Carbon Fixation Research Articles

Acute copper stress showed toxic effects on the physiological metabolism of Ulva lactuca, a common green macroalgae

The pollution by heavy metals in coastal waters has gradually intensified due to industrial development. In this study, physiological responses of Ulva lactuca, one of the most common green seaweeds with important ecological and economic value in the global intertidal zone, to acute copper stress were investigated. Results showed that an increase in copper ions concentration significantly inhibited photosynthetic activity and inorganic nitrogen utilization by U. lactuca but, increased its respiration. Copper stress limited the activity and gene expression of enzymes related to carbon and nitrogen assimilation of U. lactuca. Under moderate copper stress, U. lactuca had higher soluble carbohydrate and soluble protein contents, whereas under high copper stress, these components decreased sharply. Copper stress increased malonaldehyde content, and relative electrical conductivity in U. lactuca, but changes in antioxidant enzyme activities were not significant and even slightly decreased. Moreover, the contents of 8-hydroxy-deoxyguanosine and polyADP ribose polymerase in U. lactuca increased by high Cu2+ concentration culture, indicating that oxidative damage caused by high Cu2+ level involved its DNA damage and interfered with DNA repair in the alga. Copper stress seemed to be more damaging to the carbon assimilation process of U. lactuca, resulting in weakened resistance to copper stress and lower growth rate. This reflected the threat of coastal high copper stress to intertidal biodiversity. This provided ecological reference for the assessment of offshore heavy metal pollution represented by copper.

Characteristics, impacts and future research directions of Mongolian peatlands

Mongolia is an important peatland distribution area in the world. Over the past few decades, Mongolian peatlands have undergone significant degradation due to climate change and human activities, yet there remains substantial uncertainty about the impacts of Mongolian peatland changes on regional environment and human society. Here, compiling the data of peatland distribution, climate, human activity, as well as the permafrost, we systematically review the distribution, changes, and the ecosystem service values of the Mongolian peatlands in the face of climate warming and intensifying human activities. The current data show that the total area of peatland in the Mongolian is 15500~27000 km2, and most of the peatlands are distributed in permafrost regions, while the accuracies of these maps were not assessed. In addition to climate warming, overgrazing, mining activities, and transportation, we suggest permafrost degradation also poses significant threatens on the peatlands. Although the importance of Mongolian peatlands has been recognized, the ecosystem service values, including water provision, habitat quality, carbon fixation, soil conservation, and wind erosion prevention largely remain unknown. Currently, efforts have been made to protect the Mongolian grassland, but there are no specific measures to combat peatland degradation. To better understand the changes and roles of peatland ecosystems in regulating regional development, we propose three research directions for future studies: 1) produce a detailed map of peatland distribution based on field survey data, new remote sensing data, and new algorithms; 2) Unveil the mechanisms underlying the interaction of peat, vegetation, and permafrost; 3) Evaluate the ecosystem services of Mongolian peatlands. These knowledges are the scientific foundation to propose and implement measures to protect, maintain, and sustainably utilize peatlands in Mongolia.

Novel strategies for enhancing energy metabolism and wastewater treatment in algae-bacteria symbiotic system through carbon dots-induced photogenerated electrons: The definitive role of accelerated electron transport

The nitrogen removal efficiency of the algae-bacteria symbiotic system (ABSS) remains challenging due to competition for light capture and insufficient electron donors in aquaculture wastewater. To overcome this bottleneck issue, we first identified and reported the introduction of photogenerated electrons into ABSS by coupling them with carbon dots (CDs). The energy metabolism (21.52 %-56.25 %) and pollutant degradation efficiency (89.36 %-96.42 %) of ABSS/CDs surpassed the biochemical limit observed in traditional ABSS. Notably, the addtion of CDs facilitated an opening of the plastoquinone-pool (PQ-pool) valve and accelerated electron transfer rates, enabling photogenerated electrons to selectively target light-harvesting complexs as activation sites, thereby mobilizing photosynthesis and respiratory system activity to enhance nicotinamide adenine dinucleotide reduced (NADH) and adenosine triphosphate (ATP) production while promoting tricarboxylic acid (TCA) and Calvin cycle processes. In simulated swine wastewater treatment, ABSS/CDs achieved higher removal rates for the chemical oxygen demand (COD), total nitrogen (TN) and ammonium-nitrogen (NH4+-N) (100 %, 99.23 % and 98.62 % respectively) compared to pure culture systems alone. Network-based analysis revealed that ABSS/CDs improved microbial community structure stability within the photobioreactor while demonstrating efficient coupling between fungi, nitrifying bacteria, and denitrifying bacteria for enhanced performance in nitrogen removal processes. The upregulation of nitrogen metabolism and PQ-pool genes maintains efficient electron transport rates and contributes to nitrogen removal. This study expands our understanding of the physiological aptitudes of ABSS and provides valuable insights into applying CDs photoelectrons for enhanced wastewater treatment.

Long-Term Autotrophic Growth and Solar-to-Chemical Conversion in Shewanella Oneidensis MR-1 through Light-Driven Electron Transfer.

Members of the genus Shewanella are known for their versatile electron accepting routes, which allow them to couple decomposition of organic matter to reduction of various terminal electron acceptors for heterotrophic growth in diverse environments. Here, we report autotrophic growth of Shewanella oneidensis MR-1 with photoelectrons provided by illuminated biogenic CdS nanoparticles. This hybrid system enables photosynthetic oscillatory acetate production from CO2 for over five months, far exceeding other inorganic-biological hybrid system that can only sustain for hours or days. Biochemical, electrochemical and transcriptomic analyses reveal that the efficient electron uptake of S. oneidensis MR-1 from illuminated CdS nanoparticles supplies sufficient energy to stimulate the previously overlooked reductive glycine pathway for CO2 fixation. The continuous solar-to-chemical conversion is achieved by photon induced electric recycling in sulfur species. Overall, our findings demonstrate that this mineral-assisted photosynthesis, as a widely existing and unique model of light energy conversion, could support the sustained photoautotrophic growth of non-photosynthetic microorganisms in nutrient-lean environments and mediate the reversal of coupled carbon and sulfur cycling, consequently resulting in previously unknown environmental effects. In addition, the hybrid system provides a sustainable and flexible platform to develop a variety of solar products for carbon neutrality.

Long‐Term Autotrophic Growth and Solar‐to‐Chemical Conversion in Shewanella Oneidensis MR‐1 through Light‐Driven Electron Transfer

AbstractMembers of the genus Shewanella are known for their versatile electron accepting routes, which allow them to couple decomposition of organic matter to reduction of various terminal electron acceptors for heterotrophic growth in diverse environments. Here, we report autotrophic growth of Shewanella oneidensis MR‐1 with photoelectrons provided by illuminated biogenic CdS nanoparticles. This hybrid system enables photosynthetic oscillatory acetate production from CO2 for over five months, far exceeding other inorganic‐biological hybrid system that can only sustain for hours or days. Biochemical, electrochemical and transcriptomic analyses reveal that the efficient electron uptake of S. oneidensis MR‐1 from illuminated CdS nanoparticles supplies sufficient energy to stimulate the previously overlooked reductive glycine pathway for CO2 fixation. The continuous solar‐to‐chemical conversion is achieved by photon induced electric recycling in sulfur species. Overall, our findings demonstrate that this mineral‐assisted photosynthesis, as a widely existing and unique model of light energy conversion, could support the sustained photoautotrophic growth of non‐photosynthetic microorganisms in nutrient‐lean environments and mediate the reversal of coupled carbon and sulfur cycling, consequently resulting in previously unknown environmental effects. In addition, the hybrid system provides a sustainable and flexible platform to develop a variety of solar products for carbon neutrality.

Interpreting the complexities of the plastid genome in dinoflagellates: a mini-review of recent advances.

Photosynthetic dinoflagellates play crucial roles in global primary production and carbon fixation. Despite their success in filling various ecological niches, numerous mysteries about their plastid evolution and plastid genomes remain unsolved. The plastid genome of dinoflagellates presents one of the most complex lineages in the biological realm, mainly due to multiple endosymbiotic plastid events in their evolutionary history. Peridinin-containing dinoflagellates possess the most reduced and fragmented genome, with only a few genes located on multiple "minicircles", whereas replacement plastids in dinoflagellate lineages have undergone different degrees of endosymbiotic gene transfer. Recent advancements in high-throughput sequencing have improved our understanding of plastid genomes and plastid-encoded gene expression in many dinoflagellate species. Plastid transcripts of dinoflagellates exhibit two unconventional processing pathways: the addition of a 3' poly(U) tail and substitutional RNA editing. These pathways are widely employed across dinoflagellate lineages, which are possibly retained from the ancestral peridinin plastid. This mini-review summarizes the developments in the plastid genomes of dinoflagellates and pinpoints the research areas that necessitate further exploration, aiming to provide valuable insights into plastid evolution in these fascinating and important organisms.

Biological Acclimatization of Micropropagated Al-Taif Rose (Rosa damascena f. trigintipetala (Diek) R. Keller) Plants Using Arbuscular Mycorrhizal Fungi Rhizophagus fasciculatus

Tissue culture is used to multiply Al-Taif rose (Rosa damascena f. trigintipetala (Diek) R. Keller) plants in order to meet the demands of the fragrance, cosmetic, and floriculture industries. The use of arbuscular mycorrhizal fungus (AMF) could potentially improve plant growth and acclimatization performance to ex vitro conditions. Thus, in the current study, we investigated how AMF Rhizophagus fasciculatus influences the growth, establishment, and physiological performance of micropropagated Al-Taif rose plants during the acclimatization stage. The growth and physiological parameters of the AMF-treated plants were evaluated after a 12 week growth period in the growth chambers. The plants treated with AMF exhibited greater height (25.53 cm) and biomass growth values for both shoot fresh weight (0.93 g/plant) and dry weight (0.030 g/plant), more leaves (11.3/plant), more leaf area (66.15 cm2), longer main roots (15.05 cm/plant), total root length (172.16 cm/plant), total root area (64.36 cm2/plant), and biomass from both fresh weight (383 mg/plant) and dry weight (80.00 mg/plant) of the plants. The plants treated with AMF also exhibited increased rates of net CO2 assimilation, stomatal conductance, and transpiration compared to the control plants. The proline content in the leaves and roots was significantly lower in the AMF-treated plants than untreated plants. The Fv/Fm ratio, which serves as an indicator of the intrinsic or maximal efficacy of Photosystem II (PSII) demonstrated a notable decline in the untreated Al-Taif rose plants. These results elucidate the advantageous impact of AMF colonization on micropropagated Al-Taif rose plants, thereby enhancing their resilience against adverse ex vitro conditions.

Mixed-Linker Zr-Metal-Organic Framework with Improved Lewis Acidic Sites for CO2 Fixation Reaction Catalysis.

Applying the mixed-linker strategy in synthesizing metal-organic frameworks (MOFs) has drawn considerable attention as a heterogeneous catalyst owing to their easy synthesis and different functional ligands in their frameworks. Following this strategy, we have developed a mixed linker Zr(IV)-based MOF, [Zr6O4(OH)4(FUM)n(PZDC-NO2)6-n] (PZDC-NO2 = 4-nitro-3,5-pyrazoledicarboxylic acid, FUM = fumaric acid) denoted as MOF-801(PZDC-NO2) synthesized via this strategy which possess an electron-withdrawing group (-NO2) on secondary linkers. The MOF-801(PZDC-NO2) has been fully characterized via various analyses, such as Fourier transform infrared, powder X-ray diffraction, 13C/1H nuclear magnetic resonance, XPS, TGA, and N2 adsorption/desorption, SEM, EDX, etc. By considering the concurrent existence of acid-base active sites and the synergistic role of these sites, this mixed-linker MOF was used as a catalyst for the cycloaddition reaction of CO2 and epoxides under mild without-solvent conditions. MOF-801(PZDC-NO2) displays significant catalytic performance by producing the highest catalytic conversion of epoxide to cyclic carbonate (93%) with a turnover number of 130.7 in 8 h reaction time and 100 °C temperature under low-pressure CO2 pressure. The mixed-linker Zr-MOF exhibits exceptional stability and reusability, maintaining its structure and functionality after consecutive cycles of utilization. Finally, the reaction mechanism was further investigated by density functional theory calculations. The total energy of the reactants, intermediates, and products involved in the process.

The Influence of Exogenous CdS Nanoparticles on the Growth and Carbon Assimilation Efficiency of Escherichia coli.

This study investigated the impact of CdS nanoparticles (NPs) on Escherichia coli growth and metabolism under varying conditions. Under illumination, CdS NPs significantly enhanced bacterial growth, glucose assimilation, and biomass accumulation. Key metabolic and stress response genes showed increased expression, indicating improved ATP synthesis and oxidative stress resistance. Additionally, CdS NPs enhanced the electrochemical properties of E. coli, promoting efficient electron transfer. No significant changes were observed in the dark. These findings suggest that light-activated CdS NPs promote E. coli growth and metabolic efficiency by upregulating crucial genes involved in growth and oxidative stress management.

Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus

The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl-CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP/4HB cycle of Thaumarchaeota.

Exploring the Impact of Environmental Conditions and Bioreactors on Microalgae Growth and Applications

Microalgae and their bioproducts have diverse applications, including wastewater remediation, CO2 fixation, and the synthesis of nutraceuticals, pharmaceuticals, and biofuels. However, the production of these organisms heavily relies upon environmental conditions, which can significantly impact growth. Furthermore, microalgae cultivation itself can be a source of economic and environmental concerns. Thus, microalgae growth systems have become a critical consideration for both research and industry, to bolster microalgae cultivation and address its accompanying issues. Both open and closed systems, such as raceway ponds and photobioreactors, respectively, are commonly used during the growth process but have their own advantages and drawbacks. However, for microalgae growth, photobioreactors may address most concerns as the system’s design lowers the risk of contamination and provides the ability to control the delivery of desired growth factors. To determine the appropriate system for targeted microalgae cultivation, it is crucial to determine factors such as the scale of cultivation and growth and productivity targets. Additionally, efficient usage of these growth systems and carefully selected incubation factors can aid in addressing some of the economic and environmental issues associated with microalgae production. This review will summarize the current applications of bioreactors in both research and industrial capacities and summarize growth and incubation factors for microalgae.

A cluster-nanozyme-coenzyme system mimicking natural photosynthesis for CO2 reduction under intermittent light irradiation

Natural photosynthesis utilizes solar energy to convert water and atmospheric CO2 into carbohydrates through all-weather light/dark reactions based on molecule-based enzymes and coenzymes, inspiring extensive development of artificial photosynthesis. However, development of efficient artificial photosynthetic systems free of noble metals, as well as rational integration of functional units into a single system at the molecular level, remain challenging. Here we report an artificial system, the assembly system of Cu6 cluster and cobalt terpyridine complex, that mimics natural photosynthesis through precise integration of nanozyme complexes and ubiquinone (coenzyme Q) on Cu6 clusters. This biomimetic system efficiently reduces CO2 to CO in light reaction, achieving a production rate of 740.7 μmol·g−1·h−1 with high durability for at least 188 hours. Notably, our system realizes the decoupling of light and dark reactions, utilizing the phenol-evolutive coenzyme Q acting as an electron reservoir. By regulating the stabilizer of coenzyme Q, the dark reaction time can be extended up to 8.5 hours, which fully meets the natural day/night cycle requirements. Our findings advance the molecular design of artificial systems that replicate the comprehensive functions of natural photosynthesis.

Exogenous 5-aminolevulinic acid enhanced saline-alkali tolerance in pepper seedlings by regulating photosynthesis, oxidative damage, and glutathione metabolism.

A plant growth regulator, 5-aminolevulinic acid, enhanced the saline-alkali tolerance via photosynthetic, oxidative-reduction, and glutathione metabolism pathways in pepper seedlings. Saline-alkali stress is a prominent environmental problem, hindering growth and development of pepper. 5-Aminolevulinic acid (ALA) application effectively improves plant growth status under various abiotic stresses. Here, we evaluated morphological, physiological, and transcriptomic differences in saline-alkali-stressed pepper seedlings after ALA application to explore the impact of ALA on saline-alkali stress. The results indicated that saline-alkali stress inhibited plant growth, decreased biomass and photosynthesis, altered the osmolyte content and antioxidant system, and increased reactive oxygen species (ROS) accumulation and proline content in pepper seedlings. Conversely, the application of exogenous ALA alleviated this damage by increasing the photosynthetic rate, osmolyte content, antioxidant enzyme activity, and antioxidants, including superoxide dismutase, catalase, glutathione reductase, and glutathione peroxidase, and reducing glutathione to reduce ROS accumulation and malonaldehyde content. Moreover, the transcriptomic analysis revealed the differentially expressed genes were mainly associated with photosynthesis, oxidation-reduction process, and glutathione metabolism in saline-alkali stress + ALA treatment compared to saline-alkali treatment. Among them, the change in expression level in CaGST, CaGR, and CaGPX was close to the variation of corresponding enzyme activity. Collectively, our findings revealed the alleviating effect of ALA on saline-alkali stress in pepper seedlings, broadening the application of ALA and providing a feasible strategy for utilize saline-alkali soil.

Short-term reoxygenation is not enough for the recovery of soybean plants exposed to saline waterlogging

The ability of plants to recover after stressful events is crucial for resuming growth and development and is a key trait when studying stress tolerance. However, there is a lack of information on the physiological responses and the time required to restore homeostasis after the stress experience. This study aimed to (i) enhance understanding of soybean photosynthesis performance during saline waterlogging and (ii) investigate the effects of this combined stress during the reoxygenation and recovery period. Soybean plants (cultivar PELBR10-6049 RR) were subjected to waterlogging, NaCl, or hypoxia + NaCl for 3 and 6 days. Afterward, plants were drained and allowed to recover for an additional two (short-term) and seven days (long-term). Compared to plants exposed to single stress, the combined hypoxia + NaCl treatment resulted in a lower net CO2 assimilation rate, ФPSII, and levels of photosynthetic pigments during the waterlogging period. Furthermore, hypoxia + NaCl increased foliar electrolyte leakage during waterlogging. In response to short-term reoxygenation, these negative effects were amplified, while prolonged reoxygenation resulted in a slight increase in biomass accumulation. In conclusion, full recovery was not achieved under any condition during the reoxygenation periods tested. Notably, the brief reoxygenation phase imposed greater stress than the initial stress conditions for plants facing combined stress. Although extended recovery increased biomass accumulation, it remained lower in plants previously subjected to saline waterlogging.

Engineering quantitative stomatal trait variation and local adaptation potential by cis-regulatory editing.

Cis-regulatory element editing can generate quantitative trait variation that mitigates extreme phenotypes and harmful pleiotropy associated with coding sequence mutations. Here, we applied a multiplexed CRISPR/Cas9 approach, informed by bioinformatic datasets, to generate genotypic variation in the promoter of OsSTOMAGEN, a positive regulator of rice stomatal density. Engineered genotypic variation corresponded to broad and continuous variation in stomatal density, ranging from 70% to 120% of wild-type stomatal density. This panel of stomatal variants was leveraged in physiological assays to establish discrete relationships between stomatal morphological variation and stomatal conductance, carbon assimilation and intrinsic water use efficiency in steady-state and fluctuating light conditions. Additionally, promoter alleles were subjected to vegetative drought regimes to assay the effects of the edited alleles on developmental response to drought. Notably, the capacity for drought-responsive stomatal density reprogramming in stomagen and two cis-regulatory edited alleles was reduced. Collectively our data demonstrate that cis-regulatory element editing can generate near-isogenic trait variation that can be leveraged for establishing relationships between anatomy and physiology, providing a basis for optimizing traits across diverse environments.

Dynamic behavior and transfer characteristics of CO2-enriched bubbles within Spirulina sp. suspension under various aeration conditions using the high-speed imaging technique

The biological CO2 fixation method through microalgae photosynthesis has received considerable attention to alleviate the trend of global warming. CO2-enriched gas is generally aerated into the microalgae suspension in the form of bubbles through the gas distributors. Dynamic behavior and transfer characteristics of CO2-enriched bubbles are crucial to microalgae cells growth and CO2 bio-fixation. A visual experimental system based on the high-speed camera was constructed in this work to obtain the dynamic behavior and transfer characteristics of CO2-enriched bubbles within Spirulina sp. suspension. CO2-enriched bubbles movement and dissolution characteristics were comprehensively investigated under various CO2 concentrations, gas distributor aperture size, aeration rates, and Spirulina sp. biomass densities. Experimental results indicate that the optimal CO2 dissolution mass transfer and absorption rate were attained under the CO2 concentration of 5 %, gas distributor aperture diameter of 10 μm, and aeration rate of 0.1–0.3 vvm. Moreover, as Spirulina sp. biomass density increased, the bubble average diameter decreased, and rising velocity slowed while the volumetric mass transfer coefficient and CO2 absorption rate elevated. To summarize, this work may guide future efforts to enhance the photobioreactors (PBRs) performance from the perspective of aeration conditions optimization.

Integrating Natural Photosynthesis, Artificial Photosynthesis, and Biohydrogen Production for a Sustainable Energy Future

The interrelated topics of artificial photosynthesis, natural photosynthesis, and biohydrogen production are examined in this thorough analysis as viable avenues for achieving sustainable energy solutions. This piece offers a comprehensive assessment of the present situation and prospective future applications of these technologies by looking at the underlying dynamics of these processes, recent technological developments, and enduring difficulties. Combining knowledge from natural photosynthetic pathways with the latest findings in artificial photosynthesis and developing techniques for producing biohydrogen offers a multifaceted strategy to meet the world's energy needs while reducing the effects of climate change. By clarifying the potential of these technologies to transform the production of renewable energy, lessen reliance on fossil fuels, and offer creative solutions for waste management and carbon sequestration, this analysis benefits society. This article intends to stimulate more interdisciplinary research and development towards a sustainable energy future by highlighting the synergies between various sectors.

Amine-tethered DMAP Cation Catalysts: An Efficient Organocatalytic System for the Chemical Fixation of CO2 to Five-Membered Cyclic

Introduction: In this study, three amine-tethered DMAP cation bromide catalysts were prepared using two different mole ratios of 4-dimethylpyridine (DMAP) and 3-bromopropylamine hydrobromide (BPA·HBr) in two different solvents, namely, acetonitrile and ethanol. Then, prepared catalysts were employed for CO2 cycloaddition with styrene and propylene epoxides under metal- and solvent-free conditions. Method: The impact of mole ratio and solvent selection to prepare the designed product using a simple and cost-effective procedure was demonstrated systematically and was discussed in detail. Moreover, the influence of amine-tethered DMAP cation catalyst structures and reaction conditions on the cycloaddition was investigated, and the CO2 conversion proceeded smoothly at 80°C and 0.2 MPa for the synthesis of cyclic carbonates in good to excellent yields and high selectivity. Results: The current protocol could be a promising process at an industrial scale due to the high recyclability of the catalyst (10 cycles). Conclusion: In summary, three catalytic systems bearing amine-tethered DMAP cation have been investigated for the chemical fixation of CO2 into five-membered cyclic carbonates at mild conditions.

Measuring CO2 assimilation of Arabidopsis thaliana whole plants and seedlings

Photosynthesis is an essential process in plants that synthesizes sugars used for growth and development, highlighting the importance of establishing robust methods to monitor photosynthetic activity. Infrared gas analysis (IRGA) can be used to track photosynthetic rates by measuring plant CO2 assimilation and release. Although much progress has been made in the development of IRGA technologies, challenges remain when using this technique on small herbaceous plants such as Arabidopsis thaliana. The use of whole plant chambers can overcome the difficulties associated with applying bulky leaf clamps to small delicate leaves. However, respiration from the roots and from soil-based microorganisms may skew these gas exchange measurements. Here, we present a simple method to efficiently perform IRGA on A. thaliana plants using a whole plant chamber that removes the confounding effects of respiration from roots and soil-based microorganisms from the measurements. We show that this method can be used to detect subtle changes in photosynthetic rates measured at different times of day, under different growth conditions, and between wild-type and plants with deficiencies in the photosynthetic machinery. Furthermore, we show that this method can be used to detect changes in photosynthetic rates even at very young developmental stages such as 10 d-old seedlings. This method contributes to the array of techniques currently used to perform IRGA on A. thaliana and can allow for the monitoring of photosynthetic rates of whole plants from young ages.

Profiling of Key Hub Genes Using a Two-State Weighted Gene Co-Expression Network of 'Jao Khao' Rice under Soil Salinity Stress Based on Time-Series Transcriptome Data.

RNA-sequencing enables the comprehensive detection of gene expression levels at specific time points and facilitates the identification of stress-related genes through co-expression network analysis. Understanding the molecular mechanisms and identifying key genes associated with salt tolerance is crucial for developing rice varieties that can thrive in saline environments, particularly in regions affected by soil salinization. In this study, we conducted an RNA-sequencing-based time-course transcriptome analysis of 'Jao Khao', a salt-tolerant Thai rice variety, grown under normal or saline (160 mM NaCl) soil conditions. Leaf samples were collected at 0, 3, 6, 12, 24, and 48 h. In total, 36 RNA libraries were sequenced. 'Jao Khao' was found to be highly salt-tolerant, as indicated by the non-significant differences in relative water content, cell membrane stability, leaf greenness, and chlorophyll fluorescence over a 9-day period under saline conditions. Plant growth was slightly retarded during days 3-6 but recovered by day 9. Based on time-series transcriptome data, we conducted differential gene expression and weighted gene co-expression network analyses. Through centrality change from normal to salinity network, 111 key hub genes were identified among 1,950 highly variable genes. Enriched genes were involved in ATP-driven transport, light reactions and response to light, ATP synthesis and carbon fixation, disease resistance and proteinase inhibitor activity. These genes were upregulated early during salt stress and RT-qPCR showed that 'Jao Khao' exhibited an early upregulation trend of two important genes in energy metabolism: RuBisCo (LOC_Os10g21268) and ATP synthase (LOC_Os10g21264). Our findings highlight the importance of managing energy requirements in the initial phase of the plant salt-stress response. Therefore, manipulation of the energy metabolism should be the focus in plant resistance breeding and the genes identified in this work can serve as potentially effective candidates.