Integrating Transcriptomics and Metabolomics to Characterize Metabolic Regulation to Elevated CO2 in Chlamydomonas Reinhardtii

Heatwaves increase the polystyrene nanoplastic-induced toxicity to marine diatoms through interfacial interaction regulation

Marine heatwaves, prolonged high-temperature extreme events in the ocean, have increased worldwide in recent decades. Plastic pollution is widespread in the ocean, and the continuous weathering of plastics leads to a substantial release of nanoplastics (NPs). However, the interactive impacts and in-depth mechanisms of heatwaves and NPs on diatoms are largely unknown. Here, we show that a heatwave intensity of 4 °C amplified the toxicity of polystyrene NPs to the globally important diatom Chaetoceros gracilis (C. gracilis), with reductions of 5.62 % and 9.46 % in growth rate and photosynthesis, respectively. Notably, NPs significantly inhibited the cell-specific C assimilation rate by 18.28 % under heatwave conditions. The enhanced NP-induced toxicity to C. gracilis was attributed to decreased mechanical strength and increased NP adsorption under heatwave conditions, which increased membrane damage and oxidative stress. Transcriptomic analysis demonstrated that NPs disturbed redox homeostasis and caused mechanical stress to C. gracilis under heatwave conditions. Moreover, NP treatment downregulated genes (psbA and rbcL) encoding photosynthesis core proteins and the pivotal carbon-fixing enzyme RubisCo under heatwave conditions, resulting in decreased growth and C fixation rates. These findings demonstrate that heatwaves render C. gracilis susceptible to NPs and emphasize the reduced primary productivity caused by NPs under global warming.

Warming degrades nutritional quality of periphyton in stream ecosystems: evidence from a mesocosm experiment

Periphyton, which is rich in polyunsaturated fatty acids (PUFA), serves as an indispensable high-quality basal resource for consumers in stream food webs. However, with global warming, how fatty acid composition of periphyton changes and consequent effects on their transfer to higher trophic level consumers remain unclear. By carrying out a manipulative mesocosm experiment with a 4°C increase, warming led to a significant decrease in the proportions of PUFA and Long-chain PUFA (LC-PUFA, >20 C) in periphyton from 13.32% to 9.90% and from 3.05% to 2.18%, respectively. The proportions of three PUFAs-α-linolenic acid (18:3ω3), arachidonic acid (ARA, 20:4ω6), and docosahexaenoic acid (22:6ω3)-also declined significantly (P < .05). Notably, the fatty acid profile of the consumer-Bellamya aeruginosa reflected the changes in basal resources, with a decrease in PUFA from 40.14% to 36.27%, and a significant decrease in LC-PUFA from 34.58% to 30.11%. Although algal community composition in biofilms did not significantly change with warming, significant transcriptomic alterations were observed, with most differentially expressed genes related to fatty acid synthesis in lipid metabolism and photosynthesis down-regulated. Our findings indicate that warming may hinder the production and transfer of high-quality carbon evaluated by LC-PUFA to consumers, consequently affect the complexity and stability of stream food webs.

The accumulation and inhibition mechanism of extracellular polymeric substances of Chlorella vulgaris during cycling cultivation under different light qualities

The secretion, accumulation, and composition of extracellular polymeric substances (EPS) are pivotal factors influencing microalgal growth as well as wastewater recycling. Until now, the accumulation and inhibition mechanism of EPS of Chlorella vulgaris during cycling cultivation is not fully understood. The purpose of this study was to explore how different light qualities regulate the secretion, chemical composition, and structure of microalgal EPS, and subsequently influence the recycling of culture wastewater. After four cycles of cultivation, C. vulgaris under green light produced the highest EPS production and lowest biomass production, which were 82% higher and 17% lower, respectively, compared to white light, which yielded the least EPS production and the highest biomass production. EPS under different light qualities all exhibited a fibrillar structure with a sheet-like surface, but differed in composition. Compared with the other groups, EPS under green light showed a significant increase in polysaccharides, proteins, and humic acid-like compounds, as well as an increased proportion of arabinose and rhamnose, according to monosaccharide composition analysis. Transcriptome analysis indicated that the up-regulation of metabolic pathways linked to glycolysis/gluconeogenesis, TCA cycle, lipid synthesis, and ABC transporters promoted EPS accumulation. Additionally, EPS could target light-harvesting complex (LHC) and electron transport chain, down-regulating the photosynthetic pathway, which ultimately inhibited microalgal growth under green light. This study provides a theoretical foundation for the light regulation and circulation culture of microalgae, as well as for microalgal wastewater treatment.

Elevated temperature as the dominant stressor on the harmful algal bloom-causing dinoflagellate Prorocentrum obtusidens in a future ocean scenario

Marine dinoflagellates are increasingly affected by ongoing global climate changes. While understanding of their physiological and molecular responses to individual stressors anticipated in the future ocean has improved, their responses to multiple concurrent stressors remain poorly understood. Here, we investigated the individual and combined effects of elevated temperature (26 °C relative to 22 °C), increased pCO2 (1000 μatm relative to 400 μatm), and high nitrogen: phosphorus ratio (180:1 relative to 40:1) on a harmful algal bloom-causing dinoflagellate Prorocentrum obtusidens under short-term (28 days) exposure. Elevated temperature was the most dominant stressor affecting P. obtusidens at physiological and transcriptomic levels. It significantly increased cell growth rate and maximum photosynthetic efficiency (Fv/Fm), but reduced chlorophyll a, particulate organic carbon, particulate organic nitrogen, and particulate organic phosphorus. Elevated temperature also interacted with other stressors to produce synergistic positive effects on cell growth and Fv/Fm. Transcriptomic analysis indicated that elevated temperature promoted energy production by enhancing glycolysis, tricarboxylic acid cycle, and nitrogen and carbon assimilation, which supported rapid cell growth but reduced material storage. Increased pCO2 enhanced the expression of genes involved in ionic acid-base regulation and oxidative stress resistance, whereas a high N:P ratio inhibited photosynthesis, compromising cell viability, although the effect was alleviated by elevated temperature. The combined effect of these multiple stressors resulted in increased energy metabolism and up-regulation of material-synthesis pathways compared to the effect caused by elevated temperature alone. Our results underscore ocean warming as the predominant stressor for dinoflagellates and highlight the complex, synergistic effects of multi-stressors on dinoflagellates.

Improved microalgae carbon fixation and microplastic sedimentation in the lake through in silico method

The impact of microplastics in lake water environments on microalgae carbon fixation and microplastic sedimentation has attracted global attention. The molecular dynamic simulation method was used to design microplastic additive proportioning schemes for improving microalgae carbon fixation and microplastic sedimentation. Results showed that the harm of microplastics can be effectively alleviated by adjusting the proportioning scheme of plastic additives. Besides, the decabromodiphenyl oxide (DBDPO) was identified as the main additive that affect the microalgae carbon fixation and microplastic sedimentation. Thus, a molecular modification based on CiteSpace visual analysis was firstly used and 12 DBDPO derivatives were designed. After the screening, DBDPO-2 and DBDPO-5 became the environmentally friendly DBDPO alternatives, with the highest microalgae carbon fixation and microplastic sedimentation ability enhancement of over 25 %. Compared to DBDPO, DBDPO derivatives were found easier to stimulate the adsorption and binding ability of surrounding hotspot amino acids to CO2 and ribulose-5-phosphate, increasing the solvent-accessible surface area of microplastics, thus improving the microalgae carbon fixation and microplastic sedimentation ability. This study provides theoretical support for simultaneously promoting the microalgae carbon fixation and microplastic sedimentation in the lake water environment and provides scientific basis for the protection and sustainable development of lake water ecosystem.

Physcomitrium patens response to elevated CO2 is flexible and determined by an interaction between sugar and nitrogen availability

Mosses hold a unique position in plant evolution and are crucial for protecting natural, long-term carbon storage systems such as permafrost and bogs. Due to small stature, mosses grow close to the soil surface and are exposed to high levels of CO2 , produced by soil respiration. However, the impact of elevated CO2 (eCO2 ) levels on mosses remains underexplored. We determined the growth responses of the moss Physcomitrium patens to eCO2 in combination with different nitrogen levels and characterized the underlying physiological and metabolic changes. Three distinct growth characteristics, an early transition to caulonema, the development of longer, highly pigmented rhizoids, and increased biomass, define the phenotypic responses of P. patens to eCO2 . Elevated CO2 impacts growth by enhancing the level of a sugar signaling metabolite, T6P. The quantity and form of nitrogen source influences these metabolic and phenotypic changes. Under eCO2 , P. patens exhibits a diffused growth pattern in the presence of nitrate, but ammonium supplementation results in dense growth with tall gametophores, demonstrating high phenotypic plasticity under different environments. These results provide a framework for comparing the eCO2 responses of P. patens with other plant groups and provide crucial insights into moss growth that may benefit climate change models.

Physiological and transcriptomic analysis reveal the crucial factors in heat stress response of red raspberry 'Polka' seedlings

With global climate warming, recurring extreme heat and high temperatures irreversibly damage plants. Raspberries, known for their nutritional and medicinal value, are in high demand worldwide. Thus, it is important to study how high-temperature stress (HTS) affects raspberries. The physiological and biochemical responses and molecular genetic mechanisms of raspberry leaves to different HTS treatments were investigated: mild high temperature at 35°C (HT35), severe high temperature at 40°C (HT40), and the control at room temperature of 25°C (CK). The physiological results suggested that leaves in both the 35°C and 40°C treatments showed maximum relative conductivity at 4 d of stress, increasing by 28.54% and 43.36%, respectively, compared to CK. Throughout the stress period (0-4 d), malondialdehyde (MDA) and soluble protein contents of raspberry leaves increased under HT35 and HT40 treatments, while soluble sugar content first decreased and then increased. Catalase (CAT) activity increased, superoxide dismutase (SOD) activity first increased and then decreased, and peroxidase (POD) activity gradually decreased. Photosynthetic and fluorescence responses of raspberry leaves showed the most severe impairment after 4 d of stress. Transcriptomics results revealed significant alterations in 42 HSP family genes, two SOD-related differentially expressed genes (DEGs), 25 POD-related DEGs, three CAT-related DEGs, and 38 photosynthesis-related DEGs under HTS. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these DEGs were mainly enriched in photosynthesis-antenna proteins, pentose and glucuronide interconversion, phenylpropane biosynthesis, and indole alkaloid biosynthesis. HTS induced excessive ROS accumulation in raspberry leaves, causing oxidative damage in plant cells and subsequently reducing photosynthesis in raspberry leaves. This reduction in photosynthesis, in turn, affects photosynthetic carbon fixation and starch and sucrose metabolism, which, combined with phenol propane biosynthesis, mitigates the HTS-induced damage.

Effects of Trophic Acclimation on Growth and Expression Profiles of Genes Encoding Enzymes of Primary Metabolism and Plastid Transporters of Chlamydomonas reinhardtii

In this paper, the effect of prolonged trophic acclimation on the subsequent growth of Chlamydomonas reinhardtii batch cultures was studied. The mixotrophic (light + acetate) acclimation stimulated subsequent growth at both mixotrophy and autotrophy conditions and altered the expression profile of genes encoding enzymes of primary metabolism and plastid transporters. Besides the trophic effect, the influence of Chlamydomonas culture growth stage on gene expression was determined. Under mixotrophic conditions, this effect was most pronounced in the first half of the exponential growth with partial retention of the previous acclimation period traits. The autotrophy acclimation effect was more complex and its significance was enhanced at the end of the growth and in the stationary phase.

Chlamydomonas reinhardtii, a Reference Organism to Study Algal-Microbial Interactions: Why Can't They Be Friends?

The stability and harmony of ecological niches rely on intricate interactions between their members. During evolution, organisms have developed the ability to thrive in different environments, taking advantage of each other. Among these organisms, microalgae are a highly diverse and widely distributed group of major primary producers whose interactions with other organisms play essential roles in their habitats. Understanding the basis of these interactions is crucial to control and exploit these communities for ecological and biotechnological applications. The green microalga Chlamydomonas reinhardtii, a well-established model, is emerging as a model organism for studying a wide variety of microbial interactions with ecological and economic significance. In this review, we unite and discuss current knowledge that points to C. reinhardtii as a model organism for studying microbial interactions.

Transcriptome-based analysis of key pathways relating to yield formation stage of foxtail millet under different drought stress conditions

Although foxtail millet, as small Panicoid crop, is of drought resilient, drought stress has a significant effect on panicle of foxtail millet at the yield formation stage. In this study, the changes of panicle morphology, photosynthesis, antioxidant protective enzyme system, reactive oxygen species (ROS) system, and osmotic regulatory substance and RNA-seq of functional leaves under light drought stress (LD), heavy drought stress (HD), light drought control (LDCK) and heavy drought control (HDCK) were studied to get a snap-shot of specific panicle morphological changes, physiological responses and related molecular mechanisms. The results showed that the length and weight of panicle had decreased, but with increased empty abortive rate, and then yield dropped off 14.9% and 36.9%, respectively. The photosynthesis of millet was significantly decreased, like net photosynthesis rate, stomatal conductance and transpiration rate, especially under HD treatment with reluctant recovery from rehydration. Under LD and HD treatment, the peroxidase (POD) was increased by 34% and 14% and the same as H₂O₂ by 34.7% and 17.2% compared with LDCK and HDCK. The ability to produce and inhibit O^2- free radicals under LD treatment was higher than HD. The content of soluble sugar was higher under LD treatment but the proline was higher under HD treatment. Through RNA-seq analysis, there were 2,393 and 3,078 different genes expressed under LD and HD treatment. According to the correlation analysis between weighted gene coexpression network analysis (WGCNA) and physiological traits, the co-expression network of several modules with high correlation was constructed, and some hub genes of millet in response to drought stress were found. The expression changes relating to carbon fixation, sucrose and starch synthesis, lignin synthesis, gibberellin synthesis, and proline synthesis of millet were specifically analyzed. These findings provide a full perspective on how drought affects the yield formation of foxtail millet by constructing one work model thereby providing theoretical foundation for hub genes exploration and drought resistance breeding of foxtail millet.

Integrative Application of Transcriptomics and Metabolomics Provides Insights into Unsynchronized Growth in Sea Cucumber (Stichopus monotuberculatus)

Ever-increasing consumer demand for sea cucumbers mainly leads to huge damage to wild sea cucumber resources, including Stichopus monotuberculatus, which in turn exerts negative impacts on marine environments due to the lack of ecological functions performed by sea cucumbers. Aquaculture of sea cucumbers is an effective way to meet consumer demand and restore their resources. Unsynchronous growth is a prominent problem in the aquaculture of sea cucumbers which has concealed unelucidated molecular mechanisms until now. In this study, we carried out an integrative analysis of transcriptomics and metabolomics on fast-growing (SMF) and slow-growing (SMS) groups of S. monotuberculatus cultured in the same environmental conditions. The results revealed that a total of 2054 significantly differentially expressed genes (DEGs) were identified, which are mainly involved in fat digestion and absorption, histidine metabolism, arachidonic acid metabolism, and glutathione metabolism. 368 differential metabolites (DMs) were screened out between the SMF group and the SMS group; these metabolites are mainly involved in glycerophospholipid metabolism, purine metabolism, biosynthesis of unsaturated fatty acids, pyrimidine metabolism, arachidonic acid metabolism, and other metabolic pathways. The integrative analysis of transcriptomics and metabolomics of S. monotuberculatus suggested that the SMF group had a higher capacity for lipid metabolism and protein synthesis, and had a more frequent occurrence of apoptosis events, which are likely to be related to coping with environmental stresses. The results of this study provide potential values for the aquaculture of sea cucumbers which may promote their resource enhancement.

Untargeted metabolomics of the alkaliphilic cyanobacterium Plectonema terebrans elucidated novel stress-responsive metabolic modulations

Alkaliphilic cyanobacteria are suitable candidates to study the effect of alkaline wastewater cultivation on molecular metabolic responses. In the present study, the impact of wastewater, alkalinity, and alkaline wastewater cultivation was studied on the biomass production, biochemical composition, and the alkalinity responsive molecular mechanism through metabolomics. The results suggested a 1.29 to 1.44-fold higher biomass production along with improved lipid, carbohydrate, and pigment production under alkaline wastewater cultivation. The metabolomics analysis showed 1.2-fold and 5.54-fold increase in the indole-acetic acid and phytoene biosynthesis which contributed to overall enhanced cell differentiation and photo-protectiveness. Furthermore, lower levels of Ribulose-1,5-bisphosphate (RuBP), and higher levels of 2-phosphoglycerate and 3-phosphoglycerate suggested the efficient fixation of CO₂ into biomass, and storage compounds including polysaccharides, lipids, and sterols. Interestingly, except L-histidine and L-phenylalanine, all the metabolites related to protein biosynthesis were downregulated in response to wastewater and alkaline wastewater cultivation. The cells protected themselves from alkalinity and nutrient stress by improving the biosynthesis of sterols, non-toxic antioxidants, and osmo-protectants. Alkaline wastewater cultivation regulated the activation of carbon concentration mechanism (CCM), glycolysis, fatty-acid biosynthesis, and shikimate pathway. The data revealed the importance of alkaline wastewater cultivation for improved CO₂ fixation, wastewater treatment, and producing valuable bioproducts including phytoene, Lyso PC 18:0, and sterols. These metabolic pathways could be future targets of metabolic engineering for improving biomass and metabolite production. SIGNIFICANCE: Alkalinity is an imperative factor, responsible for the contamination control and biochemical regulation in cyanobactera, especially during the wastewater cultivation. Currently, understanding of alkaline wastewater responsive molecular mechanism is lacking and most of the studies are focused on transcriptomics of model organisms for this purpose. In this study, untargeted metabolomics was employed to analyze the impact of wastewater and alkaline wastewater on the growth, CO₂ assimilation, nutrient uptake, and associated metabolic modulations of the alkaliphilic cyanobacterium Plectonema terebrans BERC10. Results unveiled that alkaline wastewater cultivation regulated the activation of carbon concentration mechanism (CCM), glycolysis, fatty-acid biosynthesis, and shikimate pathway. It indicated the feasibility of alkaline wastewater as promising low-cost media for cyanobacterium cultivation. The identified stress-responsive pathways could be future genetic targets for strain improvement.

Insights into the genetic and metabolic engineering approaches to enhance the competence of microalgae as biofuel resource: A review

Conventional fuel resources are overburden with speedy global energy demand which ensued the urgent need of alternate energy resources. Biofuel generation efficiency of microalgae is notable due to their comparatively rapid biomass production rate and high oil content. But, the employment of microalgae as biofuel resource is in infancy due to low productivity and high production cost. The issues can be addressed by employing engineered microalgal strains that would be able to efficiently generate enhanced levels of biomass with augmented lipid and/or carbohydrate content for proficient biofuel production. Genetic alterations and metabolic engineering of microalgal species might be helpful in developing high stress-tolerant strains with improved properties for biofuel generation. Various omics approaches appeared significant to upgrade the microalgal lipid production. Intervention of genetic and metabolic engineering approaches would facilitate the development of microalgae as a competent biofuel resource and inflate the economic commercialization of biofuels.

Adaptive Laboratory Evolution of Microalgae: A Review of the Regulation of Growth, Stress Resistance, Metabolic Processes, and Biodegradation of Pollutants

Adaptive laboratory evolution (ALE) experiments are a serviceable method for the industrial utilization of the microalgae, which can improve the phenotype, performance, and stability of microalgae to obtain strains containing beneficial mutations. In this article, we reviewed the research into the microalgae ALE test and assessed the improvement of microalgae growth, tolerance, metabolism, and substrate utilization by ALE. In addition, the principles of ALE and the key factors of experimental design, as well as the issues and drawbacks of the microalgae ALE method were discussed. In general, improving the efficiency of ALE and verifying the stability of ALE resulting strains are the primary problems that need to be solved in future research, making it a promising method for the application of microalgae biotechnology.