Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142

Genome-scale metabolic models have proven useful for answering fundamental questions about metabolic capabilities of a variety of microorganisms, as well as informing their metabolic engineering. However, only a few models are available for oxygenic photosynthetic microorganisms, particularly in cyanobacteria in which photosynthetic and respiratory electron transport chains (ETC) share components. We addressed the complexity of cyanobacterial ETC by developing a genome-scale model for the diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142. The resulting metabolic reconstruction, iCce806, consists of 806 genes associated with 667 metabolic reactions and includes a detailed representation of the ETC and a biomass equation based on experimental measurements. Both computational and experimental approaches were used to investigate light-driven metabolism in Cyanothece sp. ATCC 51142, with a particular focus on reductant production and partitioning within the ETC. The simulation results suggest that growth and metabolic flux distributions are substantially impacted by the relative amounts of light going into the individual photosystems. When growth is limited by the flux through photosystem I, terminal respiratory oxidases are predicted to be an important mechanism for removing excess reductant. Similarly, under photosystem II flux limitation, excess electron carriers must be removed via cyclic electron transport. Furthermore, in silico calculations were in good quantitative agreement with the measured growth rates whereas predictions of reaction usage were qualitatively consistent with protein and mRNA expression data, which we used to further improve the resolution of intracellular flux values.     

Carbon dioxide assimilation by Thiobacillus novellus under nutrient-limited mixotrophic conditions

The contribution of CO2 to cell material synthesis in Thiobacillus novellus under nutrient-limited conditions was estimated by comparing 14CO2 uptake rates of steady-state autotrophic cultures with that of heterotrophic and mixotrophic cultures at a given dilution rate. Under heterotrophic conditions, some 13% of the cell carbon was derived from CO2; this is similar to the usual anaplerotic CO2 fixation in batch cultures of heterotrophic bacteria. Under mixotrophic conditions, the contribution of CO2 to cell material synthesis increased with increasing S2O3 2- -to-glucose ratio in the medium inflow; at a ratio of 10, ca. 32% of the cell carbon was synthesized from CO2. We speculate that the use of CO2 as carbon source, even when the glucose provided is sufficient to fulfill the biosynthetic needs, may augment the growth rate of the bacterium under such nutrient-limited conditions and could therefore be of survival value in nature. Some of the CO2 assimilated was excreted into the medium as organic compounds under all growth conditions, but in large amounts only in autotrophic environments as very low dilution rates.     

Root production and mortality under elevated atmospheric carbon dioxide

An essential component of an understanding of carbon flux is the quantification of movement through the root carbon pool. Although estimates have been made using radiocarbon, the use of minirhizotrons provides a direct measurement of rates of root birth and death. We have measured root demographic parameters under a semi-natural grassland and for wheat. The grassland was studied along a natural altitudinal gradient in northern England, and similar turf from the site was grown in elevated CO₂ in solardomes. Root biomass was enhanced under elevated CO₂. Root birth and death rates were both increased to a similar extent in elevated CO₂, so that the throughput of carbon was greater than in ambient CO₂, but root half-lives were shorter under elevated CO₂ only under a Juncus/Nardus sward on a peaty gley soil, and not under a Festuca turf on a brown earth soil. In a separate experiment, wheat also responded to elevated CO₂ by increased root production, and there was a marked shift towards surface rooting: root development at a depth of 80–85 cm was both reduced and delayed. In conjunction with published results for trees, these data suggest that the impact of elevated CO₂ will be system-dependent, affecting the spatio-temporal pattern of root growth in some ecosystems and the rate of turnover in others. Turrnover is also sensitive to temperature, soil fertility and other environmental variables, all of which are likely to change in tandem with atmospheric CO₂ concentrations. Differences in turnover and time and location of rhizodeposition may have a large effect on rates of carbon cycling.     

Soil carbon dioxide partial pressure and dissolved inorganic carbonate chemistry under elevated carbon dioxide and ozone

Global emissions of atmospheric CO₂ and tropospheric O₃ are rising and expected to impact large areas of the Earths forests. While CO₂ stimulates net primary production, O₃ reduces photosynthesis, altering plant C allocation and reducing ecosystem C storage. The effects of multiple air pollutants can alter belowground C allocation, leading to changes in the partial pressure of CO₂ (pCO₂) in the soil , chemistry of dissolved inorganic carbonate (DIC) and the rate of mineral weathering. As this system represents a linkage between the long- and short-term C cycles and sequestration of atmospheric CO₂, changes in atmospheric chemistry that affect net primary production may alter the fate of C in these ecosystems. To date, little is known about the combined effects of elevated CO₂ and O₃ on the inorganic C cycle in forest systems. Free air CO₂ and O₃ enrichment (FACE) technology was used at the Aspen FACE project in Rhinelander, Wisconsin to understand how elevated atmospheric CO₂ and O₃ interact to alter pCO₂ and DIC concentrations in the soil. Ambient and elevated CO₂ levels were 360±16 and 542±81 l l^–1, respectively; ambient and elevated O₃ levels were 33±14 and 49±24 nl l^–1, respectively. Measured concentrations of soil CO₂ and calculated concentrations of DIC increased over the growing season by 14 and 22%, respectively, under elevated atmospheric CO₂ and were unaffected by elevated tropospheric O₃. The increased concentration of DIC altered inorganic carbonate chemistry by increasing system total alkalinity by 210%, likely due to enhanced chemical weathering. The study also demonstrated the close coupling between the seasonal ¹³C of soil pCO₂ and DIC, as a mixing model showed that new atmospheric CO₂ accounted for approximately 90% of the C leaving the system as DIC. This study illustrates the potential of using stable isotopic techniques and FACE technology to examine long- and short-term ecosystem C sequestration.     

Increased mercury in forest soils under elevated carbon dioxide

Fossil fuel combustion is the primary anthropogenic source of both CO₂ and Hg to the atmosphere. On a global scale, most Hg that enters ecosystems is derived from atmospheric Hg that deposits onto the land surface. Increasing concentrations of atmospheric CO₂ may affect Hg deposition to terrestrial systems and storage in soils through CO₂-mediated changes in plant and soil properties. We show, using free-air CO₂ enrichment (FACE) experiments, that soil Hg concentrations are almost 30% greater under elevated atmospheric CO₂ in two temperate forests. There were no direct CO₂ effects, however, on litterfall, throughfall or stemflow Hg inputs. Soil Hg was positively correlated with percent soil organic matter (SOM), suggesting that CO₂-mediated changes in SOM have influenced soil Hg concentrations. Through its impacts on SOM, elevated atmospheric CO₂ may increase the Hg storage capacity of soils and modulate the movement of Hg through the biosphere. Such effects of rising CO₂, ones that transcend the typically studied effects on C and nutrient cycling, are an important next phase for research on global environmental change.     

The unicellular freshwater cyanobacterium Synechococcus and mixotrophic flagellates: evidence for a functional association in an oligotrophic, subalpine lake

1. We applied Reynolds's approach to the study of phytoplankton ecology through functional associations of species to identify possible algal species, which associate with the freshwater cyanobacterium Synechococcus. Previously an association among Synechococcus spp. and small‐celled chlorophytes (association Z) has been recognised by evaluating phytoplankton associations according to functional criteria. 2. Biomass data for phytoplankton and picocyanobacteria from Lago Maggiore spanning more years were organised in a matrix and a cluster analysis was performed. The results showed four groups separated at a linkage distance of 0.20. Mixotrophic species which clustered with Synechococcus spp. were Ceratium hirundinella, Chrysochromulina parva, Cryptomonas erosa, Cryptomonas ovata, Dinobryon bavaricum, Dinobryon sociale, Rhodomonas minuta and Uroglena americana. The redundancy analysis (RDA) consolidated the association of Synechococcus with C. hirundinella and R. minuta showing greater probability of occurrence than random aggregates of species. 3. The association Synechococcus spp. –C. hirundinella also appeared from temporal variation of their biomass. In early summer both these species increased at the same time; later, the peak of C. hirundinella (potential predator) coincided with a minimum of Synechococcus spp. suggesting a possible predator‐prey interaction. This implied that phytoplankton assemblages which form a functional group cannot only have similar adaptations and requirements but can also exhibit trophic interactions. 4. We propose to enlarge the association Z and create an association Z_MX (where _MX stands for mixotrophs) which would include Synechococcus spp. and C. hirundinella as the most representative of the mixotrophic species found in the oligotrophic Lago Maggiore.     

Isolation and characterization of the unicellular diazotrophic cyanobacterium Group C TW3 from the tropical western Pacific Ocean

A unicellular diazotrophic cyanobacterium strain of Group C, designated TW3, was isolated from the oligotrophic Kuroshio Current of the western Pacific Ocean. To our knowledge, this represents the first successful laboratory culture of a Group C unicellular diazotroph from oceanic water. TW3 cells are green rods, 2.5-3.0 μm in width and 4.0-6.0 μm in length. Phylogenetic analyses of both 16S rRNA and nifH gene fragments indicated that the TW3 sequences were over 98% identical to those of the previously isolated Cyanothece sp. ATCC51142 and Gloeocapsa sp., suggesting that TW3 is a member of the Group C unicellular diazotrophs. In addition, both TW3 and Cyanothece sp. ATCC51142 share morphological characteristics; both strains are sheathless and rod-shaped, display binary fission in a single plane, and possess dispersed thylakoids. TW3 grows aerobically in nitrogen-deficient artificial seawater, and exhibited the highest observed growth rate of 0.035 h(-1) when cultured at 30°C and 140 μmol m(-2) s(-1) of light intensity. The nitrogen fixation rate, when grown optimally using a 12 h/12 h light-dark cycle, was 7.31 × 10(-15) mol N cell(-1) day(-1) . Immunocytochemical staining using Trichodesmium sp. NIBB1067 nitrogenase antiserum revealed the existence of diazotrophic cells sharing morphological characteristics of TW3 in the Kuroshio water from which TW3 was isolated.     

Using elevated carbon dioxide to enhance copper accumulation in Pteridium revolutum, a copper-tolerant plant, under experimental conditions

In our survey in the copper (Cu) mining area of China, a sun fern (Pteridium revolutum) was found to accumulate 30-567 mg Cu kg(-1) DW (33 samples) in its fronds with a large frond biomass. Cu translocation factors in the plants varied from 0.09 to 3.88. In a greenhouse pot experiment, the effect of an elevated CO2 concentration (700 microL L(-1)) on Cu accumulation in plants was studied using three fern species (P. revolutum, Pteridium aquilinum, and Pteris vittata) grown in the Cu-contaminated soil. P. revolutum showed a higher Cu tolerance but its Cu translocation factor was lower than 1. At the elevated CO2 concentration, frond biomass of all species was significantly increased, as was the total Cu content in the fronds of P. revolutum and P. aquilinum. Our study suggests that P. revolutum could serve as a good candidate for phytoextraction of Cu-contaminated soils and that doubling the ambient CO2 concentration will facilitate its use in phytoextraction.     

Photosynthetic acclimation of maize to growth under elevated levels of carbon dioxide

The effects of elevated CO₂ concentrations on the photochemistry, biochemistry and physiology of C₄ photosynthesis were studied in maize (Zea mays L.). Plants were grown at ambient (350 μL L⁻¹) or ca. 3 times ambient (1100 μL L⁻¹) CO₂ levels under high light conditions in a greenhouse for 30 d. Relative to plants grown at ambient CO₂ levels, plants grown under elevated CO₂ accumulated ca. 20% more biomass and 23% more leaf area. When measured at the CO₂ concentration of growth, mature leaves of high-CO₂-grown plants had higher light-saturated rates of photosynthesis (ca. 15%), lower stomatal conductance (71%), higher water-use efficiency (225%) and higher dark respiration rates (100%). High-CO₂-grown plants had lower carboxylation efficiencies (23%), measured under limiting CO₂, and lower leaf protein contents (22%). Activities of a number of C₃ and C₄ cycle enzymes decreased on a leaf-area basis in the high-CO₂-grown plants by 5–30%, with NADP-malate dehydrogenase exhibiting the greatest decrease. In contrast, activities of fructose 1,6-bisphosphatase and ADP-glucose pyrophosphorylase increased significantly under elevated CO₂ condition (8% and 36%, respectively). These data show that the C₄ plant maize may benefit from elevated CO₂ through acclimation in the capacities of certain photosynthetic enzymes. The increased capacity to synthesize sucrose and starch, and to utilize these end-products of photosynthesis to produce extra energy by respiration, may contribute to the enhanced growth of maize under elevated CO₂. Received: 30 April 1999 / Accepted: 17 June 1999     

Photosynthesis and nutrient composition of spinach and fenugreek grown under elevated carbon dioxide concentration

The effect of elevated carbon dioxide concentration on the changes in the biomass, photosynthesis and nutrient composition was investigated in two leafy vegetables. Spinach (Spinacia oleracea L.) and fenugreek (Trigonella foenum-graecum L.) plants were grown in open top chambers under either ambient (ACO₂, 350 ± 50 μmol mol⁻¹) or elevated (ECO₂, 600 ± 50 μmol mol⁻¹) CO₂ concentration and analyzed 40, 60 and 80 days after exposure. The plants grown in ECO₂ had higher net photosynthetic rate and lower stomatal conductance when compared with the plants grown in ACO₂. ECO₂ also changed the nutrient composition: a lower N, Mg and Fe contents and higher C and Ca contents were observed in the leaves of plants exposed to ECO₂ than in those grown at ACO₂.     

Polysaccharide hydrolysis accelerated by adding carbon dioxide under hydrothermal conditions

Polysaccharides such as agar, guar gum, starch, and xylan were hydrolyzed to produce mono- and oligosaccharides under hydrothermal conditions with and without carbon dioxide in a small batch reactor. The molecular weight distributions of the polysaccharide hydrolyzates shifted to lower molecular weights by increasing the carbon dioxide load, corresponding to higher pressures of carbon dioxide. For example, the yield of glucose produced from the hydrolysis of starch at 200 degrees C was increased significantly from 3.7% to 53.0% (on a carbon weight basis) of the initial polysaccharide by increasing carbon dioxide load in a reaction time of 15 min. Carbonic acid generated from water and carbon dioxide appeared to lower the pH of high-temperature and high-pressure water. Polysaccharide hydrolysis under hydrothermal conditions in the presence of carbon dioxide is an environmentally benign method to produce mono- and oligosaccharides because the process does not require the use of conventional acids and bases followed by neutralization and separation.     

Active transport and accumulation of bicarbonate by a unicellular cyanobacterium

The rates of inorganic carbon accumulation and carbon fixation in light by the unicellular cyanobacterim Coccohloris peniocystis have been determined. Cells incubated in the light in medium containing H14CO3- were rapidly separated from the medium by centrifugation through silicone oil into a strongly basic terminating solution. Samples of these inactivated cells were assayed to determine total 14C accumulation, and acid-treated samples were assayed to determine 14C fixation. The rate of transport of inorganic into illuminated cells was faster than the rate of CO2 production in the medium from HCO3- dehydration. This evidence for HCO3- transport in these cells is in agreement with our previous results based upon measurements of photosynthetic O2 evolution. A substantial pool of inorganic carbon was bulit up within the cells presumably as HCO3- before the onset of the maximum rate of photosynthesis. Large accumulation ratios were observed, greater than 1,000 times the external HCO3- concentration. Accumulation did not occur in the dark and was greatly suppressed by the photosynthesis inhibitors 3-(3,4-dichlorophenyl)-1,1-dimethyl urea and 3-chloro-carbonylcyanide phenylhydrazone. These results indicate that the accumulation of inorganic carbon in these cells involves a light-dependent active transport process.     

Plant nitrogen acquisition and interactions under elevated carbon dioxide: impact of endophytes and mycorrhizae

Both endophytic and mycorrhizal fungi interact with plants to form symbiosis in which the fungal partners rely on, and sometimes compete for, carbon (C) sources from their hosts. Changes in photosynthesis in host plants caused by atmospheric carbon dioxide (CO₂) enrichment may, therefore, influence those mutualistic interactions, potentially modifying plant nutrient acquisition and interactions with other coexisting plant species. However, few studies have so far examined the interactive controls of endophytes and mycorrhizae over plant responses to atmospheric CO₂ enrichment. Using Festuca arundinacea Schreb and Plantago lanceolata L. as model plants, we examined the effects of elevated CO₂ on mycorrhizae and endophyte (Neotyphodium coenophialum) and plant nitrogen (N) acquisition in two microcosm experiments, and determined whether and how mycorrhizae and endophytes mediate interactions between their host plant species. Endophyte‐free and endophyte‐infected F. arundinacea varieties, P. lanceolata L., and their combination with or without mycorrhizal inocula were grown under ambient (400 μmol mol⁻¹) and elevated CO₂ (ambient + 330 μmol mol⁻¹). A ¹⁵N isotope tracer was used to quantify the mycorrhiza‐mediated plant acquisition of N from soil. Elevated CO₂ stimulated the growth of P. lanceolata greater than F. arundinacea, increasing the shoot biomass ratio of P. lanceolata to F. arundinacea in all the mixtures. Elevated CO₂ also increased mycorrhizal root colonization of P. lanceolata, but had no impact on that of F. arundinacea. Mycorrhizae increased the shoot biomass ratio of P. lanceolata to F. arundinacea under elevated CO₂. In the absence of endophytes, both elevated CO₂ and mycorrhizae enhanced ¹⁵N and total N uptake of P. lanceolata but had either no or even negative effects on N acquisition of F. arundinacea, altering N distribution between these two species in the mixture. The presence of endophytes in F. arundinacea, however, reduced the CO₂ effect on N acquisition in P. lanceolata, although it did not affect growth responses of their host plants to elevated CO₂. These results suggest that mycorrhizal fungi and endophytes might interactively affect the responses of their host plants and their coexisting species to elevated CO₂.     

Effect of mixed carbon substrate on exopolysaccharide production of cyanobacterium Nostoc flagelliforme in mixotrophic cultures

The effects of organic carbon sources on cell growth and exopolysaccharide (EPS) production of dissociated Nostoc flagelliforme cells under mixotrophic batch culture were investigated. After 7?days of cultivation, glycerol, acetate, sucrose, and glucose increased the final cell density and final EPS concentrations, and mixotrophic growth achieved higher biomass concentrations. The increase in cell growth was particularly high when glucose was added as the sole carbon source. On the other hand, EPS production per dry cell weight was significantly enhanced by adding acetate. For more effective EPS production, the effects of the mixture of glucose and acetate were investigated. Increasing the ratio of glucose to acetate resulted in higher growth rate with BG-11 medium and higher EPS productivity with BG-11₀ medium (without NaNO₃). When the medium was supplemented with a mixture of glucose (4.0?g?L^?1) and acetate (2.0?g?L^?1), 1.79?g?L^?1 biomass with BG-11 medium and 879.6?mg?L^?1 of EPS production with BG-11₀ medium were achieved. Adopting this optimal ratio of glucose to acetate established in flask culture, the culture was also conducted in a 20-L photobioreactor with BG-11 medium for 7?days. A maximum biomass of 2.32?g?L^?1 was achieved, and the EPS production was 634.6?mg?L^?1.     

Changes in prairie vegetation under elevated carbon dioxide levels and two soil moisture regimes

Abstract. It is important to know how increasing levels of atmospheric CO₂ will affect native vegetation. The objective of this study was to determine the effect of elevated CO₂ concentrations on species composition in a tallgrass prairie kept at a high water level (730 mm of water in a 2000 mm soil profile) and a low water level (660 mm of water in 2000 mm). 16 cylindrical plastic chambers were placed on the prairie to maintain two levels of CO₂ (ambient or twice ambient) during two growing seasons in 1989 and 1990. Frequency of species was determined on 25 July 1989 and on 5 and 10 October 1990. At the beginning of the study, Poa pratensis (Kentucky bluegrass), the dominant C₃ species, had the highest frequency of 43.3%, but decreased with time. However, at the end of the experiment and under the high soil-water level, there were more P. pratensis plants in the elevated CO₂ treatment (frequency: 13.5%) than in the ambient CO₂ treatment (1.0%). Under the low soil water regime, the reverse occurred (frequencies: 3.6% and 11.0% for high and low CO₂, respectively). The frequency of major C₄ plants, Andropogon gerardii (big bluestem), A. scoparius (little bluestem) and Sorghastrum nutans (Indian grass) was not affected by CO₂. However, water did affect their frequency. Under low water, the frequency of A. gerardii decreased between 1989 and 1990. Under both soil moisture levels, the frequencies of S. nutans and A. scoparius increased. At the end of the study, Indian grass grown with high water had the highest frequency of all species on the prairie (frequency at the end of the study in October, 1990, of 44.4% and 47.4% for the high and low CO₂ levels, respectively). Unlike Indian grass, little bluestem grew better under low water conditions than under high water conditions. These results suggest that, if the climate becomes drier, A. scoparius will flourish more than S. nutans or A. gerardii, and P. pratensis may die out. Elevated CO₂ might not increase survival of C₃ plants under dry conditions, if temperatures are too high for them.     

Growth and physiology of Thiobacillus novellus under nutrient-limited mixotrophic conditions.

Thiobacillus novellus was cultivated in a chemostate under the individual limitations of thiosulfate, glucose, and thiosulfate plus glucose. At dilution rate (D) of 0.05 h-1 or lower, the steady-state biomass concentration in mixotrophic medium was additive of the heterotrophic and autotrophic biomass at corresponding D values. The ambient concentrations of thiosulfate, glucose, or both in the various cultures were low and were very similar in mixotrophic, heterotrophic, and autotrophic environments at a given D value. At D = 0.05 h-1, mixotrophic cells possessed higher activities of sulfite oxidase and thiosulfate oxidation compared to autotrophic cells, as well as higher activities of glucose enzymes and glucose oxidation than heterotrophic cells. Thus, in contrast to nutrient-excess conditions, in nutrient-limited mixotrophic environments at these D values, T. novellus did not exhibit characteristics of uncoupled substrate oxidation, inhibition of substrate utilization, and repression of enzymes of energy metabolism. It is concluded that T. novellus responds to mixotrophic growth conditions differently in environments of different nutritional status, and the ecological and physiological significance of this finding is discussed.     

Effect of organics on sulfur-utilizing autotrophic denitrification under mixotrophic conditions

Thiol groups were introduced to dermal bovine collagen (DBC) by the reaction with gamma-thiobutyrolactone. Thiolated DBC reacted with 2-pyridyl disulfide group introduced to lysozyme to form DBC-lysozyme conjugate through disulfide bridge. The enzymatic activity of freshly prepared conjugate was almost unchanged during ten consecutive runs over one month. The DBC-lysozyme conjugate showed the maximum activity at pH 6.3, on the contrary, that of native lysozyme was pH 9.0. Thermal stability of lysozyme was enhanced by the conjugation with DBC. The present results showed that the conjugation using thiolated collagen could be one of the useful alternative approaches to modify collagen with bioactive molecules.