Principles of resilient coding for plant ecophysiologists.

Plant ecophysiology is founded on a rich body of physical and chemical theory, but it is challenging to connect theory with data in unambiguous, analytically rigorous and reproducible ways. Custom scripts written in computer programming languages (coding) enable plant ecophysiologists to model plant processes and fit models to data reproducibly using advanced statistical techniques. Since many ecophysiologists lack formal programming education, we have yet to adopt a unified set of coding principles and standards that could make coding easier to learn, use and modify. We identify eight principles to help in plant ecophysiologists without much programming experience to write resilient code: (i) standardized nomenclature, (ii) consistency in style, (iii) increased modularity/extensibility for easier editing and understanding, (iv) code scalability for application to large data sets, (v) documented contingencies for code maintenance, (vi) documentation to facilitate user understanding; (vii) extensive tutorials and (viii) unit testing and benchmarking. We illustrate these principles using a new R package, {photosynthesis}, which provides a set of analytical and simulation tools for plant ecophysiology. Our goal with these principles is to advance scientific discovery in plant ecophysiology by making it easier to use code for simulation and data analysis, reproduce results and rapidly incorporate new biological understanding and analytical tools.

Is desiccation tolerance and avoidance reflected in xylem and phloem anatomy of two coexisting arid-zone coniferous trees?

Plants close their stomata during drought to avoid excessive water loss, but species differ in respect to the drought severity at which stomata close. The stomatal closure point is related to xylem anatomy and vulnerability to embolism, but it also has implications for phloem transport and possibly phloem anatomy to allow sugar transport at low water potentials. Desiccation-tolerant plants that close their stomata at severe drought should have smaller xylem conduits and/or fewer and smaller interconduit pits to reduce vulnerability to embolism but more phloem tissue and larger phloem conduits compared with plants that avoid desiccation. These anatomical differences could be expected to increase in response to long-term reduction in precipitation. To test these hypotheses, we used tridimensional synchroton X-ray microtomograph and light microscope imaging of combined xylem and phloem tissues of 2 coniferous species: one-seed juniper (Juniperus monosperma) and piñon pine (Pinus edulis) subjected to precipitation manipulation treatments. These species show different xylem vulnerability to embolism, contrasting desiccation tolerance, and stomatal closure points. Our results support the hypothesis that desiccation tolerant plants require higher phloem transport capacity than desiccation avoiding plants, but this can be gained through various anatomical adaptations in addition to changing conduit or tissue size.

A multi-species synthesis of physiological mechanisms in drought-induced tree mortality.

Widespread tree mortality associated with drought has been observed on all forested continents and global change is expected to exacerbate vegetation vulnerability. Forest mortality has implications for future biosphere-atmosphere interactions of carbon, water and energy balance, and is poorly represented in dynamic vegetation models. Reducing uncertainty requires improved mortality projections founded on robust physiological processes. However, the proposed mechanisms of drought-induced mortality, including hydraulic failure and carbon starvation, are unresolved. A growing number of empirical studies have investigated these mechanisms, but data have not been consistently analysed across species and biomes using a standardized physiological framework. Here, we show that xylem hydraulic failure was ubiquitous across multiple tree taxa at drought-induced mortality. All species assessed had 60% or higher loss of xylem hydraulic conductivity, consistent with proposed theoretical and modelled survival thresholds. We found diverse responses in non-structural carbohydrate reserves at mortality, indicating that evidence supporting carbon starvation was not universal. Reduced non-structural carbohydrates were more common for gymnosperms than angiosperms, associated with xylem hydraulic vulnerability, and may have a role in reducing hydraulic function. Our finding that hydraulic failure at drought-induced mortality was persistent across species indicates that substantial improvement in vegetation modelling can be achieved using thresholds in hydraulic function.

Tree water dynamics in a drying and warming world.

Disentangling the relative impacts of precipitation reduction and vapour pressure deficit (VPD) on plant water dynamics and determining whether acclimation may influence these patterns in the future is an important challenge. Here, we report sap flux density (FD ), stomatal conductance (Gs ), hydraulic conductivity (KL ) and xylem anatomy in piñon pine (Pinus edulis) and juniper (Juniperus monosperma) trees subjected to five years of precipitation reduction, atmospheric warming (elevated VPD) and their combined effects. No acclimation occurred under precipitation reduction: lower Gs and FD were found for both species compared to ambient conditions. Warming reduced the sensibility of stomata to VPD for both species but resulted in the maintenance of Gs and FD to ambient levels only for piñon. For juniper, reduced soil moisture under warming negated benefits of stomatal adjustments and resulted in reduced FD , Gs and KL . Although reduced stomatal sensitivity to VPD also occurred under combined stresses, reductions in Gs , FD and KL took place to similar levels as under single stresses for both species. Our results show that stomatal conductance adjustments to high VPD could minimize but not entirely prevent additive effects of warming and drying on water use and carbon acquisition of trees in semi-arid regions.

Responses of two semiarid conifer tree species to reduced precipitation and warming reveal new perspectives for stomatal regulation.

Relatively anisohydric species are predicted to be more predisposed to hydraulic failure than relatively isohydric species, as they operate with narrower hydraulic safety margins. We subjected co-occurring anisohydric Juniperus monosperma and isohydric Pinus edulis trees to warming, reduced precipitation, or both, and measured their gas exchange and hydraulic responses. We found that reductions in stomatal conductance and assimilation by heat and drought were more frequent during relatively moist periods, but these effects were not exacerbated in the combined heat and drought treatment. Counter to expectations, both species exhibited similar gs temporal dynamics in response to drought. Further, whereas P. edulis exhibited chronic embolism, J. monosperma showed very little embolism due to its conservative stomatal regulation and maintenance of xylem water potential above the embolism entry point. This tight stomatal control and low levels of embolism experienced by juniper refuted the notion that very low water potentials during drought are associated with loose stomatal control and with the hypothesis that anisohydric species are more prone to hydraulic failure than isohydric species. Because direct association of stomatal behaviour with embolism resistance can be misleading, we advocate consideration of stomatal behaviour relative to embolism resistance for classifying species drought response strategies.

Prolonged experimental drought reduces plant hydraulic conductance and transpiration and increases mortality in a piñon-juniper woodland.

Plant hydraulic conductance (k s) is a critical control on whole-plant water use and carbon uptake and, during drought, influences whether plants survive or die. To assess long-term physiological and hydraulic responses of mature trees to water availability, we manipulated ecosystem-scale water availability from 2007 to 2013 in a piñon pine (Pinus edulis) and juniper (Juniperus monosperma) woodland. We examined the relationship between k s and subsequent mortality using more than 5 years of physiological observations, and the subsequent impact of reduced hydraulic function and mortality on total woody canopy transpiration (E C) and conductance (G C). For both species, we observed significant reductions in plant transpiration (E) and k s under experimentally imposed drought. Conversely, supplemental water additions increased E and k s in both species. Interestingly, both species exhibited similar declines in k s under the imposed drought conditions, despite their differing stomatal responses and mortality patterns during drought. Reduced whole-plant k s also reduced carbon assimilation in both species, as leaf-level stomatal conductance (g s) and net photosynthesis (A n) declined strongly with decreasing k s. Finally, we observed that chronically low whole-plant k s was associated with greater canopy dieback and mortality for both piñon and juniper and that subsequent reductions in woody canopy biomass due to mortality had a significant impact on both daily and annual canopy E C and G C. Our data indicate that significant reductions in k s precede drought-related tree mortality events in this system, and the consequence is a significant reduction in canopy gas exchange and carbon fixation. Our results suggest that reductions in productivity and woody plant cover in piñon-juniper woodlands can be expected due to reduced plant hydraulic conductance and increased mortality of both piñon pine and juniper under anticipated future conditions of more frequent and persistent regional drought in the southwestern United States.

Regulation and acclimation of leaf gas exchange in a piñon-juniper woodland exposed to three different precipitation regimes.

Leaf gas-exchange regulation plays a central role in the ability of trees to survive drought, but forecasting the future response of gas exchange to prolonged drought is hampered by our lack of knowledge regarding potential acclimation. To investigate whether leaf gas-exchange rates and sensitivity to drought acclimate to precipitation regimes, we measured the seasonal variations of leaf gas exchange in a mature piñon-juniper Pinus edulis-Juniperus monosperma woodland after 3 years of precipitation manipulation. We compared trees receiving ambient precipitation with those in an irrigated treatment (+30% of ambient precipitation) and a partial rainfall exclusion (-45%). Treatments significantly affected leaf water potential, stomatal conductance and photosynthesis for both isohydric piñon and anisohydric juniper. Leaf gas exchange acclimated to the precipitation regimes in both species. Maximum gas-exchange rates under well-watered conditions, leaf-specific hydraulic conductance and leaf water potential at zero photosynthetic assimilation all decreased with decreasing precipitation. Despite their distinct drought resistance and stomatal regulation strategies, both species experienced hydraulic limitation on leaf gas exchange when precipitation decreased, leading to an intraspecific trade-off between maximum photosynthetic assimilation and resistance of photosynthesis to drought. This response will be most detrimental to the carbon balance of piñon under predicted increases in aridity in the southwestern USA.

Increased susceptibility to drought-induced mortality in Sequoia sempervirens (Cupressaceae) trees under Cenozoic atmospheric carbon dioxide starvation.

PREMISE OF THE STUDY: Climate-induced forest retreat has profound ecological and biogeochemical impacts, but the physiological mechanisms underlying past tree mortality are poorly understood, limiting prediction of vegetation shifts with climate variation. Climate, drought, fire, and grazing represent agents of tree mortality during the late Cenozoic, but the interaction between drought and declining atmospheric carbon dioxide ([CO2]a) from high to near-starvation levels ∼34 million years (Ma) ago has been overlooked. Here, this interaction frames our investigation of sapling mortality through the interdependence of hydraulic function, carbon limitation, and defense metabolism. • METHODS: We recreated a changing Cenozoic [CO2]a regime by growing Sequoia sempervirens trees within climate-controlled growth chambers at 1500, 500, or 200 ppm [CO2]a, capturing the decline toward minimum concentrations from 34 Ma. After 7 months, we imposed drought conditions and measured key physiological components linking carbon utilization, hydraulics, and defense metabolism as hypothesized interdependent mechanisms of tree mortality. • KEY RESULTS: Catastrophic failure of hydraulic conductivity, carbohydrate starvation, and tree death occurred at 200 ppm, but not 500 or 1500 ppm [CO2]a. Furthermore, declining [CO2]a reduced investment in carbon-rich foliar defense compounds that would diminish resistance to biotic attack, likely exacerbating mortality. • CONCLUSIONS: Low-[CO2]a-driven tree mortality under drought is consistent with Pleistocene pollen records charting repeated Californian Sequoia forest contraction during glacial periods (180-200 ppm [CO2]a) and may even have contributed to forest retreat as grasslands expanded on multiple continents under low [CO2]a over the past 10 Ma. In this way, geologic intervals of low [CO2]a coupled with drought could impose a demographic bottleneck in tree recruitment, driving vegetation shifts through forest mortality.

Early vessel evolution and the diverisification of wood function: Insights from Malagasy Canellales.

Xylem vessels have long been proposed as a key innovation for the ecological diversification of angiosperms by providing a breakthrough in hydraulic efficiency to support high rates of photosynthesis and growth. However, recent studies demonstrated that angiosperm woods with structurally "primitive" vessels did not have greater whole stem hydraulic capacities as compared to vesselless angiosperms. As an alternative to the hydraulic superiority hypothesis, the heteroxylly hypothesis proposes that subtle hydraulic efficiencies of primitive vessels over tracheids enabled new directions of functional specialization in the wood. However, the functional properties of early heteroxyllous wood remain unknown. We selected the two species of Canellales from Madagascar to test the heteroxylly hypothesis because Canellaceae (represented by Cinnamosma madagascariensis) produces wood with vessels of an ancestral form, while Winteraceae, the sister clade (represented by Takhtajania perrieri) is vesselless. We found that heteroxylly correlated with increased wood functional diversity related predominantly to biomechanical specialization. However, vessels were not associated with greater stem hydraulic efficiency or increased shoot hydraulic capacity. Our results support the heteroxylly hypothesis and highlight the importance integrating a broader ecological context to understand the evolution of vessels.