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.     

Carbon: freshwater plants

δ¹³C values for freshwater aquatic plant matter varies from ?11 to ?50‰ and is not a clear indicator of photosynthetic pathway as in terrestrial plants. Several factors affect δ¹³C of aquatic plant matter. These include: (1) The δ¹³C signature of the source carbon has been observed to range from +1‰ for HCO₃^? derived from limestone to ?30‰ for CO₂ derived from respiration. (2) Some plants assimilate HCO₃^?, which is –7 to –11‰ less negative than CO₂. (3) C₃, C₄, and CAM photosynthetic pathways are present in aquatic plants. (4) Diffusional resistances are orders of magnitude greater in the aquatic environment than in the aerial environment. The greater viscosity of water acts to reduce mixing of the carbon pool in the boundary layer with that of the bulk solution. In effect, many aquatic plants draw from a finite carbon pool, and as in terrestrial plants growing in a closed system, biochemical discrimination is reduced. In standing water, this factor results in most aquatic plants having a δ¹³C value similar to the source carbon. Using Farquhar's equation and other physiological data, it is possible to use δ¹³C values to evaluate various parameters affecting photosynthesis, such as limitations imposed by CO₂ diffusion and carbon source.     

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.     

Silicon isotope fractionation in rice plants, an experimental study on rice growth under hydroponic conditions

Silicon (Si) isotope composition and Si distribution among different rice plant organs and different parts of rice leaf at maturity were studied, which may provide new insights into the mechanism of Si accumulation in plants and biogeochemical Si cycle. An isotope ratio mass spectrometer (IRMS) was used to examine Si isotope fractionation by rice plant grown in a hydroponic system. The observed ³⁰Si-depletion (about 0.3‰) of whole plant relative to external nutrient solutions suggested biologically mediated Si isotope fractionation occurred during uptake. However, it was not possible to judge the Si uptake mechanism with the data. For δ³⁰Si variation within plant, there was a consistent increasing trend from lower to upper tissues (stem < leaf < husk < grain; leaf sheath < leaf blade base <leaf blade middle < leaf blade top). The phenomenon, reflecting kinetic isotope effects, could be explained that isotope fractionation during Si deposition in rice plant was a Rayleigh-like behavior. The range (−2.7‰ to 2.3‰) of δ³⁰Si variation among rice plant tissues in present experiment exceeded that (−1.7‰ to 2.5‰) of phytoliths observed previously in continents, which would enhance understanding the role of phytoliths on globe Si isotope balance.     

Carbon isotope fractionation between diet and bioapatite in ungulate mammals and implications for ecological and paleoecological studies

 The isotope enrichment ɛ* of ¹³C between tooth enamel of large ruminant mammals and their diet is 14.1 ± 0.5‰. This value was obtained by analyzing both the dental enamel of a variety of wild and captive mammals and the vegetation that comprised their foodstuffs. This isotope enrichment factor applies to a wide variety of ruminant mammals. Non-ruminant ungulates have a similar isotope enrichment, although our data cannot determine if it is significantly different. We also found a ¹³C isotope enrichment ɛ* of 3.1 ± 0.7‰ for horn relative to diet, and 11.1 ± 0.8‰ for enamel relative to horn for ruminant mammals. Tooth enamel is a faithful recorder of diet. Its isotopic composition can be used to track changes in the isotopic composition of the atmosphere, determine the fraction of C₃ or C₄ biomass in diets of modern or fossil mammals, distinguish between mammals using different subpathways of C₄ photosynthesis,and identify those mammals whose diet is derived from closed-canopy habitats. Received: 1 July 1998 / Accepted: 9 February 1999     

Carbon isotope fractionation of methyl bromideduring agricultural soil fumigations

The isotopic composition ofmethyl bromide (CH₃Br) has been suggestedto be a potentially useful tracer forconstraining the global CH₃Br budget. Inorder to determine the carbon isotopiccomposition of CH₃Br emitted from the mostsignificant anthropogenic application(pre-plant fumigation) we directly measured the¹³C of CH₃Br released duringcommercial fumigation. We also measured theisotopic fractionation associated withdegradation in agricultural soil under typicalfield fumigation conditions. The isotopiccomposition of CH₃Br collected in soilseveral hours after injection of the fumigantwas –44.5 and this value increased to –20.7over the following three days. The mean kineticisotope effect (KIE) associated withdegradation of CH₃Br in agricultural soil(12) was smaller than the reported value formethylotrophic bacterial strain IMB-1, isolatedfrom previously fumigated agricultural soil,but was similar to methylotrophic bacterialstrain CC495, isolated from a pristine forestlitter zone. Using this fractionationassociated with the degradation of CH₃Brin agricultural soil and the mean¹³C of the industriallymanufactured CH₃Br (–54.4), we calculatethat the agricultural soil fumigation sourcehas a carbon isotope signature that ranges from–52.8 to –42.0. Roughly 65% ofindustrially manufactured CH₃Br is usedfor field fumigations. The remaining 35% isused for structural and post-harvestfumigations with a minor amount used duringindustrial chemical manufacturing. Assumingthat the structural and post-harvest fumigationsources of CH₃Br are emitted withoutsubstantial fractionation, we calculate thatthe ¹³C of anthropogenicallyemitted CH₃Br ranges from –53.2 to –47.5.     

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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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 discrimination and the integration of carbon assimilation pathways in terrestrial CAM plants

Measurement of carbon isotope discrimination (Δ) of organic plant material integrates the combination of C₄ and C₃ carboxylation processes during the phases of CAM through dark and light periods. These processes are tempered by environmental conditions which regulate CAM activity at the molecular, biochemical and ecological level. The factors contributing to short-term changes in Δ are discussed in terms of the day-night changes in metabolite pools and integration via on-line, instantaneous discrimination techniques. Thus, the isotope signature of newly fixed carbon in malic acid reflects the balance between diffusion and carboxylation limitation together with direct and indirect effects of respiratory metabolism. Leakage of CO₂ during decarboxylation leads to greater discrimination being expressed than is predicted from existing models. Over the timescales of seasonal growth and productivity, most constitutive CAM and C₃-CAM intermediate plants show little variation in Δ (2–4‰). The changes induced by developmental and environmental signals and genetic regulation of CAM are compared for stem and leaf succulents. The role of CAM as a potentially highly productive photosynthetic pathway is contrasted with the induction of CAM as a maintenance mechanism in response to environmental stresses. Analyses of Δ have already contributed much to our understanding of the distribution and regulation of CAM, and in turn can also be used to analyse phylogenetic relationships and the origins of CAM as determined from palaoecological evidence.     

双向标记培养植物测定大气二氧化碳稳定碳同位素组成

基于植物能够利用体内的碳酸酐酶来催化碳酸氢根离子生成二氧化碳和水作为底物进行光合作用的特性,采用两种δ13CPDB值差值大于10‰的碳酸氢钠分别作为外源碳酸氢根离子的碳同位素标记物,通过室内双向水培诸葛菜和芥菜型油菜实验,分别向水培处理液里添加已知δ13CPDB值的碳酸氢钠并培养24 h,利用同位素比值质谱(IRMS)技术,测定并计算了两个时间、两种环境下的大气二氧化碳稳定碳同位素日平均组成。结果表明:在环境1(不同浓度的Na HCO3处理液)下所得到的δCa值与添加到处理液中的碳酸氢根离子的浓度有关;在环境2(不同浓度的PEG处理液)下所得到的δCa值与添加到处理液中的PEG的浓度无关;两种环境下所测得的大气二氧化碳稳定碳同位素日平均组成δCa值与实验中培养的植物种类无关,而与添加到培养液中碳酸氢根离子的浓度及植物的生长速率有关。数据重现性好,结果准确可靠,可以高精度的测定不同待测环境下大气二氧化碳稳定碳同位素比值,其可为以后监测不同时间、不同地点的大气二氧化碳碳同位素组成及来源提供非常有效的方法和信息。     

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.     

Non-statistical isotope fractionation as a novel “retro-biosynthetic” approach to understanding alkaloid metabolic pathways

During the biosynthesis of natural products, isotope fractionation occurs due to the selectivity of enzymes for the heavier or lighter isotopomers. As only some of the positions in the molecule are implicated in a given reaction mechanism, position-specific fractionation occurs. Thus, the position-specific ¹³C/¹²C ratios in these compounds can be related to their known precursors and to the known isotope effects of enzymes involved in their biosynthesis, or similar reaction mechanisms. This can be accessed by isotope ratio monitoring NMR spectrometry. In this short review, how isotope fractionation occurs and when it is manifest is described. Then, the way that ¹³C NMR spectrometry has been applied to study certain aspects of the biosynthesis of the solanaceous alkaloids S-(−)-nicotine and tropine is outlined. Notably, it is shown how similar isotope fractionation is found in the steps of the pathway to the common intermediate, N-methyl-Δ¹-pyrrolinium, but that in the moieties derived from different origins no such similarity is found, the isotopic composition of these atoms reflecting their specific metabolic ancestry. In a second example, tramadol, it is shown how this technique can be used in retro-biosynthesis to give direction as to what precursors and pathway intermediates are probable. It is shown how the observed fractionation in the site-specific ¹³C/¹²C ratios can be effectively explained by known metabolism and the properties of enzymes proposed for the pathway. Furthermore, it can give indications of possible mechanisms of those enzymes that are as yet to be described for a number of key steps.     

Nitrogen allocation and carbon isotope fractionation in relation to intercepted radiation and position in a young Pinus radiata D. Don tree

The three dimensional distribution of intercepted radiation, intercellular CO₂ concentration (C_i) and late summer needle nitrogen (N) concentration were determined at the tips of all 54 branches in a 6·2-m-tall Pinus radiata D. Don tree growing in a New Zealand plantation. Measurements included above- and below-canopy irradiance, leaf stable carbon isotopic composition (δ¹³C) and tree canopy architecture. The radiation absorption component of the model, MAESTRO, was tested on site and then used to determine the branch tip distribution of intercepted radiation. We hypothesized that in branch tip needles: (i) the allocation of nitrogen and other nutrients would be closely associated with the distribution of intercepted radiation, reflecting carbon gain optimization theory, and (ii) C_i would predominantly reflect changes in photosynthetic rate (A) rather than stomatal conductance (g_s), indicating that the increase in A for a given increase in N concentration was larger than the corresponding increase in g_s. Needle nitrogen concentration was poorly related to intercepted radiation, regardless of the period over which the latter was calculated. At a given height, there was a large azimuthal variation in intercepted radiation but N concentration was remarkably uniform around the tree canopy. There was, however, a linear and positive correspondence between N concentration and δ¹³C and needle height above ground (r² = 0·73 and 0·68, respectively). The very strong linear correspondence between N concentration and C_i (r² = 0·71) was interpreted, using gas exchange measurements, as supporting our second hypothesis. Recognizing the strong apical control in P. radiata and possible effects of leaf nitrogen storage in an evergreen species, we propose that the tree leader must have constituted a very strong carbon sink throughout the growing season, and that the proximity of branch tip needles to the leader affected their photosynthetic capacity and nutrient concentration, independent of intercepted radiation. This implies an integrated internal determination of resource allocation within the tree and challenges the current convention that resources are optimally distributed according to the profile of intercepted radiation.     

Hydrogen isotope fractionation during water uptake by woody xerophytes

Stable isotope measurements are employed extensively in plant–water relations research to investigate physiological and hydrological processes from whole plant to ecosystem scales. Stable isotopes of hydrogen and oxygen are routinely measured to identify plant source water. This application relies on the assumption that no fractionation of oxygen and hydrogen isotopes in water occurs during uptake by roots. However, a large fraction of the water taken up through roots in halophytic and xerophytic plants transverses cell membranes in the endodermis before entering the root xylem. Passage of water through this symplastic pathway has been hypothesized to cause fractionation leading to a decrease in ²H of root xylem water relative to that in the surrounding soil medium. We examined 16 woody halophytic and xerophytic plant species in controlled conditions for evidence of hydrogen isotope fractionation during uptake at the root–soil interface. Isotopic separation (Δ²H = δ²H_{soil water} − δ²H_{xylem water}) ranging from 3‰ to 9‰ was observed in 12 species. A significant positive correlation between salinity tolerance and the magnitude of Δ²H was observed. Water in whole stem segments, sapwood, and roots had significantly lower δ²H values relative to soil water in Prosopis velutina Woot., the species expressing the greatest Δ²H values among the 16 species examined. Pressurized water flow through intact root systems of Artemisia tridentata Nutt. and Atriplex canescens (Pursh) Nutt. caused the δ²H values to decrease as flow rate increased. This relationship was not observed in P. velutina. Destroying the plasma membranes of root cells by excessive heat from boiling did not significantly alter the relationship between δ²H of expressed water and flow rate. In light of these results, care should be taken when using the stable isotope method to examine source-water use in halophytic and xerophytic species.     

The influence of (photo)respiration on carbon isotope discrimination in plants

The contribution which (photo)respiration makes to carbon isotope discrimination (Δ¹³C) was examined by conducting simultaneous gas exchange measurements and isotopic analysis of carbon dioxide passing over leaves of Triticum aestivum and Phaseolus vulgaris, via manipulations of the carbon isotope composition (δ¹³C) of source CO₂ during growth and measurement. Dark respiration only altered net Δ¹³C (Δ_obs) at low CO₂ assimilation, and was sensitive to source CO₂δ¹³C during measurement. Photorespiration reduced Δ_obs relative to Δ¹³C predicted from p_i/p_a (Δ_i) over the full range of CO₂ assimilation, to a greater degree under elevated oxygen partial pressure (pO₂), indicating fractionation during photorespiration (f) in T. aestivum. For P. vulgaris, Δ_obs was insensitive to elevated pO₂ at higher assimilation rates, suggesting that f was minimal. A model was developed to calculate gross discrimination (Δ_ps), independent of (photo)respiration, from which estimates of f were obtained for T. aestivum (3.3‰) and P. vulgaris (0.5‰). Because photorespiratory fractionation varies interspecifically, and influences net Δ¹³C which is directly reflected in leaf δ¹³C, consideration of (photo)respiratory fractionation is necessary when interpreting δ¹³C of leaf material, especially under conditions where (photo)respiratory CO₂ losses make a large relative contribution to total plant carbon budgets.     

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.     

The influence of water content and leaf anatomy on carbon isotope discrimination and photosynthesis in Sphagnum

The relative effect of diffusional resistance due to water films (r_wf) and leaf anatomy (r_p) on rates of net photosynthesis and on-line measures of carbon isotope discrimination (Δ=Δδ¹³C) was investigated in Sphagnum. Sphagnum species differ in the exposure of photosynthetic cells at the leaf surface. In S. affine, photosynthetic cells are widely exposed at the surface, whereas in S. magellanicum, photo-synthetic cells are enclosed within water-filled hyaline cells. This difference is expected to lead to variation in diffusive resistance within leaves (r_p). Net photosynthesis and on-line Δ were measured at two water contents: greenhouse water content (wet) and blotted dry (dry). Without correcting for respiration, on-line Δ values differed significantly between wet (23.7%_o) and dry (30.9%_o) plants. However, there was no significant difference between species means and no species × water content interaction. Corrections for respiration lowered Δ values by approximately 8.1%_o and reduced the mean difference to 3.1%_o, but did not alter the rank order of treatments. Net photosynthesis also decreased by 16% in wet plants, but there was no significant difference between the two species. In addition, five populations of S. affine and S. magellanicum grown in a common garden were analysed for their organic matter carbon isotope composition (δ¹³C). These values varied more within each species (0.9–1.2%_o) than between the two species (0.6%_o). Therefore, we conclude that variation in surface water films leads to a greater difference in resistance to CO₂ uptake and carbon isotope discrimination than that due to variation in leaf anatomical properties in Sphagnum.