"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.

The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.

Multi-sensor spectral synergies for crop stress detection and monitoring in the optical domain: A review.

Remote detection and monitoring of the vegetation responses to stress became relevant for sustainable agriculture. Ongoing developments in optical remote sensing technologies have provided tools to increase our understanding of stress-related physiological processes. Therefore, this study aimed to provide an overview of the main spectral technologies and retrieval approaches for detecting crop stress in agriculture. Firstly, we present integrated views on: i) biotic and abiotic stress factors, the phases of stress, and respective plant responses, and ii) the affected traits, appropriate spectral domains and corresponding methods for measuring traits remotely. Secondly, representative results of a systematic literature analysis are highlighted, identifying the current status and possible future trends in stress detection and monitoring. Distinct plant responses occurring under shortterm, medium-term or severe chronic stress exposure can be captured with remote sensing due to specific light interaction processes, such as absorption and scattering manifested in the reflected radiance, i.e. visible (VIS), near infrared (NIR), shortwave infrared, and emitted radiance, i.e. solar-induced fluorescence and thermal infrared (TIR). From the analysis of 96 research papers, the following trends can be observed: increasing usage of satellite and unmanned aerial vehicle data in parallel with a shift in methods from simpler parametric approaches towards more advanced physically-based and hybrid models. Most study designs were largely driven by sensor availability and practical economic reasons, leading to the common usage of VIS-NIR-TIR sensor combinations. The majority of reviewed studies compared stress proxies calculated from single-source sensor domains rather than using data in a synergistic way. We identified new ways forward as guidance for improved synergistic usage of spectral domains for stress detection: (1) combined acquisition of data from multiple sensors for analysing multiple stress responses simultaneously (holistic view); (2) simultaneous retrieval of plant traits combining multi-domain radiative transfer models and machine learning methods; (3) assimilation of estimated plant traits from distinct spectral domains into integrated crop growth models. As a future outlook, we recommend combining multiple remote sensing data streams into crop model assimilation schemes to build up Digital Twins of agroecosystems, which may provide the most efficient way to detect the diversity of environmental and biotic stresses and thus enable respective management decisions.

Maximum fluorescence and electron transport kinetics determined by light-induced fluorescence transients (LIFT) for photosynthesis phenotyping.

Photosynthetic phenotyping requires quick characterization of dynamic traits when measuring large plant numbers in a fluctuating environment. Here, we evaluated the light-induced fluorescence transient (LIFT) method for its capacity to yield rapidly fluorometric parameters from 0.6 m distance. The close approximation of LIFT to conventional chlorophyll fluorescence (ChlF) parameters is shown under controlled conditions in spinach leaves and isolated thylakoids when electron transport was impaired by anoxic conditions or chemical inhibitors. The ChlF rise from minimum fluorescence (Fo) to maximum fluorescence induced by fast repetition rate (Fm-FRR) flashes was dominated by reduction of the primary electron acceptor in photosystem II (QA). The subsequent reoxidation of QA- was quantified using the relaxation of ChlF in 0.65 ms (Fr1) and 120 ms (Fr2) phases. Reoxidation efficiency of QA- (Fr1/Fv, where Fv = Fm-FRR - Fo) decreased when electron transport was impaired, while quantum efficiency of photosystem II (Fv/Fm) showed often no significant effect. ChlF relaxations of the LIFT were similar to an independent other method. Under increasing light intensities, Fr2'/Fq' (where Fr2' and Fq' represent Fr2 and Fv in the light-adapted state, respectively) was hardly affected, whereas the operating efficiency of photosystem II (Fq'/Fm') decreased due to non-photochemical quenching. Fm-FRR was significantly lower than the ChlF maximum induced by multiple turnover (Fm-MT) flashes. However, the resulting Fv/Fm and Fq'/Fm' from both flashes were highly correlated. The LIFT method complements Fv/Fm with information about efficiency of electron transport. Measurements in situ and from a distance facilitate application in high-throughput and automated phenotyping.

Pampered inside, pestered outside? Differences and similarities between plants growing in controlled conditions and in the field.

I. 839 II. 839 III. 841 IV. 845 V. 847 VI. 848 VII. 849 VIII. 851 851 852 References 852 Appendix A1 854 SUMMARY: Plant biologists often grow plants in growth chambers or glasshouses with the ultimate aim to understand or improve plant performance in the field. What is often overlooked is how results from controlled conditions translate back to field situations. A meta-analysis showed that lab-grown plants had faster growth rates, higher nitrogen concentrations and different morphology. They remained smaller, however, because the lab plants had grown for a much shorter time. We compared glasshouse and growth chamber conditions with those in the field and found that the ratio between the daily amount of light and daily temperature (photothermal ratio) was consistently lower under controlled conditions. This may strongly affect a plant's source : sink ratio and hence its overall morphology and physiology. Plants in the field also grow at higher plant densities. A second meta-analysis showed that a doubling in density leads on average to 34% smaller plants with strong negative effects on tiller or side-shoot formation but little effect on plant height. We found the r2 between lab and field phenotypic data to be rather modest (0.26). Based on these insights, we discuss various alternatives to facilitate the translation from lab results to the field, including several options to apply growth regimes closer to field conditions.

Impact of domestication on the phenotypic architecture of durum wheat under contrasting nitrogen fertilization.

The process of domestication has led to dramatic morphological and physiological changes in crop species due to adaptation to cultivation and to the needs of farmers. To investigate the phenotypic architecture of shoot- and root-related traits and quantify the impact of primary and secondary domestication, we examined a collection of 36 wheat genotypes under optimal and nitrogen-starvation conditions. These represented three taxa that correspond to key steps in the recent evolution of tetraploid wheat (i.e. wild emmer, emmer, and durum wheat). Overall, nitrogen starvation reduced the shoot growth of all genotypes, while it induced the opposite effect on root traits, quantified using the automated phenotyping platform GROWSCREEN-Rhizo. We observed an overall increase in all of the shoot and root growth traits from wild emmer to durum wheat, while emmer was generally very similar to wild emmer but intermediate between these two subspecies. While the differences in phenotypic diversity due to the effects of primary domestication were not significant, the secondary domestication transition from emmer to durum wheat was marked by a large and significant decrease in the coefficient of additive genetic variation. In particular, this reduction was very strong under the optimal condition and less intense under nitrogen starvation. Moreover, although under the optimal condition both root and shoot traits showed significantly reduced diversity due to secondary domestication, under nitrogen starvation the reduced diversity was significant only for shoot traits. Overall, a considerable amount of phenotypic variation was observed in wild emmer and emmer, which could be exploited for the development of pre-breeding strategies.

Pore size regulates operating stomatal conductance, while stomatal densities drive the partitioning of conductance between leaf sides.

BACKGROUND AND AIMS: Leaf gas exchange is influenced by stomatal size, density, distribution between the leaf adaxial and abaxial sides, as well as by pore dimensions. This study aims to quantify which of these traits mainly underlie genetic differences in operating stomatal conductance (gs) and addresses possible links between anatomical traits and regulation of pore width. METHODS: Stomatal responsiveness to desiccation, gs-related anatomical traits of each leaf side and estimated gs (based on these traits) were determined for 54 introgression lines (ILs) generated by introgressing segments of Solanum pennelli into the S. lycopersicum 'M82'. A quantitative trait locus (QTL) analysis for stomatal traits was also performed. KEY RESULTS: A wide genetic variation in stomatal responsiveness to desiccation was observed, a large part of which was explained by stomatal length. Operating gs ranged over a factor of five between ILs. The pore area per stomatal area varied 8-fold among ILs (2-16 %), and was the main determinant of differences in operating gs between ILs. Operating gs was primarily positioned on the abaxial surface (60-83 %), due to higher abaxial stomatal density and, secondarily, to larger abaxial pore area. An analysis revealed 64 QTLs for stomatal traits in the ILs, most of which were in the direction of S. pennellii. CONCLUSIONS: The data indicate that operating and maximum gs of non-stressed leaves maintained under stable conditions deviate considerably (by 45-91 %), because stomatal size inadequately reflects operating pore area (R(2) = 0·46). Furthermore, it was found that variation between ILs in both stomatal sensitivity to desiccation and operating gs is associated with features of individual stoma. In contrast, genotypic variation in gs partitioning depends on the distribution of stomata between the leaf adaxial and abaxial epidermis.

Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation.

We systematically analyzed a developmental gradient of the third maize (Zea mays) leaf from the point of emergence into the light to the tip in 10 continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, and photosynthetic rate measurements showed that the maize leaf undergoes a sink-to-source transition without an intermediate phase of C(3) photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination, showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C(4) photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C(4) photosynthesis. All data sets are included within the publication to serve as a resource for maize leaf systems biology.

Control of transpiration by radiation.

The terrestrial hydrological cycle is strongly influenced by transpiration--water loss through the stomatal pores of leaves. In this report we present studies showing that the energy content of radiation absorbed by the leaf influences stomatal control of transpiration. This observation is at odds with current concepts of how stomata sense and control transpiration, and we suggest an alternative model. Specifically, we argue that the steady-state water potential of the epidermis in the intact leaf is controlled by the difference between the radiation-controlled rate of water vapor production in the leaf interior and the rate of transpiration. Any difference between these two potentially large fluxes is made up by evaporation from (or condensation on) the epidermis, causing its water potential to pivot around this balance point. Previous work established that stomata in isolated epidermal strips respond by opening with increasing (and closing with decreasing) water potential. Thus, stomatal conductance and transpiration rate should increase when there is condensation on (and decrease when there is evaporation from) the epidermis, thus tending to maintain homeostasis of epidermal water potential. We use a model to show that such a mechanism would have control properties similar to those observed with leaves. This hypothesis provides a plausible explanation for the regulation of leaf and canopy transpiration by the radiation load and provides a unique framework for studies of the regulation of stomatal conductance by CO(2) and other factors.

From genes to policy: mission-oriented governance of plant-breeding research and technologies.

Mission-oriented governance of research focuses on inspirational, yet attainable goals and targets the sustainable development goals through innovation pathways. We disentangle its implications for plant breeding research and thus impacting the sustainability transformation of agricultural systems, as it requires improved crop varieties and management practices. Speedy success in plant breeding is vital to lower the use of chemical fertilizers and pesticides, increase crop resilience to climate stresses and reduce postharvest losses. A key question is how this success may come about? So far plant breeding research has ignored wider social systems feedbacks, but governance also failed to deliver a set of systemic breeding goals providing directionality and organization to research policy of the same. To address these challenges, we propose a heuristic illustrating the core elements needed for governing plant breeding research: Genetics, Environment, Management and Social system (GxExMxS) are the core elements for defining directions for future breeding. We illustrate this based on historic cases in context of current developments in plant phenotyping technologies and derive implications for governing research infrastructures and breeding programs. As part of mission-oriented governance we deem long-term investments into human resources and experimental set-ups for agricultural systems necessary to ensure a symbiotic relationship for private and public breeding actors and recommend fostering collaboration between social and natural sciences for working towards transdisciplinary collaboration.

GXP: Analyze and Plot Plant Omics Data in Web Browsers.

Next-generation sequencing and metabolomics have become very cost and work efficient and are integrated into an ever-growing number of life science research projects. Typically, established software pipelines analyze raw data and produce quantitative data informing about gene expression or concentrations of metabolites. These results need to be visualized and further analyzed in order to support scientific hypothesis building and identification of underlying biological patterns. Some of these tools already exist, but require installation or manual programming. We developed "Gene Expression Plotter" (GXP), an RNAseq and Metabolomics data visualization and analysis tool entirely running in the user's web browser, thus not needing any custom installation, manual programming or uploading of confidential data to third party servers. Consequently, upon receiving the bioinformatic raw data analysis of RNAseq or other omics results, GXP immediately enables the user to interact with the data according to biological questions by performing knowledge-driven, in-depth data analyses and candidate identification via visualization and data exploration. Thereby, GXP can support and accelerate complex interdisciplinary omics projects and downstream analyses. GXP offers an easy way to publish data, plots, and analysis results either as a simple exported file or as a custom website. GXP is freely available on GitHub (see introduction).

Photosynthesis in lightfleck areas of homobaric and heterobaric leaves.

Leaves within a canopy are exposed to a spatially and temporally fluctuating light environment which may cause lateral gradients in leaf internal CO(2) concentration and diffusion between shaded and illuminated areas. In previous studies it was hypothesized that lateral CO(2) diffusion may support leaf photosynthesis, but the magnitude of this effect is still not well understood. In the present study homobaric leaves of Vicia faba or heterobaric leaves of Glycine max were illuminated with lightflecks of different sizes, mimicking sunflecks. Photosynthetic properties of the lightfleck areas were assessed with combined gas exchange measurements and chlorophyll fluorescence imaging. Lateral diffusion in homobaric leaves with an interconnected intercellular air space stimulated photosynthesis and the effect was largest in small lightfleck areas, in particular when plants were under drought stress. Such effects were not observed in the heterobaric leaves with strongly compartmented intercellular gas spaces. It is concluded that lateral diffusion may significantly contribute to photosynthesis of lightfleck areas of homobaric leaves depending on lightfleck size, lateral diffusivity, and stomatal conductance. Since homobaric leaf structures have been reported for many plant species, it is hypothesized that leaf homobary may have an impact on overall plant performance under conditions with a highly heterogeneous light environment.

The Warburg-effects: basic metabolic processes with reference to cancer development and global photosynthesis.

One century ago (1920), Otto Warburg (1883-1970) discovered that in liquid cultures of unicellular green algae (Chlorella sp.) molecular oxygen (O2) exerts an inhibitory effect on photosynthesis. Decades later, O2 dependent suppression of photosynthetic carbon dioxide (CO2) assimilation (the "green" Warbur geffect) was confirmed on the leaves of seed plants. Here, we summarize the history of this discovery and elucidate the consequences of the photorespiratory pathway in land plants with reference to unpublished CO2 exchange data measured on the leaves of sunflower (Helianthus annuus) plants. In addition, we discuss the inefficiency of the key enzyme Rubisco and analyze data concerning the productivity of C3 vs. C4 crop species (sunflower vs. maize, Zea mays). Warburg's discovery inaugurated a research agenda in the biochemistry of photosynthetic CO2 assimilation that continues to the present. In addition, we briefly discuss Warburg's model of metabolic processes in cancer, net primary production (global photosynthesis) with respect to climate change, trees and other land plants as CO2 removers, and potential climate mitigators in the Anthropocene.

Distributed feedback diode laser spectrometer at 2.7 microm for sensitive, spatially resolved H2O vapor detection.

A new, compact, spatially scanning, open-path 2.7 microm tunable diode laser absorption spectrometer with short absorption path lengths below 10 cm was developed to analyze the spatiotemporal dynamics of one-dimensional (1D) spatial water vapor gradients. This spectrometer, which is based on a room-temperature distributed feedback diode laser, is capable of measuring absolute, calibration-free, line-of-sight averaged, but laterally resolved 1D H(2)O concentration profiles with a minimum fractional optical resolution of 2.1x10(-3) optical density (OD) (2.5x10(-4) OD after a background subtraction procedure), which permits a signal-to-noise-ratio of 407 (3400) at 10,000 parts in 10(6) (ppm)H(2)O, or normalized sensitivities of 2.6 ppm x m (0.32 ppm m) at 0.5 Hz duty cycle. The spectrometer's lateral spatial resolution (governed by the 500 microm sampling beam diameter) was validated by analyzing a well-defined laminar jet of nitrogen gas in humidified air. This scanning setup was then used to (a) quantitatively investigate for what we believe to be the first time the H(2)O boundary layer from 0.7 to 11 mm beneath the stomatous side of a single, undetached plant leaf, and (b) to study the temporal boundary layer dynamics and its dependence on stepwise light stimulation of the photosynthetic system. In addition the 2.7 microm diode laser was carefully characterized in terms of spectral purity, beam profile, as well as quasi-static and dynamic wavelength tuning coefficients.

Plant Phenotyping: Past, Present, and Future.

A plant develops the dynamic phenotypes from the interaction of the plant with the environment. Understanding these processes that span plant's lifetime in a permanently changing environment is essential for the advancement of basic plant science and its translation into application including breeding and crop management. The plant research community was thus confronted with the need to accurately measure diverse traits of an increasingly large number of plants to help plants to adapt to resource-limiting environment and low-input agriculture. In this overview, we outline the development of plant phenotyping as a multidisciplinary field. We sketch the technological advancement that laid the foundation for the development of phenotyping centers and evaluate the upcoming challenges for further advancement of plant phenotyping specifically with respect to standardization of data acquisition and reusability. Finally, we describe the development of the plant phenotyping community as an essential step to integrate the community and effectively use the emerging synergies.

Genotype Specific Photosynthesis x Environment Interactions Captured by Automated Fluorescence Canopy Scans Over Two Fluctuating Growing Seasons.

Photosynthesis reacts dynamic and in different time scales to changing conditions. Light and temperature acclimation balance photosynthetic processes in a complex interplay with the fluctuating environment. However, due to limitations in the measurements techniques, these acclimations are often described under steady-state conditions leading to inaccurate photosynthesis estimates in the field. Here we analyze the photosynthetic interaction with the fluctuating environment and canopy architecture over two seasons using a fully automated phenotyping system. We acquired over 700,000 chlorophyll fluorescence transients and spectral measurements under semi-field conditions in four crop species including 28 genotypes. As expected, the quantum efficiency of the photosystem II (Fv/Fm in the dark and Fq'/Fm' in the light) was determined by light intensity. It was further significantly affected by spectral indices representing canopy structure effects. In contrast, a newly established parameter, monitoring the efficiency of electron transport (Fr2/Fv in the dark respective Fr2'/Fq' in the light), was highly responsive to temperature (R2 up to 0.75). This parameter decreased with temperature and enabled the detection of cold tolerant species and genotypes. We demonstrated the ability to capture and model the dynamic photosynthesis response to the environment over entire growth seasons. The improved linkage of photosynthetic performance to canopy structure, temperature and cold tolerance offers great potential for plant breeding and crop growth modeling.

Quantitative Estimation of Leaf Heat Transfer Coefficients by Active Thermography at Varying Boundary Layer Conditions.

Quantifying heat and mass exchanges processes of plant leaves is crucial for detailed understanding of dynamic plant-environment interactions. The two main components of these processes, convective heat transfer, and transpiration, are inevitably coupled as both processes are restricted by the leaf boundary layer. To measure leaf heat capacity and leaf heat transfer coefficient, we thoroughly tested and applied an active thermography method that uses a transient heat pulse to compute τ, the time constant of leaf cooling after release of the pulse. We validated our approach in the laboratory on intact leaves of spring barley (Hordeum vulgare) and common bean (Phaseolus vulgaris), and measured τ-changes at different boundary layer conditions.By modeling the leaf heat transfer coefficient with dimensionless numbers, we could demonstrate that τ improves our ability to close the energy budget of plant leaves and that modeling of transpiration requires considerations of convection. Applying our approach to thermal images we obtained spatio-temporal maps of τ, providing observations of local differences in thermal responsiveness of leaf surfaces. We propose that active thermography is an informative methodology to measure leaf heat transfer and derive spatial maps of thermal responsiveness of leaves contributing to improve models of leaf heat transfer processes.

Photosynthesis can be enhanced by lateral CO2 diffusion inside leaves over distances of several millimeters.

This study examines the extent to which lateral gas diffusion can influence intercellular CO(2) concentrations (c(i)) and thus photosynthesis in leaf areas with closed stomata. Leaves were partly greased to close stomata artificially, and effects of laterally diffusing CO(2) into the greased areas were studied by gas-exchange measurement and chlorophyll fluorescence imaging. Effective quantum yields (Delta F/F(m)') across the greased areas were analysed with an image-processing tool and transposed into c(i) profiles, and lateral CO(2) diffusion coefficients (D(C'lat)), directly proportional to lateral conductivities (), were estimated using a one-dimensional (1D) diffusion model. Effective CO(2) diffusion distances in Vicia faba (homobaric), Commelina vulgaris (homobaric) and Phaseolus vulgaris (heterobaric) leaves clearly differed, and were dependent on D(C'lat), light intensity, [CO(2)], and [O(2)]: largest distances were approx. 7.0 mm for homobaric leaves (with high D(C'lat)) and approx. 1.9 mm for heterobaric leaves (low D(C'lat)). Modeled lateral CO(2) fluxes indicate large support of photosynthesis over submillimeter distances for leaves with low D(C'lat), whereas in leaves with large D(C'lat), photosynthesis can be stimulated over distances of several millimeters. For the plant species investigated, the surplus CO(2) assimilation rates of the greased leaf areas (A(gr)) differed clearly, depending on lateral conductivities of the respective leaves.