Microgravity effects on leaf morphology, cell structure, carbon metabolism and mRNA expression of dwarf wheat

Combining clinostating and proton irradiation for modeling the space environment: a case study with a Chernobyl accession of Arabidopsis thaliana

PURPOSE

The study of mechanisms of plant responses to extreme conditions, particularly, microgravity and ionizing radiation, is crucial for space exploration. Modern space biology of plants focuses on increasing plant tolerance to harsh conditions of space environment. Given the limited access to the International Space Station, we designed and assembled the 3D clinostat for mimicking microgravity, which, in combination with proton irradiation, allows simulating space conditions. As a case study for testing the device, we studied the effect of clinostating on Arabidopsis thaliana accession originating from the Chernobyl exclusion zone.

MATERIALS AND METHODS

Using the combined clinostating and proton irradiation, we simulated the conditions of long-term space flight for Arabidopsis thaliana plants of the Chernobyl accession - progeny of chronically irradiated plants, grown from field-collected (Masa-0) and laboratory-cultivated (Masa-0-1) seeds, and for wild-type Col-8. The clinostating and irradiation of plants were also carried out separately. Plant responses were studied as photosynthetic and phenotypic endpoints of seedlings.

RESULTS AND CONCLUSIONS

Parameters of chlorophyll fluorescence estimated immediately after exposure showed that Masa-0-1 plants were resistant to the simulated space conditions, while Masa-0 demonstrated modulation of non-photochemical fluorescence quenching. Proton irradiation generally inhibited photosynthesis of Masa-0, Masa-0-1, and Col-8 seedlings. The combined effect of irradiation and clinostating modulated the photosynthetic activity of Col-8 seedlings. The leaf area of seedlings did not change after exposure to simulated conditions. The 3D clinostat model and software are published along with this article for researchers interested in the field of space biology.

Prolonged exposure to hypergravity increases number and size of cells and enhances lignin deposition in the stem of Arabidopsis thaliana

We have performed a lab-based hypergravity cultivation experiment using a centrifuge equipped with a lighting system and examined long-term effects of hypergravity on the development of the main axis of the Arabidopsis (Arabidopsis thaliana (L.) Heynh.) primary inflorescence, which comprises the rachis and peduncle, collectively referred to as the main stem for simplicity. Plants grown under 1 × g (gravitational acceleration on Earth) conditions for 20-23 days and having the first visible flower bud were exposed to hypergravity at 8 × g for 10 days. We analyzed the effect of prolonged hypergravity conditions on growth, lignin deposition, and tissue anatomy of the main stem. As a result, the length of the main stem decreased and cross-sectional area, dry mass per unit length, cell number, and lignin content of the main stem significantly increased under hypergravity. Lignin content in the rosette leaves also increased when they were exposed to hypergravity during their development. Except for interfascicular fibers, cross-sectional areas of the tissues composing the internode significantly increased under hypergravity in most types of the tissues in the basal part than the apical part of the main stem, indicating that the effect of hypergravity is more pronounced in the basal part than the apical part. The number of cells in the fascicular cambium and xylem significantly increased under hypergravity both in the apical and basal internodes of the main stem, indicating a possibility that hypergravity stimulates procambium activity to produce xylem element more than phloem element. The main stem was suggested to be strengthened through changes in its morphological characteristics as well as lignin deposition under prolonged hypergravity conditions.

Database of space life investigations and information on spaceflight plant biology

Extensive spaceflight life investigations (SLIs) have revealed observable space effects on plants, particularly their growth, nutrition yield, and secondary metabolite production. Knowledge of these effects not only facilitates space agricultural and biopharmaceutical technology development but also provides unique perspectives to ground-based investigations. SLIs are specialized experimental protocols and notable biological phenomena. These require specialized databases, leading to the development of the NASA Science Data Archive, Erasmus Experiment Archive, and NASA GeneLab. The increasing interests of SLIs across diverse fields demand resources with comprehensive content, convenient search facilities, and friendly information presentation. A new database SpaceLID (Space Life Investigation Database http://bidd.group/spacelid/ ) was developed with detailed menu search tools and categorized contents about the phenomena, protocols, and outcomes of 459 SLIs (including 106 plant investigations) of 92 species, where 236 SLIs and 57 plant investigations are uncovered by the existing databases. The usefulness of SpaceLID as an SLI information source is illustrated by the literature-reported analysis of metabolite, nutrition, and symbiosis variations of spaceflight plants. In conclusion, this study extensively investigated the impact of the space environment on plant biology, utilizing SpaceLID as an information source and examining various plant species, including Arabidopsis thaliana, Brassica rapa L., and Glycyrrhiza uralensis Fisch. The findings provide valuable insights into the effects of space conditions on plant physiology and metabolism.

Brachypodium distachyon Seedlings Display Accession-Specific Morphological and Transcriptomic Responses to the Microgravity Environment of the International Space Station

Plants have been recognized as key components of bioregenerative life support systems for space exploration, and many experiments have been carried out to evaluate their adaptability to spaceflight. Unfortunately, few of these experiments have involved monocot plants, which constitute most of the crops used on Earth as sources of food, feed, and fiber. To better understand the ability of monocot plants to adapt to spaceflight, we germinated and grew Brachypodium distachyon seedlings of the Bd21, Bd21-3, and Gaz8 accessions in a customized growth unit on the International Space Station, along with 1-g ground controls. At the end of a 4-day growth period, seedling organ’s growth and morphologies were quantified, and root and shoot transcriptomic profiles were investigated using RNA-seq. The roots of all three accessions grew more slowly and displayed longer root hairs under microgravity conditions relative to ground control. On the other hand, the shoots of Bd21-3 and Gaz-8 grew at similar rates between conditions, whereas those of Bd21 grew more slowly under microgravity. The three Brachypodium accessions displayed dramatically different transcriptomic responses to microgravity relative to ground controls, with the largest numbers of differentially expressed genes (DEGs) found in Gaz8 (4527), followed by Bd21 (1353) and Bd21-3 (570). Only 47 and six DEGs were shared between accessions for shoots and roots, respectively, including DEGs encoding wall-associated proteins and photosynthesis-related DEGs. Furthermore, DEGs associated with the “Oxidative Stress Response” GO group were up-regulated in the shoots and down-regulated in the roots of Bd21 and Gaz8, indicating that Brachypodium roots and shoots deploy distinct biological strategies to adapt to the microgravity environment. A comparative analysis of the Brachypodium oxidative-stress response DEGs with the Arabidopsis ROS wheel suggests a connection between retrograde signaling, light response, and decreased expression of photosynthesis-related genes in microgravity-exposed shoots. In Gaz8, DEGs were also found to preferentially associate with the “Plant Hormonal Signaling” and “MAP Kinase Signaling” KEGG pathways. Overall, these data indicate that Brachypodium distachyon seedlings exposed to the microgravity environment of ISS display accession- and organ-specific responses that involve oxidative stress response, wall remodeling, photosynthesis inhibition, expression regulation, ribosome biogenesis, and post-translational modifications. The general characteristics of these responses are similar to those displayed by microgravity-exposed Arabidopsis thaliana seedlings. However, organ- and accession-specific components of the response dramatically differ both within and between species. These results suggest a need to directly evaluate candidate-crop responses to microgravity to better understand their specific adaptability to this novel environment and develop cultivation strategies allowing them to strive during spaceflight.

Simulated microgravity shapes the endophytic bacterial community by affecting wheat root metabolism

To improve nutrient utilization and pathogenic resistance of plants in space, it is crucial to understand the effects of microgravity on the plant root microbiome. However, the finer details of whether and how microgravity affects the root microbiome remain unclear. Here, we found that simulated microgravity elicits no significant changes in fungal community composition and diversity, whether rhizosphere or endophytic. However, simulated microgravity caused a significant change in the composition and diversity of endophytic bacteria of wheat seedlings, but not in rhizosphere bacteria. The alteration of endophytic bacterial communities demonstrates that wheat seedlings adopt strategies to recruit additional endophytic Enterobacteriaceae and increase the stability of the endophytic bacterial network to respond to the challenge of simulated microgravity. Furthermore, our results also suggest that the corresponding changes in endophytic bacteria under simulated microgravity is closely related to a significant decrease in metabolites of the host's carbon metabolism, flavonoid biosynthesis, benzoxazinoid biosynthesis, and tryptophan metabolism pathways. Our findings reveal details important to our understanding of the impact of gravity on the microbial community of plant seedlings and the theoretical basis for manipulation of microorganisms to ensure efficient plant production in space. This article is protected by copyright. All rights reserved.

Physiological responses of orchids to prolonged clinorotation

Creation of plant-based bioregenerative life support systems is crucial for future long-duration space exploring missions. Microgravity is one of the major stresses affecting plant growth and development under space flight conditions. Search for higher plant genotypes resilient to microgravity as well as revealing of biological features which could be used as markers of such resilience is rather urgently needed. The objective of this study was to analyze physiological and biochemical responses of three orchid species representing different life forms (terrestrial and epiphytic), growth types (monopodial and sympodial) and pathways of CO2 fixation to long-term (24 months) clinorotation which modeled the combined effect of two stress factors: hermetic conditions and microgravity. Three years old meristematic orchids Cypripedium flavum, Angraecum eburneum, Epidendrum radicans, representing different life forms, types of branching shoot system and pathways of CO2 fixation, were used as test-plants. The microgravity was simulated using three-dimensional (3-D) clinostat equipped with two rotation axes placed at right angles (rotation frequency was 3 rpm) in controlled conditions of air temperature, illumination, air humidity and substrate moisture. The control plants were grown in the similar plastic vessels but not hermetically sealed and without clinorotating in the same environmental conditions. The vital state of the test plants was assessed using characteristics of mineral nutrition, content of photosynthetic pigments, free amino acids, soluble proteins, DNA and RNA, enzymatic and non-enzymatic antioxidants. The results of this study confirmed that orchids grown under simulated microgravity and kept in hermetically-sealed vessels were subjected to oxidative stress, which could be responsible for the observed inhibition of basic physiological processes such as mineral nutrition, metabolism of aminoacids, protein biosynthesis and photosynthesis. Monopodial orchids C. flavum and A. eburneum demonstrated better adaptation to prolonged clinorotation as compared to sympodial E. radicans. In particular, the latter demonstrated some stimulation of mineral nutrition processes (i.e. K, N, Fe, Mn, Zn accumulation), content of photosynthetic pigments, proline and superoxide dismutase activity. Long-lasting clinorotation induced adaptive changes of antioxidant systems in the studied orchids (e.i. increase in carotenoids and proline content and stimulation of superoxide dismutase activity), which helped to maintain the main physiological functions at stable level in the above-mentioned stressful conditions. The following biochemical characteristics in the studied orchids could be considered as markers of resilience to simulated microgravity and hermetic conditions: 1) an increase in the accumulation of non-enzymatic (proline, carotenoids) and enzymatic antioxidants (superoxide dismutase); 2) ability to maintain stable balance of mineral nutrients; 3) increase in the content of photosynthetic pigments; 4) increase in the content of proteinogenic amino acids and soluble proteins; 5) increase in the DNA content or RNA/DNA ratio. Our studies have also demonstrated a correlation between orchid ecomorphological characteristics such as type of branching with their adaptive responses to prolonged clinorotation. We observed no correlation between the studied life form of orchids, ecotype or the pathway of CO2 fixation and their resilience to prolonged clinorotation. This research can be a starting point for studying the relationships between ecomorphological features of various orchids and their resilience to microgravity conditions in the search for biological markers of microgravity tolerance in species of higher plants.

Physiological responses of orchids to prolonged clinorotation

Creation of plant-based bioregenerative life support systems is crucial for future long-duration space exploring missions. Microgravity is one of the major stresses affecting plant growth and development under space flight conditions. Search for higher plant genotypes resilient to microgravity as well as revealing of biological features which could be used as markers of such resilience is rather urgently needed. The objective of this study was to analyze physiological and biochemical responses of three orchid species representing different life forms (terrestrial and epiphytic), growth types (monopodial and sympodial) and pathways of CO2 fixation to long-term (24 months) clinorotation which modeled the combined effect of two stress factors: hermetic conditions and microgravity. Three years old meristematic orchids Cypripedium flavum, Angraecum eburneum, Epidendrum radicans, representing different life forms, types of branching shoot system and pathways of CO2 fixation, were used as test-plants. The microgravity was simulated using three-dimensional (3-D) clinostat equipped with two rotation axes placed at right angles (rotation frequency was 3 rpm) in controlled conditions of air temperature, illumination, air humidity and substrate moisture. The control plants were grown in the similar plastic vessels but not hermetically sealed and without clinorotating in the same environmental conditions. The vital state of the test plants was assessed using characteristics of mineral nutrition, content of photosynthetic pigments, free amino acids, soluble proteins, DNA and RNA, enzymatic and non-enzymatic antioxidants. The results of this study confirmed that orchids grown under simulated microgravity and kept in hermetically-sealed vessels were subjected to oxidative stress, which could be responsible for the observed inhibition of basic physiological processes such as mineral nutrition, metabolism of aminoacids, protein biosynthesis and photosynthesis. Monopodial orchids C. flavum and A. eburneum demonstrated better adaptation to prolonged clinorotation as compared to sympodial E. radicans. In particular, the latter demonstrated some stimulation of mineral nutrition processes (i.e. K, N, Fe, Mn, Zn accumulation), content of photosynthetic pigments, proline and superoxide dismutase activity. Long-lasting clinorotation induced adaptive changes of antioxidant systems in the studied orchids (e.i. increase in carotenoids and proline content and stimulation of superoxide dismutase activity), which helped to maintain the main physiological functions at stable level in the above-mentioned stressful conditions. The following biochemical characteristics in the studied orchids could be considered as markers of resilience to simulated microgravity and hermetic conditions: 1) an increase in the accumulation of non-enzymatic (proline, carotenoids) and enzymatic antioxidants (superoxide dismutase); 2) ability to maintain stable balance of mineral nutrients; 3) increase in the content of photosynthetic pigments; 4) increase in the content of proteinogenic amino acids and soluble proteins; 5) increase in the DNA content or RNA/DNA ratio. Our studies have also demonstrated a correlation between orchid ecomorphological characteristics such as type of branching with their adaptive responses to prolonged clinorotation. We observed no correlation between the studied life form of orchids, ecotype or the pathway of CO2 fixation and their resilience to prolonged clinorotation. This research can be a starting point for studying the relationships between ecomorphological features of various orchids and their resilience to microgravity conditions in the search for biological markers of microgravity tolerance in species of higher plants.

Plant biology for space exploration - Building on the past, preparing for the future

A review of past insights of space experiments with plants outlines basic space and gravity effects as well as gene expression. Efforts to grow plants in space gradually incorporated basic question on plant productivity, stress response and cultivation. The prospect of extended space missions as well as colonization of the Moon and Mars require better understanding and therefore research efforts on biomass productivity, substrate and water relations, atmospheric composition, pressure and temperature and substrate and volume (growth space) requirements. The essential combination of using plants not only for food production but also for regeneration of waste, and recycling of carbon and oxygen production requires integration of complex biological and engineering aspects. We combine a historical account of plant space research with considerations for future research on plant cultivation, selection, and productivity based on space-related environmental conditions.

Plant responses to real and simulated microgravity

Plant biology experiments in real and simulated microgravity have significantly contributed to our understanding of physiology and behavior of plants. How do plants perceive microgravity? How that perception translates into stimulus? And in turn plant's response and adaptation to microgravity through physiological, cellular, and molecular changes have been reasonably well documented in the literature. Knowledge gained through these plant biology experiments in microgravity helped to successfully cultivate crops in space. For instance, salad crop such as red romaine lettuce grown on the International Space Station (ISS) is allowed to incorporate into the crew's supplementary diet. However, the use of plants as a sustainable bio-regenerative life support system (BLSS) to produce fresh food and O2, reduce CO2 level, recycle metabolic waste, and efficient water management for long-duration space exploration missions requires critical gap filling research. Hence, it is inevitable to reflect and review plant biology microgravity research findings time and again with a new set of data available in the literature. With that in focus, the current article discusses phenotypic, physiological, biochemical, cell cycle, cell wall changes and molecular responses of plants to microgravity both in real and simulated conditions with the latest literature.

From Spaceflight to Mars g-Levels: Adaptive Response of A. Thaliana Seedlings in a Reduced Gravity Environment Is Enhanced by Red-Light Photostimulation

The response of plants to the spaceflight environment and microgravity is still not well understood, although research has increased in this area. Even less is known about plants' response to partial or reduced gravity levels. In the absence of the directional cues provided by the gravity vector, the plant is especially perceptive to other cues such as light. Here, we investigate the response of Arabidopsis thaliana 6-day-old seedlings to microgravity and the Mars partial gravity level during spaceflight, as well as the effects of red-light photostimulation by determining meristematic cell growth and proliferation. These experiments involve microscopic techniques together with transcriptomic studies. We demonstrate that microgravity and partial gravity trigger differential responses. The microgravity environment activates hormonal routes responsible for proliferation/growth and upregulates plastid/mitochondrial-encoded transcripts, even in the dark. In contrast, the Mars gravity level inhibits these routes and activates responses to stress factors to restore cell growth parameters only when red photostimulation is provided. This response is accompanied by upregulation of numerous transcription factors such as the environmental acclimation-related WRKY-domain family. In the long term, these discoveries can be applied in the design of bioregenerative life support systems and space farming.

Growth and photosynthetic responses of Chinese cabbage (Brassica rapa L. cv. Tokyo Bekana) to continuously elevated carbon dioxide in a simulated Space Station "Veggie" crop-production environment

Among candidate leafy vegetable species initially considered for astronauts to pick and eat from the Veggie plant-growth unit on the International Space Station (ISS), Chinese cabbage (Brassica rapa L. cv. Tokyo Bekana) ranked high in ground-based screening studies. However, subsequent attempts to optimize growth within rigorous ISS-like growth environments on the ground were frustrated by development of leaf chlorosis, necrosis, and uneven growth. 'Tokyo Bekana' ('TB') grown on ISS during the VEG-03B and C flights developed similar stress symptoms. After lengthy troubleshooting efforts to identify causes of sub-par growth in highly controlled environments, the super-elevated CO₂ concentrations that plants on ISS are exposed to continuously (average of 2,800 µmol/mol) emerged as a candidate environmental condition responsible for the observed plant-stress symptoms. Subsequent ground-based studies found continuous exposure to ISS levels of CO₂ under Veggie environmental and cultural conditions to significantly inhibit growth of 'TB' compared to near-Earth-normal CO₂ controls. The present study investigated growth and gas-exchange responses of 'TB' to sub-ISS but still elevated CO₂ levels (900 or 1,350 µmol/mol) in combination with other potential stressors related to ISS/Veggie compared to 450 µmol/mol CO₂ controls. Shoot dry mass of plants grown at 450 µmol•mol^-1 CO₂ for 28 days was 96% and 80% higher than that of plants grown at 900 µmol•mol^-1 CO₂ and 1,350 µmol•mol^-1 CO_2, respectively. Leaf number and leaf area of controls were significantly higher than those of plants grown at 1,350 µmol•mol^-1 CO₂. Photosynthetic rate measured using a leaf cuvette was significantly lower for plants grown at 900 µmol•mol^-1 CO₂ than for controls. The ratio of leaf internal CO₂ concentration (C_i) to cuvette ambient CO₂ concentration (C_a) was significantly lower for plants grown at 450 µmol•mol^-1 CO₂ than for plants grown at elevated CO₂. Thus, continuously elevated CO₂ in combination with a Veggie cultivation system decreased growth, leaf area, and photosynthetic efficiency of Chinese cabbage 'Tokyo Bekana'. The results of this study suggest that 'Tokyo Bekana' is very sensitive to continuously elevated CO₂ in such a growth environment, and indicate the need for improved environmental control of CO₂ and possibly root-zone factors for successful crop production in the ISS spaceflight environment. Differential sensitivity of other salad crops to an ISS/Veggie growth environment also is possible, so it is important to mimic controllable ISS-like environmental conditions as precisely as possible during ground-based screening.

Exploration of space to achieve scientific breakthroughs

Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.

RNA-seq analyses of Arabidopsis thaliana seedlings after exposure to blue-light phototropic stimuli in microgravity

PREMISE

Plants synthesize information from multiple environmental stimuli when determining their direction of growth. Gravity, being ubiquitous on Earth, plays a major role in determining the direction of growth and overall architecture of the plant. Here, we utilized the microgravity environment on board the International Space Station (ISS) to identify genes involved influencing growth and development of phototropically stimulated seedlings of Arabidopsis thaliana.

METHODS

Seedlings were grown on the ISS, and RNA was extracted from 7 samples (pools of 10-15 plants) grown in microgravity (μg) or Earth gravity conditions (1-g). Transcriptomic analyses via RNA sequencing (RNA-seq) of differential gene expression was performed using the HISAT2-Stringtie-DESeq2 RNASeq pipeline. Differentially expressed genes were further characterized by using Pathway Analysis and enrichment for Gene Ontology classifications.

RESULTS

For 296 genes that were found significantly differentially expressed between plants in microgravity compared to 1-g controls, Pathway Analysis identified eight molecular pathways that were significantly affected by reduced gravity conditions. Specifically, light-associated pathways (e.g., photosynthesis-antenna proteins, photosynthesis, porphyrin, and chlorophyll metabolism) were significantly downregulated in microgravity.

CONCLUSIONS

Gene expression in A. thaliana seedlings grown in microgravity was significantly altered compared to that of the 1-g control. Understanding how plants grow in conditions of microgravity not only aids in our understanding of how plants grow and respond to the environment but will also help to efficiently grow plants during long-range space missions.

Photosynthetic Performance of Rice Seedlings Originated from Seeds Exposed to Spaceflight Conditions

The mechanism of the regulation on photosynthesis after spaceflight has not been fully understood. To learn more information about this, we conducted a series of experiments of photosystem, including photosynthetic physiological characteristics (fluorescence parameters, pigment contents), gene expression and proteomic change. We want to examine the response of rice (Oryza sativaDN416), whose seeds were placed in Bio-Radiation Box on the ShiJian-10(SJ-10) recoverable satellite. Our results demonstrated that the photosynthesis capacity of plants after spaceflight declined, compared to ground control plants. Specifically, Fv/Fm is significantly reduced for 7.5%. Chlorophyll content decreased in the three growth stages of rice, trefoil, tillering and mature stages. To further analyze changes under spaceflight environment, quantitative real-time PCR technology and isobaric tags for relative and absolute quantization (iTRAQ) labeling technology were deployed. We found that the gene expression of important subunits of key enzymes and important structures had been decreased after spaceflight. As for the results of changes in proteins, we discovered that the content of proteins related to electron transport and photosynthesis key enzyme declined. Our experiments can provide reference for further research to learn more about the effects of spaceflight on photosynthesis.

Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

BACKGROUND

Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of spaceflight aboard the International Space Station (ISS), an environment completely outside their evolutionary history, they respond with unique alterations to their gene expression profile. Identifying the genes important for physiological adaptation to spaceflight and dissecting the biological processes and pathways engaged by plants during spaceflight has helped reveal spaceflight adaptation, and has furthered understanding of terrestrial growth processes. However, the underlying regulatory mechanisms responsible for these changes in gene expression patterns are just beginning to be explored. Epigenetic modifications, such as DNA methylation at position five in cytosine, has been shown to play a role in the physiological adaptation to adverse terrestrial environments, and may play a role in spaceflight as well.

RESULTS

Whole Genome Bisulfite Sequencing of DNA of Arabidopsis grown on the ISS from seed revealed organ-specific patterns of differential methylation compared to ground controls. The overall levels of methylation in CG, CHG, and CHH contexts were similar between flight and ground DNA, however, thousands of specifically differentially methylated cytosines were discovered, and there were clear organ-specific differences in methylation patterns. Spaceflight leaves had higher methylation levels in CHG and CHH contexts within protein-coding genes in spaceflight; about a fifth of the leaf genes were also differentially regulated in spaceflight, almost half of which were associated with reactive oxygen signaling.

CONCLUSIONS

The physiological adaptation of plants to spaceflight is likely nuanced by epigenomic modification. This is the first examination of differential genomic methylation from plants grown completely in the spaceflight environment of the ISS in plant growth hardware developed for informing exploration life support strategies. Yet even in this optimized plant habitat, plants respond as if stressed. These data suggest that gene expression associated with physiological adaptation to spaceflight is regulated in part by methylation strategies similar to those engaged with familiar terrestrial stress responses. The differential methylation maps generated here provide a useful reference for elucidating the layers of regulation of spaceflight responses.

Energy saving and improvement of metabolism of cultured tobacco cells upon exposure to 2-D clinorotation

Studies have confirmed that on the ground, the plant cells must expend energy to maintain positional homeostasis against gravity. Under microgravity conditions, such energy may be saved for other process such as biosynthesis of beneficial metabolites for growth. This hypothesis was examined on a cell line of tobacco (Nicotiana tabacum cv. Burley 21). The cells were continuously treated with 2-D clinostat for 1 week. Exposure to clinorotation conditions increased biomass and total protein. Total content of soluble sugar also increased which may provide more precursors for Krebs cycle and adenosine triphosphate (ATP) production. In the case of 2-D clinorotation, the expression and activity of glutamate producing enzyme, glutamate dehydrogenase (GDH) increased, whereas the activity of glutamate decarboxylase (GAD) decreased. Regarding the role of GAD in initiation of gamma amino butyric acid (GABA) shunt, it is plausible that under clinorotation condition, the tobacco cells directed their metabolism toward saving energy for Krebs cycling and more production of ATP rather than shifting to side paths such as GABA shunt. Improvement of radical scavenging enzymes activity and increase of the contents of phenolic compounds and certain peroxide neutralizing amino acids, e.g., His, Pro, Ser, and Asp under clinorotation conditions decreased membrane lipid peroxidation and maintained the growth potential of tobacco cells.

HSFA2 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight

Heat Shock Factor A2 (HsfA2) is part of the Heat Shock Factor (HSF) network, and plays an essential role beyond heat shock in environmental stress responses and cellular homeostatic control. Arabidopsis thaliana cell cultures derived from wild type (WT) ecotype Col-0 and a knockout line deficient in the gene encoding HSFA2 (HSFA2 KO) were grown aboard the International Space Station (ISS) to ascertain whether the HSF network functions in the adaptation to the novel environment of spaceflight. Microarray gene expression data were analyzed using a two-part comparative approach. First, genes differentially expressed between the two environments (spaceflight to ground) were identified within the same genotype, which represented physiological adaptation to spaceflight. Second, gene expression profiles were compared between the two genotypes (HSFA2 KO to WT) within the same environment, which defined genes uniquely required by each genotype on the ground and in spaceflight-adapted states. Results showed that the endoplasmic reticulum (ER) stress and unfolded protein response (UPR) define the HSFA2 KO cells' physiological state irrespective of the environment, and likely resulted from a deficiency in the chaperone-mediated protein folding machinery in the mutant. Results further suggested that additional to its universal stress response role, HsfA2 also has specific roles in the physiological adaptation to spaceflight through cell wall remodeling, signal perception and transduction, and starch biosynthesis. Disabling HsfA2 altered the physiological state of the cells, and impacted the mechanisms induced to adapt to spaceflight, and identified HsfA2-dependent genes that are important to the adaption of wild type cells to spaceflight. Collectively these data indicate a non-thermal role for the HSF network in spaceflight adaptation.

Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth

Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis.

Elevated CO2 enhances photosynthetic efficiency, ion uptake and antioxidant activity of Gynura bicolor DC. grown in a porous-tube nutrient delivery system under simulated microgravity

It is well known that plants can grow under space conditions, however, perturbations of many biological phenomena have been highlighted due to the effect of altered gravity and its possible interaction with other factors (e.g., CO2 , ion radiation, etc. Our aim was to test whether elevated CO2 could provide 'protection' to Gynura bicolor against the damaging effects of simulated microgravity (SM) on photosynthesis, ion uptake and antioxidant activity. As compared to G. bicolor grown in ambient CO2 with no SM (ACO2 ), growth and yield of the plants increased under elevated ambient CO2 with no SM (ECO2 ) and decreased under ACO2 +SM, whereas there was no significant effect on ECO2 +SM. Reductions in the content of Chl a, carotenoids and Chl a+b were 17.9%, 20.7% and 17.9% under ACO2 +SM, respectively, but under ECO2 there was a significant effect on all photosynthetic pigments except Chl b, compared to ACO2 . Photosynthesis was improved under ECO2 with SM and such an improvement was associated with improved water use efficiency and instantaneous carboxylation efficiency. Furthermore, SM caused a reduction in ion absorption rate, except for Ca(2+) , while ECO2 increased the uptake rate. Finally, the activity of SOD, POD and the content of MDA and H2 O2 were enhanced under SM treatments and were highest in ACO2 +SM. In contrast, T-AOC activity and GSH content significantly declined in ACO2 +SM compared to other treatments. These results suggest that ACO2 is not sufficient to counteract SM impact, but the increase is usually caused by improvement in CO2 nutrition in ECO2 +SM in comparison with ACO2 +SM.

A Bird's-Eye View of Molecular Changes in Plant Gravitropism Using Omics Techniques

During evolution, plants have developed mechanisms to adapt to a variety of environmental stresses, including drought, high salinity, changes in carbon dioxide levels and pathogens. Central signaling hubs and pathways that are regulated in response to these stimuli have been identified. In contrast to these well studied environmental stimuli, changes in transcript, protein and metabolite levels in response to a gravitational stimulus are less well understood. Amyloplasts, localized in statocytes of the root tip, in mesophyll cells of coleoptiles and in the elongation zone of the growing internodes comprise statoliths in higher plants. Deviations of the statocytes with respect to the earthly gravity vector lead to a displacement of statoliths relative to the cell due to their inertia and thus to gravity perception. Downstream signaling events, including the conversion from the biophysical signal of sedimentation of distinct heavy mass to a biochemical signal, however, remain elusive. More recently, technical advances, including clinostats, drop towers, parabolic flights, satellites, and the International Space Station, allowed researchers to study the effect of altered gravity conditions - real and simulated micro- as well as hypergravity on plants. This allows for a unique opportunity to study plant responses to a purely anthropogenic stress for which no evolutionary program exists. Furthermore, the requirement for plants as food and oxygen sources during prolonged manned space explorations led to an increased interest in the identi-fication of genes involved in the adaptation of plants to microgravity. Transcriptomic, proteomic, phosphoproteomic, and metabolomic profiling strategies provide a sensitive high-throughput approach to identify biochemical alterations in response to changes with respect to the influence of the gravitational vector and thus the acting gravitational force on the transcript, protein and metabolite level. This review aims at summarizing recent experimental approaches and discusses major observations.

Clinorotation impacts root apex respiration and the ultrostructure of mitochondria

Mitochondrial respiration in plants provides energy for biosynthesis, and its balance with photosynthesis determines the rate of plant biomass accumulation. However, there are very limited data on the influence of altered gravity on the functional status of plant mitochondria. In the given paper, we presented the results of our investigations of root respiration, the mitochondrion ultrastructure, and AOX expression of pea 1-, 3- and 5-day old seedlings grown under slow horizontal clinorotation by using an inhibitor analysis, electron microscopy, and quantitative real-time RT-PCR. It was in the first time shown that enhancement of the respiration rate in root apices of pea etiolated seedlings at the 5th day of clinorotation does not connected with increasing of both alternative oxidize capacity and AOX expression. We assumed this phenomenon is provided by more intensive oxidation of respiratory substrates. At the structural level, mitochondria in cells of the distal elongation zone were the most sensitive to clinorotation that confirms the special physiological status of this zone. The performed investigation revealed an enough resistance of plant mitochondria to the influence of altered gravity that, on our opinion, is one of components providing plant adaptation to microgravity in space flight.

Role of the plant cell wall in gravity resistance

Gravity resistance, mechanical resistance to the gravitational force, is a principal graviresponse in plants, comparable to gravitropism. The cell wall is responsible for the final step of gravity resistance. The gravity signal increases the rigidity of the cell wall via the accumulation of its constituents, polymerization of certain matrix polysaccharides due to the suppression of breakdown, stimulation of cross-link formation, and modifications to the wall environment, in a wide range of situations from microgravity in space to hypergravity. Plants thus develop a tough body to resist the gravitational force via an increase in cell wall rigidity and the modification of growth anisotropy. The development of gravity resistance mechanisms has played an important role in the acquisition of responses to various mechanical stresses and the evolution of land plants.

Differential protein expression profiling of Arabidopsis thaliana callus under microgravity on board the Chinese SZ-8 spacecraft

Exposure of Arabidopsis callus to microgravity has a significant impact on the expression of proteins involved in stress responses, carbohydrate metabolism, protein synthesis, intracellular trafficking, signaling, and cell wall biosynthesis. Microgravity is among the main environmental stress factors that affect plant growth and development in space. Understanding how plants acclimate to space microgravity is important to develop bioregenerative life-support systems for long-term space missions. To evaluate the spaceflight-associated stress and identify molecular events important for acquired microgravity tolerance, we compared proteomic profiles of Arabidopsis thaliana callus grown under microgravity on board the Chinese spacecraft SZ-8 with callus grown under 1g centrifugation (1g control) in space. Alterations in the proteome induced by microgravity were analyzed by high performance liquid chromatography-electrospray ionization-tandem mass spectrometry with isobaric tags for relative and absolute quantitation labeling. Forty-five proteins showed significant (p < 0.05) and reproducible quantitative differences in expression between the microgravity and 1g control conditions. Of these proteins, the expression level of 24 proteins was significantly up-regulated and that of 21 proteins was significantly down-regulated. The functions of these proteins were involved in a wide range of cellular processes, including general stress responses, carbohydrate metabolism, protein synthesis/degradation, intracellular trafficking/transportation, signaling, and cell wall biosynthesis. Several proteins not previously known to be involved in the response to microgravity or gravitational stimuli, such as pathogenesis-related thaumatin-like protein, leucine-rich repeat extension-like protein, and temperature-induce lipocalin, were significantly up- or down-regulated by microgravity. The results imply that either the normal gravity-response signaling is affected by microgravity exposure or that microgravity might inappropriately induce altered responses to other environmental stresses.

The Utilization of Plant Facilities on the International Space Station-The Composition, Growth, and Development of Plant Cell Walls under Microgravity Conditions

In the preparation for missions to Mars, basic knowledge of the mechanisms of growth and development of living plants under microgravity (micro-g) conditions is essential. Focus has centered on the g-effects on rigidity, including mechanisms of signal perception, transduction, and response in gravity resistance. These components of gravity resistance are linked to the evolution and acquisition of responses to various mechanical stresses. An overview is given both on the basic effect of hypergravity as well as of micro-g conditions in the cell wall changes. The review includes plant experiments in the US Space Shuttle and the effect of short space stays (8-14 days) on single cells (plant protoplasts). Regeneration of protoplasts is dependent on cortical microtubules to orient the nascent cellulose microfibrils in the cell wall. The space protoplast experiments demonstrated that the regeneration capacity of protoplasts was retarded. Two critical factors are the basis for longer space experiments: a. the effects of gravity on the molecular mechanisms for cell wall development, b. the availability of facilities and hardware for performing cell wall experiments in space and return of RNA/DNA back to the Earth. Linked to these aspects is a description of existing hardware functioning on the International Space Station.

A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8

The Simbox mission was the first joint space project between Germany and China in November 2011. Eleven-day-old Arabidopsis thaliana wild type semisolid callus cultures were integrated into fully automated plant cultivation containers and exposed to spaceflight conditions within the Simbox hardware on board of the spacecraft Shenzhou 8. The related ground experiment was conducted under similar conditions. The use of an in-flight centrifuge provided a 1 g gravitational field in space. The cells were metabolically quenched after 5 days via RNAlater injection. The impact on the Arabidopsis transcriptome was investigated by means of whole-genome gene expression analysis. The results show a major impact of nonmicrogravity related spaceflight conditions. Genes that were significantly altered in transcript abundance are mainly involved in protein phosphorylation and MAPK cascade-related signaling processes, as well as in the cellular defense and stress responses. In contrast to short-term effects of microgravity (seconds, minutes), this mission identified only minor changes after 5 days of microgravity. These concerned genes coding for proteins involved in the plastid-associated translation machinery, mitochondrial electron transport, and energy production.

Spaceflight induces specific alterations in the proteomes of Arabidopsis

Life in spaceflight demonstrates remarkable acclimation processes within the specialized habitats of vehicles subjected to the myriad of unique environmental issues associated with orbital trajectories. To examine the response processes that occur in plants in space, leaves and roots from Arabidopsis (Arabidopsis thaliana) seedlings from three GFP reporter lines that were grown from seed for 12 days on the International Space Station and preserved on orbit in RNAlater were returned to Earth and analyzed by using iTRAQ broad-scale proteomics procedures. Using stringent criteria, we identified over 1500 proteins, which included 1167 leaf proteins and 1150 root proteins we were able to accurately quantify. Quantification revealed 256 leaf proteins and 358 root proteins that showed statistically significant differential abundance in the spaceflight samples compared to ground controls, with few proteins differentially regulated in common between leaves and roots. This indicates that there are measurable proteomics responses to spaceflight and that the responses are organ-specific. These proteomics data were compared with transcriptome data from similar spaceflight samples, showing that there is a positive but limited relationship between transcriptome and proteome regulation of the overall spaceflight responses of plants. These results are discussed in terms of emergence understanding of plant responses to spaceflight particularly with regard to cell wall remodeling, as well as in the context of deriving multiple omics data sets from a single on-orbit preservation and operations approach.

Variation in stem morphology and movement of amyloplasts in white spruce grown in the weightless environment of the International Space Station

One-year-old white spruce (Picea glauca) seedlings were studied in microgravity conditions in the International Space Station (ISS) and compared with seedlings grown on Earth. Leaf growth was clearly stimulated in space whereas data suggest a similar trend for the shoots. Needles on the current shoots of ground-based seedlings were more inclined towards the stem base than those of seedlings grown in the ISS. Amyloplasts sedimented in specialized cells of shoots and roots in seedlings grown on Earth while they were distributed at random in similar cells of seedlings tested in the ISS. In shoots, such amyloplasts were found in starch sheath cells located between leaf traces and cortical cells whereas in roots they were constituents of columella cells of the cap. Nuclei were regularly observed just above the sedimented amyloplasts in both organs. It was also frequent to detect vacuoles with phenolic compounds and endoplasmic reticulum (ER) close to the sedimented amyloplasts. The ER was mainly observed just under these amyloplasts. Thus, when amyloplasts sediment, the pressure exerted on the ER, the organelle that can for instance secrete proteins destined for the plasma membrane, might influence their functioning and play a role in signaling pathways involved in gravity-sensing white spruce cells.

Spaceflight exploration in plant gravitational biology

Before there was access to space, all experiments on plant tropisms were conducted upon the background of gravity. The gravity vector could be disrupted, such as with clinorotation and random positioning machines, and by manipulating incident angles of root growth with respect to gravity, such as with Darwin's plants on slanted plates, but gravity could not be removed from the experimental equation. Access to microgravity through spaceflight has opened new doors to plant research. Here we provide an overview of some of the methodologies of conducting plant research in the unique spaceflight environment.

Expression of small heat shock protein (sHSP) genes in the garden pea (Pisum sativum) under slow horizontal clinorotation

Plant cells respond to stress conditions, such as high temperatures, by synthesizing small heat shock proteins (sHSPs). sHSPs are molecular chaperones that assist in protein folding and prevent irreversible protein aggregation. Although many sHSP genes are temperature-inducible, other variables, such as altered gravity, can induce significant changes in plant cell gene expression. Furthermore, not all subfamilies of sHSP genes share the same expression pattern. The objective of our research was to determine the effect of simulated microgravity (clinorotation) on the expression of sHSP gene subfamilies with different subcellular locations in etiolated pea (Pisum sativum) seedlings. sHSP gene expression levels were examined using quantitative real-time RT-PCR (qPCR). qPCR results demonstrated that sHSP genes were constitutively expressed in seedlings. High temperatures increased the expression of sHSP genes by several thousand-fold. However, simulated microgravity did not have any significant effects on sHSP gene expression.

Microgravity induces changes in microsome-associated proteins of Arabidopsis seedlings grown on board the international space station

The "GENARA A" experiment was designed to monitor global changes in the proteome of membranes of Arabidopsis thaliana seedlings subjected to microgravity on board the International Space Station (ISS). For this purpose, 12-day-old seedlings were grown either in space, in the European Modular Cultivation System (EMCS) under microgravity or on a 1 g centrifuge, or on the ground. Proteins associated to membranes were selectively extracted from microsomes and identified and quantified through LC-MS-MS using a label-free method. Among the 1484 proteins identified and quantified in the 3 conditions mentioned above, 80 membrane-associated proteins were significantly more abundant in seedlings grown under microgravity in space than under 1 g (space and ground) and 69 were less abundant. Clustering of these proteins according to their predicted function indicates that proteins associated to auxin metabolism and trafficking were depleted in the microsomal fraction in µg space conditions, whereas proteins associated to stress responses, defence and metabolism were more abundant in µg than in 1 g indicating that microgravity is perceived by plants as a stressful environment. These results clearly indicate that a global membrane proteomics approach gives a snapshot of the cell status and its signaling activity in response to microgravity and highlight the major processes affected.

Plant biology in space: recent accomplishments and recommendations for future research

Gravity has shaped the evolution of life since its origin. However, experiments in the absence of this overriding force, necessary to precisely analyse its role, e.g. for growth, development, and orientation of plants and single cells, only became possible with the advent of spaceflight. Consequently, this research has been supported especially by space agencies around the world for decades, mainly for two reasons: first, to enable fundamental research on gravity perception and transduction during growth and development of plants; and second, to successfully grow plants under microgravity conditions with the goal of establishing a bioregenerative life support system providing oxygen and food for astronauts in long-term exploratory missions. For the second time, the International Space Life Sciences Working Group (ISLSWG), comprised of space agencies with substantial life sciences programmes in the world, organised a workshop on plant biology research in space. The present contribution summarises the outcome of this workshop. In the first part, an analysis is undertaken, if and how the recommendations of the first workshop held in Bad Honnef, Germany, in 1996 have been implemented. A chapter summarising major scientific breakthroughs obtained in the last 15 years from plant research in space concludes this first part. In the second part, recommendations for future research in plant biology in space are put together that have been elaborated in the various discussion sessions during the workshop, as well as provided in written statements from the session chairs. The present paper clearly shows that plant biology in space has contributed significantly to progress in plant gravity perception, transduction and responses - processes also relevant for general plant biology, including agricultural aspects. In addition, the interplay between light and gravity effects has increasingly received attention. It also became evident that plants will play a major role as components of bioregenerative life support and energy systems that are necessary to complement physico-chemical systems in upcoming long-term exploratory missions. In order to achieve major progress in the future, however, standardised experimental conditions and more advanced analytical tools, such as state-of-the-art onboard analysis, are required.

Cytosolic calcium, hydrogen peroxide and related gene expression and protein modulation in Arabidopsis thaliana cell cultures respond immediately to altered gravitation: parabolic flight data

Callus cell cultures of Arabidopsis thaliana (cv. Columbia) were exposed to parabolic flights in order to assess molecular, short-term responses to altered gravity fields. Using transgenic cell lines, hydrogen peroxide (H2 O2 ) and cytosolic Ca(2+) were continuously monitored. In parallel, the metabolism of samples was chemically quenched (RNAlater, Ambion for RNA; acid/base for NADPH, NADP) at typical stages of a parabola [1 g before pull up; end of pull up (1.8 g), end of microgravity (20 s) and end of pull out (1.8 g)]. Cells exhibited an increase in both Ca(2+) and H2 O2 with the onset of microgravity, and a decline thereafter. This behaviour was accompanied by a decrease of the NADPH/NADP redox ratio, indicating Ca(2+) -dependent activation of a NADPH oxidase. Microarray analyses revealed concomitant expression profiles. At the end of the microgravity phase, 396 transcripts were specifically up-, while 485 were down-regulated. Up-regulation was dominated by Ca(2+) - and ROS-related gene products. The same material was also used for analysis of phosphopeptides with 2-D SDS PAGE. Relevant spots were identified by liquid chromatography-MS. With the exception of a chaperone (HSP 70-3), hypergravity (1.8 g) and microgravity modified different sets of proteins. These are partly involved in primary metabolism (glycolysis, gluconeogenesis, citrate cycle) and detoxification of ROS. Taken together, these data show that both gene expression and protein modulation jointly respond within seconds to alterations in the gravity field, with a focus on metabolic adaptation, signalling and control of ROS.

Gravity-dependent differentiation and root coils in Arabidopsis thaliana wild type and phospholipase-A-I knockdown mutant grown on the International Space Station

Arabidopsis roots on 45° tilted agar in 1-g grow in wave-like figures. In addition to waves, formation of root coils is observed in several mutants compromised in gravitropism and/or auxin transport. The knockdown mutant ppla-I-1 of patatin-related phospholipase-A-I is delayed in root gravitropism and forms increased numbers of root coils. Three known factors contribute to waving: circumnutation, gravisensing and negative thigmotropism. In microgravity, deprivation of wild type (WT) and mutant roots of gravisensing and thigmotropism and circumnutation (known to slow down in microgravity, and could potentially lead to fewer waves or increased coiling in both WT and mutant). To resolve this, mutant ppla-I-1 and WT were grown in the BIOLAB facility in the International Space Station. In 1-g, roots of both types only showed waving. In the first experiment in microgravity, the mutant after 9 days formed far more coils than in 1-g but the WT also formed several coils. After 24 days in microgravity, in both types the coils were numerous with slightly more in the mutant. In the second experiment, after 9 days in microgravity only the mutant formed coils and the WT grew arcuated roots. Cell file rotation (CFR) on the mutant root surface in microgravity decreased in comparison to WT, and thus was not important for coiling. Several additional developmental responses (hypocotyl elongation, lateral root formation, cotyledon expansion) were found to be gravity-influenced. We tentatively discuss these in the context of disturbances in auxin transport, which are known to decrease through lack of gravity.

Plant cell gravisensitivity and adaptation to microgravity

A short overview on the effects of real and simulated microgravity on certain cell components and processes, including new information obtained recently, is presented. Attention is focused on the influence of real and simulated microgravity on plant cells that are not specialised to gravity perception and on seed formation. The paper considers the possibility of full adaptation of plants to microgravity, and suggests some questions for future plant research in order to make decisions on fundamental and applied problems of plant space biology.

Transcriptome analyses of Arabidopsis thaliana seedlings grown in space: implications for gravity-responsive genes

The transcriptome of seedlings was analyzed from experiments performed on the International Space Station to study the interacting effects of light and gravity on plant tropisms (project named TROPI-2; Kiss et al. 2012). Seeds of Arabidopsis were germinated in space, and seedlings were then grown in the European Modular Cultivation System for 4 days at ~1g followed by exposure to a range of gravitational accelerations (from microgravity to 1g) and two light treatments (blue light with or without a 1 h pretreatment with red). At the end of the experiments, the cassettes containing the seedlings were frozen in the minus eighty laboratory freezer and returned to Earth on space shuttle mission STS-131. The RNA was extracted from whole seedlings and used for the transcriptome analyses. A comparison of 1g spaceflight samples with 1g ground controls identified 230 genes that were differentially regulated at least twofold, emphasizing the need for "in situ" tissue fixation on a 1g centrifuge as an important control for spaceflight experiments. A further comparison of all spaceflight samples with ground controls identified approximately 280 genes that were differentially regulated at least twofold. Of these genes, several were involved in regulating cell polarity (i.e., auxin, calcium, lipid metabolism), cell-wall development, oxygen status, and cell defense or stress. However, when the transcriptome of the all g-treated spaceflight samples was compared with microgravity samples, only ~130 genes were identified as being differently regulated (P ≤ 0.01). Of this subset, only 27 genes were at least twofold differently regulated between microgravity and 1g space samples and included putative/pseudo/undefined genes (14), transposable elements (5), an expansin (ATEXP24; At1g21240), a cell-wall kinase (WAK3; At1g21240), a laccase-like flavonoid oxidase (TT10; At5g48100), among others.

Characterization of photosystem I in rice (Oryza sativa L.) seedlings upon exposure to random positioning machine

To gain a better understanding of how photosynthesis is adapted under altered gravity forces, photosynthetic apparatus and its functioning were investigated in rice (Oryza sativa L.) seedlings grown in a random positioning machine (RPM). A decrease in fresh weight and dry weight was observed in rice seedlings grown under RPM condition. No significant changes were found in the chloroplast ultrastructure and total chlorophyll content between the RPM and control samples. Analyses of chlorophyll fluorescence and thermoluminescence demonstrate that PSII activity was unchanged under RPM condition. However, PSI activity decreased significantly under RPM condition. 77 K fluorescence emission spectra show a blue-shift and reduction of PSI fluorescence emission peak in the RPM seedlings. In addition, RPM caused a significant decrease in the amplitude of absorbance changes of P700 at 820 nm (A 820) induced by saturated far-red light. Moreover, the PSI efficiency (Φ I) decreased significantly under RPM condition. Immunoblot and blue native gel analyses further illustrate that accumulation of PSI proteins was greatly decreased in the RPM seedlings. Our results suggest that PSI, but not PSII, is down-regulated under RPM condition.

Organ-specific remodeling of the Arabidopsis transcriptome in response to spaceflight

BACKGROUND

Spaceflight presents a novel environment that is outside the evolutionary experience of terrestrial organisms. Full activation of the International Space Station as a science platform complete with sophisticated plant growth chambers, laboratory benches, and procedures for effective sample return, has enabled a new level of research capability and hypothesis testing in this unique environment. The opportunity to examine the strategies of environmental sensing in spaceflight, which includes the absence of unit gravity, provides a unique insight into the balance of influence among abiotic cues directing plant growth and development: including gravity, light, and touch. The data presented here correlate morphological and transcriptome data from replicated spaceflight experiments.

RESULTS

The transcriptome of Arabidopsis thaliana demonstrated organ-specific changes in response to spaceflight, with 480 genes showing significant changes in expression in spaceflight plants compared with ground controls by at least 1.9-fold, and 58 by more than 7-fold. Leaves, hypocotyls, and roots each displayed unique patterns of response, yet many gene functions within the responses are related. Particularly represented across the dataset were genes associated with cell architecture and growth hormone signaling; processes that would not be anticipated to be altered in microgravity yet may correlate with morphological changes observed in spaceflight plants. As examples, differential expression of genes involved with touch, cell wall remodeling, root hairs, and cell expansion may correlate with spaceflight-associated root skewing, while differential expression of auxin-related and other gravity-signaling genes seemingly correlates with the microgravity of spaceflight. Although functionally related genes were differentially represented in leaves, hypocotyls, and roots, the expression of individual genes varied substantially across organ types, indicating that there is no single response to spaceflight. Rather, each organ employed its own response tactics within a shared strategy, largely involving cell wall architecture.

CONCLUSIONS

Spaceflight appears to initiate cellular remodeling throughout the plant, yet specific strategies of the response are distinct among specific organs of the plant. Further, these data illustrate that in the absence of gravity plants rely on other environmental cues to initiate the morphological responses essential to successful growth and development, and that the basis for that engagement lies in the differential expression of genes in an organ-specific manner that maximizes the utilization of these signals--such as the up-regulation of genes associated with light-sensing in roots.

A method for preparing spaceflight RNAlater-fixed Arabidopsis thaliana (Brassicaceae) tissue for scanning electron microscopy

PREMISE OF THE STUDY

In spaceflight experiments, tissues for morphologic study are fixed in 3% glutaraldehyde, while tissues for molecular study are fixed in RNAlater; thus, an experiment containing both study components requires multiple fixation strategies. The possibility of using RNAlater-fixed materials for standard SEM-based morphometric investigation was explored to expand the library of tissues available for analysis and maximize usage of samples returned from spaceflight, but these technologies have wide application to any situation where recovery of biological resources is limited. •

METHODS AND RESULTS

RNAlater-fixed samples were desalinated in distilled water, dehydrated through graded methanol, plunged into liquid ethane, and transferred to cryovials for freeze-substitution. Sample tissues were critical point dried, mounted, sputter-coated, and imaged. •

CONCLUSIONS

The protocol resulted in acceptable SEM images from RNAlater-fixed Arabidopsis thaliana tissue. The majority of the tissues remained intact, including general morphology and finer details such as root hairs and trichomes.

Cereal grass pulvini: agronomically significant models for studying gravitropism signaling and tissue polarity

Cereal grass pulvini have emerged as model systems that are not only valuable for the study of gravitropism, but are also of agricultural and economic significance. The pulvini are regions of tissue that are apical to each node and collectively return a reoriented stem to a more vertical position. They have proven to be useful for the study of gravisensing and response and are also providing clues about the establishment of polarity across tissues. This review will first highlight the agronomic significance of these stem regions and their benefits for use as model systems and provide a brief historical overview. A detailed discussion of the literature focusing on cell signaling and early changes in gene expression will follow, culminating in a temporal framework outlining events in the signaling and early growth phases of gravitropism in this tissue. Changes in cell wall composition and gene expression that occur well into the growth phase will be touched upon briefly. Finally, some ongoing research involving both maize and wheat pulvini will be introduced along with prospects for future investigations.

Fundamental plant biology enabled by the space shuttle

The relationship between fundamental plant biology and space biology was especially synergistic in the era of the Space Shuttle. While all terrestrial organisms are influenced by gravity, the impact of gravity as a tropic stimulus in plants has been a topic of formal study for more than a century. And while plants were parts of early space biology payloads, it was not until the advent of the Space Shuttle that the science of plant space biology enjoyed expansion that truly enabled controlled, fundamental experiments that removed gravity from the equation. The Space Shuttle presented a science platform that provided regular science flights with dedicated plant growth hardware and crew trained in inflight plant manipulations. Part of the impetus for plant biology experiments in space was the realization that plants could be important parts of bioregenerative life support on long missions, recycling water, air, and nutrients for the human crew. However, a large part of the impetus was that the Space Shuttle enabled fundamental plant science essentially in a microgravity environment. Experiments during the Space Shuttle era produced key science insights on biological adaptation to spaceflight and especially plant growth and tropisms. In this review, we present an overview of plant science in the Space Shuttle era with an emphasis on experiments dealing with fundamental plant growth in microgravity. This review discusses general conclusions from the study of plant spaceflight biology enabled by the Space Shuttle by providing historical context and reviews of select experiments that exemplify plant space biology science.

Plant growth strategies are remodeled by spaceflight

BACKGROUND

Arabidopsis plants were grown on the International Space Station within specialized hardware that combined a plant growth habitat with a camera system that can capture images at regular intervals of growth. The Imaging hardware delivers telemetric data from the ISS, specifically images received in real-time from experiments on orbit, providing science without sample return. Comparable Ground Controls were grown in a sister unit that is maintained in the Orbital Environment Simulator at Kennedy Space Center. One of many types of biological data that can be analyzed in this fashion is root morphology. Arabidopsis seeds were geminated on orbit on nutrient gel Petri plates in a configuration that encouraged growth along the surface of the gel. Photos were taken every six hours for the 15 days of the experiment.

RESULTS

In the absence of gravity, but the presence of directional light, spaceflight roots remained strongly negatively phototropic and grew in the opposite direction of the shoot growth; however, cultivars WS and Col-0 displayed two distinct, marked differences in their growth patterns. First, cultivar WS skewed strongly to the right on orbit, while cultivar Col-0 grew with little deviation away from the light source. Second, the Spaceflight environment also impacted the rate of growth in Arabidopsis. The size of the Flight plants (as measured by primary root and hypocotyl length) was uniformly smaller than comparably aged Ground Control plants in both cultivars.

CONCLUSIONS

Skewing and waving, thought to be gravity dependent phenomena, occur in spaceflight plants. In the presence of an orienting light source, phenotypic trends in skewing are gravity independent, and the general patterns of directional root growth typified by a given genotype in unit gravity are recapitulated on orbit, although overall growth patterns on orbit are less uniform. Skewing appears independent of axial orientation on the ISS - suggesting that other tropisms (such as for oxygen and temperature) do not influence skewing. An aspect of the spaceflight environment also retards the rate of early Arabidopsis growth.

Microarray analysis of differentially expressed genes engaged in fruit development between Prunus mume and Prunus armeniaca

Microarray analysis is a technique that can be employed to provide expression profiles of single genes and new insights to elucidate the biological mechanisms responsible for fruit development. To evaluate expression of genes mostly engaged in fruit development between Prunus mume and Prunus armeniaca, we first identified differentially expressed transcripts along the entire fruit life cycle by using microarrays spotted with 10,641 ESTs collected from P. mume and other Prunus EST sequences. A total of 1418 ESTs were selected after quality control of microarray spots and analysis for differential gene expression patterns during fruit development of P. mume and P. Armeniaca. From these, 707 up-regulated and 711 down-regulated genes showing more than two-fold differences in expression level were annotated by GO based on biological processes, molecular functions and cellular components. These differentially expressed genes were found to be involved in several important pathways of carbohydrate, galactose, and starch and sucrose metabolism as well as in biosynthesis of other secondary metabolites via KEGG. This could provide detailed information on the fruit quality differences during development and ripening of these two species. With the results obtained, we provide a practical database for comprehensive understanding of molecular events during fruit development and also lay a theoretical foundation for the cloning of genes regulating in a series of important rate-limiting enzymes involved in vital metabolic pathways during fruit development.

Spaceflight transcriptomes: unique responses to a novel environment

The spaceflight environment presents unique challenges to terrestrial biology, including but not limited to the direct effects of gravity. As we near the end of the Space Shuttle era, there remain fundamental questions about the response and adaptation of plants to orbital spaceflight conditions. We address a key baseline question of whether gene expression changes are induced by the orbital environment, and then we ask whether undifferentiated cells, cells presumably lacking the typical gravity response mechanisms, perceive spaceflight. Arabidopsis seedlings and undifferentiated cultured Arabidopsis cells were launched in April, 2010, as part of the BRIC-16 flight experiment on STS-131. Biologically replicated DNA microarray and averaged RNA digital transcript profiling revealed several hundred genes in seedlings and cell cultures that were significantly affected by launch and spaceflight. The response was moderate in seedlings; only a few genes were induced by more than 7-fold, and the overall intrinsic expression level for most differentially expressed genes was low. In contrast, cell cultures displayed a more dramatic response, with dozens of genes showing this level of differential expression, a list comprised primarily of heat shock-related and stress-related genes. This baseline transcriptome profiling of seedlings and cultured cells confirms the fundamental hypothesis that survival of the spaceflight environment requires adaptive changes that are both governed and displayed by alterations in gene expression. The comparison of intact plants with cultures of undifferentiated cells confirms a second hypothesis: undifferentiated cells can detect spaceflight in the absence of specialized tissue or organized developmental structures known to detect gravity.

Parabolic flight induces changes in gene expression patterns in Arabidopsis thaliana

Our primary objective was to evaluate gene expression changes in Arabidopsis thaliana in response to parabolic flight as part of a comprehensive approach to the molecular biology of spaceflight-related adaptations. In addition, we wished to establish parabolic flight as a tractable operations platform for molecular biology studies. In a succession of experiments on NASA's KC-135 and C-9 parabolic aircraft, Arabidopsis plants were presented with replicated exposure to parabolic flight. Transcriptome profiling revealed that parabolic flight caused changes in gene expression patterns that stood the statistical tests of replication on three different flight days. The earliest response, after 20 parabolas, was characterized by a prominence of genes associated with signal transduction. After 40 parabolas, this prominence was largely replaced by genes associated with biotic and abiotic stimuli and stress. Among these responses, three metabolic processes stand out in particular: the induction of auxin metabolism and signaling, the differential expression of genes associated with calcium-mediated signaling, and the repression of genes associated with disease resistance and cell wall biochemistry. Many, but not all, of these responses are known to be involved in gravity sensing in plants. Changes in auxin-related gene expression were also recorded by reporter genes tuned to auxin signal pathways. These data demonstrate that the parabolic flight environment is appropriate for molecular biology research involving the transition to microgravity, in that with replication, proper controls, and analyses, gene expression changes can be observed in the time frames of typical parabolic flight experiments.

Gene expression changes in Arabidopsis seedlings during short- to long-term exposure to 3-D clinorotation

Seedlings of Arabidopsis thaliana (cv. Columbia) were used to evaluate dynamic transcriptional-level genome responses to simulated microgravity condition created by 3-D clinorotation. The DNA chip data analysis showed that the plant may respond to simulated microgravity by dynamic induction (up- and down-regulations) of the responsive genes in the genome. The qRT-PCR results on the investigated genes showed that the expression patterns of the genes (molecular response) were generally similar to the physiological response patterns detected in stress-challenged plants. Expression patterns were categorized into short or continual up- or down-regulated patterns, as well as stochastic changes from short- to long-term simulated microgravity stress. The induced genes are then assumed to establish a new molecular plasticity to the newly adjusted genome status in the basic milieu of maintaining homeostasis during the process of adaptation to simulated microgravity.

Lunar plant biology--a review of the Apollo era

Recent plans for human return to the Moon have significantly elevated scientific interest in the lunar environment with emphasis on the science to be done in preparation for the return and while on the lunar surface. Since the return to the Moon is envisioned as a dedicated and potentially longer-term commitment to lunar exploration, questions of the lunar environment and particularly its impact on biology and biological systems have become a significant part of the lunar science discussion. Plants are integral to the discussion of biology on the Moon. Plants are envisioned as important components of advanced habitats and fundamental components of advanced life-support systems. Moreover, plants are sophisticated multicellular eukaryotic life-forms with highly orchestrated developmental processes, well-characterized signal transduction pathways, and exceedingly fine-tuned responses to their environments. Therefore, plants represent key test organisms for understanding the biological impact of the lunar environment on terrestrial life-forms. Indeed, plants were among the initial and primary organisms that were exposed to returned lunar regolith from the Apollo lunar missions. This review discusses the original experiments involving plants in association with the Apollo samples, with the intent of understanding those studies within the context of the first lunar exploration program and drawing from those experiments the data to inform the studies critical within the next lunar exploration science agenda.

Effects of a spaceflight environment on heritable changes in wheat gene expression

Once it was established that the spaceflight environment was not a drastic impediment to plant growth, a remaining space biology question was whether long-term spaceflight exposure could cause changes in subsequent generations, even if they were returned to a normal Earth environment. In this study, we used a genomic approach to address this question. We tested whether changes in gene expression patterns occur in wheat plants that are several generations removed from growth in space, compared to wheat plants with no spaceflight exposure in their lineage. Wheat flown on Mir for 167 days in 1991 formed viable seeds back on Earth. These seeds were grown on the ground for three additional generations. Gene expression of fourth-generation Mir flight leaves was compared to that of the control leaves by using custom-made wheat microarrays. The data were evaluated using analysis of variance, and transcript abundance of each gene was contrasted among samples with t-tests. After corrections were made for multiple tests, none of the wheat genes represented on the microarrays showed a statistically significant difference in expression between wheat that has spaceflight exposure in their lineage and plants with no spaceflight exposure. This suggests that exposure to the spaceflight environment in low Earth orbit space stations does not cause significant, heritable changes in gene expression patterns in plants.

Transcriptional profiling of hexaploid wheat (Triticum aestivum L.) roots identifies novel, dehydration-responsive genes

We used a long-oligonucleotide microarray to identify transcripts that increased or decreased in abundance in roots of dehydration-tolerant hexaploid bread wheat, in response to withholding of water. We observed that the major classes of dehydration-responsive genes (e.g. osmoprotectants, compatible solutes, proteases, glycosyltransferases/hydrolases, signal transducers components, ion transporters) were generally similar to those observed previously in other species and osmotic stresses. More specifically, we highlighted increases in transcript expression for specific genes including those putatively related to the synthesis of asparagine, trehalose, oligopeptide transporters, metal-binding proteins, the gamma-aminobutyric acid (GABA) shunt and transcription factors. Conversely, we noted a decrease in transcript abundance for diverse classes of glutathione and sulphur-related enzymes, specific amino acids, as well as MATE-efflux carrier proteins. From these data, we identified a novel, dehydration-induced putative AP2/ERF transcription factor, which we predict to function as a transcriptional repressor. We also identified a dehydration-induced 'little protein' (LitP; predicted mass: 8 kDa) that is highly conserved across spermatophytes. Using qRT-PCR, we compared the expression patterns of selected genes between two related wheat genotypes that differed in their susceptibility to dehydration, and confirmed that these novel genes were highly inducible by water limitation in both genotypes, although the magnitude of induction differed.