Melvin J. Oliver

The evolution of vegetative desiccation tolerance in land plants

Vegetative desiccation tolerance is a widespread but uncommon occurrence in the plant kingdom generally. The majority of vegetative desiccation-tolerant plants are found in the less complex clades that constitute the algae, lichens and bryophytes. However, within the larger and more complex groups of vascular land plants there are some 60 to 70 species of ferns and fern allies, and approximately 60 species of angiosperms that exhibit some degree of vegetative desiccation tolerance. In this report we analyze the evidence for the differing mechanisms of desiccation tolerance in different plants, including differences in cellular protection and cellular repair, and couple this evidence with a phylogenetic framework to generate a working hypothesis as to the evolution of desiccation tolerance in land plants. We hypothesize that the initial evolution of vegetative desiccation tolerance was a crucial step in the colonization of the land by primitive plants from an origin in fresh water. The primitive mechanism of tolerance probably involved constitutive cellular protection coupled with active cellular repair, similar to that described for modern-day desiccation-tolerant bryophytes. As plant species evolved, vegetative desiccation tolerance was lost as increased growth rates, structural and morphological complexity, and mechanisms that conserve water within the plant and maintain efficient carbon fixation were selected for. Genes that had evolved for cellular protection and repair were, in all likelihood, recruited for different but related processes such as response to water stress and the desiccation tolerance of reproductive propagules. We thus hypothesize that the mechanism of desiccation tolerance exhibited in seeds, a developmentally induced cellular protection system, evolved from the primitive form of vegetative desiccation tolerance. Once established in seeds, this system became available for induction in vegetative tissues by environmental cues related to drying. The more recent, modified vegetative desiccation tolerance mechanism in angiosperms evolved from that programmed into seed development as species spread into very arid environments. Most recently, certain desiccation-tolerant monocots evolved the strategy of poikilochlorophylly to survive and compete in marginal habitats with variability in water availability.

Desiccation-tolerance in bryophytes: a review

Abstract Desiccation-tolerance (DT), the ability to lose virtually all free intracellular water and then recover normal function upon rehydration, is one of the most remarkable features of bryophytes. The physiology of bryophytes differs in major respects from that of vascular plants by virtue of their smaller size; unlike vascular plants, the leafy shoots of bryophytes equilibrate rapidly with the water potential in their surroundings and tend to be either fully hydrated or desiccated and metabolically inactive. The time required to recover from desiccation increases and degree of recovery decreases with length of desiccation; both also depend upon temperature and intensity of desiccation. Tolerance in at least some species shows phenotypic plasticity. Recovery of respiration, photosynthesis and protein synthesis takes place within minutes or an hour or two; recovery of the cell cycle, food transport and the cytoskeleton may take 24 hours or more. Positive carbon balance is essential to survival of repeated cycles of drying and wetting; significant growth requires continuously wet periods of a few days or more. Male and female gametophytes, and gametophyte and sporophyte, may differ in tolerance. Desiccation-tolerance is essential to dispersal and establishment of spores and vegetative propagules. The mechanisms of DT in bryophytes, including expression of LEA proteins, high content of non-reducing sugars and effective antioxidant and photo-protection, are at least partly constitutive, allowing survival of rapid drying, but changes in gene expression resulting from mRNA sequestration and alterations in translational controls elicited upon rehydration are also important to repair processes following re-wetting. Phylogenetic and ecological considerations suggest that DT is a primitive character of land plants, lost in the course of evolution of the homoiohydric vascular-plant shoot system, but retained in spores, pollen and seeds, and re-evolved in the vegetative tissues of vascular “resurrection plants.” Bryophytes have retained the poikilohydry and DT that are probably the optimal pattern of adaptation at their scale, but modern bryophytes are specialized and diverse, and are removed by the same span of evolutionary time as the flowering plants from their primitive origins.

Desiccation Tolerance in Bryophytes: A Reflection of the Primitive Strategy for Plant Survival in Dehydrating Habitats?

Abstract Bryophytes are a non-monophyletic group of three major lineages (liverworts, hornworts, and mosses) that descend from the earliest branching events in the phylogeny of land plants. We postulate that desiccation tolerance is a primitive trait, thus mechanisms by which the first land plants achieved tolerance may be reflected in how extant desiccation-tolerant bryophytes survive drying. Evidence is consistent with extant bryophytes employing a tolerance strategy of constitutive cellular protection coupled with induction of a recovery/repair mechanism upon rehydration. Cellular structures appear intact in the desiccated state but are disrupted by rapid uptake of water upon rehydration, but cellular integrity is rapidly regained. The photosynthetic machinery appears to be protected such that photosynthetic activity recovers quickly. Gene expression responds following rehydration and not during drying. Gene expression is translationally controlled and results in the synthesis of a number of proteins, collectively called rehydrins. Some prominent rehydrins are similar to Late Embryogenesis Abundant (LEA) proteins, classically ascribed a protection function during desiccation. The role of LEA proteins in a rehydrating system is unknown but data indicates a function in stabilization and reconstitution of membranes. Phylogenetic studies using a Tortula ruralis LEA-like rehydrin led to a re-examination of the evolution of desiccation tolerance. A new phylogenetic analysis suggests that: (i) the basic mechanisms of tolerance seen in modern day bryophytes have changed little from the earliest manifestations of desiccation tolerance in land plants, and (ii) vegetative desiccation tolerance in the early land plants may have evolved from a mechanism present first in spores.

A Sister Group Contrast Using Untargeted Global Metabolomic Analysis Delineates the Biochemical Regulation Underlying Desiccation Tolerance in Sporobolus stapfianus

The desiccation-tolerant Sporobolus stapfianus and desiccation-sensitive Sporobolus pyramidalis form a sister group contrast to investigate adaptive metabolic responses to dehydration using untargeted global metabolomic analysis. The metabolic profiles obtained reveal a state of preparedness and a cascade of biochemical regulation strategies critical to the survival of S. stapfianus under desiccation. Understanding how plants tolerate dehydration is a prerequisite for developing novel strategies for improving drought tolerance. The desiccation-tolerant (DT) Sporobolus stapfianus and the desiccation-sensitive (DS) Sporobolus pyramidalis formed a sister group contrast to reveal adaptive metabolic responses to dehydration using untargeted global metabolomic analysis. Young leaves from both grasses at full hydration or at 60% relative water content (RWC) and from S. stapfianus at lower RWCs were analyzed using liquid and gas chromatography linked to mass spectrometry or tandem mass spectrometry. Comparison of the two species in the fully hydrated state revealed intrinsic differences between the two metabolomes. S. stapfianus had higher concentrations of osmolytes, lower concentrations of metabolites associated with energy metabolism, and higher concentrations of nitrogen metabolites, suggesting that it is primed metabolically for dehydration stress. Further reduction of the leaf RWC to 60% instigated a metabolic shift in S. stapfianus toward the production of protective compounds, whereas S. pyramidalis responded differently. The metabolomes of S. stapfianus leaves below 40% RWC were strongly directed toward antioxidant production, nitrogen remobilization, ammonia detoxification, and soluble sugar production. Collectively, the metabolic profiles obtained uncovered a cascade of biochemical regulation strategies critical to the survival of S. stapfianus under desiccation.

“To dryness and beyond” – Preparation for the dried state and rehydration in vegetative desiccation-tolerant plants

The ability of vegetative plant tissues to survive desiccation is an uncommon trait, although plants that are able to do this represent all major classes of plants. Two classes of vegetative desiccation-tolerant plants exist; those that are modified desiccation-tolerant and can only survive desiccation if drying rates are slow, and those that are fully desiccation-tolerant and can survive even rapid drying rates. Investigations into the cellular level responses of these two types of plants has lead to an understanding of the underlying mechanisms of desiccation-tolerance. The following proposed mechanisms for desiccation-tolerance are presented. Modified desiccation-tolerant plants utilize inducible cellular protection systems supplemented in part by a minor rehydration induced repair component. Fully desiccation-tolerant plants utilize a rehydration induced repair system that is complemented by a constitutive protection component. This minireview explores the evidence for these proposed mechanisms in an attempt to lay the theoretical ground work for future work in this area.

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BackgroundBLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality.ResultsW.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files.ConclusionW.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from http://liru.ars.usda.gov/mainbioinformatics.html. With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum.

The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis : transcript classification and analysis

BackgroundThe cellular response of plants to water-deficits has both economic and evolutionary importance directly affecting plant productivity in agriculture and plant survival in the natural environment. Genes induced by water-deficit stress have been successfully enumerated in plants that are relatively sensitive to cellular dehydration, however we have little knowledge as to the adaptive role of these genes in establishing tolerance to water loss at the cellular level. Our approach to address this problem has been to investigate the genetic responses of plants that are capable of tolerating extremes of dehydration, in particular the desiccation-tolerant bryophyte, Tortula ruralis. To establish a sound basis for characterizing the Tortula genome in regards to desiccation tolerance, we analyzed 10,368 expressed sequence tags (ESTs) from rehydrated rapid-dried Tortula gametophytes, a stage previously determined to exhibit the maximum stress induced change in gene expression.ResultsThe 10, 368 ESTs formed 5,563 EST clusters (contig groups representing individual genes) of which 3,321 (59.7%) exhibited similarity to genes present in the public databases and 2,242 were categorized as unknowns based on protein homology scores. The 3,321 clusters were classified by function using the Gene Ontology (GO) hierarchy and the KEGG database. The results indicate that the transcriptome contains a diverse population of transcripts that reflects, as expected, a period of metabolic upheaval in the gametophyte cells. Much of the emphasis within the transcriptome is centered on the protein synthetic machinery, ion and metabolite transport, and membrane biosynthesis and repair. Rehydrating gametophytes also have an abundance of transcripts that code for enzymes involved in oxidative stress metabolism and phosphorylating activities. The functional classifications reflect a remarkable consistency with what we have previously established with regards to the metabolic activities that are important in the recovery of the gametophytes from desiccation. A comparison of the GO distribution of Tortula clusters with an identical analysis of 9,981 clusters from the desiccation sensitive bryophyte species Physcomitrella patens, revealed, and accentuated, the differences between stressed and unstressed transcriptomes. Cross species sequence comparisons indicated that on the whole the Tortula clusters were more closely related to those from Physcomitrella than Arabidopsis (complete genome BLASTx comparison) although because of the differences in the databases there were more high scoring matches to the Arabidopsis sequences. The most abundant transcripts contained within the Tortula ESTs encode Late Embryogenesis Abundant (LEA) proteins that are normally associated with drying plant tissues. This suggests that LEAs may also play a role in recovery from desiccation when water is reintroduced into a dried tissue.ConclusionThe establishment of a rehydration EST collection for Tortula ruralis, an important plant model for plant stress responses and vegetative desiccation tolerance, is an important step in understanding the genome level response to cellular dehydration. The type of transcript analysis performed here has laid the foundation for more detailed functional and genome level analyses of the genes involved in desiccation tolerance in plants.

Bryophytes as experimental models for the study of environmental stress tolerance: Tortula ruralis and desiccation-tolerance in mosses

The development of a complete understanding of how plants interact with the environment at the cellular level is a crucial step in advancing our ability to unravel the complexities of plant ecology particularly with regard to the role that many of the less complex plants (i.e., algae, lichens, and bryophytes) play in plant communities and in establishing areas for colonization by their more complex brothers. One of the main barriers to the advancement of this area of plant biology has been the paucity of simple and appropriate experimental models that would enable the researcher to biochemically and genetically dissect the response of less complex plants to environmental stress. A number of bryophytes model systems have been developed and they have been powerful experimental tools for the elucidation of complex biological processes in plants. Recently there has been a resurgent interest in bryophytes as models systems due to the discovery and development of homologous recombination technologies in the moss Physcomitrella patens (Hedw.) Brach & Schimp. In this report we introduce the desiccation-tolerant moss Tortula ruralis (Hedw.) Gaert., Meyer, and Scherb, as a model for stress tolerance mechanisms that offers a great deal of promise for advancing our efforts to understand how plants respond to and survive the severest of stressful environments. T. ruralis, a species native to Northern and Western North America, has been the most intensely studied of all bryophytes with respect to its physiological, biochemical, and cellular responses, to the severest of water stresses, desiccation. It is our hope that the research conducted using this bryophyte will lay the foundationfor not only the ecology of bryophytes and other less complex plants but also for the role of desiccation-tolerance in the evolution of land plants and the determination of mechanisms by which plant cells can withstand environmental insults. We will focus the discussion on the research we and others have conducted in an effort to understand the ability of T. ruralis to withstand the complete loss of free water from the protoplasm of its cells.

The evolution of desiccation tolerance in angiosperm plants: a rare yet common phenomenon

In a minute proportion of angiosperm species, rehydrating foliage can revive from airdryness or even from equilibration with air of ~0% RH. Such desiccation tolerance is known from vegetative cells of some species of algae and of major groups close to the evolutionary path of the angiosperms. It is also found in the reproductive structures of some algae, moss spores and probably the aerial spores of other terrestrial cryptogamic taxa. The occurrence of desiccation tolerance in the seed plants is overwhelmingly in the aerial reproductive structures; the pollen and seed embryos. Spatially and temporally, pollen and embryos are close ontogenetic derivatives of the angiosperm microspores and megaspores respectively. This suggests that the desiccation tolerance of pollen and embryos derives from the desiccation tolerance of the spores of antecedent taxa and that the basic pollen/embryo mechanism of desiccation tolerance has eventually become expressed also in the vegetative tissue of certain angiosperm species whose drought avoidance is inadequate in micro-habitats that suffer extremely xeric episodes. The protective compounds and processes that contribute to desiccation tolerance in angiosperms are found in the modern groups related to the evolutionary path leading to the angiosperms and are also present in the algae and in the cyanobacteria. The mechanism of desiccation tolerance in the angiosperms thus appears to have its origins in algal ancestors and possibly in the endosymbiotic cyanobacteria-related progenitor of chloroplasts and the bacteria-related progenitor of mitochondria. The mechanism may involve the regulation and timing of the accumulation of protective compounds and of other contributing substances and processes.

Transgenic perennial biofuel feedstocks and strategies for bioconfinement

The use of transgenic tools for the improvement of plant feedstocks will be required to realize the full economic and environmental benefits of cellulosic and other biofuels, particularly from perennial plants. Traits that are targets for improvement of biofuels crops include herbicide resistance, pest, drought, cold and salt tolerance, nutrient use efficiency, altered cell wall composition and improved processing and end-use characteristics. However, controlling gene flow is a major issue and there is no regulatory experience with perennial plants as dedicated biofuels feedstocks. Bioconfinement of transgenes is thus an obvious regulatory and biosafety objective to the release and commercialization of transgenic bioenergy feedstocks. In this article, we review bioconfinement strategies that target pollen or seeds that can be applied to perennial plants used as biofuels. These include male sterility, integration of transgenes into plastid genomes, removal of transgenes in pollen and seeds, transgene expression in vegetative organs for harvest before appearance of reproductive structures or gene use restriction technologies.