Maximum CO2 diffusion inside leaves is limited by the scaling of cell size and genome size

High photosynthesis rates in Brassiceae species are mediated by leaf anatomy enabling high biochemical capacity, rapid CO2 diffusion and efficient light use

Certain species in the Brassicaceae family exhibit high photosynthesis rates, potentially providing a valuable route toward improving agricultural productivity. However, factors contributing to their high photosynthesis rates are still unknown. We compared Hirschfeldia incana, Brassica nigra, Brassica rapa and Arabidopsis thaliana, grown under two contrasting light intensities. Hirschfeldia incana matched B. nigra and B. rapa in achieving very high photosynthesis rates under high growth-light condition, outperforming A. thaliana. Photosynthesis was relatively more limited by maximum photosynthesis capacity in H. incana and B. rapa and by mesophyll conductance in A. thaliana and B. nigra. Leaf traits such as greater exposed mesophyll specific surface enabled by thicker leaf or high-density small palisade cells contributed to the variation in mesophyll conductance among the species. The species exhibited contrasting leaf construction strategies and acclimation responses to low light intensity. High-light plants distributed Chl deeper in leaf tissue, ensuring even distribution of photosynthesis capacity, unlike low-light plants. Leaf anatomy of H. incana, B. nigra and B. rapa facilitated effective CO2 diffusion, efficient light use and provided ample volume for their high maximum photosynthetic capacity, indicating that a combination of adaptations is required to increase CO2-assimilation rates in plants.

Genome size is positively correlated with extinction risk in herbaceous angiosperms

Angiosperms with large genomes experience nuclear-, cellular-, and organism-level constraints that may limit their phenotypic plasticity and ecological niche, which could increase their risk of extinction. Therefore, we test the hypotheses that large-genomed species are more likely to be threatened with extinction than those with small genomes, and that the effect of genome size varies across three selected covariates: life form, endemism, and climatic zone. We collated genome size and extinction risk information for a representative sample of angiosperms comprising 3250 species, which we analyzed alongside life form, endemism, and climatic zone variables using a phylogenetic framework. Genome size is positively correlated with extinction risk, a pattern driven by a signal in herbaceous but not woody species, regardless of climate and endemism. The influence of genome size is stronger in endemic herbaceous species, but is relatively homogenous across different climates. Beyond its indirect link via endemism and climate, genome size is associated with extinction risk directly and significantly. Genome size may serve as a proxy for difficult-to-measure parameters associated with resilience and vulnerability in herbaceous angiosperms. Therefore, it merits further exploration as a useful biological attribute for understanding intrinsic extinction risk and augmenting plant conservation efforts.

The long and tortuous path towards improving photosynthesis by engineering elevated mesophyll conductance

The growing demand for global food production is likely to be a defining issue facing humanity over the next 50 years. To tackle this challenge, there is a desire to bioengineer crops with higher photosynthetic efficiencies, to increase yields. Recently, there has been a growing interest in engineering leaves with higher mesophyll conductance (gm), which would allow CO2 to move more efficiently from the substomatal cavities to the chloroplast stroma. However, if crop yield gains are to be realised through this approach, it is essential that the methodological limitations associated with estimating gm are fully appreciated. In this review, we summarise these limitations, and outline the uncertainties and assumptions that can affect the final estimation of gm. Furthermore, we critically assess the predicted quantitative effect that elevating gm will have on assimilation rates in crop species. We highlight the need for more theoretical modelling to determine whether altering gm is truly a viable route to improve crop performance. Finally, we offer suggestions to guide future research on gm, which will help mitigate the uncertainty inherently associated with estimating this parameter.

The global distribution of angiosperm genome size is shaped by climate

Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.

Amphistomy increases leaf photosynthesis more in coastal than montane plants of Hawaiian 'ilima (Sida fallax)

PREMISE

The adaptive significance of amphistomy (stomata on both upper and lower leaf surfaces) is unresolved. A widespread association between amphistomy and open, sunny habitats suggests the adaptive benefit of amphistomy may be greatest in these contexts, but this hypothesis has not been tested experimentally. Understanding amphistomy informs its potential as a target for crop improvement and paleoenvironment reconstruction.

METHODS

We developed a method to quantify "amphistomy advantage" (AA $\text{AA}$ ) as the log-ratio of photosynthesis in an amphistomatous leaf to that of the same leaf but with gas exchange blocked through the upper surface (pseudohypostomy). Humidity modulated stomatal conductance and thus enabled comparing photosynthesis at the same total stomatal conductance. We estimatedAA $\text{AA}$ and leaf traits in six coastal (open, sunny) and six montane (closed, shaded) populations of the indigenous Hawaiian species 'ilima (Sida fallax).

RESULTS

Coastal 'ilima leaves benefit 4.04 times more from amphistomy than montane leaves. Evidence was equivocal with respect to two hypotheses: (1) that coastal leaves benefit more because they are thicker and have lower CO2 conductance through the internal airspace and (2) that they benefit more because they have similar conductance on each surface, as opposed to most conductance being through the lower surface.

CONCLUSIONS

This is the first direct experimental evidence that amphistomy increases photosynthesis, consistent with the hypothesis that parallel pathways through upper and lower mesophyll increase CO2 supply to chloroplasts. The prevalence of amphistomatous leaves in open, sunny habitats can partially be explained by the increased benefit of amphistomy in "sun" leaves, but the mechanistic basis remains uncertain.

A rapid freezing method to determine tissue layer thickness in drought-stressed leaves

Plants have been affected by water stress ever since they settled on dry land. In severe and persisting drought, plant leaves are wilting. However, a documentation at the anatomical level of the minute changes that occur before wilting is challenging. On the other hand, understanding the anatomical alteration in plant leaves with respect to water stress provides a stronger basis to study molecular and submolecular processes through which plants enhance drought tolerance. In this work, we applied an affordable method to visualise mesophyll layers of Arabidopsis thaliana cell lines without preparation steps that would alter the volume of the cells. We rapidly plunge-froze the leaves in liquid nitrogen, cut them while in the N2 bath, and immediately imaged the mesophyll cross sections in a scanning electron microscope. We applied a reduction of watering from 60 to 40 to 20 mL per day and investigated two time points, 7 and 12 days, respectively. Interestingly, the overall thickness of leaves increased in water stress conditions. Our results showed that the palisade and spongy layers behaved differently under varying watering regimes. Moreover, the results showed that this method can be used to image leaf sections after drought stress without the risk of artefacts or swelling caused by contact to liquids as during chemical fixation.

Conserved cellular patterning in the mesophyll of rice leaves

The mesophyll cells of grass leaves, such as rice, are traditionally viewed as displaying a relatively uniform pattern, in contrast to the clear distinctions of palisade and spongy layers in typical eudicot leaves. This quantitative analysis of mesophyll cell size and shape in rice leaves reveals that there is an inherent pattern in which cells in the middle layer of the mesophyll are larger and less circular and have a distinct orientation of their long axis compared to mesophyll cells in other layers. Moreover, this pattern was observed in a range of rice cultivars and species. The significance of this pattern with relation to potential photosynthetic function and the implication of the widespread use of middle layer mesophyll cells as typical of the rice leaf have been investigated and discussed.

From genome size to trait evolution during angiosperm radiation

Angiosperm diversity arises from trait flexibility and repeated evolutionary radiations, but the role of genomic characters in these radiations remains unclear. In this opinion article, we discuss how genome size can influence angiosperm diversification via its intricate link with cell size, tissue packing, and physiological processes which, in turn, influence the macroevolution of functional traits. We propose that integrating genome size, functional traits, and phylogenetic data across a wide range of lineages allows us to test whether genome size decrease consistently leads to increased trait flexibility, while genome size increase constrains trait evolution. Combining theories from molecular biology, functional ecology and macroevolution, we provide a framework to better understand the role of genome size in trait evolution, evolutionary radiations, and the global distribution of angiosperms.

Genome-material costs and functional trade-offs in the autopolyploid Solidago gigantea (giant goldenrod) series

PREMISE

Increased genome-material costs of N and P atoms inherent to organisms with larger genomes have been proposed to limit growth under nutrient scarcities and to promote growth under nutrient enrichments. Such responsiveness may reflect a nutrient-dependent diploid versus polyploid advantage that could have vast ecological and evolutionary implications, but direct evidence that material costs increase with ploidy level and/or influence cytotype-dependent growth, metabolic, and/or resource-use trade-offs is limited.

METHODS

We grew diploid, autotetraploid, and autohexaploid Solidago gigantea plants with one of four ambient or enriched N:P ratios and measured traits related to material costs, primary and secondary metabolism, and resource-use.

RESULTS

Relative to diploids, polyploids invested more N and P into cells, and tetraploids grew more with N enrichments, suggesting that material costs increase with ploidy level. Polyploids also generally exhibited strategies that could minimize material-cost constraints over both long (reduced monoploid genome size) and short (more extreme transcriptome downsizing, reduced photosynthesis rates and terpene concentrations, enhanced N-use efficiencies) evolutionary time periods. Furthermore, polyploids had lower transpiration rates but higher water-use efficiencies than diploids, both of which were more pronounced under nutrient-limiting conditions.

CONCLUSIONS

N and P material costs increase with ploidy level, but material-cost constraints might be lessened by resource allocation/investment mechanisms that can also alter ecological dynamics and selection. Our results enhance mechanistic understanding of how global increases in nutrients might provide a release from material-cost constraints in polyploids that could impact ploidy (or genome-size)-specific performances, cytogeographic patterning, and multispecies community structuring.

Creating a virtual leaf

When microscopy meets modelling the exciting concept of a 'virtual leaf' is born. The goal of a 'virtual leaf' is to capture complex physiology in a virtual environment, resulting in the capacity to run experiments computationally. One example of a 'virtual leaf' application is capturing 3D anatomy from volume microscopy data and estimating where water evaporates in the leaf and the proportions of apoplastic, symplastic and gas phase water transport. The same 3D anatomy could then be used to improve established 3D reaction-diffusion models, providing a better understanding of the transport of CO₂ across the stomata, through the airspace and across the mesophyll cell wall. This viewpoint discusses recent progress that has been made in transitioning from a bulk leaf approach to a 3D understanding of leaf physiology, in particular, the movement of CO₂ and H₂O within the leaf.

Hydraulic differences between flowers and leaves are driven primarily by pressure-volume traits and water loss

Flowers are critical for successful reproduction and have been a major axis of diversification among angiosperms. As the frequency and severity of droughts are increasing globally, maintaining water balance of flowers is crucial for food security and other ecosystem services that rely on flowering. Yet remarkably little is known about the hydraulic strategies of flowers. We characterized hydraulic strategies of leaves and flowers of ten species by combining anatomical observations using light and scanning electron microscopy with measurements of hydraulic physiology (minimum diffusive conductance (g _min) and pressure-volume (PV) curves parameters). We predicted that flowers would exhibit higher g _min and higher hydraulic capacitance than leaves, which would be associated with differences in intervessel pit traits because of their different hydraulic strategies. We found that, compared to leaves, flowers exhibited: 1) higher g _min, which was associated with higher hydraulic capacitance (C _T); 2) lower variation in intervessel pit traits and differences in pit membrane area and pit aperture shape; and 3) independent coordination between intervessel pit traits and other anatomical and physiological traits; 4) independent evolution of most traits in flowers and leaves, resulting in 5) large differences in the regions of multivariate trait space occupied by flowers and leaves. Furthermore, across organs intervessel pit trait variation was orthogonal to variation in other anatomical and physiological traits, suggesting that pit traits represent an independent axis of variation that have as yet been unquantified in flowers. These results suggest that flowers, employ a drought-avoidant strategy of maintaining high capacitance that compensates for their higher g _min to prevent excessive declines in water potentials. This drought-avoidant strategy may have relaxed selection on intervessel pit traits and allowed them to vary independently from other anatomical and physiological traits. Furthermore, the independent evolution of floral and foliar anatomical and physiological traits highlights their modular development despite being borne from the same apical meristem.

Seed Priming with Single-Walled Carbon Nanotubes Grafted with Pluronic P85 Preserves the Functional and Structural Characteristics of Pea Plants

The engineering of carbon nanotubes in the last decades resulted in a variety of applications in electronics, electrochemistry, and biomedicine. A number of reports also evidenced their valuable application in agriculture as plant growth regulators and nanocarriers. In this work, we explored the effect of seed priming with single-walled carbon nanotubes grafted with Pluronic P85 polymer (denoted P85-SWCNT) on Pisum sativum (var. RAN-1) seed germination, early stages of plant development, leaf anatomy, and photosynthetic efficiency. We evaluated the observed effects in relation to hydro- (control) and P85-primed seeds. Our data clearly revealed that seed priming with P85-SWCNT is safe for the plant since it does not impair the seed germination, plant development, leaf anatomy, biomass, and photosynthetic activity, and even increases the amount of photochemically active photosystem II centers in a concentration-dependent manner. Only 300 mg/L concentration exerts an adverse effect on those parameters. The P85 polymer, however, was found to exhibit a number of negative effects on plant growth (i.e., root length, leaf anatomy, biomass accumulation and photoprotection capability), most probably related to the unfavorable interaction of P85 unimers with plant membranes. Our findings substantiate the future exploration and exploitation of P85-SWCNT as nanocarriers of specific substances promoting not only plant growth at optimal conditions but also better plant performance under a variety of environmental stresses.

Realizing the Full Potential of Advanced Microscopy Approaches for Interrogating Plant-Microbe Interactions

Microscopy has served as a fundamental tool for insight and discovery in plant-microbe interactions for centuries. From classical light and electron microscopy to corresponding specialized methods for sample preparation and cellular contrasting agents, these approaches have become routine components in the toolkit of plant and microbiology scientists alike to visualize, probe and understand the nature of host-microbe relationships. Over the last three decades, three-dimensional perspectives led by the development of electron tomography, and especially, confocal techniques continue to provide remarkable clarity and spatial detail of tissue and cellular phenomena. Confocal and electron microscopy provide novel revelations that are now commonplace in medium and large institutions. However, many other cutting-edge technologies and sample preparation workflows are relatively unexploited yet offer tremendous potential for unprecedented advancement in our understanding of the inner workings of pathogenic, beneficial, and symbiotic plant-microbe interactions. Here, we highlight key applications, benefits, and challenges of contemporary advanced imaging platforms for plant-microbe systems with special emphasis on several recently developed approaches, such as light-sheet, single molecule, super-resolution, and adaptive optics microscopy, as well as ambient and cryo-volume electron microscopy, X-ray microscopy, and cryo-electron tomography. Furthermore, the potential for complementary sample preparation methodologies, such as optical clearing, expansion microscopy, and multiplex imaging, will be reviewed. Our ultimate goal is to stimulate awareness of these powerful cutting-edge technologies and facilitate their appropriate application and adoption to solve important and unresolved biological questions in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Diverse mangroves deviate from other angiosperms in their genome size, leaf cell size and cell packing density relationships

BACKGROUND AND AIMS

While genome size limits the minimum sizes and maximum numbers of cells that can be packed into a given leaf volume, mature cell sizes can be substantially larger than their meristematic precursors and vary in response to abiotic conditions. Mangroves are iconic examples of how abiotic conditions can influence the evolution of plant phenotypes.

METHODS

Here, we examined the coordination between genome size, leaf cell sizes, cell packing densities and leaf size in 13 mangrove species across four sites in China. Four of these species occurred at more than one site, allowing us to test the effect of climate on leaf anatomy.

RESULTS

We found that genome sizes of mangroves were very small compared to other angiosperms, but, like other angiosperms, mangrove cells were always larger than the minimum size defined by genome size. Increasing mean annual temperature of a growth site led to higher packing densities of veins (Dv) and stomata (Ds) and smaller epidermal cells but had no effect on stomatal size. In contrast to other angiosperms, mangroves exhibited (1) a negative relationship between guard cell size and genome size; (2) epidermal cells that were smaller than stomata; and (3) coordination between Dv and Ds that was not mediated by epidermal cell size. Furthermore, mangrove epidermal cell sizes and packing densities covaried with leaf size.

CONCLUSIONS

While mangroves exhibited coordination between veins and stomata and attained a maximum theoretical stomatal conductance similar to that of other angiosperms, the tissue-level tradeoffs underlying these similar relationships across species and environments were markedly different, perhaps indicative of the unique structural and physiological adaptations of mangroves to their stressful environments.

Analyzing anatomy over three dimensions unpacks the differences in mesophyll diffusive area between sun and shade Vitis vinifera leaves

Leaves grown at different light intensities exhibit considerable differences in physiology, morphology and anatomy. Because plant leaves develop over three dimensions, analyses of the leaf structure should account for differences in lengths, surfaces, as well as volumes. In this manuscript, we set out to disentangle the mesophyll surface area available for diffusion per leaf area (S m,LA) into underlying one-, two- and three-dimensional components. This allowed us to estimate the contribution of each component to S m,LA, a whole-leaf trait known to link structure and function. We introduce the novel concept of a 'stomatal vaporshed,' i.e. the intercellular airspace unit most closely connected to a single stoma, and use it to describe the stomata-to-diffusive-surface pathway. To illustrate our new theoretical framework, we grew two cultivars of Vitis vinifera L. under high and low light, imaged 3D leaf anatomy using microcomputed tomography (microCT) and measured leaf gas exchange. Leaves grown under high light were less porous and thicker. Our analysis showed that these two traits and the lower S m per mesophyll cell volume (S m,Vcl) in sun leaves could almost completely explain the difference in S m,LA. Further, the studied cultivars exhibited different responses in carbon assimilation per photosynthesizing cell volume (A Vcl). While Cabernet Sauvignon maintained A Vcl constant between sun and shade leaves, it was lower in Blaufränkisch sun leaves. This difference may be related to genotype-specific strategies in building the stomata-to-diffusive-surface pathway.

The Plant DNA C-Values Database: A One-Stop Shop for Plant Genome Size Data

Genome size is a plant character with far-reaching implications, ranging from impacts on the financial and computing feasibility of sequencing and assembling genomes all the way to influencing the very ecology and evolution of species. The increasing recognition of the role of genome size in plant science has led to a rising demand for comprehensive and easily accessible sources of genome size data. The Plant DNA C-values database has established itself as a trusted and widely used central hub for users needing to access available plant genome size data, complemented with related cytogenetic (ploidy level) and karyological (chromosome number) information where available. Since its inception in 2001, the database has undergone six major updates to incorporate newly available genome size information, leading to the most recent release (Release 7.1), which comprises data for 12,273 species across all the major land plant and some algal lineages. Here we describe how to use the database efficiently, making use of its different query and filtering settings.

Nitrogen-based symbioses, phosphorus availability, and accounting for a modern world more productive than the Paleozoic

Evolution of high-productivity angiosperms has been regarded as a driver of Mesozoic ecosystem restructuring. However, terrestrial productivity is limited by availability of rock-derived nutrients such as phosphorus for which permanent increases in weathering would violate mass balance requirements of the long-term carbon cycle. The potential reality of productivity increases sustained since the Mesozoic is supported here with documentation of a dramatic increase in the evolution of nitrogen-fixing or nitrogen-scavenging symbioses, including more than 100 lineages of ectomycorrhizal and lichen-forming fungi and plants with specialized microbial associations. Given this evidence of broadly increased nitrogen availability, we explore via carbon cycle modeling how enhanced phosphorus availability might be sustained without violating mass balance requirements. Volcanism is the dominant carbon input, dictating peaks in weathering outputs up to twice modern values. However, times of weathering rate suppression may be more important for setting system behavior, and the late Paleozoic was the only extended period over which rates are expected to have remained lower than modern. Modeling results are consistent with terrestrial organic matter deposition that accompanied Paleozoic vascular plant evolution having suppressed weathering fluxes by providing an alternative sink of atmospheric CO₂ . Suppression would have then been progressively lifted as the crustal reservoir's holding capacity for terrestrial organic matter saturated back toward steady state with deposition of new organic matter balanced by erosion of older organic deposits. Although not an absolute increase, weathering fluxes returning to early Paleozoic conditions would represent a novel regime for the complex land biota that evolved in the interim. Volcanism-based peaks in Mesozoic weathering far surpass the modern rates that sustain a complex diversity of nitrogen-based symbioses; only in the late Paleozoic might these ecologies have been suppressed by significantly lower rates. Thus, angiosperms are posited to be another effect rather than proximal cause of Mesozoic upheaval.

Localized growth and remodelling drives spongy mesophyll morphogenesis

The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides mechanical stability. Unlike many other biological tissues, which remain confluent throughout development, the spongy mesophyll must develop from an initially confluent tissue into a tortuous network of cells with a large proportion of intercellular airspace. How the airspace in the spongy mesophyll develops while the tissue remains mechanically stable is unknown. Here, we use computer simulations of deformable polygons to develop a purely mechanical model for the development of the spongy mesophyll tissue. By stipulating that cell wall growth and remodelling occurs only near void space, our computational model is able to recapitulate spongy mesophyll development observed in Arabidopsis thaliana leaves. We find that robust generation of pore space in the spongy mesophyll requires a balance of cell growth, adhesion, stiffness and tissue pressure to ensure cell networks become porous yet maintain mechanical stability. The success of this mechanical model of morphogenesis suggests that simple physical principles can coordinate and drive the development of complex plant tissues like the spongy mesophyll.

Potassium availability influences the mesophyll structure to coordinate the conductance of CO2 and H2 O during leaf expansion

Leaf growth relies on photosynthesis and hydraulics to provide carbohydrates and expansion power; in turn, leaves intercept light and construct organism systems for functioning. Under potassium (K) deficiency stress, leaf area, photosynthesis and hydraulics are all affected by alterations in leaf structure. However, the connection between changes in leaf growth and function caused by the structure under K regulation is unclear. Consequently, the leaf hydraulic conductance (K_leaf ) and photosynthetic rate (A) combined with leaf anatomical characteristics of Brassica napus were continuously observed during leaf growth under different K supply levels. The results showed that K_leaf and A decreased simultaneously after leaf area with the increasing K deficiency stress. K deficiency significantly increased longitudinal mesophyll cell investment, leading to a reduced volume fraction of intercellular air-space (f_ias ) and decreased leaf expansion rate. Furthermore, reduced f_ias decreased mesophyll and chloroplast surfaces exposed to intercellular airspace and gas phase H₂ O transport, which induced coordinated changes in CO₂ mesophyll conductance and hydraulic conductance in extra-xylem pathways. Adequate K supply facilitated higher f_ias through smaller palisade tissue cell density (loose mesophyll cell arrangement) and smaller spongy tissue cell size, which coordinated CO₂ and H₂ O conductance and promoted leaf area expansion.

Genome evolution: On the nature of trade-offs with polyploidy and endopolyploidy

A new study uncovers a novel trade-off in polyploid plants. While the larger cells of polyploids benefit from increased cell storage and water retention, this comes at the cost of reduced structural stability, potentially impacting survival.

A workflow for segmenting soil and plant X-ray computed tomography images with deep learning in Google's Colaboratory

X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google's Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

Stoichiometry versus ecology: the relationships between genome size and guanine-cytosine content, and tissue nitrogen and phosphorus in grassland herbs

BACKGROUND AND AIMS

Plant tissue nitrogen (N) and phosphorus (P) and genome traits, such as genome size and guanine-cytosine (GC) content, scale with growth or metabolic rates and are linked to plant ecological strategy spectra. Tissue NP stoichiometry and genome traits are reported to affect plant growth, metabolic rates or ecological strategies in contrasting ways, although the elemental costs for building and maintaining DNA are typically overlooked.

METHODS

We formulated stoichiometry- and ecology-based predictions on the relationship between genome size and GC content to tissue N, P and N : P and tested them on a set of 130 herbaceous species from a temperate grassland using ordinary, phylogenetic and quantile regression.

KEY RESULTS

Genome size was only negatively linked to plant N and N : P in species with very small genomes. We found no link between genome size and plant P. GC content was negatively linked to plant N and P but we found these significant links consistently in both GC-rich and GC-poor species. Finally, GC content correlated positively with plant N : P but only in species with GC-rich genomes.

CONCLUSIONS

Our results provide stronger support for the ecology-based predictions than the stoichiometry-based predictions, and for the links between GC content and plant N and P stoichiometry than for genome size. We argue that the theories of plant metabolic rates and ecological strategies (resource-acquisitive vs. conservative or ruderal vs. stress-tolerator spectra) better explain interspecific genome-NP stoichiometry relationships at the tissue level (although relatively weakly) than the stoichiometric theory based on the elemental costs for building and maintaining DNA.

The Secondary Metabolites Profile in Horse Chestnut Leaves Infested with Horse-Chestnut Leaf Miner

Natural defensive substances synthesized by plants that could replace synthetic pesticides in the protection of plants against insect invasions are constantly being sought. The study assessed changes in the qualitative and quantitative composition of secondary metabolites in horse chestnut leaves collected in different locations and differing in the sensitivity of the plant to the invasion by the horse-chestnut leaf miner. An attempt was made to identify compounds that are most responsible for the increased plant resistance to this threat. Additionally, changes in the anatomy of chestnut leaves affected by the pest were presented. It was noticed that the trees differed in the composition of secondary metabolites already in the initial growing season, which should be related to the influence of habitat conditions. The analysis of the profile of the compounds in non-infested and infested horse chestnut leaves revealed a clear response of the plant to the stress factor, i.e., the foraging of the horse-chestnut leaf miner. Catechins seem to be compounds involved in plant resistance. The leaf anatomy showed enhanced accumulation of phenolic compounds at the pest foraging sites. Hypertrophy and thickened and cracked cell walls of the spongy parenchyma were visible in the vicinity of the mines.

The Leaf Trichome, Venation, and Mesophyll Structural Traits Play Important Roles in the Physiological Responses of Oak Seedlings to Water-Deficit Stress

In this study, we investigated the effects of water-deficit stress on the leaf anatomical traits, physiological traits, and stem starch content in Quercus acutissima Carruth and Quercus serrata Murray by subjecting their seedlings to well-watered (WW) and water-deficit stress (WS) treatments. The water stress-induced changes in trichome density, trichome-to-stomata ratio, mesophyll thickness, vein density, vein distance, vein loopiness, vessel diameter, transpiration (E), stomatal conductance (gs), water use efficiency (WUE), and starch content were analyzed between two time points. While trichome density did not vary between treatments in Q. acutissima, it dramatically increased in Q. serrata (62.63–98.96 trichomes mm−2) at the final week. The WS-treated seedlings had a thicker palisade mesophyll (162.85–169.56 µm) than the WW-treated samples (118.56–132.25 µm) in both species. The vein density and loopiness increased significantly in the WS-treated Q. serrata seedlings. Small-sized vessels (10–50 µm) were more frequent in the WS than the WW in Q. serrata. The E, gs, WUE, and starch content declined significantly in the WS-treated seedlings compared with WW-treated samples in both species. Further, principal component analysis revealed significant relationships between anatomical and physiological traits, particularly in the WS-treated seedlings of Q. serrata. The coordinated changes in leaf anatomical traits, physiological traits, and stem starch content indicate an important role in the survival of Q. acutissima and Q. serrata seedlings in water-deficit stress environments, although Q. serrata may show higher survivability under prolonged water stress than Q. acutissima.

The structural correlations and the physiological functions of stomatal morphology and leaf structures in C3 annual crops

This study suggests that stomatal and leaf structures are highly correlated, and mesophyll cell size is an important anatomical trait determining the coordination between stomatal size and mesophyll porosity. A comprehensive study of the correlations between the structural traits and on their relationships with gas exchange parameters may provide some useful information into leaf development and improvement in efficiencies of photosynthetic CO₂ fixation and transpirational water loss. In the present study, nine plant materials from eight crop species were pot grown in a growth chamber. Leaf structural traits, gas exchange, and leaf nitrogen content were measured. We found that stomatal size, mesophyll cell size (MCS), and mesophyll porosity were positively correlated and that the surface areas of mesophyll cells and chloroplasts facing intercellular air spaces were positively correlated with both stomatal density and stomatal area per leaf area (SA). These results suggested that the developments of stomata and mesophyll cells are highly correlated among different crop species. Additionally, MCS was positively correlated with leaf thickness and negatively correlated with leaf density and leaf mass per area, which indicated that MCS might play an important role in leaf structural investments and physiological functions among species. In summary, this study illustrates the correlations between stomatal and mesophyll structures, and it highlights the importance of considering the covariations among leaf traits with the intent of improving photosynthesis and iWUE.

Scaling relationships of leaf vein and areole traits versus leaf size for nine Magnoliaceae species differing in venation density

PREMISE

Across species, main leaf vein density scales inversely with leaf area (A). Yet, minor vein density manifests no clear relationship with respect to A, despite having the potential to provide important insights into the trade-off among the investments in leaf mechanical support, hydraulics, and light interception.

METHODS

To examine this phenomenon, the leaves of nine Magnoliaceae leaves were sampled, and the scaling relationships among A and midrib length (ML), total vein length (TVL), total vein area (TVA), total areole area (TAA), and mean areole area (MAA) were determined. The scaling relationships between MAA and areole density (the number of areoles per unit leaf area) and between MAA and A were also analyzed.

RESULTS

For five of the nine species, A was proportional to ML² . For eight of the nine species, TVL and TVA were both proportional to A. The numerical values of the scaling exponents for TAA vs. A were between 1.0 and 1.07 for eight species; i.e., as expected, TAA was isometrically proportional to A. There was no correlation between MAA and A, but MAA scaled inversely with respect to areole density for each species.

CONCLUSIONS

The correlation between midrib "density" (i.e., ML/A) and A, and the lack of correlation between total leaf vein density and A result from the A ∝$\propto $ ML² scaling relationship and the proportional relationship between TVL and A, respectively. Leaves with the same size can have widely varying MAA. Thus, leaf size itself does not directly constrain leaf hydraulic efficiency and redundancy.

Scaling relationships of leaf vein and areole traits versus leaf size for nine Magnoliaceae species differing in venation density

PREMISE

Across species, main leaf vein density scales inversely with leaf area (A). Yet, minor vein density manifests no clear relationship with respect to A, despite having the potential to provide important insights into the trade-off among the investments in leaf mechanical support, hydraulics, and light interception.

METHODS

To examine this phenomenon, the leaves of nine Magnoliaceae leaves were sampled, and the scaling relationships among A and midrib length (ML), total vein length (TVL), total vein area (TVA), total areole area (TAA), and mean areole area (MAA) were determined. The scaling relationships between MAA and areole density (the number of areoles per unit leaf area) and between MAA and A were also analyzed.

RESULTS

For five of the nine species, A was proportional to ML² . For eight of the nine species, TVL and TVA were both proportional to A. The numerical values of the scaling exponents for TAA vs. A were between 1.0 and 1.07 for eight species; i.e., as expected, TAA was isometrically proportional to A. There was no correlation between MAA and A, but MAA scaled inversely with respect to areole density for each species.

CONCLUSIONS

The correlation between midrib "density" (i.e., ML/A) and A, and the lack of correlation between total leaf vein density and A result from the A ∝$\propto $ ML² scaling relationship and the proportional relationship between TVL and A, respectively. Leaves with the same size can have widely varying MAA. Thus, leaf size itself does not directly constrain leaf hydraulic efficiency and redundancy.

Structural organization of the spongy mesophyll

Many plant leaves have two layers of photosynthetic tissue: the palisade and spongy mesophyll. Whereas palisade mesophyll consists of tightly packed columnar cells, the structure of spongy mesophyll is not well characterized and often treated as a random assemblage of irregularly shaped cells. Using micro-computed tomography imaging, topological analysis, and a comparative physiological framework, we examined the structure of the spongy mesophyll in 40 species from 30 genera with laminar leaves and reticulate venation. A spectrum of spongy mesophyll diversity encompassed two dominant phenotypes: first, an ordered, honeycomblike tissue structure that emerged from the spatial coordination of multilobed cells, conforming to the physical principles of Euler's law; and second, a less-ordered, isotropic network of cells. Phenotypic variation was associated with transitions in cell size, cell packing density, mesophyll surface-area-to-volume ratio, vein density, and maximum photosynthetic rate. These results show that simple principles may govern the organization and scaling of the spongy mesophyll in many plants and demonstrate the presence of structural patterns associated with leaf function. This improved understanding of mesophyll anatomy provides new opportunities for spatially explicit analyses of leaf development, physiology, and biomechanics.

Desiccation of the leaf mesophyll and its implications for CO2 diffusion and light processing

Leaves balance CO₂ and radiative absorption while maintaining water transport to maximise photosynthesis. Related species with contrasting leaf anatomy can provide insights into inherent and stress-induced links between structure and function for commonly measured leaf traits for important crops. We used two walnut species with contrasting mesophyll anatomy to evaluate these integrated exchange processes under non-stressed and drought conditions using a combination of light microscopy, X-ray microCT, gas exchange, hydraulic conductance, and chlorophyll distribution profiles through leaves. Juglans regia had thicker palisade mesophyll, higher fluorescence in the palisade, and greater low-mesophyll porosity that were associated with greater gas-phase diffusion (g_IAS ), stomatal and mesophyll (g_m ) conductances and carboxylation capacity. More and highly-packed mesophyll cells and bundle sheath extensions (BSEs) in Juglans microcarpa led to higher fluorescence in the spongy and in proximity to the BSEs. Both species exhibited drought-induced reductions in mesophyll cell volume, yet the associated increases in porosity and g_IAS were obscured by declines in biochemical activity that decreased g_m . Inherent differences in leaf anatomy between the species were linked to differences in gas exchange, light absorption and photosynthetic capacity, and drought-induced changes in leaf structure impacted performance via imposing species-specific limitations to light absorption, gas exchange and hydraulics.

Remote sensing of cytotype and its consequences for canopy damage in quaking aspen

Mapping geographic mosaics of genetic variation and their consequences via genotype x environment interactions at large extents and high resolution has been limited by the scalability of DNA sequencing. Here, we address this challenge for cytotype (chromosome copy number) variation in quaking aspen, a drought-impacted foundation tree species. We integrate airborne imaging spectroscopy data with ground-based DNA sequencing data and canopy damage data in 391 km² of southwestern Colorado. We show that (1) aspen cover and cytotype can be remotely sensed at 1 m spatial resolution, (2) the geographic mosaic of cytotypes is heterogeneous and interdigitated, (3) triploids have higher leaf nitrogen, canopy water content, and carbon isotope shifts (δ¹³ C) than diploids, and (4) canopy damage varies among cytotypes and depends on interactions with topography, canopy height, and trait variables. Triploids are at higher risk in hotter and drier conditions.

A comparative study on the leaf anatomical structure of Camellia oleifera in a low-hot valley area in Guizhou Province, China

The leaf serves as an important assimilation organ of plants, and the anatomical structure of leaves can reflect the adaptability of the plant to the environment to a certain extent. The current study aimed to cultivate superior local cultivars, and 35 healthy individual plants were selected from the Camellia oleifera germplasm resource nursery for a comparative study of the leaf structure. In July 2019, the leaves were collected from 35 selected healthy C. oleifera plants, and the leaf structure was observed by using the paraffin section method. Healthy individual plants were screened using variance analysis, correlation analysis and cluster analysis. The representative indices were selected according to the cluster membership, correlation indices and coefficient of variation (C/V) for a comprehensive evaluation of drought resistance via the membership function. There were extremely significant differences in 11 indices of leaf structure for these 35 healthy plants. C18 had the greatest leaf thickness, C7 the largest spongy tissue, and C38 the largest ratio of palisade tissue thickness to spongy tissue thickness (P/S). The clustering results of the healthy individual plants differed significantly. The membership function showed that the drought resistance of 35 C. oleifera plants was divided into five categories. C18 had very strong drought resistance, and C3, C7 and C40 had strong drought resistance. There were significant differences in terms of the upper epidermis, P/S ratio and spongy tissue among the C. oleifera plants. C18, C3, C7 and C40 exhibited satisfactory drought resistance. Although C39 and C26 had moderate drought resistance, their P/S ratios were high, which might be used to cultivate high-yield and drought-resistant C. oleifera varieties. The leaf P/S ratio of C. oleifera from low-hot valley areas was high. Among various leaf structures, spongy tissue, upper epidermis, P/S ratio and cuticle constitute the drought resistance evaluation indices for C. oleifera grown in low-hot valley areas.

Fifteen compelling open questions in plant cell biology

As scientists, we are at least as excited about the open questions-the things we do not know-as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such "rules" conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.

The three-dimensional construction of leaves is coordinated with water use efficiency in conifers

Conifers prevail in the canopies of many terrestrial biomes, holding a great ecological and economic importance globally. Current increases in temperature and aridity are imposing high transpirational demands and resulting in conifer mortality. Therefore, identifying leaf structural determinants of water use efficiency is essential for predicting physiological impacts due to environmental variation. Using synchrotron-generated microtomography imaging, we extracted leaf volumetric anatomy and stomatal traits in 34 species across conifers with a special focus on Pinus, the richest conifer genus. We show that intrinsic water use efficiency (WUE_i ) is positively driven by leaf vein volume. Needle-like leaves of Pinus, as opposed to flat leaves or flattened needles of other genera, showed lower mesophyll porosity, decreasing the relative mesophyll volume. This led to increased ratios of stomatal pore number per mesophyll or intercellular airspace volume, which emerged as powerful explanatory variables, predicting both stomatal conductance and WUE_i . Our results clarify how the three-dimensional organisation of tissues within the leaf has a direct impact on plant water use and carbon uptake. By identifying a suite of structural traits that influence important physiological functions, our findings can help to understand how conifers may respond to the pressures exerted by climate change.

Early spring flowers rely on xylem hydration but are not limited by stem xylem conductivity

Many woody plants produce large floral displays early in the spring when xylem transport can be variable and often reduced. To determine whether stem hydraulics impact floral water use, we quantified floral transpiration and tested whether it was correlated with stem xylem conductivity in five temperate woody species that flower before producing leaves. We measured inflorescence gas exchange, examined the relationship between diffusive conductance and inflorescence morphology, and estimated the amount of water supplied to an inflorescence by the phloem. We also tested for correlation between transpiration and native stem xylem conductivity for branches with leaves and branches with flowers. The flowers of our study species obtain most of their water from the xylem. Diffusive conductance was higher in small inflorescences, but water content and daily transpiration rates were greater for larger inflorescences. We found no correlation between floral transpiration per branch and stem xylem conductivity within species. The data suggest that inflorescence water loss during anthesis is not limited by the xylem in our study species. We highlight the impact of floral morphology on hydraulic traits and encourage exploration into temporal shifts in floral hydration.

Genome Size and Labellum Epidermal Cell Size Are Evolutionarily Correlated With Floral Longevity in Paphiopedilum Species

Genome size is known to influence phenotypic traits in leaves and seeds. Although genome size is closely related to cellular and developmental traits across biological kingdoms, floral longevity is a floral trait with important fitness consequence, but less is known about the link between floral longevity and sizes of genomes and cells. In this study, we examined evolutionary coordination between genome size, floral longevity, and epidermal cell size in flowers and leaves in 13 Paphiopedilum species. We found that, across all the study species, the genome size was positively correlated with floral longevity but negatively associated with labellum epidermal cell size, and a negative relationship was found between floral longevity and labellum epidermal cell size. This suggested that genome size is potentially correlated with floral longevity, and genome size has an important impact on life-history trait. In addition, genome size was positively correlated with leaf epidermal cell size, which was different from the relationship in flower due to different selective pressures they experienced or different functions they performed. Therefore, genome size constraints floral longevity, and it is a strong predictor of cell size. The impact of genome size on reproduction might have more implications for the evolution of flowering plants and pollination ecology.

Exploring environmental selection on genome size in angiosperms

Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO₂-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.

Reintegrating Biology Through the Nexus of Energy, Information, and Matter

Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that comprise this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, and matter can provide a common currency that helps link phenomena across levels of biological organization. The propagation of energy and information through levels of biological organization can result in emergent properties and system-wide changes that impact other hierarchical levels. Deeper consideration of measured imbalances in energy, information, and matter can help researchers identify key factors that influence system function at one scale, highlighting avenues to link phenomena across levels of biological organization and develop predictive models of biological systems.

Understanding airspace in leaves: 3D anatomy and directional tortuosity

The leaf intercellular airspace is a tortuous environment consisting of cells of different shapes, packing densities, and orientation, all of which have an effect on the travelling distance of molecules from the stomata to the mesophyll cell surfaces. Tortuosity, the increase in displacement over the actual distance between two points, is typically defined as encompassing the whole leaf airspace, but heterogeneity in pore dimensions and orientation between the spongy and palisade mesophyll likely result in heterogeneity in tortuosity along different axes and would predict longer traveling distance along the path of least tortuosity, such as vertically within the columnar cell matrix of the palisade layer. Here, we compare a previously established geometric method to a random walk approach, novel for this analysis in plant leaves, in four different Eucalyptus species. The random walk method allowed us to quantify directional tortuosity across the whole leaf profile, and separately for the spongy and palisade mesophyll. For all species tortuosity was higher in the palisade mesophyll than the spongy mesophyll and horizontal (parallel to the epidermis) tortuosity was consistently higher than vertical (from epidermis to epidermis) tortuosity. We demonstrate that a random walk approach improves on previous geometric approaches and is valuable for investigating CO₂ and H₂ O transport within leaves.

The Optical Properties of Leaf Structural Elements and Their Contribution to Photosynthetic Performance and Photoprotection

Leaves have evolved to effectively harvest light, and, in parallel, to balance photosynthetic CO2 assimilation with water losses. At times, leaves must operate under light limiting conditions while at other instances (temporally distant or even within seconds), the same leaves must modulate light capture to avoid photoinhibition and achieve a uniform internal light gradient. The light-harvesting capacity and the photosynthetic performance of a given leaf are both determined by the organization and the properties of its structural elements, with some of these having evolved as adaptations to stressful environments. In this respect, the present review focuses on the optical roles of particular leaf structural elements (the light capture module) while integrating their involvement in other important functional modules. Superficial leaf tissues (epidermis including cuticle) and structures (epidermal appendages such as trichomes) play a crucial role against light interception. The epidermis, together with the cuticle, behaves as a reflector, as a selective UV filter and, in some cases, each epidermal cell acts as a lens focusing light to the interior. Non glandular trichomes reflect a considerable part of the solar radiation and absorb mainly in the UV spectral band. Mesophyll photosynthetic tissues and biominerals are involved in the efficient propagation of light within the mesophyll. Bundle sheath extensions and sclereids transfer light to internal layers of the mesophyll, particularly important in thick and compact leaves or in leaves with a flutter habit. All of the aforementioned structural elements have been typically optimized during evolution for multiple functions, thus offering adaptive advantages in challenging environments. Hence, each particular leaf design incorporates suitable optical traits advantageously and cost-effectively with the other fundamental functions of the leaf.