Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

Background  

Photosynthetic organisms convert atmospheric carbon dioxide into numerous metabolites along the pathways to make new biomass. Aquatic photosynthetic organisms, which fix almost half of global inorganic carbon, have great potential: as a carbon dioxide fixation method, for the economical production of chemicals, or as a source for lipids and starch which can then be converted to biofuels. To harness this potential through metabolic engineering and to maximize production, a more thorough understanding of photosynthetic metabolism must first be achieved. A model algal species, C. reinhardtii, was chosen and the metabolic network reconstructed. Intracellular fluxes were then calculated using flux balance analysis (FBA).     

Microbial contributions to the evolution of the ‘steady state’ carbon dioxide system

Various processes for the production of carbon dioxide by microorganisms are presented. It is postulated that a microniche developed in a reducing environment; a symbiotic relationship between alga-like organisms and bacterium-like organisms in the microniche governed the production of carbon dioxide resulting in the establishment of the steady state carbon dioxide system in the sea.     

Rubisco: the enzyme that keeps on giving

In cyanobacteria, the RbcX protein enhances the production of Rubisco, the multisubunit enzyme that catalyzes the first step of carbon dioxide fixation in most autotrophic organisms. In this issue of Cell, Saschenbrecker et al. (2007) report that RbcX acts as a specific assembly chaperone that mobilizes the large subunits of Rubisco to a specific oligomeric core that can then combine with the small subunits of Rubisco to form the functional holoenzyme.     

Biofixation of carbon dioxide by Spirulina sp. and Scenedesmus obliquus cultivated in a three-stage serial tubular photobioreactor

The increase in the concentration of atmospheric carbon dioxide is considered to be one of the main causes of global warming. As estimated by the Intergovernmental Panel on Climate Change (IPCC) criteria, about 10-15% of the gases emitted from the combustion coal being in the form of carbon dioxide. Microalgae and cyanobacteria can contribute to the reduction of atmospheric carbon dioxide by using this gas as carbon source. We cultivated the Scenedesmus obliquus and Spirulina sp. at 30 degrees C in a temperature-controlled three-stage serial tubular photobioreactor and determined the resistance of these organisms to limitation and excess of carbon dioxide and the capacity of the system to fix this greenhouse gas. After 5 days of cultivation under conditions of carbon limitation both organisms showed cell death. Spirulina sp. presenting better results for all parameters than S. obliquus. For Spirulina sp. the maximum specific growth rate and maximum productivity was 0.44 d(-1), 0.22 g L(-1)d(-1), both with 6% (v/v) carbon dioxide and maximum cellular concentration was 3.50 g L(-1) with 12% (v/v) carbon dioxide. Maximum daily carbon dioxide biofixation was 53.29% for 6% (v/v) carbon dioxide and 45.61% for 12% carbon dioxide to Spirulina sp. corresponding values for S. obliquus being 28.08% for 6% (v/v) carbon dioxide and 13.56% for 12% (v/v) carbon dioxide. The highest mean carbon dioxide fixation rates value was 37.9% to Spirulina sp. in the 6% carbon dioxide runs.     

The Challenges of Living in Hypoxic and Hypercapnic Aquatic Environments

Organisms living in coastal waters, and especially estuaries,have long been known to have behavioral or physiological mechanismsthat enable them toexist in water containing low amounts ofoxygen. However, the respiratory consumption of oxygen thatgenerates hypoxia is also responsible for producing significantamounts of carbon dioxide. An elevation of carbon dioxide pressurein water will cause a significant acidosis in most aquatic organisms.Thus, the combination of low oxygen and elevated carbon dioxidethat occurs in estuaries represents a significant environmentalchallenge to organisms living in this habitat. Organisms maymaintain oxygen uptake in declining oxygen conditions by usinga respiratory pigment and/or by making adjustments in the convectiveflow of water and blood past respiratory surfaces (i.e., increasecardiac output and ventilation rate). Severe hypoxia may resultin an organism switching partially or completely to anaerobicbiochemical pathways to sustain metabolic rate. There is alsoevidence to suggest that organisms lower their metabolism duringhypoxic stress. Elevated water CO₂ (hypercapnia) produces anacidosis in the tissues of organisms that breathe it. This acidosismay be wholly or partially compensated (i.e., mechanisms returnpH to pre-exposure levels), or may be uncompensated. Some studieshave examined the effects on organisms of exposure simultaneouslyto hypoxia and hypercapnia. This article reviews some of thespecific adaptations and responses of organisms to low oxygen,to high carbon dioxide, and to the cooccurrence of low oxygenand high carbon dioxide     

Respiration of plankton in two small,polyhumic lakes

The respiration of plankton of two polyhumic lakes was measured as production of carbon dioxide in dark bottles. The method proved to be enough sensitive for use in oligotrophic lakes with low alkalinity. The respiration of plankton followed broadly changes in temperature. However, the primary production of phytoplankton was probably the main factor governing the seasonal pattern of respiration. During summer the respiration of plankton was more than three times higher than the primary production of phytoplankton. This suggests that allochthonous humic substances are an important source of carbon and energy for organisms of polyhumic lakes.     

The mechanism of carbon isotope fractionation in the metabolic process]

The mechanism of carbon isotope fractionation in metabolic paths of autotrophic organisms is considered. The principal features of the mechanism proposed are: 1) the emergence of a one-stage kinetic isotope effect of pyruvate decarboxylation during respiration resulting in the formation of two flows of the carbon substrate with different isotope compositions; 2) the multiplication of the one-stage isotope effect by means of the repeated circulation of a light isotope fraction (C2-fragments) in lipid-carbohydrate metabolism and by the simultaneous removal of a heavy isotope carbon dioxide in the Krebs cycle. On the basis of the above mechanism carbon isotope effects are explained of CO2 assimilation and respiration as well as sequential decrease of 13C content in the series of lipids, carbohydrates and proteins. The cuase of the enrichment of the whole organisms in the light isotope in respect to the carbon dioxide of the environment is discussed.     

Effects of carbon dioxide on ethylene production and action in intact sunflower plants

A continuous flow system was used to study the interactions between carbon dioxide and ethylene in intact sunflower (Helianthus annuus L.) plants. An increase in the concentration of carbon dioxide above the ambient level (0.033%) in the atmosphere surrounding the plants increased the rate of ethylene production, and a decrease in carbon dioxide concentration resulted in a decrease in the rate of ethylene production. The change in the rate of ethylene production was evident within the first 15 minutes of the carbon dioxide treatment. Continuous treatment with carbon dioxide was required to maintain increased rate of ethylene production. The rate of carbon dioxide fixation increased in response to high carbon dioxide treatment up to 1.0%. Further increases in carbon dioxide concentration had no additional effect on carbon dioxide fixation. Carbon dioxide concentrations higher than 0.11% induced hyponasty of the leaves whereas treatment with 1 microliter per liter ethylene induced epinasty of the leaves.     

Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing

Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.     

Gas Exchange of Algae: III. Relation between the Concentration of Carbon Dioxide in the Nutrient Medium and the Oxygen Production of Chlorella pyrenoidosa

The oxygen production of a photosynthetic gas exchanger containing Chlorella pyrenoidosa (1% packed cell volume) was measured when various concentrations of carbon dioxide were present within the culture unit. The internal carbon dioxide concentrations were obtained by manipulating the entrance gas concentration and the flow rate. Carbon dioxide percentages were monitored by means of electrodes placed directly in the nutrient medium. The concentration of carbon dioxide in the nutrient medium which produced maximal photosynthesis was in the range of 1.5 to 2.5% by volume. Results were unaffected by either the level of carbon dioxide in the entrance gas or the rate of gas flow. Entrance gases containing 2% carbon dioxide flowing at 320 ml/min, 3% carbon dioxide at 135 ml/min, and 4% carbon dioxide at 55 ml/min yielded optimal carbon dioxide concentrations in the particular unit studied. By using carbon dioxide electrodes implanted directly in the gas exchanger to optimize the carbon dioxide concentration throughout the culture medium, it should be possible to design more efficient large-scale units.     

Nutrient availability affects the response of the calcifying chlorophyte Halimeda opuntia (L.) J.V. Lamouroux to low pH

Atmospheric carbon dioxide emissions cause a decrease in the pH and aragonite saturation state of surface ocean water. As a result, calcifying organisms are expected to suffer under future ocean conditions, but their physiological responses may depend on their nutrient status. Because many coral reefs experience high inorganic nutrient loads or seasonal changes in nutrient availability, reef organisms in localized areas will have to cope with elevated carbon dioxide and changes in inorganic nutrients. Halimeda opuntia is a dominant calcifying primary producer on coral reefs that contributes to coral reef accretion. Therefore, we investigated the carbon and nutrient balance of H. opuntia exposed to elevated carbon dioxide and inorganic nutrients. We measured tissue nitrogen, phosphorus and carbon content as well as the activity of enzymes involved in inorganic carbon uptake and nitrogen assimilation (external carbonic anhydrase and nitrate reductase, respectively). Inorganic carbon content was lower in algae exposed to high CO₂, but calcification rates were not significantly affected by CO₂ or inorganic nutrients. Organic carbon was positively correlated to external carbonic anhydrase activity, while inorganic carbon showed the opposite correlation. Carbon dioxide had a significant effect on tissue nitrogen and organic carbon content, while inorganic nutrients affected tissue phosphorus and N:P ratios. Nitrate reductase activity was highest in algae grown under elevated CO₂ and inorganic nutrient conditions and lowest when phosphate was limiting. In general, we found that enzymatic responses were strongly influenced by nutrient availability, indicating its important role in dictating the local responses of the calcifying primary producer H. opuntia to ocean acidification.     

Study of the effect of volatile metabolites of Trichoderma hamatum on the growth of phytopathogenic soilborne fungi.

Volatile compounds produced by Trichoderma hamatum were tested for their capacity to suppress in vitro the growth of Alternaria citri, Bipolaris cynodontis, Bipolaris sorokiniana, Curvularia brachyspora, Curvularia lunata, Curvularia oryzae-sativae, Drechslera tritici-repentis, Rhizoctonia solani, Sclerotinia minor and Sclerotium rolfsii. The organisms were cultured in an apparatus made with two Erlenmeyer flasks assembled by their top parts. With the aid of the gas chromatographic technique the variation of carbon dioxide, oxygen and ethylene in the internal system was determined. Acetaldehyde and ethanol were not found. Due to the respiratory metabolism of T. hamatum the carbon dioxide level progressively increased while the oxygen content decreased. Ethylene production was low and after three days remained constant. Excepting C. oryzae-sativae and B. cynodontis the other species showed changes in the growth and development. These results suggest the inhibitory volatiles of T. hamatum as one possible mechanism of biological control.     

Hydrogenobacter thermophilus: its unusual physiological properties and phylogenic position in the microbial world

Abstract Hydrogenobacter thermophilus (IAM12695) is an obligately autotrophic, thermophilic and aerobic hydrogen-oxidizing bacterium. Chemotaxonomic studies revealed various unusual features of this microorganism. H. thermophilus operates a reductive TCA cycle, which is the only confirmed example of the operation of a non-Calvin type carbon dioxide fixation pathway among aerobic organisms. Isolation of strains similar to Hydrogenobacter from different areas suggests a possible role of these microorganisms as primary producers of organic compounds from carbon dioxide in geothermal and/or aquatic environments.     

Algae biofuels: versatility for the future of bioenergy

The world continues to increase its energy use, brought about by an expanding population and a desire for a greater standard of living. This energy use coupled with the realization of the impact of carbon dioxide on the climate, has led us to reanalyze the potential of plant-based biofuels. Of the potential sources of biofuels the most efficient producers of biomass are the photosynthetic microalgae and cyanobacteria. These versatile organisms can be used for the production of bioethanol, biodiesel, biohydrogen, and biogas. In fact, one of the most economic methods for algal biofuels production may be the combined biorefinery approach where multiple biofuels are produced from one biomass source.     

Systematic error in the calculated specific acid production rate in anaerobic fermentation of Lactococcus lactis in the presence of carbon dioxide

Summary The lactococci are commonly grown anaerobically, blanketed with a mixture of nitrogen and carbon dioxide. Specific acid production rate is often determined by alkali usage in constant pH fermentations. The combination of these methods leads to incorrect acid production figures because the added carbon dioxide reacts with some of the alkali.     

Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria

Extremophiles - Acetogenic bacteria are a polyphyletic group of organisms that fix carbon dioxide under anaerobic, non-phototrophic conditions by reduction of two mol of CO2 to acetyl-CoA via the...     

Pathways of Propionate Degradation by Enriched Methanogenic Cultures

A mixed methanogenic culture was highly enriched in a growth medium containing propionate as the sole organic carbon and energy source. With this culture, the pathways of propionate degradation were studied by use of ¹⁴C-radiotracers. Propionate was first metabolized to acetate, carbon dioxide, and hydrogen by nonmethanogenic organisms. Formate was not excreted. The carbon dioxide originated exclusively from the carboxyl group of propionate, whereas both [2-¹⁴C]- and [3-¹⁴C]propionate lead to the production of radioactive acetate. The methyl and carboxyl groups of the acetate produced were equally labeled, regardless of whether [2-¹⁴C]- or [3-¹⁴C]propionate was used. These observations suggest that in the culture, propionate was degraded through a randomizing pathway.     

Storage of poultry meat under modified atmospheres or vacuum packs: possible role of microbial metabolites as indicator of spoilage

The effect of carbon dioxide (100%), nitrogen (100%), carbon dioxide/oxygen (20% : 80%) or vacuum pack at 3 and 10°C was studied on the microbial flora, in skinless poultry breast fillets or thigh meat. Lactic acid bacteria and Brochothrix thermosphacta were the predominant organisms in samples stored in vacuum packs, carbon dioxide and nitrogen. Pseudomonads grew only in oxygen/carbon dioxide packaging systems. The concentration of lactate diminished in both thigh and breast meat during storage at 3 and 10°C. This decrease was more pronounced in thigh meat stored under 20% : 80% carbon dioxide/oxygen. Acetate increased to varying degrees in all samples regardless of the storage conditions.     

Influence of some aliphatic alcohols on the metabolism of rat liver slices

The influence of some aliphatic alcohols on oxygen uptake, carbon dioxide production, acid formation and lactate and pyruvate concentrations of rat liver slices was studied. At the concentrations used, none of the alcohols was found to influence oxygen uptake. Of the alcohols that are not oxidized by liver alcohol dehydrogenase, methanol increased carbon dioxide production, propan-2-ol decreased it and 2-methylpropan-2-ol was without influence. All the alcohols that are oxidized by the enzyme strongly decreased carbon dioxide production. The alcohols that are not oxidized had no marked effect on the lactate/pyruvate concentration ratio, whereas the other alcohols strongly increased the ratio. A highly significant correlation was found between the effects of the alcohol on pyruvate concentration and carbon dioxide production. It is assumed that the shift in the redox potential inhibits the function of the tricarboxylic acid cycle of the liver.     

Effect of furfural on the energy metabolism of fodder yeasts]

The effect of furfurol on the rate of oxygen uptake and carbon dioxide production by Candida tropicalis cells was studied. Furfurol was shown to inhibit significantly the yeast respiration, inducing aerobic glycolysis. Enhanced carbon dioxide production in the presence of furfurol was followed by an intensive degradation of trehalose and ethanol accumulation in the medium.