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Carbon Flow (carbon + flow)
Selected AbstractsCarbon flow in an upland grassland: effect of liming on the flux of recently photosynthesized carbon to rhizosphere soilGLOBAL CHANGE BIOLOGY, Issue 12 2004J. Ignacio Rangel-Castro Abstract The effect of liming on the flow of recently photosynthesized carbon to rhizosphere soil was studied using 13CO2 pulse labelling, in an upland grassland ecosystem in Scotland. The use of 13C enabled detection, in the field, of the effect of a 4-year liming period of selected soil plots on C allocation from plant biomass to soil, in comparison with unlimed plots. Photosynthetic rates and carbon turnover were higher in plants grown in limed soils than in those from unlimed plots. Higher ,13C, values were detected in shoots from limed plants than in those from unlimed plants in samples clipped within 15 days of the end of pulse labelling. Analysis of the aboveground plant production corresponding to the 4-year period of liming indicated that the standing biomass was higher in plots that received lime. Lower ,13C, values in limed roots compared with unlimed roots were found, whereas no significant difference was detected between soil samples. Extrapolation of our results indicated that more C has been lost through the soil than has been gained via photosynthetic assimilation because of pasture liming in Scotland during the period 1990,1998. However, the uncertainty associated with such extrapolation based on this single study is high and these estimates are provided only to set our findings in the broader context of national soil carbon emissions. [source] Effects of increased temperature and nutrient enrichment on the stoichiometry of primary producers and consumers in temperate shallow lakesFRESHWATER BIOLOGY, Issue 7 2008M. VENTURA Summary 1. We studied the effects of increased water temperatures (0,4.5 °C) and nutrient enrichment on the stoichiometric composition of different primary producers (macrophytes, epiphytes, seston and sediment biofilm) and invertebrate consumers in 24 mesocosm ecosystems created to mimic shallow pond environments. The nutrient ratios of primary producers were used as indicative of relative nitrogen (N) or phosphorus (P) limitation. We further used carbon stable isotopic composition (,13C) of the different primary producers to elucidate differences in the degree of CO2 limitation. 2. Epiphytes were the only primary producer with significantly higher ,13C in the enriched mesocosms. No temperature effects were observed in ,13C composition of any primary producer. Independently of the treatment effects, the four primary producers had different ,13C signatures indicative of differences in CO2 limitation. Seston had signatures indicating negligible or low CO2 limitation, followed by epiphytes and sediment biofilm, with moderate CO2 limitation, while macrophytes showed the strongest CO2 limitation. CO2 together with biomass of epiphytes were the key variables explaining between 50 and 70% of the variability in ,13C of the different primary producers, suggesting that epiphytes play an important role in carbon flow of temperate shallow lakes. 3. The ratio of carbon to chlorophyll a decreased with increasing temperature and enrichment in both epiphytes and seston. The effects of temperature were mainly attributed to changes in algal Chl a content, while the decrease with enrichment was probably a result of a higher proportion of algae in the seston and epiphytes. 4. Macrophytes, epiphytes and seston decreased their C : N with enrichment, probably as an adaptation to the different N availability levels. The C : N of epiphytes and Elodea canadensis decreased with increasing temperature in the control mesocosms. Sediment biofilm was the only primary producer with lower C : P and N : P with enrichment, probably as a result of higher P accumulation in the sediment. 5. Independently of nutrient level and increased temperature effects the four primary producers had significantly different stoichiometric compositions. Macrophytes had higher C : N and C : P and, together with epiphytes, also the highest N : P. Seston had no N or P limitation, while macrophytes and epiphytes may have been P limited in a few mesocosms. Sediment biofilm indicated strong N deficiency. 6. Consumers had strongly homeostatic stoichiometric compositions in comparison to primary producers, with weak or no significant treatment effects in any of the groups (insects, leeches, molluscs and crustaceans). Among consumers, predators had significantly higher N content and lower C : N than grazers. [source] Determination of isotope fractionation factors and quantification of carbon flow by stable carbon isotope signatures in a methanogenic rice root model systemGEOBIOLOGY, Issue 2 2006H. PENNING ABSTRACT Methanogenic processes can be quantified by stable carbon isotopes, if necessary modeling parameters, especially fractionation factors, are known. Anoxically incubated rice roots are a model system with a dynamic microbial community and thus suitable to investigate principal geochemical processes in anoxic natural systems. Here we applied an inhibitor of acetoclastic methanogenesis (methyl fluoride), calculated the thermodynamics of the involved processes, and analyzed the carbon stable isotope signatures of CO2, CH4, propionate, acetate and the methyl carbon of acetate to characterize the carbon flow during anaerobic degradation of rice roots to the final products CO2 and CH4. Methyl fluoride inhibited acetoclastic methanogenesis and thus allowed to quantify the fractionation factor of CH4 production from H2/CO2. Since our model system was not affected by H2 gradients, the fractionation factor could alternatively be determined from the Gibbs free energies of hydrogenotrophic methanogenesis. The fractionation factor of acetoclastic methanogenesis was also experimentally determined. The data were used for successfully modeling the carbon flow. The model results were in agreement with the measured process data, but were sensitive to even small changes in the fractionation factor of hydrogenotrophic methanogenesis. Our study demonstrates that stable carbon isotope signatures are a proper tool to quantify carbon flow, if fractionation factors are determined precisely. [source] Intra-lake stable isotope ratio variation in selected fish species and their possible carbon sources in Lake Kyoga (Uganda): implications for aquatic food web studiesAFRICAN JOURNAL OF ECOLOGY, Issue 3 2010Dismas Mbabazi Abstract The stable isotopes of nitrogen (,15N) and carbon (,13C) provide powerful tools for quantifying trophic relationships and carbon flow to consumers in food webs; however, the isotopic signatures of organisms vary within a lake. Assessment of carbon and nitrogen isotopic signatures in a suite of plants, invertebrates, and fishes in Lake Kyoga, indicated significant variation between two sites for ,13C (paired t = 6.305; df = 14, P < 0.001 and ,15N paired t = 1.292; df = 14; P < 0.05). The fish fauna in Bukungu was generally more 13C enriched (mean ,13C = ,16.37 ± 1.64,) than in Iyingo (mean ,13C = ,20.80 ± 2.41,) but more ,15N depleted (mean ,15N = 5.57 ± 0.71,) than in Iyingo (mean ,15N = 6.92 ± 0.83,). The simultaneous shifts in phytoplankton and consumer signatures confirmed phytoplankton as the major source of carbon for the food chain leading to fish. Limited sampling coverage within lakes may affect lake wide stable isotope signatures, and the same error is transferred into trophic position estimation. Consideration of potential intra-lake spatial variability in isotope ratios and size is essential in evaluating the spatial and trophic structure of fish assemblages. Résumé Les isotopes stables d'azote (,15N) et de carbone (,13C) sont des outils intéressants pour quantifier les relations trophiques et le flux de carbone vers les consommateurs de chaînes alimentaires; cependant, la signature isotopique des organismes varie au sein d'un même lac. L'évaluation des signatures isotopiques du carbone et de l'azote dans une suite de plantes, d'invertébrés et de poissons du lac Kyoga indiquait une variation significative entre deux sites pour ,13C (test t apparié = 6.305; df = 14; P < 0.05). La faune piscicole de Bukungu était généralement plus enrichie en ,13C (moyenne de ,13C = ,16.37 ± 1.64,) qu'à Iyingo (moyenne de ,13C = ,20.80 ± 2.41,) mais plus dépourvue de ,15N (moyenne de ,15N = 5.57 ± 0.71,) qu'Inyingo (moyenne de ,15N = 6.92 ± 0.83,). Les glissements simultanés des signatures du phytoplancton et des consommateurs confirmaient que le phytoplancton est la source principale de carbone de la chaîne alimentaire qui aboutit aux poissons. Une couverture limitée de l'échantillonnage dans les lacs peut affecter la signature des isotopes stables de tout le lac, et cette même erreur est reportée dans l'estimation de la situation trophique. Il est essentiel de tenir compte de la variabilité spatiale possible des taux et de la taille des isotopes dans les lacs lorsque l'on évalue la structure spatiale et trophique des assemblages de poissons. [source] Positive regulation of Bacillus subtilis ackA by CodY and CcpA: establishing a potential hierarchy in carbon flowMOLECULAR MICROBIOLOGY, Issue 3 2006Robert P. Shivers Summary Conversion of pyruvate to acetate via the phosphotransacetylase-acetate kinase pathway generates ATP and is a major overflow pathway under conditions of carbon and nitrogen excess. In Bacillus subtilis, this pathway is positively regulated by CcpA, a global regulator of carbon metabolism genes. Transcription of the acetate kinase gene (ackA) proved to be activated as well by a second global regulatory protein, CodY. Expression of an ackA,lacZ fusion was reduced in a codY mutant strain. CodY was found to bind in vitro to two sites in the ackA promoter region and to stimulate ackA transcription in a run-off transcription assay. This is the first known case of direct positive regulation by CodY. CodY and CcpA were found to bind to neighbouring sites and their effects were additive both in vivo and in vitro. Surprisingly, positive regulation by CodY, unlike repression, responded primarily to only one type of effector molecule. That is, branched-chain amino acids (BCAAs) served as more potent co-activators of CodY-dependent ackA transcription than did GTP. Given the roles of CcpA and CodY in regulating genes whose products determine the metabolic fate of pyruvate, these two proteins may act together to mediate a hierarchical conversion of pyruvate to its many potential products. [source] Cell wall biochemistry and biomechanics of harvested white asparagus shoots as affected by temperatureANNALS OF APPLIED BIOLOGY, Issue 3 2008W.B. Herppich Abstract The effects of temperature on the dynamics of changes in shoot mechanical properties, cell wall components, relevant soluble sugars and respiration activity of harvested white asparagus spears were investigated during a 7-day storage period. All functional cell wall components of asparagus spears increased closely temperature dependent. The content of soluble glucose declined with a similar temporal dynamics and to a comparable degree, indicating a major carbon flow of this storage sugar into cell walls (60,70%). Irrespective of temperature, the contents of stored soluble fructose and sucrose remained more or less constant. Lower temperatures reduced cell wall development but do not significantly affect the relative carbon flow from storage sugars into cell walls or maintenance respiration. Compared with cell walls, maintenance respiration is by far the smaller carbon sink in stored asparagus spears. Temperature differentially affects the absolute amount and the relative contribution of the different cell wall components and the temporal dynamics of changes in structural carbohydrate and lignin content. At higher temperatures, secondary cell wall thickening resulted mainly from a large increase in cellulose content. The pronounced increase in the fractions of cellulose and especially lignin may stress the important role of lignin in cell wall strengthening. While the fraction of cell wall proteins decreased, those of hemicellulose and the pectic components were not influenced. [source] Kinetic characterization of vero cell metabolism in a serum-free batch culture processBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2010Emma Petiot Abstract A global kinetic study of the central metabolism of Vero cells cultivated in a serum-free medium is proposed in the present work. Central metabolism including glycolysis, glutaminolysis, and tricarboxylic acid cycle (TCA) was demonstrated to be saturated by high flow rates of consumption of the two major substrates, glucose, and glutamine. Saturation was reavealed by an accumulation of metabolic intermediates and amino acids, by a high production of lactate needed to balance the redox pathway, and by a low participation of the carbon flow to the TCA cycle supply. Different culture conditions were set up to reduce the central metabolism saturation and to better balance the metabolic flow rates between lactate production and energetic pathways. From these culture conditions, substitutions of glutamine by other carbon sources, which have lower transport rates such as asparagine, or pyruvate in order to shunt the glycolysis pathway, were successful to better balance the central metabolism. As a result, an increase of the cell growth with a concomitant decrease of cell death and a better distribution of the carbon flow between TCA cycle and lactate production occurred. We also demonstrated that glutamine was a major carbon source to supply the TCA cycle in Vero cells and that a reduction of lactate production did not necessary improve the efficiency of the Vero cell metabolism. Thus, to adapt the formulation of the medium to the Vero cell needs, it is important to provide carbon substrates inducing a regulated supply of carbon in the TCA cycle either through the glycolysis or through other pathways such as glutaminolysis. Finally, this study allowed to better understand the Vero cell behavior in serum-free medium which is a valuable help for the implementation of this cell line in serum-free industrial production processes. Biotechnol. Bioeng. 2010;107: 143,153. © 2010 Wiley Periodicals, Inc. [source] A study of D-lactate and extracellular methylglyoxal production in lactate Re-Utilizing CHO culturesBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2010Tomas Paoli Abstract In large-scale mammalian cell culture, the key toxic by-products assessed and monitored are lactate and ammonia. Often no distinction between the two isoforms of lactate is made. Here, we present profiles of both D - and L -lactate. D -Lactate is the end molecule of the methylglyoxal pathway. D -Lactate unlike L -lactate is not re-utilized, and although during normal culture time frames it represents one-tenth of total lactate, during lactate re-use it represents nearly 35%. This indicates significant carbon flow through pathways not associated with primary metabolites. We have observed that the behavior of D -lactate is radically different from that of L -lactate with the level of one isoform changing, whilst the concentration of the other remains constant. This is an example of an alternate carbon flow pathway containing metabolic intermediates that may potentially have a detrimental effect on cells. The activity of the methylglyoxal pathway when measured as a proportion of glucose consumption in this study far exceeds any previously reported. This highlights the potential importance of "non-primary" metabolisms to long lifespan mammalian fermentation practices. Biotechnol. Bioeng. 2010;107: 182,189. © 2010 Wiley Periodicals, Inc. [source] Active and inactive metabolic pathways in tumor spheroids: Determination by GC,MSBIOTECHNOLOGY PROGRESS, Issue 3 2010Michael G. Hunnewell Abstract Active metabolic pathways in three-dimensional cancer-cell cultures are potential chemotherapeutic targets that would be effective throughout tumors. Chaotic vasculature creates cellular regions in tumors with distinct metabolic behavior that are only present in aggregate cell masses. To quantify cancer cell metabolism, transformed mouse fibroblasts were grown as spheroids and fed isotopically labeled culture medium. Metabolite uptake and production rates were measured as functions of time. Gas chromatography,mass spectrometry was used to quantify the extent of labeling on amino acids present in cytoplasmic extracts. The labeling pattern identified several active and inactive metabolic pathways: Glutaminolysis was found to be active, and malic enzyme and gluconeogenesis were inactive. Transformed cells in spheroids were also found to actively synthesize serine, cysteine, alanine, aspartate, glutamate, and proline; and not synthesize glutamine. The activities of these pathways suggest that cancer cells consume glutamine for biosynthesis and not to provide cellular energy. Determining active metabolic pathways indicates how cells direct carbon flow and may lead to the discovery of novel molecular targets for anticancer therapy. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] Evaluating the impacts of climate and elevated carbon dioxide on tropical rainforests of the western Amazon basin using ecosystem models and satellite dataGLOBAL CHANGE BIOLOGY, Issue 1 2010HIROFUMI HASHIMOTO Abstract Forest inventories from the intact rainforests of the Amazon indicate increasing rates of carbon gain over the past three decades. However, such estimates have been questioned because of the poor spatial representation of the sampling plots and the incomplete understanding of purported mechanisms behind the increases in biomass. Ecosystem models, when used in conjunction with satellite data, are useful in examining the carbon budgets in regions where the observations of carbon flows are sparse. The purpose of this study is to explain observed trends in normalized difference vegetation index (NDVI) using climate observations and ecosystem models of varying complexity in the western Amazon basin for the period of 1984,2002. We first investigated trends in NDVI and found a positive trend during the study period, but the positive trend in NDVI was observed only in the months from August to December. Then, trends in various climate parameters were calculated, and of the climate variables considered, only shortwave radiation was found to have a corresponding significant positive trend. To compare the impact of each climate component, as well as increasing carbon dioxide (CO2) concentrations, on evergreen forests in the Amazon, we ran three ecosystem models (CASA, Biome-BGC, and LPJ), and calculated monthly net primary production by changing a climate component selected from the available climate datasets. As expected, CO2 fertilization effects showed positive trends throughout the year and cannot explain the positive trend in NDVI, which was observed only for the months of August to December. Through these simulations, we demonstrated that the positive trend in shortwave radiation can explain the positive trend in NDVI observed for the period from August to December. We conclude that the positive trend in shortwave radiation is the most likely driver of the increasing trend in NDVI and the corresponding observed increases in forest biomass. [source] | ||||||||||||||||||||||