ALBERT

Description: 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.

Description: 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.

Description: Echolocation has evolved in different groups of animals, from bats and cetaceans to birds and humans, and enables localization and tracking of objects in a dynamic environment, where light levels may be very low or absent. Nature has shaped echolocation, an active sense that engages audiomotor feedback systems, which operates in diverse environments and situations. Echolocation production and perception vary across species, and signals are often adapted to the environment and task. In the last several decades, researchers have been studying the echolocation behavior of animals, both in the air and underwater, using different methodologies and perspectives. The result of these studies has led to rich knowledge on sound production mechanisms, directionality of the sound beam, signal design, echo reception and perception. Active control over echolocation signal production and the mechanisms for echo processing ultimately provide animals with an echoic scene or image of their surroundings. Sonar signal features directly influence the information available for the echolocating animal to perceive images of its environment. In many echolocating animals, the information processed through echoes elicits a reaction in motor systems, including adjustments in subsequent echolocation signals. We are interested in understanding how echolocating animals deal with different environments (e.g. clutter, light levels), tasks, distance to targets or objects, different prey types or other food sources, presence of conspecifics or certain predators, ambient and anthropogenic noise. In recent years, some researchers have presented new data on the origins of echolocation, which can provide a hint of its evolution. Theoreticians have addressed several issues that bear on echolocation systems, such as frequency or time resolution, target localization and beam-forming mechanisms. In this Research Topic we compiled recent work that elucidates how echolocation – from sound production, through echolocation signals to perception- has been shaped by nature functioning in different environments and situations. We strongly encouraged comparative approaches that would deepen our understanding of the processes comprising this active sense.

Description: 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.

Description: 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.

Description: 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.

Description: 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.

Description: 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.

Description: 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.

Description: 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.