Transcriptomic reprogramming of the oceanic diatom Skeletonema dohrnii under warming ocean and acidification

Proteomics analysis reveals the antagonistic interaction between high CO2 and warming in the adaptation of the marine diatom Thalassiosira weissflogii in future oceans

While it is known that warming and rising CO2 level might interactively affect the long-term adaptation of marine diatoms, the molecular and physiological mechanisms underlying these interactions in the marine diatom Thalassiosira weissflogii on an evolutionary scale remain largely unexplored. In this study, we investigated the changes in metabolic pathways and physiological responses of T. weissflogii under long-term ocean acidification and/or warming conditions (∼3.5 years), integrating proteomics analyses and physiological measurements. Our findings reveal that proteins involved in central carbon metabolisms (e.g., tricarboxylic acid cycle and glycolysis) and fatty acid metabolism were significantly up-regulated in the long-term warming-adapted populations. However, the long-term adaptation to high CO2 acted antagonistically with warming, slowing down the central carbon metabolism and fatty acid metabolism by down-regulating protein expressions in the key metabolic pathways of the glycolysis and tricarboxylic acid cycle. Additionally, amino acid synthesis was accelerated in the long-term warming and its combination with high CO2-adapted populations. Physiological measurements further supported these findings, showing altered growth rates and metabolic activity under the combined warming and high CO2 conditions. Our results provide new insights into the molecular mechanisms underpinning the antagonistic interaction between high CO2 and warming on marine phytoplankton in the context of global change.

Distinct interspecies thermal resistance strategies exhibited by euplanktonic, tychoplanktonic and benthic diatoms under marine heatwaves

Extreme climate events, such as marine heatwaves (MHWs), are expected to occur more frequently and intensely in the future, resulting in a substantial impact on marine life. The way that diatoms respond to MHWs may have crucial effects on global primary production and biogeochemical cycles. Euplanktonic diatoms appear to benefit from MHWs directly, but this phenomenon needs an explanation. As concerns tychoplanktonic and benthic diatoms, no studies have been addressed on their thermal response strategies. To address this, we investigated the responses and underlying mechanisms of three typical growth forms of diatoms, Pseudo-nitzschia multiseries (euplanktonic), Paralia guyana (tychoplanktonic) and Navicula avium (benthic), under heat stress by combining a growth experiment with transcriptomic analysis. Our results showed that the physiological responses of diatoms to MHWs and underlying molecular mechanisms are largely related to their growth forms. The euplanktonic diatom was first depressed, but then had a distinct increase in the growth rate accompanied by inducing zeatin and unsaturated fatty acid biosynthesis and repressing substance assimilation and energy metabolism. Contrarily, the benthic diatom showed elevated substance and energy demands for macromolecules accumulation by reducing cell division and increasing photosynthesis and nitrogen assimilation. The tychoplanktonic diatom exhibited higher physiological plasticity to maintain growth and cellular homeostasis. Our results indicate the increased rate of cell division in euplanktonic diatoms under heat stress is likely an emergency response strategy promoting diatom dispersal for survival, but at the cost of disturbances of metabolic balance.

The trade-offs associated with the adaptions of marine microalgae to high CO2 and warming

Trade-offs play vital roles in evolutionary theory, linking organism performance to changing environments in the context of global change. Marine microalgae, as one of the most important groups of primary producers in the biosphere, exhibit significant trade-offs across multiple traits in response to environmental changes, such as elevated CO2 (and consequent ocean acidification) and warming. In this review, we synthesize recent findings on the trade-offs associated with both short-term phenotypic acclimation and long-term genotypic adaptation of marine microalgae. Specifically, we discuss distinct classes of trade-offs (i.e., allocation trade-offs, acquisition trade-offs and specialist-generalist trade-offs) between multiple traits, such as growth rate, photosynthesis, nutrient acquisition, and stress tolerance. We also explored the underlying mechanisms driving these trade-offs. Finally, we discuss the broader ecological consequences of these trade-offs, such as potential shifts in species composition and ecosystem functions, and outline key research directions to better predict marine ecosystem responses to future global change scenarios.

The adaptive mechanisms of the marine diatom Thalassiosira weissflogii to long-term high CO2 and warming

While it is known that increased dissolved CO2 concentrations and rising sea surface temperature (ocean warming) can act interactively on marine phytoplankton, the ultimate molecular mechanisms underlying this interaction on a long-term evolutionary scale are relatively unexplored. Here, we performed transcriptomics and quantitative metabolomics analyses, along with a physiological trait analysis, on the marine diatom Thalassiosira weissflogii adapted for approximately 3.5 years to warming and/or high CO2 conditions. We show that long-term warming has more pronounced impacts than elevated CO2 on gene expression, resulting in a greater number of differentially expressed genes (DEGs). The largest number of DEGs was observed in populations adapted to warming + high CO2, indicating a potential synergistic interaction between these factors. We further identified the metabolic pathways in which the DEGs function and the metabolites with significantly changed abundances. We found that ribosome biosynthesis-related pathways were upregulated to meet the increased material and energy demands after warming or warming in combination with high CO2. This resulted in the upregulation of energy metabolism pathways such as glycolysis, photorespiration, the tricarboxylic acid cycle, and the oxidative pentose phosphate pathway, as well as the associated metabolites. These metabolic changes help compensate for reduced photochemical efficiency and photosynthesis. Our study emphasizes that the upregulation of ribosome biosynthesis plays an essential role in facilitating the adaptation of phytoplankton to global ocean changes and elucidates the interactive effects of warming and high CO2 on the adaptation of marine phytoplankton in the context of global change.

First regional reference database of northern Adriatic diatom transcriptomes

Marine microbial communities form the basis for the functioning of marine ecosystems and the conservation of biodiversity. With the application of metagenomics and metatranscriptomics in marine environmental studies, significant progress has been made in analysing the functioning of microbial communities as a whole. These molecular techniques are highly dependent on reliable, well-characterised, comprehensive and taxonomically diverse sequenced reference transcriptomes of microbial organisms. Here we present a set of 12 individual transcriptome assemblies derived from 6 representative diatom species from the northern Adriatic Sea grown under 2 environmentally relevant growth conditions (phosphate replete vs. phosphate deprived). After filtering the reads and assembly, an average number of 64,932 transcripts per assembly was obtained, of which an average of 8856 were assigned to functionally known proteins. Of all assigned transcripts, an average of 6483 proteins were taxonomically assigned to diatoms (Bacillariophyta). On average, a higher number of assigned proteins was detected in the transcriptome assemblies of diatoms grown under replete media condition. On average, 50% of the mapped proteins were shared between the two growth conditions. All recorded proteins in the dataset were classified into 24 COG categories, with approximately 25% belonging to the unknown function and the remaining 75% belonging to all other categories. The resulting diatom reference database for the northern Adriatic, focussing on the response to nutrient limitation as characteristic for the region and predicted for the future world oceans, provides a valuable resource for analysing environmental metatranscriptome and metagenome data. Each northern Adriatic transcriptome can also be used by itself as a reference database for the (meta)transcriptomes and gene expression studies of the associated species that will be generated in the future.

Integrated FT-ICR MS and metabolome reveals diatom-derived organic matter by bacterial transformation under warming and acidification

Bacterial transformation and processing of diatom-derived organic matter (OM) is extremely important for the cycling of production and energy in marine ecosystems; this process contributes to the production of microbial food webs. In this study, a cultivable bacterium (Roseobacter sp. SD-R1) from the marine diatom Skeletonema dohrnii were isolated and identified. A combined Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)/untargeted metabolomics approach was used to synthesize the results of bacterial transformation with dissolved OM (DOM) and lysate OM (LOM) under warming and acidification through laboratory experiments. Roseobacter sp. SD-R1 had different preferences for the conversion of molecules in S. dohrnii-derived DOM and LOM treatments. The effects of warming and acidification contribute to the increased number and complexity of molecules of carbon, hydrogen, oxygen, nitrogen, and sulfur after the bacterial transformation of OM. The chemical complexity generated by bacterial metabolism provides new insights into the mechanisms that shape OM complexity.

The cellular response to ocean warming in Emiliania huxleyi

Marine phytoplankton contribute substantially to the global flux of carbon from the atmosphere to the deep ocean. Sea surface temperatures will inevitably increase in line with global climate change, altering the performance of marine phytoplankton. Differing sensitivities of photosynthesis and respiration to temperature, will likely shift the strength of the future oceanic carbon sink. To further clarify the molecular mechanisms driving these alterations in phytoplankton function, shotgun proteomic analysis was carried out on the globally-occurring coccolithophore Emiliania huxleyi exposed to moderate- (23°C) and elevated- (28°C) warming. Compared to the control (17°C), growth of E. huxleyi increased under elevated temperatures, with higher rates recorded under moderate- relative to elevated- warming. Proteomic analysis revealed a significant modification of the E. huxleyi cellular proteome as temperatures increased: at lower temperature, ribosomal proteins and photosynthetic machinery appeared abundant, as rates of protein translation and photosynthetic performance are restricted by low temperatures. As temperatures increased, evidence of heat stress was observed in the photosystem, characterized by a relative down-regulation of the Photosystem II oxygen evolving complex and ATP synthase. Acclimation to elevated warming (28°C) revealed a substantial alteration to carbon metabolism. Here, E. huxleyi made use of the glyoxylate cycle and succinate metabolism to optimize carbon use, maintain growth and maximize ATP production in heat-damaged mitochondria, enabling cultures to maintain growth at levels significantly higher than those recorded in the control (17°C). Based on the metabolic changes observed, we can predict that warming may benefit photosynthetic carbon fixation by E. huxleyi in the sub-optimal to optimal thermal range. Past the thermal optima, increasing rates of respiration and costs of repair will likely constrain growth, causing a possible decline in the contribution of this species to the oceanic carbon sink depending on the evolvability of these temperature thresholds.

Combined effects of microplastics and warming enhance algal carbon and nitrogen storage

Algae dominate primary production in groundwater and oceans and play a critical role in global carbon dioxide fixation and climate change but are threatened by ongoing global warming events (such as heatwaves) and increasing microplastic (MP) pollution. However, whether and how ecologically important phytoplankton respond to the combined effects of warming and MPs remain poorly understood. We thus investigated the combined effects of these factors on carbon and nitrogen storage and the mechanisms underlying the alterations in the physiological performance of a model diatom, Phaeodactylum tricornutum, exposed to a warming stressor (25 °C compared with 21 °C) and polystyrene MP acclimation. Although warmer conditions decreased the cell viability, the diatoms subjected to the synergistic effects of MPs and warming showed significant increases in the growth rate (1.10-fold) and nitrogen uptake rate (1.26-fold). Metabolomics and transcriptomic analyses revealed that MPs and warming mainly promoted fatty acid metabolism, the urea cycle, glutamine and glutamate production, and the tricarboxylic acid (TCA) cycle due to an increased level of 2-oxoglutarate, which is the hub of carbon and nitrogen metabolism and accounts for the acquisition and utilization of carbon and nitrogen. Our findings emphasize the nonnegligible effects of MPs and HWs on the algal carbon and nitrogen cycles in waters.

Long-term adaptation to elevated temperature but not CO2 alleviates the negative effects of ultraviolet-B radiation in a marine diatom

Multifaceted changes in marine environments as a result of anthropogenic activities are likely to have a compounding impact on the physiology of marine phytoplankton. Most studies on the combined effects of rising pCO₂, sea surface temperature, and UVB radiation on marine phytoplankton were only conducted in the short-term, which does not allow to test the adaptive capacity of phytoplankton and associated potential trade-offs. Here, we investigated populations of the diatom Phaeodactylum tricornutum that were long-term (∼3.5 years, ∼3000 generations) adapted to elevated CO₂ and/or elevated temperatures, and their physiological responses to short-term (∼2 weeks) exposure of two levels of ultraviolet-B (UVB) radiation. Our results showed that while elevated UVB radiation showed predominantly negative effects on the physiological performance of P. tricornutum regardless of adaptation regimes. Elevated temperature alleviated these effects on most of the measured physiological parameters (e.g., photosynthesis). We also found that elevated CO₂ can modulate these antagonistic interactions, and conclude that long-term adaptation to sea surface warming and rising CO₂ may alter this diatom's sensitivity to elevated UVB radiation in the environment. Our study provides new insights into marine phytoplankton's long-term responses to the interplay of multiple environmental changes driven by climate change.

Response mechanism of harmful algae Phaeocystis globosa to ocean warming and acidification

Simultaneous ocean warming and acidification will alter marine ecosystem structure and directly affect marine organisms. The alga Phaeocystis globosa commonly causes harmful algal blooms in coastal areas of eastern China. P. globosa often outcompetes other species due to its heterotypic life cycle, primarily including colonies and various types of solitary cells. However, little is known about the adaptive response of P. globosa to ocean warming and acidification. This study aimed to reveal the global molecular regulatory networks implicated in the response of P. globosa to simultaneous warming and acidification. After exposure to warming and acidification, the phosphatidylinositol (PI) and mitogen-activated protein kinase (MAPK) signaling pathways of P. globosa were activated to regulate other molecular pathways in the cell, while the light harvesting complex (LHC) genes were downregulated to decrease photosynthesis. Exposure to warming and acidification also altered the intracellular energy flow, with more energy allocated to the TCA cycle rather than to the biosynthesis of fatty acids and hemolytic substances. The upregulation of genes associated with glycosaminoglycan (GAG) degradation prevented the accumulation of polysaccharides, which led to a reduction in colony formation. Finally, the upregulation of the Mre11 and Rad50 genes in response to warming and acidification implied an increase in meiosis, which may be used by P. globosa to increase the number of solitary cells. The increase in genetic diversity through sexual reproduction may be a strategy of P. globosa that supports rapid response to complex environments. Thus, the life cycle of P. globosa underwent a transition from colonies to solitary cells in response to warming and acidification, suggesting that this species may be able to rapidly adapt to future climate changes through life cycle transitions.

Ocean warming and acidification affect the transitional C:N:P ratio and macromolecular accumulation in the harmful raphidophyte Heterosigma akashiwo

Despite an increase in ocean warming and acidification that is expected to increase the number of harmful algal species worldwide, the population of the raphidophyte Heterosigma akashiwo has been reported to be reduced. However, how this species physically and metabolically modifies transitional C:N:P ratio and macromolecule accumulation is unknown. Considering 1st, 10th, and 20th culture generations under present (low-temperature; low-carbon-dioxide [LTLC] 21 °C; pCO2 400 ppm) and future (high-temperature; high-carbon-dioxide [HTHC] 25 °C; pCO2 1000 ppm) ocean conditions, we examined transitional C:N:P ratio and macromolecule level changes and performed transcriptome sequencing. The results showed that compared to 1st generation cells, 20th generation cells under HTHC conditions showed a large decrease in carbon quota (QC: 34%), nitrogen quota (QN: 36%), and phosphorus quota (QP: 32%), which were reflected in an overall reduction in DNA and RNA quantity. Decreased activation of photosynthetic, carbon fixation and lipid metabolic pathways coincided with changes in photosynthetic efficiency, carbon concentration, and lipid accumulation after long-term (20th generation) exposure to HTHC conditions. We observed that these variations in internal metabolic pathways were caused by external changes in temperature, which activated the (Ca+) signaling pathway, and external changes in pCO2, which altered proton exchange pathways. Our results suggest that H. akashiwo in a temperate environment will undergo profound changes in C:N:P ratio and macromolecular properties, leading to programmed cell death, in the future.

Transitional traits determine the acclimation characteristics of the coccolithophore Chrysotila dentata to ocean warming and acidification

Ocean warming and acidification interactively affect the coccolithophore physiology and drives major biogeochemical changes. While numerous studies investigated coccolithophore under short-term conditions, knowledge on how different transitional periods over long-exposure could influence the element, macromolecular and metabolic changes for its acclimation are largely unknown. We cultured the coccolithophore Chrysotila dentata, (culture generations of 1st, 10th, and 20th) under present (low-temperature low-carbon-dioxide [LTLC]) and projected (high-temperature high-carbon-dioxide [HTHC]) ocean conditions. We examined elemental and macromolecular component changes and sequenced a transcriptome. We found that with long-exposure, most physiological responses in HTHC cells decreased when compared with those in LTLC, however, HTHC cell physiology showed constant elevation between each generation. Specifically, compared to 1st generation, the 20th generation HTHC cells showed increases in quota carbon (Qc:29%), nitrogen (Q_N :101%), and subsequent changes in C:N-ratio (68%). We observed higher lipid accumulation than carbohydrates within HTHC cells under long-exposure, suggesting that lipids were used as an alternative energy source for cellular acclimation. Protein biosynthesis pathways increased their efficiency during long-term HTHC condition, indicating that cells produced more proteins than required to initiate acclimation. Our findings suggest that the coccolithophore resilience increased between the 1st-10th generation to initiate the acclimation process under ocean warming and acidifying conditions.

Elevated CO2 reduces copper accumulation and toxicity in the diatom Thalassiosira pseudonana

The projected ocean acidification (OA) associated with increasing atmospheric CO₂ alters seawater chemistry and hence the bio-toxicity of metal ions. However, it is still unclear how OA might affect the long-term resilience of globally important marine microalgae to anthropogenic metal stress. To explore the effect of increasing pCO₂ on copper metabolism in the diatom Thalassiosira pseudonana (CCMP 1335), we employed an integrated eco-physiological, analytical chemistry, and transcriptomic approach to clarify the effect of increasing pCO₂ on copper metabolism of Thalassiosira pseudonana across different temporal (short-term vs. long-term) and spatial (indoor laboratory experiments vs. outdoor mesocosms experiments) scales. We found that increasing pCO₂ (1,000 and 2,000 μatm) promoted growth and photosynthesis, but decreased copper accumulation and alleviated its bio-toxicity to T. pseudonana. Transcriptomics results indicated that T. pseudonana altered the copper detoxification strategy under OA by decreasing copper uptake and enhancing copper-thiol complexation and copper efflux. Biochemical analysis further showed that the activities of the antioxidant enzymes glutathione peroxidase (GPX), catalase (CAT), and phytochelatin synthetase (PCS) were enhanced to mitigate oxidative damage of copper stress under elevated CO₂. Our results provide a basis for a better understanding of the bioremediation capacity of marine primary producers, which may have profound effect on the security of seafood quality and marine ecosystem sustainability under further climate change.

Acclimation traits determine the macromolecular basis of harmful dinoflagellate Alexandrium minutum in response to changing climate conditions

Ocean warming and acidification are expected to have profound impacts on the marine ecosystem, although the dinoflagellate Alexandrium minutum is reported to be acclimated to such conditions. However, it is unknown on the transition time scale how this species physiologically adjusts their element accumulation and associated resource allocation for this process. We designed a set of experiments to examine how different culture generations (1^st, 5^th, and 10^th) change their cell physiology, cellular quotas and macromolecular cellular contents related to functional processes in A. minutum grown with future (pCO₂, 1000 ppm; 25°C) and present (pCO₂, 400 ppm; 21°C) ocean conditions. The differing cell sizes and storage capacity at different generations confirmed that compared to ancestors (1^st generation), acclimation cells (10^th generation) gained increases in quota carbon (Q_C; 55%; [p < 0.05]) and quota phosphate (Q_P; 23% [ p < 0.05]). This variation in C:P and N:P influences was transition-specific and largely determined by phosphate-based molecules. It was observed that A. minutum was initially dependent on P molecules, which help cells act as alternative lipids for quick acclimation until N molecules resume carbon-based lipids for their long-term acclimation. Our study demonstrated that rising temperature and pCO₂ concentrations in ocean may increase A. minutum based on the comprehensive analysis of different physiological modifications, including its growth, element accumulation, transformation, and functional allocation.

Regulation strategy for nutrient-dependent carbon and nitrogen stoichiometric homeostasis in freshwater phytoplankton

Phytoplankton carbon (C) and nitrogen (N) stoichiometric homeostasis plays an important role in aquatic ecosystems. Their C:N ratio is a result of cellular metabolic balance, and the relevant regulatory strategy for its plasticity is still unclear. Therefore, a field survey of seven reservoirs in Tianjin, North China, was conducted to understand variations in phytoplankton C:N ratios, and a laboratory culture of Chlamydomonas reinhardtii was performed to understand the relevant regulation strategy for cellular C-N stoichiometric homeostasis under different C and N availability by using transcriptome sequencing and Nano SIMS and C stable isotope analyses. The results indicated that CO₂ limitation had no significant effect on the phytoplankton C:N ratio in either scene, whereas limitation of dissolved inorganic N induced a 35% higher ratio in the field and a 138% higher ratio in the laboratory. Under CO₂ limitation, algal CO₂-concentrating mechanisms were operated to ensure a C supply, and coupled C-N molecular regulation remained the cellular C:N ratio stable. Under nitrate limitation, differentially expressed gene-regulated intensities increase enormously, and their increasing proportion was comparable to that of the algal C:N ratio; cellular metabolism was reorganized to form a "subhealthy" C-N stoichiometric state with high C:N ratios. In addition, the N transport system had a specific role under CO₂ and nitrate limitations. Our study implies that algal stoichiometric homeostasis depends on the involved limitation element and will help to deepen the understanding of C-N stoichiometric homeostasis in freshwater phytoplankton.

Simulated ocean acidification altered community composition and growth of a coastal phytoplankton assemblage (South West coast of India, eastern Arabian Sea)

Marine phytoplankton can be highly sensitive to ocean acidification; however, their responses are diverse and therefore, phytoplankton response study on the regional scale is of high research priority. The present study documented the community shift and growth responses of a natural phytoplankton assemblage from the South West coastal water of India (South Eastern Arabian Sea) under ambient CO₂ (A-CO₂ ≈ 400 µatm) and high CO₂ (H-CO₂ ≈ 830 µatm) levels in microcosms during the winter monsoon. A doubling of pCO₂ resulted in increased cell density, particulate organic carbon and nitrogen (POC, PON) contents, and C:N ratios. The depleted values of δ¹³C_POC in the H-CO₂-incubated cells indicated a higher diffusive CO₂ influx. HPLC marker pigment analysis revealed that the community was microphytoplankton dominated (mostly diatoms); nanoplanktonic prymnesiophytic algae and picoplanktonic cyanobacteria showed insignificant response to the simulated ocean acidification. A high CO₂-induced increased growth rate was noticed in 6 diatoms (Leptocylindrus danicus; Rhizosolenia setigera; Navicula sp., Asterionella glacialis, Dactyliosolen fragilissimus, and Thalassiosira sp.). The cell volumes of Thalassionema frauenfeldii, Asterionella glacialis, and Cylindrotheca closterium increased significantly, whereas Rhizosolenia setigera and Thalassiosira sp. showed decreased cell volume at the elevated CO₂ levels. These changes in growth rate, cell volume, and elemental stoichiometry could be related to CO₂ acquisition and the nutritional status of the cells. Some phytoplankton genera from this region are probably acclimatized to pCO₂ fluctuations and are likely to benefit from the future increase in CO₂ levels. Higher POC production and increased C:N ratio along with variable cell volume may impact the trophic transfer and cycling of organic carbon in this coastal water. However, a multi-stressor approach in a longer experimental exposure should be considered in future research.

Transformations of Diatom-Derived Dissolved Organic Matter by Bacillus pumilus Under Warming and Acidification Conditions

Heterotrophic bacteria are assumed to play an important role in processing of phytoplankton-derived dissolved organic matter (DOM). Although the algae-derived organic matter is commonly studied, the transformation and processing of DOM by epiphytic bacteria for phytoplankton have rarely been investigated, especially under warming and acidification. In this study, Bacillus pumilus is used to explore the ecologically important marine diatom Skeletonema dohrnii-derived DOM under different conditions (temperature, 27°C and 31°C; pCO2, 400 and 1,000 ppm), utilizing fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC). Fluorescence regional integration and the peak selecting method are used to generate B, T, N, A, M, and C peaks in the EEM fluorescence spectroscopy. The main known fluorophores including that protein-like components (peaks B and T), unknown components (peak N), and humic-like component (peaks A, M, and C). Our experimental results showed that under higher temperature and pressure of CO2 (pCO2) conditions, S. dohrnii-derived DOM fluorescence was dominated by a protein-like signal that slower waning throughout the experiment, becoming an increasingly humic-like substance, implying that processing by the epiphytic bacteria (B. pumilus) produced more complex molecules. In addition, spectroscopic indices (e.g., fluorescence index, biological index, freshness index β/α, and humification index) were changed in varying degrees. This study reveals and confirms the direct participation of heterotrophic bacteria in the transformation and generation of algae-derived DOM in the laboratory, underlining the influence of global warming and ocean acidification on this process.

The responses of harmful dinoflagellate Karenia mikimotoi to simulated ocean acidification at the transcriptional level

The HAB-forming, toxic dinoflagellate Karenia mikimotoi, previously found to benefit from ocean acidification (OA), was cultivated to investigate its transcriptional response to simulated OA for 30 generations. Batch cultures were grown under two CO₂ concentrations, 450 (control) and 1100 (simulated OA) μatm, and physiological parameters [growth, pigments, catalase (CAT), glutathione reductase (GR), and superoxide dismutase (SOD) activity], as well as transcriptomes (obtained via RNA-seq), were compared. Chlorophyll a (Chl a) and carotenoid (Caro) contents, as well as CAT and GR activities, were significantly increased under OA conditions. Transcriptomic analysis revealed 2,490 differentially expressed unigenes in response to OA, which comprised 1.54% of all unigenes. A total of 1,121 unigenes were upregulated, and 1,369 unigenes were downregulated in OA compared to control conditions. The downregulated expression of bicarbonate transporter and carbonic anhydrase genes was a landmark of OA acclimation. Key genes involved in energy metabolism, e.g., photosynthesis, tricarboxylic acid cycle, oxidative phosphorylation, and nitrogen metabolism, were highly upregulated under OA, contributing to increases in the Chl a (55.05%) and Caro (28.37%). The enhanced antioxidant enzyme activities (i.e. CAT, GR) and upregulated genes (i.e. glutathione peroxidase, ascorbate peroxidase, heat shock protein, 20S proteasome, aldehyde dehydrogenase, and apolipoprotein) benefit cells against the potential lower pH stress condition under OA. In addition, the downregulation of four genes associated with motility suggested that the preserved energy could further boost growth. In conclusion, the present study suggests that K. mikimotoi exhibits efficient gene expression regulation for the utilization of energy and resistance to OA-induced stress. Taken together, K. mikimotoi appeared as a tolerant species in response to OA. Thus, more extensive algal blooms that threaten marine organisms are likely in the future. These findings expand current knowledge on the gene expression of HAB-forming species in response to future OA.

Response of Chlorophyll Fluorescence Characteristics and Dissolved Organic Matter for Marine Diatom Skeletonema dohrnii under Stress from Penicillin and Zn2

Skeletonema dohrnii is a good model diatom for studying environmental stress and has promising applications and prospects in various fields. Antibiotics and heavy metals are commonly exceeded in the nearshore marine habitats. In this work, we investigated the effects of an antibiotic (penicillin, 2 µg/L) and a heavy metal ion (Zn2+, 10 µmol/L) stress on marine diatom S. dohrnii, mainly using excitation-emission matrices (EEMs) fluorescence methods and OJIP test. Results indicated that algal cells grown with the antibiotic showed higher biomass, specific growth rate, doubling time, chlorophyll a, and chlorophyll fluorescence variables. Moreover, excess zinc had negative effects on S. dohrnii. We found that zinc not only inhibited the relative photosynthetic electron transfer efficiency but also reduced the Chl a content, which ultimately affected algal growth and organic matter production. In addition, the combined effect of penicillin and Zn2+ further affected the physiological state of S. dohrnii. The dissolved organic matter (DOM) characteristics of the four cultures were also different, including fluorescence indices (fluorescence index, biological index, β/α, and humification index) and fluorescence peaks (peaks A, C, M and T). In brief, characterization of chlorophyll fluorescence characteristics and DOM-related variables are important for understanding the effects of environmental stress on microalgae.

Transcriptomes of an oceanic diatom reveal the initial and final stages of acclimation to copper deficiency

Copper (Cu) concentration is greatly reduced in the open sea so that phytoplankton must adjust their uptake systems and acclimate to sustain growth. Acclimation to low Cu involves changes to the photosynthetic apparatus and specific biochemical reactions that use Cu, but little is known how Cu affects cellular metabolic networks. Here we report results of whole transcriptome analysis of a plastocyanin-containing diatom, Thalassiosira oceanica 1005, during its initial stages of acclimation and after long-term adaptation in Cu-deficient seawater. Gene expression profiles, used to identify Cu-regulated metabolic pathways, show downregulation of anabolic and energy-yielding reactions in Cu-limited cells. These include the light reactions of photosynthesis, carbon fixation, nitrogen assimilation and glycolysis. Reduction of these pathways is consistent with reduced growth requirements for C and N caused by slower rates of photosynthetic electron transport. Upregulation of oxidative stress defence systems persists in adapted cells, suggesting cellular damage by increased reactive oxygen species (ROS) occurs even after acclimation. Copper deficiency also alters fatty acid metabolism, possibly in response to an increase in lipid peroxidation and membrane damage driven by ROS. During the initial stages of Cu-limitation the majority of differentially regulated genes are associated with photosynthetic metabolism, highlighting the chloroplast as the primary target of low Cu availability. The results provide insights into the mechanisms of acclimation and adaptation of T. oceanica to Cu deficiency.

Integrated RNA-seq and Proteomic Studies Reveal Resource Reallocation towards Energy Metabolism and Defense in Skeletonema marinoi in Response to CO2 Increase

Rising atmospheric CO2 concentrations are causing ocean acidification (OA) with significant consequences for marine organisms. Because CO2 is essential for photosynthesis, the effect of elevated CO2 on phytoplankton is more complex and the mechanism is poorly understood. Here we applied RNA-seq and iTRAQ proteomics to investigate the impacts of CO2 increase (from ∼400 to 1000 ppm) on the temperate coastal marine diatom Skeletonema marinoi We identified 32,389 differentially expressed genes (DEGs) and 1,826 differentially expressed proteins (DEPs) from elevated CO2 conditions, accounting for 48.5% of total genes and 25.9% of total proteins we detected, respectively. Elevated pCO2 significantly inhibited the growth of S marinoi, and the 'omic' data suggested that this might be due to compromised photosynthesis in the chloroplast and raised mitochondrial energy metabolism. Furthermore, many genes/proteins associated with nitrogen metabolism, transcriptional regulation, and translational regulation were markedly up-regulated, suggesting enhanced protein synthesis. In addition, S marinoi exhibited higher capacity of ROS production and resistance to oxidative stress. Overall, elevated pCO2 seems to repress photosynthesis and growth of S marinoi, and through massive gene expression reconfiguration induce cells to increase investment in protein synthesis, energy metabolism and antioxidative stress defense, likely to maintain pH homeostasis and population survival. This survival strategy may deprive this usually dominant diatom in temperate coastal waters of its competitive advantages in acidified environments.Importance Rising atmospheric CO2 concentrations are causing ocean acidification with significant consequences for marine organisms. Chain-forming centric diatoms of Skeletonema is one of the most successful groups of eukaryotic primary producers with widespread geographic distribution. Among the recognized 28 species, S. marinoi can be a useful model for investigating the ecological, genetic, physiological, and biochemical characteristics of diatoms in temperate coastal regions. In this study, we found that the elevated pCO2 seems to repress photosynthesis and growth of S. marinoi, and through massive gene expression reconfiguration induce cells to increase investment in protein synthesis, energy metabolism and antioxidative stress defense, likely to maintain pH homeostasis and population survival. This survival strategy may deprive this usually dominant diatom in temperate coastal waters of its competitive advantages in acidified environments.

Comparative Proteomic Analysis Reveals New Insights Into the Common and Specific Metabolic Regulation of the Diatom Skeletonema dohrnii to the Silicate and Temperature Availability

Silicate (Si) and temperature are essential drivers for diatom growth and development in the ocean. Response of diatoms to these particular stress has been investigated; however, their common and specific responses to regulate intracellular development and growth are not known. Here, we investigated the combination of physiological characteristics and comparative proteomics of the diatom Skeletonema dohrnii grown in silicate- and temperature-limited conditions. Results show that cell carbon and lipid quotas were higher at lower-temperature cells, whereas cellular phosphate was higher in cells grown with lower Si. In silicate-limited cells, nitrate transporters were downregulated and resulted in lower nitrate assimilation, whereas the phosphate transporters and its assimilation were reduced in lower-temperature conditions. In photosynthesis, lower silicate caused impact in the linear electron flow and NADPH production, whereas cycling electron transport and ATP production were affected by the lower temperature. Concerning cell cycle, imbalances in the translation process were observed in lower-silicate cells, whereas impact in the transcription mechanism was observed in lower-temperature cells. However, proteins associated with carbon fixation and photorespiration were downregulated in both stress conditions, while the carbohydrate and lipid synthesis proteins were upregulated. Our results showed new insights into the common and specific responses on the proteome and physiology of S. dohrnii to silicate and temperature limitation, providing particular nutrient (Si)- and temperature-dependent mechanisms in diatoms.