Gas phase in plants: integrating physiology, ecology and environmental sciences

Plants act as active bridges between the Earth’s surface and the atmosphere, moving vast amounts of gas between land and air. Plant tissues contain gases that are both dissolved in cellular aqueous phases and accumulated in intercellular air spaces. These gases can be transported within the plant by mass flow or diffusion. Gases in plants originate from multiple sources, including volatile compounds produced by the plant, uptake from ambient air through plant surfaces and gases generated by anaerobic microbial activity. As a result, plants maintain dynamic internal gas environments. These gas phases influence photosynthesis, respiration, transpiration, water transport, freezing dynamics, chemical signalling and broader carbon cycling processes. Yet, until recently, this world of gases inside plants was largely invisible (Jansen et al. 2022). The first International Meeting on the Gas Phase in Plants (Hyytiälä Forest Station, Finland, 11–14 September 2023) revealed how much these hidden gas reservoirs and pathways matter. The meeting followed a series of online meetings (Jansen et al. 2022) and gathered experts on gases in leaves, stems and roots, including not only carbon dioxide (CO2), oxygen (O2) and water vapor, but also, e.g., methane (CH4) and volatile organic compounds (VOCs), as well as gases in plant–microbiome interactions. This convergence of disciplines has led to the present special issue of Tree Physiology on the ‘gas phase in plants’. Taken together, the research papers and methodological advances presented here showcase how the gas phase is reshaping our understanding of plant functions across scales. A common theme that emerged from the meeting was the importance of gases as dynamic mediators in plant–environment interactions under stress, underscored by contributions exploring photorespiration and VOCs emissions. Abiotic stress disrupts gas exchange and metabolic balance in plants, triggering the formation of signalling molecules. Among these stress-responsive pathways, photorespiration—the oxygenation reaction of Rubisco—reduces net carbon assimilation and generates hydrogen peroxide (H₂O₂), a reactive oxygen species with an important signalling role. Alongi et al. (2024) report that drought and heat interactively modulate photorespiration in silver fir (Abies alba) seedlings. Mild drought led to a slight enhancement of photorespiration, whereas severe drought suppressed photorespiratory activity and decreased foliar H₂O₂ concentrations. Conversely, exposure to a 1-day heat treatment stimulated photorespiration only under non-limiting soil moisture conditions. Enhanced peroxidase activity under heat prevented H₂O₂ accumulation despite increased photorespiration. These findings show that carbon loss via photorespiration and oxidative signalling are tightly regulated and vary with the severity and combination of stresses. At the other side of the stress spectrum, VOCs provide thermotolerance and defence. Meischner et al. (2024) exposed Norway spruce (Picea abies) saplings to jasmonic acid and heat and monitored VOCs emissions and CO₂ exchange simultaneously from needles and roots. The team observed that jasmonic acid treatment strongly increased needle VOCs emissions—particularly sesquiterpenes—while root VOCs emissions (mainly acetone and monoterpenes) markedly declined. Jasmonic acid also suppressed CO₂ assimilation, leading to daytime net respiration, whereas root respiration remained unchanged. Nevertheless, VOCs responses under combined jasmonic acid and heat stress were attenuated, suggesting heat buffered the jasmonic acid-induced defence response. Overall, plants appeared to allocate gaseous carbon resources locally, enhancing volatile release in affected tissues while limiting belowground emissions and maintaining root metabolism under multiple stressors. Complementing this, Wang et al. (2024) offer novel insights into the biochemical regulation of isoprene emissions. Isoprene, the most abundant plant-emitted VOC, protects photosystems and alters atmospheric chemistry. Wang et al. (2024) analysed short-term isoprene regulation by isolating the role of chloroplast redox state. They developed an index of chloroplast redox state and predicted that the isoprene emission rate would respond to it with similar velocity irrespective of whether CO₂ concentration, light intensity or leaf temperature was varied. Experiments confirmed that the isoprene emission increased at comparable rates to the increase in the index of chloroplast redox state caused by these environmental manipulations, supporting the hypothesis that chloroplast redox/energy state, not cytosolic phosphoenolpyruvate carboxylation, governs isoprene biosynthesis. Together, these three papers link gas-phase metabolism to stress tolerance and signalling. They highlight how the gas phase in leaves—from oxygenation reactions to volatile emissions—mediates plant responses to abiotic stresses such as drought or heat. Understanding the gas phase requires reliable measurements of gases dissolved in sap or trapped in tissues in gaseous form. Several papers in this issue advance methodological tools that make the invisible measurable. Marion et al. (2024) built custom semi-permeable membrane probes inserted directly into a silver fir tree’s xylem and linked them to a portable mass spectrometer. Their approach measured the abundances of helium, argon, krypton, nitrogen gas, O₂ and CO₂ continuously in situ for weeks. Diurnal fluctuations in CO₂ and O₂ reflected tree physiological activity, and irrigation with helium-enriched water allowed estimation of sap flow velocity. Crucially, measuring inert noble gases alongside reactive species separated physical transport processes from metabolic reactions. The authors note that their technique is the first successful continuous method for measuring dissolved gases in tree sap, non-invasively, and applicable to studies of water and gas uptake, diffusion, respiration and embolism. Two methodological papers tackle embolism detection, i.e., the formation of gas bubbles and further blockages of water transport in xylem conduits. De Boeck and Steppe (2025) refine the non-destructive acoustic emission method used to construct vulnerability curves. By developing the clustering of acoustic emission signals based on their frequency features, they separated embolism-related events from unrelated noise and pinpointed the true endpoint of 100% embolism. Applying and testing this approach with four temperate tree species reduced subjectivity of embolism detection with acoustic emissions and broadened the applicability of the method across species. Miranda et al. (2024) revisit the pneumatic method, which extracts gas from dehydrating samples to estimate the amount of embolism. They found that residual sap in cut-open conduits can increase gas discharge during early dehydration, which is an artefact unrelated to embolism. By analysing the slope of vulnerability curves over time, the authors propose a correction for this artefact to improve pneumatic estimates of embolization. Lastly, Silva et al. (2024) scrutinize flow-centrifuge methods for constructing vulnerability curves. They demonstrate that embolism formation depends not only on pressure but also on spin time; measuring hydraulic conductivity (Kh) over 15 min at each speed revealed shifts of vulnerability curves toward higher water potentials with increasing spin time. Correcting for time-dependent changes in Kh improved statistical significance for five of six studied species, indicating that slow gas diffusion during embolism propagation can bias centrifuge measurements. These three methodological papers emphasize that accurate quantification of gas-phase processes hinges on recognizing method artefacts. Epron and Mochidome (2024) explore CH₄ accumulation in the heartwood of four tree species. Monthly measurements over 15 months revealed heartwood CH₄ concentrations ranging from less than 100 p.p.m. to higher than 200,000 p.p.m. Concentrations varied among individuals and were not primarily controlled by trunk temperature. Emissions from the trunk surface correlated weakly with internal concentrations, and the apparent diffusion coefficient varied widely, suggesting that CH₄ production sites and internal transport resistances differ between trees. The authors conclude that simulating tree-level CH₄ emissions remains challenging. Still, these findings underline that stems can act as significant CH₄ sources and sinks. Robinson et al. (2024) address a long-standing question in maple physiology: Do sugar maples maintain an osmotic barrier between xylem fibres and vessels that stabilizes gas bubbles? Using synchrotron micro-computed tomography, the team perfused maple stem segments with either water or a 2% sucrose solution. Perfusion with water markedly reduced gas in xylem fibres, whereas perfusion with sucrose had little effect. These results support the existence of an osmotic barrier that prevents sucrose from diffusing into fibres and keeps gas bubbles from dissolving. Such barriers help sugar maples develop elevated stem pressures during freeze–thaw cycles and exemplify how wood structure and sap composition govern gas stability. Plants are active bridges between the Earth’s surface and the atmosphere, and much research has been devoted to leaf gas exchange. However, gases are also exchanged through all other surfaces, including the bark. Zhou et al. (2024) studied bark water vapor conductance (gbark) in branches of 15 temperate forest species and found mean gbark values ranging from 2.22 to 12.02 mmol m−2 s−1. Bending stems, to simulate wind, increased gbark by 23%, while flooding saplings had no effect after 38 days but reduced gbark by 41% after 69 days post-flood. Relationships between gbark and bark traits such as thickness or lenticel density were inconsistent, indicating that bark gas exchange is variable and mutable. Their study highlights how mechanical disturbance and flooding can alter gas diffusion through bark, affecting tree water balance during subsequent droughts. The gas phase in plants spans scales from molecular signals to ecosystem fluxes. The research in this special issue, born from discussions at the first International Meeting on the Gas Phase in Plants in Hyytiälä, Finland, shows that gases inside plants are integral players in plant physiology. Photorespiration, isoprene and other VOCs link gas exchange to plant stress responses and climate feedbacks; CH₄ in heartwood, maple sap pressure and bark conductance reveal how stems store and modulate gases and method innovations are making it possible to monitor these processes in vivo. Collectively, these recent advances emphasize three themes, each reflecting a different facet of scaling—from cellular and biochemical regulation, to organ integration, to whole-plant and ecosystem implications. Integration across organs is key. Studies on gases in leaves, stems and roots show that gas-phase processes in these organs are interconnected and can be decoupled in ways that matter for whole-plant carbon and water balance. For instance, VOCs emissions from needles can be decoupled from root emissions, while CH₄ produced by heartwood microbes may exit via bark or dissolve in sap. Recognizing these linkages is essential for moving from organ-level measurements to whole-plant representations of gas exchange. Methodological rigour and innovation are advancing rapidly. Continuous in-situ gas measurements, and refined methods and analyses related to acoustic, pneumatic and flow-centrifuge techniques are enabling more accurate quantification of gases and embolism. These developments improve comparability across studies and provide the mechanistic basis required to parameterize and validate models across scales. Implications for climate and ecosystem functioning are substantial—and represent an open frontier. Gas-phase processes influence atmospheric chemistry (isoprene and other VOCs), carbon budgets (photorespiration and CH₄), drought resilience (embolism and bark conductance) and freeze–thaw hydraulics (osmotic barriers). While most contributions in this issue focus on plant- and organ-level physiology, they identify processes that can be upscaled through integration with canopy flux measurements, remote sensing constraints and ecosystem/land-surface modelling. Establishing these links is increasingly important as extreme weather events become more frequent. Gas-phase research can inform breeding and management strategies to enhance plant resilience to climate change including drought, heat or flooding. The 2023 Hyytiälä meeting marked a turning point by bringing together researchers who often work in parallel—leaf gas exchange and VOCs biochemistry, xylem conductance and embolism, stem and root gas storage and plant–microbiome gas production—under a shared framing of gas reservoirs and pathways inside plants. This convergence has helped consolidate an emerging community around the ‘gas phase in plants’ as a unifying concept, and the present special issue reflects that momentum. Looking forward, there is clear interest within this community in maintaining exchange and coordination beyond the 2023 meeting. This interest reflects the rapid scientific progress in the area, particularly the emergence of new tools and analyses that make internal gas pools and flux pathways quantifiable, and that enable more mechanistic tests across organs, species and stress contexts. A follow-up meeting is being planned to continue sharing methodological advances, harmonizing terminology and protocols and refining conceptual models. Details about timing and the venue have yet to be confirmed. Future work must embrace cross-scale integration. Most contributions in this special issue focus on plant and organ-level physiology, but they also identify processes with plausible consequences for canopy fluxes and ecosystem budgets (e.g., VOCs emissions and atmospheric chemistry, photorespiration and carbon balance, CH₄ storage and release, non-stomatal exchange through bark and embolism dynamics affecting drought resilience). Making these links more direct will likely require coordinated campaigns that pair within-plant measurements (dissolved gases, internal storage, VOCs and CH₄ dynamics) with canopy-scale observations (e.g., micrometeorological flux methods), together with tracer approaches, imaging and modelling that can explicitly bridge organ processes to stand-level exchange. Progress will benefit from sustained interaction across disciplines—plant physiology, ecology, micrometeorology, atmospheric chemistry and modelling—as well as collaboration with physicists and engineers to tackle the complex and dynamic gas–liquid–solid interfaces in plants, and with microbiologists to illuminate how endophytes and methanogens shape internal gas composition. These collaborations will support the integration of gas-phase processes into models of carbon cycling, hydraulic functioning and climate feedbacks, improving predictions of ecosystem responses to global change. Gases are everywhere in plants, in constant flux between the liquid and the gas phase. The latter deserves more attention than it has received in the past. By peering into this hidden phase, we not only refine our understanding of plant function but also uncover new levers for mitigating climate change and safeguarding forest functioning. We hope the insights from this special issue inspire researchers to continue exploring the dynamic, invisible and vital gas phase in plants, help consolidate a durable community and accelerate cross-scale integration of gas-phase processes, from mechanisms to whole-plant function and ecosystem fluxes. R.L.-d.-V. wrote the manuscript with input from all authors. All authors declare that they have no conflicts of interest. R.L.-d.-V. was supported by FCT—Fundação para a Ciência e a Tecnologia, I.P., through a researcher contract CEECIND/02735/2018 (DOI: http://dx.doi.org/10.54499/CEECIND/02735/2018/CP1563/CT0001) and the projects UID/00239/2025 (DOI: http://dx.doi.org/10.54499/UID/00239/2025) and UID/PRR/00239/2025 (DOI: http://dx.doi.org/10.54499/UID/PRR/00239/2025) of the Forest Research Centre and LA/P/0092/2020 (DOI: http://dx.doi.org/10.54499/LA/P/0092/2020) of the Associate Laboratory TERRA. A.L. was funded by the Research Council of Finland, grant no. 355142. A.K. was funded by the Academy of Finland fellowship PEATSTRESS, grant no. 360071. No new data were generated or analysed in support of this editorial.