) and from AVHRR (thermal channels 4 & 5 from NOAA-18), and land surface reflectances from MODIS Terra (channels 1 and 2 at 250m resolution). These three satellite sensors overpass at approximately the same time of day and provide independent observations of the land surface at different wavelengths. The observed brightness temperatures are used as constraints on the coupled energy balance/microwave radiative transfer model, and a canopy optical model was inverted to retrieve leaf area indices from observed

  2. Carbon- and Nitrogen-Based Organic Frameworks.

    PubMed

    Sakaushi, Ken; Antonietti, Markus

    2015-06-16

    This Account provides an overview of organic, covalent, porous frameworks and solid-state materials mainly composed of the elements carbon and nitrogen. The structures under consideration are rather diverse and cover a wide spectrum. This Account will summarize current works on the synthetic concepts leading toward those systems and cover the application side where emphasis is set on the exploration of those systems as candidates for unusual high-performance catalysis, electrocatalysis, electrochemical energy storage, and artificial photosynthesis. These issues are motivated by the new global energy cycles and the fact that sustainable technologies should not be based on rare and expensive resources. We therefore present the strategic design of functionality in cost-effective, affordable artificial materials starting from a spectrum of simple synthetic options to end up with carbon- and nitrogen-based porous frameworks. Following the synthetic strategies, we demonstrate how the electronic structure of polymeric frameworks can be tuned and how this can modify property profiles in a very unexpected fashion. Covalent triazine-based frameworks (CTFs), for instance, showed both enormously high energy and high power density in lithium and sodium battery systems. Other C,N-based organic frameworks, such as triazine-based graphitic carbon nitride, are suggested to show promising band gaps for many (photo)electrochemical reactions. Nitrogen-rich carbonaceous frameworks, which are developed from C,N-based organic framework strategies, are highlighted in order to address their promising electrocatalytic properties, such as in the hydrogen evolution reaction, oxygen reduction reaction (ORR), and oxygen evolution reaction (OER). With careful design, those materials can be multifunctional catalysts, such as a bifunctional ORR/OER electrocatalyst. Although the majority of new C,N-based materials are still not competitive with the best (usually nonsustainable candidates) for each

  3. 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.

  4. “Variable localization” in an ensemble Kalman filter: Application to the carbon cycle data assimilation

    NASA Astrophysics Data System (ADS)

    Kang, Ji-Sun; Kalnay, Eugenia; Liu, Junjie; Fung, Inez; Miyoshi, Takemasa; Ide, Kayo

    2011-05-01

    In ensemble Kalman filter, space localization is used to reduce the impact of long-distance sampling errors in the ensemble estimation of the forecast error covariance. When two variables are not physically correlated, their error covariance is still estimated by the ensemble and, therefore, it is dominated by sampling errors. We introduce a "variable localization" method, zeroing out such covariances between unrelated variables to the problem of assimilating carbon dioxide concentrations into a dynamical model using the local ensemble transform Kalman filter (LETKF) in an observing system simulation experiments (OSSE) framework. A system where meteorological and carbon variables are simultaneously assimilated is used to estimate surface carbon fluxes that are not directly observed. A range of covariance structures are explored for the LETKF, with emphasis on configurations allowing nonzero error covariance between carbon variables and the wind field, which affects transport of atmospheric CO2, but not between CO2 and the other meteorological variables. Such variable localization scheme zeroes out the background error covariance among prognostic variables that are not physically related, thus reducing sampling errors. Results from the identical twin experiments show that the performance in the estimation of surface carbon fluxes obtained using variable localization is much better than that using a standard full covariance approach. The relative improvement increases when the surface fluxes change with time and model error becomes significant.

  5. R2R3-type MYB transcription factor, CmMYB1, is a central nitrogen assimilation regulator in Cyanidioschyzon merolae

    PubMed Central

    Imamura, Sousuke; Kanesaki, Yu; Ohnuma, Mio; Inouye, Takayuki; Sekine, Yasuhiko; Fujiwara, Takayuki; Kuroiwa, Tsuneyoshi; Tanaka, Kan

    2009-01-01

    Plant cells sense environmental nitrogen levels and alter their gene expression accordingly to survive; however, the underlying regulatory mechanisms still remains to be elucidated. Here, we identified and characterized a transcription factor that is responsible for expression of nitrogen assimilation genes in a unicellular red alga Cyanidioschyzon merolae. DNA microarray and Northern blot analyses revealed that transcript of the gene encoding CmMYB1, an R2R3-type MYB transcription factor, increased 1 h after nitrogen depletion. The CmMYB1 protein started to accumulate after 2 h and reached a peak after 4 h after nitrogen depletion, correlating with the expression of key nitrogen assimilation genes, such as CmNRT, CmNAR, CmNIR, CmAMT, and CmGS. Although the transcripts of these nitrogen assimilation genes were detected in nitrate-grown cells, they disappeared upon the addition of preferred nitrogen source such as ammonium or glutamine, suggesting the presence of a nitrogen catabolite repression (NCR) mechanism. The nitrogen depletion-induced gene expression disappeared in a CmMYB1-null mutant, and the mutant showed decreased cell viability after exposure to the nitrogen-depleted conditions compared with the parental strain. Chromatin immunoprecipitation analysis demonstrated that CmMYB1 specifically occupied these nitrogen-responsive promoter regions only under nitrogen-depleted conditions, and electrophoretic mobility shift assays using crude cell extract revealed specific binding of CmMYB1, or a complex containing CmMYB1, to these promoters. Thus, the presented results indicated that CmMYB1 is a central nitrogen regulator in C. merolae. PMID:19592510

  6. R2R3-type MYB transcription factor, CmMYB1, is a central nitrogen assimilation regulator in Cyanidioschyzon merolae.

    PubMed

    Imamura, Sousuke; Kanesaki, Yu; Ohnuma, Mio; Inouye, Takayuki; Sekine, Yasuhiko; Fujiwara, Takayuki; Kuroiwa, Tsuneyoshi; Tanaka, Kan

    2009-07-28

    Plant cells sense environmental nitrogen levels and alter their gene expression accordingly to survive; however, the underlying regulatory mechanisms still remains to be elucidated. Here, we identified and characterized a transcription factor that is responsible for expression of nitrogen assimilation genes in a unicellular red alga Cyanidioschyzon merolae. DNA microarray and Northern blot analyses revealed that transcript of the gene encoding CmMYB1, an R2R3-type MYB transcription factor, increased 1 h after nitrogen depletion. The CmMYB1 protein started to accumulate after 2 h and reached a peak after 4 h after nitrogen depletion, correlating with the expression of key nitrogen assimilation genes, such as CmNRT, CmNAR, CmNIR, CmAMT, and CmGS. Although the transcripts of these nitrogen assimilation genes were detected in nitrate-grown cells, they disappeared upon the addition of preferred nitrogen source such as ammonium or glutamine, suggesting the presence of a nitrogen catabolite repression (NCR) mechanism. The nitrogen depletion-induced gene expression disappeared in a CmMYB1-null mutant, and the mutant showed decreased cell viability after exposure to the nitrogen-depleted conditions compared with the parental strain. Chromatin immunoprecipitation analysis demonstrated that CmMYB1 specifically occupied these nitrogen-responsive promoter regions only under nitrogen-depleted conditions, and electrophoretic mobility shift assays using crude cell extract revealed specific binding of CmMYB1, or a complex containing CmMYB1, to these promoters. Thus, the presented results indicated that CmMYB1 is a central nitrogen regulator in C. merolae. PMID:19592510

  7. Water dispersible, highly graphitic and nitrogen-doped carbon nanobubbles.

    PubMed

    Soll, Sebastian; Fellinger, Tim-Patrick; Wang, Xinchen; Zhao, Qiang; Antonietti, Markus; Yuan, Jiayin

    2013-12-20

    Dispersible, highly graphitic, and nitrogen-doped carbon hollow nanospheres (25-90 nm), termed 'nanobubbles', are prepared via confined carbonization through a silica nanocasting technique. Poly(ionic liquid) nanoparticles are employed as easy-to-make and multifunctional templates, which simultaneously act as both the carbon and nitrogen source. The promising potential of the nanobubbles in oxygen reduction reactions for fuel cells is demonstrated. PMID:23847129

  8. 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

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    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 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.

  11. The influence of ecosystem nitrogen status on carbon cycling in forests

    NASA Astrophysics Data System (ADS)

    Ollinger, S. V.; Smith, M.; Richardson, A.; Hollinger, D. Y.; Martin, M.; Jenkins, J.

    2006-12-01

    The carbon and nitrogen cycles in terrestrial ecosystems are tightly coupled through a shared set of biological processes. The N status of plant canopies exerts a direct influence on carbon assimilation through its well-known effect on net photosynthesis. In soils, both the accumulation of N and the decay of organic matter are often related to the initial C/N ratio of litterfall. Similarly, respiration rates in both roots and foliage have been shown to be positively correlated with tissue N concentrations. These linkages suggest that the N status of ecosystems may provide a useful indicator of their overall C metabolism. Further, evidence from both CO2 and N enrichment experiments indicates that alteration of one cycle can have important implications for the other. This is significant in that global cycles of both C and N have been greatly perturbed by humans. Despite the well-known influence of nitrogen availability on fluxes of carbon, few studies have explicitly examined the role of nitrogen as it pertains to spatial and temporal variation in carbon cycling. This is due, in part, to limited crossover between different scientific communities, but also stems from some very real methodological limitations that make regional-scale assessment of N status difficult. Here, we report on an NACP investigation that examines the degree to which rates of carbon assimilation and growth in forests can be related to both local and regional variation in ecosystem N status. Field measurements from a series of forested research sites within the AmeriFlux network have been combined with hyperspectral remote sensing data from the AVIRIS and Hyperion instruments. Results from a cross-site synthesis indicate a positive relationship between canopy N and the maximum rate of carbon assimilation, as measured by flux towers. Because existing methods of canopy N detection are restricted to small landscapes, a parallel investigation involves developing generalizeable canopy N detection

  12. 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

  13. 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. PMID:25216023

  14. 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

  15. 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.

  16. 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.

  17. 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. PMID:26865488

  18. 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-.

  19. Relationships between nutrient status, carbon assimilation and water use efficiency in Pinus radiata (D. Don) needles.

    PubMed

    Sheriff, D. W.; Nambiar, E. K. S.; Fife, D. N.

    1986-12-01

    The productivity of Pinus radiata D. Don plantations can be increased on many soils by N and P fertilization. Foliar analyses are usually taken as a guide for nutrient management, but there is little information about the relationship of foliar nutrient status to foliar physiology. This paper provides such information from N and P fertilization experiments. The concentrations and contents of N and P in the needles of P. radiata change because of accumulation during needle growth, retranslocation during shoot growth, and replenishment from current uptake during periods of little shoot growth. Up to 60% P and 50% N may be retranslocated in a single growing season from needles less than one year old. Three years after fertilizer application to a 10-year-old thinned P. radiata stand, net carbon assimilation rate per unit leaf area was in the order NP>P>N. There were positive associations between foliar P and assimilation at full sunlight, diffusive conductance and quantum yield. Foliar N was negatively associated with these variables. Higher concentrations of P and N were both accompanied by higher instantaneous water use efficiency by the foliage. Estimated trends in whole tree assimilation were similar to those in aboveground biomass accumulation. The interplay between the dynamic nature of nutrients in the foliage and their influence on the physiology of needles is discussed. PMID:14975843

  20. 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.

  1. 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.

  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

    2016-05-01

    uc(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. 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

  4. Assimilation of cellulose-derived carbon by microeukaryotes in oxic and anoxic slurries of an aerated soil.

    PubMed

    Chatzinotas, Antonis; Schellenberger, Stefanie; Glaser, Karin; Kolb, Steffen

    2013-09-01

    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-(13)C]cellulose under oxic conditions. A previous study using the same soil suggested that cellulolytic Bacteria assimilated (13)C 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

  5. Unexpected capacity for organic carbon assimilation by Thermosynechococcus elongatus, a crucial photosynthetic model organism.

    PubMed

    Zilliges, Yvonne; Dau, Holger

    2016-04-01

    Genetic modification of key residues of photosystems is essential to identify functionally crucial processes by spectroscopic and crystallographic investigation; the required protein stability favours use of thermophilic species. The currently unique thermophilic photosynthetic model organism is the cyanobacterial genus Thermosynechococcus. We report the ability of Thermosynechococcus elongatus to assimilate organic carbon, specifically D-fructose. Growth in the presence of a photosynthesis inhibitor opens the door towards crucial amino acid substitutions in photosystems by the rescue of otherwise lethal mutations. Yet depression of batch-culture growth after 7 days implies that additional developments are needed. PMID:26935247

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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. PMID:26706056

  13. 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. PMID:26494284

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

    PubMed Central

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

    2015-01-01

    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 NH4+ 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. PMID:26494284

  15. 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

  16. 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

  17. 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. PMID:25958969

  18. 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.

  19. 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.

  20. [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. PMID:12682972

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

    NASA Astrophysics Data System (ADS)

    Safta, C.; Ricciuto, D. M.; Sargsyan, K.; Debusschere, B.; Najm, H. N.; Williams, M.; Thornton, P. 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.

  3. CARBON EFFECTS ON NITROGEN RETENTION AND NITROGEN TRANSFORMING MICROBIAL POPULATIONS

    EPA Science Inventory

    Approach: A factorial design with three levels of ammonium chloride (0, 100 and 1000 kg N/ha), and two forms of carbon (glucose and tannic acid), each with three levels (0, 100 and 1000 kg C/ha) has been replicated three times at each of two old-field sites in southeastern Oklah...

  4. 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.

  5. 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

  6. Rootstock and Vineyard Floor Management Influence on 'Cabernet Sauvignon' Grape Yeast Assimilable Nitrogen (YAN)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This is a study on the influence two rootstocks (110R, high vigor; 420A, low vigor) and three vineyard floor management regimes (tilled resident vegetation – usual practice in California, and barley cover crops that were either mowed or tilled) had upon grape nitrogen containing compounds (mainly am...

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

    DOEpatents

    Huynh, My Hang V.; Hiskey, Michael A.

    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.

  9. 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., III; 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.

  10. 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

  11. Cadmium tolerance of carbon assimilation enzymes and chloroplast in Zn/Cd hyperaccumulator Picris divaricata.

    PubMed

    Ying, Rong-Rong; Qiu, Rong-Liang; Tang, Ye-Tao; Hu, Peng-Jie; Qiu, Hao; Chen, Hong-Ru; Shi, Tai-Hong; Morel, Jean-Louis

    2010-01-15

    To better understand the photosynthesis under stress, the effect of cadmium on carbon assimilation and chloroplast ultrastructure of a newly found Zn/Cd hyperaccumulator Picris divaricata in China was investigated in solution culture. The shoot and root Cd concentrations increased with increase in Cd supply, reaching maxima of 1109 and 5604mgkg(-1) dry weight at 75microM Cd, respectively. As Cd supply to P. divaricata increased, the shoot and root dry weight, leaf water content (except 75microM Cd), concentrations of chlorophyll a and b, chlorophyll a/b ratio and the concentration of carotenoids were not depressed at high Cd. However, the stomatal conductance, transpiration rate, net photosynthetic rate and intercellular CO(2) concentration were significantly affected when the Cd concentration reached 10, 10, 25 and 75microM, respectively. Meanwhile, carbonic anhydrase (CA; EC 4.2.1.1) activity and Rubisco (EC 4.1.1.39) content reached maxima in the presence of 50 and 5microM Cd, respectively. In addition, CA activity correlated positively with shoot Cd in plants treated with Cd at a range of 0-50microM. Moreover, the activities of NADP(+)-glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.13), Rubisco and fructose-1, 6-bisphosphatase (EC 3.1.3.11) were not significantly suppressed by increased Cd supply. Although the mesophyll cell size was reduced, chloroplast ultrastructure remained intact at the highest Cd treatment. Our finding revealed that P. divaricata chloroplast and the enzymes of carbon assimilation tolerate high levels of Cd, demonstrating its potential in possible application in phytoremediation. PMID:19683362

  12. 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

  13. 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

  14. 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.

  15. Nitrogen Oxyanion-dependent Dissociation of a Two-component Complex That Regulates Bacterial Nitrate Assimilation*

    PubMed Central

    Luque-Almagro, Victor M.; Lyall, Verity J.; Ferguson, Stuart J.; Roldán, M. Dolores; Richardson, David J.; Gates, Andrew J.

    2013-01-01

    Nitrogen is an essential nutrient for growth and is readily available to microbes in many environments in the form of ammonium and nitrate. Both ions are of environmental significance due to sustained use of inorganic fertilizers on agricultural soils. Diverse species of bacteria that have an assimilatory nitrate/nitrite reductase system (NAS) can use nitrate or nitrite as the sole nitrogen source for growth when ammonium is limited. In Paracoccus denitrificans, the pathway-specific two-component regulator for NAS expression is encoded by the nasT and nasS genes. Here, we show that the putative RNA-binding protein NasT is a positive regulator essential for expression of the nas gene cluster (i.e. nasABGHC). By contrast, a nitrogen oxyanion-binding sensor (NasS) is required for nitrate/nitrite-responsive control of nas gene expression. The NasS and NasT proteins co-purify as a stable heterotetrameric regulatory complex, NasS-NasT. This protein-protein interaction is sensitive to nitrate and nitrite, which cause dissociation of the NasS-NasT complex into monomeric NasS and an oligomeric form of NasT. NasT has been shown to bind the leader RNA for nasA. Thus, upon liberation from the complex, the positive regulator NasT is free to up-regulate nas gene expression. PMID:24005668

  16. 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. PMID:27387802

  17. Nitrogen, Carbon, and Sulfur Metabolism in Natural Thioploca Samples

    PubMed Central

    Otte, Sandra; Kuenen, J. Gijs; Nielsen, Lars P.; Paerl, Hans W.; Zopfi, Jakob; Schulz, Heide N.; Teske, Andreas; Strotmann, Bettina; Gallardo, Victor A.; Jørgensen, Bo B.

    1999-01-01

    Filamentous sulfur bacteria of the genus Thioploca occur as dense mats on the continental shelf off the coast of Chile and Peru. Since little is known about their nitrogen, sulfur, and carbon metabolism, this study was undertaken to investigate their (eco)physiology. Thioploca is able to store internally high concentrations of sulfur globules and nitrate. It has been previously hypothesized that these large vacuolated bacteria can oxidize sulfide by reducing their internally stored nitrate. We examined this nitrate reduction by incubation experiments of washed Thioploca sheaths with trichomes in combination with 15N compounds and mass spectrometry and found that these Thioploca samples produce ammonium at a rate of 1 nmol min−1 mg of protein−1. Controls showed no significant activity. Sulfate was shown to be the end product of sulfide oxidation and was observed at a rate of 2 to 3 nmol min−1 mg of protein−1. The ammonium and sulfate production rates were not influenced by the addition of sulfide, suggesting that sulfide is first oxidized to elemental sulfur, and in a second independent step elemental sulfur is oxidized to sulfate. The average sulfide oxidation rate measured was 5 nmol min−1 mg of protein−1 and could be increased to 10.7 nmol min−1 mg of protein−1 after the trichomes were starved for 45 h. Incorporation of 14CO2 was at a rate of 0.4 to 0.8 nmol min−1 mg of protein−1, which is half the rate calculated from sulfide oxidation. [2-14C]acetate incorporation was 0.4 nmol min−1 mg of protein−1, which is equal to the CO2 fixation rate, and no 14CO2 production was detected. These results suggest that Thioploca species are facultative chemolithoautotrophs capable of mixotrophic growth. Microautoradiography confirmed that Thioploca cells assimilated the majority of the radiocarbon from [2-14C]acetate, with only a minor contribution by epibiontic bacteria present in the samples. PMID:10388716

  18. Canopy carbon net assimilation of an urban, naturally assembled brownfield forest

    NASA Astrophysics Data System (ADS)

    Schafer, K. V.; Wadhwa, S.; Tripathee, R.; Gallagher, F. J.

    2010-12-01

    In this study, we have been investigating an urban brownfield at Liberty State Park that has been abandoned approximately for 40 years. Natural colonization has taken place that allowed a pioneer forest to grow with primarily Betula populifera and Populus spec. Despite soil metal contamination this urban forest exhibits moderate annual productivity and serves as a carbon sink. Diameters at breast height (DBH, 1.35 m above ground) of all trees in a study plot were measured. Aboveground biomass equations were determined for both species through destructive sampling. Aboveground net primary production was about 770 gC m-2 a-1 in 2009. Canopy net assimilation (AnC) was modeled with the canopy conductance constrained assimilation (4CA) model using measured sapflux derived conductance and photosynthetic parameters measured with a LICOR 6400. Annual AnC in 2009 was approximately 1500 gC m-2 a-1 thus with a partitioning of biomass and respiration in the same range of most natural forest with less anthropogenic induced stress. Urban brownfields thus can serve as C sinks and provide phytostabilization of contaminants.

  19. Evaluation and simplification of the assimilable organic carbon nutrient bioassay for bacterial growth in drinking water.

    PubMed

    Kaplan, L A; Bott, T L; Reasoner, D J

    1993-05-01

    A modified assimilable organic carbon (AOC) bioassay is proposed. We evaluated all aspects of the AOC bioassay technique, including inoculum, incubation water, bioassay vessel, and enumeration technique. Other concerns included eliminating the need to prepare organic carbon-free glassware and minimizing the risks of bacterial and organic carbon contamination. Borosilicate vials (40 ml) with Teflon-lined silicone septa are acceptable incubation vessels. Precleaned vials are commercially available, and the inoculum can be injected directly through the septa. Both bioassay organisms, Pseudomonas fluorescens P-17 and Spirillum sp. strain NOX, are available from the American Type Culture Collection and grow well on R2A agar, making this a convenient plating medium. Turbid raw waters need to be filtered prior to an AOC analysis. Glass fiber filters used with either a peristaltic pump or a syringe-type filter holder are recommended for this purpose. A sampling design that emphasizes replication of the highest experimental level, individual batch cultures, is the most efficacious way to reduce the total variance associated with the AOC bioassay. Quality control for the AOC bioassay includes an AOC blank and checks for organic carbon limitation and inhibition of the bioassay organisms. PMID:8517748

  20. 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.

  1. Acetate Dissimilation and Assimilation in Mycobacterium tuberculosis Depend on Carbon Availability

    PubMed Central

    Rücker, Nadine; Billig, Sandra; Bücker, René; Jahn, Dieter; Wittmann, Christoph

    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

  2. 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

  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. Eutectic Syntheses of Graphitic Carbon with High Pyrazinic Nitrogen Content.

    PubMed

    Fechler, Nina; Zussblatt, Niels P; Rothe, Regina; Schlögl, Robert; Willinger, Marc-Georg; Chmelka, Bradley F; Antonietti, Markus

    2016-02-10

    Mixtures of phenols/ketones and urea show eutectic behavior upon gentle heating. These mixtures possess liquid-crystalline-like phases that can be processed. The architecture of phenol/ketone acts as structure-donating motif, while urea serves as melting-point reduction agent. Condensation at elevated temperatures results in nitrogen-containing carbons with remarkably high nitrogen content of mainly pyrazinic nature. PMID:26178584

  5. 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.

  6. 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.

  7. 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

  8. 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. PMID:27372113

  9. [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. PMID:27506038

  10. Bioelectrochemical conversion of urea to nitrogen using aminated carbon electrode.

    PubMed

    Watanabe, Hiroaki; Nishi, Hideki; Hamana, Hiroshi; Sekioka, Naoyuki; Wang, Xiuyun; Uchiyama, Shunichi

    2009-01-01

    Urea decomposes to ammonia and carbon dioxide via carbamic acid, and amine groups can be introduced to the glassy carbon electrode surface during the electrode oxidation of carbamic acid. This modified carbon electrode has excellent catalytic activity of the oxidation of carbamic acid, and can be used to electrooxidize urea by combining urease reaction and electrode oxidation. We found that nitrogen gas is finally produced by the carbamic acid produced from urea. The production of nitrogen was confirmed by gas chromatography-mass spectrometry, and fragment pattern of hydrazine was also detected in the electrolyzed solution of urea. We intend to describe new electrochemical conversion system of urea to harmless nitrogen gas. The electrode oxidation current of urea was decreased by addition of radical trapping agent such as DMPO (5,5-dimethyl-1-pyrroline N-oxide), and this fact suggests that carbamic acid radical couples to form nitrogen-nitrogen bond, and this dimer is oxidized to nitrogen. The electrode oxidation current of urea became larger when oxygen was removed. This fact indicates that the intermediate species (probably hydrazine) produced by the electrolysis is oxidized by not only electrode reaction but also oxygen. PMID:25084444

  11. Assimilable organic carbon (AOC) in soil water extracts using Vibrio Harveyi BB721 and its implication for microbial biomass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  12. 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...

  13. tert-Butanesulfinamides as Nitrogen Nucleophiles in Carbon-Nitrogen Bond Forming Reactions.

    PubMed

    Ramirez Hernandez, Johana; Chemla, Fabrice; Ferreira, Franck; Jackowski, Olivier; Oble, Julie; Perez-Luna, Alejandro; Poli, Giovanni

    2016-01-01

    The use of tert-butanesulfinamides as nitrogen nucleophiles in carbon-nitrogen bond forming reactions is reviewed. This field has grown in the shadow of the general interest in N-tert-butanesulfinyl imines for asymmetric synthesis and occupies now an important place in its own right in the chemistry of the chiral amine reagent tert-butanesulfinamide. This article provides an overview of the area and emphasizes recent contributions wherein the tert-butanesulfinamides act as chiral auxiliaries or perform as nitrogen donors in metal-catalyzed amination reactions. PMID:26931222

  14. 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. PMID:25214080

  15. 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.

  16. General Nitrogen Regulation of Nitrate Assimilation Regulatory Gene nasR Expression in Klebsiella oxytoca M5al

    PubMed Central

    Wu, Stephen Qitu; Chai, Weihang; Lin, Janine T.; Stewart, Valley

    1999-01-01

    Klebsiella oxytoca can assimilate nitrate and nitrite by using enzymes encoded by the nasFEDCBA operon. Expression of the nasF operon is controlled by general nitrogen regulation (Ntr) via the NtrC transcription activator and by pathway-specific nitrate and nitrite induction via the NasR transcription antiterminator. This paper reports our analysis of nasR gene expression. We constructed strains bearing single-copy Φ(nasR-lacZ) operon fusions within the chromosomal rhaBAD-rhaSR locus. The expression of ΔrhaBS::[Φ(nasR-lacZ)] operon fusions was induced about 10-fold during nitrogen-limited growth. Induction was reduced in both ntrC and rpoN null mutants, indicating that Ntr control of nasR gene expression requires the NtrC and ςN (ς54) proteins. Sequence inspection of the nasR control region reveals an apparent ςN-dependent promoter but no apparent NtrC protein binding sites. Analysis of site-specific mutations coupled with primer extension analysis authenticated the ςN-dependent nasR promoter. Fusion constructs with only about 70 nucleotides (nt) upstream of the transcription initiation site exhibited patterns of β-galactosidase expression indistinguishable from Φ(nasR-lacZ) constructs with about 470 nt upstream. Expression was independent of the Nac protein, implying that NtrC is a direct activator of nasR transcription. Together, these results indicate that nasR gene expression does not require specific upstream NtrC-binding sequences, as previously noted for argT gene expression in Salmonella typhimurium (G. Schmitz, K. Nikaido, and G. F.-L. Ames, Mol. Gen. Genet. 215:107–117, 1988). PMID:10572131

  17. General nitrogen regulation of nitrate assimilation regulatory gene nasR expression in Klebsiella oxytoca M5al.

    PubMed

    Wu, S Q; Chai, W; Lin, J T; Stewart, V

    1999-12-01

    Klebsiella oxytoca can assimilate nitrate and nitrite by using enzymes encoded by the nasFEDCBA operon. Expression of the nasF operon is controlled by general nitrogen regulation (Ntr) via the NtrC transcription activator and by pathway-specific nitrate and nitrite induction via the NasR transcription antiterminator. This paper reports our analysis of nasR gene expression. We constructed strains bearing single-copy Phi(nasR-lacZ) operon fusions within the chromosomal rhaBAD-rhaSR locus. The expression of DeltarhaBS::[Phi(nasR-lacZ)] operon fusions was induced about 10-fold during nitrogen-limited growth. Induction was reduced in both ntrC and rpoN null mutants, indicating that Ntr control of nasR gene expression requires the NtrC and sigma(N) (sigma(54)) proteins. Sequence inspection of the nasR control region reveals an apparent sigma(N)-dependent promoter but no apparent NtrC protein binding sites. Analysis of site-specific mutations coupled with primer extension analysis authenticated the sigma(N)-dependent nasR promoter. Fusion constructs with only about 70 nucleotides (nt) upstream of the transcription initiation site exhibited patterns of beta-galactosidase expression indistinguishable from Phi(nasR-lacZ) constructs with about 470 nt upstream. Expression was independent of the Nac protein, implying that NtrC is a direct activator of nasR transcription. Together, these results indicate that nasR gene expression does not require specific upstream NtrC-binding sequences, as previously noted for argT gene expression in Salmonella typhimurium (G. Schmitz, K. Nikaido, and G. F.-L. Ames, Mol. Gen. Genet. 215:107-117, 1988). PMID:10572131

  18. Temperature and Carbon Assimilation Regulate the Chlorosome Biogenesis in Green Sulfur Bacteria

    PubMed Central

    Tang, Joseph Kuo-Hsiang; Saikin, Semion K.; Pingali, Sai Venkatesh; Enriquez, Miriam M.; Huh, Joonsuk; Frank, Harry A.; Urban, Volker S.; Aspuru-Guzik, Alán

    2013-01-01

    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. PMID:24047985

  19. Landscape level differences in soil carbon and nitrogen: implications for soil carbon sequestration

    SciTech Connect

    Garten Jr, 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 ({ge}53 {micro}m) and mineral-associated organic matter (<53 {micro}m). 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.

  20. 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.

  1. 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

  2. Nitrogen-doped, carbon-rich, highly photoluminescent carbon dots from ammonium citrate

    NASA Astrophysics Data System (ADS)

    Yang, Zhi; Xu, Minghan; Liu, Yun; He, Fengjiao; Gao, Feng; Su, Yanjie; Wei, Hao; Zhang, Yafei

    2014-01-01

    The synthesis of water-soluble nitrogen-doped carbon dots has received great attention, due to their wide applications in oxygen reduction reaction, cell imaging, sensors, and drug delivery. Herein, nitrogen-doped, carbon-rich, highly photoluminescent carbon dots have been synthesized for the first time from ammonium citrate under hydrothermal conditions. The obtained nitrogen-doped carbon dots possess bright blue luminescence, short fluorescence lifetime, pH-sensitivity and excellent stability at a high salt concentration. They have potential to be used for pH sensors, cell imaging, solar cells, and photocatalysis.The synthesis of water-soluble nitrogen-doped carbon dots has received great attention, due to their wide applications in oxygen reduction reaction, cell imaging, sensors, and drug delivery. Herein, nitrogen-doped, carbon-rich, highly photoluminescent carbon dots have been synthesized for the first time from ammonium citrate under hydrothermal conditions. The obtained nitrogen-doped carbon dots possess bright blue luminescence, short fluorescence lifetime, pH-sensitivity and excellent stability at a high salt concentration. They have potential to be used for pH sensors, cell imaging, solar cells, and photocatalysis. Electronic supplementary information (ESI) available: The curve of photoluminescence and absorbance of N-doped CDs and quinine sulfate, and the table showing XPS detailed information. See DOI: 10.1039/c3nr05380f

  3. 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. PMID:11283356

  4. Soil Carbon and Nitrogen Mineralization with Flexible Soil and Microbial C:N Ratios

    NASA Astrophysics Data System (ADS)

    Wang, G.; Mayes, M. A.; Thornton, P. E.; Hoffman, F. M.

    2014-12-01

    Microbial assimilation of C-N and the physicochemical protection of soil organic matter (SOM) play fundamental roles in regulating land-atmosphere interactions. However, these microbial and physicochemical processes are not explicitly represented in current region/global terrestrial ecosystem models, e.g., the Community Land Model (CLM). The lack of explicit representation of microbial pools and functions results in unrealistic fixed-C:N ratios in SOM pools currently in CLM. Thus current soil C-N model configuration is inadequate to model the effects of litter inputs or fertilization on soil carbon and nitrogen mineralization and linkages between plant litter C:N ratios and soil or microbial C:N ratios. We propose a coupled C-N model that allows for flexible C:N ratios in microbe and SOM pools and thus the ability to represent the decomposition response to fertilization and/or litter inputs with various C:N ratios. Our preliminary analysis has shown that the C:N ratios in SOM, dissolved organic matter (DOM), and microbial pools can be well constrained by the new C-N model and microbes regulate the C:N ratios in SOM and DOM pools. We will use this new model framework to evaluate the soil carbon and nitrogen mineralization processes under conditions of excess organic C, excess organic N, or limited mineral N.

  5. 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.

  6. 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.

  7. 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.

  8. Landscape controls on carbon and nitrogen cycling in boreal forests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Climate change in the boreal forest biome is having a large impact on two of the main controllers of carbon (C) and nitrogen (N) cycling within this region: permafrost and fire. Permafrost, and its effects on soil drainage, controls the inputs and losses of C and N via net primary productivity (NP...

  9. Nitrogen fertilization effects on irrigated no-till corn production and soil carbon and nitrogen

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Converting from conventional tillage (CT) to a no-till (NT) production system can affect N requirements for optimizing corn (Zea mays L.) yields while enhancing soil organic carbon (SOC) and N levels. Nitrogen fertilization impacts on irrigated, NT continuous-corn grain, stalk, cob, and stover yiel...

  10. Spatial heterogeneity of forest soil carbon and nitrogen controls nitrogen transformations and trace gas production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Small-scale spatial heterogeneity of soil nitrogen (N) and carbon (C) pools and net transformation processes in forested ecosystems are not well understood. Two forests in central Oregon (Black Butte and Santiam Pass) were used to test the hypothesis that spatial distribution of soil nutrients cont...

  11. 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. PMID:25956882

  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. 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

  14. Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs

    PubMed Central

    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

    2013-01-01

    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. PMID:24270626

  15. [Assimilation of carbon dioxide and oxidation of methane in various zones of the Rainbow hyperthermophilic field zones].

    PubMed

    Pimenov, N V; Lein, A Iu; Sagalevich, A M; Ivanov, M V

    2000-01-01

    Rates of carbon dioxide assimilation and methane oxidation were determined in various zones of the Rainbow Hydrothermal Field (36 degrees N) of the Mid-Atlantic Ridge. In the plume above the hydrothermal field, anomalously high methane content was recorded; the microbial population density (up to 10(5) cells/ml) was an order of magnitude higher than the background values; and the CO2 assimilation rate varied from 0.01 to 1.1 micrograms C/(1 day). Based on the data on CO2 assimilation, the production of organic carbon due to bacterial chemosynthesis in the plume was calculated to be 930 kg/day or 340 tons/year (about 29% of the organic carbon production in the photic zone). In the black smoke above active smokers, the microbial population density was as high as 10(6) cells/ml; the rate of CO2 assimilation made up 5-10 micrograms C/(1 day); the methane oxidation rate varied from 0.15 to 12.7 mu/(1 day); and the methane concentration ranged from 1.05 to 70.6 mu/l. In bottom sediments enriched with sulfides, the rate of CO2 assimilation was at least an order of magnitude higher than in oxidized metal-bearing sediments. At the base of an active construction site, whitish sediment was found, which was characterized by a methane high content (92 mu/dm3) and a high rate of oxidation (1.7 mu/(dm3 day)). PMID:11195582

  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. Effectiveness of Nitrogen Assimilation in the Non-Tidal Chesapeake Bay Watershed: Evaluations Based on Thirty Years of Data

    NASA Astrophysics Data System (ADS)

    Zhang, Q.; Wei, H.; Ha, D.; Ball, W. P.

    2014-12-01

    Control of watershed nutrient input has long been a priority of Chesapeake Bay watershed management for alleviating hypoxia in the Bay. Therefore, systematic evaluations of historical watershed nutrient inputs and responses of river water quality can help managers to assess the effectiveness of nutrient management across the Bay watershed. Toward that end, we conducted a comprehensive comparison of multi-decadal total nitrogen (TN) watershed input and riverine output for the nine major rivers in the non-tidal Bay watershed. Specifically, we (1) compiled available data regarding multi-decadal TN input from four major sources, (2) obtained updated estimates of TN flux at downstream (edge-of-tide) river locations ('output'), and (3) used these inputs and outputs to quantify the watersheds' land/river effectiveness (LRE) factors in regard to TN assimilation, including an investigation of relationships between LRE and TN input. Our compiled data for N sources confirmed known trends regarding the two largest of the four TN sources (atmospheric deposition and fertilizer loadings) - i.e., that the former has declined significantly in all river basins, whereas the latter has decreased in most of the river basins. For the other two sources, point sources have declined most dramatically in the Patuxent River but exhibited various trends in other basins, whereas manure sources have increased statistically significantly in most of the river basins. The riverine output results were observed to follow watershed inputs in a non-linear manner. Finally, the LRE of the various basins were observed to correlate inversely with the watersheds' input loadings, whereas temporal correlations within a given basin were less consistent. In addition, the Susquehanna sub-watersheds show lower LREs compared with other river basins, with riverine output similar to or even larger than input, implying that greater management effort at these locations could be especially fruitful for load reduction.

  18. Effect of Saccharomyces cerevisiae inoculum size on wine fermentation aroma compounds and its relation with assimilable nitrogen content.

    PubMed

    Carrau, Francisco; Medina, Karina; Fariña, Laura; Boido, Eduardo; Dellacassa, Eduardo

    2010-09-30

    Different commercial Saccharomyces cerevisiae strains have been applied at the winemaking level, trying to establish a dominant population of selected strains from the start of fermentation and ensuring the complete consumption of sugars. Although a large population of active yeast cells can be introduced in the inoculated wines, resulting in a complete fermentation, this does not necessarily mean an improvement of the sensory characteristics of the wines. The impact of the size of the inocula in wine quality parameters has been very little studied, and in no case the nutrient balance of the grape must utilized was taken into account. In this work we present results obtained for wine aroma compounds at three inoculum levels (10(4), 10(5) and 10(6)cells/mL), and two different yeast assimilable nitrogen (YAN) in a white grape must, using two S. cerevisiae strains commonly used for winemaking. A significant effect in the final concentrations of higher alcohols, esters, fatty acids, free monoterpenes and lactones was attributed to the size of inoculum in both strains but not in an easily predictable way. However, a consistent increase of desired aroma compounds (esters, lactones and free monoterpenes), and a decrease of less desired compounds for white wine (higher alcohols and medium chain fatty acids), was shown at inoculum sizes of 10(5)cells/mL for both strains in real winemaking conditions. In a discriminant analysis six aroma compounds discriminate the three inoculum sizes for all wine samples: 1,8-terpine, hodiol I (trans-3,7-dimethyl-1,5-octadiene-3,7-diol), isobutyl alcohol, iso C4 acid, ethyl C6 ester and C8 acid. PMID:20692063

  19. Methods of detection and identificationoc carbon- and nitrogen-containing materials

    DOEpatents

    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.

  20. 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.

  1. Mechanism of Carbonate Assimilation in the Middle Ordovician Hortavær Igneous Complex, north-central Norway

    NASA Astrophysics Data System (ADS)

    Barnes, C.; Li, Y.; Prestvik, T.; Barnes, M. A.

    2008-12-01

    The Hortavær igneous complex consists primarily of mafic to intermediate magmas emplaced as sheets into marble, calc-silicate, semipelitic, and quartzofeldspathic rocks as well as coeval, cogenetic syenitic magmas. Parental mafic magmas have arc-like trace element signatures and were H2O -rich. Carbonate assimilation was a heterogeneous process and the degree of assimilation varied by locality from 0 to 20 wt percent. Trace element and isotopic compositions of magmatic calcite, compositions of grossular-andradite garnet in endoskarns, and field evidence for partial melting of the endoskarns indicate that carbonate assimilation was a multistage process. Initially, H2O -rich fluid from mafic magmas infiltrated calc-silicate xenoliths/screens, resulting in lowering of their solidus. Partial melting of these screens increased their porosity and decreased their strength, leading to disruption and mingling with mafic magmas as well as bringing carbonate-rich melt into contact with the surrounding silicate magmas. This process also permitted infiltration of silicate melt into the partially melted calc-silicate rocks, enhancing development of garnet ferrohedenbergite ± wollastonite melasyenitic endoskarn. Carbonate melt from the xenoliths mixed with the surrounding mafic magmas by reactive assimilation; this process can sensibly be described as reaction of olivine and calcite components in melt phases to form augitic (fassaitic) clinopyroxene (cpx) and CO2. This enhanced stability of cpx is reflected in the presence of cpx-rich cumulates, fractionation of which resulted in alkali enrichment and formation of abundant syenitic magma. During later stages of magma evolution (monzonitic to syenitic and granitic composition), assimilation of quartzofeldspathic to pelitic rocks became dominant, and magma compositions evolved from nepheline- to quartz-normative. The large amount of host rock (carbonate, calc-silicate or pelite) assimilation in the Hortavær complex was enhanced

  2. 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

  3. 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.

  4. Controlled release of alendronate from nitrogen-doped mesoporous carbon

    DOE PAGESBeta

    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 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. 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. PMID:27098229

  6. 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).

  7. 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.

  8. 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

  9. Influence of carbon to nitrogen ratios on soybean somatic embryo (cv. Jack) growth and composition

    PubMed Central

    Truong, Quyen; Koch, Kaelynn; Yoon, Jong Moon; Everard, John D.; Shanks, Jacqueline V.

    2013-01-01

    Soybean [Glycine max (L.) Merr.] seed are valued for their protein and oil content. Soybean somatic embryos cultured in Soybean Histodifferentiation and Maturation (SHaM) medium were examined for their suitability as a model system for developing an understanding of assimilate partitioning and metabolic control points for protein and oil biosynthesis in soybean seed. This report describes the growth dynamics and compositional changes of SHaM embryos in response to change in the carbon to nitrogen ratio of the medium. It was postulated that at media compositions that were sufficient to support maximal growth rates, changes in the C:N ratio are likely to influence the partitioning of resources between the various storage products, especially protein and oil. As postulated, at steady-state growth rates, embryo protein content was strongly correlated with decreasing C:N ratios and increasing glutamine consumption rates. However, oil content remained relatively unchanged across the C:N ratio range tested, and resources were instead directed towards the starch and residual biomass (estimated by mass balance) pools in response to increasing C:N ratios. Protein and oil were inversely related only at concentrations of sucrose in the medium <88mM, where carbon limited growth and no starch was found to accumulate in the tissues. These observations and the high reproducibility in the data indicate that SHaM embryos are an ideal model system for the application of metabolic flux analysis studies designed to test hypotheses regarding assimilate partitioning in developing soybean seeds. PMID:23740932

  10. 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.