Dissecting Low Atmospheric Pressure Stress: Transcriptome Responses to the Components of Hypobaria in Arabidopsis

Transcriptome and Metabolome Analysis of Low-Pressure Regulation in Saussurea involucrata Leaves

Saussurea involucrata, an endangered medicinal plant, thrives in high mountain regions at altitudes ranging from 3500 to 5000 m. Being a plant that grows at high altitudes means it possesses unique physiological mechanisms and stress-responsive genes that regulate and adapt to the high-altitude environment. While many cold-resistant genes have been cloned and their mechanisms studied, the genes and molecular mechanisms involved in adaptation to hypobaric hypoxia remain largely unexplored. This study conducted transcriptomic and metabolomic analyses on the leaves of S. involucrata under normal atmosphere (101 kPa) and low pressure (60 kPa). A total of 2383 differentially expressed genes (DEGs) and 336 differentially accumulated metabolites (DAMs) were identified utilizing RNA-seq and UPLS-MS techniques. The results indicated that S. involucrata exhibits responses to hypobaric hypoxia environments by engaging in DNA repair, membrane transport, hypoxic response, reproductive processes, and various metabolic activities associated with nutrient uptake and the effective utilization of chemical components. It is worth noting that under low-pressure treatment, flavonoids are predominantly negatively regulated, whereas terpenoids are primarily positively regulated. These findings identify key genes and metabolites in S. involucrata that respond to hypobaric hypoxia treatment, providing a theoretical basis for the development of its medicinal value and for low-altitude cultivation.

Short-term impact of low air pressure on plants' functional traits

Lower atmospheric pressure affects biologically relevant physical parameters such as gas partial pressure and concentration, leading to increased water vapor diffusivity and greater soil water content loss through evapotranspiration. This might impact plant photosynthetic activity, resource allocation, water relations, and growth. However, the direct impact of low air pressure on plant physiology is largely unknown. This study examined the effects of low air pressure, alone and combined with two water inputs, on different functional traits of three plant species transplanted from montane grasslands at 1,500 m a.s.l. during the first four weeks of their early phenological stage: Trifolium pratense, Hieracium pilosella, and Brachypodium rupestre. Using the terraXcube Ecotron facility which can simulate different climatic conditions, we isolated the effect of air pressure from those of other, related environmental factors (temperature, humidity, and solar radiation) by simulating three different elevations with corresponding air pressures: 1,500 m a.s.l. (85 kPa, control scenario), 2,500 m a.s.l. (75 kPa), and 4,000 m a.s.l. (62 kPa) and we used two different water regimes to observe the combined effect of low air pressure and the impact of varying water inputs on plants. In T. pratense and H. pilosella, we observed an increase in stomatal conductance but a reduction in aboveground biomass at the lowest pressure compared to the control scenario after four weeks of incubation. Contrastingly, B. rupestre showed an interactive effect of air pressure and water treatment on chlorophyll and biomass nitrogen content, which were reduced under higher soil water conditions at 85kPa. This study serves as an initial step in isolating the specific impact of air pressure on plant physiology, demonstrating the potential of the facility for future research. The mixed response patterns across species highlight that atmospheric pressure could be a driving factor to consider when assessing plant responses along elevational gradient.

The physiology of plants in the context of space exploration

The stress that the space environment can induce on plant physiology is of both abiotic and biotic nature. The abiotic space environment is characterized by ionizing radiation and altered gravity, geomagnetic field (GMF), pressure, and light conditions. Biotic interactions include both pathogenic and beneficial interactions. Here, we provide an overall picture of the effects of abiotic and biotic space-related factors on plant physiology. The knowledge required for the success of future space missions will lead to a better understanding of fundamental aspects of plant physiological responses, thus providing useful tools for plant breeding and agricultural practices on Earth.

Effects of hypobaria, hyperoxia, and nitrogen form on the growth and nutritional quality of lettuce

The objectives of this research were to investigate the impact of hypobaria, hyperoxia, and nitrogen form on the growth and nutritional quality of plants. Pre-culture 20-day-old lettuce (Lactuca sativa L. var. Rome) seedlings grew for 25 days under three levels of total atmospheric pressure (101, 54, and 30 kPa), two levels of oxygen partial pressure (21 and 28 kPa), and two forms of nitrogen (NO3N and NH4N). The ratios of NO3N to NH4N included 3: 1, 4: 0, 2: 2, and 0: 4. The nitrogen quantity included two levels, i.e. N1, 0.1 g N kg-1 dry matrix and N2, 0.2 g N kg-1 dry matrix. The growth status of lettuce plants in different treatments differentiated markedly. Regardless of the nitrogen factor, the growth status of lettuce plants treated with total atmospheric pressure/oxygen partial pressure at 54/21 was equivalent to the treatment of 101/21. Under the hypobaric condition (54 kPa), compared with 21 kPa oxygen partial pressure, hyperoxia (28 kPa) significantly inhibited the growth of lettuce plants and the biomass (fresh weight) decreased by 60.9%-69.9% compared with that under 101/21 treatment. At the N1 level, the sequence of the biomass of lettuce plants supplied with different ratios of NO3N to NH4N was 3: 1 > 4: 0 > 2: 2 > 0: 4, and there were higher concentrations of chlorophyll and carotenoid of lettuce plants supplied with the higher ratio of NO3 to NH4. At the N2 level, the effects of different ratios of NO3N to NH4N on lettuce plants were similar to those at the N1 level. The high nitrogen (N2) promoted the growth of lettuce plants such as 54/21/N2 treatments. Both form and nitrogen level did not affect the stress resistance of lettuce plants. Hypobaria (54 kPa) increased the contents of N, P, and K and hyperoxia (28 kPa) decreased the content of organic carbon in lettuce plants. The high nitrogen (N2) improved the content of total N and the N uptake. The ratios of NO3N to NH4N were 4: 0 and 3: 1, lettuce could absorb and utilize N effectively. This study demonstrated that hyperoxia (28 kPa) inhibited the growth of lettuce plants under the hypobaric condition (54 kPa), and high level of nitrogen (0.2 g N kg-1 dry matrix) and NO3N: NH4N at 3: 1 markedly enhanced the growth, the contents of mineral elements and the nutritional quality of lettuce plants.

Carnobacterium Species Capable of Growth at Pressures Ranging Over 5 Orders of Magnitude, from the Surface of Mars (103 Pa) to Deep Oceans (107 Pa) in the Solar System

Several permanently cold solar system bodies are being investigated with regard to their potential habitability, including Mars and icy moons. In such locations, microbial life would have to cope with low temperatures and both high and low pressures, ranging from ∼10² to 10³ Pa on the surface of Mars to upward of ∼10⁸-10⁹ Pa in the subsurface oceans of icy moons. The bacterial genus Carnobacterium consists of species that were previously shown to be capable of growth in the absence of oxygen at low temperatures and at either low pressure or high pressure, but to date the entire pressure range of the genus has not been explored. In the present study, we subjected 14 Carnobacterium strains representing 11 species to cultivation in a complex liquid medium under anaerobic conditions at 2°C and at a range of pressures spanning 5 orders of magnitude, from 10³ to 10⁷ Pa. Eleven of the 14 strains showed measurable growth rates at all pressures tested, representing the first demonstration of terrestrial life forms capable of growth under such a wide range of pressures. These findings expand the physical boundaries of the capabilities of life to occur in extreme extraterrestrial environments.

Utilizing the KSC Fixation Tube to Conduct Human-Tended Plant Biology Experiments on a Suborbital Spaceflight

Suborbital spaceflights now enable human-tended research investigating short-term gravitational effects in biological systems, eliminating the need for complex automation. Here, we discuss a method utilizing KSC Fixation Tubes (KFTs) to both carry biology to suborbital space as well as fix that biology at certain stages of flight. Plants on support media were inserted into the sample side of KFTs preloaded with RNAlater in the fixation chamber. The KFTs were activated at various stages of a simulated flight to fix the plants. RNA-seq analysis conducted on tissue samples housed in KFTs, showed that plants behaved consistently in KFTs when compared to petri-plates. Over the time course, roots adjusted to hypoxia and leaves adjusted to changes in photosynthesis. These responses were due in part to the environment imposed by the encased triple containment of the KFTs, which is a requirement for flight in human spacecraft. While plants exhibited expected reproducible transcriptomic alteration over time in the KFTs, responses to clinorotation during the simulated flight suggest that transcriptomic responses to suborbital spaceflight can be examined using this approach.

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.

Network Analysis of Local Gene Regulators in Arabidopsis thaliana under Spaceflight Stress

Spaceflight microgravity affects normal plant growth in several ways. The transcriptional dataset of the plant model organism Arabidopsis thaliana grown in the international space station is mined using graph-theoretic network analysis approaches to identify significant gene transcriptions in microgravity essential for the plant’s survival and growth in altered environments. The photosynthesis process is critical for the survival of the plants in spaceflight under different environmentally stressful conditions such as lower levels of gravity, lesser oxygen availability, low atmospheric pressure, and the presence of cosmic radiation. Lasso regression method is used for gene regulatory network inferencing from gene expressions of four different ecotypes of Arabidopsis in spaceflight microgravity related to the photosynthetic process. The individual behavior of hub-genes and stress response genes in the photosynthetic process and their impact on the whole network is analyzed. Logistic regression on centrality measures computed from the networks, including average shortest path, betweenness centrality, closeness centrality, and eccentricity, and the HITS algorithm is used to rank genes and identify interactor or target genes from the networks. Through the hub and authority gene interactions, several biological processes associated with photosynthesis and carbon fixation genes are identified. The altered conditions in spaceflight have made all the ecotypes of Arabidopsis sensitive to dehydration-and-salt stress. The oxidative and heat-shock stress-response genes regulate the photosynthesis genes that are involved in the oxidation-reduction process in spaceflight microgravity, enabling the plant to adapt successfully to the spaceflight environment.

An Oxygen Delivery Polymer Enhances Seed Germination in a Martian-like Environment

Critical to the success of establishing a sustainable human presence on Mars is the ability to economically grow crop plants. Several environmental factors make it difficult to fully rely on local resources for agriculture. These include nutrient sparse regolith, low and fluctuating temperatures, a high amount of ultraviolet radiation, and water trapped locally in the form of ice or metal oxides. While the 96% CO2 martian atmosphere is ideal to support photosynthesis, high CO2 concentrations inhibit germination. An added difficulty is the fact that a vast majority of crop plants require oxygen for germination. Here, we report the production of a polymer-based oxygen delivery system that supports the germination and growth of cress seeds (Lepidium sativum) in a martian regolith simulant under a martian atmosphere at 101 kPa. The oxygen-donating system is based on a low-density lightly cross-linked polyacrylate that is foamed and converted into a dry powder. It is lightweight, added in low amounts to regolith simulant, and efficiently donates enough oxygen throughout the volume of hydrated regolith simulant to fully support seed germination and plant growth. Germination rates, plant development, and plant mass are nearly identical for L. sativum grown in 100% CO2 in the presence of the oxygen-donating lightly cross-linked polyacrylate compared with plants grown in air. The polymer system also serves to protect root structures and better anchors plants in the regolith simulant.

Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight

PREMISE OF THE STUDY

The root apex is an important region involved in environmental sensing, but comprises a very small part of the root. Obtaining root apex transcriptomes is therefore challenging when the samples are limited. The feasibility of using tiny root sections for transcriptome analysis was examined, comparing RNA sequencing (RNA-Seq) to microarrays in characterizing genes that are relevant to spaceflight.

METHODS

Arabidopsis thaliana Columbia ecotype (Col-0) roots were sectioned into Zone 1 (0.5 mm; root cap and meristematic zone) and Zone 2 (1.5 mm; transition, elongation, and growth-terminating zone). Differential gene expression in each was compared.

RESULTS

Both microarrays and RNA-Seq proved applicable to the small samples. A total of 4180 genes were differentially expressed (with fold changes of 2 or greater) between Zone 1 and Zone 2. In addition, 771 unique genes and 19 novel transcriptionally active regions were identified by RNA-Seq that were not detected in microarrays. However, microarrays detected spaceflight-relevant genes that were missed in RNA-Seq.

DISCUSSION

Single root tip subsections can be used for transcriptome analysis using either RNA-Seq or microarrays. Both RNA-Seq and microarrays provided novel information. These data suggest that techniques for dealing with small, rare samples from spaceflight can be further enhanced, and that RNA-Seq may miss some spaceflight-relevant changes in gene expression.

Data for characterization of SALK_084889, a T-DNA insertion line of Arabidopsis thaliana

In this article we report the identification of T-DNA (transfer DNA) insertion sites within two different gene regions in the genome of an Arabidopsis mutant line, SALK_084889. The T-DNA positions are in the 3′ UTR (untranslated region) of DREB2A (Dehydration-responsive element-binding protein 2A) (AT5G05410) and promoter of LOX1 (Lipoxygenase 1) (AT1G55020) as determined by DNA-PCR and sanger sequencing. The expression levels of DREB2A and LOX1 were also analyzed using quantitative realtime PCR (qPCR) in SALK_084889 and wild type Arabidopsis (Col, Columbia). Further, the comparison of drought and heat tolerance between Col and SALK_084889 were conducted by stress treatments. The present data indicate that in SALK_084889, the expression of DREB2A is not downregulated under normal growth conditions but can be affected only in roots under drought treatment, while LOX1 is significantly downregulated in both roots and shoots under all tested conditions. These data are original and have not been published elsewhere.