Investigating Forest Photosynthetic Response to Elevated CO2 Using UAV-Based Measurements of Solar Induced Fluorescence

The response of ecosystems to increasing atmospheric CO2 will have significant, but still uncertain, impacts on the global carbon and water cycles. A lot of infounation has been gained from Free Air CO2 Enrichment (FACE) experiments, but the response of mature forest ecosystems remains a significant knowledge gap. One of the challenges in FACE studies is obtaining an integrated measure of canopy photosynthesis at the scale of the treatment ring. A new remote sensing approach for measuring photosynthetic activity is based on Solar Induced Fluorescence (SIF), which is emitted by plants during photosynthesis, and is closely linked to the rates and regulation of photosynthesis. We proposed that UAV-based SIF measurements, that enable the spectrometer field of view to be targeted to the treatment ring, provide a unique opportunity for investigating the dynamics of photosynthetic responses to elevated CO2. We have successfully tested this approach in a new FACE site, located in a mature oak forest in the UK. We flew a series of flights across the experiment arrays, collecting a number of spectra. We combined these with ground-based physiological and optical measurements, and see great promise in the use of UAV-based SIF measurements in FACE and other global change experiments.Peer reviewe

Functional phenomics for improved climate resilience in Nordic agriculture

The five Nordic countries span the most northern region for field cultivation in the world. This presents challenges per se with short growing seasons, long days and a need for frost tolerance. Climate change has additionally increased risks for micro-droughts and water logging as well as pathogens and pests expanding northwards. Thus, Nordic agriculture demands crops that are adapted to the special Nordic growth conditions and future climate scenarios. A focus on crop varieties and traits important to Nordic agriculture, including the unique resource of nutritious wild crops, can meet these needs. In fact, with a future longer growing season due to climate change the region could contribute proportionally more to the global agricultural production. This also applies to other northern regions, including the Arctic. To address current growth conditions, mitigate impacts of climate change and meet market demands, the adaptive capacity of crops that both perform well in northern latitudes and are more climate resilient has to be increased, and better crop management systems be built. This requires functional phenomics approaches that integrate versatile high-throughput phenotyping, physiology and bioinformatics. This review stresses key target traits, the opportunities of latitudinal studies and infrastructure needs for phenotyping to support Nordic agriculture.Peer reviewe

Functional phenomics for improved climate resilience in Nordic agriculture

The five Nordic countries span the most northern region for field cultivation in the world. This presents challenges per se with short growing seasons, long days and a need for frost tolerance. Climate change has additionally increased risks for micro-droughts and water logging as well as pathogens and pests expanding northwards. Thus, Nordic agriculture demands crops that are adapted to the special Nordic growth conditions and future climate scenarios. A focus on crop varieties and traits important to Nordic agriculture, including the unique resource of nutritious wild crops, can meet these needs. In fact, with a future longer growing season due to climate change the region could contribute proportionally more to the global agricultural production. This also applies to other northern regions, including the Arctic. To address current growth conditions, mitigate impacts of climate change and meet market demands, the adaptive capacity of crops that both perform well in northern latitudes and are more climate resilient has to be increased, and better crop management systems be built. This requires functional phenomics approaches that integrate versatile high-throughput phenotyping, physiology and bioinformatics. This review stresses key target traits, the opportunities of latitudinal studies and infrastructure needs for phenotyping to support Nordic agriculture.Peer reviewe

Hyperspectral, thermal and LiDAR remote sensing for red band needle blight detection in pine plantation forests

PhD ThesisClimate change indirectly affects the distribution and abundance of forest insect pests and pathogens, as well as the severity of tree diseases. Red band needle blight is a disease which has a particularly significant economic impact on pine plantation forests worldwide, affecting diameter and height growth. Monitoring its spread and intensity is complicated by the fact that the diseased trees are often only visible from aircraft in the advanced stages of the epidemic. There is therefore a need for a more robust method to map the extent and severity of the disease. This thesis examined the use of a range of remote sensing techniques and instrumentation, including thermography, hyperspectral imaging and laser scanning, for the identification of tree stress symptoms caused by the onset of red band needle blight. Three study plots, located in a plantation forest within the Loch Lomond and the Trossachs National Park that exhibited a range of red band needle blight infection levels, were established and surveyed. Airborne hyperspectral and LiDAR data were acquired for two Lodgepole pine stands, whilst for one Scots pine stand, airborne LiDAR and Unmanned Aerial Vehicle-borne (UAV-borne) thermal imagery were acquired alongside leaf spectroscopic measurements. Analysis of the acquired data demonstrated the potential for the use of thermographic, hyperspectral and LiDAR sensors for detection of red band needle blight-induced changes in pine trees. The three datasets were sensitive to different disease symptoms, i.e. thermography to alterations in transpiration, LiDAR to defoliation, and hyperspectral imagery to changes in leaf biochemical properties. The combination of the sensors could therefore enhance the ability to diagnose the infection.Natural Environment Research Council (NERC) for funding this PhD program (studentship award 1368552) and providing access to specialist equipment through a Field Spectroscopy Facility loan (710.114). I would like to thank NERC Airborne Research Facility for providing airborne data (grant: GB 14-04) that made the PhD a challenge, to say the least. My sincere gratitude goes to the Douglas Bomford Trust for providing additional funds, which allowed for completion of the UAV-borne part of this research

The data concept behind the data: From metadata models and labelling schemes towards a generic spectral library

Spectral libraries play a major role in imaging spectroscopy. They are commonly used to store end-member and spectrally pure material spectra, which are primarily used for mapping or unmixing purposes. However, the development of spectral libraries is time consuming and usually sensor and site dependent. Spectral libraries are therefore often developed, used and tailored only for a specific case study and only for one sensor. Multi-sensor and multi-site use of spectral libraries is difficult and requires technical effort for adaptation, transformation, and data harmonization steps. Especially the huge amount of urban material specifications and its spectral variations hamper the setup of a complete spectral library consisting of all available urban material spectra. By a combined use of different urban spectral libraries, besides the improvement of spectral inter- and intra-class variability, missing material spectra could be considered with respect to a multi-sensor/ -site use. Publicly available spectral libraries mostly lack the metadata information that is essential for describing spectra acquisition and sampling background, and can serve to some extent as a measure of quality and reliability of the spectra and the entire library itself. In the GenLib project, a concept for a generic, multi-site and multi-sensor usable spectral library for image spectra on the urban focus was developed. This presentation will introduce a 1) unified, easy-to-understand hierarchical labeling scheme combined with 2) a comprehensive metadata concept that is 3) implemented in the SPECCHIO spectral information system to promote the setup and usability of a generic urban spectral library (GUSL). The labelling scheme was developed to ensure the translation of individual spectral libraries with their own labelling schemes and their usually varying level of details into the GUSL framework. It is based on a modified version of the EAGLE classification concept by combining land use, land cover, land characteristics and spectral characteristics. The metadata concept consists of 59 mandatory and optional attributes that are intended to specify the spatial context, spectral library information, references, accessibility, calibration, preprocessing steps, and spectra specific information describing library spectra implemented in the GUSL. It was developed on the basis of existing metadata concepts and was subject of an expert survey. The metadata concept and the labelling scheme are implemented in the spectral information system SPECCHIO, which is used for sharing and holding GUSL spectra. It allows easy implementation of spectra as well as their specification with the proposed metadata information to extend the GUSL. Therefore, the proposed data model represents a first fundamental step towards a generic usable and continuously expandable spectral library for urban areas. The metadata concept and the labelling scheme also build the basis for the necessary adaptation and transformation steps of the GUSL in order to use it entirely or in excerpts for further multi-site and multi-sensor applications

Evaluating wheat for genetic variation in radiation use efficiency: scaling traits from leaves to canopies

Wheat yields are stagnating or declining in many regions of the planet, requiring efforts to improve the light conversion efficiency, i.e., radiation use efficiency (RUE). RUE is a key trait in plant physiology because it links light capture and primary metabolism with biomass accumulation and yield. High-throughput phenotyping (HTP) was used among a population of field grown wheat with variation in RUE and photosynthetic traits to build predictive models of RUE, biomass and intercepted photosynthetically active radiation (IPAR). The use of remote sensing models predicted RUE with up to 70% accuracy compared to ground truth data. Wheat yield can be defined as the product of solar radiation intercepted throughout the crop cycle, radiation use efficiency and harvest index. Photosynthesis is a central component of RUE but normally measured in the upper layers of the canopy where light conditions are saturating. Significant relationships were found between light saturated photosynthetic rates measured at initiation of booting in the top, middle and bottom layers of the canopy and yield. These findings indicate that there is an opportunity for yield improvement if we consider the requirements of photosynthesis in the middle and bottom layers of wheat canopies where conditions are not light saturating. The study of photosynthesis in the field is constrained by low throughput and lack of integrative measurements at canopy level. Partial least squares regression (PLSR) modelling was used to build predictive models of photosynthetic, biophysical and biochemical traits at the top, middle and bottom layers of wheat canopies. The combined layer model predictions performed better than individual layer predictions. Using HTP allowed us to increase phenotyping capacity 30-fold compared to conventional phenotyping methods and our models can be used to screen varieties for high and low RUE. There is clear consensus in the physiological and breeding communities that improving RUE will be key to boost wheat yield. In the previous years of RUE research little has been explored on the role of root biomass accumulation and its interaction with aboveground biomass accumulation, RUE and yield. Strong positive associations were found between above and belowground biomass accumulation with RUE and root biomass during the vegetative period, and negative associations between yield components and root biomass accumulation, suggesting there is a coordination between roots and shoot in the vegetative period to maximize growth. However, if too much energy is invested in root biomass this will have an effect in decreasing aboveground biomass during grain filling. More research will be needed to explore new hypothesis in the field that accounts the effect of root biomass in canopy RUE and yield

Characterization of plant water flows in Controlled environment -PLANT SMART SENSORS

The present thesis project "Characterization of water flows in Controlled Environment -PLANT SMART SENSORS" has a multidisciplinary core and aimed towards the creation of synergies between the world of scientific research and the industry. By applying research results to technological development, this research targeted at innovation in the Agrotechnology and Aerospace sectors. Indeed, the introduction of new technologies is pivotal for controlled environment production on Earth to feed a growing population as well as for human permanence in Space in longterm missions where plants are used to regenerate resources (e.g. oxygen, water) and as source of fresh high-nutritious food. The realization of these systems must be based on a precise knowledge of plant morpho-anatomical development and its physiological behavior in closed growth systems, which are strongly influenced by numerous environmental factors including the relative humidity or more specifically the Vapour Pressure Deficit (VPD). In a protected environment (e.g. in Space greenhouses, vertical farm, indoor growing-modules), the control of relative humidity represents a significant problem, which has often been neglected. For instance, in conditions of poor aeration, too high humidity can occur with consequent low values of VPD which reduces the plant transpiration, slowing or stopping the water flow through the SPAC (Soil-plant-atmosphere-continuum), and ultimately blocking the photosynthesis, yield and biomass production. Even though there have been many studies regarding the VPD control, alone and/or in combination with other environmental factors, certain points are still unclear or controversial, providing contrasting results in different or even in the same species. This happens mainly due to the complex interactions between many microclimatic factors and plant physiological behaviour at different phenological stages. In a context of climate change, the efficient regulation of VPD can be applied to greenhouse and indoor-module production in order to enhance crop productivity, improve WUE and reduce total water consumption to design irrigation strategies, considering the balance between the amount of water saved and the quantity used to regulate the VPD. The regulation of the VPD and related environmental parameters need to be designed according to the species and its adaptive plasticity at morphophysiological levels.  Thus, the characterization and modeling of water flows in model plants in different growth chamber scenarios (from small modules intended for the spatialization for Space applications, up to structures that can be used in protected cultivation on Earth), as well as the real-time monitoring of the water status of plants, become fundamental for the management of precision agriculture both in support of Space exploration and for the sustainability of urban agriculture. To date, most of the research has focused on either specific physiological/structural aspect at the single-plant level, or on cultivation management or even on technological aspects, with only a few interlinks of knowledge. The aim of this thesis is to develop knowledge to help filling this gap to improve the understanding of VPD effects on crop productivity, with the creation of synergies among different expertise (e.g., plant physiology, crop science, engineering). To do so, it is fundamental to study the complexity of plant morpho/physiological responses, since without a deep knowledge of mechanisms behind plant responses to the environment it is difficult to determine how and to which extent plants can adapt to any changes in the environmental conditions. The application of a multidisciplinary approach in research will allow crop production in a sustainable way, even in harsh environments, where a "climate smart-agriculture" becomes necessary to improve crop yield and quality. The present thesis is organized as follows: Chapter 1 is a review which presents the current state of knowledge on how VPD influences plant morpho-physiological traits in controlled environment agriculture. The study has been published as a review article in Annals of Applied Biology (Amitrano et al., 2019 https://doi.org/10.1111/aab.12544). It covers main important aspects of VPD influence on plant growth, morpho-anatomical development, and physiology, emphasizing the possible interaction between VPD and other microclimatic factors in protected cultivation. Furthermore, the rewiew identifies and discusses future research areas, which should be explored further, based on needed synergies among different expertise from biological and horticultural fields. Chapter 2 presents evidence that the modulation of relative humidity (RH) together with other important cultivation factors such as light (presence/absence), can influence morpho-anatomical development and improve antioxidant content, even at the early stages of plant life cycle (germination, seedling establishment). The combined effect of RH and light was studied during the germination and seedling development of Vigna radiata L. (mung bean), a species widespread throughout the world also due to the high nutritional value of its edible sprouts. A manuscript reporting these data has been published in Plants (Amitrano et al., 2020a https://doi.org/10.3390/plants9091093). In Chapter 3, the role of leaf anatomical traits (e.g. leaf mesophyll features, stomata and vein traits) in photosynthetic acclimation to short- and long-term changes in VPD was examined in Vigna radiata L. adult plants. In this study, we underlined the key role of leaf structure in photosynthetic acclimation to air VPD. The long-term exposure to different VPD levels determined a pre-acclimation at the leaf morpho-anatomical level which influenced the extent of leaf physiological plasticity, changing plant ability to acclimate to any changes in the surrounding microclimate. This different leaf anatomy-related capacity of pre-acclimating becomes therefore fundamental in the present climate-change scenario due to its key role in the adaptation process under changing environmental conditions. A manuscript reporting these data has been published in Environmental and Experimental Botany (Amitrano et al., 2021a https://doi.org/10.1016/j.envexpbot.2021.104453). In Chapter 4, the effect of VPD on morpho-physiological traits also incorporating the trade-off between transpiration and carbon gain was evaluated in two cultivars of Salanova lettuce (Lactuca sativa L.) with green and red leaves, in a growth-chamber experiment. Low-VPD turned out to significantly improve growth, stomata development and hydraulic-related traits which led to higher photosynthesis and a reduced water consumption compared to the high-VPD condition. A manuscript reporting these data was published in Agronomy (Amitrano et al., 2021b https://doi.org/10.3390/agronomy11071396).  Chapter 5 represents a clear interlink of knowledge between plant scientists, engineers, mathematician and modelists. In this study, published in Sensors (Amitrano et al., 2020b https://doi.org/10.3390/s20113110), we used experimental data, based on morpho-anatomical analyses of lettuce plants, to run the Energy Cascade Model (MEC), a model already used to predict biomass production and photosynthetic efficiency in advanced life support systems studies (Space-oriented research). Here, the modification of the model is discussed together with possible improvements and applications. Chapter 6 focuses on how to modulate the micro-environment, and in particular the VPD levels, in protected cultivation to improve plant antioxidant content in crops. More specifically, the exposure of the same lettuce cultivars mentioned in previous chapters to high VPD determined an improved phytochemical content in lettuce leaves, especially in the red cultivar. Here we discussed a further possibility to use short-term high VPD treatments as a mild stress to boost the phytochemical production in lettuce plants. A Manuscript reporting these data has been published in Horticulturae (Amitrano et al., 2021c http://doi.org/10.3390/horticulturae7020032). Chapter 7 is a deep focus on how the VPD drives the coordination among morpho-anatomical traits in leaves of the above-mentioned lettuce cultivars, also exploring the variability of traits along the leaf lamina. More specifically, the attention is focused on how stomata and vein develop within lettuce leaves and how these traits are coordinated with leaf size under different VPDs. Results from this study suggest that VPD triggers a different response in lettuce plants in terms of balance of leaf 4 traits and highlight the possibility of further exploring the microenvironment (combined influence of light and VPD) to adjust the development of stomata and vein densities, thus providing optimal water and gas fluxes through the leaves. In Chapter 8, the experiments conducted during the period spent at the Controlled Environment Agriculture Center of the University of Arizona (UA-CEAC) are reported. The experiments reported here were conducted on the same species of the previous chapters (Salanvoa lettuce with green and red leaves) in a multi-layer vertical farm to test the interaction between VPD and other microclimatic factors on plant morpho-physiological development. More specifically two experimental trials are reported (E1 and E2). In E1, the interaction between VPD levels (low and high) and increasing DLI (Daily Light Integral - 8.6, 12.9, 15.5) was tested to study morpho-physiological changes and to determine the optimal combination of DLI and VPD for lettuce growth. In E2, a sudden salt stress was applied to the cultivation and then CO2 enrichment was provided, based on the hypothesis that the CO2 enrichment would mitigate the salt stress, modifying the plant carbon gain/water balance. We evaluated whether the mechanisms of salt stress mitigation due to CO2 enrichment were different under high and low VPD conditions, depending on the different morphoanatomical leaf structure.   Chapter 9 reports on experiments conducted at the IPK-Leibniz institute of plant genetics and crop plant research (Gatersleeben, Germany) in the framework of the EPPN2020 transnational access (https://eppn2020.plant-phenotyping.eu/EPPN_Transnational_Access). A report with obtained results is showed in this chapter. These experiments concern the application of high-throughput phenotyping combined with morpho-anatomical analyses on Salanova green and red plants acclimated to a VPD level and then subjected to short-term changes in the VPD. The project submitted to the EPPN transnational access and winner of the grant is presented in Appendix 1. Chapter 10 and 11 report on the possible industrial applications after the collaboration with the partner company "Kayser Italia srl" (http://www.kayser.it/). Chapter 10 is a study for the definition of scientific and technical requirements for the realization of a miniaturized phenotyping growth chamber to grow microgreens or small crops in Space. The structure of the chamber is based on the "Kubik" incubator, an incubator facility of the European Space Agency with the shape of a cube of about 40 cm that has been operating aboard the International Space Station for more than 12 years, carrying different life science experiments. In the chapter, technical and scientific requirements are listed and a preliminary schedule for the project realization is provided. At the end of the chapter, open issues are also discussed. In Chapter 11, the set-up of a prototype miniaturized cultivation chamber for use in Space is described and the results of validation tests, carried out at Kayser Italia with brassica microgreens (Brassica rapa subsp. sylvestris var. esculenta) under different air relative humidities (VPD), are reported. In Appendix 1, the project submitted to the EPPN transnational access (PHEW- Automated phenotyping platform to improve lettuce water use efficiency under different VPD and watering regimens) and winner of the grant is presented. In Appendix 2, a brief recap on the activities conducted during the Ph.D. program is presented

Multi-sensor remote sensing for drought characterization: current status, opportunities and a roadmap for the future

Satellite based remote sensing offers one of the few approaches able to monitor the spatial and temporal development of regional to continental scale droughts. A unique element of remote sensing platforms is their multi-sensor capability, which enhances the capacity for characterizing drought from a variety of perspectives. Such aspects include monitoring drought influences on vegetation and hydrological responses, as well as assessing sectoral impacts (e.g., agriculture). With advances in remote sensing systems along with an increasing range of platforms available for analysis, this contribution provides a timely and systematic review of multi-sensor remote sensing drought studies, with a particular focus on drought related datasets, drought related phenomena and mechanisms, and drought modeling. To explore this topic, we first present a comprehensive summary of large-scale remote sensing datasets that can be used for multi-sensor drought studies. We then review the role of multi-sensor remote sensing for exploring key drought related phenomena and mechanisms, including vegetation responses to drought, land-atmospheric feedbacks during drought, drought-induced tree mortality, drought-related ecosystem fires, post-drought recovery and legacy effects, flash drought, as well as drought trends under climate change. A summary of recent modeling advances towards developing integrated multi-sensor remote sensing drought indices is also provided. We conclude that leveraging multi-sensor remote sensing provides unique benefits for regional to global drought studies, particularly in: 1) revealing the complex drought impact mechanisms on ecosystem components; 2) providing continuous long-term drought related information at large scales; 3) presenting real-time drought information with high spatiotemporal resolution; 4) providing multiple lines of evidence of drought monitoring to improve modeling and prediction robustness; and 5) improving the accuracy of drought monitoring and assessment efforts. We specifically highlight that more mechanism-oriented drought studies that leverage a combination of sensors and techniques (e.g., optical, microwave, hyperspectral, LiDAR, and constellations) across a range of spatiotemporal scales are needed in order to progress and advance our understanding, characterization and description of drought in the future