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Abstract. Stable isotope analysis is a powerful tool for assessing plant carbon and water relations and their impact on biogeochemical processes at different scales. Our processbased understanding of stable isotope signals, as well as technological developments, has progressed significantly, opening new frontiers in ecological and interdisciplinary research. This has promoted the broad utilisation of carbon, oxygen and hydrogen isotope applications to gain insight into plant carbon and water cycling and their interaction with the atmosphere and pedosphere. Here, we highlight specific areas of recent progress and new research challenges in plant carbon and water relations, using selected examples covering scales from the leaf to the regional scale. Further, we discuss strengths and limitations of recent technological Published by Copernicus Publications on behalf of the European Geosciences Union. C. Werner et al.: Progress and challenges in using stable isotopesdevelopments and approaches and highlight new opportunities arising from unprecedented temporal and spatial resolution of stable isotope measurements.

Recent advances in understanding the metabolic origin and the temporal dynamics in delta(13)C of dark-respired CO(2) (delta(13)C(res)) have led to an increasing awareness of the importance of plant isotopic fractionation in respiratory processes. Pronounced dynamics in delta(13)C(res) have been observed in a number of species and three main hypotheses have been proposed: first, diurnal changes in delta(13)C of respiratory substrates; second, post-photosynthetic discrimination in respiratory pathways; and third, dynamic decarboxylation of enriched carbon pools during the post-illumination respiration period. Since different functional groups exhibit distinct diurnal patterns in delta(13)C(res) (ranging from 0 to 10 per thousand diurnal increase), we explored these hypotheses for different ecotypes and environmental (i.e. growth light) conditions. Mass balance calculations revealed that the effect of respiratory substrates on diurnal changes in delta(13)C(res) was negligible in all investigated species. Further, rapid post-illumination changes in delta(13)C(res) (30 min), which increased from 2.6 per thousand to 5 per thousand over the course of the day, were examined by positional (13)C-labelling to quantify changes in pyruvate dehydrogenase (PDH) and Krebs cycle (KC) activity. We investigated the origin of these dynamics with Rayleigh mass balance calculations based on theoretical assumptions on fractionation processes. Neither the estimated changes of PDH and KC, nor decarboxylation of a malate pool entirely explained the observed pattern in delta(13)C(res). However, a Rayleigh fractionation of (12)C-discriminating enzymes and/or a rapid decline in the decarboxylation rate of an enriched substrate pool may explain the post-illumination peak in delta(13)C(res). These results are highly relevant since delta(13)C(res) is used in large-scale carbon cycle studies.

Summary• Temporal dynamics in carbon isotope ratios of ecosystem respiration ( δ 13 C R ) were evaluated on hourly, daily and annual timescales in a Mediterranean woodland. Emphasis was given to the periods of transition from wet to dry season and vice versa, when the system turns from a net carbon sink to a source. The constancy of nocturnal δ 13 C R was tested.• The relationship between δ 13 C R (determined through Keeling plots) and environmental factors was evaluated through time-lag analysis.• δ 13 C R exhibited high annual variation ( > 7‰). During the transition periods, δ 13 C R correlated significantly with factors influencing photosynthetic discrimination, soil respiration, and whole-canopy conductance. Time-lags differed between belowand above-ground variables, and between seasons. A shift in regression parameters with environmental factors indicated seasonal differences in ecosystem responsiveness (e.g. temperature acclimation). δ 13 C R exhibited substantial nocturnal enrichment ( > 4‰) from dusk to dawn.• These data indicate pronounced short-term dynamics in δ 13 C R at hourly to daily timescales and a modulated response to environmental drivers. Substantial shortterm changes in nocturnal δ 13 C R may have important implications for the sampling protocols of nocturnal Keeling plots.

Combining C flux measurements with information on their isotopic composition can yield a process-based understanding of ecosystem C dynamics. We studied the variations in both respiratory fluxes and their stable C isotopic compositions (delta(13)C) for all major components (trees, understory, roots and soil microorganisms) in a Mediterranean oak savannah during a period with increasing drought. We found large drought-induced and diurnal dynamics in isotopic compositions of soil, root and foliage respiration (delta(13)C(res)). Soil respiration was the largest contributor to ecosystem respiration (R (eco)), exhibiting a depleted isotopic signature and no marked variations with increasing drought, similar to ecosystem respired delta(13)CO(2), providing evidence for a stable C-source and minor influence of recent photosynthate from plants. Short-term and diurnal variations in delta(13)C(res) of foliage and roots (up to 8 and 4 per thousand, respectively) were in agreement with: (1) recent hypotheses on post-photosynthetic fractionation processes, (2) substrate changes with decreasing assimilation rates in combination with increased respiratory demand, and (3) decreased phosphoenolpyruvate carboxylase activity in drying roots, while altered photosynthetic discrimination was not responsible for the observed changes in delta(13)C(res). We applied a flux-based and an isotopic flux-based mass balance, yielding good agreement at the soil scale, while the isotopic mass balance at the ecosystem scale was not conserved. This was mainly caused by uncertainties in Keeling plot intercepts at the ecosystem scale due to small CO(2) gradients and large differences in delta(13)C(res) of the different component fluxes. Overall, stable isotopes provided valuable new insights into the drought-related variations of ecosystem C dynamics, encouraging future studies but also highlighting the need of improved methodology to disentangle short-term dynamics of isotopic composition of R (eco).

Future climate scenarios for the Iberian Peninsula predict increasingly variable precipitation regimes, challenging key ecosystem processes in the Mediterranean biome. This study presents a large-scale water manipulation experiment, exposing the understorey vegetation in a Mediterranean oak woodland to simulations of precipitation variability. We hypothesized that, with no net changes in rainfall quantity, large infrequent precipitation events extend the period of soil moisture deficit, thereby decreasing productivity and soil nitrogen availability, accompanied by changes in plant community structure. However, the herbaceous understorey was highly resilient to increased precipitation variability. Extending the dry period between precipitation events from three to six weeks had no effect on productivity and community structure, this lack of responsiveness being attributed to phenotypic and physiological adaptations of the vegetation. However, vegetation senesced earlier, the shorter life cycle potentially influencing reproductive success. Additionally, experimental water manipulation did not affect soil nitrogen dynamics, with nitrogen being limiting in both treatments. In comparison, non-manipulated control plots experienced a severe natural wintertime drought, significantly reducing productivity and affecting species composition, but showed less indication of nitrogen limitation. Thus, although the understorey vegetation was resilient to changes in precipitation variability, long drought periods exerted highly negative effects, with the vegetation not being able to buffer the drought effects through adaptive strategies when the length of the dry period exceeded ∼10 weeks. Our results highlight the necessity for further studies investigating how climate change will influence the co-limitation of water and nitrogen availability, which in turn might affect plant productivity in Mediterranean ecosystems.

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