A Perspective on Plant Phenomics: Coupling Deep Learning and Near-Infrared Spectroscopy

The trait-based approach in plant ecology aims at understanding and classifying the diversity of ecological strategies by comparing plant morphology and physiology across organisms. The major drawback of the approach is that the time and financial cost of measuring the traits on many individuals and environments can be prohibitive. We show that combining near-infrared spectroscopy (NIRS) with deep learning resolves this limitation by quickly, non-destructively, and accurately measuring a suite of traits, including plant morphology, chemistry, and metabolism. Such an approach also allows to position plants within the well-known CSR triangle that depicts the diversity of plant ecological strategies. The processing of NIRS through deep learning identifies the effect of growth conditions on trait values, an issue that plagues traditional statistical approaches. Together, the coupling of NIRS and deep learning is a promising high-throughput approach to capture a range of ecological information on plant diversity and functioning and can accelerate the creation of extensive trait databases.

Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana?

BACKGROUND AND AIMS

Determining within-species large-scale variation in phenotypic traits is central to elucidate the drivers of species' ranges. Intraspecific comparisons offer the opportunity to understand how trade-offs and biogeographical history constrain adaptation to contrasted environmental conditions. Here we test whether functional traits, ecological strategies from the CSR scheme and phenotypic plasticity in response to abiotic stress vary along a latitudinal or a center- margins gradient within the native range of Arabidopsis thaliana.

METHODS

We experimentally examined the phenotypic outcomes of plant adaptation at the center and margins of its geographic range using 30 accessions from southern, central and northern Europe. We characterized the variation of traits related to stress tolerance, resource use, colonization ability, CSR strategy scores, survival and fecundity in response to high temperature (34 °C) or frost (- 6 °C), combined with a water deficit treatment.

KEY RESULTS

We found evidence for both a latitudinal and a center-margins differentiation for the traits under scrutiny. Age at maturity, leaf dry matter content, specific leaf area and leaf nitrogen content varied along a latitudinal gradient. Northern accessions presented a greater survival to stress than central and southern accessions. Leaf area, C-scores, R-scores and fruit number followed a center-margins differentiation. Central accessions displayed a higher phenotypic plasticity than northern and southern accessions for most studied traits.

CONCLUSIONS

Traits related to an acquisitive/conservative resource-use trade-off followed a latitudinal gradient. Traits associated with a competition/colonization trade-off differentiated along the historic colonization of the distribution range and then followed a center-margins differentiation. Our findings pinpoint the need to consider the joint effect of evolutionary history and environmental factors when examining phenotypic variation across the distribution range of a species.

A Detailed Investigation of the Onion Structure of Exchanged Coupled Magnetic Fe3-δO4@CoFe2O4@Fe3-δO4 Nanoparticles

Nanoparticles that combine several magnetic phases offer wide perspectives for cutting edge applications because of the high modularity of their magnetic properties. Besides the addition of the magnetic characteristics intrinsic to each phase, the interface that results from core-shell and, further, from onion structures leads to synergistic properties such as magnetic exchange coupling. Such a phenomenon is of high interest to overcome the superparamagnetic limit of iron oxide nanoparticles which hampers potential applications such as data storage or sensors. In this manuscript, we report on the design of nanoparticles with an onion-like structure which has been scarcely reported yet. These nanoparticles consist of a Fe_3-δO₄ core covered by a first shell of CoFe₂O₄ and a second shell of Fe_3-δO₄, e.g., a Fe_3-δO₄@CoFe₂O₄@Fe_3-δO₄ onion-like structure. They were synthesized through a multistep seed-mediated growth approach which consists consists in performing three successive thermal decomposition of metal complexes in a high-boiling-point solvent (about 300 °C). Although TEM micrographs clearly show the growth of each shell from the iron oxide core, core sizes and shell thicknesses markedly differ from what is suggested by the size increasing. We investigated very precisely the structure of nanoparticles in performing high resolution (scanning) TEM imaging and geometrical phase analysis (GPA). The chemical composition and spatial distribution of atoms were studied by electron energy loss spectroscopy (EELS) mapping and spectroscopy. The chemical environment and oxidation state of cations were investigated by ⁵⁷Fe Mössbauer spectrometry, soft X-ray absorption spectroscopy (XAS) and X-ray magnetic circular dichroism (XMCD). The combination of these techniques allowed us to estimate the increase of Fe²⁺ content in the iron oxide core of the core@shell structure and the increase of the cobalt ferrite shell thickness in the core@shell@shell one, whereas the iron oxide shell appears to be much thinner than expected. Thus, the modification of the chemical composition as well as the size of the Fe_3-δO₄ core and the thickness of the cobalt ferrite shell have a high impact on the magnetic properties. Furthermore, the growth of the iron oxide shell also markedly modifies the magnetic properties of the core-shell nanoparticles, thus demonstrating the high potential of onion-like nanoparticles to accurately tune the magnetic properties of nanoparticles according to the desired applications.

PhenoSpace: A Shiny application to visualize trait data in the phenotypic space of the global spectrum of plant form and function

A recent analysis of variation in six major traits conducted on a large worldwide sample of vascular plant species showed that three-quarters of trait variation was captured by a two-dimensional global spectrum of plant form and function ("global spectrum" hereafter). We developed the PhenoSpace application, whose aim is to visualize and export the position of any individual/population/species in the phenotypic space of the global spectrum.PhenoSpace is a Shiny application that helps users to manipulate and visualize data pertaining to the global spectrum of plant form and function. It is freely accessible at the following URL: https://shiny.cefe.cnrs.fr/PhenoSpace/.PhenoSpace has three main functionalities. First, it allows users to visualize the phenotypic space of the global spectrum using different combinations of traits and growth forms. Second, trait data from any new user-defined dataset can be projected onto the phenotypic space of the global spectrum, provided that at least two of the six traits are available. Finally, figures produced and loadings of the imported data on the PCA axes can be downloaded, allowing users to conduct further analyses.PhenoSpace fulfills the practical goal of positioning plants in the phenotypic space of the global spectrum, making it possible to compare trait variation at any level of organization against the worldwide background. This serves a major aim of comparative plant ecology, which is to put specific sets of individuals, populations or species into a broader context, facilitating comparison and synthesis of results across different continents and environments using relevant indicators of plant design and function.

Highly chelating stellate mesoporous silica nanoparticles for specific iron removal from biological media

In this work, the design of a new generation of functionalized large pore silica nanoparticles is addressed for the specific removal of iron from biological environments. Herein, mesoporous silica with a large pore stellate morphology, denoted STMS, were grafted with the highly specific iron chelating agent desferrioxamine B, DFoB. The challenge of this work was the step by step elaboration of the nanoplatform and the evaluation of its chelating efficiency and selectivity. Hence, the controlled covalent grafting of DFoB specific iron chelator, was successfully achieved ensuring a high grafting rate of chelating ligand of 730 nmol·mg^-1 (i.e., 0.85 ligand·nm^-2). Furthermore, these highly chelating STMS silica were able to capture iron(III) stabilized with nitrilotriacetic acid (NTA) in solution at physiological pH with a fast kinetics (less than 30 min). For a stoichiometry 0.85:1 (FeNTA : DFoB), the STMS-DFoB nanoparticles allowed reaching capture capacity and efficiency of 480 nmolFe³⁺/mg SiO₂ and 78%, respectively. Regarding the selectivity features of the removal process, studies were performed with two different media composed of various metal ions: (i) an equimolar solution of various metal cations and (ii) a Barth's buffer mimicking the brain solution composition. In both cases, the chelating STMS-DFoB showed a high selectivity for iron versus other ions at the same (Al³⁺) or different valency (Na⁺, K⁺…). Finally, this work paves the way for new nanosystems for metal overload treatments as well as for future highly chelating nanoplatforms that can be used at the interface between depollution and nanomedecine.

Trait differentiation between native and introduced populations of the invasive plant Sonchus oleraceus L. (Asteraceae)

There is growing evidence that rapid adaptation to novel environments drives successful establishment and spread of invasive plant species. However, the mechanisms driving trait adaptation, such as selection pressure from novel climate niche envelopes, remain poorly tested at global scales. In this study, we investigated differences in 20 traits (relating to growth, resource acquisition, reproduction, phenology and defence) amongst 14 populations of the herbaceous plant Sonchus oleraceus L. (Asteraceae) across its native (Europe and North Africa) and introduced (Australia and New Zealand) ranges. We compared traits amongst populations grown under standard glasshouse conditions. Introduced S. oleraceus plants seemed to outperform native plants, i.e. possessing higher leaf and stem dry matter content, greater number of leaves and were taller at first flowering stage. Although introduced plants produced fewer seeds, they had a higher germination rate than native plants. We found strong evidence for adaptation along temperature and precipitation gradients for several traits (e.g. shoot height, biomass, leaf and stem dry matter contents increased with minimum temperatures, while germination rate decreased with annual precipitations and temperatures), which suggests that similar selective forces shape populations in both the native and invaded ranges. We detected significant shifts in the relationships (i.e. trade-offs) (i) between plant height and flowering time and (ii) between leaf-stem biomass and grain yield between native and introduced plants, indicating that invasion was associated with changes to life-history dynamics that may confer competitive advantages over native vegetation. Specifically, we found that, at first flowering, introduced plants tended to be taller than native ones and that investment in leaf and stem biomass was greater in introduced than in native plants for equivalent levels of grain yield. Our study has demonstrated that climatic conditions may drive rapid adaption to novel environments in invasive plant species.

Secondary metabolites have more influence than morphophysiological traits on litter decomposability across genotypes of Arabidopsis thaliana

Although interspecific variation in plant phenotype is recognised to impact afterlife processes such as litter decomposability, it is still unclear which traits and selection pressures explain these relationships. Examining intraspecific variation is crucial to identify and compare trait effects on decomposability, and investigate the potential role of natural selection. We studied the genetic variability and relationships between decomposability, plant traits typically related to decomposability at species level (morphophysiological traits), and leaf metabolites among a set of genotypes of Arabidopsis thaliana grown under controlled conditions. We also investigated correlations between decomposability and environmental variables at genotypes collection site. We investigated the genetic architecture of decomposability with genome-wide association studies (GWAS). There was large genetic variability in decomposability that was correlated with precipitation. Morphophysiological traits had a minor effect, while secondary metabolites, especially glucosinolates, were correlated with decomposability. Consistently, GWAS suggested that genes and metabolites related to the composition of cell membranes and envelopes control the variation of decomposability across genotypes. Our study suggests that decomposability varies within species as a result of metabolic adaptation to climate. Our findings highlight that subtle variations of defence-related metabolites like glucosinolates may strongly influence after-life processes such as decomposability.

Leaf economics and slow-fast adaptation across the geographic range of Arabidopsis thaliana

Life history strategies of most organisms are constrained by resource allocation patterns that follow a 'slow-fast continuum'. It opposes slow growing and long-lived organisms with late investment in reproduction to those that grow faster, have earlier and larger reproductive effort and a short longevity. In plants, the Leaf Economics Spectrum (LES) depicts a leaf-level trade-off between the rate of carbon assimilation and leaf lifespan, as stressed in functional ecology from interspecific comparative studies. However, it is still unclear how the LES is connected to the slow-fast syndrome. Interspecific comparisons also impede a deep exploration of the linkage between LES variation and adaptation to climate. Here, we measured growth, morpho-physiological and life-history traits, at both the leaf and whole-plant levels, in 378 natural accessions of Arabidopsis thaliana. We found that the LES is tightly linked to variation in whole-plant functioning, and aligns with the slow-fast continuum. A genetic analysis further suggested that phenotypic differentiation results from the selection of different slow-fast strategies in contrasted climates. Slow growing and long-lived plants were preferentially found in cold and arid habitats while fast growing and short-lived ones in more favorable habitats. Our findings shed light on the role of the slow-fast continuum for plant adaptation to climate. More broadly, they encourage future studies to bridge functional ecology, genetics and evolutionary biology to improve our understanding of plant adaptation to environmental changes.

Strong interfacial coupling through exchange interactions in soft/hard core-shell nanoparticles as a function of cationic distribution

Exchange coupled core-shell nanoparticles present high potential to tune adequately the magnetic properties for specific applications such as nanomedicine or spintronics. Here, we report on the design of core-shell nanoparticles by performing the successive thermal decomposition of Fe and Co complexes. Depending on the thermal stability and the concentration of the Co precursor, we were able to control the formation of a hard ferrimagnetic (FiM) Co-ferrite shell or an antiferromagnetic (AFM) CoO shell at the surface of a soft FiM Fe3-δO4 core. The formation of the Co-ferrite shell was also found to occur through two different mechanisms: the diffusion of Co or the growth at the iron oxide surface. The structural properties of core-shell nanoparticles were investigated by a wide panel of techniques such as HAADF, STEM and XRD. The distribution of Fe and Co elements in the crystal structure was described accurately by XAS and XMCD. The operating conditions influenced significantly the oxidation rate of Fe2+ in the core as well as the occupancy of Oh sites by Fe2+ and Co2+ cations. The structural properties of nanoparticles were correlated with their magnetic properties which were investigated by SQUID magnetometry. Each core-shell nanoparticle displayed enhanced effective magnetic anisotropy energy (Eeff) in comparison with pristine Fe3-δO4 nanoparticles because of magnetic coupling at the core-shell interface. The Co-ferrite FiM shells resulted in better enhancement of Eeff than a CoO AFM shell. In addition, the magnetic properties were also influenced by the core size. The coercive field (HC) was increased by core reduction while the blocking temperature (TB) was increased by a larger core. Element-specific XMCD measurements showed the fine coupling of Fe and Co cations which agree with Co-ferrite in each sample, e.g. the formation of a Co-doped interfacial layer in the Fe3-δO4@CoO nanoparticles.

Room Temperature Blocked Magnetic Nanoparticles Based on Ferrite Promoted by a Three-Step Thermal Decomposition Process

Exchange coupled nanoparticles that combine hard and soft magnetic phases are very promising to enhance the effective magnetic anisotropy while preserving sizes below 20 nm. However, the core-shell structure is usually insufficient to produce rare earth-free ferro(i)magnetic blocked nanoparticles at room temperature. We report on onion-type magnetic nanoparticles prepared by a three-step seed mediated growth based on the thermal decomposition method. The core@shell@shell structure consists of a core and an external shell of Fe_3-δO₄ separated by an intermediate Co-doped ferrite shell. The double exchange coupling at both core@shell and shell@shell interfaces results in such an increased of the magnetic anisotropy energy, that onion-type nanoparticles of 16 nm mainly based on iron oxide are blocked at room temperature. We envision that these results are very appealing for potential applications based on permanent magnets.

Climate as a driver of adaptive variations in ecological strategies in Arabidopsis thaliana

BACKGROUND AND AIMS

The CSR classification categorizes plants as stress tolerators (S), ruderals (R) and competitors (C). Initially proposed as a general framework to describe ecological strategies across species, this scheme has recently been used to investigate the variation of strategies within species. For instance, ample variation along the S-R axis was found in Arabidopsis thaliana, with stress-tolerator accessions predominating in hot and dry regions, which was interpreted as a sign of functional adaptation to climate within the species.

METHODS

In this study the range of CSR strategies within A. thaliana was evaluated across 426 accessions originating from North Africa to Scandinavia. A position in the CSR strategy space was allocated for every accession based on three functional traits: leaf area, leaf dry matter content (LDMC) and specific leaf area (SLA). Results were related to climate at origin and compared with a previous study performed on the same species. Furthermore, the role of natural selection in phenotypic differentiation between lineages was investigated with QST-FST comparisons, using the large amount of genetic information available for this species.

KEY RESULTS

Substantial variation in ecological strategies along the S-R axis was found in A. thaliana. By contrast with previous findings, stress-tolerator accessions predominated in cold climates, notably Scandinavia, where late flowering was associated with traits related to resource conservation, such as high LDMC and low SLA. Because of trait plasticity, variations in CSR classification in relation to growth conditions were also observed for the same genotypes.

CONCLUSIONS

There is a latitudinal gradient of ecological strategies in A. thaliana as a result of within-species adaptation to climate. Our study also underlines the importance of growth conditions and of the methodology used for trait measurement, notably age versus stage measurement, to infer the strength and direction of trait-environment relationships. This highlights the potential and limitations of the CSR classification in explaining functional adaptation to the environment.

Asymmetric evolutionary responses to sex-specific selection in a hermaphrodite

Sex allocation theory predicts that simultaneous hermaphrodites evolve to an evolutionary stable resource allocation, whereby any increase in investment to male reproduction leads to a disproportionate cost on female reproduction and vice versa. However, empirical evidence for sexual trade-offs in hermaphroditic animals is still limited. Here, we tested how male and female reproductive traits evolved under conditions of reduced selection on either male or female reproduction for 40 generations in a hermaphroditic snail. This selection favors a reinvestment of resources from the sex function under relaxed selection toward the other function. We found no such evolutionary response. Instead, juvenile survival and male reproductive success significantly decreased in lines where selection on the male function (i.e., sexual selection) was relaxed, while relaxing selection on the female function had no effect. Our results suggest that most polymorphisms under selection in these lines were not sex-antagonistic. Rather, they were deleterious mutations affecting juvenile survival (thus reducing both male and female fitness) with strong pleiotropic effects on male success in a sexual selection context. These mutations accumulated when sexual selection was relaxed, which supports the idea that sexual selection in hermaphrodites contributes to purge the mutation load from the genome as in separate-sex organisms.