|
| ||
|
|
||
Carbon Flux (carbon + flux)
Kinds of Carbon Flux Selected AbstractsMetabolic Carbon Fluxes and Biosynthesis of Polyhydroxyalkanoates in Ralstonia eutropha on Short Chain Fatty AcidsBIOTECHNOLOGY PROGRESS, Issue 4 2004Jian Yu Short chain fatty acids such as acetic, propionic, and butyric acids can be synthesized into polyhydroxyalkanoates (PHAs) by Ralstonia eutropha. Metabolic carbon fluxes of the acids in living cells have significant effect on the yield, composition, and thermomechanical properties of PHA bioplastics. Based on the general knowledge of central metabolism pathways and the unusual metabolic pathways in R. eutropha,a metabolic network of 41 bioreactions is constructed to analyze the carbon fluxes on utilization of the short chain fatty acids. In fed-batch cultures with constant feeding of acid media, carbon metabolism and distribution in R. eutropha were measured involving CO2, PHA biopolymers, and residual cell mass. As the cells underwent unsteady state metabolism and PHA biosynthesis under nitrogen-limited conditions, accumulative carbon balance was applied for pseudo-steady-state analysis of the metabolic carbon fluxes. Cofactor NADP/NADPH balanced between PHA synthesis and the C3/C4 pathway provided an independent constraint for solution of the underdetermined metabolic network. A major portion of propionyl-CoA was directed to pyruvate via the 2-methylcitrate cycle and further decarboxylated to acetyl-CoA. Only a small amount of propionate carbon (<15% carbon) was directly condensed with acetyl-CoA for 3-hydroxyvalerate. The ratio of glyoxylate shunt to TCA cycle varies from 0 to 0.25, depending on the intracellular acetyl-CoA level and acetic acid in the medium. Malate is the node of the C3/C4 pathway and TCA cycle and its decarboxylation to dehydrogenation ranges from 0.33 to 1.28 in response to the demands on NADPH and oxaloacetate for short chain fatty acids utilization. [source] Carbon flux from plants to soil: roots are a below-ground source of phenolic secondary compounds in an alpine ecosystemJOURNAL OF ECOLOGY, Issue 3 2008Courtney L. Meier Summary 1Phenolics are an important, biologically reactive component of the carbon (C) pool that moves from plants to soil. Once in soil, phenolics can regulate plant,soil feedbacks because of their influence on soil nitrogen biogeochemistry. 2Roots are a largely overlooked potential source of below-ground phenolic C. We examined phenolic fluxes from plants to soil in an alpine ecosystem, where phenolics are associated with slow rates of nutrient cycling. Using a phenolic-rich forb (Acomastylis rossii) and a grass with low tissue phenolics (Deschampsia caespitosa), we asked whether leaves, leaf litter or roots are the dominant source of soil phenolics during the growing season. We also determined whether the composition of root-derived phenolics differed from that of leaf litter. 3Both labile low molecular weight phenolics and tannins disappeared from A. rossii leaf litter over the winter. Evidence from this study and others indicates litter phenolics are not a significant source of labile C for soil microbes throughout the growing season. 4In the field, levels of phenolics were higher under A. rossii canopies than under D. caespitosa canopies throughout the growing season. We also estimated significantly higher phenolic fluxes into soils for A. rossii than for D. caespitosa in the glasshouse. Field and glasshouse results suggest roots are an important source of these compounds. Furthermore, the phenolic chemistry of roots was different from that of leaf litter, indicating that the effects of root phenolics on soil processes and neighbouring plant growth may differ from those associated with leaves. 5Synthesis. Based on our results, labile phenolic inputs from roots are likely to have a more important influence on soil nutrient dynamics during the alpine growing season than phenolic inputs from leaf litter. We suggest that roots may be the dominant input of labile phenolics to soil during the growing season in other ecosystems with seasonal patterns of plant growth and senescence. These observations are critical to our understanding of how phenolic-rich species may interact with soil microbes to influence soil nutrient cycling and shape the soil resource environment. [source] Mass invariance of population nitrogen flux by terrestrial mammalian herbivores: an extension of the energetic equivalence ruleECOLOGY LETTERS, Issue 9 2008Christopher W. Habeck Abstract According to the energetic equivalence rule, energy use by a population is independent of average adult body mass. Energy use can be equated with carbon flux, and it has been suggested that population fluxes of other materials, such as nitrogen and phosphorus, might also be independent of body mass. We compiled data on individual nitrogen deposition rates (via faeces and urine) and average population densities of 26 species of mammalian herbivores to test the hypothesis of elemental equivalence for nitrogen. We found that the mass scaling of individual nitrogen flux was opposite to that of population density for the species in our dataset. By computing the product of individual nitrogen flux and average population density for each species in our dataset, we found that population-level nitrogen flux was independent of species mass, averaging c. 3.22 g N ha,1 day,1. Results from this analysis can be used to understand the influence of mammalian herbivore communities on nitrogen cycling in terrestrial ecosystems. [source] Lymantria dispar herbivory induces rapid changes in carbon transport and partitioning in Populus nigraENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, Issue 1 2008Benjamin A. Babst Abstract We tested for rapid changes in photosynthate transport and partitioning in response to Lymantria dispar (L.) (Lepidoptera: Lymantriidae) (gypsy moth) herbivory in Populus nigra L. (Salicaceae). Transport and partitioning of [11C]-photosynthate from young mature leaves were measured in vivo before and 18 h after leaf chewing by gypsy moth larvae, which were caged on three older leaves. Following herbivory, there was an increase in export speed of recently fixed carbon from younger mature leaves. The increased export speed was due to a quicker transit time of 11C through the leaf, rather than a change in transport speed through the phloem. Additionally, basipetal partitioning of [11C]-photosynthate was increased following herbivory. Neither of these changes was observed in control plants. This enhancement of export occurs even though herbivores are well known to induce increases in carbon allocation to secondary metabolites within leaves. Our results demonstrate that the use of non-destructive imaging of 11C tracer is a powerful tool for examining plant responses to herbivory. Although the mechanisms underlying the rapid increase in carbon flux to stems and roots remain to be elucidated, our results raise the possibility of a coordinated whole plant response to herbivory. Thus, even when the herbivore specializes on only one plant tissue type, a whole plant approach may be key to understanding how plants respond to herbivory. [source] Kinetic and biochemical analyses on the reaction mechanism of a bacterial ATP-citrate lyaseFEBS JOURNAL, Issue 14 2002Tadayoshi Kanao The prokaryotic ATP-citrate lyase is considered to be a key enzyme of the carbon dioxide-fixing reductive tricarboxylic acid (RTCA) cycle. Kinetic examination of the ATP-citrate lyase from the green sulfur bacterium Chlorobium limicola (Cl -ACL), an ,4,4 heteromeric enzyme, revealed that the enzyme displayed typical Michaelis-Menten kinetics toward ATP with an apparent Km value of 0.21 ± 0.04 mm. However, strong negative cooperativity was observed with respect to citrate binding, with a Hill coefficient (nH) of 0.45. Although the dissociation constant of the first citrate molecule was 0.057 ± 0.008 mm, binding of the first citrate molecule to the enzyme drastically decreased the affinity of the enzyme for the second molecule by a factor of 23. ADP was a competitive inhibitor of ATP with a Ki value of 0.037 ± 0.006 mm. Together with previous findings that the enzyme catalyzed the reaction only in the direction of citrate cleavage, these kinetic features indicated that Cl -ACL can regulate both the direction and carbon flux of the RTCA cycle in C. limicola. Furthermore, in order to gain insight on the reaction mechanism, we performed biochemical analyses of Cl -ACL. His273 of the , subunit was indicated to be the phosphorylated residue in the catalytic center, as both catalytic activity and phosphorylation of the enzyme by ATP were abolished in an H273A mutant enzyme. We found that phosphorylation of the subunit was reversible. Nucleotide preference for activity was in good accordance with the preference for phosphorylation of the enzyme. Although residues interacting with nucleotides in the succinyl-CoA synthetase from Escherichia coli were conserved in AclB, AclA alone could be phoshorylated with the same nucleotide specificity observed in the holoenzyme. However, AclB was necessary for enzyme activity and contributed to enhance phosphorylation and stabilization of AclA. [source] Role of reserve carbohydrates in the growth dynamics of Saccharomyces cerevisiae,FEMS YEAST RESEARCH, Issue 8 2004Vincent Guillou Abstract The purpose of this study was to explore the role of glycogen and trehalose in the ability of Saccharomyces cerevisiae to respond to a sudden rise of the carbon flux. To this end, aerobic glucose-limited continuous cultures were challenged with a sudden increase of the dilution rate from 0.05 to 0.15 h,1. Under this condition, a rapid mobilization of glycogen and trehalose was observed which coincided with a transient burst of budding and a decrease of cell biomass. Experiments carried out with mutants defective in storage carbohydrates indicated a predominant role of glycogen in the adaptation to this perturbation. However, the real importance of trehalose in this response was veiled by the unexpected phenotypes harboured by the tps1 mutant, chosen for its inability to synthesize trehalose. First, the biomass yield of this mutant was 25% lower than that of the isogenic wild-type strain at dilution rate of 0.05 h,1, and this difference was annulled when cultures were run at a higher dilution rate of 0.15 h,1. Second, the tps1 mutant was more effective to sustain the dilution rate shift-up, apparently because it had a faster glycolytic rate and an apparent higher capacity to consume glucose with oxidative phosphorylation than the wild type. Consequently, a tps1gsy1gsy2 mutant was able to adapt to the dilution rate shift-up after a long delay, likely because the detrimental effects from the absence of glycogen was compensated for by the tps1 mutation. Third, a glg1,glg2, strain, defective in glycogen synthesis because of the lack of the glycogen initiation protein, recovered glycogen accumulation upon further deletion of TPS1. This recovery, however, required glycogen synthase. Finally, we demonstrated that the rapid breakdown of reserve carbohydrates triggered by the shift-up is merely due to changes in the concentrations of hexose-6-phosphate and UDPglucose, which are the main metabolic effectors of the rate-limiting enzymes of glycogen and trehalose pathways. [source] Plant functional group identity influences short-term peatland ecosystem carbon flux: evidence from a plant removal experimentFUNCTIONAL ECOLOGY, Issue 2 2009Susan E. Ward Summary 1Northern hemisphere peatlands are globally important stores of organic soil carbon. We examined effects of plant functional group identity on short-term carbon (C) flux in an ombrotrophic peatland in northern England, UK, by selectively removing one of each of the three dominant plant functional groups (ericoid dwarf-shrubs, graminoids and bryophytes). Carbon dynamics were quantified by a combination of CO2 flux measurements and 13CO2 stable isotope pulse labelling approaches. 2Significant effects of plant functional group removals on CO2 fluxes and tracer 13C uptake and turnover were detected. Removal of ericoid dwarf-shrubs had the greatest influence on gross CO2 flux, increasing rates of respiration and photosynthesis by > 200% relative to the undisturbed control. After pulse labelling with 13CO2, we found that turnover of recent photosynthate, measured as respired 13CO2, was also greatest in the absence of dwarf-shrubs. 3Analysis of 13C tracer enrichment in leaf tissues from all plant removal treatments showed that the rate of fixation of 13CO2 and turnover of 13C labelled photosynthate in leaf tissue was greatest in graminoids and lowest in bryophytes. Furthermore, graminoid leaf 13C enrichment was greatest when growing in the absence of dwarf-shrubs, suggesting that the presence of dwarf-shrubs reduced the photosynthetic activity of graminoids. 4We conclude that plant functional groups differentially influence the uptake and short-term flux of carbon in peatlands, suggesting that changes in the functional composition of vegetation resulting from global change have the potential to alter short-term patterns of carbon exchange in peatland. [source] Below-ground carbon flux and partitioning: global patterns and response to temperatureFUNCTIONAL ECOLOGY, Issue 6 2008C. M. Litton Summary 1The fraction of gross primary production (GPP) that is total below-ground carbon flux (TBCF) and the fraction of TBCF that is below-ground net primary production (BNPP) represent globally significant C fluxes that are fundamental in regulating ecosystem C balance. However, global estimates of the partitioning of GPP to TBCF and of TBCF to BNPP, as well as the absolute size of these fluxes, remain highly uncertain. 2Efforts to model below-ground processes are hindered by methodological difficulties for estimating below-ground C cycling, the complexity of below-ground interactions, and an incomplete understanding of the response of GPP, TBCF and BNPP to climate change. Due to a paucity of available data, many terrestrial ecosystem models and ecosystem-level studies of whole stand C use efficiency rely on assumptions that: (i) C allocation patterns across large geographic, climatic and taxonomic scales are fixed; and (ii) c. 50% of TBCF is BNPP. 3Here, we examine available information on GPP, TBCF, BNPP, TBCF : GPP and BNPP : TBCF from a diverse global data base of forest ecosystems to understand patterns in below-ground C flux and partitioning, and their response to mean annual temperature (MAT). 4MAT and mean annual precipitation (MAP) covaried strongly across the global forest data base (37 mm increase in MAP for every 1 °C increase in MAT). In all analyses, however, MAT was the most important variable explaining observed patterns in below-ground C processes. 5GPP, TBCF and BNPP all increased linearly across the global scale range of MAT. TBCF : GPP increased significantly with MAT for temperate and tropical ecosystems (> 5 °C), but variability was high across the data set. BNPP : TBCF varied from 0·26 to 0·53 across the entire MAT gradient (,5 to 30 °C), with a much narrower range of 0·42 to 0·53 for temperate and tropical ecosystems (5 to 30 °C). 6Variability in the data sets was moderate and clear exceptions to the general patterns exist that likely relate to other factors important for determining below-ground C flux and partitioning, in particular water availability and nutrient supply. Still, our results highlight global patterns in below-ground C flux and partitioning in forests in response to MAT that in part confirm previously held assumptions. [source] Biodiversity and ecosystem function in soilFUNCTIONAL ECOLOGY, Issue 3 2005A. H. FITTER Summary 1Soils are one of the last great frontiers for biodiversity research and are home to an extraordinary range of microbial and animal groups. Biological activities in soils drive many of the key ecosystem processes that govern the global system, especially in the cycling of elements such as carbon, nitrogen and phosphorus. 2We cannot currently make firm statements about the scale of biodiversity in soils, or about the roles played by soil organisms in the transformations of organic materials that underlie those cycles. The recent UK Soil Biodiversity Programme (SBP) has brought a unique concentration of researchers to bear on a single soil in Scotland, and has generated a large amount of data concerning biodiversity, carbon flux and resilience in the soil ecosystem. 3One of the key discoveries of the SBP was the extreme diversity of small organisms: researchers in the programme identified over 100 species of bacteria, 350 protozoa, 140 nematodes and 24 distinct types of arbuscular mycorrhizal fungi. Statistical analysis of these results suggests a much greater ,hidden diversity'. In contrast, there was no unusual richness in other organisms, such as higher fungi, mites, collembola and annelids. 4Stable-isotope (13C) technology was used to measure carbon fluxes and map the path of carbon through the food web. A novel finding was the rapidity with which carbon moves through the soil biota, revealing an extraordinarily dynamic soil ecosystem. 5The combination of taxonomic diversity and rapid carbon flux makes the soil ecosystem highly resistant to perturbation through either changing soil structure or removing selected groups of organisms. [source] Quantifying root lateral distribution and turnover using pine trees with a distinct stable carbon isotope signatureFUNCTIONAL ECOLOGY, Issue 1 2005K. JOHNSEN Summary 1In order to help assess spatial competition for below-ground resources, we quantified the effects of fertilization on root biomass quantity and lateral root distribution of mid-rotation Pinus taeda trees. Open-top chambers exposed trees to ambient or ambient plus 200 µmol mol,1 atmospheric CO2 for 31 months. 2Tank CO2 was depleted in atmospheric 13C; foliage of elevated CO2 trees had ,13C of ,42·9, compared with ,29·1 for ambient CO2 trees. 3Roots 1 m from the base of elevated CO2 -grown trees had more negative ,13C relative to control trees, and this difference was detected, on average, up to 5·8, 3·7 and 3·7 m away from the trees for 0,2, 2,5 and >5 mm root-size classes, respectively. Non-fertilized tree roots extended as far as fertilized trees despite the fact that their above-ground biomass was less than half that of fertilized trees. 4These results are informative with respect to root sampling intensity and protocol, and the distances required between experimental manipulations to evaluate below-ground processes of independent treatments. 5Fine-root turnover has usually been estimated to range from weeks to 3 years, representing a major avenue of carbon flux. Using a mixing model we calculated that 0,2 mm roots had a mean residence time of 4·5 years indicating relatively slow fine-root turnover, a result that has major implications in modelling C cycling. [source] Litter decomposition in grasslands of Central North America (US Great Plains)GLOBAL CHANGE BIOLOGY, Issue 5 2009ELIANA E. BONTTI Abstract One of the major concerns about global warming is the potential for an increase in decomposition and soil respiration rates, increasing CO2 emissions and creating a positive feedback between global warming and soil respiration. This is particularly important in ecosystems with large belowground biomass, such as grasslands where over 90% of the carbon is allocated belowground. A better understanding of the relative influence of climate and litter quality on litter decomposition is needed to predict these changes accurately in grasslands. The Long-Term Intersite Decomposition Experiment Team (LIDET) dataset was used to evaluate the influence of climatic variables (temperature, precipitation, actual evapotranspiration, and climate decomposition index), and litter quality (lignin content, carbon : nitrogen, and lignin : nitrogen ratios) on leaf and root decomposition in the US Great Plains. Wooden dowels were used to provide a homogeneous litter quality to evaluate the relative importance of above and belowground environments on decomposition. Contrary to expectations, temperature did not explain variation in root and leaf decomposition, whereas precipitation partially explained variation in root decomposition. Percent lignin was the best predictor of leaf and root decomposition. It also explained most variation in root decomposition in models which combined litter quality and climatic variables. Despite the lack of relationship between temperature and root decomposition, temperature could indirectly affect root decomposition through decreased litter quality and increased water deficits. These results suggest that carbon flux from root decomposition in grasslands would increase, as result of increasing temperature, only if precipitation is not limiting. However, where precipitation is limiting, increased temperature would decrease root decomposition, thus likely increasing carbon storage in grasslands. Under homogeneous litter quality, belowground decomposition was faster than aboveground and was best predicted by mean annual precipitation, which also suggests that the high moisture in soil accelerates decomposition belowground. [source] A non-native invasive grass increases soil carbon flux in a Hawaiian tropical dry forestGLOBAL CHANGE BIOLOGY, Issue 4 2008CREIGHTON M. LITTON Abstract Non-native plants are invading terrestrial ecosystems across the globe, yet little is known about how invasions impact carbon (C) cycling or how these impacts will be influenced by climate change. We quantified the effect of a non-native C4 grass invasion on soil C pools and fluxes in a Hawaiian tropical dry forest over 2 years in which annual precipitation was average (Year 1) and ,60% higher than average (Year 2). Work was conducted in a series of forested plots where the grass understory was completely removed (removal plots) or left intact (grass plots) for 3 years before experiment initiation. We hypothesized that grass invasion would: (i) not change total soil C pools, (ii) increase the flux of C into and out of soils, and (iii) increase the sensitivity of soil C flux to variability in precipitation. In grass plots, grasses accounted for 25,34% of litter layer C and ,70% of fine root C. However, no differences were observed between treatments in the size of any soil C pools. Moreover, grass-derived C constituted a negligible fraction of the large mineral soil C pool (< 3%) despite being present in the system for ,50 years. Tree litterfall was ,45% lower in grass plots, but grass-derived litterfall more than compensated for this reduction in both years. Annual cumulative soil-surface CO2 efflux (Rsoil) was ,40% higher in grass plots in both years, and increased in both treatments by ,36% in the wetter Year 2. Despite minimal grass-derived mineral soil C, > 75% of Rsoil in grass plots was of C4 (i.e. grass) origin. These results demonstrate that grass invasion in forest ecosystems can increase the flux of C into and out of soils without changing total C pools, at least over the short term and as long as the native tree canopy remains intact, and that invasion-mediated changes in belowground C cycling are sensitive to precipitation. [source] Net regional ecosystem CO2 exchange from airborne and ground-based eddy covariance, land-use maps and weather observationsGLOBAL CHANGE BIOLOGY, Issue 3 2007F. MIGLIETTA Abstract Measurements of regional net ecosystem exchange (NEE) were made over a period of 21 days in summer 2002 in the South-Central part of the Netherlands and extrapolated to an area of 13 000 km2 using a combination of flux measurements made by a Sky Arrow ERA research aircraft, half-hourly eddy covariance data from four towers, half-hourly weather data recorded by three weather stations and detailed information on regional land use. The combination of this type of information allowed to estimate the net contribution of the terrestrial ecosystems to the overall regional carbon flux and to map dynamically the temporal and spatial variability of the fluxes. A regional carbon budget was calculated for the study period and the contributions of the different land uses to the overall regional flux, were assessed. Ecosystems were, overall, a small source of carbon to the atmosphere equivalent to to 0.23±0.025 g C m,2 day,1. When considered separately, arable and grasslands were a source of, respectively, 0.68±0.022 and 1.28±0.026 g C m,2 day,1. Evergreen and deciduous forests were instead a sink of ,1.42±0.015 g C m,2 day,1. During the study period, forests offset approximately 3.5% of anthropogenic carbon emission estimates obtained from inventory data. Lacking of a robust validation, NEE values obtained with this method were compared with independent state of art estimates of the regional carbon balance that were obtained by applying a semi-empirical model of NEE driven by MODIS satellite fAPAR data. The comparison showed an acceptable matching for the carbon balance of forest that was a sink in both cases, while a much larger difference for arable and grassland was found. Those ecosystems were a sink for satellite-based estimates while they were a source for the combined aircraft and tower estimates. Possible causes of such differences are discussed and partly addressed. The importance of new methods for determining carbon balance at the regional scale, is outlined. [source] On the variability of respiration in terrestrial ecosystems: moving beyond Q10GLOBAL CHANGE BIOLOGY, Issue 2 2006ERIC A. DAVIDSON Abstract Respiration, which is the second most important carbon flux in ecosystems following gross primary productivity, is typically represented in biogeochemical models by simple temperature dependence equations. These equations were established in the 19th century and have been modified very little since then. Recent applications of these equations to data on soil respiration have produced highly variable apparent temperature sensitivities. This paper searches for reasons for this variability, ranging from biochemical reactions to ecosystem-scale substrate supply. For a simple membrane-bound enzymatic system that follows Michaelis,Menten kinetics, the temperature sensitivities of maximum enzyme activity (Vmax) and the half-saturation constant that reflects the affinity of the enzyme for the substrate (Km) can cancel each other to produce no net temperature dependence of the enzyme. Alternatively, when diffusion of substrates covaries with temperature, then the combined temperature sensitivity can be higher than that of each individual process. We also present examples to show that soluble carbon substrate supply is likely to be important at scales ranging from transport across membranes, diffusion through soil water films, allocation to aboveground and belowground plant tissues, phenological patterns of carbon allocation and growth, and intersite differences in productivity. Robust models of soil respiration will require that the direct effects of substrate supply, temperature, and desiccation stress be separated from the indirect effects of temperature and soil water content on substrate diffusion and availability. We speculate that apparent Q10 values of respiration that are significantly above about 2.5 probably indicate that some unidentified process of substrate supply is confounded with observed temperature variation. [source] Patterns of rhizosphere carbon flux in sugar maple (Acer saccharum) and yellow birch (Betula allegheniensis) saplingsGLOBAL CHANGE BIOLOGY, Issue 6 2005Richard P. Phillips Abstract Despite its importance in the terrestrial C cycle rhizosphere carbon flux (RCF) has rarely been measured for intact root,soil systems. We measured RCF for 8-year-old saplings of sugar maple (Acer saccharum) and yellow birch (Betula allegheniensis) collected from the Hubbard Brook Experimental Forest (HBEF), NH and transplanted into pots with native soil horizons intact. Five saplings of each species were pulse labeled with 13CO2 at ambient CO2 concentrations for 4,6 h, and the 13C label was chased through rhizosphere and bulk soil pools in organic and mineral horizons for 7 days. We hypothesized yellow birch roots would supply more labile C to the rhizosphere than sugar maple roots based on the presumed greater C requirements of ectomycorrhizal roots. We observed appearance of the label in rhizosphere soil of both species within the first 24 h, and a striking difference between species in the timing of 13C release to soil. In sugar maple, peak concentration of the label appeared 1 day after labeling and declined over time whereas in birch the label increased in concentration over the 7-day chase period. The sum of root and rhizomicrobial respiration in the pots was 19% and 26% of total soil respiration in sugar maple and yellow birch, respectively. Our estimate of the total amount of RCF released by roots was 6.9,7.1% of assimilated C in sugar maple and 11.2,13.0% of assimilated C in yellow birch. These fluxes extrapolate to 55,57 and 90,104 g C m,2 yr,1 from sugar maple and yellow birch roots, respectively. These results suggest RCF from both arbuscular mycorrhizal and ectomycorrhizal roots represents a substantial flux of C to soil in northern hardwood forests with important implications for soil microbial activity, nutrient availability and C storage. [source] Variation in wood density determines spatial patterns inAmazonian forest biomassGLOBAL CHANGE BIOLOGY, Issue 5 2004Timothy R. Baker Abstract Uncertainty in biomass estimates is one of the greatest limitations to models of carbon flux in tropical forests. Previous comparisons of field-based estimates of the aboveground biomass (AGB) of trees greater than 10 cm diameter within Amazonia have been limited by the paucity of data for western Amazon forests, and the use of site-specific methods to estimate biomass from inventory data. In addition, the role of regional variation in stand-level wood specific gravity has not previously been considered. Using data from 56 mature forest plots across Amazonia, we consider the relative roles of species composition (wood specific gravity) and forest structure (basal area) in determining variation in AGB. Mean stand-level wood specific gravity, on a per stem basis, is 15.8% higher in forests in central and eastern, compared with northwestern Amazonia. This pattern is due to the higher diversity and abundance of taxa with high specific gravity values in central and eastern Amazonia, and the greater diversity and abundance of taxa with low specific gravity values in western Amazonia. For two estimates of AGB derived using different allometric equations, basal area explains 51.7% and 63.4%, and stand-level specific gravity 45.4% and 29.7%, of the total variation in AGB. The variation in specific gravity is important because it determines the regional scale, spatial pattern of AGB. When weighting by specific gravity is included, central and eastern Amazon forests have significantly higher AGB than stands in northwest or southwest Amazonia. The regional-scale pattern of species composition therefore defines a broad gradient of AGB across Amazonia. [source] Net grassland carbon flux over a subambient to superambient CO2 gradientGLOBAL CHANGE BIOLOGY, Issue 7 2001P. C. Mielnick Abstract Increasing atmospheric CO2 concentrations may have a profound effect on the structure and function of plant communities. A previously grazed, central Texas grassland was exposed to a 200-µmol mol,1 to 550 µmol mol,1 CO2 gradient from March to mid-December in 1998 and 1999 using two, 60-m long, polyethylene- covered chambers built directly onto the site. One chamber was operated at subambient CO2 concentrations (200,360 µmol mol,1 daytime) and the other was regulated at superambient concentrations (360,550 µmol mol,1). Continuous CO2 gradients were maintained in each chamber by photosynthesis during the day and respiration at night. Net ecosystem CO2 flux and end-of-year biomass were measured in each of 10, 5-m long sections in each chamber. Net CO2 fluxes were maximal in late May (c. day 150) in 1998 and in late August in 1999 (c. day 240). In both years, fluxes were near zero and similar in both chambers at the beginning and end of the growing season. Average daily CO2 flux in 1998 was 13 g CO2 m,2 day,1 in the subambient chamber and 20 g CO2 m,2 day,1 in the superambient chamber; comparable averages were 15 and 26 g CO2 m,2 day,1 in 1999. Flux was positively and linearly correlated with end-of-year above-ground biomass but flux was not linearly correlated with CO2 concentration; a finding likely to be explained by inherent differences in vegetation. Because C3 plants were the dominant functional group, we adjusted average daily flux in each section by dividing the flux by the average percentage C3 cover. Adjusted fluxes were better correlated with CO2 concentration, although scatter remained. Our results indicate that after accounting for vegetation differences, CO2 flux increased linearly with CO2 concentration. This trend was more evident at subambient than superambient CO2 concentrations. [source] Hydrological and biogeochemical processes in a changing Amazon: results from small watershed studies and the large-scale biosphere-atmosphere experimentHYDROLOGICAL PROCESSES, Issue 12 2006Christopher Neill Abstract The Amazon Basin is the world's largest tropical forest region and one where rapid human changes to land cover have the potential to cause significant changes to hydrological and biogeochemical processes. The Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA) is a multidisciplinary, multinational research program led by Brazil. The goal of LBA is to understand how the Amazon Basin functions as a regional entity in the earth system and how these functions are changing as a result of ongoing human activity. This compilation of nine papers focuses on a central LBA question in the area of nutrient dynamics and surface water chemistry,how do changes in land use alter fluxes of dissolved and particulate materials from uplands across riparian zones and down the channels of river corridors? These papers cover work conducted in small watersheds on a wide range of topics within the spirit and geographical focus area of LBA: water balance and runoff generation, nutrient transformations in riparian zones and stream channels, carbon fluxes in water moving from land to water and the influence of soils on flowpath structure and stream chemistry. Important new insights can be gained from these and other studies. Forest clearing for pastures results in a decrease in soil hydraulic conductivity that forces water into surficial flowpaths throughout most of the rainy season across wide regions of the Amazon. Riparian zones along small forest streams appear to be very effective in removing nitrate arriving from the uplands, while forest streams take up nitrate at very low rates, allowing them to travel downstream for long distances. Although substantial, the contribution of dissolved organic C (DOC) to the carbon flux from forests to streams appears to be lower than the flux of dissolved inorganic C that is subsequently outgassed as CO2. Remaining key challenges within LBA will be to synthesize existing data sets on river networks, soils, climate, land use and planned infrastructure for the Amazon to develop models capable of predicting hydrologic and biogeochemical fluxes at a variety of scales relevant to the development of strategies for sustainable management of the Amazon's remarkable forest, soil and freshwater resources. Copyright © 2006 John Wiley & Sons, Ltd. [source] Quantifying uncertainty in the biospheric carbon flux for England and WalesJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES A (STATISTICS IN SOCIETY), Issue 1 2008Marc Kennedy Summary., A crucial issue in the current global warming debate is the effect of vegetation and soils on carbon dioxide (CO2) concentrations in the atmosphere. Vegetation can extract CO2 through photosynthesis, but respiration, decay of soil organic matter and disturbance effects such as fire return it to the atmosphere. The balance of these processes is the net carbon flux. To estimate the biospheric carbon flux for England and Wales, we address the statistical problem of inference for the sum of multiple outputs from a complex deterministic computer code whose input parameters are uncertain. The code is a process model which simulates the carbon dynamics of vegetation and soils, including the amount of carbon that is stored as a result of photosynthesis and the amount that is returned to the atmosphere through respiration. The aggregation of outputs corresponding to multiple sites and types of vegetation in a region gives an estimate of the total carbon flux for that region over a period of time. Expert prior opinions are elicited for marginal uncertainty about the relevant input parameters and for correlations of inputs between sites. A Gaussian process model is used to build emulators of the multiple code outputs and Bayesian uncertainty analysis is then used to propagate uncertainty in the input parameters through to uncertainty on the aggregated output. Numerical results are presented for England and Wales in the year 2000. It is estimated that vegetation and soils in England and Wales constituted a net sink of 7.55 Mt C (1 Mt C = 1012 g of carbon) in 2000, with standard deviation 0.56 Mt C resulting from the sources of uncertainty that are considered. [source] Experimentally testing the role of foundation species in forests: the Harvard Forest Hemlock Removal ExperimentMETHODS IN ECOLOGY AND EVOLUTION, Issue 2 2010Aaron M. Ellison Summary 1.,Problem statement, Foundation species define and structure ecological systems. In forests around the world, foundation tree species are declining due to overexploitation, pests and pathogens. Eastern hemlock (Tsuga canadensis), a foundation tree species in eastern North America, is threatened by an exotic insect, the hemlock woolly adelgid (Adelges tsugae). The loss of hemlock is hypothesized to result in dramatic changes in assemblages of associated species with cascading impacts on food webs and fluxes of energy and nutrients. We describe the setting, design and analytical framework of the Harvard Forest Hemlock Removal Experiment (HF-HeRE), a multi-hectare, long-term experiment that overcomes many of the major logistical and analytical challenges of studying system-wide consequences of foundation species loss. 2.,Study design, HF-HeRE is a replicated and blocked Before-After-Control-Impact experiment that includes two hemlock removal treatments: girdling all hemlocks to simulate death by adelgid and logging all hemlocks >20 cm diameter and other merchantable trees to simulate pre-emptive salvage operations. These treatments are paired with two control treatments: hemlock controls that are beginning to be infested in 2010 by the adelgid and hardwood controls that represent future conditions of most hemlock stands in eastern North America. 3.,Ongoing measurements and monitoring, Ongoing long-term measurements to quantify the magnitude and direction of forest ecosystem change as hemlock declines include: air and soil temperature, light availability, leaf area and canopy closure; changes in species composition and abundance of the soil seed-bank, understorey vegetation, and soil-dwelling invertebrates; dynamics of coarse woody debris; soil nitrogen availability and net nitrogen mineralization; and soil carbon flux. Short-term or one-time-only measurements include initial tree ages, hemlock-decomposing fungi, wood-boring beetles and throughfall chemistry. Additional within-plot, replicated experiments include effects of ants and litter-dwelling microarthoropods on ecosystem functioning, and responses of salamanders to canopy change. 4.,Future directions and collaborations, HF-HeRE is part of an evolving network of retrospective studies, natural experiments, large manipulations and modelling efforts focused on identifying and understanding the role of single foundation species on ecological processes and dynamics. We invite colleagues from around the world who are interested in exploring complementary questions to take advantage of the HF-HeRE research infrastructure. [source] Root carbon flux: measurements versus mechanismsNEW PHYTOLOGIST, Issue 1 2009Paul J. Hanson No abstract is available for this article. [source] Direct and indirect effects of elevated CO2 on leaf respiration in a forest ecosystemPLANT CELL & ENVIRONMENT, Issue 9 2001J. G. Hamilton Abstract We measured the short-term direct and long-term indirect effects of elevated CO2 on leaf dark respiration of loblolly pine (Pinus taeda) and sweetgum (Liquidambar styraciflua) in an intact forest ecosystem. Trees were exposed to ambient or ambient + 200 µmol mol,1 atmospheric CO2 using free-air carbon dioxide enrichment (FACE) technology. After correcting for measurement artefacts, a short-term 200 µmol mol,1 increase in CO2 reduced leaf respiration by 7,14% for sweetgum and had essentially no effect on loblolly pine. This direct suppression of respiration was independent of the CO2 concentration under which the trees were grown. Growth under elevated CO2 did not appear to have any long-term indirect effects on leaf maintenance respiration rates or the response of respiration to changes in temperature (Q10, R0). Also, we found no relationship between mass-based respiration rates and leaf total nitrogen concentrations. Leaf construction costs were unaffected by growth CO2 concentration, although leaf construction respiration decreased at elevated CO2 in both species for leaves at the top of the canopy. We conclude that elevated CO2 has little effect on leaf tissue respiration, and that the influence of elevated CO2 on plant respiratory carbon flux is primarily through increased biomass. [source] New insights into plant transaldolaseTHE PLANT JOURNAL, Issue 1 2005Maxime Caillau Summary The oxidative pentose phosphate pathway (OPPP) provides plants with important substrates for both primary and secondary metabolism via the oxidation of glucose-6-phosphate. The OPPP is also thought to generate large amounts of reducing power to drive various anabolic processes. In animals this major pathway is located within the cytoplasm of cells, but in plants its subcellular compartmentation is far from clear. Although several enzymes of the OPPP were demonstrated to have both cytosolic and plastidic counterparts, there is yet no evidence for a full set of functional enzymes in each compartment. We report here the isolation of two coding sequences from tomato (Lycopersicon esculentum L.) which encode phylogenetically distant sequences (ToTal1 and ToTal2) that putatively encode distinct plastidic TA isoforms. The kinetic characterization of ToTal1 revealed that, unlike other enzymes of the non-oxidative branch of the OPPP, ToTal1 does not follow a Michaelis,Menten mode of catalysis which has implications for its role in regulating carbon flux between primary and secondary metabolism. TA genes appear to be differentially regulated at the level of gene expression in plant tissues and in response to environmental factors which suggests that TA isoforms have a non-overlapping role for plant metabolism. [source] Metabolic and transcriptional response of recombinant Escherichia coli to elevated dissolved carbon dioxide concentrationsBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009Antonino Baez Abstract The effect of dissolved carbon dioxide (dCO2) concentration on the stoichiometric and kinetic constants and by-product accumulation was determined for Escherichia coli cells producing recombinant green fluorescent protein (GFP). Constant dCO2, in the range of 20,300,mbar, was maintained during batch cultures by manipulating the inlet gas composition. As dCO2 increased, specific growth rate (µ) decreased, and acetate accumulation and the time for onset of GFP production increased. Maximum biomass yield on glucose and GFP concentration were affected for dCO2 above 70 and 150,mbar, respectively. Expression analysis of 16 representative genes showed that E. coli can respond at the transcriptional level upon exposure to increasing dCO2, and revealed possible mechanisms responsible for the detrimental effects of high dCO2. Genes studied included those involved in decarboxylation reactions (aceF, icdA, lpdA, sucA, sucB), genes from pathways of production and consumption of acetate (ackA, poxB, acs, aceA, fadR), genes from gluconeogenic and anaplerotic metabolism (pckA, ppc), genes from the acid resistance (AR) systems (adiA, gadA, gadC), and the heterologous gene (gfp). The transcription levels of tricarboxylic acid (TCA) cycle genes (icdA, sucA, sucB) and glyoxylate shunt (aceA) decreased as dCO2 increased, whereas fadR (that codes for a negative regulator of the glyoxylate operon) and poxB (that codes for PoxB which is involved in acetate production from pyruvate) were up-regulated as dCO2 increased up to 150,mbar. Furthermore, transcription levels of genes from the AR systems increased as dCO2 increased up to 150,mbar, indicating that elevated dCO2 triggers an acid stress response in E. coli cells. Altogether, such results suggest that the increased acetate accumulation and reduction in µ, biomass yield and maximum GFP concentration under high dCO2 resulted from a lower carbon flux to TCA cycle, the concomitant accumulation of acetyl-CoA or pyruvate, and the acidification of the cytoplasm. Biotechnol. Bioeng. 2009; 104: 102,110 © 2009 Wiley Periodicals, Inc. [source] Stimulation, Monitoring, and Analysis of Pathway Dynamics by Metabolic Profiling in the Aromatic Amino Acid PathwayBIOTECHNOLOGY PROGRESS, Issue 6 2004M. Oldiges Using a concerted approach of biochemical standard preparation, analytical access via LC-MS/MS, glucose pulse, metabolic profiling, and statistical data analysis, the metabolism dynamics in the aromatic amino acid pathway has been stimulated, monitored, and analyzed in different tyrosine-auxotrophic l -phenylalanine-producing Escherichiacoli strains. During the observation window from ,4 s (before) up to 27 s after the glucose pulse, the dynamics of the first five enzymatic reactions in the aromatic amino acid pathway was observed by measuring intracellular concentrations of 3-deoxy- d -arabino-heptulosonate 7-phosphate DAH(P), 3-dehydroquinate (3-DHQ), 3-dehydroshikimate (3-DHS), shikimate 3-phosphate (S3P), and shikimate (SHI), together with the pathway precursors phosphoenolpyruvate (PEP) and P5P, the lumped pentose phosphate pool as an alternative to the nondetectable erythrose 4-phosphate (E4P). Provided that a sufficient fortification of the carbon flux into the pathway of interest is ensured, respective metabolism dynamics can be observed. On the basis of the intracellular pool measurements, the standardized pool velocities were calculated, and a simple, data-driven criterion-called "pool efflux capacity" (PEC)-is derived. Despite its simplifying system description, the criterion managed to identify the well-known AroB limitation in the E. coli strain A (genotype ,( pheA tyrA aroF)/pJF119EH aroFfbrpheAfbramp) and it also succeeded to identify AroL and AroA (in strain B, genotype ,( pheA tyrA aroF)/pJF119EH aroFfbrpheAfbraroB amp) as promising metabolic engineering targets to alleviate respective flux control in subsequent l -Phe producing strains. Furthermore, using of a simple correlation analysis, the reconstruction of the metabolite sequence of the observed pathway was enabled. The results underline the necessity to extend the focus of glucose pulse experiments by studying not only the central metabolism but also anabolic pathways. [source] Understanding and Improving NADPH-Dependent Reactions by Nongrowing Escherichia coli CellsBIOTECHNOLOGY PROGRESS, Issue 2 2004Adam Z. Walton We have shown that whole Escherichia coli cells overexpressing NADPH-dependent cyclohexanone monooxygenase carry out a model Baeyer-Villiger oxidation with high volumetric productivity (0.79 g ,-caprolactone/L·h ) under nongrowing conditions (Walton, A. Z.; Stewart, J. D. Biotechnol. Prog.2002, 18, 262,268). This is approximately 20-fold higher than the space-time yield for reactions that used growing cells of the same strain. Here, we show that the intracellular stability of cyclohexanone monooxygenase and the rate of substrate transport across the cell membrane were the key limitations on the overall reaction duration and rate, respectively. Directly measuring the levels of intracellular nicotinamide cofactors under bioprocess conditions suggested that E. coli cells could support even more efficient NADPH-dependent bioconversions if a more suitable enzyme-substrate pair were identified. This was demonstrated by reducing ethyl acetoacetate with whole cells of an E. coli strain that overexpressed an NADPH-dependent, short-chain dehydrogenase from bakerapos;s yeast ( Saccharomyces cerevisiae). Under glucose-fed, nongrowing conditions, this reduction proceeded with a space-time yield of 2.0 g/L·h and a final product titer of 15.8 g/L using a biocatalyst:substrate ratio (g/g) of only 0.37. These values are significantly higher than those obtained previously. Moreover, the stoichiometry linking ketone reduction and glucose consumption (2.3 ± 0.1) suggested that the citric acid cycle supplied the bulk of the intracellular NADPH under our process conditions. This information can be used to improve the efficiency of glucose utilization even further by metabolic engineering strategies that increase carbon flux through the pentose phosphate pathway. [source] Alterations in Taxol Production in Plant Cell Culture via Manipulation of the Phenylalanine Ammonia Lyase PathwayBIOTECHNOLOGY PROGRESS, Issue 6 2002Michelle C. Brincat One approach to increasing secondary metabolite production in plant cell culture is to manipulate metabolic pathways to utilize more resources toward production of one desired compound or class of compounds, such as diverting carbon flux from competing secondary pathways. Since phenylalanine provides both the phenylisoserine side chain and the benzoyl moiety at C-2 of Taxol, we speculated that blockage of the phenylpropanoid pathway might divert phenylalanine into Taxol biosynthesis. We used specific enzyme inhibitors to target the first enzyme in the phenylpropanoid pathway, phenylalanine ammonia lyase (PAL), the critical control point for conversion of l -phenylalanine to trans -cinnamic acid. Cinnamic acid acted quickly in reducing PAL activity by 40,50%, without affecting total protein levels, but it generally inhibited the taxane pathway, reducing Taxol by 90% of control levels. Of the taxanes produced, 13-acetyl-9-dihydro-baccatin III and 9-dihydrobaccatin III doubled as a percentage of total taxanes in C93AD and CO93P cells treated with 0.20 and 0.25 mM cinnamic acid, when all other taxanes were lowered. The PAL inhibitor ,-aminooxyacetic acid (AOA) almost entirely shut down Taxol production at both 0.5 and 1.5 mM, whereas l -,-aminooxy-,-phenylpropionic acid (AOPP) had the opposite effect, slightly enhancing Taxol production at 1 ,M but having no effect at 10 ,M. The discrepancy in the effectiveness of AOA and AOPP and the lack of effect with addition of phenylalanine or benzoic acid derivatives further indicates that the impact of cinnamic acid on Taxol is related not to its effect on PAL but rather to a specific effect on the taxane pathway. On the basis of these results, a less direct route for inhibiting the phenylpropanoid pathway may be required to avoid unwanted side effects and potentially enhance Taxol production. [source] Precursor Balancing for Metabolic Engineering of Lycopene Production in Escherichia coliBIOTECHNOLOGY PROGRESS, Issue 1 2001William R. Farmer One issue that must be addressed in the rational design of metabolic pathways is the elimination of potential bottlenecks in the upstream pathways. We have reconstructed the isoprenoid pathway to overproduce the carotenoid lycopene in Escherichia coli. Here we show that the distribution between pyruvate and glyceraldehyde 3-phosphate (G3P), the originating precursors of the isoprenoid pathway, is a major factor that can limit isoprenoid production yields in E. coli. In particular, alterations in the central metabolism that redirect flux from pyruvate back to G3P enhance lycopene production, while alterations that channel carbon flux away from the G3P pool have the opposite effect. These results suggest that G3P may be limiting in the biosynthesis of lycopene, and modifications that achieve a more equitable distribution between the two precursors are able to increase the lycopene yield in metabolically engineered E. coli. [source] Organic matter quality of a forest soil subjected to repeated drying and different re-wetting intensitiesEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 2 2010A. Schmitt Extended drought periods followed by heavy rainfall may increase in many regions of the Earth, but the consequences for the quality of soil organic matter and soil microbial communities are poorly understood. Here, we investigated the effect of repeated drying and re-wetting on microbial communities and the quality of particulate and dissolved organic matter in a Haplic Podzol from a Norway spruce stand. After air-drying, undisturbed soil columns were re-wetted at different intensities (8, 20 and 50 mm per day) and time intervals, so that all treatments received the same amount of water per cycle (100 mm). After the third cycle, SOM pools of the treatments were compared with those of non-dried control columns. Lignin phenols were not systematically affected in the O horizons by the treatments whereas fewer lignin phenols were found in the A horizon of the 20- and 50-mm treatments. Microbial biomass and the ratio of fungi to bacteria were generally not altered, suggesting that most soil microorganisms were well adapted to drying and re-wetting in this soil. However, gram-positive bacteria and actinomycetes were reduced whereas gram-negative bacteria and protozoa were stimulated by the treatments. The increase in the (cy 17: 0 + cy 19: 0)/(16:1,7c + 18:1,7c) ratio indicates physiological or nutritional stress for the bacterial communities in the O, A and B horizons with increasing re-wetting intensity. Drying and re-wetting reduced the amount of hydrolysable plant and microbial sugars in all soil horizons. However, CO2 and dissolved organic carbon fluxes could not explain these losses. We postulate that drying and re-wetting triggered chemical alterations of hydrolysable sugar molecules in organic and mineral soil horizons. [source] Improved automated extraction and separation procedure for soil lipid analysesEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 2 2004G. L. B. Wiesenberg Summary Analysis of soil lipids may contribute to an improved understanding of atmosphere to soil carbon fluxes, soil organic matter source differentiation and pollutant accumulation. Soil lipids, mostly originating from plants and microorganisms, have traditionally been analysed by non-automated extraction and separation methods, which produce several lipid fractions, operationally defined by polarity. Here we present a combination of fast, automated and reproducible techniques, adopted from organic geochemical studies, for preparative separation of individual soil lipid fractions with increasing polarity. These techniques involve commercially available instruments, including accelerated solvent extraction and a two-step automated medium-pressure liquid chromatography procedure. The method yields eight lipid fractions consisting of five fractions fully amenable to gas chromatography/mass spectrometry (GC/MS) (aliphatic hydrocarbons, aromatic hydrocarbons, ketones, alcohols, carboxylic acids), and three fractions of highly polar or high molecular weight compounds (bases, very long-chain wax esters (C40+), high polarity compounds) that were not measurable with GC/MS under standard conditions. We tested the method on five agricultural soils. Results show that (i) mass recoveries for the individual fractions are reproducible, (ii) within individual fractions compound distribution patterns are reproducible, as demonstrated for alkanes and carboxylic acids, and (iii) individual fractions represent distinct and clean compound classes, free of interfering substances detectable by GC/MS. Thus, automated separation can be a fast, effective and reproducible procedure for fractionation of complex mixtures of soil lipids into clean compound classes, directly suitable for a variety of molecular (e.g. GC/MS) and isotopic characterizations (e.g. gas chromatography coupled with isotope ratio monitoring mass spectrometry or accelerator mass spectrometry). [source] | |||||||||||||||||||||||||||||||