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Sample records for yeast assimilable nitrogen

  1. Free amino nitrogen concentration correlates to total yeast assimilable nitrogen concentration in apple juice.

    PubMed

    Boudreau, Thomas F; Peck, Gregory M; O'Keefe, Sean F; Stewart, Amanda C

    2018-01-01

    Yeast assimilable nitrogen (YAN) is essential for yeast growth and metabolism during apple ( Malus x domestica Borkh.) cider fermentation. YAN concentration and composition can impact cider fermentation kinetics and the formation of volatile aroma compounds by yeast. The YAN concentration and composition of apples grown in Virginia, USA over the course of two seasons was determined through analysis of both free amino nitrogen (FAN) and ammonium ion concentration. FAN was the largest fraction of YAN, with a mean value of 51 mg N L -1 FAN compared to 9 mg N L -1 ammonium. Observed YAN values ranged from nine to 249 mg N L -1 , with a mean value of 59 mg N L -1 . Ninety-four percent of all samples analyzed in this study contained <140 mg N L -1 YAN, a concentration generally considered the minimum level needed in grape-based wines for yeast to fully utilize all of the fermentable sugars. FAN concentration was correlated with total YAN concentration, but ammonium concentration was not. Likewise, there was no correlation between FAN and ammonium concentration.

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

    PubMed

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

    2008-11-01

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

  3. Non-Saccharomyces Yeasts Nitrogen Source Preferences: Impact on Sequential Fermentation and Wine Volatile Compounds Profile

    PubMed Central

    Gobert, Antoine; Tourdot-Maréchal, Raphaëlle; Morge, Christophe; Sparrow, Céline; Liu, Youzhong; Quintanilla-Casas, Beatriz; Vichi, Stefania; Alexandre, Hervé

    2017-01-01

    Nitrogen sources in the must are important for yeast metabolism, growth, and performance, and wine volatile compounds profile. Yeast assimilable nitrogen (YAN) deficiencies in grape must are one of the main causes of stuck and sluggish fermentation. The nitrogen requirement of Saccharomyces cerevisiae metabolism has been described in detail. However, the YAN preferences of non-Saccharomyces yeasts remain unknown despite their increasingly widespread use in winemaking. Furthermore, the impact of nitrogen consumption by non-Saccharomyces yeasts on YAN availability, alcoholic performance and volatile compounds production by S. cerevisiae in sequential fermentation has been little studied. With a view to improving the use of non-Saccharomyces yeasts in winemaking, we studied the use of amino acids and ammonium by three strains of non-Saccharomyces yeasts (Starmerella bacillaris, Metschnikowia pulcherrima, and Pichia membranifaciens) in grape juice. We first determined which nitrogen sources were preferentially used by these yeasts in pure cultures at 28 and 20°C (because few data are available). We then carried out sequential fermentations at 20°C with S. cerevisiae, to assess the impact of the non-Saccharomyces yeasts on the availability of assimilable nitrogen for S. cerevisiae. Finally, 22 volatile compounds were quantified in sequential fermentation and their levels compared with those in pure cultures of S. cerevisiae. We report here, for the first time, that non-Saccharomyces yeasts have specific amino-acid consumption profiles. Histidine, methionine, threonine, and tyrosine were not consumed by S. bacillaris, aspartic acid was assimilated very slowly by M. pulcherrima, and glutamine was not assimilated by P. membranifaciens. By contrast, cysteine appeared to be a preferred nitrogen source for all non-Saccharomyces yeasts. In sequential fermentation, these specific profiles of amino-acid consumption by non-Saccharomyces yeasts may account for some of the

  4. Non-Saccharomyces Yeasts Nitrogen Source Preferences: Impact on Sequential Fermentation and Wine Volatile Compounds Profile.

    PubMed

    Gobert, Antoine; Tourdot-Maréchal, Raphaëlle; Morge, Christophe; Sparrow, Céline; Liu, Youzhong; Quintanilla-Casas, Beatriz; Vichi, Stefania; Alexandre, Hervé

    2017-01-01

    Nitrogen sources in the must are important for yeast metabolism, growth, and performance, and wine volatile compounds profile. Yeast assimilable nitrogen (YAN) deficiencies in grape must are one of the main causes of stuck and sluggish fermentation. The nitrogen requirement of Saccharomyces cerevisiae metabolism has been described in detail. However, the YAN preferences of non- Saccharomyces yeasts remain unknown despite their increasingly widespread use in winemaking. Furthermore, the impact of nitrogen consumption by non- Saccharomyces yeasts on YAN availability, alcoholic performance and volatile compounds production by S. cerevisiae in sequential fermentation has been little studied. With a view to improving the use of non- Saccharomyces yeasts in winemaking, we studied the use of amino acids and ammonium by three strains of non- Saccharomyces yeasts ( Starmerella bacillaris, Metschnikowia pulcherrima , and Pichia membranifaciens ) in grape juice. We first determined which nitrogen sources were preferentially used by these yeasts in pure cultures at 28 and 20°C (because few data are available). We then carried out sequential fermentations at 20°C with S. cerevisiae , to assess the impact of the non- Saccharomyces yeasts on the availability of assimilable nitrogen for S. cerevisiae . Finally, 22 volatile compounds were quantified in sequential fermentation and their levels compared with those in pure cultures of S. cerevisiae . We report here, for the first time, that non- Saccharomyces yeasts have specific amino-acid consumption profiles. Histidine, methionine, threonine, and tyrosine were not consumed by S. bacillaris , aspartic acid was assimilated very slowly by M. pulcherrima , and glutamine was not assimilated by P. membranifaciens . By contrast, cysteine appeared to be a preferred nitrogen source for all non- Saccharomyces yeasts. In sequential fermentation, these specific profiles of amino-acid consumption by non- Saccharomyces yeasts may account for

  5. Nitrogen assimilation in denitrifier Bacillus azotoformans LMG 9581T.

    PubMed

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

    2017-12-01

    Until recently, it has not been generally known that some bacteria can contain the gene inventory for both denitrification and dissimilatory nitrate (NO 3 - )/nitrite (NO 2 - ) reduction to ammonium (NH 4 + ) (DNRA). Detailed studies of these microorganisms could shed light on the differentiating environmental drivers of both processes without interference of organism-specific variation. Genome analysis of Bacillus azotoformans LMG 9581 T shows a remarkable redundancy of dissimilatory nitrogen reduction, with multiple copies of each denitrification gene as well as DNRA genes nrfAH, but a reduced capacity for nitrogen assimilation, with no nas operon nor amtB gene. Here, we explored nitrogen assimilation in detail using growth experiments in media with different organic and inorganic nitrogen sources at different concentrations. Monitoring of growth, NO 3 - NO 2 - , NH 4 + concentration and N 2 O production revealed that B. azotoformans LMG 9581 T could not grow with NH 4 + as sole nitrogen source and confirmed the hypothesis of reduced nitrogen assimilation pathways. However, NH 4 + could be assimilated and contributed up to 50% of biomass if yeast extract was also provided. NH 4 + also had a significant but concentration-dependent influence on growth rate. The mechanisms behind these observations remain to be resolved but hypotheses for this deficiency in nitrogen assimilation are discussed. In addition, in all growth conditions tested a denitrification phenotype was observed, with all supplied NO 3 - converted to nitrous oxide (N 2 O).

  6. Yeast identification: reassessment of assimilation tests as sole universal identifiers.

    PubMed

    Spencer, J; Rawling, S; Stratford, M; Steels, H; Novodvorska, M; Archer, D B; Chandra, S

    2011-11-01

    To assess whether assimilation tests in isolation remain a valid method of identification of yeasts, when applied to a wide range of environmental and spoilage isolates. Seventy-one yeast strains were isolated from a soft drinks factory. These were identified using assimilation tests and by D1/D2 rDNA sequencing. When compared to sequencing, assimilation test identifications (MicroLog™) were 18·3% correct, a further 14·1% correct within the genus and 67·6% were incorrectly identified. The majority of the latter could be attributed to the rise in newly reported yeast species. Assimilation tests alone are unreliable as a universal means of yeast identification, because of numerous new species, variability of strains and increasing coincidence of assimilation profiles. Assimilation tests still have a useful role in the identification of common species, such as the majority of clinical isolates. It is probable, based on these results, that many yeast identifications reported in older literature are incorrect. This emphasizes the crucial need for accurate identification in present and future publications. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  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. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Fermentative activity and production of volatile compounds by Saccharomyces grown in synthetic grape juice media deficient in assimilable nitrogen and/or pantothenic acid.

    PubMed

    Wang, X D; Bohlscheid, J C; Edwards, C G

    2003-01-01

    To understand the impact of assimilable nitrogen and pantothenic acid on fermentation rate and synthesis of volatile compounds by Saccharomyces under fermentative conditions. A 2 x 3 factorial experimental design was employed with the concentrations of yeast assimilable nitrogen (YAN) (60 and 250 mg l(-1)) and pantothenic acid (10, 50 and 250 microg l(-1)) as variables. In media containing 250 microg l(-1) pantothenic acid, H2S production by two different species of Saccharomyces decreased when YAN was increased from 60 to 250 mg l(-1). Conversely, H2S production was significantly higher when the concentration of assimilable nitrogen was increased if pantothenic acid was deficient (10 or 50 microg l(-1)). Yeast synthesis of other volatile compounds were impacted by both assimilable nitrogen and pantothenic acid. While growth and fermentative rate of Saccharomyces was more influenced by nitrogen than by pantothenic acid, complicated interactions exist between these nutrients that affect the synthesis of volatile compounds including H2S. This study has important implications for the winemaking industry where a better understanding of the nutritional requirements of Saccharomyces is necessary to reduce fermentation problems and to improve final product quality.

  9. Nitrogen availability of grape juice limits killer yeast growth and fermentation activity during mixed-culture fermentation with sensitive commercial yeast strains.

    PubMed Central

    Medina, K; Carrau, F M; Gioia, O; Bracesco, N

    1997-01-01

    The competition between selected or commercial killer strains of type K2 and sensitive commercial strains of Saccharomyces cerevisiae was studied under various conditions in sterile grape juice fermentations. The focus of this study was the effect of yeast inoculation levels and the role of assimilable nitrogen nutrition on killer activity. A study of the consumption of free amino nitrogen (FAN) by pure and mixed cultures of killer and sensitive cells showed no differences between the profiles of nitrogen assimilation in all cases, and FAN was practically depleted in the first 2 days of fermentation. The effect of the addition of assimilable nitrogen and the size of inoculum was examined in mixed killer and sensitive strain competitions. Stuck and sluggish wine fermentations were observed to depend on nitrogen availability when the ratio of killer to sensitive cells was low (1:10 to 1:100). A relationship between the initial assimilable nitrogen content of must and the proportion of killer cells during fermentation was shown. An indirect relationship was found between inoculum size and the percentage of killer cells: a smaller inoculum resulted in a higher proportion of killer cells in grape juice fermentations. In all cases, wines obtained with pure-culture fermentations were preferred to mixed-culture fermentations by sensory analysis. The reasons why killer cells do not finish fermentation under competitive conditions with sensitive cells are discussed. PMID:9212430

  10. The interactive effect of fungicide residues and yeast assimilable nitrogen on fermentation kinetics and hydrogen sulfide production during cider fermentation.

    PubMed

    Boudreau, Thomas F; Peck, Gregory M; O'Keefe, Sean F; Stewart, Amanda C

    2017-01-01

    Fungicide residues on fruit may adversely affect yeast during cider fermentation, leading to sluggish or stuck fermentation or the production of hydrogen sulfide (H 2 S), which is an undesirable aroma compound. This phenomenon has been studied in grape fermentation but not in apple fermentation. Low nitrogen availability, which is characteristic of apples, may further exacerbate the effects of fungicides on yeast during fermentation. The present study explored the effects of three fungicides: elemental sulfur (S 0 ) (known to result in increased H 2 S in wine); fenbuconazole (used in orchards but not vineyards); and fludioxonil (used in post-harvest storage of apples). Only S 0 led to increased H 2 S production. Fenbuconazole (≥0.2 mg L -1 ) resulted in a decreased fermentation rate and increased residual sugar. An interactive effect of yeast assimilable nitrogen (YAN) concentration and fenbuconazole was observed such that increasing the YAN concentration alleviated the negative effects of fenbuconazole on fermentation kinetics. Cidermakers should be aware that residual fenbuconazole (as low as 0.2 mg L -1 ) in apple juice may lead to stuck fermentation, especially when the YAN concentration is below 250 mg L -1 . These results indicate that fermentation problems attributed to low YAN may be caused or exacerbated by additional factors such as fungicide residues, which have a greater impact on fermentation performance under low YAN conditions. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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

    PubMed Central

    Salmon, Jean-Michel; Barre, Pierre

    1998-01-01

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

  12. Optimization of carbon and nitrogen medium components for biomass production using non-Saccharomyces wine yeasts.

    PubMed

    Schnierda, T; Bauer, F F; Divol, B; van Rensburg, E; Görgens, J F

    2014-05-01

    The impact of different nitrogen and carbon sources on biomass production of the non-Saccharomyces wine yeast species Lachancea thermotolerans, Metschnikowia pulcherrima and Issatchenkia orientalis was assessed. Using a molasses-based medium, yeast extract and corn steep liquor as well as ammonium sulphate and di-ammonium phosphate (DAP) as nitrogen sources were compared in shake-flask cultures. A medium with 20 g l⁻¹ sugar (diluted molasses) and 500 mg l⁻¹ total yeast assimilable nitrogen, from yeast extract, gave the highest biomass concentrations and yields. Invertase pretreatment was required for cultures of M. pulcherrima and I. orientalis, and respective biomass yields of 0.7 and 0.8 g g⁻¹ were achieved in aerobic bioreactor cultures. The absence of ethanol production suggested Crabtree-negative behaviour by these yeasts, whereas Crabtree-positive behaviour by L. thermotolerans resulted in ethanol and biomass concentrations of 5.5 and 11.1 g l⁻¹, respectively. Recent studies demonstrate that non-Saccharomyces yeasts confer positive attributes to the final composition of wine. However, optimal process conditions for their biomass production have not been described, thereby limiting commercial application. In this study, industrial media and methods of yeast cultivation were investigated to develop protocols for biomass production of non-Saccharomyces yeast starter cultures for the wine industry. © 2014 The Society for Applied Microbiology.

  13. How exogenous nitric oxide regulates nitrogen assimilation in wheat seedlings under different nitrogen sources and levels

    PubMed Central

    Balotf, Sadegh; Islam, Shahidul; Kavoosi, Gholamreza; Kholdebarin, Bahman; Juhasz, Angela

    2018-01-01

    Nitrogen (N) is one of the most important nutrients for plants and nitric oxide (NO) as a signaling plant growth regulator involved in nitrogen assimilation. Understanding the influence of exogenous NO on nitrogen metabolism at the gene expression and enzyme activity levels under different sources of nitrogen is vitally important for increasing nitrogen use efficiency (NUE). This study investigated the expression of key genes and enzymes in relation to nitrogen assimilation in two Australian wheat cultivars, a popular high NUE cv. Spitfire and a normal NUE cv. Westonia, under different combinations of nitrogen and sodium nitroprusside (SNP) as the NO donor. Application of NO increased the gene expressions and activities of nitrogen assimilation pathway enzymes in both cultivars at low levels of nitrogen. At high nitrogen supplies, the expressions and activities of N assimilation genes increased in response to exogenous NO only in cv. Spitfire but not in cv. Westonia. Exogenous NO caused an increase in leaf NO content at low N supplies in both cultivars, while under high nitrogen treatments, cv. Spitfire showed an increase under ammonium nitrate (NH4NO3) treatment but cv. Westonia was not affected. N assimilation gene expression and enzyme activity showed a clear relationship between exogenous NO, N concentration and N forms in primary plant nitrogen assimilation. Results reveal the possible role of NO and different nitrogen sources on nitrogen assimilation in Triticum aestivum plants. PMID:29320529

  14. How exogenous nitric oxide regulates nitrogen assimilation in wheat seedlings under different nitrogen sources and levels.

    PubMed

    Balotf, Sadegh; Islam, Shahidul; Kavoosi, Gholamreza; Kholdebarin, Bahman; Juhasz, Angela; Ma, Wujun

    2018-01-01

    Nitrogen (N) is one of the most important nutrients for plants and nitric oxide (NO) as a signaling plant growth regulator involved in nitrogen assimilation. Understanding the influence of exogenous NO on nitrogen metabolism at the gene expression and enzyme activity levels under different sources of nitrogen is vitally important for increasing nitrogen use efficiency (NUE). This study investigated the expression of key genes and enzymes in relation to nitrogen assimilation in two Australian wheat cultivars, a popular high NUE cv. Spitfire and a normal NUE cv. Westonia, under different combinations of nitrogen and sodium nitroprusside (SNP) as the NO donor. Application of NO increased the gene expressions and activities of nitrogen assimilation pathway enzymes in both cultivars at low levels of nitrogen. At high nitrogen supplies, the expressions and activities of N assimilation genes increased in response to exogenous NO only in cv. Spitfire but not in cv. Westonia. Exogenous NO caused an increase in leaf NO content at low N supplies in both cultivars, while under high nitrogen treatments, cv. Spitfire showed an increase under ammonium nitrate (NH4NO3) treatment but cv. Westonia was not affected. N assimilation gene expression and enzyme activity showed a clear relationship between exogenous NO, N concentration and N forms in primary plant nitrogen assimilation. Results reveal the possible role of NO and different nitrogen sources on nitrogen assimilation in Triticum aestivum plants.

  15. Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation

    DOE PAGES

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

    2016-04-05

    Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using 15NO 3 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 N2E2more » strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. In conclusion, the use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.« less

  16. Global isotope metabolomics reveals adaptive strategies for nitrogen assimilation

    SciTech Connect

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

    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 15NO 3 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 N2E2more » strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. In conclusion, the use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.« less

  17. Leaf nitrogen assimilation and partitioning differ among subtropical forest plants in response to canopy addition of nitrogen treatments.

    PubMed

    Liu, Nan; Wu, Shuhua; Guo, Qinfeng; Wang, Jiaxin; Cao, Ce; Wang, Jun

    2018-05-12

    Global increases in nitrogen deposition may alter forest structure and function by interfering with plant nitrogen metabolism (e.g., assimilation and partitioning) and subsequent carbon assimilation, but it is unclear how these responses to nitrogen deposition differ among species. In this study, we conducted a 2-year experiment to investigate the effects of canopy addition of nitrogen (CAN) on leaf nitrogen assimilation and partitioning in three subtropical forest plants (Castanea henryi, Ardisia quinquegona, and Blastus cochinchinensis). We hypothesized that responses of leaf nitrogen assimilation and partitioning to CAN differ among subtropical forest plants. CAN increased leaf nitrate reductase (NR) activity, and leaf nitrogen and chlorophyll contents but reduced leaf maximum photosynthetic rate (A max ), photosynthetic nitrogen use efficiency (PNUE), ribulose-1,5-bisphosphate carboxylase (Rubisco) activity, and metabolic protein content of an overstory tree species C. henryi. In an understory tree A. quinquegona, CAN increased NR activity and glutamine synthetase activity and therefore increased metabolic protein synthesis (e.g., Rubisco) in leaves. In the shrub B. cochinchinensis, CAN increased A max , PNUE, Rubisco content, metabolic protein content, and Rubisco activity in leaves. Leaf nitrogen assimilation and partitioning results indicated that A. quinquegona and B. cochinchinensis may better acclimate to CAN than C. henryi and that the acclimation mechanism differs among the species. Results from this study suggest that long-term elevated atmospheric nitrogen deposition has contributed to the ongoing transformation of subtropical forests into communities dominated by small trees and shrubs. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Leaf nitrogen assimilation and partitioning differ among subtropical forest plants in response to canopy addition of nitrogen treatments

    Treesearch

    Nan Liu; Shuhua Wu; Qinfeng Guo; Jiaxin Wang; Ce Cao; Jun Wang

    2018-01-01

    Global increases in nitrogen deposition may alter forest structure and function by interferingwith plant nitrogen metabolism (e.g., assimilation and partitioning) and subsequent carbon assimilation, but it is unclear how these responses to nitrogen deposition differ among species. In this study, we conducted a 2-year experiment to investigate the effects of canopy...

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

    PubMed

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

    2016-06-13

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

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

    PubMed

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

    2011-11-08

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

  1. Carbon and nitrogen assimilation in deep subseafloor microbial cells

    PubMed Central

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

    2011-01-01

    Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individual microbial cells from 219-m-deep lower Pleistocene (460,000 y old) sediments from the northwestern Pacific off the Shimokita Peninsula of Japan. Sediment samples were incubated in vitro with 13C- and/or 15N-labeled glucose, pyruvate, acetate, bicarbonate, methane, ammonium, and amino acids. Significant incorporation of 13C and/or 15N and growth occurred in response to glucose, pyruvate, and amino acids (∼76% of total cells), whereas acetate and bicarbonate were incorporated without fostering growth. Among those substrates, a maximum substrate assimilation rate was observed at 67 × 10−18 mol/cell per d with bicarbonate. Neither carbon assimilation nor growth was evident in response to methane. The atomic ratios between nitrogen incorporated from ammonium and the total cellular nitrogen consistently exceeded the ratios of carbon, suggesting that subseafloor microbes preferentially require nitrogen assimilation for the recovery in vitro. Our results showed that the most deeply buried subseafloor sedimentary microbes maintain potentials for metabolic activities and that growth is generally limited by energy but not by the availability of C and N compounds. PMID:21987801

  2. Construction of a lactose-assimilating strain of baker's yeast.

    PubMed

    Adam, A C; Prieto, J A; Rubio-Texeira, M; Polaina, J

    1999-09-30

    A recombinant strain of baker's yeast has been constructed which can assimilate lactose efficiently. This strain has been designed to allow its propagation in whey, the byproduct resulting from cheese-making. The ability to metabolize lactose is conferred by the functional expression of two genes from Kluyveromyces lactis, LAC12 and LAC4, which encode a lactose permease and a beta-galactosidase, respectively. To make the recombinant strain more acceptable for its use in bread-making, the genetic transformation of the host baker's yeast was carried out with linear fragments of DNA of defined sequence, carrying as the only heterologous material the coding regions of the two K. lactis genes. Growth of the new strain on cheese whey affected neither the quality of bread nor the yeast gassing power. The significance of the newly developed strain is two-fold: it affords a cheap alternative to the procedure generally used for the propagation of baker's yeast, and it offers a profitable use for cheese whey. Copyright 1999 John Wiley & Sons, Ltd.

  3. 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.

  4. 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.

  5. 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.

  6. 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 regulationmore » 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.« less

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

    PubMed Central

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

    2014-01-01

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

  8. Mycobacterium tuberculosis nitrogen assimilation and host colonization require aspartate

    PubMed Central

    Gouzy, Alexandre; Larrouy-Maumus, Gérald; Wu, Ting-Di; Peixoto, Antonio; Levillain, Florence; Lugo-Villarino, Geanncarlo; Gerquin-Kern, Jean-Luc; de Carvalho, Luiz Pedro Sório; Poquet, Yannick; Neyrolles, Olivier

    2013-01-01

    Here we identify the amino acid transporter AnsP1 as the unique aspartate importer in the human pathogen Mycobacterium tuberculosis. Metabolomic analysis of a mutant inactivated in AnsP1 revealed the transporter is essential for M. tuberculosis to assimilate nitrogen from aspartate. Virulence of the AnsP1 mutant is impaired in vivo, revealing aspartate is a primary nitrogen source required for host colonization by the tuberculosis bacillus. PMID:24077180

  9. 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

  10. Yeast nitrogen utilization in the phyllosphere during plant lifespan under regulation of autophagy

    PubMed Central

    Shiraishi, Kosuke; Oku, Masahide; Kawaguchi, Kosuke; Uchida, Daichi; Yurimoto, Hiroya; Sakai, Yasuyoshi

    2015-01-01

    Recently, microbe-plant interactions at the above-ground parts have attracted great attention. Here we describe nitrogen metabolism and regulation of autophagy in the methylotrophic yeast Candida boidinii, proliferating and surviving on the leaves of Arabidopsis thaliana. After quantitative analyses of yeast growth on the leaves of A. thaliana with the wild-type and several mutant yeast strains, we showed that on young leaves, nitrate reductase (Ynr1) was necessary for yeast proliferation, and the yeast utilized nitrate as nitrogen source. On the other hand, a newly developed methylamine sensor revealed appearance of methylamine on older leaves, and methylamine metabolism was induced in C. boidinii, and Ynr1 was subjected to degradation. Biochemical and microscopic analysis of Ynr1 in vitro during a shift of nitrogen source from nitrate to methylamine revealed that Ynr1 was transported to the vacuole being the cargo for biosynthetic cytoplasm-to-vacuole targeting (Cvt) pathway, and degraded. Our results reveal changes in the nitrogen source composition for phyllospheric yeasts during plant aging, and subsequent adaptation of the yeasts to this environmental change mediated by regulation of autophagy. PMID:25900611

  11. 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.

  12. Fermentation performances and aroma production of non-conventional wine yeasts are influenced by nitrogen preferences.

    PubMed

    Rollero, Stéphanie; Bloem, Audrey; Ortiz-Julien, Anne; Camarasa, Carole; Divol, Benoit

    2018-05-07

    Saccharomyces cerevisiae is currently the most important yeast involved in food fermentations, particularly in oenology. However, several other yeast species occur naturally in grape must that are highly promising for diversifying and improving the aromatic profile of wines. If the nitrogen requirement of S. cerevisiae has been described in detail, those of non-Saccharomyces yeasts remain poorly studied despite their increasingly widespread use in winemaking. With a view to improving the use of non-Saccharomyces yeasts in winemaking, we explored the fermentation performances, the utilization of nitrogen sources and the volatile compound production of ten strains of non-conventional yeasts in pure culture. Two different conditions were tested: one mimicking the grape juice's nitrogen composition and one with all the nitrogen sources at the same level. We highlighted the diversity in terms of nitrogen preference and amount consumed among the yeast strains. Some nitrogen sources (arginine, glutamate, glycine, tryptophan and GABA) displayed the largest variations between strains throughout the fermentation. Several non-Saccharomyces strains produced important aroma compounds such as higher alcohols, acetate and ethyl esters in significantly higher quantities than S. cerevisiae.

  13. Assimilation of Remotely Sensed Leaf Area Index into the Community Land Model with Explicit Carbon and Nitrogen Components using Data Assimilation Research Testbed

    NASA Astrophysics Data System (ADS)

    Ling, X.; Fu, C.; Yang, Z. L.; Guo, W.

    2017-12-01

    Information of the spatial and temporal patterns of leaf area index (LAI) is crucial to understand the exchanges of momentum, carbon, energy, and water between the terrestrial ecosystem and the atmosphere, while both in-situ observation and model simulation usually show distinct deficiency in terms of LAI coverage and value. Land data assimilation, combined with observation and simulation together, is a promising way to provide variable estimation. The Data Assimilation Research Testbed (DART) developed and maintained by the National Centre for Atmospheric Research (NCAR) provides a powerful tool to facilitate the combination of assimilation algorithms, models, and real (as well as synthetic) observations to better understanding of all three. Here we systematically investigated the effects of data assimilation on improving LAI simulation based on NCAR Community Land Model with the prognostic carbon-nitrogen option (CLM4CN) linked with DART using the deterministic Ensemble Adjustment Kalman Filter (EAKF). Random 40-member atmospheric forcing was used to drive the CLM4CN with or without LAI assimilation. The Global Land Surface Satellite LAI data (GLASS LAI) LAI is assimilated into the CLM4CN at a frequency of 8 days, and LAI (and leaf carbon / nitrogen) are adjusted at each time step. The results show that assimilating remotely sensed LAI into the CLM4CN is an effective method for improving model performance. In detail, the CLM4-CN simulated LAI systematically overestimates global LAI, especially in low latitude with the largest bias of 5 m2/m2. While if updating both LAI and leaf carbon and leaf nitrogen simultaneously during assimilation, the analyzed LAI can be corrected, especially in low latitude regions with the bias controlled around ±1 m2/m2. Analyzed LAI could also represent the seasonal variation except for the Southern Temperate (23°S-90°S). The obviously improved regions located in the center of Africa, Amazon, the South of Eurasia, the northeast of

  14. 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

  15. Mapping Genetic Variants Underlying Differences in the Central Nitrogen Metabolism in Fermenter Yeasts

    PubMed Central

    García, Verónica; Salinas, Francisco; Aguilera, Omayra; Liti, Gianni; Martínez, Claudio

    2014-01-01

    Different populations within a species represent a rich reservoir of allelic variants, corresponding to an evolutionary signature of withstood environmental constraints. Saccharomyces cerevisiae strains are widely utilised in the fermentation of different kinds of alcoholic beverages, such as, wine and sake, each of them derived from must with distinct nutrient composition. Importantly, adequate nitrogen levels in the medium are essential for the fermentation process, however, a comprehensive understanding of the genetic variants determining variation in nitrogen consumption is lacking. Here, we assessed the genetic factors underlying variation in nitrogen consumption in a segregating population derived from a cross between two main fermenter yeasts, a Wine/European and a Sake isolate. By linkage analysis we identified 18 main effect QTLs for ammonium and amino acids sources. Interestingly, majority of QTLs were involved in more than a single trait, grouped based on amino acid structure and indicating high levels of pleiotropy across nitrogen sources, in agreement with the observed patterns of phenotypic co-variation. Accordingly, we performed reciprocal hemizygosity analysis validating an effect for three genes, GLT1, ASI1 and AGP1. Furthermore, we detected a widespread pleiotropic effect on these genes, with AGP1 affecting seven amino acids and nine in the case of GLT1 and ASI1. Based on sequence and comparative analysis, candidate causative mutations within these genes were also predicted. Altogether, the identification of these variants demonstrate how Sake and Wine/European genetic backgrounds differentially consume nitrogen sources, in part explaining independently evolved preferences for nitrogen assimilation and representing a niche of genetic diversity for the implementation of practical approaches towards more efficient strains for nitrogen metabolism. PMID:24466135

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

    PubMed

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

    2017-01-10

    Tropical corals are associated with a diverse community of dinitrogen (N 2 )-fixing prokaryotes (diazotrophs) providing the coral an additional source of bioavailable nitrogen (N) in oligotrophic waters. The overall activity of these diazotrophs changes depending on the current environmental conditions, but to what extent it affects the assimilation of diazotroph-derived N (DDN) by corals is still unknown. Here, in a series of 15 N 2 tracer experiments, we directly quantified DDN assimilation by scleractinian corals from the Red Sea exposed to different environmental conditions. We show that DDN assimilation strongly varied with the corals' metabolic status or with phosphate availability in the water. The very autotrophic shallow-water (~5 m) corals showed low or no DDN assimilation, which significantly increased under elevated phosphate availability (3 µM). Corals that depended more on heterotrophy (i.e., bleached and deep-water [~45 m] corals) assimilated significantly more DDN, which contributed up to 15% of the corals' N demand (compared to 1% in shallow corals). Furthermore, we demonstrate that a substantial part of the DDN assimilated by deep corals was likely obtained from heterotrophic feeding on fixed N compounds and/or diazotrophic cells in the mucus. Conversely, in shallow corals, the net release of mucus, rich in organic carbon compounds, likely enhanced diazotroph abundance and activity and thereby the release of fixed N to the pelagic and benthic reef community. Overall, our results suggest that DDN assimilation by corals varies according to the environmental conditions and is likely linked to the capacity of the coral to acquire nutrients from seawater. Tropical corals are associated with specialized bacteria (i.e., diazotrophs) able to transform dinitrogen (N 2 ) gas into a bioavailable form of nitrogen, but how much of this diazotroph-derived nitrogen (DDN) is assimilated by corals under different environmental conditions is still unknown. Here

  17. Genetic Basis of Variations in Nitrogen Source Utilization in Four Wine Commercial Yeast Strains

    PubMed Central

    Gutiérrez, Alicia; Beltran, Gemma; Warringer, Jonas; Guillamón, Jose M.

    2013-01-01

    The capacity of wine yeast to utilize the nitrogen available in grape must directly correlates with the fermentation and growth rates of all wine yeast fermentation stages and is, thus, of critical importance for wine production. Here we precisely quantified the ability of low complexity nitrogen compounds to support fast, efficient and rapidly initiated growth of four commercially important wine strains. Nitrogen substrate abundance in grape must failed to correlate with the rate or the efficiency of nitrogen source utilization, but well predicted lag phase length. Thus, human domestication of yeast for grape must growth has had, at the most, a marginal impact on wine yeast growth rates and efficiencies, but may have left a surprising imprint on the time required to adjust metabolism from non growth to growth. Wine yeast nitrogen source utilization deviated from that of the lab strain experimentation, but also varied between wine strains. Each wine yeast lineage harbored nitrogen source utilization defects that were private to that strain. By a massive hemizygote analysis, we traced the genetic basis of the most glaring of these defects, near inability of the PDM wine strain to utilize methionine, as consequence of mutations in its ARO8, ADE5,7 and VBA3 alleles. We also identified candidate causative mutations in these genes. The methionine defect of PDM is potentially very interesting as the strain can, in some circumstances, overproduce foul tasting H2S, a trait which likely stems from insufficient methionine catabolization. The poor adaptation of wine yeast to the grape must nitrogen environment, and the presence of defects in each lineage, open up wine strain optimization through biotechnological endeavors. PMID:23826223

  18. The role of nitrogen uptake on the competition ability of three vineyard Saccharomyces cerevisiae strains.

    PubMed

    Vendramini, Chiara; Beltran, Gemma; Nadai, Chiara; Giacomini, Alessio; Mas, Albert; Corich, Viviana

    2017-10-03

    Three vineyard strains of Saccharomyces cerevisiae, P301.4, P304.4 and P254.12, were assayed in comparison with a commercial industrial strain, QA23. The aim was to understand if nitrogen availability could influence strain competition ability during must fermentation. Pairwise-strain fermentations and co-fermentations with the simultaneous presence of the four strains were performed in synthetic musts at two nitrogen levels: control nitrogen condition (CNC) that assured the suitable assimilable nitrogen amount required by the yeast strains to complete the fermentation and low nitrogen condition (LNC) where nitrogen is present at very low level. Results suggested a strong involvement of nitrogen availability, as the frequency in must of the vineyard strains, respect to QA23, in LNC was always higher than that found in CNC. Moreover, in CNC only strain P304.4 reached the same strain frequency as QA23. P304.4 competition ability increased during the fermentation, indicating better performance when nitrogen availability was dropping down. P301.4 was the only strain sensitive to QA23 killer toxin. In CNC, when it was co-inoculated with the industrial strain QA23, P301.4 was never detected. In LNC, P301.4 after 12h accounted for 10% of the total population. This percentage increased after 48h (20%). Single-strain fermentations were also run in both conditions and the nitrogen metabolism further analyzed. Fermentation kinetics, ammonium and amino-acid consumptions and the expression of genes under nitrogen catabolite repression evidenced that vineyard yeasts, and particularly strain P304.4, had higher nitrogen assimilation rate than the commercial control. In conclusion, the high nitrogen assimilation rate seems to be an additional strategy that allowed vineyard yeasts successful competition during the growth in grape musts. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. 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

  20. Assimilation of Nitrogen from Nitrite and Trinitrotoluene in Pseudomonas putida JLR11

    PubMed Central

    Caballero, Antonio; Esteve-Núñez, Abraham; Zylstra, Gerben J.; Ramos, Juan L.

    2005-01-01

    Pseudomonas putida JLR11 releases nitrogen from the 2,4,6-trinitrotoluene (TNT) ring as nitrite or ammonium. These processes can occur simultaneously, as shown by the observation that a nasB mutant impaired in the reduction of nitrite to ammonium grew at a slower rate than the parental strain. Nitrogen from TNT is assimilated via the glutamine syntethase-glutamate synthase (GS-GOGAT) pathway, as evidenced by the inability of GOGAT mutants to use TNT. This pathway is also used to assimilate ammonium from reduced nitrate and nitrite. Three mutants that had insertions in ntrC, nasT, and cnmA, which encode regulatory proteins, failed to grow on nitrite but grew on TNT, although slower than the wild type. PMID:15601726

  1. Production of sensory compounds by means of the yeast Dekkera bruxellensis in different nitrogen sources with the prospect of producing cachaça.

    PubMed

    Castro Parente, Denise; Vidal, Esteban Espinosa; Leite, Fernanda Cristina Bezerra; de Barros Pita, Will; de Morais, Marcos Antonio

    2015-01-01

    The distilled spirit made from sugar cane juice, also known as cachaça, is a traditional Brazilian beverage that in recent years has increased its market share among international distilled beverages. Several volatile compounds produced by yeast cells during the fermentation process are responsible for the unique taste and aroma of this drink. The yeast Dekkera bruxellensis has acquired increasing importance in the fermented beverage production, as the different metabolites produced by this yeast may be either beneficial or harmful to the end-product. Since D. bruxellensis is often found in the fermentation processes carried out in ethanol fuel distillation in Brazil, we employed this yeast to analyse the physiological profile and production of aromatic compounds and to examine whether it is feasible to regard it as a cachaça-producing microorganism. The assays were performed on a small scale and simulated the conditions for the production of handmade cachaça. The results showed that the presence of aromatic and branched-chain amino acids in the medium has a strong influence on the metabolism and production of flavours by D. bruxellensis. The assimilation of these alternative nitrogen sources led to different fermentation yields and the production of flavouring compounds. The influence of the nitrogen source on the metabolism of fusel alcohols and esters in D. bruxellensis highlights the need for further studies of the nitrogen requirements to obtain the desired level of sensory compounds in the fermentation. Our results suggest that D. bruxellensis has the potential to play a role in the production of cachaça. Copyright © 2014 John Wiley & Sons, Ltd.

  2. Saccharomyces cerevisiae vineyard strains have different nitrogen requirements that affect their fermentation performances.

    PubMed

    Lemos Junior, W J F; Viel, A; Bovo, B; Carlot, M; Giacomini, A; Corich, V

    2017-11-01

    In this work the fermentation performances of seven vineyard strains, together with the industrial strain EC1118, have been investigated at three differing yeast assimilable nitrogen (YAN) concentrations (300 mg N l -1 , 150 mg N l -1 and 70 mg N l -1 ) in synthetic musts. The results indicated that the response to different nitrogen levels is strain dependent. Most of the strains showed a dramatic decrease of the fermentation at 70 mg N l -1 but no significant differences in CO 2 production were found when fermentations at 300 mg N l -1 and 150 mg N l -1 were compared. Only one among the vineyard strains showed a decrease of the fermentation when 150 mg N l -1 were present in the must. These results contribute to shed light on strain nitrogen requirements and offer new perspectives to manage the fermentation process during winemaking. Selected vineyard Saccharomyces cerevisiae strains can improve the quality and the complexity of local wines. Wine quality is also influenced by nitrogen availability that modulates yeast fermentation activity. In this work, yeast nitrogen assimilation was evaluated to clarify the nitrogen requirements of vineyard strains. Most of the strains needed high nitrogen levels to express the best fermentation performances. The results obtained indicate the critical nitrogen levels. When the nitrogen concentration was above the critical level, the fermentation process increased, but if the level of nitrogen was further increased no effect on the fermentation was found. © 2017 The Society for Applied Microbiology.

  3. 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

  4. Assimilation of diazotrophic nitrogen into pelagic food webs.

    PubMed

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

    2013-01-01

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

  5. Effects of inorganic nitrogen sources on the production of PP-V [(10Z)-12-carboxyl-monascorubramine] and the Expression of the nitrate assimilation gene cluster by Penicillium sp. AZ.

    PubMed

    Arai, Teppei; Umemura, Sara; Ota, Tamaki; Ogihara, Jun; Kato, Jun; Kasumi, Takafumi

    2012-01-01

    A fungal strain, Penicillium sp. AZ, produced the azaphilone Monascus pigment homolog when cultured in a medium composed of soluble starch, ammonium nitrate, yeast extract, and citrate buffer, pH 5.0. One of the typical features of violet pigment PP-V [(10Z)-12-carboxyl-monascorubramine] is that pyranoid oxygen is replaced with nitrogen. In this study, we found that ammonia and nitrate nitrogen are available for PP-V biosynthesis, and that ammonia nitrogen was much more effective than nitrate nitrogen. Further, we isolated nitrate assimilation gene cluster, niaD, niiA, and crnA, and analyzed the expression of these genes. The expression levels of all these genes increased with sodium nitrate addition to the culture medium. The results obtained here strongly suggest that Penicillium sp. AZ produced PP-V using nitrate in the form of ammonium reduced from nitrate through a bioprocess assimilatory reaction.

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

    PubMed

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

    2015-08-21

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

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

    PubMed

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

    2017-12-01

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

  8. Biomass Content Governs Fermentation Rate in Nitrogen-Deficient Wine Musts

    PubMed Central

    Varela, Cristian; Pizarro, Francisco; Agosin, Eduardo

    2004-01-01

    Problematic fermentations are common in the wine industry. Assimilable nitrogen deficiency is the most prevalent cause of sluggish fermentations and can reduce fermentation rates significantly. A lack of nitrogen diminishes a yeast's metabolic activity, as well as the biomass yield, although it has not been clear which of these two interdependent factors is more significant in sluggish fermentations. Under winemaking conditions with different initial nitrogen concentrations, metabolic flux analysis was used to isolate the effects. We quantified yeast physiology and identified key metabolic fluxes. We also performed cell concentration experiments to establish how biomass yield affects the fermentation rate. Intracellular analysis showed that trehalose accumulation, which is highly correlated with ethanol production, could be responsible for sustaining cell viability in nitrogen-poor musts independent of the initial assimilable nitrogen content. Other than the higher initial maintenance costs in sluggish fermentations, the main difference between normal and sluggish fermentations was that the metabolic flux distributions in nitrogen-deficient cultures revealed that the specific sugar uptake rate was substantially lower. The results of cell concentration experiments, however, showed that in spite of lower sugar uptake, adding biomass from sluggish cultures not only reduced the time to finish a problematic fermentation but also was less likely to affect the quality of the resulting wine as it did not alter the chemistry of the must. PMID:15184136

  9. 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

  10. Comparison of nitrogen depletion and repletion on lipid production in yeast and fungal species

    DOE PAGES

    Yang, Shihui; Wang, Wei; Wei, Hui; ...

    2016-08-29

    Although it is well known that low nitrogen stimulates lipid accumulation, especially for algae and some oleaginous yeast, few studies have been conducted in fungal species, especially on the impact of different nitrogen deficiency strategies. In this study, we use two promising consolidated bioprocessing (CBP) candidates to examine the impact of two nitrogen deficiency strategies on lipid production, which are the extensively investigated oleaginous yeast Yarrowia lipolytica, and the commercial cellulase producer Trichoderma reesei. We first utilized bioinformatics approaches to reconstruct the fatty acid metabolic pathway and demonstrated the presence of a triacylglycerol (TAG) biosynthesis pathway in Trichoderma reesei. Wemore » then examined the lipid production of Trichoderma reesei and Y. lipomyces in different media using two nitrogen deficiency strategies of nitrogen natural repletion and nitrogen depletion through centrifugation. Our results demonstrated that nitrogen depletion was better than nitrogen repletion with about 30% lipid increase for Trichoderma reesei and Y. lipomyces, and could be an option to improve lipid production in both oleaginous yeast and filamentous fungal species. The resulting distinctive lipid composition profiles indicated that the impacts of nitrogen depletion on yeast were different from those for fungal species. Under three types of C/N ratio conditions, C16 and C18 fatty acids were the predominant forms of lipids for both Trichoderma reesei and Y. lipolytica. In addition, while the overall fatty acid methyl ester (FAME) profiles of Trichoderma reesei were similar, the overall FAME profiles of Y. lipolytica observed a shift. The fatty acid metabolic pathway reconstructed in this work supports previous reports of lipid production in T. reesei, and provides a pathway for future omics studies and metabolic engineering efforts. Further investigation to identify the genetic targets responsible for the effect of nitrogen depletion

  11. Comparison of nitrogen depletion and repletion on lipid production in yeast and fungal species

    SciTech Connect

    Yang, Shihui; Wang, Wei; Wei, Hui

    Although it is well known that low nitrogen stimulates lipid accumulation, especially for algae and some oleaginous yeast, few studies have been conducted in fungal species, especially on the impact of different nitrogen deficiency strategies. In this study, we use two promising consolidated bioprocessing (CBP) candidates to examine the impact of two nitrogen deficiency strategies on lipid production, which are the extensively investigated oleaginous yeast Yarrowia lipolytica, and the commercial cellulase producer Trichoderma reesei. We first utilized bioinformatics approaches to reconstruct the fatty acid metabolic pathway and demonstrated the presence of a triacylglycerol (TAG) biosynthesis pathway in Trichoderma reesei. Wemore » then examined the lipid production of Trichoderma reesei and Y. lipomyces in different media using two nitrogen deficiency strategies of nitrogen natural repletion and nitrogen depletion through centrifugation. Our results demonstrated that nitrogen depletion was better than nitrogen repletion with about 30% lipid increase for Trichoderma reesei and Y. lipomyces, and could be an option to improve lipid production in both oleaginous yeast and filamentous fungal species. The resulting distinctive lipid composition profiles indicated that the impacts of nitrogen depletion on yeast were different from those for fungal species. Under three types of C/N ratio conditions, C16 and C18 fatty acids were the predominant forms of lipids for both Trichoderma reesei and Y. lipolytica. In addition, while the overall fatty acid methyl ester (FAME) profiles of Trichoderma reesei were similar, the overall FAME profiles of Y. lipolytica observed a shift. The fatty acid metabolic pathway reconstructed in this work supports previous reports of lipid production in T. reesei, and provides a pathway for future omics studies and metabolic engineering efforts. Further investigation to identify the genetic targets responsible for the effect of nitrogen depletion

  12. 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

  13. Impact of nutrient imbalance on wine alcoholic fermentations: nitrogen excess enhances yeast cell death in lipid-limited must.

    PubMed

    Tesnière, Catherine; Delobel, Pierre; Pradal, Martine; Blondin, Bruno

    2013-01-01

    We evaluated the consequences of nutritional imbalances, particularly lipid/nitrogen imbalances, on wine yeast survival during alcoholic fermentation. We report that lipid limitation (ergosterol limitation in our model) led to a rapid loss of viability during the stationary phase of fermentation and that the cell death rate is strongly modulated by nitrogen availability and nature. Yeast survival was reduced in the presence of excess nitrogen in lipid-limited fermentations. The rapidly dying yeast cells in fermentations in high nitrogen and lipid-limited conditions displayed a lower storage of the carbohydrates trehalose and glycogen than observed in nitrogen-limited cells. We studied the cell stress response using HSP12 promoter-driven GFP expression as a marker, and found that lipid limitation triggered a weaker stress response than nitrogen limitation. We used a SCH9-deleted strain to assess the involvement of nitrogen signalling pathways in the triggering of cell death. Deletion of SCH9 increased yeast viability in the presence of excess nitrogen, indicating that a signalling pathway acting through Sch9p is involved in this nitrogen-triggered cell death. We also show that various nitrogen sources, but not histidine or proline, provoked cell death. Our various findings indicate that lipid limitation does not elicit a transcriptional programme that leads to a stress response protecting yeast cells and that nitrogen excess triggers cell death by modulating this stress response, but not through HSP12. These results reveal a possibly negative role of nitrogen in fermentation, with reported effects referring to ergosterol limitation conditions. These effects should be taken into account in the management of alcoholic fermentations.

  14. Impact of Nutrient Imbalance on Wine Alcoholic Fermentations: Nitrogen Excess Enhances Yeast Cell Death in Lipid-Limited Must

    PubMed Central

    Tesnière, Catherine; Delobel, Pierre; Pradal, Martine; Blondin, Bruno

    2013-01-01

    We evaluated the consequences of nutritional imbalances, particularly lipid/nitrogen imbalances, on wine yeast survival during alcoholic fermentation. We report that lipid limitation (ergosterol limitation in our model) led to a rapid loss of viability during the stationary phase of fermentation and that the cell death rate is strongly modulated by nitrogen availability and nature. Yeast survival was reduced in the presence of excess nitrogen in lipid-limited fermentations. The rapidly dying yeast cells in fermentations in high nitrogen and lipid-limited conditions displayed a lower storage of the carbohydrates trehalose and glycogen than observed in nitrogen-limited cells. We studied the cell stress response using HSP12 promoter-driven GFP expression as a marker, and found that lipid limitation triggered a weaker stress response than nitrogen limitation. We used a SCH9-deleted strain to assess the involvement of nitrogen signalling pathways in the triggering of cell death. Deletion of SCH9 increased yeast viability in the presence of excess nitrogen, indicating that a signalling pathway acting through Sch9p is involved in this nitrogen-triggered cell death. We also show that various nitrogen sources, but not histidine or proline, provoked cell death. Our various findings indicate that lipid limitation does not elicit a transcriptional programme that leads to a stress response protecting yeast cells and that nitrogen excess triggers cell death by modulating this stress response, but not through HSP12. These results reveal a possibly negative role of nitrogen in fermentation, with reported effects referring to ergosterol limitation conditions. These effects should be taken into account in the management of alcoholic fermentations. PMID:23658613

  15. Root Ideotype Influences Nitrogen Transport and Assimilation in Maize

    PubMed Central

    Dechorgnat, Julie; Francis, Karen L.; Dhugga, Kanwarpal S.; Rafalski, J. A.; Tyerman, Stephen D.; Kaiser, Brent N.

    2018-01-01

    Maize (Zea mays, L.) yield is strongly influenced by external nitrogen inputs and their availability in the soil solution. Overuse of nitrogen-fertilizers can have detrimental ecological consequences through increased nitrogen pollution of water and the release of the potent greenhouse gas, nitrous oxide. To improve yield and overall nitrogen use efficiency (NUE), a deeper understanding of nitrogen uptake and utilization is required. This study examines the performance of two contrasting maize inbred lines, B73 and F44. F44 was selected in Florida on predominantly sandy acidic soils subject to nitrate leaching while B73 was selected in Iowa on rich mollisol soils. Transcriptional, enzymatic and nitrogen transport analytical tools were used to identify differences in their N absorption and utilization capabilities. Our results show that B73 and F44 differ significantly in their genetic, enzymatic, and biochemical root nitrogen transport and assimilatory pathways. The phenotypes show a strong genetic relationship linked to nitrogen form, where B73 showed a greater capacity for ammonium transport and assimilation whereas F44 preferred nitrate. The contrasting phenotypes are typified by differences in root system architecture (RSA) developed in the presence of both nitrate and ammonium. F44 crown roots were longer, had a higher surface area and volume with a greater lateral root number and density than B73. In contrast, B73 roots (primary, seminal, and crown) were more abundant but lacked the defining features of the F44 crown roots. An F1 hybrid between B73 and F44 mirrored the B73 nitrogen specificity and root architecture phenotypes, indicating complete dominance of the B73 inbred. This study highlights the important link between RSA and nitrogen management and why both variables need to be tested together when defining NUE improvements in any selection program. PMID:29740466

  16. 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.

  17. 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.

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

    PubMed

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

    2017-04-01

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

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

    PubMed

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

    2015-02-01

    The photosynthetic performance, carbon assimilation, and triacylglycerol accumulation of Isochrysis zhangjiangensis under nitrogen-deplete conditions were studied to understand the intrinsic correlations between them. The nitrogen-deplete period was divided into two stages based on the photosynthetic parameters. During the first stage, carbon assimilation was not reduced compared with that under favorable conditions. The marked increase in triacylglycerols and the variation in the fatty acid profile suggested that triacylglycerols were mainly derived from de novo synthesized acyl groups. In the second stage, the triacylglycerol content continued increasing while the carbohydrate content decreased from 44.0% to 26.3%. These results indicated that the intracellular conversion of carbohydrates to triacylglycerols occurred. Thus, we propose that sustainable carbon assimilation and incremental triacylglycerol production can be achieved by supplying appropriate amounts of nitrogen in medium to protect the photosynthetic process from severe damage using the photosynthetic parameters as indicators. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. 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.

  1. Characterization of the nitrogen compounds released during yeast autolysis in a model wine system.

    PubMed

    Martínez-Rodríguez, A J; Polo, M C

    2000-04-01

    The nitrogen composition of wines aged with yeast for a long period of time, as in the case of sparkling wines, depends on the composition of the base wine and on the compounds released by the yeast. In this paper, the release of the different classes of nitrogen compounds during autolysis of one of the strains of yeast used in the manufacture of sparkling wines has been studied. The yeast, Saccharomyces bayanus, was suspended in a model wine buffer, pH 3.0 and 10% ethanol, and incubated at 30 degrees C. Samples of the autolysate were taken after 4, 24, 48, 72, 168, and 360 h of autolysis. An electrophoretic and chromatographic study was conducted of the proteins, peptides with molecular weights higher and lower than 700 Da, and amino acids released during the autolysis. Using SDS-PAGE, it was observed that it was predominantly polypeptides with molecular weights lower than 10 000 that were released. Through HPLC of the fraction lower than 10 000 Da, it was observed that it is polypeptides with molecular weights of between 10 000 and 700 Da that are released first and that these later break up to give rise to peptides with molecular weights lower than 700 Da, which in turn break down into amino acids. This indicates that the nature of the nitrogen compounds present in wines aged with yeast depends on the aging time, being less polymerized as the aging time increases.

  2. 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

  3. 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

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

    PubMed

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

    2014-01-01

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

  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. Effects of wort gravity and nitrogen level on fermentation performance of brewer's yeast and the formation of flavor volatiles.

    PubMed

    Lei, Hongjie; Zhao, Haifeng; Yu, Zhimin; Zhao, Mouming

    2012-03-01

    Normal gravity wort and high gravity wort with different nitrogen levels were used to examine their effects on the fermentation performance of brewer's yeast and the formation of flavor volatiles. Results showed that both the wort gravity and nitrogen level had significant impacts on the growth rate, viability, flocculation, and gene expression of brewer's yeast and the levels of flavor volatiles. The sugar (glucose, maltose, and maltotriose) consumption rates and net cell growth decreased when high gravity worts were used, while these increased with increasing nitrogen level. Moreover, high gravity resulted in lower expression levels of ATF1, BAP2, BAT1, HSP12, and TDH, whereas the higher nitrogen level caused higher expression levels for these genes. Furthermore, the lower nitrogen level resulted in increases in the levels of higher alcohols and esters at high wort gravity. All these results demonstrated that yeast physiology and flavor balance during beer brewing were significantly affected by the wort gravity and nitrogen level.

  7. Wickerhamomyces xylosica sp. nov. and Candida phayaonensis sp. nov., two xylose-assimilating yeast species from soil.

    PubMed

    Limtong, Savitree; Nitiyon, Sukanya; Kaewwichian, Rungluk; Jindamorakot, Sasitorn; Am-In, Somjit; Yongmanitchai, Wichien

    2012-11-01

    Two strains (NT29(T) and NT31(T)) of xylose-assimilating yeasts were obtained from soils collected in northern Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer region, the two strains were found to represent two novel ascomycete yeast species. Strain NT29(T) was assigned to the genus Candida belonging to the Pichia clade as a representative of Candida phayaonensis sp. nov.; the type strain is NT29(T) (=BCC 47634(T)=NBRC 108868(T)=CBS 12319(T)). Strain NT31(T) represented a novel Wickerhamomyces species, which was named Wickerhamomyces xylosica sp. nov.; the type strain is NT31(T) (=BCC 47635(T)=NBRC 108869(T)=CBS 12320(T)).

  8. Assessing the Mechanisms Responsible for Differences between Nitrogen Requirements of Saccharomyces cerevisiae Wine Yeasts in Alcoholic Fermentation

    PubMed Central

    Brice, Claire; Sanchez, Isabelle; Tesnière, Catherine

    2014-01-01

    Nitrogen is an essential nutrient for Saccharomyces cerevisiae wine yeasts during alcoholic fermentation, and its abundance determines the fermentation rate and duration. The capacity to ferment under conditions of nitrogen deficiency differs between yeasts. A characterization of the nitrogen requirements of a set of 23 strains revealed large differences in their fermentative performances under nitrogen deficiency, and these differences reflect the nitrogen requirements of the strains. We selected and compared two groups of strains, one with low nitrogen requirements (LNRs) and the other with high nitrogen requirements (HNRs). A comparison of various physiological traits indicated that the differences are not related to the ability to store nitrogen or the protein content. No differences in protein synthesis activity were detected between strains with different nitrogen requirements. Transcriptomic analysis revealed expression patterns specific to each of the two groups of strains, with an overexpression of stress genes in HNR strains and a stronger expression of biosynthetic genes in LNR strains. Our data suggest that differences in glycolytic flux may originate from variations in nitrogen sensing and signaling under conditions of starvation. PMID:24334661

  9. Nitrogen recycling from fuel-extracted algal biomass: residuals as the sole nitrogen source for culturing Scenedesmus acutus.

    PubMed

    Gu, Huiya; Nagle, Nick; Pienkos, Philip T; Posewitz, Matthew C

    2015-05-01

    In this study, the reuse of nitrogen from fuel-extracted algal residues was investigated. The alga Scenedesmus acutus was found to be able to assimilate nitrogen contained in amino acids, yeast extracts, and proteinaceous alga residuals. Moreover, these alternative nitrogen resources could replace nitrate in culturing media. The ability of S. acutus to utilize the nitrogen remaining in processed algal biomass was unique among the promising biofuel strains tested. This alga was leveraged in a recycling approach where nitrogen is recovered from algal biomass residuals that remain after lipids are extracted and carbohydrates are fermented to ethanol. The protein-rich residuals not only provided an effective nitrogen resource, but also contributed to a carbon "heterotrophic boost" in subsequent culturing, improving overall biomass and lipid yields relative to the control medium with only nitrate. Prior treatment of the algal residues with Diaion HP20 resin was required to remove compounds inhibitory to algal growth. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Isolation and characterization of yeasts capable of efficient utilization of hemicellulosic hydrolyzate as the carbon source.

    PubMed

    Cassa-Barbosa, L A; Procópio, R E L; Matos, I T S R; Filho, S A

    2015-09-28

    Few yeasts have shown the potential to efficiently utilize hemicellulosic hydrolyzate as the carbon source. In this study, microorganisms isolated from the Manaus region in Amazonas, Brazil, were characterized based on their utilization of the pentoses, xylose, and arabinose. The yeasts that showed a potential to assimilate these sugars were selected for the better utilization of lignocellulosic biomass. Two hundred and thirty seven colonies of unicellular microorganisms grown on hemicellulosic hydrolyzate, xylose, arabinose, and yeast nitrogen base selective medium were analyzed. Of these, 231 colonies were subjected to sugar assimilation tests. One hundred and twenty five of these were shown to utilize hydrolyzed hemicellulose, xylose, or arabinose as the carbon source for growth. The colonies that showed the best growth (N = 57) were selected, and their internal transcribed spacer-5.8S rDNA was sequenced. The sequenced strains formed four distinct groups in the phylogenetic tree, and showed a high percentage of similarity with Meyerozyma caribbica, Meyerozyma guilliermondii, Trichosporon mycotoxinivorans, Trichosporon loubieri, Pichia kudriavzevii, Candida lignohabitans, and Candida ethanolica. The discovery of these xylose-fermenting yeasts could attract widespread interest, as these can be used in the cost-effective production of liquid fuel from lignocellulosic materials.

  11. Concerted evolution of life stage performances signals recent selection on yeast nitrogen use.

    PubMed

    Ibstedt, Sebastian; Stenberg, Simon; Bagés, Sara; Gjuvsland, Arne B; Salinas, Francisco; Kourtchenko, Olga; Samy, Jeevan K A; Blomberg, Anders; Omholt, Stig W; Liti, Gianni; Beltran, Gemma; Warringer, Jonas

    2015-01-01

    Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that an organism's life stages are exposed to the same environmental variations, we reasoned that fitness components, such as the lag, rate, and efficiency of growth, directly reflecting performance in these life stages, should often be selected in concert. We therefore conjectured that correlations between fitness components over natural isolates, in a particular environmental context, would constitute a robust signal of recent selection. Critically, this test for selection requires fitness components to be determined by different genetic loci. To explore our conjecture, we exhaustively evaluated the lag, rate, and efficiency of asexual population growth of natural isolates of the model yeast Saccharomyces cerevisiae in a large variety of nitrogen-limited environments. Overall, fitness components were well correlated under nitrogen restriction. Yeast isolates were further crossed in all pairwise combinations and coinheritance of each fitness component and genetic markers were traced. Trait variations tended to map to quantitative trait loci (QTL) that were private to a single fitness component. We further traced QTLs down to single-nucleotide resolution and uncovered loss-of-function mutations in RIM15, PUT4, DAL1, and DAL4 as the genetic basis for nitrogen source use variations. Effects of SNPs were unique for a single fitness component, strongly arguing against pleiotropy between lag, rate, and efficiency of reproduction under nitrogen restriction. The strong correlations between life stage performances that cannot be explained by pleiotropy compellingly support adaptive differentiation of yeast nitrogen source use and suggest a generic approach for detecting selection. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e

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

    PubMed Central

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

  14. Cryptococcus friedmannii, a new species of yeast from the Antarctic

    NASA Technical Reports Server (NTRS)

    Vishniac, H. S.

    1985-01-01

    Cryptococcus friedmannii Vishniac sp. nov. from an Antarctic cryptoendolithic community is a psychrophilic basidioblastomycete characterized by cream-colored colonies of cells with smooth, layered walls, budding monopolarly, producing amylose and extracellular proteinase, utilizing nitrate and D-alanine (inter alia) as nitrogen sources and L-arabinose, arbutin, cellobiose, D-glucuronate, maltose, melezitose, salicin, soluble starch, trehalose, and D-xylose as carbon sources. This species differs from all other basidiomycetous yeasts in possessing the following combination of characters: amylose production (positive), assimilation of cellobiose (positive), D-galactose (negative), myo-inositol (negative), D-mannitol (negative), and sucrose (negative).

  15. Nitrogen-source preference in blueberry (Vaccinium sp.): Enhanced shoot nitrogen assimilation in response to direct supply of nitrate.

    PubMed

    Alt, Douglas S; Doyle, John W; Malladi, Anish

    2017-09-01

    Blueberry (Vaccinium sp.) is thought to display a preference for the ammonium (NH 4 + ) form over the nitrate (NO 3 - ) form of inorganic nitrogen (N). This N-source preference has been associated with a generally low capacity to assimilate the NO 3 - form of N, especially within the shoot tissues. Nitrate assimilation is mediated by nitrate reductase (NR), a rate limiting enzyme that converts NO 3 - to nitrite (NO 2 - ). We investigated potential limitations of NO 3 - assimilation in two blueberry species, rabbiteye (Vaccinium ashei) and southern highbush (Vaccinium corymbosum) by supplying NO 3 - to the roots, leaf surface, or through the cut stem. Both species displayed relatively low but similar root uptake rates for both forms of inorganic N. Nitrate uptake through the roots transiently increased NR activity by up to 3.3-fold and root NR gene expression by up to 4-fold. However, supplying NO 3 - to the roots did not increase its transport in the xylem, nor did it increase NR activity in the leaves, indicating that the acquired N was largely assimilated or stored within the roots. Foliar application of NO 3 - increased leaf NR activity by up to 3.5-fold, but did not alter NO 3 - metabolism-related gene expression, suggesting that blueberries are capable of post translational regulation of NR activity in the shoots. Additionally, supplying NO 3 - to the cut ends of stems resulted in around a 5-fold increase in NR activity, a 10-fold increase in NR transcript accumulation, and up to a 195-fold increase in transcript accumulation of NITRITE REDUCTASE (NiR1) which codes for the enzyme catalyzing the conversion of NO 2 - to NH 4 + . These data indicate that blueberry shoots are capable of assimilating NO 3 - when it is directly supplied to these tissues. Together, these data suggest that limitations in the uptake and translocation of NO 3 - to the shoots may limit overall NO 3 - assimilation capacity in blueberry. Copyright © 2017 Elsevier GmbH. All rights reserved.

  16. 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.

  17. Bioconversion of Xylan to triglycerides by oil-rich yeasts. [Cryptococcus albidus; Cryptococcus terricoluus; Trichosporon

    SciTech Connect

    Fall, R.; Phelps, P.; Spindler, D.

    A series of lipid-accumulating yeasts was examined for their potential to saccharify xylan and accumulate triglyceride. Of the genera tested, including Candida, Cryptococcus, Lipomyces, Rhodosporidium, Rhodotorula, and Trichosporon, only Crytococcus and Trichosporon isolates saccharified xylan. All of the strains could assimilate xylose and accumuate triglyceride under nitrogen-limiting conditions. Strains of Cryptococcus albidus were found to be especially useful for a one-step saccharification of xylan coupled to triglyceride synthesis. Crytococcus terricolus, a strain constitutive for lipid accumulation, lacked extracellular xylanase, but did assimilate xylose and xylobiose and was able to continuously convert xylan to triglyceride if the culture medium was supplementedmore » with xylanase. 22 references.« less

  18. Peptide (Lys-Leu) and amino acids (Lys and Leu) supplementations improve physiological activity and fermentation performance of brewer's yeast during very high-gravity (VHG) wort fermentation.

    PubMed

    Yang, Huirong; Zong, Xuyan; Cui, Chun; Mu, Lixia; Zhao, Haifeng

    2017-12-22

    Lys and Leu were generally considered as the key amino acids for brewer's yeast during beer brewing. In the present study, peptide Lys-Leu and a free amino acid (FAA) mixture of Lys and Leu (Lys + Leu) were supplemented in 24 °P wort to examine their effects on physiological activity and fermentation performance of brewer's yeast during very high-gravity (VHG) wort fermentation. Results showed that although both peptide Lys-Leu and their FAA mixture supplementations could increase the growth and viability, intracellular trehalose and glycerol content, wort fermentability, and ethanol content for brewer's yeast during VHG wort fermentation, and peptide was better than their FAA mixture at promoting growth and fermentation for brewer's yeast when the same dose was kept. Moreover, peptide Lys-Leu supplementation significantly increased the assimilation of Asp, but decreased the assimilation of Gly, Ala, Val, (Cys)2, Ile, Leu, Tyr, Phe, Lys, Arg, and Pro. However, the FAA mixture supplementation only promoted the assimilation of Lys and Leu, while reduced the absorption of total amino acids to a greater extent. Thus, the peptide Lys-Leu was more effective than their FAA mixture on the improvement of physiological activity, fermentation performance, and nitrogen metabolism of brewer's yeast during VHG wort fermentation. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

  19. 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

  20. Nitrate signals determine the sensing of nitrogen through differential expression of genes involved in nitrogen uptake and assimilation in finger millet.

    PubMed

    Gupta, Alok Kumar; Gaur, Vikram Singh; Gupta, Sanjay; Kumar, Anil

    2013-06-01

    In order to understand the molecular basis of high nitrogen use efficiency of finger millet, five genes (EcHNRT2, EcLNRT1, EcNADH-NR, EcGS, and EcFd-GOGAT) involved in nitrate uptake and assimilation were isolated using conserved primer approaches. Expression profiles of these five genes along with the previously isolated EcDof1 was studied under increased KNO3 concentrations (0.15 to 1,500 μM) for 2 h as well as at 1.5 μM for 24 h in the roots and shoots of 25 days old nitrogen deprived two contrasting finger millet genotypes (GE-3885 and GE-1437) differing in grain protein content (13.76 and 6.15 %, respectively). Time kinetics experiment revealed that, all the five genes except EcHNRT2 in the leaves of GE-3885 were induced within 30 min of nitrate exposure indicating that there might be a greater nitrogen deficit in leaves and therefore quick transportation of nitrate signals to the leaves. Exposing the plants to increasing nitrate concentrations for 2 h showed that in roots of GE-3885, NR was strongly induced while GS was repressed; however, the pattern was found to be reversed in leaves of GE-1437 indicating that in GE-3885, most of the nitrate might be reduced in the roots but assimilated in leaves and vice-versa. Furthermore, compared with the low-protein genotype, expression of HNRT2 was strongly induced in both roots and shoots of high-protein genotype at the least nitrate concentration supplied. This further indicates that GE-3885 is a quick sensor of nitrogen compared with the low-protein genotype. Furthermore, expression of EcDof1 was also found to overlap the expression of NR, GS, and GOGAT indicating that Dof1 probably regulates the expression of these genes under different conditions by sensing the nitrogen fluctuations around the root zone.

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

    PubMed

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

    2016-11-22

    Most investigations of biogeochemically important microbes have focused on plastic (short-term) phenotypic responses in the absence of genetic change, whereas few have investigated adaptive (long-term) responses. However, no studies to date have investigated the molecular progression underlying the transition from plasticity to adaptation under elevated CO 2 for a marine nitrogen-fixer. To address this gap, we cultured the globally important cyanobacterium Trichodesmium at both low and high CO 2 for 4.5 y, followed by reciprocal transplantation experiments to test for adaptation. Intriguingly, fitness actually increased in all high-CO 2 adapted cell lines in the ancestral environment upon reciprocal transplantation. By leveraging coordinated phenotypic and transcriptomic profiles, we identified expression changes and pathway enrichments that rapidly responded to elevated CO 2 and were maintained upon adaptation, providing strong evidence for genetic assimilation. These candidate genes and pathways included those involved in photosystems, transcriptional regulation, cell signaling, carbon/nitrogen storage, and energy metabolism. Conversely, significant changes in specific sigma factor expression were only observed upon adaptation. These data reveal genetic assimilation as a potentially adaptive response of Trichodesmium and importantly elucidate underlying metabolic pathways paralleling the fixation of the plastic phenotype upon adaptation, thereby contributing to the few available data demonstrating genetic assimilation in microbial photoautotrophs. These molecular insights are thus critical for identifying pathways under selection as drivers in plasticity and adaptation.

  2. The influence of nitrogen and biotin interactions on the performance of Saccharomyces in alcoholic fermentations.

    PubMed

    Bohlscheid, J C; Fellman, J K; Wang, X D; Ansen, D; Edwards, C G

    2007-02-01

    To study the impact of assimilable nitrogen, biotin and their interaction on growth, fermentation rate and volatile formation by Saccharomyces. Fermentations of synthetic grape juice media were conducted in a factorial design with yeast assimilable nitrogen (YAN) (60 or 250 mg l(-1)) and biotin (0, 1 or 10 microg l(-1)) as variables. All media contained 240 g l(-1) glucose + fructose (1 : 1) and were fermented using biotin-depleted Saccharomyces cerevisiae strains EC1118 or UCD 522. Both strains exhibited weak growth and sluggish fermentation rates without biotin. Increased nitrogen concentration resulted in higher maximum fermentation rates, while adjusting biotin from 1 to 10 microg l(-1) had no effect. Nitrogen x biotin interactions influenced fermentation time, production of higher alcohols and hydrogen sulfide (H(2)S). Maximum H(2)S production occurred in the medium containing 60 mg l(-1) YAN and 1 microg l(-1) biotin. Nitrogen x biotin interactions affect fermentation time and volatile production by Saccharomyces depending on strain. Biotin concentrations sufficient to complete fermentation may affect the organoleptic impact of wine. This study demonstrates the necessity to consider nutrient interactions when diagnosing problem fermentations.

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

    PubMed

    Esen, Merve; Ozturk Urek, Raziye

    2015-01-01

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

  4. Influence of carbon and nitrogen source on production of volatile fragrance and flavour metabolites by the yeast Kluyveromyces marxianus.

    PubMed

    Gethins, Loughlin; Guneser, Onur; Demirkol, Aslı; Rea, Mary C; Stanton, Catherine; Ross, R Paul; Yuceer, Yonca; Morrissey, John P

    2015-01-01

    The yeast Kluyveromyces marxianus produces a range of volatile molecules with applications as fragrances or flavours. The purpose of this study was to establish how nutritional conditions influence the production of these metabolites. Four strains were grown on synthetic media, using a variety of carbon and nitrogen sources and volatile metabolites analysed using gas chromatography-mass spectrometry (GC-MS). The nitrogen source had pronounced effects on metabolite production: levels of the fusel alcohols 2-phenylethanol and isoamyl alcohol were highest when yeast extract was the nitrogen source, and ammonium had a strong repressing effect on production of 2-phenylethyl acetate. In contrast, the nitrogen source did not affect production of isoamyl acetate or ethyl acetate, indicating that more than one alcohol acetyl transferase activity is present in K. marxianus. Production of all acetate esters was low when cells were growing on lactose (as opposed to glucose or fructose), with a lower intracellular pool of acetyl CoA being one explanation for this observation. Bioinformatic and phylogenetic analysis of the known yeast alcohol acetyl transferases ATF1 and ATF2 suggests that the ancestral protein Atf2p may not be involved in synthesis of volatile acetate esters in K. marxianus, and raises interesting questions as to what other genes encode this activity in non-Saccharomyces yeasts. Identification of all the genes involved in ester synthesis will be important for development of the K. marxianus platform for flavour and fragrance production. Copyright © 2014 John Wiley & Sons, Ltd.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  6. Specific phenotypic traits of Starmerella bacillaris regarding nitrogen source consumption and central carbon metabolites production during wine fermentation.

    PubMed

    Englezos, Vasileios; Cocolin, Luca; Rantsiou, Kalliopi; Ortiz-Julien, Anne; Bloem, Audrey; Dequin, Sylvie; Camarasa, Carole

    2018-06-01

    Over the last past years, the potential of non-Saccharomyces yeasts to improve the sensory quality of wine has been well recognized. In particular, the use of Starmerella bacillaris in mixed fermentations with Saccharomyces cerevisiae was reported as an appropriate way to enhance glycerol formation and reduce ethanol production. However, during sequential fermentation, many factors as the inoculation timing, strain combination and physical and biochemical interactions can affect yeast growth, fermentation process and/or metabolite synthesis. Among them, yeast assimilable nitrogen (YAN) availability, due to its role in the control of growth and fermentation, has been identified as a key parameter. Consequently, a comprehensive understanding of the metabolic specificities and the nitrogen requirements would be valuable to better exploit the potential of Starm. bacillaris during wine fermentation. In this study, marked differences in the consumption of the total and individual nitrogen sources were registered between the two species, while the two Starm. bacillaris strains generally behaved uniformly. Starm. bacillaris strains are differentiated by their preferential uptake of ammonium compared with amino acids that are poorly assimilated or even produced (alanine). Otherwise, the non- Saccharomyces yeast exhibits low activity through the acetaldehyde pathway, which triggers an important redistribution of fluxes through the central carbon metabolic network. In particular, the formation of metabolites deriving from the two glycolytic intermediates glyceraldehyde-3-phosphate and pyruvate is substantially increased during fermentations by Starm. bacillaris This knowledge will be useful to better control the fermentation process in mixed fermentation with Starm. bacillaris and S. cerevisiae IMPORTANCE Mixed fermentations using a controlled inoculation of Starm. bacillaris and S. cerevisiae starter cultures represent a feasible way to modulate wine composition that takes

  7. Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses.

    PubMed

    Cubillos, Francisco A; Brice, Claire; Molinet, Jennifer; Tisné, Sebastién; Abarca, Valentina; Tapia, Sebastián M; Oporto, Christian; García, Verónica; Liti, Gianni; Martínez, Claudio

    2017-06-07

    Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1 , PDC1 , CPS1 , ASI2 , LYP1 , and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics. Copyright © 2017 Cubillos et al.

  8. Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

    PubMed Central

    Cubillos, Francisco A.; Brice, Claire; Molinet, Jennifer; Tisné, Sebastién; Abarca, Valentina; Tapia, Sebastián M.; Oporto, Christian; García, Verónica; Liti, Gianni; Martínez, Claudio

    2017-01-01

    Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics. PMID:28592651

  9. Arxula adeninivorans (Blastobotrys adeninivorans) — A Dimorphic Yeast of Great Biotechnological Potential

    NASA Astrophysics Data System (ADS)

    Böer, Erik; Steinborn, Gerhard; Florschütz, Kristina; Körner, Martina; Gellissen, Gerd; Kunze, Gotthard

    The dimorphic ascomycetous yeast Arxula adeninivorans exhibits some unusual properties. Being a thermo- and halotolerant species it is able to assimilate and ferment many compounds as sole carbon and/or nitrogen source. It utilises n-alkanes and is capable of degrading starch. Due to these unusual biochemical properties A. adeninivorans can be exploited as a gene donor for the production of enzymes with attractive biotechnological characteristics. Examples of A. adeninivorans-derived genes that are overexpressed include the ALIP1 gene encoding a secretory lipase, the AINV encoding invertase, the AXDH encoding xylitol dehydrogenase and the APHY encoding a secretory phosphatase with phytase activity.

  10. A set of nutrient limitations trigger yeast cell death in a nitrogen-dependent manner during wine alcoholic fermentation

    PubMed Central

    Duc, Camille; Pradal, Martine; Sanchez, Isabelle; Noble, Jessica; Tesnière, Catherine

    2017-01-01

    Yeast cell death can occur during wine alcoholic fermentation. It is generally considered to result from ethanol stress that impacts membrane integrity. This cell death mainly occurs when grape musts processing reduces lipid availability, resulting in weaker membrane resistance to ethanol. However the mechanisms underlying cell death in these conditions remain unclear. We examined cell death occurrence considering yeast cells ability to elicit an appropriate response to a given nutrient limitation and thus survive starvation. We show here that a set of micronutrients (oleic acid, ergosterol, pantothenic acid and nicotinic acid) in low, growth-restricting concentrations trigger cell death in alcoholic fermentation when nitrogen level is high. We provide evidence that nitrogen signaling is involved in cell death and that either SCH9 deletion or Tor inhibition prevent cell death in several types of micronutrient limitation. Under such limitations, yeast cells fail to acquire any stress resistance and are unable to store glycogen. Unexpectedly, transcriptome analyses did not reveal any major changes in stress genes expression, suggesting that post-transcriptional events critical for stress response were not triggered by micronutrient starvation. Our data point to the fact that yeast cell death results from yeast inability to trigger an appropriate stress response under some conditions of nutrient limitations most likely not encountered by yeast in the wild. Our conclusions provide a novel frame for considering both cell death and the management of nutrients during alcoholic fermentation. PMID:28922393

  11. Production of Bakers' Yeast in Cheese Whey Ultrafiltrate †

    PubMed Central

    Champagne, C. P.; Goulet, J.; Lachance, R. A.

    1990-01-01

    A process for the production of bakers' yeast in whey ultrafiltrate (WU) is described. Lactose in WU was converted to lactic acid and galactose by fermentation. Streptococcus thermophilus was selected for this purpose. Preculturing of S. thermophilus in skim milk considerably reduced its lag. Lactic fermentation in 2.3×-concentrated WU was delayed compared with that in unconcentrated whey, and fermentation could not be completed within 60 h. The growth rate of bakers' yeast in fermented WU differed among strains. The rate of galactose utilization was similar for all strains, but differences in lactic acid utilization occurred. Optimal pH ranges for galactose and lactic acid utilization were 5.5 to 6.0 and 5.0 to 5.5, respectively. The addition of 4 g of corn steep liquor per liter to fermented WU increased cell yields. Two sources of nitrogen were available for growth of Saccharomyces cerevisiae: amino acids (corn steep liquor) and ammonium (added during the lactic acid fermentation). Ammonium was mostly assimilated during growth on lactic acid. This process could permit the substitution of molasses by WU for the industrial production of bakers' yeast. PMID:16348117

  12. TORC1 activity is partially reduced under nitrogen starvation conditions in sake yeast Kyokai no. 7, Saccharomyces cerevisiae.

    PubMed

    Nakazawa, Nobushige; Sato, Aya; Hosaka, Masahiro

    2016-03-01

    Industrial yeasts are generally unable to sporulate but treatment with the immunosuppressive drug rapamycin restores this ability in a sake yeast strain Kyokai no. 7 (K7), Saccharomyces cerevisiae. This finding suggests that TORC1 is active under sporulation conditions. Here, using a reporter gene assay, Northern and Western blots, we tried to gain insight into how TORC1 function under nitrogen starvation conditions in K7 cells. Similarly to a laboratory strain, RPS26A transcription was repressed and Npr1 was dephosphorylated in K7 cells, indicative of the expected loss of TORC1 function under nitrogen starvation. The expression of nitrogen catabolite repression-sensitive genes, however, was not induced, the level of Cln3 remained constant, and autophagy was more slowly induced than in a laboratory strain, all suggestive of active TORC1. We conclude that TORC1 activity is partially reduced under nitrogen starvation conditions in K7 cells. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  13. A mutated hygromycin resistance gene is functional in the n-alkane-assimilating yeast Candida tropicalis.

    PubMed

    Hara, A; Ueda, M; Misawa, S; Matsui, T; Furuhashi, K; Tanaka, A

    2000-03-01

    Development of a transformation system in the n-alkane-assimilating diploid yeast Candida tropicalis requires an antibiotic resistance gene in order to establish a selectable marker. The resistance gene for hygromycin B has often been used as a selectable marker in yeast transformation. However, C. tropicalis harboring the hygromycin resistance gene (HYG) was as sensitive to hygromycin B as the wild-type strain. Nine CTG codons were found in the ORF of the HYG gene. This codon has been reported to be translated as serine rather than leucine in Candida species. Analysis of the tRNA gene in C. tropicalis with the anticodon CAG [tRNA(CAG) gene], which is complementary to the codon CTG, showed that the sequence was highly similar to that of the C. maltosa tRNA(CAG) gene. In C. maltosa, the codon CTG is read as serine and not leucine. These results suggested that the HYG gene was not functional due to the nonuniversal usage of the CTG codon. Each of the nine CTG codons in the ORF of the HYG gene was changed to a CTC codon, which is read as leucine, by site-directed mutagenesis. When a plasmid containing the mutated HYG gene (HYG#) was constructed and introduced into C. tropicalis, hygromycin-resistant transformants were successfully obtained. This mutated hygromycin resistance gene may be useful for direct selection of C. tropicalis transformants.

  14. Target of rapamycin complex 1 and Tap42-associated phosphatases are required for sensing changes in nitrogen conditions in the yeast Saccharomyces cerevisiae.

    PubMed

    Li, Jinmei; Yan, Gonghong; Liu, Sichi; Jiang, Tong; Zhong, Mingming; Yuan, Wenjie; Chen, Shaoxian; Zheng, Yin; Jiang, Yong; Jiang, Yu

    2017-12-01

    In yeast target of rapamycin complex 1 (TORC1) and Tap42-associated phosphatases regulate expression of genes involved in nitrogen limitation response and the nitrogen discrimination pathway. However, it remains unclear whether TORC1 and the phosphatases are required for sensing nitrogen conditions. Utilizing temperature sensitive mutants of tor2 and tap42, we examined the role of TORC1 and Tap42 in nuclear entry of Gln3, a key transcription factor in yeast nitrogen metabolism, in response to changes in nitrogen conditions. Our data show that TORC1 is essential for Gln3 nuclear entry upon nitrogen limitation and downshift in nitrogen quality. However, Tap42-associated phosphatases are required only under nitrogen limitation condition. In cells grown in poor nitrogen medium, the nitrogen permease reactivator kinase (Npr1) inhibits TORC1 activity and alters its association with Tap42, rendering Tap42-associated phosphatases unresponsive to nitrogen limitation. These findings demonstrate a direct role for TORC1 and Tap42-associated phosphatases in sensing nitrogen conditions and unveil an Npr1-dependent mechanism that controls TORC1 and the phosphatases in response to changes in nitrogen quality. © 2017 John Wiley & Sons Ltd.

  15. Rootstock and vineyard floor management influence on 'Cabernet Sauvignon' grape yeast assimilable nitrogen (YAN).

    PubMed

    Lee, Jungmin; Steenwerth, Kerri L

    2011-08-01

    This is a study on the influence that two rootstocks (110R, high vigour; 420A, low vigour) and three vineyard floor management regimes (tilled resident vegetation - usual practise in California, and barley cover crops that were either mowed or tilled) had upon grape nitrogen-containing compounds (mainly ammonia and free amino acids recalculated as YAN), sugars, and organic acids in 'Cabernet Sauvignon' clone 8. A significant difference was observed for some of the free amino acids between rootstocks. In both sample preparation methods (juiced or chemically extracted), 110R rootstock grapes were significantly higher in SER, GLN, THR, ARG, VAL, ILE, LEU, and YAN than were 420A rootstock grapes. Differences in individual free amino acid profiles and concentrations were observed between the two sample preparations, which indicate that care should be taken when comparing values from dissimilar methods. No significant differences among vineyard floor treatments were detected, which suggests that mowing offers vineyard managers a sustainable practise, alternative to tilling, without negatively affecting grape nitrogen compounds, sugars, or organic acids. Published by Elsevier Ltd.

  16. Extracellular enzymatic activities and physiological profiles of yeasts colonizing fruit trees.

    PubMed

    Molnárová, Jana; Vadkertiová, Renáta; Stratilová, Eva

    2014-07-01

    Yeasts form a significant and diverse part of the phyllosphere microbiota. Some yeasts that inhabit plants have been found to exhibit extracellular enzymatic activities. The aim of the present study was to investigate the ability of yeasts isolated from leaves, fruits, and blossoms of fruit trees cultivated in Southwest Slovakia to produce extracellular enzymes, and to discover whether the yeasts originating from these plant organs differ from each other in their physiological properties. In total, 92 strains belonging to 29 different species were tested for: extracellular protease, β-glucosidase, lipase, and polygalacturonase activities; fermentation abilities; the assimilation of xylose, saccharose and alcohols (methanol, ethanol, glycerol); and for growth in a medium with 33% glucose. The black yeast Aureobasidium pullulans showed the largest spectrum of activities of all the species tested. Almost 70% of the strains tested demonstrated some enzymatic activity, and more than 90% utilized one of the carbon compounds tested. Intraspecies variations were found for the species of the genera Cryptococcus and Pseudozyma. Interspecies differences of strains exhibiting some enzymatic activities and utilizing alcohols were also noted. The largest proportion of the yeasts exhibited β-glucosidase activity and assimilated alcohols independently of their origin. The highest number of strains positive for all activities tested was found among the yeasts associated with leaves. Yeasts isolated from blossoms assimilated saccharose and D-xylose the most frequently of all the yeasts tested. The majority of the fruit-inhabiting yeasts grew in the medium with higher osmotic pressure. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. CHROMagar Candida as the Sole Primary Medium for Isolation of Yeasts and as a Source Medium for the Rapid-Assimilation-of-Trehalose Test

    PubMed Central

    Murray, Melissa P.; Zinchuk, Riva; Larone, Davise H.

    2005-01-01

    The chromogenic medium BBL CHROMagar Candida (CAC) was evaluated as a sole primary medium for the isolation of yeasts from clinical specimens in which yeasts are the primary concern. Additionally, the reliability of the rapid-assimilation-of-trehalose (RAT) test in yielding correct results with isolates taken from CAC was assessed. A total of 270 throat, urine, and genital (TUG) specimens were streaked onto CAC, Sabouraud dextrose agar (SDA), inhibitory mold agar (IMA), and Mycosel (MYC). A total of 69 blood culture broths that were smear positive for yeast were streaked onto CAC and SDA. A 1-h RAT test (NCCLS M35-A) was performed simultaneously on isolates from CAC and SDA. A total of 112 TUG specimens yielded yeast colonies (CAC, 111 colonies; IMA, 105; SDA, 103; MYC, 91). The 69 blood culture yeasts grew on both CAC and SDA. Mixed cultures of yeasts were detected on 11 CAC plates but were unrecognized on other media. Colonies suspected of being C. glabrata on 32 CAC plates were all RAT test positive and confirmed to be C. glabrata; of 59 colonies with various characteristics of color and morphology on CAC, none were RAT positive, and all were conventionally identified as yeasts other than C. glabrata (sensitivity and specificity, 100%). The same isolates from SDA tested for RAT produced six false negatives and no false positives (sensitivity, 81%; specificity, 100%). The results show that CAC can be used as the sole primary medium for recovery of yeasts from clinical specimens. Additionally, isolates grown on CAC yield excellent results with the RAT test utilized in this study. PMID:15750085

  18. CHROMagar Candida as the sole primary medium for isolation of yeasts and as a source medium for the rapid-assimilation-of-trehalose test.

    PubMed

    Murray, Melissa P; Zinchuk, Riva; Larone, Davise H

    2005-03-01

    The chromogenic medium BBL CHROMagar Candida (CAC) was evaluated as a sole primary medium for the isolation of yeasts from clinical specimens in which yeasts are the primary concern. Additionally, the reliability of the rapid-assimilation-of-trehalose (RAT) test in yielding correct results with isolates taken from CAC was assessed. A total of 270 throat, urine, and genital (TUG) specimens were streaked onto CAC, Sabouraud dextrose agar (SDA), inhibitory mold agar (IMA), and Mycosel (MYC). A total of 69 blood culture broths that were smear positive for yeast were streaked onto CAC and SDA. A 1-h RAT test (NCCLS M35-A) was performed simultaneously on isolates from CAC and SDA. A total of 112 TUG specimens yielded yeast colonies (CAC, 111 colonies; IMA, 105; SDA, 103; MYC, 91). The 69 blood culture yeasts grew on both CAC and SDA. Mixed cultures of yeasts were detected on 11 CAC plates but were unrecognized on other media. Colonies suspected of being C. glabrata on 32 CAC plates were all RAT test positive and confirmed to be C. glabrata; of 59 colonies with various characteristics of color and morphology on CAC, none were RAT positive, and all were conventionally identified as yeasts other than C. glabrata (sensitivity and specificity, 100%). The same isolates from SDA tested for RAT produced six false negatives and no false positives (sensitivity, 81%; specificity, 100%). The results show that CAC can be used as the sole primary medium for recovery of yeasts from clinical specimens. Additionally, isolates grown on CAC yield excellent results with the RAT test utilized in this study.

  19. Efficient resource recycling from liquid digestate by microalgae-yeast mixed culture and the assessment of key gene transcription related to nitrogen assimilation in microalgae.

    PubMed

    Qin, Lei; Liu, Lu; Wang, Zhongming; Chen, Weining; Wei, Dong

    2018-05-18

    To determine the feasibility of microalgae-yeast mixed culture using the liquid digestate of dairy wastewater (LDDW) for biofuels and single cell protein (SCP) production, the cell growth, nutrient removal and outputs evaluation of the mono and mixed culture of Chlorella vulgaris and Yarrowia lipolytica in LDDW were investigated by adding glycerol as carbon source. The results showed that the mixed culture could enhance the biological utilization efficiency of nitrogen and phosphorus, and obtain higher yield of biomass (1.62 g/L), lipid (0.31 g/L), protein (0.51 g/L), and higher heating value (34.06 KJ/L). Compared with the mono culture of C. vulgaris, a decline of the transcription level in nitrate reductase and glutamine synthetase II genes in C. vulgaris was observed in the mixed culture when ammonia was sufficient. The results suggest the possibility of using the mixed culture for the efficient treatment of LDDW and resources recycling. Copyright © 2018. Published by Elsevier Ltd.

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

    EPA Science Inventory

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

  1. Nitrogen requirements of commercial wine yeast strains during fermentation of a synthetic grape must.

    PubMed

    Gutiérrez, Alicia; Chiva, Rosana; Sancho, Marta; Beltran, Gemma; Arroyo-López, Francisco Noé; Guillamon, José Manuel

    2012-08-01

    Nitrogen deficiencies in grape musts are one of the main causes of stuck or sluggish wine fermentations. Currently, the most common method for dealing with nitrogen-deficient fermentations is adding supplementary nitrogen (usually ammonium phosphate). However, it is important to know the specific nitrogen requirement of each strain, to avoid excessive addition that can lead to microbial instability and ethyl carbamate accumulation. In this study, we aimed to determine the effect of increasing nitrogen concentrations of three different nitrogen sources on growth and fermentation performance in four industrial wine yeast strains. This task was carried out using statistical modeling techniques. The strains PDM and RVA showed higher growth-rate and maximum population size and consumed nitrogen much more quickly than strains ARM and TTA. Likewise, the strains PDM and RVA were also the greatest nitrogen demanders. Thus, we can conclude that these differences in nitrogen demand positively correlated with higher growth rate and higher nitrogen uptake rate. The most direct effect of employing an adequate nitrogen concentration is the increase in biomass, which involves a higher fermentation rate. However, the impact of nitrogen on fermentation rate is not exclusively due to the increase in biomass because the strain TTA, which showed the worst growth behavior, had the best fermentation activity. Some strains may adapt a strategy whereby fewer cells with higher metabolic activity are produced. Regarding the nitrogen source used, all the strains showed the better and worse fermentation performance with arginine and ammonium, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Oxygen response of the wine yeast Saccharomyces cerevisiae EC1118 grown under carbon-sufficient, nitrogen-limited enological conditions.

    PubMed

    Aceituno, Felipe F; Orellana, Marcelo; Torres, Jorge; Mendoza, Sebastián; Slater, Alex W; Melo, Francisco; Agosin, Eduardo

    2012-12-01

    Discrete additions of oxygen play a critical role in alcoholic fermentation. However, few studies have quantitated the fate of dissolved oxygen and its impact on wine yeast cell physiology under enological conditions. We simulated the range of dissolved oxygen concentrations that occur after a pump-over during the winemaking process by sparging nitrogen-limited continuous cultures with oxygen-nitrogen gaseous mixtures. When the dissolved oxygen concentration increased from 1.2 to 2.7 μM, yeast cells changed from a fully fermentative to a mixed respirofermentative metabolism. This transition is characterized by a switch in the operation of the tricarboxylic acid cycle (TCA) and an activation of NADH shuttling from the cytosol to mitochondria. Nevertheless, fermentative ethanol production remained the major cytosolic NADH sink under all oxygen conditions, suggesting that the limitation of mitochondrial NADH reoxidation is the major cause of the Crabtree effect. This is reinforced by the induction of several key respiratory genes by oxygen, despite the high sugar concentration, indicating that oxygen overrides glucose repression. Genes associated with other processes, such as proline uptake, cell wall remodeling, and oxidative stress, were also significantly affected by oxygen. The results of this study indicate that respiration is responsible for a substantial part of the oxygen response in yeast cells during alcoholic fermentation. This information will facilitate the development of temporal oxygen addition strategies to optimize yeast performance in industrial fermentations.

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

    PubMed

    Liseron-Monfils, Christophe; Bi, Yong-Mei; Downs, Gregory S; Wu, Wenqing; Signorelli, Tara; Lu, Guangwen; Chen, Xi; Bondo, Eddie; Zhu, Tong; Lukens, Lewis N; Colasanti, Joseph; Rothstein, Steven J; Raizada, Manish N

    2013-10-01

    Nitrogen is considered the most limiting nutrient for maize (Zea mays L.), but there is limited understanding of the regulation of nitrogen-related genes during maize development. An Affymetrix 82K maize array was used to analyze the expression of ≤ 46 unique nitrogen uptake and assimilation probes in 50 maize tissues from seedling emergence to 31 d after pollination. Four nitrogen-related expression clusters were identified in roots and shoots corresponding to, or overlapping, juvenile, adult, and reproductive phases of development. Quantitative real time PCR data was consistent with the existence of these distinct expression clusters. Promoters corresponding to each cluster were screened for over-represented cis-acting elements. The 8-bp distal motif of the Arabidopsis 43-bp nitrogen response element (NRE) was over-represented in nitrogen-related maize gene promoters. This conserved motif, referred to here as NRE43-d8, was previously shown to be critical for nitrate-activated transcription of nitrate reductase (NIA1) and nitrite reductase (NIR1) by the NIN-LIKE PROTEIN 6 (NLP6) in Arabidopsis. Here, NRE43-d8 was over-represented in the promoters of maize nitrate and ammonium transporter genes, specifically those that showed peak expression during early-stage vegetative development. This result predicts an expansion of the NRE-NLP6 regulon and suggests that it may have a developmental component in maize. We also report leaf expression of putative orthologs of nitrite transporters (NiTR1), a transporter not previously reported in maize. We conclude by discussing how each of the four transcriptional modules may be responsible for the different nitrogen uptake and assimilation requirements of leaves and roots at different stages of maize development.

  4. Regulation of nitrate assimilation in cyanobacteria.

    PubMed

    Ohashi, Yoshitake; Shi, Wei; Takatani, Nobuyuki; Aichi, Makiko; Maeda, Shin-ichi; Watanabe, Satoru; Yoshikawa, Hirofumi; Omata, Tatsuo

    2011-02-01

    Nitrate assimilation by cyanobacteria is inhibited by the presence of ammonium in the growth medium. Both nitrate uptake and transcription of the nitrate assimilatory genes are regulated. The major intracellular signal for the regulation is, however, not ammonium or glutamine, but 2-oxoglutarate (2-OG), whose concentration changes according to the change in cellular C/N balance. When nitrogen is limiting growth, accumulation of 2-OG activates the transcription factor NtcA to induce transcription of the nitrate assimilation genes. Ammonium inhibits transcription by quickly depleting the 2-OG pool through its metabolism via the glutamine synthetase/glutamate synthase cycle. The P(II) protein inhibits the ABC-type nitrate transporter, and also nitrate reductase in some strains, by an unknown mechanism(s) when the cellular 2-OG level is low. Upon nitrogen limitation, 2-OG binds to P(II) to prevent the protein from inhibiting nitrate assimilation. A pathway-specific transcriptional regulator NtcB activates the nitrate assimilation genes in response to nitrite, either added to the medium or generated intracellularly by nitrate reduction. It plays an important role in selective activation of the nitrate assimilation pathway during growth under a limited supply of nitrate. P(II) was recently shown to regulate the activity of NtcA negatively by binding to PipX, a small coactivator protein of NtcA. On the basis of accumulating genome information from a variety of cyanobacteria and the molecular genetic data obtained from the representative strains, common features and group- or species-specific characteristics of the response of cyanobacteria to nitrogen is summarized and discussed in terms of ecophysiological significance.

  5. Nitrogen and carbon source balance determines longevity, independently of fermentative or respiratory metabolism in the yeast Saccharomyces cerevisiae.

    PubMed

    Santos, Júlia; Leitão-Correia, Fernanda; Sousa, Maria João; Leão, Cecília

    2016-04-26

    Dietary regimens have proven to delay aging and age-associated diseases in several eukaryotic model organisms but the input of nutritional balance to longevity regulation is still poorly understood. Here, we present data on the role of single carbon and nitrogen sources and their interplay in yeast longevity. Data demonstrate that ammonium, a rich nitrogen source, decreases chronological life span (CLS) of the prototrophic Saccharomyces cerevisiae strain PYCC 4072 in a concentration-dependent manner and, accordingly, that CLS can be extended through ammonium restriction, even in conditions of initial glucose abundance. We further show that CLS extension depends on initial ammonium and glucose concentrations in the growth medium, as long as other nutrients are not limiting. Glutamine, another rich nitrogen source, induced CLS shortening similarly to ammonium, but this effect was not observed with the poor nitrogen source urea. Ammonium decreased yeast CLS independently of the metabolic process activated during aging, either respiration or fermentation, and induced replication stress inhibiting a proper cell cycle arrest in G0/G1 phase. The present results shade new light on the nutritional equilibrium as a key factor on cell longevity and may contribute for the definition of interventions to promote life span and healthy aging.

  6. Filamentous invasive growth of mutants of the genes encoding ammonia-metabolizing enzymes in the fission yeast Schizosaccharomyces pombe.

    PubMed

    Sasaki, Yoshie; Kojima, Ayumi; Shibata, Yuriko; Mitsuzawa, Hiroshi

    2017-01-01

    The fission yeast Schizosaccharomyces pombe undergoes a switch from yeast to filamentous invasive growth in response to certain environmental stimuli. Among them is ammonium limitation. Amt1, one of the three ammonium transporters in this yeast, is required for the ammonium limitation-induced morphological transition; however, the underlying molecular mechanism remains to be understood. Cells lacking Amt1 became capable of invasive growth upon increasing concentrations of ammonium in the medium, suggesting that the ammonium taken up into the cell or a metabolic intermediate in ammonium assimilation might serve as a signal for the ammonium limitation-induced morphological transition. To investigate the possible role of ammonium-metabolizing enzymes in the signaling process, deletion mutants were constructed for the gdh1, gdh2, gln1, and glt1 genes, which were demonstrated by enzyme assays to encode NADP-specific glutamate dehydrogenase, NAD-specific glutamate dehydrogenase, glutamine synthetase, and glutamate synthase, respectively. Growth tests on various nitrogen sources revealed that a gln1Δ mutant was a glutamine auxotroph and that a gdh1Δ mutant had a defect in growth on ammonium, particularly at high concentrations. The latter observation indicates that the NADP-specific glutamate dehydrogenase of S. pombe plays a major role in ammonium assimilation under high ammonium concentrations. Invasive growth assays showed that gdh1Δ and glt1Δ mutants underwent invasive growth to a lesser extent than did wild-type strains. Increasing the ammonium concentration in the medium suppressed the invasive growth defect of the glt1Δ mutant, but not the gdh1Δ mutant. These results suggest that the nitrogen status of the cell is important in the induction of filamentous invasive growth in S. pombe.

  7. Phenotypic and metabolic traits of commercial Saccharomyces cerevisiae yeasts

    PubMed Central

    2014-01-01

    Currently, pursuing yeast strains that display both a high potential fitness for alcoholic fermentation and a favorable impact on quality is a major goal in the alcoholic beverage industry. This considerable industrial interest has led to many studies characterizing the phenotypic and metabolic traits of commercial yeast populations. In this study, 20 Saccharomyces cerevisiae strains from different geographical origins exhibited high phenotypic diversity when their response to nine biotechnologically relevant conditions was examined. Next, the fermentation fitness and metabolic traits of eight selected strains with a unique phenotypic profile were evaluated in a high-sugar synthetic medium under two nitrogen regimes. Although the strains exhibited significant differences in nitrogen requirements and utilization rates, a direct relationship between nitrogen consumption, specific growth rate, cell biomass, cell viability, acetic acid and glycerol formation was only observed under high-nitrogen conditions. In contrast, the strains produced more succinic acid under the low-nitrogen regime, and a direct relationship with the final cell biomass was established. Glucose and fructose utilization patterns depended on both yeast strain and nitrogen availability. For low-nitrogen fermentation, three strains did not fully degrade the fructose. This study validates phenotypic and metabolic diversity among commercial wine yeasts and contributes new findings on the relationship between nitrogen availability, yeast cell growth and sugar utilization. We suggest that measuring nitrogen during the stationary growth phase is important because yeast cells fermentative activity is not exclusively related to population size, as previously assumed, but it is also related to the quantity of nitrogen consumed during this growth phase. PMID:24949272

  8. Phenotypic and metabolic traits of commercial Saccharomyces cerevisiae yeasts.

    PubMed

    Barbosa, Catarina; Lage, Patrícia; Vilela, Alice; Mendes-Faia, Arlete; Mendes-Ferreira, Ana

    2014-01-01

    Currently, pursuing yeast strains that display both a high potential fitness for alcoholic fermentation and a favorable impact on quality is a major goal in the alcoholic beverage industry. This considerable industrial interest has led to many studies characterizing the phenotypic and metabolic traits of commercial yeast populations. In this study, 20 Saccharomyces cerevisiae strains from different geographical origins exhibited high phenotypic diversity when their response to nine biotechnologically relevant conditions was examined. Next, the fermentation fitness and metabolic traits of eight selected strains with a unique phenotypic profile were evaluated in a high-sugar synthetic medium under two nitrogen regimes. Although the strains exhibited significant differences in nitrogen requirements and utilization rates, a direct relationship between nitrogen consumption, specific growth rate, cell biomass, cell viability, acetic acid and glycerol formation was only observed under high-nitrogen conditions. In contrast, the strains produced more succinic acid under the low-nitrogen regime, and a direct relationship with the final cell biomass was established. Glucose and fructose utilization patterns depended on both yeast strain and nitrogen availability. For low-nitrogen fermentation, three strains did not fully degrade the fructose. This study validates phenotypic and metabolic diversity among commercial wine yeasts and contributes new findings on the relationship between nitrogen availability, yeast cell growth and sugar utilization. We suggest that measuring nitrogen during the stationary growth phase is important because yeast cells fermentative activity is not exclusively related to population size, as previously assumed, but it is also related to the quantity of nitrogen consumed during this growth phase.

  9. Oxygen Response of the Wine Yeast Saccharomyces cerevisiae EC1118 Grown under Carbon-Sufficient, Nitrogen-Limited Enological Conditions

    PubMed Central

    Aceituno, Felipe F.; Orellana, Marcelo; Torres, Jorge; Mendoza, Sebastián; Slater, Alex W.; Melo, Francisco

    2012-01-01

    Discrete additions of oxygen play a critical role in alcoholic fermentation. However, few studies have quantitated the fate of dissolved oxygen and its impact on wine yeast cell physiology under enological conditions. We simulated the range of dissolved oxygen concentrations that occur after a pump-over during the winemaking process by sparging nitrogen-limited continuous cultures with oxygen-nitrogen gaseous mixtures. When the dissolved oxygen concentration increased from 1.2 to 2.7 μM, yeast cells changed from a fully fermentative to a mixed respirofermentative metabolism. This transition is characterized by a switch in the operation of the tricarboxylic acid cycle (TCA) and an activation of NADH shuttling from the cytosol to mitochondria. Nevertheless, fermentative ethanol production remained the major cytosolic NADH sink under all oxygen conditions, suggesting that the limitation of mitochondrial NADH reoxidation is the major cause of the Crabtree effect. This is reinforced by the induction of several key respiratory genes by oxygen, despite the high sugar concentration, indicating that oxygen overrides glucose repression. Genes associated with other processes, such as proline uptake, cell wall remodeling, and oxidative stress, were also significantly affected by oxygen. The results of this study indicate that respiration is responsible for a substantial part of the oxygen response in yeast cells during alcoholic fermentation. This information will facilitate the development of temporal oxygen addition strategies to optimize yeast performance in industrial fermentations. PMID:23001663

  10. Cocoa butter-like lipid production ability of non-oleaginous and oleaginous yeasts under nitrogen-limited culture conditions.

    PubMed

    Wei, Yongjun; Siewers, Verena; Nielsen, Jens

    2017-05-01

    Cocoa butter (CB) extracted from cocoa beans is the main raw material for chocolate production. However, growing chocolate demands and limited CB production has resulted in a shortage of CB supply. CB is mainly composed of three different kinds of triacylglycerols (TAGs), POP (C16:0-C18:1-C16:0), POS (C16:0-C18:1-C18:0), and SOS (C18:0-C18:1-C18:0). The storage lipids of yeasts, mainly TAGs, also contain relative high-level of C16 and C18 fatty acids and might be used as CB-like lipids (CBL). In this study, we cultivated six different yeasts, including one non-oleaginous yeast strain, Saccharomyces cerevisiae CEN.PK113-7D, and five oleaginous yeast strains, Trichosporon oleaginosus DSM11815, Rhodotorula graminis DSM 27356, Lipomyces starkeyi DSM 70296, Rhodosporidium toruloides DSM 70398, and Yarrowia lipolytica CBS 6124, in nitrogen-limited medium and compared their CBL production ability. Under the same growth conditions, we found that TAGs were the main lipids in all six yeasts and that T. oleaginosus can produce more TAGs than the other five yeasts. Less than 3% of the total TAGs were identified as potential SOS in the six yeasts. However, T. oleaginosus produced 27.8% potential POP and POS at levels of 378 mg TAGs/g dry cell weight, hinting that this yeast may have potential as a CBL production host after further metabolic engineering in future.

  11. 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

  12. Potent L-lactic acid assimilation of the fermentative and heterothallic haploid yeast Saccharomyces cerevisiae NAM34-4C.

    PubMed

    Tomitaka, Masataka; Taguchi, Hisataka; Matsuoka, Masayoshi; Morimura, Shigeru; Kida, Kenji; Akamatsu, Takashi

    2014-01-01

    We screened an industrial thermotolerant Saccharomyces cerevisiae strain, KF7, as a potent lactic-acid-assimilating yeast. Heterothallic haploid strains KF7-5C and KF7-4B were obtained from the tetrads of the homothallic yeast strain KF7. The inefficient sporulation and poor spore viability of the haploid strains were improved by two strategies. The first strategy was as follows: (i) the KF7-5C was crossed with the laboratory strain SH6710; (ii) the progenies were backcrossed with KF7-5C three times; and (iii) the progenies were inbred three times to maintain a genetic background close to that of KF7. The NAM12 diploid between the cross of the resultant two strains, NAM11-9C and NAM11-13A, showed efficient sporulation and exhibited excellent growth in YPD medium (pH 3.5) at 35°C with 1.4-h generation time, indicating thermotolerance and acid tolerance. The second strategy was successive intrastrain crosses. The resultant two strains, KFG4-6B and KFG4-4B, showed excellent mating capacity. A spontaneous mutant of KFG4-6B, KFG4-6BD, showed a high growth rate with a generation time of 1.1 h in YPD medium (pH 3.0) at 35°C. The KFG4-6BD strain produced ascospores, which were crossed with NAM11-2C and its progeny to produce tetrads. These tetrads were crossed with KFG4-4B to produce NAM26-14A and NAM26-15A. The latter strain had a generation time of 1.6 h at 35°C in pH 2.5, thus exhibiting further thermotolerance and acid tolerance. A progeny from a cross of NAM26-14A and NAM26-15A yielded the strain NAM34-4C, which showed potent lactic acid assimilation and high transformation efficiency, better than those of a standard laboratory strain. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  13. Yeast Biomass Production in Brewery's Spent Grains Hemicellulosic Hydrolyzate

    NASA Astrophysics Data System (ADS)

    Duarte, Luís C.; Carvalheiro, Florbela; Lopes, Sónia; Neves, Ines; Gírio, Francisco M.

    Yeast single-cell protein and yeast extract, in particular, are two products which have many feed, food, pharmaceutical, and biotechnological applications. However, many of these applications are limited by their market price. Specifically, the yeast extract requirements for culture media are one of the major technical hurdles to be overcome for the development of low-cost fermentation routes for several top value chemicals in a biorefinery framework. A potential biotechnical solution is the production of yeast biomass from the hemicellulosic fraction stream. The growth of three pentose-assimilating yeast cell factories, Debaryomyces hansenii, Kluyveromyces marxianus, and Pichia stipitis was compared using non-detoxified brewery's spent grains hemicellulosic hydrolyzate supplemented with mineral nutrients. The yeasts exhibited different specific growth rates, biomass productivities, and yields being D. hansenii as the yeast species that presented the best performance, assimilating all sugars and noteworthy consuming most of the hydrolyzate inhibitors. Under optimized conditions, D. hansenii displayed a maximum specific growth rate, biomass yield, and productivity of 0.34 h-1, 0.61 g g-1, and 0.56 g 1-1 h-1, respectively. The nutritional profile of D. hansenii was thoroughly evaluated, and it compares favorably to others reported in literature. It contains considerable amounts of some essential amino acids and a high ratio of unsaturated over saturated fatty acids.

  14. 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

  15. Prevention of GABA reduction during dough fermentation using a baker's yeast dal81 mutant.

    PubMed

    Ando, Akira; Nakamura, Toshihide

    2016-10-01

    γ-Aminobutyric acid (GABA) is consumed by yeasts during fermentation. To prevent GABA reduction in bread dough, a baker's yeast mutant AY77 deficient in GABA assimilation was characterized and utilized for wheat dough fermentation. An amber mutation in the DAL81 gene, which codes for a positive regulator of multiple nitrogen degradation pathways, was found in the AY77 strain. The qPCR analyses of genes involved in nitrogen utilization showed that transcriptional levels of the UGA1 and DUR3 genes encoding GABA transaminase and urea transporter, respectively, are severely decreased in the AY77 cells. The AY77 strain cultivated by fed-batch culture using cane molasses exhibited inferior gas production during dough fermentation compared to that of wild-type strain AY13. However, when fed with molasses containing 0.5% ammonium sulfate, the mutant strain exhibited gas production comparable to that of the AY13 strain. In contrast to the AY13 strain, which completely consumed GABA in dough within 5 h, the AY77 strain consumed no GABA under either culture condition. Dough fermentation with the dal81 mutant strain should be useful for suppression of GABA reduction in breads. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  16. Isolation of 2-deoxy-scyllo-inosose (DOI)-assimilating yeasts and cloning and characterization of the DOI reductase gene of Cryptococcus podzolicus ND1.

    PubMed

    Ara, Satoshi; Yamazaki, Harutake; Takaku, Hiroaki

    2018-04-01

    2-Deoxy-scyllo-inosose (DOI) is the first intermediate in the 2-deoxystreptamine-containing aminoglycoside antibiotic biosynthesis pathway and has a six-membered carbocycle structure. DOI is a valuable material because it is easily converted to aromatic compounds and carbasugar derivatives. In this study, we isolated yeast strains capable of assimilating DOI as a carbon source. One of the strains, Cryptococcus podzolicus ND1, mainly converted DOI to scyllo-quercitol and (-)-vibo-quercitol, which is a valuable compound used as an antihypoglycemia agent and as a heat storage material. An NADH-dependent DOI reductase coding gene, DOIR, from C. podzolicus ND1 was cloned and successfully overexpressed in Escherichia coli. The purified protein catalyzed the irreversible reduction of DOI with NADH and converted DOI into (-)-vibo-quercitol. The enzyme had an optimal pH of 8.5 and optimal temperature of 35°C, respectively. The k cat of this enzyme was 9.98 s -1 , and the K m values for DOI and NADH were 4.38 and 0.24 mM, respectively. The enzyme showed a strong preference for NADH and showed no activity with NADPH. Multiple-alignment analysis of DOI reductase revealed that it belongs to the GFO_IDH_MocA protein family and is an inositol dehydrogenase homolog in other fungi, such as Cryptococcus gattii, and bacteria, such as Bacillus subtilis. This is the first identification of a DOI-assimilating yeast and a gene involved in DOI metabolism in fungi. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  17. Study of the Plasma Membrane Proteome Dynamics Reveals Novel Targets of the Nitrogen Regulation in Yeast.

    PubMed

    Villers, Jennifer; Savocco, Jérôme; Szopinska, Aleksandra; Degand, Hervé; Nootens, Sylvain; Morsomme, Pierre

    2017-09-01

    Yeast cells, to be able to grow on a wide variety of nitrogen sources, regulate the set of nitrogen transporters present at their plasma membrane. Such regulation relies on both transcriptional and post-translational events. Although microarray studies have identified most nitrogen-sensitive genes, nitrogen-induced post-translational regulation has only been studied for very few proteins among which the general amino acid permease Gap1. Adding a preferred nitrogen source to proline-grown cells triggers Gap1 endocytosis and vacuolar degradation in an Rsp5-Bul1/2-dependent manner. Here, we used a proteomic approach to follow the dynamics of the plasma membrane proteome after addition of a preferred nitrogen source. We identified new targets of the nitrogen regulation and four transporters of poor nitrogen sources-Put4, Opt2, Dal5, and Ptr2-that rapidly decrease in abundance. Although the kinetics is different for each transporter, we found that three of them-Put4, Dal5, and Ptr2-are endocytosed, like Gap1, in an Rsp5-dependent manner and degraded in the vacuole. Finally, we showed that Gap1 stabilization at the plasma membrane, through deletion of Bul proteins, regulates the abundance of Put4, Dal5 and Ptr2. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Structure theorems and the dynamics of nitrogen catabolite repression in yeast

    PubMed Central

    Boczko, Erik M.; Cooper, Terrance G.; Gedeon, Tomas; Mischaikow, Konstantin; Murdock, Deborah G.; Pratap, Siddharth; Wells, K. Sam

    2005-01-01

    By using current biological understanding, a conceptually simple, but mathematically complex, model is proposed for the dynamics of the gene circuit responsible for regulating nitrogen catabolite repression (NCR) in yeast. A variety of mathematical “structure” theorems are described that allow one to determine the asymptotic dynamics of complicated systems under very weak hypotheses. It is shown that these theorems apply to several subcircuits of the full NCR circuit, most importantly to the URE2–GLN3 subcircuit that is independent of the other constituents but governs the switching behavior of the full NCR circuit under changes in nitrogen source. Under hypotheses that are fully consistent with biological data, it is proven that the dynamics of this subcircuit is simple periodic behavior in synchrony with the cell cycle. Although the current mathematical structure theorems do not apply to the full NCR circuit, extensive simulations suggest that the dynamics is constrained in much the same way as that of the URE2–GLN3 subcircuit. This finding leads to the proposal that mathematicians study genetic circuits to find new geometries for which structure theorems may exist. PMID:15814615

  19. The Rewiring of Ubiquitination Targets in a Pathogenic Yeast Promotes Metabolic Flexibility, Host Colonization and Virulence

    PubMed Central

    Childers, Delma S.; Raziunaite, Ingrida; Mol Avelar, Gabriela; Mackie, Joanna; Budge, Susan; Stead, David; Gow, Neil A. R.; Lenardon, Megan D.; Ballou, Elizabeth R.; MacCallum, Donna M.; Brown, Alistair J. P.

    2016-01-01

    Efficient carbon assimilation is critical for microbial growth and pathogenesis. The environmental yeast Saccharomyces cerevisiae is “Crabtree positive”, displaying a rapid metabolic switch from the assimilation of alternative carbon sources to sugars. Following exposure to sugars, this switch is mediated by the transcriptional repression of genes (carbon catabolite repression) and the turnover (catabolite inactivation) of enzymes involved in the assimilation of alternative carbon sources. The pathogenic yeast Candida albicans is Crabtree negative. It has retained carbon catabolite repression mechanisms, but has undergone posttranscriptional rewiring such that gluconeogenic and glyoxylate cycle enzymes are not subject to ubiquitin-mediated catabolite inactivation. Consequently, when glucose becomes available, C. albicans can continue to assimilate alternative carbon sources alongside the glucose. We show that this metabolic flexibility promotes host colonization and virulence. The glyoxylate cycle enzyme isocitrate lyase (CaIcl1) was rendered sensitive to ubiquitin-mediated catabolite inactivation in C. albicans by addition of a ubiquitination site. This mutation, which inhibits lactate assimilation in the presence of glucose, reduces the ability of C. albicans cells to withstand macrophage killing, colonize the gastrointestinal tract and cause systemic infections in mice. Interestingly, most S. cerevisiae clinical isolates we examined (67%) have acquired the ability to assimilate lactate in the presence of glucose (i.e. they have become Crabtree negative). These S. cerevisiae strains are more resistant to macrophage killing than Crabtree positive clinical isolates. Moreover, Crabtree negative S. cerevisiae mutants that lack Gid8, a key component of the Glucose-Induced Degradation complex, are more resistant to macrophage killing and display increased virulence in immunocompromised mice. Thus, while Crabtree positivity might impart a fitness advantage for

  20. Growth of non-Saccharomyces yeasts affects nutrient availability for Saccharomyces cerevisiae during wine fermentation.

    PubMed

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

    2012-07-02

    Yeast produces numerous secondary metabolites during fermentation that impact final wine quality. Although it is widely recognized that growth of diverse non-Saccharomyces (NS) yeast can positively affect flavor complexity during Saccharomyces cerevisiae wine fermentation, the inability to control spontaneous or co-fermentation processes by NS yeast has restricted their use in winemaking. We selected two NS yeasts from our Uruguayan native collection to study NS-S. cerevisiae interactions during wine fermentation. The selected strains of Hanseniaspora vineae and Metschnikowia pulcherrima had different yeast assimilable nitrogen consumption profiles and had different effects on S. cerevisiae fermentation and growth kinetics. Studies in which we varied inoculum size and using either simultaneous or sequential inoculation of NS yeast and S. cerevisiae suggested that competition for nutrients had a significant effect on fermentation kinetics. Sluggish fermentations were more pronounced when S. cerevisiae was inoculated 24h after the initial stage of fermentation with a NS strain compared to co-inoculation. Monitoring strain populations using differential WL nutrient agar medium and fermentation kinetics of mixed cultures allowed for a better understanding of strain interactions and nutrient addition effects. Limitation of nutrient availability for S. cerevisiae was shown to result in stuck fermentations as well as to reduce sensory desirability of the resulting wine. Addition of diammonium phosphate (DAP) and a vitamin mix to a defined medium allowed for a comparison of nutrient competition between strains. Addition of DAP and the vitamin mix was most effective in preventing stuck fermentations. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Genomic Evolution of the Ascomycete Yeasts

    SciTech Connect

    Riley, Robert; Haridas, Sajeet; Salamov, Asaf

    2015-03-16

    Yeasts are important for industrial and biotechnological processes and show remarkable metabolic and phylogenetic diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. Phylogenetic analysis of these and previously published yeast genomes helped resolve the placement of species including Saitoella complicata, Babjeviella inositovora, Hyphopichia burtonii, and Metschnikowia bicuspidata. Moreover, we find that alternative nuclear codon usage, where CUG encodes serine instead of leucine, are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes, and amore » tendency towards more introns in early-diverging species. Analysis of enzyme phylogeny gives insights into the evolution of metabolic capabilities such as methanol utilization and assimilation of alternative carbon sources.« less

  2. Interaction of Yna1 and Yna2 Is Required for Nuclear Accumulation and Transcriptional Activation of the Nitrate Assimilation Pathway in the Yeast Hansenula polymorpha.

    PubMed

    Silvestrini, Lucia; Rossi, Beatrice; Gallmetzer, Andreas; Mathieu, Martine; Scazzocchio, Claudio; Berardi, Enrico; Strauss, Joseph

    2015-01-01

    A few yeasts, including Hansenula polymorpha are able to assimilate nitrate and use it as nitrogen source. The genes necessary for nitrate assimilation are organised in this organism as a cluster comprising those encoding nitrate reductase (YNR1), nitrite reductase (YNI1), a high affinity transporter (YNT1), as well as the two pathway specific Zn(II)2Cys2 transcriptional activators (YNA1, YNA2). Yna1p and Yna2p mediate induction of the system and here we show that their functions are interdependent. Yna1p activates YNA2 as well as its own (YNA1) transcription thus forming a nitrate-dependent autoactivation loop. Using a split-YFP approach we demonstrate here that Yna1p and Yna2p form a heterodimer independently of the inducer and despite both Yna1p and Yna2p can occupy the target promoter as mono- or homodimer individually, these proteins are transcriptionally incompetent. Subsequently, the transcription factors target genes containing a conserved DNA motif (termed nitrate-UAS) determined in this work by in vitro and in vivo protein-DNA interaction studies. These events lead to a rearrangement of the chromatin landscape on the target promoters and are associated with the onset of transcription of these target genes. In contrast to other fungi and plants, in which nuclear accumulation of the pathway-specific transcription factors only occur in the presence of nitrate, Yna1p and Yna2p are constitutively nuclear in H. polymorpha. Yna2p is needed for this nuclear accumulation and Yna1p is incapable of strictly positioning in the nucleus without Yna2p. In vivo DNA footprinting and ChIP analyses revealed that the permanently nuclear Yna1p/Yna2p heterodimer only binds to the nitrate-UAS when the inducer is present. The nitrate-dependent up-regulation of one partner protein in the heterodimeric complex is functionally similar to the nitrate-dependent activation of nuclear accumulation in other systems.

  3. Effects of vine water status on dimethyl sulfur potential, ammonium, and amino acid contents in Grenache Noir grapes (Vitis vinifera).

    PubMed

    De Royer Dupré, N; Schneider, R; Payan, J C; Salançon, E; Razungles, A

    2014-04-02

    We studied the effect of vine water status on the dimethyl sulfur potential (DMSP), ammonium, and amino acid contents of the berry during the maturation of Grenache Noir grapes. Water deficit increased the accumulation of amino acids in berries and favored yeast assimilable amino nitrogen. Similarly, ammonium content was higher in berries from vines subjected to moderate water deficit. DMSP content followed the same trend as yeast assimilable amino acid content, with higher concentrations observed in the berries of vines subjected to water deficit. The high DMSP and yeast assimilable nitrogen contents of musts from vines subjected to water deficit resulted in a better preservation of DMSP during winemaking. The wines produced from these musts had a higher DMSP level and would therefore probably have a higher aroma shelf life, because the DMSP determines the rate of release of dimethyl sulfur during wine storage, and this compound enhances fruity notes.

  4. Nitrate assimilation is inhibited by elevated CO2 in field-grown wheat

    NASA Astrophysics Data System (ADS)

    J. Bloom, Arnold; Burger, Martin; A. Kimball, Bruce; J. Pinter, Paul, Jr.

    2014-06-01

    Total protein and nitrogen concentrations in plants generally decline under elevated CO2 atmospheres. Explanations for this decline include that plants under elevated CO2 grow larger, diluting the protein within their tissues; that carbohydrates accumulate within leaves, downregulating the amount of the most prevalent protein Rubisco; that carbon enrichment of the rhizosphere leads to progressively greater limitations of the nitrogen available to plants; and that elevated CO2 directly inhibits plant nitrogen metabolism, especially the assimilation of nitrate into proteins in leaves of C3 plants. Recently, several meta-analyses have indicated that CO2 inhibition of nitrate assimilation is the explanation most consistent with observations. Here, we present the first direct field test of this explanation. We analysed wheat (Triticum aestivum L.) grown under elevated and ambient CO2 concentrations in the free-air CO2 enrichment experiment at Maricopa, Arizona. In leaf tissue, the ratio of nitrate to total nitrogen concentration and the stable isotope ratios of organic nitrogen and free nitrate showed that nitrate assimilation was slower under elevated than ambient CO2. These findings imply that food quality will suffer under the CO2 levels anticipated during this century unless more sophisticated approaches to nitrogen fertilization are employed.

  5. Molecular Components of Nitrate and Nitrite Efflux in Yeast

    PubMed Central

    Cabrera, Elisa; González-Montelongo, Rafaela; Giraldez, Teresa; de la Rosa, Diego Alvarez

    2014-01-01

    Some eukaryotes, such as plant and fungi, are capable of utilizing nitrate as the sole nitrogen source. Once transported into the cell, nitrate is reduced to ammonium by the consecutive action of nitrate and nitrite reductase. How nitrate assimilation is balanced with nitrate and nitrite efflux is unknown, as are the proteins involved. The nitrate assimilatory yeast Hansenula polymorpha was used as a model to dissect these efflux systems. We identified the sulfite transporters Ssu1 and Ssu2 as effective nitrate exporters, Ssu2 being quantitatively more important, and we characterize the Nar1 protein as a nitrate/nitrite exporter. The use of strains lacking either SSU2 or NAR1 along with the nitrate reductase gene YNR1 showed that nitrate reductase activity is not required for net nitrate uptake. Growth test experiments indicated that Ssu2 and Nar1 exporters allow yeast to cope with nitrite toxicity. We also have shown that the well-known Saccharomyces cerevisiae sulfite efflux permease Ssu1 is also able to excrete nitrite and nitrate. These results characterize for the first time essential components of the nitrate/nitrite efflux system and their impact on net nitrate uptake and its regulation. PMID:24363367

  6. Phenol degradation and heavy metal tolerance of Antarctic yeasts.

    PubMed

    Fernández, Pablo Marcelo; Martorell, María Martha; Blaser, Mariana G; Ruberto, Lucas Adolfo Mauro; de Figueroa, Lucía Inés Castellanos; Mac Cormack, Walter Patricio

    2017-05-01

    In cold environments, biodegradation of organic pollutants and heavy metal bio-conversion requires the activity of cold-adapted or cold-tolerant microorganisms. In this work, the ability to utilize phenol, methanol and n-hexadecane as C source, the tolerance to different heavy metals and growth from 5 to 30 °C were evaluated in cold-adapted yeasts isolated from Antarctica. Fifty-nine percent of the yeasts were classified as psychrotolerant as they could grow in all the range of temperature tested, while the other 41% were classified as psychrophilic as they only grew below 25 °C. In the assimilation tests, 32, 78, and 13% of the yeasts could utilize phenol, n-hexadecane, and methanol as C source, respectively, but only 6% could assimilate the three C sources evaluated. In relation to heavy metals ions, 55, 68, and 80% were tolerant to 1 mM of Cr(VI), Cd(II), and Cu(II), respectively. Approximately a half of the isolates tolerated all of them. Most of the selected yeasts belong to genera previously reported as common for Antarctic soils, but several other genera were also isolated, which contribute to the knowledge of this cold environment mycodiversity. The tolerance to heavy metals of the phenol-degrading cold-adapted yeasts illustrated that the strains could be valuable as inoculant for cold wastewater treatment in extremely cold environments.

  7. Efficient assimilation of cyanobacterial nitrogen by water hyacinth.

    PubMed

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

    2017-10-01

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

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

    DOE PAGES

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

    2015-11-27

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

  9. On the resilience of nitrogen assimilation by intact roots under starvation, as revealed by isotopic and metabolomic techniques.

    PubMed

    Bathellier, Camille; Tcherkez, Guillaume; Mauve, Caroline; Bligny, Richard; Gout, Elizabeth; Ghashghaie, Jaleh

    2009-09-01

    The response of root metabolism to variations in carbon source availability is critical for whole-plant nitrogen (N) assimilation and growth. However, the effect of changes in the carbohydrate input to intact roots is currently not well understood and, for example, both smaller and larger values of root:shoot ratios or root N uptake have been observed so far under elevated CO(2). In addition, previous studies on sugar starvation mainly focused on senescent or excised organs while an increasing body of data suggests that intact roots may behave differently with, for example, little protein remobilization. Here, we investigated the carbon and nitrogen primary metabolism in intact roots of French bean (Phaseolus vulgaris L.) plants maintained under continuous darkness for 4 days. We combined natural isotopic (15)N/(14)N measurements, metabolomic and (13)C-labeling data and show that intact roots continued nitrate assimilation to glutamate for at least 3 days while the respiration rate decreased. The activity of the tricarboxylic acid cycle diminished so that glutamate synthesis was sustained by the anaplerotic phosphoenolpyruvate carboxylase fixation. Presumably, the pentose phosphate pathway contributed to provide reducing power for nitrate reduction. All the biosynthetic metabolic fluxes were nevertheless down-regulated and, consequently, the concentration of all amino acids decreased. This is the case of asparagine, strongly suggesting that, as opposed to excised root tips, protein remobilization in intact roots remained very low for 3 days in spite of the restriction of respiratory substrates. Copyright (c) 2009 John Wiley & Sons, Ltd.

  10. Synthetic control of a fitness tradeoff in yeast nitrogen metabolism

    PubMed Central

    Bayer, Travis S; Hoff, Kevin G; Beisel, Chase L; Lee, Jack J; Smolke, Christina D

    2009-01-01

    Background Microbial communities are involved in many processes relevant to industrial and medical biotechnology, such as the formation of biofilms, lignocellulosic degradation, and hydrogen production. The manipulation of synthetic and natural microbial communities and their underlying ecological parameters, such as fitness, evolvability, and variation, is an increasingly important area of research for synthetic biology. Results Here, we explored how synthetic control of an endogenous circuit can be used to regulate a tradeoff between fitness in resource abundant and resource limited environments in a population of Saccharomyces cerevisiae. We found that noise in the expression of a key enzyme in ammonia assimilation, Gdh1p, mediated a tradeoff between growth in low nitrogen environments and stress resistance in high ammonia environments. We implemented synthetic control of an endogenous Gdh1p regulatory network to construct an engineered strain in which the fitness of the population was tunable in response to an exogenously-added small molecule across a range of ammonia environments. Conclusion The ability to tune fitness and biological tradeoffs will be important components of future efforts to engineer microbial communities. PMID:19118500

  11. Contribution of yeast and base wine supplementation to sparkling wine composition.

    PubMed

    Martí-Raga, Maria; Martín, Valentina; Gil, Mariona; Sancho, Marta; Zamora, Fernando; Mas, Albert; Beltran, Gemma

    2016-12-01

    The differential characteristic of sparkling wine is the formation of foam, which is dependent, among other factors, on yeast autolysis, aging and oenological practices. In this study, we analyzed the effects of yeast strain, nutrient supplementation to the base wine and aging process on the sparkling wine composition and its foamability. We determined that the addition of inorganic nitrogen promoted nitrogen liberation to the extracellular medium, while the addition of inactive dry yeast to the base wine caused an increase in the polysaccharide concentration and foaming properties of the sparkling wine. The use of synthetic and natural base wines allowed us to discriminate that the differences in high-molecular-weight polysaccharides and oligosaccharides could be attributed to the yeast cells and that the higher nitrogen content in the natural wine could be due to external proteolysis. The practices of nitrogen addition and supplementation of inactive dry yeast could modulate the main characteristics of the sparkling wine and be a critical element for the design of this kind of wine. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  12. The Fitness Advantage of Commercial Wine Yeasts in Relation to the Nitrogen Concentration, Temperature, and Ethanol Content under Microvinification Conditions

    PubMed Central

    García-Ríos, Estéfani; Gutiérrez, Alicia; Salvadó, Zoel; Arroyo-López, Francisco Noé

    2014-01-01

    The effect of the main environmental factors governing wine fermentation on the fitness of industrial yeast strains has barely received attention. In this study, we used the concept of fitness advantage to measure how increasing nitrogen concentrations (0 to 200 mg N/liter), ethanol (0 to 20%), and temperature (4 to 45°C) affects competition among four commercial wine yeast strains (PDM, ARM, RVA, and TTA). We used a mathematical approach to model the hypothetical time needed for the control strain (PDM) to out-compete the other three strains in a theoretical mixed population. The theoretical values obtained were subsequently verified by competitive mixed fermentations in both synthetic and natural musts, which showed a good fit between the theoretical and experimental data. Specifically, the data show that the increase in nitrogen concentration and temperature values improved the fitness advantage of the PDM strain, whereas the presence of ethanol significantly reduced its competitiveness. However, the RVA strain proved to be the most competitive yeast for the three enological parameters assayed. The study of the fitness of these industrial strains is of paramount interest for the wine industry, which uses them as starters of their fermentations. Here, we propose a very simple method to model the fitness advantage, which allows the prediction of the competitiveness of one strain with respect to different abiotic factors. PMID:24242239

  13. Amino acid metabolism in maize earshoots. Implications for assimilate preconditioning and nitrogen signaling.

    PubMed

    Seebauer, Juliann R; Moose, Stephen P; Fabbri, Bradon J; Crossland, Lyle D; Below, Frederick E

    2004-12-01

    Nitrogen (N) is an essential requirement for kernel growth in maize (Zea mays); however, little is known about how N assimilates are metabolized in young earshoots during seed development. The objective of this study was to assess amino acid metabolism in cob and spikelet tissues during the critical 2 weeks following silking. Two maize hybrids were grown in the field for 2 years at two levels of supplemental N fertilizer (0 and 168 kg N/ha). The effects of the reproductive sink on cob N metabolism were examined by comparing pollinated to unpollinated earshoots. Earshoots were sampled at 2, 8, 14, and 18 d after silking; dissected into cob, spikelet, and/or pedicel and kernel fractions; then analyzed for amino acid profiles and key enzyme activities associated with amino acid metabolism. Major amino acids in the cob were glutamine (Gln), aspartic acid (Asp), asparagine (Asn), glutamate, and alanine. Gln concentrations dropped dramatically from 2 to 14 d after silking in both pollinated and unpollinated cobs, whereas all other measured amino acids accumulated over time in unpollinated spikelets and cobs, especially Asn. N supply had a variable effect on individual amino acid levels in young cobs and spikelets, with Asn being the most notably enhanced. We found that the cob performs significant enzymatic interconversions among Gln, alanine, Asp, and Asn during early reproductive development, which may precondition the N assimilate supply for sustained kernel growth. The measured amino acid profiles and enzymatic activities suggest that the Asn to Gln ratio in cobs may be part of a signal transduction pathway involving aspartate aminotransferase, Gln synthetase, and Asn synthetase to indicate plant N status for kernel development.

  14. Understanding nitrate assimilation and its regulation in microalgae

    PubMed Central

    Sanz-Luque, Emanuel; Chamizo-Ampudia, Alejandro; Llamas, Angel; Galvan, Aurora; Fernandez, Emilio

    2015-01-01

    Nitrate assimilation is a key process for nitrogen (N) acquisition in green microalgae. Among Chlorophyte algae, Chlamydomonas reinhardtii has resulted to be a good model system to unravel important facts of this process, and has provided important insights for agriculturally relevant plants. In this work, the recent findings on nitrate transport, nitrate reduction and the regulation of nitrate assimilation are presented in this and several other algae. Latest data have shown nitric oxide (NO) as an important signal molecule in the transcriptional and posttranslational regulation of nitrate reductase and inorganic N transport. Participation of regulatory genes and proteins in positive and negative signaling of the pathway and the mechanisms involved in the regulation of nitrate assimilation, as well as those involved in Molybdenum cofactor synthesis required to nitrate assimilation, are critically reviewed. PMID:26579149

  15. 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.

  16. 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.

  17. Rates of nitrification and nitrate assimilation in the Changjiang River estuary and adjacent waters based on the nitrogen isotope dilution method

    NASA Astrophysics Data System (ADS)

    Wang, Wentao; Yu, Zhiming; Wu, Zaixing; Song, Shuqun; Song, Xiuxian; Yuan, Yongquan; Cao, Xihua

    2018-07-01

    Being supplied from both terrestrial inputs and internal regeneration, nitrate is usually in excess in the Changjiang River estuary (CRE) and adjacent waters (CREAW). As significant reactions in the nitrogen cycle, nitrate assimilation and nitrification rates were calculated by field incubation experiments following the isotope dilution method during June and November 2014. Besides this, distribution of other field parameters in the CREAW were also investigated. The results showed that the nitrate assimilation rates were higher in nearshore areas and lower in offshore areas. The nitrate assimilation rates were also higher during June, at 0.3-11.9 μmol L-1 d-1, whereas the rates were 0-3.2 μmol L-1 d-1 in November. The highest rate was observed in the surface water of the estuary, where the chlorophyll-a (chl-a) concentration reached 11.02 μg L-1. In addition, the phytoplankton community structure affected the nitrate assimilation rates, and dinoflagellates presented weaker nitrate assimilation abilities than those of diatoms. By contrast, the nitrification rates were higher in nearshore areas in June but higher in offshore areas in November. The nitrification rates were 0-4.1 μmol L-1 d-1 and 0-3.6 μmol L-1 d-1 in June and November, respectively. At most sites, the nitrification rates were positively correlated with the ammonium concentrations and were higher in November, which might be attributable to the higher temperature. Moreover, a theoretical calculation was used to study the regional nitrate flux throughout the vertical water column. The results showed that a gradual supplement from nitrification might replenish the nitrate consumed by assimilation far from the CRE. The overall result was that terrestrial input remained the primary source of estuarine nitrate; however, the role of internal nitrate regeneration, which would be effective for primary production in the CREAW, should also be highlighted as a source of nitrate, especially in offshore areas.

  18. Lead toxicity in Brassica pekinensis Rupr.: effect on nitrate assimilation and growth.

    PubMed

    Xiong, Zhi-Ting; Zhao, Fei; Li, Min-jing

    2006-04-01

    Lead is a major heavy-metal contaminant in the environment that has various anthropogenic and natural sources. To study the phytotoxic effects of Pb on the popular vegetable Chinese cabbage (Brassica pekinensis Rupr.) via depression of nitrogen assimilation, pot culture experiments with three concentrations of treatment with Pb (0, 4, and 8 mmol/kg dry soil) were carried out. Our results demonstrated adverse effects of Pb on nitrogen assimilation and plant growth. The addition of Pb in the soil resulted in elevated accumulation of Pb in the shoots of the plants: Pb concentrations of 14.3, 202.3, and 418.2 mg/kg (DW) in the shoots were detected with the 0, 4, and 8 mmol/kg treatments, respectively. Compared to the control, Pb exposure (4 and 8 mmol/kg) significantly decreased shoot nitrate content (71% and 80% of the control), nitrate reductase activity (104% and 49% of the control), and free amino acid content (81% and 82% of the control), indicating decreased nitrogen assimilation in the plants. The effect of Pb also was shown by the progressive decline in shoot biomass with increasing Pb concentration in plant shoots and in the soil. However, at the treatment levels used in this study, lead did not induce visible toxic symptoms. The lowest-concentration Pb treatment (4 mmol/kg) stimulated chlorophyll b content but did not influence chlorophyll a content. The results suggested that the toxicity of Pb to the plants occurred at least partly via depression of nitrogen assimilation. Copyright 2006 Wiley Periodicals, Inc.

  19. Impact of fermentation rate changes on potential hydrogen sulfide concentrations in wine.

    PubMed

    Butzke, Christian E; Park, Seung Kook

    2011-05-01

    The correlation between alcoholic fermentation rate, measured as carbon dioxide (CO2) evolution, and the rate of hydrogen sulfide (H2S) formation during wine production was investigated. Both rates and the resulting concentration peaks in fermentor headspace H2S were directly impacted by yeast assimilable nitrogenous compounds in the grape juice. A series of model fermentations was conducted in temperature-controlled and stirred fermentors using a complex model juice with defined concentrations of ammonium ions and/or amino acids. The fermentation rate was measured indirectly by noting the weight loss of the fermentor; H2S was quantitatively trapped in realtime using a pre-calibrated H2S detection tube which was inserted into a fermentor gas relief port. Evolution rates for CO2 and H2S as well as the relative ratios between them were calculated. These fermentations confirmed that total sulfide formation was strongly yeast strain-dependent, and high concentrations of yeast assimilable nitrogen did not necessarily protect against elevated H2S formation. High initial concentrations of ammonium ions via addition of diammonium phosphate (DAP) caused a higher evolution of H2S when compared with a non-supplemented but nondeficient juice. It was observed that the excess availability of a certain yeast assimilable amino acid, arginine, could result in a more sustained CO2 production rate throughout the wine fermentation. The contribution of yeast assimilable amino acids from conventional commercial yeast foods to lowering of the H2S formation was marginal.

  20. Interactive Effects of CO2 Concentration and Water Regime on Stable Isotope Signatures, Nitrogen Assimilation and Growth in Sweet Pepper.

    PubMed

    Serret, María D; Yousfi, Salima; Vicente, Rubén; Piñero, María C; Otálora-Alcón, Ginés; Del Amor, Francisco M; Araus, José L

    2017-01-01

    Sweet pepper is among the most widely cultivated horticultural crops in the Mediterranean basin, being frequently grown hydroponically under cover in combination with CO 2 fertilization and water conditions ranging from optimal to suboptimal. The aim of this study is to develop a simple model, based on the analysis of plant stable isotopes in their natural abundance, gas exchange traits and N concentration, to assess sweet pepper growth. Plants were grown in a growth chamber for near 6 weeks. Two [CO 2 ] (400 and 800 μmol mol -1 ), three water regimes (control and mild and moderate water stress) and four genotypes were assayed. For each combination of genotype, [CO 2 ] and water regime five plants were evaluated. Water stress applied caused significant decreases in water potential, net assimilation, stomatal conductance, intercellular to atmospheric [CO 2 ], and significant increases in water use efficiency, leaf chlorophyll content and carbon isotope composition, while the relative water content, the osmotic potential and the content of anthocyanins did change not under stress compared to control conditions support this statement. Nevertheless, water regime affects plant growth via nitrogen assimilation, which is associated with the transpiration stream, particularly at high [CO 2 ], while the lower N concentration caused by rising [CO 2 ] is not associated with stomatal closure. The stable isotope composition of carbon, oxygen, and nitrogen (δ 13 C, δ 18 O, and δ 15 N) in plant matter are affected not only by water regime but also by rising [CO 2 ]. Thus, δ 18 O increased probably as response to decreases in transpiration, while the increase in δ 15 N may reflect not only a lower stomatal conductance but a higher nitrogen demand in leaves or shifts in nitrogen metabolism associated with decreases in photorespiration. The way that δ 13 C explains differences in plant growth across water regimes within a given [CO 2 ], seems to be mediated through its direct

  1. Interactive Effects of CO2 Concentration and Water Regime on Stable Isotope Signatures, Nitrogen Assimilation and Growth in Sweet Pepper

    PubMed Central

    Serret, María D.; Yousfi, Salima; Vicente, Rubén; Piñero, María C.; Otálora-Alcón, Ginés; del Amor, Francisco M.; Araus, José L.

    2018-01-01

    Sweet pepper is among the most widely cultivated horticultural crops in the Mediterranean basin, being frequently grown hydroponically under cover in combination with CO2 fertilization and water conditions ranging from optimal to suboptimal. The aim of this study is to develop a simple model, based on the analysis of plant stable isotopes in their natural abundance, gas exchange traits and N concentration, to assess sweet pepper growth. Plants were grown in a growth chamber for near 6 weeks. Two [CO2] (400 and 800 μmol mol−1), three water regimes (control and mild and moderate water stress) and four genotypes were assayed. For each combination of genotype, [CO2] and water regime five plants were evaluated. Water stress applied caused significant decreases in water potential, net assimilation, stomatal conductance, intercellular to atmospheric [CO2], and significant increases in water use efficiency, leaf chlorophyll content and carbon isotope composition, while the relative water content, the osmotic potential and the content of anthocyanins did change not under stress compared to control conditions support this statement. Nevertheless, water regime affects plant growth via nitrogen assimilation, which is associated with the transpiration stream, particularly at high [CO2], while the lower N concentration caused by rising [CO2] is not associated with stomatal closure. The stable isotope composition of carbon, oxygen, and nitrogen (δ13C, δ18O, and δ15N) in plant matter are affected not only by water regime but also by rising [CO2]. Thus, δ18O increased probably as response to decreases in transpiration, while the increase in δ15N may reflect not only a lower stomatal conductance but a higher nitrogen demand in leaves or shifts in nitrogen metabolism associated with decreases in photorespiration. The way that δ13C explains differences in plant growth across water regimes within a given [CO2], seems to be mediated through its direct relationship with N

  2. Alterations in leaf nitrogen metabolism indicated the structural changes of subtropical forest by canopy addition of nitrogen.

    PubMed

    Liu, Nan; Wang, Jiaxin; Guo, Qinfeng; Wu, Shuhua; Rao, Xingquan; Cai, Xi'an; Lin, Zhifang

    2018-09-30

    Globally, nitrogen deposition increment has caused forest structural changes due to imbalanced plant nitrogen metabolism and subsequent carbon assimilation. Here, a 2 consecutive-year experiment was conducted to reveal the effects of canopy addition of nitrogen (CAN) on nitrogen absorption, assimilation, and allocation in leaves of three subtropical forest woody species (Castanea henryi, Ardisia quinquegona, and Blastus cochinchinensis). We hypothesized that CAN altered leaf nitrogen absorption, assimilation and partitioning of different plants in different ways in subtropical forest. It shows that CAN increased maximum photosynthetic rate (A max ), photosynthetic nitrogen use efficiency (PNUE), and metabolic protein content of the two understory species A. quinquegona and B. cochinchinensis. By contrary, for the overstory species, C. henryi, A max , PNUE, and metabolic protein content were significantly reduced in response to CAN. We found that changes in leaf nitrogen metabolism were mainly due to the differences in enzyme (e.g. Ribulose-1,5-bisphosphate carboxylase, nitrate reductase, nitrite reductase and glutamine synthetase) activities under CAN treatment. Our results indicated that C. henryi may be more susceptible to CAN treatment, and both A. quinquegona and B. cochinchinensis could better adapt to CAN treatment but in different ways. Our findings may partially explain the ongoing degradation of subtropical forest into a community dominated by small trees and shrubs in recent decades. It is possible that persistent high levels of atmospheric nitrogen deposition will lead to the steady replacement of dominant woody species in this subtropical forest. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Carbon: Nitrogen Interaction Regulates Expression of Genes Involved in N-Uptake and Assimilation in Brassica juncea L.

    PubMed Central

    Goel, Parul; Bhuria, Monika; Kaushal, Mamta

    2016-01-01

    In plants, several cellular and metabolic pathways interact with each other to regulate processes that are vital for their growth and development. Carbon (C) and Nitrogen (N) are two main nutrients for plants and coordination of C and N pathways is an important factor for maintaining plant growth and development. In the present work, influence of nitrogen and sucrose (C source) on growth parameters and expression of genes involved in nitrogen transport and assimilatory pathways was studied in B. juncea seedlings. For this, B. juncea seedlings were treated with four combinations of C and N source viz., N source alone (-Suc+N), C source alone (+Suc-N), with N and C source (+Suc+N) or without N and C source (-Suc-N). Cotyledon size and shoot length were found to be increased in seedlings, when nitrogen alone was present in the medium. Distinct expression pattern of genes in both, root and shoot tissues was observed in response to exogenously supplied N and C. The presence or depletion of nitrogen alone in the medium leads to severe up- or down-regulation of key genes involved in N-uptake and transport (BjNRT1.1, BjNRT1.8) in root tissue and genes involved in nitrate reduction (BjNR1 and BjNR2) in shoot tissue. Moreover, expression of several genes, like BjAMT1.2, BjAMT2 and BjPK in root and two genes BjAMT2 and BjGS1.1 in shoot were found to be regulated only when C source was present in the medium. Majority of genes were found to respond in root and shoot tissues, when both C and N source were present in the medium, thus reflecting their importance as a signal in regulating expression of genes involved in N-uptake and assimilation. The present work provides insight into the regulation of genes of N-uptake and assimilatory pathway in B. juncea by interaction of both carbon and nitrogen. PMID:27637072

  4. Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes.

    PubMed

    Ghoshroy, Sohini; Robertson, Deborah L

    2015-01-01

    Nitrogen assimilation is a highly regulated process requiring metabolic coordination of enzymes and pathways in the cytosol, chloroplast, and mitochondria. Previous studies of prasinophyte genomes revealed that genes encoding nitrate and ammonium transporters have a complex evolutionary history involving both vertical and horizontal transmission. Here we examine the evolutionary history of well-conserved nitrogen-assimilating enzymes to determine if a similar complex history is observed. Phylogenetic analyses suggest that genes encoding glutamine synthetase (GS) III in the prasinophytes evolved by horizontal gene transfer from a member of the heterokonts. In contrast, genes encoding GSIIE, a canonical vascular plant and green algal enzyme, were found in the Micromonas genomes but have been lost from Ostreococcus. Phylogenetic analyses placed the Micromonas GSIIs in a larger chlorophyte/vascular plant clade; a similar topology was observed for ferredoxin-dependent nitrite reductase (Fd-NiR), indicating the genes encoding GSII and Fd-NiR in these prasinophytes evolved via vertical transmission. Our results show that genes encoding the nitrogen-assimilating enzymes in Micromonas and Ostreococcus have been differentially lost and as well as recruited from different evolutionary lineages, suggesting that the regulation of nitrogen assimilation in prasinophytes will differ from other green algae.

  5. [The homogeneity of a population of yeasts from Camembert cheeses].

    PubMed

    Schmidt, J L; Daudin, J J

    1983-01-01

    Yeasts are found to a large extent in cheeses, more particularly in soft cheeses such as Camembert. The proximity between two species previously identified by standard methods was studied using a factorial discriminant analysis on 326 strains. Twenty-three fermentation and assimilation tests (discriminant variables) gave a fairly good discrimination between species. This treatment has allowed us to confirm the present tendencies noticed in yeast classification and has also enabled us to group some of the species.

  6. Improvement of growth, fermentative efficiency and ethanol tolerance of Kloeckera africana during the fermentation of Agave tequilana juice by addition of yeast extract.

    PubMed

    Díaz-Montaño, Dulce M; Favela-Torres, Ernesto; Córdova, Jesus

    2010-01-30

    The aim of this work was to improve the productivity and yield of tequila fermentation and to propose the use of a recently isolated non-Saccharomyces yeast in order to obtain a greater diversity of flavour and aroma of the beverage. For that, the effects of the addition of different nitrogen (N) sources to Agave tequilana juice on the growth, fermentative capacity and ethanol tolerance of Kloeckera africana and Saccharomyces cerevisiae were studied and compared. Kloeckera africana K1 and S. cerevisiae S1 were cultured in A. tequilana juice supplemented with ammonium sulfate, diammonium phosphate or yeast extract. Kloeckera africana did not assimilate inorganic N sources, while S. cerevisiae utilised any N source. Yeast extract stimulated the growth, fermentative capacity and alcohol tolerance of K. africana, giving kinetic parameter values similar to those calculated for S. cerevisiae. This study revealed the importance of supplementing A. tequilana juice with a convenient N source to achieve fast and complete conversion of sugars in ethanol, particularly in the case of K. africana. This yeast exhibited similar growth and fermentative capacity to S. cerevisiae. The utilisation of K. africana in the tequila industry is promising because of its variety of synthesised aromatic compounds, which would enrich the attributes of this beverage. (c) 2009 Society of Chemical Industry.

  7. Quantifying the Stress Responses of Brassica Rapa Genotypes, With Experimental Drought in Two Nitrogen Treatments

    NASA Astrophysics Data System (ADS)

    Hickerson, J. L.; Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B. E.; Weinig, C.

    2014-12-01

    In a greenhouse study designed to quantify and compare stress responses of four genotypes of Brassica rapa, broccolette (bro), cabbage (cab), turnip (tur), and oil, leaf water potential and net CO2 assimilations were measured. Individuals from each genotype, grown either with high or low nitrogen, were exposed to experimental drought of the same duration. One hypothesis was that the genotypes would differ significantly in their responses to periodic drought. The other hypothesis was that the nitrogen treatment versus no nitrogen treatment would play a significant role in the stress responses during drought. It would be expected that the nitrogen treated would have greater dry leaf mass. A LI-6400 XT portable photosynthesis system was used to obtain A/Ci curves (net CO2 assimilation rate versus substomatal CO2) for each treatment group. Predawn and midday water potentials were obtained throughout the hydrated and drought periods using a Model 670 pressure chamber. The dry leaf mass was significantly greater among the high nitrogen group versus the low nitrogen group for each genotype. Nitrogen and genotype were both determinants in variation of water potentials and net CO2 assimilation. Bro and cab genotypes with high nitrogen showed the highest net CO2 assimilation rates during hydration, but the assimilation rates dropped to the lowest during droughts. The water potentials for bro and cab were lower than values for tur and oil. Nitrogen treated genotypes had lower water potentials, but higher net CO2 assimilation rates. Bayesian ecophysiological modeling with the TREES model showed significant differences in trait expression, quantified in terms of differences in model parameter posteriors, among the four genotypes.

  8. Effects of nitrogen availability on polymalic acid biosynthesis in the yeast-like fungus Aureobasidium pullulans.

    PubMed

    Wang, Yongkang; Song, Xiaodan; Zhang, Yongjun; Wang, Bochu; Zou, Xiang

    2016-08-22

    Polymalic acid (PMA) is a novel polyester polymer that has been broadly used in the medical and food industries. Its monomer, L-malic acid, is also a potential C4 platform chemical. However, little is known about the mechanism of PMA biosynthesis in the yeast-like fungus, Aureobasidium pullulans. In this study, the effects of different nitrogen concentration on cell growth and PMA biosynthesis were investigated via comparative transcriptomics and proteomics analyses, and a related signaling pathway was also evaluated. A high final PMA titer of 44.00 ± 3.65 g/L (49.9 ± 4.14 g/L of malic acid after hydrolysis) was achieved in a 5-L fermentor under low nitrogen concentration (2 g/L of NH4NO3), which was 18.3 % higher yield than that obtained under high nitrogen concentration (10 g/L of NH4NO3). Comparative transcriptomics profiling revealed that a set of genes, related to the ribosome, ribosome biogenesis, proteasome, and nitrogen metabolism, were significantly up- or down-regulated under nitrogen sufficient conditions, which could be regulated by the TOR signaling pathway. Fourteen protein spots were identified via proteomics analysis, and were found to be associated with cell division and growth, energy metabolism, and the glycolytic pathway. qRT-PCR further confirmed that the expression levels of key genes involved in the PMA biosynthetic pathway (GLK, CS, FUM, DAT, and MCL) and the TOR signaling pathway (GS, TOR1, Tap42, and Gat1) were upregulated due to nitrogen limitation. Under rapamycin stress, PMA biosynthesis was obviously inhibited in a dose-dependent manner, and the transcription levels of TOR1, MCL, and DAT were also downregulated. The level of nitrogen could regulate cell growth and PMA biosynthesis. Low concentration of nitrogen was beneficial for PMA biosynthesis, which could upregulate the expression of key genes involved in the PMA biosynthesis pathway. Cell growth and PMA biosynthesis might be mediated by the TOR signaling pathway in

  9. Methanol Expression Regulator 1 (Mxr1p) Is Essential for the Utilization of Amino Acids as the Sole Source of Carbon by the Methylotrophic Yeast, Pichia pastoris.

    PubMed

    Sahu, Umakant; Rangarajan, Pundi N

    2016-09-23

    Unlike Saccharomyces cerevisiae, the methylotrophic yeast Pichia pastoris can assimilate amino acids as the sole source of carbon and nitrogen. It can grow in media containing yeast extract and peptone (YP), yeast nitrogen base (YNB) + glutamate (YNB + Glu), or YNB + aspartate (YNB + Asp). Methanol expression regulator 1 (Mxr1p), a zinc finger transcription factor, is essential for growth in these media. Mxr1p regulates the expression of several genes involved in the utilization of amino acids as the sole source of carbon and nitrogen. These include the following: (i) GDH2 encoding NAD-dependent glutamate dehydrogenase; (ii) AAT1 and AAT2 encoding mitochondrial and cytosolic aspartate aminotransferases, respectively; (iii) MDH1 and MDH2 encoding mitochondrial and cytosolic malate dehydrogenases, respectively; and (iv) GLN1 encoding glutamine synthetase. Synthesis of all these enzymes is regulated by Mxr1p at the level of transcription except GDH2, whose synthesis is regulated at the level of translation. Mxr1p activates the transcription of AAT1, AAT2, and GLN1 in cells cultured in YP as well as in YNB + Glu media, whereas transcription of MDH1 and MDH2 is activated in cells cultured in YNB + Glu but not in YP. A truncated Mxr1p composed of 400 N-terminal amino acids activates transcription of target genes in cells cultured in YP but not in YNB + Glu. Mxr1p binds to Mxr1p response elements present in the promoters of AAT2, MDH2, and GLN1 We conclude that Mxr1p is essential for utilization of amino acids as the sole source of carbon and nitrogen, and it is a global regulator of multiple metabolic pathways in P. pastoris. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. 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.

  11. Influence of nitrogen sources on growth and fermentation performance of different wine yeast species during alcoholic fermentation.

    PubMed

    Kemsawasd, Varongsiri; Viana, Tiago; Ardö, Ylva; Arneborg, Nils

    2015-12-01

    In this study, the influence of twenty different single (i.e. 19 amino acids and ammonium sulphate) and two multiple nitrogen sources (N-sources) on growth and fermentation (i.e. glucose consumption and ethanol production) performance of Saccharomyces cerevisiae and of four wine-related non-Saccharomyces yeast species (Lachancea thermotolerans, Metschnikowia pulcherrima, Hanseniaspora uvarum and Torulaspora delbrueckii) was investigated during alcoholic fermentation. Briefly, the N-sources with beneficial effects on all performance parameters (or for the majority of them) for each yeast species were alanine, arginine, asparagine, aspartic acid, glutamine, isoleucine, ammonium sulphate, serine, valine and mixtures of 19 amino acids and of 19 amino acids plus ammonium sulphate (for S. cerevisiae), serine (for L. thermotolerans), alanine (for H. uvarum), alanine and asparagine (for M. pulcherrima), arginine, asparagine, glutamine, isoleucine and mixture of 19 amino acids (for T. delbrueckii). Furthermore, our results showed a clear positive effect of complex mixtures of N-sources on S. cerevisiae and on T. delbrueckii (although to a lesser extent) as to all performance parameters studied, whereas for L. thermotolerans, H. uvarum and M. pulcherrima, single amino acids affected growth and fermentation performance to the same extent as the mixtures. Moreover, we found groups of N-sources with similar effects on the growth and/or fermentation performance of two or more yeast species. Finally, the influences of N-sources observed for T. delbrueckii and H. uvarum resembled those of S. cerevisiae the most and the least, respectively. Overall, this work contributes to an improved understanding of how different N-sources affect growth, glucose consumption and ethanol production of wine-related yeast species under oxygen-limited conditions, which, in turn, may be used to, e.g. optimize growth and fermentation performance of the given yeast upon N-source supplementation during

  12. 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.

  13. VARIATION IN THE ABUNDANCE OF SYNECHOCOCCUS SP. CC9311 NARB MRNA RELATIVE TO CHANGES IN LIGHT, NITROGEN GROWTH CONDITIONS AND NITRATE ASSIMILATION(1).

    PubMed

    Paerl, Ryan W; Tozzi, Sasha; Kolber, Zbigniew S; Zehr, Jonathan P

    2012-08-01

    Synechococcus- and Prochlorococcus-specific narB genes that encode for an assimilatory nitrate reductase are found in coastal to open-ocean waters. However, it remains uncertain if these picocyanobacteria assimilate nitrate in situ. This unknown can potentially be addressed by examining narB mRNA from the environment, but this requires a better understanding of the influence of environmental factors on narB gene transcription. In laboratory experiments with Synechococcus sp. CC9311 cultures exposed to diel light fluctuations and grown on nitrate or ammonium, there was periodic change in narB transcript abundance. This periodicity was broken in cultures subjected to a doubling of irradiance (40-80 μmol photons · m(-2)  · s(-1) ) during the mid-light period. Therefore, the irradiance level, not circadian rhythm, was the dominant factor controlling narB transcription. In nitrate-grown cultures, diel change in narB transcript abundance and nitrate assimilation rate did not correlate; suggesting narB mRNA levels better indicate nitrate assimilation activity than assimilation rate. Growth history also affected narB transcription, as changes in narB mRNA levels in nitrogen-deprived CC9311 cultures following nitrate amendment were distinct from cultures grown solely on nitrate. Environmental sampling for narB transcripts should consider time, irradiance, and the growth status of cells to ecologically interpret narB transcript abundances. © 2012 Phycological Society of America.

  14. Exogenous trehalose improves growth under limiting nitrogen through upregulation of nitrogen metabolism.

    PubMed

    Lin, Yingchao; Zhang, Jie; Gao, Weichang; Chen, Yi; Li, Hongxun; Lawlor, David W; Paul, Matthew J; Pan, Wenjie

    2017-12-19

    The trehalose (Tre) pathway has strong effects on growth and development in plants through regulation of carbon metabolism. Altering either Tre or trehalose 6-phosphate (T6P) can improve growth and productivity of plants as observed under different water availability. As yet, there are no reports of the effects of modification of Tre orT6P on plant performance under limiting nutrition. Here we report that nitrogen (N) metabolism is positively affected by exogenous application of Tre in nitrogen-deficient growing conditions. Spraying foliage of tobacco (Nicotiana tabacum) with trehalose partially alleviated symptoms of nitrogen deficiency through upregulation of nitrate and ammonia assimilation and increasing activities of nitrate reductase (NR), glycolate oxidase (GO), glutamine synthetase (GS) and glutamine oxoglutarate aminotransferase (GOGAT) with concomitant changes in ammonium (NH 4 + ) and nitrate (NO 3 - ) concentrations, glutamine and amino acids. Chlorophyll and total nitrogen content of leaves and rates of photosynthesis were increased compared to nitrogen-deficient plants without applied Tre. Total plant biomass accumulation was also higher in Tre -fed nitrogen-deficient plants, with a smaller proportion of dry weight partitioned to roots, compared to nitrogen-deficient plants without applied Tre. Consistent with higher nitrogen assimilation and growth, Tre application reduced foliar starch. Minimal effects of Tre feeding were observed on nitrogen-sufficient plants. The data show, for the first time, significant stimulatory effects of exogenous Tre on nitrogen metabolism and growth in plants growing under deficient nitrogen. Under such adverse conditions metabolism is regulated for survival rather than productivity. Application of Tre can alter this regulation towards maintenance of productive functions under low nitrogen. This has implications for considering approaches to modifying the Tre pathway for to improve crop nitrogen-use efficiency and

  15. Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen

    PubMed Central

    2011-01-01

    Background Studies of nuclear function in many organisms, especially those with tough cell walls, are limited by lack of availability of simple, economical methods for large-scale preparation of clean, undamaged nuclei. Findings Here we present a useful method for nuclear isolation from the important model organism, the fission yeast, Schizosaccharomyces pombe. To preserve in vivo molecular configurations, we flash-froze the yeast cells in liquid nitrogen. Then we broke their tough cell walls, without damaging their nuclei, by grinding in a precision-controlled motorized mortar-and-pestle apparatus. The cryo-ground cells were resuspended and thawed in a buffer designed to preserve nuclear morphology, and the nuclei were enriched by differential centrifugation. The washed nuclei were free from contaminating nucleases and have proven well-suited as starting material for genome-wide chromatin analysis and for preparation of fragile DNA replication intermediates. Conclusions We have developed a simple, reproducible, economical procedure for large-scale preparation of endogenous-nuclease-free, morphologically intact nuclei from fission yeast. With appropriate modifications, this procedure may well prove useful for isolation of nuclei from other organisms with, or without, tough cell walls. PMID:22088094

  16. Integrity of chromatin and replicating DNA in nuclei released from fission yeast by semi-automated grinding in liquid nitrogen.

    PubMed

    Givens, Robert M; Mesner, Larry D; Hamlin, Joyce L; Buck, Michael J; Huberman, Joel A

    2011-11-16

    Studies of nuclear function in many organisms, especially those with tough cell walls, are limited by lack of availability of simple, economical methods for large-scale preparation of clean, undamaged nuclei. Here we present a useful method for nuclear isolation from the important model organism, the fission yeast, Schizosaccharomyces pombe. To preserve in vivo molecular configurations, we flash-froze the yeast cells in liquid nitrogen. Then we broke their tough cell walls, without damaging their nuclei, by grinding in a precision-controlled motorized mortar-and-pestle apparatus. The cryo-ground cells were resuspended and thawed in a buffer designed to preserve nuclear morphology, and the nuclei were enriched by differential centrifugation. The washed nuclei were free from contaminating nucleases and have proven well-suited as starting material for genome-wide chromatin analysis and for preparation of fragile DNA replication intermediates. We have developed a simple, reproducible, economical procedure for large-scale preparation of endogenous-nuclease-free, morphologically intact nuclei from fission yeast. With appropriate modifications, this procedure may well prove useful for isolation of nuclei from other organisms with, or without, tough cell walls.

  17. Biochemical characteristics of a free cyanide and total nitrogen assimilating Fusarium oxysporum EKT01/02 isolate from cyanide contaminated soil.

    PubMed

    Akinpelu, Enoch A; Adetunji, Adewole T; Ntwampe, Seteno K O; Nchu, Felix; Mekuto, Lukhanyo

    2017-10-01

    Sustainability of nutrient requirements for microbial proliferation on a large scale is a challenge in bioremediation processes. This article presents data on biochemical properties of a free cyanide resistant and total nitrogen assimilating fungal isolate from the rhizosphere of Zea mays (maize) growing in soil contaminated with a cyanide-based pesticide. DNA extracted from this isolate were PCR amplified using universal primers; TEF1-α and ITS. The raw sequence files are available on the NCBI database. Characterisation using biochemical data was obtained using colorimetric reagents analysed with VITEK ® 2 software version 7.01. The data will be informative in selection of biocatalyst for environmental engineering application.

  18. 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

  19. Symbiotic effects of a lipase-secreting bacterium, Burkholderia arboris SL1B1, and a glycerol-assimilating yeast, Candida cylindracea SL1B2, on triacylglycerol degradation.

    PubMed

    Matsuoka, Hiroshi; Miura, Atsuto; Hori, Katsutoshi

    2009-04-01

    Although microbial degradation of oils and fats has been developed for application in wastewater treatment, microbial degraders are not always effective in the field, for example, in grease-traps installed for the treatment of wastewater from restaurants and food industries. Wastewater in grease-traps is usually in a pH range of 5.5 to 6.5 due to hydrolysis of triacylglycerol (TAG). Because many microorganisms commercialized for use in grease-traps cannot grow at pH 6.0, we screened oil-degrading microorganisms from the environment by growing in a medium at pH 6.0 containing canola oil as the sole carbon source. We succeeded in isolating the bacterial strain Burkholderia arboris SL1B1, which secretes lipase and assimilates fatty acids, and the yeast strain Candida cylindracea SL1B2, which assimilates glycerol. The former cannot utilize glycerol as a carbon source while the latter shows only faint lipase activity that cannot support its active growth on TAG. Canola oil was degraded rapidly by a pure culture of SL1B1 at pH 6.0. However, the degradation was markedly enhanced by a mixed culture of SL1B1 and SL1B2, although lipase activity during cultivation was similar between the pure and mixed cultures. This suggests that the reversible reaction proceeds in the direction of hydrolysis of TAG due to consumption of the reaction product, glycerol, by the symbiotic yeast strain. The optimum pH and temperature of lipase secreted by B. arboris SL1B1 were 8.0 and 60 degrees C, respectively. This lipase showed highly thermal stability; the residual activity after incubation at 70 degrees C for 2 h did not decline.

  20. Ecological Physiology of Synechococcus sp. Strain SH-94-5, a Naturally Occurring Cyanobacterium Deficient in Nitrate Assimilation

    PubMed Central

    Miller, Scott R.; Castenholz, Richard W.

    2001-01-01

    Synechococcus sp. strain SH-94-5 is a nitrate assimilation-deficient cyanobacterium which was isolated from an ammonium-replete hot spring in central Oregon. While this clone could grow on ammonium and some forms of organic nitrogen as sole nitrogen sources, it could not grow on either nitrate or nitrite, even under conditions favoring passive diffusion. It was determined that this clone does not express functional nitrate reductase or nitrite reductase and that the lack of activity of either enzyme is not due to inactivation of the cyanobacterial nitrogen control protein NtcA. A few other naturally occurring cyanobacterial strains are also nitrate assimilation deficient, and phylogenetic analyses indicated that the ability to utilize nitrate has been independently lost at least four times during the evolutionary history of the cyanobacteria. This phenotype is associated with the presence of environmental ammonium, a negative regulator of nitrate assimilation gene expression, which may indicate that natural selection to maintain functional copies of nitrate assimilation genes has been relaxed in these habitats. These results suggest how the evolutionary fates of conditionally expressed genes might differ between environments and thereby effect ecological divergence and biogeographical structure in the microbial world. PMID:11425713

  1. Ecological physiology of Synechococcus sp. strain SH-94-5, a naturally occurring cyanobacterium deficient in nitrate assimilation

    NASA Technical Reports Server (NTRS)

    Miller, S. R.; Castenholz, R. W.

    2001-01-01

    Synechococcus sp. strain SH-94-5 is a nitrate assimilation-deficient cyanobacterium which was isolated from an ammonium-replete hot spring in central Oregon. While this clone could grow on ammonium and some forms of organic nitrogen as sole nitrogen sources, it could not grow on either nitrate or nitrite, even under conditions favoring passive diffusion. It was determined that this clone does not express functional nitrate reductase or nitrite reductase and that the lack of activity of either enzyme is not due to inactivation of the cyanobacterial nitrogen control protein NtcA. A few other naturally occurring cyanobacterial strains are also nitrate assimilation deficient, and phylogenetic analyses indicated that the ability to utilize nitrate has been independently lost at least four times during the evolutionary history of the cyanobacteria. This phenotype is associated with the presence of environmental ammonium, a negative regulator of nitrate assimilation gene expression, which may indicate that natural selection to maintain functional copies of nitrate assimilation genes has been relaxed in these habitats. These results suggest how the evolutionary fates of conditionally expressed genes might differ between environments and thereby effect ecological divergence and biogeographical structure in the microbial world.

  2. Bioprospection of cold-adapted yeasts with biotechnological potential from Antarctica.

    PubMed

    Martorell, María Martha; Ruberto, Lucas Adolfo Mauro; Fernández, Pablo Marcelo; Castellanos de Figueroa, Lucía Inés; Mac Cormack, Walter Patricio

    2017-06-01

    The aim of this study was to investigate the ability to produce extracellular hydrolytic enzymes at low temperature of yeasts isolated from 25 de Mayo island, Antarctica, and to identify those exhibiting one or more of the evaluated enzymatic activities. A total of 105 yeast isolates were obtained from different samples and 66 were identified. They belonged to 12 basidiomycetous and four ascomycetous genera. Most of the isolates were ascribed to the genera Cryptococcus, Mrakia, Cystobasidium, Rhodotorula, Gueomyces, Phenoliferia, Leucosporidium, and Pichia. Results from enzymes production at low temperatures revealed that the Antarctic environment contains metabolically diverse cultivable yeasts, which represent potential tools for biotechnological applications. While most the isolates proved to produce 2-4 of the investigated exoenzymes, two of them evidenced the six evaluated enzymatic activities: Pichia caribbica and Guehomyces pullulans, which were characterized as psycrotolerant and psycrophilic, respectively. In addition, P. caribbica could assimilate several n-alkanes and diesel fuel. The enzyme production profile and hydrocarbons assimilation capacity, combined with its high level of biomass production and the extended exponential growth phase make P. caribbica a promising tool for cold environments biotechnological purposes in the field of cold-enzymes production and oil spills bioremediation as well. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Effect on White Grape Must of Multiflora Bee Pollen Addition during the Alcoholic Fermentation Process.

    PubMed

    Amores-Arrocha, Antonio; Roldán, Ana; Jiménez-Cantizano, Ana; Caro, Ildefonso; Palacios, Víctor

    2018-05-31

    The aim of the present study was to compare and analyze the impact of using bee pollen doses (0.1, 0.25, 1, 5, 10 and 20 g/L) as activator in the alcoholic fermentation process of Palomino fino and Riesling wines. In this regard, its influence on the musts composition, the fermentative kinetics, the evolution of the populations of Saccharomyces cerevisiae , the evolution of yeast-assimilable nitrogen and physico-chemical characteristics of final wines has been analyzed. Bee pollen addition produces significant increases in yeast-assimilable nitrogen and maximum yeasts population and exponential velocity reached during alcoholic fermentation. Bee pollen showed an important effect on yeast survival during the death phase. Final wines showed significantly increase in volatile acidity above doses higher than 10 g/L and Comisión Internacional de L'Eclairage parameters (CIELab), color intensity and Abs 420 nm, from 1 g/L. Therefore, pollen could be used as fermentative activator for the alcoholic fermentation of white wines applying doses below of 1 g/L.

  4. Pathways of nitrogen assimilation in cowpea nodules studied using /sup 15/N/sub 2/ and allopurinol. [Vigna unguiculata L. Walp. cv Vita

    SciTech Connect

    Atkins, C.A.; Storer, P.J.; Pate, J.S.

    1988-01-01

    In the presence of 0.5 millimolar allopurinol (4-hydroxypyrazolo (3,4-d)pyrimidine), an inhibitor of NAD:xanthine oxidoreductase (EC 1.2.3.2), intact attached nodules of cowpea (vigna unguiculata L. Walp. cv Vita 3) formed (/sup 15/N)xanthine from /sup 15/N/sub 2/ at rates equivalent to those of ureide synthesis, confirming the direct assimilation of fixed nitrogen into purines. Xanthine accumulated in nodules and was exported in increasing amounts in xylem of allopurinol-treated plants. Other intermediates of purine oxidation, de novo purine synthesis, and ammonia assimilation did not increase and, over the time course of experiments (4 hours), allopurinol had no effect on nitrogenase (EC 1.87.99.2) activity.more » Negligible /sup 15/N -labeling of asparagine from /sup 15/N/sub 2/ was observed, suggesting that the significant pool (up to 14 micromoles per gram of nodule fresh weight) of this amide in cowpea nodules was not formed directly from fixation but may have accumulated as a consequence of phloem delivery.« less

  5. Salinity stress induced alterations in antioxidant metabolism and nitrogen assimilation in wheat (Triticum aestivum L) as influenced by potassium supplementation.

    PubMed

    Ahanger, Mohammad Abass; Agarwal, R M

    2017-06-01

    Experiments were conducted on two wheat (Triticum aestivum L) cultivars exposed to NaCl stress with and without potassium (K) supplementation. Salt stress induced using NaCl caused oxidative stress resulting into enhancement in lipid peroxidation and altered growth as well as yield. Added potassium led to significant improvement in growth having positive effects on the attributes including nitrogen and antioxidant metabolism. NaCl-induced stress triggered the antioxidant defence system nevertheless, the activity of antioxidant enzymes and the content of non-enzymatic antioxidants increased in K fed plants. Enhancement in the accumulation of osmolytes comprising free proline, sugars and amino acids was observed at both the developmental stages with K supplementation associated with improvement of the relative water content and ultimately yield. Potassium significantly increased uptake and assimilation of nitrogen with concomitant reduction in the Na ions and consequently Na/K ratio. Optimal K can be used as a potential tool for alleviating NaCl stress in wheat to some extent. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  6. Flux balance analysis of ammonia assimilation network in E. coli predicts preferred regulation point.

    PubMed

    Wang, Lu; Lai, Luhua; Ouyang, Qi; Tang, Chao

    2011-01-25

    Nitrogen assimilation is a critical biological process for the synthesis of biomolecules in Escherichia coli. The central ammonium assimilation network in E. coli converts carbon skeleton α-ketoglutarate and ammonium into glutamate and glutamine, which further serve as nitrogen donors for nitrogen metabolism in the cell. This reaction network involves three enzymes: glutamate dehydrogenase (GDH), glutamine synthetase (GS) and glutamate synthase (GOGAT). In minimal media, E. coli tries to maintain an optimal growth rate by regulating the activity of the enzymes to match the availability of the external ammonia. The molecular mechanism and the strategy of the regulation in this network have been the research topics for many investigators. In this paper, we develop a flux balance model for the nitrogen metabolism, taking into account of the cellular composition and biosynthetic requirements for nitrogen. The model agrees well with known experimental results. Specifically, it reproduces all the (15)N isotope labeling experiments in the wild type and the two mutant (ΔGDH and ΔGOGAT) strains of E. coli. Furthermore, the predicted catalytic activities of GDH, GS and GOGAT in different ammonium concentrations and growth rates for the wild type, ΔGDH and ΔGOGAT strains agree well with the enzyme concentrations obtained from western blots. Based on this flux balance model, we show that GS is the preferred regulation point among the three enzymes in the nitrogen assimilation network. Our analysis reveals the pattern of regulation in this central and highly regulated network, thus providing insights into the regulation strategy adopted by the bacteria. Our model and methods may also be useful in future investigations in this and other networks.

  7. 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.

    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% lessmore » 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.« less

  8. Functional expression of a heterologous nickel-dependent, ATP-independent urease in Saccharomyces cerevisiae.

    PubMed

    Milne, N; Luttik, M A H; Cueto Rojas, H F; Wahl, A; van Maris, A J A; Pronk, J T; Daran, J M

    2015-07-01

    In microbial processes for production of proteins, biomass and nitrogen-containing commodity chemicals, ATP requirements for nitrogen assimilation affect product yields on the energy producing substrate. In Saccharomyces cerevisiae, a current host for heterologous protein production and potential platform for production of nitrogen-containing chemicals, uptake and assimilation of ammonium requires 1 ATP per incorporated NH3. Urea assimilation by this yeast is more energy efficient but still requires 0.5 ATP per NH3 produced. To decrease ATP costs for nitrogen assimilation, the S. cerevisiae gene encoding ATP-dependent urease (DUR1,2) was replaced by a Schizosaccharomyces pombe gene encoding ATP-independent urease (ure2), along with its accessory genes ureD, ureF and ureG. Since S. pombe ure2 is a Ni(2+)-dependent enzyme and Saccharomyces cerevisiae does not express native Ni(2+)-dependent enzymes, the S. pombe high-affinity nickel-transporter gene (nic1) was also expressed. Expression of the S. pombe genes into dur1,2Δ S. cerevisiae yielded an in vitro ATP-independent urease activity of 0.44±0.01 µmol min(-1) mg protein(-1) and restored growth on urea as sole nitrogen source. Functional expression of the Nic1 transporter was essential for growth on urea at low Ni(2+) concentrations. The maximum specific growth rates of the engineered strain on urea and ammonium were lower than those of a DUR1,2 reference strain. In glucose-limited chemostat cultures with urea as nitrogen source, the engineered strain exhibited an increased release of ammonia and reduced nitrogen content of the biomass. Our results indicate a new strategy for improving yeast-based production of nitrogen-containing chemicals and demonstrate that Ni(2+)-dependent enzymes can be functionally expressed in S. cerevisiae. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  9. Impact of available nitrogen and sugar concentration in musts on alcoholic fermentation and subsequent wine spoilage by Brettanomyces bruxellensis.

    PubMed

    Childs, Bradford C; Bohlscheid, Jeffri C; Edwards, Charles G

    2015-04-01

    The level of yeast assimilable nitrogen (YAN) supplementation required for Saccharomyces cerevisiae to complete fermentation of high sugar musts in addition to the impact of non-metabolized nitrogen on post-alcoholic spoilage by Brettanomyces bruxellensis was studied. A 2 × 3 factorial design was employed using a synthetic grape juice medium with YAN (150 or 250 mg N/L) and equal proportions of glucose/fructose (230, 250, or 270 g/L) as variables. S. cerevisiae ECA5 (low nitrogen requirement) or Uvaferm 228 (high nitrogen requirement) were inoculated at 10(5) cfu/mL while B. bruxellensis E1 or B2 were added once alcoholic fermentation ceased. Regardless of YAN concentration, musts that contained 230 or 250 g/L glucose/fructose at either nitrogen level attained dryness (mean = 0.32 g/L fructose) while those containing 270 g/L generally did not (mean = 2.5 g/L fructose). Higher concentrations of YAN present in musts yielded wines with higher amounts of α-amino acids and ammonium but very little (≤ 6 mg N/L) was needed by B. bruxellensis to attain populations ≥ 10(7) cfu/mL. While adding nitrogen to high sugar musts does not necessarily ensure completion of alcoholic fermentation, residual YAN did not affect B. bruxellensis growth as much as ethanol concentration. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Nitrogen metabolism and nitrogen control in corynebacteria: variations of a common theme.

    PubMed

    Walter, Britta; Hänssler, Eva; Kalinowski, Jörn; Burkovski, Andreas

    2007-01-01

    The published genome sequences of Corynebacterium diphtheriae, Corynebacterium efficiens, Corynebacterium glutamicum and Corynebacterium jeikeium were screened for genes encoding central components of nitrogen source uptake, nitrogen assimilation and nitrogen control systems. Interestingly, the soil-living species C. efficiens and C. glutamicum exhibit a broader spectrum of genes for nitrogen transport and metabolism than the pathogenic species C. diphtheriae and C. jeikeium. The latter are characterized by gene decay and loss of functions like urea metabolism and nitrogen-dependent transcription control. The global regulator of nitrogen regulation AmtR and its DNA-binding motif are conserved in C. diphtheriae, C. efficiens and C. glutamicum, while in C. jeikeium, an AmtR-encoding gene as well as putative AmtR-binding motifs are missing. Copyright (c) 2007 S. Karger AG, Basel.

  11. Determination of yeast assimilable nitrogen content in wine fermentations by sequential injection analysis with spectrophotometric detetection.

    PubMed

    Muik, Barbara; Edelmann, Andrea; Lendl, Bernhard; Ayora-Cañada, María José

    2002-09-01

    An automated method for measuring the primary amino acid concentration in wine fermentations by sequential injection analysis with spectrophotometric detection was developed. Isoindole-derivatives from the primary amino acid were formed by reaction with o-phthaldialdehyde and N-acetyl- L-cysteine and measured at 334 nm with respect to a baseline point at 700 nm to compensate the observed Schlieren effect. As the reaction kinetic was strongly matrix dependent the analytical readout at the final reaction equilibrium has been evaluated. Therefore four parallel reaction coils were included in the flow system to be capable of processing four samples simultaneously. Using isoleucine as the representative primary amino acid in wine fermentations a linear calibration curve from 2 to 10 mM isoleucine, corresponding to 28 to 140 mg nitrogen/L (N/L) was obtained. The coefficient of variation of the method was 1.5% at a throughput of 12 samples per hour. The developed method was successfully used to monitor two wine fermentations during alcoholic fermentation. The results were in agreement with an external reference method based on high performance liquid chromatography. A mean-t-test showed no significant differences between the two methods at a confidence level of 95%.

  12. Air Quality Modeling Using the NASA GEOS-5 Multispecies Data Assimilation System

    NASA Technical Reports Server (NTRS)

    Keller, Christoph A.; Pawson, Steven; Wargan, Krzysztof; Weir, Brad

    2018-01-01

    The NASA Goddard Earth Observing System (GEOS) data assimilation system (DAS) has been expanded to include chemically reactive tropospheric trace gases including ozone (O3), nitrogen dioxide (NO2), and carbon monoxide (CO). This system combines model analyses from the GEOS-5 model with detailed atmospheric chemistry and observations from MLS (O3), OMI (O3 and NO2), and MOPITT (CO). We show results from a variety of assimilation test experiments, highlighting the improvements in the representation of model species concentrations by up to 50% compared to an assimilation-free control experiment. Taking into account the rapid chemical cycling of NO2 when applying the assimilation increments greatly improves assimilation skills for NO2 and provides large benefits for model concentrations near the surface. Analysis of the geospatial distribution of the assimilation increments suggest that the free-running model overestimates biomass burning emissions but underestimates lightning NOx emissions by 5-20%. We discuss the capability of the chemical data assimilation system to improve atmospheric composition forecasts through improved initial value and boundary condition inputs, particularly during air pollution events. We find that the current assimilation system meaningfully improves short-term forecasts (1-3 day). For longer-term forecasts more emphasis on updating the emissions instead of initial concentration fields is needed.

  13. From mannan to bioethanol: cell surface co-display of β-mannanase and β-mannosidase on yeast Saccharomyces cerevisiae.

    PubMed

    Ishii, Jun; Okazaki, Fumiyoshi; Djohan, Apridah Cameliawati; Hara, Kiyotaka Y; Asai-Nakashima, Nanami; Teramura, Hiroshi; Andriani, Ade; Tominaga, Masahiro; Wakai, Satoshi; Kahar, Prihardi; Yopi; Prasetya, Bambang; Ogino, Chiaki; Kondo, Akihiko

    2016-01-01

    Mannans represent the largest hemicellulosic fraction in softwoods and also serve as carbohydrate stores in various plants. However, the utilization of mannans as sustainable resources has been less advanced in sustainable biofuel development. Based on a yeast cell surface-display technology that enables the immobilization of multiple enzymes on the yeast cell walls, we constructed a recombinant Saccharomyces cerevisiae strain that co-displays β-mannanase and β-mannosidase; this strain is expected to facilitate ethanol fermentation using mannan as a biomass source. Parental yeast S. cerevisiae assimilated mannose and glucose as monomeric sugars, producing ethanol from mannose. We constructed yeast strains that express tethered β-mannanase and β-mannosidase; co-display of the two enzymes on the cell surface was confirmed by immunofluorescence staining and enzyme activity assays. The constructed yeast cells successfully hydrolyzed 1,4-β-d-mannan and produced ethanol by assimilating the resulting mannose without external addition of enzymes. Furthermore, the constructed strain produced ethanol from 1,4-β-d-mannan continually during the third batch of repeated fermentation. Additionally, the constructed strain produced ethanol from ivory nut mannan; ethanol yield was improved by NaOH pretreatment of the substrate. We successfully displayed β-mannanase and β-mannosidase on the yeast cell surface. Our results clearly demonstrate the utility of the strain co-displaying β-mannanase and β-mannosidase for ethanol fermentation from mannan biomass. Thus, co-tethering β-mannanase and β-mannosidase on the yeast cell surface provides a powerful platform technology for yeast fermentation toward the production of bioethanol and other biochemicals from lignocellulosic materials containing mannan components.

  14. Npr1 Ser/Thr Protein Kinase Links Nitrogen Source Quality and Carbon Availability with the Yeast Nitrate Transporter (Ynt1) Levels*

    PubMed Central

    Martín, Yusé; González, Yelvis V.; Cabrera, Elisa; Rodríguez, Celia; Siverio, José M.

    2011-01-01

    Ynt1, the single high affinity nitrate and nitrite transporter of the yeast Hansenula polymorpha, is regulated by the quality of nitrogen sources. Preferred nitrogen sources cause Ynt1 dephosphorylation, ubiquitinylation, endocytosis, and vacuolar degradation. In contrast, under nitrogen limitation Ynt1 is phosphorylated and sorted to the plasma membrane. We show here the involvement of the Ser/Thr kinase HpNpr1 in Ynt1 phosphorylation and regulation of Ynt1 levels in response to nitrogen source quality and the availability of carbon. In Δnpr1, Ynt1 phosphorylation does not take place, although Ynt1 ubiquitin conjugates increase. As a result, in this strain Ynt1 is sorted to the vacuole, from both plasma membrane and the later biosynthetic pathway in nitrogen-free conditions and nitrate. In contrast, overexpression of NPR1 blocks down-regulation of Ynt1, increasing Ynt1 phosphorylation at Ser-244 and -246 and reducing ubiquitinylation. Furthermore, Npr1 is phosphorylated in response to the preferred nitrogen sources, and indeed it is dephosphorylated in nitrogen-free medium. Under conditions where Npr1 is phosphorylated, Ynt1 is not and vice versa. We show for the first time that carbon starvation leads to Npr1 phosphorylation, whereas Ynt1 is dephosphorylated and degraded in the vacuole. Rapamycin prevents this, indicating a possible role of the target of rapamycin signaling pathway in this process. We concluded that Npr1 plays a key role in adapting Ynt1 levels to the nitrogen quality and availability of a source of carbon. PMID:21652715

  15. Ammonia Assimilation in Zea mays L. Infected with a Vesicular-Arbuscular Mycorrhizal Fungus Glomus fasciculatum.

    PubMed

    Cliquet, J. B.; Stewart, G. R.

    1993-03-01

    To investigate nitrogen assimilation and translocation in Zea mays L. colonized by the vesicular-arbuscular mycorrhizal (VAM) fungus Glomus fasciculatum (Thax. sensu Gerd.), we measured key enzyme activities, 15N incorporation into free amino acids, and 15N translocation from roots to shoots. Glutamine synthetase and nitrate reductase activities were increased in both roots and shoots compared with control plants, and glutamate dehydrogenase activity increased in roots only. In the presence of [15N]ammonium, glutamine amide was the most heavily labeled product. More label was incorporated into amino acids in VAM plants. The kinetics of 15N labeling and effects of methionine sulfoximine on distribution of 15N-labeled products were entirely consistent with the operation of the glutamate synthase cycle. No evidence was found for ammonium assimilation via glutamate dehydrogenase. 15N translocation from roots to shoots through the xylem was higher in VAM plants compared with control plants. These results establish that, in maize, VAM fungi increase ammonium assimilation, glutamine production, and xylem nitrogen translocation. Unlike some ectomycorrhizal fungi, VAM fungi do not appear to alter the pathway of ammonium assimilation in roots of their hosts.

  16. Yeast Methylotrophy and Autophagy in a Methanol-Oscillating Environment on Growing Arabidopsis thaliana Leaves

    PubMed Central

    Kawaguchi, Kosuke; Yurimoto, Hiroya; Oku, Masahide; Sakai, Yasuyoshi

    2011-01-01

    The yeast Candida boidinii capable of growth on methanol proliferates and survives on the leaves of Arabidopsis thaliana. The local methanol concentration at the phyllosphere of growing A. thaliana exhibited daily periodicity, and yeast cells responded by altering both the expression of methanol-inducible genes and peroxisome proliferation. Even under these dynamically changing environmental conditions, yeast cells proliferated 3 to 4 times in 11 days. Among the C1-metabolic enzymes, enzymes in the methanol assimilation pathway, but not formaldehyde dissimilation or anti-oxidizing enzymes, were necessary for yeast proliferation at the phyllosphere. Furthermore, both peroxisome assembly and pexophagy, a selective autophagy pathway that degrades peroxisomes, were necessary for phyllospheric proliferation. Thus, the present study sheds light on the life cycle and physiology of yeast in the natural environment at both the molecular and cellular levels. PMID:21966472

  17. Demonstration of Both a Photosynthetic and a Nonphotosynthetic CO(2) Requirement for NH(4) Assimilation in the Green Alga Selenastrum minutum.

    PubMed

    Amory, A M; Vanlerberghe, G C; Turpin, D H

    1991-01-01

    Nitrogen-limited and nitrogen-sufficient cell cultures of Selenastrum minutum (Naeg.) Collins (Chlorophyta) were used to investigate the dependence of NH(4) (+) assimilation on exogenous CO(2). N-sufficient cells were only able to assimilate NH(4) (+) maximally in the presence of CO(2) and light. Inhibition of photosynthesis with 3-(3,4-dichlorophenyl)-1,1-dimethylurea, diuron also inhibited NH(4) (+) assimilation. These results indicate that NH(4) (+) assimilation by N-sufficient cells exhibited a strict requirement for photosynthetic CO(2) fixation. N-limited cells assimilated NH(4) (+) both in the dark and in the light in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea, diuron, indicating that photosynthetic CO(2) fixation was not required for NH(4) (+) assimilation. Using CO(2) removal techniques reported previously in the literature, we were unable to demonstrate CO(2)-dependent NH(4) (+) assimilation in N-limited cells. However, employing more stringent CO(2) removal techniques we were able to show a CO(2) dependence of NH(4) (+) assimilation in both the light and dark, which was independent of photosynthesis. The results indicate two independent CO(2) requirements for NH(4) (+) assimilation. The first is as a substrate for photosynthetic CO(2) fixation, whereas the second is a nonphoto-synthetic requirement, presumably as a substrate for the anaplerotic reaction catalyzed by phosphoenolpyruvate carboxylase.

  18. Comparative Transcriptomic Analysis Reveals Similarities and Dissimilarities in Saccharomyces cerevisiae Wine Strains Response to Nitrogen Availability

    PubMed Central

    Barbosa, Catarina; García-Martínez, José; Pérez-Ortín, José E.; Mendes-Ferreira, Ana

    2015-01-01

    Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12h, 24h and 96h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape

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

    PubMed

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

    2014-02-01

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

  20. Occurrence of yeasts, enterococci and other enteric bacteria in subgingival biofilm of HIV-positive patients with chronic gingivitis and necrotizing periodontitis

    PubMed Central

    Gaetti-Jardim Júnior, Elerson; Nakano, Viviane; Wahasugui, Thais C.; Cabral, Fátima C.; Gamba, Rosa; Avila-Campos, Mario Julio

    2008-01-01

    The purpose of this study was to determine the prevalence of enteric bacteria and yeasts in biofilm of 80 HIV-positive patients with plaque-associated gingivitis or necrotizing periodontitis. Patients were subjected to extra, intra oral and radiographic examinations. The oral hygiene, bleeding on probing, gingival conditions, and attachment loss were evaluated. Clinical specimens were collected from gingival crevices or periodontal pockets, transferred to VMGA III, diluted and transferred to Sabouraud Dextrose agar with 100 μg/ml of chloramphenicol, peptone water, EVA broth, EMB agar, SS agar, Bile esculin agar and Brilliant green agar. Isolation of yeasts was carried out at room temperature, for 3-7 days; and for the isolation of enteric microorganisms plates were incubated at 37°C, for 24-48 h. The yeasts identification was performed according to the carbon and nitrogen assimilation, fermentation of carbohydrates and germ tube formation. Bacteria were identified according to their colonial and cellular morphologies and biochemical tests. Yeasts were identified as Candida albicans and its occurrence was more common in patients with CD4+ below 200/mm3 and was affected by the extension of periodontal involvement (P = 0.0345). Enteric bacteria recovered from clinical specimens were identified as Enterobacter sakazakii, Enterobacter cloacae, Serratia liquefaciens, Klebsiella oxytoca and Enterococcus sp. Enterobacteriaceae and enterococci were detected in 32.5% of clinical samples from patients with necrotizing periodontitis. In conclusion, non-oral pathogenic bacteria and C. albicans were more prevalent in periodontal sites of HIV-positive patients with necrotizing periodontitis and chronic gingivitis. PMID:24031212

  1. Demonstration of Both a Photosynthetic and a Nonphotosynthetic CO2 Requirement for NH4+ Assimilation in the Green Alga Selenastrum minutum1

    PubMed Central

    Amory, Alan M.; Vanlerberghe, Greg C.; Turpin, David H.

    1991-01-01

    Nitrogen-limited and nitrogen-sufficient cell cultures of Selenastrum minutum (Naeg.) Collins (Chlorophyta) were used to investigate the dependence of NH4+ assimilation on exogenous CO2. N-sufficient cells were only able to assimilate NH4+ maximally in the presence of CO2 and light. Inhibition of photosynthesis with 3-(3,4-dichlorophenyl)-1,1-dimethylurea, diuron also inhibited NH4+ assimilation. These results indicate that NH4+ assimilation by N-sufficient cells exhibited a strict requirement for photosynthetic CO2 fixation. N-limited cells assimilated NH4+ both in the dark and in the light in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea, diuron, indicating that photosynthetic CO2 fixation was not required for NH4+ assimilation. Using CO2 removal techniques reported previously in the literature, we were unable to demonstrate CO2-dependent NH4+ assimilation in N-limited cells. However, employing more stringent CO2 removal techniques we were able to show a CO2 dependence of NH4+ assimilation in both the light and dark, which was independent of photosynthesis. The results indicate two independent CO2 requirements for NH4+ assimilation. The first is as a substrate for photosynthetic CO2 fixation, whereas the second is a nonphoto-synthetic requirement, presumably as a substrate for the anaplerotic reaction catalyzed by phosphoenolpyruvate carboxylase. PMID:16667950

  2. Proteome analysis of yeast response to various nutrient limitations

    PubMed Central

    Kolkman, Annemieke; Daran-Lapujade, Pascale; Fullaondo, Asier; Olsthoorn, Maurien M A; Pronk, Jack T; Slijper, Monique; Heck, Albert J R

    2006-01-01

    We compared the response of Saccharomyces cerevisiae to carbon (glucose) and nitrogen (ammonia) limitation in chemostat cultivation at the proteome level. Protein levels were differentially quantified using unlabeled and 15N metabolically labeled yeast cultures. A total of 928 proteins covering a wide range of isoelectric points, molecular weights and subcellular localizations were identified. Stringent statistical analysis identified 51 proteins upregulated in response to glucose limitation and 51 upregulated in response to ammonia limitation. Under glucose limitation, typical glucose-repressed genes encoding proteins involved in alternative carbon source utilization, fatty acids β-oxidation and oxidative phosphorylation displayed an increased protein level. Proteins upregulated in response to nitrogen limitation were mostly involved in scavenging of alternative nitrogen sources and protein degradation. Comparison of transcript and protein levels clearly showed that upregulation in response to glucose limitation was mainly transcriptionally controlled, whereas upregulation in response to nitrogen limitation was essentially controlled at the post-transcriptional level by increased translational efficiency and/or decreased protein degradation. These observations underline the need for multilevel analysis in yeast systems biology. PMID:16738570

  3. Single-cell Protein and Xylitol Production by a Novel Yeast Strain Candida intermedia FL023 from Lignocellulosic Hydrolysates and Xylose.

    PubMed

    Wu, Jiaqiang; Hu, Jinlong; Zhao, Shumiao; He, Mingxiong; Hu, Guoquan; Ge, Xiangyang; Peng, Nan

    2018-05-01

    Yeasts are good candidates to utilize the hydrolysates of lignocellulose, the most abundant bioresource, for bioproducts. This study aimed to evaluate the efficiencies of single-cell protein (SCP) and xylitol production by a novel yeast strain, Candida intermedia FL023, from lignocellulosic hydrolysates and xylose. This strain efficiently assimilated hexose, pentose, and cellubiose for cell mass production with the crude protein content of 484.2 g kg -1 dry cell mass. SCP was produced by strain FL023 using corncob hydrolysate and urea as the carbon and nitrogen sources with the dry cell mass productivity 0.86 g L -1  h -1 and the yield of 0.40 g g -1 sugar. SCP was also produced using NaOH-pretreated Miscanthus sinensis straw and corn steep liquor as the carbon and nitrogen sources through simultaneous saccharification and fermentation with the dry cell productivity of 0.23 g L -1  h -1 and yield of 0.17 g g -1 straw. C. intermedia FL023 was tolerant to 0.5 g L -1 furfural, acetic acid, and syringaldehyde in xylitol fermentation and produced 45.7 g L -1 xylitol from xylose with the productivity of 0.38 g L -1  h -1 and the yield of 0.57 g g -1 xylose. This study provides feasible methods for feed and food additive production from the abundant lignocellulosic bioresources.

  4. Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress

    PubMed Central

    Levitan, Orly; Dinamarca, Jorge; Zelzion, Ehud; Lun, Desmond S.; Guerra, L. Tiago; Kim, Min Kyung; Kim, Joomi; Van Mooy, Benjamin A. S.; Bhattacharya, Debashish; Falkowski, Paul G.

    2015-01-01

    Diatoms are unicellular algae that accumulate significant amounts of triacylglycerols as storage lipids when their growth is limited by nutrients. Using biochemical, physiological, bioinformatics, and reverse genetic approaches, we analyzed how the flux of carbon into lipids is influenced by nitrogen stress in a model diatom, Phaeodactylum tricornutum. Our results reveal that the accumulation of lipids is a consequence of remodeling of intermediate metabolism, especially reactions in the tricarboxylic acid and the urea cycles. Specifically, approximately one-half of the cellular proteins are cannibalized; whereas the nitrogen is scavenged by the urea and glutamine synthetase/glutamine 2-oxoglutarate aminotransferase pathways and redirected to the de novo synthesis of nitrogen assimilation machinery, simultaneously, the photobiological flux of carbon and reductants is used to synthesize lipids. To further examine how nitrogen stress triggers the remodeling process, we knocked down the gene encoding for nitrate reductase, a key enzyme required for the assimilation of nitrate. The strain exhibits 40–50% of the mRNA copy numbers, protein content, and enzymatic activity of the wild type, concomitant with a 43% increase in cellular lipid content. We suggest a negative feedback sensor that couples photosynthetic carbon fixation to lipid biosynthesis and is regulated by the nitrogen assimilation pathway. This metabolic feedback enables diatoms to rapidly respond to fluctuations in environmental nitrogen availability. PMID:25548193

  5. Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

    PubMed Central

    Airoldi, Edoardo M.; Miller, Darach; Athanasiadou, Rodoniki; Brandt, Nathan; Abdul-Rahman, Farah; Neymotin, Benjamin; Hashimoto, Tatsu; Bahmani, Tayebeh; Gresham, David

    2016-01-01

    Cell growth rate is regulated in response to the abundance and molecular form of essential nutrients. In Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen is a major determinant of cell growth rate, supporting growth rates that vary at least threefold. Transcriptional control of nitrogen use is mediated in large part by nitrogen catabolite repression (NCR), which results in the repression of specific transcripts in the presence of a preferred nitrogen source that supports a fast growth rate, such as glutamine, that are otherwise expressed in the presence of a nonpreferred nitrogen source, such as proline, which supports a slower growth rate. Differential expression of the NCR regulon and additional nitrogen-responsive genes results in >500 transcripts that are differentially expressed in cells growing in the presence of different nitrogen sources in batch cultures. Here we find that in growth rate–controlled cultures using nitrogen-limited chemostats, gene expression programs are strikingly similar regardless of nitrogen source. NCR expression is derepressed in all nitrogen-limiting chemostat conditions regardless of nitrogen source, and in these conditions, only 34 transcripts exhibit nitrogen source–specific differential gene expression. Addition of either the preferred nitrogen source, glutamine, or the nonpreferred nitrogen source, proline, to cells growing in nitrogen-limited chemostats results in rapid, dose-dependent repression of the NCR regulon. Using a novel means of computational normalization to compare global gene expression programs in steady-state and dynamic conditions, we find evidence that the addition of nitrogen to nitrogen-limited cells results in the transient overproduction of transcripts required for protein translation. Simultaneously, we find that that accelerated mRNA degradation underlies the rapid clearing of a subset of transcripts, which is most pronounced for the highly expressed NCR

  6. Metabolic reconstruction and flux analysis of industrial Pichia yeasts.

    PubMed

    Chung, Bevan Kai-Sheng; Lakshmanan, Meiyappan; Klement, Maximilian; Ching, Chi Bun; Lee, Dong-Yup

    2013-03-01

    Pichia yeasts have been recognized as important microbial cell factories in the biotechnological industry. Notably, the Pichia pastoris and Pichia stipitis species have attracted much research interest due to their unique cellular physiology and metabolic capability: P. pastoris has the ability to utilize methanol for cell growth and recombinant protein production, while P. stipitis is capable of assimilating xylose to produce ethanol under oxygen-limited conditions. To harness these characteristics for biotechnological applications, it is highly required to characterize their metabolic behavior. Recently, following the genome sequencing of these two Pichia species, genome-scale metabolic networks have been reconstructed to model the yeasts' metabolism from a systems perspective. To date, there are three genome-scale models available for each of P. pastoris and P. stipitis. In this mini-review, we provide an overview of the models, discuss certain limitations of previous studies, and propose potential future works that can be conducted to better understand and engineer Pichia yeasts for industrial applications.

  7. Succinic acid production by Actinobacillus succinogenes using hydrolysates of spent yeast cells and corn fiber.

    PubMed

    Chen, Ke-Quan; Li, Jian; Ma, Jiang-Feng; Jiang, Min; Wei, Ping; Liu, Zhong-Min; Ying, Han-Jie

    2011-01-01

    The enzymatic hydrolysate of spent yeast cells was evaluated as a nitrogen source for succinic acid production by Actinobacillus succinogenes NJ113, using corn fiber hydrolysate as a carbon source. When spent yeast cell hydrolysate was used directly as a nitrogen source, a maximum succinic acid concentration of 35.5 g/l was obtained from a glucose concentration of 50 g/l, with a glucose utilization of 95.2%. Supplementation with individual vitamins showed that biotin was the most likely factor to be limiting for succinic acid production with spent yeast cell hydrolysate. After supplementing spent yeast cell hydrolysate and 90 g/l of glucose with 150 μg/l of biotin, cell growth increased 32.5%, glucose utilization increased 37.6%, and succinic acid concentration was enhanced 49.0%. As a result, when biotin-supplemented spent yeast cell hydrolysate was used with corn fiber hydrolysate, a succinic acid yield of 67.7% was obtained from 70.3 g/l of total sugar concentration, with a productivity of 0.63 g/(l h). Our results suggest that biotin-supplemented spent yeast cell hydrolysate may be an alternative nitrogen source for the efficient production of succinic acid by A. succinogenes NJ113, using renewable resources. Crown Copyright © 2010. Published by Elsevier Ltd. All rights reserved.

  8. Saccharomyces and non-Saccharomyces Competition during Microvinification under Different Sugar and Nitrogen Conditions

    PubMed Central

    Lleixà, Jessica; Manzano, Maria; Mas, Albert; Portillo, María del C.

    2016-01-01

    The inoculation of wines with autochthonous yeast allows obtaining complex wines with a peculiar microbial footprint characteristic from a wine region. Mixed inoculation of non-Saccharomyces yeasts and S. cerevisiae is of interest for the wine industry for technological and sensory reasons. However, the interactions between these yeasts are not well understood, especially those regarding the availability of nutrients. The aim of the present study was to analyze the effect of nitrogen and sugar concentration on the evolution of mixed yeast populations on controlled laboratory-scale fermentations monitored by density, plate culturing, PCR-DGGE and sugar and nitrogen consumption. Furthermore, the effect of the time of inoculation of Saccharomyces cerevisiae respect the initial co-inoculation of three non-Saccharomyces yeasts was evaluated over the evolution of fermentation. Our results have shown that S. cerevisiae inoculation during the first 48 h conferred a stabilizing effect over the fermentations with non-Saccharomyces strains tested and, generally, reduced yeast diversity at the end of the fermentation. On the other hand, nitrogen limitation increased the time of fermentation and also the proportion of non-Saccharomyces yeasts at mid and final fermentation. High sugar concentration resulted in different proportions of the inoculated yeast depending on the time of S. cerevisiae inoculation. This work emphasizes the importance of the concentration of nutrients on the evolution of mixed fermentations and points to the optimal conditions for a stable fermentation in which the inoculated yeasts survived until the end. PMID:27994585

  9. Characterization of culturable yeast species associating with whole crop corn and total mixed ration silage

    PubMed Central

    Wang, Huili; Hao, Wei; Ning, Tingting; Zheng, Mingli; Xu, Chuncheng

    2018-01-01

    Objective This study investigated the association of yeast species with improved aerobic stability of total mixed ration (TMR) silages with prolonged ensiling, and clarified the characteristics of yeast species and their role during aerobic deterioration. Methods Whole crop corn (WCC) silages and TMR silages formulated with WCC were ensiled for 7, 14, 28, and 56 d and used for an aerobic stability test. Predominant yeast species were isolated from different periods and identified by sequencing analyses of the 26S rRNA gene D1/D2 domain. Characteristics (assimilation and tolerance) of the yeast species and their role during aerobic deterioration were investigated. Results In addition to species of Candida glabrata and Pichia kudriavzevii (P. kudriavzevii) previously isolated in WCC and TMR, Pichia manshurica (P. manshurica), Candida ethanolica (C. ethanolica), and Zygosaccharomyces bailii (Z. bailii) isolated at great frequency during deterioration, were capable of assimilating lactic or acetic acid and tolerant to acetic acid and might function more in deteriorating TMR silages at early fermentation (7 d and 14 d). With ensiling prolonged to 28 d, silages became more (p<0.01) stable when exposed to air, coinciding with the inhibition of yeast to below the detection limit. Species of P. manshurica that were predominant in deteriorating WCC silages were not detectable in TMR silages. In addition, the predominant yeast species of Z. bailii in deteriorating TMR silages at later fermentation (28 d and 56 d) were not observed in both WCC and WCC silages. Conclusion The inhibition of yeasts, particularly P. kudriavzevii, probably account for the improved aerobic stability of TMR silages at later fermentation. Fewer species seemed to be involved in aerobic deterioration of silages at later fermentation and Z. bailii was most likely to initiate the aerobic deterioration of TMR silages at later fermentation. The use of WCC in TMR might not influence the predominant yeast

  10. Characterization of culturable yeast species associating with whole crop corn and total mixed ration silage.

    PubMed

    Wang, Huili; Hao, Wei; Ning, Tingting; Zheng, Mingli; Xu, Chuncheng

    2018-02-01

    This study investigated the association of yeast species with improved aerobic stability of total mixed ration (TMR) silages with prolonged ensiling, and clarified the characteristics of yeast species and their role during aerobic deterioration. Whole crop corn (WCC) silages and TMR silages formulated with WCC were ensiled for 7, 14, 28, and 56 d and used for an aerobic stability test. Predominant yeast species were isolated from different periods and identified by sequencing analyses of the 26S rRNA gene D1/D2 domain. Characteristics (assimilation and tolerance) of the yeast species and their role during aerobic deterioration were investigated. In addition to species of Candida glabrata and Pichia kudriavzevii ( P. kudriavzevii ) previously isolated in WCC and TMR, Pichia manshurica ( P. manshurica ), Candida ethanolica ( C. ethanolica ), and Zygosaccharomyces bailii ( Z. bailii ) isolated at great frequency during deterioration, were capable of assimilating lactic or acetic acid and tolerant to acetic acid and might function more in deteriorating TMR silages at early fermentation (7 d and 14 d). With ensiling prolonged to 28 d, silages became more (p<0.01) stable when exposed to air, coinciding with the inhibition of yeast to below the detection limit. Species of P. manshurica that were predominant in deteriorating WCC silages were not detectable in TMR silages. In addition, the predominant yeast species of Z. bailii in deteriorating TMR silages at later fermentation (28 d and 56 d) were not observed in both WCC and WCC silages. The inhibition of yeasts, particularly P. kudriavzevii , probably account for the improved aerobic stability of TMR silages at later fermentation. Fewer species seemed to be involved in aerobic deterioration of silages at later fermentation and Z. bailii was most likely to initiate the aerobic deterioration of TMR silages at later fermentation. The use of WCC in TMR might not influence the predominant yeast species during aerobic

  11. Genome and metabolic engineering in non-conventional yeasts: Current advances and applications.

    PubMed

    Löbs, Ann-Kathrin; Schwartz, Cory; Wheeldon, Ian

    2017-09-01

    Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisia e is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.

  12. Active role of a human genomic insert in replication of a yeast artificial chromosome.

    PubMed

    van Brabant, A J; Fangman, W L; Brewer, B J

    1999-06-01

    Yeast artificial chromosomes (YACs) are a common tool for cloning eukaryotic DNA. The manner by which large pieces of foreign DNA are assimilated by yeast cells into a functional chromosome is poorly understood, as is the reason why some of them are stably maintained and some are not. We examined the replication of a stable YAC containing a 240-kb insert of DNA from the human T-cell receptor beta locus. The human insert contains multiple sites that serve as origins of replication. The activity of these origins appears to require the yeast ARS consensus sequence and, as with yeast origins, additional flanking sequences. In addition, the origins in the human insert exhibit a spacing, a range of activation efficiencies, and a variation in times of activation during S phase similar to those found for normal yeast chromosomes. We propose that an appropriate combination of replication origin density, activation times, and initiation efficiencies is necessary for the successful maintenance of YAC inserts.

  13. Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency.

    PubMed

    Kant, Surya; Bi, Yong-Mei; Rothstein, Steven J

    2011-02-01

    Development of genetic varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Generally, NUE can be divided into two parts. First, assimilation efficiency involves nitrogen (N) uptake and assimilation and second utilization efficiency involves N remobilization. Understanding the mechanisms regulating these processes is crucial for the improvement of NUE in crop plants. One important approach is to develop an understanding of the plant response to different N regimes, especially to N limitation, using various methods including transcription profiling, analysing mutants defective in their normal response to N limitation, and studying plants that show better growth under N-limiting conditions. One can then attempt to improve NUE in crop plants using the knowledge gained from these studies. There are several potential genetic and molecular approaches for the improvement of crop NUE discussed in this review. Increased knowledge of how plants respond to different N levels as well as to other environmental conditions is required to achieve this.

  14. Yeasts associated with the curculionid beetle Xyloterinus politus: Candida xyloterini sp. nov., Candida palmyrensis sp. nov. and three common ambrosia yeasts.

    PubMed

    Suh, Sung-Oui; Zhou, Jianlong

    2010-07-01

    Seven yeast strains were isolated from the body surface and galleries of Xyloterinus politus, the ambrosia beetle that attacks black oak trees. Based on rDNA sequence comparisons and other taxonomic characteristics, five of the strains were identified as members of the species Saccharomycopsis microspora, Wickerhamomyces hampshirensis and Candida mycetangii, which have been reported previously as being associated with insects. The remaining two yeast strains were proposed as representatives of two novel species, Candida xyloterini sp. nov. (type strain ATCC 62898(T)=CBS 11547(T)) and Candida palmyrensis sp. nov. (type strain ATCC 62899(T)=CBS 11546(T)). C. xyloterini sp. nov. is a close sister taxon to Ogataea dorogensis and assimilates methanol as a sole carbon source but lacks ascospores. On the other hand, C. palmyrensis sp. nov. is phylogenetically distinct from any other ambrosia yeast reported so far. The species was placed near Candida sophiae-reginae and Candida beechii based on DNA sequence analyses, but neither of these were close sister taxa to C. palmyrensis sp. nov.

  15. Effects of lanthanum(III) on nitrogen metabolism of soybean seedlings under elevated UV-B radiation.

    PubMed

    Cao, Rui; Huang, Xiao-hua; Zhou, Qing; Cheng, Xiao-ying

    2007-01-01

    The hydroponic culture experiments of soybean bean seedlings were conducted to investigate the effect of lanthanum (La) on nitrogen metabolism under two different levels of elevated UV-B radiation (UV-B, 280-320 nm). The whole process of nitrogen metabolism involves uptake and transport of nitrate, nitrate assimilation, ammonium assimilation, amino acid biosynthesis, and protein synthesis. Compared with the control, UV-B radiation with the intensity of low level 0.15 W/m2 and high level 0.45 W/m2 significantly affected the whole nitrogen metabolism in soybean seedlings (p < 0.05). It restricted uptake and transport of NO3(-), inhibited activity of some key nitrogen-metabolism-related enzymes, such as: nitrate reductase (NR) to the nitrate reduction, glutamine systhetase (GS) and glutamine synthase (GOGAT) to the ammonia assimilation, while it increased the content of free amino acids and decreased that of soluble protein as well. The damage effect of high level of UV-B radiation on nitrogen metabolism was greater than that of low level. And UV-B radiation promoted the activity of the anti-adversity enzyme glutamate dehydrogenase (GDH), which reduced the toxicity of excess ammonia in plant. After pretreatment with the optimum concentration of La (20 mg/L), La could increase the activity of NR, GS, GOGAT, and GDH, and ammonia assimilation, but decrease nitrate and ammonia accumulation. In conclusion, La could relieve the damage effect of UV-B radiation on plant by regulating nitrogen metabolism process, and its alleviating effect under low level was better than that under the high one.

  16. [Treatment of oil-manufacturing wastewater by yeast-SBR system].

    PubMed

    Lü, Wen-zhou; Liu, Ying; Huang, Yi-zhen

    2008-04-01

    Eight yeast strains were applied to a sequencing batch reactor (SBR) to treat high-strength oil-containing wastewater. The removal performance, yeast cultivation method and key factors affecting the stability of system were discussed. The results show yeast sludge with MLSS of 19 g/L and SVI of 35 mL/g can be obtained in 6 d in an open system without any molds and bacteria inhibitor addition; In 30 d continuous wastewater treatment, COD and oil removal rate achieve 86.8%-96.9% and above 99.5% respectively under the influent conditions of the COD of 9000-23000 mg/L and oil of 4500-16000 mg/L; Short period of pH impact brings reversible effects on the system and the sludge retention time can affect the SVI of the yeast; Absence of nitrogen induces morphology conversion of some yeast cells from single cell to filamentous one and impairs the settling capability of the yeast.

  17. Flor Yeast: New Perspectives Beyond Wine Aging

    PubMed Central

    Legras, Jean-Luc; Moreno-Garcia, Jaime; Zara, Severino; Zara, Giacomo; Garcia-Martinez, Teresa; Mauricio, Juan C.; Mannazzu, Ilaria; Coi, Anna L.; Bou Zeidan, Marc; Dequin, Sylvie; Moreno, Juan; Budroni, Marilena

    2016-01-01

    The most important dogma in white-wine production is the preservation of the wine aroma and the limitation of the oxidative action of oxygen. In contrast, the aging of Sherry and Sherry-like wines is an aerobic process that depends on the oxidative activity of flor strains of Saccharomyces cerevisiae. Under depletion of nitrogen and fermentable carbon sources, these yeast produce aggregates of floating cells and form an air–liquid biofilm on the wine surface, which is also known as velum or flor. This behavior is due to genetic and metabolic peculiarities that differentiate flor yeast from other wine yeast. This review will focus first on the most updated data obtained through the analysis of flor yeast with -omic tools. Comparative genomics, proteomics, and metabolomics of flor and wine yeast strains are shedding new light on several features of these special yeast, and in particular, they have revealed the extent of proteome remodeling imposed by the biofilm life-style. Finally, new insights in terms of promotion and inhibition of biofilm formation through small molecules, amino acids, and di/tri-peptides, and novel possibilities for the exploitation of biofilm immobilization within a fungal hyphae framework, will be discussed. PMID:27148192

  18. Cryptococcus cyanovorans sp. nov., a basidiomycetous yeast isolated from cyanide-contaminated soil.

    PubMed

    Motaung, Thabiso E; Albertyn, Jacobus; Kock, Johan L F; Pohl, Carolina H

    2012-05-01

    Eighteen yeast strains were isolated and identified from cyanide-contaminated soil in South Africa. According to sequence-based analyses using the D1/D2 region of the large ribosomal subunit and ITS region, three of these strains were found to be identical and represent a novel species. Phylogenetic analysis based on the combined dataset of the D1/D2 and ITS regions revealed a grouping with Cryptococcus curvatus, representing a defined clade (Curvatus) in the order Trichosporonales. The three strains were demarcated from Cryptococcus curvatus by standard physiological tests such as assimilation of lactose, xylitol, 5-keto-D-gluconate, succinate and citrate as well as growth on media containing 10 % (w/v) NaCl and 5 % (w/v) glucose. In addition, it was established that these strains could utilize up to 10 mM NaCN as sole carbon source on solid media and as sole nitrogen source in liquid media. On the basis of these findings, it is suggested that the three strains represent a novel species for which the name Cryptococcus cyanovorans sp. nov. is given (type strain CBS 11948(T) = NRRL Y-48730(T)).

  19. Yeast succession in the Amazon fruit Parahancornia amapa as resource partitioning among Drosophila spp.

    PubMed Central

    Morais, P B; Martins, M B; Klaczko, L B; Mendonça-Hagler, L C; Hagler, A N

    1995-01-01

    The succession of yeasts colonizing the fallen ripe amapa fruit, from Parahancornia amapa, was examined. The occupation of the substrate depended on both the competitive interactions of yeast species, such as the production of killer toxins, and the selective dispersion by the drosophilid guild of the amapa fruit. The yeast community associated with this Amazon fruit differed from those isolated from other fruits in the same forest. The physiological profile of these yeasts was mostly restricted to the assimilation of a few simple carbon sources, mainly L-sorbose, D-glycerol, DL-lactate, cellobiose, and salicin. Common fruit-associated yeasts of the genera Kloeckera and Hanseniaspora, Candida guilliermondii, and Candida krusei colonized fruits during the first three days after the fruit fell. These yeasts were dispersed and served as food for the invader Drosophila malerkotliana. The resident flies of the Drosophila willistoni group fed selectively on patches of yeasts colonizing fruits 3 to 10 days after the fruit fell. The killer toxin-producing yeasts Pichia kluyveri var. kluyveri and Candida fructus were probably involved in the exclusion of some species during the intermediate stages of fruit deterioration. An increase in pH, inhibiting toxin activity and the depletion of simple sugars, may have promoted an increase in yeast diversity in the later stages of decomposition. The yeast succession provided a patchy environment for the drosophilids sharing this ephemeral substrate. PMID:8534092

  20. Effect of carbon sources on the growth and ethanol production of native yeast Pichia kudriavzevii ITV-S42 isolated from sweet sorghum juice.

    PubMed

    Díaz-Nava, L E; Montes-Garcia, N; Domínguez, J M; Aguilar-Uscanga, M G

    2017-07-01

    The importance of non-Saccharomyces yeast species in fermentation processes is widely acknowledged. Within this group, Pichia kudriavzevii ITV-S42 yeast strain shows particularly desirable characteristics for ethanol production. Despite this fact, a thorough study of the metabolic and kinetic characteristics of this strain is currently unavailable. The aim of this work is to study the nutritional requirements of Pichia kudriavzevii ITV-S42 strain and the effect of different carbon sources on the growth and ethanol production. Results showed that glucose and fructose were both assimilated and fermented, achieving biomass and ethanol yields of 0.37 and 0.32 gg -1 , respectively. Glycerol was assimilated but not fermented; achieving a biomass yield of 0.88 gg -1 . Xylose and sucrose were not metabolized by the yeast strain. Finally, the use of a culture medium enriched with salts and yeast extract favored glucose consumption both for growth and ethanol production, improving ethanol tolerance reported for this genre (35 g L -1 ) to 90 g L -1 maximum ethanol concentration (over 100%). Furthermore Pichia kudriavzevii ITV-S42 maintained its fermentative capacity up to 200 g L -1 initial glucose, demonstrating that this yeast is osmotolerant.

  1. Significance of Phosphoenolpyruvate Carboxylase during Ammonium Assimilation

    PubMed Central

    Guy, Robert D.; Vanlerberghe, Greg C.; Turpin, David H.

    1989-01-01

    The effect of N-assimilation on the partitioning of carbon fixation between phosphoenolpyruvate carboxylase (PEPcase) and ribulose bisphosphate carboxylase/oxygenase (Rubisco) was determined by measuring stable carbon isotope discrimination during photosynthesis by an N-limited green alga, Selenastrum minutum (Naeg.) Collins. This was facilitated by a two process model accounting for simultaneous CO2 fixation and respiratory CO2 release. Discrimination by control cells was consistent with the majority of carbon being fixed by Rubisco. During nitrogen assimilation however, discrimination was greatly reduced indicating an enhanced flux through PEPcase which accounted for upward of 70% of total carbon fixation. This shift toward anaplerotic metabolism supports a large increase in tricarboxylic acid cycle activity primarily between oxaloacetate and α-ketoglutarate thereby facilitating the provision of carbon skeletons for amino acid synthesis. This provides an example of a unique set of conditions under which anaplerotic carbon fixation by PEPcase exceeds photosynthetic carbon fixation by Rubisco in a C3 organism. Images Figure 6 PMID:16666678

  2. Assimilative and non-assimilative color spreading in the watercolor configuration.

    PubMed

    Kimura, Eiji; Kuroki, Mikako

    2014-01-01

    A colored line flanking a darker contour will appear to spread its color onto an area enclosed by the line (watercolor effect). The watercolor effect has been characterized as an assimilative effect, but non-assimilative color spreading has also been demonstrated in the same spatial configuration; e.g., when a black inner contour (IC) is paired with a blue outer contour (OC), yellow color spreading can be observed. To elucidate visual mechanisms underlying these different color spreading effects, this study investigated the effects of luminance ratio between the double contours on the induced color by systematically manipulating the IC and the OC luminance (Experiment 1) as well as the background luminance (Experiment 2). The results showed that the luminance conditions suitable for assimilative and non-assimilative color spreading were nearly opposite. When the Weber contrast of the IC to the background luminance (IC contrast) was smaller in size than that of the OC (OC contrast), the induced color became similar to the IC color (assimilative spreading). In contrast, when the OC contrast was smaller than or equal to the IC contrast, the induced color became yellow (non-assimilative spreading). Extending these findings, Experiment 3 showed that bilateral color spreading, i.e., assimilative spreading on one side and non-assimilative spreading on the other side, can also be observed in the watercolor configuration. These results suggest that the assimilative and the non-assimilative spreading were mediated by different visual mechanisms. The properties of the assimilative spreading are consistent with the model proposed to account for neon color spreading (Grossberg and Mingolla, 1985) and extended for the watercolor effect (Pinna and Grossberg, 2005). However, the present results suggest that additional mechanisms are needed to account for the non-assimilative color spreading.

  3. Astaxanthinogenesis in the yeast Phaffia rhodozyma - optimization of low-cost culture media and yeast cell-wall lysis

    SciTech Connect

    Fontana, J.D.; Baron, M.; Guimaraes, M.F.

    Astaxanthin is a diketo-dihydroxy-carotenoid produced by Phaffia rhodozyma, a basidiomicetous yeast. A low-cost fermentation medium consisting of raw sugarcane juice and urea was developed to exploit the active sucrolytic/urelolytic enzyme apparatus inherent to the yeast. As compared to the beneficial effect of 0.1 g% urea, a ready nitrogen source, mild phosphoric pre inversion of juice sucrose to glucose and fructose, promptly fermentable carbon sources, resulted in smaller benefits. Corn steep liquor (CSL) was found to be a valuable supplement for both yeast biomass yield (9.2 g dry cells/L) and astaxanthin production (1.3 mg/g cells). Distillery effluent (vinace), despite only amore » slightly positive effect on yeast growth, allowed for the highest pigment productivity (1.9 mg/g cells). Trace amounts of Ni{sup 2} (1 mg/L, as a cofactor for urease) resulted in controversial effects, namely, biomass decrease and astaxanthin increase, with no effect on the release (and uptake) of ammonium ion from urea. 13 refs., 6 figs.« less

  4. Nitrogen use strategies of seedlings from neotropical tree species of distinct successional groups.

    PubMed

    Oliveira, Halley Caixeta; da Silva, Ligia Maria Inocêncio; de Freitas, Letícia Dias; Debiasi, Tatiane Viegas; Marchiori, Nidia Mara; Aidar, Marcos Pereira Marinho; Bianchini, Edmilson; Pimenta, José Antonio; Stolf-Moreira, Renata

    2017-05-01

    Few studies have analyzed the strategies of neotropical tree seedlings for absorbing, translocating and assimilating the nitrogen. Here, we compared the nitrogen use strategies of seedlings from six tree species that are native to the Brazilian Atlantic Forest and that belong to different successional groups: Trema micrantha, Heliocarpus popayanensis and Cecropia pachystachya (pioneers), Cariniana estrellensis, Eugenia brasiliensis and Guarea kunthiana (non-pioneers). The effects of cultivating seedlings with nitrate or ammonium on the growth, physiology and nitrogen metabolism were analyzed. Nitrate-grown pioneer species had much higher leaf nitrate reductase activity than non-pioneer ones, but non-pioneer seedlings were also able to use nitrate as a nitrogen source. In addition to this remarkable difference between the groups in the capacity for leaf nitrate assimilation, substantial variations in the nitrogen use strategies were observed within the successional classes. Differently from the other non-pioneers, the canopy species C. estrellensis seemed to assimilate nitrate mainly in the leaves. Morphophysiological analyses showed a gradient of ammonium toxicity response, with E. brasiliensis as the most tolerant species, and T. micrantha and H. popayanensis as the most sensitive ones. Guarea kunthiana showed a relatively low tolerance to ammonium and an unusual high translocation of this cation in the xylem sap. In contrast to the other pioneers, C. pachystachya had a high plasticity in the use of nitrogen sources. Overall, these results suggest that nitrogen use strategies of neotropical tree seedlings were not determined solely by their successional position. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  5. Nutrient depletion modifies cell wall adsorption activity of wine yeast.

    PubMed

    Sidari, R; Caridi, A

    2016-06-01

    Yeast cell wall is a structure that helps yeasts to manage and respond to many environmental stresses. The mannosylphosphorylation is a modification in response to stress that provides the cell wall with negative charges able to bind compounds present in the environment. Phenotypes related to the cell wall modification such as the filamentous growth in Saccharomyces cerevisiae are affected by nutrient depletion. The present work aimed at describing the effect of carbon and/or nitrogen limitation on the aptitude of S. cerevisiae strains to bind coloured polyphenols. Carbon- and nitrogen-rich or deficient media supplemented with grape polyphenols were used to simulate different grape juice conditions-early, mid, 'adjusted' for nitrogen, and late fermentations. In early fermentation condition, the R+G+B values range from 106 (high adsorption, strain Sc1128) to 192 (low adsorption, strain Σ1278b), in mid-fermentation the values range from 111 (high adsorption, strain Sc1321) to 258 (low adsorption, strain Sc2306), in 'adjusted' for nitrogen conditions the values range from 105 (high adsorption, strain Sc1321) to 194 (low adsorption, strain Sc2306) while in late fermentation conditions the values range from 101 (high adsorption, strain Sc384) to 293 (low adsorption, strain Sc2306). The effect of nutrient availability is not univocal for all the strains and the different media tested modified the strains behaviour. In all the media the strains show significant differences. Results demonstrate that wine yeasts decrease/increase their parietal adsorption activity according to the nutrient availability. The wide range of strain variability observed could be useful in selecting wine starters.

  6. NaCl stress effects on enzymes involved in nitrogen assimilation pathway in tomato "Lycopersicon esculentum" seedlings.

    PubMed

    Debouba, Mohamed; Gouia, Houda; Suzuki, Akira; Ghorbel, Mohamed Habib

    2006-12-01

    Tomato plants (Lycopersicon esculentum Mill, cv. Chibli F1) grown for 10 days on control medium were exposed to differing concentrations of NaCl (0, 25, 50, and 100mM). Increasing salinity led to a decrease of dry weight (DW) production and protein contents in the leaves and roots. Conversely, the root to shoot (R/S) DW ratio was increased by salinity. Na(+) and Cl(-) accumulation were correlated with a decline of K(+) and NO(3)(-) in the leaves and roots. Under salinity, the activities of nitrate reductase (NR, EC 1.6.6.1) and glutamine synthetase (GS, EC 6.3.1.2) were repressed in the leaves, while they were enhanced in the roots. Nitrite reductase (NiR, EC 1.7.7.1) activity was decreased in both the leaves and roots. Deaminating activity of glutamate dehydrogenase (GDH, EC 1.4.1.2) was inhibited, whereas the aminating function was significantly stimulated by salinity in the leaves and roots. At a high salt concentration, the nicotinamide adenine dinucleotide reduced (NADH)-GDH activity was stimulated concomitantly with the increasing NH(4)(+) contents and proteolysis activity in the leaves and roots. With respect to salt stress, the distinct sensitivity of the enzymes involved in nitrogen assimilation is discussed.

  7. Molecular mechanism for the operation of nitrogen control in cyanobacteria.

    PubMed Central

    Luque, I; Flores, E; Herrero, A

    1994-01-01

    In cyanobacteria, ammonium exerts a negative regulation of the expression of proteins involved in the assimilation of nitrogen sources alternative to ammonium. In Synechococcus, mRNA levels of genes encoding proteins for nitrate and ammonium assimilation were observed to be negatively regulated by ammonium, and ammonium-regulated transcription start points were identified for those genes. The NtcA protein is a positive regulator of genes subjected to nitrogen control by ammonium. Mutants lacking NtcA exhibited only basal mRNA levels of the regulated genes, even in the absence of ammonium, indicating that NtcA exerts its regulatory action by positively influencing mRNA levels of the nitrogen-regulated genes. NtcA was observed to bind directly to the promoters of nitrogen-regulated genes, and the palindromic DNA sequence GTAN8TAC was identified as a sequence signature for NtcA-target sites. The structure of the nitrogen-, NtcA-regulated promoters of Synechococcus was determined to be constituted by a -10, Pribnow-like box in the form TAN3T, and an NtcA-binding site that substituted for the canonical -35 box. Images PMID:8026471

  8. Relationship of nitrogen use efficiency with the activities of enzymes involved in nitrogen uptake and assimilation of finger millet genotypes grown under different nitrogen inputs.

    PubMed

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

    2012-01-01

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

  9. The occurrence and growth of yeasts in Camembert and blue-veined cheeses.

    PubMed

    Roostita, R; Fleet, G H

    1996-01-01

    Yeast populations greater than 10(6) cfu/g were found in approximately 54% and 36%, respectively in surface samples of retail Camembert (85 samples) and Blue-veined (45 samples) cheeses. The most predominant species isolated were Debaryomyces hansenii, Candida catenulata, C. lipolytica, C. kefyr, C. intermedia, Saccharomyces cerevisiae, Cryptococcus albidus and Kluyveromyces marxianus. The salt concentration of the surface samples of the cheeses varied between 2.5-5.5% (w/w) (Camembert) and 7.5-8.3 (Blue-veined), depending upon brand, and influenced the yeast ecology, especially the presence of S. cerevisiae. Yeasts grew to populations of 10(6)-10(8) cfu/g when cheeses were stored at either 25 degrees C or 10 degrees C. These populations decreased on continued storage at 25 degrees C, but such decreases were not so evident on storage at 10 degrees C. The properties of yeasts influencing their occurrence and growth in cheese were: fermentation/assimilation of lactose; production of extracellular lipolytic and proteolytic enzymes, utilisation of lactic and citric acids; and growth at 10 degrees C.

  10. Isolation and functional characterization of an ammonium transporter gene, PyAMT1, related to nitrogen assimilation in the marine macroalga Pyropia yezoensis (Rhodophyta).

    PubMed

    Kakinuma, Makoto; Nakamoto, Chika; Kishi, Kazuki; Coury, Daniel A; Amano, Hideomi

    2017-07-01

    Ammonium and nitrate are the primary nitrogen sources in natural environments, and are essential for growth and development in photosynthetic eukaryotes. In this study, we report on the isolation and characterization of an ammonium transporter gene (PyAMT1) which performs a key function in nitrogen (N) metabolism of Pyropia yezoensis thalli. The predicted length of PyAMT1 was 483 amino acids (AAs). The AA sequence included 11 putative transmembrane domains and showed approximately 33-44% identity to algal and plant AMT1 AA sequences. Functional complementation in an AMT-defective yeast mutant indicated that PyAMT1 mediated ammonium transport across the plasma membrane. Expression analysis showed that the PyAMT1 mRNA level was strongly induced by N-deficiency, and was more highly suppressed by resupply of inorganic-N than organic-N. These results suggest that PyAMT1 plays important roles in the ammonium transport system, and is highly regulated in response to external/internal N-status. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Sulfur assimilation and the role of sulfur in plant metabolism: a survey.

    PubMed

    Droux, Michel

    2004-01-01

    Sulfur occurs in two major amino-acids, cysteine (Cys) and methionine (Met), essential for the primary and secondary metabolism of the plant. Cys, as the first carbon/nitrogen-reduced sulfur product resulting from the sulfate assimilation pathway, serves as a sulfur donor for Met, glutathione, vitamins, co-factors, and sulfur compounds that play a major role in the growth and development of plant cells. This sulfur imprinting occurs in a myriad of fundamental processes, from photosynthesis to carbon and nitrogen metabolism. Cys and Met occur in proteins, with the former playing a wide range of functions in proteins catalysis. In addition, the sulfur atom in proteins forms part of a redox buffer, as for glutathione, through specific detoxification/protection mechanisms. In this review, a survey of sulfur assimilation from sulfate to Cys, Met and glutathione is presented with highlights on open questions on their respective biosynthetic pathways and regulations that derived from recent findings. These are addressed at the biochemical and molecular levels with respect to the fate of Cys and Met throughout the plant-cell metabolism.

  12. Use of corn steep liquor as an economical nitrogen source for biosuccinic acid production by Actinobacillus succinogenes

    NASA Astrophysics Data System (ADS)

    Tan, J. P.; Jahim, J. M.; Wu, T. Y.; Harun, S.; Mumtaz, T.

    2016-06-01

    Expensive raw materials are the driving force that leads to the shifting of the petroleum-based succinic acid production into bio-based succinic acid production by microorganisms. Cost of fermentation medium is among the main factors contributing to the total production cost of bio-succinic acid. After carbon source, nitrogen source is the second largest component of the fermentation medium, the cost of which has been overlooked for the past years. The current study aimed at replacing yeast extract- a costly nitrogen source with corn steep liquor for economical production of bio-succinic acid by Actinobacillus succinogenes 130Z. In this study, a final succinic acid concentration of 20.6 g/L was obtained from the use of corn steep liquor as the nitrogen source, which was comparable with the use of yeast extract as the nitrogen source that had a final succinate concentration of 21.4 g/l. In terms of economical wise, corn steep liquor was priced at 200 /ton, which was one fifth of the cost of yeast extract at 1000 /ton. Therefore, corn steep liquor can be considered as a potential nitrogen source in biochemical industries instead of the costly yeast extract.

  13. A light-dependent ammonia-assimilating mechanism in the ctenidia of a giant clam

    NASA Astrophysics Data System (ADS)

    Hiong, Kum C.; Choo, Celine Y. L.; Boo, Mel V.; Ching, Biyun; Wong, Wai P.; Chew, Shit F.; Ip, Yuen K.

    2017-03-01

    Giant clams harbor symbiotic zooxanthellae and manifest light-enhanced calcification. In light, they also increase the absorption and assimilation of exogenous ammonia, but the roles of the host and symbionts are unclear and the reason for light dependency remains enigmatic. Here, we report the complete coding cDNA sequence of a glutamine synthetase (GS), from the ctenidia (gill) of Tridacna squamosa. The deduced GS amino acid sequence was closely related to other animal GSs, indicating a host origin. The GS/GS transcript level and protein abundance increased significantly in the ctenidia after 12 h of light exposure. These results denote the ctenidia as the site of light-enhanced ammonia absorption with the absorbed ammonia being assimilated to glutamine by the host GS. Immunofluorescence microscopy confirmed that GS was expressed predominantly in the cytoplasm of the epithelial cells separating the tertiary water channels from the hemolymph inside the ctenidia. Hence, unlike symbiotic cnidarians, the host clam probably supplies exogenous nitrogen as glutamine from the ctenidia, through the hemolymph and tubular fluid, to the nitrogen-deficient zooxanthellae which reside extracellularly in the extensible outer mantle. This is the first report on light-dependent gene and protein expression of a host enzyme involved in nitrogen metabolism in an alga-invertebrate association.

  14. 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

  15. Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeast species.

    PubMed

    Sitepu, Irnayuli R; Sestric, Ryan; Ignatia, Laura; Levin, David; German, J Bruce; Gillies, Laura A; Almada, Luis A G; Boundy-Mills, Kyria L

    2013-09-01

    Oleaginous yeasts have been studied for oleochemical production for over 80 years. Only a few species have been studied intensely. To expand the diversity of oleaginous yeasts available for lipid research, we surveyed a broad diversity of yeasts with indicators of oleaginicity including known oleaginous clades, and buoyancy. Sixty-nine strains representing 17 genera and 50 species were screened for lipid production. Yeasts belonged to Ascomycota families, Basidiomycota orders, and the yeast-like algal genus Prototheca. Total intracellular lipids and fatty acid composition were determined under different incubation times and nitrogen availability. Thirteen new oleaginous yeast species were discovered, representing multiple ascomycete and basidiomycete clades. Nitrogen starvation generally increased intracellular lipid content. The fatty acid profiles varied with the growth conditions regardless of taxonomic affiliation. The dominant fatty acids were oleic acid, palmitic acid, linoleic acid, and stearic acid. Yeasts and culture conditions that produced fatty acids appropriate for biodiesel were identified. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Manipulation of culture conditions alters lipid content and fatty acid profiles of a wide variety of known and new oleaginous yeasts species

    PubMed Central

    Sitepu, Irnayuli R.; Sestric, Ryan; Ignatia, Laura; Levin, David; German, J. Bruce; Gillies, Laura A.; Almada, Luis A.G.; Boundy-Mills, Kyria L.

    2013-01-01

    Oleaginous yeasts have been studied for oleochemical production for over 80 years. Only a few species have been studied intensely. To expand the diversity of oleaginous yeasts available for lipid research, we surveyed a broad diversity of yeasts with indicators of oleaginicity including known oleaginous clades, and buoyancy. Sixty-nine strains representing 17 genera and 50 species were screened for lipid production. Yeasts belonged to Ascomycota families, Basidiomycota orders, and the yeast-like algal genus Prototheca. Total intracellular lipids and fatty acid composition were determined under different incubation times and nitrogen availability. Thirteen new oleaginous yeast species were discovered, representing multiple ascomycete and basidiomycete clades. Nitrogen starvation generally increased intracellular lipid content. The fatty acid profiles varied with the growth conditions regardless of taxonomic affiliation. The dominant fatty acids were oleic acid, palmitic acid, linoleic acid, and stearic acid. Yeasts and culture conditions that produced fatty acids appropriate for biodiesel were identified. PMID:23891835

  17. Brucella, nitrogen and virulence.

    PubMed

    Ronneau, Severin; Moussa, Simon; Barbier, Thibault; Conde-Álvarez, Raquel; Zuniga-Ripa, Amaia; Moriyon, Ignacio; Letesson, Jean-Jacques

    2016-08-01

    The brucellae are α-Proteobacteria causing brucellosis, an important zoonosis. Although multiplying in endoplasmic reticulum-derived vacuoles, they cause no cell death, suggesting subtle but efficient use of host resources. Brucellae are amino-acid prototrophs able to grow with ammonium or use glutamate as the sole carbon-nitrogen source in vitro. They contain more than twice amino acid/peptide/polyamine uptake genes than the amino-acid auxotroph Legionella pneumophila, which multiplies in a similar vacuole, suggesting a different nutritional strategy. During these two last decades, many mutants of key actors in nitrogen metabolism (transporters, enzymes, regulators, etc.) have been described to be essential for full virulence of brucellae. Here, we review the genomic and experimental data on Brucella nitrogen metabolism and its connection with virulence. An analysis of various aspects of this metabolism (transport, assimilation, biosynthesis, catabolism, respiration and regulation) has highlighted differences and similarities in nitrogen metabolism with other α-Proteobacteria. Together, these data suggest that, during their intracellular life cycle, the brucellae use various nitrogen sources for biosynthesis, catabolism and respiration following a strategy that requires prototrophy and a tight regulation of nitrogen use.

  18. Analysis of Possibility of Yeast Production Increase at Maintained Carbon Dioxide Emission Level

    NASA Astrophysics Data System (ADS)

    Włodarczyk, Barbara; Włodarczyk, Paweł P.

    2016-12-01

    Main parameters polluting of technological wastewater (dregs from decantation and thicken of the wort) from yeast industry are: nitrogen, potassium and COD. Such wastewater are utilized mostly on agricultural fields. Unfortunately, these fields can only accept a limited amount of wastes. The basic parameter limiting there the amount of wastewater is nitrogen. When capacity of the production is large sewages are often pretreated at an evaporator station. However, due to the fairly high running costs of the evaporator station currently such a solution is applied only to a small amount of wastes (just to meet legal requirements). Replacement of the earth gas with a biomass being supplied to the evaporator station from the agricultural fields will both allow to maintain the carbon dioxide emission level and enable the production growth. Moreover, the biomass growing on the agricultural fields being fertilized with the wastewater coming from the yeast production allows consequently to utilize the greater volume of wastewater. Theoretically, the possible increase in the yeasts production, with maintaining the carbon dioxide emission level, can reach even 70%. Therefore, the solution presented in this paper combines both intensification of the yeasts production and maintaining the carbon dioxide emission level.

  19. CO2 enrichment inhibits shoot nitrate assimilation in C3 but not C4 plants and slows growth under nitrate in C3 plants.

    PubMed

    Bloom, Arnold J; Asensio, Jose Salvador Rubaio; Randall, Lesley; Rachmilevitch, Shimon; Cousins, Asaph B; Carlisle, Eli A

    2012-02-01

    The CO2 concentration in Earth's atmosphere may double during this century. Plant responses to such an increase depend strongly on their nitrogen status, but the reasons have been uncertain. Here, we assessed shoot nitrate assimilation into amino acids via the shift in shoot CO2 and O2 fluxes when plants received nitrate instead of ammonium as a nitrogen source (deltaAQ). Shoot nitrate assimilation became negligible with increasing CO2 in a taxonomically diverse group of eight C3 plant species, was relatively insensitive to CO2 in three C4 species, and showed an intermediate sensitivity in two C3-C4 intermediate species. We then examined the influence of CO2 level and ammonium vs. nitrate nutrition on growth, assessed in terms of changes in fresh mass, of several C3 species and a Crassulacean acid metabolism (CAM) species. Elevated CO2 (720 micromol CO2/mol of all gases present) stimulated growth or had no effect in the five C3 species tested when they received ammonium as a nitrogen source but inhibited growth or had no effect if they received nitrate. Under nitrate, two C3 species grew faster at sub-ambient (approximately 310 micromol/mol) than elevated CO2. A CAM species grew faster at ambient than elevated or sub-ambient CO2 under either ammonium or nitrate nutrition. This study establishes that CO2 enrichment inhibits shoot nitrate assimilation in a wide variety of C3 plants and that this phenomenon can have a profound effect on their growth. This indicates that shoot nitrate assimilation provides an important contribution to the nitrate assimilation of an entire C3 plant. Thus, rising CO2 and its effects on shoot nitrate assimilation may influence the distribution of C3 plant species.

  20. Hanseniaspora nodinigri, a new yeast species found in black knots (Dibotryon morbosum) of Prunus virginiana.

    PubMed

    Lachance, M A

    1981-07-01

    The new yeast species Hanseniaspora nodinigri is described to accommodate members of the genus Hanseniaspora that are unable to assimilate glucono-sigma-lactone and isolated from stromatal tissue of black knots (Dobotryon morbosum) of chokecherry, Prunus virginiana. The newly described taxon shows much resemblance, by other criteria, to H. vineae van der Walt et Tscheuschner and H. osmophila (Niehaus) Phaff, Miller et Shifrine.

  1. Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

    PubMed Central

    2014-01-01

    Background The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. Results We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Conclusions Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning. PMID:24708438

  2. Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit.

    PubMed

    Hoefman, Sven; van der Ha, David; Boon, Nico; Vandamme, Peter; De Vos, Paul; Heylen, Kim

    2014-04-04

    The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.

  3. Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum

    SciTech Connect

    Rydzak, Thomas; Garcia, David; Stevenson, David M.

    Clostridium thermocellum rapidly deconstructs cellulose and ferments resulting hydrolysis products into ethanol and other products, and is thus a promising platform organism for the development of cellulosic biofuel production via consolidated bioprocessing. And while recent metabolic engineering strategies have targeted eliminating canonical fermentation products (acetate, lactate, formate, and H 2), C. thermocellum also secretes amino acids, which has limited ethanol yields in engineered strains to approximately 70% of the theoretical maximum. To decrease amino acid secretion, we attempted to reduce ammonium assimilation by deleting the Type I glutamine synthetase (glnA) in C. thermocellum. Deletion of glnA reduced levels of secretedmore » valine and total amino acids by 53% and 44% respectively, and increased ethanol yields by 53%. RNA-seq analysis revealed that genes encoding the RNF-complex were more highly expressed in ΔglnA and may have a role in improving NADH-availability for ethanol production. While a significant up-regulation of genes involved in nitrogen assimilation and urea uptake suggested that deletion of glnA induces a nitrogen starvation response, metabolomic analysis showed an increase in intracellular glutamine and α-ketoglutarate levels indicative of nitrogen-rich conditions. Here, we propose that deletion of glnA causes deregulation of nitrogen metabolism, leading to overexpression of nitrogen metabolism genes and, in turn, elevated glutamine/α-ketoglutarate levels. Here we demonstrate that perturbation of nitrogen assimilation is a promising strategy to redirect flux from the production of nitrogenous compounds toward biofuels in C. thermocellum.« less

  4. Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum.

    PubMed

    Rydzak, Thomas; Garcia, David; Stevenson, David M; Sladek, Margaret; Klingeman, Dawn M; Holwerda, Evert K; Amador-Noguez, Daniel; Brown, Steven D; Guss, Adam M

    2017-05-01

    Clostridium thermocellum rapidly deconstructs cellulose and ferments resulting hydrolysis products into ethanol and other products, and is thus a promising platform organism for the development of cellulosic biofuel production via consolidated bioprocessing. While recent metabolic engineering strategies have targeted eliminating canonical fermentation products (acetate, lactate, formate, and H 2 ), C. thermocellum also secretes amino acids, which has limited ethanol yields in engineered strains to approximately 70% of the theoretical maximum. To investigate approaches to decrease amino acid secretion, we attempted to reduce ammonium assimilation by deleting the Type I glutamine synthetase (glnA) in an essentially wild type strain of C. thermocellum. Deletion of glnA reduced levels of secreted valine and total amino acids by 53% and 44% respectively, and increased ethanol yields by 53%. RNA-seq analysis revealed that genes encoding the RNF-complex were more highly expressed in ΔglnA and may have a role in improving NADH-availability for ethanol production. While a significant up-regulation of genes involved in nitrogen assimilation and urea uptake suggested that deletion of glnA induces a nitrogen starvation response, metabolomic analysis showed an increase in intracellular glutamine levels indicative of nitrogen-rich conditions. We propose that deletion of glnA causes deregulation of nitrogen metabolism, leading to overexpression of nitrogen metabolism genes and, in turn, elevated glutamine levels. Here we demonstrate that perturbation of nitrogen assimilation is a promising strategy to redirect flux from the production of nitrogenous compounds toward biofuels in C. thermocellum. Copyright © 2017. Published by Elsevier Inc.

  5. Metabolic engineering of microbial competitive advantage for industrial fermentation processes.

    PubMed

    Shaw, A Joe; Lam, Felix H; Hamilton, Maureen; Consiglio, Andrew; MacEwen, Kyle; Brevnova, Elena E; Greenhagen, Emily; LaTouf, W Greg; South, Colin R; van Dijken, Hans; Stephanopoulos, Gregory

    2016-08-05

    Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment. Copyright © 2016, American Association for the Advancement of Science.

  6. Nitrogen balance for wheat canopies (Triticum aestivum cv. Veery 10) grown under elevated and ambient CO2 concentrations

    NASA Technical Reports Server (NTRS)

    Smart, D. R.; Ritchie, K.; Bloom, A. J.; Bugbee, B. B.

    1998-01-01

    We examined the hypothesis that elevated CO2 concentration would increase NO3- absorption and assimilation using intact wheat canopies (Triticum aestivum cv. Veery 10). Nitrate consumption, the sum of plant absorption and nitrogen loss, was continuously monitored for 23 d following germination under two CO2 concentrations (360 and 1000 micromol mol-1 CO2) and two root zone NO3- concentrations (100 and 1000 mmol m3 NO3-). The plants were grown at high density (1780 m-2) in a 28 m3 controlled environment chamber using solution culture techniques. Wheat responded to 1000 micromol mol-1 CO2 by increasing carbon allocation to root biomass production. Elevated CO2 also increased root zone NO3- consumption, but most of this increase did not result in higher biomass nitrogen. Rather, nitrogen loss accounted for the greatest part of the difference in NO3- consumption between the elevated and ambient [CO2] treatments. The total amount of NO3(-)-N absorbed by roots or the amount of NO3(-)-N assimilated per unit area did not significantly differ between elevated and ambient [CO2] treatments. Instead, specific leaf organic nitrogen content declined, and NO3- accumulated in canopies growing under 1000 micromol mol-1 CO2. Our results indicated that 1000 micromol mol-1 CO2 diminished NO3- assimilation. If NO3- assimilation were impaired by high [CO2], then this offers an explanation for why organic nitrogen contents are often observed to decline in elevated [CO2] environments.

  7. The IRC7 gene encodes cysteine desulphydrase activity and confers on yeast the ability to grow on cysteine as a nitrogen source.

    PubMed

    Santiago, Margarita; Gardner, Richard C

    2015-07-01

    Although cysteine desulphydrase activity has been purified and characterized from Saccharomyces cerevisiae, the gene encoding this activity in vivo has never been defined. We show that the full-length IRC7 gene, encoded by the YFR055W open reading frame, encodes a protein with cysteine desulphydrase activity. Irc7p purified to homogeneity is able to utilize l-cysteine as a substrate, producing pyruvate and hydrogen sulphide as products of the reaction. Purified Irc7p also utilized l-cystine and some other cysteine conjugates, but not l-cystathionine or l-methionine, as substrates. We further show that, in vivo, the IRC7 gene is both necessary and sufficient for yeast to grow on l-cysteine as a nitrogen source, and that overexpression of the gene results in increased H2 S production. Strains overexpressing IRC7 are also hypersensitive to a toxic analogue, S-ethyl-l-cysteine. While IRC7 has been identified as playing a critical role in converting cysteine conjugates to volatile thiols that are important in wine aroma, its biological role in yeast cells is likely to involve regulation of cysteine and redox homeostasis. Copyright © 2015 John Wiley & Sons, Ltd.

  8. Isolation and Characterization of Hydrocarbon-Degrading Yeast Strains from Petroleum Contaminated Industrial Wastewater.

    PubMed

    Gargouri, Boutheina; Mhiri, Najla; Karray, Fatma; Aloui, Fathi; Sayadi, Sami

    2015-01-01

    Two yeast strains are enriched and isolated from industrial refinery wastewater. These strains were observed for their ability to utilize several classes of petroleum hydrocarbons substrates, such as n-alkanes and aromatic hydrocarbons as a sole carbon source. Phylogenetic analysis based on the D1/D2 variable domain and the ITS-region sequences indicated that strains HC1 and HC4 were members of the genera Candida and Trichosporon, respectively. The mechanism of hydrocarbon uptaking by yeast, Candida, and Trichosporon has been studied by means of the kinetic analysis of hydrocarbons-degrading yeasts growth and substrate assimilation. Biodegradation capacity and biomass quantity were daily measured during twelve days by gravimetric analysis and gas chromatography coupled with mass spectrometry techniques. Removal of n-alkanes indicated a strong ability of hydrocarbon biodegradation by the isolated yeast strains. These two strains grew on long-chain n-alkane, diesel oil, and crude oil but failed to grow on short-chain n-alkane and aromatic hydrocarbons. Growth measurement attributes of the isolates, using n-hexadecane, diesel oil, and crude oil as substrates, showed that strain HC1 had better degradation for hydrocarbon substrates than strain HC4. In conclusion, these yeast strains can be useful for the bioremediation process and decreasing petroleum pollution in wastewater contaminated with petroleum hydrocarbons.

  9. Rice Ferredoxin-Dependent Glutamate Synthase Regulates Nitrogen-Carbon Metabolomes and Is Genetically Differentiated between japonica and indica Subspecies.

    PubMed

    Yang, Xiaolu; Nian, Jinqiang; Xie, Qingjun; Feng, Jian; Zhang, Fengxia; Jing, Hongwei; Zhang, Jian; Dong, Guojun; Liang, Yan; Peng, Juli; Wang, Guodong; Qian, Qian; Zuo, Jianru

    2016-11-07

    Plants assimilate inorganic nitrogen absorbed from soil into organic forms as Gln and Glu through the glutamine synthetase/glutamine:2-oxoglutarate amidotransferase (GS/GOGAT) cycle. Whereas GS catalyzes the formation of Gln from Glu and ammonia, GOGAT catalyzes the transfer of an amide group from Gln to 2-oxoglutarate to produce two molecules of Glu. However, the regulatory role of the GS/GOGAT cycle in the carbon-nitrogen balance is not well understood. Here, we report the functional characterization of rice ABNORMAL CYTOKININ RESPONSE 1 (ABC1) gene that encodes a ferredoxin-dependent (Fd)-GOGAT. The weak mutant allele abc1-1 mutant shows a typical nitrogen-deficient syndrome, whereas the T-DNA insertional mutant abc1-2 is seedling lethal. Metabolomics analysis revealed the accumulation of an excessive amount of amino acids with high N/C ratio (Gln and Asn) and several intermediates in the tricarboxylic acid cycle in abc1-1, suggesting that ABC1 plays a critical role in nitrogen assimilation and carbon-nitrogen balance. Five non-synonymous single-nucleotide polymorphisms were identified in the ABC1 coding region and characterized as three distinct haplotypes, which have been highly and specifically differentiated between japonica and indica subspecies. Collectively, these results suggest that ABC1/OsFd-GOGAT is essential for plant growth and development by modulating nitrogen assimilation and the carbon-nitrogen balance. Copyright © 2016 The Author. Published by Elsevier Inc. All rights reserved.

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

    PubMed Central

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

    2017-01-01

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

  11. Processing watershed-derived nitrogen in a well-flushed New England estuary

    USGS Publications Warehouse

    Tobias, C.R.; Cieri, M.; Peterson, B.J.; Deegan, Linda A.; Vallino, J.; Hughes, J.

    2003-01-01

    Isotopically labeled nitrate (15NO3-) was added continuously to the Rowley estuary, Massachusetts, for 22 d to assess the transport, uptake, and cycling of terrestrially derived nitrogen during a period of high river discharge and low phytoplankton activity. Isotopic enrichment of the 3.5-km tidal prism (150,000 m3) was achieved for the 3 weeks and allowed us to construct a nitrogen mass balance model for the upper estuary. Mean ??15NO3- in the estuary ranged from 300??? to 600???, and approximately 75%-80% of the 15N was exported conservatively as 15NO 3- to the coastal ocean. Essentially all of the 20%-25% of the 15N processed in the estuary occurred in the benthos and was evenly split between direct denitrification and autotrophic assimilation. The lack of water-column 15N uptake was attributed to low phytoplankton stocks and short water residence times (1.2-1.4 d). Uptake of water-column NO3- by benthic autotrophs (enriched in excess of 100???) was a function of NO3- concentration and satisfied up to 15% and 25% of the total nitrogen demand for benthic microalgae and macroalgae, respectively. Approximately 10% of tracer assimilated by benthic autotrophs was mineralized and released back to the water column as 15NH4+. By the end of the study, 15N storage in sediments and marsh macrophytes accounted for 50%-70% of the 15N assimilated in the estuary. These compartments may sequester watershed-derived nitrogen in the estuary for time scales of months to years.

  12. Growth and fermentation patterns of Saccharomyces cerevisiae under different ammonium concentrations and its implications in winemaking industry.

    PubMed

    Mendes-Ferreira, A; Mendes-Faia, A; Leão, C

    2004-01-01

    To study the effects of assimilable nitrogen concentration on growth profile and on fermentation kinetics of Saccharomyces cerevisiae. Saccharomyces cerevisiae was grown in batch in a defined medium with glucose (200 g l(-1)) as the only carbon and energy source, and nitrogen supplied as ammonium sulphate or phosphate forms under different concentrations. The initial nitrogen concentration in the media had no effect on specific growth rates of the yeast strain PYCC 4072. However, fermentation rate and the time required for completion of the alcoholic fermentation were strongly dependent on nitrogen availability. At the stationary phase, the addition of ammonium was effective in increasing cell population, fermentation rate and ethanol. The yeast strain required a minimum of 267 mg N l(-1) to attain complete dryness of media, within the time considered for the experiments. Lower levels were enough to support growth, although leading to sluggish or stuck fermentation. The findings reported here contribute to elucidate the role of nitrogen on growth and fermentation performance of wine yeast. This information might be useful to the wine industry where excessive addition of nitrogen to prevent sluggish or stuck fermentation might have a negative impact on wine stability and quality. Copyright 2004 The Society for Applied Microbiology

  13. Metabolic peculiarities of the citric acid overproduction from glucose in yeasts Yarrowia lipolytica.

    PubMed

    Kamzolova, Svetlana V; Morgunov, Igor G

    2017-11-01

    Comparative study of 43 natural yeast strains belonging to 20 species for their capability for overproduction of citric acid (CA) from glucose under nitrogen limitation of cell growth was carried out. As a result, natural strain Yarrowia lipolytica VKM Y-2373 was selected. The effect of growth limitation by biogenic macroelements (nitrogen, phosphorus, or sulfur) on the CA production by the selected strain was studied. It was shown that yeasts Y. lipolytica grown under deficiency of nitrogen, phosphorus, or sulfur were able to excrete CA in industrially sufficient amounts (80-85g/L with the product yield (Y CA ) of 0.70-0.75g/g and the process selectivity of 92.5-95.3%). Based on the obtained data on activities of enzymes involved in the initial stages of glucose oxidation, the cycle of tricarboxylic acids, and the glyoxylate cycle, the conception of the mechanism responsible for the CA overproduction from glucose in Y. lipolytica was formulated. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Potential benefits of the application of yeast starters in table olive processing.

    PubMed

    Arroyo-López, Francisco N; Romero-Gil, Verónica; Bautista-Gallego, Joaquín; Rodríguez-Gómez, Francisco; Jiménez-Díaz, Rufino; García-García, Pedro; Querol, Amparo; Garrido-Fernández, Antonio

    2012-01-01

    Yeasts play an important role in the food and beverage industry, especially in products such as bread, wine, and beer, among many others. However, their use as a starter in table olive processing has not yet been studied in detail. The candidate yeast strains should be able to dominate fermentation, together with lactic acid bacteria, but should also provide a number of beneficial advantages. Technologically, yeasts should resist low pH and high salt concentrations, produce desirable aromas, improve lactic acid bacteria growth, and inhibit spoilage microorganisms. Nowadays, they are being considered as probiotic agents because many species are able to resist the passage through the gastrointestinal tract and show favorable effects on the host. In this way, yeasts may improve the health of consumers by means of the degradation of non-assimilated compounds (such as phytate complexes), a decrease in cholesterol levels, the production of vitamins and antioxidants, the inhibition of pathogens, an adhesion to intestinal cell line Caco-2, and the maintenance of epithelial barrier integrity. Many yeast species, usually found in table olive processing (Wickerhamomyces anomalus, Saccharomyces cerevisiae, Pichia membranifaciens, and Kluyveromyces lactis, among others), have exhibited some of these properties. Thus, the selection of the most appropriate strains to be used as starters in this fermented vegetable, alone or in combination with lactic acid bacteria, is a promising research line to develop in the near future.

  15. Potential benefits of the application of yeast starters in table olive processing

    PubMed Central

    Arroyo-López, Francisco N.; Romero-Gil, Verónica; Bautista-Gallego, Joaquín; Rodríguez-Gómez, Francisco; Jiménez-Díaz, Rufino; García-García, Pedro; Querol, Amparo; Garrido-Fernández, Antonio

    2012-01-01

    Yeasts play an important role in the food and beverage industry, especially in products such as bread, wine, and beer, among many others. However, their use as a starter in table olive processing has not yet been studied in detail. The candidate yeast strains should be able to dominate fermentation, together with lactic acid bacteria, but should also provide a number of beneficial advantages. Technologically, yeasts should resist low pH and high salt concentrations, produce desirable aromas, improve lactic acid bacteria growth, and inhibit spoilage microorganisms. Nowadays, they are being considered as probiotic agents because many species are able to resist the passage through the gastrointestinal tract and show favorable effects on the host. In this way, yeasts may improve the health of consumers by means of the degradation of non-assimilated compounds (such as phytate complexes), a decrease in cholesterol levels, the production of vitamins and antioxidants, the inhibition of pathogens, an adhesion to intestinal cell line Caco-2, and the maintenance of epithelial barrier integrity. Many yeast species, usually found in table olive processing (Wickerhamomyces anomalus, Saccharomyces cerevisiae, Pichia membranifaciens, and Kluyveromyces lactis, among others), have exhibited some of these properties. Thus, the selection of the most appropriate strains to be used as starters in this fermented vegetable, alone or in combination with lactic acid bacteria, is a promising research line to develop in the near future.

  16. Thermospheric Data Assimilation

    DTIC Science & Technology

    2016-05-05

    forecasting longer than 3 days. Furthermore, validation of assimilation analyses with independent CHAMP mass density observations confirms that the...approach developed in this project. 15. SUBJECT TERMS Data assimilation, Ensemble forecasting , Thermosphere-ionosphere coupled data assimilation...Neutral mass density specification and forecasting , 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 6 19a. NAME

  17. Candida queiroziae sp. nov., a cellobiose-fermenting yeast species isolated from rotting wood in Atlantic Rain Forest.

    PubMed

    Santos, Renata O; Cadete, Raquel M; Badotti, Fernanda; Mouro, Adriane; Wallheim, Daniela O; Gomes, Fátima C O; Stambuk, Boris U; Lachance, Marc-André; Rosa, Carlos A

    2011-03-01

    Eight strains of a novel yeast species were isolated from rotting wood and wood-boring insects in Atlantic Rain Forest ecosystems in Brazil. Sequences of the D1/D2 domains of the large subunit of the rRNA gene showed that the yeast belongs to the Scheffersomyces clade and that it is related to Candida lignicola and Candida coipomoensis. The new species was isolated from rotting wood of three different localities and a wood-boring insect suggesting that these substrates are its ecological niche. This new yeast species is able to assimilate cellobiose and other compounds related to rotting wood. Strong fermentation of cellobiose in Durham tubes was observed for the strains of this new yeast. The new species produced an intracellular β-glucosidase responsible for cellobiose hydrolysis. The novel species, Candida queiroziae sp. nov., is proposed to accommodate these isolates. The type strain of C. queiroziae is UFMG-CLM 5.1(T) (=CBS 11853(T) = NRRL Y-48722(T)).

  18. Modeling of nitrogen transformation in an integrated multi-trophic aquaculture (IMTA)

    NASA Astrophysics Data System (ADS)

    Silfiana; Widowati; Putro, S. P.; Udjiani, T.

    2018-03-01

    The dynamic model of nitrogen transformation in IMTA (Integrated Multi-Trophic Aquaculture) is purposed. IMTA is a polyculture with several biotas maintained in it to optimize waste recycling as a food source. The purpose of this paper is to predict nitrogen decrease and nitrogen transformation in IMTA consisting of ammonia (NH3), Nitrite (NO2) and Nitrate (NO3). Nitrogen transformation of several processes, nitrification, assimilation, and volatilization. Numerical simulations are performed by providing initial parameters and values based on a review of previous research. The numerical results show that the rate of change in nitrogen concentration in IMTA decrease and reaches stable at different times.

  19. Identification of yeasts isolated from raffia wine (Raphia hookeri) produced in Côte d'Ivoire and genotyping of Saccharomyces cerevisiae strains by PCR inter-delta.

    PubMed

    Tra Bi, Charles Y; N'guessan, Florent K; Kouakou, Clémentine A; Jacques, Noemie; Casaregola, Serge; Djè, Marcellin K

    2016-08-01

    Raffia wine is a traditional alcoholic beverage produced in several African countries where it plays a significant role in traditional customs and population diet. Alcoholic fermentation of this beverage is ensured by a complex natural yeast flora which plays a decisive role in the quality of the final product. This present study aims to evaluate the distribution and the diversity of the yeast strains isolated in raffia wine from four sampling areas (Abengourou, Alépé, Grand-Lahou and Adzopé) in Côte d'Ivoire. Based on the D1/D2 domain of the LSU rDNA sequence analysis, nine species belonging to six genera were distinguished. With a percentage of 69.5 % out of 171 yeast isolates, Saccharomyces cerevisiae was the predominant species in the raffia wine, followed by Kodamaea ohmeri (20.4 %). The other species isolated were Candida haemulonii (4.1 %), Candida phangngensis (1.8 %), Pichia kudriavzevii (1.2 %), Hanseniaspora jakobsenii (1.2 %), Candida silvae (0.6 %), Hanseniaspora guilliermondii (0.6 %) and Meyerozyma caribbica (0.6 %). The molecular characterization of S. cerevisiae isolates at the strain level using the PCR-interdelta method revealed the presence of 21 profiles (named I to XXI) within 115 isolates. Only four profiles (I, III, V and XI) were shared by the four areas under study. Phenotypic characterization of K. ohmeri strains showed two subgroups for sugar fermentation and no diversity for the nitrogen compound assimilations and the growth at different temperatures.

  20. Quantifying the production of dissolved organic nitrogen in headwater streams using 15N tracer additions

    Treesearch

    Laura T. Johnson; Jennifer L. Tank; Robert O. Hall; Patrick J. Mullholland; Stephen K. Hamilton; H. Maurice Valett; Jackson R. Webster; Melody J. Bernot; William H. McDowell; Bruce J. Peterson; Suzanne M. Thomas

    2013-01-01

    Most nitrogen (N) assimilation in lake and marine ecosystems is often subsequently released via autochthonous dissolved organic nitrogen (DON) production, but autochthonous DON production has yet to be quantified in flowing waters. We measured in-stream DON production following 24 h 15N-nitrate (NO3-...

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

    PubMed Central

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

    2011-01-01

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

  2. Candida aechmeae sp. nov. and Candida vrieseae sp. nov., novel yeast species isolated from the phylloplane of bromeliads in Southern Brazil.

    PubMed

    Landell, Melissa Fontes; Billodre, Raisa; Ramos, Jesus P; Leoncini, Orílio; Vainstein, Marilene H; Valente, Patrícia

    2010-01-01

    Two novel yeast species, Candida aechmeae sp. nov. and Candida vrieseae sp. nov., were isolated from bromeliads in Itapuã Park, Rio Grande do Sul, Brazil. These species are genetically isolated from all other currently recognized ascomycetous yeasts based on their sequence divergence in the D1/D2 domain of the LSU rRNA gene. C. aechmeae sp. nov. is phylogenetically close to Candida ubatubensis, a species also isolated from bromeliads in Brazil, but the novel species can be differentiated on the basis of differences in the D1/D2 domain and positive results for the assimilation of l-arabinose, raffinose, inulin and citrate. Candida vrieseae sp. nov. is phylogenetically placed in a clade near Candida membranifaciens that is composed of several species associated with insects, but the novel species can be differentiated from them by the D1/D2 and ITS gene sequences, positive results for the assimilation of nitrite and a negative result for the assimilation of ethylamine. The type strain for Candida aechmeae sp. nov. is BI153(T) (=CBS 10831(T)=NRRL Y-48456(T)) and the type strain for C. vrieseae sp. nov. is BI146(T) (=CBS 10829(T)=NRRL Y-48461(T)).

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  4. Biomass assimilation in coupled ecohydrodynamical model of the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Crispi, G.; Bournaski, E.; Crise, A.

    2003-04-01

    Data assimilation has raised new interest in the last years in the context of the environmental sciences. The swift increment of the attention paid to it in oceanography is due to the coming age of operational services for the marine environment which is going to dramatically increase the demand for accurate, timely and reliable estimates of the space and time distribution both for physical and in a near future for biogeochemical fields. Data assimilation combines information derived from measurements with knowledge of the rules that govern the evolution of the system of interest through formalization and implementation in numerical models. The importance of ocean data assimilation has been recognized by several international programmes as JGOFS, GOOS and CLIVAR. This work presents an eco-hydrodynamic model of the Mediterranean Sea developed at the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy. It includes 3-D MOM-based hydrodynamics of the Mediterranean Sea, coupled with biochemical model of Nitrogen, Phytoplankton, Zooplankton, and Detritus (NPZD). Monthly mean wind forcings are adopted to force this MOM-NPZD model. For better prediction and analysis of N, P, Z and D distributions in the sea the model needs data assimilation from biomass observations on the sea surface. Chosen approach for evaluating performances of data assimilation techniques in coupled model is the definition of a twin experiment testbed where a reference run is carried out assuming its result as the truth. We define a sampling strategy to obtain different datasets to be incorporated in another ecological model in successive runs in order to appraise the potential of the data assimilation and sampling strategy. The runs carried out with different techniques and different spatio-temporal coverages are compared in order to evaluate the sensitivity to different coverage of dataset. The discussed alternative way is to assume the ecosystem at steady state and

  5. Active role of fatty acid amino acid conjugates in nitrogen metabolism in Spodoptera litura larvae

    PubMed Central

    Yoshinaga, Naoko; Aboshi, Takako; Abe, Hiroaki; Nishida, Ritsuo; Alborn, Hans T.; Tumlinson, James H.; Mori, Naoki

    2008-01-01

    Since the first fatty acid amino acid conjugate (FAC) was isolated from regurgitant of Spodoptera exigua larvae in 1997 [volicitin: N-(17-hydroxylinolenoyl)-l-glutamine], their role as elicitors of induced responses in plants has been well documented. However, studies of the biosyntheses and the physiological role of FACs in the insect have been minimal. By using 14C-labeled glutamine, glutamic acid, and linolenic acid in feeding studies of Spodoptera litura larvae, combined with tissue analyses, we found glutamine in the midgut cells to be a major source for biosynthesis of FACs. Furthermore, 20% of the glutamine moiety of FACs was derived from glutamic acid and ammonia through enzymatic reaction of glutamine synthetase (GS). To determine whether FACs improve GS productivity, we studied nitrogen assimilation efficiency of S. litura larvae fed on artificial diets containing 15NH4Cl and glutamic acid. When the diet was enriched with linolenic acid, the nitrogen assimilation efficiency improved from 40% to >60%. In the lumen, the biosynthesized FACs are hydrolyzed to fatty acids and glutamine, which are reabsorbed into tissues and hemolymph. These results strongly suggested that FACs play an active role in nitrogen assimilation in Lepidoptera larva and that glutamine containing FACs in the gut lumen may function as a form of storage of glutamine, a key compound of nitrogen metabolism. PMID:18997016

  6. Optimum production and characterization of an acid protease from marine yeast Metschnikowia reukaufii W6b

    NASA Astrophysics Data System (ADS)

    Li, Jing; Peng, Ying; Wang, Xianghong; Chi, Zhenming

    2010-12-01

    The marine yeast strain W6b isolated from sediment of the South China Sea was found to produce a cell-bound acid protease. The crude acid protease produced by this marine yeast showed the highest activity at pH 3.5 and 40 °C. The optimal pH and temperature for the crude acid protease were in agreement with those for acid protease produced by the terrestrial yeasts. The optimal medium of the acid protease production was seawater containing 1.0% glucose, 1.5% casein, and 0.5% yeast extract, and the optimal cultivation conditions of the acid protease production were pH 4.0, a temperature of 25 °C and a shaking speed of 140 rmin-1. Under the optimal conditions, 72.5 UmL-1 of acid protease activity could be obtained in cell suspension within 48 h of fermentation at shake flask level. The acid protease production was induced by high-molecular-weight nitrogen sources and repressed by low-molecular-weight nitrogen sources. Skimmed-milk-clotting test showed that the crude acid protease from the cell suspension of the yeast W6b had high skimmed milk coagulability. The acid protease produced by M. reukaufii W6b may have highly potential applications in cheese, food and fermentation industries.

  7. L-histidine inhibits biofilm formation and FLO11-associated phenotypes in Saccharomyces cerevisiae flor yeasts.

    PubMed

    Bou Zeidan, Marc; Zara, Giacomo; Viti, Carlo; Decorosi, Francesca; Mannazzu, Ilaria; Budroni, Marilena; Giovannetti, Luciana; Zara, Severino

    2014-01-01

    Flor yeasts of Saccharomyces cerevisiae have an innate diversity of Flo11p which codes for a highly hydrophobic and anionic cell-wall glycoprotein with a fundamental role in biofilm formation. In this study, 380 nitrogen compounds were administered to three S. cerevisiae flor strains handling Flo11p alleles with different expression levels. S. cerevisiae strain S288c was used as the reference strain as it cannot produce Flo11p. The flor strains generally metabolized amino acids and dipeptides as the sole nitrogen source, although with some exceptions regarding L-histidine and histidine containing dipeptides. L-histidine completely inhibited growth and its effect on viability was inversely related to Flo11p expression. Accordingly, L-histidine did not affect the viability of the Δflo11 and S288c strains. Also, L-histidine dramatically decreased air-liquid biofilm formation and adhesion to polystyrene of the flor yeasts with no effect on the transcription level of the Flo11p gene. Moreover, L-histidine modified the chitin and glycans content on the cell-wall of flor yeasts. These findings reveal a novel biological activity of L-histidine in controlling the multicellular behavior of yeasts [corrected].

  8. L-Histidine Inhibits Biofilm Formation and FLO11-Associated Phenotypes in Saccharomyces cerevisiae Flor Yeasts

    PubMed Central

    Bou Zeidan, Marc; Zara, Giacomo; Viti, Carlo; Decorosi, Francesca; Mannazzu, Ilaria; Budroni, Marilena; Giovannetti, Luciana; Zara, Severino

    2014-01-01

    Flor yeasts of Saccharomyces cerevisiae have an innate diversity of FLO11 which codes for a highly hydrophobic and anionic cell-wall glycoprotein with a fundamental role in biofilm formation. In this study, 380 nitrogen compounds were administered to three S. cerevisiae flor strains handling FLO11 alleles with different expression levels. S. cerevisiae strain S288c was used as the reference strain as it cannot produce FLO11p. The flor strains generally metabolized amino acids and dipeptides as the sole nitrogen source, although with some exceptions regarding L-histidine and histidine containing dipeptides. L-histidine completely inhibited growth and its effect on viability was inversely related to FLO11 expression. Accordingly, L-histidine did not affect the viability of the Δflo11 and S288c strains. Also, L-histidine dramatically decreased air–liquid biofilm formation and adhesion to polystyrene of the flor yeasts with no effect on the transcription level of the FLO11 gene. Moreover, L-histidine modified the chitin and glycans content on the cell-wall of flor yeasts. These findings reveal a novel biological activity of L-histidine in controlling the multicellular behavior of yeasts. PMID:25369456

  9. The production of aromatic alcohols in non-Saccharomyces wine yeast is modulated by nutrient availability.

    PubMed

    González, Beatriz; Vázquez, Jennifer; Morcillo-Parra, M Ángeles; Mas, Albert; Torija, María Jesús; Beltran, Gemma

    2018-09-01

    Aromatic alcohols (tryptophol, phenylethanol, tyrosol) positively contribute to organoleptic characteristics of wines, and are also described as bioactive compounds and quorum sensing molecules. These alcohols are produced by yeast during alcoholic fermentation via the Erhlich pathway, although in non-Saccharomyces this production has been poorly studied. We studied how different wine yeast species modulate the synthesis patterns of aromatic alcohol production depending on glucose, nitrogen and aromatic amino acid availability. Nitrogen limitation strongly promoted the production of aromatic alcohols in all strains, whereas low glucose generally inhibited it. Increased aromatic amino acid concentrations stimulated the production of aromatic alcohols in all of the strains and conditions tested. Thus, there was a clear association between the nutrient conditions and production of aromatic alcohols in most of the wine yeast species analysed. Additionally, the synthesis pattern of these alcohols has been evaluated for the first time in Torulaspora delbrueckii, Metschnikowia pulcherrima and Starmellera bacillaris. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Three novel species of d-xylose-assimilating yeasts, Barnettozyma xylosiphila sp. nov., Barnettozyma xylosica sp. nov. and Wickerhamomyces xylosivorus f.a., sp. nov.

    PubMed

    Kobayashi, Ryuichi; Kanti, Atit; Kawasaki, Hiroko

    2017-10-01

    This study describes three novel xylose-assimilating yeasts, which were isolated from decayed wood collected from Bung Hatta Botanical Garden in West Sumatra and Cibodas Botanic Garden in West Java, or from litter from Eka Karya Bali Botanic Garden in Bali, Indonesia. Phylogenetic analysis was performed based on the sequences of the D1/D2 domains of the large ribosomal subunit (LSU), the small ribosomal subunit (SSU), the internal transcribed spacer (ITS) and elongation factor-1α (EF-1α), and the three strains were found to represent three novel species belonging to genera Barnettozyma or Wickerhamomyces. The morphological, biochemical and physiological characteristics indicated that the strains were distinct from other closely related species. Strains 13Y206 T and 14Y196 T belonging to the Barnettozyma clade are described as the type strains of Barnettozyma xylosiphila sp. nov. (type strain 13Y206 T =NBRC 110202 T =InaCC Y726 T ; MycoBank MB808598) and Barnettozyma xylosica sp. nov. (type strain 14Y196 T =NBRC 111558 T =InaCC Y1030 T ; MycoBank MB819485). Strain 14Y125 T belonging to the Wickerhamomyces clade is described as the type strain of Wickerhamomyces xylosivorus f.a., sp. nov. (type strain 14Y125 T =NBRC 111553 T =InaCC Y1026 T ; MycoBank MB819484).

  11. Estimation of forest canopy nitrogen concentration. Chapter 15

    Treesearch

    Marie-Louise Smith; David Y. Hollinger; Scott Ollinger

    2008-01-01

    The ability to detect patterns of carbon assimilation by vegetation is a key component of the North American Carbon Program. Because photosynthetic potential is strongly related to biochemical constituents such as nitrogen and chlorophyll concentrations in foliage, the ability to incorporate canopy chemistry into landscape- to regional-scale carbon cycling research...

  12. Temporal variation of nitrogen balance within constructed wetlands treating slightly polluted water using a stable nitrogen isotope experiment.

    PubMed

    Zhang, Wanguang; Lei, Qiongye; Li, Zhengkui; Han, Huayang

    2016-02-01

    Slightly polluted water has become one of the main sources of nitrogen contaminants in recent years, for which constructed wetlands (CW) is a typical and efficient treatment. However, the knowledge about contribution of individual nitrogen removal pathways and nitrogen balance in constructed wetlands is still limited. In this study, a stable-isotope-addition experiment was performed in laboratory-scale constructed wetlands treating slightly polluted water to determine quantitative contribution of different pathways and temporal variation of nitrogen balance using Na(15)NO3 as tracer. Microbial conversion and substrate retention were found to be the dominant pathways in nitrogen removal contributing 24.4-79.9 and 8.9-70.7 %, respectively, while plant contributed only 4.6-11.1 % through direct assimilation but promoted the efficiency of other pathways. In addition, microbial conversion became the major way to remove N whereas nitrogen retained in substrate at first was gradually released to be utilized by microbes and plants over time. The findings indicated that N2 emission representing microbial conversion was not only the major but also permanent nitrogen removal process, thus keeping a high efficiency of microbial conversion is important for stable and efficient nitrogen removal in constructed wetlands.

  13. Isolation and Characterization of Hydrocarbon-Degrading Yeast Strains from Petroleum Contaminated Industrial Wastewater

    PubMed Central

    Gargouri, Boutheina; Mhiri, Najla; Karray, Fatma; Aloui, Fathi; Sayadi, Sami

    2015-01-01

    Two yeast strains are enriched and isolated from industrial refinery wastewater. These strains were observed for their ability to utilize several classes of petroleum hydrocarbons substrates, such as n-alkanes and aromatic hydrocarbons as a sole carbon source. Phylogenetic analysis based on the D1/D2 variable domain and the ITS-region sequences indicated that strains HC1 and HC4 were members of the genera Candida and Trichosporon, respectively. The mechanism of hydrocarbon uptaking by yeast, Candida, and Trichosporon has been studied by means of the kinetic analysis of hydrocarbons-degrading yeasts growth and substrate assimilation. Biodegradation capacity and biomass quantity were daily measured during twelve days by gravimetric analysis and gas chromatography coupled with mass spectrometry techniques. Removal of n-alkanes indicated a strong ability of hydrocarbon biodegradation by the isolated yeast strains. These two strains grew on long-chain n-alkane, diesel oil, and crude oil but failed to grow on short-chain n-alkane and aromatic hydrocarbons. Growth measurement attributes of the isolates, using n-hexadecane, diesel oil, and crude oil as substrates, showed that strain HC1 had better degradation for hydrocarbon substrates than strain HC4. In conclusion, these yeast strains can be useful for the bioremediation process and decreasing petroleum pollution in wastewater contaminated with petroleum hydrocarbons. PMID:26339653

  14. [Effects of postponed basal nitrogen application with reduced nitrogen rate on grain yield and nitrogen use efficiency of south winter wheat].

    PubMed

    Zhang, Lei; Shao, Yu Hang; Gu, Shi Lu; Hu, Hang; Zhang, Wei Wei; Tian, Zhong Wei; Jiang, Dong; Dai, Ting Bo

    2016-12-01

    Excessive nitrogen (N) fertilizer application has led to a reduction of nitrogen use efficiency and environmental problems. It was of great significance for high-yield and high-efficiency cultivation to reduce N fertilizer application with modified application strategies. A two-year field experiment was conducted to study effects of different N application rates at basal and seedling application stages on grain yield and nitrogen use efficiency. Taking the conventional nitrogen application practice (240 kg N·hm -2 with application at basal, jointing, and booting stages at ratios of 5:3:2, respectively) as control, a field trial was conducted at different N application rates (240, 180 and 150 kg N·hm -2 , N 240 , N 180 and N 150 , respectively) and different application times [basal (L 0 ), fourth (L 4 ) and sixth leaf stage (L 6 )] to investigate the effects on grain yield and nitrogen use efficiency. The results indicated that grain yield decreased along with reducing the N application rate, but it had no significant difference between N 240 and N 180 while decreased significantly under N 150 . Nitrogen agronomy and recovery efficiency were all highest under N 180 . Among different N application stages, grain yield and nitrogen use efficiency were highest under L 4 . N 180 L 4 had no signifi-cant difference with control in grain yield, but its nitrogen use efficiency was significantly higher. The leaf area index, flag leaf photosynthesis rate, leaf nitrogen content, activity of nitrogen reductase and glutamine synthase in flag leaf, dry matter and N accumulation after jointing of N 180 L 4 had no significant difference with control. In an overall view, postponing basal N fertilizer application at reduced nitrogen rate could maintain high yield and improve nitrogen use efficiency through improving photosynthetic production capacity and promoting nitrogen uptake and assimilation.

  15. Extraction of brewer's yeasts using different methods of cell disruption for practical biodiesel production.

    PubMed

    Řezanka, Tomáš; Matoulková, Dagmar; Kolouchová, Irena; Masák, Jan; Viden, Ivan; Sigler, Karel

    2015-05-01

    The methods of preparation of fatty acids from brewer's yeast and its use in production of biofuels and in different branches of industry are described. Isolation of fatty acids from cell lipids includes cell disintegration (e.g., with liquid nitrogen, KOH, NaOH, petroleum ether, nitrogenous basic compounds, etc.) and subsequent processing of extracted lipids, including analysis of fatty acid and computing of biodiesel properties such as viscosity, density, cloud point, and cetane number. Methyl esters obtained from brewer's waste yeast are well suited for the production of biodiesel. All 49 samples (7 breweries and 7 methods) meet the requirements for biodiesel quality in both the composition of fatty acids and the properties of the biofuel required by the US and EU standards.

  16. A Global Carbon Assimilation System using a modified EnKF assimilation method

    NASA Astrophysics Data System (ADS)

    Zhang, S.; Zheng, X.; Chen, Z.; Dan, B.; Chen, J. M.; Yi, X.; Wang, L.; Wu, G.

    2014-10-01

    A Global Carbon Assimilation System based on Ensemble Kalman filter (GCAS-EK) is developed for assimilating atmospheric CO2 abundance data into an ecosystem model to simultaneously estimate the surface carbon fluxes and atmospheric CO2 distribution. This assimilation approach is based on the ensemble Kalman filter (EnKF), but with several new developments, including using analysis states to iteratively estimate ensemble forecast errors, and a maximum likelihood estimation of the inflation factors of the forecast and observation errors. The proposed assimilation approach is tested in observing system simulation experiments and then used to estimate the terrestrial ecosystem carbon fluxes and atmospheric CO2 distributions from 2002 to 2008. The results showed that this assimilation approach can effectively reduce the biases and uncertainties of the carbon fluxes simulated by the ecosystem model.

  17. Elementary budget of stag beetle larvae associated with selective utilization of nitrogen in decaying wood.

    PubMed

    Tanahashi, Masahiko; Ikeda, Hiroshi; Kubota, Kôhei

    2018-05-03

    Wood degradation by insects plays important roles for the forest matter cycling. Since wood is deficient in nitrogen compared to the insect body, wood-feeding insects need to assimilate the nitrogen selectively and discard an excess carbon. Such a stoichiometric imbalance between food and body will cause high metabolic cost; therefore, wood-feeding insects may somehow alleviate the stoichiometric imbalance. Here, we investigated the carbon and nitrogen budgets of the larvae of stag beetle, Dorcus rectus, which feed on decaying wood. Assimilation efficiency of ingested wood was 22%, and those values based on the carbon and nitrogen were 27 and 45%, respectively, suggesting the selective digestion of nitrogen in wood. Element-based gross growth efficiency was much higher for nitrogen (45%) than for carbon (3%). As a result, the larvae released 24% of the ingested carbon as volatile, whereas almost no gaseous exchange was observed for nitrogen. Moreover, solubility-based elementary analysis revealed that the larvae mainly utilized alkaline-soluble-water-insoluble fraction of wood, which is rich in nitrogen. Actually, the midgut of the larvae was highly alkaline (pH 10.3). Stag beetle larvae are known to exhibit coprophagy, and here we also confirmed that alkaline-soluble-water-insoluble nitrogen increased again from fresh feces to old feces in the field. Stable isotope analysis suggested the utilization of aerial nitrogen by larvae; however, its actual contribution is still disputable. Those results suggest that D. rectus larvae selectively utilize alkaline-soluble nitrogenous substrates by using their highly alkaline midgut, and perhaps associate with microbes that enhance the nitrogen recycling in feces.

  18. Elementary budget of stag beetle larvae associated with selective utilization of nitrogen in decaying wood

    NASA Astrophysics Data System (ADS)

    Tanahashi, Masahiko; Ikeda, Hiroshi; Kubota, Kôhei

    2018-06-01

    Wood degradation by insects plays important roles for the forest matter cycling. Since wood is deficient in nitrogen compared to the insect body, wood-feeding insects need to assimilate the nitrogen selectively and discard an excess carbon. Such a stoichiometric imbalance between food and body will cause high metabolic cost; therefore, wood-feeding insects may somehow alleviate the stoichiometric imbalance. Here, we investigated the carbon and nitrogen budgets of the larvae of stag beetle, Dorcus rectus, which feed on decaying wood. Assimilation efficiency of ingested wood was 22%, and those values based on the carbon and nitrogen were 27 and 45%, respectively, suggesting the selective digestion of nitrogen in wood. Element-based gross growth efficiency was much higher for nitrogen (45%) than for carbon (3%). As a result, the larvae released 24% of the ingested carbon as volatile, whereas almost no gaseous exchange was observed for nitrogen. Moreover, solubility-based elementary analysis revealed that the larvae mainly utilized alkaline-soluble-water-insoluble fraction of wood, which is rich in nitrogen. Actually, the midgut of the larvae was highly alkaline (pH 10.3). Stag beetle larvae are known to exhibit coprophagy, and here we also confirmed that alkaline-soluble-water-insoluble nitrogen increased again from fresh feces to old feces in the field. Stable isotope analysis suggested the utilization of aerial nitrogen by larvae; however, its actual contribution is still disputable. Those results suggest that D. rectus larvae selectively utilize alkaline-soluble nitrogenous substrates by using their highly alkaline midgut, and perhaps associate with microbes that enhance the nitrogen recycling in feces.

  19. Respiration-dependent utilization of sugars in yeasts: a determinant role for sugar transporters.

    PubMed

    Goffrini, Paola; Ferrero, Iliana; Donnini, Claudia

    2002-01-01

    In many yeast species, including Kluyveromyces lactis, growth on certain sugars (such as galactose, raffinose, and maltose) occurs only under respiratory conditions. If respiration is blocked by inhibitors, mutation, or anaerobiosis, growth does not take place. This apparent dependence on respiration for the utilization of certain sugars has often been suspected to be associated with the mechanism of the sugar uptake step. We hypothesized that in many yeast species, the permease activities for these sugars are not sufficient to ensure the high substrate flow that is necessary for fermentative growth. By introducing additional sugar permease genes, we have obtained K. lactis strains that were capable of growing on galactose and raffinose in the absence of respiration. High dosages of both the permease and maltase genes were indeed necessary for K. lactis cells to grow on maltose in the absence of respiration. These results strongly suggest that the sugar uptake step is the major bottleneck in the fermentative assimilation of certain sugars in K. lactis and probably in many other yeasts.

  20. Respiration-Dependent Utilization of Sugars in Yeasts: a Determinant Role for Sugar Transporters

    PubMed Central

    Goffrini, Paola; Ferrero, Iliana; Donnini, Claudia

    2002-01-01

    In many yeast species, including Kluyveromyces lactis, growth on certain sugars (such as galactose, raffinose, and maltose) occurs only under respiratory conditions. If respiration is blocked by inhibitors, mutation, or anaerobiosis, growth does not take place. This apparent dependence on respiration for the utilization of certain sugars has often been suspected to be associated with the mechanism of the sugar uptake step. We hypothesized that in many yeast species, the permease activities for these sugars are not sufficient to ensure the high substrate flow that is necessary for fermentative growth. By introducing additional sugar permease genes, we have obtained K. lactis strains that were capable of growing on galactose and raffinose in the absence of respiration. High dosages of both the permease and maltase genes were indeed necessary for K. lactis cells to grow on maltose in the absence of respiration. These results strongly suggest that the sugar uptake step is the major bottleneck in the fermentative assimilation of certain sugars in K. lactis and probably in many other yeasts. PMID:11751819

  1. CHARACTERIZATION OF THE ALKANE-INDUCIBLE CYTOCHROME P450 (P450ALK) GENE FROM THE YEAST CANDIDA TROPICALIS: IDENTIFICATION OF A NEW P450 FAMILY

    EPA Science Inventory

    The P450alk gene, which is inducible by the assimilation of alkane in Candida tropicalis, was sequenced and characterized. Structural features described in promoter and terminator regions of Saccharomyces yeast genes are present in the P450alk gene and some particular structures ...

  2. Assimilation for skin SST in the NASA GEOS atmospheric data assimilation system.

    PubMed

    Akella, Santha; Todling, Ricardo; Suarez, Max

    2017-01-01

    The present article describes the sea surface temperature (SST) developments implemented in the Goddard Earth Observing System, Version 5 (GEOS-5) Atmospheric Data Assimilation System (ADAS). These are enhancements that contribute to the development of an atmosphere-ocean coupled data assimilation system using GEOS. In the current quasi-operational GEOS-ADAS, the SST is a boundary condition prescribed based on the OSTIA product, therefore SST and skin SST (Ts) are identical. This work modifies the GEOS-ADAS Ts by modeling and assimilating near sea surface sensitive satellite infrared (IR) observations. The atmosphere-ocean interface layer of the GEOS atmospheric general circulation model (AGCM) is updated to include near surface diurnal warming and cool-skin effects. The GEOS analysis system is also updated to directly assimilate SST-relevant Advanced Very High Resolution Radiometer (AVHRR) radiance observations. Data assimilation experiments designed to evaluate the Ts modification in GEOS-ADAS show improvements in the assimilation of radiance observations that extends beyond the thermal IR bands of AVHRR. In particular, many channels of hyperspectral sensors, such as those of the Atmospheric Infrared Sounder (AIRS), and Infrared Atmospheric Sounding Interferometer (IASI) are also better assimilated. We also obtained improved fit to withheld, in-situ buoy measurement of near-surface SST. Evaluation of forecast skill scores show marginal to neutral benefit from the modified Ts.

  3. Assimilation for skin SST in the NASA GEOS atmospheric data assimilation system

    PubMed Central

    Akella, Santha; Todling, Ricardo; Suarez, Max

    2018-01-01

    The present article describes the sea surface temperature (SST) developments implemented in the Goddard Earth Observing System, Version 5 (GEOS-5) Atmospheric Data Assimilation System (ADAS). These are enhancements that contribute to the development of an atmosphere-ocean coupled data assimilation system using GEOS. In the current quasi-operational GEOS-ADAS, the SST is a boundary condition prescribed based on the OSTIA product, therefore SST and skin SST (Ts) are identical. This work modifies the GEOS-ADAS Ts by modeling and assimilating near sea surface sensitive satellite infrared (IR) observations. The atmosphere-ocean interface layer of the GEOS atmospheric general circulation model (AGCM) is updated to include near surface diurnal warming and cool-skin effects. The GEOS analysis system is also updated to directly assimilate SST-relevant Advanced Very High Resolution Radiometer (AVHRR) radiance observations. Data assimilation experiments designed to evaluate the Ts modification in GEOS-ADAS show improvements in the assimilation of radiance observations that extends beyond the thermal IR bands of AVHRR. In particular, many channels of hyperspectral sensors, such as those of the Atmospheric Infrared Sounder (AIRS), and Infrared Atmospheric Sounding Interferometer (IASI) are also better assimilated. We also obtained improved fit to withheld, in-situ buoy measurement of near-surface SST. Evaluation of forecast skill scores show marginal to neutral benefit from the modified Ts. PMID:29628531

  4. Assimilation for Skin SST in the NASA GEOS Atmospheric Data Assimilation System

    NASA Technical Reports Server (NTRS)

    Akella, Santha; Todling, Ricardo; Suarez, Max

    2017-01-01

    The present article describes the sea surface temperature (SST) developments implemented in the Goddard Earth Observing System, Version 5 (GEOS) Atmospheric Data Assimilation System (ADAS). These are enhancements that contribute to the development of an atmosphere-ocean coupled data assimilation system using GEOS. In the current quasi-operational GEOS-ADAS, the SST is a boundary condition prescribed based on the OSTIA product, therefore SST and skin SST (Ts) are identical. This work modifies the GEOS-ADAS Ts by modelling and assimilating near sea surface sensitive satellite infrared (IR) observations. The atmosphere-ocean interface layer of the GEOS atmospheric general circulation model (AGCM) is updated to include near-surface diurnal warming and cool-skin effects. The GEOS analysis system is also updated to directly assimilate SST-relevant Advanced Very High Resolution Radiometer (AVHRR) radiance observations. Data assimilation experiments designed to evaluate the Ts modification in GEOS-ADAS show improvements in the assimilation of radiance observations that extend beyond the thermal infrared bands of AVHRR. In particular, many channels of hyperspectral sensors, such as those of the Atmospheric Infrared Sounder (AIRS), and Infrared Atmospheric Sounding Interferometer (IASI) are also better assimilated. We also obtained improved fit to withheld insitu buoy measurement of near-surface SST. Evaluation of forecast skill scores show neutral to marginal benefit from the modified Ts.

  5. Pullulan production by Aureobasidium pullulans grown on ethanol stillage as a nitrogen source.

    PubMed

    West, T P; Strohfus, B

    1996-01-01

    Pullulan production by Aureobasidium pullulans strain RP-1 using thin stillage from fuel ethanol production as a nitrogen source was studied in a medium using corn syrup as a carbon source. The use of 1% thin stillage as a nitrogen source instead of ammonium sulphate elevated polysaccharide production by strain RP-1 cells when grown on a concentration of up to 7.5% corn syrup, independent of yeast extract supplementation. Dry weights of cells grown in medium containing ammonium sulphate as the nitrogen source were higher than the stillage-grown cells after 7 days of growth. The viscosity of the polysaccharide on day 7 was higher for cells grown on thin stillage rather than ammonium sulphate as a nitrogen source. The pullulan content of the polysaccharide elaborated by ammonium sulphate-grown cells on day 7 was higher than the pullulan content of polysaccharide produced by stillage-grown cells regardless of whether yeast extract was added to the culture medium.

  6. [Evaluation of mass spectrometry for the identification of clinically interesting yeasts].

    PubMed

    Galán, Fátima; García-Agudo, Lidia; Guerrero, Inmaculada; Marín, Pilar; García-Tapia, Ana; García-Martos, Pedro; Rodríguez-Iglesias, Manuel

    2015-01-01

    Identification of yeasts is based on morphological, biochemical and nutritional characteristics, and using molecular methods. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, a new method for the identification of microorganisms, has demonstrated to be very useful. The aim of this study is to evaluate this new method in the identification of yeasts. A total of 600 strains of yeasts isolated from clinical specimens belonging to 9 genera and 43 species were tested. Identification was made by sequencing of the ITS regions of ribosomal DNA, assimilation of carbon compounds (ID 32C), and mass spectrometry on a Microflex spectrometer (Bruker Daltonics GmbH, Germany). A total of 569 strains (94.8%) were identified to species level by ID 32C, and 580 (96.7%) by MALDI-TOF. Concordance between both methods was observed for 553 strains (92.2%), with 100% in clinically relevant species: C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and almost 100% in C. krusei. MALDI-TOF identified species requiring molecular methods: Candida dubliniensis, C. nivariensis, C. metapsilosis and C. orthopsilosis. Some irregularities were observed in the identification of arthroconidia yeast and basidiomycetes. MALDI-TOF is a rapid, effective and economic method, which enables the identification of most clinically important yeasts and the differentiation of closely related species. It would be desirable to include more species in its database to expand its performance. Copyright © 2014 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  7. Metabolic and transcriptomic response of the wine yeast Saccharomyces cerevisiae strain EC1118 after an oxygen impulse under carbon-sufficient, nitrogen-limited fermentative conditions.

    PubMed

    Orellana, Marcelo; Aceituno, Felipe F; Slater, Alex W; Almonacid, Leonardo I; Melo, Francisco; Agosin, Eduardo

    2014-05-01

    During alcoholic fermentation, Saccharomyces cerevisiae is exposed to continuously changing environmental conditions, such as decreasing sugar and increasing ethanol concentrations. Oxygen, a critical nutrient to avoid stuck and sluggish fermentations, is only discretely available throughout the process after pump-over operation. In this work, we studied the physiological response of the wine yeast S. cerevisiae strain EC1118 to a sudden increase in dissolved oxygen, simulating pump-over operation. With this aim, an impulse of dissolved oxygen was added to carbon-sufficient, nitrogen-limited anaerobic continuous cultures. Results showed that genes related to mitochondrial respiration, ergosterol biosynthesis, and oxidative stress, among other metabolic pathways, were induced after the oxygen impulse. On the other hand, mannoprotein coding genes were repressed. The changes in the expression of these genes are coordinated responses that share common elements at the level of transcriptional regulation. Beneficial and detrimental effects of these physiological processes on wine quality highlight the dual role of oxygen in 'making or breaking wines'. These findings will facilitate the development of oxygen addition strategies to optimize yeast performance in industrial fermentations. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  8. Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia.

    PubMed

    Carro, Lorena; Pujic, Petar; Alloisio, Nicole; Fournier, Pascale; Boubakri, Hasna; Hay, Anne E; Poly, Franck; François, Philippe; Hocher, Valerie; Mergaert, Peter; Balmand, Severine; Rey, Marjolaine; Heddi, Abdelaziz; Normand, Philippe

    2015-08-01

    Actinorhizal plant growth in pioneer ecosystems depends on the symbiosis with the nitrogen-fixing actinobacterium Frankia cells that are housed in special root organs called nodules. Nitrogen fixation occurs in differentiated Frankia cells known as vesicles. Vesicles lack a pathway for assimilating ammonia beyond the glutamine stage and are supposed to transfer reduced nitrogen to the plant host cells. However, a mechanism for the transfer of nitrogen-fixation products to the plant cells remains elusive. Here, new elements for this metabolic exchange are described. We show that Alnus glutinosa nodules express defensin-like peptides, and one of these, Ag5, was found to target Frankia vesicles. In vitro and in vivo analyses showed that Ag5 induces drastic physiological changes in Frankia, including an increased permeability of vesicle membranes. A significant release of nitrogen-containing metabolites, mainly glutamine and glutamate, was found in N2-fixing cultures treated with Ag5. This work demonstrates that the Ag5 peptide is central for Frankia physiology in nodules and uncovers a novel cellular function for this large and widespread defensin peptide family.

  9. Highly Dynamic Cellular-Level Response of Symbiotic Coral to a Sudden Increase in Environmental Nitrogen

    PubMed Central

    Kopp, C.; Pernice, M.; Domart-Coulon, I.; Djediat, C.; Spangenberg, J. E.; Alexander, D. T. L.; Hignette, M.; Meziane, T.; Meibom, A.

    2013-01-01

    ABSTRACT Metabolic interactions with endosymbiotic photosynthetic dinoflagellate Symbiodinium spp. are fundamental to reef-building corals (Scleractinia) thriving in nutrient-poor tropical seas. Yet, detailed understanding at the single-cell level of nutrient assimilation, translocation, and utilization within this fundamental symbiosis is lacking. Using pulse-chase 15N labeling and quantitative ion microprobe isotopic imaging (NanoSIMS; nanoscale secondary-ion mass spectrometry), we visualized these dynamic processes in tissues of the symbiotic coral Pocillopora damicornis at the subcellular level. Assimilation of ammonium, nitrate, and aspartic acid resulted in rapid incorporation of nitrogen into uric acid crystals (after ~45 min), forming temporary N storage sites within the dinoflagellate endosymbionts. Subsequent intracellular remobilization of this metabolite was accompanied by translocation of nitrogenous compounds to the coral host, starting at ~6 h. Within the coral tissue, nitrogen is utilized in specific cellular compartments in all four epithelia, including mucus chambers, Golgi bodies, and vesicles in calicoblastic cells. Our study shows how nitrogen-limited symbiotic corals take advantage of sudden changes in nitrogen availability; this opens new perspectives for functional studies of nutrient storage and remobilization in microbial symbioses in changing reef environments. PMID:23674611

  10. Polysaccharides, oligosaccharides and nitrogenous compounds change during the ageing of Tempranillo and Verdejo sparkling wines.

    PubMed

    Martínez-Lapuente, Leticia; Apolinar-Valiente, Rafael; Guadalupe, Zenaida; Ayestarán, Belén; Pérez-Magariño, Silvia; Williams, Pascale; Doco, Thierry

    2018-01-01

    Verdejo and Tempranillo are traditional varieties for producing still wines; however, they could provide an alternative for the manufacturing of sparkling wines. Sparkling wines were elaborated by the traditional method, followed by ageing on lees for 9 months. A study on the changes that take place in polysaccharides, oligosaccharides and nitrogenous compounds during the ageing on lees of Tempranillo and Verdejo sparkling wines has been undertaken. Mannoproteins and the glucose residue of oligosaccharides were the major carbohydrates detected in all vinification stages. Yeast polysaccharides and glucan-like structures of the oligosaccharides increased after 3 months of ageing. The evolution of yeast polysaccharides and the composition of PRAG-like structure were different among grape varieties. A decrease in amino acids and biogenic amines was observed during the ageing. The contents of polysaccharides, oligosaccharides and nitrogenous compound were significantly higher in Tempranillo than in Verdejo sparkling wines at the end of the ageing period. Polysaccharides and oligosaccharides from yeast were more significant autolysis markers of sparkling wines than the nitrogenous compounds. Our data suggest a potential cultivar effect on the evolution of yeast polysaccharides and on the composition of PRAG, which may influence the physico-chemical and sensory properties of sparkling wines. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  11. Issues in identifying germ tube positive yeasts by conventional methods.

    PubMed

    Yazdanpanah, Atta; Khaithir, Tzar Mohd Nizam

    2014-01-01

    Candida speciation is vital for epidemiology and management of candidiasis. Nonmolecular conventional methods often fail to identify closely related germ tube positive yeasts from clinical specimens. The present study was conducted to identify these yeasts and to highlight issues in conventional versus molecular methods of identification. A total of 98 germ tube positive yeasts from high vaginal swabs were studied over a 12-month period. Isolates were examined with various methods including growth at 42 °C and 45 °C on Sabouraud dextrose agar (SDA), color development on CHROMagar Candida medium, chlamydospore production on corn meal agar at 25 °C, carbohydrate assimilation using ID 32C system, and polymerase chain reaction using a single pair of primers targeting the hyphal wall protein 1 (Hwp1) gene. Of all the isolates studied, 97 were molecularly confirmed as C. albicans and one isolate was identified as C. dubliniensis. No C. africana was detected in this study. The molecular method used in our study was an accurate and useful tool for discriminating C. albicans, C. dubliniensis, and C. africana. The conventional methods, however, were less accurate and riddled with many issues that will be discussed in further details. © 2013 Wiley Periodicals, Inc.

  12. Magnesium deficiency results in damage of nitrogen and carbon cross-talk of maize and improvement by cerium addition.

    PubMed

    Zhao, Haiquan; Zhou, Qiuping; Zhou, Min; Li, Chunxiao; Gong, Xiaolan; Liu, Chao; Qu, Chunxiang; Si, Wenhui; Hong, Fashui

    2012-07-01

    Magnesium (Mg) deficiency has been reported to affect plant photosynthesis and growth, and cerium (Ce) was considered to be able to improve plant growth. However, the mechanisms of Mg deficiency and Ce on plant growth remain poorly understood. The main aim of this work is to identify whether or not Mg deprivation affects the interdependent nitrogen and carbon assimilations in the maize leaves and whether or not Ce modulates the assimilations in the maize leaves under Mg deficiency. Maize plants were cultivated in Hoagland’s solution. They were subjected to Mg deficiency and to cerium chloride administration in the Mg-present Hoagland’s media and Mg-deficient Hoagland’s media.After 2 weeks,we measured chlorophyll (Chl) a fluorescence and the activities of nitrate reductase (NR), sucrose-phosphate synthase(SPS), and phosphoenolpyruvate carboxylase (PEPCase)in metabolic checkpoints coordinating primary nitrogen and carbon assimilations in the maize leaves. The results showed that Mg deficiency significantly inhibited plant growth and decreased the activities of NR, SPS, and PEPCase and the synthesis of Chl and protein. Mg deprivation in maize also significantly decreased the oxygen evolution, electron transport,and efficiency of photochemical energy conversion by photosystem II (PSII). However, Ce addition may promote nitrogen and carbon assimilations, increase PSII activities,and improve maize growth under Mg deficiency. Moreover,our findings would help promote usage of Mg or Ce fertilizers in maize production.

  13. Diagnostics of sources of tropospheric ozone using data assimilation during the KORUS-AQ campaign

    NASA Astrophysics Data System (ADS)

    Gaubert, B.; Emmons, L. K.; Miyazaki, K.; Buchholz, R. R.; Tang, W.; Arellano, A. F., Jr.; Tilmes, S.; Barré, J.; Worden, H. M.; Raeder, K.; Anderson, J. L.; Edwards, D. P.

    2017-12-01

    Atmospheric oxidative capacity plays a crucial role in the fate of greenhouse gases and air pollutants as well as in the formation of secondary pollutants such as tropospheric ozone. The attribution of sources of tropospheric ozone is a difficult task because of biases in input parameters and forcings such as emissions and meteorology in addition to errors in chemical schemes. We assimilate satellite remote sensing observations of ozone precursors such as carbon monoxide (CO) and nitrogen dioxide (NO2) in the global coupled chemistry-transport model: Community Atmosphere Model with Chemistry (CAM-Chem). The assimilation is completed using an Ensemble Adjustment Kalman Filter (EAKF) in the Data Assimilation Research Testbed (DART) framework which allows estimates of unobserved parameters and potential constraints on secondary pollutants and emissions. The ensemble will be constructed using perturbations in chemical kinetics, different emission fields and by assimilating meteorological observations to fully assess uncertainties in the chemical fields of targeted species. We present a set of tools such as emission tags (CO and propane), combined with diagnostic analysis of chemical regimes and perturbation of emissions ratios to estimate a regional budget of primary and secondary pollutants in East Asia and their sensitivity to data assimilation. This study benefits from the large set of aircraft and ozonesonde in-situ observations from the Korea-United States Air Quality (KORUS-AQ) campaign that occurred in South Korea in May-June 2016.

  14. Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

    PubMed Central

    2013-01-01

    Background Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves the interplay of signalling pathways and transcriptional regulation of nitrogen assimilation and scavenging genes. In the soil dwelling saprophyte Mycobacterium smegmatis the OmpR-type response regulator GlnR is thought to mediate the transcriptomic response to nitrogen limitation. However, to date only ten genes have been shown to be in the GlnR regulon, a vastly reduced number compared to other organisms. Results We investigated the role of GlnR in the nitrogen limitation response and determined the entire GlnR regulon, by combining expression profiling of M. smegmatis wild type and glnR deletion mutant, with GlnR-specific chromatin immunoprecipitation and high throughput sequencing. We identify 53 GlnR binding sites during nitrogen limitation that control the expression of over 100 genes, demonstrating that GlnR is the regulator controlling the assimilation and utilisation of nitrogen. We also determine a consensus GlnR binding motif and identify key residues within the motif that are required for specific GlnR binding. Conclusions We have demonstrated that GlnR is the global nitrogen response regulator in M. smegmatis, directly regulating the expression of more than 100 genes. GlnR controls key nitrogen stress survival processes including primary nitrogen metabolism pathways, the ability to utilise nitrate and urea as alternative nitrogen sources, and the potential to use cellular components to provide a source of ammonium. These studies further our understanding of how mycobacteria survive nutrient limiting conditions. PMID:23642041

  15. Comparison of different assimilation schemes in an operational assimilation system with Ensemble Kalman Filter

    NASA Astrophysics Data System (ADS)

    Yan, Yajing; Barth, Alexander; Beckers, Jean-Marie; Candille, Guillem; Brankart, Jean-Michel; Brasseur, Pierre

    2016-04-01

    In this paper, four assimilation schemes, including an intermittent assimilation scheme (INT) and three incremental assimilation schemes (IAU 0, IAU 50 and IAU 100), are compared in the same assimilation experiments with a realistic eddy permitting primitive equation model of the North Atlantic Ocean using the Ensemble Kalman Filter. The three IAU schemes differ from each other in the position of the increment update window that has the same size as the assimilation window. 0, 50 and 100 correspond to the degree of superposition of the increment update window on the current assimilation window. Sea surface height, sea surface temperature, and temperature profiles at depth collected between January and December 2005 are assimilated. Sixty ensemble members are generated by adding realistic noise to the forcing parameters related to the temperature. The ensemble is diagnosed and validated by comparison between the ensemble spread and the model/observation difference, as well as by rank histogram before the assimilation experiments The relevance of each assimilation scheme is evaluated through analyses on thermohaline variables and the current velocities. The results of the assimilation are assessed according to both deterministic and probabilistic metrics with independent/semi-independent observations. For deterministic validation, the ensemble means, together with the ensemble spreads are compared to the observations, in order to diagnose the ensemble distribution properties in a deterministic way. For probabilistic validation, the continuous ranked probability score (CRPS) is used to evaluate the ensemble forecast system according to reliability and resolution. The reliability is further decomposed into bias and dispersion by the reduced centered random variable (RCRV) score in order to investigate the reliability properties of the ensemble forecast system.

  16. Identification of oleaginous yeast strains able to accumulate high intracellular lipids when cultivated in alkaline pretreated corn stover

    PubMed Central

    Sitepu, Irnayuli R.; Jin, Mingjie; Fernandez, J. Enrique; da Costa Sousa, Leonardo; Balan, Venkatesh; Boundy-Mills, Kyria L.

    2015-01-01

    Microbial oil is a potential alternative to food/plant-derived biodiesel fuel. Our previous screening studies identified a wide range of oleaginous yeast species, using a defined laboratory medium known to stimulate lipid accumulation. In this study, the ability of these yeasts to grow and accumulate lipids was further investigated in synthetic hydrolysate (SynH) and authentic ammonia fiber expansion (AFEX™)-pretreated corn stover hydrolysate (ACSH). Most yeast strains tested were able to accumulate lipids in SynH, but only a few were able to grow and accumulate lipids in ACSH medium. Cryptococcus humicola UCDFST 10-1004 was able to accumulate as high as 15.5 g/L lipids, out of a total of 36 g/L cellular biomass when grown in ACSH, with a cellular lipid content of 40% of cell dry weight. This lipid production is among the highest reported values for oleaginous yeasts grown in authentic hydrolysate. Pre-culturing in SynH media with xylose as sole carbon source enabled yeasts to assimilate both glucose and xylose more efficiently in the subsequent hydrolysate medium. This study demonstrates that ACSH is a suitable medium for certain oleaginous yeasts to convert lignocellullosic sugars to triacylglycerols for production of biodiesel and other valuable oleochemicals. PMID:25052467

  17. Efficient Methods to Assimilate Satellite Retrievals Based on Information Content. Part 2; Suboptimal Retrieval Assimilation

    NASA Technical Reports Server (NTRS)

    Joiner, J.; Dee, D. P.

    1998-01-01

    One of the outstanding problems in data assimilation has been and continues to be how best to utilize satellite data while balancing the tradeoff between accuracy and computational cost. A number of weather prediction centers have recently achieved remarkable success in improving their forecast skill by changing the method by which satellite data are assimilated into the forecast model from the traditional approach of assimilating retrievals to the direct assimilation of radiances in a variational framework. The operational implementation of such a substantial change in methodology involves a great number of technical details, e.g., pertaining to quality control procedures, systematic error correction techniques, and tuning of the statistical parameters in the analysis algorithm. Although there are clear theoretical advantages to the direct radiance assimilation approach, it is not obvious at all to what extent the improvements that have been obtained so far can be attributed to the change in methodology, or to various technical aspects of the implementation. The issue is of interest because retrieval assimilation retains many practical and logistical advantages which may become even more significant in the near future when increasingly high-volume data sources become available. The central question we address here is: how much improvement can we expect from assimilating radiances rather than retrievals, all other things being equal? We compare the two approaches in a simplified one-dimensional theoretical framework, in which problems related to quality control and systematic error correction are conveniently absent. By assuming a perfect radiative transfer model and perfect knowledge of radiance and background error covariances, we are able to formulate a nonlinear local error analysis for each assimilation method. Direct radiance assimilation is optimal in this idealized context, while the traditional method of assimilating retrievals is suboptimal because it

  18. P. brasiliensis Virulence Is Affected by SconC, the Negative Regulator of Inorganic Sulfur Assimilation

    PubMed Central

    Menino, João Filipe; Saraiva, Margarida; Gomes-Rezende, Jéssica; Sturme, Mark; Pedrosa, Jorge; Castro, António Gil; Ludovico, Paula; Goldman, Gustavo H.; Rodrigues, Fernando

    2013-01-01

    Conidia/mycelium-to-yeast transition of Paracoccidioides brasiliensis is a critical step for the establishment of paracoccidioidomycosis, a systemic mycosis endemic in Latin America. Thus, knowledge of the factors that mediate this transition is of major importance for the design of intervention strategies. So far, the only known pre-requisites for the accomplishment of the morphological transition are the temperature shift to 37°C and the availability of organic sulfur compounds. In this study, we investigated the auxotrophic nature to organic sulfur of the yeast phase of Paracoccidioides , with special attention to P. brasiliensis species. For this, we addressed the role of SconCp, the negative regulator of the inorganic sulfur assimilation pathway, in the dimorphism and virulence of this pathogen. We show that down-regulation of SCONC allows initial steps of mycelium-to-yeast transition in the absence of organic sulfur compounds, contrarily to the wild-type fungus that cannot undergo mycelium-to-yeast transition under such conditions. However, SCONC down-regulated transformants were unable to sustain yeast growth using inorganic sulfur compounds only. Moreover, pulses with inorganic sulfur in SCONC down-regulated transformants triggered an increase of the inorganic sulfur metabolism, which culminated in a drastic reduction of the ATP and NADPH cellular levels and in higher oxidative stress. Importantly, the down-regulation of SCONC resulted in a decreased virulence of P. brasiliensis, as validated in an in vivo model of infection. Overall, our findings shed light on the inability of P. brasiliensis yeast to rely on inorganic sulfur compounds, correlating its metabolism with cellular energy and redox imbalances. Furthermore, the data herein presented reveal SconCp as a novel virulence determinant of P. brasiliensis. PMID:24066151

  19. The pitcher plant Sarracenia purpurea can directly acquire organic nitrogen and short-circuit the inorganic nitrogen cycle.

    PubMed

    Karagatzides, Jim D; Butler, Jessica L; Ellison, Aaron M

    2009-07-07

    Despite the large stocks of organic nitrogen in soil, nitrogen availability limits plant growth in many terrestrial ecosystems because most plants take up only inorganic nitrogen, not organic nitrogen. Although some vascular plants can assimilate organic nitrogen directly, only recently has organic nitrogen been found to contribute significantly to the nutrient budget of any plant. Carnivorous plants grow in extremely nutrient-poor environments and carnivory has evolved in these plants as an alternative pathway for obtaining nutrients. We tested if the carnivorous pitcher plant Sarracenia purpurea could directly take up intact amino acids in the field and compared uptake of organic and inorganic forms of nitrogen across a gradient of nitrogen deposition. We hypothesized that the contribution of organic nitrogen to the nitrogen budget of the pitcher plant would decline with increasing nitrogen deposition. At sites in Canada (low nitrogen deposition) and the United States (high nitrogen deposition), individual pitchers were fed two amino acids, glycine and phenylalanine, and inorganic nitrogen (as ammonium nitrate), individually and in mixture. Plants took up intact amino acids. Acquisition of each form of nitrogen provided in isolation exceeded uptake of the same form in mixture. At the high deposition site, uptake of organic nitrogen was higher than uptake of inorganic nitrogen. At the low deposition site, uptake of all three forms of nitrogen was similar. Completeness of the associated detritus-based food web that inhabits pitcher-plant leaves and breaks down captured prey had no effect on nitrogen uptake. By taking up intact amino acids, Sarracenia purpurea can short-circuit the inorganic nitrogen cycle, thus minimizing potential bottlenecks in nitrogen availability that result from the plant's reliance for nitrogen mineralization on a seasonally reconstructed food web operating on infrequent and irregular prey capture.

  20. The Pitcher Plant Sarracenia purpurea Can Directly Acquire Organic Nitrogen and Short-Circuit the Inorganic Nitrogen Cycle

    PubMed Central

    Karagatzides, Jim D.; Butler, Jessica L.; Ellison, Aaron M.

    2009-01-01

    Background Despite the large stocks of organic nitrogen in soil, nitrogen availability limits plant growth in many terrestrial ecosystems because most plants take up only inorganic nitrogen, not organic nitrogen. Although some vascular plants can assimilate organic nitrogen directly, only recently has organic nitrogen been found to contribute significantly to the nutrient budget of any plant. Carnivorous plants grow in extremely nutrient-poor environments and carnivory has evolved in these plants as an alternative pathway for obtaining nutrients. We tested if the carnivorous pitcher plant Sarracenia purpurea could directly take up intact amino acids in the field and compared uptake of organic and inorganic forms of nitrogen across a gradient of nitrogen deposition. We hypothesized that the contribution of organic nitrogen to the nitrogen budget of the pitcher plant would decline with increasing nitrogen deposition. Methodology and Principal Findings At sites in Canada (low nitrogen deposition) and the United States (high nitrogen deposition), individual pitchers were fed two amino acids, glycine and phenylalanine, and inorganic nitrogen (as ammonium nitrate), individually and in mixture. Plants took up intact amino acids. Acquisition of each form of nitrogen provided in isolation exceeded uptake of the same form in mixture. At the high deposition site, uptake of organic nitrogen was higher than uptake of inorganic nitrogen. At the low deposition site, uptake of all three forms of nitrogen was similar. Completeness of the associated detritus-based food web that inhabits pitcher-plant leaves and breaks down captured prey had no effect on nitrogen uptake. Conclusions and Significance By taking up intact amino acids, Sarracenia purpurea can short-circuit the inorganic nitrogen cycle, thus minimizing potential bottlenecks in nitrogen availability that result from the plant's reliance for nitrogen mineralization on a seasonally reconstructed food web operating on

  1. Inhibition of nitrogen-fixing activity of the cyanobiont affects the localization of glutamine synthetase in hair cells of Azolla.

    PubMed

    Uheda, Eiji; Maejima, Kazuhiro

    2009-10-15

    In the Azolla-Anabaena association, the host plant Azolla efficiently incorporates and assimilates ammonium ions that are released from the nitrogen-fixing cyanobiont, probably via glutamine synthetase (GS; EC 6.3.1.2) in hair cells, which are specialized cells protruding into the leaf cavity. In order to clarify the regulatory mechanism underlying ammonium assimilation in the Azolla-Anabaena association, Azolla plants were grown under an argon environment (Ar), in which the nitrogen-fixing activity of the cyanobiont was inhibited specifically and completely. The localization of GS in hair cells was determined by immunoelectron microscopy and quantitative analysis of immunogold labeling. Azolla plants grew healthily under Ar when nitrogen sources, such as NO(3)(-) and NH(4)(+), were provided in the growth medium. Both the number of cyanobacterial cells per leaf and the heterocyst frequency of the plants under Ar were similar to those of plants in a nitrogen environment (N(2)). In hair cells of plants grown under Ar, regardless of the type of nitrogen source provided, only weak labeling of GS was observed in the cytoplasm and in chloroplasts. In contrast, in hair cells of plants grown under N(2), abundant labeling of GS was observed in both sites. These findings indicate that specific inhibition of the nitrogen-fixing activity of the cyanobiont affects the localization of GS isoenzymes. Ammonium fixed and released by the cyanobiont could stimulate GS synthesis in hair cells. Simultaneously, the abundant GS, probably GS1, in these cells, could assimilate ammonium rapidly.

  2. [Effect of excess ethanol on the growth of yeasts of the genus Candida during continuous cultivation].

    PubMed

    Shkidchenko, A N; Shul'ga, A V; Gurina, L V

    1988-01-01

    The effect of flow rates and a specific ethanol load on the growth of Candida utilis and Candida krusei was studied in the process of one-step and three-step cultivation. The productive capacity of fermenters and the economic coefficient of yeast biomass production were shown to depend on the ability of microbial populations to assimilate a certain quantity of a carbon substrate per unit time. When a specific ethanol load exceeds the optimal one, the respiratory activity of a population and the economic coefficient of growth fall down whereas the accumulation of metabolites in the cultural broth increases. The steady state of biomass can be maintained in the process of continuous cultivation by inhibiting the yeast growth with an excess of ethanol.

  3. Identification of the fitness determinants of budding yeast on a natural substrate

    PubMed Central

    Filteau, Marie; Charron, Guillaume; Landry, Christian R

    2017-01-01

    The budding yeasts are prime models in genomics and cell biology, but the ecological factors that determine their success in non-human-associated habitats is poorly understood. In North America Saccharomyces yeasts are present on the bark of deciduous trees, where they feed on bark and sap exudates. In the North East, Saccharomyces paradoxus is found on maples, which makes maple sap a natural substrate for this species. We measured growth rates of S. paradoxus natural isolates on maple sap and found variation along a geographical gradient not explained by the inherent variation observed under optimal laboratory conditions. We used a functional genomic screen to reveal the ecologically relevant genes and conditions required for optimal growth in this substrate. We found that the allantoin degradation pathway is required for optimal growth in maple sap, in particular genes necessary for allantoate utilization, which we demonstrate is the major nitrogen source available to yeast in this environment. Growth with allantoin or allantoate as the sole nitrogen source recapitulated the variation in growth rates in maple sap among strains. We also show that two lineages of S. paradoxus display different life-history traits on allantoin and allantoate media, highlighting the ecological relevance of this pathway. PMID:27935595

  4. Identification of the fitness determinants of budding yeast on a natural substrate.

    PubMed

    Filteau, Marie; Charron, Guillaume; Landry, Christian R

    2017-04-01

    The budding yeasts are prime models in genomics and cell biology, but the ecological factors that determine their success in non-human-associated habitats is poorly understood. In North America Saccharomyces yeasts are present on the bark of deciduous trees, where they feed on bark and sap exudates. In the North East, Saccharomyces paradoxus is found on maples, which makes maple sap a natural substrate for this species. We measured growth rates of S. paradoxus natural isolates on maple sap and found variation along a geographical gradient not explained by the inherent variation observed under optimal laboratory conditions. We used a functional genomic screen to reveal the ecologically relevant genes and conditions required for optimal growth in this substrate. We found that the allantoin degradation pathway is required for optimal growth in maple sap, in particular genes necessary for allantoate utilization, which we demonstrate is the major nitrogen source available to yeast in this environment. Growth with allantoin or allantoate as the sole nitrogen source recapitulated the variation in growth rates in maple sap among strains. We also show that two lineages of S. paradoxus display different life-history traits on allantoin and allantoate media, highlighting the ecological relevance of this pathway.

  5. Comparison between assimilated and non-assimilated experiments of the MACCii global reanalysis near surface ozone

    NASA Astrophysics Data System (ADS)

    Tsikerdekis, Athanasios; Katragou, Eleni; Zanis, Prodromos; Melas, Dimitrios; Eskes, Henk; Flemming, Johannes; Huijnen, Vincent; Inness, Antje; Kapsomenakis, Ioannis; Schultz, Martin; Stein, Olaf; Zerefos, Christos

    2014-05-01

    In this work we evaluate near surface ozone concentrations of the MACCii global reanalysis using measurements from the EMEP and AIRBASE database. The eight-year long reanalysis of atmospheric composition data covering the period 2003-2010 was constructed as part of the FP7-funded Monitoring Atmospheric Composition and Climate project by assimilating satellite data into a global model and data assimilation system (Inness et al., 2013). The study mainly focuses in the differences between the assimilated and the non-assimilated experiments and aims to identify and quantify any improvements achieved by adding data assimilation to the system. Results are analyzed in eight European sub-regions and region-specific Taylor plots illustrate the evaluation and the overall predictive skill of each experiment. The diurnal and annual cycles of near surface ozone are evaluated for both experiments. Furthermore ozone exposure indices for crop growth (AOT40), human health (SOMO35) and the number of days that 8-hour ozone averages exceeded 60ppb and 90ppb have been calculated for each station based on both observed and simulated data. Results indicate mostly improvement of the assimilated experiment with respect to the high near surface ozone concentrations, the diurnal cycle and range and the bias in comparison to the non-assimilated experiment. The limitations of the comparison between assimilated and non-assimilated experiments for near surface ozone are also discussed.

  6. [Effects of carbon and nitrogen sources on 5-keto-gluconic acid production].

    PubMed

    Tan, Zhilei; Wang, Hongcui; Wei, Yuqiao; Li, Yanyan; Zhong, Cheng; Jia, Shiru

    2014-01-01

    Gluconobacter oxydans is known to oxidize glucose to gluconic acid (GA), and subsequently, to 2-keto-gluconic acid (2KGA) and 5-keto-gluconic acid (5KGA), while 5KGA can be converted to L-(+)-tartaric acid. In order to increase the production of 5KGA, Gluconobacter oxydans HGI-1 that converts GA to 5KGA exclusively was chosen in this study, and effects of carbon sources (lactose, maltose, sucrose, amylum and glucose) and nitrogen sources (yeast extract, fish meal, corn steep liquor, soybean meal and cotton-seed meal) on 5KGA production were investigated. Results of experiment in 500 mL shake-flask show that the highest yield of 5KGA (98.20 g/L) was obtained using 100 g/L glucose as carbon source. 5KGA reached 100.20 g/L, 109.10 g/L, 99.83 g/L with yeast extract, fish meal and corn steep liquor as nitrogen source respectively, among which the optimal nitrogen source was fish meal. The yield of 5KGA by corn steep liquor is slightly lower than that by yeast extract. For the economic reason, corn steep liquor was selected as nitrogen source and scaled up to 5 L stirred-tank fermentor, and the final concentration of 5KGA reached 93.80 g/L, with its maximum volumetric productivity of 3.48 g/(L x h) and average volumetric productivity of 1.56 g/(L x h). The result obtained in this study showed that carbon and nitrogen sourses for large-scale production of 5KGA by Gluconobacter oxydans HGI-1 were glucose and corn steep liquor, respectively, and the available glucose almost completely (85.93%) into 5KGA.

  7. New Insights into Sulfur Metabolism in Yeasts as Revealed by Studies of Yarrowia lipolytica

    PubMed Central

    Hébert, Agnès; Forquin-Gomez, Marie-Pierre; Roux, Aurélie; Aubert, Julie; Junot, Christophe; Heilier, Jean-François; Landaud, Sophie; Bonnarme, Pascal

    2013-01-01

    Yarrowia lipolytica, located at the frontier of hemiascomycetous yeasts and fungi, is an excellent candidate for studies of metabolism evolution. This yeast, widely recognized for its technological applications, in particular produces volatile sulfur compounds (VSCs) that fully contribute to the flavor of smear cheese. We report here a relevant global vision of sulfur metabolism in Y. lipolytica based on a comparison between high- and low-sulfur source supplies (sulfate, methionine, or cystine) by combined approaches (transcriptomics, metabolite profiling, and VSC analysis). The strongest repression of the sulfate assimilation pathway was observed in the case of high methionine supply, together with a large accumulation of sulfur intermediates. A high sulfate supply seems to provoke considerable cellular stress via sulfite production, resulting in a decrease of the availability of the glutathione pathway's sulfur intermediates. The most limited effect was observed for the cystine supply, suggesting that the intracellular cysteine level is more controlled than that of methionine and sulfate. Using a combination of metabolomic profiling and genetic experiments, we revealed taurine and hypotaurine metabolism in yeast for the first time. On the basis of a phylogenetic study, we then demonstrated that this pathway was lost by some of the hemiascomycetous yeasts during evolution. PMID:23220962

  8. High-Gravity Brewing: Effects of Nutrition on Yeast Composition, Fermentative Ability, and Alcohol Production

    PubMed Central

    Casey, Gregory P.; Magnus, Carol A.; Ingledew, W. M.

    1984-01-01

    A number of economic and product quality advantages exist in brewing when high-gravity worts of 16 to 18% dissolved solids are fermented. Above this level, production problems such as slow or stuck fermentations and poor yeast viability occur. Ethanol toxicity has been cited as the main cause, as brewers' yeasts are reported to tolerate only 7 to 9% (vol/vol) ethanol. The inhibitory effect of high osmotic pressure has also been implicated. In this report, it is demonstrated that the factor limiting the production of high levels of ethanol by brewing yeasts is actually a nutritional deficiency. When a nitrogen source, ergosterol, and oleic acid are added to worts up to 31% dissolved solids, it is possible to produce beers up to 16.2% (vol/vol) ethanol. Yeast viability remains high, and the yeasts can be repitched at least five times. Supplementation does not increase the fermentative tolerance of the yeasts to ethanol but increases the length and level of new yeast cell mass synthesis over that seen in unsupplemented wort (and therefore the period of more rapid wort attenuation). Glycogen, protein, and sterol levels in yeasts were examined, as was the importance of pitching rate, temperature, and degree of anaerobiosis. The ethanol tolerance of brewers' yeast is suggested to be no different than that of sake or distillers' yeast. PMID:16346630

  9. Nitrogen Metabolite Repression of Metabolism and Virulence in the Human Fungal Pathogen Cryptococcus neoformans

    PubMed Central

    Lee, I. Russel; Chow, Eve W. L.; Morrow, Carl A.; Djordjevic, Julianne T.; Fraser, James A.

    2011-01-01

    Proper regulation of metabolism is essential to maximizing fitness of organisms in their chosen environmental niche. Nitrogen metabolite repression is an example of a regulatory mechanism in fungi that enables preferential utilization of easily assimilated nitrogen sources, such as ammonium, to conserve resources. Here we provide genetic, transcriptional, and phenotypic evidence of nitrogen metabolite repression in the human pathogen Cryptococcus neoformans. In addition to loss of transcriptional activation of catabolic enzyme-encoding genes of the uric acid and proline assimilation pathways in the presence of ammonium, nitrogen metabolite repression also regulates the production of the virulence determinants capsule and melanin. Since GATA transcription factors are known to play a key role in nitrogen metabolite repression, bioinformatic analyses of the C. neoformans genome were undertaken and seven predicted GATA-type genes were identified. A screen of these deletion mutants revealed GAT1, encoding the only global transcription factor essential for utilization of a wide range of nitrogen sources, including uric acid, urea, and creatinine—three predominant nitrogen constituents found in the C. neoformans ecological niche. In addition to its evolutionarily conserved role in mediating nitrogen metabolite repression and controlling the expression of catabolic enzyme and permease-encoding genes, Gat1 also negatively regulates virulence traits, including infectious basidiospore production, melanin formation, and growth at high body temperature (39°–40°). Conversely, Gat1 positively regulates capsule production. A murine inhalation model of cryptococcosis revealed that the gat1Δ mutant is slightly more virulent than wild type, indicating that Gat1 plays a complex regulatory role during infection. PMID:21441208

  10. Nitrogen Transformation and Microbial Spatial Distribution in Drinking Water Biofilter

    NASA Astrophysics Data System (ADS)

    Qian, Yongxing; Zhang, Huining; Jin, Huizheng; Wu, Chengxia

    2018-02-01

    Well understanding the rule of nitrogen mutual transformation in biofilters is important for controlling the DBPs formation in the subsequent disinfection process. Ammonia nitrogen removal effect and nitrogen transformation approach in biofilter of drinking water was researched in the study. The biofilter removed ammonia of 48.5% and total phosphorus of 72.3%. And the removal rate of TN, NO3 --N, DON were 37.1%, 33.1%, 46.9%, respectively. Biomass and bioactivity of different depth of the biofilter were determined, too. The overall distribution of biomass showed a decreasing trend from top to bottom. The bioactivity in lower layer gradually increased. Especially the bioactivity of heterotrophic microorganisms showed a gradual increase trend. The amount of the nitrogen loss was 3.06mg/L. Non-nitrification pathway of “nitrogen loss” phenomenon in biofilter might exist assimilation, nitrification and denitrification in autotrophic.

  11. Exploring New Pathways in Precipitation Assimilation

    NASA Technical Reports Server (NTRS)

    Hou, Arthur; Zhang, Sara Q.

    2004-01-01

    Precipitation assimilation poses a special challenge in that the forward model for rain in a global forecast system is based on parameterized physics, which can have large systematic errors that must be rectified to use precipitation data effectively within a standard statistical analysis framework. We examine some key issues in precipitation assimilation and describe several exploratory studies in assimilating rainfall and latent heating information in NASA's global data assimilation systems using the forecast model as a weak constraint. We present results from two research activities. The first is the assimilation of surface rainfall data using a time-continuous variational assimilation based on a column model of the full moist physics. The second is the assimilation of convective and stratiform latent heating retrievals from microwave sensors using a variational technique with physical parameters in the moist physics schemes as a control variable. We will show the impact of assimilating these data on analyses and forecasts. Among the lessons learned are (1) that the time-continuous application of moisture/temperature tendency corrections to mitigate model deficiencies offers an effective strategy for assimilating precipitation information, and (2) that the model prognostic variables must be allowed to directly respond to an improved rain and latent heating field within an analysis cycle to reap the full benefit of assimilating precipitation information. of microwave radiances versus retrieval information in raining areas, and initial efforts in developing ensemble techniques such as Kalman filter/smoother for precipitation assimilation. Looking to the future, we discuss new research directions including the assimilation

  12. Volatile sulphur compounds and pathways of L-methionine catabolism in Williopsis yeasts.

    PubMed

    Tan, Amelia W J; Lee, Pin-Rou; Seow, Yi-Xin; Ong, Peter K C; Liu, Shao-Quan

    2012-08-01

    Volatile sulphur compounds (VSCs) are important to the food industry due to their high potency and presence in many foods. This study assessed for the first time VSC production and pathways of L: -methionine catabolism in yeasts from the genus Williopsis with a view to understanding VSC formation and their potential flavour impact. Five strains of Williopsis saturnus (var. saturnus, var. subsufficiens, var. suavolens, var. sargentensis and var. mrakii) were screened for VSC production in a synthetic medium supplemented with L: -methionine. A diverse range of VSCs were produced including dimethyl disulphide, dimethyl trisulphide, 3-(methylthio)-1-propanal (methional), 3-(methylthio)-1-propanol (methionol), 3-(methylthio)-1-propene, 3-(methylthio)-1-propyl acetate, 3-(methylthio)-1-propanoic acid (methionic acid) and ethyl 3-(methylthio)-1-propanoate, though the production of these VSCs varied between yeast strains. W. saturnus var. saturnus NCYC22 was selected for further studies due to its relatively high VSC production. VSC production was characterised step-wise with yeast strain NCYC22 in coconut cream at different L: -methionine concentrations (0.00-0.20%) and under various inorganic sulphate (0.00-0.20%) and nitrogen (ammonia) supplementation (0.00-0.20%), respectively. Optimal VSC production was obtained with 0.1% of L: -methionine, while supplementation of sulphate had no significant effect. Nitrogen supplementation showed a dramatic inhibitory effect on VSC production. Based on the production of VSCs, the study suggests that the Ehrlich pathway of L: -methionine catabolism is operative in W. saturnus yeasts and can be manipulated by adjusting certain nutrient parameters to control VSC production.

  13. Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609.

    PubMed

    Sambles, Christine; Middelhaufe, Sabine; Soanes, Darren; Kolak, Dagmara; Lux, Thomas; Moore, Karen; Matoušková, Petra; Parker, David; Lee, Rob; Love, John; Aves, Stephen J

    2017-09-01

    Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, Rhodotorula ( Rhodosporidium ) toruloides (Pucciniomycotina) is known to produce high quantities of lipids when grown in nitrogen-limiting media, and has potential for biodiesel production. The genome of the CGMCC 2.1609 strain of this oleaginous red yeast was sequenced using a hybrid of Roche 454 and Illumina technology generating 13 × coverage. The de novo assembly was carried out using MIRA and scaffolded using MAQ and BAMBUS. The sequencing and assembly resulted in 365 scaffolds with total genome size of 33.4 Mb. The complete genome sequence of this strain was deposited in GenBank and the accession number is LKER00000000. The annotation is available on Figshare (doi:10.6084/m9.figshare.4754251).

  14. Fate and effects of nitrogen and phosphorus in shallow vegetated aquatic ecosystems

    USGS Publications Warehouse

    Fairchild, James F.; Vradenburg, Leigh Ann

    2006-01-01

    Nitrate concentrations have greatly increased in streams and rivers draining agricultural regions of the Midwestern United States, increasing nitrate transport to the Gulf of Mexico has been implicated in the hypoxic conditions that threaten the productivity of marine fisheries. Increases in nitrate concentrations have been attributed to a combination of factors including agricultural expansion, increased nitrogen application rates, increased tile drainage, and loss of riparian Wetlands, These landscape-level changes have resulted in a decreased natural capacity for nitrogen uptake, removal, and cycling back to the atmosphere. Land managers are increasingly interested in using wetland construction and rehabilitation as a management practice to reduce loss of nitrate from the terrestrial systems. Yet, relatively little is known about the limnological factors involved in nitrate removal by Wetland systems.We conducted a series of studies from 1999-2000 to investigate the functional capacity of shallow, macrophyte-dominated pond wetland systems for uptake, assimilation, and retention of nitrogen (N) and phosphorus (P). We evaluated four factors that were hypothesized to influence nutrient uptake and assimilation: 1) nitrate loading rates; 2) nitrogen to phosphorus (N.P) ratios; 3) frequency of dosing/application; and 4) timing of dose initiation.Nutrient assimilation was rapid; store than 90% of added nutrients were removed from the water column in all treatments. Neither variation in N:P ratios (evaluated range, <13:1 to -114.1), frequency of application (weekly or bi-weekly), nor liming of dose initiation relative to macrophyte development (0%, 15-25%, or 75-90% maximum biomass) had significant effects on nutrient assimilation of wetland community dynamics. Maximum loading of nitrate (60 g N/m2 2.4 g P/m2) applied as six weekly doses stimulated algal communities, but inhibited macrophyte communities.Predicted shifts from a stable state of macrophyte- to

  15. Bioactive Compounds Derived from the Yeast Metabolism of Aromatic Amino Acids during Alcoholic Fermentation

    PubMed Central

    Guillamon, Jose Manuel; Torija, Maria Jesus; Beltran, Gemma; Troncoso, Ana M.; Garcia-Parrilla, M. Carmen

    2014-01-01

    Metabolites resulting from nitrogen metabolism in yeast are currently found in some fermented beverages such as wine and beer. Their study has recently attracted the attention of researchers. Some metabolites derived from aromatic amino acids are bioactive compounds that can behave as hormones or even mimic their role in humans and may also act as regulators in yeast. Although the metabolic pathways for their formation are well known, the physiological significance is still far from being understood. The understanding of this relevance will be a key element in managing the production of these compounds under controlled conditions, to offer fermented food with specific enrichment in these compounds or even to use the yeast as nutritional complements. PMID:24895623

  16. A Cyanide-Induced 3-Cyanoalanine Nitrilase in the Cyanide-Assimilating Bacterium Pseudomonas pseudoalcaligenes Strain CECT 5344

    PubMed Central

    Acera, Felipe; Carmona, María Isabel; Castillo, Francisco; Quesada, Alberto

    2017-01-01

    ABSTRACT Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a sole nitrogen source. Under this growth condition, a 3-cyanoalanine nitrilase enzymatic activity was induced. This activity was encoded by nit4, one of the four nitrilase genes detected in the genome of this bacterium, and its expression in Escherichia coli enabled the recombinant strain to fully assimilate 3-cyanoalanine. P. pseudoalcaligenes CECT 5344 showed a weak growth level with 3-cyanoalanine as the N source, unless KCN was also added. Moreover, a nit4 knockout mutant of P. pseudoalcaligenes CECT 5344 became severely impaired in its ability to grow with 3-cyanoalanine and cyanide as nitrogen sources. The native enzyme expressed in E. coli was purified up to electrophoretic homogeneity and biochemically characterized. Nit4 seems to be specific for 3-cyanoalanine, and the amount of ammonium derived from the enzymatic activity doubled in the presence of exogenously added asparaginase activity, which demonstrated that the Nit4 enzyme had both 3-cyanoalanine nitrilase and hydratase activities. The nit4 gene is located downstream of the cyanide resistance transcriptional unit containing cio1 genes, whose expression levels are under the positive control of cyanide. Real-time PCR experiments revealed that nit4 expression was also positively regulated by cyanide in both minimal and LB media. These results suggest that this gene cluster including cio1 and nit4 could be involved both in cyanide resistance and in its assimilation by P. pseudoalcaligenes CECT 5344. IMPORTANCE Cyanide is a highly toxic molecule present in some industrial wastes due to its application in several manufacturing processes, such as gold mining and the electroplating industry. The biodegradation of cyanide from contaminated wastes could be an attractive alternative to physicochemical treatment. P. pseudoalcaligenes CECT 5344 is a bacterial strain able to assimilate cyanide under alkaline conditions

  17. A Cyanide-Induced 3-Cyanoalanine Nitrilase in the Cyanide-Assimilating Bacterium Pseudomonas pseudoalcaligenes Strain CECT 5344.

    PubMed

    Acera, Felipe; Carmona, María Isabel; Castillo, Francisco; Quesada, Alberto; Blasco, Rafael

    2017-05-01

    Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a sole nitrogen source. Under this growth condition, a 3-cyanoalanine nitrilase enzymatic activity was induced. This activity was encoded by nit4 , one of the four nitrilase genes detected in the genome of this bacterium, and its expression in Escherichia coli enabled the recombinant strain to fully assimilate 3-cyanoalanine. P. pseudoalcaligenes CECT 5344 showed a weak growth level with 3-cyanoalanine as the N source, unless KCN was also added. Moreover, a nit4 knockout mutant of P. pseudoalcaligenes CECT 5344 became severely impaired in its ability to grow with 3-cyanoalanine and cyanide as nitrogen sources. The native enzyme expressed in E. coli was purified up to electrophoretic homogeneity and biochemically characterized. Nit4 seems to be specific for 3-cyanoalanine, and the amount of ammonium derived from the enzymatic activity doubled in the presence of exogenously added asparaginase activity, which demonstrated that the Nit4 enzyme had both 3-cyanoalanine nitrilase and hydratase activities. The nit4 gene is located downstream of the cyanide resistance transcriptional unit containing cio1 genes, whose expression levels are under the positive control of cyanide. Real-time PCR experiments revealed that nit4 expression was also positively regulated by cyanide in both minimal and LB media. These results suggest that this gene cluster including cio1 and nit4 could be involved both in cyanide resistance and in its assimilation by P. pseudoalcaligenes CECT 5344. IMPORTANCE Cyanide is a highly toxic molecule present in some industrial wastes due to its application in several manufacturing processes, such as gold mining and the electroplating industry. The biodegradation of cyanide from contaminated wastes could be an attractive alternative to physicochemical treatment. P. pseudoalcaligenes CECT 5344 is a bacterial strain able to assimilate cyanide under alkaline conditions, thus

  18. Assimilation of surface NO2 and O3 observations into the SILAM chemistry transport model

    NASA Astrophysics Data System (ADS)

    Vira, J.; Sofiev, M.

    2014-08-01

    This paper describes assimilation of trace gas observations into the chemistry transport model SILAM using the 3D-Var method. Assimilation results for year 2012 are presented for the prominent photochemical pollutants ozone (O3) and nitrogen dioxide (NO2). Both species are covered by the Airbase observation database, which provides the observational dataset used in this study. Attention is paid to the background and observation error covariance matrices, which are obtained primarily by iterative application of a posteriori diagnostics. The diagnostics are computed separately for two months representing summer and winter conditions, and further disaggregated by time of day. This allows deriving background and observation error covariance definitions which include both seasonal and diurnal variation. The consistency of the obtained covariance matrices is verified using χ2 diagnostics. The analysis scores are computed for a control set of observation stations withheld from assimilation. Compared to a free-running model simulation, the correlation coefficient for daily maximum values is improved from 0.8 to 0.9 for O3 and from 0.53 to 0.63 for NO2.

  19. Seabird nutrient subsidies benefit non-nitrogen fixing trees and alter species composition in South American coastal dry forests.

    PubMed

    Havik, Gilles; Catenazzi, Alessandro; Holmgren, Milena

    2014-01-01

    Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing species, increasing the relative abundance of non-nitrogen fixing species close to seashore. Moreover, we proposed that herbivores can alter the effects of nutrient supplementation by preferentially feeding on high nutrient plants. We studied the effects of nutrient fertilization by seabird guano on tree recruitment and how these effects can be modulated by herbivorous lizards in the coastal dry forests of northwestern Peru. We combined field studies, experiments and stable isotope analysis to study the response of the two most common tree species in these forests, the nitrogen-fixing Prosopis pallida and the non-nitrogen-fixing Capparis scabrida. We did not find differences in herbivore pressure along the sea-inland gradient. We found that the non-nitrogen fixing C. scabrida assimilates marine-derived nitrogen and is more abundant than P. pallida closer to guano-rich soil. We conclude that the input of marine-derived nitrogen through guano deposited by seabirds feeding in the Pacific Ocean affects the two dominant tree species of the coastal dry forests of northern Peru in contrasting ways. The non-nitrogen fixing species, C. scabrida may benefit from sea nutrient subsidies by incorporating guano-derived nitrogen into its foliar tissues, whereas P. pallida, capable of atmospheric fixation, does not.

  20. Seabird Nutrient Subsidies Benefit Non-Nitrogen Fixing Trees and Alter Species Composition in South American Coastal Dry Forests

    PubMed Central

    Havik, Gilles; Catenazzi, Alessandro; Holmgren, Milena

    2014-01-01

    Marine-derived nutrients can increase primary productivity and change species composition of terrestrial plant communities in coastal and riverine ecosystems. We hypothesized that sea nutrient subsidies have a positive effect on nitrogen assimilation and seedling survival of non-nitrogen fixing species, increasing the relative abundance of non-nitrogen fixing species close to seashore. Moreover, we proposed that herbivores can alter the effects of nutrient supplementation by preferentially feeding on high nutrient plants. We studied the effects of nutrient fertilization by seabird guano on tree recruitment and how these effects can be modulated by herbivorous lizards in the coastal dry forests of northwestern Peru. We combined field studies, experiments and stable isotope analysis to study the response of the two most common tree species in these forests, the nitrogen-fixing Prosopis pallida and the non-nitrogen-fixing Capparis scabrida. We did not find differences in herbivore pressure along the sea-inland gradient. We found that the non-nitrogen fixing C. scabrida assimilates marine-derived nitrogen and is more abundant than P. pallida closer to guano-rich soil. We conclude that the input of marine-derived nitrogen through guano deposited by seabirds feeding in the Pacific Ocean affects the two dominant tree species of the coastal dry forests of northern Peru in contrasting ways. The non-nitrogen fixing species, C. scabrida may benefit from sea nutrient subsidies by incorporating guano-derived nitrogen into its foliar tissues, whereas P. pallida, capable of atmospheric fixation, does not. PMID:24466065

  1. A Novel Flucytosine-Resistant Yeast Species, Candida pseudoaaseri, Causes Disease in a Cancer Patient ▿

    PubMed Central

    Pfüller, Roland; Gräser, Yvonne; Erhard, Marcel; Groenewald, Marizeth

    2011-01-01

    Some members of the genus Candida are among the most common human fungal pathogens and cause serious diseases especially in immunocompromised people. A yeast was isolated from a blood culture from an immunocompromised cancer patient who suffered from acute pneumonia. The growth characteristics of the yeast on CHROMagar Candida were similar to those of Candida tropicalis, whereas the API ID 32C system identified the yeast as Candida silvicola. On the basis of the nucleotide divergence in the D1/D2 domain of the 26S nuclear rRNA (nrRNA) gene, as well as the internal transcribed spacer (ITS) domain of the nrRNA gene region, a new species, Candida pseudoaaseri sp. nov. with type strain VK065094 (CBS 11170T), which was found to be closely related to Candida aaseri, is proposed. While C. aaseri strains were susceptible to all tested antifungals, the new species is resistant to flucytosine and may also be distinguished from C. aaseri by its ability to assimilate l-rhamnose, whereas its colony morphology on CHROMagar Candida may be helpful for differentiation. PMID:21976765

  2. Biological data assimilation for parameter estimation of a phytoplankton functional type model for the western North Pacific

    NASA Astrophysics Data System (ADS)

    Hoshiba, Yasuhiro; Hirata, Takafumi; Shigemitsu, Masahito; Nakano, Hideyuki; Hashioka, Taketo; Masuda, Yoshio; Yamanaka, Yasuhiro

    2018-06-01

    Ecosystem models are used to understand ecosystem dynamics and ocean biogeochemical cycles and require optimum physiological parameters to best represent biological behaviours. These physiological parameters are often tuned up empirically, while ecosystem models have evolved to increase the number of physiological parameters. We developed a three-dimensional (3-D) lower-trophic-level marine ecosystem model known as the Nitrogen, Silicon and Iron regulated Marine Ecosystem Model (NSI-MEM) and employed biological data assimilation using a micro-genetic algorithm to estimate 23 physiological parameters for two phytoplankton functional types in the western North Pacific. The estimation of the parameters was based on a one-dimensional simulation that referenced satellite data for constraining the physiological parameters. The 3-D NSI-MEM optimized by the data assimilation improved the timing of a modelled plankton bloom in the subarctic and subtropical regions compared to the model without data assimilation. Furthermore, the model was able to improve not only surface concentrations of phytoplankton but also their subsurface maximum concentrations. Our results showed that surface data assimilation of physiological parameters from two contrasting observatory stations benefits the representation of vertical plankton distribution in the western North Pacific.

  3. Nitrogen Fixation by Anaerobes is Stimulated by Low Oxygen and Insensitive to Combined Nitrogen in Coastal Sediments

    NASA Astrophysics Data System (ADS)

    Jenkins, B. D.; Spinette, R.; Jones, A.; Puggioni, G.; Ehrlich, A.; Brown, S. M.

    2016-02-01

    Coastal sediments are typically zones of nitrogen removal via coupled nitrification-denitrification pathways. Increasingly, there are reports of nitrogen fixation in anthropogenically impacted sediments containing ample combined nitrogen. In previous work in the estuarine sediments of Narragansett Bay, we found that anaerobes related to Desulfovibrio spp. and in the Desulfuromonadales express genes for nitrogen fixation (nifH). We also determined that nitrogen fixation rates and gene expression are elevated during periods of seasonal hypoxia. Statistical modeling shows that a combination of elevated phytoplankton biomass as with a duration of hypoxia for a week or longer lead to conditions that promote nitrogen fixation as measured by acetylene reduction. Interestingly, diazotrophs closely related to those identified in Narragansett Bay are present and active in other low oxygen systems, suggesting that expansion of hypoxic events may lead to unanticipated consequences for the benthic nitrogen cycle in many ecosystems. To determine controls on diazotrophy on the organismal level, we isolated and sequenced the genomes of two Narragansett Bay members of the Desulfovibrio. We found that these organisms are insensitive to nitrate and urea, as they are missing the genes to assimilate these nitrogen sources. However, their nitrogen fixation is suppressed by increasing concentrations of ammonium, indicating that they may be sensitive to this nitrogen source in the environment. The paradox of detectable nitrogen fixation in the background of measurable ammonium in estuarine systems is a newly emergent theme and suggests that there are complex microbial interactions and/or structure to the nutrient regimes allowing for fixation.

  4. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage

    PubMed Central

    Gonçalves, Carla; Wisecaver, Jennifer H; Kominek, Jacek; Oom, Madalena Salema; Leandro, Maria José; Shen, Xing-Xing; Opulente, Dana A; Zhou, Xiaofan; Peris, David; Hittinger, Chris Todd; Rokas, Antonis

    2018-01-01

    Fructophily is a rare trait that consists of the preference for fructose over other carbon sources. Here, we show that in a yeast lineage (the Wickerhamiella/Starmerella, W/S clade) comprised of fructophilic species thriving in the high-sugar floral niche, the acquisition of fructophily is concurrent with a wider remodeling of central carbon metabolism. Coupling comparative genomics with biochemical and genetic approaches, we gathered ample evidence for the loss of alcoholic fermentation in an ancestor of the W/S clade and subsequent reinstatement through either horizontal acquisition of homologous bacterial genes or modification of a pre-existing yeast gene. An enzyme required for sucrose assimilation was also acquired from bacteria, suggesting that the genetic novelties identified in the W/S clade may be related to adaptation to the high-sugar environment. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events. PMID:29648535

  5. Assimilative capacity-based emission load management in a critically polluted industrial cluster.

    PubMed

    Panda, Smaranika; Nagendra, S M Shiva

    2017-12-01

    In the present study, a modified approach was adopted to quantify the assimilative capacity (i.e., the maximum emission an area can take without violating the permissible pollutant standards) of a major industrial cluster (Manali, India) and to assess the effectiveness of adopted air pollution control measures at the region. Seasonal analysis of assimilative capacity was carried out corresponding to critical, high, medium, and low pollution levels to know the best and worst conditions for industrial operations. Bottom-up approach was employed to quantify sulfur dioxide (SO 2 ), nitrogen dioxide (NO 2 ), and particulate matter (aerodynamic diameter <10 μm; PM 10 ) emissions at a fine spatial resolution of 500 × 500 m 2 in Manali industrial cluster. AERMOD (American Meteorological Society/U.S. Environmental Protection Agency Regulatory Model), an U.S. Environmental Protection Agency (EPA) regulatory model, was used for estimating assimilative capacity. Results indicated that 22.8 tonnes/day of SO 2 , 7.8 tonnes/day of NO 2 , and 7.1 tonnes/day of PM 10 were emitted from the industries of Manali. The estimated assimilative capacities for SO 2 , NO 2 , and PM 10 were found to be 16.05, 17.36, and 19.78 tonnes/day, respectively. It was observed that the current SO 2 emissions were exceeding the estimated safe load by 6.7 tonnes/day, whereas PM 10 and NO 2 were within the safe limits. Seasonal analysis of assimilative capacity showed that post-monsoon had the lowest load-carrying capacity, followed by winter, summer, and monsoon seasons, and the allowable SO 2 emissions during post-monsoon and winter seasons were found to be 35% and 26% lower, respectively, when compared with monsoon season. The authors present a modified approach for quantitative estimation of assimilative capacity of a critically polluted Indian industrial cluster. The authors developed a geo-coded fine-resolution PM 10 , NO 2 , and SO 2 emission inventory for Manali industrial area and further

  6. Nitrogen sources affect productivity, desiccation tolerance and storage stability of Beauveria bassiana blastospores.

    PubMed

    Mascarin, G M; Kobori, N N; Jackson, M A; Dunlap, C A; Delalibera, Í

    2018-03-01

    Nitrogen is a critical element in industrial fermentation media. This study investigated the influence of various nitrogen sources on blastospore production, desiccation tolerance and storage stability using two strains of the cosmopolitan insect-pathogenic fungus Beauveria bassiana. Complex organic sources of nitrogen such as soy flour, autolysed yeast and cottonseed flour induced great numbers of blastospores after 2-3 days of fermentation, which also survived drying and remained viable (32-56% survival) after 9 months storage at 4°C, although variations were found between strains. Nitrogen availability in the form of free amino acids directly influenced blastospore production and resistance to desiccation. Increasing glucose and nitrogen concentrations up to 120 and 30 g l -1 , respectively, did not improve blastospore production but enhanced desiccation tolerance. Cell viability after drying and upon fast-rehydration was increased when ≥25 g acid-hydrolysed casein per litre was supplemented in the liquid culture medium. These findings indicate that low-cost complex nitrogen compounds are suitable to enhance yeast-like growth by B. bassiana with good desiccation tolerance and therefore support its further scale-up production as a mycoinsecticide. Nitrogen is the most expensive nutrient in liquid media composition, but this study underscores the feasibility of using low-cost nitrogen compounds composed mainly of agro-industrial by-products for rapid production of desiccation-tolerant B. bassiana blastospores by liquid culture fermentation. © 2018 The Society for Applied Microbiology.

  7. Management of Multiple Nitrogen Sources during Wine Fermentation by Saccharomyces cerevisiae.

    PubMed

    Crépin, Lucie; Truong, Nhat My; Bloem, Audrey; Sanchez, Isabelle; Dequin, Sylvie; Camarasa, Carole

    2017-03-01

    During fermentative growth in natural and industrial environments, Saccharomyces cerevisiae must redistribute the available nitrogen from multiple exogenous sources to amino acids in order to suitably fulfill anabolic requirements. To exhaustively explore the management of this complex resource, we developed an advanced strategy based on the reconciliation of data from a set of stable isotope tracer experiments with labeled nitrogen sources. Thus, quantifying the partitioning of the N compounds through the metabolism network during fermentation, we demonstrated that, contrary to the generally accepted view, only a limited fraction of most of the consumed amino acids is directly incorporated into proteins. Moreover, substantial catabolism of these molecules allows for efficient redistribution of nitrogen, supporting the operative de novo synthesis of proteinogenic amino acids. In contrast, catabolism of consumed amino acids plays a minor role in the formation of volatile compounds. Another important feature is that the α-keto acid precursors required for the de novo syntheses originate mainly from the catabolism of sugars, with a limited contribution from the anabolism of consumed amino acids. This work provides a comprehensive view of the intracellular fate of consumed nitrogen sources and the metabolic origin of proteinogenic amino acids, highlighting a strategy of distribution of metabolic fluxes implemented by yeast as a means of adapting to environments with changing and scarce nitrogen resources. IMPORTANCE A current challenge for the wine industry, in view of the extensive competition in the worldwide market, is to meet consumer expectations regarding the sensory profile of the product while ensuring an efficient fermentation process. Understanding the intracellular fate of the nitrogen sources available in grape juice is essential to the achievement of these objectives, since nitrogen utilization affects both the fermentative activity of yeasts and the

  8. Management of Multiple Nitrogen Sources during Wine Fermentation by Saccharomyces cerevisiae

    PubMed Central

    Crépin, Lucie; Truong, Nhat My; Bloem, Audrey; Sanchez, Isabelle; Dequin, Sylvie

    2017-01-01

    ABSTRACT During fermentative growth in natural and industrial environments, Saccharomyces cerevisiae must redistribute the available nitrogen from multiple exogenous sources to amino acids in order to suitably fulfill anabolic requirements. To exhaustively explore the management of this complex resource, we developed an advanced strategy based on the reconciliation of data from a set of stable isotope tracer experiments with labeled nitrogen sources. Thus, quantifying the partitioning of the N compounds through the metabolism network during fermentation, we demonstrated that, contrary to the generally accepted view, only a limited fraction of most of the consumed amino acids is directly incorporated into proteins. Moreover, substantial catabolism of these molecules allows for efficient redistribution of nitrogen, supporting the operative de novo synthesis of proteinogenic amino acids. In contrast, catabolism of consumed amino acids plays a minor role in the formation of volatile compounds. Another important feature is that the α-keto acid precursors required for the de novo syntheses originate mainly from the catabolism of sugars, with a limited contribution from the anabolism of consumed amino acids. This work provides a comprehensive view of the intracellular fate of consumed nitrogen sources and the metabolic origin of proteinogenic amino acids, highlighting a strategy of distribution of metabolic fluxes implemented by yeast as a means of adapting to environments with changing and scarce nitrogen resources. IMPORTANCE A current challenge for the wine industry, in view of the extensive competition in the worldwide market, is to meet consumer expectations regarding the sensory profile of the product while ensuring an efficient fermentation process. Understanding the intracellular fate of the nitrogen sources available in grape juice is essential to the achievement of these objectives, since nitrogen utilization affects both the fermentative activity of yeasts and

  9. Downstream change in leucine aminopeptidase activity and leucine assimilation by epilithic microbiota along the River Swale, northern England.

    PubMed

    Ainsworth, A M; Goulder, R

    2000-05-05

    Parallel determinations of epilithic extracellular leucine aminopeptidase activity and leucine assimilation were made at five sites along 112 km of the River Swale and also in two tributaries, the River Wiske and Cod Beck. Epilithic leucine aminopeptidase activity along the Swale increased with distance downstream; this increase was gradual, rather than stepwise in response to specific sewage-works outfalls. Epilithic leucine assimilation, in contrast, did not consistently increase along the river. Epilithic leucine aminopeptidase activity and leucine assimilation were both potentially controlled by epilithic microbial variables (bacterial abundance and chlorophyll a) while leucine aminopeptidase activity was also strongly related to water-quality variables, especially temperature, pH and conductivity. Epilithic leucine aminopeptidase activity and leucine assimilation were coupled, but the magnitude of aminopeptidase activity was always substantially greater than that of leucine assimilation. Arguments are presented, however, which suggest that this did not necessarily indicate the constant availability of excess leucine, and by inference amino-acid nitrogen, to epilithic bacteria. Values of epilithic leucine aminopeptidase activity and leucine assimilation, expressed relative to rates in overlying water, suggested that most activity and assimilation was epilithic rather than planktonic, although the planktonic contribution was proportionately greater at the deeper, more downstream, sites. In the tributaries, River Wiske and Cod Beck, values of epilithic leucine aminopeptidase activity and epilithic microbial abundance, as well as those of many water-quality variables, resembled values in the middle and lower Swale. Thus, these tributaries were essentially lowland, enriched watercourses being very different from the headstreams of the main river.

  10. The carbon consumption pattern of the spoilage yeast Brettanomyces bruxellensis in synthetic wine-like medium.

    PubMed

    Smith, Brendan D; Divol, Benoit

    2018-08-01

    The wine matrix contains limited carbon compounds to sustain microbial life. Brettanomyces bruxellensis is one of very few yeast species that has adapted to this environment. Indeed, the presence of growth-inhibiting compounds and conditions do not prevent its proliferation. Literature regarding the nutritional requirements of this yeast is surprisingly poor, given the observation that B. bruxellensis produces biomass with apparently less nutrients than other yeasts. In this study, various carbon sources were screened in a synthetic wine medium, under anaerobic and semi-aerobic growth conditions, in order to determine which compounds B. bruxellensis assimilates. Slight differences were observed between strains but overall, B. bruxellensis produced biomass from limited nutrients consumed in a specific order regardless of the oxygen conditions. Upon initial consumption of the simple sugars, B. bruxellensis was able to remain viable, by concurrently utilising ethanol (only in the presence of oxygen) and malic acid. Although initially beneficial, oxygen was found detrimental in the long term. Formation of volatile phenols occurred during the consumption of the sugars but not as a mechanism to help correct the redox imbalance. The study confirms that B. bruxellensis is able to survive using limited amount of nutrients, making this yeast a challenge for winemakers. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Phosphoenolpyruvate carboxylase intrinsically located in the chloroplast of rice plays a crucial role in ammonium assimilation

    PubMed Central

    Masumoto, Chisato; Miyazawa, Shin-Ichi; Ohkawa, Hiroshi; Fukuda, Takuya; Taniguchi, Yojiro; Murayama, Seiji; Kusano, Miyako; Saito, Kazuki; Fukayama, Hiroshi; Miyao, Mitsue

    2010-01-01

    Phosphoenolpyruvate carboxylase (PEPC) is a key enzyme of primary metabolism in bacteria, algae, and vascular plants, and is believed to be cytosolic. Here we show that rice (Oryza sativa L.) has a plant-type PEPC, Osppc4, that is targeted to the chloroplast. Osppc4 was expressed in all organs tested and showed high expression in the leaves. Its expression in the leaves was confined to mesophyll cells, and Osppc4 accounted for approximately one-third of total PEPC protein in the leaf blade. Recombinant Osppc4 was active in the PEPC reaction, showing Vmax comparable to cytosolic isozymes. Knockdown of Osppc4 expression by the RNAi technique resulted in stunting at the vegetative stage, which was much more marked when rice plants were grown with ammonium than with nitrate as the nitrogen source. Comparison of leaf metabolomes of ammonium-grown plants suggested that the knockdown suppressed ammonium assimilation and subsequent amino acid synthesis by reducing levels of organic acids, which are carbon skeleton donors for these processes. We also identified the chloroplastic PEPC gene in other Oryza species, all of which are adapted to waterlogged soil where the major nitrogen source is ammonium. This suggests that, in addition to glycolysis, the genus Oryza has a unique route to provide organic acids for ammonium assimilation that involves a chloroplastic PEPC, and that this route is crucial for growth with ammonium. This work provides evidence for diversity of primary ammonium assimilation in the leaves of vascular plants. PMID:20194759

  12. Nitrogen stress response and stringent response are coupled in Escherichia coli

    PubMed Central

    Brown, Daniel R.; Barton, Geraint; Pan, Zhensheng; Buck, Martin; Wigneshweraraj, Sivaramesh

    2014-01-01

    Assimilation of nitrogen is an essential process in bacteria. The nitrogen regulation stress response is an adaptive mechanism used by nitrogen-starved Escherichia coli to scavenge for alternative nitrogen sources and requires the global transcriptional regulator NtrC. In addition, nitrogen-starved E. coli cells synthesize a signal molecule, guanosine tetraphosphate (ppGpp), which serves as an effector molecule of many processes including transcription to initiate global physiological changes, collectively termed the stringent response. The regulatory mechanisms leading to elevated ppGpp levels during nutritional stresses remain elusive. Here, we show that transcription of relA, a key gene responsible for the synthesis of ppGpp, is activated by NtrC during nitrogen starvation. The results reveal that NtrC couples these two major bacterial stress responses to manage conditions of nitrogen limitation, and provide novel mechanistic insights into how a specific nutritional stress leads to elevating ppGpp levels in bacteria. PMID:24947454

  13. A proteomic network for symbiotic nitrogen fixation efficiency in Bradyrhizobium elkanii

    USDA-ARS?s Scientific Manuscript database

    Rhizobia bacteroids colonize legumes and reduce N2 to NH3 in root nodules. The current model is that bacteroids avoid assimilating this NH3. Instead, the legume forms glutamine from it, the nitrogen of which is returned to the bacteroid as leucine, isoleucine, valine, dicarboxylates, and peptides. I...

  14. Production of astaxanthin rich feed supplement for animals from Phaffia rhodozyma yeast at low cost

    NASA Astrophysics Data System (ADS)

    Irtiza, Ayesha; Shatunova, Svetlana; Glukhareva, Tatiana; Kovaleva, Elena

    2017-09-01

    Dietary nutrients such as amino acids, vitamins, minerals and antioxidants can play a significant role in determining meat quality and also the growth rate of poultry or animal. Phaffia rhodozyma was grown on waste from brewery industry to produce astaxanthin rich feed supplements at a very low cost. Phaffia rhodozyma is yeast specie that has ability to produce carotenoids and approximately 80% of its total carotenoid content is astaxanthin, which is highly valuable carotenoid for food, feed and aquaculture industry. This study was carried out to test yeast extract of spent yeast from brewing industry waste (residual yeast) as potential nitrogen source for growth of Phaffia rhodozyma. Cultivation was carried out in liquid media prepared by yeast extracts and other components (glucose and peptone). Carotenoids from the biomass were released into biomass by suspending cells in DMSO for destruction of cells followed by extraction with petroleum ether. The extracted carotenoids were studied by spectrophotometry to identify and quantify astaxanthin and other carotenoids produced.

  15. Sulfate Assimilation Mediates Tellurite Reduction and Toxicity in Saccharomyces cerevisiae▿†

    PubMed Central

    Ottosson, Lars-Göran; Logg, Katarina; Ibstedt, Sebastian; Sunnerhagen, Per; Käll, Mikael; Blomberg, Anders; Warringer, Jonas

    2010-01-01

    Despite a century of research and increasing environmental and human health concerns, the mechanistic basis of the toxicity of derivatives of the metalloid tellurium, Te, in particular the oxyanion tellurite, Te(IV), remains unsolved. Here, we provide an unbiased view of the mechanisms of tellurium metabolism in the yeast Saccharomyces cerevisiae by measuring deviations in Te-related traits of a complete collection of gene knockout mutants. Reduction of Te(IV) and intracellular accumulation as metallic tellurium strongly correlated with loss of cellular fitness, suggesting that Te(IV) reduction and toxicity are causally linked. The sulfate assimilation pathway upstream of Met17, in particular, the sulfite reductase and its cofactor siroheme, was shown to be central to tellurite toxicity and its reduction to elemental tellurium. Gene knockout mutants with altered Te(IV) tolerance also showed a similar deviation in tolerance to both selenite and, interestingly, selenomethionine, suggesting that the toxicity of these agents stems from a common mechanism. We also show that Te(IV) reduction and toxicity in yeast is partially mediated via a mitochondrial respiratory mechanism that does not encompass the generation of substantial oxidative stress. The results reported here represent a robust base from which to attack the mechanistic details of Te(IV) toxicity and reduction in a eukaryotic organism. PMID:20675578

  16. Iron deficiency affects nitrogen metabolism in cucumber (Cucumis sativus L.) plants

    PubMed Central

    2012-01-01

    Background Nitrogen is a principal limiting nutrient in plant growth and development. Among factors that may limit NO3- assimilation, Fe potentially plays a crucial role being a metal cofactor of enzymes of the reductive assimilatory pathway. Very few information is available about the changes of nitrogen metabolism occurring under Fe deficiency in Strategy I plants. The aim of this work was to study how cucumber (Cucumis sativus L.) plants modify their nitrogen metabolism when grown under iron deficiency. Results The activity of enzymes involved in the reductive assimilation of nitrate and the reactions that produce the substrates for the ammonium assimilation both at root and at leaf levels in Fe-deficient cucumber plants were investigated. Under Fe deficiency, only nitrate reductase (EC 1.7.1.1) activity decreased both at the root and leaf level, whilst for glutamine synthetase (EC 6.3.1.2) and glutamate synthase (EC 1.4.1.14) an increase was found. Accordingly, the transcript analysis for these enzymes showed the same behaviour except for root nitrate reductase which increased. Furthermore, it was found that amino acid concentration greatly decreased in Fe-deficient roots, whilst it increased in the corresponding leaves. Moreover, amino acids increased in the xylem sap of Fe-deficient plants. Conclusions The data obtained in this work provided new insights on the responses of plants to Fe deficiency, suggesting that this nutritional disorder differentially affected N metabolism in root and in leaf. Indeed under Fe deficiency, roots respond more efficiently, sustaining the whole plant by furnishing metabolites (i.e. aa, organic acids) to the leaves. PMID:23057967

  17. The effect of yeast (Saccharomyces cerevisiae) on nutrient intake, digestibility and finishing performance of lambs fed a diet based on dried molasses sugar beet-pulp.

    PubMed

    Payandeh, S; Kafilzadeh, F

    2007-12-15

    This experiment was conducted to determine the effect of yeast (Saccharomyces cerevisiae, SC47) on finishing performance, digestibility, some blood metabolites and carcass characteristics of male lambs fed a diet based on dried Molasses Sugar Beet-Pulp (MSBP). Eighteen Sanjabi male lambs (20.95 +/- 2.7 kg initial body weight and 3 month of age) were used in a completely randomized design. Animals were assigned to one of the two dietary treatments (with or without yeast). Digestibility and nitrogen balance experiment was carried out using six mature rams on finishing diet with and without yeast. Serum metabolites were determined in samples taken from lambs at the end of finishing period. Dry matter digestibility of finishing diet was significantly increased by yeast addition. However, yeast did not have any significant effect on apparent digestibility of OM, NDF, CP and energy. Nitrogen retention was also not affected by yeast addition. Yeast resulted in a significant increase in the average daily gain, dry matter and organic matter intake. However, feed conversion ratio was not significantly affected by addition of yeast. The concentration of the serum metabolites including glucose, urea, cholesterol, sodium, potassium, calcium, phosphorous and cratinine were not affected significantly by yeast supplementation, but triglyceride concentrations increased significantly when yeast was fed. Addition of yeast to the diet did not have any significant effect on the carcass characteristics. Results of this study suggest that feeding saccharomyces cerevisiae with a diet based on MSBP can improve the performance of fattening lambs without any change in carcass characteristics or cuts.

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

    DOE PAGES

    Franklin, Oskar; Cambui, Camila Aguetoni; Gruffman, Linda; ...

    2016-06-29

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

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

    SciTech Connect

    Franklin, Oskar; Cambui, Camila Aguetoni; Gruffman, Linda

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

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

    PubMed Central

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

    2016-01-01

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

  1. Species Distribution and Susceptibility to Azoles of Vaginal Yeasts Isolated Prostitutes

    PubMed Central

    Gross, Norma T.; Arias, M. L.; Moraga, M.; Baddasarow, Y.; Jarstrand, C.

    2007-01-01

    Objective. We investigated the use of miconazole among female prostitutes in Costa Rica as well as the distribution of vaginal yeasts and the susceptibility pattern to azoles of strains obtained from this population. Our intention was to relate a frequent use of miconazole to occurrence of vaginal yeasts resistant to azoles. Methods. Vaginal samples were taken from 277 patients that have previously used azoles. Vaginal swabs were obtained for direct microscopy and culture. Yeast isolates were identified by germ tube test and assimilation pattern. Susceptibility testing was determined using a tablet diffusion method. Results. The number of clinical Candida isolates (one from each patient) was 57 (20.6%). C. albicans was the predominant species (70%), followed by C. parapsilosis (12%), C. tropicalis (5.3%), C. glabrata and C. famata (3.5% each), C. krusei, C. inconspicua and C. guilliermondii (1.7% each). The majority of vaginal Candida isolates were susceptible to ketoconazole (91%), fluconazole (96.5%), and itraconazole (98%). A lower susceptibility of some isolates to miconazole (63%) was observed as compared to the other azoles tested. Moreover, the strains, nonsusceptible to miconazole, were more often obtained from patients that have used this antifungal at least four times within the last year before taking the samples as compared to those with three or less treatments (P<.01). Conclusion. An indiscriminate use of miconazole, such as that observed among female prostitutes in Costa Rica, results in a reduced susceptibility of vaginal yeasts to miconazole but not to other azoles. PMID:18273407

  2. Modeling and optimization of lipid accumulation by Yarrowia lipolytica from glucose under nitrogen depletion conditions.

    PubMed

    Robles-Rodríguez, Carlos E; Muñoz-Tamayo, Rafael; Bideaux, Carine; Gorret, Nathalie; Guillouet, Stéphane E; Molina-Jouve, Carole; Roux, Gilles; Aceves-Lara, César A

    2018-05-01

    Oleaginous yeasts have been seen as a feasible alternative to produce the precursors of biodiesel due to their capacity to accumulate lipids as triacylglycerol having profiles with high content of unsaturated fatty acids. The yeast Yarrowia lipolytica is a promising microorganism that can produce lipids under nitrogen depletion conditions and excess of the carbon source. However, under these conditions, this yeast also produces citric acid (overflow metabolism) decreasing lipid productivity. This work presents two mathematical models for lipid production by Y. lipolytica from glucose. The first model is based on Monod and inhibition kinetics, and the second one is based on the Droop quota model approach, which is extended to yeast. The two models showed good agreements with the experimental data used for calibration and validation. The quota based model presented a better description of the dynamics of nitrogen and glucose dynamics leading to a good management of N/C ratio which makes this model interesting for control purposes. Then, quota model was used to evaluate, by means of simulation, a scenario for optimizing lipid productivity and lipid content. For that, a control strategy was designed by approximating the flow rates of glucose and nitrogen with piecewise linear functions. Simulation results achieved productivity of 0.95 g L -1  hr -1 and lipid content fraction of 0.23 g g -1 , which indicates that this strategy is a promising alternative for the optimization of lipid production. © 2017 Wiley Periodicals, Inc.

  3. The role of oyster restoration and aquaculture in nitrogen removal within a Rhode Island estuary

    EPA Science Inventory

    Coastal systems are increasingly impacted by over-enrichment of nutrients, which has cascading effects for ecosystem functioning. Oyster aquaculture and restoration are hypothesized to mitigate excessive nitrogen (N) loads via assimilation, burial, or benthic denitrification. Stu...

  4. Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum.

    PubMed

    Alipanah, Leila; Winge, Per; Rohloff, Jens; Najafi, Javad; Brembu, Tore; Bones, Atle M

    2018-01-01

    Phosphorus, an essential element for all living organisms, is a limiting nutrient in many regions of the ocean due to its fast recycling. Changes in phosphate (Pi) availability in aquatic systems affect diatom growth and productivity. We investigated the early adaptive mechanisms in the marine diatom Phaeodactylum tricornutum to P deprivation using a combination of transcriptomics, metabolomics, physiological and biochemical experiments. Our analysis revealed strong induction of gene expression for proteins involved in phosphate acquisition and scavenging, and down-regulation of processes such as photosynthesis, nitrogen assimilation and nucleic acid and ribosome biosynthesis. P deprivation resulted in alterations of carbon allocation through the induction of the pentose phosphate pathway and cytosolic gluconeogenesis, along with repression of the Calvin cycle. Reorganization of cellular lipids was indicated by coordinated induced expression of phospholipases, sulfolipid biosynthesis enzymes and a putative betaine lipid biosynthesis enzyme. A comparative analysis of nitrogen- and phosphorus-deprived P. tricornutum revealed both common and distinct regulation patterns in response to phosphate and nitrate stress. Regulation of central carbon metabolism and amino acid metabolism was similar, whereas unique responses were found in nitrogen assimilation and phosphorus scavenging in nitrogen-deprived and phosphorus-deprived cells, respectively.

  5. GlnR-mediated regulation of nitrogen metabolism in the actinomycete Saccharopolyspora erythraea.

    PubMed

    Yao, Li-Li; Liao, Cheng-Heng; Huang, Gang; Zhou, Ying; Rigali, Sebastien; Zhang, Buchang; Ye, Bang-Ce

    2014-09-01

    Nitrogen source sensing, uptake, and assimilation are central for growth and development of microorganisms which requires the participation of a global control of nitrogen metabolism-associated genes at the transcriptional level. In soil-dwelling antibiotic-producing actinomycetes, this role is played by GlnR, an OmpR family regulator. In this work, we demonstrate that SACE_7101 is the ortholog of actinomycetes' GlnR global regulators in the erythromycin producer Saccharopolyspora erythraea. Indeed, the chromosomal deletion of SACE_7101 severely affects the viability of S. erythraea when inoculated in minimal media supplemented with NaNO3, NaNO2, NH4Cl, glutamine, or glutamate as sole nitrogen source. Combination of in silico prediction of cis-acting elements, subsequent in vitro (through gel shift assays) and in vivo (real-time reverse transcription polymerase chain reaction) validations of the predicted target genes revealed a very large GlnR regulon aimed at adapting the nitrogen metabolism of S. erythraea. Indeed, enzymes/proteins involved in (i) uptake and assimilation of ammonium, (ii) transport and utilization of urea, (iii) nitrite/nitrate, (iv) glutamate/glutamine, (v) arginine metabolism, (vi) nitric oxide biosynthesis, and (vii) signal transduction associated with the nitrogen source supplied have at least one paralog gene which expression is controlled by GlnR. Our work highlights a GlnR-binding site consensus sequence (t/gna/cAC-n6-GaAAc) which is similar although not identical to the consensus sequences proposed for other actinomycetes. Finally, we discuss the distinct and common features of the GlnR-mediated transcriptional control of nitrogen metabolism between S. erythraea and the model organism Streptomyces coelicolor.

  6. Empowering Geoscience with Improved Data Assimilation Using the Data Assimilation Research Testbed "Manhattan" Release.

    NASA Astrophysics Data System (ADS)

    Raeder, K.; Hoar, T. J.; Anderson, J. L.; Collins, N.; Hendricks, J.; Kershaw, H.; Ha, S.; Snyder, C.; Skamarock, W. C.; Mizzi, A. P.; Liu, H.; Liu, J.; Pedatella, N. M.; Karspeck, A. R.; Karol, S. I.; Bitz, C. M.; Zhang, Y.

    2017-12-01

    The capabilities of the Data Assimilation Research Testbed (DART) at NCAR have been significantly expanded with the recent "Manhattan" release. DART is an ensemble Kalman filter based suite of tools, which enables researchers to use data assimilation (DA) without first becoming DA experts. Highlights: significant improvement in efficient ensemble DA for very large models on thousands of processors, direct read and write of model state files in parallel, more control of the DA output for finer-grained analysis, new model interfaces which are useful to a variety of geophysical researchers, new observation forward operators and the ability to use precomputed forward operators from the forecast model. The new model interfaces and example applications include the following: MPAS-A; Model for Prediction Across Scales - Atmosphere is a global, nonhydrostatic, variable-resolution mesh atmospheric model, which facilitates multi-scale analysis and forecasting. The absence of distinct subdomains eliminates problems associated with subdomain boundaries. It demonstrates the ability to consistently produce higher-quality analyses than coarse, uniform meshes do. WRF-Chem; Weather Research and Forecasting + (MOZART) Chemistry model assimilates observations from FRAPPÉ (Front Range Air Pollution and Photochemistry Experiment). WACCM-X; Whole Atmosphere Community Climate Model with thermosphere and ionosphere eXtension assimilates observations of electron density to investigate sudden stratospheric warming. CESM (weakly) coupled assimilation; NCAR's Community Earth System Model is used for assimilation of atmospheric and oceanic observations into their respective components using coupled atmosphere+land+ocean+sea+ice forecasts. CESM2.0; Assimilation in the atmospheric component (CAM, WACCM) of the newly released version is supported. This version contains new and extensively updated components and software environment. CICE; Los Alamos sea ice model (in CESM) is used to assimilate

  7. The General Amino Acid Permease FfGap1 of Fusarium fujikuroi Is Sorted to the Vacuole in a Nitrogen-Dependent, but Npr1 Kinase-Independent Manner

    PubMed Central

    Pfannmüller, Andreas; Wagner, Dominik; Sieber, Christian; Schönig, Birgit; Boeckstaens, Mélanie; Marini, Anna Maria; Tudzynski, Bettina

    2015-01-01

    The rice pathogenic fungus Fusarium fujikuroi is well known for the production of a broad spectrum of secondary metabolites (SMs) such as gibberellic acids (GAs), mycotoxins and pigments. The biosynthesis of most of these SMs strictly depends on nitrogen availability and of the activity of permeases of nitrogen sources, e.g. the ammonium and amino acid permeases. One of the three ammonium permeases, MepB, was recently shown to act not only as a transporter but also as a nitrogen sensor affecting the production of nitrogen-repressed SMs. Here we describe the identification of a general amino acid permease, FfGap1, among the 99 putative amino acid permeases (AAPs) in the genome of F. fujikuroi. FfGap1 is able to fully restore growth of the yeast gap1∆ mutant on several amino acids including citrulline and tryptophane. In S. cerevisiae, Gap1 activity is regulated by shuttling between the plasma membrane (nitrogen limiting conditions) and the vacuole (nitrogen sufficiency), which we also show for FfGap1. In yeast, the Npr1 serine/threonine kinase stabilizes the Gap1 position at the plasma membrane. Here, we identified and characterized three NPR1-homologous genes, encoding the putative protein kinases FfNpr1-1, FfNpr1-2 and FfNpr1-3 with significant similarity to yeast Npr1. Complementation of the yeast npr1Δ mutant with each of the three F. fujikuroi NPR1 homologues, resulted in partial restoration of ammonium, arginine and proline uptake by FfNPR1-1 while none of the three kinases affect growth on different nitrogen sources and nitrogen-dependent sorting of FfGap1 in F. fujikuroi. However, exchange of the putative ubiquitin-target lysine 9 (K9A) and 15 (K15A) residues of FfGap1 resulted in extended localization to the plasma membrane and increased protein stability independently of nitrogen availability. These data suggest a similar regulation of FfGap1 by nitrogen-dependent ubiquitination, but differences regarding the role of Fusarium Npr1 homologues compared to

  8. Alleviation of Nitrogen and Sulfur Deficiency and Enhancement of Photosynthesis in Arabidopsis thaliana by Overexpression of Uroporphyrinogen III Methyltransferase (UPM1)

    PubMed Central

    Garai, Sampurna; Tripathy, Baishnab C.

    2018-01-01

    Siroheme, an iron-containing tetrapyrrole, is the prosthetic group of nitrite reductase (NiR) and sulfite reductase (SiR); it is synthesized from uroporphyrinogen III, an intermediate of chlorophyll biosynthesis, and is required for nitrogen (N) and sulfur (S) assimilation. Further, uroporphyrinogen III methyltransferase (UPM1), responsible for two methylation reactions to form dihydrosirohydrochlorin, diverts uroporphyrinogen III from the chlorophyll biosynthesis pathway toward siroheme synthesis. AtUPM1 [At5g40850] was used to produce both sense and antisense plants of Arabidopsis thaliana in order to modulate siroheme biosynthesis. In our experiments, overexpression of AtUPM1 signaled higher NiR (NII) and SiR gene and gene product expression. Increased NII expression was found to regulate and enhance the transcript and protein abundance of nitrate reductase (NR). We suggest that elevated NiR, NR, and SiR expression must have contributed to the increased synthesis of S containing amino acids in AtUPM1overexpressors, observed in our studies. We note that due to higher N and S assimilation in these plants, total protein content had increased in these plants. Consequently, chlorophyll biosynthesis increased in these sense plants. Higher chlorophyll and protein content of plants upregulated photosynthetic electron transport and carbon assimilation in the sense plants. Further, we have observed increased plant biomass in these plants, and this must have been due to increased N, S, and C assimilation. On the other hand, in the antisense plants, the transcript abundance, and protein content of NiR, and SiR was shown to decrease, resulting in reduced total protein and chlorophyll content. This led to a decrease in photosynthetic electron transport rate, carbon assimilation and plant biomass in these antisense plants. Under nitrogen or sulfur starvation conditions, the overexpressors had higher protein content and photosynthetic electron transport rate than the wild type

  9. Genetic basis of priority effects: insights from nectar yeast

    PubMed Central

    Hartwig, Thomas

    2016-01-01

    Priority effects, in which the order of species arrival dictates community assembly, can have a major influence on species diversity, but the genetic basis of priority effects remains unknown. Here, we suggest that nitrogen scavenging genes previously considered responsible for starvation avoidance may drive priority effects by causing rapid resource depletion. Using single-molecule sequencing, we de novo assembled the genome of the nectar-colonizing yeast, Metschnikowia reukaufii, across eight scaffolds and complete mitochondrion, with gap-free coverage over gene spaces. We found a high rate of tandem gene duplication in this genome, enriched for nitrogen metabolism and transport. Both high-capacity amino acid importers, GAP1 and PUT4, present as tandem gene arrays, were highly expressed in synthetic nectar and regulated by the availability and quality of amino acids. In experiments with competitive nectar yeast, Candida rancensis, amino acid addition alleviated suppression of C. rancensis by early arrival of M. reukaufii, corroborating that amino acid scavenging may contribute to priority effects. Because niche pre-emption via rapid resource depletion may underlie priority effects in a broad range of microbial, plant and animal communities, nutrient scavenging genes like the ones we considered here may be broadly relevant to understanding priority effects. PMID:27708148

  10. Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage.

    PubMed

    Gonçalves, Carla; Wisecaver, Jennifer H; Kominek, Jacek; Oom, Madalena Salema; Leandro, Maria José; Shen, Xing-Xing; Opulente, Dana A; Zhou, Xiaofan; Peris, David; Kurtzman, Cletus P; Hittinger, Chris Todd; Rokas, Antonis; Gonçalves, Paula

    2018-04-12

    Fructophily is a rare trait that consists of the preference for fructose over other carbon sources. Here, we show that in a yeast lineage (the Wickerhamiella / Starmerella , W/S clade) comprised of fructophilic species thriving in the high-sugar floral niche, the acquisition of fructophily is concurrent with a wider remodeling of central carbon metabolism. Coupling comparative genomics with biochemical and genetic approaches, we gathered ample evidence for the loss of alcoholic fermentation in an ancestor of the W/S clade and subsequent reinstatement through either horizontal acquisition of homologous bacterial genes or modification of a pre-existing yeast gene. An enzyme required for sucrose assimilation was also acquired from bacteria, suggesting that the genetic novelties identified in the W/S clade may be related to adaptation to the high-sugar environment. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events. © 2018, Gonçalves et al.

  11. Ocean Data Assimilation Systems for GODAE

    DTIC Science & Technology

    2009-09-01

    we describe some of the ocean data assimilation systems that have been developed within the Global Ocean Data Assimilation Experiment (GODAE...assimilation systems in the post-GODAF. time period beyond 2008. 15. SUBJECT TERMS Global Ocean Data Assimilation Experiment, ARGO, subsurface...E. R. Franchi , 7000 Public Affairs (Unclassified/ Unlimited Only), Code 703o 4 yj ?>-* i o’ 1. Release of this paper is approved. 2. To the

  12. Exopolysaccharides from yeast: insight into optimal conditions for biosynthesis, chemical composition and functional properties - review.

    PubMed

    Gientka, Iwona; Błażejak, Stanisław; Stasiak-Różańska, Lidia; Chlebowska-Śmigiel, Anna

    2015-01-01

    xopolysaccharides (EPS) are not a well-established group of metabolites. An industrial scale    of this EPS production is limited mainly by low yield biosynthesis. Until now, enzymes and biosynthesis pathways, as well as the role of regulatory genes, have not been described. Some of yeast EPS show antitumor, immunostimulatory and antioxidant activity. Others, absorb heavy metals and can function as bioactive components of food. Also, the potential of yeast EPS as thickeners or stabilizers can be found. Optimal conditions for the biosynthesis of yeast exopolysaccharides require strong oxygenation and low temperature of the culture, due to the physiology of the producer strains. The medium should contain sucrose as a carbon source and ammonium sulfate as inorganic nitrogen source, wherein the C:N ratio in the substrate should be 15:1. The cultures are long and the largest accumulation of polymers is observed after 4 or 5 days of culturing. The structure of yeast EPS is complex which affects the strain and culture condition. The EPS from yeast are linear mannans, pullulan, glucooligosaccharides, galactooligosaccharides and other heteropolysaccharides containing α-1,2; α-1,3; α-1,6; β-1,3; β-1,4 bonds. Mannose and glucose have the largest participation of carbohydrates for. t exopolysaccharides (EPS) are not a well-established group of metabolites. An industrial scale    of this EPS production is limited mainly by low yield biosynthesis. Until now, enzymes and biosynthesis pathways, as well as the role of regulatory genes, have not been described. Some of yeast EPS show antitumor, immunostimulatory and antioxidant activity. Others, absorb heavy metals and can function as bioactive components of food. Also, the potential of yeast EPS as thickeners or stabilizers can be found. Optimal conditions for the biosynthesis of yeast exopolysaccharides require strong oxygenation and low temperature of the culture, due to the physiology of the producer strains. The

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

    PubMed

    Macler, B A

    1988-11-01

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

  14. Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica

    SciTech Connect

    Pomraning, Kyle R.; Bredeweg, Erin L.; Baker, Scott E.

    ABSTRACT Fungi accumulate lipids in a manner dependent on the quantity and quality of the nitrogen source on which they are growing. In the oleaginous yeastYarrowia lipolytica, growth on a complex source of nitrogen enables rapid growth and limited accumulation of neutral lipids, while growth on a simple nitrogen source promotes lipid accumulation in large lipid droplets. Here we examined the roles of nitrogen catabolite repression and its regulation by GATA zinc finger transcription factors on lipid metabolism inY. lipolytica. Deletion of the GATA transcription factor genesgzf3andgzf2resulted in nitrogen source-specific growth defects and greater accumulation of lipids when the cells weremore » growing on a simple nitrogen source. Deletion ofgzf1, which is most similar to activators of genes repressed by nitrogen catabolite repression in filamentous ascomycetes, did not affect growth on the nitrogen sources tested. We examined gene expression of wild-type and GATA transcription factor mutants on simple and complex nitrogen sources and found that expression of enzymes involved in malate metabolism, beta-oxidation, and ammonia utilization are strongly upregulated on a simple nitrogen source. Deletion ofgzf3results in overexpression of genes with GATAA sites in their promoters, suggesting that it acts as a repressor, whilegzf2is required for expression of ammonia utilization genes but does not grossly affect the transcription level of genes predicted to be controlled by nitrogen catabolite repression. Both GATA transcription factor mutants exhibit decreased expression of genes controlled by carbon catabolite repression via the repressormig1, including genes for beta-oxidation, highlighting the complex interplay between regulation of carbon, nitrogen, and lipid metabolism. IMPORTANCENitrogen source is commonly used to control lipid production in industrial fungi. Here we identified regulators of nitrogen catabolite repression in the oleaginous yeast

  15. 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.

  16. Screening of a thiamine-auxotrophic yeast for alpha-ketoglutaric acid overproduction.

    PubMed

    Zhou, Jingwen; Zhou, Haiyan; Du, Guocheng; Liu, Liming; Chen, Jian

    2010-09-01

    To obtain a thiamine-auxotrophic yeast strain that overproduces alpha-ketoglutaric acid (alpha-KG) from glycerol and to investigate nutrient effects on alpha-KG production. Yeast strain WSH-Z06, a thiamine auxotroph that gave high yields of alpha-KG from glycerol, was obtained by screening for ampicillin/kanamycin resistance and thiamine auxotrophy. The strain was identified as Yarrowia lipolytica based on physiological, chemical, and phylogenetic analysis. The ability of the strain to convert glycerol to alpha-KG was analysed by investigating the effects of nutritional factors, including thiamine, riboflavin, nitrogen sources, and calcium ion. Thiamine and calcium ion concentration had the greatest effect on alpha-KG accumulation. Under optimal conditions, a yield of 39.2 g l(-1)alpha-KG was obtained from 100 g l(-1) glycerol, with 16.84 g l(-1) pyruvate as a by-product. The current work provides a method for screening for an alpha-KG overproducer. Nutrients have a significant impact on alpha-KG production in the yeast strain presented here. The alpha-KG-overproducing yeast strain Y. lipolytica WSH-Z06 is a promising parent strain for further metabolic engineering to lower by-product accumulation and accelerate glycerol utilization.

  17. Process Analysis of Variables for Standardization of Antifungal Susceptibility Testing of Nonfermentative Yeasts

    PubMed Central

    Zaragoza, Oscar; Mesa-Arango, Ana C.; Gómez-López, Alicia; Bernal-Martínez, Leticia; Rodríguez-Tudela, Juan Luis; Cuenca-Estrella, Manuel

    2011-01-01

    Nonfermentative yeasts, such as Cryptococcus spp., have emerged as fungal pathogens during the last few years. However, standard methods to measure their antifungal susceptibility (antifungal susceptibility testing [AST]) are not completely reliable due to the impaired growth of these yeasts in standard media. In this work, we have compared the growth kinetics and the antifungal susceptibilities of representative species of nonfermentative yeasts such as Cryptococcus neoformans, Cryptococcus gattii, Cryptococcus albidus, Rhodotorula spp., Yarrowia lipolytica, Geotrichum spp., and Trichosporon spp. The effect of the growth medium (RPMI medium versus yeast nitrogen base [YNB]), glucose concentration (0.2% versus 2%), nitrogen source (ammonium sulfate), temperature (30°C versus 35°C), shaking, and inoculum size (103, 104, and 105 cells) were analyzed. The growth rate, lag phase, and maximum optical density were obtained from each growth experiment, and after multivariate analysis, YNB-based media demonstrated a significant improvement in the growth of yeasts. Shaking, an inoculum size of 105 CFU/ml, and incubation at 30°C also improved the growth kinetics of organisms. Supplementation with ammonium sulfate and with 2% glucose did not have any effect on growth. We also tested the antifungal susceptibilities of all the isolates by the reference methods of the CLSI and EUCAST, the EUCAST method with shaking, YNB under static conditions, and YNB with shaking. MIC values obtained under different conditions showed high percentages of agreement and significant correlation coefficient values between them. MIC value determinations according to CLSI and EUCAST standards were rather complicated, since more than half of isolates tested showed a limited growth index, hampering endpoint determinations. We conclude that AST conditions including YNB as an assay medium, agitation of the plates, reading after 48 h of incubation, an inoculum size of 105 CFU/ml, and incubation at 30

  18. Optimality in Data Assimilation

    NASA Astrophysics Data System (ADS)

    Nearing, Grey; Yatheendradas, Soni

    2016-04-01

    It costs a lot more to develop and launch an earth-observing satellite than it does to build a data assimilation system. As such, we propose that it is important to understand the efficiency of our assimilation algorithms at extracting information from remote sensing retrievals. To address this, we propose that it is necessary to adopt completely general definition of "optimality" that explicitly acknowledges all differences between the parametric constraints of our assimilation algorithm (e.g., Gaussianity, partial linearity, Markovian updates) and the true nature of the environmetnal system and observing system. In fact, it is not only possible, but incredibly straightforward, to measure the optimality (in this more general sense) of any data assimilation algorithm as applied to any intended model or natural system. We measure the information content of remote sensing data conditional on the fact that we are already running a model and then measure the actual information extracted by data assimilation. The ratio of the two is an efficiency metric, and optimality is defined as occurring when the data assimilation algorithm is perfectly efficient at extracting information from the retrievals. We measure the information content of the remote sensing data in a way that, unlike triple collocation, does not rely on any a priori presumed relationship (e.g., linear) between the retrieval and the ground truth, however, like triple-collocation, is insensitive to the spatial mismatch between point-based measurements and grid-scale retrievals. This theory and method is therefore suitable for use with both dense and sparse validation networks. Additionally, the method we propose is *constructive* in the sense that it provides guidance on how to improve data assimilation systems. All data assimilation strategies can be reduced to approximations of Bayes' law, and we measure the fractions of total information loss that are due to individual assumptions or approximations in the

  19. Nitrogen processing by grazers in a headwater stream: riparian connections

    DOE PAGES

    Hill, Walter R.; Griffiths, Natalie A.

    2016-10-19

    Primary consumers play important roles in the cycling of nutrients in headwater streams, storing assimilated nutrients in growing tissue and recycling them through excretion. Though environmental conditions in most headwater streams and their surrounding terrestrial ecosystems vary considerably over the course of a year, relatively little is known about the effects of seasonality on consumer nutrient recycling these streams. Here, we measured nitrogen accumulated through growth and excreted by the grazing snail Elimia clavaeformis (Pleuroceridae) over the course of 12 months in Walker Branch, identifying close connections between in-stream nitrogen processing and seasonal changes in the surrounding forest.

  20. Assimilation of surface NO2 and O3 observations into the SILAM chemistry transport model

    NASA Astrophysics Data System (ADS)

    Vira, J.; Sofiev, M.

    2015-02-01

    This paper describes the assimilation of trace gas observations into the chemistry transport model SILAM (System for Integrated modeLling of Atmospheric coMposition) using the 3D-Var method. Assimilation results for the year 2012 are presented for the prominent photochemical pollutants ozone (O3) and nitrogen dioxide (NO2). Both species are covered by the AirBase observation database, which provides the observational data set used in this study. Attention was paid to the background and observation error covariance matrices, which were obtained primarily by the iterative application of a posteriori diagnostics. The diagnostics were computed separately for 2 months representing summer and winter conditions, and further disaggregated by time of day. This enabled the derivation of background and observation error covariance definitions, which included both seasonal and diurnal variation. The consistency of the obtained covariance matrices was verified using χ2 diagnostics. The analysis scores were computed for a control set of observation stations withheld from assimilation. Compared to a free-running model simulation, the correlation coefficient for daily maximum values was improved from 0.8 to 0.9 for O3 and from 0.53 to 0.63 for NO2.

  1. Time-series resolution of gradual nitrogen starvation and its impact on photosynthesis in the cyanobacterium Synechocystis PCC 6803.

    PubMed

    Krasikov, Vladimir; Aguirre von Wobeser, Eneas; Dekker, Henk L; Huisman, Jef; Matthijs, Hans C P

    2012-07-01

    Sequential adaptation to nitrogen deprivation and ultimately to full starvation requires coordinated adjustment of cellular functions. We investigated changes in gene expression and cell physiology of the cyanobacterium Synechocystis PCC 6803 during 96 h of nitrogen starvation. During the first 6 h, the transcriptome showed activation of nitrogen uptake and assimilation systems and of the core nitrogen and carbon assimilation regulators. However, the nitrogen-deprived cells still grew at the same rate as the control and even showed transiently increased expression of phycobilisome genes. After 12 h, cell growth decreased and chlorosis started with degradation of the nitrogen-rich phycobilisomes. During this phase, the transcriptome showed suppression of genes for phycobilisomes, for carbon fixation and for de novo protein synthesis. Interestingly, photosynthetic activity of both photosystem I (PSI) and photosystem II was retained quite well. Excess electrons were quenched by the induction of terminal oxidase and hydrogenase genes, compensating for the diminished carbon fixation and nitrate reduction activity. After 48 h, the cells ceased most activities. A marked exception was the retained PSI gene transcription, possibly this supports the viability of Synechocystis cells and enables rapid recovery after relieving from nitrogen starvation. During early recovery, many genes changed expression, supporting the resumed cellular activity. In total, our results distinguished three phases during gradual nitrogen depletion: (1) an immediate response, (2) short-term acclimation and (3) long-term survival. This shows that cyanobacteria respond to nitrogen starvation by a cascade of physiological adaptations reflected by numerous changes in the transcriptome unfolding at different timescales. Copyright © Physiologia Plantarum 2012.

  2. Climate-mediated nitrogen and carbon dynamics in a tropical watershed

    NASA Astrophysics Data System (ADS)

    Ballantyne, A. P.; Baker, P. A.; Fritz, S. C.; Poulter, B.

    2011-06-01

    Climate variability affects the capacity of the biosphere to assimilate and store important elements, such as nitrogen and carbon. Here we present biogeochemical evidence from the sediments of tropical Lake Titicaca indicating that large hydrologic changes in response to global glacial cycles during the Quaternary were accompanied by major shifts in ecosystem state. During prolonged glacial intervals, lake level was high and the lake was in a stable nitrogen-limited state. In contrast, during warm dry interglacials lake level fell and rates of nitrogen concentrations increased by a factor of 4-12, resulting in a fivefold to 24-fold increase in organic carbon concentrations in the sediments due to increased primary productivity. Observed periods of increased primary productivity were also associated with an apparent increase in denitrification. However, the net accumulation of nitrogen during interglacial intervals indicates that increased nitrogen supply exceeded nitrogen losses due to denitrification, thereby causing increases in primary productivity. Although primary productivity in tropical ecosystems, especially freshwater ecosystems, tends to be nitrogen limited, our results indicate that climate variability may lead to changes in nitrogen availability and thus changes in primary productivity. Therefore some tropical ecosystems may shift between a stable state of nitrogen limitation and a stable state of nitrogen saturation in response to varying climatic conditions.

  3. Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Jones, Emlyn M.; Baird, Mark E.; Mongin, Mathieu; Parslow, John; Skerratt, Jenny; Lovell, Jenny; Margvelashvili, Nugzar; Matear, Richard J.; Wild-Allen, Karen; Robson, Barbara; Rizwi, Farhan; Oke, Peter; King, Edward; Schroeder, Thomas; Steven, Andy; Taylor, John

    2016-12-01

    Skillful marine biogeochemical (BGC) models are required to understand a range of coastal and global phenomena such as changes in nitrogen and carbon cycles. The refinement of BGC models through the assimilation of variables calculated from observed in-water inherent optical properties (IOPs), such as phytoplankton absorption, is problematic. Empirically derived relationships between IOPs and variables such as chlorophyll-a concentration (Chl a), total suspended solids (TSS) and coloured dissolved organic matter (CDOM) have been shown to have errors that can exceed 100 % of the observed quantity. These errors are greatest in shallow coastal regions, such as the Great Barrier Reef (GBR), due to the additional signal from bottom reflectance. Rather than assimilate quantities calculated using IOP algorithms, this study demonstrates the advantages of assimilating quantities calculated directly from the less error-prone satellite remote-sensing reflectance (RSR). To assimilate the observed RSR, we use an in-water optical model to produce an equivalent simulated RSR and calculate the mismatch between the observed and simulated quantities to constrain the BGC model with a deterministic ensemble Kalman filter (DEnKF). The traditional assumption that simulated surface Chl a is equivalent to the remotely sensed OC3M estimate of Chl a resulted in a forecast error of approximately 75 %. We show this error can be halved by instead using simulated RSR to constrain the model via the assimilation system. When the analysis and forecast fields from the RSR-based assimilation system are compared with the non-assimilating model, a comparison against independent in situ observations of Chl a, TSS and dissolved inorganic nutrients (NO3, NH4 and DIP) showed that errors are reduced by up to 90 %. In all cases, the assimilation system improves the simulation compared to the non-assimilating model. Our approach allows for the incorporation of vast quantities of remote-sensing observations

  4. Continuing Themes in Assimilation Through Education.

    ERIC Educational Resources Information Center

    Strouse, Joan

    1987-01-01

    Discusses assimilation and adaptation of immigrants in the United States. Summarizes major sociological theories on assimilation. Focuses on schools as instruments of assimilation that attempt to force Anglo-conformity upon students. The refugee student's perceptions of his or her problems and opportunities are discussed. (PS)

  5. Apple Aminoacid Profile and Yeast Strains in the Formation of Fusel Alcohols and Esters in Cider Production.

    PubMed

    Eleutério Dos Santos, Caroline Mongruel; Pietrowski, Giovana de Arruda Moura; Braga, Cíntia Maia; Rossi, Márcio José; Ninow, Jorge; Machado Dos Santos, Tâmisa Pires; Wosiacki, Gilvan; Jorge, Regina Maria Matos; Nogueira, Alessandro

    2015-06-01

    The amino acid profile in dessert apple must and its effect on the synthesis of fusel alcohols and esters in cider were established by instrumental analysis. The amino acid profile was performed in nine apple musts. Two apple musts with high (>150 mg/L) and low (<75 mg/L) nitrogen content, and four enological yeast strains, were used in cider fermentation. The aspartic acid, asparagine and glutamic acid amino acids were the majority in all the apple juices, representing 57.10% to 81.95%. These three amino acids provided a high consumption (>90%) during fermentation in all the ciders. Principal component analysis (PCA) explained 81.42% of data variability and the separation of three groups for the analyzed samples was verified. The ciders manufactured with low nitrogen content showed sluggish fermentation and around 50% less content of volatile compounds (independent of the yeast strain used), which were mainly 3-methyl-1-butanol (isoamyl alcohol) and esters. However, in the presence of amino acids (asparagine, aspartic acid, glutamic acid and alanine) there was a greater differentiation between the yeasts in the production of fusel alcohols and ethyl esters. High contents of these aminoacids in dessert apple musts are essential for the production of fusel alcohols and most of esters by aromatic yeasts during cider fermentation. © 2015 Institute of Food Technologists®

  6. Land Surface Data Assimilation

    NASA Astrophysics Data System (ADS)

    Houser, P. R.

    2012-12-01

    Information about land surface water, energy and carbon conditions is of critical importance to real-world applications such as agricultural production, water resource management, flood prediction, water supply, weather and climate forecasting, and environmental preservation. While ground-based observational networks are improving, the only practical way to observe these land surface states on continental to global scales is via satellites. Remote sensing can make spatially comprehensive measurements of various components of the terrestrial system, but it cannot provide information on the entire system (e.g. evaporation), and the observations represent only an instant in time. Land surface process models may be used to predict temporal and spatial terrestrial dynamics, but these predictions are often poor, due to model initialization, parameter and forcing, and physics errors. Therefore, an attractive prospect is to combine the strengths of land surface models and observations (and minimize the weaknesses) to provide a superior terrestrial state estimate. This is the goal of land surface data assimilation. Data Assimilation combines observations into a dynamical model, using the model's equations to provide time continuity and coupling between the estimated fields. Land surface data assimilation aims to utilize both our land surface process knowledge, as embodied in a land surface model, and information that can be gained from observations. Both model predictions and observations are imperfect and we wish to use both synergistically to obtain a more accurate result. Moreover, both contain different kinds of information, that when used together, provide an accuracy level that cannot be obtained individually. Model biases can be mitigated using a complementary calibration and parameterization process. Limited point measurements are often used to calibrate the model(s) and validate the assimilation results. This presentation will provide a brief background on land

  7. Biosynthesis of higher alcohol flavour compounds by the yeast Saccharomyces cerevisiae: impact of oxygen availability and responses to glucose pulse in minimal growth medium with leucine as sole nitrogen source.

    PubMed

    Espinosa Vidal, Esteban; de Morais, Marcos Antonio; François, Jean Marie; de Billerbeck, Gustavo M

    2015-01-01

    Higher alcohol formation by yeast is of great interest in the field of fermented beverages. Among them, medium-chain alcohols impact greatly the final flavour profile of alcoholic beverages, even at low concentrations. It is widely accepted that amino acid metabolism in yeasts directly influences higher alcohol formation, especially the catabolism of aromatic and branched-chain amino acids. However, it is not clear how the availability of oxygen and glucose metabolism influence the final higher alcohol levels in fermented beverages. Here, using an industrial Brazilian cachaça strain of Saccharomyces cerevisiae, we investigated the effect of oxygen limitation and glucose pulse on the accumulation of higher alcohol compounds in batch cultures, with glucose (20 g/l) and leucine (9.8 g/l) as the carbon and nitrogen sources, respectively. Fermentative metabolites and CO2 /O2 balance were analysed in order to correlate the results with physiological data. Our results show that the accumulation of isoamyl alcohol by yeast is independent of oxygen availability in the medium, depending mainly on leucine, α-keto-acids and/or NADH pools. High-availability leucine experiments showed a novel and unexpected accumulation of isobutanol, active amyl alcohol and 2-phenylethanol, which could be attributed to de novo biosynthesis of valine, isoleucine and phenylalanine and subsequent outflow of these pathways. In carbon-exhausted conditions, our results also describe, for the first time, the metabolization of isoamyl alcohol, isobutanol, active amyl alcohol but not of 2-phenylethanol, by yeast strains in stationary phase, suggesting a role for these higher alcohols as carbon source for cell maintenance and/or redox homeostasis during this physiological phase. Copyright © 2014 John Wiley & Sons, Ltd.

  8. Biological limits on nitrogen use for plant photosynthesis: a quantitative revision comparing cultivated and wild species.

    PubMed

    Rotundo, José L; Cipriotti, Pablo A

    2017-04-01

    The relationship between leaf photosynthesis and nitrogen is a critical production function for ecosystem functioning. Cultivated species have been studied in terms of this relationship, focusing on improving nitrogen (N) use, while wild species have been studied to evaluate leaf evolutionary patterns. A comprehensive comparison of cultivated vs wild species for this relevant function is currently lacking. We hypothesize that cultivated species show increased carbon assimilation per unit leaf N area compared with wild species as associated with artificial selection for resource-acquisition traits. We compiled published data on light-saturated photosynthesis (A max ) and leaf nitrogen (LN area ) for cultivated and wild species. The relationship between A max and LN area was evaluated using a frontier analysis (90 th percentile) to benchmark the biological limit of nitrogen use for photosynthesis. Carbon assimilation in relation to leaf N was not consistently higher in cultivated species; out of 14 cultivated species, only wheat, rice, maize and sorghum showed higher ability to use N for photosynthesis compared with wild species. Results indicate that cultivated species have not surpassed the biological limit on nitrogen use observed for wild species. Future increases in photosynthesis based on natural variation need to be assisted by bioengineering of key enzymes to increase crop productivity. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  9. Functional indicators of response mechanisms to nitrogen deposition, ozone, and their interaction in two Mediterranean tree species

    PubMed Central

    Palma, Adriano; Salvatori, Elisabetta; Basile, Adriana; Maresca, Viviana; Asadi Karam, Elham; Manes, Fausto

    2017-01-01

    The effects of nitrogen (N) deposition, tropospheric ozone (O3) and their interaction were investigated in two Mediterranean tree species, Fraxinus ornus L. (deciduous) and Quercus ilex L. (evergreen), having different leaf habits and resource use strategies. An experiment was conducted under controlled condition to analyse how nitrogen deposition affects the ecophysiological and biochemical traits, and to explore how the nitrogen-induced changes influence the response to O3. For both factors we selected realistic exposures (20 kg N ha-1 yr-1 and 80 ppb h for nitrogen and O3, respectively), in order to elucidate the mechanisms implemented by the plants. Nitrogen addition resulted in higher nitrogen concentration at the leaf level in F. ornus, whereas a slight increase was detected in Q. ilex. Nitrogen enhanced the maximum rate of assimilation and ribulose 1,5-bisphosphate regeneration in both species, whereas it influenced the light harvesting complex only in the deciduous F. ornus that was also affected by O3 (reduced assimilation rate and accelerated senescence-related processes). Conversely, Q. ilex developed an avoidance mechanism to cope with O3, confirming a substantial O3 tolerance of this species. Nitrogen seemed to ameliorate the harmful effects of O3 in F. ornus: the hypothesized mechanism of action involved the production of nitrogen oxide as the first antioxidant barrier, followed by enzymatic antioxidant response. In Q. ilex, the interaction was not detected on gas exchange and photosystem functionality; however, in this species, nitrogen might stimulate an alternative antioxidant response such as the emission of volatile organic compounds. Antioxidant enzyme activity was lower in plants treated with both O3 and nitrogen even though reactive oxygen species production did not differ between the treatments. PMID:28973038

  10. Functional indicators of response mechanisms to nitrogen deposition, ozone, and their interaction in two Mediterranean tree species.

    PubMed

    Fusaro, Lina; Palma, Adriano; Salvatori, Elisabetta; Basile, Adriana; Maresca, Viviana; Asadi Karam, Elham; Manes, Fausto

    2017-01-01

    The effects of nitrogen (N) deposition, tropospheric ozone (O3) and their interaction were investigated in two Mediterranean tree species, Fraxinus ornus L. (deciduous) and Quercus ilex L. (evergreen), having different leaf habits and resource use strategies. An experiment was conducted under controlled condition to analyse how nitrogen deposition affects the ecophysiological and biochemical traits, and to explore how the nitrogen-induced changes influence the response to O3. For both factors we selected realistic exposures (20 kg N ha-1 yr-1 and 80 ppb h for nitrogen and O3, respectively), in order to elucidate the mechanisms implemented by the plants. Nitrogen addition resulted in higher nitrogen concentration at the leaf level in F. ornus, whereas a slight increase was detected in Q. ilex. Nitrogen enhanced the maximum rate of assimilation and ribulose 1,5-bisphosphate regeneration in both species, whereas it influenced the light harvesting complex only in the deciduous F. ornus that was also affected by O3 (reduced assimilation rate and accelerated senescence-related processes). Conversely, Q. ilex developed an avoidance mechanism to cope with O3, confirming a substantial O3 tolerance of this species. Nitrogen seemed to ameliorate the harmful effects of O3 in F. ornus: the hypothesized mechanism of action involved the production of nitrogen oxide as the first antioxidant barrier, followed by enzymatic antioxidant response. In Q. ilex, the interaction was not detected on gas exchange and photosystem functionality; however, in this species, nitrogen might stimulate an alternative antioxidant response such as the emission of volatile organic compounds. Antioxidant enzyme activity was lower in plants treated with both O3 and nitrogen even though reactive oxygen species production did not differ between the treatments.

  11. Assimilation of MLS and OMI Ozone Data

    NASA Technical Reports Server (NTRS)

    Stajner, I.; Wargan, K.; Chang, L.-P.; Hayashi, H.; Pawson, S.; Froidevaux, L.; Livesey, N.

    2005-01-01

    Ozone data from Aura Microwave Limb Sounder (MLS) and Ozone Monitoring Instrument (OMI) were assimilated into the ozone model at NASA's Global Modeling and Assimilation Office (GMAO). This assimilation produces ozone fields that are superior to those from the operational GMAO assimilation of Solar Backscatter Ultraviolet (SBUV/2) instrument data. Assimilation of Aura data improves the representation of the "ozone hole" and the agreement with independent Stratospheric Aerosol and Gas Experiment (SAGE) III and ozone sonde data. Ozone in the lower stratosphere is captured better: mean state, vertical gradients, spatial and temporal variability are all improved. Inclusion of OMI and MLS data together, or separately, in the assimilation system provides a way of checking how consistent OMI and MLS data are with each other, and with the ozone model. We found that differences between OMI total ozone column data and model forecasts decrease after MLS data are assimilated. This indicates that MLS stratospheric ozone profiles are consistent with OMI total ozone columns. The evaluation of error characteristics of OMI and MLS ozone will continue as data from newer versions of retrievals becomes available. We report on the initial step in obtaining global assimilated ozone fields that combine measurements from different Aura instruments, the ozone model at the GMAO, and their respective error characteristics. We plan to use assimilated ozone fields in estimation of tropospheric ozone. We also plan to investigate impacts of assimilated ozone fields on numerical weather prediction through their use in radiative models and in the assimilation of infrared nadir radiance data from NASA's Advanced Infrared Sounder (AIRS).

  12. Impact of Assimilation on Heavy Rainfall Simulations Using WRF Model: Sensitivity of Assimilation Results to Background Error Statistics

    NASA Astrophysics Data System (ADS)

    Rakesh, V.; Kantharao, B.

    2017-03-01

    Data assimilation is considered as one of the effective tools for improving forecast skill of mesoscale models. However, for optimum utilization and effective assimilation of observations, many factors need to be taken into account while designing data assimilation methodology. One of the critical components that determines the amount and propagation observation information into the analysis, is model background error statistics (BES). The objective of this study is to quantify how BES in data assimilation impacts on simulation of heavy rainfall events over a southern state in India, Karnataka. Simulations of 40 heavy rainfall events were carried out using Weather Research and Forecasting Model with and without data assimilation. The assimilation experiments were conducted using global and regional BES while the experiment with no assimilation was used as the baseline for assessing the impact of data assimilation. The simulated rainfall is verified against high-resolution rain-gage observations over Karnataka. Statistical evaluation using several accuracy and skill measures shows that data assimilation has improved the heavy rainfall simulation. Our results showed that the experiment using regional BES outperformed the one which used global BES. Critical thermo-dynamic variables conducive for heavy rainfall like convective available potential energy simulated using regional BES is more realistic compared to global BES. It is pointed out that these results have important practical implications in design of forecast platforms while decision-making during extreme weather events

  13. The pleiotropic transcriptional regulator NlpR contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci.

    PubMed

    Hernández, Martín A; Lara, Julia; Gago, Gabriela; Gramajo, Hugo; Alvarez, Héctor M

    2017-01-01

    The regulatory mechanisms involved in lipogenesis and triacylglycerol (TAG) accumulation are largely unknown in oleaginous rhodococci. In this study a regulatory protein (here called NlpR: Nitrogen lipid Regulator), which contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci was identified. Under nitrogen deprivation conditions, in which TAG accumulation is stimulated, the nlpR gene was significantly upregulated, whereas a significant decrease of its expression and TAG accumulation occurred when cerulenin was added. The nlpR disruption negatively affected the nitrate/nitrite reduction as well as lipid biosynthesis under nitrogen-limiting conditions. In contrast, its overexpression increased TAG production during cultivation of cells in nitrogen-rich media. A putative 'NlpR-binding motif' upstream of several genes related to nitrogen and lipid metabolisms was found. The nlpR disruption in RHA1 strain led to a reduced transcription of genes involved in nitrate/nitrite assimilation, as well as in fatty acid and TAG biosynthesis. Purified NlpR was able to bind to narK, nirD, fasI, plsC and atf3 promoter regions. It was suggested that NlpR acts as a pleiotropic transcriptional regulator by activating of nitrate/nitrite assimilation genes and others genes involved in fatty acid and TAG biosynthesis, in response to nitrogen deprivation. © 2016 John Wiley & Sons Ltd.

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

    PubMed

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

    2017-01-01

    The importance of organic nitrogen (N) for plant nutrition and productivity is increasingly being recognized. Here we show that it is not only the availability in the soil that matters, but also the effects on plant growth. The chemical form of N taken up, whether inorganic (such as nitrate) or organic (such as amino acids), may significantly influence plant shoot and root growth, and nitrogen use efficiency (NUE). We analysed these effects by synthesizing results from multiple laboratory experiments on small seedlings (Arabidopsis, poplar, pine and spruce) based on a tractable plant growth model. A key point is that the carbon cost of assimilating organic N into proteins is lower than that of inorganic N, mainly because of its carbon content. This carbon bonus makes it more beneficial for plants to take up organic than inorganic N, even when its availability to the roots is much lower - up to 70% lower for Arabidopsis seedlings. At equal growth rate, root:shoot ratio was up to three times higher and nitrogen productivity up to 20% higher for organic than inorganic N, which both are factors that may contribute to higher NUE in crop production. © 2016 The Authors Plant, Cell & Environment Published by John Wiley & Sons Ltd.

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  16. Candida xylanilytica sp. nov., a xylan-degrading yeast species isolated from Thailand.

    PubMed

    Boonmak, Chanita; Limtong, Savitree; Jindamorakot, Sasitorn; Am-In, Somjit; Yongmanitchai, Wichien; Suzuki, Ken-ichiro; Nakase, Takashi; Kawasaki, Hiroko

    2011-05-01

    Xylan is a major component of hemicellulose, which constitutes about 40 % of plant biomass. Hydrolysis of xylan into simple sugars is one of the important steps in the conversion of lignocellulosic material to value-added products. During an investigation of cellulose- and xylan-degrading yeasts, two yeast strains that were able to use cellulose and xylan as sole carbon source were found to represent a phylogenetically distinct species in the Spathaspora clade. The closest species in terms of pairwise sequence similarity in the D1/D2 domain of the LSU rRNA gene was Candida subhashii. The novel species can be distinguished from the other species in the Spathaspora clade based on the ability to assimilate methanol and raffinose, growth in medium containing 60 % glucose, and growth at 42 °C. It ferments glucose but not other carbohydrates. The name Candida xylanilytica sp. nov. is proposed for this species. The type strain is KU-Xn11(T) ( = NBRC 106499(T)  = BCC 34694(T)  = CBS 11761(T)).

  17. The environmental and intrinsic yeast diversity of Cuban cocoa bean heap fermentations.

    PubMed

    Fernández Maura, Yurelkys; Balzarini, Tom; Clapé Borges, Pablo; Evrard, Pierre; De Vuyst, Luc; Daniel, H-M

    2016-09-16

    The environmental yeast diversity of spontaneous cocoa bean fermentations in east Cuba was investigated. Seven fermentations, 25 equipment- and handling-related samples, and 115 environmental samples, such as flowers, leaf and cocoa pod surfaces, as well as drosophilid insects, were analysed. The basic fermentation parameters temperature and pH were recorded during five fermentations for at least six days. A total of 435 yeast isolates were identified by a combination of PCR-fingerprinting of genomic DNA with the M13 primer and sequence analysis of DNA from representative isolates, using the internal transcribed spacer region, the D1/D2 region of the large subunit rRNA gene, and an actin gene-encoding fragment, as required. Among 65 yeast species detected, Pichia manshurica and Hanseniaspora opuntiae were the most frequently isolated species, obtained from five and four fermentations, followed in frequency by Pichia kudriavzevii from two fermentations. Saccharomyces cerevisiae was isolated only occasionally. Cocoa fermentation yeast species were also present on processing equipment. The repeated isolation of a preliminarily as Yamadazyma sp. classified species, a group of strains similar to Saccharomycopsis crataegensis from fermentations and equipment, and the isolation of fifteen other potentially novel yeast species in low numbers provides material for further studies. Environmental samples showed higher yeast diversity compared to the fermentations, included the most frequent fermentation species, whereas the most frequently isolated environmental species were Candida carpophila, Candida conglobata, and Candida quercitrusa. Potential selective advantages of the most frequently isolated species were only partly explained by the physiological traits tested. For instance, tolerance to higher ethanol concentrations was more frequent in strains of Pichia spp. and S. cerevisiae compared to Hanseniaspora spp.; the ability to also assimilate ethanol might have

  18. Highly dynamic cellular-level response of symbiotic coral to a sudden increase in environmental nitrogen.

    PubMed

    Kopp, C; Pernice, M; Domart-Coulon, I; Djediat, C; Spangenberg, J E; Alexander, D T L; Hignette, M; Meziane, T; Meibom, A

    2013-05-14

    Metabolic interactions with endosymbiotic photosynthetic dinoflagellate Symbiodinium spp. are fundamental to reef-building corals (Scleractinia) thriving in nutrient-poor tropical seas. Yet, detailed understanding at the single-cell level of nutrient assimilation, translocation, and utilization within this fundamental symbiosis is lacking. Using pulse-chase (15)N labeling and quantitative ion microprobe isotopic imaging (NanoSIMS; nanoscale secondary-ion mass spectrometry), we visualized these dynamic processes in tissues of the symbiotic coral Pocillopora damicornis at the subcellular level. Assimilation of ammonium, nitrate, and aspartic acid resulted in rapid incorporation of nitrogen into uric acid crystals (after ~45 min), forming temporary N storage sites within the dinoflagellate endosymbionts. Subsequent intracellular remobilization of this metabolite was accompanied by translocation of nitrogenous compounds to the coral host, starting at ~6 h. Within the coral tissue, nitrogen is utilized in specific cellular compartments in all four epithelia, including mucus chambers, Golgi bodies, and vesicles in calicoblastic cells. Our study shows how nitrogen-limited symbiotic corals take advantage of sudden changes in nitrogen availability; this opens new perspectives for functional studies of nutrient storage and remobilization in microbial symbioses in changing reef environments. The methodology applied, combining transmission electron microscopy with nanoscale secondary-ion mass spectrometry (NanoSIMS) imaging of coral tissue labeled with stable isotope tracers, allows quantification and submicrometric localization of metabolic fluxes in an intact symbiosis. This study opens the way for investigations of physiological adaptations of symbiotic systems to nutrient availability and for increasing knowledge of global nitrogen and carbon biogeochemical cycling.

  19. Data Assimilation for Applied Meteorology

    NASA Astrophysics Data System (ADS)

    Haupt, S. E.

    2012-12-01

    Although atmospheric models provide a best estimate of the future state of the atmosphere, due to sensitivity to initial condition, it is difficult to predict the precise future state. For applied problems, however, users often depend on having accurate knowledge of that future state. To improve prediction of a particular realization of an evolving flow field requires knowledge of the current state of that field and assimilation of local observations into the model. This talk will consider how dynamic assimilation can help address the concerns of users of atmospheric forecasts. First, we will look at the value of assimilation for the renewable energy industry. If the industry decision makers can have confidence in the wind and solar power forecasts, they can build their power allocations around the expected renewable resource, saving money for the ratepayers as well as reducing carbon emissions. We will assess the value to that industry of assimilating local real-time observations into the model forecasts and the value that is provided. The value of the forecasts with assimilation is important on both short (several hour) to medium range (within two days). A second application will be atmospheric transport and dispersion problems. In particular, we will look at assimilation of concentration data into a prediction model. An interesting aspect of this problem is that the dynamics are a one-way coupled system, with the fluid dynamic equations affecting the concentration equation, but not vice versa. So when the observations are of the concentration, one must infer the fluid dynamics. This one-way coupled system presents a challenge: one must first infer the changes in the flow field from observations of the contaminant, then assimilate that to recover both the advecting flow and information on the subgrid processes that provide the mixing. To accomplish such assimilation requires a robust method to match the observed contaminant field to that modeled. One approach is

  20. Source Attribution of Near-surface Ozone in the Western US: Improved Estimates by TF HTAP2 Multi-model Experiment and Multi-scale Chemical Data Assimilation

    NASA Astrophysics Data System (ADS)

    Huang, M.; Bowman, K. W.; Carmichael, G. R.; Lee, M.; Park, R.; Henze, D. K.; Chai, T.; Flemming, J.; Lin, M.; Weinheimer, A. J.; Wisthaler, A.; Jaffe, D. A.

    2014-12-01

    Near-surface ozone in the western US can be sensitive to transported background pollutants from the free troposphere over the eastern Pacific, as well as various local emissions sources. Accurately estimating ozone source contributions in this region has strong policy-relevant significance as the air quality standards tend to go down. Here we improve modeled contributions from local and non-local sources to western US ozone base on the HTAP2 (Task Force on Hemispheric Transport of Air Pollution) multi-model experiment, along with multi-scale chemical data assimilation. We simulate western US air quality using the STEM regional model on a 12 km horizontal resolution grid, during the NASA ARCTAS field campaign period in June 2008. STEM simulations use time-varying boundary conditions downscaled from global GEOS-Chem model simulations. Standard GEOS-Chem simulation overall underpredicted ozone at 1-5 km in the eastern Pacific, resulting in underestimated contributions from the transported background pollutants to surface ozone inland. These negative biases can be reduced by using the output from several global models that support the HTAP2 experiment, which all ran with the HTAP2 harmonized emission inventory and also calculated the contributions from east Asian anthropogenic emissions. We demonstrate that the biases in GEOS-Chem boundary conditions can be more efficiently reduced via assimilating satellite ozone profiles from the Tropospheric Emission Spectrometer (TES) instrument using the three dimensional variational (3D-Var) approach. Base upon these TES-constrained GEOS-Chem boundary conditions, we then update regional nitrogen dioxide and isoprene emissions in STEM through the four dimensional variational (4D-Var) assimilation of the Ozone Monitoring Instrument (OMI) nitrogen dioxide columns and the NASA DC-8 aircraft isoprene measurements. The 4D-Var assimilation spatially redistributed the emissions of nitrogen oxides and isoprene from various US sources, and

  1. Towards a Comprehensive Dynamic-chemistry Assimilation for Eos-Chem: Plans and Status in NASA's Data Assimilation Office

    NASA Technical Reports Server (NTRS)

    Pawson, Steven; Lin, Shian-Jiann; Rood, Richard B.; Stajner, Ivanka; Nebuda, Sharon; Nielsen, J. Eric; Douglass, Anne R.

    2000-01-01

    In order to support the EOS-Chem project, a comprehensive assimilation package for the coupled chemical-dynamical system is being developed by the Data Assimilation Office at NASA GSFC. This involves development of a coupled chemistry/meteorology model and of data assimilation techniques for trace species and meteorology. The model is being developed using the flux-form semi-Lagrangian dynamical core of Lin and Rood, the physical parameterizations from the NCAR Community Climate Model, and atmospheric chemistry modules from the Atmospheric Chemistry and Dynamics branch at NASA GSFC. To date the following results have been obtained: (i) multi-annual simulations with the dynamics-radiation model show the credibility of the package for atmospheric simulations; (ii) initial simulations including a limited number of middle atmospheric trace gases reveal the realistic nature of transport mechanisms, although there is still a need for some improvements. Samples of these results will be shown. A meteorological assimilation system is currently being constructed using the model; this will form the basis for the proposed meteorological/chemical assimilation package. The latter part of the presentation will focus on areas targeted for development in the near and far terms, with the objective of Providing a comprehensive assimilation package for the EOS-Chem science experiment. The first stage will target ozone assimilation. The plans also encompass a reanalysis (ReSTS) for the 1991-1995 period, which includes the Mt. Pinatubo eruption and the time when a large number of UARS observations were available. One of the most challenging aspects of future developments will be to couple theoretical advances in tracer assimilation with the practical considerations of a real environment and eventually a near-real-time assimilation system.

  2. Improvement of the ammonia assimilation for enhancing L-arginine production of Corynebacterium crenatum.

    PubMed

    Guo, Jing; Man, Zaiwei; Rao, Zhiming; Xu, Meijuan; Yang, Taowei; Zhang, Xian; Xu, Zhenghong

    2017-03-01

    There are four nitrogen atoms in L-arginine molecule and the nitrogen content is 32.1%. By now, metabolic engineering for L-arginine production strain improvement was focused on carbon flux optimization. In previous work, we obtained an L-arginine-producing Corynebacterium crenatum SDNN403 (ARG) through screening and mutation breeding. In this paper, a strain engineering strategy focusing on nitrogen supply and ammonium assimilation for L-arginine production was performed. Firstly, the effects of nitrogen atom donor (L-glutamate, L-glutamine and L-aspartate) addition on L-arginine production of ARG were studied, and the addition of L-glutamine and L-aspartate was beneficial for L-arginine production. Then, the glutamine synthetase gene glnA and aspartase gene aspA from E. coli were overexpressed in ARG for increasing the L-glutamine and L-aspartate synthesis, and the L-arginine production was effectively increased. In addition, the L-glutamate supply re-emerged as a limiting factor for L-arginine biosynthesis. Finally, the glutamate dehydrogenase gene gdh was co-overexpressed for further enhancement of L-arginine production. The final strain could produce 53.2 g l -1 of L-arginine, which was increased by 41.5% compared to ARG in fed-batch fermentation.

  3. Influence of the yeast strain on the changes of the amino acids, peptides and proteins during sparkling wine production by the traditional method.

    PubMed

    Martínez-Rodríguez, A J; Carrascosa, A V; Martín-Alvarez, P J; Moreno-Arribas, V; Polo, M C

    2002-12-01

    The influence of five yeast strains on the nitrogen fractions, amino acids, peptides and proteins, during 12 months of aging of sparkling wines produced by the traditional or Champenoise method, was studied. High-performance liquid chromatography (HPLC) techniques were used for analysis of the amino acid and peptide fractions. Proteins plus polypeptides were determined by the colorimetric Bradford method. Four main stages were detected in the aging of wines with yeast. In the first stage, a second fermentation took place; amino acids and proteins plus polypeptides diminished, and peptides were liberated. In the second stage, there was a release of amino acids and proteins, and peptides were degraded. In the third stage, the release of proteins and peptides predominated. In the fourth stage, the amino acid concentration diminished. The yeast strain used influenced the content of free amino acids and peptides and the aging time in all the nitrogen fractions.

  4. A one-dimensional, steady-state, dissolved-oxygen model and waste-load assimilation study for Duck Creek, Madison, Tipton, and Hamilton counties, Indiana

    USGS Publications Warehouse

    Crawford, Charles G.; Wilber, William G.; Peters, James G.

    1980-01-01

    The Indiana State Board of Health is developing a State water-quality plan that includes establishing limits for wastewater effluents discharged into Indiana streams. A digital model calibrated to conditions in Duck Creek was used to develop alternatives for future waste loadings that would be compatible with Indiana stream water-quality standards defined for two critical hydrologic conditions, summer and winter low flows. The major point-source waste load affecting Duck Creek is the Elwood wastewater-treatment facility. Natural streamflow during the low flow is zero, so no benefit from dilution is provided. Natural reaeration at the low-flow condition (approximately 3 cubic feet per second), also low, is estimated to be less than 1 per day (base e at 20 Celsius). Consequently, the wasteload assimilative capacity of the stream is low. Effluent ammonia-nitrogen concentrations, projected by the Indiana State Board of Health, will result in stream ammonia-nitrogen concentrations that exceed the State ammonia-nitrogen toxicity standards (2.5 milligrams per liter from April to October and 4.0 milligrams per liter from November through March). The projected effluent ammonia-nitrogen load will also result in the present Indiana stream dissolved-oxygen standard (5.0 milligrams per liter) not being met. Benthic-oxygen demand may also affect stream water quality. During the summer low-flow, a benthic-oxygen demand of only 0.6 gram per square meter per day would utilize all the streams 's available assimilative capacity. (USGS)

  5. Assimilation of Satellite Ozone Observations

    NASA Technical Reports Server (NTRS)

    Stajner, I.; Winslow, N.; Wargan, K.; Hayashi, H.; Pawson, S.; Rood, R.

    2003-01-01

    This talk will discuss assimilation of ozone data from satellite-borne instruments. Satellite observations of ozone total columns and profiles have been measured by a series of Total Ozone Mapping Spectrometer (TOMS), Solar Backscatter Ultraviolet (SBUV) instruments, and more recently by the Global Ozone Monitoring Experiment. Additional profile data are provided by instruments on NASA's Upper Atmosphere Research Satellite and by occultation instruments on other platforms. Instruments on Envisat' and future EOS Aura satellite will supply even more comprehensive data about the ozone distribution. Satellite data contain a wealth of information, but they do not provide synoptic global maps of ozone fields. These maps can be obtained through assimilation of satellite data into global chemistry and transport models. In the ozone system at NASA's Data Assimilation Office (DAO) any combination of TOMS, SBUV, and Microwave Limb sounder (MLS) data can be assimilated. We found that the addition of MLS to SBUV and TOMS data in the system helps to constrain the ozone distribution, especially in the polar night region and in the tropics. The assimilated ozone distribution in the troposphere and lower stratosphere is sensitive also to finer changes in the SBUV and TOMS data selection and to changes in error covariance models. All results are established by comparisons of assimilated ozone with independent profiles from ozone sondes and occultation instruments.

  6. Plant nitrogen regulatory P-PII polypeptides

    DOEpatents

    Coruzzi, Gloria M.; Lam, Hon-Ming; Hsieh, Ming-Hsiun

    2004-11-23

    The present invention generally relates to plant nitrogen regulatory PII gene (hereinafter P-PII gene), a gene involved in regulating plant nitrogen metabolism. The invention provides P-PII nucleotide sequences, expression constructs comprising said nucleotide sequences, and host cells and plants having said constructs and, optionally expressing the P-PII gene from said constructs. The invention also provides substantially pure P-PII proteins. The P-PII nucleotide sequences and constructs of the invention may be used to engineer organisms to overexpress wild-type or mutant P-PII regulatory protein. Engineered plants that overexpress or underexpress P-PII regulatory protein may have increased nitrogen assimilation capacity. Engineered organisms may be used to produce P-PII proteins which, in turn, can be used for a variety of purposes including in vitro screening of herbicides. P-PII nucleotide sequences have additional uses as probes for isolating additional genomic clones having the promoters of P-PII gene. P-PII promoters are light- and/or sucrose-inducible and may be advantageously used in genetic engineering of plants.

  7. The role of glutamine synthetase and glutamate dehydrogenase in nitrogen assimilation and possibilities for improvement in the nitrogen utilization of crops.

    PubMed

    Miflin, Ben J; Habash, Dimah Z

    2002-04-01

    This short review outlines the central role of glutamine synthetase (GS) in plant nitrogen metabolism and discusses some possibilities for crop improvement. GS functions as the major assimilatory enzyme for ammonia produced from N fixation, and nitrate or ammonia nutrition. It also reassimilates ammonia released as a result of photorespiration and the breakdown of proteins and nitrogen transport compounds. GS is distributed in different subcellular locations (chloroplast and cytoplasm) and in different tissues and organs. This distribution probably changes as a function of the development of the tissue, for example, GS1 appears to play a key role in leaf senescence. The enzyme is the product of multiple genes with complex promoters that ensure the expression of the genes in an organ- and tissue-specific manner and in response to a number of environmental variables affecting the nutritional status of the cell. GS activity is also regulated post-translationally in a manner that involves 14-3-3 proteins and phosphorylation. GS and plant nitrogen metabolism is best viewed as a complex matrix continually changing during the development cycle of plants. Along with GS, a number of other enzymes play key roles in maintaining the balance of carbon and nitrogen. It is proposed that one of these is glutamate dehydrogenase (GDH). There is considerable evidence for a GDH shunt to return the carbon in amino acids back into reactions of carbon metabolism and the tri-carboxylic acid cycle. Results with transgenic plants containing transferred GS genes suggest that there may be ways in which it is possible to improve the efficiency with which crop plants use nitrogen. Marker-assisted breeding may also bring about such improvements.

  8. Effects of Nitrogen Fertilization on Synthesis of Primary and Secondary Metabolites in Three Varieties of Kacip Fatimah (Labisia Pumila Blume)

    PubMed Central

    Ibrahim, Mohd Hafiz; Jaafar, Hawa Z.E.; Rahmat, Asmah; Rahman, Zaharah Abdul

    2011-01-01

    A split plot 3 by 4 experiment was designed to examine the impact of 15-week variable levels of nitrogen fertilization (0, 90, 180 and 270 kg N/ha) on the characteristics of total flavonoids (TF), total phenolics (TP), total non structurable carbohydrate (TNC), net assimilation rate, leaf chlorophyll content, carbon to nitrogen ratio (C/N), phenyl alanine lyase activity (PAL) and protein content, and their relationships, in three varieties of Labisia pumila Blume (alata, pumila and lanceolata). The treatment effects were solely contributed by nitrogen application; there was neither varietal nor interaction effect observed. As nitrogen levels increased from 0 to 270 kg N/ha, the production of TNC was found to decrease steadily. Production of TF and TP reached their peaks under 0 followed by 90, 180 and 270 kg N/ha treatment. However, net assimilation rate was enhanced as nitrogen fertilization increased from 0 to 270 kg N/ha. The increase in production of TP and TF under low nitrogen levels (0 and 90 kg N/ha) was found to be correlated with enhanced PAL activity. The enhancement in PAL activity was followed by reduction in production of soluble protein under low nitrogen fertilization indicating more availability of amino acid phenyl alanine (phe) under low nitrogen content that stimulate the production of carbon based secondary metabolites (CBSM). The latter was manifested by high C/N ratio in L. pumila plants. PMID:21954355

  9. Methodological Developments in Geophysical Assimilation Modeling

    NASA Astrophysics Data System (ADS)

    Christakos, George

    2005-06-01

    This work presents recent methodological developments in geophysical assimilation research. We revisit the meaning of the term "solution" of a mathematical model representing a geophysical system, and we examine its operational formulations. We argue that an assimilation solution based on epistemic cognition (which assumes that the model describes incomplete knowledge about nature and focuses on conceptual mechanisms of scientific thinking) could lead to more realistic representations of the geophysical situation than a conventional ontologic assimilation solution (which assumes that the model describes nature as is and focuses on form manipulations). Conceptually, the two approaches are fundamentally different. Unlike the reasoning structure of conventional assimilation modeling that is based mainly on ad hoc technical schemes, the epistemic cognition approach is based on teleologic criteria and stochastic adaptation principles. In this way some key ideas are introduced that could open new areas of geophysical assimilation to detailed understanding in an integrated manner. A knowledge synthesis framework can provide the rational means for assimilating a variety of knowledge bases (general and site specific) that are relevant to the geophysical system of interest. Epistemic cognition-based assimilation techniques can produce a realistic representation of the geophysical system, provide a rigorous assessment of the uncertainty sources, and generate informative predictions across space-time. The mathematics of epistemic assimilation involves a powerful and versatile spatiotemporal random field theory that imposes no restriction on the shape of the probability distributions or the form of the predictors (non-Gaussian distributions, multiple-point statistics, and nonlinear models are automatically incorporated) and accounts rigorously for the uncertainty features of the geophysical system. In the epistemic cognition context the assimilation concept may be used to

  10. Coupled assimilation for an intermediated coupled ENSO prediction model

    NASA Astrophysics Data System (ADS)

    Zheng, Fei; Zhu, Jiang

    2010-10-01

    The value of coupled assimilation is discussed using an intermediate coupled model in which the wind stress is the only atmospheric state which is slavery to model sea surface temperature (SST). In the coupled assimilation analysis, based on the coupled wind-ocean state covariance calculated from the coupled state ensemble, the ocean state is adjusted by assimilating wind data using the ensemble Kalman filter. As revealed by a series of assimilation experiments using simulated observations, the coupled assimilation of wind observations yields better results than the assimilation of SST observations. Specifically, the coupled assimilation of wind observations can help to improve the accuracy of the surface and subsurface currents because the correlation between the wind and ocean currents is stronger than that between SST and ocean currents in the equatorial Pacific. Thus, the coupled assimilation of wind data can decrease the initial condition errors in the surface/subsurface currents that can significantly contribute to SST forecast errors. The value of the coupled assimilation of wind observations is further demonstrated by comparing the prediction skills of three 12-year (1997-2008) hindcast experiments initialized by the ocean-only assimilation scheme that assimilates SST observations, the coupled assimilation scheme that assimilates wind observations, and a nudging scheme that nudges the observed wind stress data, respectively. The prediction skills of two assimilation schemes are significantly better than those of the nudging scheme. The prediction skills of assimilating wind observations are better than assimilating SST observations. Assimilating wind observations for the 2007/2008 La Niña event triggers better predictions, while assimilating SST observations fails to provide an early warning for that event.

  11. Yeast Based Sensors

    NASA Astrophysics Data System (ADS)

    Shimomura-Shimizu, Mifumi; Karube, Isao

    Since the first microbial cell sensor was studied by Karube et al. in 1977, many types of yeast based sensors have been developed as analytical tools. Yeasts are known as facultative anaerobes. Facultative anaerobes can survive in both aerobic and anaerobic conditions. The yeast based sensor consisted of a DO electrode and an immobilized omnivorous yeast. In yeast based sensor development, many kinds of yeast have been employed by applying their characteristics to adapt to the analyte. For example, Trichosporon cutaneum was used to estimate organic pollution in industrial wastewater. Yeast based sensors are suitable for online control of biochemical processes and for environmental monitoring. In this review, principles and applications of yeast based sensors are summarized.

  12. Mineral nitrogen sources differently affect root glutamine synthetase isoforms and amino acid balance among organs in maize.

    PubMed

    Prinsi, Bhakti; Espen, Luca

    2015-04-03

    Glutamine synthetase (GS) catalyzes the first step of nitrogen assimilation in plant cell. The main GS are classified as cytosolic GS1 and plastidial GS2, of which the functionality is variable according to the nitrogen sources, organs and developmental stages. In maize (Zea mays L.) one gene for GS2 and five genes for GS1 subunits are known, but their roles in root metabolism are not yet well defined. In this work, proteomic and biochemical approaches have been used to study root GS enzymes and nitrogen assimilation in maize plants re-supplied with nitrate, ammonium or both. The plant metabolic status highlighted the relevance of root system in maize nitrogen assimilation during both nitrate and ammonium nutrition. The analysis of root proteomes allowed a study to be made of the accumulation and phosphorylation of six GS proteins. Three forms of GS2 were identified, among which only the phosphorylated one showed an accumulation trend consistent with plastidial GS activity. Nitrogen availabilities enabled increments in root total GS synthetase activity, associated with different GS1 isoforms according to the nitrogen sources. Nitrate nutrition induced the specific accumulation of GS1-5 while ammonium led to up-accumulation of both GS1-1 and GS1-5, highlighting co-participation. Moreover, the changes in thermal sensitivity of root GS transferase activity suggested differential rearrangements of the native enzyme. The amino acid accumulation and composition in roots, xylem sap and leaves deeply changed in response to mineral sources. Glutamine showed the prevalent changes in all nitrogen nutritions. Besides, the ammonium nutrition was associated with an accumulation of asparagine and reducing sugars and a drop in glutamic acid level, significantly alleviated by the co-provision with nitrate. This work provides new information about the multifaceted regulation of the GS enzyme in maize roots, indicating the involvement of specific isoenzymes/isoforms, post

  13. User's Guide - WRF Lightning Assimilation

    EPA Pesticide Factsheets

    This document describes how to run WRF with the lightning assimilation technique described in Heath et al. (2016). The assimilation method uses gridded lightning data to trigger and suppress sub-grid deep convection in Kain-Fritsch.

  14. Herbicide glufosinate inhibits yeast growth and extends longevity during wine fermentation.

    PubMed

    Vallejo, Beatriz; Picazo, Cecilia; Orozco, Helena; Matallana, Emilia; Aranda, Agustín

    2017-09-29

    Glufosinate ammonium (GA) is a widely used herbicide that inhibits glutamine synthetase. This inhibition leads to internal amino acid starvation which, in turn, causes the activation of different nutrient sensing pathways. GA also inhibits the enzyme of the yeast Saccharomyces cerevisiae in such a way that, although it is not used as a fungicide, it may alter yeast performance in industrial processes like winemaking. We describe herein how GA indeed inhibits the yeast growth of a wine strain during the fermentation of grape juice. In turn, GA extends longevity in a variety of growth media. The biochemical analysis indicates that GA partially inhibits the nutrient sensing TORC1 pathway, which may explain these phenotypes. The GCN2 kinase mutant is hypersensitive to GA. Hence the control of translation and amino acid biosynthesis is required to also deal with the damaging effects of this pesticide. A global metabolomics analysis under winemaking conditions indicated that an increase in amino acid and in polyamines occurred. In conclusion, GA affects many different biochemical processes during winemaking, which provides us with some insights into both the effect of this herbicide on yeast physiology and into the relevance of the metabolic step for connecting nitrogen and carbon metabolism.

  15. Ste12/Fab1 phosphatidylinositol-3-phosphate 5-kinase is required for nitrogen-regulated mitotic commitment and cell size control

    PubMed Central

    Schauries, Marie; Kaczmarek, Adrian; Franz-Wachtel, Mirita; Du, Wei; Krug, Karsten; Maček, Boris; Petersen, Janni

    2017-01-01

    Tight coupling of cell growth and cell cycle progression enable cells to adjust their rate of division, and therefore size, to the demands of proliferation in varying nutritional environments. Nutrient stress promotes inhibition of Target Of Rapamycin Complex 1 (TORC1) activity. In fission yeast, reduced TORC1 activity advances mitotic onset and switches growth to a sustained proliferation at reduced cell size. A screen for mutants, that failed to advance mitosis upon nitrogen stress, identified a mutant in the PIKFYVE 1-phosphatidylinositol-3-phosphate 5-kinase fission yeast homolog Ste12. Ste12PIKFYVE deficient mutants were unable to advance the cell cycle to reduce cell size after a nitrogen downshift to poor nitrogen (proline) growth conditions. While it is well established that PI(3,5)P2 signalling is required for autophagy and that Ste12PIKFYVE mutants have enlarged vacuoles (yeast lysosomes), neither a block to autophagy or mutants that independently have enlarged vacuoles had any impact upon nitrogen control of mitotic commitment. The addition of rapamycin to Ste12PIKFYVE deficient mutants reduced cell size at division to suggest that Ste12PIKFYVE possibly functions upstream of TORC1. ste12 mutants display increased Torin1 (TOR inhibitor) sensitivity. However, no major impact on TORC1 or TORC2 activity was observed in the ste12 deficient mutants. In summary, Ste12PIKFYVE is required for nitrogen-stress mediated advancement of mitosis to reduce cell size at division. PMID:28273166

  16. Organic and Inorganic Nitrogen Impact Chlorella variabilis Productivity and Host Quality for Viral Production and Cell Lysis.

    PubMed

    Cheng, Yu-Shen; Labavitch, John; VanderGheynst, Jean S

    2015-05-01

    Microalgae have been proposed as a potential feedstock for biofuel production; however, cell disruption is usually required for collection and utilization of cytoplasmic polysaccharides and lipids. Virus infection might be one approach to disrupt the cell wall. The concentration of yeast extract and presence of KNO3 in algae cultivation media were investigated to observe their effects on Chlorella variabilis NC64A physiology and composition and the subsequent effect on production of Chlorella virus and disruption of infected cells. Cytoplasmic starch accumulation increased from 5% to approximately 35% of the total dry weight when yeast extract decreased from 1 to 0.25 g L(-1). When cells were cultured with the lowest nitrogen levels, the total polysaccharide accounted for more than 50% of the cell wall, which was 1.7 times higher than the content in cells cultured with the highest nitrogen levels. The C/N ratio of the algal biomass decreased by a factor of approximately 2 when yeast extract increased from 0.25 to 1 g L(-1). After virus infection, cells with a low C/N ratio produced a 7.6 times higher burst size than cells with a high C/N ratio, suggesting that the nitrogen content in C. variabilis has a large influence on viral production and cell lysis. The results have implications on management of nitrogen for both the synthesis of products from algae and product recovery via viral lysis.

  17. Genetic variations in ARE1 mediate grain yield by modulating nitrogen utilization in rice.

    PubMed

    Wang, Qing; Nian, Jinqiang; Xie, Xianzhi; Yu, Hong; Zhang, Jian; Bai, Jiaoteng; Dong, Guojun; Hu, Jiang; Bai, Bo; Chen, Lichao; Xie, Qingjun; Feng, Jian; Yang, Xiaolu; Peng, Juli; Chen, Fan; Qian, Qian; Li, Jiayang; Zuo, Jianru

    2018-02-21

    In crops, nitrogen directly determines productivity and biomass. However, the improvement of nitrogen utilization efficiency (NUE) is still a major challenge in modern agriculture. Here, we report the characterization of are1, a genetic suppressor of a rice fd-gogat mutant defective in nitrogen assimilation. ARE1 is a highly conserved gene, encoding a chloroplast-localized protein. Loss-of-function mutations in ARE1 cause delayed senescence and result in 10-20% grain yield increases, hence enhance NUE under nitrogen-limiting conditions. Analysis of a panel of 2155 rice varieties reveals that 18% indica and 48% aus accessions carry small insertions in the ARE1 promoter, which result in a reduction in ARE1 expression and an increase in grain yield under nitrogen-limiting conditions. We propose that ARE1 is a key mediator of NUE and represents a promising target for breeding high-yield cultivars under nitrogen-limiting condition.

  18. Candida wancherniae sp. nov. and Candida morakotiae sp. nov., two novel ascomycetous anamorphic yeast species found in Thailand.

    PubMed

    Nakase, Takashi; Jindamorakot, Sasitorn; Ninomiya, Shinya; Imanishi, Yumi; Kawasaki, Hiroko

    2009-04-01

    Seven yeast strains isolated from natural substrates of Thailand were found to represent two novel species of Candida, an ascomycetous anamorphic genus. Three strains, ST-233, ST-259 and ST-260, isolated from insect frass and plant leaves were found to represent a single novel species related to Metschnikowia agaves in a tree based on the D1/D2 domain sequences of the 26S rRNA genes. This species is clearly discriminated from M. agaves by the carbon assimilation patterns and required vitamins. The remaining four strains, ST-18, ST-261, ST-606 and ST-658, isolated from the fruit body of a mushroom, insect frass, decayed jack fruit and an unidentified flower, were found to represent a single species which is related to Candida corydali, a recently described insect-associated species, in a neighbor-joining tree based on the D1/D2 sequences. This species is clearly discriminated from C. corydali by the ability to assimilate propane-1,2-diol and the inability to assimilate glucono-delta-lactone. They are described as Candida wancherniae sp. nov. and Candida morakotiae sp. nov., respectively.

  19. Soluble carbohydrate allocation to roots, photosynthetic rate of leaves, and nitrate assimilation as affected by nitrogen stress and irradiance

    NASA Technical Reports Server (NTRS)

    Henry, L. T.; Raper, C. D. Jr

    1991-01-01

    Upon resupply of exogenous nitrogen to nitrogen-stressed plants, uptake rate of nitrogen is enhanced relative to nonstressed plants. Absorption of nitrogen presumably is dependent on availability of carbohydrates in the roots. A buildup in soluble carbohydrates thus should occur in roots of nitrogen-stressed plants, and upon resupply of exogenous nitrogen the increased uptake rate should be accompanied by a rapid decline in carbohydrates to prestress levels. To evaluate this relationship, three sets of tobacco plants growing in a complete hydroponic solution containing 1.0 mM NO3- were either continued in the complete solution for 21 d, transferred to a minus-nitrogen solution for 21 d, or transferred to a minus-nitrogen solution for 8-9 d and then returned to the 1.0 mM NO3- solution. These nitrogen treatments were imposed upon plants growing at photosynthetic photon flux densities of 700 and 350 micromoles m-2 s-1. Soluble carbohydrate levels in roots increased during onset of nitrogen stress to levels that were fourfold greater than in roots of non-stressed plants. Following resupply of external nitrogen, a rapid resumption of nitrogen uptake was accompanied by a decline in soluble carbohydrates in roots to levels characteristic of nonstressed plants. This pattern of soluble carbohydrate levels in roots during onset of and recovery from nitrogen stress occurred at both irradiance levels. The response of net photosynthetic rate to nitrogen stress could be expressed as a nonlinear function of concentration of reduced nitrogen in leaves. The net photosynthetic rate at a given concentration of reduced nitrogen, however, averaged 10% less at the lower than at the higher irradiance. The decline in net photosynthetic rate per unit of reduced nitrogen in leaves at the lower irradiance was accompanied by an increase in the nitrate fraction of total nitrogen in leaves from 20% at the higher irradiance to 38% at the lower irradiance.

  20. Salinity Effects on Photosynthesis, Carbon Allocation, and Nitrogen Assimilation in the Red Alga, Gelidium coulteri1

    PubMed Central

    Macler, Bruce A.

    1988-01-01

    The long-term effects of altered salinities on the physiology of the intertidal red alga Gelidium coulteri Harv. were assessed. Plants were transfered from 30 grams per liter salinity to media with salinities from 0 to 50 grams per liter. Growth rate, agar, photosynthesis, respiration, and various metabolites were quantified after 5 days and 5 weeks adaptation. After 5 days, growth rates were lower for plants at all altered salinities. Growth rates recovered from these values with 5 weeks adaptation, except for salinities of 10 grams per liter and below, where tissues bleached and died. Photosynthetic O2 evolution was lower than control values at both higher and lower salinities after 5 days and did not change over time. Carbon fixation at the altered salinities was unchanged after 5 days, but decreased below 25 grams per liter and above 40 grams per liter after 5 weeks. Respiration increased at lower salinities. Phycobili-protein and chlorophyll were lower for all altered salinities after 5 days. These decreases continued at lower salinities, then were stable after 5 weeks. Chlorophyll recovered over time at higher salinities. Decreases in protein at lower salinities were quantitatively attributable to phycobili-protein loss. Total N levels and C:N ratios were nearly constant across all salinities tested. Carbon flow into glutamate and aspartate decreased with both decreasing and increasing salinities. Glycine, serine, and glycolate levels increased with both increasing and decreasing salinity, indicating a stimulation of photorespiration. The cell wall component agar increased with decreasing salinity, although biosynthesis was inhibited at both higher and lower salinities. The storage compound floridoside increased with increasing salinity. The evidence suggests stress responses to altered salinities that directly affected photosynthesis, respiration, and nitrogen assimilation and indirectly affected photosynthate flow. At low salinities, respiration and

  1. Manganese nanoparticles: impact on non-nodulated plant as a potent enhancer in nitrogen metabolism and toxicity study both in vivo and in vitro.

    PubMed

    Pradhan, Saheli; Patra, Prasun; Mitra, Shouvik; Dey, Kushal Kumar; Jain, Sneha; Sarkar, Samapd; Roy, Shuvrodeb; Palit, Pratip; Goswami, Arunava

    2014-09-03

    Mung bean plants were grown under controlled conditions and supplemented with macro- and micronutrients. The objective of this study was to determine the response of manganese nanoparticles (MnNP) in nitrate uptake, assimilation, and metabolism compared with the commercially used manganese salt, manganese sulfate (MS). MnNP was modulated to affect the assimilatory process by enhancing the net flux of nitrogen assimilation through NR-NiR and GS-GOGAT pathways. This study was associated with toxicological investigation on in vitro and in vivo systems to promote MnNP as nanofertilizer and can be used as an alternative to MS. MnNP did not impart any toxicity to the mice brain mitochondria except in the partial inhibition of complex II-III activity in ETC. Therefore, mitochondrial dysfunction and neurotoxicity, which were noted by excess usage of elemental manganese, were prevented. This is the first attempt to highlight the nitrogen uptake, assimilation, and metabolism in a plant system using a nanoparticle to promote a biosafe nanomicronutrient-based crop management.

  2. Role of Nitrogen and Carbon Transport, Regulation, and Metabolism Genes for Saccharomyces cerevisiae Survival In Vivo†

    PubMed Central

    Kingsbury, Joanne M.; Goldstein, Alan L.; McCusker, John H.

    2006-01-01

    Saccharomyces cerevisiae is both an emerging opportunistic pathogen and a close relative of pathogenic Candida species. To better understand the ecology of fungal infection, we investigated the importance of pathways involved in uptake, metabolism, and biosynthesis of nitrogen and carbon compounds for survival of a clinical S. cerevisiae strain in a murine host. Potential nitrogen sources in vivo include ammonium, urea, and amino acids, while potential carbon sources include glucose, lactate, pyruvate, and fatty acids. Using mutants unable to either transport or utilize these compounds, we demonstrated that no individual nitrogen source was essential, while glucose was the most significant primary carbon source for yeast survival in vivo. Hydrolysis of the storage carbohydrate glycogen made a slight contribution for in vivo survival compared with a substantial requirement for trehalose hydrolysis. The ability to sense and respond to low glucose concentrations was also important for survival. In contrast, there was little or no requirement in vivo in this assay for any of the nitrogen-sensing pathways, nitrogen catabolite repression, the ammonium- or amino acid-sensing pathways, or general control. By using auxotrophic mutants, we found that some nitrogenous compounds (polyamines, methionine, and lysine) can be acquired from the host, while others (threonine, aromatic amino acids, isoleucine, and valine) must be synthesized by the pathogen. Our studies provide insights into the yeast-host environment interaction and identify potential antifungal drug targets. PMID:16682459

  3. Assimilation of Gridded GRACE Terrestrial Water Storage Estimates in the North American Land Data Assimilation System

    NASA Technical Reports Server (NTRS)

    Kumar, Sujay V.; Zaitchik, Benjamin F.; Peters-Lidard, Christa D.; Rodell, Matthew; Reichle, Rolf; Li, Bailing; Jasinski, Michael; Mocko, David; Getirana, Augusto; De Lannoy, Gabrielle; hide

    2016-01-01

    The objective of the North American Land Data Assimilation System (NLDAS) is to provide best available estimates of near-surface meteorological conditions and soil hydrological status for the continental United States. To support the ongoing efforts to develop data assimilation (DA) capabilities for NLDAS, the results of Gravity Recovery and Climate Experiment (GRACE) DA implemented in a manner consistent with NLDAS development are presented. Following previous work, GRACE terrestrial water storage (TWS) anomaly estimates are assimilated into the NASA Catchment land surface model using an ensemble smoother. In contrast to many earlier GRACE DA studies, a gridded GRACE TWS product is assimilated, spatially distributed GRACE error estimates are accounted for, and the impact that GRACE scaling factors have on assimilation is evaluated. Comparisons with quality-controlled in situ observations indicate that GRACE DA has a positive impact on the simulation of unconfined groundwater variability across the majority of the eastern United States and on the simulation of surface and root zone soil moisture across the country. Smaller improvements are seen in the simulation of snow depth, and the impact of GRACE DA on simulated river discharge and evapotranspiration is regionally variable. The use of GRACE scaling factors during assimilation improved DA results in the western United States but led to small degradations in the eastern United States. The study also found comparable performance between the use of gridded and basin averaged GRACE observations in assimilation. Finally, the evaluations presented in the paper indicate that GRACE DA can be helpful in improving the representation of droughts.

  4. Anaerobic Carbon Metabolism by the Tricarboxylic Acid Cycle : Evidence for Partial Oxidative and Reductive Pathways during Dark Ammonium Assimilation.

    PubMed

    Vanlerberghe, G C; Horsey, A K; Weger, H G; Turpin, D H

    1989-12-01

    Nitrogen-limited cells of Selenastrum minutum (Naeg.) Collins are able to assimilate NH(4) (+) in the dark under anaerobic conditions. Addition of NH(4) (+) to anaerobic cells results in a threefold increase in tricarboxylic acid cycle (TCAC) CO(2) efflux and an eightfold increase in the rate of anaplerotic carbon fixation via phosphoenolpyruvate carboxylase. Both of these observations are consistent with increased TCAC carbon flow to supply intermediates for amino acid biosynthesis. Addition of H(14)CO(3) (-) to anaerobic cells assimilating NH(4) (+) results in the incorporation of radiolabel into the alpha-carboxyl carbon of glutamic acid. Incorporation of radiolabel into glutamic acid is not simply a short-term phenomenon following NH(4) (+) addition as the specific activity of glutamic acid increases over time. This indicates that this alga is able to maintain partial oxidative TCAC carbon flow while under anoxia to supply alpha-ketoglutarate for glutamate production. During dark aerobic NH(4) (+) assimilation, no radiolabel appears in fumarate or succinate and only a small amount occurs in malate. During anaerobic NH(4) (+) assimilation, these metabolites contain a large proportion of the total radiolabel and radiolabel accumulates in succinate over time. Also, the ratio of dark carbon fixation to NH(4) (+) assimilation is much higher under anaerobic than aerobic conditions. These observations suggest the operation of a partial reductive TCAC from oxaloacetic acid to malate, fumarate, and succinate. Such a pathway might contribute to redox balance in an anaerobic cell maintaining partial oxidative TCAC activity.

  5. Extracellular Polysaccharides Produced by Yeasts and Yeast-Like Fungi

    NASA Astrophysics Data System (ADS)

    van Bogaert, Inge N. A.; de Maeseneire, Sofie L.; Vandamme, Erick J.

    Several yeasts and yeast-like fungi are known to produce extracellular polysaccharides. Most of these contain D-mannose, either alone or in combination with other sugars or phosphate. A large chemical and structural variability is found between yeast species and even among different strains. The types of polymers that are synthesized can be chemically characterized as mannans, glucans, phosphoman-nans, galactomannans, glucomannans and glucuronoxylomannans. Despite these differences, almost all of the yeast exopolysaccharides display some sort of biological activity. Some of them have already applications in chemistry, pharmacy, cosmetics or as probiotic. Furthermore, some yeast exopolysaccharides, such as pullulan, exhibit specific physico-chemical and rheological properties, making them useful in a wide range of technical applications. A survey is given here of the production, the characteristics and the application potential of currently well studied yeast extracellular polysaccharides.

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

    NASA Technical Reports Server (NTRS)

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

    2007-01-01

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

  7. Yeast Infection (Vaginal)

    MedlinePlus

    Yeast infection (vaginal) Overview A vaginal yeast infection is a fungal infection that causes irritation, discharge and intense itchiness ... symptoms Causes The fungus candida causes a vaginal yeast infection. Your vagina naturally contains a balanced mix of yeast, including ...

  8. Overview of Chinese GRAPES Data Assimilation System

    NASA Astrophysics Data System (ADS)

    Liu, Yan

    2017-04-01

    The development of data assimilation system of Global and Regional Assimilation and Prediction System (GRAPES in short) which is Chinese new generation operational numerical weather prediction system completed in recent years is reviewed in this paper, including the design scheme and main characteristics. GRAPES adopts the variational approach with stresses at application of various remote sensing observational data. Its development path is from three dimensional to four dimensional assimilation. It may be implemented with limited area or global configurations. The three dimensional variational data assimilation systems have been operational in the national and a few of regional meteorological centers. The global four dimensional assimilation system is in pre-operational experiments, and will be upgraded. After a brief introduction to the GRAPES data assimilation system, results of a series of validations of GRAPES analyses against the observation data and analyses derived from other operational NWP center to assess its performance are presented.

  9. Data Assimilation Results from PLASMON

    NASA Astrophysics Data System (ADS)

    Jorgensen, A. M.; Lichtenberger, J.; Duffy, J.; Friedel, R. H.; Clilverd, M.; Heilig, B.; Vellante, M.; Manninen, J. K.; Raita, T.; Rodger, C. J.; Collier, A.; Reda, J.; Holzworth, R. H.; Ober, D. M.; Boudouridis, A.; Zesta, E.; Chi, P. J.

    2013-12-01

    VLF and magnetometer observations can be used to remotely sense the plasmasphere. VLF whistler waves can be used to measure the electron density and magnetic Field Line Resonance (FLR) measurements can be used to measure the mass density. In principle it is then possible to remotely map the plasmasphere with a network of ground-based stations which are also less expensive and more permanent than satellites. The PLASMON project, funded by the EU FP-7 program, is in the process of doing just this. A large number of ground-based observations will be input into a data assimilative framework which models the plasmasphere structure and dynamics. The data assimilation framework combines the Ensemble Kalman Filter with the Dynamic Global Core Plasma Model. In this presentation we will describe the plasmasphere model, the data assimilation approach that we have taken, PLASMON data and data assimilation results for specific events.

  10. Evaluation of Different Yeast Species for Improving In vitro Fermentation of Cereal Straws

    PubMed Central

    Wang, Zuo; He, Zhixiong; Beauchemin, Karen A.; Tang, Shaoxun; Zhou, Chuanshe; Han, Xuefeng; Wang, Min; Kang, Jinhe; Odongo, Nicholas E.; Tan, Zhiliang

    2016-01-01

    Information on the effects of different yeast species on ruminal fermentation is limited. This experiment was conducted in a 3×4 factorial arrangement to explore and compare the effects of addition of three different live yeast species (Candida utilis 1314, Saccharomyces cerevisiae 1355, and Candida tropicalis 1254) at four doses (0, 0.25×107, 0.50×107, and 0.75×107 colony-forming unit [cfu]) on in vitro gas production kinetics, fiber degradation, methane production and ruminal fermentation characteristics of maize stover, and rice straw by mixed rumen microorganisms in dairy cows. The maximum gas production (Vf), dry matter disappearance (IVDMD), neutral detergent fiber disappearance (IVNDFD), and methane production in C. utilis group were less (p<0.01) than other two live yeast supplemented groups. The inclusion of S. cerevisiae reduced (p<0.01) the concentrations of ammonia nitrogen (NH3-N), isobutyrate, and isovalerate compared to the other two yeast groups. C. tropicalis addition generally enhanced (p<0.05) IVDMD and IVNDFD. The NH3-N concentration and CH4 production were increased (p<0.05) by the addition of S. cerevisiae and C. tropicalis compared with the control. Supplementation of three yeast species decreased (p<0.05) or numerically decreased the ratio of acetate to propionate. The current results indicate that C. tropicalis is more preferred as yeast culture supplements, and its optimal dose should be 0.25×107 cfu/500 mg substrates in vitro. PMID:26732448

  11. The Ustilago maydis Nit2 Homolog Regulates Nitrogen Utilization and Is Required for Efficient Induction of Filamentous Growth

    PubMed Central

    Horst, Robin J.; Zeh, Christine; Saur, Alexandra; Sonnewald, Sophia; Sonnewald, Uwe

    2012-01-01

    Nitrogen catabolite repression (NCR) is a regulatory strategy found in microorganisms that restricts the utilization of complex and unfavored nitrogen sources in the presence of favored nitrogen sources. In fungi, this concept has been best studied in yeasts and filamentous ascomycetes, where the GATA transcription factors Gln3p and Gat1p (in yeasts) and Nit2/AreA (in ascomycetes) constitute the main positive regulators of NCR. The reason why functional Nit2 homologs of some phytopathogenic fungi are required for full virulence in their hosts has remained elusive. We have identified the Nit2 homolog in the basidiomycetous phytopathogen Ustilago maydis and show that it is a major, but not the exclusive, positive regulator of nitrogen utilization. By transcriptome analysis of sporidia grown on artificial media devoid of favored nitrogen sources, we show that only a subset of nitrogen-responsive genes are regulated by Nit2, including the Gal4-like transcription factor Ton1 (a target of Nit2). Ustilagic acid biosynthesis is not under the control of Nit2, while nitrogen starvation-induced filamentous growth is largely dependent on functional Nit2. nit2 deletion mutants show the delayed initiation of filamentous growth on maize leaves and exhibit strongly compromised virulence, demonstrating that Nit2 is required to efficiently initiate the pathogenicity program of U. maydis. PMID:22247264

  12. Chitosan inactivates spoilage yeasts but enhances survival of Escherichia coli O157:H7 in apple juice.

    PubMed

    Kiskó, G; Sharp, R; Roller, S

    2005-01-01

    To develop new measures for controlling both spoilage and pathogenic micro-organisms in unpasteurized apple juice using chitosan. Micro-organisms were isolated and identified from apple juice treated or untreated with chitosan using enrichment, selective media, microscopy, substrate assimilation patterns and ribosomal DNA profiling. Chitosan (0.05-0.1%) delayed spoilage by yeasts at 25 degrees C for up to 12 days but the effect was species specific: Kloeckera apiculata and Metschnikowia pulcherrima were inactivated but Saccharomyces cerevisiae and Pichia spp. multiplied slowly. In challenge experiments at 25 degrees C, total yeast counts were 3-5 log CFU ml(-1) lower in chitosan-treated juices than in the controls for 4 days but the survival of Escherichia coli O157:H7 was extended from 1 to 2 days; at 4 degrees C, chitosan reduced the yeast counts by 2-3 log CFU ml(-1) for up to 10 days but survival of the pathogen was prolonged from 3 to 5 days. The survival of Salmonella enterica serovar Typhimurium was unaffected by chitosan at either temperature. The addition of chitosan to apple juice delayed spoilage by yeasts but enhanced the survival of E. coli O157:H7. The results suggest that the use of chitosan in the treatment of fruit juices may potentially lead to an increased risk of food poisoning from E. coli O157:H7.

  13. Skill Assessment in Ocean Biological Data Assimilation

    NASA Technical Reports Server (NTRS)

    Gregg, Watson W.; Friedrichs, Marjorie A. M.; Robinson, Allan R.; Rose, Kenneth A.; Schlitzer, Reiner; Thompson, Keith R.; Doney, Scott C.

    2008-01-01

    There is growing recognition that rigorous skill assessment is required to understand the ability of ocean biological models to represent ocean processes and distributions. Statistical analysis of model results with observations represents the most quantitative form of skill assessment, and this principle serves as well for data assimilation models. However, skill assessment for data assimilation requires special consideration. This is because there are three sets of information in the free-run model, data, and the assimilation model, which uses Data assimilation information from both the flee-run model and the data. Intercom parison of results among the three sets of information is important and useful for assessment, but is not conclusive since the three information sets are intertwined. An independent data set is necessary for an objective determination. Other useful measures of ocean biological data assimilation assessment include responses of unassimilated variables to the data assimilation, performance outside the prescribed region/time of interest, forecasting, and trend analysis. Examples of each approach from the literature are provided. A comprehensive list of ocean biological data assimilation and their applications of skill assessment, in both ecosystem/biogeochemical and fisheries efforts, is summarized.

  14. Aerosol Data Assimilation at GMAO

    NASA Technical Reports Server (NTRS)

    da Silva, Arlindo M.; Buchard, Virginie

    2017-01-01

    This presentation presents an overview of the aerosol data assimilation work performed at GMAO. The GMAO Forward Processing system and the biomass burning emissions from QFED are first presented. Then, the current assimilation of Aerosol Optical Depth (AOD), performed by means of the analysis splitting method is briefly described, followed by some results on the quality control of observations using a Neural Network trained using AERONET AOD. Some applications are shown such as the Mount Pinatubo eruption in 1991 using the MERRA-2 aerosol dataset. Finally preliminary results on the EnKF implementation for aerosol assimilation are presented.

  15. Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts.

    PubMed

    Gonçalves, Margarida; Pontes, Ana; Almeida, Pedro; Barbosa, Raquel; Serra, Marta; Libkind, Diego; Hutzler, Mathias; Gonçalves, Paula; Sampaio, José Paulo

    2016-10-24

    Beer is one of the oldest alcoholic beverages and is produced by the fermentation of sugars derived from starches present in cereal grains. Contrary to lager beers, made by bottom-fermenting strains of Saccharomyces pastorianus, a hybrid yeast, ale beers are closer to the ancient beer type and are fermented by S. cerevisiae, a top-fermenting yeast. Here, we use population genomics to investigate (1) the closest relatives of top-fermenting beer yeasts; (2) whether top-fermenting yeasts represent an independent domestication event separate from those already described; (3) whether single or multiple beer yeast domestication events can be inferred; and (4) whether top-fermenting yeasts represent non-recombinant or recombinant lineages. Our results revealed that top-fermenting beer yeasts are polyphyletic, with a main clade composed of at least three subgroups, dominantly represented by the German, British, and wheat beer strains. Other beer strains were phylogenetically close to sake, wine, or bread yeasts. We detected genetic signatures of beer yeast domestication by investigating genes previously linked to brewing and using genome-wide scans. We propose that the emergence of the main clade of beer yeasts is related with a domestication event distinct from the previously known cases of wine and sake yeast domestication. The nucleotide diversity of the main beer clade more than doubled that of wine yeasts, which might be a consequence of fundamental differences in the modes of beer and wine yeast domestication. The higher diversity of beer strains could be due to the more intense and different selection regimes associated to brewing. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Contrasted Reactivity to Oxygen Tensions in Frankia sp. Strain CcI3 throughout Nitrogen Fixation and Assimilation

    PubMed Central

    Ghodhbane-Gtari, Faten; Hezbri, Karima; Ktari, Amir; Sbissi, Imed; Beauchemin, Nicholas; Gtari, Maher; Tisa, Louis S.

    2014-01-01

    Reconciling the irreconcilable is a primary struggle in aerobic nitrogen-fixing bacteria. Although nitrogenase is oxygen and reactive oxygen species-labile, oxygen tension is required to sustain respiration. In the nitrogen-fixing Frankia, various strategies have been developed through evolution to control the respiration and nitrogen-fixation balance. Here, we assessed the effect of different oxygen tensions on Frankia sp. strain CcI3 growth, vesicle production, and gene expression under different oxygen tensions. Both biomass and vesicle production were correlated with elevated oxygen levels under both nitrogen-replete and nitrogen-deficient conditions. The mRNA levels for the nitrogenase structural genes (nifHDK) were high under hypoxic and hyperoxic conditions compared to oxic conditions. The mRNA level for the hopanoid biosynthesis genes (sqhC and hpnC) was also elevated under hyperoxic conditions suggesting an increase in the vesicle envelope. Under nitrogen-deficient conditions, the hup2 mRNA levels increased with hyperoxic environment, while hup1 mRNA levels remained relatively constant. Taken together, these results indicate that Frankia protects nitrogenase by the use of multiple mechanisms including the vesicle-hopanoid barrier and increased respiratory protection. PMID:24987692

  17. Coupled Data Assimilation in Navy ESPC

    NASA Astrophysics Data System (ADS)

    Barron, C. N.; Spence, P. L.; Frolov, S.; Rowley, C. D.; Bishop, C. H.; Wei, M.; Ruston, B.; Smedstad, O. M.

    2017-12-01

    Data assimilation under global coupled Earth System Prediction Capability (ESPC) presents significantly greater challenges than data assimilation in forecast models of a single earth system like the ocean and atmosphere. In forecasts of a single component, data assimilation has broad flexibility in adjusting boundary conditions to reduce forecast errors; coupled ESPC requires consistent simultaneous adjustment of multiple components within the earth system: air, ocean, ice, and others. Data assimilation uses error covariances to express how to consistently adjust model conditions in response to differences between forecasts and observations; in coupled ESPC, these covariances must extend from air to ice to ocean such that changes within one fluid are appropriately balanced with corresponding adjustments in the other components. We show several algorithmic solutions that allow us to resolve these challenges. Specifically, we introduce the interface solver method that augments existing stand-alone systems for ocean and atmosphere by allowing them to be influenced by relevant measurements from the coupled fluid. Plans are outlined for implementing coupled data assimilation within ESPC for the Navy's global coupled model. Preliminary results show the impact of assimilating SST-sensitive radiances in the atmospheric model and first results of hybrid DA in a 1/12 degree model of the global ocean.

  18. Environmental and Genetic Determinants of Colony Morphology in Yeast

    PubMed Central

    Granek, Joshua A.; Magwene, Paul M.

    2010-01-01

    Nutrient stresses trigger a variety of developmental switches in the budding yeast Saccharomyces cerevisiae. One of the least understood of such responses is the development of complex colony morphology, characterized by intricate, organized, and strain-specific patterns of colony growth and architecture. The genetic bases of this phenotype and the key environmental signals involved in its induction have heretofore remained poorly understood. By surveying multiple strain backgrounds and a large number of growth conditions, we show that limitation for fermentable carbon sources coupled with a rich nitrogen source is the primary trigger for the colony morphology response in budding yeast. Using knockout mutants and transposon-mediated mutagenesis, we demonstrate that two key signaling networks regulating this response are the filamentous growth MAP kinase cascade and the Ras-cAMP-PKA pathway. We further show synergistic epistasis between Rim15, a kinase involved in integration of nutrient signals, and other genes in these pathways. Ploidy, mating-type, and genotype-by-environment interactions also appear to play a role in the controlling colony morphology. Our study highlights the high degree of network reuse in this model eukaryote; yeast use the same core signaling pathways in multiple contexts to integrate information about environmental and physiological states and generate diverse developmental outputs. PMID:20107600

  19. Tropopause sharpening by data assimilation

    NASA Astrophysics Data System (ADS)

    Pilch Kedzierski, R.; Neef, L.; Matthes, K.

    2016-08-01

    Data assimilation was recently suggested to smooth out the sharp gradients that characterize the tropopause inversion layer (TIL) in systems that did not assimilate TIL-resolving observations. We investigate whether this effect is present in the ERA-Interim reanalysis and the European Centre for Medium-Range Weather Forecasts (ECMWF) operational forecast system (which assimilate high-resolution observations) by analyzing the 4D-Var increments and how the TIL is represented in their data assimilation systems. For comparison, we also diagnose the TIL from high-resolution GPS radio occultation temperature profiles from the COSMIC satellite mission, degraded to the same vertical resolution as ERA-Interim and ECMWF operational analyses. Our results show that more recent reanalysis and forecast systems improve the representation of the TIL, updating the earlier hypothesis. However, the TIL in ERA-Interim and ECMWF operational analyses is still weaker and farther away from the tropopause than GPS radio occultation observations of the same vertical resolution.

  20. A Global Data Assimilation System for Atmospheric Aerosol

    NASA Technical Reports Server (NTRS)

    daSilva, Arlindo

    1999-01-01

    We will give an overview of an aerosol data assimilation system which combines advances in remote sensing of atmospheric aerosols, aerosol modeling and data assimilation methodology to produce high spatial and temporal resolution 3D aerosol fields. Initially, the Goddard Aerosol Assimilation System (GAAS) will assimilate TOMS, AVHRR and AERONET observations; later we will include MODIS and MISR. This data assimilation capability will allows us to integrate complementing aerosol observations from these platforms, enabling the development of an assimilated aerosol climatology as well as a global aerosol forecasting system in support of field campaigns. Furthermore, this system provides an interactive retrieval framework for each aerosol observing satellites, in particular TOMS and AVHRR. The Goddard Aerosol Assimilation System (GAAS) takes advantage of recent advances in constituent data assimilation at DAO, including flow dependent parameterizations of error covariances and the proper consideration of model bias. For its prognostic transport model, GAAS will utilize the Goddard Ozone, Chemistry, Aerosol, Radiation and Transport (GOCART) model developed at NASA/GSFC Codes 916 and 910.3. GOCART includes the Lin-Rood flux-form, semi-Langrangian transport model with parameterized aerosol chemistry and physical processes for absorbing (dust and black carbon) and non-absorbing aerosols (sulfate and organic carbon). Observations and model fields are combined using a constituent version of DAO's Physical-space Statistical Analysis System (PSAS), including its adaptive quality control system. In this talk we describe the main components of this assimilation system and present preliminary results obtained by assimilating TOMS data.

  1. QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice.

    PubMed

    Senthilvel, Senapathy; Vinod, Kunnummal Kurungara; Malarvizhi, Palaniappan; Maheswaran, Marappa

    2008-09-01

    Agricultural environments deteriorate due to excess nitrogen application. Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input. Rice genotypes respond variably to soil available nitrogen. The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits. Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena. Three nitrogen regimes namely, native (0 kg/ha; no nitrogen applied), optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments. The parents and DH lines were significantly varying for all traits under different nitrogen regimes. All traits except plant height recorded significant genotype x environment interaction. Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake. Sixteen QTLs were detected by composite interval mapping. Eleven QTLs showed significant QTL x environment interactions. On chromosome 3, seven QTLs were detected associated with nitrogen use, plant yield and associated traits. A QTL region between markers RZ678, RZ574 and RZ284 was associated with nitrogen use and yield. This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.

  2. Morphodynamic data assimilation used to understand changing coasts

    USGS Publications Warehouse

    Plant, Nathaniel G.; Long, Joseph W.

    2015-01-01

    Morphodynamic data assimilation blends observations with model predictions and comes in many forms, including linear regression, Kalman filter, brute-force parameter estimation, variational assimilation, and Bayesian analysis. Importantly, data assimilation can be used to identify sources of prediction errors that lead to improved fundamental understanding. Overall, models incorporating data assimilation yield better information to the people who must make decisions impacting safety and wellbeing in coastal regions that experience hazards due to storms, sea-level rise, and erosion. We present examples of data assimilation associated with morphologic change. We conclude that enough morphodynamic predictive capability is available now to be useful to people, and that we will increase our understanding and the level of detail of our predictions through assimilation of observations and numerical-statistical models.

  3. A short note on the assimilation of collocated and concurrent GPS and ionosonde data into the Electron Density Assimilative Model

    NASA Astrophysics Data System (ADS)

    Angling, M. J.; Jackson-Booth, N. K.

    2011-12-01

    The Electron Density Assimilative Model (EDAM) has been developed to provide real-time characterizations of the ionosphere by assimilating diverse data sets into a background model. Techniques have been developed to assimilate virtual height ionogram traces rather than relying on true height inversions. A test assimilation has been conducted using both GPS and ionosonde data as input. Postassimilation analysis shows that foF2 residuals can be degraded when only GPS data are assimilated. It has also been demonstrated that by using both data types it is possible to have low total electron content and foF2 residuals and that this is achieved by modifying the ionospheric slab thickness.

  4. Herbivory alters plant carbon assimilation, patterns of biomass allocation and nitrogen use efficiency

    NASA Astrophysics Data System (ADS)

    Peschiutta, María Laura; Scholz, Fabián Gustavo; Goldstein, Guillermo; Bucci, Sandra Janet

    2018-01-01

    Herbivory can trigger physiological processes resulting in leaf and whole plant functional changes. The effects of chronic infestation by an insect on leaf traits related to carbon and nitrogen economy in three Prunus avium cultivars were assessed. Leaves from non-infested trees (control) and damaged leaves from infested trees were selected. The insect larvae produce skeletonization of the leaves leaving relatively intact the vein network of the eaten leaves and the abaxial epidermal tissue. At the leaf level, nitrogen content per mass (Nmass) and per area (Narea), net photosynthesis per mass (Amass) and per area (Aarea), photosynthetic nitrogen-use efficiency (PNUE), leaf mass per area (LMA) and total leaf phenols content were measured in the three cultivars. All cultivars responded to herbivory in a similar fashion. The Nmass, Amass, and PNUE decreased, while LMA and total content of phenols increased in partially damaged leaves. Increases in herbivore pressure resulted in lower leaf size and total leaf area per plant across cultivars. Despite this, stem cumulative growth tended to increase in infected plants suggesting a change in the patterns of biomass allocation and in resources sequestration elicited by herbivory. A larger N investment in defenses instead of photosynthetic structures may explain the lower PNUE and Amass observed in damaged leaves. Some physiological changes due to herbivory partially compensate for the cost of leaf removal buffering the carbon economy at the whole plant level.

  5. Ecological Assimilation of Land and Climate Observations - the EALCO model

    NASA Astrophysics Data System (ADS)

    Wang, S.; Zhang, Y.; Trishchenko, A.

    2004-05-01

    Ecosystems are intrinsically dynamic and interact with climate at a highly integrated level. Climate variables are the main driving factors in controlling the ecosystem physical, physiological, and biogeochemical processes including energy balance, water balance, photosynthesis, respiration, and nutrient cycling. On the other hand, ecosystems function as an integrity and feedback on the climate system through their control on surface radiation balance, energy partitioning, and greenhouse gases exchange. To improve our capability in climate change impact assessment, a comprehensive ecosystem model is required to address the many interactions between climate change and ecosystems. In addition, different ecosystems can have very different responses to the climate change and its variation. To provide more scientific support for ecosystem impact assessment at national scale, it is imperative that ecosystem models have the capability of assimilating the large scale geospatial information including satellite observations, GIS datasets, and climate model outputs or reanalysis. The EALCO model (Ecological Assimilation of Land and Climate Observations) is developed for such purposes. EALCO includes the comprehensive interactions among ecosystem processes and climate, and assimilates a variety of remote sensing products and GIS database. It provides both national and local scale model outputs for ecosystem responses to climate change including radiation and energy balances, water conditions and hydrological cycles, carbon sequestration and greenhouse gas exchange, and nutrient (N) cycling. These results form the foundation for the assessment of climate change impact on ecosystems, their services, and adaptation options. In this poster, the main algorithms for the radiation, energy, water, carbon, and nitrogen simulations were diagrammed. Sample input data layers at Canada national scale were illustrated. Model outputs including the Canada wide spatial distributions of net

  6. Tol1, a fission yeast phosphomonoesterase, is an in vivo target of lithium, and its deletion leads to sulfite auxotrophy.

    PubMed

    Miyamoto, R; Sugiura, R; Kamitani, S; Yada, T; Lu, Y; Sio, S O; Asakura, M; Matsuhisa, A; Shuntoh, H; Kuno, T

    2000-07-01

    Lithium is the drug of choice for the treatment of bipolar affective disorder. The identification of an in vivo target of lithium in fission yeast as a model organism may help in the understanding of lithium therapy. For this purpose, we have isolated genes whose overexpression improved cell growth under high LiCl concentrations. Overexpression of tol1(+), one of the isolated genes, increased the tolerance of wild-type yeast cells for LiCl but not for NaCl. tol1(+) encodes a member of the lithium-sensitive phosphomonoesterase protein family, and it exerts dual enzymatic activities, 3'(2'),5'-bisphosphate nucleotidase and inositol polyphosphate 1-phosphatase. tol1(+) gene-disrupted cells required high concentrations of sulfite in the medium for growth. Consistently, sulfite repressed the sulfate assimilation pathway in fission yeast. However, tol1(+) gene-disrupted cells could not fully recover from their growth defect and abnormal morphology even when the medium was supplemented with sulfite, suggesting the possible implication of inositol polyphosphate 1-phosphatase activity for cell growth and morphology. Given the remarkable functional conservation of the lithium-sensitive dual-specificity phosphomonoesterase between fission yeast and higher-eukaryotic cells during evolution, it may represent a likely in vivo target of lithium action across many species.

  7. Selection and identification of oleaginous yeast isolated from soil, animal feed and ruminal fluid for use as feed supplement in dairy cattle.

    PubMed

    Paserakung, A; Pattarajinda, V; Vichitphan, K; Froetschel, M A

    2015-10-01

    The purpose of this study was to select oleaginous yeast for microbial lipid production. Sixty-four yeast isolates were obtained from soil (GSY1-12), animal feeds (FDY1-21), and ruminal fluid (RMY1-31) using yeast extract peptone dextrose (YPD) agar. The cultivation of these isolates on nitrogen limited-medium revealed that GSY2 to GSY6, GSY10, FDY2, FDY12 and FDY14 accumulated lipid over 20% of dry biomass. Therefore, they were preliminarily classified as oleaginous yeast. In subsequent experiment, an 8 × 3 factorial in completely randomized design was conducted to examine the effect of eight oleaginous yeast strains and three nitrogen sources (peptone, (NH4 )2 SO4 , urea) on lipid accumulation when using molasses as substrate. The result illustrated that only GSY3 and GSY10 accumulated lipid over 20% of biomass when using peptone or (NH4 )2 SO4 but urea did not. However, GSY10 gave higher biomass and lipid yield than GSY3 (P < 0·05). Identification of GSY10 using 26S rDNA illustrated that GSY10 belongs to Trichosporon asahii. Fatty acid profiles of this strain contained unsaturated fats up to 62·5% of which oleic acid (C18:1 ) was predominant. In conclusion, T. asahii GSY10 was the most promising oleaginous yeast for microbial lipid production from molasses. This study illustrated the ability of T. asahii GSY10 to utilize molasses and (NH4 )2 SO4 for synthesizing and accumulating cellular lipid of which oleic acid (C18:1 ) was predominant. This yeast would be used for microbial lipid production used as feed supplement in dairy cattle. © 2015 The Society for Applied Microbiology.

  8. Microbiological Characteristics of Wild Yeast Strain Pichia anomala Y197-13 for Brewing Makgeolli

    PubMed Central

    Kim, Hye Ryun; Kim, Jae-Ho; Bai, Dong-Hoon

    2013-01-01

    Makgeolli is a traditional cloudy-white Korean rice wine with an alcohol content of 6~7%. The present study investigated the morphological characteristics, carbon-utilizing ability, fatty acid composition, alcohol resistance, glucose tolerance, and flocculence of Saccharomyces cerevisiae Y98-5 and Pichia anomala Y197-13, non-S. cerevisiae isolated from Nuruk, which is used in brewing Makgeolli. Similar morphological characteristics were observed for both isolated wild yeast strains; and the carbon source assimilation of Y197-13 differed from that of other P. anomala strains. Strain Y197-13 was negative for D-trehalose, mannitol, arbutin, I-erythritol, and succinic acid. The major cellular fatty acids of strain Y197-13 included C18:2n6c (33.94%), C18:1n9c (26.97%) and C16:0 (20.57%). Strain Y197-13 was Crabtree-negative, with 60% cell viability at 12% (v/v) ethanol. The flocculation level of strain Y197-13 was 8.38%, resulting in its classification as a non-flocculent yeast. PMID:24198668

  9. Detection of yeast Saccharomyces cerevisiae with ionic liquid mediated carbon dots.

    PubMed

    Wang, Jia-Li; Teng, Ji-Yuan; Jia, Te; Shu, Yang

    2018-02-01

    Hydrophobic nitrogen-doped carbon dots are prepared with energetic ionic liquid (1,3-dibutylimidazolium dicyandiamide, BbimDCN) as carbon source. A yield of as high as 58% is obtained for the carbon dots, shortly termed as BbimDCN-OCDs, due to the presence of thermal-instable N(CN) 2 - moiety. BbimDCN-OCDs exhibit favorable biocompability and excellent imaging capacity for fluorescence labelling of yeast cell Saccharomyces cerevisiae. In addition, chitosan-modified Dy 3+ -doped magnetic nanoparticles (shortly as Chitosan@Fe 2.75 Dy 0.25 O 4 ) with superparamagnetism are prepared. The electrostatic attraction between positively charged magnetic nanoparticles and negatively charged yeast cells facilitates exclusive recognition/isolation of S. cerevisiae. In practice, S. cerevisiae is labelled by BbimDCN-OCDs and adhered onto the Chitosan@Fe 2.75 Dy 0.25 O 4 . The yeast/ BbimDCN-OCDs/Chitosan@Fe 2.75 Dy 0.25 O 4 composite is then isolated with an external magnet and the fluorescence from BbimDCN-OCDs incorporated in S. cerevisiae is monitored. The fluorescence intensity is linearly correlated with the content of yeast cell, showing a calibration graph of F = 3.01log[C]+11.7, offering a detection limit of 5×10 2 CFU/mL. S. cerevisiae content in various real sample matrixes are quantified by using this protocol. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Global CO emission estimates inferred from assimilation of MOPITT and IASI CO data, together with observations of O3, NO2, HNO3, and HCHO.

    NASA Astrophysics Data System (ADS)

    Zhang, X.; Jones, D. B. A.; Keller, M.; Jiang, Z.; Bourassa, A. E.; Degenstein, D. A.; Clerbaux, C.; Pierre-Francois, C.

    2017-12-01

    Atmospheric carbon monoxide (CO) emissions estimated from inverse modeling analyses exhibit large uncertainties, due, in part, to discrepancies in the tropospheric chemistry in atmospheric models. We attempt to reduce the uncertainties in CO emission estimates by constraining the modeled abundance of ozone (O3), nitrogen dioxide (NO2), nitric acid (HNO3), and formaldehyde (HCHO), which are constituents that play a key role in tropospheric chemistry. Using the GEOS-Chem four-dimensional variational (4D-Var) data assimilation system, we estimate CO emissions by assimilating observations of CO from the Measurement of Pollution In the Troposphere (MOPITT) and the Infrared Atmospheric Sounding Interferometer (IASI), together with observations of O3 from the Optical Spectrograph and InfraRed Imager System (OSIRIS) and IASI, NO2 and HCHO from the Ozone Monitoring Instrument (OMI), and HNO3 from the Microwave Limb Sounder (MLS). Our experiments evaluate the inferred CO emission estimates from major anthropogenic, biomass burning and biogenic sources. Moreover, we also infer surface emissions of nitrogen oxides (NOx = NO + NO2) and isoprene. Our results reveal that this multiple species chemical data assimilation produces a chemical consistent state that effectively adjusts the CO-O3-OH coupling in the model. The O3-induced changes in OH are particularly large in the tropics. Overall, our analysis results in a better constrained tropospheric chemical state.

  11. Metabolism of organic acids, nitrogen and amino acids in chlorotic leaves of 'Honeycrisp' apple (Malus domestica Borkh) with excessive accumulation of carbohydrates.

    PubMed

    Wang, Huicong; Ma, Fangfang; Cheng, Lailiang

    2010-07-01

    Metabolite profiles and activities of key enzymes in the metabolism of organic acids, nitrogen and amino acids were compared between chlorotic leaves and normal leaves of 'Honeycrisp' apple to understand how accumulation of non-structural carbohydrates affects the metabolism of organic acids, nitrogen and amino acids. Excessive accumulation of non-structural carbohydrates and much lower CO(2) assimilation were found in chlorotic leaves than in normal leaves, confirming feedback inhibition of photosynthesis in chlorotic leaves. Dark respiration and activities of several key enzymes in glycolysis and tricarboxylic acid (TCA) cycle, ATP-phosphofructokinase, pyruvate kinase, citrate synthase, aconitase and isocitrate dehydrogenase were significantly higher in chlorotic leaves than in normal leaves. However, concentrations of most organic acids including phosphoenolpyruvate (PEP), pyruvate, oxaloacetate, 2-oxoglutarate, malate and fumarate, and activities of key enzymes involved in the anapleurotic pathway including PEP carboxylase, NAD-malate dehydrogenase and NAD-malic enzyme were significantly lower in chlorotic leaves than in normal leaves. Concentrations of soluble proteins and most free amino acids were significantly lower in chlorotic leaves than in normal leaves. Activities of key enzymes in nitrogen assimilation and amino acid synthesis, including nitrate reductase, glutamine synthetase, ferredoxin and NADH-dependent glutamate synthase, and glutamate pyruvate transaminase were significantly lower in chlorotic leaves than in normal leaves. It was concluded that, in response to excessive accumulation of non-structural carbohydrates, glycolysis and TCA cycle were up-regulated to "consume" the excess carbon available, whereas the anapleurotic pathway, nitrogen assimilation and amino acid synthesis were down-regulated to reduce the overall rate of amino acid and protein synthesis.

  12. Impact of assimilating GOES imager clear-sky radiance with a rapid refresh assimilation system for convection-permitting forecast over Mexico

    NASA Astrophysics Data System (ADS)

    Yang, Chun; Liu, Zhiquan; Gao, Feng; Childs, Peter P.; Min, Jinzhong

    2017-05-01

    The Geostationary Operational Environmental Satellite (GOES) imager data could provide a continuous image of the evolutionary pattern of severe weather phenomena with its high spatial and temporal resolution. The capability to assimilate the GOES imager radiances has been developed within the Weather Research and Forecasting model's data assimilation system. Compared to the benchmark experiment with no GOES imager data, the impact of assimilating GOES imager radiances on the analysis and forecast of convective process over Mexico in 7-10 March 2016 was assessed through analysis/forecast cycling experiments using rapid refresh assimilation system with hybrid-3DEnVar scheme. With GOES imager radiance assimilation, better analyses were obtained in terms of the humidity, temperature, and simulated water vapor channel brightness temperature distribution. Positive forecast impacts from assimilating GOES imager radiance were seen when verified against the Tropospheric Airborne Meteorological Data Reporting observation, GOES imager observation, and Mexico station precipitation data.

  13. Assimilation of MODIS Snow Cover Through the Data Assimilation Research Testbed and the Community Land Model Version 4

    NASA Technical Reports Server (NTRS)

    Zhang, Yong-Fei; Hoar, Tim J.; Yang, Zong-Liang; Anderson, Jeffrey L.; Toure, Ally M.; Rodell, Matthew

    2014-01-01

    To improve snowpack estimates in Community Land Model version 4 (CLM4), the Moderate Resolution Imaging Spectroradiometer (MODIS) snow cover fraction (SCF) was assimilated into the Community Land Model version 4 (CLM4) via the Data Assimilation Research Testbed (DART). The interface between CLM4 and DART is a flexible, extensible approach to land surface data assimilation. This data assimilation system has a large ensemble (80-member) atmospheric forcing that facilitates ensemble-based land data assimilation. We use 40 randomly chosen forcing members to drive 40 CLM members as a compromise between computational cost and the data assimilation performance. The localization distance, a parameter in DART, was tuned to optimize the data assimilation performance at the global scale. Snow water equivalent (SWE) and snow depth are adjusted via the ensemble adjustment Kalman filter, particularly in regions with large SCF variability. The root-mean-square error of the forecast SCF against MODIS SCF is largely reduced. In DJF (December-January-February), the discrepancy between MODIS and CLM4 is broadly ameliorated in the lower-middle latitudes (2345N). Only minimal modifications are made in the higher-middle (4566N) and high latitudes, part of which is due to the agreement between model and observation when snow cover is nearly 100. In some regions it also reveals that CLM4-modeled snow cover lacks heterogeneous features compared to MODIS. In MAM (March-April-May), adjustments to snowmove poleward mainly due to the northward movement of the snowline (i.e., where largest SCF uncertainty is and SCF assimilation has the greatest impact). The effectiveness of data assimilation also varies with vegetation types, with mixed performance over forest regions and consistently good performance over grass, which can partly be explained by the linearity of the relationship between SCF and SWE in the model ensembles. The updated snow depth was compared to the Canadian Meteorological

  14. Understanding nitrate uptake, signaling and remobilisation for improving plant nitrogen use efficiency.

    PubMed

    Kant, Surya

    2018-02-01

    The majority of terrestrial plants use nitrate as their main source of nitrogen. Nitrate also acts as an important signalling molecule in vital physiological processes required for optimum plant growth and development. Improving nitrate uptake and transport, through activation by nitrate sensing, signalling and regulatory processes, would enhance plant growth, resulting in improved crop yields. The increased remobilisation of nitrate, and assimilated nitrogenous compounds, from source to sink tissues further ensures higher yields and quality. An updated knowledge of various transporters, genes, activators, and microRNAs, involved in nitrate uptake, transport, remobilisation, and nitrate-mediated root growth, is presented. An enhanced understanding of these components will allow for their orchestrated fine tuning in efforts to improving nitrogen use efficiency in plants. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  15. Effects of nitrogen and carbon sources on the production of inulinase from strain Bacillus sp. SG113

    NASA Astrophysics Data System (ADS)

    Gavrailov, Simeon; Ivanova, Viara

    2016-03-01

    The effects of the carbon and nitrogen substrates on the growth of Bacillus sp. SG113 strain were studied. The use of organic nitrogen sources (peptone, beef extract, yeast extract, casein) leads to rapid cellular growth and the best results for the Bacillus strain were obtained with casein hydrolysate. From the inorganic nitrogen sources studied, the (NH4) 2SO4 proved to be the best nitrogen source. Casein hydrolysate and (NH4) 2SO4 stimulated the invertase synthesis. In the presence of Jerusalem artichoke, onion and garlic extracts as carbon sources the strain synthesized from 6 to 10 times more inulinase.

  16. Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass.

    PubMed

    Yun, Eun Ju; Oh, Eun Joong; Liu, Jing-Jing; Yu, Sora; Kim, Dong Hyun; Kwak, Suryang; Kim, Kyoung Heon; Jin, Yong-Su

    2018-01-01

    Understanding the global metabolic network, significantly perturbed upon promiscuous activities of foreign enzymes and different carbon sources, is crucial for systematic optimization of metabolic engineering of yeast Saccharomyces cerevisiae . Here, we studied the effects of promiscuous activities of overexpressed enzymes encoded by foreign genes on rerouting of metabolic fluxes of an engineered yeast capable of assimilating sugars from renewable biomass by profiling intracellular and extracellular metabolites. Unbiased metabolite profiling of the engineered S. cerevisiae strain EJ4 revealed promiscuous enzymatic activities of xylose reductase and xylitol dehydrogenase on galactose and galactitol, respectively, resulting in accumulation of galactitol and tagatose during galactose fermentation. Moreover, during glucose fermentation, a trisaccharide consisting of glucose accumulated outside of the cells probably owing to the promiscuous and transglycosylation activity of β-glucosidase expressed for hydrolyzing cellobiose. Meanwhile, higher accumulation of fatty acids and secondary metabolites was observed during xylose and cellobiose fermentations, respectively. The heterologous enzymes functionally expressed in S. cerevisiae showed promiscuous activities that led to unintended metabolic rerouting in strain EJ4. Such metabolic rerouting could result in a low yield and productivity of a final product due to the formation of unexpected metabolites. Furthermore, the global metabolic network can be significantly regulated by carbon sources, thus yielding different patterns of metabolite production. This metabolomic study can provide useful information for yeast strain improvement and systematic optimization of yeast metabolism to manufacture bio-based products.

  17. Sampling, feasibility, and priors in data assimilation

    DOE PAGES

    Tu, Xuemin; Morzfeld, Matthias; Miller, Robert N.; ...

    2016-03-01

    Importance sampling algorithms are discussed in detail, with an emphasis on implicit sampling, and applied to data assimilation via particle filters. Implicit sampling makes it possible to use the data to find high-probability samples at relatively low cost, making the assimilation more efficient. A new analysis of the feasibility of data assimilation is presented, showing in detail why feasibility depends on the Frobenius norm of the covariance matrix of the noise and not on the number of variables. A discussion of the convergence of particular particle filters follows. A major open problem in numerical data assimilation is the determination ofmore » appropriate priors, a progress report on recent work on this problem is given. The analysis highlights the need for a careful attention both to the data and to the physics in data assimilation problems.« less

  18. 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

  19. Autophagy is required for efficient meiosis progression and proper meiotic chromosome segregation in fission yeast.

    PubMed

    Matsuhara, Hirotada; Yamamoto, Ayumu

    2016-01-01

    Autophagy is a conserved intracellular degradation system, which contributes to development and differentiation of various organisms. Yeast cells undergo meiosis under nitrogen-starved conditions and require autophagy for meiosis initiation. However, the precise roles of autophagy in meiosis remain unclear. Here, we show that autophagy is required for efficient meiosis progression and proper meiotic chromosome segregation in fission yeast. Autophagy-defective strains bearing a mutation in the autophagy core factor gene atg1, atg7, or atg14 exhibit deformed nuclear structures during meiosis. These mutant cells require an extracellular nitrogen supply for meiosis progression following their entry into meiosis and show delayed meiosis progression even with a nitrogen supply. In addition, they show frequent chromosome dissociation from the spindle together with spindle overextension, forming extra nuclei. Furthermore, Aurora kinase, which regulates chromosome segregation and spindle elongation, is significantly increased at the centromere and spindle in the mutant cells. Aurora kinase down-regulation eliminated delayed initiation of meiosis I and II, chromosome dissociation, and spindle overextension, indicating that increased Aurora kinase activity may cause these aberrances in the mutant cells. Our findings show a hitherto unrecognized relationship of autophagy with the nuclear structure, regulation of cell cycle progression, and chromosome segregation in meiosis. © 2015 The Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.

  20. Regulation Effects of Water and Nitrogen on the Source-Sink Relationship in Potato during the Tuber Bulking Stage

    PubMed Central

    Li, Wenting; Xiong, Binglin; Wang, Shiwen; Deng, Xiping; Yin, Lina; Li, Hongbing

    2016-01-01

    The source-sink relationship determines crop yield, and it is largely regulated by water and nutrients in agricultural production. This has been widely investigated in cereals, but fewer studies have been conducted in root and tuber crops such as potato (Solanum tuberosum L.). The objective of this study was to investigate the source-sink relationship in potato and the regulation of water and nitrogen on the source-sink relationship during the tuber bulking stage. A pot experiment using virus-free plantlets of the Atlantic potato cultivar was conducted, using three water levels (50%, 70% and 90% of field capacity) and three nitrogen levels (0, 0.2, 0.4 g N∙kg−1 soil). The results showed that, under all water and nitrogen levels, plant source capacity were small at the end of the experiment, since photosynthetic activity in leaves were low and non-structural reserves in underground stems were completely remobilized. While at this time, there were very big differences in maximum and minimum tuber number and tuber weight, indicating that the sink tuber still had a large potential capacity to take in assimilates. These results suggest that the source-supplied assimilates were not sufficient enough to meet the demands of sink growth. Thus, we concluded that, unlike cereals, potato yield is more likely to be source-limited than sink-limited during the tuber bulking stage. Water and nitrogen are two key factors in potato production management. Our results showed that water level, nitrogen level and the interaction between water and nitrogen influence potato yield mainly through affecting source capacity via the net photosynthetic rate, total leaf area and leaf life span. Well-watered, sufficient nitrogen and well-watered combined with sufficient nitrogen increased yield mainly by enhancing the source capacity. Therefore, this suggests that increasing source capacity is more crucial to improve potato yield. PMID:26752657

  1. Pelagic Nitrogen Cycle Observations In The Arctic Ocean - How Might They Change In Response To Ocean Acidification?

    NASA Astrophysics Data System (ADS)

    Clark, D. R.; Rees, A.; Brown, I.; Al-Moosawi, L.; Cripps, G.

    2016-02-01

    Phytoplankton forms the base of marine food webs by assimilating nutrients and generating biomass that supports higher trophic levels. Conversely, marine heterotrophs degrade organic matter produced by phytoplankton and recycle nutrients, maintaining food web integrity. We investigated the assimilation and regeneration of dissolved inorganic nitrogen (DIN) at stations located in the Arctic Ocean. In addition, we measured the concentration of nitrous oxide, a by-product of N-regeneration (specifically nitrification) and a climatically active gas. Measurements demonstrated the simultaneous regeneration and assimilation of ammonium, nitrite and nitrate at open ocean, ice-edge and within-ice locations. Ammonium was regenerated and assimilated within the range 0.2-4.5 nmol·L-1·h-1 and 0.5-24.8 nmol·L-1·h-1 respectively. Nitrite was regenerated and assimilated within the range 0.1-9.2 nmol·L-1·h-1 and 0.0-6.9 nmol·L-1·h-1 respectively. Nitrate was regenerated and assimilated within the range 0.3-372.7 nmol·L-1·h-1 and 0.1-48.3 nmol·L-1·h-1 respectively. Results indicated that the ice-edge was associated with enhanced DIN assimilation. The concentration of nitrous oxide (<100m) averaged 11.8±2.2 nmol·L-1, which was approximately 15% higher than measured in the European shelf seas and most likely related only to temperature. In separate experiments, the influence of ocean acidification (OA) upon nitrogen cycle processes was investigated.