Carbon dioxide-concentrating mechanism and the development of extracellular carbonic anhydrase in the marine picoeukaryote Micromonas pusilla

A range of marine photosynthetic picoeukaryote phytoplankton species grown in culture were screened for the presence of extracellular carbonic anhydrase (CA_ext), a key enzyme in inorganic carbon acquisition under carbon- limiting conditions in some larger marine phytoplankton species. Of the species tested, extracellular carbonic anhydrase was detected only in Micromonas pusilla Butcher. The rapid, light-dependent development of CA_ext when cells were transferred from carbon-replete to carbon-limiting conditions was regulated by the available free- CO₂ concentration and not by total dissolved inorganic carbon. Kinetic studies provided support for a CO₂- concentrating mechanism in that the K _0.5[CO₂] (i.e. the CO₂ concentration required for the half-maximal rate of photosynthesis) was substantially lower than the K _m[CO₂] of Rubisco from related taxa, whilst the intracellular carbon pool was at least seven fold greater than the extracellular DIC concentration, for extracellular DIC values 1.0 m m .
It is proposed that when the flux of CO₂ into the cell is insufficient to support the photosynthetic rate at an optimum photon irradiance, the development of CA_ext increases the availability of CO₂ at the plasma membrane. This ensures rapid acclimation to environmental change and provides an explanation for the central role of M. pusilla as a carbon sink in oligotrophic environments.     

Biofumigation potential of brassicas

The relationship of global climate change to plant growth and the role of forests as sites of carbon sequestration have encouraged the refinement of the estimates of root biomass and production. However, tremendous controversy exists in the literature as to which is the best method to determine fine root biomass and production. This lack of consensus makes it difficult for researchers to determine which methods are most appropriate for their system. The sequential root coring method was the most commonly used method to collect root biomass data in the past and is still commonly used. But within the last decade the use of minirhizotrons has become a favorite method of many researchers. In addition, due to the high labor-intensive requirements of many of the direct approaches to determine root biomass, there has been a shift to develop indirect methods that would allow fine root biomass and production to be predicted using data on easily monitored variables that are highly correlated to root dynamics. Discussions occur as to which method should be used but without gathering data from the same site using different methods, these discussions can be futile. This paper discusses and compares the results of the most commonly used direct and indirect methods of determining root biomass and production: sequential root coring, ingrowth cores, minirhizotrons, carbon fluxes approach, nitrogen budget approach and correlations with abiotic resources. No consistent relationships were apparent when comparing several sites where at least one of the indirect and direct methods were used on the same site. Until the different root methods can be compared to some independently derived root biomass value obtained from total carbon budgets for systems, one root method cannot be stated to be the best and the method of choice will be determined from researcher's personal preference, experiences, equipment, and/or finances.     

Long-term growth at elevated carbon dioxide stimulates methane emission in tropical paddy rice

Recent anthropogenic emissions of key atmospheric trace gases (e.g. CO₂ and CH₄) which absorb infra-red radiation may lead to an increase in mean surface temperatures and potential changes in climate. Although sources of each gas have been evaluated independently, little attention has focused on potential interactions between gases which could influence emission rates. In the current experiment, the effect of enhanced CO₂ (300 μL L^–1 above ambient) and/or air temperature (4 °C above ambient) on methane generation and emission were determined for the irrigated tropical paddy rice system over 3 consecutive field seasons (1995 wet and dry seasons 1996 dry season). For all three seasons, elevated CO₂ concentration resulted in a significant increase in dissolved soil methane relative to the ambient control. Consistent with the observed increases in soil methane, measurements of methane flux per unit surface area during the 1995 wet and 1996 dry seasons also showed a significant increase at elevated carbon dioxide concentration relative to the ambient CO₂ condition (+49 and 60% for each season, respectively). Growth of rice at both increasing CO₂ concentration and air temperature did not result in additional stimulation of either dissolved or emitted methane compared to growth at elevated CO₂ alone. The observed increase in methane emissions were associated with a large, consistent, CO₂-induced stimulation of root growth. Results from this experiment suggest that as atmospheric CO₂ concentration increases, methane emissions from tropical paddy rice could increase above current projections.     

Dissolved organic carbon and fluorescence in Lake Hovsgol: factors reducing humic content of the lake water

 Lake Hovsgol is a large tectonic lake located in northern Mongolia, which has extremely transparent lake water. In our survey, the dissolved organic carbon of the lake water was 80–100 μM-C, and the fluorescence intensity in an excitation and emission matrix was very low. The brown color and high content of humic substances in river water flowing from a watershed consisting of grassland and forests rapidly declined in the coastal area of the lake. The decrease in humic content may be due not only to dilution by the lake water but also to flocculation and photobleaching. Among tectonic lakes in Asia, Lake Hovsgol would appear to have unique biological and hydrological features that reduce humic content and help to maintain water transparency. Received: June 25, 2002 / Accepted: January 10, 2003 Acknowledgments The authors acknowledge helpful discussion with Dr. J. Urabe. We thank Dr. T. Galbaatar, Mongolian Academy of Science, Mongolia, for his arrangements on the expeditions in 1999. We are also indebted to Mr. D. Hadbaatar, B. Ganbat, and the cruise staff of the R/V Suchbaatar for their assistance in the course of the study. This study was supported by Grant-in-Aid No. 09041159 and 13575034 for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology of Japan. Correspondence to:K. Hayakawa     

Activity of the Enzymes of Carbon Metabolism in Sulfobacillus sibiricus under Various Conditions of Cultivation

The thermoacidophilic iron-oxidizing chemolithotroph Sulfobacillus sibiricus N1^T is characterized by steady growth and amplified cell yield when grown in vigorously aerated medium containing Fe²⁺, glucose, and yeast extract as energy sources. In this case, carbon dioxide, glucose, and yeast extract are used as carbon sources. Glucose is assimilated through the fructose-bisphosphate pathway and the pentose-phosphate pathway. The glyoxylate bypass does not function in S. sibiricus, and the tricarboxylic acid cycle is disrupted at the level of 2-oxoglutarate dehydrogenase. The presence of ribulose-bisphosphate carboxylase indicates that carbon dioxide fixation proceeds through the Calvin cycle. The activity of ribulose-bisphosphate carboxylase is highest in autotrophically grown cells. The cells also contain pyruvate carboxylase, phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and phosphoenolpyruvate carboxytransphosphorylase.     

Function of methanofuran,tetrahydromethanopterin, and coenzyme F420 in Archaeoglobus fulgidus

Archaeoglobus fulgidus is an extremely thermophilic archaebacterium that can grow at the expense of lactate oxidation with sulfate to CO₂ and H₂S. The organism contains coenzyme F₄₂₀, tetrahydromethanopterin, and methanofuran which are coenzymes previously thought to be unique for methanogenic bacteria. We report here that the bacterium contains methylenetetrahydromethanopterin: F₄₂₀ oxidoreductase (20 U/mg), methenyltetrahydromethanopterin cyclohydrolase (0.9 U/mg), formyltetrahydromethanopterin: methanofuran formyltransferase (4.4 U/mg), and formylmethanofuran: benzyl viologen oxidoreductase (35 mU/mg). Besides these enzymes carbon monoxide: methyl viologen oxidoreductase (5 U/mg), pyruvate: methyl viologen oxidoreductase (0.7 U/mg), and membranebound lactate: dimethylnaphthoquinone oxidoreductase (0.1 U/mg) were found. 2-Oxoglutarate dehydrogenase, which is a key enzyme of the citric acid cycle, was not detectable. From the enzyme outfit it is concluded that in A. fulgidus lactate is oxidized to CO₂ via a modified acetyl-CoA/carbon monoxide dehydrogenase pathway involving C₁-intermediates otherwise only used by methanogenic bacteria.Non-standard abbreviations APS adenosine 5-phosphosulfate - BV benzyl viologen - DCPIP 2,6-dichlorophenolindophenol - DMN 2,3-dimethyl-1,4-naphthoquinone - DTT DL-1,4-dithiothreitol - H₄F tetrahydrofolate - H₄MPT tetrahydromethanopterin - CH₂ H₄MPT, methylene-H₄MPT - CH H₄MPT, methenyl-H₄MPT - Mes morpholinoethane sulfonic acid - MFR methanofuran - Mops morpholinopropane sulfonic acid - MV methyl viologen - Tricine N-tris(hydroxymethyl)-methylglycine - U mol product formed per min     

High internal resistance to CO2 uptake by submerged macrophytes that use HCO3 −: measurements in air,nitrogen and helium

Previous studies have shown that in water the affinity of submerged macrophytes for CO₂ is higher for species restricted to CO₂ than for species with an additional ability to use bicarbonate. We measured slopes of CO₂ uptake versus CO₂ concentration in the gas phase in air, nitrogen and helium for pairs of species, having or lacking the ability to use bicarbonate, but with similar leaf morphology. For species restricted to CO₂, the slope in nitrogen and helium was 1.5 times and 3.2 times greater than in air. The increased slope in nitrogen results from a suppression of photorespiration. The further increase in helium reflects the increased rate of diffusion of CO₂ and shows that, even in gas, external diffusion through the boundary layer is a significant hindrance to CO₂ uptake. In contrast, in species able to use bicarbonate, the uptake slope was not affected by gas composition, suggesting that photorespiration is absent or photorespired CO₂ is efficiently trapped and that internal resistance is high relative to external resistance. Elodea canadensis specimens grown under high concentrations of CO₂ de-regulated their ability to use bicarbonate, and slopes of CO₂ uptake in helium were significantly greater than in air or nitrogen. Overall, these results are consistent with the notion that while a high affinity for CO₂ will maximise carbon uptake in species restricted to CO₂, for species able to use bicarbonate, a high internal resistance would reduce loss of CO₂ and help maintain high concentrations of CO₂ at the site of fixation. This revised version was published online in August 2006 with corrections to the Cover Date.     

Denitrification in a seashore sandy deposit influenced by groundwater discharge

The chemical compositions of ground water and organic matter in sediments were investigated at a sandy shore of Tokyo Bay, Japan to determine the fate of ground water NO₃ ^–. On the basis of Cl^– distribution in ground water, the beach was classified into freshwater (FR)-, transition (TR)-, and seawater (SW)-zones from the land toward the shoreline. The NO₃ ^– and N₂O did not behave conservatively with respect to Cl^– during subsurface mixing of freshwater and seawater, suggesting NO₃ ^– consumption and N₂O production in the TR-zone. Absence of beach vegetation indicated that NO₃ ^– assimilation by higher plants was not as important as NO₃ ^– sink. Low NH₄ ⁺ concentrations in ground water revealed little reduction of NO₃ ^– to NH₄ ⁺. These facts implied that microbial denitrification and assimilation were the likely sinks for ground water NO₃ ^–. The potential activity and number of denitrifiers in water-saturated sediment were highest in the low-chlorinity part of the TR-zone. The location of the highest potential denitrification activity (DN-zone) overlapped with that of the highest NO₃ ^– concentration. The C/N ratio and carbon isotope ratio (¹³C) of organic matter in sediment (< 100 -m) varied from 12.0 to 22.5 and from –22.5 to –25.5, respectively. The ¹³C value was inversely related to the C/N ratio (r ² = 0.968, n = 11), which was explained by the mixing of organic matters of terrestrial and marine origins. In the DN-zone, the fine sediments were rich in organic matters with high C/N ratios and low ¹³C values, implying that dissolved organic matters of terrestrial origin might have been immobilized under slightly saline conditions. A concurrent supply of NO₃ ^– and organic matter to the TR-zone by ground water discharge probably generates favorable conditions for denitrifiers. Ground water NO₃ ^– discharged to the beach is thus partially denitrified and fixed as microbial biomass before it enters the sea. Further studies are necessary to determine the relative contribution of these processes for NO₃ ^– removal.     

Affixing the O to Rubisco: discovering the source of photorespiratory glycolate and its regulation

The source of glycolate in photorespiration and its control, a particularly active and controversial research topic in the 1970s, was resolved in large part by several discoveries and observations described here. George Bowes discovered that the key carboxylation enzyme Rubisco (ribulosebisphosphate carboxylase/oxygenase) is competitively inhibited by O₂ and that O₂ substitutes for CO₂ in the initial `dark' reaction of photosynthesis to yield glycolate-P, the substrate for photorespiration. William Laing derived an equation from basic enzyme kinetics that describes the CO₂, O₂, and temperature dependence of photosynthesis, photorespiration, and the CO₂ compensation point in C₃ plants. Jerome Servaites established that photosynthesis cannot be increased by inhibiting the photorespiratory pathway prior to the release of photorespiratory CO₂, and Douglas Jordan discovered substantial natural variation in the Rubisco oxygenase/carboxylase ratio. A mutant Arabidopsis plant with defective glycolate-P phosphatase, isolated by Chris Somerville, definitively established the role of O₂ and Rubisco in providing photorespiratory glycolate. Selection techniques to isolate photorespiration-deficient plants were devised by Jack Widholm and by Somerville, but no plants with reduced photorespiration were found. Somerville's approach, directed mutagenesis of Arabidopsis plants, was subsequently successful in the isolation of numerous other classes of mutants and revolutionized the science of plant biology. This revised version was published online in August 2006 with corrections to the Cover Date.