Physical and chemical basis of carbon isotope fractionation in plants

Naturally-occurring variations in the abundances of the stable isotopes of carbon and other elements can be used to understand the dynamics of natural processes in chemistry, biochemistry, biology, medicine, ecology and other fields. The use of carbon-13 isotopic abundances as an indicator of photosynthetic function in plants has become common. The purpose of this article is to describe the physical and chemical processes that contribute to the abundances of carbon-13 in plant materials, and to provide a framework for understanding how those processes control the isotopic contents of natural materials.     

Evidence for the mechanisms of zinc uptake by rice using isotope fractionation

In an earlier study, we found that rice (Oryza sativa) grown in nutrient solution well‐supplied with Zn preferentially took up light ⁶⁴Zn over ⁶⁶Zn, probably as a result of kinetic fractionation in membrane transport processes. Here, we measure isotope fractionation by rice in a submerged Zn‐deficient soil with and without Zn fertilizer. We grew the same genotype as in the nutrient solution study plus low‐Zn tolerant and intolerant lines from a recombinant inbred population. In contrast to the nutrient solution, in soil with Zn fertilizer we found little or heavy isotopic enrichment in the plants relative to plant‐available Zn in the soil, and in soil without Zn fertilizer we found consistently heavy enrichment, particularly in the low‐Zn tolerant line. These observations are only explicable by complexation of Zn by a complexing agent released from the roots and uptake of the complexed Zn by specific root transporters. We show with a mathematical model that, for realistic rates of secretion of the phytosiderophore deoxymugineic acid (DMA) by rice, and realistic parameters for the Zn‐solubilizing effect of DMA in soil, solubilization and uptake by this mechanism is necessary and sufficient to account for the measured Zn uptake and the differences between genotypes.     

Calcium isotope fractionation by intracellular amorphous calcium carbonate (ACC) forming cyanobacteria

The formation of intracellular amorphous calcium carbonate (ACC) by various cyanobacteria is a widespread biomineralization process, yet its mechanism and importance in past and modern environments remain to be fully comprehended. This study explores whether calcium (Ca) isotope fractionation, linked to ACC-forming cyanobacteria, can serve as a reliable tracer for detecting these microorganisms in modern and ancient settings. Accordingly, we measured stable Ca isotope fractionation during Ca uptake by the intracellular ACC-forming cyanobacterium Cyanothece sp. PCC 7425. Our results show that Cyanothece sp. PCC 7425 cells are enriched in lighter Ca isotopes relative to the solution. This finding is consistent with the kinetic isotope effects observed in the Ca isotope fractionation during biogenic carbonate formation by marine calcifying organisms. The Ca isotope composition of Cyanothece sp. PCC 7425 was accurately modeled using a Rayleigh fractionation model, resulting in a Ca isotope fractionation factor (Δ⁴⁴Ca) equal to −0.72 ± 0.05‰. Numerical modeling suggests that Ca uptake by these cyanobacteria is primarily unidirectional, with minimal back reaction observed over the duration of the experiment. Finally, we compared our Δ⁴⁴Ca values with those of other biotic and abiotic carbonates, revealing similarities with organisms that form biogenic calcite. These similarities raise questions about the effectiveness of using the Ca isotope fractionation factor as a univocal tracer of ACC-forming cyanobacteria in the environment. We propose that the use of Δ⁴⁴Ca in combination with other proposed tracers of ACC-forming cyanobacteria such as Ba and Sr isotope fractionation factors and/or elevated Ba/Ca and Sr/Ca ratios may provide a more reliable approach.     

An indirect method for estimating 15N isotope fractionation during nitrogen fixation by a legume under field conditions

A new technique is proposed for measuring ¹⁵N isotope fractionation during N fixation that obviates some of the possible disadvantages of existing methods. Accurate calculation of N fixation by legumes using the ¹⁵N natural abundance technique requires a value for the isotopic composition of fixed N as an input. Isotopic fractionation in fixed N in legumes has usually been measured using N- free solution culture but results can vary with Rhizobium strain and growth conditions. The proposed method avoids these problems and can be used as an integral part of a field experiment for evaluating N fixation.The technique is essentially a process of adjusting values of ¹⁵ N for fixed N until % N fixation calculated by the ¹⁵N natural abundance method best matches % N fixation estimated by the ¹⁵N enrichment method. The use of high % N fixation values improves the sensitivity and reliability of the method.A field evaluation of this comparison technique using chickpea (Cicer arietinum L.) provided a ¹⁵N isotope fractionation factor (–2.37) for fixed N close to that obtained by N-free solution culture methods (–2.10). The availability of these two independent techniques allowed mutual corroboration of estimates of ¹⁵N isotope fractionation during N fixation.

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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.     

Factors controlling the carbon isotope fractionation of tetra- and trichloroethene during reductive dechlorination by Sulfurospirillum ssp. and Desulfitobacterium sp. strain PCE-S

Carbon stable isotope fractionation of tetrachloroethene (PCE) and trichloroethene (TCE) was investigated during reductive dechlorination. Growing cells of Sulfurospirillum multivorans, Sulfurospirillum halorespirans, or Desulfitobacterium sp. strain PCE-S, the respective crude extracts and the abiotic reaction with cyanocobalamin (vitamin B(12)) were used. Fractionation of TCE (alphaC=1.0132-1.0187) by S. multivorans was more than one order of magnitude higher than values previously observed for tetrachloroethene (PCE) (alphaC=1.00042-1.0017). Similar differences in fractionation were observed during reductive dehalogenation by the close relative S. halorespirans with alphaC=1.0046-1.032 and alphaC=1.0187-1.0229 for PCE and TCE respectively. TCE carbon isotope fractionation (alphaC=1.0150) by the purified PCE-reductive dehalogenase from S. multivorans was more than one order of magnitude higher than fractionation of PCE (alphaC=1.0017). Carbon isotope fractionation of TCE by Desulfitobacterium sp. strain PCE-S (alphaC=1.0109-1.0122) as well as during the abiotic reaction with cyanocobalamin (alphaC=1.0154) was in a similar range to previously reported values for fractionation by mixed microbial cultures. In contrast with previous results with PCE, no effects due to rate limitations, uptake or transport of the substrate to the reactive site could be observed during TCE dechlorination. Our results show that prior to a mechanistic interpretation of stable isotope fractionation factors it has to be carefully verified how other factors such as uptake or transport affect the isotope fractionation during degradation experiments with microbial cultures.     

Decarboxylation of glycine contributes to carbon isotope fractionation in photosynthetic organisms

Carbon isotope effects were investigated for the reaction catalyzed by the glycine decarboxylase complex (GDC; EC 2.1.2.10). Mitochondria isolated from leaves of pea (Pisum sativum L.) and spinach (Spinacia oleracea L.) were incubated with glycine, and the CO₂ evolved was analyzed for the carbon isotope ratio (δ¹³C). Within the range of parameters tested (temperature, pH, combination of cofactors NAD⁺, ADP, pyridoxal 5-phosphate), carbon isotope shifts of CO₂ relative to the C₁-carboxyl carbon of glycine varied from +14‰ to −7‰. The maximum effect of cofactors was observed for NAD⁺, the removal of which resulted in a strong ¹²C enrichment of the CO₂ evolved. This indicates the possibility of isotope effects with both positive and negative signs in the GDC reaction. The measurement of δ¹³C in the leaves of the GDC-deficient barley (Hordeum vulgare L.) mutant (LaPr 87/30) plants indicated that photorespiratory carbon isotope fractionation, opposite in sign when compared to the carbon isotope effect during CO₂ photoassimilation, takes place in vivo. Thus the key reaction of photorespiration catalyzed by GDC, together with the key reaction of CO₂ fixation catalyzed by ribulose-1,5-bisphosphate carboxylase, both contribute to carbon isotope fractionation in photosynthesis. This revised version was published online in June 2006 with corrections to the Cover Date.     

Carbon isotope fractionation in species of the torrenticolous families Podostemaceae and Hydrostachyaceae

Carbon isotope ratios of herbarium material from members of the fresh-water families Podostemaceae and Hydrostachyaceae (Rosidae) were analyzed. The levels of ¹³C were highly variable (Podostemaceae −12.8‰ to −38.55‰; Hydrostachyaceae −10.78‰ to −30.42‰), across as well as within species and across a wide geographic range.

We suggest that the high variance observed is due neither to a constant attribute of the species like the photosynthetic CO₂-carboxylase (in water plants with very high discrimination of the ¹³CO₂ probably Rubisco) nor to the constant structural peculiarities of these species. Rather, it is likely due to the ‘diffusional resistance’ for the CO₂-flux from the turbulent and/or fast flowing water, causing a very variable boundary layer on the plant surface.     

Effects of RuBisCO and CO2 concentration on cyanobacterial growth and carbon isotope fractionation

Carbon isotope biosignatures preserved in the Precambrian geologic record are primarily interpreted to reflect ancient cyanobacterial carbon fixation catalyzed by Form I RuBisCO enzymes. The average range of isotopic biosignatures generally follows that produced by extant cyanobacteria. However, this observation is difficult to reconcile with several environmental (e.g., temperature, pH, and CO₂ concentrations), molecular, and physiological factors that likely would have differed during the Precambrian and can produce fractionation variability in contemporary organisms that meets or exceeds that observed in the geologic record. To test a specific range of genetic and environmental factors that may impact ancient carbon isotope biosignatures, we engineered a mutant strain of the model cyanobacterium Synechococcus elongatus PCC 7942 that overexpresses RuBisCO across varying atmospheric CO₂ concentrations. We hypothesized that changes in RuBisCO expression would impact the net rates of intracellular CO₂ fixation versus CO₂ supply, and thus whole-cell carbon isotope discrimination. In particular, we investigated the impacts of RuBisCO overexpression under changing CO₂ concentrations on both carbon isotope biosignatures and cyanobacterial physiology, including cell growth and oxygen evolution rates. We found that an increased pool of active RuBisCO does not significantly affect the ¹³C/¹²C isotopic discrimination (ε_p) at all tested CO₂ concentrations, yielding ε_p of ≈ 23‰ for both wild-type and mutant strains at elevated CO₂. We therefore suggest that expected variation in cyanobacterial RuBisCO expression patterns should not confound carbon isotope biosignature interpretation. A deeper understanding of environmental, evolutionary, and intracellular factors that impact cyanobacterial physiology and isotope discrimination is crucial for reconciling microbially driven carbon biosignatures with those preserved in the geologic record.     

Stable isotope fractionation of strontium in coccolithophore calcite: Influence of temperature and carbonate chemistry

Marine calcifying eukaryotic phytoplankton (coccolithophores) is a major contributor to the pelagic production of CaCO₃ and plays an important role in the biogeochemical cycles of C, Ca and other divalent cations present in the crystal structure of calcite. The geochemical signature of coccolithophore calcite is used as palaeoproxy to reconstruct past environmental conditions and to understand the underlying physiological mechanisms (vital effects) and precipitation kinetics. Here, we present the stable Sr isotope fractionation between seawater and calcite (Δ^88/86Sr) of laboratory cultured coccolithophores in individual dependence of temperature and seawater carbonate chemistry. Coccolithophores were cultured within a temperature and a pCO₂ range from 10 to 25°C and from 175 to 1,240 μatm, respectively. Both environmental drivers induced a significant linear increase in coccolith stable Sr isotope fractionation. The temperature correlation at constant pCO₂ for Emiliania huxleyi and Coccolithus braarudii is expressed as Δ^88/86Sr = ?7.611 × 10^?3 T + 0.0061. The relation of Δ^88/86Sr to pCO₂ was tested in Emiliania huxleyi at 10 and 20°C and resulted in Δ^88/86Sr = ?5.394 × 10^?5 pCO₂ – 0.0920 and Δ^88/86Sr = ?5.742 × 10^?5 pCO₂ – 0.1351, respectively. No consistent relationship was found between coccolith Δ^88/86Sr and cellular physiology impeding a direct application of fossil coccolith Δ^88/86Sr as coccolithophore productivity proxy. An overall significant correlation was detected between the elemental distribution coefficient (D_Sr) and Δ^88/86Sr similar to inorganic calcite with a physiologically induced offset. Our observations indicate (i) that temperature and pCO₂ induce specific effects on coccolith Δ^88/86Sr values and (ii) that strontium elemental ratios and stable isotope fractionation are mainly controlled by precipitation kinetics when embedded into the crystal lattice and subject to vital effects during the transmembrane transport from seawater to the site of calcification. These results provide an important step to develop a coccolith Δ^88/86Sr palaeoproxy complementing the existing toolbox of palaeoceanography.     

Biological fractionation of stable carbon isotopes at the aerobic/anaerobic water interface of meromictic water bodies

Mass-spectrometric investigation of carbon isotope composition (δ¹³C) was carried out for suspended organic matter and dissolved mineral compounds for the water column of some meromictic water bodies differing in salinity and trophic state. As a rule, a more pronounced carbon isotope fractionation (resulting from the metabolism of phytoplankton and anoxygenic phototrophic bacteria) was revealed in the zones of enhanced oxygenic and anoxygenic photosynthesis. Carbon isotope fractionation at the border between oxidized and reduced waters depends both on the activity of microbial communities and on the dominant species of phototrophic microorganisms. Analysis of the distribution profiles of the isotopic composition of suspended organic matter and dissolved mineral carbon revealed active mineralization of the organic matter newly formed via anoxygenic photosynthesis in the monimolimnion by microbial communities, resulting in the release of isotopically light carbon dioxide. Mineral carbon in the anaerobic zones of highly productive meromictic water bodies is therefore enriched with the light ¹²C isotope.     

Experimental determination of nitrogen kinetic isotope fractionation: Some principles; illustration for the denitrification and nitrification processes

Summary A few principles relative to the presentation and use of nitrogen stable isotopic data are briefly reviewed. Some classical relationships between the isotope composition of a substrate undergoing a single-step unidirectional reaction, are introduced. They are illustrated through controlled experiments on denitrification in a soil, and through nitrification by pure cultures ofNitrosomonas europaea. In the latter case, the isotope fractionation is calculated from the isotopic composition of the residual substrate, then of the product and the result is shown to be statistically the same for the two procedures. The isotopic enrichment factor for denitrification is −29.4±2.4‰ at 20°C, and −24.6±0.9‰ at 30°C; for nitrification this factor is −34.7±2.5‰ under the experimental conditions employed.     

Effects of light on respiration and oxygen isotope fractionation in soybean cotyledons

Light effects on electron flow through the cyanide-resistant respiratory pathway, oxygen isotope fractionation and total respiration were studied in soybean (Glycine max L.) cotyledons. During the first 12 h of illumination there was an increase in both electron partitioning through the alternative pathway and oxygen isotope fractionation by the alternative oxidase. The latter probably indicates a change in the properties of the alternative oxidase. There was no engagement of the alternative oxidase in darkness and its fractionation was 27‰. In green cotyledons 60% of the respiration flux was through the alternative pathway and the alternative oxidase fractionation was 32‰. Exposing previously illuminated tissue to continuous darkness induced a decrease in the electron partitioning through the alternative pathway. However, this decrease was not directly linked with the low cellular sugar concentration resulting from the lack of light because 5 min of light every 12 h was sufficient to keep the alternative pathway engaged to the same extent as plants grown under control conditions.     

Variation in oxygen isotope fractionation during cellulose synthesis: intramolecular and biosynthetic effects

The oxygen isotopic composition of plant cellulose is commonly used for the interpretations of climate, ecophysiology and dendrochronology in both modern and palaeoenvironments. Further applications of this analytical tool depends on our in-depth knowledge of the isotopic fractionations associated with the biochemical pathways leading to cellulose. Here, we test two important assumptions regarding isotopic effects resulting from the location of oxygen in the carbohydrate moiety and the biosynthetic pathway towards cellulose synthesis. We show that the oxygen isotopic fractionation of the oxygen attached to carbon 2 of the glucose moieties differs from the average fractionation of the oxygens attached to carbons 3-6 from cellulose by at least 9%, for cellulose synthesized within seedlings of two different species (Triticum aestivum L. and Ricinus communis L.). The fractionation for a given oxygen in cellulose synthesized by the Triticum seedlings, which have starch as their primary carbon source, is different than the corresponding fractionation in Ricinus seedlings, within which lipids are the primary carbon source. This observation shows that the biosynthetic pathway towards cellulose affects oxygen isotope partitioning, a fact heretofore undemonstrated. Our findings may explain the species-dependent variability in the overall oxygen isotope fractionation during cellulose synthesis, and may provide much-needed insight for palaeoclimate reconstruction using fossil cellulose.     

Seasonal water uptake and movement in root systems of Australian phraeatophytic plants of dimorphic root morphology: a stable isotope investigation

A natural abundance hydrogen stable isotope technique was used to study seasonal changes in source water utilization and water movement in the xylem of dimorphic root systems and stem bases of several woody shrubs or trees in mediterranean-type ecosystems of south Western Australia. Samples collected from the native treeBanksia prionotes over 18 months indicated that shallow lateral roots and deeply penetrating tap (sinker) roots obtained water of different origins over the course of a winter-wet/summer-dry annual cycle. During the wet season lateral roots acquired water mostly by uptake of recent precipitation (rain water) contained within the upper soil layers, and tap roots derived water from the underlying water table. The shoot obtained a mixture of these two water sources. As the dry season approached dependence on recent rain water decreased while that on ground water increased. In high summer, shallow lateral roots remained well-hydrated and shoots well supplied with ground water taken up by the tap root. This enabled plants to continue transpiration and carbon assimilation and thus complete their seasonal extension growth during the long (4–6 month) dry season. Parallel studies of other native species and two plantation-grown species ofEucalyptus all demonstrated behavior similar to that ofB. prionotes. ForB. prionotes, there was a strong negative correlation between the percentage of water in the stem base of a plant which was derived from the tap root (ground water) and the amount of precipitation which fell at the site. These data suggested that during the dry season plants derive the majority of the water they use from deeper sources while in the wet season most of the water they use is derived from shallower sources supplied by lateral roots in the upper soil layers. The data collected in this study supported the notion that the dimorphic rooting habit can be advantageous for large woody species of floristically-rich, open, woodlands and heathlands where the acquisition of seasonally limited water is at a premium.     

Isotope fractionation during root water uptake by Acacia caven is enhanced by arbuscular mycorrhizas

Plant and Soil - A growing number of studies show a discrepancy between the isotopic composition of xylem water and plant water sources. We tested the effect of arbuscular mycorrhizal fungi (AMF)...     

Silicon isotope fractionation dynamics during uptake and translocation by various crop species under three soil types

Plant and Soil - Silicon is important for both plant growth and the soil biogeochemical cycle. Si uptake and accumulation ability varies in plants, which are defined as Si accumulators,...     

Hydrogen uptake by Robinia pseudoacacia nodules

Summary Hydrogen uptake is thought to increase the efficiency of nitrogen fixation by recycling H₂ produced by nitrogenase that would otherwise be lost by diffusion. Here we demonstrate the capacity of eight Rhizobium strains to take up molecular hydrogen. Uptake by nodule homogenates from Robinia pseudoacacia was measured amperometrically under nitrogenase repression. Markedly lower activities were found than in soybean nodules. In addition hydrogenase activity was detected by the ability of bacteroids to reduce methylene blue in the presence of hydrogen. It was demonstrated that hydrogenase structural genes are present in the black locust symbiont, Rhizobium sp. strain R1, using hybridization with a plasmid, which contained hydrogenase genes from R. leguminosarum bv. viceae.