Paleoecology, Ploidy, Paleoatmospheric Composition, and Developmental Biology: A Review of the Multiple Uses of Fossil Stomata

Stomatal evolution and plant adaptation to future climate

Global climate change is affecting plant photosynthesis and transpiration processes, as well as increasing weather extremes impacting socio-political and environmental events and decisions for decades to come. One major research challenge in plant biology and ecology is the interaction of photosynthesis with the environment. Stomata control plant gas exchange and their evolution was a crucial innovation that facilitated the earliest land plants to colonize terrestrial environments. Stomata couple homoiohydry, together with cuticles, intercellular gas space, with the endohydric water-conducting system, enabling plants to adapt and diversify across the planet. Plants control stomatal movement in response to environmental change through regulating guard cell turgor mediated by membrane transporters and signaling transduction. However, the origin, evolution, and active control of stomata remain controversial topics. We first review stomatal evolution and diversity, providing fossil and phylogenetic evidence of their origins. We summarize functional evolution of guard cell membrane transporters in the context of climate changes and environmental stresses. Our analyses show that the core signaling elements of stomatal movement are more ancient than stomata, while genes involved in stomatal development co-evolved de novo with the earliest stomata. These results suggest that novel stomatal development-specific genes were acquired during plant evolution, whereas genes regulating stomatal movement, especially cell signaling pathways, were inherited ancestrally and co-opted by dynamic functional differentiation. These two processes reflect the different adaptation strategies during land plant evolution.

Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multiclade perspective

PREMISE

The proportion of polyploid plants in a community increases with latitude, and different hypotheses have been proposed about which factors drive this pattern. Here, we aimed to understand the historical causes of the latitudinal polyploidy gradient using a combination of ancestral state reconstruction methods. Specifically, we assessed whether (1) polyploidization enables movement to higher latitudes (i.e., polyploidization precedes occurrences in higher latitudes) or (2) higher latitudes facilitate polyploidization (i.e., occurrence in higher latitudes precedes polyploidization).

METHODS

We reconstructed the ploidy states and ancestral niches of 1032 angiosperm species at four paleoclimatic time slices ranging from 3.3 million years ago to the present, comprising taxa from four well-represented clades: Onagraceae, Primulaceae, Solanum (Solanaceae), and Pooideae (Poaceae). We used ancestral niche reconstruction models alongside a customized discrete character evolution model to allow reconstruction of states at specific time slices. Patterns of latitudinal movement were reconstructed and compared in relation to inferred ploidy shifts.

RESULTS

No single hypothesis applied equally well across all analyzed clades. While significant differences in median latitudinal occurrence were detected in the largest clade, Poaceae, no significant differences were detected in latitudinal movement in any clade.

CONCLUSIONS

Our preliminary study is the first to attempt to connect ploidy changes to continuous latitudinal movement, but we cannot favor one hypothesis over another. Given that patterns seem to be clade-specific, more clades must be analyzed in future studies for generalities to be drawn.

Functional traits of fossil plants

A minuscule fraction of the Earth's paleobiological diversity is preserved in the geological record as fossils. What plant remnants have withstood taphonomic filtering, fragmentation, and alteration in their journey to become part of the fossil record provide unique information on how plants functioned in paleo-ecosystems through their traits. Plant traits are measurable morphological, anatomical, physiological, biochemical, or phenological characteristics that potentially affect their environment and fitness. Here, we review the rich literature of paleobotany, through the lens of contemporary trait-based ecology, to evaluate which well-established extant plant traits hold the greatest promise for application to fossils. In particular, we focus on fossil plant functional traits, those measurable properties of leaf, stem, reproductive, or whole plant fossils that offer insights into the functioning of the plant when alive. The limitations of a trait-based approach in paleobotany are considerable. However, in our critical assessment of over 30 extant traits we present an initial, semi-quantitative ranking of 26 paleo-functional traits based on taphonomic and methodological criteria on the potential of those traits to impact Earth system processes, and for that impact to be quantifiable. We demonstrate how valuable inferences on paleo-ecosystem processes (pollination biology, herbivory), past nutrient cycles, paleobiogeography, paleo-demography (life history), and Earth system history can be derived through the application of paleo-functional traits to fossil plants.

Targeting editing of tomato SPEECHLESS cis-regulatory regions generates plants with altered stomatal density in response to changing climate conditions

Flexible developmental programs enable plants to customize their organ size and cellular composition. In leaves of eudicots, the stomatal lineage produces two essential cell types, stomata and pavement cells, but the total numbers and ratio of these cell types can vary. Central to this flexibility is the stomatal lineage initiating transcription factor, SPEECHLESS (SPCH). Here we show, by multiplex CRISPR/Cas9 editing of SlSPCH cis-regulatory sequences in tomato, that we can identify variants with altered stomatal development responses to light and temperature cues. Analysis of tomato leaf development across different conditions, aided by newly-created tools for live-cell imaging and translational reporters of SlSPCH and its paralogues SlMUTE and SlFAMA, revealed the series of cellular events that lead to the environmental change-driven responses in leaf form. Plants bearing the novel SlSPCH variants generated in this study are powerful resources for fundamental and applied studies of tomato resilience in response to climate change.

What we talk about when we talk about the long-term carbon cycle

The terrestrial biota is a crucial part of the long-term carbon cycle via the deposition of biomass as coal and other sedimentary organic matter and the impact of plants, fungi, and microbial life on the weathering of silicate minerals. Understanding these processes and their changes through time requires both geochemical modeling of the system as well as expertise in the living and fossil biotas and their ecological interactions, but details of these components are often lost in translation between disciplines. Here, we highlight misconceptions of the long-term carbon cycle that most frequently infiltrate the literature and hamper progress: mass balance requirements, the nature and duration of perturbations, opposing timescale constraints on biological and geological processes, and the role of models.

Micromorphology of Pine Needle Primordia and Young Needles after Bud Dormancy Breaking

Using a scanning electron microscope, the micromorphologies of needle primordia and the young needles of seven pine species (Pinus cembra, P. mugo, P. nigra, P. rigida, P. sylvestris, P. strobus, and P. uncinata) were analyzed at phenological stages B2 and B3 (according to Debazac). In B2, needle tips were rounded or pointed, depending on the species. In P. cembra and P. strobus, teeth were noted on the tips. Teeth were also visible on the margins in P. mugo, P. cembra, and P. strobus. Stomata became visible in the late B2 phase (P. sylvestris, P. mugo, and P. nigra) near the needle tips and were arranged in rows. In the B3 phase, needle tips were pointed. Only in P. strobus was the needle tip slightly rounded. The teeth on the margin in all the species were pointed. In P. strobus, their size and density along the margin decreased basipetally. In B3 for all the species, numerous stomata were visible. In P. sylvestris, P. cembra, and P. strobus, Florin rings were also observed. These observations could be useful in pine systematics but also in palaeobotanical or physiological studies. To the best of our knowledge, this is the first study on the micromorphology of very young needles in representatives of the genus Pinus.

Stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus

Stomatal density and guard cell length of 274 global core germplasms of rapeseed reveal that the stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. Stomata are microscopic structures of plants for the regulation of CO₂ assimilation and transpiration. Stomatal morphology has changed substantially in the adaptation to the external environment during land plant evolution. Brassica napus is a major crop to produce oil, livestock feed and biofuel in the world. However, there are few studies on the regulatory genes controlling stomatal development and their interaction with environmental factors as well as the genetic mechanism of adaptive variation in B. napus. Here, we characterized stomatal density (SD) and guard cell length (GL) of 274 global core germplasms at seedling stage. It was found that among the significant phenotypic variation, European germplasms are mostly winter rapeseed with high stomatal density and small guard cell length. However, the germplasms from Asia (especially China) are semi-winter rapeseed, which is characterized by low stomatal density and large guard cell length. Through selective sweep analysis and homology comparison, we identified several candidate genes related to stomatal density and guard cell length, including Epidermal Patterning Factor2 (EPF2; BnaA09g23140D), Epidermal Patterning Factor Like4 (EPFL4; BnaC01g22890D) and Suppressor of LLP1 (SOL1 BnaC01g22810D). Haplotype and phylogenetic analysis showed that natural variation in EPF2, EPFL4 and SOL1 is closely associated with the winter, spring, and semi-winter rapeseed ecotypes. In summary, this study demonstrated for the first time the relation between stomatal phenotypic variation and ecological adaptation in rapeseed, which is useful for future molecular breeding of rapeseed in the context of evolution and domestication of key stomatal traits and global climate change.

Evolvability and Macroevolution: Overview and Synthesis

Evolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats.

The origin and evolution of stomata

The acquisition of stomata is one of the key innovations that led to the colonisation of the terrestrial environment by the earliest land plants. However, our understanding of the origin, evolution and the ancestral function of stomata is incomplete. Phylogenomic analyses indicate that, firstly, stomata are ancient structures, present in the common ancestor of land plants, prior to the divergence of bryophytes and tracheophytes and, secondly, there has been reductive stomatal evolution, especially in the bryophytes (with complete loss in the liverworts). From a review of the evidence, we conclude that the capacity of stomata to open and close in response to signals such as ABA, CO₂ and light (hydroactive movement) is an ancestral state, is present in all lineages and likely predates the divergence of the bryophytes and tracheophytes. We reject the hypothesis that hydroactive movement was acquired with the emergence of the gymnosperms. We also conclude that the role of stomata in the earliest land plants was to optimise carbon gain per unit water loss. There remain many other unanswered questions concerning the evolution and especially the origin of stomata. To address these questions, it will be necessary to: find more fossils representing the earliest land plants, revisit the existing early land plant fossil record in the light of novel phylogenomic hypotheses and carry out more functional studies that include both tracheophytes and bryophytes.

Stomatal density in Pinus sylvestris as an indicator of temperature rather than CO2 : Evidence from a pan-European transect

The commonly observed negative relationship between stomatal density (SD) and atmospheric CO₂ has led to SD being proposed as an indicator of atmospheric CO₂ concentration. The use of SD as a proxy for CO₂ , however, has been hampered by an insufficient understanding of the intraspecific variation of this trait. We hypothesized that SD in Pinus sylvestris, a widely distributed conifer, varies geographically and that this variation is determined by major climatic variables. By sampling needles from naturally growing trees along a latitudinal range of 32.25°, equivalent to 13.7°C gradient of mean annual temperature (MAT) across Europe, we found that SD decreased from the warmest southern sites to the coldest sites in the north at a rate of 4 stomata per mm² for each 1°C, with MAT explaining 44% of the variation. Additionally, samples from a provenance trial exhibited a positive relationship between SD and the MAT of the original localities, suggesting that high SD is an adaptation to warm temperature. Our study revealed one of the strongest intraspecific relationships between SD and climate in any woody species, supporting the utility of SD as a temperature, rather than direct CO₂ , proxy. In addition, our results predict the response of SD to climate warming.

Quantifying the effect of shade on cuticle morphology and carbon isotopes of sycamores: present and past

PREMISE

Reconstructing the light environment and architecture of the plant canopy from the fossil record requires the use of proxies, such as those derived from cell wall undulation, cell size, and carbon isotopes. All approaches assume that plant taxa will respond predictably to changes in light environments. However, most species-level studies looking at cell wall undulation only consider "sun" or "shade" leaves; therefore, we need a fully quantitative taxon-specific method.

METHODS

We quantified the response of cell wall undulation, cell size, and carbon isotopes of Platanus occidentalis using two experimental setups: (1) two growth chambers at low and high light and (2) a series of outdoor growth experiments using green and black shade cloth at different densities. We then developed and applied a proxy for daily light integral (DLI) to fossil Platanites leaves from two early Paleocene floras from the San Juan Basin in New Mexico.

RESULTS

All traits responded to light environment. Cell wall undulation was the most useful trait for reconstructing DLI in the geological record. Median reconstructed DLI from early Paleocene leaves was ~44 mol m^-2  d^-1 , with values from 28 to 54 mol m^-2  d^-1 .

CONCLUSIONS

Cell wall undulation of P. occidentalis is a robust, quantifiable measurement of light environment that can be used to reconstruct the paleo-light environment from fossil leaves. The distribution of high DLI values from fossil leaves may provide information on canopy architecture; indicating that either (1) most of the canopy mass is within the upper portion of the crown or (2) leaves exposed to more sunlight are preferentially preserved.

Geometric and topological approaches to shape variation in Ginkgo leaves

Leaf shape is a key plant trait that varies enormously. The range of applications for data on this trait requires frequent methodological development so that researchers have an up-to-date toolkit with which to quantify leaf shape. We generated a dataset of 468 leaves produced by Ginkgo biloba, and 24 fossil leaves produced by evolutionary relatives of extant Ginkgo. We quantified the shape of each leaf by developing a geometric method based on elastic curves and a topological method based on persistent homology. Our geometric method indicates that shape variation in modern leaves is dominated by leaf size, furrow depth and the angle of the two lobes at the leaf base that is also related to leaf width. Our topological method indicates that shape variation in modern leaves is dominated by leaf size and furrow depth. We have applied both methods to modern and fossil material: the methods are complementary, identifying similar primary patterns of variation, but also revealing different aspects of morphological variation. Our topological approach distinguishes long-shoot leaves from short-shoot leaves, both methods indicate that leaf shape influences or is at least related to leaf area, and both could be applied in palaeoclimatic and evolutionary studies of leaf shape.

Fossil cells

Philip Donoghue introduces the fossil record of cells.

Moss stomata do not respond to light and CO2 concentration but facilitate carbon uptake by sporophytes: a gas exchange, stomatal aperture, and 13 C-labelling study

Stomata exert control on fluxes of CO₂ and water (H₂ O) in the majority of vascular plants and thus are pivotal for planetary fluxes of carbon and H₂ O. However, in mosses, the significance and possible function of the sporophytic stomata are not well understood, hindering understanding of the ancestral function and evolution of these key structures of land plants. Infrared gas analysis and ¹³ CO₂ labelling, with supporting data from gravimetry and optical and scanning electron microscopy, were used to measure CO₂ assimilation and water exchange on young, green, ± fully expanded capsules of 11 moss species with a range of stomatal numbers, distributions, and aperture sizes. Moss sporophytes are effectively homoiohydric. In line with their open fixed apertures, moss stomata, contrary to those in tracheophytes, do not respond to light and CO₂ concentration. Whereas the sporophyte cuticle is highly impermeable to gases, stomata are the predominant sites of ¹³ CO₂ entry and H₂ O loss in moss sporophytes, and CO₂ assimilation is closely linked to total stomatal surface areas. Higher photosynthetic autonomy of moss sporophytes, consequent on the presence of numerous stomata, may have been the key to our understanding of evolution of large, gametophyte-independent sporophytes at the onset of plant terrestrialization.

Stomatal Lineage Control by Developmental Program and Environmental Cues

Stomata are micropores that allow plants to breathe and play a critical role in photosynthesis and nutrient uptake by regulating gas exchange and transpiration. Stomatal development, therefore, is optimized for survival and growth of the plant despite variable environmental conditions. Signaling cascades and transcriptional networks that determine the birth, proliferation, and differentiation of a stomate have been identified. These networks ensure proper stomatal patterning, density, and polarity. Environmental cues also influence stomatal development. In this review, we highlight recent findings regarding the developmental program governing cell fate and dynamics of stomatal lineage cells at the cell state- or single-cell level. We also overview the control of stomatal development by environmental cues as well as developmental plasticity associated with stomatal function and physiology. Recent advances in our understanding of stomatal development will provide a route to improving photosynthesis and water-stress resilience of crop plants in the climate change we currently face.

Rice Stomatal Mega-Papillae Restrict Water Loss and Pathogen Entry

Rice (Oryza sativa) is a water-intensive crop, and like other plants uses stomata to balance CO₂ uptake with water-loss. To identify agronomic traits related to rice stomatal complexes, an anatomical screen of 64 Thai and 100 global rice cultivars was undertaken. Epidermal outgrowths called papillae were identified on the stomatal subsidiary cells of all cultivars. These were also detected on eight other species of the Oryza genus but not on the stomata of any other plant species we surveyed. Our rice screen identified two cultivars that had "mega-papillae" that were so large or abundant that their stomatal pores were partially occluded; Kalubala Vee had extra-large papillae, and Dharia had approximately twice the normal number of papillae. These were most accentuated on the flag leaves, but mega-papillae were also detectable on earlier forming leaves. Energy dispersive X-Ray spectrometry revealed that silicon is the major component of stomatal papillae. We studied the potential function(s) of mega-papillae by assessing gas exchange and pathogen infection rates. Under saturating light conditions, mega-papillae bearing cultivars had reduced stomatal conductance and their stomata were slower to close and re-open, but photosynthetic assimilation was not significantly affected. Assessment of an F₃ hybrid population treated with Xanthomonas oryzae pv. oryzicola indicated that subsidiary cell mega-papillae may aid in preventing bacterial leaf streak infection. Our results highlight stomatal mega-papillae as a novel rice trait that influences gas exchange, stomatal dynamics, and defense against stomatal pathogens which we propose could benefit the performance of future rice crops.

Links between environment and stomatal size through evolutionary time in Proteaceae

The size of plant stomata (adjustable pores that determine the uptake of CO₂ and loss of water from leaves) is considered to be evolutionarily important. This study uses fossils from the major Southern Hemisphere family Proteaceae to test whether stomatal cell size responded to Cenozoic climate change. We measured the length and abundance of guard cells (the cells forming stomata), the area of epidermal pavement cells, stomatal index and maximum stomatal conductance from a comprehensive sample of fossil cuticles of Proteaceae, and extracted published estimates of past temperature and atmospheric CO₂. We developed a novel test based on stochastic modelling of trait evolution to test correlations among traits. Guard cell length increased, and stomatal density decreased significantly with decreasing palaeotemperature. However, contrary to expectations, stomata tended to be smaller and more densely packed at higher atmospheric CO₂. Thus, associations between stomatal traits and palaeoclimate over the last 70 million years in Proteaceae suggest that stomatal size is significantly affected by environmental factors other than atmospheric CO₂. Guard cell length, pavement cell area, stomatal density and stomatal index covaried in ways consistent with coordinated development of leaf tissues.

Plant responses to decadal scale increments in atmospheric CO2 concentration: comparing two stomatal conductance sampling methods

MAIN CONCLUSION

Our study demonstrated that the species respond non-linearly to increases in CO2 concentration when exposed to decadal changes in CO2, representing the year 1987, 2025, 2051, and 2070, respectively. There are several lines of evidence suggesting that the vast majority of C3 plants respond to elevated atmospheric CO2 by decreasing their stomatal conductance (gs). However, in the majority of CO2 enrichment studies, the response to elevated CO2 are tested between plants grown under ambient (380-420 ppm) and high (538-680 ppm) CO2 concentrations and measured usually at single time points in a diurnal cycle. We investigated gs responses to simulated decadal increments in CO2 predicted over the next 4 decades and tested how measurements of gs may differ when two alternative sampling methods are employed (infrared gas analyzer [IRGA] vs. leaf porometer). We exposed Populus tremula, Popolus tremuloides and Sambucus racemosa to four different CO2 concentrations over 126 days in experimental growth chambers at 350, 420, 490 and 560 ppm CO2; representing the years 1987, 2025, 2051, and 2070, respectively (RCP4.5 scenario). Our study demonstrated that the species respond non-linearly to increases in CO2 concentration when exposed to decadal changes in CO2. Under natural conditions, maximum operational gs is often reached in the late morning to early afternoon, with a mid-day depression around noon. However, we showed that the daily maximum gs can, in some species, shift later into the day when plants are exposed to only small increases (70 ppm) in CO2. A non-linear decreases in gs and a shifting diurnal stomatal behavior under elevated CO2, could affect the long-term daily water and carbon budget of many plants in the future, and therefore alter soil-plant-atmospheric processes.

δ13C of terrestrial vegetation records Toarcian CO2 and climate gradients

Throughout Earth's history, variations in atmospheric CO2 concentration modulated climate. Understanding changes in atmospheric carbon cycle is therefore pivotal in predicting consequences of recent global warming. Here, we report stable carbon isotopes (δ13C) of molecular land plant fossils complemented by bulk organic and inorganic carbon fractions for early Toarcian (Early Jurassic) sediments that coincided with global warming and a carbon cycle perturbation. The carbon cycle perturbation is expressed by a negative excursion in the δ13C records established for the different substrates. Based on differences in the magnitude of the carbon isotope excursion recorded in land plants and marine substrates we infer that the early Toarcian warming was paralleled by an increase in atmospheric CO2 levels from ~500 ppmv to ~1000 ppmv. Our data suggest that rising atmospheric CO2 levels resulted from the injection of  12C-enriched methane and its subsequent oxidation to CO2. Based on the cyclic nature of the CIE we concluded that methane was released from climate sensitive reservoirs, in particular permafrost areas. Moderate volcanic CO2 emissions led to a destabilization of the labile permafrost carbon pool triggering the onset of Toarcian climate change only. The main carbon cycle perturbation then subsequently was driven by a self-sustained demise of a carbon-rich cryosphere progressing from mid to high latitudes as reflected by latitudinal climate gradients recorded in land plant carbon isotopes.

Plant carbon assimilation rates in atmospheric CO2 reconstructions

Fossil plant gas-exchange-based CO₂ reconstructions use carbon (C) assimilation rates of extant plant species as substitutes for assimilation rates of fossil plants. However, assumptions in model species adoption can lead to systematic error propagation. We used a dataset of c. 2500 extant species to investigate the role of phylogenetic relatedness and ecology in determining C assimilation, an essential variable in gas-exchange-based CO₂ models. We evaluated the effect on random and systematic error propagation in atmospheric CO₂ caused by adopting different model species. Phylogenetic relatedness, growth form, and solar exposure are important predictors of C assimilation rate. CO₂ reconstructions that apply C assimilation rates from modern species based solely on phylogenetic relatedness to fossil species can result in CO₂ estimates that are systematically biased by a factor of > 2. C assimilation rates used in CO₂ reconstructions should be determined by averaging assimilation rates of modern plant species that are (1) in the same family and (2) have a similar habit and habitat as the fossil plant. In addition, systematic bias potential and random error propagation are greatly reduced when CO₂ is reconstructed from multiple fossil plant species with different modern relatives at the same site.

Is Amphistomy an Adaptation to High Light? Optimality Models of Stomatal Traits along Light Gradients

Stomata regulate the supply of CO2 for photosynthesis and the rate of water loss out of the leaf. The presence of stomata on both leaf surfaces, termed amphistomy, increases photosynthetic rate, is common in plants from high light habitats, and rare otherwise. In this study I use optimality models based on leaf energy budget and photosynthetic models to ask why amphistomy is common in high light habitats. I developed an R package leafoptimizer to solve for stomatal traits that optimally balance carbon gain with water loss in a given environment. The model predicts that amphistomy is common in high light because its marginal effect on carbon gain is greater than in the shade, but only if the costs of amphistomy are also lower under high light than in the shade. More generally, covariation between costs and benefits may explain why stomatal and other traits form discrete phenotypic clusters.

StomataCounter: a neural network for automatic stomata identification and counting

Stomata regulate important physiological processes in plants and are often phenotyped by researchers in diverse fields of plant biology. Currently, there are no user-friendly, fully automated methods to perform the task of identifying and counting stomata, and stomata density is generally estimated by manually counting stomata. We introduce StomataCounter, an automated stomata counting system using a deep convolutional neural network to identify stomata in a variety of different microscopic images. We use a human-in-the-loop approach to train and refine a neural network on a taxonomically diverse collection of microscopic images. Our network achieves 98.1% identification accuracy on Ginkgo scanning electron microscropy micrographs, and 94.2% transfer accuracy when tested on untrained species. To facilitate adoption of the method, we provide the method in a publicly available website at http://www.stomata.science/.

Stomatal frequency of Quercus glauca from three material sources shows the same inverse response to atmospheric pCO2

BACKGROUND AND AIMS

The inverse correlation between atmospheric CO2 partial pressure (pCO2) and stomatal frequency in many plants has been widely used to estimate palaeo-CO2 levels. However, apparent discrepancies exist among the obtained estimates. This study attempts to find a potential proxy for palaeo-CO2 concentrations by analysing the stomatal frequency of Quercus glauca (section Cyclobalanopsis, Fagaceae), a dominant species in East Asian sub-tropical forests with abundant fossil relatives.

METHODS

Stomatal frequencies of Q. glauca from three material sources were analysed: seedlings grown in four climatic chambers with elevated CO2 ranging from 400 to 1300 ppm; extant samples collected from 14 field sites at altitudes ranging from 142 to 1555 m; and 18 herbarium specimens collected between 1930 and 2011. Stomatal frequency-pCO2 correlations were determined using samples from these three sources.

KEY RESULTS

An inverse correlation between stomatal frequency and pCO2 was found for Q. glauca through cross-validation of the three material sources. The combined calibration curves integrating data of extant altitudinal samples and historical herbarium specimens improved the reliability and accuracy of the curves. However, materials in the climatic chambers exhibited a weak response and relatively high stomatal frequency possibly due to insufficient treatment time.

CONCLUSIONS

A new inverse stomatal frequency-pCO2 correlation for Q. glauca was determined using samples from three sources. These three material types show the same response, indicating that Q. glauca is sensitive to atmospheric pCO2 and is an ideal proxy for palaeo-CO2 levels. Quercus glauca is a nearest living relative (NLR) of section Cyclobalanopsis fossils, which are widely distributed in the strata of East Asia ranging from the Eocene to Pliocene, thereby providing excellent materials to reconstruct the atmospheric CO2 concentration history of the Cenozoic. Quercus glauca will add to the variety of proxies that can be widely used in addition to Ginkgo and Metasequoia.

The prospects for constraining productivity through time with the whole-plant physiology of fossils

Anatomically preserved fossils allow estimation of hydraulic parameters, potentially providing constraints on interpreting whole-plant physiology. However, different organ systems have typically been considered in isolation - a problem given common mismatches of high and low conductance components coupled in the hydraulic path of the same plant. A recent paper addressed the issue of how to handle resistance mismatches in fossil plant hydraulics, focusing on Carboniferous medullosan seed plants and arborescent lycopsids. Among other problems, however, a fundamental error was made: the transpiration stream consists of resistances in series (where resistances are additive and the component with the largest resistance can dominate the behavior of the system), but emphasis was instead placed on the lowest resistance, effectively treating the system as resistances in parallel (where the component with the smallest resistance will dominate the behavior). Instead of possessing high assimilation capacities to match high specific stem conductances, it is argued here that individual high conductance components in these Paleozoic plants are nonetheless associated with low whole-plant productivity, just as can be commonly seen in living plants. Resolution of how to handle these issues may have broad implications for the Earth system including geobiological feedbacks to rock weathering, atmospheric composition, and climate.

Is Amphistomy an Adaptation to High Light? Optimality Models of Stomatal Traits along Light Gradients

Stomata regulate the supply of CO2 for photosynthesis and the rate of water loss out of the leaf. The presence of stomata on both leaf surfaces, termed amphistomy, increases photosynthetic rate, is common in plants from high light habitats, and rare otherwise. In this study I use optimality models based on leaf energy budget and photosynthetic models to ask why amphistomy is common in high light habitats. I developed an R package leafoptimizer to solve for stomatal traits that optimally balance carbon gain with water loss in a given environment. The model predicts that amphistomy is common in high light because its marginal effect on carbon gain is greater than in the shade, but only if the costs of amphistomy are also lower under high light than in the shade. More generally, covariation between costs and benefits may explain why stomatal and other traits form discrete phenotypic clusters.

Convergence in Maximum Stomatal Conductance of C3 Woody Angiosperms in Natural Ecosystems Across Bioclimatic Zones

Stomatal conductance (g s) in terrestrial vegetation regulates the uptake of atmospheric carbon dioxide for photosynthesis and water loss through transpiration, closely linking the biosphere and atmosphere and influencing climate. Yet, the range and pattern of g s in plants from natural ecosystems across broad geographic, climatic, and taxonomic ranges remains poorly quantified. Furthermore, attempts to characterize g s on such scales have predominantly relied upon meta-analyses compiling data from many different studies. This approach may be inherently problematic as it combines data collected using unstandardized protocols, sometimes over decadal time spans, and from different habitat groups. Using a standardized protocol, we measured leaf-level g s using porometry in 218 C3 woody angiosperm species in natural ecosystems representing seven bioclimatic zones. The resulting dataset of 4273 g s measurements, which we call STraits (Stomatal Traits), was used to determine patterns in maximum g s (g smax) across bioclimatic zones and whether there was similarity in the mean g smax of C3 woody angiosperms across ecosystem types. We also tested for differential g smax in two broadly defined habitat groups - open-canopy and understory-subcanopy - within and across bioclimatic zones. We found strong convergence in mean g smax of C3 woody angiosperms in the understory-subcanopy habitats across six bioclimatic zones, but not in open-canopy habitats. Mean g smax in open-canopy habitats (266 ± 100 mmol m-2 s-1) was significantly higher than in understory-subcanopy habitats (233 ± 86 mmol m-2 s-1). There was also a central tendency in the overall dataset to operate toward a g smax of ∼250 mmol m-2 s-1. We suggest that the observed convergence in mean g smax of C3 woody angiosperms in the understory-subcanopy is due to a buffering of g smax against macroclimate effects which will lead to differential response of C3 woody angiosperm vegetation in these two habitats to future global change. Therefore, it will be important for future studies of g smax to categorize vegetation according to habitat group.

The plant stomatal lineage at a glance

Stomata are structures on the surfaces of most land plants that are required for gas exchange between plants and their environment. In Arabidopsis thaliana, stomata comprise two kidney bean-shaped epidermal guard cells that flank a central pore overlying a cavity in the mesophyll. These guard cells can adjust their shape to occlude or facilitate access to this pore, and in so doing regulate the release of water vapor and oxygen from the plant, in exchange for the intake of carbon dioxide from the atmosphere. Stomatal guard cells are the end product of a specialized lineage whose cell divisions and fate transitions ensure both the production and pattern of cells in aerial epidermal tissues. The stomatal lineage is dynamic and flexible, altering stomatal production in response to environmental change. As such, the stomatal lineage is an excellent system to study how flexible developmental transitions are regulated in plants. In this Cell Science at a Glance article and accompanying poster, we will summarize current knowledge of the divisions and fate decisions during stomatal development, discussing the role of transcriptional regulators, cell-cell signaling and polarity proteins. We will highlight recent work that links the core regulators to systemic or environmental information and provide an evolutionary perspective on stomata lineage regulators in plants.

Multiple haploids, triploids, and tetraploids found in modern-day "living fossil" Ginkgo biloba

Ginkgo biloba, the last extant representative of a lineage of Mesozoic gymnosperms, is one of the few seed plants with an exceptionally long (~300 Myr) evolutionary history free of genome-wide duplications (polyploidy). Despite this genome conservatism, we have recently found a viable spontaneous tetraploid Ginkgo sapling during routine screening of several plants, demonstrating that natural polyploidy is possible in Ginkgo. Here we provide a much wider flow cytometry survey of ploidy in some European Ginkgo collections, and own seedlings (>2200 individuals and ~200 cultivars). We found a surprisingly high level of ploidy variation in modern-day Ginkgo and documented altogether 13 haploid, 3 triploid, and 10 tetraploid Ginkgo plants or cultivars, most of them being morphologically distinct from common diploids. Haploids frequently produced polyploid (dihaploid) buds or branches. Tetraploids showed some genome size variation. The surveyed plants provide a unique resource for future Ginkgo research and breeding, and they might be used to accelerate the modern diversification of this nearly extinct plant lineage.

Light and growth form interact to shape stomatal ratio among British angiosperms

In most plants, stomata are located only on the abaxial leaf surface (hypostomy), but many plants have stomata on both surfaces (amphistomy). High light and herbaceous growth form have been hypothesized to favor amphistomy, but these hypotheses have not been rigorously tested together using phylogenetic comparative methods. I leveraged a large dataset including stomatal ratio, Ellenberg light indicator value, growth form and phylogenetic relationships for 372 species of British angiosperms. I used phylogenetic comparative methods to test how light and/or growth form influence stomatal ratio and density. High light and herbaceous growth form are correlated with amphistomy, as predicted, but they also interact; the effect of light is pronounced in therophytes (annuals) and perennial herbs, but muted in phanerophytes (shrubs and trees). Furthermore, amphistomy and stomatal density evolve together in response to light. Comparative analyses of British angiosperms reveal two major insights. First, light and growth form interact to shape stomatal ratio; amphistomy is common under high light, but mostly for herbs. Second, coordinated evolution of adaxial stomatal density and light tolerance indicates that amphistomy helps to optimally balance light acquisition with gas exchange. Stomatal ratio may have potential as a functional trait for paleoecology and crop improvement.

Diurnal Variation in Gas Exchange: The Balance between Carbon Fixation and Water Loss

Stomatal control of transpiration is critical for maintaining important processes, such as plant water status, leaf temperature, as well as permitting sufficient CO2 diffusion into the leaf to maintain photosynthetic rates (A). Stomatal conductance often closely correlates with A and is thought to control the balance between water loss and carbon gain. It has been suggested that a mesophyll-driven signal coordinates A and stomatal conductance responses to maintain this relationship; however, the signal has yet to be fully elucidated. Despite this correlation under stable environmental conditions, the responses of both parameters vary spatially and temporally and are dependent on species, environment, and plant water status. Most current models neglect these aspects of gas exchange, although it is clear that they play a vital role in the balance of carbon fixation and water loss. Future efforts should consider the dynamic nature of whole-plant gas exchange and how it represents much more than the sum of its individual leaf-level components, and they should take into consideration the long-term effect on gas exchange over time.

Evolution of the Stomatal Regulation of Plant Water Content

Changes in the function of stomata from the earliest bryophytes to derived angiosperms are examined.