ALBERT

Beschreibung: It has become more evident that many microalgae respond very differently than land plants to diverse stimuli. Therefore, we cannot reduce microalgae biology to what we have learned from land plants biology. However, we are still at the beginning of a comprehensive understanding of microalgae biology. Microalgae have been posited several times as prime candidates for the development of sustainable energy platforms, making thus the in-depth understanding of their biological features an important objective. Thus, the knowledge related to the basics of microalgae biology must be acquired and shared rapidly, fostering the development of potential applications. Microalgae biology has been studied for more than forty years now and more intensely since the 1970’s, when genetics and molecular biology approaches were integrated into the research programs. Recently, studies on the molecular physiology of microalgae have provided evidences on the particularities of these organisms, mainly in model species, such as Chlamydomonas reinhardtii. Of note, cellular responses in microalgae produce very interesting phenotypes, such as high lipid content in nitrogen deprived cells, increased protein content in cells under high CO2 concentrations, the modification of flagella structure and motility in basal body mutant strains, the different ancient proteins that microalgae uses to dissipate the harmful excess of light energy, the hydrogen production in cells under sulfur deprivation, to mention just a few. Moreover, several research groups are using high-throughput and data-driven technologies, including “omics” approaches to investigate microalgae cellular responses at a system-wide level, revealing new features of microalgae biology, highlighting differences between microalgae and land plants. It has been amazing to observe the efforts towards the development and optimization of new technologies required for the proper study of microalgae, including methods that opened new paths to the investigation of important processes such as regulatory mechanisms, signaling crosstalk, chemotactic mechanisms, light responses, chloroplast controlled mechanisms, among others. This is an exciting moment in microalgae research when novel data are been produced and applied by research groups from different areas, such as bioprocesses and biotechnology. Moreover, there has been an increased amount of research groups focused in the study of microalgae as a sustainable source for bioremediation, synthesis of bioproducts and development of bioenergy. Innovative strategies are combining the knowledge of basic sciences on microalgae into their applied processes, resulting in the progression of many applications that hopefully, will achieve the necessary degree of optimization for economically feasible large-scale applications. Advances on the areas of basic microalgae biology and novelties on the essential cellular processes were revealed. Progress in the applied science showed the use of the basic science knowledge into fostering translational research, proposing novel strategies for a sustainable world scenario. In this present e-book, articles presented by research groups from different scientific areas showed, successfully, the increased development of the microalgae research. Herewith, you will find articles ranging from bioprospecting regional microalgae species, through advances in microalgae molecular physiology to the development of techniques for characterization of biomass and the use of biomass into agriculture and bioenergy production. This e-book is an excellent source of knowledge for those working with microalgae basic and applied sciences, and a great opportunity for researchers from both areas to have an overview of the amazing possibilities we have for building an environmentally sustainable future once the knowledge is translated into novel applications.

Beschreibung: Virus-caused asthma, we now call a phenotype of asthma. Regardless of the significance and popularity of this disease, the etiology of the virus-induced asthma have not well understood. In addition, a few effective vaccines have been applied to prevent respiratory virus infection. To solve the issues, it is essential to clarify and delineate both aspects of the virus and host defense systems including acute/chronic inflammation and airway tissue remodeling. To deeply review and discuss pathophysiology and epidemiology of virus-induced asthma, this topics includes new findings of the host immunity, pathology, epidemiology, and virology of asthma/chronic obstructive pulmonary disease (COPD). We believe that these works are well summarized and informative to glimpse the field of virus- associated asthma and COPD, and may help understanding the basic and clinical aspects of the diseases.

Beschreibung: Transfer cells are anatomically specialized cells optimized to support high levels of nutrient transport in plants. These cells trans-differentiate from existing cell types by developing extensive and localized wall ingrowth labyrinths to amplify plasma membrane surface area which in turn supports high densities of membrane transporters. Unsurprisingly, therefore, transfer cells are found at key anatomical sites for nutrient acquisition, distribution and exchange. Transfer cells are involved in delivery of nutrients between generations and in the development of reproductive organs and also facilitate the exchange of nutrients that characterize symbiotic associations. Transfer cells occur across all taxonomic groups in higher plants and also in algae and fungi. Deposition of wall ingrowth-like structures are also seen in “syncytia” and “giant cells” which function as feeding sites for cyst and root-knot nematodes, respectively, following their infection of roots. Consequently, the formation of highly localized wall ingrowth structures in diverse cell types appears to be an ancient anatomical adaption to facilitate enhanced rates of apoplasmic transport of nutrients in plants. In some systems a role for transfer cells in the formation of an anti-pathogen protective barrier at these symplastic discontinuities has been inferred. Remarkably, the extent of cell wall ingrowth development at a particular site can show high plasticity, suggesting that transfer cell differentiation might be a dynamic process adapted to the transport requirements of each physiological condition. Recent studies exploiting different experimental systems to investigate transfer cell biology have identified signaling pathways inducing transfer cell development and genes/gene networks that define transfer cell identity and/or are involved in building the wall ingrowth labyrinths themselves. Further studies have defined the structure and composition of wall ingrowths in different systems, leading in many instances to the conclusion that this process may involve previously uncharacterized mechanisms for localized wall deposition in plants. Since transfer cells play important roles in plant development and productivity, the latter being relevant to crop yield, especially so in major agricultural species such as wheat, barley, soybean and maize, understanding the molecular and cellular events leading to wall ingrowth deposition holds exciting promise to develop new strategies to improve plant performance, a key imperative in addressing global food security. This Research Topic presents a timely and comprehensive treatise on transfer cell biology to help define critical questions for future research and thereby generating a deeper understanding of these fascinating and important cells in plant biology.

Beschreibung: Photosystem II is a 700-kDa membrane-protein super-complex responsible for the light-driven splitting of water in oxygenic photosynthesis. The photosystem is comprised of two 350-kDa complexes each made of 20 different polypeptides and over 80 co-factors. While there have been major advances in understanding the mature structure of this photosystem many key protein factors involved in the assembly of the complex do not appear in the holoenzyme. The mechanism for assembling this super-complex is a very active area of research with newly discovered assembly factors and subcomplexes requiring characterization. Additionally the ability to split water is inseparable from light-induced photodamage that arises from radicals and reactive O2 species generated by Photosystem II chemistry. Consequently, to sustain water splitting, a “self repair” cycle has evolved whereby damaged protein is removed and replaced so as to extend the working life of the complex. Understanding how the biogenesis and repair processes are coordinated is among several important questions that remain to be answered. Other questions include: how and when are the inorganic cofactors inserted during the assembly and repair processes and how are the subcomplexes protected from photodamage during assembly? Evidence has also been obtained for Photosystem II biogenesis centers in cyanobacteria but do these also exist in plants? Do the molecular mechanisms associated with Photosystem II assembly shed fresh light on the assembly of other major energy-transducing complexes such as Photosystem I or the cytochrome b6/f complex or indeed other respiratory complexes? The contributions to this Frontiers in Plant Science Research Topic are likely to reveal new details applicable to the assembly of a range of membrane-protein complexes, including aspects of self-assembly and solar energy conversion that may be applied to artificial photosynthetic systems. In addition, a deeper understanding of Photosystem II assembly — particularly in response to changing environmental conditions — will provide new knowledge underpinning photosynthetic yields which may contribute to improved food production and long-term food security.

Beschreibung: Biotic and abiotic stress factors deliver a huge impact on plant life. Biotic stress factors such as damage through pathogens or herbivore attack, as well as abiotic stress factors like variation in temperature, rainfall and salinity, have placed the plant kingdom under constant challenges for survival. As a consequence, global agricultural and horticultural productivity has been disturbed to a large extent. Being sessile in nature, plants cannot escape from the stress, and instead adapt changes within their system to overcome the adverse conditions. These changes include physiological, developmental and biochemical alterations within the plant body which influences the genome, proteome and metabolome profiles of the plant. Since proteins are the ultimate players of cellular behavior, proteome level alterations during and recovery period of stress provide direct implications of plant responses towards stress factors. With current advancement of modern high-throughput technologies, much research has been carried out in this field. This e-book highlights the research and review articles that cover proteome level changes during the course or recovery period of various stress factors in plant life. Overall, the chapters in this e-book has provided a wealth of information on how plants deal with stress from a proteomics perspective.

Beschreibung: As a consequence of the global climate change, both the reduction on yield potential and the available surface area of cultivated species will compromise the production of food needed for a constant growing population. There is consensus about the significant gap between world food consumption projected for the coming decades and the expected crop yield-improvements, which are estimated to be insufficient to meet the demand. The complexity of this scenario will challenge breeders to develop cultivars that are better adapted to adverse environmental conditions, therefore incorporating a new set of morpho-physiological and physico-chemical traits; a large number of these traits have been found to be linked to heat and drought tolerance. Currently, the only reasonable way to satisfy all these demands is through acquisition of high-dimensional phenotypic data (high-throughput phenotyping), allowing researchers with a holistic comprehension of plant responses, or ‘Phenomics’. Phenomics is still under development. This Research Topic aims to be a contribution to the progress of methodologies and analysis to help understand the performance of a genotype in a given environment.

Beschreibung: The onset of flowering is an important step during the lifetime of a flowering plant. During the past two decades, there has been enormous progress in our understanding of how internal and external (environmental) cues control the transition to reproductive growth in plants. Many flowering time regulators have been identified from the model plant Arabidopsis thaliana. Most of them are assembled in regulatory pathways, which converge to central integrators which trigger the transition of the vegetative into an inflorescence meristem. For crop cultivation, the time of flowering is of upmost importance, because it determines yield. Phenotypic variation for this trait is largely controlled by genes, which were often modified during domestication or crop improvement. Understanding the genetic basis of flowering time regulation offers new opportunities for selection in plant breeding and for genome editing and genetic modification of crop species.

Beschreibung: Autophagy (also known as macroautophagy) is an evolutionarily conserved process by which cytoplasmic components are nonselectively enclosed within a double-membrane vesicle known as the autophagosome and delivered to the vacuole for degradation of toxic components and recycling of needed nutrients. This catabolic process is required for the adequate adaptation and response of the cell, and correspondingly the whole organism, to different types of stress including nutrient starvation or oxidative damage. Autophagy has been extensively investigated in yeasts and mammals but the identification of autophagy-related (ATG) genes in plant and algal genomes together with the characterization of autophagy-deficient mutants in plants have revealed that this process is structurally and functionally conserved in photosynthetic eukaryotes. Recent studies have demonstrated that autophagy is active at a basal level under normal growth in plants and is upregulated during senescence and in response to nutrient limitation, oxidative stress, salt and drought conditions and pathogen attack. Autophagy was initially considered as a non-selective pathway, but numerous observations mainly obtained in yeasts revealed that autophagy can also selectively eliminate specific proteins, protein complexes and organelles. Interestingly, several types of selective autophagy appear to be also conserved in plants, and the degradation of protein aggregates through specific adaptors or the delivery of chloroplast material to the vacuole via autophagy has been reported. This research topic aims to gather recent progress on different aspects of autophagy in plants and algae. We welcome all types of articles including original research, methods, opinions and reviews that provide new insights about the autophagy process and its regulation.

Beschreibung: In this century the human being must face the challenges of producing enough to feed a growing population in a sustainable and environmentally friendly way. The yields are with increasing frequency affected by abiotic stresses such as salinity, drought, and high temperature or by new diseases and plagues. The Research Topic on Induced Resistance for Plant Defense focuses on the understanding the mechanisms underlying plant resistance or tolerance since these will help us to develop fruitful new agricultural strategies for a sustainable crop protection. This topic and its potential applications provide a new sustainable approach to crop protection. This technology currently can offer promising molecules capable to provide new long lasting treatments for crop protection against biotic or abiotic stresses. The aim of this Research Topic is to review and discuss current knowledge of the mechanisms regulating plant induced resistance and how from our better understanding of these mechanisms we can find molecules capable of inducing this defence response in the plant, thereby contributing to sustainable agriculture we need for the next challenges of the XXI century.

Beschreibung: Phytopathogenic bacteria of the Xanthomonas genus cause severe diseases on hundreds of host plants, including economically important crops, such as bean, cabbage, cassava, citrus, hemp, pepper, rice, sugarcane, tomato or wheat. Diseases occurring in nature comprise bacterial blight, canker, necrosis, rot, scald, spot, streak or wilt. Xanthomonas spp. are distributed worldwide and pathogenic and nonpathogenic strains are essentially found in association to plants. Some phytopathogenic strains are emergent or re-emergent and, consequently, dramatically impact agriculture, economy and food safety. During the last decades, massive efforts were undertaken to decipher Xanthomonas biology. So far, more than one hundred complete or draft genomes from diverse Xanthomonas species have been sequenced (http://www.xanthomonas.org), thus providing powerful tools to study genetic determinants triggering pathogenicity and adaptation to plant habitats. Xanthomonas spp. employ an arsenal of virulence factors to invade its host, including extracellular polysaccharides, plant cell wall-degrading enzymes, adhesins and secreted effectors. In most xanthomonads, type III secretion (T3S) system and secreted effectors (T3Es) are essential to bacterial pathogenicity through the inhibition of plant immunity or the induction of plant susceptibility (S) genes, as reported for Transcription Activation-Like (TAL) effectors. Yet, toxins can also be major virulence determinants in some xanthomonads while nonpathogenic Xanthomonas species do live in sympatry with plant without any T3S systems nor T3Es. In a context of ever increasing international commercial exchanges and modifications of the climate, monitoring and regulating pathogens spread is of crucial importance for food security. A deep knowledge of the genomic diversity of Xanthomonas spp. is required for scientists to properly identify strains, to help preventing future disease outbreaks and to achieve knowledge-informed sustainable disease resistance in crops. This Research Topic published in the ‘Plant Biotic Interactions’ section of Frontiers in Plant Science and Frontiers in Microbiology aims at illustrating several of the recent achievements of the Xanthomonas community. We collected twelve manuscripts dealing with comparative genomics or T3E repertoires, including five focusing on TAL effectors which we hope will contribute to advance research on plant pathogenic bacteria.

Beschreibung: Over the last decades, nitric oxide (NO) has emerged as an essential player in redox signalling. Reactive oxygen species (ROS) also act as signals throughout all stages of plant life. Because they are potentially harmful for cellular integrity, ROS and NO levels must be tightly controlled, especially by the classical antioxidant system and additional redox-active metabolites and proteins. Recent work provided evidence that NO and ROS influence each other’s biosynthesis and removal. Moreover, novel signalling molecules resulting from the chemical reaction between NO, ROS and plant metabolites have been highlighted, including N2O3, ONOO-, NO2, S-nitrosoglutathione and 8-NO2 cGMP. They are involved in diverse plant physiological processes, the best characterized being stomata regulation and stress defense. Taken together, these new data demonstrate the complex interactions between NO, ROS signalling and the antioxidant system. This Frontiers in Plant Science Research Topic aims to provide an updated and complete overview of this important and rapidly expanding area through original article and detailed reviews.

Beschreibung: Parasitic weeds are severe constraint to agriculture and major crop production, and the efficacy of available means to control them is minimal. Control strategies have centred around agronomic practices, resistant varieties and the use of herbicides. Novel integrated control programmes should be sympathetic to agricultural extensification while exerting minimal harmful effects on the environment. This eBook covers recent advances in biology, physiology of parasitism, genetics, population dynamics, resistance, host-parasite relationships, regulation of seed germination, etc., in order to offer an outstanding windows to these enigmatic plants, and contribute to their practical management.

Beschreibung: Plant organ abscission is a developmental process regulated by the environment, stress, pathogens and the physiological status of the plant. In particular, seed and fruit abscission play an important role in seed dispersion and plant reproductive success and are common domestication traits with important agronomic consequences for many crop species. Indeed, in natural populations, shedding of the seed or fruit at the correct time is essential for reproductive success, while for crop species the premature or lack of abscission may be either beneficial or detrimental to crop productivity. The use of model plants, in particular Arabidopsis and tomato, have led to major advances in our understanding of the molecular and cellular mechanisms underlying organ abscission, and now many workers pursue the translation of these advances to crop species. Organ abscission involves specialized cell layers called the abscission zone (AZ), where abscission signals are perceived and cell separation takes place for the organ to be shed. A general model for plant organ abscission includes (1) the differentiation of the AZ, (2) the acquisition of AZ cells to become competent to respond to various abscission signals, (3) response to signals and the activation of the molecular and cellular processes that lead to cell separation in the AZ and (4) the post-abscission events related to protection of exposed cells after the organ has been shed. While this simple four-phase framework is helpful to describe the abscission process, the exact mechanisms of each stage, the differences between organ types and amongst diverse species, and in response to different abscission inducing signals are far from elucidated. For an organ to be shed, AZ cells must transduce a multitude of both endogenous and exogenous signals that lead to transcriptional and cellular and ultimately cell wall modifications necessary for adjacent cells to separate. How these key processes have been adapted during evolution to allow for organ abscission to take place in different locations and under different conditions is unknown. The aim of the current collection of articles is to present and be able to compare recent results on our understanding of organ abscission from model and crop species, and to provide a basis to understand both the evolution of abscission in plants and the translation of advances with model plants for applications in crop species.

Beschreibung: Many of the most prevalent and devastating human and animal pathogens have part of their lifecycle out-with the animal host. These pathogens have a remarkably wide capacity to adapt to a range of quite different environments: physical, chemical and biological, which is part of the key to their success. Many of the well-known pathogens that are able to jump between hosts in different biological kingdoms are transmitted through the faecal-oral and direct transmission pathways, and as such have become important food-borne pathogens. Some high-profile examples include fresh produce-associated outbreaks of Escherichia coli O157:H7 and Salmonella enterica. Other pathogens may be transmitted via direct contact or aerosols are include important zoonotic pathogens. It is possible to make a broad division between those pathogens that are passively transmitted via vectors and need the animal host for replication (e.g. virus and parasites), and those that are able to actively interact with alternative hosts, where they can proliferate (e.g. the enteric bacteria). This research topic will focus on plants as alternative hosts for human pathogens, and the role of plants in their transmission back to humans. The area is particularly exciting because it opens up new aspects to the biology of some microbes already considered to be very well characterised. One aspect of cross-kingdom host colonisation is in the comparison between the hosts and how the microbes are able to use both common and specific adaptations for each situation. The area is still in relative infancy and there are far more questions than answers at present. We aim to address important questions underlying the interactions for both the microbe and plant host in this research topic.

Beschreibung: Due to their bacterial endosymbiotic origin plastids are organelles with both nuclear-encoded and plastid-encoded proteins. Therefore, a highly integrated modulation of gene expression between the nucleus and the plastome is needed in plant cell development. Plastids have retained for the most part a prokaryotic gene expression machinery but, differently from prokaryotes and eukaryotes, they have largely abandoned transcriptional control and switched to predominantly translational control of their gene expression. Some transcriptional regulation is known to occur, but the coordinate expression between the nucleus and the plastome takes place mainly through translational regulation. However, the regulatory mechanisms of plastid gene expression (PGE) are mediated by intricate plastid-nuclear interactions and are still far from being fully understood. Although, for example, translational autoregulation mechanisms in algae have been described for subunits of heteromeric protein complexes and termed control by epistasy of synthesis (CES), only few autoregulatory proteins have been identified in plant plastids. It should be noted of course that PGE in C. reinhardtii is different from that in plants in many aspects. Another example of investigation in this research area is to understand the interactions that occur during RNA binding between nucleus-encoded RNA-binding proteins and the respective RNA sequences, and how this influences the translation initiation process. In addition to this, the plastid retains a whole series of mechanisms for the preservation of its protein balance (proteostasis), including specific proteases, as well as molecular chaperones and enzymes useful in protein folding. After synthesis, plastid proteins must rapidly fold into stable three dimensional structures and often undergo co- and posttranslational modifications to perform their biological mission, avoiding aberrant folding, aggregation and targeting with the help of molecular chaperones and proteases. We believe that this topic is highly interesting for many research areas because the regulation of PGE is not only of wide interest for plant biologists but has also biotechnological implications. Indeed, plastid transformation turns out to be a very promising tool for the production of recombinant proteins in plants, yet some limitations must still be overcome and we believe that this is mainly due to our limited knowledge of the mechanisms in plastids influencing the maintenance of proteostasis.

Beschreibung: The Frontiers in Chemistry Editorial Office team are delighted to present the inaugural “Frontiers in Chemistry: Rising Stars” article collection, showcasing the high-quality work of internationally recognized researchers in the early stages of their independent careers. All Rising Star researchers featured within this collection were individually nominated by the Journal’s Chief Editors in recognition of their potential to influence the future directions in their respective fields. The work presented here highlights the diversity of research performed across the entire breadth of the chemical sciences, and presents advances in theory, experiment and methodology with applications to compelling problems. This Editorial features the corresponding author(s) of each paper published within this important collection, ordered by section alphabetically, highlighting them as the great researchers of the future. The Frontiers in Chemistry Editorial Office team would like to thank each researcher who contributed their work to this collection. We would also like to personally thank our Chief Editors for their exemplary leadership of this article collection; their strong support and passion for this important, community-driven collection has ensured its success and global impact.

Beschreibung: The flexible filamentous plant viruses are responsible for more than half of all agricultural loss worldwide. Potexvirus is one of the two most important flexible filamentous plant viruses. Bamboo mosaic virus (BaMV), a single-stranded positive-sense RNA virus, is a member of the Potexvirus genus of Alphaflexiviridae. It can infect at least 12 species of bamboo, causing a huge economic impact on the bamboo industry in Taiwan. The study of BaMV did not start extensively until the completion of the full-length sequencing of genomic RNA of BaMV and generation of the BaMV infectious cDNA clone in the early 1990s. Since then, BaMV has been extensively studied at the molecular, cellular and ecological level, covering both basic and applied researches, by a group of researchers in Taiwan. In this eBook, the content comprises 6 reviews and 4 articles. Seven of them are involved in the infection of BaMV covering viral RNA replication, viral RNA trafficking, and the host factors. Two of them are related to the vector transmission and the ecology of BaMV. The last one is the application of using BaMV as a viral vector to produce vaccines in plants.

Beschreibung: The great diversity of land plants (especially angiosperms) is mainly reflected in the diversity of various reproductive organs of plants. However, despite long time intensive investigations, there are still uncertainties and sometimes misunderstandings over the nature and evolution of reproductive organs in land plants. With the new advances made in various fields of botany (especially at molecular level), there is increasing light shed on some aspects of flowers (reproductive organs of angiosperms). In this ebook, we collect 15 papers reporting new understanding on plant reproductive organs. These works range from morphology and anatomy to molecular regulatory networks underlying traditional observations. We understand this single book cannot reach our goal, but we do hope that this book can contribute to or initiate some efforts leading to the final solution of some problems concerning the homology and evolution of reproductive organs in plants.

Beschreibung: Until recently, a majority of the applications of X-ray computed tomography (CT) scanning in plant sciences remained descriptive; some included a quantification of the plant materials when the root-soil isolation or branch-leaf separation was satisfactory; and a few involved the modeling of plant biology processes or the assessment of treatment or disease effects on plant biomass and structures during growth. In the last decade, repeated CT scanning of the same plants was reported in an increasing number of studies in which moderate doses of X-rays had been used. Besides the general objectives of Frontiers in Plant Science research topics, “Branching and Rooting Out with a CT Scanner” was proposed to meet specific objectives: (i) providing a non-technical update on knowledge about the application of CT scanning technology to plants, starting with the type of CT scanning data collected (CT images vs. CT numbers) and their processing in the graphical and numerical approaches; (ii) drawing the limits of the CT scanning approach, which because it is based on material density can distinguish materials with contrasting or moderately overlapping densities (e.g., branches vs. leaves, roots vs. non-organic soils) but not the others (e.g., roots vs. organic soils); (iii) explaining with a sufficient level of detail the main procedures used for graphical, quantitative and statistical analyses of plant CT scanning data, including fractal complexity measures and statistics appropriate for repeated plant CT scanning, in experiments where the research hypotheses are about biological processes such as light interception by canopies, root disease development and plant growth under stress conditions; (iv) comparing plant CT scanning with an alternative technology that applies to plants, such as the phenomics platforms which target leaf canopies; and (v) providing current and potential users of plant CT scanning with up-to-date information and exhaustive documentation, including clear perspectives and well-defined goals for the future, for them to be even more efficient or most efficient from start in their research work.

Beschreibung: Growing plants have a constitutive demand for sulfur to synthesize proteins, sulfolipids and other essential sulfur containing molecules for growth and development. The uptake and subsequent distribution of sulfate is regulated in response to demand and environmental cues. The importance of sulfate for plant growth and vigor and hence crop yield and nutritional quality for human and animal diets has been clearly recognized. The acquisition of sulfur by plants, however, has become an increasingly important concern for the agriculture due to the decreasing S-emissions from industrial sources and the consequent limitation of inputs from atmospheric deposition. Molecular characterization involving transcriptomics, proteomics and metabolomics in Arabidopsis thaliana as well as in major crops revealed that sulfate uptake, distribution and assimilation are finely regulated depending on sulfur status and demand, and that these regulatory networks are integrated with cell cycle, photosynthesis, carbohydrate metabolism, hormonal signaling, uptake and assimilation of other nutrients, etc., to enable plant growth, development, and reproduction even under different biotic and abiotic stresses. This knowledge can be used to underpin approaches to enhance plant growth and nutritional quality of major food crops around the world. Although considerable progress has been made regarding the central role of sulfur metabolism in plant growth, development and stress response, several frontiers need to be explored to reveal the mechanisms of the cross-talk between sulfur metabolism and these processes. In this research topic the knowledge on plant sulfur metabolism is reviewed and updated. Focus is put not only on molecular mechanisms of control of sulfur metabolism but also on its integration with other vital metabolic events. The topic covers 4 major areas of sulfur research: sulfate uptake, assimilation and metabolism, regulation, and role in stress response. We hope that the topic will promote interaction between researchers with different expertise and thus contribute to a more integrative approach to study sulfur metabolism in plants.

Beschreibung: Grain legumes, together with quinoa and amaranth (pseudocereals) and other crops are attractive candidates to satisfy the growing demand for plant protein production worldwide for food and feed. Despite their high value, many protein crops have not been adequately assessed and numerous species are underutilized. Special attention has to be paid to genetic diversity and landraces, and to the key limiting factors affecting yield, including water deficiency and other abiotic and biotic stresses, in order to obtain stable, reliable and sustainable crop production through the introduction and local adaptation of genetically improved varieties. Legumes, the main protein crops worldwide, contribute to the sustainable improvement of the environment due to their ability to fix nitrogen and their beneficial effects on the soil. They play a key role in the crop diversification and sustainable intensification of agriculture, particularly in light of new and urgent challenges, such as climate change and food security. In addition, the role of legumes in nutrition has been recognized as a relevant source of plant protein, together with other benefits for health. Chapters dealing with common bean, lupine, soybean, lentil, cowpea and Medicago are included in this book. Most contributions deal with legumes, but the significant number of papers on different aspects of quinoa gives an idea of the increasing importance of this protein crop. Pseudocereals, such as quinoa and amaranth, are good sources of proteins. Quinoa and amaranth seeds contain lysine, an essential amino acid that is limited in other grains. Nutritional evaluations of quinoa indicate that it constitutes a source of complete protein with a good balance among all of the amino acids needed for human diet, and also important minerals, vitamins, high quality oils and flavonoids. Other protein crops also included in this book are hemp, cotton and cereals (maize, wheat and rice). Although cereals protein content is not high, their seeds are largely used for human consumption. In this book are included articles dealing with all different aspects of protein crops, including nutritional value, breeding, genetic diversity, biotic and abiotic stress, cropping systems or omics, which may be considered crucial to help provide the plant proteins of the future. Overall, the participation of 169 authors in 29 chapters in this book indicates an active scientific community in the field, which appears to be an encouraging reflect of the global awareness of the need for sustainability and the promising future of proteins crops as a source of food and feed.

Beschreibung: Mycorrhizal symbiosis is a mutualistic association of plant roots and fungi that plays a major role in ecosystem function and diversification, as well as its stability and productivity. It also plays a key role in the biology and ecology of forest trees, affecting growth, water and nutrient absorption and protection against soil-borne pathogens. However, the mycorrhizal research in tropical and neotropical ecosystems remains largely unexplored despite its importance in tropical and neotropical ecosystems. These ecosystems represent more than 0.6% of the total land ecosystems and they have a crucial role in the Earth’s biogeochemical cycling and climate. Threats to tropical forest biodiversity should therefore encourage investigations and inventories of mycorrhizal diversity, function and ecology in tropical latitudes because they concern ecologically and economically important plant species. This Research Topic aims to provide an overview of the knowledge of mycorrhizal symbioses in tropical and neotropical ecosystems. For this Research Topic, we welcome articles that address the diversity, ecology and function of mycorrhiza associated with plants, the impacts of mycorrhiza on plant diversity and composition, the regeneration and dynamics of ecosystems, and biomass production in ecosystems.

Beschreibung: An increasing population faces the growing demand for agricultural products and accurate global climate models that account for individual plant morphologies to predict favorable human habitat. Both demands are rooted in an improved understanding of the mechanistic origins of plant development. Such understanding requires geometric and topological descriptors to characterize the phenotype of plants and its link to genotypes. However, the current plant phenotyping framework relies on simple length and diameter measurements, which fail to capture the exquisite architecture of plants. The Research Topic “Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences” is the result of a workshop held at National Institute for Mathematical and Biological Synthesis (NIMBioS) in Knoxville, Tennessee. From 2.-4. September 2015 over 40 scientists from mathematics, computer science, engineering, physics and biology came together to set new frontiers in combining plant phenotyping with recent results from shape theory at the interface of geometry and topology. In doing so, the Research Topic synthesizes the views from multiple disciplines to reveal the potential of new mathematical concepts to analyze and quantify the relationship between morphological plant features. As such, the Research Topic bundles examples of new mathematical techniques including persistent homology, graph-theory, and shape statistics to tackle questions in crop breeding, developmental biology, and vegetation modeling. The challenge to model plant morphology under field conditions is a central theme of the included papers to address the problems of climate change and food security, that require the integration of plant biology and mathematics from geometry and topology research applied to imaging and simulation techniques. The introductory white paper written by the workshop participants identifies future directions in research, education and policy making to integrate biological and mathematical approaches and to strengthen research at the interface of both disciplines.

Beschreibung: Natural diversity has been extensively used to understand plant biology and improve crops. However, studies were commonly based on visual phenotypes or on a few measurable parameters. Nowadays, a large number of parameters can be measured thanks to next generation sequencing, metabolomics, proteomics, and transcriptomics thus providing an unprecedented resolution in the detection of natural diversity. This enhanced resolution offers new possibilities in terms of understanding plant biology. Technology advances also contribute to a better assessment of the biodiversity loss currently taking place. Hence, the topic presents an overview on efforts for maintaining biological diversity in crops, on possibilities offered by recent technologies in the assessment of natural variation, and ends with examples of the diversity found even at the cellular level.

Beschreibung: The life of proteins starts and ends as amino acids. In addition to the primary function as protein building blocks, amino acids serve multiple other purposes to make a plant's life worth living. This is true especially for the amino acids of the glutamate family, namely glutamate (Glu), glutamine (Gln), proline (Pro) and arginine (Arg), as well as the product of Glu decarboxylation, ?-aminobutyric acid (GABA). Synthesis, accumulation, interconversion and degradation of these five compounds contribute in many ways to the regulation of plant development and to responses to environmental challenges. Glu and Gln hold key positions as entry points and master regulators of nitrogen metabolism in plants, and have a pivotal role in the regulatory interplay between carbon and nitrogen metabolism. Pro and GABA are among the best-studied compatible osmolytes that accumulate in response to water deficit, yet the full range of protective functions is still to be revealed. Arg, with its exceptionally high nitrogen-to-carbon ratio, has long been recognized as a major storage form of organic nitrogen. Most of the enzymes involved in metabolism of the amino acids of the glutamate family in plants have been identified or can be predicted according to similarity with animal or microbial homologues. However, for some of these enzymes the detailed biochemical properties still remain to be determined in order to understand activities in vivo. Additionally, uncertainties regarding the subcellular localization of proteins and especially the lack of knowledge about intracellular transport proteins leave significant gaps in our understanding of the metabolic network connecting Glu, Gln, Pro, GABA and Arg. While anabolic reactions are distributed between the cytosol and chloroplasts, catabolism of the amino acids of the glutamate family takes place in mitochondria and has been implicated in fueling energy-demanding physiological processes such as root elongation, recovery from stress, bolting and pollen tube elongation. Exceeding the metabolic functions, the amino acids of the glutamate family were recently identified as important signaling molecules in plants. Extracellular Glu, GABA and a range of other metabolites trigger responses in plant cells that resemble the actions of Glu and GABA as neurotransmitters in animals. Plant homologues of the Glu-gated ion channels from mammals and protein kinase signaling cascades have been implicated in these responses. Pollen tube growth and guidance depend on GABA signaling and the root architecture is specifically regulated by Glu. GABA and Pro signaling or metabolism were shown to contribute to the orchestration of defense and programmed cell death in response to pathogen attacks. Pro signaling was additionally proposed to regulate developmental processes and especially sexual reproduction. Arg is tightly linked to nitric oxide (NO) production and signaling in plants, although Arg-dependent NO-synthases could still not be identified. Potentially Arg-derived polyamines constitute the missing link between Arg and NO signaling in response to stress. Taken together, the amino acids of the glutamate family emerge as important signaling molecules that orchestrate plant growth and development by integrating the metabolic status of the plant with environmental signals, especially in stressful conditions. This research topic collects contributions from different facets of glutamate family amino acid signaling or metabolism to bring together, and integrate in a comprehensive view the latest advances in our understanding of the multiple functions of Glu-derived amino acids in plants.

Beschreibung: Fleshy Fruits are a late acquisition of plant evolution. In addition of protecting the seeds, these specialized organs unique to plants were developed to promote seed dispersal via the contribution of frugivorous animals. Fruit development and ripening is a complex process and understanding the underlying genetic and molecular program is a very active field of research. Part of the ripening process is directed to build up quality traits such as color, texture and aroma that make the fruit attractive and palatable. As fruit consumers, humans have developed a time long interaction with fruits which contributed to make the fruit ripening attributes conform our needs and preferences. This issue of Frontiers in Plant Science is intended to cover the most recent advances in our understanding of different aspects of fleshy fruit biology, including the genetic, molecular and metabolic mechanisms associated to each of the fruit quality traits. It is also of prime importance to consider the effects of environmental cues, cultural practices and postharvest methods, and to decipher the mechanism by which they impact fruit quality traits. Most of our knowledge of fleshy fruit development, ripening and quality traits comes from work done in a reduced number of species that are not only of economic importance but can also benefit from a number of genetic and genomic tools available to their specific research communities. For instance, working with tomato and grape offers several advantages since the genome sequences of these two fleshy fruit species have been deciphered and a wide range of biological and genetic resources have been developed. Ripening mutants are available for tomato which constitutes the main model system for fruit functional genomics. In addition, tomato is used as a reference species for climacteric fruit which ripening is controlled by the phytohormone ethylene. Likewise, grape is a reference species for non-climacteric fruit even though no single master switches controlling ripening initiation have been uncovered yet. In the last period, the genome sequence of an increased number of fruit crop species became available which creates a suitable situation for research communities around crops to get organized and information to be shared through public repositories. On the other hand, the availability of genome-wide expression profiling technologies has enabled an easier study of global transcriptional changes in fruit species where the sequenced genome is not yet available. In this issue authors will present recent progress including original data as well as authoritative reviews on our understanding of fleshy fruit biology focusing on tomato and grape as model species.

Beschreibung: One of the distinguishing features of plants is the presence of membrane-bound organelles called plastids. Starting from proplastids (undifferentiated plastids) they readily develop into specialised types, which are involved in a range of cellular functions such as photosynthesis, nitrogen assimilation, biosynthesis of sucrose, starch, chlorophyll, carotenoids, fatty acids, amino acids, and secondary metabolites as well as a number of metabolic reactions. The central role of plastids in many aspects of plant cell biology means an in-depth understanding is key for a holistic view of plant physiology. Despite the vast amount of research, the molecular details of many aspects of plastid biology remains limited. Plastids possess their own high-copy number genome known as the plastome. Manipulation of the plastid genome has been developed as an alternative way to developing transgenic plants for various biotechnological applications. High-copy number of the plastome, site-specific integration of transgenes through homologous recombination, and potential to express proteins at high levels (〉70% of total soluble proteins has been reported in some cases) are some of the technologies being developed. Additionally, plastids are inherited maternally, providing a natural gene containment system, and do not follow Mendelian laws of inheritance, allowing each individual member of the progeny of a transplastomic line to uniformly express transgene(s). Both algal and higher plant chloroplast transformation has been demonstrated, and with the ability to be propagated either in bioreactors or in the field, both systems are well suited for scale up of production. The manipulation of chloroplast genes is also essential for many approaches that attempt to increase biomass accumulation or re-routing metabolic pathways for biofortification, food and fuel production. This includes metabolic engineering for lipid production, adapting the light harvesting apparatus to improve solar conversion efficiencies and engineering means of suppressing photorespiration in crop species, which range from the introduction of artificial carbon concentrating mechanisms, or those pre-existing elsewhere in nature, to bypassing ribulose bisphosphate carboxylase/oxygenase entirely. The purpose of this eBook is to provide a compilation of the latest research on various aspects of plastid biology including basic biology, biopharming, metabolic engineering, bio-fortification, stress physiology, and biofuel production.One of the distinguishing features of plants is the presence of membrane-bound organelles called plastids. Starting from proplastids (undifferentiated plastids) they readily develop into specialised types, which are involved in a range of cellular functions such as photosynthesis, nitrogen assimilation, biosynthesis of sucrose, starch, chlorophyll, carotenoids, fatty acids, amino acids, and secondary metabolites as well as a number of metabolic reactions. The central role of plastids in many aspects of plant cell biology means an in-depth understanding is key for a holistic view of plant physiology. Despite the vast amount of research, the molecular details of many aspects of plastid biology remains limited. Plastids possess their own high-copy number genome known as the plastome. Manipulation of the plastid genome has been developed as an alternative way to developing transgenic plants for various biotechnological applications. High-copy number of the plastome, site-specific integration of transgenes through homologous recombination, and potential to express proteins at high levels (〉70% of total soluble proteins has been reported in some cases) are some of the technologies being developed. Additionally, plastids are inherited maternally, providing a natural gene containment system, and do not follow Mendelian laws of inheritance, allowing each individual member of the progeny of a transplastomic line to uniformly express transgene(s). Both algal and higher plant chloroplast transformation has been demonstrated, and with the ability to be propagated either in bioreactors or in the field, both systems are well suited for scale up of production. The manipulation of chloroplast genes is also essential for many approaches that attempt to increase biomass accumulation or re-routing metabolic pathways for biofortification, food and fuel production. This includes metabolic engineering for lipid production, adapting the light harvesting apparatus to improve solar conversion efficiencies and engineering means of suppressing photorespiration in crop species, which range from the introduction of artificial carbon concentrating mechanisms, or those pre-existing elsewhere in nature, to bypassing ribulose bisphosphate carboxylase/oxygenase entirely. The purpose of this eBook is to provide a compilation of the latest research on various aspects of plastid biology including basic biology, biopharming, metabolic engineering, bio-fortification, stress physiology, and biofuel production.

Beschreibung: Alterations in gene expression are essential during growth and development phases and when plants are exposed to environmental challenges. Stress conditions induce gene expression modifications, which are associated with changes in the biochemical and physiological processes that help plants to avoid or reduce potential damage resulting from these stresses.After exposure to stress, surviving plants tend to flower earlier than normal and therefore transfer the accumulated epigenetic information to their progenies, given that seeds, where this information is stored, are formed at a later stage of plant development.DNA methylation is correlated with expression repression. Likewise, miRNA produced in the cell can reduce the transcript abundance or even prevent translation of mRNA. However, histone modulation, such as histone acetylation, methylation, and ubiquitination, can show distinct effects on gene expression. These alterations can be inherited, especially if the plants are consistently exposed to a particular environmental stress. Retrotransposons and retroviruses are foreign movable DNA elements that play an important role in plant evolution. Recent studies have shown that epigenetic alterations control the movement and the expression of genes harbored within these elements. These epigenetic modifications have an impact on the morphology, and biotic and abiotic tolerance in the subsequent generations because they can be inherited through the transgenerational memory in plants. Therefore, epigenetic modifications, including DNA methylation, histone modifications, and small RNA interference, serve not only to alter gene expression but also may enhance the evolutionary process in eukaryotes.In this E-book, original research and review articles that cover issues related to the role of DNA methylation, histone modifications, and small RNA in plant transgenerational epigenetic memory were published.The knowledge published on this topic may add new insight on the involvement of epigenetic factors in natural selection and environmental adaptation. This information may also help to generate a modeling system to study the epigenetic role in evolution.

Beschreibung: Unfolded protein response (UPR) is a cellular adaptive response for restoring endoplasmic reticulum (ER) homeostasis in response to ER stress. Perturbation of the UPR and failure to restore ER homeostasis inevitably leads to diseases. It has now become evident that perturbation of the UPR is the cause of many important human diseases such as neurodegenerative diseases, cystic fibrosis, diabetes and cancer. It has recently emerged that virus infections can trigger the UPR but the relationship between virus infections and host UPR is intriguing. On one hand, UPR is harmful to the virus and virus has developed means to subvert the UPR. On the other hand, virus exploits the host UPR to assist in its own infection, gene expression, establishment of persistence, reactivation from latency and to evade the immune response. When this delicate balance of virus-host UPR interaction is broken down, it may cause diseases. This is particularly challenging for viruses that establish a chronic infection to maintain this balance. Each virus interacts with the host UPR in a different way to suit their life style and how the virus interacts with the host UPR can define the characteristic of a particular virus infection. Understanding how a particular virus interacts with the host UPR may pave the way to the design of a new class of anti-viral that targets this particular pathway to skew the response towards anti-virus. This knowledge can also be translated into the clinics to help re-design oncolytic virotherapy and gene therapy. In this research topic we aimed to compile a collection of focused review articles, original research articles, commentary, opinion, hypothesis and methods to highlight the current advances in this burgeoning area of research, in an attempt to provide an in-depth understanding of how viruses interact with the host UPR, which may be beneficial to the future combat of viral and human diseases.

Beschreibung: Chloroplasts are plant cell organelles that convert light energy into relatively stable chemical energy via the photosynthetic process. By doing so, they sustain life on Earth. Chloroplasts also provide diverse metabolic activities for plant cells, including the synthesis of fatty acids, membrane lipids, isoprenoids, tetrapyrroles, starch, and hormones. The biogenesis, morphogenesis, protection and senescence of chloroplasts are essential for maintaining a proper structure and function of chloroplasts, which will be the theme of this Research Topic. Chloroplasts are enclosed by an envelope of two membranes which encompass a third complex membrane system, the thylakoids, including grana and lamellae. In addition, starch grains, plastoglobules, stromules, eyespots, pyrenoids, etc. are also important structures of chloroplasts. It is widely accepted that chloroplasts evolved from a free-living photosynthetic cyanobacterium, which was engulfed by a eukaryotic cell. Chloroplasts retain a minimal genome, most of the chloroplast proteins are encoded by nuclear genes and the gene products are transported into the chloroplast through complex import machinery. The coordination of nuclear and plastid genome expressions establishes the framework of both anterograde and retrograde signaling pathways. As the leaf develops from the shoot apical meristem, proplastids and etioplastids differentiate into chloroplasts. Chloroplasts are divided by a huge protein complex, also called the plastid-dividing (PD) machinery, and their division is also regulated by many factors to get an optimized number and size of chloroplasts in the cell. These processes are fundamental for the biogenesis and three-dimensional dynamic structure of chloroplasts. During the photosynthesis, reactive oxygen species (ROS) and other cellular signals can be made. As an important metabolic hub of the plant cell, the chloroplast health has been found critical for a variety of abiotic and biotic stresses, including drought, high light, cold, heat, oxidative stresses, phosphate deprivation, and programmed cell death at sites of infection. Therefore, a better understanding the responses of chloroplasts to these stresses is part of knowing how the plant itself responds. Ultimately, this knowledge will be necessary to engineer crops more resistant to common stresses. With the current global environment changes, world population growth, and the pivotal role of chloroplasts in carbon metabolism, it is of great significance to represent the advancement in this field, for science and society. Tremendous progresses have been made in the field of chloroplast biology in recent years. Through concerted efforts from the community, greater discoveries definitely will emerge in the future.

Beschreibung: Ethylene is a simple gaseous phytohormone with multiple roles in regulation of metabolism at cellular, molecular, and whole plant level. It influences performance of plants under optimal and stressful environments by interacting with other signaling molecules. Understanding the ethylene biosynthesis and action through the plant’s life can contribute to improve the knowledge of plant functionality and use of this plant hormone may drive adaptation and defense of plants from the adverse environmental conditions. The action of ethylene depends on its concentration in cell and the sensitivity of plants to the hormone. In recent years, research on ethylene has been focused, due to its dual action, on the regulation of plant processes at physiological and molecular level. The involvement of ethylene in the regulation of transcription needs to be widely explored involving the interaction with other key molecular regulators. The aim of the current research topic was to explore and update our understanding on its regulatory role in plant developmental mechanisms at cellular or whole plant level under optimal and changing environmental conditions. The present edited volume includes original research papers and review articles describing ethylene’s regulatory role in plant development during plant ontogeny and also explains how it interacts with biotic and abiotic stress factors. This comprehensive collection of researches provide evidence that ethylene is essential in different physiological processes and does not always work alone, but in coordinated manner with other plant hormones. This research topic is also a source of tips for further works that should be addressed for the biology and molecular effects on plants.

Beschreibung: "Phenomics" is an emerging area of research whose aspiration is the systematic measurement of the physical, physiological and biochemical traits (the phenome) belonging to a given individual or collection of individuals. Non-destructive or minimally invasive techniques allow repeated measurements across time to follow phenotypes as a function of developmental time. These longitudinal traits promise new insights into the ways in which crops respond to their environment including how they are managed. To maximize the benefit, these approaches should ideally be scalable so that large populations in multiple environments can be sampled repeatedly at reasonable cost. Thus, the development and validation of non-contact sensing technologies remains an area of intensive activity that ranges from Remote Sensing of crops within the landscape to high resolution at the subcellular level. Integration of this potentially highly dimensional data and linking it with variation at the genetic level is an ongoing challenge that promises to release the potential of both established and under-exploited crops.

Beschreibung: Epigenetics is a new field that explains gene expression at the chromatin structure and organization level. Three principal epigenetic mechanisms are known and hundreds of combinations among them can develop different phenotypic characteristics. DNA methylation, histone modifications and small RNAs have been identified, and their functions are being studied in order to understand the mechanisms of interaction and regulation among the different biological processes in plants. Although, fundamental epigenetic mechanisms in crop plants are beginning to be elucidated, the comprehension of the different epigenetic mechanisms, by which plant gene regulation and phenotype are modified, is a major topic to develop in the near future in order to increase crop productivity. Thus, the importance of epigenetics in improving crop productivity is undoubtedly growing. Current research on epigenetics suggest that DNA methylation, histone modifications and small RNAs are involved in almost every aspect of plant life including agronomically important traits such as flowering time, fruit development, responses to environmental factors, defense response and plant growth. The aim of this Research Topic is to explore the recent advances concerning the role of epigenetics in crop biotechnology, as well as to enhance and promote interactions among high quality researchers from different disciplines such as genetics, cell biology, pathology, microbiology, and evolutionary biology in order to join forces and decipher the epigenetic mechanisms in crop productivity.

Beschreibung: In response to environmental stresses, or during development, plant cells will produce lipids that will act as intracellular or intercellular mediators. Glycerophospholipid and/or sphingolipid second messengers resulting from the action of lipid metabolizing enzymes (e.g. lipid-kinases or lipases) are commonly found within cells. The importance of such mediating lipids in plants has become increasingly apparent. Responses to biotic and abiotic stresses, and to plant hormones, all appear to involve and require lipid signals. Likewise, developmental processes, in particular polarized growth, seem also to involve signalling lipids. Amongst these lipids, phosphatidic acid (PA) has received the most attention. It can be produced by phospholipases D, but also by diacylglycerol kinases coupled to phospholipases C. Proteins that bind phosphatidic acid, and for which the activity is altered upon binding, have been identified. Furthermore, other lipids are also important in signalling processes. PA can be phosphorylated into diacylglycerol-pyrophosphate, and plants are one of the first biological models where the production of this lipid has been reported, and its implication in signal transduction have been demonstrated. PA can also be deacylated into lyso- phosphatidic acid. The phosphorylated phosphatidylinositols, i.e. the phosphoinositides, can act as substrate of phospholipases C, but are also mediating lipids per se, since proteins that bind them have been identified. Other important lipid mediators belong to the sphingolipid family such the phosphorylated phytosphingosine, or long-chain bases. Many questions remain unanswered concerning lipid signalling in plants. Understanding and discussing current knowledge on these mechanisms will provide insights into plant mechanisms in response to constraints, either developmental or environmental.

Beschreibung: The broad host range pathogenic bacterium Agrobacterium tumefaciens has been widely studied as a model system to understand horizontal gene flow, secretion of effector proteins into host cells, and plant-pathogen interactions. Agrobacterium-mediated plant transformation also is the major method for generating transgenic plants for research and biotechnology purposes. Agrobacterium species have the natural ability to conduct interkingdom genetic transfer from bacteria to eukaryotes, including most plant species, yeast, fungi, and even animal cells. In nature, A. tumefaciens causes crown gall disease resulting from expression in plants of auxin and cytokinin biosynthesis genes encoded by the transferred (T-) DNA. Gene transfer from A. tumefaciens to host cells requires virulence (vir) genes that reside on the resident tumor-inducing (Ti) plasmid. In addition to T-DNA, several Virulence (Vir) effector proteins are also translocated to host cells through a bacterial type IV secretion system. These proteins aid in T-DNA trafficking through the host cell cytoplasm, nuclear targeting, and T-DNA integration. Genes within native T-DNAs can be replaced by any gene of interest, making Agrobacterium species important tools for plant research and genetic engineering. In this research topic, we provided updated information on several important areas of Agrobacterium biology and its use for biotechnology purposes.

Beschreibung: In all living organisms, essential micronutrients are cofactors of many ubiquitous proteins that participate in crucial metabolic pathways, but can also be toxic when present in excessive concentrations. In order to achieve correct homeostasis, plants need to control uptake of metals from the environment, their distribution to organs and tissues, and their subcellular compartmentalization. They also have to avoid deleterious accumulation of metals and metalloids such as Cd, As and Al. These multiple steps are controlled by their transport across various membrane structures and their storage in different organelles. Thus, integration of these transport systems required for micronutrient trafficking within the plant is necessary for physiological processes to work efficiently. To cope with the variable availability of micronutrients, plants have evolved an intricate collection of physiological and developmental processes, which are under tight control of short- and long-range signaling pathways. Understanding how plants perceive and deal with different micronutrient concentrations, from regulation to active transport, is important to completing the puzzle of plant metal homeostasis. This is an essential area of research, with several implications for plant biology, agriculture and human nutrition. There is a rising interest in developing plants that efficiently mobilize specific metals and prosper in soils with limited micronutrient availability, as well as those that can selectively accumulate beneficial micronutrients in the edible parts while avoiding contaminants such as Cd and As. However, there is still an important gap in our understanding of how nutrients reach the seeds and the relative contribution of each step in the long pathway from the rhizosphere to the seed. Possible rate-limiting steps for micronutrient accumulation in grains should be the primary targets of biotechnological interventions aiming at biofortification. Over the last 10 years, many micronutrient uptake- and transport-related processes have been identified at the molecular and physiological level. The systematic search for mutants and transcriptional responses has allowed analysis of micronutrient-signaling pathways at the cellular level, whereas physiological approaches have been particularly useful in describing micronutrient-signaling processes at the organ and whole-plant level. Large-scale elemental profiling using high-throughput analytical methodologies and their integration with both bioinformatics and genetic tools, along with metal speciation, have been used to decipher the functions of genes that control micronutrients homeostasis. In this research topic, we will follow the pathway of metal movement from the soil to the seed and describe the suggested roles of identified gene products in an effort to understand how plants acquire micronutrients from the soil, how they partition among different tissues and subcellular organelles, and how they regulate their deficiency and overload responses. We also highlight the current work on heavy metals and metalloids uptake and accumulation, the studies on metal selectivity in transporters and the cross-talk between micro and macronutrients. Thus, we believe a continued dialogue and sharing of ideas amongst plant scientists is critical to a better understanding of metal movement into and within the plant.

Beschreibung: The plant factory is a facility that aids the steady production of high-quality vegetables all year round by artificially controlling the cultivation environment (e.g., light, temperature, humidity, carbon dioxide concentration, and culture solution), allowing growers to plan production. By controlling theinternal environment,plant factories can produce vegetables about two to four times faster than by typical outdoor cultivation. In addition, as multiple cultivation shelves (a multi-shelf system) are used, the mass production of vegetables in a small space is facilitated. This research topic presents some new trends on intelligent measuring systems; environment controlled and optimization; favonoids; phenylpropanoids, transcriptomes, and bacteria.

Beschreibung: The nucleolus is a prominent nuclear domain that is common to eukaryotes. Since the nucleolus was first described in the 1830s, its identity had remained a mystery for longer than 100 years. Major advances in understanding of the nucleolus were achieved through electron microscopic and biochemical studies in the 1960s to 1970s followed by molecular biological studies. These studies finally established the view of the nucleolus that it is a large aggregate of RNA-protein complexes associated with the rRNA gene region of chromosome DNA, serving mainly as a site of ribosome biogenesis, where pre-rRNA transcription, pre-rRNA processing, and ribosome assembly occur. This function of the nucleolus appears to indicate that the nucleolus plays a constitutive and essential role in fundamental cellular activities by producing ribosomes. Recent research has shown, however, that the nucleolus is more dynamic and can have more specific and wider functions. In plants, nucleolar functions have been implicated in developmental regulations and environmental responses by accumulating pieces of evidence obtained mostly from genetic studies of nucleolar factor-related mutants. Comprehensive analysis of nucleolar proteins and molecular cytological characterization of sub-nucleolar and peri-nucelolar bodies have also provided new insights into behaviors and functions of the plant nucleolus.〈/p〉In this Research Topic, we would like to collect physiological and molecular links between the nucleolus to plant growth and development, shed light on novel aspects of nucleolar functions beyond its classical view, and stimulate research activities focusing on the nucleolus across various fields of plant science, including molecular biology, cell biology, genetics, developmental biology, physiology, and evolutionary biology.

Beschreibung: Natural and anthropogenic grasslands such as prairies, meadows, rangelands, and pastures cover more than 40% of the planet’s surface and provide a wealth of ecological services. Grasslands alone store one third of the global carbon stocks and grass roots, through their specific architectures, ensure water cycling and prevent the erosion of fertile topsoil. In addition, grasslands are of vital importance for human food production as vast areas of rangelands and pastures provide feed for livestock. Pastoral legumes mobilize atmospheric nitrogen and improve fertility of arable soils. Not least, grasslands are an essential genetic resource. The three major crop species that feed half of the global population have been bred from wild grasses. Ancestors of our contemporary turf cultivars, common components of urban landscapes and recreation spaces, originated from wild grasslands. Although natural and managed grasslands represent pivotal ecosystems, many aspects of how they function are poorly understood. To date, most attention has focused on grassland primary producers (i.e. forage plants) and mammalian grazers but invertebrates are likely to play an equally, if not more important role in grassland ecosystem functioning. In Australian pastures, for example, the biomass of root-feeding scarab beetles can often exceed that of sheep and plant damage caused by invertebrates is sometimes equivalent to an average dairy cow’s grass consumption. Indeed, grasslands are one of the most densely populated ecosystems with invertebrates being probably the most important engineers that shape both plant communities and the grassland as a whole. In a rapidly changing world with increasing anthropogenic pressure on grasslands, this Research Topic focuses on: 1. How grassland habitats shape invertebrate biodiversity 2. Impacts of climate change on grassland-invertebrate interactions 3. Plant and invertebrate pest monitoring and management 4. Plant-mediated multitrophic interactions and biological control in grasslands 5. Land use and grassland invertebrates 6. Plant resistance to invertebrate pests Given the increasing demand for food and land for human habitation, unprecedented threats to grasslands are anticipated. Resilient to some extent, these key ecosystems need to be better comprehended to guarantee their sustainable management and ecosystem services.

Beschreibung: Plants, as sessile organisms, are exposed to a large array of challenging external and internal alterations that may restrict plant growth. These limiting growth conditions activate plant signalling responses which eventually target the protein synthesis machinery to rapidly reprogram plant metabolism to adapt to the new situation. Thus, the control of mRNA translation is one key regulatory step of gene expression and it is an essential molecular mechanism used by plants to bring about impressive growth plasticity. Compared to the vast number of studies aimed to identify plant transcriptional changes upon hormonal or environmental cues, the subsequent steps of mRNA transport, stability, storage, and eventually translational regulation, have been less studied in plants. This lack of knowledge concerns not only the fate of protein-coding transcripts in plants, but also the biogenesis and maturation of rRNAs, tRNAs and the plant translation factors involved. In this eBook we have focused on how internal cues and external signals of either biotic or abiotic origin impact translation to adjust plant growth and development. We have collected altogether ten scientific contributions to extend the knowledge on plant post-transcriptional and translational events that regulate the production of proteins that execute the required cellular functions. We hope that this compilation of original research articles and reviews will provide the readers with a detailed update on the state of knowledge in this field, and also with additional motivation to improve plant growth adaptation to future environmental challenges.

Beschreibung: Besides increasing crop yield to feed the growing population, improving crop quality is a challenging and key issue. Indeed, quality determines consumer acceptability and increases the attractivity of fresh and processed products. In this respect, fruit and vegetables, which represent a main source of vitamins and other health compounds, play a major role in human diet. This is the case in developing countries where populations are prone to nutritional deficiencies, but this is also a pending issue worldwide, where the growing middle class is increasingly aware and in search of healthy food. So a future challenge for the global horticultural industry will be to answer the demand for better quality food in a changing environment, where many resources will be limited. This e-collection collates state-of-the-art research on the quality of horticultural crops, covering the underlying physiological processes, the genetic and environmental controls during plant and organ development and the postharvest evolution of quality during storage and processing.

Beschreibung: Secretomics describes the global study of proteins that are secreted by a cell, a tissue or an organism, and has recently emerged as a field for which interest is rapidly growing. The term secretome was first coined at the turn of the millennium and was defined to comprise not only the native secreted proteins released into the extracellular space but also the components of machineries for protein secretion. Two secretory pathways have been described in fungi: i) the canonical pathway through which proteins bearing a N-terminal peptide signal can traverse the endoplasmic reticulum and Golgi apparatus, and ii) the unconventional pathway for proteins lacking a peptide signal. Protein secretion systems are more diverse in bacteria, in which types I to VII pathways as well as Sec or two-arginine (Tat) pathways have been described. In oomycete species, effectors are mostly small proteins containing an N-terminal signal peptide for secretion and additional C-terminal motifs such as RXLRs and CRNs for host targeting. It has recently been shown that oomycetes exploit non-conventional secretion mechanisms to transfer certain proteins to the extracellular environment. Other non-classical secretion systems involved in plant-fugal interaction include extracellular vesicles (EVs, Figure 1 from Samuel et al 2016 Front. Plant Sci. 6:766.). The versatility of oomycetes, fungi and bacteria allows them to associate with plants in many ways depending on whether they are biotroph, hemibiotroph, necrotroph, or saprotroph. When interacting with a live organism, a microbe will invade its plant host and manipulate its metabolisms either detrimentally if it is a pathogen or beneficially if it is a symbiote. Deciphering secretomes became a crucial biological question when an increasing body of evidence indicated that secreted proteins were the main effectors initiating interactions, whether of pathogenic or symbiotic nature, between microbes and their plant hosts. Secretomics may help to contribute to the global food security and to the ecosystem sustainability by addressing issues in i) plant biosecurity, with the design of crops resistant to pathogens, ii) crop yield enhancement, for example driven by arbuscular mycorrhizal fungi helping plant hosts utilise phosphate from the soil hence increase biomass, and iii) renewable energy, through the identification of microbial enzymes able to augment the bio-conversion of plant lignocellulosic materials for the production of second generation biofuels that do not compete with food production. To this day, more than a hundred secretomics studies have been published on all taxa and the number of publications is increasing steadily. Secretory pathways have been described in various species of microbes and/or their plant hosts, yet the functions of proteins secreted outside the cell remain to be fully grasped. This Research Topic aims at discussing how secretomics can assist the scientists in gaining knowledge about the mechanisms underpinning plant-microbe interactions.

Beschreibung: Reversible ubiquitylation plays an important regulatory role in almost all aspects of cellular and organismal processes in plants. Its pervasive regulatory role in plant biology is primarily due to the involvement of a large set of ubiquitin system constituents (encoded by approximately 6% Arabidopsis genome), the huge number of important cellular proteins targeted as substrates, and various drastic effects on the modified proteins. The major components of the ubiquitin system include a large set of enzymes and proteins involved in ubiquitin conjugation (E1s, E2s, and E3s) and deconjugation (deubiquitinases of different classes) and post ubiquitin conjugation components such as ubiquitin receptors, endocytic machineries, and 26S proteasome. The established substrates include transcriptional activators and repressors, signaling components, key metabolic enzymes, and critical mechanistic components of major cellular processes and regulatory mechanisms. Post-translational modification of proteins by reversible ubiquitylation could drastically affects the modified proteins by proteolytic processing and turnover, altering catalytic activity, subcellular targeting, and protein-protein interaction. Continued efforts are being carried out to identify novel substrates critical for various cellular and organismal processes, to determine effects of reversible ubiquitylation on the modified substrates, to determine signaling determinants triggering reversible ubiquitylation of specific substrates, to illustrate individual components of the ubiquitin system for their in vivo functions and involved mechanistic roles, and to determine mechanistic roles of modification acting on critical components of major cellular processes and regulatory mechanisms. The aim of this special topic is to serve as a platform to report most recent advances on those above listed current research endeavors. We welcome article types including original research, review, mini review, method, and perspective/opinion/hypothesis.

Beschreibung: Aquaporins (AQPs), a class of integral membrane proteins, form channels facilitating movement of water and many other solutes. In solute transport systems of all living organisms including plants, animals and fungi, AQPs play a vital role. Plants contain a much higher number of AQP genes compared to animals, the likely consequence of genome duplication events and higher ploidy levels. As a result of duplication and subsequent diversification, plant AQPs have evolved several subfamilies with very diverse functions. Plant AQPs are highly selective for specific solutes because of their unique structural features. For instance, ar/R selectivity filters and NPA domains have been found to be key elements in governing solute permeability through the AQP channels. Combination of conserved motifs and specific amino acids influencing pore morphology appears to regulate the permeability of specific solutes such as water, urea, CO2, H2O2, boric acid, silicic acid and many more. The discovery of novel AQPs has been accelerated over the last few years with the increasing availability of genomic and transcriptomic data. The expanding number of well characterised AQPs provides opportunities to understand factors influencing water transport, nutritional uptake, and elemental balance. Homology-based search tools and phylogenetic analyses offer efficient strategies for AQP identification. Subsequent characterization can be based on different approaches involving proteomics, genomics, and transcriptomic tools. The combination of these technological advances make it possible to efficiently study the inter-dependency of AQPs, regulation through phosphorylation and reversible phosphorylation, networking with other transporters, structural features, pH gating systems, trafficking and degradation. Several studies have supported the role of AQPs in differential phenotypic responses to abiotic and biotic stress in plants. Crop improvement programs aiming for the development of cultivars with higher tolerance against stresses like drought, flooding, salinity and many biotic diseases, can explore and exploit the finely tuned AQP-regulated transport system. For instance, a promising approach in crop breeding programs is the utilization of genetic variation in AQPs for the development of stress tolerant cultivars. Similarly, transgenic and mutagenesis approaches provide an opportunity to better understand the AQP transport system with subsequent applications for the development of climate-smart drought-tolerant cultivars. The contributions to this Frontiers in Plant Science Research Topic have highlighted the evolution and phylogenetic distribution of AQPs in several plant species. Numerous aspects of regulation that seek to explain AQP-mediated transport system have been addressed. These contributions will help to improve our understanding of AQPs and their role in important physiological aspects and will bring AQP research closer to practical applications.

Beschreibung: Understanding plant responses to abiotic stresses is central to our ability to predict the impact of global change and environmental pollution on the production of food, feed and forestry. Besides increasing carbon dioxide concentration and rising global temperature, increasingly frequent and severe climatic events (e.g. extended droughts, heat waves, flooding) are expected in the coming decades. Additionally, pollution (e.g. heavy metals, gaseous pollutants such as ozone or sulfur dioxide) is an important factor in many regions, decreasing plant productivity and product quality. This Research topic focuses on stress responses at the level of whole plants, addressing biomass-related processes (development of the root system, root respiration/fermentation, leaf expansion, stomatal regulation, photosynthetic capacity, leaf senescence, yield) and interactions between organs (transport via xylem and phloem, long-distance signaling and secondary metabolites). Comparisons between species and between varieties of the same species are helpful to evaluate the potential for species selection and genetic improvement. This research topic is focused on the following abiotic stresses and interactions between them: - Increased carbon dioxide concentration in ambient air is an important parameter influenced by global change and affects photosynthesis, stomatal regulation, plant growth and finally yield. - Elevated temperature: both the steady rise in average temperature and extreme events of shorter duration (heat waves) must be considered in the context of alterations in carbon balance through increased photorespiration, decreased Rubisco activation and carboxylation efficiency, damage to photosynthetic apparatus, as well as loss of water via transpiration and stomatal sensitivity. - Low temperatures (late frosts, prolonged cold phases, freezing temperature) can decrease overwintering survival rates, productivity of crop plants and species composition in meadows. - Water availability: More frequent, severe and extended drought periods have been predicted by climate change models. The timing and duration of a drought period is crucial to determining plant responses, particularly if the drought event coincides with an increase in temperature. Drought causes stomatal closure, decreasing the cooling potential of transpiration and potentially leading to thermal stress as leaf temperature rises. Waterlogging may become also more relevant during the next decades and is especially important for seedlings and young plants. It is not the presence of water itself that causes the stress, but the exclusion of oxygen from the soil which causes a decrease in respiration and an increase in fermentation rates followed by a period of potential oxidative stress as water recedes. - Salinity: high salt concentration in soil influences soil water potential, the water status of the plant and hence affects productivity. Salt tolerance will become an important trait driven by increased competition for land and the need to exploit marginal lands.

Beschreibung: Competitiveness describes a key ability important for plants to grow and survive abiotic and biotic stresses. Under optimal, but particularly under non-optimal conditions, plants compete for resources including nutrients, light, water, space, pollinators and other. Competition occurs above- and belowground. In resource-poor habitats, competition is generally considered to be more pronounced than in resource-rich habitats. Although competition occurs between different players within an ecosystem such as between plants and soil microorganisms, our topic focusses on plant-plant interactions and includes inter-specific competition between different species of similar and different life forms and intra-specific competition. Strategies for securing resources via spatial or temporal separation and different resource needs generally reduce competition. Increasingly important is the effect of invasive plants and subsequent decline in biodiversity and ecosystem function. Current knowledge and future climate predictions suggest that in some situations competition will be intensified with occurrence of increased abiotic (e.g. water and nutrient limitations) and biotic stresses (e.g. mass outbreak of insects), but competition might also decrease in situations where plant productivity and survival declines (e.g. habitats with degraded soils). Changing interactions, climate change and biological invasions place new challenges on ecosystems. Understanding processes and mechanisms that underlie the interactions between plants and environmental factors will aid predictions and intervention. There is much need to develop strategies to secure ecosystem services via primary productivity and to prevent the continued loss of biodiversity. This Research Topic provides an up-to-date account of knowledge on plant-plant interactions with a focus on identifying the mechanisms underpinning competitive ability. The Research Topic aims to showcase knowledge that links ecological relevance with physiological processes to better understanding plant and ecosystem function.

Beschreibung: Fungi of the order Pucciniales cause rust diseases on many plants including important crops and trees widely used in agriculture, forestry and bioenergy programs; these encompass gymnosperms and angiosperms, monocots and dicots, perennial and annual plant species. These fungi are obligate biotrophs and -except for a few cases- cannot be cultivated outside their hosts in a laboratory. For this reason, standard functional and molecular genetic approaches to study these pathogens are very challenging and the means to study their biology, i.e. how they infect, develop and reproduce on plant hosts, are rather limited, even though they rank among the most devastating pathogens. Among fungal plant pathogens, rust fungi display the most complex lifecycles with up to five different spore forms and for many rust fungi, unrelated alternate hosts on which sexual and clonal reproduction are achieved. The genomics revolution and particularly the application of new generation sequencing technologies have greatly changed the way we now address biological studies and has in particular accelerated and made feasible, molecular studies on non-model species, such as rust fungi. The goal of this research topic is to gather articles that present recent advances in the understanding of rust fungi biology, their complex lifecycles and obligate biotrophic interactions with their hosts, through the means of genomics. This includes genome sequencing and/or resequencing of isolates, RNA-Seq or large-scale transcriptome analyses, genome-scale detailed annotation of gene families, and comparative analyses among the various rust fungi and, where feasible, with other obligate biotrophs or fungi displaying distinct trophic modes. This Research Topic provides a great opportunity to provide an up-to-date account of rust fungus biology through the lens of genomics, including state-of-the-art technologies developed to achieve this knowledge.

Beschreibung: Chloroplasts and mitochondria both have a prokaryotic origin, carry essential genes on their own highly reduced genome and generate energy in the form of ATP for the plant cell. The ion composition and concentration in these bioenergetic organelles impact photosynthesis, respiration and stress responses in plants. Early electrophysiological and biochemical studies provided strong evidence for the presence of ion channels and ion transporters in chloroplast and mitochondrial membranes. However, it wasn’t until the last decade that the development of model organisms such as Arabidopsis thaliana and Chlamydomonas reinhardtii along with improved genetic tools to study cell physiolgy have led to the discovery of several genes encoding for ion transport proteins in chloroplasts and mitochondria. For the first time, these discoveries have enabled detailed studies on the essential physiological function of the organellar ion flux. This Research Topic welcomed updated overviews and comprehensive investigations on already identified and novel ion transport components involved in physiology of chloroplasts and mitochondria in green organisms.

Beschreibung: Life presumably arose in the primeval oceans with similar or even greater salinity than the present ocean, so the ancient cells were designed to withstand salinity. However, the immediate ancestors of land plants most likely lived in fresh, or slightly brackish, water. The fresh/brackish water origins might explain why many land plants, including some cereals, can withstand moderate salinity, but only 1 – 2 % of all the higher plant species were able to re-discover their saline origins again and survive at increased salinities close to that of seawater. From a practical side, salinity is among the major threats to agriculture, having been one of the reasons for the demise of the ancient Mesopotamian Sumer civilisation and in the present time causing huge annual economic losses of over 10 billion USD. The effects of salinity on plants include osmotic stress, disruption of membrane ion transport, direct toxicity of high cytoplasmic concentrations of sodium and chloride on cellular processes and induced oxidative stress. Ion transport is the crucial starting point that determines salinity tolerance in plants. Transport via membranes is mediated mostly by the ion channels and transporters, which ensure selective passage of specific ions. The molecular and structural diversity of these ion channels and transporters is amazing. Obtaining the detailed descriptions of distinct ion channels and transporters present in halophytes, marine algae and salt-tolerant fungi and then progressing to the cellular and the whole organism mechanisms, is one of the logical ways to understand high salinity tolerance. Transfer of the genes from halophytes to agricultural crops is a means to increase salt tolerance of the crops. The theoretical scientific approaches involve protein chemistry, structure-function relations of membrane proteins, synthetic biology, systems biology and physiology of stress and ion homeostasis. At the time of compiling this e-book many aspects of ion transport under salinity stress are not yet well understood. The e-book has attracted researchers in ion transport and salinity tolerance. We have combined our efforts to achieve a wider, more detailed understanding of salt tolerance in plants mediated by ion transport, to understand present and future ways to modify and manipulate ion transport and salinity tolerance and also to find natural limits for the modifications.

Beschreibung: The World population will reach 9 billion by 2050, with the majority of this growth occurring in developing countries. On the other hand, one in nine of the World's population suffers from chronic hunger, the vast majority of which live in developing countries. We therefore need to find new and sustainable solutions to feed this increasing population and alleviate the predicted negative impact of global changes on crop production. This e-Book deals with new strategies to improve food security and livelihoods in rural communities, reduce vulnerability, increase resilience and mitigate lthe impact of climate change and land degradation on agriculture. This collection of 18 articles addresses the major abiotic factors limiting crop production worldwide, how to characterize and exploit the available plant biodiversity to increase production and sustainability in agrosystems, and the use of beneficial microbes to improve production and reduce the use of fertilizers and pesticides.

Beschreibung: The study of plant cell physiology is currently experiencing a profound transformation. Novel techniques allow dynamic in vivo imaging with subcellular resolution, covering a rapidly growing range of plant cell physiology. Several basic biological questions that have been inaccessible by the traditional combination of biochemical, physiological and cell biological approaches now see major progress. Instead of grinding up tissues, destroying their organisation, or describing cell- and tissue structure, without a measure for its function, novel imaging approaches can provide the critical link between localisation, function and dynamics. Thanks to a fast growing collection of available fluorescent protein variants and sensors, along with innovative new microscopy technologies and quantitative analysis tools, a wide range of plant biology can now be studied in vivo, including cell morphology & migration, protein localization, topology & movement, protein-protein interaction, organelle dynamics, as well as ion, ROS & redox dynamics. Within the cell, genetic targeting of fluorescent protein probes to different organelles and subcellular locations has started to reveal the stringently compartmentalized nature of cell physiology and its sophisticated spatiotemporal regulation in response to environmental stimuli. Most importantly, such cellular processes can be monitored in their natural 3D context, even in complex tissues and organs – a condition not easily met in studies on mammalian cells. Recent new insights into plant cell physiology by functional imaging have been largely driven by technological developments, such as the design of novel sensors, innovative microscopy & imaging techniques and the quantitative analysis of complex image data. Rapid further advances are expected which will require close interdisciplinary interaction of plant biologists with chemists, physicists, mathematicians and computer scientists. High-throughput approaches will become increasingly important, to fill genomic data with ‘life’ on the scale of cell physiology. If the vast body of information generated in the -omics era is to generate actual mechanistic understanding of how the live plant cell works, functional imaging has enormous potential to adopt the role of a versatile standard tool across plant biology and crop breeding. We welcome original research papers, methodological papers, reviews and mini reviews, with particular attention to contributions in which novel imaging techniques enhance our understanding of plant cell physiology and permits to answer questions that cannot be easily addressed with other techniques.

Beschreibung: Plastids are plant cell-specific organelles of endosymbiotic origin that contain their own genome, the so-called plastome. Its proper expression is essential for faithful chloroplast biogenesis during seedling development and for the establishment of photosynthetic and other biosynthetic functions in the organelle. The structural organisation, replication and expression of this plastid genome, thus, has been studied for many years, but many essential steps are still not understood. Especially, the structural and functional involvement of various regulatory proteins in these processes is still a matter of research. Studies from the last two decades demonstrated that a plethora of proteins act as specific regulators during replication, transcription, post-transcription, translation and post-translation accommodating a proper inheritance and expression of the plastome. Their number exceeds by far the number of the genes encoded by the plastome suggesting that a strong evolutionary pressure is maintaining the plastome in its present stage. The plastome gene organisation in vascular plants was found to be highly conserved, while algae exhibit a certain flexibility in gene number and organisation. These regulatory proteins are, therefore, an important determinant for the high degree of conservation in plant plastomes. A deeper understanding of individual roles and functions of such proteins would improve largely our understanding of plastid biogenesis and function, a knowledge that will be essential in the development of more efficient and productive plants for agriculture. The latter represents a major socio-economic need of fast growing mankind that asks for increased supply of food, fibres and biofuels in the coming decades despite the threats exerted by global change and fast spreading urbanisation.

Beschreibung: The charophytes are the group of green algae that are anestral and most closely related to land plants. Today, these organisms are not only important in evoutionary studies but have become outstanding model organisms for plant research.

Beschreibung: In this Frontiers topic, we explore how the functions and fates of plant silicon interact with other organisms and ecosystem processes. By bringing together new data from multiple disciplines and scales, we present a cross-section of novel explorations into how plants use silicon and the implications for agriculture and ecosystems. Key aims in this field are to understand the determinants of plant silicon uptake and cycling, and the benefits that silicon uptake confers on plants, including reducing the impacts of stresses such as herbivory. Current research explores inter-specific interactions, including co-evolutionary relationships between plant silicon and animals, particularly morphological adaptations, behavioural responses and the potential for plant silicon to regulate mammal populations. Another emerging area of research is understanding silicon fluxes in soils and vegetation communities and scaling this up to better understand the global silicon cycle. New methods for measuring plant silicon are contributing to progress in this field. Silicon could help plants mitigate some effects of climate change through alleviation of biotic and abiotic stress and silicon is a component of some carbon sinks. Therefore, understanding the role of plant silicon across ecological, agricultural and biogeochemical disciplines is increasingly important in the context of global environmental change.

Beschreibung: In contrast to the situation in heterotrophic organisms, plant genomes code for a significantly larger number of oxidoreductases such as thioredoxins (TRXs) and glutaredoxins (GRXs). These proteins provide a biochemical mechanism that allows the rapid and reversible activation or deactivation of protein functions in response to changing environmental conditions, as oxidative conditions caused by excessive photosynthesis. Indeed, owing to the fact that cysteines are sensitive to oxidation, TRXs and GRXs play an essential role in controlling the redox state of protein thiol groups. These redox-dependent post-translational modifications have proven to be critical for many cellular functions constituting regulatory, signalling or protective mechanisms. The articles contained in this Research Topic provide timely overviews and new insights into thiol-dependent redox regulation mechanisms with a focus on TRX- and GRX-based reduction systems in plants. The different contexts discussed take into account physiological, developmental and environmental conditions.

Beschreibung: This eBook presents all 10 articles published under the Frontiers Research Topic "Evolutionary Feedbacks Between Population Biology and Genome Architecture", edited by Scott V. Edwards and Tariq Ezaz. With the rise of rapid genome sequencing across the Tree of Life, challenges arise in understanding the major evolutionary forces influencing the structure of microbial and eukaryotic genomes, in particular the prevalence of natural selection versus genetic drift in shaping those genomes. Additional complexities in understanding genome architecture arise with the increasing incidence of interspecific hybridization as a force for shaping genotypes and phenotypes. A key paradigm shift facilitating a more nuanced interpretation of genomes came with the rise of the nearly neutral theory in the 1970s, followed by a greater appreciation for the contribution of nonadaptive forces such as genetic drift to genome structure in the 1990s and 2000s. The articles published in this eBook grapple with these issues and provide an update as to the ways in which modern population genetics and genome informatics deepen our understanding of the subtle interplay between these myriad forces. From intraspecific to macroevolutionary studies, population biology and population genetics are now major tools for understanding the broad landscape of how genomes evolve across the Tree of Life. This volume is a celebration across diverse taxa of the contributions of population genetics thinking to genome studies. We hope it spurs additional research and clarity in the ongoing search for rules governing the evolution of genomes.

Beschreibung: Abiotic stresses such as high temperature, low-temperature, drought and salinity limit crop productivity worldwide. Understanding plant responses to these stresses is essential for rational engineering of crop plants. In Arabidopsis, the signal transduction pathways for abiotic stresses, light, several phytohormones and pathogenesis have been elucidated. A significant portion of plant genomes (Arabidopsis and rice were mostly studied) encodes for proteins involves in signaling such as receptor, sensors, kinases, phosphatases, transcription factors and transporters/channels. Despite decades of physiological and molecular effort, knowledge pertaining to how plants sense and transduce low and high temperature, low-water availability (drought), water-submergence, microgravity and salinity signals is still a major question for plant biologist. One major constraint hampering our understanding of these signal transduction processes in plants has been the lack or slow pace of application of molecular genomic and genetics knowledge in the form of gene function. In the post-genomic era, one of the major challenges is investigation and understanding of multiple genes and gene families regulating a particular physiological and developmental aspect of plant life cycle. One of the important physiological processes is regulation of stress response, which leads to adaptation or adjustment in response to adverse stimuli. With the holistic understanding of the signaling pathways involving not only one gene family but multiple genes or gene families, plant biologist can lay a foundation for designing and generating future crops, which can withstand the higher degree of environmental stresses (especially abiotic stresses, which are the major cause of crop loss throughout the world) without losing crop yield and productivity. Therefore, in this e-Book, we intend to incorporate the contribution from leading plant biologists to elucidate several aspects of stress signaling by functional genomics approaches.

Beschreibung: Mitochondrial biogenesis is an extremely complex process. A hint of this complexity is clearly indicated by the many steps and factors required to assemble the respiratory complexes involved in oxidative phosphorylation. These steps include the expression of genes present in both the nucleus and the organelle, intricate post-transcriptional RNA processing events, the coordinated synthesis, transport and assembly of the different subunits, the synthesis and assembly of co-factors and, finally, the formation of supercomplexes or respirasomes. It can be envisaged, and current knowledge supports this view, that plants have evolved specific mechanisms for the biogenesis of respiratory complexes. For example, expression of the mitochondrial genome in plants has special features, not present in other groups of eukaryotes. Moreover, plant mitochondrial biogenesis and function should be considered in the context of the presence of the chloroplast, a second organelle involved in energetic and redox metabolism. It implies the necessity to discriminate between proteins destined for each organelle and requires the establishment of functional interconnections between photosynthesis and respiration. In recent years, our knowledge of the mechanisms involved in these different processes in plants has considerably increased. As a result, the many events and factors necessary for the correct expression of proteins encoded in the mitochondrial genome, the cis acting elements and factors responsible for the expression of nuclear genes encoding respiratory chain components, the signals and mechanisms involved in the import of proteins synthesized in the cytosol and the many factors required for the synthesis and assembly of the different redox co-factors (heme groups, iron-sulfur clusters, copper centers) are beginning to be recognized at the molecular level. However, detailed knowledge of these processes is still not complete and, especially, little is known about how these processes are interconnected. Questions such as how the proteins, once synthesized in the mitochondrial matrix, are inserted into the membrane and assembled with other components, including those imported from the cytosol, how the expression of both genomes is coordinated and responds to changes in mitochondrial function, cellular requirements or environmental cues, or which factors and conditions influence the assembly of complexes and supercomplexes are still open and will receive much attention in the near future. This Research Topic is aimed at establishing a collection of articles that focus on the different processes involved in the biogenesis of respiratory complexes in plants as a means to highlight recent advances. In this way, it intends to help to construct a picture of the whole process and, not less important, to expose the existing gaps that need to be addressed to fully understand how plant cells build and modulate the complex structures involved in respiration.

Beschreibung: Quantifying temporal changes in plant geometry as a result of genetic, developmental, or environmental causes is essential to improve our understanding of the structure and function relationships in plants. Over the last decades, optical imaging and remote sensing developed fundamental working tools to monitor and quantify our environment and plants in particular. Increased efficiency of methods lowered the barrier to compare, integrate, and interpret the optically obtained plant data across larger spatial scales and across scales of biological organization. In particular, acquisition speed at high resolutions reached levels that allow capturing the temporal dynamics in plants in three dimensions along with multi-spectral information beyond human visual senses. These advanced imaging capabilities have proven to be essential to detect and focus on analyzing temporal dynamics of plant geometries. The focus of this Research Topic is on optical techniques developed to study geometrical changes at the plant level detected within the wavelength spectrum between near-UV to near infrared. Such techniques typically involve photogrammetric, LiDAR, or imaging spectroscopy approaches but are not exclusively restricted to these. Instruments operating within this range of wavelengths allow capturing a wide range of temporal scales ranging from sub-second to seasonal changes that result from plant development, environmental effects like wind and heat, or genetically controlled adaption to environmental conditions. The Research Topic covered a plethora of methodological approaches as suggestions for best practices in the light of a particular research question and to a wider view to different research disciplines and how they utilize their state-of-the-art techniques in demonstrating potential use cases across different scales.

Beschreibung: There is a scarcity of detailed information regarding the ecophysiology of root systems and the way root system functioning is affected by both internal and external factors. Furthermore, global climate change is expected to increase the intensity of climate extremes, such as severe drought, heat waves and periods of heavy rainfall; in addition other stresses such as salinization of soils are increasing world-wide. Recently an increasing awareness has developed that understanding plant traits will play a major role in breeding of future crop plants. For example, there is increasing evidence that the traits of root systems are defined by the properties of individual roots. However, further knowledge on the functional importance of root segments and the molecular/physiological mechanisms underlying root system functioning and persistence is needed, and would specifically allow modifying (crop) root system functionality and efficiency in the future. Another major gap in knowledge is localized at the root-soil interface and in regard to the potential adaptive plasticity of root-rhizosphere interactions under abiotic stress and/or competition. It is currently unknown whether adaptations in microbe communities occur, for example due to modified exudation rates, and what are the subsequent influences on nutrient mobilization and uptake. Furthermore, uncovering the mechanisms by which roots perceive neighboring roots may not only contribute to our understanding of plant developmental strategies, but also has important implications on the study of competitive interactions in natural communities, and in optimizing plant performance and resource use in agricultural and silvicultural systems. In this Research Topic, we aimed to provide an on-line, open-access snapshot of the current state of the art of the field of root ecology and physiology, with special focus on the translation of root structure to function, and how root systems are influenced by interplay with internal and external factors such as abiotic stress, microbes and plant-plant interaction. We welcomed original research papers, but reviews of specific topics, articles formulating opinions or describing cutting-edge methods were also gladly accepted.

Beschreibung: Polyamines are small aliphatic polycations which have been involved in key stress and developmental processes in plants. In the recent years, compelling genetic and molecular evidences point to polyamines as essential metabolites required for resistance to drought, freezing, salinity, oxidative stress among other type of abiotic and biotic stresses. In addition to their role as stress-protective compounds, polyamines participate in key developmental processes mediated by specific signaling pathways or in cross-regulation with other plant hormones. Our Research Topic aims to integrate the multiple stress and developmental regulatory functions of polyamines in plants under a genetic, molecular and evolutionary perspective with special focus on signaling networks, mechanisms of action and metabolism regulation.

Beschreibung: Growing demographic trends require sustainable technologies to improve quality and yield of future food productions. However, there is uncertainty about plant protection strategies in many agro-ecosystems. Pests, diseases, and weeds are overwhelmingly controlled by chemicals which pose health risks and cause other undesirable effects.Therefore, an increasing concern on control measures emerged in recent years. Many chemicals became questioned with regard to their sustainability and are (or will be) banned. Alternative management tools are studied, relying on biological, and low impact solutions. This ResearchTopic concerns microbial biocontrol agents, root-associated microbiomes, and rhizosphere networks. Understanding how they interact or respond to (a)biotic environmental cues is instrumental for an effective and sustainable impact. The rhizosphere is in this regard a fundamental object of study, because of its role in plant productivity. This e-book provides a polyhedral perspective on many issues in which beneficial microorganisms are involved. Data indeed demonstrate that they represent an as yet poorly-explored resource, whose exploitation may actively sustain plant protection and crop production. Given the huge number of microbial species present on the planet, the microorganisms studied represent just the tip of an iceberg. Data produced are, however, informative enough about their genetic and functional biodiversity, as well as about the ecosystem services they provide to underp in crop production. Challenges for future research work concern not only the biology of these species, but also the practices required to protect their biodiversity and to extend their application in the wide range of agricultural soils and systems present in the world. Agriculture cannot remain successfully and sustainable unless plant germplasm and useful microbial species are integrated, a goal for which new knowledge and information-based approaches are urgently needed.Growing demographic trends require sustainable technologies to improve quality and yield of future food productions. However, there is uncertainty about plant protection strategies in many agro-ecosystems. Pests, diseases, and weeds are overwhelmingly controlled by chemicals which pose health risks and cause other undesirable effects.Therefore, an increasing concern on control measures emerged in recent years. Many chemicals became questioned with regard to their sustainability and are (or will be) banned. Alternative management tools are studied, relying on biological, and low impact solutions. This ResearchTopic concerns microbial biocontrol agents, root-associated microbiomes, and rhizosphere networks. Understanding how they interact or respond to (a)biotic environmental cues is instrumental for an effective and sustainable impact. The rhizosphere is in this regard a fundamental object of study, because of its role in plant productivity. This e-book provides a polyhedral perspective on many issues in which beneficial microorganisms are involved. Data indeed demonstrate that they represent an as yet poorly-explored resource, whose exploitation may actively sustain plant protection and crop production. Given the huge number of microbial species present on the planet, the microorganisms studied represent just the tip of an iceberg. Data produced are, however, informative enough about their genetic and functional biodiversity, as well as about the ecosystem services they provide to underp in crop production. Challenges for future research work concern not only the biology of these species, but also the practices required to protect their biodiversity and to extend their application in the wide range of agricultural soils and systems present in the world. Agriculture cannot remain successfully and sustainable unless plant germplasm and useful microbial species are integrated, a goal for which new knowledge and information-based approaches are urgently needed.

Beschreibung: This topic covers emerging knowledge about the properties and functions of the outer membranes of chloroplasts and mitochondria. These outer membranes house various processes necessary for efficient communication and thus integration of the organelles with and into their surroundings in the cytoplasm. Such processes include, but are not limited to, protein import, organelle division, organelle movement, metabolism, and metabolite/ion transport. Recent molecular genetic, biochemical and cell biological studies have revealed functions of various outer membrane proteins. These findings have helped address and generate diverse biological and evolutionary questions at molecular, cellular and whole organism levels. The topic should encourage contributions of scientists from various disciplines and thus would provide the field with opportunities to "think outside the box" and to develop potential collaborations. The topic is also aimed to stimulate interests of general audience in the outer membranes of chloroplasts and mitochondria.

Beschreibung: Agricultural land is subjected to a variety of societal pressures, as demands for food, animal feed, and biomass production increase, with an added requirement to simultaneously maintain natural areas and mitigate climatic and environmental impacts. The biotic elements of agricultural systems interact with the abiotic environment to generate a number of ecosystem functions that offer services benefiting humans across many scales of time and space. The intensification of agriculture generally reduces biodiversity including that within soil, and impacts negatively upon a number of regulating and supporting ecosystem services. There is a global need toward achieving sustainable agricultural systems, as also highlighted in the United Nations Sustainable Development Goals. There is hence a need for management regimes that enhance both agricultural production and the associated provision of multiple ecosystem services. The articles of this Research Topic enhance our knowledge of how management practices applied to agricultural systems affect the delivery of multiple ecosystem services and how trade-offs between provisioning, regulating, and supporting services can be handled both above- and below-ground. They also show the diversity of topics that need to be considered within the framework of ecosystem services delivered by agricultural systems, from knowledge on basic concepts and newly-proposed frameworks, to a focus on specific ecosystem types such as grasslands and high nature-value farmlands, pollinator habitats, and soil habitats. This diversity of topics indicates the need for broader-scope research, integrated with targeted scientific research to promote sustainable agricultural practices and to ensure food security.

Beschreibung: RNA enveloped viruses comprise several families belonging to plus and minus strand RNA viruses, such as retroviruses, flavoviruses and orthomyxoviruses. Viruses utilize cellular lipids during critical steps of replication like entry, assembly and egress. Growing evidence indicate important roles for lipids and lipid nanodomains in virus assembly. This special topic covers key aspects of virus-membrane interactions during assembly and egress, especially those of retroviruses and Ebola virus (EBOV). Virus assembly and release involve specific and nonspecific interactions between viral proteins and membrane compartments. Retroviral Gag proteins assemble predominantly on the PM. Despite the great progress in identifying the factors that modulate retroviral Gag assembly on the PM, there are still gaps in our understanding of precise mechanisms of Gag-membrane interactions. Studies over the last two decades have focused on the mechanisms by which other retroviral Gag proteins interact with membranes during assembly. These include human immunodeficiency virus (HIV), Rous sarcoma virus (RSV), equine infectious anemia virus (EIAV), Mason-Pfizer monkey virus (M-PMV), murine leukemia virus (MLV), and human T-lymphotropic virus type (HTLV-1). Additionally, assembly of filoviruses such as EBOV also occurs on the inner leaflet of the PM. The articles published under this special topic highlight the latest understanding of the role of membrane lipids during virus assembly, egress and release.

Beschreibung: Ecosystems are the stage on which the play of evolution is acted, and ecosystems are complex, spatially structured and temporally varying. The purpose of this Research Topic is to explore critical challenges and opportunities for the transition from landscape genetics to landscape genomics. Landscape genetics has focused on the spatial analysis of small genetic datasets, typically comprised of less than 20 microsatellite markers, taken from clusters of individuals in putative populations or distributed individuals across landscapes. The recent emergence of large scale genomic datasets produced by next generation sequencing methods poses tremendous challenge and opportunity to the field. Perhaps the greatest is to produce, process, curate, archive and analyze spatially referenced genomic datasets in a way such that research is led by a priori hypotheses regarding how environmental heterogeneity and temporal dynamics interact to affect gene flow and selection. The papers in the Research Topic cover a broad range of topics under this area of focus, from reviews of the emergence of landscape genetics, to best practices in spatial analysis of genetic data. The compilation, like the emerging field itself, is eclectic and illustrates the scope of both the challenges and opportunities of this emerging field.

Beschreibung: Trees are among the longest-living organisms. They are sensitive to extreme climatic events and document the effects of environmental changes in form of structural modifications of their tissues. These modifications represent an integrated signal of complex biological responses enforced by the environment. For example, temporal change in stem increment integrates multiple information of tree performance, and wood anatomical traits may be altered by climatic extremes or environmental stress. Recent developments in preparative tools and computational image analysis enable to quantify changes in wood anatomical features, like vessel density or vessel size. Thus, impacts on their functioning can be related to climatic forcing factors. Similarly, new developments in monitoring (cambial) phenology and mechanistic modelling are enlightening the interrelationships between environmental factors, wood formation and tree performance and mortality. Quantitative wood anatomy is a reliable indicator of drought occurrence during the growing season, and therefore has been studied intensively in recent years. The variability in wood anatomy not only alters the biological and hydraulic functioning of a tree, but may also influence the technological properties of wood, with substantial impacts in forestry. On a larger scale, alterations of sapwood and phloem area and their ratios to other functional traits provide measures to detect changes in a tree’s life functions, and increasing risk of drought-induced mortality with possible impacts on hydrological processes and species composition of plant communities. Genetic variability within and across populations is assumed to be crucial for species survival in an unpredictable future world. The magnitude of genetic variation and heritability of adaptive traits might define the ability to adapt to climate change. Is there a relation between genetic variability and resilience to climate change? Is it possible to link genetic expression and climate change to obtain deeper knowledge of functional genetics? To derive precise estimates of genetic determinism it is important to define adaptive traits in wood properties and on a whole-tree scale. Understanding the mechanisms ruling these processes is fundamental to assess the impact of extreme climate events on forest ecosystems, and to provide realistic scenarios of tree responses to changing climates. Wood is also a major carbon sink with a long-term residence, impacting the global carbon cycle. How well do we understand the link between wood growth dynamics, wood carbon allocation and the global carbon cycle? Papers contribution to this Research Topic will cover a wide range of ecosystems. However, special relevance will be given to Mediterranean-type areas. These involve coastal regions of four continents, making Mediterranean-type ecosystems extremely interesting for investigating the potential impacts of global change on growth and for studying responses of woody plants under extreme environmental conditions. For example, the ongoing trend towards warmer temperatures and reduced precipitation can increase the susceptibility to fire and pests. The EU-funded COST Action STREeSS (Studying Tree Responses to extreme Events: a SynthesiS) addresses such crucial tree biological and forest ecological issues by providing a collection of important methodological and scientific insights, about the current state of knowledge, and by opinions for future research needs.

Beschreibung: Plants synthesize a wide variety of unique glycan structures which play essential roles during the life cycle of the plant. Being omnipresent throughout the plant kingdom, ranging from simple green algae to modern flowering plants, glycans contribute to many diverse processes. Glycans can function as structural components in the plant cell wall, assist in the folding of nascent proteins, act as signaling molecules in plant defense responses or (ER) stress pathways, or serve within the energy metabolism of a plant. In most cases, glycans are attached to other macromolecules to form so-called glycoconjugates (e.g. glycoproteins, proteoglycans and glycolipids), but they can also be present as free entities residing in the plant cell. Next to the broad, complex set of glycans, plants also evolved an elaborate collection of lectins or proteins with a lectin-like domain, which can recognize and bind to endogenous (plants-own) or exogenous (foreign) glycans. Though still poorly understood in plants, the dynamic interactions between lectins and carbohydrate structures are suggested to be involved in gene transcription, protein folding, protein transport, cell adhesion, signaling as well as defense responses. As such, a complex and largely undetermined glycan-interactome is established inside plant cells, between cells and their surrounding matrix, inside the extracellular matrix, and even between organisms. Studying the biological roles of plant glycans will enable to better understand plant development and physiology in order to fully exploit plants for food, feed and production of pharmaceutical proteins. In this Research Topic, we want to provide a platform for articles describing the latest research, perspectives and methodologies related to the fascinating world of plant glycobiology, with a focus on following subjects: 1. Identification and characterization of plant glycans, their biosynthetic and degradation enzymes 2. Characterization of plant lectins and glycoproteins 3. Plant glycans in the plant’s energy metabolism 4. Role of plant glycans in plant defense signaling 5. Use of plant lectins in pest control 6. Plant lectins as new tools in human medicine 7. Glyco-engineering in plants

Beschreibung: Plant gene transfer achieved in the early ‘80s paved the way for the exploitation of the potential of gene engineering to add novel agronomic traits and/or to design plants as factories for high added value molecules. For this latter area of research, the term "Molecular Farming" was coined in reference to agricultural applications in that major crops like maize and tobacco were originally used basically for pharma applications. The concept of the “green biofactory” implies different advantages over the typical cell factories based on animal cell or microbial cultures already when considering the investment and managing costs of fermenters. Although yield, stability, and quality of the molecules may vary among different heterologous systems and plants are competitive on a case-to-case basis, still the “plant factory” attracts scientists and technologists for the challenging features of low production cost, product safety and easy scale up. Once engineered, a plant is among the cheapest and easiest eukaryotic system to be bred with simple know-how, using nutrients, water and light. Molecules that are currently being produced in plants vary from industrial and pharmaceutical proteins, including medical diagnostics proteins and vaccine antigens, to nutritional supplements such as vitamins, carbohydrates and biopolymers. Convergence among disciplines as distant as plant physiology and pharmacology and, more recently, as omic sciences, bioinformatics and nanotechnology, increases the options of research on the plant cell factory. “Farming for Pharming” biologics and small-molecule medicines is a challenging area of plant biotechnology that may break the limits of current standard production technologies. The recent success on Ebola fighting with plant-made antibodies put a spotlight on the enormous potential of next generation herbal medicines made especially in the name of the guiding principle of reduction of costs, hence reduction of disparities of health rights and as a tool to guarantee adequate health protection in developing countries.Plant gene transfer achieved in the early ‘80s paved the way for the exploitation of the potential of gene engineering to add novel agronomic traits and/or to design plants as factories for high added value molecules. For this latter area of research, the term "Molecular Farming" was coined in reference to agricultural applications in that major crops like maize and tobacco were originally used basically for pharma applications. The concept of the “green biofactory” implies different advantages over the typical cell factories based on animal cell or microbial cultures already when considering the investment and managing costs of fermenters. Although yield, stability, and quality of the molecules may vary among different heterologous systems and plants are competitive on a case-to-case basis, still the “plant factory” attracts scientists and technologists for the challenging features of low production cost, product safety and easy scale up. Once engineered, a plant is among the cheapest and easiest eukaryotic system to be bred with simple know-how, using nutrients, water and light. Molecules that are currently being produced in plants vary from industrial and pharmaceutical proteins, including medical diagnostics proteins and vaccine antigens, to nutritional supplements such as vitamins, carbohydrates and biopolymers. Convergence among disciplines as distant as plant physiology and pharmacology and, more recently, as omic sciences, bioinformatics and nanotechnology, increases the options of research on the plant cell factory. “Farming for Pharming” biologics and small-molecule medicines is a challenging area of plant biotechnology that may break the limits of current standard production technologies. The recent success on Ebola fighting with plant-made antibodies put a spotlight on the enormous potential of next generation herbal medicines made especially in the name of the guiding principle of reduction of costs, hence reduction of disparities of health rights and as a tool to guarantee adequate health protection in developing countries.

Beschreibung: Abiotic stresses are the major cause that limits productivity of crop plants worldwide. Plants have developed intricate machinery to respond and adapt over these adverse environmental conditions both at physiological and molecular levels. Due to increasing problems of abiotic stresses, plant biotechnologists and breeders need to employ new approaches to improve abiotic stress tolerance in crop plants. Although current research has divulged several key genes, gene regulatory networks and quantitative trait loci that mediate plant responses to various abiotic stresses, the comprehensive understanding of this complex trait is still not available. This e-book is focused on molecular genetics and genomics approaches to understand the plant response/adaptation to various abiotic stresses. It includes different types of articles (original research, method, opinion and review) that provide current insights into different aspects of plant responses and adaptation to abiotic stresses.

Beschreibung: The understanding of biological complexity has been greatly facilitated by cross-disciplinary, holistic approaches that allow insights into the function and regulation of biological processes that cannot be captured by dissecting them into their individual components. In addition, the development of novel tools has dramatically increased our ability to interrogate information at the nucleic acid, protein and metabolite level. The integration and interpretation of disparate data sets, however, still remain a major challenge in systems biology. Roots provide an excellent model for studying physiological, developmental, and metabolic processes. The availability of genetic resources, along with sequenced genomes has allowed important discoveries in root biochemistry, development and function. Roots are transparent, allowing optical investigation of gene activity in individual cells and experimental manipulation. In addition, the predictable fate of cells emerging from the root meristem and the continuous development of roots throughout the life of the plant, which permits simultaneous observation of different developmental stages, provide ideal premises for the analysis of growth and differentiation. Moreover, a genetically fixed cellular organization allows for studying the utilization of positional information and other non-cell-autonomous phenomena, which are of utmost importance in plant development. Although their ontogeny is largely invariant under standardized experimental conditions, roots possess an extraordinary capacity to respond to a plethora of environmental signals, resulting in distinct phenotypic readouts. This high phenotypic plasticity allows research into acclimative and adaptive strategies, the understanding of which is crucial for germplasm enhancement and crop improvement. With the aim of providing a current snapshot on the function and development of roots at the systems level, this Research Topic collated original research articles, methods articles, reviews, mini reviews and perspective, opinion and hypotheses articles that communicate breakthroughs in root biology, as well as recent advances in research technologies and data analysis.

Beschreibung: As the amount of biological information and its diversity accumulates massively there is a critical need to facilitate the integration of this data to allow new and unexpected conclusions to be drawn from it. The Semantic Web is a new wave of web- based technologies that allows the linking of data between diverse data sets via standardised data formats (“big data”). Semantic Biology is the application of semantic web technology in the biological domain (including medical and health informatics). The Special Topic encompasses papers in this very broad area, including not only ontologies (development and applications), but also text mining, data integration and data analysis making use of the technologies of the Semantic Web. Ontologies are a critical requirement for such integration as they allow conclusions drawn about biological experiments, or descriptions of biological entities, to be understandable and integratable despite being contained in different databases and analysed by different software systems. Ontologies are the standard structures used in biology, and more broadly in computer science, to hold standardized terminologies for particular domains of knowledge. Ontologies consist of sets of standard terms, which are defined and may have synonyms for ease of searching and to accommodate different usages by different communities. These terms are linked by standard relationships, such as “is_a” (an eye “is_a” sense organ) or “part_of” (an eye is “part_of” a head). By linking terms in this way, more detailed, or granular, terms can be linked to broader terms, allowing computation to be carried out that takes these relationships into account.

Beschreibung: A plant growing under field conditions is not a simple individual; it is a community. We now know that there is a community of microbes associated with all parts of the plant, and that the root associated community is particularly large. This microbial community, the phytomicrobiome, is complex, regulated and the result of almost half a billion years of evolution. Circumstances that benefit the plant generally benefit the phytomicrobiome, and vice versa. Members of the holobiont modulate each other's activities, in part, through molecular signals, acting as the hormones of the holobiont. The plant plus the phytomicrobiome constitute the holobiont, the resulting entity that is that community. The phytomicrobiome is complex, well developed and well-orchestrated, and there is considerable potential in managing this system. The use of “biologicals” will develop during the 21st century and play as large a role as agro-chemistry did in the 20th century. Biologicals can be deployed to enhance plant pathogen resistance, improve plant access to nutrients and improve stress tolerance. They can be used to enhance crop productivity, to meet the expanding demands for plant material as food, fibre and fuel. They can assist crop plants in dealing with the more frequent and more extreme episodes of stress that will occur as climate change conditions continue to develop. The path is clear and we have started down it; there is a considerable distance remaining.

Beschreibung: The study of plant-microbe associations by new techniques has significantly improved our understanding of the structure and specificity of the plant microbiome. Yet, microbiome function and the importance of the plant’s microbiome in the context of human and plant health are largely unexplored. Comparable with our human microbiome, millions of microbes inhabit plants, forming complex ecological communities that influence plant growth and health through its collective metabolic activities and host interactions. Viewing the microbiota from an ecological perspective can provide insight into how to promote plant health and stress tolerance of their hosts or how to adapt to a changing climate by targeting this microbial community. Moreover, the plant microbiome has a substantial impact on human health by influencing our gut microbiome by eating raw plants such as lettuce and herbs but also by influencing the microbiome of our environment through airflow. This research topic comprising reviews, original and opinion articles highlights the current knowledge regarding plant microbiomes, their specificity, diversity and function as well as all aspects studying the management of plant microbiomes to enhance plant growth, health quality and stress tolerance.

Beschreibung: Global warming has dramatically increased the frequency and severity of flooding events worldwide. As a result, many man-made and natural ecosystems have become flood-prone. For plants, the main consequence of flooding is the drastic reduction of oxygen availability that restricts respiratory energy production and finally affects survival. Flooding can negatively influence crop production and wild plant distributions, since most plants are sensitive to excessively wet conditions. However, plants have evolved a broad spectrum of adaptive responses to oxygen deficiency that eventually leads to tolerance. Many of these morphological and physiological adaptations have been described in some crops and wild plant species and considerable progress has been made in understanding the molecular aspects governing tolerance traits. Moreover, the molecular mechanism of plant oxygen sensing has been recently elucidated. However, many other aspects concerning plant acclimation responses to flooding remain unanswered. With this research topic we seek to build an online collection of articles addressing various aspects relating to “plant responses to flooding’’ which will reflect the exciting new developments and current state of the art in this vibrant and dynamic research field. All kinds of articles, including original research articles, short reviews, methods and opinions are welcome, in the attempt to broadly and freely disseminate research information, tools and protocols.

Beschreibung: Plant architecture is a major determinant of the resource use efficiency of crops. The architecture of a plant shows ontogenetic structural changes which are modified by multiple environmental factors: Plant canopies are exposed to natural fluctuations in light quantity and the dynamically changing canopy architecture induces local variations in light quality. Changing temperature conditions or water availability during growth additionally affect plant architecture and thus crop productivity, because plants have various options to adapt their architecture to the available resources. Meeting the challenge of ensuring food security we must understand the plant’s mechanisms for integrating and responding to an orchestra of environmental factors. ‘Virtual plants’ describe plant architecture in silico. Virtual plants have the potential to help us understanding the complex feedback processes between canopy architecture, multiple environmental factors and crop productivity. As a research tool, they have become increasingly popular within the last decade due to their great power of realistically visualizing the plant’s architecture. This Research Topic highlights current research carried out on modeling plant architecture in changing environments.

Beschreibung: With global populations expected to exceed 9.2 billion by 2050 and available land and water resources devoted to crop production dwindling, we face significant challenges to secure global food security. Only 12 plant species feed 80% of the world’s population, with just three crop species (wheat, rice and maize) accounting for food consumed by 50% of the global population. Annual losses to crop pests and pathogens are significant, thought to be equivalent to that required to feed a billion people, at a time when crop productivity has plateaued. With pesticide applications becoming increasingly unfeasible on cost, efficacy and environmental grounds, there is growing interest in exploiting plant resistance and tolerance traits for crop protection. Indeed, mankind has been selectively breeding plants for desirable traits for thousands of years. However, resistance and tolerance traits have not always been those most desired, and in many cases have been inadvertently lost during the domestication process: crops have been effectively ‘disarmed by domestication’. Moreover, mechanistic understanding of how resistance and tolerance traits operate is often incomplete, which makes identifying the right combination for crop protection difficult. We aimed to address this Research Topic by inviting authors to contribute their knowledge of appropriate resistance and tolerance traits, explore what is known about durability and breakdown of defensive traits and, finally, asking what are the prospects for exploiting these traits for crop protection. The research topic summarised in this book addresses some of the most important issues in the future sustainability of global crop production.

Beschreibung: Terrestrial plants are sessile organisms that, differently from animals, can not move in searching of the nutrients and water they need. Instead, they have to change continuously their physiology and morphology to adapt to the environmental changes. When plants suffer from a nutrient deficiency, they develop physiological and morphological responses (mainly in their roots) aimed to facilitate the acquisition and mobilization of such a nutrient. Physiological responses include some ones like acidification of the rizhosphere and release of chelating agents into the medium; and morphological responses include others, like changes in root architecture and development of root hairs. The regulation of these responses is not totally known but in the last years different plant hormones and signaling substances, such as auxin, ethylene, cytokinins and nitric oxide, have been involved in their control. Besides hormones, oxidative stress has also been related with most of the nutrient deficiencies. The relationship of ethylene with the regulation of responses to nutrient deficiencies came from the nineties, when some works presented data suggesting its involvement in the regulation of responses to Fe and P deficiency. In the last years, the role of ethylene has been extended to many other nutrient deficiencies, such as K deficiency, Mg deficiency, S deficiency, N deficiency, and others. In most of the cases, it has been found that ethylene production, as well as the expression of ethylene synthesis genes, increases under these nutrient deficiencies. Furthermore, it has also been found that ethylene controls the expression of genes related to responses to different deficiencies. The involvement of ethylene in so many deficiencies suggests that it should act in conjunction with other signals that would confer nutrient-specificity to the distinct nutrient responses. These other signals could be plant hormones (auxin, cytokinins, etc) as well as other substances (nitric oxide, microRNAs, peptides, glutathione, etc), either originated in the roots or coming from the shoots through the phloem. The role of ethylene in the mineral nutrition of plants is even more complex that the one related to its role in the responses to nutrient deficiencies. Ethylene has also been implicated in the N2 fixation of legume plants; in salt tolerance responses; and in responses to heavy metals, such as Cd toxicity. All these processes are related to ion uptake and, consequently, are related to plant mineral nutrition. We consider a good opportunity to review all this information in a coordinated way. This Research Topic will provide an overview about the role of the plant hormone ethylene on the regulation of physiological and morphological responses to different nutrient deficiencies. In addition, it will cover other aspects of ethylene related to plant nutrition such as its role on salinity, N2 fixation and tolerance to heavy metals.

Beschreibung: Environmental stresses and metabolic by-products can severely affect the integrity of genetic information by inducing DNA damage and impairing genome stability. As a consequence, plant growth and productivity are irreversibly compromised. To overcome genotoxic injury, plants have evolved complex strategies relying on a highly efficient repair machinery that responds to sophisticated damage perception/signaling networks. The DNA damage signaling network contains several key components: DNA damage sensors, signal transducers, mediators, and effectors. Most of these components are common to other eukaryotes but some features are unique to the plant kingdom. ATM and ATR are well-conserved members of PIKK family, which amplify and transduce signals to downstream effectors. ATM primarily responds to DNA double strand breaks while ATR responds to various forms of DNA damage. The signals from the activated transducer kinases are transmitted to the downstream cell-cycle regulators, such as CHK1, CHK2, and p53 in many eukaryotes. However, plants have no homologue of CHK1, CHK2 nor p53. The finding of Arabidopsis transcription factor SOG1 that seems functionally but not structurally similar to p53 suggests that plants have developed unique cell cycle regulation mechanism. The double strand break repair, recombination repair, postreplication repair, and lesion bypass, have been investigated in several plants. The DNA double strand break, a most critical damage for organisms are repaired non-homologous end joining (NHEJ) or homologous recombination (HR) pathway. Damage on template DNA makes replication stall, which is processed by translesion synthesis (TLS) or error-free postreplication repair (PPR) pathway. Deletion of the error-prone TLS polymerase reduces mutation frequencies, suggesting PPR maintains the stalled replication fork when TLS is not available. Unveiling the regulation networks among these multiple pathways would be the next challenge to be completed. Some intriguing issues have been disclosed such as the cross-talk between DNA repair, senescence and pathogen response and the involvement of non-coding RNAs in global genome stability. Several studies have highlighted the essential contribution of chromatin remodeling in DNA repair. DNA damage sensing, signaling and repair have been investigated in relation to environmental stresses, seed quality issues, mutation breeding in both model and crop plants and all these studies strengthen the idea that components of the plant response to genotoxic stress might represent tools to improve stress tolerance and field performance. This focus issue gives researchers the opportunity to gather and interact by providing Mini-Reviews, Commentaries, Opinions, Original Research and Method articles which describe the most recent advances and future perspectives in the field of DNA damage sensing, signaling and repair in plants. A comprehensive overview of the current progresses dealing with the genotoxic stress response in plants will be provided looking at cellular and molecular level with multidisciplinary approaches. This will hopefully bring together valuable information for both plant biotechnologists and breeders.

Beschreibung: The small phenolic compound salicylic acid (SA) is critical for plant defense against a broad spectrum of pathogens. SA is also involved in multi-layered defense responses, from pathogen-associated molecular pattern triggered basal defense, resistance gene-mediated defense, to systemic acquired resistance. Recent decades have witnessed tremendous progress towards our understanding of SA-mediated signaling networks. Many genes have been identified to have direct or indirect effect on SA biosynthesis or to regulate SA accumulation. Several SA receptors have been identified and characterization of these receptors has shed light on the mechanisms of SA-mediated defense signaling, which encompass chromosomal remodeling, DNA repair, epigenetics, to transcriptional reprogramming. Molecules from plant-associated microbes have been identified, which manipulate SA levels and/or SA signaling. SA does not act alone. It engages in crosstalk with other signaling pathways, such as those mediated by other phytohormones, in an agonistic or antagonistic manner, depending on hormones and pathosystems. Besides affecting plant innate immunity, SA has also been implicated in other cellular processes, such as flowering time determination, lipid metabolism, circadian clock control, and abiotic stress responses, possibly contributing to the regulation of plant development. The multifaceted function of SA makes it critically important to further identify genes involved in SA signaling networks, understand their modes of action, and delineate interactions among the components of SA signaling networks. In addition, genetic manipulation of genes involved in SA signaling networks has also provided a promising approach to enhance disease resistance in economically important plants. This ebook collects articles in the Research Topic "Salicylic Acid Signaling Networks". For this collection we solicited reviews, perspectives, and original research articles that highlight recent exciting progress on the understanding of molecular mechanisms underlying SA-mediated defense, SA-crosstalk with other pathways and how microbes impact these events.

Beschreibung: During the 1970s, renewed interest in plant mechanical signaling led to the discovery that plants subjected to mechanical stimulation develop shorter and thicker axes than undisturbed plants, a syndrome called thigmomorphogenesis. Currently, mechanosensing is being intensively studied because of its involvement in many physiological processes in plants and particularly in the control of plant morphogenesis. From an ecological point of view, the shaping of plant architecture has to be precisely organized in space to ensure light capture as well as mechanical stability. In natural environments terrestrial plants are subjected to mechanical stimulation mainly due to wind, but also due to precipitation, while aquatic and marine plants are subjected to current and wave energy. Plants acclimate to mechanically challenging environments by sensing mechanical stimulations and modifying their growth in length and diameter and their tissue properties to reduce potential for buckling or breakage. From a morphogenetic point of view, both external and internal mechanical cues play an important role in the control of cell division and meristem development likely by modulating microtubule orientation. How mechanical stimulations are being sensed by plants is an area of intense research. Different types of mechanosensors have been discovered or proposed, including ion channels gated by membrane tension (stretch activation) and plasma membrane receptor-like kinases that monitor the cell wall deformations. Electrophysiologists have measured the conductances of some stretch-activated channels and have showed that SAC of different structures can exhibit different conductances. The role of these differences in conductance has not yet been established. Once a mechanical stimulus has been perceived, it must be converted into a biological signal that can lead to variations of plant phenotype. Calcium has been shown to function as an early second messenger, tightly linked with changes in cytosolic and apoplastic pH. Transcriptional analyses of the effect of mechanical stimulation have revealed a considerable number of differentially expressed genes, some of which appear to be specific to mechanical signal transduction. These genes can thus serve as markers of mechanosensing, for example, in studies attempting to define signalling threshold, or variations of mechanosensitivity (accommodation). Quantitative biomechanical studies have lead to a model of mechanoperception which links mechanical state and plant responses, and provides an integrative tool to study the regulation of mechanosensing. This model includes parameters (sensitivity and threshold) that can be estimated experimentally. It has also been shown that plants are desensitized when exposed to multiple mechanical signals as a function of their mechanical history. Finally, mechanosensing is also involved in osmoregulation or cell expansion. The links between these different processes involving mechanical signalling need further investigation. This frontier research topic provides an overview of the different aspects of mechanical signaling in plants, spanning perception, effects on plant growth and morphogenesis, and broad ecological significance.During the 1970s, renewed interest in plant mechanical signaling led to the discovery that plants subjected to mechanical stimulation develop shorter and thicker axes than undisturbed plants, a syndrome called thigmomorphogenesis. Currently, mechanosensing is being intensively studied because of its involvement in many physiological processes in plants and particularly in the control of plant morphogenesis. From an ecological point of view, the shaping of plant architecture has to be precisely organized in space to ensure light capture as well as mechanical stability. In natural environments terrestrial plants are subjected to mechanical stimulation mainly due to wind, but also due to precipitation, while aquatic and marine plants are subjected to current and wave energy. Plants acclimate to mechanically challenging environments by sensing mechanical stimulations and modifying their growth in length and diameter and their tissue properties to reduce potential for buckling or breakage. From a morphogenetic point of view, both external and internal mechanical cues play an important role in the control of cell division and meristem development likely by modulating microtubule orientation. How mechanical stimulations are being sensed by plants is an area of intense research. Different types of mechanosensors have been discovered or proposed, including ion channels gated by membrane tension (stretch activation) and plasma membrane receptor-like kinases that monitor the cell wall deformations. Electrophysiologists have measured the conductances of some stretch-activated channels and have showed that SAC of different structures can exhibit different conductances. The role of these differences in conductance has not yet been established. Once a mechanical stimulus has been perceived, it must be converted into a biological signal that can lead to variations of plant phenotype. Calcium has been shown to function as an early second messenger, tightly linked with changes in cytosolic and apoplastic pH. Transcriptional analyses of the effect of mechanical stimulation have revealed a considerable number of differentially expressed genes, some of which appear to be specific to mechanical signal transduction. These genes can thus serve as markers of mechanosensing, for example, in studies attempting to define signalling threshold, or variations of mechanosensitivity (accommodation). Quantitative biomechanical studies have lead to a model of mechanoperception which links mechanical state and plant responses, and provides an integrative tool to study the regulation of mechanosensing. This model includes parameters (sensitivity and threshold) that can be estimated experimentally. It has also been shown that plants are desensitized when exposed to multiple mechanical signals as a function of their mechanical history. Finally, mechanosensing is also involved in osmoregulation or cell expansion. The links between these different processes involving mechanical signalling need further investigation. This frontier research topic provides an overview of the different aspects of mechanical signaling in plants, spanning perception, effects on plant growth and morphogenesis, and broad ecological significance.

Beschreibung: Doubled haploids (DHs) are powerful tools to reduce the time and costs needed to produce pure lines to be used in breeding programs. DHs are also useful for genetic mapping of complex qualitative traits, to avoid transgenic hemizygotes, for studies of linkage and estimation of recombination fractions, for screening of recessive mutants. These are just some of the advantages that make DH technology one of the most exciting fields of present and future plant biotechnology. All of the DH methods have model species where these technologies have been developed, or that respond every efficiently to their corresponding induction treatment. However, not all the species of economical/agronomical interest respond to these methodologies as they should be in order to obtain DHs on a routine basis. Indeed, many of them are still considered as low-responding or recalcitrant to these treatments, including many of the most important crops worldwide. Although many groups are making significant progresses in the understanding of these intriguing experimental pathways, little is known about the origin, causes and ways to overcome recalcitrancy. It would be very important to shed light on the particularities of recalcitrant species and the special conditions they need to be induced. In parallel, the knowledge gained from the study of basic aspects in model species could also be beneficial to overcome recalcitrancy. In this e-book, we present a compilation of different approaches leading to the generation of DHs in model and in recalcitrant species, and different studies on new and relevant aspects of this process, useful to extract common traits and features, to know better these processes, and eventually, to elucidate how to make DH technology more efficient.

Beschreibung: There are few more active frontiers in plant science than helping understand and predict the ecological consequences of on-going, global changes in climate, land use and cover, nutrient cycling, and acidity. This collection of research papers and reviews focuses on how these changes are likely to interact with two important factors, clonal growth in plants and the introduction of species into new regions by humans, to reshape the ecology of our world. Clonal growth is vegetative reproduction in which offspring remain attached to the parent at least until establishment. Clonal growth is associated with the invasiveness of introduced species, their tendency to spread after introduction and negatively affect other species. Will changes in climate, land cover, or nutrients further increase biological invasions by introduced, clonal plants? The articles in this book seek to address this question with new research and theory on clonal growth and its interactions with invasiveness and other components of global change.

Beschreibung: Today's biodiversity is the spectacular product of hundreds of millions of years of evolution. Understanding how this diversity of living organisms appeared is one of the most intriguing and challenging question in biology. Because organismal morphology is established during embryonic development, and because morphological traits diversified from ancestral forms during evolution, it can be inferred that changes in the mechanisms controlling embryonic development are instrumental for morphological evolution. This syllogism lies at the very heart of a new discipline called Evo-Devo which is centered in the identification of the cellular and genetic mechanisms that, through modifications in developmental programmes, were at the base of morphological innovations during evolution. After the discovery of the broad conservation of gene content and regulatory networks in the animal kingdom, as well as in plants, Evo-Devo is orienting towards the study of differences through experimental and functional approaches. Given the wide range of species, gene families, and developmental processes considered, a concerted effort is still required to shed light on the genetic, cellular and molecular mechanisms involved in phenotypic evolution. It is a particularly exciting time for this field of evolutionary developmental biology, as the advent of novel imaging, genome editing and sequencing technologies allows the study of almost any organism in ways that were unthinkable only a few years ago. Therefore, the aim of this Frontiers Research Topic is to gather an original collection of experimental approaches, concepts and hypotheses reflecting the current diversity of the Evo-Devo field. We have organized the articles according to the mechanistic depth with which they tackle specific evolutionary issues. Hence, comparisons of expression patterns have been grouped in Chapter 1, changes in regulatory interactions and gene networks are presented in Chapter 2, while Chapter 3 focuses on the evolution of developmental processes and biological patterns.

Beschreibung: The phenotype of a plant in response to a stress condition is the reflection of the molecular responses in different cell-types composing the plant. The multicellular complexity represents a challenge when accessing specific responses of each cell or cell type composing the plant. To overcome this difficulty and allow the clear characterization of the plant cell molecular mechanisms, the research community is now focusing on studying a single cell and single cell-types. The isolation of plant single cells is limited by the cell wall that confers the rigidity of the plant and its overall structure. Various methods have been developed for isolating plant cells (e.g. laser capture microdissection; cell sorting of Green Fluorescent Protein (GFP)-tagged protoplasts, differential protoplastization of cells such as guard cells, isolation of easily accessible cell types such as cotton fiber, pollen cells, trichomes and root hair cells). The development of these innovative approaches to isolate single plant cells or cell-types combined with the application of sensitive and high-throughput technologies allows a better analysis of the developmental processes and response to environmental stresses. Ultimately, single plant cell and cell-type biology will lead to establishment of more reliable and accurate -molecular regulatory networks at the resolution of basic life unit. The goal of this Research Topic is to cover new technological and biological advances in the study of plant single cell, cell-type and systems biology.

Beschreibung: Plant reproduction is essential not only for producing offspring but also for increasing crop quality and yield. Moreover, plant reproduction entails complex growth and developmental processes, which provide a variety of opportunities for elucidating fundamental principles in biology. The combinational employment of molecular genetic approaches and emerging technologies, such as florescence-based imaging techniques and next generation sequencing, has led to important progresses in plant reproduction using model plants, crops, and trees. This e-book compiles 31 articles, including 1 hypothesis and theory, 4 perspectives, 12 reviews, and 14 original research papers. We hope that this E-book will draw attention of all plant biologists to exciting advances in the field of plant reproduction and help solve remaining challenging questions in the future. We wish to express our appreciation to all the authors, reviewers, and the Frontiers editorial office for their excellent contributions that made the publication of this e-book possible.

Beschreibung: Silicon (Si) is gaining increased attention in the farming sector because of its beneficial effects observed in several crop species, particularly under stress conditions. The magnitude of benefits is predominantly observed in plant species that can accumulate Si above a certain threshold. Therefore, deciphering the molecular mechanisms and genetic factors conferring a plant ability to take up silicon is necessary. Along these lines, several efforts have been made to identify the specific genes regulating Si uptake and distribution in plant tissues. This information finds its usefulness in identifying Si-competent species, and could eventually lead to improving this ability in low-accumulating species. The successful exploitation of Si in agriculture depends highly on the understanding of different Si properties including plant-available Si from the soil, transport within tissues, deposition in planta, and Si effect on different metabolic and physiological processes. In addition, a better comprehension of external factors influencing Si uptake and deposition in plant tissue remains important. A plant can take up Si efficiently only in the form of silicic acid and most soils, despite containing high concentrations of Si, are deficient in plant-available Si. Consequently, soil amendment with fertilizers rich in plant-available Si is now viewed as an affordable option to protect plants from the biotic and abiotic stresses and achieve more sustainable cropping management worldwide. Articles compiled in the present research topic touch upon several aspects of Si properties and functionality in plants. The information will be helpful to further our understanding of the role of Si and contribute to exploit the benefits plants derive from it.

Beschreibung: The gaseous molecule ethylene (C2H4), which is small in size and simple in structure, is a plant hormone most often associated with fruit ripening yet has a diversity of effects throughout the plant life cycle. While its agricultural effects were known even in ancient Egypt, the complexity of its mode of action and the broad spectrum of its effects and potential uses in plant physiology remain important scientific challenges today. In the last few decades, the biochemical pathway of ethylene production has been uncovered, ethylene perception and signaling have been molecularly dissected, ethylene-responsive transcription factors have been identified and numerous effects of ethylene have been described, ranging from water stress, development, senescence, reproduction plant-pathogen interactions, and of course, ripening. Thus ethylene is involved in plant development, in biotic and abiotic stress, and in reproduction. There is no stage in plant life that is not affected by ethylene, modulated by a complex and fascinating molecular machinery.

Beschreibung: Plants use the Sun's energy to synthesize the basic biomolecules that make up all the organic matter of all organisms of terrestrial ecosystems, including ourselves. Therefore, understanding their adaptive mechanisms to variations of environmental factors, both biotic and abiotic, is fundamental, and particularly relevant in the current context of rapid climate change. Some of the most important adaptive mechanisms of plants are the electrical and chemical signaling systems for the exchange of information between proximally and distally located cells. These signalling systems allow plants to dynamically coordinate the activities of all cells under a diversity of situations. In this Research Topic, we present eight articles that bring up new hypothesis and data to understand the mechanisms of systemic electrical signaling and the central role that it plays in adapting the whole plant to different stresses, as well as new findings on intracellular calcium and nitric oxide-based signaling pathways under stress, which could be extrapolated to non-plant research.

Beschreibung: Ecological and evolutionary genetics of plant-microbe interactions is of high importance for developing the plant science since the plants originated symbiotically (via incorporation of a phototrophic cyanobacterium into a heterotrophic eukaryon) and further evolve as the multipartite symbiotic systems, harboring the enormously diverse microbial communities. The Research Topic has integrated the top-level research on the genetic interactions in the plant-microbial associations required to develop the novel evolutionary approaches in the molecular and ecological genetics of different kinds of symbioses.

Beschreibung: Whilst significant advances have been made in whole organismal proteomics approaches, many researchers still rely on combinations of tissue selection and subcellular prefractionation methods to reduce the complexity of protein extracts from plants prior to proteomic analysis. Often this will allow identification of many lower abundance proteins of the target proteome and it may involve the selection of specific organs, cell types or the isolation of specific subcellular components. These subcellular proteomes provide insight into functions following various treatments and also contribute to the wider understanding of the entire organismal proteome by cataloguing a series of sub-proteome contents. The aim of this Research Topic is to bring together knowledge of sub cellular components in different plant species to provide a basis for accelerated research. It aims to provide a mini-review for each proposed section that summarizes the current understanding of a particular proteome, with the anticipation that every 5 - 10 years we can update these definitive publications.

Beschreibung: Recent developments in various “OMICs” fields have revolutionized our understanding of the vast diversity and ubiquity of microbes in the biosphere. However, most of the current paradigms of microbial cell biology, and our view of how microbes live and what they are capable of, are derived from in vitro experiments on isolated strains. Even the co-culturing of mixed species to interrogate community behavior is relatively new. But the majority of microorganisms lives in complex communities in natural environments, under varying conditions, and often cannot be cultivated. Unless we obtain a detailed understanding of the near-native 3D ultrastructure of individual community members, the 3D spatial community organization, their metabolic interdependences, coordinated gene expression and the spatial organization of their macromolecular machines inventories as well as their communication strategies, we won’t be able to truly understand microbial community life. How spatial and also temporal organization in cell–cell interactions are achieved remains largely elusive. For example, a key question in microbial ecology is what mechanisms microbes employ to respond when faced with prey, competitors or predators, and changes in external factors. Specifically, to what degree do bacterial cells in biofilms act individually or with coordinated responses? What are the spatial extent and coherence of coordinated responses? In addition, networks linking organisms across a dynamic range of physical constraints and connections should provide the basis for linked evolutionary changes under pressure from a changing environment. Therefore, we need to investigate microbial responses to altered or adverse environmental conditions (including phages, predators, and competitors) and their macromolecular, metabolic responses according to their spatial organization. We envision a diverse set of tools, including optical, spectroscopical, chemical and ultrastructural imaging techniques that will be utilized to address questions regarding e.g. intra- and inter-organism interactions linked to ultrastructure, and correlated adaptive responses in gene expression, physiological and metabolic states as a consequence of the alterations of their environment. Clearly strategies for co-evolution and in general the display of adaptive strategies of a microbial network as a response to the altered environment are of high interest. While a special focus will be placed on terrestrial sole-species or mixed biofilms, we are also interested in aquatic systems, biofilms in general and microbes living in symbiosis. In this Research Topic, we wish to summarize and review results investigating interactions and possibly networks between microbes of the same or different species, their co-occurrence, as well as spatiotemporal patterns of distribution. Our goal is to include a broad spectrum of experimental and theoretical contributions, from research and review articles to hypothesis and theory, aiming at understanding microbial interactions at a systems level.

Beschreibung: Plants are made up of a large number of distinct cell types that originate from a single fertilized egg cell. How the diversity of cell types arise in appropriate places is one of the most fascinating and attractive research areas of plant biology. During the past several decades, due to the development of new molecular techniques and tools, advances in optical microscopy, and availability of whole genome information and mutants in the model plant Arabidopsis and other plants, great advances have been made in understanding the mechanisms involved in cell fate determination in plants. Multiple mechanisms are used to generate cellular diversity. Asymmetric cell division is one of the primary mechanisms. As an example, asymmetric cell division enables one stem cell to generate a stem cell daughter and a daughter with a distinct identity. Initially equivalent cells can also differentiate to generate different cell types. This mechanism has been clearly demonstrated in the formation of multiple cell types during epidermis development in the shoot and root. Cell fate determination is influenced by both intrinsic factors, i.e, developmental regulators, as well as extrinsic signals, i.e., environmental stimuli. By using model systems like stomata, trichome, root hair and shoot and root apical meristem cells, ligands, receptors and transcription factors have been found to regulate cell fate determination. However, the details of signaling cassettes responsible for cell fate determination remain largely unknown. Plants are made up of a large number of distinct cell types that originate from a single fertilized egg cell. How the diversity of cell types arise in appropriate places is one of the most fascinating and attractive research areas of plant biology. During the past several decades, due to the development of new molecular techniques and tools, advances in optical microscopy, and availability of whole genome information and mutants in the model plant Arabidopsis and other plants, great advances have been made in understanding the mechanisms involved in cell fate determination in plants. This research topic contains 12 collected articles, including 2 Opinion Articles, 5 Reviews, 4 Mini Reviews, and 1 Original Research Article. Hopefully, these articles will expand our understanding of the regulation of cell fate determination in plants.

Beschreibung: During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.

Beschreibung: Plants have been exposed to multiple environmental stressors on long-term (seasonal) and short-term (daily) basis since their appearance on land. However, the frequency and the intensity of stress events have increased much during the last three decades because of climate change. Plants have developed, however, a multiplicity of modular and highly integrated strategies to cope with challenges imposed by novel, usually harsher environments. These strategies include migration, acclimation and adaptation. Twelve articles in this research topic exactly focus on the relative significance of these response mechanisms for the successful acclimation of plants to a wide range of novel environmental pressures. Four articles , additionally, explore how plants respond to severe stress conditions resulting from the concurrent action of multiple stressors. Ten articles mostly examine how morpho-anatomical, physiological and biochemical-related traits integrate when plants suffer from ‘novel’ threats, such as solid, gaseous, and electromagnetic pollutants. Suitable physiological indicators for developing conservation strategies are described in the last two works. This research topic highlights that bottom-up, as well as, top-down approaches will be necessary to develop in near future in the study of plants´ responses to environmental pressures.

Beschreibung: Hemipterans encompass a large group of insect pests of plants that utilize mouthparts which are modified for piercing and consuming fluids from plants. In addition, hemipterans vector viral and bacterial diseases of plants. This book brings together a set of reviews and research papers that showcase the the range of activities being undertaken to advance our understanding of the multi-organismal interaction between plant, hemipterans and microbes.

Beschreibung: Legumes crops have an extraordinary importance for the agriculture and the environment. In a world urgently requiring more sustainable agriculture, food security and healthier diets the demand for legume crops is on the rise. The International Legume Society (http://ils.nsseme.com) organizes a triannual series of conferences with the goal to serve as a forum to discuss interdisciplinary progress on legume research. The Second International Legume Society Conference (ILS2) hosted in October 2016 at Troia, Portugal was the starting point for the Research Topic “Advances in Legume Research” in FiPS, that was also open to spontaneous submissions.

Beschreibung: Nanotechnology is a fast-evolving discipline that already produces outstanding basic knowledge and industrial applications for the benefit of society. It is a new emerging and fascinating field of science, that permits advanced research in many areas. The first applications of nanotechnology mainly concerned material sciences; applications in the agriculture and food sectors are still emerging. Food science nanotechnology is an area of rising attention that unties new possibilities for the food industry. Due to the rapid population growth there is a need to produce food and beverages in a more efficient, safe and sustainable way. The application of nanotechnology in food has also gained great importance in recent years in view of its potential application to improve production of food crops, enhance nutrition, packaging and food safety overall. The new materials, products and applications are anticipated to bring lots of improvements to the food and related sectors, impacting agriculture and food production, food processing, distribution, storage, sanitation as well as the development of innovative products and sensors for effective detection of contaminants. Therefore, nanotechnology present with a large potential to provide an opportunity for the researchers of food science, food microbiology and other fields, to develop new tools for incorporation of nanoparticles into food system that could augment existing functions and add new ones. However, the number of relative publications currently available is rather small. The present Research Topic aims to provide with basic information and practical applications regarding all aspects related to the applications of nanotechnology in food science and food microbiology, namely, nanoparticle synthesis, especially through the eco-friendly perspective, potential applications in food processing, biosensor development, alternative strategies for effective pathogenic bacteria monitoring as well as the possible effects on human health and the environment.

Beschreibung: Hypericum is an important genus of the family Hypericaceae and includes almost 500 species of herbs, shrubs and trees. Being the home for many important bioactive compounds, these species have a long traditional value as medicinal plants. Currently, several species of this genus have been used in ailments as knowledge-based medicine in many countries. In the recent past, several pharmacological studies have been performed using crude extracts to evaluate the traditional knowledge. Results of those studies have revealed that Hypericum extract exert multiple pharmacological properties including antidepressant, antimicrobial, antitumor and wound healing effects. Phytochemical analyses revealed that these species produce a broad spectrum of valuable compounds, mainly naphthodianthrones (hypericin and pseudohypericin), phloroglucinols (hyperforin and adhyperforin), flavonoids (hyperoside, rutin and quercitrin), benzophenones/xanthones (garcinol and gambogic acid), and essential oils. Noticeably, Hypericum perforatum extracts have been used to treat mild to moderate depression from ancient to present times and the antidepressant efficacy of Hypericum extracts has been attributed to its hyperforin content, which is known to inhibit the re-uptake of aminergic transmitters such as serotonin and noradrenaline into synaptic nerve endings. Neurodegenerative diseases and inflammatory responses are also linked with Reactive Oxygen Species (ROS) production. A wide range of flavonoids present in Hypericum extracts, namely, rutin, quercetin, and quercitrin exhibit antioxidant/free radical scavenging activity. Hypericin, beside hyperforin, is the active molecule responsible for the antitumor ability of Hypericum extracts and is seen as a potent candidate to treat brain tumor. Recent attempts of using hypericin in patients with recurrent malignant brain tumors showed promising results. Collectively, Hypericum species contain multiple bioactive constituents, suggesting their potential to occupy a huge portion of the phytomedicine market. Today, studies on medicinal plants are rapidly increasing because of the search for new active molecules, and for the improvement in the production of plants and molecules for the herbal pharmaceutical industries. In the post genomic era, application of molecular biology and genomic tools revolutionized our understanding of major biosynthetic pathways, phytochemistry and pharmacology of Hypericum species and individual compounds. This special issue mainly focuses on the recent advancements made in the understanding of biosynthetic pathways, application of biotechnology, molecular biology, genomics, pharmacology and related areas.

Beschreibung: Biologically active small molecules have increasingly been applied in plant biology to dissect and understand biological systems. This is evident from the frequent use of potent and selective inhibitors of enzymes or other biological processes such as transcription, translation, or protein degradation. In contrast to animal systems, which are nurtured from drug research, the systematic development of novel bioactive small molecules as research tools for plant systems is a largely underexplored research area. This is surprising since bioactive small molecules bear great potential for generating new, powerful tools for dissecting diverse biological processes. In particular, when small molecules are integrated into genetic strategies (thereby defining “chemical genetics”), they may help to circumvent inherent problems of classical (forward) genetics. There are now clear examples of important, fundamental discoveries originating from plant chemical genetics that demonstrate the power, but not yet fully exploited potential, of this experimental approach. These include the unraveling of molecular mechanisms and critical steps in hormone signaling, activation of defense reactions and dynamic intracellular processes. The intention of this Research Topic of Frontiers in Plant Physiology is to summarize the current status of research at the interface between chemistry and biology and to identify future research challenges. The research topic covers diverse aspects of plant chemical biology, including the identification of bioactive small molecules through screening processes from chemical libraries and natural sources, which rely on robust and quantitative high-throughput bioassays, the critical evaluation and characterization of the compound’s activity (selectivity) and, ultimately, the identification of its protein target(s) and mode-of-action, which is yet the biggest challenge of all. Such well-characterized, selective chemicals are attractive tools for basic research, allowing the functional dissection of plant signaling processes, or for applied purposes, if designed for protection of crop plants from disease. New methods and data mining tools for assessing the bioactivity profile of compounds, exploring the chemical space for structure–function relationships, and comprehensive chemical fingerprinting (metabolomics) are also important strategies in plant chemical biology. In addition, there is a continuing need for diverse target-specific bioprobes that help profiling enzymatic activities or selectively label protein complexes or cellular compartments. To achieve these goals and to add suitable probes and methods to the experimental toolbox, plant biologists need to closely cooperate with synthetic chemists. The development of such tailored chemicals that beyond application in basic research can modify traits of crop plants or target specific classes of weeds or pests by collaboration of applied and academic research groups may provide a bright future for plant chemical biology. The current Research Topic covers the breadth of the field by presenting original research articles, methods papers, reviews, perspectives and opinions.