• biotic interactions;
  • carbon cycle;
  • carbon pools and fluxes;
  • ecosystem;
  • global environmental change;
  • plant metabolism and biochemistry;
  • plant–soil interactions;
  • stable isotope of carbon (13C)

The uptake and metabolism of carbon (C) by plants, and its subsequent partitioning to the soil microbial community and the atmosphere, have long been fundamental topics in plant biology and ecological research. Carbon cycling research is especially prominent now as a key component in our efforts to better understand and predict the trajectory and consequences of global environmental change. The stable isotope of C, 13C, has seen increased use as an important tool for understanding and quantifying C pools and fluxes in terrestrial ecosystems. In this Virtual Special Issue, we bring together 20 recent papers from New Phytologist that use 13C to explore plant and ecosystem C cycling. They cover a wide range of biological questions: basic plant metabolism and biochemistry, gaseous exchanges with the atmosphere, and plant–soil and biotic interactions. Together, this collection of papers shows how powerful 13C has become as a research tool, and how creative and sophisticated researchers have become in exploiting its use.

Andrew Benson recounted the exciting history of the rapid discovery of the path of C in photosynthesis when the newly created radioisotope of C, 14C, saw its first use in plant biology in the 1940s (Benson, 2002). Several decades later, 14C was used in investigations of C allocation in trees in forest ecosystems (McLaughlin & McConathy, 1979). However, safety and regulatory concerns have limited the application of 14C, especially in the field environment. Background levels of 14C that resulted from atmospheric testing of nuclear weapons have been very useful in ecological studies (Carbone & Trumbore, 2007), but such analysis is expensive and not widely available. The short-lived radioisotope, 11C, was used in photosynthesis research before 14C became available (Benson, 2002), but it has seen only limited use (Minchin & Thorpe, 2003) because of its very short half-life and the specialized facility its use requires. By contrast, new tools for analysis of 13C (Barbour et al., 2007) have made approaches using the stable C isotope much more widely available to many researchers.

In their Tansley review, Bowling et al. (2008) discuss the implications of systematic variation in the C isotopic composition (δ13C) in ecosystem C pools and fluxes for C cycling studies. They emphasized the importance of understanding the sources of variation related to plant metabolism and environmental influences, and how that variation is critical for interpreting ecosystem processes and the temporal and spatial variability in the isotopic composition of the atmosphere. A detailed systems approach is required to understand the metabolic pathways and fractionation between 12C and 13C that occurs during metabolism (Barbour & Hanson, 2009), and the differences in metabolic pathways between plant organs can help explain the diel and seasonal variation in δ13C measured at the ecosystem scale (Wingate, 2008). Bathellier et al. (2008) investigated the changes in isotopic signature during plant development in different plant organs of Phaseolus vulgaris. They concluded that the differences between organs were related to respiration and respiratory fractionation. In continuing studies with P. vulgaris, Bathellier et al. (2009) concluded that unless the 13C photosynthetic fractionation varies at the leaf level, the root δ13C signal hardly changes under a range of natural environmental conditions. Hence, more detailed understanding of respiratory fractionation is needed to interpret isotopic evidence at larger scales. Gessler et al. (2009) analyzed the 13C content of respired CO2 from leaves, stems and roots of Ricinus communis and related the diel variation in 13C enrichment of respiratory CO2 to intensive phosphoenolpyruvatecarboxylase-catalysed CO2 refixation in stems and roots. Carbone & Trumbore (2007) and Priault et al. (2009) interpreted 13C patterns resulting from labelling or from diurnal variation in metabolism in terms of functional group variation in allocation. Dueck et al. (2007) used a laser-based approach with 13C-labelled plants to show that there is no evidence for substantial aerobic methane emission by terrestrial plants.

Environmental influences on the 13C content of leaves and other organs within and among plant species are related in part to the initial uptake of 13CO2. Diffusion through stomata causes a discrimination against the heavier 13CO2 molecule relative to 12CO2, and the resulting δ13C in leaves can be used to estimate the balance between stomatal conductance and assimilation rate (DaMatta et al., 2008) or mesophyll resistance (Flexas et al., 2007). Sekiya & Yano (2008) explored how environmental variations, specifically the availability of soil phosphorus, water and atmospheric CO2, could affect the relationship between δ13C and stomatal density. They concluded that there was a linear relationship across all examined environments. Cernusak et al. (2007) hoped to identify indicators of differences in transpiration efficiency among tropical tree species. Although variation in transpiration efficiency was correlated with leaf N concentration and 18O enrichment, transpiration efficiency was correlated with δ13C only within a species, not across species. This contrasts with the clear and long-established difference in δ13C between C3 and C4 plants (Bender, 1971). Descolas-Gros & Scholzel (2007) exploited the C3–C4 difference to differentiate modern pollen into C3 and C4 groups based on δ13C, which should be an aid to interpretation of quaternary and older fossil sediments.

The long-term fate of C in ecosystems depends on whether it is stored in living biomass or in soils (Hyvönen et al., 2007), so the processes controlling the partitioning of C to soil must be understood. In a Tansley review on soil microbial processes that mediate soil C balance, Paterson et al. (2009) discuss how quantitative isotope labelling and partitioning methods contribute to our understanding of the C-cycling processes in soil. They discuss many of the techniques that are employed for introducing a 13C label, including pulse labelling, growing C3 plants in soil from a C4 cropping system (Hancock et al., 2007), use of a 13C-depleted CO2 source in free-air CO2 enrichment (FACE) experiments and the addition of 13C-labelled microbial substrates. Högberg et al. (2008) applied a pulse label of 13CO2 to a forest patch and demonstrated the close temporal coupling between tree canopy photosynthesis and a significant fraction of soil activity in forests. Using a tunable diode laser absorption spectrometer for high-resolution monitoring of δ13C in soil respiration, Bahn et al. (2009) similarly demonstrated a tight coupling in the plant–soil system and the importance of plant metabolism for soil CO2 fluxes in a grassland ecosystem. A 13C pulse-labelling experiment with Quercus rubra seedlings subjected to foliar herbivory led Frost & Hunter (2008) to conclude that C exudation from roots was an actively regulated component of below-ground C allocation. At a finer scale, Paterson et al. (2007) employed compound-specific isotope ratio mass spectrometry to show that utilization of 13C-labelled root exudate compounds was an important driver of microbial group abundance in organic soils.

Fine-root turnover is an important source of C flux into soil (Iversen et al., 2008), and fine-root dynamics are an important controller of the efflux of C from soil (Vargas & Allen, 2008). Distinct C isotope signatures (δ13C from 13C-depleted CO2 sources used in FACE experiments and 14C from atmospheric weapons testing) have been used to quantify fine-root turnover (Gaudinski et al., 2001; Matamala et al., 2003), but the estimates often disagree with estimates obtained from minirhizotron observations. Guo et al. (2008) explain this discrepancy through a model based on root branch order. Fungi also contribute to soil respiration, although as discussed by Bostrom et al. (2008), uncertainty about the mechanism causing the difference in 13C enrichment between fungi and plant material continues to constrain the use of stable isotopes in below-ground C-cycling studies. The detailed analysis of δ13C in respired CO2 and sporocarps of different ectomycorrhizal and saprophytic fungal groups in Bostrom et al. (2008) should help to assess hypotheses about the isotopic fractionation that occurs during microbial decomposition of soil organic matter and observations of increasing δ13C with soil depth (Taylor, 2008). Carbon isotopic analysis (13C and 14C) has also been useful for resolving uncertainties in the plant–fungal relationships in orchids (Zimmer et al., 2007, 2008; Cameron et al., 2008) and Pyroleae species (Hynson et al., 2009).

This Virtual Special Issue focuses on the use of 13C, but stable isotopes of other ecologically important elements, particularly deuterium (Keppler et al., 2007), 18O (Gessler et al., 2007) and 15N (Cameron & Seel, 2007; Pons et al., 2007), are also valuable for studying metabolic processes, fluxes and trophic-level interactions in plants and ecosystems. Combined analysis of 13C with other stable isotopes can be especially revealing (Descolas-Gros & Scholzel, 2007; Cernusak et al., 2007; Högberg et al., 2008; Taylor, 2008). As Barbour & Hanson (2009) concluded, ‘The potential for using techniques involving stable isotopes to help understand terrestrial C cycling has been recognized for many years, and it is time for this potential to be realized.’ This collection of papers demonstrates that the potential is indeed coming to reality.


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