The Evolution of Modern Eukaryotic Phytoplankton

Metabolomic and physiological analyses of two picochlorophytes from distinct oceanic latitudes under future ocean acidification and warming

Phytoplankton are cosmopolitan marine photosynthetic organisms that are vital to biogeochemical cycles and marine ecosystems. The current rise in atmospheric CO2 and surface ocean temperatures are poised to disrupt the ecological niches of phytoplankton. Picochlorophytes, a broad taxon of small green eukaryotic phytoplankton, have been shown to perform well under future rising oceanic CO2 and temperature scenarios. This study investigates the acclimation responses of cosmopolitan picochlorophytes from the Chlorella-lineage under high CO2 (1000 p.p.m.) and a rise of 4 °C (8 °C - polar picochlorophyte; 32 °C, tropical picochlorophyte). In order to determine how the future ocean warming and acidification might affect picochlorophytes, a polar strain of Chlorella and a tropical Parachlorella were selected, and their physiology and GCMS-based metabolomics were investigated. Growth rate and cellular dimensions (diameter, volume, and surface area) of Chlorella significantly increased in all environmental future scenarios compared to Parachlorella. Photosynthetic parameters of the picochlorophytes studied showed acclimation, with high temperature and high CO2 triggering the adaptation of Fv/Fm, NPQmax, and Ek of Chlorella and Parachlorella, respectively. High CO2 induced the most changes in the Chlorella metabolome, altering the levels of metabolites related to amino acids and their derivatives, glutathione production, carbohydrates, and photochemical quenching. Combined high CO2/temperature altered Parachlorella's metabolome, though with a small number of biomarkers detected. This study provided evidence to support the hypothesis that picochlorophytes could thrive in a more acidified and warmer ocean.

Cathepsin X is a conserved cell death protein involved in algal response to environmental stress

Phytoplankton are responsible for half of the global photosynthesis and form vast blooms in aquatic ecosystems. Bloom demise fuels marine microbial life and is suggested to be mediated by programmed cell death (PCD) induced by diverse environmental stressors. Despite its importance, the molecular basis for algal PCD remains elusive. Here, we reveal novel PCD genes conserved across distant algal lineages using cell-to-cell heterogeneity in the response of the diatom Phaeodactylum tricornutum to oxidative stress. Comparative transcriptomics of sorted sensitive and resilient subpopulations following oxidative stress revealed genes directly linked to their contrasting fates of cell death and survival. Comparing these genes with those found in a large-scale mutant screen in the green alga Chlamydomonas reinhardtii identified functionally relevant conserved PCD gene candidates, including the cysteine protease cathepsin X/Z (CPX). CPX mutants in P. tricornutum CPX1 and C. reinhardtii CYSTEINE ENDOPEPTIDASE 12 (CEP12) exhibited resilience to oxidative stress and infochemicals that induce PCD, supporting a conserved function of these genes in algal PCD. Phylogenetic and predictive structural analyses show that CPX is highly conserved in eukaryotes, and algae exhibit strong structural similarity to human Cathepsin X/Z (CTSZ), a protein linked to various diseases. CPX is expressed by diverse algae across the oceans and correlates with upcoming demise events during toxic Pseudo-nitzschia blooms, providing support for its ecological significance. Elucidating PCD components in algae sheds light on the evolutionary origin of PCD in unicellular organisms and on the cellular strategies employed by the population to cope with stressful conditions.

Structure of a photosystem I supercomplex from Galdieria sulphuraria close to an ancestral red alga

Red algae exhibit unique photosynthetic adaptations, characterized by photosystem I (PSI) supercomplexes containing light-harvesting complexes (LHCs), forming PSI-LHCI supercomplexes. In this study, we solved the PSI-LHCI structure of Galdieria sulphuraria NIES-3638 at 2.19-angstrom resolution using cryo-electron microscopy, revealing a PSI monomer core associated with seven LHCI subunits. Structural analysis uncovered the absence of phylloquinones, the common secondary electron acceptor in PSI of photosynthetic organisms, suggesting adaptation to a benzoquinone-like molecule. Phylogenetic analysis suggests that G. sulphuraria retains traits characteristic of an ancestral red alga, including distinctive LHCI binding and interaction patterns. Variations in LHCI composition and interactions across red algae, particularly in red-lineage chlorophyll a/b-binding-like protein and red algal LHCs, highlight evolutionary divergence and specialization. These findings not only deepen our understanding of red algal PSI-LHCI diversification but also enable us to predict features of an ancestral red algal PSI-LHCI supercomplex, providing a framework to explore evolutionary adaptations from an ancestral red alga.

Urbanization leads to convergent succession and homogenization of phytoplankton functional traits in a subtropical watershed over 11 years

Urbanization can significantly drive biodiversity loss in river ecosystems, yet the underlying mechanisms require further study. Here, we used a trait-based approach to investigate temporal succession and variation in the dissimilarity of phytoplankton community functional traits along an urbanizing subtropical river over 11 years - during which time the downstream of catchment underwent rapid urbanization. Our results indicated that urbanization altered the interannual succession of phytoplankton. The phytoplankton communities in the rural region were mainly shaped by a specialist trade-off between extreme lotic strategies (single cell, high maximum growth rate and high silica demand) in river habitat, and extreme lentic strategies (colonial, toxin production and nitrogen fixation abilities) in reservoir habitat. Conversely, in the urban region, generalist strategies with intermediate trait combinations (moderate mobility and mixotrophic ability) dominated the communities in both river and reservoir habitats. Time-lag analysis of functional dissimilarity showed lower, or even no significant variations of functional beta diversity in the urban region. Further decomposition of functional beta diversity indicated a reduced rate of functional turnover in urban river compared with that in rural river and a decrease in functional nestedness in urban reservoir. Paired differences between river and reservoir in the urban region exhibited convergent succession by functional turnover. The convergent succession and homogenization in the urban region made the variation in phytoplankton functional structure more unpredictable in a random forest model, and diminished the relationship between functional dissimilarity and environmental factors compared to the rural region. Our study shows how urbanization shapes the phytoplankton functional structure and causes homogenization in functional trait composition. The insight gained enhance our ability to assess and predict the environmental impacts of urbanization on aquatic ecosystems.

Aggregation-Induced Excitation-Energy Quenching in Fucoxanthin Chlorophyll a/c-Binding Proteins from the Diatom Phaeodactylum tricornutum

Light-harvesting complexes (LHCs) are vital for photosynthesis, capturing light energy and transferring it to photosystems I and II. In diatoms, fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) function as unique LHCs. In this study, we examined the spectral properties of untreated and aggregated FCP complexes (Untreated-FCP and Aggregated-FCP, respectively) from the diatom Phaeodactylum tricornutum. Fluorescence quantum yields and excitation-energy transfer pathways were evaluated using absolute fluorescence spectroscopy and fluorescence decay-associated (FDA) spectra. Aggregation of FCPs significantly enhanced excitation-energy quenching, with a marked decrease in fluorescence quantum yield from 37.6% in Untreated-FCP to 4.8% in Aggregated-FCP. The FDA spectra of Aggregated-FCP showed prominent fluorescence decays with relatively high amplitudes with time constants of 310 ps and 1.6 ns, reflecting distinct alterations in excitation-energy transfer among Chls upon aggregation. These changes were accompanied by long-wavelength shifts and broadening of the fluorescence-emission spectra, characteristics typically observed in aggregated LHCs in land plants. Our results suggest that the structural rearrangement of pigment molecules, driven by changes in Chl-Chl and Chl-Car interactions, underlies the observed excitation-energy quenching upon aggregation. This study provides key insights into the quenching mechanisms of diatom FCPs, offering broader implications for understanding energy regulation in photosynthetic systems.

Resolving the Snowball Earth conundrum: the role of marine dissolved organic carbon pool

The Cryogenian Sturtian (717-660 Ma) and Marinoan glacial deposits (∼650-635 Ma), typically consisting of alternating layers of glaciogenic diamictite and clast-free lithofacies, indicate dynamic glaciers or glacial-interglacial cycles during the global glaciations. This may result from ice sublimation in tropics under a Snowball Earth condition. However, this model fails to explain the deposition patterns observed in mid-latitude continents. We propose the presence of unfrozen oceans while the continents are covered, i.e., the icy-continents. The open-ocean condition requires low atmospheric pCO2 level. We argued that the mantle CO2 degassing could be counterbalanced by a growing pool of dissolved organic carbon (DOC) in the deep ocean, maintaining a small marine dissolved inorganic carbon (DIC) pool and a low atmospheric pCO2 level. The persistent marine productivity in the open ocean would support the expanded DOC pool due to reduced ocean ventilation and limited terrestrial inputs of oxidants. However, the global glaciation with open oceans was climatically unstable. The fluctuation of the DOC pool on a local or regional scale likely contributed to the frequent glacial-interglacial oscillations recorded in the rock records. Additionally, the expansion of the DOC pool removed seawater nutrients, e.g., phosphorus (P), and insufficient nutrient supply prevented the transfer of mantle-degassing carbon as DOC, ultimately leading to the termination of global glaciation. The turnover of the DOC pool, caused by deep ocean ventilation in the deglacial period, significantly increased the atmospheric pCO2 level. This event was followed by intense continental weathering, increased seawater pH, recovery of primary productivity, cap carbonate precipitation, and eventually, the emergence of new life forms and innovations in the biosphere.

Structures of PSI-FCPI from Thalassiosira pseudonana grown under high light provide evidence for convergent evolution and light-adaptive strategies in diatom FCPIs

Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for light harvesting and energy quenching under marine environments. Here we report two cryo-electron microscopic structures of photosystem I (PSI) with either 13 or five fucoxanthin chlorophyll a/c-binding protein Is (FCPIs) at 2.78 and 3.20 Å resolutions from Thalassiosira pseudonana grown under high light (HL) conditions. Among them, five FCPIs are stably associated with the PSI core, these include Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3. The eight additional Lhcr-type FCPIs are loosely associated with the PSI core and detached under the present purification conditions. The pigments of this centric diatom showed a higher proportion of chlorophylls a, diadinoxanthins, and diatoxanthins; some of the chlorophyll as and diadinoxanthins occupy the locations of fucoxanthins found in the huge PSI-FCPI from another centric diatom Chaetoceros gracilis grown under low-light conditions. These additional chlorophyll as may form more energy transfer pathways and additional diadinoxanthins may form more energy dissipation sites relying on the diadinoxanthin-diatoxanthin cycle. These results reveal the assembly mechanism of FCPIs and corresponding light-adaptive strategies of T. pseudonana PSI-FCPI, as well as the convergent evolution of the diatom PSI-FCPI structures.

Nutrient stress triggers sugar-mediated carotenoid production in algal-bacterial interactions

This study examined the impact of co-culturing Chlorella saccharophila (UTEX247) with Exiguobacterium sp. strain AMK1 on carotenoid production under nitrate-depleted conditions and 3% CO₂ supplementation. The co-culture significantly enhanced the productivity of lutein (238.31 µg.L⁻¹d⁻¹), zeaxanthin (220.72 µg.L⁻¹d⁻¹), violaxanthin (185.42 µg.L⁻¹d⁻¹), and antheraxanthin (84.07 µg.L⁻¹d⁻¹). Compared to nitrate-repleted mono-cultures, these carotenoids increased by 3.54-fold, 4.81-fold, 12.28-fold, and 9.34-fold, respectively. The violaxanthin cycle, activated by CO₂ supplementation, resulted in higher zeaxanthin production, verified through HPLC analysis. Metabolic profiling highlighted a notable rise in sucrose, an algal-specific metabolite, in the co-culture, reflecting enhanced carbon metabolism and carotenoid synthesis. Conversely, trehalose levels were significantly higher in the bacterial mono-culture (297.77 µg.mL⁻¹) than in the co-culture (88.84 µg.mL⁻¹), showing a 1.68-fold reduction as confirmed by GC-MS/MS. This suggests trehalose as a stress marker, with its reduction indicating mutualistic interactions between algal and bacterial. Overall, the co-culture strategy emerges as a promising approach to activate unexpressed pathways, generate novel metabolites, and enhance yields of valuable carotenoids like lutein and zeaxanthin. This aligns with the principles of a circular bioeconomy, leveraging bacterial biofertilizers, valorizing CO₂, and minimizing chemical dependency, thus offering potential for biorefinery applications.

The chemical ecology and physiological functions of type I polyketide natural products: the emerging picture

Covering: up to 2024.For many years, the value of complex polyketides lay in their medical properties, including their antibiotic and antifungal activities, with little consideration paid to their native functions. However, more recent evidence gathered from the study of inter-organismal interactions has revealed the influence of these metabolites upon the ecological adaptation and distribution of their hosts, as well as their modes of communication. The increasing number of sequenced genomes and associated transcriptomes has also unveiled the widespread occurrence of the underlying biosynthetic enzymes across all kingdoms of life, and the important contributions they make to physiological events specific to each organism. This review depicts the diversity of roles fulfilled by type I polyketides, particularly in light of studies carried out during the last decade, providing an initial overall picture of their diverse functions.

John Raven, FRS, FRSE: a truly great innovator in plant physiology, photosynthesis and much more

This is a tribute to a truly inspirational plant biologist, Prof. John A. Raven, FRS, FRSE (25th June 1941- 23rd May 2024), who died at the age of 82. He was a leader in the field of evolution and physiology of algae and land plants. His research touched on many areas including photosynthesis, ion transport, carbon utilisation, mineral use, such as silicon, iron and molybdenum, the evolution of phytoplankton, the evolution of root systems, the impact of global change, especially on the acidification of the oceans, carbon gain and water use in early land plants, and ways of detecting extraterrestrial photosynthesis. Beginning his research career in the Botany School, University of Cambridge, John studied ion uptake in a giant algal cell. This was at the time of great strides brought about by Peter Mitchell (1920-1992) in elucidating the role of energy generation in mitochondria and chloroplasts and the coupling of ion transport systems to energy generation. With Enid MacRobbie and Andrew Smith, John pioneered early work on the involvement of ion transport in the growth and metabolism of plant cells.On leaving Cambridge John took up a lectureship at the University of Dundee in 1971, where he was still attached upon his death. His primary focus over the years, with one of us (Paul Falkowski), was on phytoplankton, the photosynthetic microalgae of the oceans. Still, his publication list of 5 books and over 600 scientific papers spans a very broad range. The many highly cited papers (see Table 1) attest to an outstanding innovator, who influenced a multitude of students and coworkers and a very wide readership worldwide. At the personal level, John Raven was a wonderful human being; he had an extraordinary memory, dredging up facts and little-known scientific papers, like a scientific magician, but at the same time making humorous jokes and involving his colleagues in fun and sympathetic appreciation. Table 1 Ten best cited articles (from google scholar) Citations Date Aquatic Photosynthesis, 3rd Edition P.G. Falkowski & J.A. Raven Princeton University Press, 2013 3854 2013 The evolution of modern eukaryotic phytoplankton P.G. Falkowski, M.E. Katz, A.H. Knoll, A. Quigg, J.A. Raven, et al Science 305, 354-360 1790 2004 CO2 concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution M. Giordano, J. Beardall & J.A. Raven Annu. Rev. Plant Biol. 56 (1), 99-131 1648 2005 Algae as nutritional food sources: revisiting our understanding M.L. Wells, P. Potin, J.S. Craigie, J.A. Raven, S.S. Merchant, et al Journal of applied phycology 29, 949-982 1527 2017 Plant Nutrient acquisition strategies change with soil age H. Lambers, J.A. Raven, G.R. Shaver & S.E. Smith Trends in ecology & evolution 23, 95-103 1488 2008 Ocean acidification due to increasing atmospheric carbon dioxide J. Raven, K. Caldeira, H. Elderfield, O. Hoegh-Guldberg, P. Liss, et al The Royal Society, Policy Document, June 2005 1470 2005 Phytoplankton in a changing world: cell size and elemental stoichiometry Z.V. Finkel, J. Beardall, K.J. Flynn, A. Quigg, T.A.V. Rees & J.A. Raven Journal of plankton research 32, 119-137 1198 2010 Opportunities for improving phosphorus efficiency in crop plants E.J. Veneklaas, H. Lambers, J. Bragg, P.M. Finnegan, C.E. Lovelock, et al New phytologist 195, 306-320 951 2012 Adaptation of unicellular algae to irradiance: an analysis of strategies K. Richardson, J. Beardall & J.A. Raven New Phytologist 93, 157-191 914 1983 Nitrogen assimilation and transport in vascular land plants in relation to Intracellular pH regulation J.A. Raven & F.A. Smith New Phytologist 76, 415-431 893 1976 Temperature and algal growth J.A. Raven & R.J. Geider New phytologist 110, 441-461 867 1988 The role of trace metals in photosynthetic electron transport in O2 -evolving organisms J.A. Raven, M.C.W. Evans & R.E. Korb Photosynthesis Research 60, 111-150 840 1999.

Epipelagic community as prominent biosensor for sub-micron and nanoparticles uptake: Insights from field and laboratory experiments

Nowadays, ENMs/NPLs particles have not yet been extensively measured in the environment, but there is increased concern that this size fraction may be more widely distributed and hazardous than larger-sized particles. This study aimed to examine the bioaccumulation potential of engineered nanomaterials and nanoplastics (ENMs/NPLs) across marine food webs, focusing on plankton communities and commercial fish species (Engraulis encrasicolus and Scomber colias) from the Gulf of Naples. Laboratory experiments on plankton assemblages exposed to fluorescent polystyrene nanoplastics (PS-NPs, 100 nm) for 24h at concentrations ranging from 0.01 to 10 mg/L confirmed nanoplastic uptake in phytoplankton and zooplankton, indicating a dose-dependent internalization in plankton communities. Notably, in natural samples no particles were detected in fish muscle or liver tissues, suggesting limited translocation. Unexpectedly, titanium oxide particles (<1 μm) were found in natural phytoplankton, highlighting the potential presence of other nanoparticles in marine systems. These findings suggest that, despite detection challenges, plankton communities are major biosensors of ENMs/NPs contamination and highlight the need for ongoing environmental monitoring to assess ecological impacts and potential risks of nanoparticle bioaccumulation in marine ecosystems.

CyanoTag: Discovery of protein function facilitated by high-throughput endogenous tagging in a photosynthetic prokaryote

Despite their importance to aquatic ecosystems, global carbon cycling, and sustainable bioindustries, the genomes of photosynthetic bacteria contain large numbers of uncharacterized genes. Here, we develop high-throughput endogenous fluorescent protein tagging in the cyanobacterium Synechococcus elongatus PCC 7942. From 400 targets, we successfully tag over 330 proteins corresponding to >10% of the proteome. We use this collection to determine subcellular localization, relative protein abundances, and protein-protein interaction networks, providing biological insights into diverse processes-from photosynthesis to cell division. We build a high-confidence protein-protein interaction map for the major components of photosynthesis, associating previously uncharacterized proteins with different complexes and processes. In response to light changes, we visualize, on second timescales, the reversible formation, growth, and fusion of puncta by two Calvin cycle proteins, suggesting that biomolecular condensation provides spatiotemporal control of the Calvin cycle in cyanobacteria. We envision that these insights, cell lines, and optimized methods will facilitate rapid advances in cyanobacteria biology and, more broadly, all photosynthetic life.

Biochemical evidence for the diversity of LHCI proteins in PSI-LHCI from the red alga Galdieria sulphuraria NIES-3638

Red algae are photosynthetic eukaryotes whose light-harvesting complexes (LHCs) associate with photosystem I (PSI). In this study, we examined characteristics of PSI-LHCI, PSI, and LHCI isolated from the red alga Galdieria sulphuraria NIES-3638. The PSI-LHCI supercomplexes were purified using anion-exchange chromatography followed by hydrophobic-interaction chromatography, and finally by trehalose density gradient centrifugation. PSI and LHCI were similarly prepared following the dissociation of PSI-LHCI with Anzergent 3-16. Polypeptide analysis of PSI-LHCI revealed the presence of PSI and LHC proteins, along with red-lineage chlorophyll a/b-binding-like protein (RedCAP), which is distinct from LHC proteins within the LHC protein superfamily. RedCAP, rather than LHC proteins, exhibited tight binding to PSI. Carotenoid analysis of LHCI identified zeaxanthin, β-cryptoxanthin, and β-carotene, with zeaxanthin particularly enriched, which is consistent with other red algal LHCIs. A Qy peak of chlorophyll a in the LHCI absorption spectrum was blue-shifted compared with those of PSI-LHCI and PSI, and a fluorescence emission peak was similarly shifted to shorter wavelengths. Based on these results, we discuss the diversity of LHC proteins and RedCAP in red algal PSI-LHCI supercomplexes.

Synergistic effects of temperature and light on photoprotection in the model diatom Phaeodactylum tricornutum

Diatoms dominate phytoplankton communities in turbulent waters, where light fluctuations can be frequent and intense. Due to this complex environment, these heterokont microalgae display remarkable photoprotection strategies, including a fast Non-Photochemical Quenching (NPQ). However, in nature, several abiotic parameters (such as temperature) can influence the response of photosynthetic organisms to light stress in a synergistic or antagonistic manner. Yet, the combined effects of light and these other drivers on the photosynthetic and photoprotective capacity of diatoms are still poorly understood. In this work, we investigated the impact of short-term temperature and light stress on the model diatom Phaeodactylum tricornutum, combining NPQ induction-recovery assays or light curves with a broad gradient of superimposed temperature treatments (5 to 35°C). We employed mutant lines deficient in NPQ generation (vde KO) or recovery (zep3 KO) and wild type. We found that temperature and light have a synergistic effect: lower temperatures limited both the photosynthetic capacity and NPQ, while the general photophysiological performance was enhanced with warming, up to a heat-stress limit (above 30°C). We discuss the temperature effects on NPQ induction and recovery and propose that these are independent from the energy requirements of the cells and result from altered xanthophyll cycle dynamics. Namely, we found that de-epoxidation activity strongly increases with temperature, outweighing epoxidation and resulting in a positive increase of NPQ with temperature. Finally, we propose that in a short-term time frame, temperature and light have a synergistic and not antagonistic effect, with a positive relationship between increasing temperature and NPQ.

Distinct phytoplankton size classes respond differently to biotic and abiotic factors

The interplay between abiotic (resource supply, temperature) and biotic (grazing) factors determines growth and loss processes in phytoplankton through resource competition and trophic interactions, which are mediated by morphological traits like size. Here, we study the relative importance of grazers, water physics, and chemistry on the daily net accumulation rates (ARs) of individual phytoplankton from natural communities, grouped into six size classes from circa 10 to 500 μm. Using a Random Forest modelling approach and 4 years of daily data from a lake, we find that water temperature is generally a pivotal control of all phytoplankton ARs. At the same time, nutrients and light are important for the smallest and the largest classes. Mesozooplankton abundance is a key predictor of the AR for small phytoplankton, with microzooplankton being important for the middle-size range. In our data, large and small phytoplankton have different (seasonal) blooming patterns: small forms are favoured by low temperature and grazing, and high phosphorus levels. Larger forms show positive ARs at high temperatures and low phosphorus (being relatively insensitive to zooplankton grazing). These results help us understand the opportunities and limitations of using size to explain and model phytoplankton responses to biotic and abiotic environmental change.

Structural and spectroscopic insights into fucoxanthin chlorophyll a/c-binding proteins of diatoms in diverse oligomeric states

Diatoms, a group of prevalent marine algae, contribute significantly to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, facilitated by fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs), which exhibit oligomeric diversity across diatom species. Using mild clear native PAGE analysis of solubilized thylakoid membranes, we displayed monomeric, dimeric, trimeric, tetrameric, and pentameric FCPs in diatoms. Mass spectrometry analysis revealed that each oligomeric FCP has a specific protein composition, and together they constitute a large Lhcf family of FCP antennas. In addition, we resolved the structures of the Thalassiosira pseudonana FCP (Tp-FCP) homotrimer and the Chaetoceros gracilis FCP (Cg-FCP) pentamer by cryoelectron microscopy at 2.73-Å and 2.65-Å resolution, respectively. The distinct pigment compositions and organizations of various oligomeric FCPs affect their blue-green light-harvesting, excitation energy transfer pathways. Compared with dimeric and trimeric FCPs, the Cg-FCP tetramer and Cg-FCP pentamer exhibit stronger absorption by Chl c, redshifted and broader Chl a fluorescence emission, and more robust circular dichroism signals originating from Chl a-carotenoid dimers. These spectroscopic characteristics indicate that Chl a molecules in the Cg-FCP tetramer and Cg-FCP pentamer are more heterogeneous than in both dimers and the Tp-FCP trimer. The structural and spectroscopic insights provided by this study contribute to a better understanding of the mechanisms that empower diatoms to adapt to fluctuating light environments.

Structural basis for molecular assembly of fucoxanthin chlorophyll a/c-binding proteins in a diatom photosystem I supercomplex

Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll a/c-binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom Thalassiosira pseudonana CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein-protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from T. pseudonana and the diatom Chaetoceros gracilis, underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.

Microplastics and climate change: the global impacts of a tiny driver

Microplastic pollution and climate change, the two seemingly distinct phenomena of global concern, are interconnected through various pathways. The connecting links between the two include the biological carbon pumps in the oceans, the sea ice, the plastisphere involved in biogeochemical cycling and the direct emissions of greenhouse gases from microplastics. On one hand, the presence of microplastics in the water column disrupts the balance of the natural carbon sequestration by affecting the key players in the pumping of carbon, such as the phytoplankton and zooplankton. On the other hand, the effect of microplastics on the sea ice in Polar Regions is two-way, as the ice caps are transformed into sinks and sources of microplastics and at the same time, the microplastics can enhance the melting of ice by reducing the albedo. Microplastics may have more potential than larger plastic fragments to release greenhouse gases (GHGs). Microbe-mediated emission of GHGs from soils is also now altered by the microplastics present in the soil. Plastisphere, the emerging microbiome in aquatic environments, can also contribute to climate change as it hosts complex networks of microbes, many of which are involved in greenhouse gas production. To combat a global stressor like climate change, it needs to be addressed with a holistic approach and this begins with tracing the various stressors like microplastic pollution that can aggravate the impacts of climate change.

The structural basis for light harvesting in organisms producing phycobiliproteins

Cyanobacteria, red algae, and cryptophytes produce 2 classes of proteins for light harvesting: water-soluble phycobiliproteins (PBP) and membrane-intrinsic proteins that bind chlorophylls (Chls) and carotenoids. In cyanobacteria, red algae, and glaucophytes, phycobilisomes (PBS) are complexes of brightly colored PBP and linker (assembly) proteins. To date, 6 structural classes of PBS have been described: hemiellipsoidal, block-shaped, hemidiscoidal, bundle-shaped, paddle-shaped, and far-red-light bicylindrical. Two additional antenna complexes containing single types of PBP have also been described. Since 2017, structures have been reported for examples of all of these complexes except bundle-shaped PBS by cryogenic electron microscopy. PBS range in size from about 4.6 to 18 mDa and can include ∼900 polypeptides and bind >2000 chromophores. Cyanobacteria additionally produce membrane-associated proteins of the PsbC/CP43 superfamily of Chl a/b/d-binding proteins, including the iron-stress protein IsiA and other paralogous Chl-binding proteins (CBP) that can form antenna complexes with Photosystem I (PSI) and/or Photosystem II (PSII). Red and cryptophyte algae also produce CBP associated with PSI but which belong to the Chl a/b-binding protein superfamily and which are unrelated to the CBP of cyanobacteria. This review describes recent progress in structure determination for PBS and the Chl proteins of cyanobacteria, red algae, and cryptophytan algae.

Benzophenone-4 inhibition in marine diatoms: Physiological and molecular perspectives

Benzophenone-4 (BP-4), a widely utilized organic ultraviolet (UV) filter, is recognized as a pseudo-persistent contaminant in aquatic environments. To elucidate the effects and mechanisms of BP-4 on marine diatoms, an investigation was conducted on the growth rate, photosynthetic pigment content, photosynthetic parameters, antioxidant enzyme activity, malondialdehyde (MDA) levels, cellular structure, and transcriptome profile of the model species, Phaeodactylum tricornutum. The results showed a pronounced inhibition of algal growth upon exposure to BP-4, with a 144 h-EC50 value of 201 mg·L-1. In addition, BP-4 exposure resulted in a significant reduction in biomass, disruption of cell membrane integrity, and increased MDA accumulation, with levels escalating 3.57-fold at 125 mg·L-1 of BP-4. In the BP-4-treated samples, 1556 differentially expressed genes (DEGs) were identified, of which 985 were upregulated and 571 were downregulated. Gene ontology and KEGG pathway enrichment analysis revealed that the carbon fixation and carbon metabolism processes in P. tricornatum were disrupted in response to BP-4 exposure, along with excessive reactive oxygen species (ROS) production. The upregulation of genes associated with photosynthetic pigment (chlorophyll and carotenoids) synthesis, phospholipid synthesis, ribosome biogenesis, and translation-related pathways may be regarded as a component of P. tricornatum's tolerance mechanism towards BP-4. These results provide preliminary insights into the toxicity and tolerance mechanisms of BP-4 on P. tricornatum. They will contribute to a better understanding of the ecotoxicological impacts of BP-4 on the marine ecosystem and provide valuable information for elimination of BP-4 in aquatic environment by bioremediation.

Negative effects of cigarette butt leachate on freshwater phytoplankton communities

We experimentally tested the effects of different concentrations of cigarette butt leachate on freshwater phytoplankton chlorophyll-a, species richness, cell density, and community composition. For this, we sampled the phytoplankton from a eutrophic lake and acclimated it for 24 h in microcosms. We then conducted the experiment in microcosms maintained for 96 h. The experiment consisted of four treatments: control and leachate from 1 butt L-1 (T1), 5 butts L-1 (T5), and 10 butts L-1 (T10), which were prepared by diluting a stock solution of leachate from 50 butts L-1. We found that algal chlorophyll-a content was not affected by different leachate concentrations. In contrast, phytoplankton cell density decreased in a dose-dependent manner as concentrations of the leachate increased. Similarly, the number of species was highest in the control group relative to all other treatments, with T1 and T5 showing higher species richness than T10. Additionally, the exposition to different concentrations of the leachate impacted community composition across all treatments in comparison to the control group. Our results suggest that cigarette butt leachate alters the number of cells and species, as well as the distribution of abundance, without necessarily reducing chlorophyll-a concentrations. Our findings indicate that to gain a comprehensive understanding of the effects of cigarette butt leachate on freshwater ecosystems, it is essential to evaluate more realistic scenarios that incorporate aquatic communities, rather than isolated species.

Cellular uptake of multi-walled carbon nanotubes is associated to genotoxic and teratogenic effects towards the freshwater diatom Nitzschia linearis

The increase in industrial production of multi-walled carbon nanotubes (MWCNTs) raises concerns about their potential adverse effects associated to environmental releases, especially in aquatic environments where they are likely to accumulate. This study focuses on the environmental impact of MWCNTs, specifically on a benthic freshwater diatom (Nitzschia linearis), which plays a major role in the primary production of water bodies. The obtained results indicate that exposure to MWCNTs in the presence of natural organic matter (NOM) inhibits diatom's growth in a dose-dependent manner after 72 h of exposure. Interestingly, the photosystem II quantum yield (PSIIQY) in diatoms remains unaffected even after exposure to MWCNTs at 10 mg/L. After 48 h of exposure, MWCNTs are found to bind preferentially to extracellular polymeric substances (EPS) produced by diatoms, which could decrease their toxicity by limiting their interaction with this organism. However, measurement of genotoxicity and teratogenicity in diatoms exposed to MWCNTs revealed that the exposure to MWCNTs increased the occurrence of cells with micronuclei and abnormal frustules. Microscopy analyses including two-photon excitation microscopy (TPEM) revealed the internalization of MWCNTs. Investigations of the diatom's frustule structure using Scanning electron microscopy (SEM) indicated that the presence of pore structures constitutes a pathway allowing MWCNTs uptake. The presence in the diatom's cytoplasm of MWCNTs might possibly induce disturbances of the cellular components, leading to the observed genotoxic and teratogenic effects. In view of previous studies, this work underscores the need for further studies on the interaction between nanomaterials and different diatom species, given the species-specific nature of the interactions.

Connected interactions: enriching food web research by spatial and social interactions

This theme issue features 18 papers exploring ecological interactions, encompassing metabolic, social, and spatial connections alongside traditional trophic networks. This integration enriches food web research, offering insights into ecological dynamics. By examining links across organisms, populations, and ecosystems, a hierarchical approach emerges, connecting horizontal effects within organizational levels vertically across biological organization levels. The inclusion of interactions involving humans is a key focus, highlighting the need for their integration into ecology given the complex interactions between human activities and ecological systems in the Anthropocene. The comprehensive exploration in this theme issue sheds light on the interconnectedness of ecological systems and the importance of considering diverse interactions in understanding ecosystem dynamics. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance

Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Structural basis for the distinct core-antenna assembly of cryptophyte photosystem II

Photosystem II (PSII) catalyzes the light-driven charge separation and water oxidation reactions of photosynthesis. Eukaryotic PSII core is usually associated with membrane-embedded light-harvesting antennae, which greatly increase the absorbance cross-section of the core. The peripheral antennae in different phototrophs vary considerably in protein composition and arrangement. Photosynthetic cryptophytes possess chlorophyll a/c binding proteins (CACs) that serve as their antennae. How these CACs assemble with the PSII core remains unclear. Here, we report the 2.57-Å resolution structure of cryptophyte PSII-CAC purified from cells at nitrogen-limited stationary growth phase. We show that each monomer of the PSII homodimer contains a core complex, six chlorophyll a/c binding proteins (CACs) and a previously unseen chlorophyll-binding protein (termed CAL-II). Six CACs are arranged as a double-layered arc-shaped non-parallel belt, and two such belts attach to the dimeric core from opposite sides. The CAL-II simultaneously interacts with a number of core subunits and five CACs. The distinct organization of CACs and the presence of CAL-II may play a critical role in stabilizing the dimeric PSII-CAC complex under stress conditions. Our study provides mechanistic insights into the assembly and function of the PSII-CAC complex as well as the possible adaptation of cryptophytes in response to environmental stresses.

Multifaceted Dinoflagellates and the Marine Model Prorocentrum cordatum

BACKGROUND

Dinoflagellates are a monophyletic group within the taxon Alveolata, which comprises unicellular eukaryotes. Dinoflagellates have long been studied for their organismic and morphologic diversity as well as striking cellular features. They have a main size range of 10-100 µm, a complex "cell covering", exceptionally large genomes (∼1-250 Gbp with a mean of 50,000 protein-encoding genes) spread over a variable number of highly condensed chromosomes, and perform a closed mitosis with extranuclear spindles (dinomitosis). Photosynthetic, marine, and free-living Prorocentrum cordatum is a ubiquitously occurring, bloom-forming dinoflagellate, and an emerging model system, particularly with respect to systems biology.

SUMMARY

Focused ion beam/scanning electron microscopy (FIB/SEM) analysis of P. cordatum recently revealed (i) a flattened nucleus with unusual structural features and a total of 62 tightly packed chromosomes, (ii) a single, barrel-shaped chloroplast devoid of grana and harboring multiple starch granules, (iii) a single, highly reticular mitochondrion, and (iv) multiple phosphate and lipid storage bodies. Comprehensive proteomics of subcellular fractions suggested (i) major basic nuclear proteins to participate in chromosome condensation, (ii) composition of nuclear pores to differ from standard knowledge, (iii) photosystems I and II, chloroplast complex I, and chlorophyll a-b binding light-harvesting complex to form a large megacomplex (>1.5 MDa), and (iv) an extraordinary richness in pigment-binding proteins. Systems biology-level investigation of heat stress response demonstrated a concerted down-regulation of CO2-concentrating mechanisms, CO2-fixation, central metabolism, and monomer biosynthesis, which agrees with reduced growth yields.

KEY MESSAGES

FIB/SEM analysis revealed new insights into the remarkable subcellular architecture of P. cordatum, complemented by proteogenomic unraveling of novel nuclear structures and a photosynthetic megacomplex. These recent findings are put in the wider context of current understanding of dinoflagellates.

Mechanisms of hormetic effects of ofloxacin on Chlorella pyrenoidosa under environmental-relevant concentration and long-term exposure

Antibiotics are frequently detected in surface water and pose potential threats to organisms in aquatic ecosystem such as microalgae. The occurrence of biphasic dose responses raised the possibility of stimulation of microalgal biomass by antibiotics at environmental-relevant concentration and caused potential ecological risk such as algal bloom. However, the underlying mechanisms of low concentration-induced hormetic effects are not well understood. In this study, we evaluated the hormesis of ofloxacin on Chlorella pyrenoidosa under environmental-relevant concentration and long-term exposure. Results showed the hormetic effects of ofloxacin on cell density and carbon fixation rate (RC). The predicted maximum promotion was 17.45 % by 16.84 μg/L and 20.08 % by 15.78 μg/L at 21 d, respectively. The predicted maximum concentration of non-effect on cell density and RC at 21 d was 3.24 mg/L and 1.44 mg/L, respectively. Ofloxacin induced the mobilization of pigments and antioxidant enzymes to deal with oxidative stress. PCA analysis revealed Chl-a/Chl-b could act as a more sensitive biomarker under acute exposure while chlorophyll fluorescence parameters were in favor of monitoring long-term implication. The hormesis in increased secretion of extracellular organic matters was regarded as a defensive mechanism and accelerated indirect photodegradation of ofloxacin. Bioremoval was dominant and related to biomass accumulation in the total dissipation while abiotic removal appeared slight contributions. This study provided new insights into the understanding of hormesis of microalgae induced by antibiotics.

Ultrafast Energy Transfer in a Diatom Photosystem II Supercomplex

The light-harvesting complexes (LHCs) of diatoms, specifically fucoxanthin-Chl a/c binding proteins (FCPs), exhibit structural and functional diversity, as highlighted by recent structural studies of photosystem II-FCP (PSII-FCPII) supercomplexes from different diatom species. The excitation dynamics of PSII-FCPII supercomplexes isolated from the diatom Thalassiosira pseudonana was explored using time-resolved fluorescence spectroscopy and two-dimensional electronic spectroscopy at room temperature and 77 K. Energy transfer between FCPII and PSII occurred remarkably fast (<5 ps), emphasizing the efficiency of FCPII as a light-harvesting antenna. The presence of long-wavelength chlorophylls may further help concentrate excitations in the core complex and increase the efficiency of light harvesting. Structure-based calculations reveal remarkably strong excitonic couplings between chlorophylls in the FCP antenna and between FCP and the PSII core antenna that are the basis for the rapid energy transfer.

Environmental controls on the seasonal variations of diatoms and dinoflagellates in the Qingdao coastal region, the Yellow Sea

Diatoms and dinoflagellates are two typical functional groups of phytoplankton assemblages, which play a crucial role in the structure and functioning of most marine ecosystems. To date, a novel challenge in ecology and biogeochemistry is to address the influences of environmental changes associated with climate change and human activities on the dynamics of diatoms and dinoflagellates. However, the knowledge of the key environmental factors controlling the diatom-dinoflagellate dynamics remains to be improved, particularly in the coastal ecosystems. Therefore, we conducted four cruises along the Qingdao coastline in spring, summer, autumn, and winter 2022 to explore how diatoms and dinoflagellates varied in response to regional environmental changes. The results showed that the phytoplankton communities were dominated by diatoms and dinoflagellates in terms of abundance and species diversity throughout the year in the study region. Yet, there were significant seasonal variability of diatoms and dinoflagellates across the four seasons. For example, diatom species was the most diverse during autumn, and the higher average abundance was observed in the fall and winter. In contrast, the average abundance of dinoflagellates was maximum during the summer and minimum in the autumn season. Moreover, the abundance and species ratios of diatoms/dinoflagellates (dia/dino) also showed significant seasonal variations in the region. The dia/dino abundance ratio was lowest in summer, while the dia/dino species ratio showed an increasing trend from spring to fall and a slight descending trend during winter. Based on the redundancy analysis, we revealed that diatoms and dinoflagellates responded differently to various environmental variables in different seasons, of which temperature and nutrients (especially dissolved inorganic nitrogen, DIN) had highly significant correlations with both the dia/dino abundance and species ratios. Thus, we suggested that temperature and DIN were the key factors controlling the seasonal dynamics of diatoms and dinoflagellates in the Qingdao coastal area.

HSP70A promotes the photosynthetic activity of marine diatom Phaeodactylum tricornutum under high temperature

With global climate change, the high-temperature environment has severely impacted the community structure and phenotype of marine diatoms. Phaeodactylum tricornutum, a model species of marine diatom, is sensitive to high temperature, which grow slowly under high temperature. However, the regulatory mechanism of P. tricornutum in response to high-temperature is still unclear. In this study, we found that the expression level of the HSP70A in the wild type (WT) increased 28 times when exposed to high temperature (26°C) for 1 h, indicating that HSP70A plays a role in high temperature in P. tricornutum. Furthermore, overexpression and interference of HSP70A have great impact on the exponential growth phase of P. tricornutum under 26°C. Moreover, the results of Co-immunoprecipitation (Co-IP) suggested that HSP70A potentially involved in the correct folding of the photosynthetic system-related proteins (D1/D2), preventing aggregation. The photosynthetic activity results demonstrated that overexpression of HSP70A improves non-photochemical quenching (NPQ) activity under high-temperature stress. These results reveal that HSP70A regulates the photosynthetic activity of P. tricornutum under high temperatures. This study not only helps us to understand the photosynthetic activity of marine diatoms to high temperature but also provides a molecular mechanism for HSP70A in P. tricornutum under high-temperature stress.

Widespread Production of Polyunsaturated Aldehydes by Benthic Diatoms of the North Pacific Ocean's Salish Sea

Diatoms are key primary producers across marine, freshwater, and terrestrial ecosystems. They are responsible for photosynthesis and secondary production that, in part, support complex food webs. Diatoms can produce phytochemicals that have transtrophic ecological effects which increase their competitive fitness. Polyunsaturated aldehydes (PUAs) are one class of diatom-derived phytochemicals that are known to have allelopathic and anti-herbivory properties. The anti-herbivory capability of PUAs results from their negative effect on grazer fecundity. Since their discovery, research has focused on their production by pelagic marine diatoms, and their effects on copepod egg production, hatching success, and juvenile survival and development. Few investigations have explored PUA production by the prolific suite of benthic marine diatoms, despite their importance to coastal trophic systems. In this study, we tested eight species of benthic diatoms for the production of the bioactive PUAs 2,4-heptadienal, 2,4-octadienal, and 2,4-decadienal. Benthic diatom species were isolated from the Salish Sea, an inland sea within the North Pacific ecosystem. All species were found to be producers of at least two PUAs in detectable concentrations, with five species producing all three PUAs in quantifiable concentrations. Our results indicate that production of PUAs from Salish Sea benthic diatoms may be widespread, and thus these compounds may contribute to benthic coastal food web dynamics through heretofore unrecognized pathways. Future studies should expand the geographic scope of investigations into benthic diatom PUA production and explore the effects of benthic diatoms on benthic consumer fecundity.

Structure and distinct supramolecular organization of a PSII-ACPII dimer from a cryptophyte alga Chroomonas placoidea

Cryptophyte algae are an evolutionarily distinct and ecologically important group of photosynthetic unicellular eukaryotes. Photosystem II (PSII) of cryptophyte algae associates with alloxanthin chlorophyll a/c-binding proteins (ACPs) to act as the peripheral light-harvesting system, whose supramolecular organization is unknown. Here, we purify the PSII-ACPII supercomplex from a cryptophyte alga Chroomonas placoidea (C. placoidea), and analyze its structure at a resolution of 2.47 Å using cryo-electron microscopy. This structure reveals a dimeric organization of PSII-ACPII containing two PSII core monomers flanked by six symmetrically arranged ACPII subunits. The PSII core is conserved whereas the organization of ACPII subunits exhibits a distinct pattern, different from those observed so far in PSII of other algae and higher plants. Furthermore, we find a Chl a-binding antenna subunit, CCPII-S, which mediates interaction of ACPII with the PSII core. These results provide a structural basis for the assembly of antennas within the supercomplex and possible excitation energy transfer pathways in cryptophyte algal PSII, shedding light on the diversity of supramolecular organization of photosynthetic machinery.

A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components

Plants and algae use light not only for driving photosynthesis but also to sense environmental cues and to adjust their circadian clocks via photoreceptors. Aureochromes are blue-light-dependent photoreceptors that also function as transcription factors, possessing both a LOV and a bZIP domain. Aureochromes so far have only been detected in Stramenopile algae, which include the diatoms. Four paralogues of aureochromes have been identified in the pennate model diatom Phaeodactylum tricornutum: PtAureo1a, 1b, 1c, and 2. While it was shown recently that diatoms have a diel rhythm, the molecular mechanisms and components regulating it are still largely unknown. Diel gene expression analyses of wild-type P. tricornutum, a PtAureo1a knockout strain, and the respective PtAureo1 complemented line revealed that all four aureochromes have a different diel regulation and that PtAureo1a has a strong co-regulatory influence on its own transcription, as well as on that of other genes encoding different blue-light photoreceptors (CPF1, 2 and 4), proteins involved in photoprotection (Lhcx1), and specific bHLH transcription factors (RITMO1). Some of these genes completely lost their circadian expression in the PtAureo1a KO mutant. Our results suggest a major involvement of aureochromes in the molecular clock of diatoms.

Lipophilic arsenic compounds in the cultured green alga Chlamydomonas reinhardtii

In this study, arsenic (As) speciation was investigated in the freshwater alga Chlamydomonas reinhardtii treated with 20 μg/L arsenate using fractionation as well as ICP-MS/ESI-MS analyses and was compared with the known As metabolite profile of wild-grown Saccharina latissima. While the total As accumulation in C. reinhardtii was about 85% lower than in S. latissima, the relative percentage of arsenolipids was significantly higher in C. reinhardtii (57.0% vs. 5.01%). As-containing hydrocarbons and phospholipids dominated the hydrophobic As profile in S. latissima, but no As-containing hydrocarbons were detectable in C. reinhardtii. Instead for the first time, an arsenoriboside-containing phytol (AsSugPhytol) was found to dominate the hydrophobic arsenicals of C. reinhardtii. Interestingly, this compound and its relatives had so far been only found in green marine microalgae, open sea plankton (mixed assemblage), and sediments but not in brown or red macroalgae. This compound family might therefore relate to differences in the arsenic metabolism between the algae phyla.

Impact of the neurotoxin β-N-methylamino-L-alanine on the diatom Thalassiosira pseudonana using metabolomics

The neurotoxin β-N-methylamino-L-alanine (BMAA) has emerged as an environmental factor related to neurodegenerative diseases. BMAA is produced by various microorganisms including cyanobacteria and diatoms, in diverse ecosystems. In the diatom Phaeodactylum tricornutum, BMAA is known to inhibit growth. The present study investigated the impact of BMAA on the diatom Thalassiosira pseudonana by exposing it to different concentrations of exogenous BMAA. Metabolomics was predominantly employed to investigate the effect of BMAA on T. pseudonana, and MetaboAnalyst (https://www.metabo-analyst.ca/) was used to identify BMAA-associated metabolisms/pathways in T. pseudonana. Furthermore, to explore the unique response, specific metabolites were compared between treatments. When the growth was obstructed by BMAA, 17 metabolisms/pathways including nitrogen and glutathione (i.e. oxidative stress) metabolisms, were influenced in T. pseudonana. This study has further determined that 11 out of 17 metabolisms/pathways could be essentially affected by BMAA, leading to the inhibition of diatom growth.

Atlas of phytoplankton phenology indices in selected Eastern Mediterranean marine ecosystems

Phytoplankton is a fundamental component of marine food webs and play a crucial role in marine ecosystem functioning. The phenology (timing of growth) of these microscopic algae is an important ecological indicator that can be utilized to observe its seasonal dynamics, and assess its response to environmental perturbations. Ocean colour remote sensing is currently the only means of obtaining synoptic estimates of chlorophyll-a (a proxy of phytoplankton biomass) at high temporal and spatial resolution, enabling the calculation of phenology metrics. However, ocean colour observations have acknowledged weaknesses compromising its reliability, while the scarcity of long-term in situ data has impeded the validation of satellite-derived phenology estimates. To address this issue, we compared one of the longest available in situ time series (20 years) of chlorophyll-a concentrations in the Eastern Mediterranean Sea (EMS), along with concurrent remotely-sensed observations. The comparison revealed a marked coherence between the two datasets, indicating the capability of satellite-based measurements in accurately capturing the phytoplankton seasonality and phenology metrics (i.e., timing of initiation, duration, peak and termination) in the studied area. Furthermore, by studying and validating these metrics we constructed a satellite-derived phytoplankton phenology atlas, reporting in detail the seasonal patterns in several sub-regions in coastal and open seas over the EMS. The open waters host higher concentrations from late October to April, with maximum levels recorded during February and lowest during the summer period. The phytoplankton growth over the Northern Aegean Sea appeared to initiate at least a month later than the rest of the EMS (initiating in late November and terminating in late May). The coastal waters and enclosed gulfs (such as Amvrakikos and Maliakos), exhibit a distinct seasonal pattern with consistently higher levels of chlorophyll-a and prolonged growth period compared to the open seas. The proposed phenology atlas represents a useful resource for monitoring phytoplankton growth periods in the EMS, supporting water quality management practices, while enhancing our current comprehension on the relationships between phytoplankton biomass and higher trophic levels (as a food source).

Different responses of marine microalgae Phaeodactylum tricornutum upon exposures to WAF and CEWAF of crude oil: A case study coupled with stable isotopic signatures

Increasing use of chemical dispersants for oil spills highlights the need to understand their adverse effects on marine microalgae and nutrient assimilation because the toxic components of crude oil can be more bioavailable. We employed the crude oil water-accommodated fraction (WAF) and chemically enhanced WAF (CEWAF) to compare different responses in marine microalgae (Phaeodactylum tricornutum) coupled with stable isotopic signatures. The concentration and proportion of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs), which are key toxic components in crude oil, increased after dispersant addition. CEWAF exposure caused higher percent growth inhibition and a lower chlorophyll-a level of microalgae than those after WAF exposure. Compared with WAF exposure, CEWAF led to an enhancement in the self-defense mechanism of P. tricornutum, accompanied by an increased content of extracellular polymeric substances. 13C-depletion and carbon assimilation were altered in P. tricornutum, suggesting more HMW PAHs could be utilized as carbon sources by microalgae under CEWAF. CEWAF had no significant effects on the isotopic fractionation or assimilation of nitrogen in P. tricornutum. Our study unveiled the impact on the growth, physiological response, and nutrient assimilation of microalgae upon WAF and CEWAF exposures. Our data provide new insights into the ecological effects of dispersant applications for coastal oil spills.

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.

Hydraulic retention time governed the micro/nanostructures of titanium-incorporated diatoms and their photocatalytic activity

Titanium-incorporated diatoms are promising biomaterials to photodegrade micropollutants such as pharmaceuticals and personal care products (PPCPs). Hydraulic retention time (HRT) is a key parameter for diatom cultivation and the incorporation of titanium into diatom frustules. This study assessed how HRT governs the micro/nanostructures, titania (TiO2) content and distribution, and the photocatalytic activity of titanium-incorporated diatom frustules. We cultivated a diatom strain Stephanodiscus hantzschii using a feed solution containing titanium(IV) in membrane bioreactors (MBRs) at a solids retention time (SRT) of 10 d and staged HRTs from 24 to 12 and to 6 h. The decrease in HRT reduced the porosity of diatom frustules but increased their silicon and titania contents. When the HRT decreased from 24 to 12 and to 6 h, the specific surface areas of the diatom decreased from 37.65 ± 3.19 to 31.53 ± 3.71 and to 18.43 ± 2.69 m2·g-1 frustules, while the titanium (Ti) contents increased from 53 ± 14 to 71 ± 9 and to 85 ± 13 mg Ti·g-1 frustules. The increase in the influent flow rates of the MBRs with decreasing HRTs likely enhanced nutrient diffusion inside the diatom valve pores, facilitating the uptake and incorporation of silicon and titanium. The titanium-incorporated frustules were effective in removing two representative PPCPs, bisphenol A (BPA) and N,N-diethyl-meta-toluamide (DEET), from water. As photocatalytic activity depends on the amount of titanium, decreasing the HRT substantially increased the photocatalytic activity of the titanium-incorporated frustules. In batch tests under ultraviolet light, frustules from the diatom cultivated at HRTs of 24, 12, and 6 h had the pseudo-first-order removal (mainly through photodegradation) rate constants of BPA of 0.376, 0.456, and 0.683 h-1, respectively. Under the same experimental condition, the pseudo-first-order removal rate constants of DEET by the frustules cultivated at HRTs of 24, 12, and 6 h increased from 0.270 to 0.330 and to 0.480 h-1.

The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs

Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.

Pyrenoid proteomics reveals independent evolution of the CO2-concentrating organelle in chlorarachniophytes

Pyrenoids are microcompartments that are universally found in the photosynthetic plastids of various eukaryotic algae. They contain ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and play a pivotal role in facilitating CO2 assimilation via CO2-concentrating mechanisms (CCMs). Recent investigations involving model algae have revealed that pyrenoid-associated proteins participate in pyrenoid biogenesis and CCMs. However, these organisms represent only a small part of algal lineages, which limits our comprehensive understanding of the diversity and evolution of pyrenoid-based CCMs. Here we report a pyrenoid proteome of the chlorarachniophyte alga Amorphochlora amoebiformis, which possesses complex plastids acquired through secondary endosymbiosis with green algae. Proteomic analysis using mass spectrometry resulted in the identification of 154 potential pyrenoid components. Subsequent localization experiments demonstrated the specific targeting of eight proteins to pyrenoids. These included a putative Rubisco-binding linker, carbonic anhydrase, membrane transporter, and uncharacterized GTPase proteins. Notably, most of these proteins were unique to this algal lineage. We suggest a plausible scenario in which pyrenoids in chlorarachniophytes have evolved independently, as their components are not inherited from green algal pyrenoids.

Ordovician origin and subsequent diversification of the brown algae

Brown algae are the only group of heterokont protists exhibiting complex multicellularity. Since their origin, brown algae have adapted to various marine habitats, evolving diverse thallus morphologies and gamete types. However, the evolutionary processes behind these transitions remain unclear due to a lack of a robust phylogenetic framework and problems with time estimation. To address these issues, we employed plastid genome data from 138 species, including heterokont algae, red algae, and other red-derived algae. Based on a robust phylogeny and new interpretations of algal fossils, we estimated the geological times for brown algal origin and diversification. The results reveal that brown algae first evolved true multicellularity, with plasmodesmata and reproductive cell differentiation, during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna (the Great Ordovician Biodiversification Event) and a proliferation of multicellular green algae. Despite its early Paleozoic origin, the diversification of major orders within this brown algal clade accelerated only during the Mesozoic Era, coincident with both Pangea rifting and the diversification of other heterokont algae (e.g., diatoms), coccolithophores, and dinoflagellates, with their red algal-derived plastids. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous Period. These are concordant with a positive character correlation between parthenogenesis and isogamy. Our new brown algal timeline, combined with a knowledge of past environmental conditions, shed new light on brown algal diversification and the intertwined evolution of multicellularity and sexual reproduction.

Spatial and temporal patterns of phytoplankton community succession and characteristics of realized niches in Lake Taihu, China

Understanding the dynamics and succession of phytoplankton in large lakes can help inform future lake management. The study analyzed phytoplankton community variations in Lake Taihu over a 21-year period, focusing on realized niches and their impact on succession. The study developed a niche periodic table with 32 niches, revealing responses to environmental factors and the optimal number of niches. Results showed that the phytoplankton in Lake Taihu showed significant spatial and temporal heterogeneity, with biomass decreasing as one moved from the northwest to the southeast and expanding towards central lake area, and towards autumn and winter. Different phytoplankton groups in Lake Taihu occupied realized niches shaped by temperature, nitrate, and phosphate. To predict the response of eutrophic freshwater lake ecosystems to human activities and climate change, it is critical to interpret the law of phytoplankton bloom and niche succession.

Bacterial carbonic anhydrase-induced carbonates mitigate soil erosion in biological soil crusts

Soil erosion is a significant environmental issue worldwide, particularly in island regions where land resources are exceedingly scarce. Biological soil crusts play a crucial role in mitigating soil erosion, yet the precise effect and mechanism of biological soil crusts against erosion remain ambiguous. In this study, biological soil crusts at various developmental stages from a tropical coral island in the South China Sea were chosen to investigate the role of carbonic anhydrase in mitigating erosion. A cohesive strength meter, real-time quantitative PCR, and 16S rRNA gene high-throughput sequencing were employed to assess variations in soil antiscouribility as well as bacterial abundance and composition during the formation and development of biological soil crusts. Scanning electron microscopy was utilized to detect carbonates induced by bacterial carbonic anhydrase and elucidate their role in the solidification of sand particles. The findings indicate that the formation and development of biological soil crusts significantly enhance anti-scouribility. Comparison to those of bare coral sand, the shear stress increased from 0.35 to 1.11 N/m2 in the dark biocrusts. Moreover, significantly elevated carbonic anhydrase activity was observed in biological soil crusts, demonstrating a positive correlation with antiscouribility. In addition, there was a significant increase in bacterial abundance within the biological soil crusts. The enrichment of Cyanobacteriales and Chloroflexales potentially contributed to the increased carbonic anhydrase activity and antiscouribility. Furthermore, three cyanobacterial strains with carbonic anhydrase activity were isolated from biological soil crusts and subsequently confirmed to enhance sand solidification through microbial carbonate precipitation. This study presents initial evidence for the role of microbial carbonic anhydrase in enhancing the antiscouribility of biological soil crusts during their formation and development. These findings offer novel insights into the functional and mechanistic dimensions underlying the mitigation of soil erosion facilitated by biological soil crusts, which are valuable for implementing sustainable biorestoration and environmental management technologies to prevent soil erosion.

Spectral Tuning and Excitation-Energy Transfer by Unique Carotenoids in Diatom Light-Harvesting Antenna

The light-harvesting antennae of diatoms and spinach are composed of similar chromophores; however, they exhibit different absorption wavelengths. Recent advances in cryoelectron microscopy have revealed that the diatom light-harvesting antenna fucoxanthin chlorophyll a/c-binding protein (FCPII) forms a tetramer and differs from the spinach antenna in terms of the number of protomers; however, the detailed molecular mechanism remains elusive. Herein, we report the physicochemical factors contributing to the characteristic light absorption of the diatom light-harvesting antenna based on spectral calculations using an exciton model. Spectral analysis reveals the significant contribution of unique fucoxanthin molecules (fucoxanthin-S) in FCPII to the diatom-specific spectrum, and further analysis determines their essential role in excitation-energy transfer to chlorophyll. It was revealed that the specificity of these fucoxanthin-S molecules is caused by the proximity between protomers associated with the tetramerization of FCPII. The findings of this study demonstrate that diatoms employ fucoxanthin-S to harvest energy under the ocean in the absence of long-wavelength sunlight and can provide significant information about the survival strategies of photosynthetic organisms to adjust to their living environment.

Structures and organizations of PSI-AcpPCI supercomplexes from red tidal and coral symbiotic photosynthetic dinoflagellates

Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the photosynthetic properties of dinoflagellates. We report here three structures of photosystem I (PSI)-chlorophylls (Chls) a/c-peridinin protein complex (PSI-AcpPCI) from two species of dinoflagellates by single-particle cryoelectron microscopy. The crucial PsaA/B subunits of a red tidal dinoflagellate Amphidinium carterae are remarkably smaller and hence losing over 20 pigment-binding sites, whereas its PsaD/F/I/J/L/M/R subunits are larger and coordinate some additional pigment sites compared to other eukaryotic photosynthetic organisms, which may compensate for the smaller PsaA/B subunits. Similar modifications are observed in a coral symbiotic dinoflagellate Symbiodinium species, where two additional core proteins and fewer AcpPCIs are identified in the PSI-AcpPCI supercomplex. The antenna proteins AcpPCIs in dinoflagellates developed some loops and pigment sites as a result to accommodate the changed PSI core, therefore the structures of PSI-AcpPCI supercomplex of dinoflagellates reveal an unusual protein assembly pattern. A huge pigment network comprising Chls a and c and various carotenoids is revealed from the structural analysis, which provides the basis for our deeper understanding of the energy transfer and dissipation within the PSI-AcpPCI supercomplex, as well as the evolution of photosynthetic organisms.

The requirement for external carbonic anhydrase in diatoms is influenced by the supply and demand for dissolved inorganic carbon

Photosynthesis by marine diatoms contributes significantly to the global carbon cycle. Due to the low concentration of CO2 in seawater, many diatoms use extracellular carbonic anhydrase (eCA) to enhance the supply of CO2 to the cell surface. While much research has investigated how the requirement for eCA is influenced by changes in CO2 availability, little is known about how eCA contributes to CO2 supply following changes in the demand for carbon. We therefore examined how changes in photosynthetic rate influence the requirement for eCA in three centric diatoms. Modeling of cell surface carbonate chemistry indicated that diffusive CO2 supply to the cell surface was greatly reduced in large diatoms at higher photosynthetic rates. Laboratory experiments demonstrated a trend of an increasing requirement for eCA with increasing photosynthetic rate that was most pronounced in the larger species, supporting the findings of the cellular modeling. Microelectrode measurements of cell surface pH and O2 demonstrated that individual cells exhibited an increased contribution of eCA to photosynthesis at higher irradiances. Our data demonstrate that changes in carbon demand strongly influence the requirement for eCA in diatoms. Cell size and photosynthetic rate will therefore be key determinants of the mode of dissolved inorganic carbon uptake.

Allele-dependent expression and functionality of lipid enzyme phospholipid:diacylglycerol acyltransferase affect diatom carbon storage and growth

In the acyl-CoA-independent pathway of triacylglycerol (TAG) synthesis unique to plants, fungi, and algae, TAG formation is catalyzed by the enzyme phospholipid:diacylglycerol acyltransferase (PDAT). The unique PDAT gene of the model diatom Phaeodactylum tricornutum strain CCMP2561 boasts 47 single nucleotide variants within protein coding regions of the alleles. To deepen our understanding of TAG synthesis, we observed the allele-specific expression of PDAT by the analysis of 87 published RNA-sequencing (RNA-seq) data and experimental validation. The transcription of one of the two PDAT alleles, Allele 2, could be specifically induced by decreasing nitrogen concentrations. Overexpression of Allele 2 in P. tricornutum substantially enhanced the accumulation of TAG by 44% to 74% under nutrient stress; however, overexpression of Allele 1 resulted in little increase of TAG accumulation. Interestingly, a more serious growth inhibition was observed in the PDAT Allele 1 overexpression strains compared with Allele 2 counterparts. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that enzymes encoded by PDAT Allele 2 but not Allele 1 had TAG biosynthetic activity, and 7 N-terminal and 3 C-terminal amino acid variants between the 2 allele-encoded proteins substantially affected enzymatic activity. P. tricornutum PDAT, localized in the innermost chloroplast membrane, used monogalactosyldiacylglycerol and phosphatidylcholine as acyl donors as demonstrated by the increase of the 2 lipids in PDAT knockout lines, which indicated a common origin in evolution with green algal PDATs. Our study reveals unequal roles among allele-encoded PDATs in mediating carbon storage and growth in response to nitrogen stress and suggests an unsuspected strategy toward lipid and biomass improvement for biotechnological purposes.

Utilization and transformation of Chrysotila dentata-derived dissolved organic matter by phycosphere bacteria Marinobacter hydrocarbonoclasticus and Bacillus firmus

The dissolved organic matter (DOM) released from the cocoolithophores (Chrysotila dentata) was studied in laboratory experiments after co-culturing C. dentata with bacteria. Marinobacter hydrocarbonoclasticus (CA6)-γ-Proteobacteria and Bacillus firmus (CF2) were used to investigate the utilization and processing of the DOM derived from C. dentata, utilizing fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC), while measuring algal abundance and photosynthetic parameters. The experimental groups consisted of axenic C. dentata groups, filter cultured with bacteria (CA6 or CF2) groups, C. dentata co-cultured with bacteria (CA6 or CF2) groups and axenic bacteria (CA6 or CF2) groups. We then evaluated the processing of DOM by determining four fluorescence indices. The number of C. dentata cells and the photosynthetic capacity of microalgae were enhanced by CA6 and CF2. The main known fluorophores, including humic-like components and protein-like components, were present in all sample. The protein-like component of algal-bacterial co-cultures was effectively utilized by CA6 and CF2. The humic-like components increased at the end of the culture time for all cultures. Meanwhile, the average fluorescence intensity of protein-like in CA6 co-culture with algae was lower than that in CF2 co-culture with algae over time. On the other hand, the average fluorescence intensity of humic-like in CA6 was higher than CF2. However, the total change in fluorescence in humic-like and protein-like of axenic CF2 cultures was lower than that of CA6. Hence, the ability of CA6 to transform microalgal-derived DOM was superior to that of CF2, and CF2's ability to consume bacterial-derived DOM was superior to that of CA6.

Proteomes reveal the lipid metabolic network in the complex plastid of Phaeodactylum tricornutum

Phaeodactylum tricornutum plastid is surrounded by four membranes, and its protein composition and function remain mysterious. In this study, the P. tricornutum plastid-enriched fraction was obtained and 2850 proteins were identified, including 92 plastid-encoded proteins, through label-free quantitative proteomic technology. Among them, 839 nuclear-encoded proteins were further determined to be plastidial proteins based on the BLAST alignments within Plant Proteome DataBase and subcellular localization prediction, in spite of the strong contamination by mitochondria-encoded proteins and putative plasma membrane proteins. According to our proteomic data, we reconstructed the metabolic pathways and highlighted the hybrid nature of this diatom plastid. Triacylglycerol (TAG) hydrolysis and glycolysis, as well as photosynthesis, glycan metabolism, and tocopherol and triterpene biosynthesis, occur in the plastid. In addition, the synthesis of long-chain acyl-CoAs, elongation, and desaturation of fatty acids (FAs), and synthesis of lipids including TAG are confined in the four-layered-membrane plastid based on the proteomic and GFP-fusion localization data. The whole process of generation of docosahexaenoic acid (22:6) from palmitic acid (16:0), via elongation and desaturation of FAs, occurs in the chloroplast endoplasmic reticulum membrane, the outermost membrane of the plastid. Desaturation that generates 16:4 from 16:0 occurs in the plastid stroma and outer envelope membrane. Quantitative analysis of glycerolipids between whole cells and isolated plastids shows similar composition, and the FA profile of TAG was not different. This study shows that the diatom plastid combines functions usually separated in photosynthetic eukaryotes, and differs from green alga and plant chloroplasts by undertaking the whole process of lipid biosynthesis.