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1. Boolink: a graphical interface for open access Boolean network simulations and use in guard cell CO2 signaling

   https://doi.org/10.1093/plphys/kiab344  

   Karanam, Aravind; He, David; Hsu, Po-Kai; Schulze, Sebastian; Dubeaux, Guillaume; Karmakar, Richa; Schroeder, Julian I; Rappel, Wouter-Jan (July 2021, Plant Physiology)

   Abstract Signaling networks are at the heart of almost all biological processes. Most of these networks contain large number of components, and often either the connections between these components are not known or the rate equations that govern the dynamics of soluble signaling components are not quantified. This uncertainty in network topology and parameters can make it challenging to formulate detailed mathematical models. Boolean networks, in which all components are either on or off, have emerged as viable alternatives to detailed mathematical models that contain rate constants and other parameters. Therefore, open-source platforms of Boolean models for community use are desirable. Here, we present Boolink, a freely available graphical user interface that allows users to easily construct and analyze existing Boolean networks. Boolink can be applied to any Boolean network. We demonstrate its application using a previously published network for abscisic acid (ABA)-driven stomatal closure in Arabidopsis spp. (Arabidopsis thaliana). We also show how Boolink can be used to generate testable predictions by extending the network to include CO2 regulation of stomatal movements. Predictions of the model were experimentally tested, and the model was iteratively modified based on experiments showing that ABA effectively closes Arabidopsis stomata at near-zero CO2 concentrations (1.5-ppm CO2). Thus, Boolink enables public generation and the use of existing Boolean models, including the prior developed ABA signaling model with added CO2 signaling components. 

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2. Does stomatal patterning in amphistomatous leaves minimize the CO2 diffusion path length within leaves?

   https://doi.org/10.1093/aobpla/plae015  

   Watts, Jacob L; Dow, Graham J; Buckley, Thomas N; Muir, Christopher D (February 2024, AoB PLANTS)

   Salter, William (Ed.)

   Abstract Photosynthesis is co-limited by multiple factors depending on the plant and its environment. These include biochemical rate limitations, internal and external water potentials, temperature, irradiance and carbon dioxide ( CO2). Amphistomatous leaves have stomata on both abaxial and adaxial leaf surfaces. This feature is considered an adaptation to alleviate CO2 diffusion limitations in productive environments as the diffusion path length from stomate to chloroplast is effectively halved in amphistomatous leaves. Plants may also reduce CO2 limitations through other aspects of optimal stomatal anatomy: stomatal density, distribution, patterning and size. Some studies have demonstrated that stomata are overdispersed compared to a random distribution on a single leaf surface; however, despite their prevalence in nature and near ubiquity among crop species, much less is known about stomatal anatomy in amphistomatous leaves, especially the coordination between leaf surfaces. Here, we use novel spatial statistics based on simulations and photosynthesis modelling to test hypotheses about how amphistomatous plants may optimize CO2 diffusion in the model angiosperm Arabidopsis thaliana grown in different light environments. We find that (i) stomata are overdispersed, but not ideally dispersed, on both leaf surfaces across all light treatments; (ii) the patterning of stomata on abaxial and adaxial leaf surfaces is independent and (iii) the theoretical improvements to photosynthesis from abaxial–adaxial stomatal coordination are miniscule (≪1%) across the range of feasible parameter space. However, we also find that (iv) stomatal size is correlated with the mesophyll volume that it supplies with CO2, suggesting that plants may optimize CO2 diffusion limitations through alternative pathways other than ideal, uniform stomatal spacing. We discuss the developmental, physical and evolutionary constraints that may prohibit plants from reaching this theoretical adaptive peak of uniform stomatal spacing and inter-surface stomatal coordination. These findings contribute to our understanding of variation in the anatomy of amphistomatous leaves. 

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3. Anatomical adjustments of the tree hydraulic pathway decrease canopy conductance under long-term elevated CO2

   https://doi.org/10.1093/plphys/kiac482  

   Gattmann, Marielle; McAdam, Scott A; Birami, Benjamin; Link, Roman; Nadal-Sala, Daniel; Schuldt, Bernhard; Yakir, Dan; Ruehr, Nadine K (October 2022, Plant Physiology)

   Abstract The cause of reduced leaf-level transpiration under elevated CO2 remains largely elusive. Here, we assessed stomatal, hydraulic, and morphological adjustments in a long-term experiment on Aleppo pine (Pinus halepensis) seedlings germinated and grown for 22–40 months under elevated (eCO2; c. 860 ppm) or ambient (aCO2; c. 410 ppm) CO2. We assessed if eCO2-triggered reductions in canopy conductance (gc) alter the response to soil or atmospheric drought and are reversible or lasting due to anatomical adjustments by exposing eCO2 seedlings to decreasing [CO2]. To quantify underlying mechanisms, we analyzed leaf abscisic acid (ABA) level, stomatal and leaf morphology, xylem structure, hydraulic efficiency, and hydraulic safety. Effects of eCO2 manifested in a strong reduction in leaf-level gc (−55%) not caused by ABA and not reversible under low CO2 (c. 200 ppm). Stomatal development and size were unchanged, while stomatal density increased (+18%). An increased vein-to-epidermis distance (+65%) suggested a larger leaf resistance to water flow. This was supported by anatomical adjustments of branch xylem having smaller conduits (−8%) and lower conduit lumen fraction (−11%), which resulted in a lower specific conductivity (−19%) and leaf-specific conductivity (−34%). These adaptations to CO2 did not change stomatal sensitivity to soil or atmospheric drought, consistent with similar xylem safety thresholds. In summary, we found reductions of gc under elevated CO2 to be reflected in anatomical adjustments and decreases in hydraulic conductivity. As these water savings were largely annulled by increases in leaf biomass, we do not expect alleviation of drought stress in a high CO2 atmosphere. 

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4. Consistent responses of vegetation gas exchange to elevated atmospheric CO ₂ emerge from heuristic and optimization models

   https://doi.org/10.5194/bg-19-4387-2022  

   Manzoni, Stefano; Fatichi, Simone; Feng, Xue; Katul, Gabriel G.; Way, Danielle; Vico, Giulia (January 2022, Biogeosciences)

   Abstract. Elevated atmospheric CO2 concentration is expectedto increase leaf CO2 assimilation rates, thus promoting plant growthand increasing leaf area. It also decreases stomatal conductance, allowingwater savings, which have been hypothesized to drive large-scale greening,in particular in arid and semiarid climates. However, the increase in leafarea could reduce the benefits of elevated CO2 concentration through soilwater depletion. The net effect of elevated CO2 on leaf- andcanopy-level gas exchange remains uncertain. To address this question, wecompare the outcomes of a heuristic model based on the Partitioning ofEquilibrium Transpiration and Assimilation (PETA) hypothesis and three modelvariants based on stomatal optimization theory. Predicted relative changes in leaf-and canopy-level gas exchange rates are used as a metric of plant responsesto changes in atmospheric CO2 concentration. Both model approaches predictreductions in leaf-level transpiration rate due to decreased stomatalconductance under elevated CO2, but negligible (PETA) or no(optimization) changes in canopy-level transpiration due to the compensatoryeffect of increased leaf area. Leaf- and canopy-level CO2 assimilationis predicted to increase, with an amplification of the CO2fertilization effect at the canopy level due to the enhanced leaf area. Theexpected increase in vapour pressure deficit (VPD) under warmer conditions isgenerally predicted to decrease the sensitivity of gas exchange toatmospheric CO2 concentration in both models. The consistentpredictions by different models that canopy-level transpiration varieslittle under elevated CO2 due to combined stomatal conductancereduction and leaf area increase highlight the coordination ofphysiological and morphological characteristics in vegetation to maximizeresource use (here water) under altered climatic conditions. 

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5. Influence of plant ecophysiology on ozone dry deposition: comparing between multiplicative and photosynthesis-based dry deposition schemes and their responses to rising CO₂ level

   https://doi.org/10.5194/bg-19-1753-2022  

   Sun, Shihan; Tai, Amos P.; Yung, David H.; Wong, Anthony Y.; Ducker, Jason A.; Holmes, Christopher D. (January 2022, Biogeosciences)

   Abstract. Dry deposition is a key process for surface ozone(O3) removal. Stomatal uptake is a major component of O3 drydeposition, which is parameterized differently in current land surfacemodels and chemical transport models. We developed and used a standaloneterrestrial biosphere model, driven by a unified set of prescribedmeteorology, to evaluate two widely used dry deposition modeling frameworks,Wesely (1989) and Zhang et al. (2003), with different configurations ofstomatal resistance: (1) the default multiplicative method in the Weselyscheme (W89) and Zhang et al. (2003) scheme (Z03), (2) the traditionalphotosynthesis-based Farquhar–Ball–Berry (FBB) stomatal algorithm, and (3) theMedlyn stomatal algorithm (MED) based on optimization theory. We found thatusing the FBB stomatal approach that captures ecophysiological responses toenvironmental factors, especially to water stress, can generally improve thesimulated dry deposition velocities compared with multiplicative schemes.The MED stomatal approach produces higher stomatal conductance than FBB andis likely to overestimate dry deposition velocities for major vegetationtypes, but its performance is greatly improved when spatially varying slopeparameters based on annual mean precipitation are used. Large discrepancieswere also found in stomatal responses to rising CO2 levels from 390to 550 ppm: the multiplicative stomatal method with an empirical CO2response function produces reduction (−35 %) in global stomatalconductance on average much larger than that with the photosynthesis-basedstomatal method (−14 %–19 %). Our results show the potential biases inO3 sink caused by errors in model structure especially in the Weselydry deposition scheme and the importance of using photosynthesis-basedrepresentation of stomatal resistance in dry deposition schemes under achanging climate and rising CO2 concentration. 

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