The curious consistency of carbon biosignatures over billions of years of Earth-life coevolution

The oldest and most wide-ranging signal of biological activity (biosignature) on our planet is the carbon isotope composition of organic materials preserved in rocks. These biosignatures preserve the long-term evolution of the microorganism-hosted metabolic machinery responsible for producing deviations in the isotopic compositions of inorganic and organic carbon. Despite billions of years of ecosystem turnover, evolutionary innovation, organismic complexification, and geological events, the organic carbon that is a residuum of the global marine biosphere in the rock record tells an essentially static story. The ~25‰ mean deviation between inorganic and organic ¹³C/¹²C values has remained remarkably unchanged over >3.5 billion years. The bulk of this record is conventionally attributed to early-evolved, RuBisCO-mediated CO₂ fixation that, in extant oxygenic phototrophs, produces comparable isotopic effects and dominates modern primary production. However, billions of years of environmental transition, for example, in the progressive oxygenation of the Earth’s atmosphere, would be expected to have accompanied shifts in the predominant RuBisCO forms as well as enzyme-level adaptive responses in RuBisCO CO₂-specificity. These factors would also be expected to result in preserved isotopic signatures deviating from those produced by extant RuBisCO in oxygenic phototrophs. Why does the bulk carbon isotope record not reflect these expected environmental transitions and evolutionary innovations? Here, we discuss this apparent discrepancy and highlight the need for greater quantitative understanding of carbon isotope fractionation behavior in extant metabolic pathways. We propose novel, laboratory-based approaches to reconstructing ancestral states of carbon metabolisms and associated enzymes that can constrain isotopic biosignature production in ancient biological systems. Together, these strategies are crucial for integrating the complementary toolsets of biological and geological sciences and for interpretation of the oldest record of life on Earth.Subject terms: Bacterial evolution, Applied microbiology, Biogeochemistry     

Carbon isotope fractionation in plants

Plants with the C₃, C₄, and crassulacean acid metabolism (CAM) photosynthetic pathways show characteristically different discriminations against ¹³C during photosynthesis. For each photosynthetic type, no more than slight variations are observed within or among species. CAM plants show large variations in isotope fractionation with temperature, but other plants do not. Different plant organs, subcellular fractions and metabolises can show widely varying isotopic compositions. The isotopic composition of respired carbon is often different from that of plant carbon, but it is not currently possible to describe this effect in detail. The principal components which will affect the overall isotope discrimination during photosynthesis are diffusion of CO₂, interconversion of CO₂ and HCO^?₃, incorporation of CO₂ by phosphoenolpyruvate carboxylase or ribulose bisphosphate carboxylase, and respiration. Theisotope fractionations associated with these processes are summarized. Mathematical models are presented which permit prediction of the overall isotope discrimination in terms of these components. These models also permit a correlation of isotope fractionations with internal CO₂ concentrations. Analysis of existing data in terms of these models reveals that CO₂ incorporation in C₃ plants is limited principally by ribulose bisphosphate carboxylase, but CO₂ diffusion also contributes. In C₄ plants, carbon fixation is principally limited by the rate of CO₂ diffusion into the leaf. There is probably a small fractionation in C₄ plants due to ribulose bisphosphate carboxylase.     

Evolutionary trends in RuBisCO kinetics and their co‐evolution with CO2 concentrating mechanisms

RuBisCO‐catalyzed CO₂ fixation is the main source of organic carbon in the biosphere. This enzyme is present in all domains of life in different forms (III, II, and I) and its origin goes back to 3500 Mya, when the atmosphere was anoxygenic. However, the RuBisCO active site also catalyzes oxygenation of ribulose 1,5‐bisphosphate, therefore, the development of oxygenic photosynthesis and the subsequent oxygen‐rich atmosphere promoted the appearance of CO₂ concentrating mechanisms (CCMs) and/or the evolution of a more CO₂‐specific RuBisCO enzyme. The wide variability in RuBisCO kinetic traits of extant organisms reveals a history of adaptation to the prevailing CO₂/O₂ concentrations and the thermal environment throughout evolution. Notable differences in the kinetic parameters are found among the different forms of RuBisCO, but the differences are also associated with the presence and type of CCMs within each form, indicative of co‐evolution of RuBisCO and CCMs. Trade‐offs between RuBisCO kinetic traits vary among the RuBisCO forms and also among phylogenetic groups within the same form. These results suggest that different biochemical and structural constraints have operated on each type of RuBisCO during evolution, probably reflecting different environmental selective pressures. In a similar way, variations in carbon isotopic fractionation of the enzyme point to significant differences in its relationship to the CO₂ specificity among different RuBisCO forms. A deeper knowledge of the natural variability of RuBisCO catalytic traits and the chemical mechanism of RuBisCO carboxylation and oxygenation reactions raises the possibility of finding unrevealed landscapes in RuBisCO evolution.     

Ecologically and geologically relevant isotope signatures of C,N, and S: okenone producing purple sulfur bacteria part I

Purple sulfur bacteria (PSB) are known to couple the carbon, nitrogen, and sulfur cycling in euxinic environments. This is the first study with multiple strains and species of okenone‐producing PSB to examine the carbon (C), nitrogen (N), and sulfur (S) metabolisms and isotopic signatures in controlled laboratory conditions, investigating what isotopic fractionations might be recorded in modern environments and the geologic record. PSB play an integral role in the ecology of euxinic environments and produce the unique molecular fossil okenane, derived from the diagenetic alteration of the carotenoid pigment okenone. Cultures of Marichromatium purpuratum 1591 (Mpurp1591) were observed to have carbon isotope fractionations (¹³ε_{biomass – CO2}), via RuBisCO, ranging from ?16.1 to ?23.2‰ during exponential and stationary phases of growth. Cultures of Thiocapsa marina 5653 (Tmar5653) and Mpurp1591 had a nitrogen isotope fractionation (¹⁵ε_{biomass – NH4}) of ?15‰, via glutamate dehydrogenase, measured and recorded for the first time in PSB. The δ³⁴S_VCDT values and amount of stored elemental sulfur for Mpurp1591 cells grown autotrophically and photoheterotrophically were dependent upon their carbon metabolic pathways. We show that PSB may contribute to the isotopic enrichments observed in modern and ancient anoxic basins. In a photoheterotrophic culture of Mpurp1591 that switched to autotrophy once the organic substrate was consumed, there were bulk biomass δ¹³C values that span a broader range than recorded across the Late Devonian, Permian–Triassic, Triassic–Jurassic, and OAE2 mass extinction boundaries . This finding stresses the complexities in interpreting and assigning δ¹³C values to bulk organic matter preserved in the geologic record.     

SOURCES OF INORGANIC CARBON FOR PHOTOSYNTHESIS BY THREE SPECIES OF MARINE DIATOM1

The utilization of inorganic carbon by three species of marine diatom, Skeletonema costatum (Grev.) Cleve. Ditylum brightwellii (West) Grun., and Chaetoceros calcitrans Paulsen was investigated using an inorganic carbon isotopic disequilibnum technique and inorganic carbon dose-response curves. Stable carbon isotope data of the diatoms are also presented. Observed rates of photosynthetic oxygen evolution were greater than could be accounted for by the theoretical rate of CO₂ supply from the uncatalyzed dehydration of HCO₃^? in the external medium, suggesting use of HCO₃^? as an inorganic carbon source. Data from the isotopic disequilibrium experiment demonstrate the use of both HCO₃^? and CO₂ for photosynthesis. Carbon isotope discrimination values support the use of HCO₃^? by the diatoms.     

Geochemically distinct carbon isotope distributions in Allochromatium vinosum DSM 180T grown photoautotrophically and photoheterotrophically

Anoxygenic, photosynthetic bacteria are common at redox boundaries. They are of interest in microbial ecology and geosciences through their role in linking the carbon, sulfur, and iron cycles, yet much remains unknown about how their flexible carbon metabolism—permitting either autotrophic or heterotrophic growth—is recorded in the bulk sedimentary and lipid biomarker records. Here, we investigated patterns of carbon isotope fractionation in a model photosynthetic sulfur‐oxidizing bacterium, Allochromatium vinosum DSM180^T. In one treatment, A. vinosum was grown with CO₂ as the sole carbon source, while in a second treatment, it was grown on acetate. Different intracellular isotope patterns were observed for fatty acids, phytol, individual amino acids, intact proteins, and total RNA between the two experiments. Photoautotrophic CO₂ fixation yielded typical isotopic ordering for the lipid biomarkers: δ¹³C values of phytol > n‐alkyl lipids. In contrast, growth on acetate greatly suppressed intracellular isotopic heterogeneity across all molecular classes, except for a marked ¹³C‐depletion in phytol. This caused isotopic “inversion” in the lipids (δ¹³C values of phytol < n‐alkyl lipids). The finding suggests that inverse δ¹³C patterns of n‐alkanes and pristane/phytane in the geologic record may be at least in part a signal for photoheterotrophy. In both experimental scenarios, the relative isotope distributions could be predicted from an isotope flux‐balance model, demonstrating that microbial carbon metabolisms can be interrogated by combining compound‐specific stable isotope analysis with metabolic modeling. Isotopic differences among molecular classes may be a means of fingerprinting microbial carbon metabolism, both in the modern environment and the geologic record.     

13C discrimination by fossil leaves during the late-glacial climate oscillation 12-10 ka BP: measurements and physiological controls

The late-glacial climatic oscillation, 12-10 ka BP, is characterised in ice core oxygen isotope profiles by a rapid and abrupt return to glacial climate. Recent work has shown that associated with this cooling was a drop in atmospheric CO₂ concentration of ca. 50 ppm. In this paper, the impact of these environmental changes on ¹³C discrimination is reported, based on measurements made on a continuous sequence of fossil Salix herbacea leaves from a single site. The plant responses were interpreted using an integrated model of stomatal conductance, CO₂ assimilation and intercellular CO₂ concentration, influenced by external environmental factors. According to the model, temperature exerts a marked influence on ¹³C discrimination by leaves and the pattern of ¹³C changes recorded by the fossil leaves is consistent with other palaeotemperature curves for 12-10 ka BP, particularly the deuterium isotope record from Alaskan Salix woods, which generally reflects ocean temperatures. The gas exchange model correctly accounts for these changes and so permits the reconstruction of ancient rates of leaf CO₂ uptake and loss of water vapour in response to the abrupt late-glacial changes in global climate and CO₂. The approach provides the required physiological underpinning for extracting quantitative estimates of past temperatures and for contributing an ecophysiological explanation for changes in ¹³C discrimination in the fossil record.     

Carbon isotope composition of C4 grasses is influenced by light and water supply

The carbon isotope composition of C⁴ grasses has the potential to be used as an indicator of changes in the isotopic composition and concentration of atmospheric CO2, especially for climate reconstruction. The usefulness of C₄ grasses for this purpose hinges on the assumption that their photosynthetic discrimination against ¹³C remains constant in a wide range of environmental conditions. We tested this assumption by examining the effects of light and water stress on the carbon isotope composition of C₄ grasses using different biochemical subtypes (NADP-ME, NAD-ME, PCK) in glasshouse experiments. We grew 14 different C₄ grass species in four treatments: sun-watered, sun-drought, shade-watered and shade-drought. Carbon isotope discrimination (Δ) rarely remained constant. In general, Δ values were lowest in sun-watered grasses, greater for sun-drought plants and even higher for plants of the shade-watered treatment. The highest Δ values were generally found in the most stressed grasses, the shade-drought plants. Grasses of the NADP-ME subtype were the least influenced by a change in environmental variables, followed by PCK and NAD-ME subtypes. Water availability affected the carbon isotope discrimination less than light limitation in PCK and NAD-ME subtypes, but similarly in NADP-ME subtypes. In another experiment, we studied the effect of increasing light levels (150 to 1500 μmol photons m^?2 s^?1) on the Δ values of 18 well-watered C₄ grass species. Carbon isotope discrimination remained constant until photon flux density (PFD) was less than 700 μmol photons m^?2 s^?1. Below this light level, Δ values increased with decreasing irradiance for all biochemical subtypes. The change in A was less pronounced in NADP-ME and PCK than in NAD-ME grasses. Grasses grown in the field and in the glasshouse showed a similar pattern. Thus, caution should be exercised when using C4 plants under varying environmental conditions to monitor the concentration or carbon isotopic composition of atmospheric CO2 in field/glasshouse studies or climate reconstruction.     

Stable Carbon Isotope Fractionation by Sulfate-Reducing Bacteria

Biogeochemical transformations occurring in the anoxic zones of stratified sedimentary microbial communities can profoundly influence the isotopic and organic signatures preserved in the fossil record. Accordingly, we have determined carbon isotope discrimination that is associated with both heterotrophic and lithotrophic growth of pure cultures of sulfate-reducing bacteria (SRB). For heterotrophic-growth experiments, substrate consumption was monitored to completion. Sealed vessels containing SRB cultures were harvested at different time intervals, and δ¹³C values were determined for gaseous CO₂, organic substrates, and products such as biomass. For three of the four SRB, carbon isotope effects between the substrates, acetate or lactate and CO₂, and the cell biomass were small, ranging from 0 to 2‰. However, for Desulfotomaculum acetoxidans, the carbon incorporated into biomass was isotopically heavier than the available substrates by 8 to 9‰. SRB grown lithoautotrophically consumed less than 3% of the available CO₂ and exhibited substantial discrimination (calculated as isotope fractionation factors [α]), as follows: for Desulfobacterium autotrophicum, α values ranged from 1.0100 to 1.0123; for Desulfobacter hydrogenophilus, the α value was 0.0138, and for Desulfotomaculum acetoxidans, the α value was 1.0310. Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO₂ resulted in biomass with a δ¹³C composition intermediate to that of the substrates. The extent of fractionation depended on which enzymatic pathways were used, the direction in which the pathways operated, and the growth rate, but fractionation was not dependent on the growth phase. To the extent that environmental conditions affect the availability of organic substrates (e.g., acetate) and reducing power (e.g., H₂), ecological forces can also influence carbon isotope discrimination by SRB.     

Carbon isotope discrepancy between precambrian stromatolites and their modern analogs: Inferences from hypersaline microbial mats of the sinai coast

The isotopic composition of organic carbon from extant stromatolite-type microbial ecosystems is commonly slanted toward heavy ¹³ C values as compared to respective compositions of average organic matter (including that from Precambrian stromatolites). This seems the more enigmatic as the bulk of primary producers from benthic microbial communities are known to fix carbon via the C3 pathway normally entailing the sizable fractionations of the RuBP carboxylase reaction.There is reason to believe that the small fractionations displayed by aquatic microorganisms result from the limitations of a diffusion-controlled assimilatory pathway in which the isotope effect of the enzymatic reaction is largely suppressed. Apart from the diffusion-control exercised by the aqueous environment, transport of CO₂ to the photosynthetically active sites will be further impeded by the protective slime (polysaccharide) coatings commonly covering microbial mats in which gas diffusivities are extremely low. Ineffective discrimination against¹³C becomes, however, most pronounced in hypersaline environments where substantially reduced CO₂ solubilities tend to push carbon into the role of a limiting nutrient (brine habitats constitute preferential sanctuaries of mat-forming microbenthos since the emergence of Metazoan grazers 0.7 Ga ago). As the same microbial communities had been free to colonize normal marine environments during the Precambrian, the CO₂ concentration effect was irrelevant to the carbon-fixing pathway of these ancient forms. Therefore, it might not surprise that organic matter from Precambrian stromatolites displays the large fractionations commonly associated with C3 photosynthesis. Increased mixing ratios of CO₂ in the Precambrian atmosphere may have additionally contributed to the elimination of the diffusion barrier in the carbon-fixing pathways of ancient mat-forming microbiota.     

Quantum chemical modeling of the kinetic isotope effect of the carboxylation step in RuBisCO

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most important enzyme for the assimilation of carbon into biomass, features a well-known isotope effect with regards to the CO₂ carbon atom. This kinetic isotope effect α = k ₁₂/k ₁₃ for the carboxylation step of the RuBisCO reaction sequence, and its microscopic origin, was investigated with the help of cluster models and quantum chemical methods [B3LYP/6-31G(d,p)]. We use a recently proposed model for the RuBisCO active site, in which a water molecule remains close to the reaction center during carboxylation of ribulose-1,5-bisphosphate [B. Kannappan, J.E. Gready, J. Am. Chem. Soc. 130 (2008), 15063]. Alternative active-site models and/or computational approaches were also tested. An isotope effect alpha for carboxylation is found, which is reasonably close to the one measured for the overall reaction, and which originates from a simple frequency shift of the bending vibration of ¹²CO₂ compared to ¹³CO₂. The latter is the dominant mode for the product formation at the transition state.     

Modelling the discrimination of 13CO2 above and within a temperate broad-leaved forest canopy on hourly to seasonal time scales

Fluxes and concentrations of carbon dioxide and ¹³CO₂ provide information about ecosystem physiological processes and their response to environmental variation. The biophysical model, CANOAK, was adapted to compute concentration profiles and fluxes of ¹³CO₂ within and above a temperate deciduous forest (Walker Branch Watershed, Tennessee, USA). Modifications to the model are described and the ability of the new model (CANISOTOPE) to simulate concentration profiles of ¹³CO₂, its flux density across the canopy–atmosphere interface and leaf‐level photosynthetic discrimination against ¹³CO₂ is demonstrated by comparison with field measurements. The model was used to investigate several aspects of carbon isotope exchange between a forest ecosystem and the atmosphere. During the 1998 growing season, the mean photosynthetic discrimination against ¹³CO₂, by the deciduous forest canopy (Δ_canopy), was computed to be 22·4‰, but it varied between 18 and 27‰. On a diurnal basis, the greatest discrimination occurred during the early morning and late afternoon. On a seasonal time scale, the greatest diurnal range in Δ_canopy occurred early and late in the growing season. Diurnal and seasonal variations in Δ_canopy resulted from a strong dependence of Δ_canopy on photosynthetically active radiation and vapour pressure deficit of air. Model calculations also revealed that the relationship between canopy‐scale water use efficiency (CO₂ assimilation/transpiration) and Δ_canopy was positive due to complex feedbacks among fluxes, leaf temperature and vapour pressure deficit, a finding that is counter to what is predicted for leaves exposed to well‐mixed environments.     

Carbon: terrestrial C4 plants

The carbon isotope composition of terrestrial C₄ plants depends on the primary carboxylation of phosphoenolpyruvate (PEP) and on the diffusion of CO₂ to the carboxylation sites, but is also influenced by the final carboxylation of ribulose-1,5-bisphosphate (RuBP). Several models have been used for reproducing this complex situation. In the present review, a particular model is applied as a means to interpret the effects of environmental and genetically determined factors on carbon isotope discrimination during C₄ photosynthesis. As a new feature, the model considers four types of limitation of the overall CO₂ assimilation rate. Both carboxylation reactions are assumed to be limited by either maximum enzyme activity or maximum substrate regeneration rate. The model is applied to experimental data on the effects of CO₂, irradiance and water stress on short-term discrimination by leaves of several C₄ species measured simultaneously with CO₂ gas exchange characteristics. In particular, different patterns of the influence of low irradiances on carbon isotope discrimination are interpreted as due to variations in that irradiance at which a transition from limitation by PEP regeneration rate and RuBP carboxylase activity to limitation by the regeneration rates of both substrates occurs. After discussing literature data on the effects of environmental conditions on carbon isotope discrimination by C₄ plants seasonal and developmental changes in carbon isotope composition, studies on the systematic and geographic distribution of C₄ plants, evolutionary and genetical aspects, and some ecological implications are reviewed.     

Combined effects of elevated CO2 and soil drought on carbon and nitrogen allocation of the desert shrub Caragana intermedia

Impacts of either elevated CO₂ or drought stress on plant growth have been studied extensively, but interactive effects of these on plant carbon and nitrogen allocation is inadequately understood yet. In this study the response of the dominant desert shrub, Caragana intermedia Kuanget H.c.Fu, to the interaction of elevated CO₂ (700 ± 20 μmol mol⁻¹) and soil drought were determined in two large environmental growth chambers (18 m²). Elevated CO₂ increased the allocation of biomass and carbon into roots and the ratio of carbon to nitrogen (C:N) as well as the leaf soluble sugar content, but decreased the allocation of biomass and carbon into leaves, leaf nitrogen and leaf soluble protein concentrations. Elevated CO₂ significantly decreased the partitioning of nitrogen into leaves, but increased that into roots, especially under soil drought. Elevated CO₂ significantly decreased the carbon isotope discrimination (Δ) in leaves, but increased them in roots, and the ratio of Δ values between root and leaf, indicating an increased allocation into below-ground parts. It is concluded that stimulation of plant growth by CO₂ enrichment may be negated under soil drought, and under the future environment, elevated CO₂ may partially offset the negative effects of enhanced drought by regulating the partitioning of carbon and nitrogen.     

Role of carboxysomes in cyanobacterial CO2 assimilation: CO2 concentrating mechanisms and metabolon implications

Many carbon-fixing organisms have evolved CO₂ concentrating mechanisms (CCMs) to enhance the delivery of CO₂ to RuBisCO, while minimizing reactions with the competitive inhibitor, molecular O₂. These distinct types of CCMs have been extensively studied using genetics, biochemistry, cell imaging, mass spectrometry, and metabolic flux analysis. Highlighted in this paper, the cyanobacterial CCM features a bacterial microcompartment (BMC) called ‘carboxysome’ in which RuBisCO is co-encapsulated with the enzyme carbonic anhydrase (CA) within a semi-permeable protein shell. The cyanobacterial CCM is capable of increasing CO₂ around RuBisCO, leading to one of the most efficient processes known for fixing ambient CO₂. The carboxysome life cycle is dynamic and creates a unique subcellular environment that promotes activity of the Calvin–Benson (CB) cycle. The carboxysome may function within a larger cellular metabolon, physical association of functionally coupled proteins, to enhance metabolite channelling and carbon flux. In light of CCMs, synthetic biology approaches have been used to improve enzyme complex for CO₂ fixations. Research on CCM-associated metabolons has also inspired biologists to engineer multi-step pathways by providing anchoring points for enzyme cascades to channel intermediate metabolites towards valuable products.     

Origin and cycling of riverine inorganic carbon in the Sava River watershed (Slovenia) inferred from major solutes and stable carbon isotopes

The Sava River and its tributaries in Slovenia represent waters strongly influenced by chemical weathering of limestone and dolomite. The carbon isotopic compositions of dissolved inorganic carbon (DIC) and suspended organic carbon (POC) fractions as well as major solute concentrations yielded insights into the origin and fluxes of carbon in the upper Sava River system. The major solute composition was dominated by carbonic acid dissolution of calcite and dolomite. Waters were generally supersaturated with respect to calcite, and dissolved CO₂ was about fivefold supersaturated relative to the atmosphere. The δ¹³C of DIC ranged from −13.5 to −3.3‰. Mass balances for riverine inorganic carbon suggest that carbonate dissolution contributes up to 26%, degradation of organic matter ∼17% and exchange with atmospheric CO₂ up to 5%. The concentration and stable isotope diffusion models indicated that atmospheric exchange of CO₂ predominates in streams draining impermeable shales and clays while in the carbonate-dominated watersheds dissolution of the Mesozoic carbonates predominates.     

Effects of climate change on labile and structural carbon in Douglas-fir needles as estimated by δ13C and Carea measurements

Models of photosynthesis, respiration, and export predict that foliar labile carbon (C) should increase with elevated CO₂ but decrease with elevated temperature. Sugars, starch, and protein can be compared between treatments, but these compounds make up only a fraction of the total labile pool. Moreover, it is difficult to assess the turnover of labile carbon between years for evergreen foliage. Here, we combined changes in foliar C_area (C concentration on an areal basis) as needles aged with changes in foliar isotopic composition (δ¹³C) caused by inputs of ¹³C‐depleted CO₂ to estimate labile and structural C in needles of different ages in a four‐year, closed‐chamber mesocosm experiment in which Douglas‐fir (Pseudotsuga menziesii (Mirb.) Franco) seedlings were exposed to elevated temperature (ambient + 3.5 °C) and CO₂ (ambient + 179 ppm). Declines in δ ¹³C of needle cohorts as they aged indicated incorporation of newly fixed labile or structural carbon. The δ ¹³C calculations showed that new C was 41 ± 2% and 28 ± 3% of total needle carbon in second‐ and third‐year needles, respectively, with higher proportions of new C in elevated than ambient CO₂ chambers (e.g. 42 ± 2% vs. 37 ± 6%, respectively, for second‐year needles). Relative to ambient CO₂, elevated CO₂ increased labile C in both first‐ and second‐year needles. Relative to ambient temperature, elevated temperature diminished labile C in second‐year needles but not in first‐year needles, perhaps because of differences in sink strength between the two needle age classes. We hypothesize that plant‐soil feedbacks on nitrogen supply contributed to higher photosynthetic rates under elevated temperatures that partly compensated for higher turnover rates of labile C. Strong positive correlations between labile C and sugar concentrations suggested that labile C was primarily determined by carbohydrates. Labile C was negatively correlated with concentrations of cellulose and protein. Elevated temperature increased foliar %C, possibly due to a shift of labile constituents from low %C carbohydrates to relatively high %C protein. Decreased sugar concentrations and increased nitrogen concentrations with elevated temperature were consistent with this explanation. Because foliar constituents that vary in isotopic signature also vary in concentrations with leaf age or environmental conditions, inferences of c_i/c_a values from δ ¹³C of bulk leaf tissue should be done cautiously. Tracing of ¹³C through foliar carbon pools may provide new insight into foliar C constituents and turnover.     

The contribution of C<Subscript>3</Subscript> and C<Subscript>4</Subscript> plants to the carbon cycle of a tallgrass prairie: an isotopic approach

The photosynthetic pathway composition (C₃:C₄ mixture) of an ecosystem is an important controller of carbon exchanges and surface energy flux partitioning, and therefore represents a fundamental ecophysiological distinction. To assess photosynthetic mixtures at a tallgrass prairie pasture in Oklahoma, we collected nighttime above-canopy air samples along concentration and isotopic gradients throughout the 1999 and 2000 growing seasons. We analyzed these samples for their CO₂ concentration and carbon isotopic composition and calculated C₃:C₄ proportions with a two-source mixing model. In 1999, the C₄ percentage increased from 38% in spring (late April) to 86% in early fall (mid-September). The C₄ percentages inferred from ecosystem respiration measurements in 2000 indicate a smaller shift, from 67% in spring (early May) to 77% in mid-summer (late July). We also sampled daytime CO₂ concentration and carbon isotope gradients above the canopy to determine ecosystem discrimination against ¹³CO₂ during net uptake. These discrimination values were always lower than corresponding nighttime ecosystem respiration isotopic signatures would suggest. After accounting for the isotopic disequilibria between respiration and photosynthesis resulting from seasonal variations in the C₃:C₄ mixture, we estimated canopy photosynthetic discrimination. The C₄ percentage calculated from this approach agrees with the percentage determined from nighttime respiration for sampling periods in both growing seasons. Isotopic imbalances between photosynthesis and respiration are likely to be common in mixed C₃:C₄ ecosystems and must be considered when using daytime isotopic measurements to constrain ecosystem physiology. Given the global extent of such ecosystems, isotopic imbalances likely contribute to global variations in the carbon isotopic composition of atmospheric CO₂.     

Reaction of ribulose biphosphate carboxylase/oxygenase assembled on a DNA scaffold

Ribulose-1,5-biphosphate carboxylase/oxygenase (RuBisCO), an enzyme in the Calvin-Benson-Bassham cycle of photosynthesis, catalyzes the first step of CO₂ fixation in plants, algae, and photosynthetic bacteria. Despite of the important function in the global carbon cycle, RuBisCO suffers from a slow reaction rate and a competing reaction with O₂ which draw attentions to improve the enzyme efficiency. In this study, a RuBisCO dimer from Rhodospirillum rubrum was assembled on a DNA scaffold using a dimeric DNA binding protein as an adaptor. The enzyme assembly was characterized by atomic force microscopy and RuBisCO assembled on the DNA scaffold showed avid enzymatic activity with retaining its parent carboxylase function. To mimic the environment of the natural microcompartment in cyanobacterial carboxysome that encapsulate the second enzyme carbonic anhydrase (CA) with RuBisCO, RuBisCO was next co-assembled with CA on the DNA scaffold. Although the natural carboxysome assembly is believed to enhance the RuBisCO activity, the co-assembly of RuBisCO and CA reduced the RuBisCO activity, suggesting that the preferential CO₂ dehydration by CA reduced the RuBisCO reaction rate. In line with the recent study, our results suggest that the proximity in the interenzyme distance of RuBisCO and CA is not the crucial determinant for the enhanced RuBisCO activity in carboxysome. The assembly of RuBisCO and CA on DNA scaffold provides a platform for further study on the spatial control of RuBisCO and associating enzymes.     

Role of habitat and great oxidation event on the occurrence of three multisubunit inorganic carbon-uptake systems in cyanobacteria

The oxygenase reaction catalyzed by RuBisCO became an issue only after the evolution of the oxygenic photosynthesis in cyanobacteria. Several strategies were developed by autotrophic organisms as an evolutionary response to increase oxygen levels to help RuBisCO maximize its net carboxylation rate. One of the crucial advancements in this context was the development of more efficient inorganic carbon transporters which could help in increasing the influx of inorganic carbon (Ci) at the site of CO₂ fixation. We conducted a survey to find out the genes coding for cyanobacterial Ci transporters in 40 cyanobacterial phyla with respect to transporters present in Gloeobacter violaceous PCC 7421, an early-diverging cyanobacterium. An attempt was also made to correlate the prevalence of the kind of transporter present in the species with its habitat. Basically, two types of cyanobacterial inorganic carbon transporters exist, i.e. bicarbonate transporters and CO₂-uptake systems. The transporters also show variation in context to their structure as some exist as single subunit proteins (BicA and SbtA), while others exist as multisubunit proteins (namely BCT1, NdhI₃ and NdhI₄). The phylogeny and distribution of the former have been extensively studied and the present analysis provides an insight into the latter ones. The in silico analysis of the genes under study revealed that their distribution was greatly influenced by the habitat and major environmental changes such as the great oxidation event (GOE) in the course of their evolution.