Visual plant anatomy: From science to education and vice versa.

Plant biology, mainly plant anatomy, is a less attractive area for students at high school and university, but not much research has been devoted to improve this field. We therefore researched into the teaching of root, stem and leaf anatomy combined with the preparation of native microscopic slides and histochemical reaction using two selected dyes (classic phloroglucinol test combined with textile dye 'Duha green' to visualize xylem and phloem, respectively). The use of reagents in teaching had a positive effect on students' knowledge (control/ experimental class) of root (+70%), stem (+70%) and leaf anatomy (+130%) as well as vascular and mechanical tissues (+170%), leading to an overall improvement of knowledge by ca. 100%. Students' ability to identify individual tissues on microscopic slides increased and they also understood the functions of individual tissues after self-preparing and staining slides. However, we identified that some aspects were still problematic for students after the experimental education (e.g. identification of tissue providing secondary growth, significance of sclerenchyma and transpiration). We also attach correct answers for the anatomy test and worksheets used for practical exercises as motivation for wider use to improve students' knowledge of plant anatomy.

Enigmatic fossil plants with three-dimensional, arborescent-growth architecture from the earliest Carboniferous of New Brunswick, Canada.

The evolution of arborescence in Devonian plants, followed by their architectural radiation in the Carboniferous, is a transition fundamental to Earth-system processes and ecological development. However, this evolutionary transition in trees is based on preserved trunks, of which only a few known specimens possess crowns. We describe Mississippian-aged (Tournaisian) trees with a unique three-dimensional crown morphology from New Brunswick, Canada. The trees were preserved by earthquake-induced, catastrophic burial of lake-margin vegetation. The tree architecture consists of an unbranched, 16-cm-diameter trunk with compound leaves arranged in spirals of ∼13 and compressed into ∼14 cm of vertical trunk length. Compound leaves in the upper ∼0.75 m of the trunk measure >1.75 m in length and preserve alternately arranged secondary laterals beginning at 0.5 m from the trunk; the area below the trunk bears only persistent leaf bases. The principal specimen lacks either apical or basal sections, although an apex is preserved in another. Apically, the leaves become less relaxed toward horizontal and are borne straight at an acute angle at the crown. The compact leaf organization and leaf length created a crown volume of >20-30 m3. This growth strategy likely maximized light interception and reduced resource competition from groundcover. From their growth morphology, canopy size, and volume, we propose that these fossils represent the earliest evidence of arborescent subcanopy-tiering. Moreover, although systematically unresolved, this specimen shows that Early Carboniferous vegetation was more complex than realized, signaling that it was a time of experimental, possibly transitional and varied, growth architectures.

Directional epistasis is common in morphological divergence.

Epistasis is often portrayed as unimportant in evolution. While random patterns of epistasis may have limited effects on the response to selection, systematic directional epistasis can have substantial effects on evolutionary dynamics. Directional epistasis occurs when allele substitutions that change a trait also modify the effects of allele substitution at other loci in a systematic direction. In this case, trait evolution may induce correlated changes in allelic effects and additive genetic variance (evolvability) that modify further evolution. Although theory thus suggests a potentially important role for directional epistasis in evolution, we still lack empirical evidence about its prevalence and magnitude. Using a new framework to estimate systematic patterns of epistasis from line-crosses experiments, we quantify its effects on 197 size-related traits from diverging natural populations in 24 animal and 17 plant species. We show that directional epistasis is common and tends to become stronger with increasing morphological divergence. In animals, most traits displayed negative directionality toward larger size, suggesting that epistatic constraints reducing evolvability toward larger size. Dominance was also common but did not systematically alter the effects of epistasis.

Why incorporate plant architecture into trait-based ecology?

Trait-based ecology has improved our understanding of the functioning of organisms, communities, ecosystems, and beyond. However, its predictive ability remains limited as long as phenotypic integration and temporal dynamics are not considered. We highlight how the morphogenetic processes that shape the 3D development of a plant during its lifetime affect its performance. We show that the diversity of architectural traits allows us to go beyond organ-level traits in capturing the temporal and spatial dimensions of ecological niches and informing community assembly processes. Overall, we argue that consideration of multilevel topological, geometrical, and ontogenetic features provides a dynamic view of the whole-plant phenotype and a relevant framework for investigating phenotypic integration, plant adaptation and performance, and community structure and dynamics.

OPIA: an open archive of plant images and related phenotypic traits.

High-throughput plant phenotype acquisition technologies have been extensively utilized in plant phenomics studies, leading to vast quantities of images and image-based phenotypic traits (i-traits) that are critically essential for accelerating germplasm screening, plant diseases identification and biotic & abiotic stress classification. Here, we present the Open Plant Image Archive (OPIA, https://ngdc.cncb.ac.cn/opia/), an open archive of plant images and i-traits derived from high-throughput phenotyping platforms. Currently, OPIA houses 56 datasets across 11 plants, comprising a total of 566 225 images with 2 417 186 labeled instances. Notably, it incorporates 56 i-traits of 93 rice and 105 wheat cultivars based on 18 644 individual RGB images, and these i-traits are further annotated based on the Plant Phenotype and Trait Ontology (PPTO) and cross-linked with GWAS Atlas. Additionally, each dataset in OPIA is assigned an evaluation score that takes account of image data volume, image resolution, and the number of labeled instances. More importantly, OPIA is equipped with useful tools for online image pre-processing and intelligent prediction. Collectively, OPIA provides open access to valuable datasets, pre-trained models, and phenotypic traits across diverse plants and thus bears great potential to play a crucial role in facilitating artificial intelligence-assisted breeding research.

Diversity patterns of vascular and non-vascular epiphytes along tropical dry forest / Patrones de diversidad de epífitas vasculares y no vasculares a lo largo del bosque seco tropical

Abstract Introduction: Epiphytes (vascular and non-vascular) are one of the most diverse groups in the Neotropics, but despite their importance in the functioning of many ecosystems, much of their taxonomy and ecology is still unknown in the dry forest of Colombia. Objective: To compare the diversity patterns and species composition of vascular and non-vascular epiphytes along tropical dry forest remnants of Cauca Valley, Colombia. Methods: Ten permanent plots (50 x 20 m2) were established in tropical dry forest remnants. The epiphytes were sampled in 40-50 trees per plot. Alpha and gamma diversity were calculated using the richness (q0) and Shannon index (q1) (alpha was estimated as the average for phorophytes). Beta diversity was measured using the Whitaker index. To evaluate the relationship between diversities and environmental variables, GLM analysis was used. Results: We found 50 morphospecies of vascular epiphytes, 77 of bryophytes and 290 of lichens. The 𝛼 and 𝛾 diversity of bryophytes from each remnant was significantly explained by temperature. The abundance of lichens per tree was significantly related with the DBH and tree height of each remnant. The 𝛼 diversity of vascular epiphytes shown can be explained by temperature and precipitation. The 𝛾 diversity was strongly influenced by the beta diversity in bryophytes and lichens. This pattern is because the sites with high disturbance present a lower diversity, as a consequence of a homogenizing effect, that is, a low turnover of species between sampling units. Conclusions: Precipitation and temperature affected the diversity of bryophytes and vascular epiphytes, while it did not show a relationship with the lichen's diversity, for which there is not a high congruence between the diversity and composition of these epiphytes.

Resumen Introducción: Los epífitos (vasculares y no vasculares) son uno de los más diversos grupos de plantas en el Neotrópico, pero a pesar de su importancia para el funcionamiento de varios ecosistemas, existen grandes vacíos en su conocimiento taxonómico y ecológico en el bosque seco de Colombia. Objetivo: Comparar los patrones de diversidad y composición de especies de epífitas vasculares y no vasculares a lo largo de remanentes de bosque seco tropical del Valle del Cauca, Colombia. Métodos: Se establecieron diez parcelas permanentes (50 x 20 m2) en remanentes de bosque seco tropical. Las epífitas se muestrearon en 40-50 árboles por parcela. La diversidad alfa y gamma se calculó utilizando la riqueza (q0) y el índice de Shannon (q1) (alfa se estimó como el promedio para los forófitos). La diversidad beta se midió utilizando el índice de Whitaker. Para evaluar la relación entre diversidades y variables ambientales se utilizó el análisis GLM. Resultados: Se encontraron 50 morfoespecies de epífitas vasculares, 77 de briófitas y 290 de líquenes. La diversidad de 𝛼 y 𝛾 de briófitas de cada remanente fue explicada significativamente por la temperatura. La abundancia de líquenes por árbol se relacionó significativamente con el DAP y la altura del árbol de cada remanente. La diversidad 𝛼 de epífitas vasculares que se muestra puede explicarse por la temperatura y la precipitación. La diversidad 𝛾 estuvo fuertemente influenciada por la diversidad beta en briófitas y líquenes. Este patrón se debe a que los sitios con alta perturbación presentan una menor diversidad, como consecuencia de un efecto homogeneizador, es decir, un bajo recambio de especies entre unidades de muestreo. Conclusiones: La precipitación y la temperatura afectaron la diversidad de briófitas y epífitas vasculares, mientras que no mostró relación con la diversidad de líquenes, por lo que no existe una alta congruencia entre la diversidad y composición de estas epífitas.

An integrated leaf trait analysis of two Paleogene leaf floras.

Objectives: This study presents the Integrated Leaf Trait Analysis (ILTA), a workflow for the combined application of methodologies in leaf trait and insect herbivory analyses on fossil dicot leaf assemblages. The objectives were (1) to record the leaf morphological variability, (2) to describe the herbivory pattern on fossil leaves, (3) to explore relations between leaf morphological trait combination types (TCTs), quantitative leaf traits, and other plant characteristics (e.g., phenology), and (4) to explore relations of leaf traits and insect herbivory. Material and Methods: The leaves of the early Oligocene floras Seifhennersdorf (Saxony, Germany) and Suletice-Berand (Ústí nad Labem Region, Czech Republic) were analyzed. The TCT approach was used to record the leaf morphological patterns. Metrics based on damage types on leaves were used to describe the kind and extent of insect herbivory. The leaf assemblages were characterized quantitatively (e.g., leaf area and leaf mass per area (LMA)) based on subsamples of 400 leaves per site. Multivariate analyses were performed to explore trait variations. Results: In Seifhennersdorf, toothed leaves of TCT F from deciduous fossil-species are most frequent. The flora of Suletice-Berand is dominated by evergreen fossil-species, which is reflected by the occurrence of toothed and untoothed leaves with closed secondary venation types (TCTs A or E). Significant differences are observed for mean leaf area and LMA, with larger leaves tending to lower LMA in Seifhennersdorf and smaller leaves tending to higher LMA in Suletice-Berand. The frequency and richness of damage types are significantly higher in Suletice-Berand than in Seifhennersdorf. In Seifhennersdorf, the evidence of damage types is highest on deciduous fossil-species, whereas it is highest on evergreen fossil-species in Suletice-Berand. Overall, insect herbivory tends to be more frequently to occur on toothed leaves (TCTs E, F, and P) that are of low LMA. The frequency, richness, and occurrence of damage types vary among fossil-species with similar phenology and TCT. In general, they are highest on leaves of abundant fossil-species. Discussion: TCTs reflect the diversity and abundance of leaf architectural types of fossil floras. Differences in TCT proportions and quantitative leaf traits may be consistent with local variations in the proportion of broad-leaved deciduous and evergreen elements in the ecotonal vegetation of the early Oligocene. A correlation between leaf size, LMA, and fossil-species indicates that trait variations are partly dependent on the taxonomic composition. Leaf morphology or TCTs itself cannot explain the difference in insect herbivory on leaves. It is a more complex relationship where leaf morphology, LMA, phenology, and taxonomic affiliation are crucial.

Are absorptive root traits good predictors of ecosystem functioning? A test in a natural temperate forest.

Trait-based approaches provide a useful framework to predict ecosystem functions under intensifying global change. However, our current understanding of trait-functioning relationships mainly relies on aboveground traits. Belowground traits (e.g. absorptive root traits) are rarely studied although these traits are related to important plant functions. We analyzed four pairs of analogous leaf and absorptive root traits of woody plants in a temperate forest and examined how these traits are coordinated at the community-level, and to what extent the trait covariation depends on local-scale environmental conditions. We then quantified the contributions of leaf and absorptive root traits and the environmental conditions in determining two important forest ecosystem functions, aboveground carbon storage, and woody biomass productivity. The results showed that both morphological trait pairs and chemical trait pairs exhibited positive correlations at the community level. Absorptive root traits show a strong response to environmental conditions compared to leaf traits. We also found that absorptive root traits were better predictors of the two forest ecosystem functions than leaf traits and environmental conditions. Our study confirms the important role of belowground traits in modulating ecosystem functions and deepens our understanding of belowground responses to changing environmental conditions.

Seeing clearly - Plant anatomy through Katherine Esau's microscopy lens.

Describing, naming and understanding the tissues and cell types composing biological organisms underpin myriad research endeavours in the biosciences. This is obvious when the organismal structure is a direct subject of the investigation such as in analyses of structure-function relationships. However, it also applies when structure represents the context. Gene expression networks and physiological processes cannot be divorced from the spatial and structural framework of the organs in which they operate. Atlases of anatomy and a precise vocabulary are therefore key tools on which modern scientific endeavours in the life sciences are based. One of the seminal authors whose books are familiar to nearly everyone in the plant biology community is Katherine Esau (1898-1997), a phenomenal plant anatomist and microscopist whose textbooks are still used daily around the world - 70 years after their first publication. Several technical innovations in microscopy have emerged since Esau's time and plant biological studies by authors who were trained using her books are shown side-by-side with Esau's drawings.

A direct comparison of ecological theories for predicting the relationship between plant traits and growth.

Despite long-standing theory for classifying plant ecological strategies, limited data directly link organismal traits to whole-plant growth rates (GRs). We compared trait-growth relationships based on three prominent theories: growth analysis, Grime's competitive-stress tolerant-ruderal (CSR) triangle, and the leaf economics spectrum (LES). Under these schemes, growth is hypothesized to be predicted by traits related to relative biomass investment, leaf structure, or gas exchange, respectively. We also considered traits not included in these theories but that might provide potential alternative best predictors of growth. In phylogenetic analyses of 30 diverse milkweeds (Asclepias spp.) and 21 morphological and physiological traits, GR (total biomass produced per day) varied 50-fold and was best predicted by biomass allocation to leaves (as predicted by growth analysis) and the CSR traits of leaf size and leaf dry matter content. Total leaf area (LA) and plant height were also excellent predictors of whole-plant GRs. Despite two LES traits correlating with growth (mass-based leaf nitrogen and area-based leaf phosphorus contents), these were in the opposite direction of that predicted by LES, such that higher N and P contents corresponded to slower growth. The remaining LES traits (e.g., leaf gas exchange) were not predictive of plant GRs. Overall, differences in GR were driven more by whole-plant characteristics such as biomass fractions and total LA than individual leaf-level traits such as photosynthetic rate or specific leaf area. Our results are most consistent with classical growth analysis-combining leaf traits with whole-plant allocation to best predict growth. However, given that destructive biomass measures are often not feasible, applying easy-to-measure leaf traits associated with the CSR classification appear more predictive of whole-plant growth than LES traits. Testing the generality of this result across additional taxa would further improve our ability to predict whole-plant growth from functional traits across scales.

The mechanics of plant morphogenesis.

Understanding the mechanism by which patterned gene activity leads to mechanical deformation of cells and tissues to create complex forms is a major challenge for developmental biology. Plants offer advantages for addressing this problem because their cells do not migrate or rearrange during morphogenesis, which simplifies analysis. We synthesize results from experimental analysis and computational modeling to show how mechanical interactions between cellulose fibers translate through wall, cell, and tissue levels to generate complex plant tissue shapes. Genes can modify mechanical properties and stresses at each level, though the values and pattern of stresses differ from one level to the next. The dynamic cellulose network provides elastic resistance to deformation while allowing growth through fiber sliding, which enables morphogenesis while maintaining mechanical strength.

Wireless Fixed Camera Network for Greenhouse-Based Plant Phenotyping.

An indoor wireless fixed camera network was developed for an efficient, cost-effective method of extracting informative plant phenotypes in a controlled greenhouse environment. Deployed at the Donald Danforth Plant Science Center (DDPSC), this fixed camera platform implements rapid and automated plant phenotyping. The platform uses low-cost Raspberry Pi computers and digital cameras to monitor aboveground morphological and developmental plant phenotypes. The Raspberry Pi is a readily programmable, credit card-sized computer board with remote accessibility. A standard camera module connects to the Raspberry Pi computer board and generates eight-megapixel resolution images. With a fixed array, or "bramble," of Raspberry Pi computer boards and camera modules placed strategically in a greenhouse, we can capture automated, high-resolution images for 3D reconstructions of individual plants on timescales ranging from minutes to hours, capturing temporal changes in plant phenotypes.

Estimation of Leaf Area Index with a Multi-Channel Spectral Micro-Sensor for Wireless Sensing Networks.

The leaf area index (LAI) is a key parameter in the context of monitoring the development of tree crowns and plants in general. As parameters such as carbon assimilation, environmental stress on carbon, and the water fluxes within tree canopies are correlated to the leaves surface, this parameter is essential for understanding and modeling ecological processes. However, its continuous monitoring using manual state-of-the-art measurement instruments is still challenging. To address this challenge, we present an innovative sensor concept to obtain the LAI based on the cheap and easy to integrate multi-channel spectral sensor AS7341. Additionally, we present a method for processing and filtering the gathered data, which enables very high accuracy measurements with an nRMSE of only 0.098, compared to the manually-operated state-of-the-art instrument LAI-2200C (LiCor). The sensor that is embedded on a sensor node has been tested in long-term experiments, proving its suitability for continuous deployment over an entire season. It permits the estimation of both the plant area index (PAI) and leaf area index (LAI) and provides the first wireless system that obtains the LAI solely powered by solar cells. Its energy autonomy and wireless connectivity make it suitable for a massive deployment over large areas and at different levels of the tree crown. It may be upgraded to allow the parallel measurement of photosynthetic active radiation (PAR) and light quality, relevant parameters for monitoring processes within tree canopies.

Towards 3D basic theories of plant forms.

Allometric, metabolic, and biomechanical theories are the critical foundations for scientifically deciphering plant forms. Their concrete laws, however, are found to deviate for plenty of plant specimens. This phenomenon has not been extensively studied, due to technical restrictions. This bottleneck now can be overcome by the state-of-the-art three-dimensional (3D) mapping technologies, such as fine-scale terrestrial laser scanning. On these grounds, we proposed to reexamine the basic theories regarding plant forms, and then, we case validated the feasibility of upgrading them into 3D modes. As an in-time enlightening of 3D revolutionizing the related basic subject, our theoretical prospect further sorted out the potential challenges as the cutting points for advancing its future exploration, which may enable 3D reconstruction of the basic theories of plant forms and even boost life science.

The enigmatic tropical alpine flora on the African sky islands is young, disturbed, and unsaturated.

Tropical alpine floras are renowned for high endemism, spectacular giant rosette plants testifying to convergent adaptation to harsh climates with nightly frosts, and recruitment dominated by long-distance dispersal from remote areas. In contrast to the larger, more recent (late Miocene onward) and contiguous expanses of tropical alpine habitat in South America, the tropical alpine flora in Africa is extremely fragmented across small patches on distant mountains of variable age (Oligocene onward). How this has affected the colonization and diversification history of the highly endemic but species-poor afroalpine flora is not well known. Here we infer phylogenetic relationships of ∼20% of its species using novel genome skimming data and published matrices and infer a timeframe for species origins in the afroalpine region using fossil-calibrated molecular clocks. Although some of the mountains are old, and although stem node ages may substantially predate colonization, most lineages appear to have colonized the afroalpine during the last 5 or 10 My. The accumulation of species increased exponentially toward the present. Taken together with recent reports of extremely low intrapopulation genetic diversity and recent intermountain population divergence, this points to a young, unsaturated, and dynamic island scenario. Habitat disturbance caused by the Pleistocene climate oscillations likely induced cycles of colonization, speciation, extinction, and recolonization. This study contributes to our understanding of differences in the histories of recruitment on different tropical sky islands and on oceanic islands, providing insight into the general processes shaping their remarkable floras.

Environmental variation drives the decoupling of leaf and root traits within species along an elevation gradient.

BACKGROUND AND AIMS: Plant performance is enhanced by balancing above- and below-ground resource uptake through the intraspecific adjustment of leaf and root traits. It is assumed that these organ adjustments are at least partly coordinated, so that analogous leaf and root traits broadly covary. Understanding the extent of such intraspecific leaf-root trait covariation would strongly contribute to our understanding of how plants match above- and below-ground resource use strategies as their environment changes, but comprehensive studies are lacking. METHODS: We measured analogous leaf and root traits from 11 species, as well as climate, soil and vegetation properties along a 1000-m elevation gradient in the French Alps. We determined how traits varied along the gradient, to what extent this variation was determined by the way different traits respond to environmental cues acting at different spatial scales (i.e. within and between elevations), and whether trait pairs covaried within species. KEY RESULTS: Leaf and root trait patterns strongly diverged: across the 11 species along the gradient, intraspecific leaf trait patterns were largely consistent, whereas root trait patterns were highly idiosyncratic. We also observed that, when compared with leaves, intraspecific variation was greater in root traits, due to the strong effects of the local environment (i.e. at the same elevation), while landscape-level effects (i.e. at different elevations) were minor. Overall, intraspecific trait correlations between analogous leaf and root traits were nearly absent. CONCLUSIONS: Our study suggests that environmental gradients at the landscape level, as well as local heterogeneity in soil properties, are the drivers of a strong decoupling between analogous leaf and root traits within species. This decoupling of plant resource acquisition strategies highlights how plants can exhibit diverse whole-plant acclimation strategies to modify above- and below-ground resource uptake, improving their resilience to environmental change.

Comparative root anatomy and root bud development after injury in two perennial herbs.

A bud bank is a pool of dormant meristems that enable plants to resprout after injury. While the bud bank on stem organs is established prior to injury as the stem grows, the bud bank on roots is considered at least partly formed as a response to disturbance events. To date, only woody species have been examined, and the establishment of reparative buds after injury without connection to the root vascular system has been confirmed; for herbs, no data are available. We tested whether root buds are formed spontaneously or induced after plant damage by studying root anatomy following plant injury in two congeneric perennial herbs. In a pot experiment with young plants of Inula britannica (root sprouter) and I. salicina (non-root sprouter), whole aboveground biomass was removed. Roots were sampled five times at 1-week intervals after disturbance events to evaluate bud occurrence and size, root and vessel diameters, sclerenchyma areas and carbohydrate storage. Compared to non-root-sprouting I. salicina, root-sprouting I. britannica presented more secondary thickening that was connected to adventitious bud formation and improved the root storage and transport capacity necessary for resprouting. Plant injury, in contrast to expectations, did not cause increased bud formation in I. britannica, and all buds were connected to the root vascular system. No root buds were observed in I. salicina. Our study implies that plants using bud banks on roots might depend on preformed buds. Comparative studies examining more species are needed to assess the generality of our findings.

The legacy of the extinct Neotropical megafauna on plants and biomes.

Large mammal herbivores are important drivers of plant evolution and vegetation patterns, but the extent to which plant trait and ecosystem geography currently reflect the historical distribution of extinct megafauna is unknown. We address this question for South and Central America (Neotropical biogeographic realm) by compiling data on plant defence traits, climate, soil, and fire, as well as on the historical distribution of extinct megafauna and extant mammal herbivores. We show that historical mammal herbivory, especially by extinct megafauna, and soil fertility explain substantial variability in wood density, leaf size, spines and latex. We also identified three distinct regions (''antiherbiomes''), differing in plant defences, environmental conditions, and megafauna history. These patterns largely matched those observed in African ecosystems, where abundant megafauna still roams, and suggest that some ecoregions experienced savanna-to-forest shifts following megafauna extinctions. Here, we show that extinct megafauna left a significant imprint on current ecosystem biogeography.