Low CO2 results in a rearrangement of carbon metabolism to support C4 photosynthetic carbon assimilation in Thalassiosira pseudonana

Low-CO2-inducible bestrophins outside the pyrenoid sustain high photosynthetic efficacy in diatoms

Anion transporters sustain a variety of physiological states in cells. Bestrophins (BSTs) belong to a Cl- and/or HCO3- transporter family conserved in bacteria, animals, algae, and plants. Recently, putative BSTs were found in the green alga Chlamydomonas reinhardtii, where they are upregulated under low CO2 (LC) conditions and play an essential role in the CO2-concentrating mechanism (CCM). The putative BST orthologs are also conserved in diatoms, secondary endosymbiotic algae harboring red-type plastids, but their physiological functions are unknown. Here, we characterized the subcellular localization and expression profile of BSTs in the marine diatoms Phaeodactylum tricornutum (PtBST1 to 4) and Thalassiosira pseudonana (TpBST1 and 2). PtBST1, PtBST2, and PtBST4 were localized at the stroma thylakoid membrane outside of the pyrenoid, and PtBST3 was localized in the pyrenoid. Contrarily, TpBST1 and TpBST2 were both localized in the pyrenoid. These BST proteins accumulated in cells grown in LC but not in 1% CO2 (high CO2 [HC]). To assess the physiological functions, we generated knockout mutants for the PtBST1 gene by genome editing. The lack of PtBST1 decreased photosynthetic affinity for dissolved inorganic carbon to the level comparable with the HC-grown wild type. Furthermore, non-photochemical quenching in LC-grown cells was 1.5 to 2.0 times higher in the mutants than in the wild type. These data suggest that HCO3- transport at the stroma thylakoid membranes by PtBST1 is a critical part of the CO2-evolving machinery of the pyrenoid in the fully induced CCM and that PtBST1 may modulate photoprotection under CO2-limited environments in P. tricornutum.

Energy crosstalk between photosynthesis and the algal CO2-concentrating mechanisms

Microalgal photosynthesis is responsible for nearly half of the CO2 annually captured by Earth's ecosystems. In aquatic environments where the CO2 availability is low, the CO2-fixing efficiency of microalgae greatly relies on mechanisms - called CO2-concentrating mechanisms (CCMs) - for concentrating CO2 at the catalytic site of the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). While the transport of inorganic carbon (Ci) across membrane bilayers against a concentration gradient consumes part of the chemical energy generated by photosynthesis, the bioenergetics and cellular mechanisms involved are only beginning to be elucidated. Here, we review the current knowledge relating to the energy requirement of CCMs in the light of recent advances in photosynthesis regulatory mechanisms and the spatial organization of CCM components.

Regulation and integration of membrane transport in marine diatoms

Diatoms represent one of the most successful groups of marine phytoplankton and are major contributors to ocean biogeochemical cycling. They have colonized marine, freshwater and ice environments and inhabit all regions of the World's oceans, from poles to tropics. Their success is underpinned by a remarkable ability to regulate their growth and metabolism during nutrient limitation and to respond rapidly when nutrients are available. This requires precise regulation of membrane transport and nutrient acquisition mechanisms, integration of nutrient sensing mechanisms and coordination of different transport pathways. This review outlines transport mechanisms involved in acquisition of key nutrients (N, C, P, Si, Fe) by marine diatoms, illustrating their complexity, sophistication and multiple levels of control.

Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella

The primary plastid endosymbiosis (∼124 Mya) that occurred in the heterotrophic amoeba lineage, Paulinella, is at an earlier stage of evolution than in Archaeplastida, and provides an excellent model for studying organelle integration. Using genomic data from photosynthetic Paulinella, we identified a plausible mechanism for the evolution of host control of endosymbiont (termed the chromatophore) biosynthetic pathways and functions. Specifically, random gene loss from the chromatophore and compensation by nuclear-encoded gene copies enables host control of key pathways through a minimal number of evolutionary innovations. These gene losses impact critical enzymatic steps in nucleotide biosynthesis and the more peripheral components of multi-protein DNA replication complexes. Gene retention in the chromatophore likely reflects the need to maintain a specific stoichiometric balance of the encoded products (e.g., involved in DNA replication) rather than redox state, as in the highly reduced plastid genomes of algae and plants.

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Endosymbiont DNA replication cannot be completed without several key host proteins

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Endosymbiont nucleotide biosynthesis is completed by import of host proteins

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Limited gene loss allowed the host to gain control of endosymbiont division

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Paulinella regulates chromatophore function using the stringent response pathway

Mitochondrial phosphoenolpyruvate carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations

Photosynthetic carbon fixation is often limited by CO₂ availability, which led to the evolution of CO₂ concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C₄ plants, but whether biochemical CCMs are commonly found in diatoms is a subject of debate. In the diatom Phaeodactylum tricornutum, phosphoenolpyruvate carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real-time quantitative polymerase chain reaction, Western blots, and enzymatic assays to examine PEPC expression and PEPC activity, under low and high concentrations of dissolved inorganic carbon (DIC). We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double-knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double-knockout strains grown under ambient air or lower DIC availability conditions showed reduced growth and photosynthetic affinity for DIC while behaving similarly to wild-type (WT) cells at high DIC concentrations. These mutants furthermore exhibited significantly lower ¹³ C/¹² C ratios compared to the WT. Our data imply that in P. tricornutum at least parts of the CCM rely on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.

Growth-stage-related shifts in diatom endometabolome composition set the stage for bacterial heterotrophy

Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our understanding of the organic molecules transferred between these microbial groups. In an experimental bloom study consisting of three heterotrophic marine bacteria growing together with the diatom Thalassiosira pseudonana, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing. Twenty-two diatom endometabolites were annotated, with nine increasing in internal concentration in the late stage of the bloom, eight decreasing, and five showing no variation through the bloom progression. Some metabolite changes could be linked to shifts in diatom gene expression, as well as to shifts in bacterial community composition and their expression of substrate uptake and catabolism genes. Yet an overall low match indicated that endometabolome concentration was not a good predictor of exometabolite availability, and that complex physiological and ecological interactions underlie metabolite exchange. Six diatom endometabolites accumulated to higher concentrations in the bacterial co-cultures compared to axenic cultures, suggesting a bacterial influence on rates of synthesis or release of glutamate, arginine, leucine, 2,3-dihydroxypropane-1-sulfonate, glucose, and glycerol-3-phosphate. Better understanding of phytoplankton metabolite production, release, and transfer to assembled bacterial communities is key to untangling this nearly invisible yet pivotal step in ocean carbon cycling.

The Enzymology of Ocean Global Change

A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean.

The Draft Genome of the Centric Diatom Conticribra weissflogii (Coscinodiscophyceae, Ochrophyta)

Here, we present a 231 Mb draft genome of the centric diatom Conticribra weissflogii CCMP1336. Comparative genomics of C. weissflogii and other Ochrophyta support the existence of unique carbon-concentrating mechanisms and chitin metabolic processes in diatoms. The whole-genome project is available at CNSA (https://db.cngb.org/search/project/CNP0001903/).

Proteomic and biochemical responses to different concentrations of CO2 suggest the existence of multiple carbon metabolism strategies in Phaeodactylum tricornutum

BACKGROUND

Diatoms are well known for high photosynthetic efficiency and rapid growth rate, which are not only important oceanic primary producer, but also ideal feedstock for microalgae industrialization. Their high success is mainly due to the rapid response of photosynthesis to inorganic carbon fluctuations. Thus, an in-depth understanding of the photosynthetic carbon fixation mechanism of diatoms will be of great help to microalgae-based applications. This work directed toward the analysis of whether C4 photosynthetic pathway functions in the model marine diatom Phaeodactylum tricornutum, which possesses biophysical CO₂-concentrating mechanism (CCM) as well as metabolic enzymes potentially involved in C4 photosynthetic pathway.

RESULTS

For P. tricornutum, differential proteome, enzyme activities and transcript abundance of carbon metabolism-related genes especially biophysical and biochemical CCM-related genes in response to different concentrations of CO₂ were tracked in this study. The upregulated protein abundance of a carbonic anhydrases and a bicarbonate transporter suggested biophysical CCM activated under low CO₂ (LC). The upregulation of a number of key C4-related enzymes in enzymatic activity, transcript and protein abundance under LC indicated the induction of a mitochondria-mediated CCM in P. tricornutum. Moreover, protein abundance of a number of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine-urea cycle related proteins upregulated under LC, while numbers of proteins involved in the Calvin cycle and pentose phosphate pathway were downregulated. Under high CO₂ (HC), protein abundance of most central carbon metabolism and photosynthesis-related proteins were upregulated.

CONCLUSIONS

The proteomic and biochemical responses to different concentrations of CO₂ suggested multiple carbon metabolism strategies exist in P. tricornutum. Namely, LC might induce a mitochondrial-mediated C4-like CCM and the improvement of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine-urea cycle activity contribute to the energy supply and carbon and nitrogen recapture in P. tricornutum to cope with the CO₂ limitation, while P. tricornutum responds to the HC environment by improving photosynthesis and central carbon metabolism activity. These findings can not only provide evidences for revealing the global picture of biophysical and biochemical CCM in P. tricornutum, but also provide target genes for further microalgal strain modification to improve carbon fixation and biomass yield in algal-based industry.

Initiation of efficient C4 pathway in response to low ambient CO2 during the bloom period of a marine dinoflagellate

Dinoflagellates are important primary producers and major causative agents of harmful algal blooms in the global ocean. Despite the great ecological significance, the photosynthetic carbon acquisition by dinoflagellates is still poorly understood. The pathways of photosynthetic carbon assimilation in a marine dinoflagellate Prorocentrum donghaiense under both in situ and laboratory-simulated bloom conditions were investigated using a combination of metaproteomics, qPCR, stable carbon isotope and targeted metabolomics approaches. A rapid consumption of dissolved CO₂ to generate high biomass was observed as the bloom proceeded. The carbon assimilation genes and proteins including intracellular carbonic anhydrase 2, phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase and RubisCO as well as their enzyme activities were all highly expressed at the low CO₂ level, indicating that C₄ photosynthetic pathway functioned in the blooming P. donghaiense cells. Furthermore, δ¹³ C values and content of C₄ compound (malate) significantly increased with the decreasing CO₂ concentration. The transition from C₃ to C₄ pathway minimizes the internal CO₂ leakage and guarantees efficient carbon fixation at the low CO₂ level. This study demonstrates the existence of C₄ photosynthetic pathway in a marine dinoflagellate and reveals its important complementary role to assist carbon assimilation for cell proliferation during the bloom period.

Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans

Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO₂ to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO₂, which is vital information toward modeling their response to future CO₂ levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO₂ variability. The current study investigates the interlink between the environmental variability of CO₂ and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO₂ concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8-5 μm, 5-20 μm, 20-180 μm, and 180-2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO₂ levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.

Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application

Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.

Diatoms for Carbon Sequestration and Bio-Based Manufacturing

Carbon dioxide (CO2) is a major greenhouse gas responsible for climate change. Diatoms, a natural sink of atmospheric CO2, can be cultivated industrially in autotrophic and mixotrophic modes for the purpose of CO2 sequestration. In addition, the metabolic diversity exhibited by this group of photosynthetic organisms provides avenues to redirect the captured carbon into products of value. These include lipids, omega-3 fatty acids, pigments, antioxidants, exopolysaccharides, sulphated polysaccharides, and other valuable metabolites that can be produced in environmentally sustainable bio-manufacturing processes. To realize the potential of diatoms, expansion of our knowledge of carbon supply, CO2 uptake and fixation by these organisms, in conjunction with ways to enhance metabolic routing of the fixed carbon to products of value is required. In this review, current knowledge is explored, with an evaluation of the potential of diatoms for carbon capture and bio-based manufacturing.

Regulation of Carbon Metabolism by Environmental Conditions: A Perspective From Diatoms and Other Chromalveolates

Diatoms belong to a major, diverse and species-rich eukaryotic clade, the Heterokonta, within the polyphyletic chromalveolates. They evolved as a result of secondary endosymbiosis with one or more Plantae ancestors, but their precise evolutionary history is enigmatic. Nevertheless, this has conferred them with unique structural and biochemical properties that have allowed them to flourish in a wide range of different environments and cope with highly variable conditions. We review the effect of pH, light and dark, and CO2 concentration on the regulation of carbon uptake and assimilation. We discuss the regulation of the Calvin-Benson-Bassham cycle, glycolysis, lipid synthesis, and carbohydrate synthesis at the level of gene transcripts (transcriptomics), proteins (proteomics) and enzyme activity. In contrast to Viridiplantae where redox regulation of metabolic enzymes is important, it appears to be less common in diatoms, based on the current evidence, but regulation at the transcriptional level seems to be widespread. The role of post-translational modifications such as phosphorylation, glutathionylation, etc., and of protein-protein interactions, has been overlooked and should be investigated further. Diatoms and other chromalveolates are understudied compared to the Viridiplantae, especially given their ecological importance, but we believe that the ever-growing number of sequenced genomes combined with proteomics, metabolomics, enzyme measurements, and the application of novel techniques will provide a better understanding of how this important group of algae maintain their productivity under changing conditions.

PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum

Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.

Identification of candidate genes related to salt tolerance of the secretohalophyte Atriplex canescens by transcriptomic analysis

BACKGROUND

Atriplex canescens is a typical C₄ secretohalophyte with salt bladders on the leaves. Accumulating excessive Na⁺ in tissues and salt bladders, maintaining intracellular K⁺ homeostasis and increasing leaf organic solutes are crucial for A. canescens survival in harsh saline environments, and enhanced photosynthetic activity and water balance promote its adaptation to salt. However, the molecular basis for these physiological mechanisms is poorly understood. Four-week-old A. canescens seedlings were treated with 100 mM NaCl for 6 and 24 h, and differentially expressed genes in leaves and roots were identified, respectively, with Illumina sequencing.

RESULTS

In A. canescens treated with 100 mM NaCl, the transcripts of genes encoding transporters/channels for important nutrient elements, which affect growth under salinity, significantly increased, and genes involved in exclusion, uptake and vacuolar compartmentalization of Na⁺ in leaves might play vital roles in Na⁺ accumulation in salt bladders. Moreover, NaCl treatment upregulated the transcripts of key genes related to leaf organic osmolytes synthesis, which are conducive to osmotic adjustment. Correspondingly, aquaporin-encoding genes in leaves showed increased transcripts under NaCl treatment, which might facilitate water balance maintenance of A. canescens seedlings in a low water potential condition. Additionally, the transcripts of many genes involved in photosynthetic electron transport and the C₄ pathway was rapidly induced, while other genes related to chlorophyll biosynthesis, electron transport and C₃ carbon fixation were later upregulated by 100 mM NaCl.

CONCLUSIONS

We identified many important candidate genes involved in the primary physiological mechanisms of A. canescens salt tolerance. This study provides excellent gene resources for genetic improvement of salt tolerance of important crops and forages.

Genome-wide identification of genes involved in carbon fixation in Saccharina japonica and responses of putative C4-related genes to bicarbonate concentration and light intensity

Brown algae play a dominant role in the primary productivity of coastal ecosystems and may have an efficient carbon fixation. In this work, 56 genes involved in inorganic carbon fixation were identified from the Saccharina japonica genome. Sequence structure analysis of these genes showed the existence of corresponding function domains and active amino acid sites highly conserved with other stramenopile species. The predicted subcellular localizations showed that Calvin cycle-related enzymes predominantly reside in the plastid and that putative C4-related enzymes are mainly distributed in the mitochondrion. We determined the transcriptional profiles and enzymatic activities of these C4-related enzymes in response to the KHCO3 concentrations and light intensities. Pyruvate orthophosphate dikinase (PPDK) presented the greatest response to low HCO3- concentrations and high light intensity. Phosphoenolpyruvate carboxykinase (PEPCK) was up-regulated at low HCO3- concentrations to compensate for ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and might be the crucial decarboxylase in this kelp. We propose that S. japonica might possess a PPDK- and PEPCK-dependent C4-like pathway that enables its rapid growth in natural coastal environments.

The intracellular distribution of inorganic carbon fixing enzymes does not support the presence of a C4 pathway in the diatom Phaeodactylum tricornutum

Diatoms are unicellular algae and important primary producers. The process of carbon fixation in diatoms is very efficient even though the availability of dissolved CO₂ in sea water is very low. The operation of a carbon concentrating mechanism (CCM) also makes the more abundant bicarbonate accessible for photosynthetic carbon fixation. Diatoms possess carbonic anhydrases as well as metabolic enzymes potentially involved in C4 pathways; however, the question as to whether a C4 pathway plays a general role in diatoms is not yet solved. While genome analyses indicate that the diatom Phaeodactylum tricornutum possesses all the enzymes required to operate a C4 pathway, silencing of the pyruvate orthophosphate dikinase (PPDK) in a genetically transformed cell line does not lead to reduced photosynthetic carbon fixation. In this study, we have determined the intracellular location of all enzymes potentially involved in C4-like carbon fixing pathways in P. tricornutum by expression of the respective proteins fused to green fluorescent protein (GFP), followed by fluorescence microscopy. Furthermore, we compared the results to known pathways and locations of enzymes in higher plants performing C3 or C4 photosynthesis. This approach revealed that the intracellular distribution of the investigated enzymes is quite different from the one observed in higher plants. In particular, the apparent lack of a plastidic decarboxylase in P. tricornutum indicates that this diatom does not perform a C4-like CCM.

Ocean acidification conditions increase resilience of marine diatoms

The fate of diatoms in future acidified oceans could have dramatic implications on marine ecosystems, because they account for ~40% of marine primary production. Here, we quantify resilience of Thalassiosira pseudonana in mid-20th century (300 ppm CO2) and future (1000 ppm CO2) conditions that cause ocean acidification, using a stress test that probes its ability to recover from incrementally higher amount of low-dose ultraviolet A (UVA) and B (UVB) radiation and re-initiate growth in day-night cycles, limited by nitrogen. While all cultures eventually collapse, those growing at 300 ppm CO2 succumb sooner. The underlying mechanism for collapse appears to be a system failure resulting from "loss of relational resilience," that is, inability to adopt physiological states matched to N-availability and phase of the diurnal cycle. Importantly, under elevated CO2 conditions diatoms sustain relational resilience over a longer timeframe, demonstrating increased resilience to future acidified ocean conditions. This stress test framework can be extended to evaluate and predict how various climate change associated stressors may impact microbial community resilience.

Ion and metabolite transport in the chloroplast of algae: lessons from land plants

Chloroplasts are endosymbiotic organelles and play crucial roles in energy supply and metabolism of eukaryotic photosynthetic organisms (algae and land plants). They harbor channels and transporters in the envelope and thylakoid membranes, mediating the exchange of ions and metabolites with the cytosol and the chloroplast stroma and between the different chloroplast subcompartments. In secondarily evolved algae, three or four envelope membranes surround the chloroplast, making more complex the exchange of ions and metabolites. Despite the importance of transport proteins for the optimal functioning of the chloroplast in algae, and that many land plant homologues have been predicted, experimental evidence and molecular characterization are missing in most cases. Here, we provide an overview of the current knowledge about ion and metabolite transport in the chloroplast from algae. The main aspects reviewed are localization and activity of the transport proteins from algae and/or of homologues from other organisms including land plants. Most chloroplast transporters were identified in the green alga Chlamydomonas reinhardtii, reside in the envelope and participate in carbon acquisition and metabolism. Only a few identified algal transporters are located in the thylakoid membrane and play role in ion transport. The presence of genes for putative transporters in green algae, red algae, diatoms, glaucophytes and cryptophytes is discussed, and roles in the chloroplast are suggested. A deep knowledge in this field is required because algae represent a potential source of biomass and valuable metabolites for industry, medicine and agriculture.

Diverse CO2-Induced Responses in Physiology and Gene Expression among Eukaryotic Phytoplankton

With rising atmospheric CO₂, phytoplankton face shifts in ocean chemistry including increased dissolved CO₂ and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. Here we compared the physiological and gene expression responses of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (~400 ppm) and elevated (~800 ppm) CO₂. Dinoflagellates had significantly slower growth rates and higher, yet variable, chlorophyll a per cell under elevated CO₂. The other phytoplankton tended to have increased growth rates and/or decreased chlorophyll a per cell. Carbon and nitrogen partitioning of cells shifted under elevated CO₂ in some species, indicating potential changes in energy fluxes due to changes in carbon concentrating mechanisms (CCM) or photorespiration. Consistent with these phenotypic changes, gene set enrichment analyses revealed shifts in energy, carbon and nitrogen metabolic pathways, though with limited overlap between species in the genes and pathways involved. Similarly, gene expression responses across species revealed few conserved CO₂-responsive genes within CCM and photorespiration categories, and a survey of available transcriptomes found high diversity in biophysical CCM and photorespiration expressed gene complements between and within the four phyla represented by these species. The few genes that displayed similar responses to CO₂ across phyla were from understudied gene families, making them targets for further research to uncover the mechanisms of phytoplankton acclimation to elevated CO₂. These results underscore that eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO₂ perturbations and highlight the value of cross-phyla comparisons for identifying gene families that respond to environmental change.

Diversity of CO2-concentrating mechanisms and responses to CO2 concentration in marine and freshwater diatoms

The presence of CO2-concentrating mechanisms (CCMs) is believed to be one of the characteristics that allows diatoms to thrive in many environments and to be major contributors to global productivity. Here, the type of CCM and the responses to variable CO2 concentration were studied in marine and freshwater diatoms. At 400 ppm, there was a large diversity in physiological and biochemical mechanisms among the species. While Phaeodactylum tricornutum mainly used HCO3-, Thalassiosira pseudonana mainly used CO2. Carbonic anhydrase was an important component of the CCM in all species and C4 metabolism was absent, even with T. weissflogii. For all species, at 20 000 ppm, the affinity for dissolved inorganic carbon was lower than at 400 ppm CO2 and the reliance on CO2 was higher. Despite the difference in availability of inorganic carbon in marine and fresh waters, there were only small differences in CCMs between species from the two environments, and Navicula pelliculosa behaved similarly when grown in the two environments. The results suggest that species-specific differences are great, and more important than environmental differences in determining the nature and effectiveness of the CCM in diatoms.

Responses of the marine diatom Thalassiosira pseudonana to changes in CO2 concentration: a proteomic approach

The concentration of CO₂ in many aquatic systems is variable, often lower than the K_M of the primary carboxylating enzyme Rubisco, and in order to photosynthesize efficiently, many algae operate a facultative CO₂ concentrating mechanism (CCM). Here we measured the responses of a marine diatom, Thalassiosira pseudonana, to high and low concentrations of CO₂ at the level of transcripts, proteins and enzyme activity. Low CO₂ caused many metabolic pathways to be remodeled. Carbon acquisition enzymes, primarily carbonic anhydrase, stress, degradation and signaling proteins were more abundant while proteins associated with nitrogen metabolism, energy production and chaperones were less abundant. A protein with similarities to the Ca²⁺/ calmodulin dependent protein kinase II_association domain, having a chloroplast targeting sequence, was only present at low CO₂. This protein might be a specific response to CO₂ limitation since a previous study showed that other stresses caused its reduction. The protein sequence was found in other marine diatoms and may play an important role in their response to low CO₂ concentration.

Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms

Evidence suggests that diatom photorespiratory metabolism is distinct from other photosynthetic eukaryotes in that there may be at least two routes for the metabolism of the photorespiratory metabolite glycolate. One occurs primarily in the mitochondria and is similar to the C2 photorespiratory pathway, and the other processes glycolate through the peroxisomal glyoxylate cycle. Genomic analysis has identified the presence of key genes required for glycolate oxidation, the glyoxylate cycle, and malate metabolism, however, predictions of intracellular localization can be ambiguous and require verification. This knowledge gap leads to uncertainties surrounding how these individual pathways operate, either together or independently, to process photorespiratory intermediates under different environmental conditions. Here, we combine in silico sequence analysis, in vivo protein localization techniques and gene expression patterns to investigate key enzymes potentially involved in photorespiratory metabolism in the model diatom Thalassiosira pseudonana. We demonstrate the peroxisomal localization of isocitrate lyase and the mitochondrial localization of malic enzyme and a glycolate oxidase. Based on these analyses, we propose an updated model for photorespiratory metabolism in T. pseudonana, as well as a mechanism by which C2 photorespiratory metabolism and its associated pathways may operate during silicon starvation and growth arrest.

Modelling metabolism of the diatom Phaeodactylum tricornutum

Marine diatoms have potential as a biotechnological production platform, especially for lipid-derived products, including biofuels. Here we introduce some features of diatom metabolism, particularly with respect to photosynthesis, photorespiration and lipid synthesis and their differences relative to other photosynthetic eukaryotes. Since structural metabolic modelling of other photosynthetic organisms has been shown to be capable of representing their metabolic capabilities realistically, we briefly review the main approaches to this type of modelling. We then propose that genome-scale modelling of the diatom Phaeodactylum tricornutum, in response to varying light intensity, could uncover the novel aspects of the metabolic potential of this organism.

The Water to Water Cycles in Microalgae

In oxygenic photosynthesis, light produces ATP plus NADPH via linear electron transfer, i.e. the in-series activity of the two photosystems: PSI and PSII. This process, however, is thought not to be sufficient to provide enough ATP per NADPH for carbon assimilation in the Calvin-Benson-Bassham cycle. Thus, it is assumed that additional ATP can be generated by alternative electron pathways. These circuits produce an electrochemical proton gradient without NADPH synthesis, and, although they often represent a small proportion of the linear electron flow, they could have a huge importance in optimizing CO₂ assimilation. In Viridiplantae, there is a consensus that alternative electron flow comprises cyclic electron flow around PSI and the water to water cycles. The latter processes include photosynthetic O₂ reduction via the Mehler reaction at PSI, the plastoquinone terminal oxidase downstream of PSII, photorespiration (the oxygenase activity of Rubisco) and the export of reducing equivalents towards the mitochondrial oxidases, through the malate shuttle. In this review, we summarize current knowledge about the role of the water to water cycles in photosynthesis, with a special focus on their occurrence and physiological roles in microalgae.

The physiology and genetics of CO2 concentrating mechanisms in model diatoms

Diatoms, a diverse and ecologically-important group of unicellular algae, use a CO2 concentrating mechanism to enhance the performance of RubisCO and overcome the limited availability of CO2 in their habitats. The recent development of genetic manipulation techniques for the model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana and the sequencing of their genomes have enabled the rapid identification of genes involved in their CO2 concentrating mechanisms (CCMs). These include numerous carbonic anhydrases (CAs), which are localized to distinct subcellular compartments in the two diatom species, and putative bicarbonate transporters, one of which has been functionally characterized. New physiological data on the P. tricornutum CCM are consistent with this molecular data and suggest that the major driver of the CCM is a 'chloroplast-pump' that actively transports bicarbonate into the chloroplast. In T. pseudonana, the localization of a CA in the chloroplast stroma presents a paradox as this would be expected to impede function of a biophysical CCM, though the recent proposal of a modified C4 CCM offers a potential explanation.

Transcript level coordination of carbon pathways during silicon starvation-induced lipid accumulation in the diatom Thalassiosira pseudonana

Diatoms are one of the most productive and successful photosynthetic taxa on Earth and possess attributes such as rapid growth rates and production of lipids, making them candidate sources of renewable fuels. Despite their significance, few details of the mechanisms used to regulate growth and carbon metabolism are currently known, hindering metabolic engineering approaches to enhance productivity. To characterize the transcript level component of metabolic regulation, genome-wide changes in transcript abundance were documented in the model diatom Thalassiosira pseudonana on a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of coregulated genes as a key feature of global gene regulation in T. pseudonana. The identity of key enzymes for carbon metabolic pathway inputs (photosynthesis) and outputs (growth and storage) reveals these clusters are organized to synchronize these processes. Coordinated transcript level responses to silicon starvation are probably driven by signals linked to cell cycle progression and shifts in photophysiology. A mechanistic understanding of how this is accomplished will aid efforts to engineer metabolism for development of algal-derived biofuels.

Changes in Relative Thylakoid Protein Abundance Induced by Fluctuating Light in the Diatom Thalassiosira pseudonana

One of the hallmarks of marine diatom biology is their ability to cope with rapid changes in light availability due to mixing of the water column and the lens effect. We investigated how irradiance fluctuations influence the relative abundance of key photosynthetic proteins in the centric diatom Thalassiosira pseudonana by means of mass-spectrometry-based approaches for relative protein quantitation. Most notably, fluctuating-light conditions lead to a substantial overall up-regulation of light-harvesting complex proteins as well as several subunits of photosystems II and I. Despite an initial delay in growth under FL, there were no indications of FL-induced photosynthesis limitation, in contrast to other photosynthetic organisms. Our findings further strengthen the notion that diatoms use a qualitatively different mechanism of photosynthetic regulation in which chloroplast-mitochondria interaction has overtaken crucial regulatory processes of photosynthetic light reactions that are typical for the survival of land plants, green algae, and cyanobacteria.

The nature of the CO2 -concentrating mechanisms in a marine diatom, Thalassiosira pseudonana

Diatoms are widespread in aquatic ecosystems where they may be limited by the supply of inorganic carbon. Their carbon dioxide-concentrating mechanisms (CCMs) involving transporters and carbonic anhydrases (CAs) are well known, but the contribution of a biochemical CCM involving C4 metabolism is contentious. The CCM(s) present in the marine-centric diatom, Thalassiosira pseudonana, were studied in cells exposed to high or low concentrations of CO2 , using a range of approaches. At low CO2 , cells possessed a CCM based on active uptake of CO2 (70% contribution) and bicarbonate, while at high CO2 , cells were restricted to CO2 . CA was highly and rapidly activated on transfer to low CO2 and played a key role because inhibition of external CA produced uptake kinetics similar to cells grown at high CO2 . The activities of phosphoenolpyruvate (PEP) carboxylase (PEPC) and the PEP-regenerating enzyme, pyruvate phosphate dikinase (PPDK), were lower in cells grown at low than at high CO2 . The ratios of PEPC and PPDK to ribulose bisphosphate carboxylase were substantially lower than 1, even at low CO2 . Our data suggest that the kinetic properties of this species results from a biophysical CCM and not from C4 type metabolism.

Physiological Responses of a Model Marine Diatom to Fast pH Changes: Special Implications of Coastal Water Acidification

Diatoms and other phytoplankton in coastal waters experience rapid pH changes in milieu due to high biological activities and/or upwelled CO2-rich waters. While CO2 concentrating mechanisms (CCMs) are employed by all diatoms tested to counter low CO2 availability in seawater, little is known how this mechanism responds to fast pH changes. In the present study, the model diatom Thalassiosira pseudonana was acclimated for 20 generations to low pH (7.81) at an elevated CO2 of 1000 μatm (HC) or to high pH (8.18) at ambient CO2 levels of 390 μatm (LC), then its physiological characteristics were investigated as cells were shifted from HC to LC or vice versa. The maximal electron transport rate (ETRmax) in the HC-acclimated cells was immediately reduced by decreased CO2 availability, showing much lower values compared to that of the LC-acclimated cells. However, the cells showed a high capacity to regain their photochemical performance regardless of the growth CO2 levels, with their ETRmax values recovering to initial levels in about 100 min. This result indicates that this diatom might modulate its CCMs quickly to maintain a steady state supply of CO2, which is required for sustaining photosynthesis. In addition, active uptake of CO2 could play a fundamental role during the induction of CCMs under CO2 limitation, since the cells maintained high ETR even when both intracellular and periplasmic carbonic anhydrases were inhibited. It is concluded that efficient regulation of the CCM is one of the key strategies for diatoms to survive in fast changing pH environment, e.g. for the tested species, which is a dominant species in coastal waters where highly fluctuating pH is observed.