An atypical member of the light-harvesting complex stress-related protein family modulates diatom responses to light

Chassis engineering for high light tolerance in microalgae and cyanobacteria

Oxygenic photosynthesis in microalgae and cyanobacteria is considered an important chassis to accelerate energy transition and mitigate global warming. Currently, cultivation systems for photosynthetic microbes for large-scale applications encountered excessive light exposure stress. High light stress can: affect photosynthetic efficiency, reduce productivity, limit cell growth, and even cause cell death. Deciphering photoprotection mechanisms and constructing high-light tolerant chassis have been recent research focuses. In this review, we first briefly introduce the self-protection mechanisms of common microalgae and cyanobacteria in response to high light stress. These mechanisms mainly include: avoiding excess light absorption, dissipating excess excitation energy, quenching excessive high-energy electrons, ROS detoxification, and PSII repair. We focus on the species-specific differences in these mechanisms as well as recent advancements. Then, we review engineering strategies for creating high-light tolerant chassis, such as: reducing the size of the light-harvesting antenna, optimizing non-photochemical quenching, optimizing photosynthetic electron transport, and enhancing PSII repair. Finally, we propose a comprehensive exploration of mechanisms: underlying identified high light tolerant chassis, identification of new genes pertinent to high light tolerance using innovative methodologies, harnessing CRISPR systems and artificial intelligence for chassis engineering modification, and introducing plant photoprotection mechanisms as future research directions.

Identifying the gene responsible for non-photochemical quenching reversal in Phaeodactylum tricornutum

Algae such as diatoms and haptophytes have distinct photosynthetic pigments from plants, including a novel set of carotenoids. This includes a primary xanthophyll cycle comprised of diadinoxanthin and its de-epoxidation product diatoxanthin that enables the switch between light harvesting and non-photochemical quenching (NPQ)-mediated dissipation of light energy. The enzyme responsible for the reversal of this cycle was previously unknown. Here, we identified zeaxanthin epoxidase 3 (ZEP3) from Phaeodactylum tricornutum as the candidate diatoxanthin epoxidase. Knocking out the ZEP3 gene caused a loss of rapidly reversible NPQ following saturating light exposure. This correlated with the maintenance of high concentrations of diatoxanthin during recovery in low light. Xanthophyll cycling and NPQ relaxation were restored via complementation of the wild-type ZEP3 gene. The zep3 knockout strains showed reduced photosynthetic rates at higher light fluxes and reduced specific growth rate in variable light regimes, likely due to the mutant strains becoming locked in a light energy dissipation state. We were able to toggle the level of NPQ capacity in a time and dose dependent manner by placing the ZEP3 gene under the control of a β-estradiol inducible promoter. Identification of this gene provides a deeper understanding of the diversification of photosynthetic control in algae compared to plants and suggests a potential target to improve the productivity of industrial-scale cultures.

Lighting the way: Compelling open questions in photosynthesis research

Photosynthesis-the conversion of energy from sunlight into chemical energy-is essential for life on Earth. Yet there is much we do not understand about photosynthetic energy conversion on a fundamental level: how it evolved and the extent of its diversity, its dynamics, and all the components and connections involved in its regulation. In this commentary, researchers working on fundamental aspects of photosynthesis including the light-dependent reactions, photorespiration, and C4 photosynthetic metabolism pose and discuss what they view as the most compelling open questions in their areas of research.

Regulation of Microalgal Photosynthetic Electron Transfer

The global ecosystem relies on the metabolism of photosynthetic organisms, featuring the ability to harness light as an energy source. The most successful type of photosynthesis utilizes a virtually inexhaustible electron pool from water, but the driver of this oxidation, sunlight, varies on time and intensity scales of several orders of magnitude. Such rapid and steep changes in energy availability are potentially devastating for biological systems. To enable a safe and efficient light-harnessing process, photosynthetic organisms tune their light capturing, the redox connections between core complexes and auxiliary electron mediators, ion passages across the membrane, and functional coupling of energy transducing organelles. Here, microalgal species are the most diverse group, featuring both unique environmental adjustment strategies and ubiquitous protective mechanisms. In this review, we explore a selection of regulatory processes of the microalgal photosynthetic apparatus supporting smooth electron flow in variable environments.

A rapid aureochrome opto-switch enables diatom acclimation to dynamic light

Diatoms often outnumber other eukaryotic algae in the oceans, especially in coastal environments characterized by frequent fluctuations in light intensity. The identities and operational mechanisms of regulatory factors governing diatom acclimation to high light stress remain largely elusive. Here, we identified the AUREO1c protein from the coastal diatom Phaeodactylum tricornutum as a crucial regulator of non-photochemical quenching (NPQ), a photoprotective mechanism that dissipates excess energy as heat. AUREO1c detects light stress using a light-oxygen-voltage (LOV) domain and directly activates the expression of target genes, including LI818 genes that encode NPQ effector proteins, via its bZIP DNA-binding domain. In comparison to a kinase-mediated pathway reported in the freshwater green alga Chlamydomonas reinhardtii, the AUREO1c pathway exhibits a faster response and enables accumulation of LI818 transcript and protein levels to comparable degrees between continuous high-light and fluctuating-light treatments. We propose that the AUREO1c-LI818 pathway contributes to the resilience of diatoms under dynamic light conditions.

Skeletonema marinoi ecotypes show specific habitat-related responses to fluctuating light supporting high potential for growth under photobioreactor light regime

Diatoms are a diverse group of phytoplankton usually dominating areas characterized by rapidly shifting light conditions. Because of their high growth rates and interesting biochemical profile, their biomass is considered for various commercial applications. This study aimed at identifying strains with superior growth in a photobioreactor (PBR) by screening the natural intraspecific diversity of ecotypes isolated from different habitats. We investigated the effect of PBR light fluctuating on a millisecond scale (FL, simulating the light in a PBR) on 19 ecotypes of the diatom Skeletonema marinoi isolated from the North Sea-Baltic Sea area. We compare growth, pigment ratios, phylogeny, photo-physiological variables and photoacclimation strategies between all strains and perform qPCR and absorption spectra analysis on a subset of strains. Our results show that the ecotypes responded differently to FL, and have contrasting photo-physiological and photoprotective strategies. The strains from Kattegat performed better in FL, and shared common photoacclimation and photoprotection strategies that are the results of adaptation to the specific light climate of the Kattegat area. The strains that performed better with FL conditions had a high light (HL)-acclimated phenotype coupled with unique nonphotochemical quenching features. Based on their characteristics, three strains were identified as good candidates for growth in PBRs.

Structural Diversity in Eukaryotic Photosynthetic Light Harvesting

Photosynthesis has been using energy from sunlight to assimilate atmospheric CO2 for at least 3.5 billion years. Through evolution and natural selection, photosynthetic organisms have flourished in almost all aquatic and terrestrial environments. This is partly due to the diversity of light-harvesting complex (LHC) proteins, which facilitate photosystem assembly, efficient excitation energy transfer, and photoprotection. Structural advances have provided angstrom-level structures of many of these proteins and have expanded our understanding of the pigments, lipids, and residues that drive LHC function. In this review, we compare and contrast recently observed cryo-electron microscopy structures across photosynthetic eukaryotes to identify structural motifs that underlie various light-harvesting strategies. We discuss subtle monomer changes that result in macroscale reorganization of LHC oligomers. Additionally, we find recurring patterns across diverse LHCs that may serve as evolutionary stepping stones for functional diversification. Advancing our understanding of LHC protein-environment interactions will improve our capacity to engineer more productive crops.

Ultrafast energy quenching mechanism of LHCSR3-dependent photoprotection in Chlamydomonas

Photosynthetic organisms have evolved an essential energy-dependent quenching (qE) mechanism to avoid any lethal damages caused by high light. While the triggering mechanism of qE has been well addressed, candidates for quenchers are often debated. This lack of understanding is because of the tremendous difficulty in measuring intact cells using transient absorption techniques. Here, we have conducted femtosecond pump-probe measurements to characterize this photophysical reaction using micro-sized cell fractions of the green alga Chlamydomonas reinhardtii that retain physiological qE function. Combined with kinetic modeling, we have demonstrated the presence of an ultrafast excitation energy transfer (EET) pathway from Chlorophyll a (Chl a) Qy to a carotenoid (car) S1 state, therefore proposing that this carotenoid, likely lutein1, is the quencher. This work has provided an easy-to-prepare qE active thylakoid membrane system for advanced spectroscopic studies and demonstrated that the energy dissipation pathway of qE is evolutionarily conserved from green algae to land plants.

Ecophysiological responses of Ostreopsis towards temperature: A case study of benthic HAB facing ocean warming

Reports of the benthic dinoflagellate Ostreopsis spp. have been increasing in the last decades, especially in temperate areas. In a context of global warming, evidences of the effects of increasing sea temperatures on its physiology and its distribution are still lacking and need to be investigated. In this study, the influence of temperature on growth, ecophysiology and toxicity was assessed for several strains of O. cf. siamensis from the Bay of Biscay (NE Atlantic) and O. cf. ovata from NW Mediterranean Sea. Cultures were acclimated to temperatures ranging from 14.5 °C to 32 °C in order to study the whole range of each strain-specific thermal niche. Acclimation was successful for temperatures ranging from 14.5 °C to 25 °C for O. cf. siamensis and from 19 °C to 32 °C for O. cf. ovata, with the highest growth rates measured at 22 °C (0.54-1.06 d-1) and 28 °C (0.52-0.75 d-1), respectively. The analysis of cellular content of pigments and lipids revealed some aspects of thermal acclimation processes in Ostreopsis cells. Specific capacities of O. cf. siamensis to cope with stress of cold temperatures were linked with the activation of a xanthophyll cycle based on diadinoxanthin. Lipids (neutral reserve lipids and polar ones) also revealed species-specific variations, with increases in cellular content noted under extreme temperature conditions. Variations in toxicity were assessed through the Artemia franciscana bioassay. For both species, a decrease in toxicity was observed when temperature dropped under the optimal temperature for growth. No PLTX-like compounds were detected in O. cf. siamensis strains. Thus, the main part of the lethal effect observed on A. franciscana was dependent on currently unknown compounds. From a multiclonal approach, this work allowed for defining specificities in the thermal niche and acclimation strategies of O. cf. siamensis and O. cf. ovata towards temperature. Potential impacts of climate change on the toxic risk associated with Ostreopsis blooms in both NW Mediterranean Sea and NE Atlantic coast is further discussed, taking into account variations in the geographic distribution, growth abilities and toxicity of each species.

A key gene, violaxanthin de-epoxidase-like 1, enhances fucoxanthin accumulation in Phaeodactylum tricornutum

BACKGROUND

Fucoxanthin has been widely investigated owing to its beneficial biological properties, and the model diatom Phaeodactylum tricornutum, possessing fucoxanthin (Fux) chlorophyll proteins as light-harvesting systems, is considered to have the potential to become a commercial cell factory for the pigment production.

RESULTS

Here, we compared the pigment contents in 10 different P. tricornutum strains from the globe, and found that strain CCMP631 (Pt6) exhibited the highest Fux content but with a low biomass. Comparison of mRNA levels revealed that higher Fux content in Pt6 was related with the higher expression of gene violaxanthin de-epoxidase-like (VDL) protein 1 (VDL1), which encodes the enzyme catalyzing the tautomerization of violaxanthin to neoxanthin in Fux biosynthesis pathway. Single nucleotide variants of VDL1 gene and allele-specific expression in strains Pt1 (the whole genome sequenced strain CCMP632) and Pt6 were analyzed, and overexpressing of each of the 4 VDL1 alleles, two from Pt1 and two from Pt6, in strain Pt1 leads to an increase in downstream product diadinoxanthin and channels the pigments towards Fux biosynthesis. All the 8 VDL1 overexpression (OE) lines showed significant increases by 8.2 to 41.7% in Fux content without compromising growth, and VDL1 Allele 2 OE lines even exhibited the higher cell density on day 8, with an increase by 24.2-28.7% in two Pt1VDL1-allele 2 OE lines and 7.1-11.1% in two Pt6VDL1-allele 2 OE lines, respectively.

CONCLUSIONS

The results reveal VDL1, localized in the plastid stroma, plays a key role in Fux over-accumulation in P. tricornutum. Overexpressing VDL1, especially allele 2, improved both the Fux content and growth rate, which provides a new strategy for the manipulation of Fux production in the future.

Identification of promoter targets by Aureochrome 1a in the diatom Phaeodactylum tricornutum

Aureochromes (AUREOs) are unique blue light receptors and transcription factors found only in stramenopile algae. While each of the four AUREOs identified in the diatom Phaeodactylum tricornutum may have a specific function, PtAUREO1a has been shown to have a strong impact on overall gene regulation, when light changes from red to blue light conditions. Despite its significance, the molecular mechanism of PtAUREO1a is largely unexplored. To comprehend the overall process of gene regulation by PtAUREO1a, we conducted a series of in vitro and in vivo experiments, including pull-down assays, yeast one-hybrid experiments, and phenotypical characterization using recombinant PtAUREOs and diatom mutant lines expressing a modified PtAureo1a gene. We describe the distinct light absorption properties of four PtAUREOs and the formation of all combinations of their potential dimers. We demonstrate the capability of PtAUREO1a and 1b to activate the genes, diatom-specific cyclin 2, PtAureo1a, and PtAureo1c under both light and dark conditions. Using mutant lines expressing a modified PtAUREO1a protein with a considerably reduced light absorption, we found novel evidence that PtAUREO1a regulates the expression of PtLHCF15, which is essential for red light acclimation. Based on current knowledge, we present a working model of PtAUREO1a gene regulation properties.

Electric Field Susceptibility of Chlorophyll c Leads to Unexpected Excitation Dynamics in the Major Light-Harvesting Complex of Diatoms

Diatoms are one of the most abundant photosynthetic organisms on earth and contribute largely to atmospheric oxygen production. They contain fucoxanthin and chlorophyll-a/c binding proteins (FCPs) as light-harvesting complexes with a remarkable adaptation to the fluctuating light on ocean surfaces. To understand the basis of the photosynthetic process in diatoms, the excitation energy funneling within FCPs must be probed. A state-of-the-art multiscale analysis within a quantum mechanics/molecular mechanics framework has been employed. To this end, the chlorophyll (Chl) excitation energies within the FCP complex from the diatom Phaeodactylum tricornutum have been determined. The Chl-c excitation energies were found to be 5-fold more susceptible to electric fields than those of Chl-a pigments and thus are significantly lower in FCP than in organic solvents. This finding challenges the general belief that the excitation energy of Chl-c is always higher than that of Chl-a in FCP proteins and reveals that Chl-c molecules are much more sensitive to electric fields within protein scaffolds than in Chl-a pigments. The analysis of the linear absorption spectrum and the two-dimensional electronic spectra of the FCP complex strongly supports these findings and allows us to study the excitation transfer within the FCP complex.

Transcriptome analysis of the harmful alga Heterosigma akashiwo under a 24-hour light-dark cycle

The photoperiod, which is defined as the period of time within a 24-hour time frame that light is available, is an important environmental regulator of several physiological processes in phytoplankton, including harmful bloom-forming phytoplankton. The ichthyotoxic raphidophyte Heterosigma akashiwo is a globally distributed bloom-forming phytoplankton. Despite extensive studies on the ecological impact of H. akashiwo, the influence of the photoperiod on crucial biological processes of this species remains unclear. In this study, gene expression in H. akashiwo was analyzed over a 24-hour light-dark (14:10) treatment period. Approximately 36 % of unigenes in H. akashiwo were differentially expressed during this 24-hour treatment period, which is indicative of their involvement in the response to light-dark variation. Notably, the number of differentially expressed genes exhibited an initial increase followed by a subsequent decrease as the sampling time progressed (T0 vs. other time points). Unigenes associated with photosynthesis and photoprotection reached their peak expression levels after 2-4 h of illumination (T12-T14). In contrast, the expression of unigenes associated with DNA replication peaked at the starting point of the dark period (T0). Furthermore, although several unigenes annotated to photoreceptors displayed potential diel periodicity, genes from various photoreceptor families (such as phytochrome and cryptochrome) showed unique expression patterns. Collectively, our findings offer novel perspectives on the response of H. akashiwo to the light-dark cycle, serving as a valuable resource for investigating the physiology and ecology of this species.

Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum

Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an "atypical diatom" displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well-known physiology, alongside the steady increase in genome-enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.

Characterizing compensatory mechanisms in the absence of photoprotective qE in Chlamydomonas reinhardtii

Rapid fluctuations in the quantity and quality of natural light expose photosynthetic organisms to conditions when the capacity to utilize absorbed quanta is insufficient. These conditions can result in the production of reactive oxygen species and photooxidative damage. Non-photochemical quenching (NPQ) and alternative electron transport are the two most prominent mechanisms which synergistically function to minimize the overreduction of photosystems. In the green alga Chlamydomonas reinhardtii, the stress-related light-harvesting complex (LHCSR) is a required component for the rapid induction and relaxation of NPQ in the light-harvesting antenna. Here, we use simultaneous chlorophyll fluorescence and oxygen exchange measurements to characterize the acclimation of the Chlamydomonas LHCSR-less mutant (npq4lhcsr1) to saturating light conditions. We demonstrate that, in the absence of NPQ, Chlamydomonas does not acclimate to sinusoidal light through increased light-dependent oxygen consumption. We also show that the npq4lhcsr1 mutant has an increased sink capacity downstream of PSI and this energy flow is likely facilitated by cyclic electron transport. Furthermore, we show that the timing of additions of mitochondrial inhibitors has a major influence on plastid/mitochondrial coupling experiments.

Loss of CpFTSY Reduces Photosynthetic Performance and Affects Insertion of PsaC of PSI in Diatoms

The chloroplast signal recognition particle (CpSRP) receptor (CpFTSY) is a component of the CpSRP pathway that post-translationally targets light-harvesting complex proteins (LHCPs) to the thylakoid membranes in plants and green algae containing chloroplasts derived from primary endosymbiosis. In plants, CpFTSY also plays a major role in the co-translational incorporation of chloroplast-encoded subunits of photosynthetic complexes into the thylakoids. This role has not been demonstrated in green algae. So far, its function in organisms with chloroplasts derived from secondary endosymbiotic events has not been elucidated. Here, we report the generation and characterization of mutants lacking CpFTSY in the diatom Phaeodactylum tricornutum. We found that this protein is not involved in inserting LHCPs into thylakoid membranes, indicating that the post-translational part of the CpSRP pathway is not active in this group of microalgae. The lack of CpFTSY caused an increased level of photoprotection, low electron transport rates, inefficient repair of photosystem II (PSII), reduced growth, a strong decline in the PSI subunit PsaC and upregulation of proteins that might compensate for a non-functional co-translational CpSRP pathway during light stress conditions. The phenotype was highly similar to the one described for diatoms lacking another component of the co-translational CpSRP pathway, the CpSRP54 protein. However, in contrast to cpsrp54 mutants, only one thylakoid membrane protein, PetD of the Cytb6f complex, was downregulated in cpftsy. Our results point to a minor role for CpFTSY in the co-translational CpSRP pathway, suggesting that other mechanisms may partially compensate for the effect of a disrupted CpSRP pathway.

Conservation of triplet-triplet energy transfer photoprotective pathways in fucoxanthin chlorophyll-binding proteins across algal lineages

Detailed information on the photo-generated triplet states of diatom and haptophyte Fucoxanthin Chlorophyll-binding Proteins (FCPs and E-FCPs, respectively) have been obtained from a combined spectroscopic investigation involving Transient Absorption and Time-Resolved Electron Paramagnetic Resonance. Pennate diatom Phaeodactylum tricornutum FCP shows identical photoprotective Triplet-Triplet Energy Transfer (TTET) pathways to the previously investigated centric diatom Cyclotella meneghiniana FCP, with the same two chlorophyll a-fucoxanthin pairs that involve the fucoxanthins in sites Fx301 and Fx302 contributing to TTET in both diatom groups. In the case of the haptophyte Emilianina huxleyi E-FCP, only one of the two chlorophyll a-fucoxanthins pairs observed in diatoms, the one involving chlorophyll a409 and Fx301, has been shown to be active in TTET. Furthermore, despite the marked change in the pigment content of E-FCP with growth light intensity, the TTET pathway is not affected. Thus, our comparative investigation of FCPs revealed a photoprotective TTET pathway shared within these classes involving the fucoxanthin in site Fx301, a site exposed to the exterior of the antenna monomer that has no equivalent in Light-Harvesting Complexes from the green lineage.

Light-dependent signal transduction in the marine diatom Phaeodactylum tricornutum

Unlike most higher plants, unicellular algae can acclimate to changes in irradiance on time scales of hours to a few days. The process involves an enigmatic signaling pathway originating in the plastid that leads to coordinated changes in plastid and nuclear gene expression. To deepen our understanding of this process, we conducted functional studies to examine how the model diatom, Phaeodactylum tricornutum, acclimates to low light and sought to identify the molecules responsible for the phenomenon. We show that two transformants with altered expression of two putative signal transduction molecules, a light-specific soluble kinase and a plastid transmembrane protein, that appears to be regulated by a long noncoding natural antisense transcript, arising from the opposite strand, are physiologically incapable of photoacclimation. Based on these results, we propose a working model of the retrograde feedback in the signaling and regulation of photoacclimation in a marine diatom.

Light-driven processes: key players of the functional biodiversity in microalgae

Microalgae are prominent aquatic organisms, responsible for about half of the photosynthetic activity on Earth. Over the past two decades, breakthroughs in genomics and ecosystem biology, as well as the development of genetic resources in model species, have redrawn the boundaries of our knowledge on the relevance of these microbes in global ecosystems. However, considering their vast biodiversity and complex evolutionary history, our comprehension of algal biology remains limited. As algae rely on light, both as their main source of energy and for information about their environment, we focus here on photosynthesis, photoperception, and chloroplast biogenesis in the green alga Chlamydomonas reinhardtii and marine diatoms. We describe how the studies of light-driven processes are key to assessing functional biodiversity in evolutionary distant microalgae. We also emphasize that integration of laboratory and environmental studies, and dialogues between different scientific communities are both timely and essential to understand the life of phototrophs in complex ecosystems and to properly assess the consequences of environmental changes on aquatic environments globally.

Transcriptomic and metabolic signatures of diatom plasticity to light fluctuations

Unlike in terrestrial and freshwater ecosystems, light fields in oceans fluctuate due to both horizontal current and vertical mixing. Diatoms thrive and dominate the phytoplankton community in these fluctuating light fields. However, the molecular mechanisms that regulate diatom acclimation and adaptation to light fluctuations are poorly understood. Here, we performed transcriptome sequencing, metabolome profiling, and 13C-tracer labeling on the model diatom Phaeodactylum tricornutum. The diatom acclimated to constant light conditions was transferred to six different light conditions, including constant light (CL5d), short-term (1 h) high light (sHL1h), and short-term (1 h) and long-term (5 days) mild or severe light fluctuation conditions (mFL1h, sFL1h, mFL5d, and sFL5d) that mimicked land and ocean light levels. We identified 2,673 transcripts (25% of the total expressed genes) expressed differentially under different fluctuating light regimes. We also identified 497 transcription factors, 228 not reported previously, which exhibited higher expression under light fluctuations, including 7 with a light-sensitive PAS domain (Per-period circadian protein, Arnt-aryl hydrocarbon receptor nuclear translocator protein, Sim-single-minded protein) and 10 predicted to regulate genes related to light-harvesting complex proteins. Our data showed that prolonged preconditioning in severe light fluctuation enhanced photosynthesis in P. tricornutum under this condition, as evidenced by increased oxygen evolution accompanied by the upregulation of Rubisco and light-harvesting proteins. Furthermore, severe light fluctuation diverted the metabolic flux of assimilated carbon preferentially toward fatty acid storage over sugar and protein. Our results suggest that P. tricornutum use a series of complex and different responsive schemes in photosynthesis and carbon metabolism to optimize their growth under mild and severe light fluctuations. These insights underscore the importance of using more intense conditions when investigating the resilience of phytoplankton to light fluctuations.

Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros

Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.

A kaleidoscope of photosynthetic antenna proteins and their emerging roles

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

Transcriptional regulation of photoprotection in dark-to-light transition-More than just a matter of excess light energy

In nature, photosynthetic organisms are exposed to different light spectra and intensities depending on the time of day and atmospheric and environmental conditions. When photosynthetic cells absorb excess light, they induce nonphotochemical quenching to avoid photodamage and trigger expression of "photoprotective" genes. In this work, we used the green alga Chlamydomonas reinhardtii to assess the impact of light intensity, light quality, photosynthetic electron transport, and carbon dioxide on induction of the photoprotective genes (LHCSR1, LHCSR3, and PSBS) during dark-to-light transitions. Induction (mRNA accumulation) occurred at very low light intensity and was independently modulated by blue and ultraviolet B radiation through specific photoreceptors; only LHCSR3 was strongly controlled by carbon dioxide levels through a putative enhancer function of CIA5, a transcription factor that controls genes of the carbon concentrating mechanism. We propose a model that integrates inputs of independent signaling pathways and how they may help the cells anticipate diel conditions and survive in a dynamic light environment.

Impaired photoprotection in Phaeodactylum tricornutum KEA3 mutants reveals the proton regulatory circuit of diatoms light acclimation

Diatoms are successful phytoplankton clades able to acclimate to changing environmental conditions, including e.g. variable light intensity. Diatoms are outstanding at dissipating light energy exceeding the maximum photosynthetic electron transfer (PET) capacity via the nonphotochemical quenching (NPQ) process. While the molecular effectors of NPQ as well as the involvement of the proton motive force (PMF) in its regulation are known, the regulators of the PET/PMF relationship remain unidentified in diatoms. We generated mutants of the H⁺ /K⁺ antiporter KEA3 in the model diatom Phaeodactylum tricornutum. Loss of KEA3 activity affects the PET/PMF coupling and NPQ responses at the onset of illumination, during transients and in steady-state conditions. Thus, this antiporter is a main regulator of the PET/PMF coupling. Consistent with this conclusion, a parsimonious model including only two free components, KEA3 and the diadinoxanthin de-epoxidase, describes most of the feedback loops between PET and NPQ. This simple regulatory system allows for efficient responses to fast (minutes) or slow (e.g. diel) changes in light environment, thanks to the presence of a regulatory calcium ion (Ca²⁺ )-binding domain in KEA3 modulating its activity. This circuit is likely tuned by the NPQ-effector proteins, LHCXs, providing diatoms with the required flexibility to thrive in different ocean provinces.

The Fucoxanthin Chlorophyll a/c-Binding Protein in Tisochrysis lutea: Influence of Nitrogen and Light on Fucoxanthin and Chlorophyll a/c-Binding Protein Gene Expression and Fucoxanthin Synthesis

We observed differences in lhc classification in Chromista. We proposed a classification of the lhcf family with two groups specific to haptophytes, one specific to diatoms, and one specific to seaweeds. Identification and characterization of the Fucoxanthin and Chlorophyll a/c-binding Protein (FCP) of the haptophyte microalgae Tisochrysis lutea were performed by similarity analysis. The FCP family contains 52 lhc genes in T. lutea. FCP pigment binding site candidates were characterized on Lhcf protein monomers of T. lutea, which possesses at least nine chlorophylls and five fucoxanthin molecules, on average, per monomer. The expression of T. lutea lhc genes was assessed during turbidostat and chemostat experiments, one with constant light (CL) and changing nitrogen phases, the second with a 12 h:12 h sinusoidal photoperiod and changing nitrogen phases. RNA-seq analysis revealed a dynamic decrease in the expression of lhc genes with nitrogen depletion. We observed that T. lutea lhcx2 was only expressed at night, suggesting that its role is to protect \cells from return of light after prolonged darkness exposure.

Biochemical and molecular properties of LHCX1, the essential regulator of dynamic photoprotection in diatoms

Light harvesting is regulated by a process triggered by the acidification of the thylakoid lumen, known as nonphotochemical "energy-dependent quenching" (qE). In diatoms, qE is controlled by the light-harvesting complex (LHC) protein LHCX1, while the LHC stress-related (LHCSR) and photosystem II subunit S proteins are essential for green algae and plants, respectively. Here, we report a biochemical and molecular characterization of LHCX1 to investigate its role in qE. We found that, when grown under intermittent light, Phaeodactylum tricornutum forms very large qE, due to LHCX1 constitutive upregulation. This "super qE" is abolished in LHCX1 knockout mutants. Biochemical and spectroscopic analyses of LHCX1 reveal that this protein might differ in the character of binding pigments relative to the major pool of light-harvesting antenna proteins. The possibility of transient pigment binding or not binding pigments at all is discussed. Targeted mutagenesis of putative protonatable residues (D95 and E205) in transgenic P. tricornutum lines does not alter qE capacity, showing that they are not involved in sensing lumen pH, differently from residues conserved in LHCSR3. Our results suggest functional divergence between LHCX1 and LHCSR3 in qE modulation. We propose that LHCX1 evolved independently to facilitate dynamic tracking of light fluctuations in turbulent waters. The evolution of LHCX(-like) proteins in organisms with secondary red plastids, such as diatoms, might have conferred a selective advantage in the control of dynamic photoprotection, ultimately resulting in their ecological success.

Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e. fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identify 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggest that these FCPs can be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and the novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, have orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seems to be diversified in each diatom species, and the number of Lhcqs differs among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs is common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provide insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage.

Impact of Lhcx2 on Acclimation to Low Iron Conditions in the Diatom Phaeodactylum tricornutum

Iron is a cofactor of photosystems and electron carriers in the photosynthetic electron transport chain. Low concentrations of dissolved iron are, therefore, the predominant factor that limits the growth of phototrophs in large parts of the open sea like the Southern Ocean and the North Pacific, resulting in "high nutrient-low chlorophyll" (HNLC) areas. Diatoms are among the most abundant microalgae in HNLC zones. Besides efficient iron uptake mechanisms, efficient photoprotection might be one of the key traits enabling them to outcompete other algae in HNLC regions. In diatoms, Lhcx proteins play a crucial role in one of the main photoprotective mechanisms, the energy-dependent fluorescence quenching (qE). The expression of Lhcx proteins is strongly influenced by various environmental triggers. We show that Lhcx2 responds specifically and in a very sensitive manner to iron limitation in the diatom Phaeodactylum tricornutum on the same timescale as the known iron-regulated genes ISIP1 and CCHH11. By comparing Lhcx2 knockout lines with wild type cells, we reveal that a strongly increased qE under iron limitation is based on the upregulation of Lhcx2. Other observed iron acclimation phenotypes in P. tricornutum include a massively reduced chlorophyll a content/cell, a changed ratio of light harvesting and photoprotective pigments per chlorophyll a, a decreased amount of photosystem II and photosystem I cores, an increased functional photosystem II absorption cross section, and decoupled antenna complexes. H₂O₂ formation at photosystem I induced by high light is lowered in iron-limited cells, while the amount of total reactive oxygen species is rather increased. Our data indicate a possible reduction in singlet oxygen by Lhcx2-based qE, while the other iron acclimation phenotype parameters monitored are not affected by the amount of Lhcx2 and qE.

Transcriptomic and Metabolomic Response to High Light in the Charophyte Alga Klebsormidium nitens

The characterization of the molecular mechanisms, such as high light irradiance resistance, that allowed plant terrestralization is a cornerstone in evolutionary studies since the conquest of land by plants played a pivotal role in life evolution on Earth. Viridiplantae or the green lineage is divided into two clades, Chlorophyta and Streptophyta, that in turn splits into Embryophyta or land plants and Charophyta. Charophyta are used in evolutionary studies on plant terrestralization since they are generally accepted as the extant algal species most closely related to current land plants. In this study, we have chosen the facultative terrestrial early charophyte alga Klebsormidium nitens to perform an integrative transcriptomic and metabolomic analysis under high light in order to unveil key mechanisms involved in the early steps of plants terrestralization. We found a fast chloroplast retrograde signaling possibly mediated by reactive oxygen species and the inositol polyphosphate 1-phosphatase (SAL1) and 3'-phosphoadenosine-5'-phosphate (PAP) pathways inducing gene expression and accumulation of specific metabolites. Systems used by both Chlorophyta and Embryophyta were activated such as the xanthophyll cycle with an accumulation of zeaxanthin and protein folding and repair mechanisms constituted by NADPH-dependent thioredoxin reductases, thioredoxin-disulfide reductases, and peroxiredoxins. Similarly, cyclic electron flow, specifically the pathway dependent on proton gradient regulation 5, was strongly activated under high light. We detected a simultaneous co-activation of the non-photochemical quenching mechanisms based on LHC-like stress related (LHCSR) protein and the photosystem II subunit S that are specific to Chlorophyta and Embryophyta, respectively. Exclusive Embryophyta systems for the synthesis, sensing, and response to the phytohormone auxin were also activated under high light in K. nitens leading to an increase in auxin content with the concomitant accumulation of amino acids such as tryptophan, histidine, and phenylalanine.

Identification of sequence motifs in Lhcx proteins that confer qE-based photoprotection in the diatom Phaeodactylum tricornutum

Photosynthetic organisms in nature often experience light fluctuations. While low light conditions limit the energy uptake by algae, light absorption exceeding the maximal rate of photosynthesis may go along with enhanced formation of potentially toxic reactive oxygen species. To preempt high light-induced photodamage, photosynthetic organisms evolved numerous photoprotective mechanisms. Among these, energy-dependent fluorescence quenching (qE) provides a rapid mechanism to dissipate thermally the excessively absorbed energy. Diatoms thrive in all aquatic environments and thus belong to the most important primary producers on earth. qE in diatoms is provided by a concerted action of Lhcx proteins and the xanthophyll cycle pigment diatoxanthin. While the exact Lhcx activation mechanism of diatom qE is unknown, two lumen-exposed acidic amino acids within Lhcx proteins were proposed to function as regulatory switches upon light-induced lumenal acidification. By introducing a modified Lhcx1 lacking these amino acids into a Phaeodactylum tricornutum Lhcx1-null qE knockout line, we demonstrate that qE is unaffected by these two amino acids. Based on sequence comparisons with Lhcx4, being incapable of providing qE, we perform domain swap experiments of Lhcx4 with Lhcx1 and identify two peptide motifs involved in conferring qE. Within one of these motifs, we identify a tryptophan residue with a major influence on qE establishment. This tryptophan residue is located in close proximity to the diadinoxanthin/diatoxanthin-binding site based on the recently revealed diatom Lhc crystal structure. Our findings provide a structural explanation for the intimate link of Lhcx and diatoxanthin in providing qE in diatoms.

Metabolite Quantification by Fourier Transform Infrared Spectroscopy in Diatoms: Proof of Concept on Phaeodactylum tricornutum

Diatoms are feedstock for the production of sustainable biocommodities, including biofuel. The biochemical characterization of newly isolated or genetically modified strains is seminal to identify the strains that display interesting features for both research and industrial applications. Biochemical quantification of organic macromolecules cellular quotas are time-consuming methodologies which often require large amount of biological sample. Vibrational spectroscopy is an essential tool applied in several fields of research. A Fourier transform infrared (FTIR) microscopy-based imaging protocol was developed for the simultaneous cellular quota quantification of lipids, carbohydrates, and proteins of the diatom Phaeodactylum tricornutum. The low amount of sample required for the quantification allows the high throughput quantification on small volume cultures. A proof of concept was performed (1) on nitrogen-starved experimental cultures and (2) on three different P. tricornutum wild-type strains. The results are supported by the observation in situ of lipid droplets by confocal and brightfield microscopy. The results show that major differences exist in the regulation of lipid metabolism between ecotypes of P. tricornutum.

The Critical Studies of Fucoxanthin Research Trends from 1928 to June 2021: A Bibliometric Review

Fucoxanthin is a major carotenoid in brown macroalgae and diatoms that possesses a broad spectrum of health benefits. This review evaluated the research trends of the fucoxanthin field from 1928 to June 2021 using the bibliometric method. The present findings unraveled that the fucoxanthin field has grown quickly in recent years with a total of 2080 publications. Japan was the most active country in producing fucoxanthin publications. Three Japan institutes were listed in the top ten productive institutions, with Hokkaido University being the most prominent institutional contributor in publishing fucoxanthin articles. The most relevant subject area on fucoxanthin was the agricultural and biological sciences category, while most fucoxanthin articles were published in Marine Drugs. A total of four research concepts emerged based on the bibliometric keywords analysis: “bioactivities”, “photosynthesis”, “optimization of process’’, and “environment”. The “bioactivities” of fucoxanthin was identified as the priority in future research. The current analysis highlighted the importance of collaboration and suggested that global collaboration could be the key to valorizing and efficiently boosting the consumer acceptability of fucoxanthin. The present bibliometric analysis offers valuable insights into the research trends of fucoxanthin to construct a better future development of this treasurable carotenoid.

Modulation of Phototropin Signalosome with Artificial Illumination Holds Great Potential in the Development of Climate-Smart Crops

Changes in environmental conditions like temperature and light critically influence crop production. To deal with these changes, plants possess various photoreceptors such as Phototropin (PHOT), Phytochrome (PHY), Cryptochrome (CRY), and UVR8 that work synergistically as sensor and stress sensing receptors to different external cues. PHOTs are capable of regulating several functions like growth and development, chloroplast relocation, thermomorphogenesis, metabolite accumulation, stomatal opening, and phototropism in plants. PHOT plays a pivotal role in overcoming the damage caused by excess light and other environmental stresses (heat, cold, and salinity) and biotic stress. The crosstalk between photoreceptors and phytohormones contributes to plant growth, seed germination, photo-protection, flowering, phototropism, and stomatal opening. Molecular genetic studies using gene targeting and synthetic biology approaches have revealed the potential role of different photoreceptor genes in the manipulation of various beneficial agronomic traits. Overexpression of PHOT2 in Fragaria ananassa leads to the increase in anthocyanin content in its leaves and fruits. Artificial illumination with blue light alone and in combination with red light influence the growth, yield, and secondary metabolite production in many plants, while in algal species, it affects growth, chlorophyll content, lipid production and also increases its bioremediation efficiency. Artificial illumination alters the morphological, developmental, and physiological characteristics of agronomic crops and algal species. This review focuses on PHOT modulated signalosome and artificial illumination-based photo-biotechnological approaches for the development of climate-smart crops.

Robust Strategy for Photoprotection in the Light-Harvesting Antenna of Diatoms: A Molecular Dynamics Study

Diatoms generate a large portion of the oxygen produced on earth due to their exceptional light-harvesting properties involving fucoxanthin and chlorophyll-binding proteins (FCP). At the same time, an efficient adaptation of these complexes to fluctuating light conditions is necessary to protect the diatoms against photodamage. So far, structural and dynamic data for the interaction between FCP and the photoprotective LHCX family of proteins in diatoms are lacking. In this computational study, we provide a structural basis for a remarkable pH-dependent adaptation at the molecular level. Upon binding of the LHCX1 protein to the FCP complex together with a change in pH, conformational changes within the FCP protein result in a variation of the electronic coupling in a specific chlorophyll-fucoxanthin pair, leading to a change in the exciton transfer rate by almost an order of magnitude. A common strategy for photoprotection between diatoms and higher plants is identified and discussed.

SPX-related genes regulate phosphorus homeostasis in the marine phytoplankton, Phaeodactylum tricornutum

Phosphorus (P) is an essential nutrient for marine phytoplankton. Maintaining intracellular P homeostasis against environmental P variability is critical for phytoplankton, but how they achieve this is poorly understood. Here we identify a SPX gene and investigate its role in Phaeodactylum tricornutum. SPX knockout led to significant increases in the expression of phosphate transporters, alkaline phosphatases (the P acquisition machinery) and phospholipid hydrolases (a mechanism to reduce P demand). These demonstrate that SPX is a negative regulator of both P uptake and P-stress responses. Furthermore, we show that SPX regulation of P uptake and metabolism involves a phosphate starvation response regulator (PHR) as an intermediate. Additionally, we find the SPX related genes exist and operate across the phytoplankton phylogenetic spectrum and in the global oceans, indicating its universal importance in marine phytoplankton. This study lays a foundation for better understanding phytoplankton adaptation to P variability in the future changing oceans.

The fine-tuning of NPQ in diatoms relies on the regulation of both xanthophyll cycle enzymes

Diatoms possess an efficient mechanism to dissipate photons as heat in conditions of excess light, which is visualized as the Non-Photochemical Quenching of chlorophyll a fluorescence (NPQ). In most diatom species, NPQ is proportional to the concentration of the xanthophyll cycle pigment diatoxanthin formed from diadinoxanthin by the diadinoxanthin de-epoxidase enzyme. The reverse reaction is performed by the diatoxanthin epoxidase. Despite the xanthophyll cycle's central role in photoprotection, its regulation is not yet well understood. The proportionality between diatoxanthin and NPQ allowed us to calculate the activity of both xanthophyll cycle enzymes in the model diatom Phaeodactylum tricornutum from NPQ kinetics. From there, we explored the light-dependency of the activity of both enzymes. Our results demonstrate that a tight regulation of both enzymes is key to fine-tune NPQ: (i) the rate constant of diadinoxanthin de-epoxidation is low under a light-limiting regime but increases as photosynthesis saturates, probably due to the thylakoidal proton gradient ΔpH (ii) the rate constant of diatoxanthin epoxidation exhibits an optimum under low light and decreases in the dark due to an insufficiency of the co-factor NADPH as well as in higher light through an as yet unresolved inhibition mechanism, that is unlikely to be related to the ΔpH. We observed that the suppression of NPQ by an uncoupler was due to an accelerated diatoxanthin epoxidation enzyme rather than to the usually hypothesized inhibition of the diadinoxanthin de-epoxidation enzyme.

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.

Trophic Transition Enhanced Biomass and Lipid Production of the Unicellular Green Alga Scenedesmus acuminatus

Microalgal heterotrophic cultivation is an emerging technology that can enable producing high cell-density algal cell cultures, which can be coupled with photoautotrophic cultivation for valuable chemicals such as lipids manufacturing. However, how the heterotrophically grown algal cells respond to the lipid-inducing conditions has not been fully elucidated so far. In this study, when the heterotrophically grown Scenedesmus acuminatus cells were subjected to the high light (HL) and nitrogen-limited (NL) conditions, both the biomass and lipid productivity were enhanced as compared to that of the photoautotrophically grown counterparts. The chlorophyll a fluorometry analysis showed that the Fv/Fm and Y(II) of the heterotrophically grown cells subjected to the HL and NL conditions was recovered to the maximum value of 0.75 and 0.43, respectively, much higher than those of the photoautotrophically grown cells under the same stress conditions. Transcriptomic analysis revealed that heterotrophically grown cells fully expressed the genes coding for the photosystems proteins, including the key photoprotective proteins D1, PsbS, light-harvesting-complex (LHC) I and LHC II. Meanwhile, downregulation of the carotenoid biosynthesis and upregulation of the glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle and oxidative phosphorylation pathways were observed when the heterotrophically grown cells were subjected to the HL and N-limited conditions for lipid production. It was deduced that regulation of these pathways not only enhanced the light utilization but also provided the reducing power and ATP by which the biomass accumulation was significantly elevated. Besides, upregulation of the acetyl-CoA carboxylase/biotin carboxylase, digalactosyl diacylglycerol synthase and diacylglycerol acyltransferase 2 encoding genes may be attributable to the enhanced lipid production. Understanding the cellular responses during the trophic transition process could guide improvement of the strength of trophic transition enhancing microalgal biomass and lipid production.

Rapid photoacclimation during episodic deep mixing augments the biological carbon pump

Episodic deep mixing events are one component of the biological carbon pump that physically transports organic carbon into the mesopelagic. Episodic deep mixing also disrupts summertime thermal stratification thereby changing the light field and nutrient concentrations available for phytoplankton growth. Phytoplankton survival and growth below the mixed layer following restratification depends on how rapidly cells can employ a variety of photoacclimation processes in response to the environmental changes. To compare the relative timescales of summertime episodic deep mixing events with the timescales of phytoplankton photoacclimation processes, we first analyzed autonomous float data to survey the frequency and magnitude of deep mixing events in the western North Atlantic Ocean. Next, we simulated a sustained deep mixing event in the laboratory and measured rates of acclimation processes ranging from light harvesting to growth in a model diatom and green alga. In both algae increases in chlorophyll (Chl) were coupled to growth, but growth of the green alga lagged the diatom by about a day. In float profiles, significant increases in Chl and phytoplankton carbon (C _phyto) were detected below the mixed layer following episodic deep mixing events. These events pose a previously unrecognized source of new production below the mixed layer that can significantly boost the amount of carbon available for export to the deep ocean.

Regulation of Phaeodactylum plastid gene transcription by redox, light, and circadian signals

Diatoms are a diverse group of photosynthetic unicellular algae with a plastid of red-algal origin. As prolific primary producers in the ocean, diatoms fix as much carbon as all rainforests combined. The molecular mechanisms that contribute to the high photosynthetic productivity and ecological success of diatoms are however not yet fully understood. Using the model diatom Phaeodactylum tricornutum, here we show rhythmic transcript accumulation of plastid psaA, psbA, petB, and atpB genes as driven by a free running circadian clock. Treatment with the electron transport inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea overrides the circadian signal by markedly downregulating transcription of psaA, petB, and atpB genes but not the psbA gene. Changes in light quantity produce little change in plastid gene transcription while the effect of light quality seems modest with only the psaA gene responding in a pattern that is dependent on the redox state of the plastoquinone pool. The significance of these plastid transcriptional responses and the identity of the underlying genetic control systems are discussed with relevance to diatom photosynthetic acclimation.

Role of an ancient light-harvesting protein of PSI in light absorption and photoprotection

Diverse algae of the red lineage possess chlorophyll a-binding proteins termed LHCR, comprising the PSI light-harvesting system, which represent an ancient antenna form that evolved in red algae and was acquired through secondary endosymbiosis. However, the function and regulation of LHCR complexes remain obscure. Here we describe isolation of a Nannochloropsis oceanica LHCR mutant, named hlr1, which exhibits a greater tolerance to high-light (HL) stress compared to the wild type. We show that increased tolerance to HL of the mutant can be attributed to alterations in PSI, making it less prone to ROS production, thereby limiting oxidative damage and favoring growth in HL. HLR1 deficiency attenuates PSI light-harvesting capacity and growth of the mutant under light-limiting conditions. We conclude that HLR1, a member of a conserved and broadly distributed clade of LHCR proteins, plays a pivotal role in a dynamic balancing act between photoprotection and efficient light harvesting for photosynthesis.

LHCR proteins are ancient chlorophyll a-binding antennas that evolved in diverse algae of the red lineage. Here Lu et al. characterize a red lineage LHCR mutant and show reduced oxidative damage in high light but attenuated growth under low light, thus demonstrating how LHCR proteins impact the balance between photoprotection and light harvesting.

The molecular response mechanisms of a diatom Thalassiosira pseudonana to the toxicity of BDE-47 based on whole transcriptome analysis

Polybrominated diphenyl ethers (PBDEs) are ubiquitously distributed persistent organic pollutants (POPs) in marine environments. Phytoplankton are the entrance of PBDEs entering to biotic environments from abiotic environments, while the responding mechanisms of phytoplankton to PBDEs have not been full established. Therefore, we chose the model diatom Thalassiosira pseudonana in this study, by integrating whole transcriptome analysis with physiological-biochemical data, to reveal the molecular responding mechanisms of T. pseudonana to the toxicity of BDE-47. Our results indicated the changes of genes expressions correlated to the physiological-biochemical changes, and there were multiple molecular mechanisms of T. pseudonana responding to the toxicity of BDE-47: Gene expressions evidence explained the suppression of light reaction and proved the occurrence of cellular oxidative stress; In the meanwhile, up-regulations of genes in pathways involving carbon metabolisms happened, including the Calvin cycle, glycolysis, TCA cycle, fatty acid synthesis, and triacylglycerol synthesis; Lastly, DNA damage was found and three outcome including DNA repair, cell cycle arrest and programmed cell death (PCD) happened, which could finally inhibit the cell division and population growth of T. pseudonana. This study presented the most complete molecular responding mechanisms of phytoplankton cells to PBDEs, and provided valuable information of various PBDEs-sensitive genes with multiple functions for further research involving organic pollutants and phytoplankton.

Pre-purification of diatom pigment protein complexes provides insight into the heterogeneity of FCP complexes

BACKGROUND

Although our knowledge about diatom photosynthesis has made huge progress over the last years, many aspects about their photosynthetic apparatus are still enigmatic. According to published data, the spatial organization as well as the biochemical composition of diatom thylakoid membranes is significantly different from that of higher plants.

RESULTS

In this study the pigment protein complexes of the diatom Thalassiosira pseudonana were isolated by anion exchange chromatography. A step gradient was used for the elution process, yielding five well-separated pigment protein fractions which were characterized in detail. The isolation of photosystem (PS) core complex fractions, which contained fucoxanthin chlorophyll proteins (FCPs), enabled the differentiation between different FCP complexes: FCP complexes which were more closely associated with the PSI and PSII core complexes and FCP complexes which built-up the peripheral antenna. Analysis by mass spectrometry showed that the FCP complexes associated with the PSI and PSII core complexes contained various Lhcf proteins, including Lhcf1, Lhcf2, Lhcf4, Lhcf5, Lhcf6, Lhcf8 and Lhcf9 proteins, while the peripheral FCP complexes were exclusively composed of Lhcf8 and Lhcf9. Lhcr proteins, namely Lhcr1, Lhcr3 and Lhcr14, were identified in fractions containing subunits of the PSI core complex. Lhcx1, Lhcx2 and Lhcx5 proteins co-eluted with PSII protein subunits. The first fraction contained an additional Lhcx protein, Lhcx6_1, and was furthermore characterized by high concentrations of photoprotective xanthophyll cycle pigments.

CONCLUSION

The results of the present study corroborate existing data, like the observation of a PSI-specific antenna complex in diatoms composed of Lhcr proteins. They complement other data, like e.g. on the protein composition of the 21 kDa FCP band or the Lhcf composition of FCPa and FCPb complexes. They also provide interesting new information, like the presence of the enzyme diadinoxanthin de-epoxidase in the Lhcx-containing PSII fraction, which might be relevant for the process of non-photochemical quenching. Finally, the high negative charge of the main FCP fraction may play a role in the organization and structure of the native diatom thylakoid membrane. Thus, the results present an important contribution to our understanding of the complex nature of the diatom antenna system.

Freezing, Melting, and Light Stress on the Photophysiology of Ice Algae: Ex Situ Incubation of the Ice Algal diatom Fragilariopsis cylindrus (Bacillariophyceae) Using an Ice Tank

Sea ice algae contribute up to 25% of the primary productivity of polar seas and seed large-scale ice-edge blooms. Fluctuations in temperature, salinity, and light associated with the freeze/thaw cycle can significantly impact the photophysiology of ice-associated taxa. The effects of multiple co-stressors (i.e., freezing temperature and high brine salinity or sudden high light exposure) on the photophysiology of ice algae were investigated in a series of ice tank experiments with the polar diatom Fragilariopsis cylindrus under different light intensities. When algal cells were frozen into the ice, the maximum quantum yield of photosystem II photochemistry (PSII; F_v /F_m ) decreased possibly due to the damage of PSII reaction centers and/or high brine salinity stress suppressing the reduction capacity downstream of PSII. Expression of the rbcL gene was highly up-regulated, suggesting that cells initiated strategies to enhance survival upon freezing in. Algae contained within the ice-matrix displayed similar levels of F_v /F_m regardless of the light treatments. Upon melting out, cells were exposed to high light (800 μmol photons · m^-2  · s^-1 ), resulting in a rapid decline in F_v /F_m and significant up-regulation of non-photochemical quenching (NPQ). These results suggest that ice algae employed safety valves (i.e., NPQ) to maintain their photosynthetic capability during the sudden environmental changes. Our results infer that sea ice algae are highly adaptable when exposed to multiple co-stressors and that their success can, in part, be explained by the ability to rapidly modify their photosynthetic competence - a key factor contributing to algal bloom formation in the polar seas.

Sexual reproduction potential implied by functional analysis of SPO11 in Phaeodactylum tricornutum

Phaeodactylum tricornutum is a model microalgae that is widely used to study diatom physiology and ecology. Since the meiotic process and sexual cycle have never been observed directly, P. tricornutum has been considered to be an asexual species. However, phylogenetic analysis of the P. tricornutum genome has revealed a series of meiosis-specific gene homologues in this species. We identified two copies of differently transcribed SPO11 homologs that contain the conserved motifs of Winged-helix and Toprim domains. The homolog PtSPO11-3 interacts with TopoVIB in yeast two-hybrid analysis, whereas the homolog PtSPO11-2 could rescue the sporulation defect of a Spo11 yeast mutant strain. PtSPO11-2 was also found to be significantly up-regulated at low temperatures in P. tricornutum and its key catalytic residue was important to the homolog's function in sporulation. The results herein provide positive clue that meiosis and sexual reproduction could exist in this diatom.

Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle

Light is an important factor for the growth of planktonic organisms, and many of them depend on the diurnal light/dark cycle to regulate key metabolic processes. So far, most of the diel responses were only studied in single species or marine and large lake communities. Yet, we lack information on whether these processes are regulated similarly in small aquatic systems such as ponds. Here, we investigated the activity of a microeukaryotic community from a temperate, small freshwater pond in response to the diurnal cycle. For this, we took samples at midday and night during the Central European summer. We extracted pigments and RNA from samples and the sequencing of eukaryotic transcripts allowed us to obtain day and night metatranscriptomes. Differentially expressed transcripts primarily corresponded to photosynthesis-related and translational processes, and were found to be upregulated at midday with high light conditions compared to darkness. Unique gene ontology classes were found at each respective condition. During the day, ontology classes including photoreception for photosynthesis, defense, and stress mechanisms dominated, while motility, ribosomal assembly and other large, energy-consuming processes were restricted to the night. Euglenophyta and Chlorophyta dominated the active phototrophic community, as shown by the pigment composition analysis. Regarding the gene expression patterns, we could confirm that the pond community appears to follow similar diurnal dynamics as those described for larger aquatic ecosystems. Overall, combining pigment analyses, metatranscriptomics, and data on physicochemical factors yielded considerably more insight into the metabolic processes performed by the microeukaryotic community of a small freshwater ecosystem.