%0 Journal Article %J Bioengineered %D 2024 %T Exopolysaccharide from marine microalgae belonging to the \textit{Glossomastix genus: fragile gel behavior and suspension stability %A Dulong, Virginie %A Rihouey, Christophe %A Gaignard, Clément %A Bridiau, Nicolas %A Gourvil, Priscilla %A Laroche, Céline %A Pierre, Guillaume %A Varacavoudin, Tony %A Probert, Ian %A Maugard, Thierry %A Michaud, Philippe %A Picton, Luc %A Le Cerf, Didier %K fragile gel %K Glossomastix %K Microalgae %K Polysaccharide %K RCC3688 %K RCC3707 %K stabilizer %X With the aim to find new polysaccharides of rheological interest with innovated properties, rhamnofucans produced as exopolysaccharides (EPS) in a photobioreactor (PBR) and an airlift bioreactor (ABR) by the marine microalgae Glossomastix sp. RCC3707 and RCC3688 were fully studied. Chemical characterizations have been conducted (UHPLC – MS HR). Analyses by size-exclusion chromatography (SEC) coupled online with a multiangle light scattering detector (MALS) and a differential refractive index detector showed the presence of large structures with molar masses higher than 106 g.mol−1. The rheological studies of these EPS solutions, conducted at different concentrations and salinities, have evidenced interesting and rare behavior characteristic of weak and fragile hydrogels i.e. gel behavior with very low elastic moduli (between 10−2 and 10 Pa) and yield stresses (between 10−2 and 2 Pa) according to the EPS source, concentration, and salinity. These results were confirmed by diffusing wave spectroscopy. Finally, as one of potential application, solutions of EPS from Glossomastix sp. have evidenced very good properties as anti-settling stabilizers, using microcrystalline cellulose particles as model, studied by multiple light scattering (MLS) with utilization in cosmetic or food industry. Compared to alginate solution with same viscosity for which sedimentation is observed over few hours, microalgae EPS leads to a stable suspension over few days. %B Bioengineered %V 15 %P 2296257 %8 dec %G eng %U https://doi.org/10.1080/21655979.2023.2296257 %R 10.1080/21655979.2023.2296257 %0 Journal Article %J Toxins %D 2023 %T Artificial Substrates Coupled with qPCR (AS-qPCR) Assay for the Detection of the Toxic Benthopelagic Dinoflagellate Vulcanodinium rugosum %A Bouquet, Aurélien %A Felix, Christine %A Masseret, Estelle %A Reymond, Coralie %A Abadie, Eric %A Laabir, Mohamed %A Rolland, Jean Luc %K artificial substrate %K benthopelagic %K detection %K PCR %K RCC6328 %K RCC6338 %K RCC6344 %K RCC6548 %K RCC6550 %K toxins %K \textitVulcanodinium rugosum %X Vulcanodinium rugosum is an emerging benthopelagic neuro-toxic dinoflagellate species responsible for seasonal Pinnatoxins and Portimines contaminations of shellfish and marine animals. This species is challenging to detect in the environment, as it is present in low abundance and difficult to be identified using light microscopy. In this work, we developed a method using artificial substrates coupled with qPCR (AS-qPCR) to detect V. rugosum in a marine environment. This sensitive, specific and easy-to-standardize alternative to current techniques does not require specialized expertise in taxonomy. After determining the limits and specificity of the qPCR, we searched for the presence of V. rugosum in four French Mediterranean lagoons using artificial substrates collected every two weeks for one year. The AS-qPCR method revealed its occurrences in summer 2021 in every studied lagoon and detected cells in more samples than light microscopy. As V. rugosum development induces shellfish contamination even at low microalga densities, the AS-qPCR method is accurate and relevant for monitoring V. rugosum in a marine environment. %B Toxins %V 15 %P 217 %8 mar %G eng %U https://www.mdpi.com/2072-6651/15/3/217 %R 10.3390/toxins15030217 %0 Generic %D 2023 %T Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations %A Dennu, Louis %A Devic, Martine %A Rigonato, Janaina %A Falciatore, Angela %A Lozano, Jean-Claude %A Vergé, Valérie %A Mariac, Cédric %A Jaillon, Olivier %A Team, The Dark Edge genomics sampling %A Sabot, François %A Bouget, François-Yves %K RCC1615 %K RCC1868 %K RCC4222 %K RCC4752 %K RCC5417 %K RCC685 %K RCC716 %X Population-scale sequencing has become a standard practice to explore the natural genetic diversity underlying adaptation, notably in land plants. However, current sequencing initiatives for eukaryotic phytoplankton primarily concentrate on creating reference genomes for model organisms and characterizing natural communities through metagenomics approaches. Consequently, few species have been thoroughly sequenced and intraspecific genetic diversity remains virtually undescribed, limiting our understanding of diversity and adaptation mechanisms. Here we report a biological and genomic resource to explore the genetic diversity of the cosmopolitan and ecologically important Bathycoccus genus. To span broad geographical and temporal scales, we selected available strains but also isolated and genotyped strains from both the Banyuls bay (Mediterranean sea) and the Baffin bay (Arctic ocean). By combining ONT long reads and Illumina short reads technologies, we produced and annotated 28 Bathycoccus sp. de novo assembled genomes of high quality, including 24 genomes of Bathycoccus prasinos strains along a latitudinal gradient between 40° and 78° North, one reference genome of the Bathycoccus calidus species and 3 genomes of a yet undescribed Bathycoccus species named Bathycoccus catiminus. We assessed the genetic diversity of this genus through phylogenomic analyses and highlighted the central role of this genomic resource in providing new insights into the diversity of outlier chromosomal structures. The Bathycoccus biological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean. Significance statement Comparative and functional approaches for the study of eukaryotic phytoplankton and their adaptation to latitudes and seasons that rely on extensive biological and genomic resources are currently lacking. Here we report such resources and describe the natural diversity of the cosmopolitan phytoplankton Bathycoccus, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies. %I bioRxiv %8 oct %G eng %U https://www.biorxiv.org/content/10.1101/2023.10.16.562038v1 %R 10.1101/2023.10.16.562038 %0 Journal Article %J Algal Research %D 2023 %T Comparison of different small-scale cultivation methods towards the valorization of a marine benthic diatom strain for lipid production %A Arnaldo, Mary Dianne Grace %A Gamage, Nadeeshani Dehel %A Jaffrenou, Agathe %A Rabesaotra, Vony %A Mossion, Aurélie %A Wielgosz-Collin, Gaëtane %A Méléder, Vona %K RCC5813 %B Algal Research %P 103327 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S2211926423003600 %R 10.1016/j.algal.2023.103327 %0 Journal Article %J Small Structures %D 2023 %T Crystallization of Coccolith Calcite at Different Life-Cycle Phases Exhibits Distinct Degrees of Cellular Confinement %A Ben-Joseph, Oz %A de Haan, Diede %A Rechav, Katya %A Shimoni, Eyal %A Levin-Zaidman, Smadar %A Langer, Gerald %A Probert, Ian %A Wheeler, Glen L. %A Gal, Assaf %K biomineralization %K calcites %K Coccoliths %K crystal growths %K haploid–diploid life cycles %K RCC1181 %K RCC3777 %X Coccolithophores are a group of unicellular marine algae that shape global geochemical cycles via the production of calcium carbonate crystals. Interestingly, different life-cycle phases of the same coccolithophore species produce very different calcitic scales, called coccoliths. In the widely studied diploid phase, the crystals have anisotropic and complex morphologies, while haploid cells produce coccoliths consisting solely of calcite crystals with simple rhombohedral morphology. Understanding how these two life-cycle phases control crystallization is a highly sought-after goal, yet, haploid phase crystallization has rarely been studied, and the process by which they form is unknown. Herein, advanced electron microscopy is employed to elucidate the cellular architecture of the calcification process in haploid cells. The results show that in contrast to diploid-phase calcification, the coccolith-forming vesicle of haploid-phase cells is voluminous. In this solution-like environment, the crystals nucleate and grow asynchronously in a process that resembles calcite growth in bulk solution, leading to the simple morphologies of the crystals. The two distinct mineralization regimes of coccolithophore life-cycle phases suggest that cellular architecture, and specifically confinement of the crystallization process, is a pivotal determinant of biomineral morphology and assembly. %B Small Structures %V n/a %P 2200353 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1002/sstr.202200353 %R 10.1002/sstr.202200353 %0 Journal Article %J Applied Sciences %D 2023 %T The Diatom Cylindrotheca closterium and the Chlorophyll Breakdown Product Pheophorbide a for Photodynamic Therapy Applications %A Saide, Assunta %A Riccio, Gennaro %A Ianora, Adrianna %A Lauritano, Chiara %K biotechnological applications %K cancer %K Microalgae %K Pheophorbide \textita %K photodynamic therapy %K RCC1712 %K \textitCylindrotheca closterium %X Microalgae, eukaryotic unicellular plants that are distributed worldwide, have been shown to exert anti-proliferative and anticancer activities on various human cancer cell lines. An example of a microalgal bioactive compound is a chlorophyll breakdown product named Pheophorbide a (Ppa), which has been reported to have anti-proliferative properties against various cell lines. This compound has also been tested with light exposure in photodynamic therapy for cancer treatment. In this paper, we screened eleven marine microalgae against a panel of cancer cells, and evaluated the synergistic anti-proliferative effect with Pheophorbide a, with and without photo-activation. The results showed significant anti-proliferative activity against melanoma cells when Ppa was combined with fraction E of the diatom Cylindrotheca closterium plus 1 h photo-activation. Its activity was also analyzed using gene expression and Western blot experiments. Altogether, these data give new insights into the possible application of microalgae for photodynamic therapy. %B Applied Sciences %V 13 %P 2590 %G eng %U https://www.mdpi.com/2076-3417/13/4/2590 %R 10.3390/app13042590 %0 Journal Article %J Bioresources and Bioprocessing %D 2023 %T Different photosynthetic responses of haploid and diploid Emiliania huxleyi (Prymnesiophyceae) to high light and ultraviolet radiation %A Ruan, Zuoxi %A Lu, Meifang %A Lin, Hongmin %A Chen, Shanwen %A Li, Ping %A Chen, Weizhou %A Xu, Huijuan %A Qiu, Dajun %K Diploid phase %K Effective quantum yield %K Emiliania huxleyi %K Haploid phase %K rcc1217 %K Ultraviolet radiation (UVR) %X Solar radiation varies quantitatively and qualitatively while penetrating through the seawater column and thus is one of the most important environmental factors shaping the vertical distribution pattern of phytoplankton. The haploid and diploid life-cycle phases of coccolithophores might have different vertical distribution preferences. Therefore, the two phases respond differently to high solar photosynthetically active radiation (PAR, 400–700 nm) and ultraviolet radiation (UVR, 280–400 nm). To test this, the haploid and diploid Emiliania huxleyi were exposed to oversaturating irradiance. In the presence of PAR alone, the effective quantum yield was reduced by 10% more due to the higher damage rate of photosystem II in haploid cells than in diploid cells. The addition of UVR resulted in further inhibition of the quantum yield for both haploid and diploid cells in the first 25 min, partly because of the increased damage of photosystem II. Intriguingly, this UVR-induced inhibition of the haploid cells completely recovered half an hour later. This recovery was confirmed by the comparable maximum quantum yields, maximum relative electron transport rates and yields of the haploid cells treated with PAR and PAR + UVR. Our data indicated that photosynthesis of the haploid phase was more sensitive to high visible light than the diploid phase but resistant to UVR-induced inhibition, reflecting the ecological niches to which this species adapts. %B Bioresources and Bioprocessing %V 10 %P 40 %8 jul %G eng %U https://doi.org/10.1186/s40643-023-00660-5 %R 10.1186/s40643-023-00660-5 %0 Journal Article %J Cell Reports Physical Science %D 2023 %T Does the life cycle stage matter for distinguishing phytoplankton via fluoro-electrochemical microscopy? %A Yu, Jiahao %A Yang, Minjun %A Batchelor-McAuley, Christopher %A Barton, Samuel %A Rickaby, Rosalind E. M. %A Bouman, Heather A. %A Compton, Richard G. %K electrogenerated radicals %K fluoro-electrochemistry %K Green algae %K life cycle %K marine phytoplankton %K oxidative damage %K RCC1 %K remote sensing %K susceptibility library %X Phytoplankton have species-specific responses toward electrogenerated oxidants, allowing high-throughput species analysis. Herein, a fluoro-electrochemical method is used to expose single Chlamydomonas concordia vegetative cells at different points within their life cycle to electro-generated oxidants from seawater. The resulting decay in fluorescence from chlorophyll-a is measured as a function of time and drops to zero for phytoplankton adjacent to the electrode over a period of a few seconds. The chlorophyll-a transient timescale allows mother cells, which are distinctively larger and require a larger quantity of oxidants, to be distinguished from either zoospores or “growing” cells, while all the cells show the same intrinsic susceptibility modulated only by the size of the phytoplankton. These observations are essential for the future automated characterization of the speciation of phytoplankton populations as they show that there is no need to manually identify the life cycle stage. %B Cell Reports Physical Science %P 101223 %G eng %U https://www.sciencedirect.com/science/article/pii/S2666386422005410 %R 10.1016/j.xcrp.2022.101223 %0 Journal Article %J Algal Research %D 2023 %T Fine-tuning the flavor of Tetraselmis chuii by modifying nitrogen supply %A Coleman, Bert %A Van Poucke, Christof %A Dewitte, Bavo %A Casciaro, Valentina %A Moerdijk-Poortvliet, Tanja %A Muylaert, Koenraad %A Robbens, Johan %K Microalgae %K Nitrogen starvation %K RCC128 %K Sensory evaluation %K Umami %K Volatile organic compounds %X Dried Tetraselmis chuii biomass has potential as flavoring agent for the development of plant-based seafood alternatives because of its seafood-like aroma and strong umami taste. Depending on the cultivation conditions, microalgae can adapt their metabolism, resulting in a change in biochemical composition. The aim of this study was to assess if the flavor of T. chuii could be modified by changing the nitrogen (N) supply in the cultivation medium in order to maximize the potential of T. chuii as flavoring agent. The sensory evaluation by a trained panel showed that the T. chuii biomass obtained from N starved cultivation conditions (N-deplete) is characterized by a significantly stronger odor intensity and earthy-like off-odor compared to T. chuii biomass obtained from N sufficient cultivation conditions (N-replete). The analysis of volatile organic compounds (VOCs) using SPME-GC–MS showed that these odor features of N-deplete biomass are attributed to an increased formation of odor-active VOCs including 2,3-butanedione, 3-methylbutanal, 3-methylbutanol and sulfur-containing dimethyl sulfide and dimethyl disulfide. In contrast, the T. chuii N-replete biomass possessed a significantly stronger taste intensity, umami and salty taste compared to the T. chuii N-deplete biomass. The higher umami is attributed to the significantly higher free glutamic acid (Glu) and adenosine monophosphate (AMP) concentrations in N-replete biomass compared to N-deplete biomass. This study illustrates that flavor and palatability of microalgae biomass is strongly affected by cultivating conditions and modifying these conditions can be an important tool in the development of plant-based seafood alternatives. %B Algal Research %P 103208 %G eng %U https://www.sciencedirect.com/science/article/pii/S2211926423002412 %R 10.1016/j.algal.2023.103208 %0 Journal Article %J ISME Communications %D 2023 %T Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms %A Ruvindy, Rendy %A Barua, Abanti %A Bolch, Christopher J. S. %A Sarowar, Chowdhury %A Savela, Henna %A Murray, Shauna A. %K Molecular ecology %K Molecular Evolution %K RCC3145 %K RCC4874 %K RCC4876 %K RCC4877 %K RCC4879 %X The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and \textasciitilde7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell−1 /\textasciitilde127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102– 108 copies cell−1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 – 107 cell−1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20–22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0–102 copies cell−1, was significantly related to PSTs (ng cell−1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes. %B ISME Communications %V 3 %P 1–11 %8 jul %G eng %U https://www.nature.com/articles/s43705-023-00274-0 %R 10.1038/s43705-023-00274-0 %0 Journal Article %J Marine Drugs %D 2023 %T Growth Behavior, Biomass Composition and Fatty Acid Methyl Esters (FAMEs) Production Potential of Chlamydomonas reinhardtii, and Chlorella vulgaris Cultures %A López-Pacheco, Itzel Y. %A Ayala-Moreno, Victoria Guadalupe %A Mejia-Melara, Catherinne Arlette %A Rodríguez-Rodríguez, José %A Cuellar-Bermudez, Sara P. %A González-González, Reyna Berenice %A Coronado-Apodaca, Karina G. %A Farfan-Cabrera, Leonardo I. %A González-Meza, Georgia María %A Iqbal, Hafiz M. N. %A Parra-Saldívar, Roberto %K RCC2488 %X The production of biomolecules by microalgae has a wide range of applications in the development of various materials and products, such as biodiesel, food supplements, and cosmetics. Microalgae biomass can be produced using waste and in a smaller space than other types of crops (e.g., soja, corn), which shows microalgae’s great potential as a source of biomass. Among the produced biomolecules of greatest interest are carbohydrates, proteins, lipids, and fatty acids. In this study, the production of these biomolecules was determined in two strains of microalgae (Chlamydomonas reinhardtii and Chlorella vulgaris) when exposed to different concentrations of nitrogen, phosphorus, and sulfur. Results show a significant microalgal growth (3.69 g L−1) and carbohydrates (163 mg g−1) increase in C. reinhardtii under low nitrogen concentration. Also, higher lipids content was produced under low sulfur concentration (246 mg g−1). It was observed that sulfur variation could affect in a negative way proteins production in C. reinhardtii culture. In the case of C. vulgaris, a higher biomass production was obtained in the standard culture medium (1.37 g L−1), and under a low-phosphorus condition, C. vulgaris produced a higher lipids concentration (248 mg g−1). It was observed that a low concentration of nitrogen had a better effect on the accumulation of fatty acid methyl esters (FAMEs) (C16-C18) in both microalgae. These results lead us to visualize the effects that the variation in macronutrients can have on the growth of microalgae and their possible utility for the production of microalgae-based subproducts. %B Marine Drugs %V 21 %P 450 %8 aug %G eng %U https://www.mdpi.com/1660-3397/21/8/450 %R 10.3390/md21080450 %0 Journal Article %J Phycologia %D 2023 %T Morpho-molecular analysis of podolampadacean dinoflagellates (Dinophyceae), with the description of two new genera %A Mertens, Kenneth Neil %A Carbonell-Moore, M. Consuelo %A Chomérat, Nicolas %A Bilien, Gwenael %A Boulben, Sylviane %A Guillou, Laure %A Romac, Sarah %A Probert, Ian %A Ishikawa, Akira %A Nézan, Elisabeth %K Alatosphaera %K Blepharocysta %K desmoschisis %K Gaarderiella %K Lissodinium %K LSU rDNA %K Mysticella %K Podolampas %K Pseudalatosphaera %K SSU rDNA %X Sequences were obtained for 58 podolampadacean single cells from France, Reunion Island (French territories) and Japan (6 SSU rDNA only, 40 SSU+LSU and 12 LSU only). The sequenced taxa belong to five of the eight described genera: Podolampas, Blepharocysta, Lissodinium, Gaarderiella and Mysticella. Two new genera, Alatosphaera and Pseudalatosphaera, were erected to accommodate ‘Blepharocysta’ hermosillae and ‘Blepharocysta’ denticulata. Most genera are well supported by concatenated LSU–SSU rDNA phylogenies, with the least support for Lissodinium. Metabarcoding of podolampadaceans using the V4 region of SSU rDNA showed a resolution too low to discriminate genera or species. Roscoffia and Cabra are here considered podolampadaceans, whilst Lessardia is considered to belong in a separate family. The relationship of Rhinodinium to the Podolampadaceae needs further study. Desmoschisis was recorded for the first time in Alatosphaera and Pseudalatosphaera. Several ribotypes need further study to attribute a species name to them. %B Phycologia %P 1–19 %8 feb %G eng %U https://doi.org/10.1080/00318884.2022.2158281 %R 10.1080/00318884.2022.2158281 %0 Journal Article %J European Journal of Taxonomy %D 2023 %T New species of Pavlovophyceae (Haptophyta) and revision of the genera Exanthemachrysis, Rebecca and Pavlova %A Veron, Benoit %A Rougier, Etienne %A Taylor, Anthony %A Goux, Didier %K habitats %K haptophytes %K new species %K phytoplankton %K pyrenoid %K RCC1528 %K RCC1541 %X The justification of the 4 genera that currently compose the class Pavlovophyceae is based on a low number of species and a relative paucity of available, traceable and referenced cultures. Previous integrative phylogeny work revealed strains that can refine and strengthen our knowledge of the genera in the class. The application of multiple light and electron microscopy techniques allowed us to prioritize the cytomorphological characters (pyrenoid, thylakoid, stigma, knob-scales, life stage / life cycle) used for the taxonomy of these algae and to describe two new species: Exanthemachrysis fresneliae Véron sp. nov. and Rebecca billardiae Véron sp. nov. Consequently, revisions of the two genera Exanthemachrysis Lepailleur emend. Véron and Rebecca Green emend. Véron were made. In addition, the genus Pavlova Butcher emend Véron is revised in the light of these characters. Particular emphasis is placed on the life stages and habitat of the species. %B European Journal of Taxonomy %V 861 %P 21–47 %8 mar %G eng %U https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/2063 %R 10.5852/ejt.2023.861.2063 %0 Generic %D 2023 %T Novel dimethylsulfoniopropionate biosynthesis enzymes in diverse marine bacteria, cyanobacteria and abundant algae %A Wang, Jinyan %A Zhou, Shun %A Curson, Andrew %A Vieira, Ana %A Walsham, Keanu %A Monaco, Serena %A Li, Chun-Yang %A Rivera, Peter Paolo %A Wang, Xiao-Di %A Hanwell, Libby %A Zhu, Xiao-Yu %A Leão, Pedro %A Lea-Smith, David J. %A Zhang, Yuzhong %A Zhang, Xiaohua %A Todd, Jonathan %K RCC100 %K RCC2956 %K RCC4094 %K RCC4422 %K RCC6172 %X Abstract Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound[1] with roles in stress protection[2, 3], chemotaxis[4], nutrient and sulfur cycling[5] and, potentially, climate regulation[6, 7]. Marine algae and bacteria are considered significant DMSP producers, but many diverse representatives lack known DMSP synthesis genes/enzymes[8, 9]. Here, new DMSP biosynthesis enzymes were identified that considerably increase the number and diversity of potential DMSP-producing organisms, inferring new and significant global DMSP producers. A novel bifunctional DMSP biosynthesis enzyme, DsyGD, identified in the rhizobacterium Gynuella sunshinyii, produces DMSP at levels higher than any other bacterium from methylthiohydroxybutyrate (MTHB) via an N-terminal MTHB S-methyltransferase domain (termed DsyG) and a C-terminal dimethylsulfoniohydroxybutyrate (DMSHB) decarboxylase domain (termed DsyD, which is the first reported enzyme with this activity). DsyGD is also found in some filamentous cyanobacteria, not previously known to produce DMSP. Regulation of DMSP production and dsyGD transcription was consistent with their role in osmoprotection. Indeed, cloned dsyGD conferred osmotolerance to bacteria deficient in osmolyte production, something not previously demonstrated for any known DMSP synthesis gene, and which could be exploited for biotechnology e.g., engineering salt tolerance. DsyGD characterisation led to identification of phylogenetically distinct DsyG-like proteins, termed DSYE, with MTHB S-methyltransferase activity, in diverse and environmentally abundant Chlorophyta, Chlorachniophyta, Ochraphyta, Haptophyta and Bacillariophyta algae. These algae comprise a mix of low, high and previously unknown DMSP producers[10]. Algae containing DSYE, particularly bloom-forming Pelagophyceae species, which we showed to accumulate medium-high intracellular DMSP levels, were globally more abundant DMSP producers than Haptophyta, Dinophyta and Bacillariophyta with DSYB and/or TpMMT. This highlights the potential importance of Pelagophyceae and other DSYE containing algae in global DMSP production and sulfur cycling. %I In Review %8 mar %G eng %U https://www.researchsquare.com/article/rs-2678769/v1 %9 preprint %R 10.21203/rs.3.rs-2678769/v1 %0 Journal Article %J Algal Research %D 2023 %T Novel exopolysaccharide produced by the marine dinoflagellate Heterocapsa AC210: Production, characterization, and biological properties %A Concórdio-Reis, Patrícia %A Cardeira, Martim %A Macedo, Ana Catarina %A Ferreira, Sónia S. %A Serra, Ana Teresa %A Coimbra, Manuel A. %A Amorim, Ana %A Reis, Maria A. M. %A Freitas, Filomena %K Anti-inflammatory %K Cytotoxicity %K Dinoflagellates %K Exopolysaccharide production %K Marine microalgae %K RCC1514 %K sp. AC210 %X Marine microalgae are promising sources of novel valuable biomolecules such as polysaccharides. In this study, the dinoflagellate Heterocapsa sp. AC210 was described as a new exopolysaccharide (EPS) producer. The cultivation and EPS production in bioreactor was evaluated for the first time in detail. The EPS was composed of seven different sugar monomers, including fucose and glucosamine, which are quite rare and have never been reported in dinoflagellates' EPS. Moreover, the EPS had a high content of sulphate, which is often associated with biological properties. Cytotoxicity was accessed and the results showed that the EPS did not reduce cell viability for concentrations up to 1 g L−1. Additionally, antioxidant and anti-inflammatory assays demonstrated that the EPS reduced by 18 % the intracellular reactive oxygen species and decreased up to 79.3 % and 46.2 % of IL-8 and IL-6 secretion in keratinocytes, which supports its potential application in the cosmeceutical and biomedical fields. %B Algal Research %V 70 %P 103014 %G eng %U https://www.sciencedirect.com/science/article/pii/S2211926423000474 %R 10.1016/j.algal.2023.103014 %0 Generic %D 2023 %T A novel fluoro-electrochemical technique for classifying diverse marine nanophytoplankton %A Barton, Samuel %A Yang, Minjun %A Chen, Haotian %A Batchelor-McAuley, Christopher %A Compton, Richard %A Bouman, Heather %A Rickaby, Rosalind %K RCC1 %K rcc1084 %K RCC1130 %K RCC1150 %K RCC1178 %K RCC1185 %K RCC1198 %K RCC1216 %K rcc1217 %K RCC1242 %K RCC1314 %K RCC1346 %K RCC1489 %K RCC1511 %K RCC1546 %K RCC1557 %K RCC1614 %K rcc1731 %K RCC191 %K RCC2570 %K RCC3598 %K RCC3696 %K RCC3776 %K RCC3780 %K RCC4207 %K RCC4221 %K RCC4273 %K RCC4657 %K RCC4660 %K RCC6 %K RCC623 %K RCC6516 %K RCC656 %K RCC678 %K RCC69 %K RCC74 %K RCC76 %K RCC8 %K RCC80 %K RCC81 %K RCC88 %K RCC911 %K RCC950 %X

To broaden our understanding of pelagic ecosystem responses to environmental change, it is essential that we improve the spatio-temporal resolution of in situ monitoring of phytoplankton communities. A key challenge for existing methods is in classifying and quantifying cells within the nanophytoplankton size range (2-20µm). This is particularly difficult when there are similarities in morphology, making visual differentiation difficult for both trained taxonomists and machine learning based approaches. Here we present a rapid fluoro-electrochemical technique for classifying nanophytoplankton, and using a library of 52 diverse strains of nanophytoplankton we assess the accuracy of this technique based on two measurements at the individual level: charge required to reduce per cell chlorophyll a fluorescence by 50%, and cell radius. We demonstrate a high degree of accuracy overall (>90%) in categorising cells belonging to widely recognised key functional groups, however this is reduced when we consider the broader diversity of “nano-phytoflagellates”. Notably, we observe that some groups, for example calcifying Isochrysidales, have much greater resilience to electrochemically driven oxidative conditions relative to others of a similar size, making them more easily categorised by the technique. The findings of this study present a promising step forward in advancing our toolkit for monitoring phytoplankton communities. We highlight that, for improved categorisation accuracy, future iterations of the method can be enhanced by measuring additional predictor variables with minimal adjustments to the set-up. In doing so, we foresee this technique being highly applicable, and potentially invaluable, for in situ classification and enumeration of the nanophytoplankton size fraction.

%I Life Sciences %8 apr %G eng %U https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10572 %9 preprint %R 10.1002/lom3.10572 %0 Journal Article %J The ISME Journal %D 2023 %T Rapid diversification underlying the global dominance of a cosmopolitan phytoplankton %A Bendif, El Mahdi %A Probert, Ian %A Archontikis, Odysseas A. %A Young, Jeremy R. %A Beaufort, Luc %A Rickaby, Rosalind E. %A Filatov, Dmitry %K Microbial biooceanography %K phylogenomics %K population genetics %K rcc1212 %K RCC1216 %K rcc1220 %K RCC1239 %K RCC1240 %K RCC1242 %K RCC1245 %K rcc1252 %K RCC1253 %K RCC1266 %K RCC1304 %K rcc1731 %K RCC1754 %K RCC1813 %K RCC1823 %K rcc1824 %K RCC1830 %K RCC1838 %K RCC1840 %K RCC1853 %K RCC1856 %K RCC3746 %K RCC4027 %K RCC4028 %K RCC4030 %K RCC5134 %K RCC5137 %K RCC5141 %K RCC6381 %K RCC6421 %K RCC6427 %K RCC6566 %K RCC6660 %K RCC6666 %K RCC911 %K RCC963 %X Marine phytoplankton play important roles in the global ecosystem, with a limited number of cosmopolitan keystone species driving their biomass. Recent studies have revealed that many of these phytoplankton are complexes composed of sibling species, but little is known about the evolutionary processes underlying their formation. Gephyrocapsa huxleyi, a widely distributed and abundant unicellular marine planktonic algae, produces calcified scales (coccoliths), thereby significantly affects global biogeochemical cycles via sequestration of inorganic carbon. This species is composed of morphotypes defined by differing degrees of coccolith calcification, the evolutionary ecology of which remains unclear. Here, we report an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (\textasciitilde140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton. %B The ISME Journal %P 1–11 %G eng %U https://www.nature.com/articles/s41396-023-01365-5 %R 10.1038/s41396-023-01365-5 %0 Journal Article %J Algal Research %D 2023 %T Shotgun proteomics reveals temperature-dependent regulation of major nutrient metabolism in coastal Synechococcus sp. WH5701 %A Dedman, Craig J. %A Barton, Samuel %A Fournier, Marjorie %A Rickaby, Rosalind E. M. %K climate change %K Ocean warming %K phytoplankton %K Proteomics: Marine biogeochemistry %K rcc1084 %X Marine cyanobacteria are major contributors to the oceanic carbon sink and are predicted to increase in numbers in the future warmed ocean. As a result, the influence of marine cyanobacteria on marine biogeochemical cycling will likely be enhanced. Associated with elevations in temperature the ocean will undergo increased stratification, reducing supply of essential nutrients to upper phototrophic layers. It is therefore critical that we resolve the manners by which cyanobacteria respond to variations in temperature, and consequences for major nutrient metabolism which may ultimately direct global biogeochemistry and trophic transfer. In this study we use the coastal Synechococcus sp. WH5701 to examine proteomic alterations in major nutrient (C, N and P) metabolic pathways following exposure to varying temperature. In response to temperature treatments, Synechococcus displayed higher rates of growth and photosynthetic efficiency when temperatures were raised from 17 °C to 23 °C and 28 °C, associated with a significant \textasciitilde30–40 % alteration in the cellular proteome. As temperatures increased, proteomic investment towards photosynthetic machinery appeared up-regulated, whilst abundance of RuBisCO was reduced, associated with an apparent alteration in CCM composition and carbon metabolism. N demand appeared to increase in-line with temperature, associated with alterations in the GS-GOGAT pathway, likely due to increased demand for and efficiency of protein synthesis. In contrast, P demand at the highest temperature appeared reduced as investment in the ribosome declines due to improved translation efficiency, whilst luxury P-storage appeared a feature of growth at low temperature. It appears likely that as seawater temperatures rise under ocean warming, the biochemical composition of cyanobacteria will be altered, increasing cellular C- and N- to P ratios, ultimately impacting upon their contribution to oceanic biogeochemical cycling. %B Algal Research %P 103279 %8 oct %G eng %U https://www.sciencedirect.com/science/article/pii/S2211926423003120 %R 10.1016/j.algal.2023.103279 %0 Journal Article %J New Phytologist %D 2023 %T Stimulating and toxic effect of chromium on growth and photosynthesis of a marine chlorophyte %A Zhang, Qiong %A Charles, Philip D. %A Bendif, El Mahdi %A Hester, Svenja S. %A Mohammad, Shabaz %A Rickaby, Rosalind E. M. %K chromium %K Photosynthesis %K phytoplankton %K proteomics %K RCC1 %K RCC1242 %K trace metal %X Marine phytoplankton can interchange trace metals in various biochemical functions, particularly under metal-limiting conditions. Here, we investigate the stimulating and toxicity effect of chromium (Cr) on a marine Chlorophyceae Osetreococcus tauri under Fe-replete and Fe-deficient conditions. We determined the growth, photosynthesis, and proteome expressions of Osetreococcus tauri cultured under different Cr and Fe concentrations. In Fe-replete conditions, the presence of Cr(VI) stimulated significantly the growth rate and the maximum yield of photochemistry of photosystem II (Fv/Fm) of the phytoplankton, while the functional absorption cross-section of photosystem II (σPSII) did not change. Minor additions of Cr(VI) partially rescued phytoplankton growth under Fe-limited conditions. Proteomic analysis of this alga grown in Fe-replete normal and Fe-replete with Cr addition media (10 μM Cr) showed that the presence of Cr significantly decreased the expression of phosphate-transporting proteins and photosynthetic proteins, while increasing the expression of proteins related to carbon assimilation. Cr can stimulate the growth and photosynthesis of O. tauri, but the effects are dependent on both the Cr(VI) concentration and the availability of Fe. The proteomic results further suggest that Cr(VI) addition might significantly increase starch production and carbon fixation. %B New Phytologist %V n/a %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19376 %R 10.1111/nph.19376 %0 Journal Article %J mBio %D 2023 %T Transcriptional Mechanisms of Thermal Acclimation in \textit{Prochlorococcus %A Alonso-Sáez, Laura %A Palacio, Antonio S. %A Cabello, Ana M. %A Robaina-Estévez, Semidán %A González, José M. %A Garczarek, Laurence %A López-Urrutia, Ángel %E Martiny, Jennifer B. H. %K RCC3377 %X Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. %B mBio %P e03425–22 %G eng %U https://journals.asm.org/doi/10.1128/mbio.03425-22 %R 10.1128/mbio.03425-22 %0 Journal Article %J MicrobiologyOpen %D 2023 %T Transcriptomics‐guided identification of an algicidal protease of the marine bacterium Kordia algicida OT‐1 %A Syhapanha, Kristy S. %A Russo, David A. %A Deng, Yun %A Meyer, Nils %A Poulin, Remington X. %A Pohnert, Georg %K RCC75 %X In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT‐1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics‐guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real‐time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms., Algicidal bacteria shape the plankton communities of the oceans by lysing microalgae and consuming the released nutrients. Kordia algicida is an environmentally relevant marine bacterium whose algicidal activity is mediated by secreted proteases. In this study, we utilize a transcriptomics‐guided approach to identify the secreted serine protease AlpA1 as a key factor in the algicidal process. This discovery offers new approaches for the real‐time monitoring and manipulation of algicidal bacteria in algal blooms. %B MicrobiologyOpen %V 12 %P e1387 %G eng %U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565126/ %R 10.1002/mbo3.1387 %0 Journal Article %J Frontiers in Microbiology %D 2022 %T Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas %A Ferrieux, Mathilde %A Dufour, Louison %A Doré, Hugo %A Ratin, Morgane %A Guéneuguès, Audrey %A Chasselin, Léo %A Marie, Dominique %A Rigaut-jalabert, Fabienne %A Le Gall, Florence %A Sciandra, Théo %A Monier, Garance %A Hoebeke, Mark %A Corre, Erwan %A Xia, Xiaomin %A Liu, Hongbin %A Scanlan, David J. %A Partensky, Frédéric %A Garczarek, Laurence %K RCC2374 %K RCC2385 %K RCC2533 %K RCC2534 %K RCC2571 %K RCC515 %K rcc539 %K rcc791 %X Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters. %B Frontiers in Microbiology %V 13 %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2022.893413 %R 10.3389/fmicb.2022.893413 %0 Journal Article %J Journal of Marine Science and Engineering %D 2022 %T Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species %A Yung, Charmaine C. M. %A Rey Redondo, Elvira %A Sanchez, Frédéric %A Yau, Sheree %A Piganeau, Gwenael %K Biogeography %K evolution %K genomics %K mamiellophyceae %K metagenomics %K microalgae–virus interactions %K phycoDNAvirus %K RCC809 %X The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions. %B Journal of Marine Science and Engineering %V 10 %P 240 %8 feb %G eng %U https://www.mdpi.com/2077-1312/10/2/240 %R 10.3390/jmse10020240 %0 Journal Article %J Genome Biology and Evolution %D 2022 %T Diversity and evolution of pigment types in marine \textit{Synechococcus cyanobacteria %A Grébert, Théophile %A Garczarek, Laurence %A Daubin, Vincent %A Humily, Florian %A Marie, Dominique %A Ratin, Morgane %A Devailly, Alban %A Farrant, Gregory K. %A Mary, Isabelle %A Mella-Flores, Daniella %A Tanguy, Gwenn %A Labadie, Karine %A Wincker, Patrick %A Kehoe, David M. %A Partensky, Frédéric %E Angert, Esther %K RCC307 %K to add %X DNA integration and site-specific recombination, suggesting that their genomic variability relies D in part on a ‘tycheposon’-like mechanism. Comparison of the phylogenies obtained for PBS and E core genes revealed that the evolutionary history of PBS rod genes differs from the core T genome and is characterized by the co-existence of different alleles and frequent allelic P exchange. We propose a scenario for the evolution of the different pigment types and highlight E the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in C different Synechococcus lineages despite multiple speciation events. %B Genome Biology and Evolution %P evac035 %G eng %U https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac035/6547267 %R 10.1093/gbe/evac035 %0 Journal Article %J Communications Biology %D 2022 %T Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence %A Guérin, Nina %A Ciccarella, Marta %A Flamant, Elisa %A Frémont, Paul %A Mangenot, Sophie %A Istace, Benjamin %A Noel, Benjamin %A Belser, Caroline %A Bertrand, Laurie %A Labadie, Karine %A Cruaud, Corinne %A Romac, Sarah %A Bachy, Charles %A Gachenot, Martin %A Pelletier, Eric %A Alberti, Adriana %A Jaillon, Olivier %A Wincker, Patrick %A Aury, Jean-Marc %A Carradec, Quentin %K Biogeography %K comparative genomics %K metagenomics %K RCC100 %K Water microbiology %X The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata. %B Communications Biology %V 5 %P 1–14 %G eng %U https://www.nature.com/articles/s42003-022-03939-z %R 10.1038/s42003-022-03939-z %0 Journal Article %J Applied Phycology %D 2022 %T Genomic and meta-genomic insights into the functions, diversity and global distribution of haptophyte algae %A Penot, Mathias %A Dacks, Joel B. %A Read, Betsy %A Dorrell, Richard G. %K 18S rDNA %K coccolithophorid %K dispersal %K meta-genomics %K niche adaptation %K prymnesiophyte %K RCC1129 %K RCC1187 %K RCC1387 %K RCC1480 %K RCC1532 %K RCC851 %K RCC914 %K systematics %K to read %X Haptophytes are an environmentally important phylum of eukaryotic phytoplankton, forming the second most abundant algal group after diatoms in recent estimates of ocean biodiversity. Haptophytes are phylogenetically and functionally diverse, including globally distributed and bloom-forming calcifying species such as Emiliania and Coccolithus, and non-calcifying orders that may form important components of phytoplankton communities in polar (Phaeocystis, Chrysochromulina) through to sub-tropical latitudes (Pavlova). In this review, we synthesize available phylogenetic, genomic and environmental information concerning the diversity of haptophyte life, considering the origins and placement on the eukaryotic tree; the diversity of the five major orders (Pavlovophyceae, Phaeocystales, Prymnesiales, the CSZ clade, and Isochrysidales); and the contrasting biogeographical distributions of haptophyte groups across different Tara Oceans sampling stations and size fractions. We additionally consider outstanding questions within the fields of haptophyte diversity and biology, particularly in the context of newly discovered and largely uncultured major groups (DPL lineages and Rappemonads), and current gaps in our knowledge of genomic content and niche adaptation across the haptophyte tree. %B Applied Phycology %P 1–20 %G eng %U https://doi.org/10.1080/26388081.2022.2103732 %R 10.1080/26388081.2022.2103732 %0 Journal Article %J mSystems %D 2022 %T Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts %A Doré, Hugo %A Leconte, Jade %A Guyet, Ulysse %A Breton, Solène %A Farrant, Gregory K. %A Demory, David %A Ratin, Morgane %A Hoebeke, Mark %A Corre, Erwan %A Pitt, Frances D. %A Ostrowski, Martin %A Scanlan, David J. %A Partensky, Frédéric %A Six, Christophe %A Garczarek, Laurence %K RCC1086 %K RCC1695 %K RCC2369 %K rcc2380 %K RCC2553 %K RCC2556 %K RCC2570 %K rcc791 %X Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of “who is where” by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades. %B mSystems %P e00656–22 %G eng %U https://journals.asm.org/doi/full/10.1128/msystems.00656-22 %R 10.1128/msystems.00656-22 %0 Journal Article %J mBio %D 2022 %T Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation %A Haney, Allissa M. %A Sanfilippo, Joseph E. %A Garczarek, Laurence %A Partensky, Frédéric %A Kehoe, David M. %E Ruby, Edward %K rcc555 %X

Marine cyanobacteria depend on light for photosynthesis, restricting their growth to the photic zone. The upper part of this layer is exposed to strong UV radiation (UVR), a DNA mutagen that can harm these microorganisms. To thrive in UVR-rich waters, marine cyanobacteria employ photoprotection strategies that are still not well defined. Among these are photolyases, light-activated enzymes that repair DNA dimers generated by UVR. Our analysis of genomes of 81 strains of Synechococcus, Cyanobium, and Prochlorococcus isolated from the world’s oceans shows that they possess up to five genes encoding different members of the photolyase/cryptochrome family, including a photolyase with a novel domain arrangement encoded by either one or two separate genes. We disrupted the putative photolyase-encoding genes in Synechococcus sp. strain RS9916 and discovered that each gene contributes to the overall capacity of this organism to survive UVR. Additionally, each conferred increased survival after UVR exposure when transformed into Escherichia coli lacking its photolyase and SOS response. Our results provide the first evidence that this large set of photolyases endows Synechococcus with UVR resistance that is far superior to that of E. coli, but that, unlike for E. coli, these photolyases provide Synechococcus with the vast majority of its UVR tolerance.

%B mBio %V 13 %P e01511–22 %8 aug %G eng %U https://journals.asm.org/doi/10.1128/mbio.01511-22 %R 10.1128/mbio.01511-22 %0 Journal Article %J Limnology and Oceanography %D 2022 %T Nutritional response of a coccolithophore to changing pH and temperature %A Johnson, Roberta %A Langer, Gerald %A Rossi, Sergio %A Probert, Ian %A Mammone, Marta %A Ziveri, Patrizia %K RCC1832 %X Coccolithophores are a calcifying unicellular phytoplankton group that are at the base of the marine food web, and their lipid content provides a source of energy to consumers. Coccolithophores are vulnerable to ocean acidification and warming, therefore it is critical to establish the effects of climate change on these significant marine primary producers, and determine potential consequences that these changes can have on their consumers. Here, we quantified the impact of changes in pH and temperature on the nutritional condition (lipid content, particulate organic carbon/nitrogen), growth rate, and morphology of the most abundant living coccolithophore species, Emiliania huxleyi. We used a regression type approach with nine pH levels (ranging from 7.66 to 8.44) and two temperatures (15°C and 20°C). Lipid production was greater under reduced pH, and growth rates were distinctly lower at 15°C than at 20°C. The production potential of lipids, which estimates the availability of lipids to consumers, increased under 20°C, but decreased under low pH. The results indicate that, while consumers will benefit energetically under ocean warming, this benefit will be mitigated by ocean acidification. The carbon to nitrogen ratio was higher at 20°C and low pH, indicating that the nutritional quality of coccolithophores for consumers will decline under climate change. The impact of low pH on the structural integrity of the coccosphere may also mean that coccolithophores are easier to digest for consumers. Many responses suggest cellular stress, indicating that increases in temperature and reductions in pH may have a negative impact on the ecophysiology of coccolithophores. %B Limnology and Oceanography %V n/a %G eng %U http://onlinelibrary.wiley.com/doi/abs/10.1002/lno.12204 %R 10.1002/lno.12204 %0 Journal Article %J Frontiers in Marine Science %D 2022 %T Pronounced Uptake and Metabolism of Organic Substrates by Diatoms Revealed by Pulse-Labeling Metabolomics %A Meyer, Nils %A Rydzyk, Aljoscha %A Pohnert, Georg %K RCC75 %X Diatoms contribute as a dominant group of microalgae to approximately 20% of the global carbon fixation. In the plankton, these photosynthetic algae are exposed to a plethora of metabolites, especially when competing algae are lysed. It is well established that diatoms can take up specific metabolites, such as vitamins, amino acids as nitrogen source, or dimethylsulfoniopropoionate to compensate for changes in water salinity. It is, however, unclear to which extent diatoms take up other organic resources and if these are incorporated into the cell´s metabolism. Here, we explore the general scope of uptake of metabolites from competitors. Using labeled metabolites released during lysis of algae grown under a 13CO2 atmosphere, we show that the cosmopolitan diatom Chaetoceros didymus takes up even dilute organic substrates from these lysates with little bias for molecular weight or polarity. This is reflected by a high degree of labeling in the metabolome of the exposed cells. The newly developed pulse label/mass spectrometry metabolomics approach reveals that polarity and molecular weight has no detectable influence on uptake. We further show that the taken-up metabolites are partly maintained without metabolic modification within the cells, but also a substantial part is subject to catabolic and anabolic transformation. One of the most dominant phytoplankton groups thus has the potential to compete with heterotrophs, suggesting that the observed osmotrophy may substantially impact organic material fluxes in the oceans. Our findings call for the refinement of our understanding of competition in the plankton. %B Frontiers in Marine Science %V 9 %P 821167 %G eng %U https://www.frontiersin.org/articles/10.3389/fmars.2022.821167/full %R 10.3389/fmars.2022.821167 %0 Journal Article %J Molecular Phylogenetics and Evolution %D 2022 %T Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences %A Akita, Shingo %A Vieira, Christophe %A Hanyuda, Takeaki %A Rousseau, Florence %A Cruaud, Corinne %A Couloux, Arnaud %A Heesch, Svenja %A Cock, J. Mark %A Kawai, Hiroshi %K Ectocarpales %K genomics %K Heterokontophytes %K Phaeoexplorer %K Phaeophyceae %K RCC4962 %K RCC7086 %K RCC7088 %K RCC7090 %K RCC7092 %K RCC7094 %K RCC7096 %K RCC7098 %K RCC7101 %K RCC7104 %K RCC7107 %K RCC7108 %K RCC7109 %K RCC7112 %K RCC7115 %K RCC7116 %K RCC7117 %K RCC7120 %K RCC7123 %K RCC7124 %K RCC7125 %K RCC7127 %K RCC7129 %K RCC7131 %K RCC7134 %K RCC7137 %K RCC7138 %K RCC7139 %K stramenopiles %X In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling. %B Molecular Phylogenetics and Evolution %V 168 %P 107408 %8 mar %G eng %U https://www.sciencedirect.com/science/article/pii/S1055790322000215 %R 10.1016/j.ympev.2022.107408 %0 Journal Article %J Analytical Chemistry %D 2022 %T Quantifying the Extent of Calcification of a Coccolithophore Using a Coulter Counter %A Fan, Xinmeng %A Batchelor-McAuley, Christopher %A Yang, Minjun %A Barton, Samuel %A Rickaby, Rosalind E. M. %A Bouman, Heather A. %A Compton, Richard G. %K RCC1198 %K RCC1216 %K RCC1314 %X Although, in principle, the Coulter Counter technique yields an absolute measure of particle volume, in practice, calibration is nearuniversally employed. For regularly shaped and non-biological samples, the use of latex beads for calibration can provide sufficient accuracy. However, this is not the case with particles encased in biogenically formed calcite. To date, there has been no effective route by which a Coulter Counter can be calibrated to enable the calcification of coccolithophores�single cells encrusted with biogenic calcite�to be quantified. Consequently, herein, we seek to answer the following question: to what extent can a Coulter Counter be used to provide accurate information regarding the calcite content of a singlespecies coccolithophore population? Through the development of a new calibration methodology, based on the measurement and dynamic tracking of the acid-driven calcite dissolution reaction, a route by which the cellular calcite content can be determined is presented. This new method allows, for the first time, a Coulter Counter to be used to yield an absolute measurement of the amount of calcite per cell. %B Analytical Chemistry %P acs.analchem.2c01971 %8 sep %G eng %U https://pubs.acs.org/doi/10.1021/acs.analchem.2c01971 %R 10.1021/acs.analchem.2c01971 %0 Journal Article %J European Journal of Phycology %D 2022 %T Taxonomic relationship between two small-sized Chaetoceros species (Bacillariophyta): C. tenuissimus and C. salsugineus , and comparison with C. olympicus sp. nov. from Catalan coastal waters (NW Mediterranean) %A Arin, Laura %A Reñé, Albert %A Gallisai, Rachele %A Sarno, Diana %A Garcés, Esther %A Estrada, Marta %K RCC3007 %K RCC3008 %K RCC5795 %X

The majority of species of the highly diverse genus Chaetoceros are described as chain-forming, although several species are described as strictly solitary (such as C. tenuissimus) or having an alternate solitary and a chain-forming phase during their life history (such as C. salsugineus). In this study, the diversity of small forms of Chaetoceros from the NW Mediterranean coastal waters was explored through the morphological and molecular characterization of four different strains belonging to two distinct species. Based on their morphology, three of the strains were identified as C. salsugineus (Takano, 1983). The SSU and LSU rDNA sequences represented the first available for well-characterized C. salsugineus strains and were 96.6–100% similar to publicly available C. tenuissimus (Meunier, 1913) sequences. Both species share the same morphological features, such as setae and ultrastructure of the valves, as well as the rimoportula characteristics. In addition, the morphology of the solitary form of C. salsugineus matched with that of C. tenuissimus. Here, we propose the two species as synonyms (the name C. tenuissimus prevailing as it has priority for this taxon), emend the original description and designate an epitype. The fourth strain was identified as C. olympicus sp. nov., a new species, which alternates solitary and chain-forming forms within its life history. The main differential characteristics of this species are the absence of rimoportula both in terminal and intercalary valves, the setae ultrastructure, which is thin and circular in cross-section with a few, slightly twisted, rows of small rectangular poroids and some spirally arranged spines, and the morphology of the resting spores, with primary valve vaulted and covered with short to medium-sized spines, and secondary valve smaller, rounded and smooth. A comparison of C. tenuissimus and C. olympicus with other species as well as information on their life cycle and ecology is also provided.

%B European Journal of Phycology %V 57 %P 277–296 %G eng %U https://www.tandfonline.com/doi/full/10.1080/09670262.2021.1966838 %R 10.1080/09670262.2021.1966838 %0 Journal Article %J Frontiers in Plant Science %D 2021 %T Altitudinal Zonation of Green Algae Biodiversity in the French Alps %A Stewart, Adeline %A Rioux, Delphine %A Boyer, Fréderic %A Gielly, Ludovic %A Pompanon, François %A Saillard, Amélie %A Thuiller, Wilfried %A Valay, Jean-Gabriel %A Maréchal, Éric %A Coissac, Eric %K rcc %K RCC1055 %K RCC130 %K RCC1563 %K RCC2501 %K RCC2960 %K RCC3402 %K RCC443 %K RCC4743 %K RCC537 %K RCC581 %K RCC6 %K RCC7 %K RCC891 %X Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes. %B Frontiers in Plant Science %V 12 %P 1066 %G eng %U https://www.frontiersin.org/article/10.3389/fpls.2021.679428 %R 10.3389/fpls.2021.679428 %0 Journal Article %J Scientific Reports %D 2021 %T Annual phytoplankton dynamics in coastal waters from fildes bay, western antarctic peninsula %A Trefault, Nicole %A de la Iglesia, Rodrigo %A Moreno-Pino, Mario %A Lopes dos Santos, Adriana %A Gérikas Ribeiro, Catherine %A Parada-Pozo, Génesis %A Cristi, Antonia %A Marie, Dominique %A Vaulot, Daniel %K RCC2265 %K RCC2289 %K RCC4582 %K RCC4586 %K RCC5152 %X Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris , which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters. %B Scientific Reports %V 11 %P 1368 %8 dec %G eng %U http://biorxiv.org/content/early/2020/10/27/2020.10.27.356600.abstract http://www.nature.com/articles/s41598-020-80568-8 %R 10.1038/s41598-020-80568-8 %0 Journal Article %J Scientific Reports %D 2021 %T Bacteria enhance the production of extracellular polymeric substances by the green dinoflagellate Lepidodinium chlorophorum %A Roux, Pauline %A Siano, Raffaele %A Collin, Karine %A Bilien, Gwenael %A Sinquin, Corinne %A Marchand, Laetitia %A Zykwinska, Agata %A Delbarre-Ladrat, Christine %A Schapira, Mathilde %K RCC1489 %X High biomasses of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations along Southern Brittany (NE Atlantic, France). The viscosity associated to these phenomena has been related to problems in oyster cultivation. The harmful effect of L. chlorophorum might originate from the secretion of Extracellular Polymeric Substances (EPS). To understand whether the EPS are produced by L. chlorophorum or its associated bacteria, or if they are a product of their interaction, batch cultures were performed under non-axenic and pseudo-axenic conditions for three strains. Maximum dinoflagellate cell abundances were observed in pseudo-axenic cultures. The non-sinking fraction of polymers (Soluble Extracellular Polymers, SEP), mainly composed of proteins and the exopolysaccharide sulphated galactan, slightly increased in pseudo-axenic cultures. The amount of Transparent Exopolymer Particles (TEP) per cell increased under non-axenic conditions. Despite the high concentrations of Particulate Organic Carbon (POC) measured, viscosity did not vary. These results suggest that the L. chlorophorum-bacteria interaction could have a detrimental consequence on the dinoflagellate, translating in a negative effect on L. chlorophorum growth, as well as EPS overproduction by the dinoflagellate, at concentrations that should not affect seawater viscosity. %B Scientific Reports %V 11 %P 1–15 %G eng %U http://www.nature.com/articles/s41598-021-84253-2 %R 10.1038/s41598-021-84253-2 %0 Journal Article %J mSphere %D 2021 %T Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality %A Pollara, Scott B. %A Becker, Jamie W. %A Nunn, Brook L. %A Boiteau, Rene %A Repeta, Daniel %A Mudge, Miranda C. %A Downing, Grayton %A Chase, Davis %A Harvey, Elizabeth L. %A Whalen, Kristen E. %E McMahon, Katherine %K rcc1731 %X Interactions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems by controlling primary production, structuring marine food webs, mediating carbon export, and influencing global climate. Phytoplankton-bacterium interactions are facilitated by secreted compounds; however, linking these chemical signals, their mechanisms of action, and their resultant ecological consequences remains a fundamental challenge. The bacterial quorumsensing signal 2-heptyl-4-quinolone (HHQ) induces immediate, yet reversible, cellular stasis (no cell division or mortality) in the coccolithophore Emiliania huxleyi; however, the mechanism responsible remains unknown. Using transcriptomic and proteomic approaches in combination with diagnostic biochemical and fluorescent cell-based assays, we show that HHQ exposure leads to prolonged S-phase arrest in phytoplankton coincident with the accumulation of DNA damage and a lack of repair despite the induction of the DNA damage response (DDR). While this effect is reversible, HHQ-exposed phytoplankton were also protected from viral mortality, ascribing a new role of quorum-sensing signals in regulating multitrophic interactions. Furthermore, our data demonstrate that in situ measurements of HHQ coincide with areas of enhanced micro- and nanoplankton biomass. Our results suggest bacterial communication signals as emerging players that may be one of the contributing factors that help structure complex microbial communities throughout the ocean. %B mSphere %V 6 %P e00009–21, /msphere/6/3/mSph.00009–21.atom %G eng %U https://msphere.asm.org/content/6/3/e00009-21 %R 10.1128/mSphere.00009-21 %0 Journal Article %J Current Opinion in Microbiology %D 2021 %T A cell–cell atlas approach for understanding symbiotic interactions between microbes %A Alacid, Elisabet %A Richards, Thomas A %X Natural environments are composed of a huge diversity of microorganisms interacting with each other to form complex functional networks. Our understanding of the operative nature of host–symbiont associations is limited because propagating such associations in a laboratory is challenging. The advent of single-cell technologies applied to, for example, animal cells and apicomplexan parasites has revolutionized our understanding of development and disease. Such cell atlas approaches generate maps of cell-specific processes and variations within cellular populations. These methods can now be combined with cellular-imaging so that interaction stage versus transcriptome state can be quantized for microbe-microbe interactions. We predict that the combination of these methods applied to the study of symbioses will transform our understanding of many ecological interactions, including those sampled directly from natural environments. %B Current Opinion in Microbiology %V 64 %P 47–59 %G eng %U https://www.sciencedirect.com/science/article/pii/S1369527421001144 %R 10.1016/j.mib.2021.09.001 %0 Journal Article %J Environmental Science: Water Research & Technology %D 2021 %T Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters %A Robla, J. %A García-Hierrro, J. %A Alguacil, F. J. %A Dittami, S. M. %A Marie, D. %A Villa, E. %A Deragon, E. %A Guillebault, D. %A Mengs, G. %A Medlin, L. K. %K rcc %K RCC1507 %X The most important question in sampling is “Is the sample representative of the target population?” This question is necessary to understand how valid the sample taken is to the original population and if generalizations can be made from the sample. Samples taken for water quality measurement range from 1 mL for bacterial contamination to 100 mL or up to 1000 L for protozoan parasites. With larger samples taken, the confidence in detecting rare events increases dramatically. Here we illustrate that hollow fiber filters as routinely used for kidney dialysis can be adapted for environmental use. The filters retain all organisms down to viral particles and organic matter above 70 kDA, the molecular cutoff for urea, one of the waste products removed in kidney dialysis. With these filters, 50 liters of water can be filtered in about 90 minutes. Backflush of the filters recovers viable cells with minimal cell lysis that can be processed downstream for molecular analysis. Recovery rates were as high as 89% and 75% for phytoplankton and bacteria, respectively. %B Environmental Science: Water Research & Technology %V 7 %P 1230–1239 %8 jul %G eng %U https://pubs.rsc.org/en/content/articlelanding/2021/ew/d0ew00927j %R 10.1039/D0EW00927J %0 Journal Article %J The ISME Journal %D 2021 %T Experimental identification and in silico prediction of bacterivory in green algae %A Bock, Nicholas A. %A Charvet, Sophie %A Burns, John %A Gyaltshen, Yangtsho %A Rozenberg, Andrey %A Duhamel, Solange %A Kim, Eunsoo %K RCC180 %K RCC3375 %K RCC369 %K RCC618 %X While algal phago-mixotrophs play a major role in aquatic microbial food webs, their diversity remains poorly understood. Recent studies have indicated several species of prasinophytes, early diverging green algae, to be able to consume bacteria for nutrition. To further explore the occurrence of phago-mixotrophy in green algae, we conducted feeding experiments with live fluorescently labeled bacteria stained with CellTracker Green CMFDA, heat-killed bacteria stained with 5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF), and magnetic beads. Feeding was detected via microscopy and/or flow cytometry in five strains of prasinophytes when provided with live bacteria: Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, and Dolichomastix tenuilepis CCMP3274. No feeding was detected when heat-killed bacteria or magnetic beads were provided, suggesting a strong preference for live prey in the strains tested. In parallel to experimental assays, green algal bacterivory was investigated using a gene-based prediction model. The predictions agreed with the experimental results and suggested bacterivory potential in additional green algae. Our observations underline the likelihood of widespread occurrence of phago-mixotrophy among green algae, while additionally highlighting potential biases introduced when using prey proxy to evaluate bacterial ingestion by algal cells. %B The ISME Journal %P 1–14 %8 mar %G eng %U http://www.nature.com/articles/s41396-021-00899-w %R 10.1038/s41396-021-00899-w %0 Journal Article %J Frontiers in Microbiology %D 2021 %T From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains? %A Geffroy, Solène %A Lechat, Marc-Marie %A Le Gac, Mickaël %A Rovillon, Georges-Augustin %A Marie, Dominique %A Bigeard, Estelle %A Malo, Florent %A Amzil, Zouher %A Guillou, Laure %A Caruana, Amandine M. N. %K RCC2644 %K RCC2645 %K RCC3327 %K RCC4871 %K RCC4872 %K RCC4890 %K RCC7037 %K RCC7038 %K RCC7039 %X Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster (sxt). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene (sxtA4), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9–187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum. %B Frontiers in Microbiology %V 12 %P 613199 %G eng %U https://www.frontiersin.org/articles/10.3389/fmicb.2021.613199/full %R 10.3389/fmicb.2021.613199 %0 Journal Article %J Nature Communications %D 2021 %T Group 2i Isochrysidales produce characteristic alkenones reflecting sea ice distribution %A Wang, Karen Jiaxi %A Huang, Yongsong %A Majaneva, Markus %A Belt, Simon T. %A Liao, Sian %A Novak, Joseph %A Kartzinel, Tyler R. %A Herbert, Timothy D. %A Richter, Nora %A Cabedo-Sanz, Patricia %K RCC107 %K RCC1195 %K RCC1334 %K RCC5486 %X Alkenones are biomarkers produced solely by algae in the order Isochrysidales that have been used to reconstruct sea surface temperature (SST) since the 1980s. However, alkenone-based SST reconstructions in the northern high latitude oceans show significant bias towards warmer temperatures in core-tops, diverge from other SST proxies in down core records, and are often accompanied by anomalously high relative abundance of the C 37 tetra-unsaturated methyl alkenone (%C 37:4 ). Elevated %C 37:4 is widely interpreted as an indicator of low sea surface salinity from polar water masses, but its biological source has thus far remained elusive. Here we identify a lineage of Isochrysidales that is responsible for elevated C 37:4 methyl alkenone in the northern high latitude oceans through next-generation sequencing and lab-culture experiments. This Isochrysidales lineage co-occurs widely with sea ice in marine environments and is distinct from other known marine alkenone-producers, namely Emiliania huxleyi and Gephyrocapsa oceanica . More importantly, the %C 37:4 in seawater filtered particulate organic matter and surface sediments is significantly correlated with annual mean sea ice concentrations. In sediment cores from the Svalbard region, the %C 37:4 concentration aligns with the Greenland temperature record and other qualitative regional sea ice records spanning the past 14 kyrs, reflecting sea ice concentrations quantitatively. Our findings imply that %C 37:4 is a powerful proxy for reconstructing sea ice conditions in the high latitude oceans on thousand- and, potentially, on million-year timescales. %B Nature Communications %V 12 %P 15 %8 dec %G eng %U http://dx.doi.org/10.1038/s41467-020-20187-z http://www.nature.com/articles/s41467-020-20187-z %R 10.1038/s41467-020-20187-z %0 Journal Article %J Geobiology %D 2021 %T The influence of elevated SiO2(aq) on intracellular silica uptake and microbial metabolism %A Tostevin, Rosalie %A Snow, Joseph T. %A Zhang, Qiong %A Tosca, Nicholas J. %A Rickaby, Rosalind E. M. %K Archaean %K culturing %K microbial metabolism %K Proterozoic %K RCC1 %K RCC1216 %K rcc1512 %K RCC1547 %K rcc539 %K silica %X Microbes are known to accumulate intracellular SiO2(aq) up to 100s of mmol/l from modern seawater (SiO2(aq) <100 µmol/l), despite having no known nutrient requirement for Si. Before the evolution of siliceous skeletons, marine silica concentrations were likely an order of magnitude higher than the modern ocean, raising the possibility that intracellular SiO2(aq) accumulation interfered with normal cellular function in non-silicifying algae. Yet, because few culturing studies have isolated the effects of SiO2(aq) at high concentration, the potential impact of elevated marine silica on early microbial evolution is unknown. Here, we test the influence of elevated SiO2(aq) on eukaryotic algae, as well as a prokaryote species. Our results demonstrate that under SiO2(aq) concentrations relevant to ancient seawater, intracellular Si accumulates to concentrations comparable to those found in siliceous algae such as diatoms. In addition, all eukaryotic algae showed a statistically significant response to the high-Si treatment, including reduced average cell sizes and/or a reduction in the maximum growth rate. In contrast, there was no consistent response to the high-Si treatment by the prokaryote species. Our results highlight the possibility that elevated marine SiO2(aq) may have been an environmental stressor during early eukaryotic evolution. %B Geobiology %V n/a %G eng %U http://onlinelibrary.wiley.com/doi/abs/10.1111/gbi.12442 %R 10.1111/gbi.12442 %0 Journal Article %D 2021 %T Les Efflorescences de Lepidodinium chlorophorum au large de la Loire et de la Vilaine : Déterminisme et conséquences sur la qualité des masses d’eau côtières %A Schapira, Mathilde %A Roux, Pauline %A Andre, Coralie %A Mertens, Kenneth %A Bilien, Gwenael %A Terre Terrillon, Aouregan %A Le Gac-Abernot, Chantal %A Siano, Raffaele %A Quéré, Julien %A Bizzozero, Lucie %A Bonneau, Francoise %A Bouget, Jean-Francois %A Cochennec-Laureau, Nathalie %A Collin, Karine %A Fortune, Mireille %A Gabellec, Raoul %A Le Merrer, Yoann %A Manach, Soazig %A Pierre-Duplessix, Olivier %A Retho, Michael %A Schmitt, Anne %A Souchu, Philippe %A Stachowski-Haberkorn, Sabine %K ? No DOI found %K rcc %K RCC1489 %X Ce projet, organisé en trois actions, avait pour objectif de mieux évaluer les risques d’eaux colorées vertes se produisant sur le secteur côtier situé au large de la Loire et de la Vilaine, en termes (i) de fréquence de ces épisodes, (ii) d’abondance et (iii) de localisation des zones à risque. Action 1 : Amélioration du recensement des eaux vertes à L. chlorophorum Action 2 : Optimisation de l’estimation des abondances de L. chlorophorum Action 3 : Identification des zones à risque au large de la Loire et de la Vilaine. %G eng %U https://archimer.ifremer.fr/doc/00724/83598/ %0 Book Section %B Progress in the Chemistry of Organic Natural Products 116 %D 2021 %T Marine Biodiscovery in a Changing World %A Reddy, Maggie M. %A Jennings, Laurence %A Thomas, Olivier P. %E Kinghorn, A. Douglas %E Falk, Heinz %E Gibbons, Simon %E Asakawa, Yoshinori %E Liu, Ji-Kai %E Dirsch, Verena M. %K Bioprospecting %K Biorepositories %K Data management system %K Marine biodiscovery %K Marine natural products %K Screenings %K taxonomy %X The term “marine biodiscovery” has been recently been adopted to describe the area of marine natural products dedicated to the search of new drugs. Several maritime countries such as Australia, New Zealand, South Korea, and Japan as well as some European countries have invested significantly in this area of research over the last 50 years. In the late 2000s, research in this field has received significant interest and support in Ireland for exploring new marine bioresources from the nutrient-rich waters of the Northeastern Atlantic Ocean. Despite undeniable success exemplified by the marketing of new drugs, especially in oncology, the integration of new technical but also environmental aspects should be considered. Indeed, global change, particularly in our oceans, such as climate change, biodiversity loss, and the emergence of microbial pathogens, not only affects the environment but ultimately contributes to social inequalities. In this contribution, new avenues and best practices are proposed, such as the development of biorepositories and shared data for the future of marine biodiscovery research. The extension of this type of scientific work will allow humanity to finally make the optimum use of marine bioresources. %B Progress in the Chemistry of Organic Natural Products 116 %S Progress in the Chemistry of Organic Natural Products %I Springer International Publishing %C Cham %P 1–36 %@ 978-3-030-80560-9 %G eng %U https://doi.org/10.1007/978-3-030-80560-9_1 %R 10.1007/978-3-030-80560-9_1 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2021 %T Marine Synechococcus picocyanobacteria: Light utilization across latitudes %A Six, Christophe %A Ratin, Morgane %A Marie, Dominique %A Corre, Erwan %K ?? Invalid DOI %K RCC2035 %K rcc2382 %K RCC2385 %K RCC2421 %K RCC2527 %K RCC2535 %K RCC2553 %K RCC2570 %K RCC515 %K rcc539 %K rcc752 %K rcc791 %K to add %X

The most ubiquitous cyanobacteria, Synechococcus, have colonized different marine thermal niches through the evolutionary specialization of lineages adapted to different ranges of temperature seawater. We used the strains of Synechococcus temperature ecotypes to study how light utilization has evolved in the function of temperature. The tropical Synechococcus (clade II) was unable to grow under 16 °C but, at temperatures >25 °C, induced very high growth rates that relied on a strong synthesis of the components of the photosynthetic machinery, leading to a large increase in photosystem cross-section and electron flux. By contrast, the Synechococcus adapted to subpolar habitats (clade I) grew more slowly but was able to cope with temperatures <10 °C. We show that growth at such temperatures was accompanied by a large increase of the photoprotection capacities using the orange carotenoid protein (OCP). Metagenomic analyzes revealed that Synechococcus natural communities show the highest prevalence of the ocp genes in low-temperature niches, whereas most tropical clade II Synechococcus have lost the gene. Moreover, bioinformatic analyzes suggested that the OCP variants of the two cold-adapted Synechococcus clades I and IV have undergone evolutionary convergence through the adaptation of the molecular flexibility. Our study points to an important role of temperature in the evolution of the OCP. We, furthermore, discuss the implications of the different metabolic cost of these physiological strategies on the competitiveness of Synechococcus in a warming ocean. This study can help improve the current hypotheses and models aimed at predicting the changes in ocean carbon fluxes in response to global warming.

%B Proceedings of the National Academy of Sciences %V 118 %G eng %U http://www.pnas.org/content/118/38/e2111300118 %R 10.1073/pnas.2111300118 %0 Journal Article %J Current Biology %D 2021 %T The mode of speciation during a recent radiation in open-ocean phytoplankton %A Filatov, Dmitry A. %A Bendif, El Mahdi %A Archontikis, Odysseas A. %A Hagino, Kyoko %A Rickaby, Rosalind E. M. %K phytoplankton %K population genetic modeling %K rcc1212 %K rcc1238 %K RCC1239 %K RCC1253 %K RCC1281 %K RCC1296 %K RCC1310 %K RCC1314 %K RCC1562 %K RCC1836 %K RCC3370 %K RCC3711 %K RCC3733 %K RCC3862 %K RCC3898 %K RCC4002 %K RCC4028 %K RCC4030 %K RCC4032 %K RCC4033 %K RCC4034 %K RCC4035 %K RCC4036 %K RCC5119 %K RCC5134 %K RCC5137 %K RCC5141 %K RCC6566 %K RCC6730 %K secondary contact %K sequence polymorphism %K speciation %X Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton. %B Current Biology %8 oct %G eng %U https://www.sciencedirect.com/science/article/pii/S0960982221013415 %R 10.1016/j.cub.2021.09.073 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2021 %T Molecular bases of an alternative dual-enzyme system for light color acclimation of marine \textit{Synechococcus cyanobacteria %A Grébert, Théophile %A Nguyen, Adam A. %A Pokhrel, Suman %A Joseph, Kes Lynn %A Ratin, Morgane %A Dufour, Louison %A Chen, Bo %A Haney, Allissa M. %A Karty, Jonathan A. %A Trinidad, Jonathan C. %A Garczarek, Laurence %A Schluchter, Wendy M. %A Kehoe, David M. %A Partensky, Frédéric %K RCC2374 %K to add %X

Marine Synechococcus cyanobacteria owe their ubiquity in part to the wide pigment diversity of their light-harvesting complexes. In open ocean waters, cells predominantly possess sophisticated antennae with rods composed of phycocyanin and two types of phycoerythrins (PEI and PEII). Some strains are specialized for harvesting either green or blue light, while others can dynamically modify their light absorption spectrum to match the dominant ambient color. This process, called type IV chromatic acclimation (CA4), has been linked to the presence of a small genomic island occurring in two configurations (CA4-A and CA4-B). While the CA4-A process has been partially characterized, the CA4-B process has remained an enigma. Here we characterize the function of two members of the phycobilin lyase E/F clan, MpeW and MpeQ, in Synechococcus sp. strain A15-62 and demonstrate their critical role in CA4-B. While MpeW, encoded in the CA4-B island and up-regulated in green light, attaches the green light-absorbing chromophore phycoerythrobilin to cysteine-83 of the PEII α-subunit in green light, MpeQ binds phycoerythrobilin and isomerizes it into the blue light-absorbing phycourobilin at the same site in blue light, reversing the relationship of MpeZ and MpeY in the CA4-A strain RS9916. Our data thus reveal key molecular differences between the two types of chromatic acclimaters, both highly abundant but occupying distinct complementary ecological niches in the ocean. They also support an evolutionary scenario whereby CA4-B island acquisition allowed former blue light specialists to become chromatic acclimaters, while former green light specialists would have acquired this capacity by gaining a CA4-A island.

%B Proceedings of the National Academy of Sciences %V 118 %P e2019715118 %G eng %U http://www.pnas.org/lookup/doi/10.1073/pnas.2019715118 %R 10.1073/pnas.2019715118 %0 Journal Article %J Marine Drugs %D 2021 %T A New, Quick, and Simple Protocol to Evaluate Microalgae Polysaccharide Composition %A Decamp, Antoine %A Michelo, Orane %A Rabbat, Christelle %A Laroche, Céline %A Grizeau, Dominique %A Pruvost, Jérémy %A Gonçalves, Olivier %K rcc2380 %K RCC3438 %X In this work, a new methodological approach, relying on the high specificity of enzymes in a complex mixture, was developed to estimate the composition of bioactive polysaccharides produced by microalgae, directly in algal cultures. The objective was to set up a protocol to target oligomers commonly known to be associated with exopolysaccharides’ (EPS) nutraceutical and pharmaceutical activities (i.e., rhamnose, fucose, acidic sugars, etc.) without the constraints classically associated with chromatographic methods, while maintaining a resolution sufficiently high to enable their monitoring in the culture system. Determination of the monosaccharide content required the application of acid hydrolysis (2 M trifluoroacetic acid) followed by NaOH (2 M) neutralization. Quantification was then carried out directly on the fresh hydrolysate using enzyme kits corresponding to the main monosaccharides in a pre-determined composition of the polysaccharides under analysis. Initial results showed that the enzymes were not sensitive to the presence of TFA and NaOH, so the methodology could be carried out on fresh hydrolysate. The limits of quantification of the method were estimated as being in the order of the log of nanograms of monosaccharides per well, thus positioning it among the chromatographic methods in terms of analytical performance. A comparative analysis of the results obtained by the enzymatic method with a reference method (high-performance anion-exchange chromatography) confirmed good recovery rates, thus validating the closeness of the protocol. Finally, analyses of raw culture media were carried out and compared to the results obtained in miliQ water; no differences were observed. The new approach is a quick, functional analysis method allowing routine monitoring of the quality of bioactive polysaccharides in algal cultures grown in photobioreactors. %B Marine Drugs %V 19 %P 101 %G eng %U https://www.mdpi.com/1660-3397/19/2/101 %R 10.3390/md19020101 %0 Journal Article %J Angewandte Chemie International Edition %D 2021 %T Opto-Electrochemical Dissolution Reveals Coccolith Calcium Carbonate Content %A Yang, Minjun %A Batchelor-McAuley, Christopher %A Barton, Samuel %A Rickaby, Rosalind E. M. %A Bouman, Heather A. %A Compton, Richard G. %K analytical methods %K calcite dissolution %K electrochemistry %K global carbonate cycle %K marine phytoplankton %K RCC1130 %K RCC1198 %K RCC1216 %K RCC1314 %X Coccoliths are plates of biogenic calcium carbonate secreted by calcifying marine phytoplankton; annually these phytoplankton are responsible for exporting >1 billion tonnes (1015 g) of calcite to the deep ocean. Rapid and reliable methods for assessing the degree of calcification are technically challenging because the coccoliths are micron sized and contain picograms (pg) of calcite. Here we pioneer an opto-eletrochemical acid titration of individual coccoliths which allows 3D reconstruction of each individual coccolith via in situ optical imaging enabling direct inference of the coccolith mass. Coccolith mass ranging from 2 to 400 pg are reported herein, evidencing both inter- and intra-species variation over four different species. We foresee this scientific breakthrough, which is independent of knowledge regarding the species and calibration-free, will allow continuous monitoring and reporting of the degree of coccolith calcification in the changing marine environment. %B Angewandte Chemie International Edition %V 60 %P 20999–21006 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202108435 %R 10.1002/anie.202108435 %0 Journal Article %J Processes %D 2021 %T Production of Omega-3 Oil by Aurantiochytrium mangrovei Using Spent Osmotic Solution from Candied Fruit Industry as Sole Organic Carbon Source %A Russo, Giovanni L. %A Langellotti, Antonio L. %A Blasco, Thierry %A Oliviero, Maria %A Sacchi, Raffaele %A Masi, Paolo %K DHA %K food waste %K Microalgae %K PUFA %K rcc %K RCC893 %K sustainability %X Osmotic dehydration is an important phase in the production of dried products, including most fruits and vegetables, in the food industry. The drying process for candied fruit produces a liquid waste called “spent osmotic solution”, which is characterized by a high content of organic compounds, mostly dissolved sugars. The sugar content of this food by-product could be valorized through the growth of biomass with a high added value. In this study, the spent osmotic solution from the candied fruit industry was used as an organic carbon source for the growth and production of docosahexaenoic acid (DHA) in the cultivation of Aurantiochytrium mangrovei RCC893. The carbon content of the standard media was completely replaced by the sugars present in this food by-product. After that, the growth condition of this strain was optimized through response surface methodologies using a central composite design (CCD), and the optimal combination of the spent osmotic solution and nitrogen was established. Moreover, a scale-up trial was performed using the optimal conditions obtained after CCD to evaluate the scalability of the process. %B Processes %V 9 %P 1834 %8 oct %G eng %U https://www.mdpi.com/2227-9717/9/10/1834 %R 10.3390/pr9101834 %0 Journal Article %J BMC Biology %D 2021 %T Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. %A Farhat, Sarah %A Le, Phuong %A Kayal, Ehsan %A Noel, Benjamin %A Bigeard, Estelle %A Corre, Erwan %A Maumus, Florian %A Florent, Isabelle %A Alberti, Adriana %A Aury, Jean-Marc %A Barbeyron, Tristan %A Cai, Ruibo %A Silva, Corinne Da %A Istace, Benjamin %A Labadie, Karine %A Marie, Dominique %A Mercier, Jonathan %A Rukwavu, Tsinda %A Szymczak, Jeremy %A Tonon, Thierry %A Alves-de-Souza, Catharina %A Rouze, Pierre %A de Peer, Yves Van %A Wincker, Patrick %A Rombauts, Stephane %A Porcel, Betina M %A Guillou, Laure %K Dinoflagellate %K genome %K Introner elements %K Non-canonical introns %K parasite %K RCC4383 %K RCC4398 %B BMC Biology %P 1–21 %G eng %R 10.1186/s12915-020-00927-9 %0 Journal Article %J Current Biology %D 2021 %T Rappemonads are haptophyte phytoplankton %A Kawachi, Masanobu %A Nakayama, Takuro %A Kayama, Motoki %A Nomura, Mami %A Miyashita, Hideaki %A Bojo, Othman %A Rhodes, Lesley %A Sym, Stuart %A Pienaar, Richard N. %A Probert, Ian %A Inouye, Isao %A Kamikawa, Ryoma %K environmental DNA sequences %K morphological evolution %K organellar phylogenomics %K phytoplankton diversity %K RCC3430 %K transmission electron microscopy %X Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 which is responsible for around 50% of global net primary production.12,13 However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.14, 15, 16, 17 The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,15 has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities. %B Current Biology %8 mar %G eng %U https://www.sciencedirect.com/science/article/pii/S0960982221003511 %R 10.1016/j.cub.2021.03.012 %0 Journal Article %J Journal of Plankton Research %D 2021 %T Response of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas to oxidative stress in three phytoplankton species %A Royer, C %A Gypens, N %A Cardol, P %A Borges, A V %A Roberty, S %K rcc %K RCC1719 %K RCC4800 %X Several phytoplankton species produce the metabolites dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) but their intracellular roles need to be better understood. To improve the understanding of the DMSP antioxidant function suggested by Sunda et al. (2002), we exposed the diatom Skeletonema costatum, the Prymnesiophyceae Phaeocystis globosa and the dinoflagellate Heterocapsa triquetra to experimental treatments known to cause potential oxidative stress (high light intensities (HL); HL with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU); menadione sodium bisulfite (MSB)). DMSP and DMSO concentrations decreased after 6 h in all treatments indicating an interaction with Reactive Oxygen Species (ROS) produced. DMSP and DMSO-to-cell ratios in control conditions were higher for H. triquetra, while being unable to grow under HL. DMSP and DMSO-to-cell carbon were the highest for P. globosa, while the other species had similar values. During long-term treatment, these ratios were not increased in high-light grown cells of P. globosa and S. costatum. Overall, this illustrates that (1) the DMSP- and DMSO-to-cell or carbon seems to be not indicative of the capability of the species to tolerate an oxidative stress, (2) these molecules could react with ROS and lower their cellular concentration, but no clues demonstrated that these molecules are part of the antioxidant response of the cell. %B Journal of Plankton Research %V 43 %P 673–690 %8 sep %G eng %U https://doi.org/10.1093/plankt/fbab052 %R 10.1093/plankt/fbab052 %0 Journal Article %J bioRxiv %D 2021 %T Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae %A Decelle, Johan %A Veronesi, Giulia %A LeKieffre, Charlotte %A Gallet, Benoit %A Chevalier, Fabien %A Stryhanyuk, Hryhoriy %A Marro, Sophie %A Ravanel, Stéphane %A Tucoulou, Rémi %A Schieber, Nicole %A Finazzi, Giovanni %A Schwab, Yannick %A Musat, Niculina %X Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the “greenhouse-like” colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low 13C and 15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged. %B bioRxiv %P 2021.03.13.435225 %G eng %U https://www.biorxiv.org/content/10.1101/2021.03.13.435225v1 %R 10.1101/2021.03.13.435225 %0 Generic %D 2021 %T The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching %A Roquis, David %A Cosseau, Céline %A Raffalli, Kelly Brener %A Romans, Pascal %A Masanet, Patrick %A Mitta, Guillaume %A Grunau, Christoph %A Vidal-Dupiol, Jeremie %K chromatin structure %K Histone H3 clipping %K invertebrate epigenetics %K Pocillopora acuta %K Pocillopora damicornis %K rcc %K RCC4017 %X

Background: Pocillopora acuta is a hermatypic coral with strong ecological importance. Anthropogenic disturbances and global warming are major threats that can induce coral bleaching, the disruption of the mutualistic symbiosis between the coral host and its endosymbiotic algae. Previous works have shown that somaclonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. However, almost no work had been published on the P. acuta epigenome, especially on histone modifications. In this study, we aim at providing the first insight into chromatin structure of this species. Methods: We aligned the amino acid sequence of P. acuta core histones with histone sequences from various phyla. We developed a centri-filtration on sucrose gradient to separate chromatin from the host and the symbiont. The presence of histone H3 protein and specific histone modifications were then detected by western blot performed on histone extraction done from bleached and healthy corals. Finally, micrococcal nuclease (MNase) digestions were undertaken to study nucleosomal organization. Results: The centri-filtration enabled coral chromatin isolation with less than 2% of contamination by endosymbiont material. Histone sequences alignments with other species show that P. acuta displays on average \textasciitilde90% of sequence similarities with mice and \textasciitilde96% with other corals. H3 detection by western blot showed that H3 is clipped in healthy corals while it appeared to be intact in bleached corals. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure. Conclusions: These results provide a first insight into the chromatin, nucleosome and histone structure of P. acuta . The unusual patterns highlighted in this study and partly shared with other cnidarian will need to be further studied to better understand its role in corals.

%I Wellcome Open Research %8 jul %G eng %U https://wellcomeopenresearch.org/articles/6-195 %R 10.12688/wellcomeopenres.17058.1 %0 Journal Article %J The ISME Journal %D 2021 %T Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts %A Bachy, Charles %A Yung, Charmaine C. M. %A Needham, David M. %A Gazitúa, Maria Consuelo %A Roux, Simon %A Limardo, Alexander J. %A Choi, Chang Jae %A Jorgens, Danielle M. %A Sullivan, Matthew B. %A Worden, Alexandra Z. %K RCC715 %K RCC716 %X The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (\textasciitilde210 kb) than BI-Viruses and BII-V1. BII-Vs share \textasciitilde90% of their proteins, and between 65% to 83% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters. %B The ISME Journal %P 1–19 %8 may %G eng %U https://www.nature.com/articles/s41396-021-00989-9 %R 10.1038/s41396-021-00989-9 %0 Journal Article %J Elementa: Science of the Anthropocene %D 2020 %T Culturable diversity of Arctic phytoplankton during pack ice melting %A Ribeiro, Catherine Gérikas %A dos Santos, Adriana Lopes %A Gourvil, Priscillia %A Le Gall, Florence %A Marie, Dominique %A Tragin, Margot %A Probert, Ian %A Vaulot, Daniel %K RCC5197 %K RCC5198 %K RCC5199 %K RCC5200 %K RCC5201 %K RCC5202 %K RCC5203 %K RCC5204 %K RCC5205 %K RCC5206 %K RCC5207 %K RCC5208 %K RCC5209 %K RCC5210 %K RCC5211 %K RCC5212 %K RCC5213 %K RCC5214 %K RCC5215 %K RCC5216 %K RCC5217 %K RCC5218 %K RCC5219 %K RCC5220 %K RCC5221 %K RCC5222 %K RCC5223 %K RCC5224 %K RCC5225 %K RCC5226 %K RCC5227 %K RCC5228 %K RCC5229 %K RCC5230 %K RCC5231 %K RCC5232 %K RCC5233 %K RCC5234 %K RCC5235 %K RCC5236 %K RCC5237 %K RCC5238 %K RCC5239 %K RCC5240 %K RCC5241 %K RCC5242 %K RCC5243 %K RCC5244 %K RCC5245 %K RCC5246 %K RCC5247 %K RCC5248 %K RCC5249 %K RCC5250 %K RCC5251 %K RCC5252 %K RCC5253 %K RCC5254 %K RCC5255 %K RCC5256 %K RCC5257 %K RCC5258 %K RCC5259 %K RCC5260 %K RCC5261 %K RCC5262 %K RCC5263 %K RCC5264 %K RCC5265 %K RCC5266 %K RCC5267 %K RCC5268 %K RCC5269 %K RCC5270 %K RCC5271 %K RCC5272 %K RCC5273 %K RCC5274 %K RCC5275 %K RCC5276 %K RCC5277 %K RCC5278 %K RCC5279 %K RCC5280 %K RCC5281 %K RCC5282 %K RCC5283 %K RCC5284 %K RCC5285 %K RCC5286 %K RCC5287 %K RCC5288 %K RCC5289 %K RCC5290 %K RCC5291 %K RCC5292 %K RCC5293 %K RCC5294 %K RCC5295 %K RCC5296 %K RCC5297 %K RCC5298 %K RCC5299 %K RCC5300 %K RCC5301 %K RCC5302 %K RCC5303 %K RCC5304 %K RCC5305 %K RCC5306 %K RCC5307 %K RCC5308 %K RCC5309 %K RCC5310 %K RCC5311 %K RCC5312 %K RCC5313 %K RCC5314 %K RCC5315 %K RCC5316 %K RCC5317 %K RCC5318 %K RCC5319 %K RCC5320 %K RCC5321 %K RCC5322 %K RCC5323 %K RCC5324 %K RCC5325 %K RCC5326 %K RCC5327 %K RCC5328 %K RCC5329 %K RCC5330 %K RCC5331 %K RCC5332 %K RCC5333 %K RCC5334 %K RCC5335 %K RCC5336 %K RCC5337 %K RCC5338 %K RCC5339 %K RCC5340 %K RCC5341 %K RCC5342 %K RCC5343 %K RCC5344 %K RCC5345 %K RCC5346 %K RCC5347 %K RCC5348 %K RCC5349 %K RCC5350 %K RCC5351 %K RCC5352 %K RCC5353 %K RCC5354 %K RCC5355 %K RCC5356 %K RCC5357 %K RCC5358 %K RCC5359 %K RCC5360 %K RCC5361 %K RCC5362 %K RCC5363 %K RCC5364 %K RCC5365 %K RCC5366 %K RCC5367 %K RCC5368 %K RCC5369 %K RCC5370 %K RCC5371 %K RCC5372 %K RCC5373 %K RCC5374 %K RCC5375 %K RCC5376 %K RCC5377 %K RCC5378 %K RCC5379 %K RCC5380 %K RCC5381 %K RCC5382 %K RCC5383 %K RCC5384 %K RCC5385 %K RCC5386 %K RCC5387 %K RCC5388 %K RCC5389 %K RCC5390 %K RCC5391 %K RCC5392 %K RCC5393 %K RCC5394 %K RCC5395 %K RCC5396 %K RCC5397 %K RCC5398 %K RCC5399 %K RCC5400 %K RCC5401 %K RCC5402 %K RCC5403 %K RCC5404 %K RCC5405 %K RCC5406 %K RCC5407 %K RCC5408 %K RCC5409 %K RCC5410 %K RCC5411 %K RCC5412 %K RCC5413 %K RCC5414 %K RCC5415 %K RCC5416 %K RCC5417 %K RCC5418 %K RCC5419 %K RCC5420 %K RCC5421 %K RCC5422 %K RCC5423 %K RCC5424 %K RCC5425 %K RCC5426 %K RCC5427 %K RCC5428 %K RCC5429 %K RCC5430 %K RCC5431 %K RCC5432 %K RCC5433 %K RCC5434 %K RCC5435 %K RCC5436 %K RCC5437 %K RCC5438 %K RCC5439 %K RCC5440 %K RCC5441 %K RCC5442 %K RCC5443 %K RCC5444 %K RCC5445 %K RCC5446 %K RCC5447 %K RCC5448 %K RCC5449 %K RCC5450 %K RCC5451 %K RCC5452 %K RCC5453 %K RCC5454 %K RCC5455 %K RCC5456 %K RCC5457 %K RCC5458 %K RCC5459 %K RCC5460 %K RCC5461 %K RCC5462 %K RCC5463 %K RCC5464 %K RCC5465 %K RCC5466 %K RCC5467 %K RCC5468 %K RCC5469 %K RCC5470 %K RCC5471 %K RCC5472 %K RCC5473 %K RCC5474 %K RCC5475 %K RCC5476 %K RCC5477 %K RCC5478 %K RCC5479 %K RCC5480 %K RCC5481 %K RCC5482 %K RCC5483 %K RCC5484 %K RCC5485 %K RCC5486 %K RCC5487 %K RCC5488 %K RCC5489 %K RCC5490 %K RCC5491 %K RCC5492 %K RCC5493 %K RCC5494 %K RCC5495 %K RCC5496 %K RCC5497 %K RCC5498 %K RCC5499 %K RCC5500 %K RCC5501 %K RCC5502 %K RCC5503 %K RCC5504 %K RCC5505 %K RCC5506 %K RCC5507 %K RCC5508 %K RCC5509 %K RCC5510 %K RCC5511 %K RCC5512 %K RCC5513 %K RCC5514 %K RCC5515 %K RCC5516 %K RCC5517 %K RCC5518 %K RCC5519 %K RCC5520 %K RCC5521 %K RCC5522 %K RCC5523 %K RCC5524 %K RCC5525 %K RCC5526 %K RCC5527 %K RCC5528 %K RCC5529 %K RCC5530 %K RCC5531 %K RCC5532 %K RCC5533 %K RCC5534 %K RCC5535 %K RCC5536 %K RCC5537 %K RCC5538 %K RCC5539 %K RCC5540 %K RCC5541 %K RCC5542 %K RCC5543 %K RCC5544 %K RCC5545 %K RCC5546 %K RCC5547 %K RCC5548 %K RCC5549 %K RCC5550 %K RCC5551 %K RCC5552 %K RCC5553 %K RCC5554 %K RCC5555 %K RCC5556 %K RCC5557 %K RCC5558 %K RCC5559 %K RCC5560 %K RCC5561 %K RCC5562 %K RCC5563 %K RCC5564 %K RCC5565 %K RCC5566 %K RCC5567 %K RCC5568 %K RCC5569 %K RCC5570 %K RCC5571 %K RCC5572 %K RCC5573 %K RCC5574 %K RCC5575 %K RCC5576 %K RCC5577 %K RCC5578 %K RCC5579 %K RCC5580 %K RCC5581 %K RCC5582 %K RCC5583 %K RCC5584 %K RCC5585 %K RCC5586 %K RCC5587 %K RCC5588 %K RCC5589 %K RCC5590 %K RCC5591 %K RCC5592 %K RCC5593 %K RCC5594 %K RCC5595 %K RCC5596 %K RCC5597 %K RCC5598 %K RCC5599 %K RCC5600 %K RCC5601 %K RCC5602 %K RCC5603 %K RCC5604 %K RCC5605 %K RCC5606 %K RCC5607 %K RCC5608 %K RCC5609 %K RCC5610 %K RCC5611 %K RCC5612 %X Massive phytoplankton blooms develop at the Arctic ice edge, sometimes extending far under the pack ice. An extensive culturing effort was conducted before and during a phytoplankton bloom in Baffin Bay between April and July 2016. Different isolation strategies were applied, including flow cytometry cell sorting, manual single cell pipetting and serial dilution. Although all three techniques yielded the most common organisms, each technique retrieved specific taxa, highlighting the importance of using several methods to maximize the number and diversity of isolated strains. More than 1,000 cultures were obtained, characterized by 18S rRNA sequencing and optical microscopy and de-replicated to a subset of 276 strains presented in this work. Strains grouped into 57 genotypes defined by 100% 18S rRNA sequence similarity. These genotypes spread across five divisions: Heterokontophyta, Chlorophyta, Cryptophyta, Haptophyta and Dinophyta. Diatoms were the most abundant group (193 strains), mostly represented by the genera Chaetoceros and Attheya. The genera Rhodomonas and Pyramimonas were the most abundant non-diatom nanoplankton strains, while Micromonas polaris dominated the picoplankton. Diversity at the class level was higher during the peak of the bloom. Potentially new species were isolated, in particular within the genera Navicula, Nitzschia, Coscinodiscus, Thalassiosira, Pyramimonas, Mantoniella and Isochrysis. %B Elementa: Science of the Anthropocene %V 8 %P 6 %8 feb %G eng %U https://www.biorxiv.org/content/10.1101/642264v1 https://www.elementascience.org/article/10.1525/elementa.401/ %R 10.1525/elementa.401 %0 Journal Article %J Aquatic Microbial Ecology %D 2020 %T Diel oscillations in the feeding activity of heterotrophic and mixotrophic nanoplankton in the North Pacific Subtropical Gyre %A Connell, PE %A Ribalet, F %A Armbrust, EV %A White, A %A Caron, DA %K bacterivory %K diel cycles %K mixotrophy %K nanoplankton grazing %K picocyanobacteria %K RCC80 %X Daily oscillations in photosynthetically active radiation strongly influence the timing of metabolic processes in picocyanobacteria, but it is less clear how the light-dark cycle affects the activities of their consumers. We investigated the relationship between marine picocyanobacteria and nanoplanktonic consumers throughout the diel cycle to determine whether heterotrophic and mixotrophic protists (algae with phagotrophic ability) display significant periodicity in grazing pressure. Carbon biomass of Prochlorococcus and Synechococcus was estimated continuously from abundances and cell size measurements made by flow cytometry. Picocyanobacterial dynamics were then compared to nanoplankton abundances and ingestion of fluorescently labeled bacteria measured every 4 h during a 4 d survey in the North Pacific Subtropical Gyre. Grazing of the labeled bacteria by heterotrophic nanoplankton was significantly greater at night than during the day. The grazing activity of mixotrophic nanoplankton showed no diel periodicity, suggesting that they may feed continuously, albeit at lower rates than heterotrophic nanoplankton, to alleviate nutrient limitation in this oligotrophic environment. Diel changes in Prochlorococcus biomass indicated that they could support substantial growth of nanoplankton if those grazers are the main source of picocyanobacterial mortality, and that grazers may contribute to temporally stable abundances of picocyanobacteria. %B Aquatic Microbial Ecology %V 85 %P 167–181 %8 dec %G eng %U http://dx.doi.org/10.3354/ame01950 https://www.int-res.com/abstracts/ame/v85/p167-181/ %R 10.3354/ame01950 %0 Journal Article %J Journal of Experimental Marine Biology and Ecology %D 2020 %T Dissolved organic phosphorus uptake by marine phytoplankton is enhanced by the presence of dissolved organic nitrogen %A Fitzsimons, Mark F. %A Probert, Ian %A Gaillard, Fanny %A Rees, Andrew P. %K Alkaline phosphatase %K COASTAL WATERS %K Dissolved organic nitrogen %K Dissolved organic phosphorus %K Marine algae %K P-limitation %K RCC2563 %K RCC2565 %X Organic nutrients can constitute the major fractions (up to 70%) of aquatic nitrogen (N) and phosphorus (P), but their cycling is poorly understood relative to the inorganic pools. Some phytoplankton species access P from the dissolved organic phosphorus (DOP) pool through expression of alkaline phosphatase (AP), which hydrolyses orthophosphate from organic molecules, and is thought to occur either at low concentrations of dissolved inorganic P (DIP), or elevated ratios of dissolved inorganic N (DIN) to DIP. Three algal strains native to the North-East Atlantic Ocean (coccolithophore, dinoflagellate and diatom species) were grown under representative, temperate conditions, and the dissolved N and P components amended to include dissolved organic N (DON) and DOP. The activity of AP was measured to determine the rate of DOP uptake by each algal species. The addition of DON and DOP enhanced the growth of the algal species, regardless of DIN and DIP concentrations. In cultures where the total concentrations and absolute N: P ratio was unchanged but the N pool included both DON and DIN, an increase in alkaline phosphatase activity (APA) was measured. This suggested that the presence of DON triggered the selective uptake of DOP. The uptake of organic P was confirmed by detection of adenosine in DOP-amended culture media, indicating that P had been cleaved from ADP and ATP added to the media as DOP, and cellular P concentration in these cultures exceeded the calculated concentration based on uptake of DIP only. Our data demonstrates that organic nutrients can enhance and sustain marine algal productivity. The findings have implications for marine ecosystem function and health, since climate change scenarios predict variable riverine inputs to coastal areas, altered N: P ratios, and changes in the inorganic to organic balance of the nutrient pools. %B Journal of Experimental Marine Biology and Ecology %V 530-531 %P 151434 %8 sep %G eng %U https://doi.org/10.1016/j.jembe.2020.151434 https://linkinghub.elsevier.com/retrieve/pii/S0022098119304666 %R 10.1016/j.jembe.2020.151434 %0 Journal Article %J The ISME Journal %D 2020 %T Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel %A Arsenieff, Laure %A Le Gall, Florence %A Rigaut-jalabert, Fabienne %A Mahé, Frédéric %A Sarno, Diana %A Gouhier, Léna %A Baudoux, Anne-claire %A Simon, Nathalie %K RCC4657 %K RCC4658 %K RCC4659 %K RCC4660 %K RCC4661 %K RCC4662 %K RCC4663 %K RCC4664 %K RCC4665 %K RCC4666 %K RCC5154 %K RCC5839 %K RCC5840 %K RCC5841 %K RCC5842 %K RCC5843 %K RCC5844 %K RCC5845 %K RCC5846 %K RCC5847 %K RCC5848 %K RCC5849 %K RCC5850 %K RCC5851 %K RCC5852 %K RCC5853 %K RCC5854 %K RCC5855 %K RCC5856 %K RCC5857 %K RCC5859 %K RCC5860 %K RCC5861 %K RCC5862 %K RCC5863 %K RCC5864 %K RCC5865 %K RCC5866 %K RCC5867 %K RCC5868 %K RCC5869 %K RCC5870 %K RCC5871 %K RCC5872 %K RCC5873 %K RCC5875 %K RCC5876 %K RCC5877 %K RCC5878 %K RCC5879 %K RCC5880 %K RCC5881 %K RCC5882 %K RCC5883 %K RCC5884 %K RCC5885 %K RCC5886 %K RCC5887 %K RCC5921 %B The ISME Journal %8 apr %G eng %U http://dx.doi.org/10.1038/s41396-020-0659-6 http://www.nature.com/articles/s41396-020-0659-6 %R 10.1038/s41396-020-0659-6 %0 Journal Article %J Toxics %D 2020 %T Effect of 10 UV filters on the brine shrimp Artemia salina and themarinemicroalga Tetraselmis sp. %A Thorel, Evane %A Clergeaud, Fanny %A Jaugeon, Lucie %A Rodrigues, Alice M.S. %A Lucas, Julie %A Stien, Didier %A Lebaron, Philippe %K Artemia salina %K marine environment %K Marine microalgae %K RCC500 %K Toxicity tests %K UV-filters %X The presence of pharmaceutical and personal care product (PPCP) residues in the aquatic environment is an emerging issue due to their uncontrolled release through gray water, and accumulation in the environment that may affect living organisms, ecosystems and public health. The aim of this study is to assess the toxicity of benzophenone-3 (BP-3), bis-ethylhexyloxyphenol methoxyphenyl triazine (BEMT), butyl methoxydibenzoylmethane (BM), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), 2-ethylhexyl salicylate (ES), diethylaminohydroxybenzoyl hexyl benzoate (DHHB), diethylhexyl butamido triazone (DBT), ethylhexyl triazone (ET), homosalate (HS) and octocrylene (OC) on marine organisms from two major trophic levels, including autotrophs (Tetraselmis sp.) and heterotrophs (Artemia salina). In general, results showed that both HS and OC were the most toxic UV filters for our tested species, followed by a significant effect of BM on Artemia salina due to BM-but only at high concentrations (1 mg/L). ES, BP3 and DHHB affected the metabolic activity of the microalgae at 100 ??g/L. BEMT, DBT, ET, MBBT had no effect on the tested organisms, even at high concentrations (2 mg/L). OC toxicity represents a risk for those species, since concentrations used in this study are 15-90 times greater than those reported in occurrence studies for aquatic environments. For the first time in the literature, we report HS toxicity on a microalgae species at concentrations complementing those found in aquatic environments. These preliminary results could represent a risk in the future if concentrations of OC and HS continue to increase. %B Toxics %V 8 %P 29 %8 jun %G eng %U www.mdpi.com/journal/toxics %R 10.3390/TOXICS8020029 %0 Journal Article %J Frontiers in Microbiology %D 2020 %T Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria %A Doré, Hugo %A Farrant, Gregory K. %A Guyet, Ulysse %A Haguait, Julie %A Humily, Florian %A Ratin, Morgane %A Pitt, Frances D. %A Ostrowski, Martin %A Six, Christophe %A Brillet-Guéguen, Loraine %A Hoebeke, Mark %A Bisch, Antoine %A Le Corguillé, Gildas %A Corre, Erwan %A Labadie, Karine %A Aury, Jean-Marc %A Wincker, Patrick %A Choi, Dong Han %A Noh, Jae Hoon %A Eveillard, Damien %A Scanlan, David J. %A Partensky, Frédéric %A Garczarek, Laurence %K amino-acid substitutions %K comparative genomics %K evolution %K genomic islands %K marine cyanobacteria %K niche adaptation %K Prochlorococcus %K rcc1084 %K RCC1085 %K RCC1086 %K RCC1087 %K RCC156 %K RCC158 %K rcc162 %K RCC2033 %K RCC2035 %K RCC2319 %K RCC2366 %K RCC2368 %K RCC2369 %K RCC2374 %K RCC2376 %K RCC2378 %K RCC2379 %K rcc2380 %K RCC2381 %K rcc2382 %K RCC2383 %K RCC2385 %K RCC2433 %K RCC2436 %K RCC2438 %K RCC2527 %K RCC2528 %K RCC2533 %K RCC2534 %K RCC2535 %K RCC2553 %K RCC2554 %K RCC2555 %K RCC2556 %K RCC2571 %K RCC2673 %K RCC278 %K rcc296 %K RCC307 %K RCC328 %K RCC3377 %K RCC407 %K RCC515 %K rcc539 %K rcc555 %K RCC556 %K rcc752 %K RCC753 %K rcc791 %K Synechococcus %B Frontiers in Microbiology %V 11 %P 1–23 %8 sep %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2020.567431/full %R 10.3389/fmicb.2020.567431 %0 Journal Article %J Ecology Letters %D 2020 %T Evolutionary temperature compensation of carbon fixation in marine phytoplankton %A Barton, Samuel %A Jenkins, James %A Buckling, Angus %A Schaum, C.-Elisa %A Smirnoff, Nicholas %A Raven, John A. %A Yvon-Durocher, Gabriel %E Ezenwa, Vanessa %K climate change %K evolutionary ecology %K metabolism %K phytoplankton physiology %K RCC1303 %K rcc1512 %K RCC1773 %K RCC4221 %K RCC623 %K RCC626 %K RCC652 %K RCC80 %K RCC834 %K thermal performance curves %X The efficiency of carbon sequestration by the biological pump could decline in the coming decades because respiration tends to increase more with temperature than photosynthesis. Despite these differences in the short-term temperature sensitivities of photosynthesis and respiration, it remains unknown whether the long-term impacts of global warming on metabolic rates of phytoplankton can be modulated by evolutionary adaptation. We found that respiration was consistently more temperature dependent than photosynthesis across 18 diverse marine phytoplankton, resulting in universal declines in the rate of carbon fixation with short-term increases in temperature. Long-term experimental evolution under high temperature reversed the short-term stimulation of metabolic rates, resulting in increased rates of carbon fixation. Our findings suggest that thermal adaptation may therefore have an ameliorating impact on the efficiency of phytoplankton as primary mediators of the biological carbon pump. %B Ecology Letters %P ele.13469 %8 feb %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13469 %R 10.1111/ele.13469 %0 Journal Article %J Scientific Reports %D 2020 %T High resolution spatial analyses of trace elements in coccoliths reveal new insights into element incorporation in coccolithophore calcite %A Bottini, Cinzia %A Dapiaggi, Monica %A Erba, Elisabetta %A Faucher, Giulia %A Rotiroti, Nicola %K Environmental chemistry %K Environmental impact %K Marine chemistry %K Pollution remediation %K RCC1198 %K RCC1303 %X Coccolithophores are phytoplanktonic algae which produce an exoskeleton made of single platelets of calcite named coccoliths. They are widespread in all oceans and directly impact the short- and long-term C cycle. The study of coccolith size, morphology and elemental composition reveals important information regarding the ability of the cell to calcify and on the factors that influence this process. In this regard, very little is known about coccolith composition and its changes under altered environmental conditions. Here, we present high resolution (50 × 50 nm) elemental spatial distribution in pristine coccoliths of Coccolithus pelagicus and Gephyrocapsa oceanica reconstructed via X-ray fluorescence analyses at synchrotron. The studied specimens are from control culture and metal-enriched (V, Ni, Zn and Pb) experiments. The analysed specimens produced under stress conditions, display an irregular shape and are thinner, especially in the external rim, with ca. 1/3 lower Ca concentrations compared to specimens from the control. The same specimens also have higher Sr/Ca ratio with highest values in the coccolith external rim, suggesting that difficulty in calcification is additionally reflected in increased Sr/Ca ratios. Selenium is found in the coccolith as possible substitute of carbonate in the calcite. V and Pb apparently did not interact with the coccoliths while Zn and Ni were deposited on the coccolith surface. %B Scientific Reports %V 10 %P 9825 %G eng %U http://www.nature.com/articles/s41598-020-66503-x %R 10.1038/s41598-020-66503-x %0 Journal Article %J Archives of Biochemistry and Biophysics %D 2020 %T Identification and characterization of ChlreSEX4, a novel glucan phosphatase from Chlamydomonas reinhardtii green alga %A Carrillo, Julieta B. %A Torresi, Florencia %A Morales, Luisina L. %A Ricordi, Micaela %A Gomez-Casati, Diego F. %A Busi, Maria V. %A Martín, Mariana %K Chlamydomonas Reinhardtii %K ChlreSEX4 %K Glucan phosphatase %K SEX4 %K Starch phosphorylation %X Chlamydomonas reinhardtii is the best known unicellular green alga model which has long been used to investigate all kinds of cellular processes, including starch metabolism. Here we identified and characterized a novel enzyme, ChlreSEX4, orthologous to glucan phosphatase SEX4 from Arabidopsis thaliana, that is capable of binding and dephosphorylating amylopectin in vitro. We also reported that cysteine 224 and tryptophan 305 residues are critical for enzyme catalysis and substrate binding. Furthermore, we verified that ChlreSEX4 gene is expressed in vivo and that glucan phosphatase activity is measurable in Chlamydomonas protein extracts. In view of the results presented, we suggest ChlreSEX4 as a functional phosphoglucan phosphatase from C. reinhardtii. Our data obtained so far contribute to understanding the phosphoglucan phosphatases evolutionary process in the green lineage and their role in starch reversible phosphorylation. In addition, this allows to position Chlamydomonas as a potential tool to obtain starches with different degrees of phosphorylation for industrial or biotechnological purposes. %B Archives of Biochemistry and Biophysics %V 680 %P 108235 %8 feb %G eng %R 10.1016/j.abb.2019.108235 %0 Journal Article %J Journal of Phycology %D 2020 %T Influence of temperature and CO 2 on Plasma-membrane permeability to CO 2 and HCO 3 - in the marine haptophytes emiliania huxleyi and calcidiscus leptoporus (prymnesiophyceae) %A Blanco-Ameijeiras, Sonia %A Stoll, Heather M. %A Zhang, Hongrui %A Hopkinson, Brian M. %E Raven, J. %K carbon concentrating mechanism %K CO2 %K haptophyte %K membrane %K PERMEABILITY %K RCC1130 %K rcc1258 %X Membrane permeabilities to CO2 and HCO3- constrain the function of CO2 concentrating mechanisms that algae use to supply inorganic carbon for photosynthesis. In diatoms and green algae, plasma membranes are moderately to highly permeable to CO2 but effectively impermeable to HCO3-. Here, CO2 and HCO3- membrane permeabilities were measured using an 18O-exchange technique on two species of haptophyte algae, Emiliania huxleyi and Calcidiscus leptoporus, which showed that the plasma membranes of these species are also highly permeable to CO2 (0.006–0.02 cm ? s-1) but minimally permeable to HCO3-. Increased temperature and CO2 generally increased CO2 membrane permeabilities in both species, possibly due to changes in lipid composition or CO2 channel proteins. Changes in CO2 membrane permeabilities showed no association with the density of calcium carbonate coccoliths surrounding the cell, which could potentially impede passage of compounds. Haptophyte plasma-membrane permeabilities to CO2 were somewhat lower than those of diatoms but generally higher than membrane permeabilities of green algae. One caveat of these measurements is that the model used to interpret 18O-exchange data assumes that carbonic anhydrase, which catalyzes 18O-exchange, is homogeneously distributed in the cell. The implications of this assumption were tested using a two-compartment model with an inhomogeneous distribution of carbonic anhydrase to simulate 18O-exchange data and then inferring plasma-membrane CO2 permeabilities from the simulated data. This analysis showed that the inferred plasma-membrane CO2 permeabilities are minimal estimates but should be quite accurate under most conditions. %B Journal of Phycology %P jpy.13017 %8 jun %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13017 %R 10.1111/jpy.13017 %0 Journal Article %J Geochimica et Cosmochimica Acta %D 2020 %T Interactions of thallium with marine phytoplankton %A Zhang, Qiong %A Rickaby, Rosalind E.M. %K bioaccumulation %K biogeochemical cycle %K metallome %K phytoplankton %K RCC1 %K RCC1242 %K RCC1353 %K RCC1557 %K rcc174 %K RCC834 %K RCC950 %K thallium %B Geochimica et Cosmochimica Acta %V 276 %P 1–13 %G eng %U https://doi.org/10.1016/j.gca.2020.02.024 https://linkinghub.elsevier.com/retrieve/pii/S0016703720301344 %R 10.1016/j.gca.2020.02.024 %0 Journal Article %J Biomolecules %D 2020 %T Isoprostanoid profiling of marine microalgae %A Vigor, Claire %A Oger, Camille %A Reversat, Guillaume %A Rocher, Amandine %A Zhou, Bingqing %A Linares-Maurizi, Amandyne %A Guy, Alexandre %A Bultel-Poncé, Valérie %A Galano, Jean-Marie %A Vercauteren, Joseph %A Durand, Thierry %A Potin, Philippe %A Tonon, Thierry %A Leblanc, Catherine %K Isoprostanoids %K Micro-LC-MS/MS %K Microalgae %K Oxidative stress %K PUFAs %K RCC1349 %K RCC20 %K RCC69 %X ¡p¿Algae result from a complex evolutionary history that shapes their metabolic network. For example, these organisms can synthesize different polyunsaturated fatty acids, such as those found in land plants and oily fish. Due to the presence of numerous double-bonds, such molecules can be oxidized nonenzymatically, and this results in the biosynthesis of high-value bioactive metabolites named isoprostanoids. So far, there have been only a few studies reporting isoprostanoid productions in algae. To fill this gap, the current investigation aimed at profiling isoprostanoids by liquid chromatography -mass spectrometry/mass spectrometry (LC-MS/MS) in four marine microalgae. A good correlation was observed between the most abundant polyunsaturated fatty acids (PUFAs) produced by the investigated microalgal species and their isoprostanoid profiles. No significant variations in the content of oxidized derivatives were observed for Rhodomonas salina and Chaetoceros gracilis under copper stress, whereas increases in the production of C18-, C20- and C22-derived isoprostanoids were monitored in Tisochrysis lutea and Phaeodactylum tricornutum. In the presence of hydrogen peroxide, no significant changes were observed for C. gracilis and for T. lutea, while variations were monitored for the other two algae. This study paves the way to further studying the physiological roles of isoprostanoids in marine microalgae and exploring these organisms as bioresources for isoprostanoid production.¡/p¿ %B Biomolecules %V 10 %P 1073 %8 jul %G eng %U https://www.mdpi.com/2218-273X/10/7/1073 %R 10.3390/biom10071073 %0 Journal Article %J Algal Research %D 2020 %T Parallelisable non-invasive biomass, fitness and growth measurement of macroalgae and other protists with nephelometry %A Calmes, Benoît %A Strittmatter, Martina %A Jacquemin, Bertrand %A Perrineau, Marie Mathilde %A Rousseau, Céline %A Badis, Yacine %A Cock, J. Mark %A Destombe, Christophe %A Valero, Myriam %A Gachon, Claire M.M. %K Algal cultivation %K Biomass %K Biotechnology %K Nephelometry %K Phenotyping %K RCC149 %K RCC3088 %K RCC3510 %K rcc3553 %X With the exponential development of algal aquaculture and blue biotechnology, there is a strong demand for simple, inexpensive, high-throughput, quantitative phenotyping assays to measure the biomass, growth and fertility of algae and other marine protists. Here, we validate nephelometry, a method that relies on measuring the scattering of light by particles in suspension, as a non-invasive tool to measure in real-time the biomass of aquatic micro-organisms, such as microalgae, filamentous algae, as well as non-photosynthetic protists. Nephelometry is equally applicable to optic density and chlorophyll fluorescence measurements for the quantification of some microalgae, but outperforms other spectroscopy methods to quantify the biomass of biofilm-forming and filamentous algae, highly pigmented species and non-photosynthetic eukaryotes. Thanks to its insensitivity to the sample's pigmentation, nephelometry is also the method of choice when chlorophyll content varies between samples or time points, for example due to abiotic stress or pathogen infection. As examples, we illustrate how nephelometry can be combined with fluorometry or image analysis to monitor the quantity and time-course of spore release in fertile kelps or the progression of symptoms in diseased algal cultures. %B Algal Research %V 46 %P 101762 %G eng %U https://doi.org/10.1016/j.algal.2019.101762 %R 10.1016/j.algal.2019.101762 %0 Journal Article %J Frontiers in Microbiology %D 2020 %T Synergic effects of temperature and irradiance on the physiology of the marine synechococcus strain WH7803 %A Guyet, Ulysse %A Nguyen, Ngoc A. %A Doré, Hugo %A Haguait, Julie %A Pittera, Justine %A Conan, Maël %A Ratin, Morgane %A Corre, Erwan %A Le Corguillé, Gildas %A Brillet-Guéguen, Loraine %A Hoebeke, Mark %A Six, Christophe %A Steglich, Claudia %A Siegel, Anne %A Eveillard, Damien %A Partensky, Frédéric %A Garczarek, Laurence %K light stress %K marine cyanobacteria %K rcc752 %K Synechococcus %K temperature stress %K transcriptomics %K UV radiations %X Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria. %B Frontiers in Microbiology %V 11 %P 1707 %8 jul %G eng %U www.frontiersin.org %R 10.3389/fmicb.2020.01707 %0 Journal Article %J Scientific Reports %D 2020 %T Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes %A Derilus, D %A Rahman, M Z %A Pinero, F %A Massey, S E %K RCC1110 %K RCC1116 %K RCC809 %B Scientific Reports %V 10 %P 8918 %G eng %U http://dx.doi.org/10.1038/s41598-020-65476-1 http://www.nature.com/articles/s41598-020-65476-1 %R 10.1038/s41598-020-65476-1 %0 Journal Article %J Phycologia %D 2020 %T Taxonomic reassignment of \textit{Pseudohaptolina birgeri comb. nov . (Haptophyta) %A Gérikas Ribeiro, Catherine %A Lopes dos Santos, Adriana %A Probert, Ian %A Vaulot, Daniel %A Edvardsen, Bente %K RCC5268 %K RCC5270 %B Phycologia %V in press %P 1–10 %8 oct %G eng %U https://www.biorxiv.org/content/10.1101/2020.05.06.081489v1 https://www.tandfonline.com/doi/full/10.1080/00318884.2020.1830255 %R 10.1080/00318884.2020.1830255 %0 Journal Article %J bioRxiv %D 2020 %T A thermal trade-off between viral production and degradation drives phytoplankton-virus population dynamics %A Demory, David %A Weitz, Joshua S %A Baudoux, Anne-claire %A Touzeau, Suzanne %A Simon, Natalie %A Rabouille, Sophie %A Sciandra, Antoine %A Bernard, Olivier %K RCC4229 %K RCC4265 %K RCC451 %K RCC4523 %K RCC829 %K RCC834 %X Marine viruses interact with their microbial hosts in dynamic environments shaped by variations in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modeling with experimental datasets to explore the effect of temperature on three Micromonas-prasinovirus pairs. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modeling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free, or habitat loss states. Hence, we generalized our model to global sea surface temperature of present and future seas and show that climate change may influence virus-host dynamics differently depending on the virus-host pair. Our study suggests that temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro-and microorganisms . %B bioRxiv %P 2020.08.18.256156 %8 aug %G eng %U https://doi.org/10.1101/2020.08.18.256156 %R 10.1101/2020.08.18.256156 %0 Journal Article %J Science Advances %D 2020 %T Virus-host coexistence in phytoplankton through the genomic lens %A Yau, Sheree %A Krasovec, Marc %A Benites, L. Felipe %A Rombauts, Stephane %A Groussin, Mathieu %A Vancaester, Emmelien %A Aury, Jean-Marc %A Derelle, Evelyne %A Desdevises, Yves %A Escande, Marie-Line %A Grimsley, Nigel %A Guy, Julie %A Moreau, Hervé %A Sanchez-Brosseau, Sophie %A Van de Peer, Yves %A Vandepoele, Klaas %A Gourbière, Sébastien %A Piganeau, Gwenael %K RCC2590 %K RCC2596 %X Virus-microbe interactions in the ocean are commonly described by “boom and bust” dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this “accordion” chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions. %B Science Advances %V 6 %P eaay2587 %8 apr %G eng %U https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aay2587 %R 10.1126/sciadv.aay2587 %0 Journal Article %J Current Biology %D 2019 %T Algal remodeling in a ubiquitous planktonic photosymbiosis %A Decelle, Johan %A Stryhanyuk, Hryhoriy %A Gallet, Benoit %A Veronesi, Giulia %A Schmidt, Matthias %A Balzano, Sergio %A Marro, Sophie %A Uwizeye, Clarisse %A Jouneau, Pierre-Henri %A Lupette, Josselin %A Jouhet, Juliette %A Maréchal, Éric %A Schwab, Yannick %A Schieber, Nicole L. %A Tucoulou, Rémi %A Richnow, Hans %A Finazzi, Giovanni %A Musat, Niculina %K RCC1719 %X Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae. %B Current Biology %V 29 %P 968–978.e4 %8 mar %G eng %U https://www.sciencedirect.com/science/article/abs/pii/S0960982219301320#undfig1 %R 10.1016/J.CUB.2019.01.073 %0 Journal Article %J Environmental Microbiology %D 2019 %T Closely related viruses of the marine picoeukaryotic alga Ostreococcus lucimarinus exhibit different ecological strategies %A Zimmerman, Amy E. %A Bachy, Charles %A Ma, Xiufeng %A Roux, Simon %A Jang, Ho Bin %A Sullivan, Matthew B. %A Waldbauer, Jacob R. %A Worden, Alexandra Z. %K rcc3401 %K RCC393 %K RCC829 %X SUMMARY In marine ecosystems viruses are major disrupters of the direct flow of carbon and nutrients to higher trophic levels. While the genetic diversity of several eukaryotic phytoplankton virus groups has been characterized, their infection dynamics are less understood, such that the physiological and ecological implications of their diversity remain unclear. We compared genomes and infection phenotypes of the two most closely related cultured phycodnaviruses infecting the widespread picoprasinophyte Ostreococcus lucimarinus under standard- (1.3 divisions d-1) and limited-light (0.41 divisions d-1) nutrient replete conditions. OlV7 infection caused early arrest of the host cell cycle, coinciding with a significantly higher proportion of infected cells than OlV1-amended treatments, regardless of host growth rate. OlV7 treatments showed a near-50-fold increase of progeny virions at the higher host growth rate, contrasting with OlV1's 16-fold increase. However, production of OlV7 virions was more sensitive than OlV1 production to reduced host growth rate, suggesting fitness trade-offs between infection efficiency and resilience to host physiology. Moreover, while organic matter released from OlV1- and OlV7-infected hosts had broadly similar chemical composition, some distinct molecular signatures were observed. Collectively, these results suggest that current views on viral relatedness through marker and core gene analyses underplay operational divergence and consequences for host ecology. This article is protected by copyright. All rights reserved. %B Environmental Microbiology %V 00 %G eng %R 10.1111/1462-2920.14608 %0 Journal Article %J Frontiers in Marine Science %D 2019 %T Dead in the Water: The Vicious Cycle of Blanks During Natural Level 14 C Manipulation of Marine Algal Cultures %A Kusch, Stephanie %A Benthien, Albert %A Richter, Klaus-Uwe %A Rost, Björn %A Mollenhauer, Gesine %K Algal cultures %K Alkanoic acids %K alkenones %K Authentic standards %K Blank %K chlorophyll a %K Compound-specific radiocarbon analysis %K natural level 14 C manipulation %K rcc1238 %X Authentic biomarker standards were obtained from algal cultures in an attempt to accurately determine blank C added during sample processing for compound-specific radiocarbon analysis. Emiliania huxleyi and Thalassiosira pseudonana were grown under manipulated Δ14C dissolved inorganic carbon (DIC) levels and chlorophyll a and either alkenones (E. huxleyi) or low molecular weight (LMW) alkanoic acids (T. pseudonana) were isolated from the respective biomass using preparative liquid chromatography (LC), wet chemical techniques or preparative gas chromatography, respectively. DI14C in the seawater medium was determined pre- and post-growth. Biomarker Δ14C values mostly agree within 1-2? analytical uncertainties. In those cases where biomarker Δ14C values differ significantly, chlorophyll a is up to 104‰ more 14C-depleted than alkenones or LMW alkanoic acids, consistent with a larger LC blank compared to the other purification methods. However, in the majority of experimental setups pre- and post-growth DIC Δ14C values seem to be compromised by an unknown and variable blank C contribution. DIC Δ14C values deviate strongly from the anticipated Δ14C values (by up to ca. 560‰), pre- and post-growth Δ14C values differ significantly (by up to ca. 460‰), and changes are not unidirectional. Accordingly, since the substrate Δ14C value cannot unequivocally be constrained, blank C contributions for the different biomarker purification methods cannot be accurately calculated. This study illustrates the challenges and problems of producing authentic standards that are not readily commercially available and exemplifies how a laborious and time-consuming culturing approach may enter a vicious cycle of blank C contamination hampering accurate blank C determination. %B Frontiers in Marine Science %V 6 %G eng %U https://www.frontiersin.org/articles/10.3389/fmars.2019.00780/full %R 10.3389/fmars.2019.00780 %0 Journal Article %J Frontiers in Microbiology %D 2019 %T First viruses infecting the marine diatom guinardia delicatula %A Arsenieff, Laure %A Simon, Nathalie %A Rigaut-jalabert, Fabienne %A Le Gall, Florence %A Chaffron, Samuel %A Corre, Erwan %A Com, Emmanuelle %A Bigeard, Estelle %A Baudoux, Anne-claire %K diatoms %K genomics %K host-virus dynamics %K RCC1000 %K RCC2023 %K RCC3046 %K RCC3083 %K RCC3093 %K RCC3101 %K RCC4657 %K RCC4659 %K RCC4660 %K RCC4667 %K RCC4834 %K RCC5154 %K RCC5777 %K RCC5778 %K RCC5779 %K RCC5780 %K RCC5781 %K RCC5782 %K RCC5783 %K RCC5784 %K RCC5785 %K RCC5787 %K RCC5788 %K RCC5789 %K RCC5790 %K RCC5792 %K RCC5793 %K RCC5794 %K RCC80 %K single-stranded RNA viruses %K Western English Channel %B Frontiers in Microbiology %V 9 %8 jan %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2018.03235/full %R 10.3389/fmicb.2018.03235 %0 Journal Article %J Organic Geochemistry %D 2019 %T Hydrogen isotope fractionation response to salinity and alkalinity in a calcifying strain of Emiliania huxleyi %A Weiss, Gabriella M. %A Roepert, Anne %A Middelburg, Jack J. %A Schouten, Stefan %A Sinninghe Damsté, Jaap S. %A van der Meer, Marcel T.J. %K RCC2050 %B Organic Geochemistry %8 jun %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0146638019301020 %R 10.1016/j.orggeochem.2019.06.001 %0 Journal Article %J Phytochemistry %D 2019 %T NMR characterization and evaluation of antibacterial and antiobiofilm activity of organic extracts from stationary phase batch cultures of five marine microalgae (Dunaliella sp., D. salina, Chaetoceros calcitrans, C. gracilis and Tisochrysis lutea) %A Iglesias, Ma José %A Soengas, Raquel %A Probert, Ian %A Guilloud, Emilie %A Gourvil, Priscillia %A Mehiri, Mohamed %A López, Yuly %A Cepas, Virginio %A Gutiérrez-del-Río, Ignacio %A Redondo-Blanco, Saúl %A Villar, Claudio J. %A Lombó, Felipe %A Soto, Sara %A Ortiz, Fernando López %K Antibacterial %K Antibiofilm %K Chaetoceros %K Dunaliella %K Metabolite identification %K NMR %K RCC1349 %K RCC1811 %K RCC3579 %K RCC5 %K RCC5953 %K Tisochrysis %B Phytochemistry %V 164 %P 192–205 %8 aug %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0031942219300184 %R 10.1016/j.phytochem.2019.05.001 %0 Journal Article %J The ISME Journal %D 2019 %T Picoeukaryotes of the Micromonas genus: sentinels of a warming ocean %A Demory, David %A Baudoux, Anne-claire %A Monier, Adam %A Simon, Nathalie %A Six, Christophe %A Ge, Pei %A Rigaut-jalabert, Fabienne %A Marie, Dominique %A Sciandra, Antoine %A Bernard, Olivier %A Rabouille, Sophie %K Biogeography %K change ecology %K Climate %K microbial ecology %K RCC114 %K RCC1697 %K RCC1862 %K RCC2257 %K RCC2306 %K RCC299 %K RCC451 %K RCC497 %K RCC746 %K RCC829 %K RCC834 %X Photosynthetic picoeukaryotesx in the genus Micromonas show among the widest latitudinal distributions on Earth, experiencing large thermal gradients from poles to tropics. Micromonas comprises at least four different species often found in sympatry. While such ubiquity might suggest a wide thermal niche, the temperature response of the different strains is still unexplored, leaving many questions as for their ecological success over such diverse ecosystems. Using combined experiments and theory, we characterize the thermal response of eleven Micromonas strains belonging to four species. We demonstrate that the variety of specific responses to temperature in the Micromonas genus makes this environmental factor an ideal marker to describe its global distribution and diversity. We then propose a diversity model for the genus Micromonas, which proves to be representative of the whole phytoplankton diversity. This prominent primary producer is therefore a sentinel organism of phytoplankton diversity at the global scale. We use the diversity within Micromonas to anticipate the potential impact of global warming on oceanic phytoplankton. We develop a dynamic, adaptive model and run forecast simulations, exploring a range of adaptation time scales, to probe the likely responses to climate change. Results stress how biodiversity erosion depends on the ability of organisms to adapt rapidly to temperature increase. %B The ISME Journal %V 13 %P 132–146 %8 jan %G eng %U http://www.nature.com/articles/s41396-018-0248-0 %R 10.1038/s41396-018-0248-0 %0 Journal Article %J Limnology and Oceanography %D 2019 %T Susceptibility of algae to Cr toxicity reveals contrasting metal management strategies %A Wilson, Will %A Zhang, Qiong %A Rickaby, Rosalind E. M. %K RCC1 %K RCC1242 %K RCC4221 %K RCC950 %X At the Paleozoic–Mesozoic boundary, the dominance of marine eukaryotic algae shifted from the green (chlorophyll b) to the red (chlorophyll c) superfamily. Selection pressures caused by the bioavailability of trace metals associated with increasing oxygenation of the ocean may have played a key role in this algal revolution. From a scan of elemental compositions, a significant difference in the cellular Cr/P quota was found between the two superfamilies. Here, the different responses to high levels of Cr exposure reveal contrasting strategies for metal uptake and homeostasis in these algal lineages. At high Cr(VI) concentrations, red lineages experience growth inhibition through reduced photosynthetic capability, while green lineages are completely unaffected. Moreover, Cr(VI) has a more significant impact on the metallomes of red lineage algae, in which metal/P ratios increased with increasing Cr(VI) concentration for many trace elements. Green algae have higher specificity transporters to prevent Cr(VI) from entering the cell, and more specific intracellular stores of Cr within the membrane fraction than the red algae, which accumulate more Cr mistakenly in the cytosol fraction via lower affinity transport mechanisms. Green algal approaches require greater nutrient investments in the more numerous transport proteins required and management of specific metals, a strategy better adapted to the resource-rich coastal waters. By contrast, the red algae are nutrient-efficient with fewer and less discriminate metal transporters, which can be fast and better adapted in the oligotrophic, oxygenated open ocean, which has prevailed since the deepening of the oxygen minimum zones at the start of the Mesozoic era. %B Limnology and Oceanography %V 64 %P 2271–2282 %8 sep %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1002/lno.11183 %R 10.1002/lno.11183 %0 Journal Article %J New Phytologist %D 2019 %T Unveiling membrane thermoregulation strategies in marine picocyanobacteria %A Breton, Solène %A Jouhet, Juliette %A Guyet, Ulysse %A Gros, Valérie %A Pittera, Justine %A Demory, David %A Partensky, Frédéric %A Doré, Hugo %A Ratin, Morgane %A Maréchal, Éric %A Nguyen, Ngoc An %A Garczarek, Laurence %A Six, Christophe %K RCC2374 %K RCC2385 %K RCC515 %K rcc539 %B New Phytologist %P nph.16239 %8 oct %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16239 %R 10.1111/nph.16239 %0 Journal Article %J bioRxiv %D 2018 %T A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum %A Annunziata, Rossella %A Ritter, Andrés %A Fortunato, Antonio Emidio %A Cheminant-Navarro, Soizic %A Agier, Nicolas %A Huysman, Marie J. J. %A Winge, Per %A Bones, Atle %A Bouget, François-Yves %A Lagomarsino, Marco Cosentino %A Bouly, Jean Pierre %A Falciatore, Angela %K RCC2967 %X Periodic light dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular bases controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we here unveil the key function of a Phaeodactylum tricornutum bHLH-PAS protein, named Pt bHLH1a, in the regulation of light-dependent rhythms. Peak expression of Pt bHLH1a mRNA occurs at the end of the light period and it is adjusted to photoperiod changes. Ectopic over-expression of Pt bHLH1a results in lines with altered cell division and gene expression and showing a phase shift in diurnal responses, compared to the wild-type cells. Reduced oscillations in gene expression are also observed in continuous darkness, showing that the regulation of rhythmicity by Pt bHLH1a is not directly dependent on light inputs and cell division. Pt bHLH1a orthologs are widespread in both pennate and centric diatom genomes, hinting at a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but still underinvestigated branch of the tree of life. %B bioRxiv %P 271445 %G eng %U https://www.biorxiv.org/content/early/2018/02/25/271445 %R 10.1101/271445 %0 Journal Article %J Scientific Reports %D 2018 %T Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis %A Paerl, Ryan W. %A Bertrand, Erin M. %A Rowland, Elden %A Schatt, Phillippe %A Mehiri, Mohamed %A Niehaus, Thomas D. %A Hanson, Andrew D. %A Riemann, Lasse %A Yves-Bouget, Francois %K RCC4222 %K RCC745 %B Scientific Reports %V 8 %P 5940 %G eng %U http://www.nature.com/articles/s41598-018-24321-2 %R 10.1038/s41598-018-24321-2 %0 Journal Article %J Frontiers in Microbiology %D 2018 %T Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains %A Farhat, Sarah %A Florent, Isabelle %A Noel, Benjamin %A Kayal, Ehsan %A Da Silva, Corinne %A Bigeard, Estelle %A Alberti, Adriana %A Labadie, Karine %A Corre, Erwan %A Aury, Jean-Marc %A Rombauts, Stephane %A Wincker, Patrick %A Guillou, Laure %A Porcel, Betina M. %K amoebophrya %K Dinoflagellates %K Gene Expression %K infection %K oxidative stress response %K parasite %K plankton %K RCC1627 %K RCC3596 %K RCC4383 %K RCC4398 %K syndiniales %B Frontiers in Microbiology %V 9 %P 1–19 %8 oct %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full %R 10.3389/fmicb.2018.02251 %0 Journal Article %J Frontiers in Microbiology %D 2018 %T High variability in cellular stoichiometry of carbon, nitrogen, and phosphorus within classes of marine eukaryotic phytoplankton under sufficient nutrient conditions %A Garcia, Nathan S. %A Sexton, Julie %A Riggins, Tracey %A Brown, Jeff %A Lomas, Michael W. %A Martiny, Adam C. %K cell size %K Diatom %K Dinoflagellate %K eukaryote %K frontiers in microbiology %K frontiersin %K Growth %K org %K protist %K prymnesiophyte %K RCC103 %K RCC1242 %K RCC1562 %K RCC4023 %K RCC449 %K RCC931 %K temperature %K www %X Current hypotheses suggest that cellular elemental stoichiometry of marine eukaryotic phytoplankton such as the ratios of cellular carbon:nitrogen:phosphorus (C:N:P) vary between phylogenetic groups based traits like evolutionary history and cell size. To investigate how phylogenetic structure, cell volume, growth rate and temperature interact to affect the cellular elemental stoichiometry of marine eukaryotic phytoplankton, we examined the C:N:P composition in 30 isolates across 7 classes of marine phytoplankton that were grown with a sufficient supply of nutrients with nitrate as the nitrogen source. The isolates covered a wide range in cell volume (5 orders of magnitude), growth rate (¡0.01-0.9 d-1), and habitat temperature (2-24°C). Our analysis indicates that C:N:P is highly variable, with statistical model residuals accounting for over half of the total variance with no relationship between phylogeny and elemental stoichiometry. Furthermore, our data indicated that variability in C:P, N:P and C:N within Bacillariophyceae (diatoms) was as high as that among all of the isolates that we examined. In addition, a linear statistical model identified a positive relationship between diatom cell volume and C:P and N:P. Among all of the isolates that we examined, the statistical model identified temperature as a significant factor, consistent with the temperature-dependent translation efficiency model, but temperature only explained 5% of the total statistical model variance. While some of our results support data from previous field studies, the high variability of elemental ratios within Bacillariophyceae contradicts previous work that suggests that this cosmopolitan group of microalgae has consistently low C:P and N:P ratios in comparison with other groups. %B Frontiers in Microbiology %V 9 %P 1–10 %G eng %U http://journal.frontiersin.org/article/10.3389/fmicb.2018.00543/full %R 10.3389/fmicb.2018.00543 %0 Journal Article %J iScience %D 2018 %T Infection dynamics of a bloom-forming alga and its virus determine airborne coccolith emission from seawater %A Trainic, Miri %A Koren, Ilan %A Sharoni, Shlomit %A Frada, Miguel %A Segev, Lior %A Rudich, Yinon %A Vardi, Assaf %K Atmospheric Science %K Biogeoscience %K Earth Sciences %K Marine Organism %K RCC1216 %X Summary Sea spray aerosols (SSA), have a profound effect on the climate; however, the contribution of oceanic microbial activity to SSA is not fully established. We assessed aerosolization of the calcite units (coccoliths) that compose the exoskeleton of the cosmopolitan bloom-forming coccolithophore, Emiliania huxleyi. Airborne coccolith emission occurs in steady-state conditions and increases by an order of magnitude during E. huxleyi infection by E. huxleyi virus (EhV). Airborne to seawater coccolith ratio is 1:108, providing estimation of airborne concentrations from seawater concentrations. The coccoliths' unique aerodynamic structure yields a characteristic settling velocity of \~0.01 cm s-1, \~25 times slower than average sea salt particles, resulting in coccolith fraction enrichment in the air. The calculated enrichment was established experimentally, indicating that coccoliths may be key contributors to coarse mode SSA surface area, comparable with sea salt aerosols. This study suggests a coupling between key oceanic microbial interactions and fundamental atmospheric processes like SSA formation. %B iScience %8 aug %G eng %U https://www.cell.com/iscience/fulltext/S2589-0042(18)30105-6 https://linkinghub.elsevier.com/retrieve/pii/S2589004218301056 %R 10.1016/j.isci.2018.07.017 %0 Journal Article %J Scientific Reports %D 2018 %T Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms %A Rastogi, Achal %A Maheswari, Uma %A Dorrell, Richard G. %A Vieira, Fabio Rocha Jimenez %A Maumus, Florian %A Kustka, Adam %A McCarthy, James %A Allen, Andy E. %A Kersey, Paul %A Bowler, Chris %A Tirichine, Leila %K RCC2967 %X 2 3 Diatoms are one of the most successful and ecologically important groups of eukaryotic 4 phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better 5 understanding of their biological innovations, evolutionary origins, and ecological 6 underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions 7 combined with published expressed sequence tags and protein sequences from multiple taxa 8 to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 9 novel genes. The new annotation additionally permitted the discovery for the first time of 10 extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping 11 which increases the diversity of transcripts to regulate gene expression in response to nutrient 12 limitations. In addition, we have used up-to-date reference sequence libraries to dissect the 13 taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete in 14 lineage-specific genes, with up to 47% of the gene models present only possessing 15 orthologues in other stramenopile groups. Finally, we have performed a comprehensive de 16 novo annotation of repetitive elements showing novel classes of TEs such as SINE, MITE, LINE 17 and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene 18 function, evolution and ecology. %B Scientific Reports %V 8 %P 4834 %8 dec %G eng %U https://www.biorxiv.org/content/early/2017/08/14/176024%0Ahttp://dx.doi.org/10.1101/176024 http://www.nature.com/articles/s41598-018-23106-x %R 10.1038/s41598-018-23106-x %0 Journal Article %J Scientific Reports %D 2018 %T A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle %A Partensky, Frédéric %A Six, Christophe %A Ratin, Morgane %A Garczarek, Laurence %A Vaulot, Daniel %A Probert, Ian %A Calteau, Alexandra %A Gourvil, Priscillia %A Marie, Dominique %A Grébert, Théophile %A Bouchier, Christiane %A Le Panse, Sophie %A Gachenot, Martin %A Rodríguez, Francisco %A Garrido, José L. %K RCC1774 %B Scientific Reports %V 8 %P 9142 %8 dec %G eng %U http://www.nature.com/articles/s41598-018-27542-7 %R 10.1038/s41598-018-27542-7 %0 Journal Article %J Frontiers in Environmental Science %D 2018 %T Ostreococcus tauri luminescent reporter lines as biosensors for detecting pollution from copper-mine tailing effluents in coastal environments %A Henríquez-Castillo, Carlos %A Botebol, Hugo %A Mouton, Adelaide %A Ramírez-Flandes, Salvador %A Lozano, Jean-Claude %A Lelandais, Gaelle %A Andrade, Santiago %A Trefault, Nicole %A de la Iglesia, Rodrigo %A Bouget, François-Yves %K biosensors %K CDKA %K copper pollution %K ferritin %K frontiers in environmental science %K frontiersin %K luciferase reporter %K mine tailings %K org %K Ostreococcus %K RCC745 %K www %B Frontiers in Environmental Science %V 6 %P 1–11 %8 may %G eng %U https://www.frontiersin.org/article/10.3389/fenvs.2018.00022/full %R 10.3389/fenvs.2018.00022 %0 Journal Article %J bioRxiv %D 2018 %T Phenotypic variability in chloroplast redox state predicts cell fate in a marine diatom %A Mizrachi, Avia %A Graff, Shiri %A Creveld, Van %A Shapiro, Orr H %A Rosenwasser, Shilo %K RCC2967 %B bioRxiv %G eng %R 10.1101/319517 %0 Journal Article %J Genome Biology and Evolution %D 2018 %T Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends %A Klinger, Christen M %A Paoli, Lucas %A Newby, Robert J %A Wang, Matthew Yu-Wei %A Carroll, Hyrum D %A Leblond, Jeffrey D %A Howe, Christopher J %A Dacks, Joel B %A Bowler, Chris %A Cahoon, A Bruce %A Dorrell, Richard G %A Richardson, Elisabeth %K constructive neutral evolution %K Dinoflagellate %K plastid %K RCC1513 %K serial endosymbiosis %K transcript editing %X Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes. Because reports of this process have been limited to manual assessment of individual lineages, global trends concerning this RNA editing and its effect on the biological function of the plastid are largely unknown. Using novel bioinformatic methods, we examine the dynamics and evolution of RNA editing over a large multispecies data set of dinoflagellates, including novel sequence data from the peridinin dinoflagellate Pyrocystis lunula and the fucoxanthin dinoflagellate Karenia mikimotoi. We demonstrate that while most individual RNA editing events in dinoflagellate plastids are restricted to single species, global patterns, and functional consequences of editing are broadly conserved. We find that editing is biased toward specific codon positions and regions of genes, and generally corrects otherwise deleterious changes in the genome prior to translation, though this effect is more prevalent in peridinin than fucoxanthin lineages. Our results support a model for promiscuous editing application subsequently shaped by purifying selection, and suggest the presence of an underlying editing mechanism transferred from the peridinin-containing ancestor into fucoxanthin plastids postendosymbiosis, with remarkably conserved functional consequences in the new lineage. %B Genome Biology and Evolution %V 10 %P 1019–1038 %G eng %U https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evy057/4935245 %R 10.1093/gbe/evy057 %0 Journal Article %J Environmental Microbiology Reports %D 2018 %T Relative stability of ploidy in a marine Synechococcus across various growth conditions %A Perez-Sepulveda, Blanca %A Pitt, Frances %A N'Guyen, An Ngoc %A Ratin, Morgane %A Garczarek, Laurence %A Millard, Andrew %A Scanlan, David J %K rcc752 %X Marine picocyanobacteria of the genus Synechococcus are ubiquitous phototrophs in oceanic systems. Consistent with these organisms occupying vast tracts of the nutrient impoverished ocean, most marine Synechococcus so far studied are monoploid i.e. contain a single chromosome copy. The exception is the oligoploid strain Synechococcus sp. WH7803, which on average possesses around 4 chromosome copies. Here, we set out to understand the role of resource availability (through nutrient deplete growth) and physical stressors (UV, exposure to low and high temperature) in regulating ploidy level in this strain. Using qPCR to assay ploidy status we demonstrate the relative stability of chromosome copy number in Synechococcus sp. WH7803. Such robustness in maintaining an oligoploid status even under nutrient and physical stress is indicative of a fundamental role, perhaps facilitating recombination of damaged DNA regions as a result of prolonged exposure to oxidative stress, or allowing added flexibility in gene expression via possessing multiple alleles. This article is protected by copyright. All rights reserved. %B Environmental Microbiology Reports %P in press %8 feb %G eng %U http://dx.doi.org/10.1111/1758-2229.12614 http://doi.wiley.com/10.1111/1758-2229.12614 %R 10.1111/1758-2229.12614 %0 Journal Article %J PLOS ONE %D 2018 %T Temperature effects on sinking velocity of different Emiliania huxleyi strains %A Rosas-Navarro, Anaid %A Langer, Gerald %A Ziveri, Patrizia %E Johnson, Colin %K IAN01 %K rcc1252 %K rcc1710 %X The sinking properties of three strains of Emiliania huxleyi in response to temperature changes were examined. We used a recently proposed approach to calculate sinking velocities from coccosphere architecture, which has the advantage to be applicable not only to culture samples, but also to field samples including fossil material. Our data show that temperature in the sub-optimal range impacts sinking velocity of E. huxleyi. This response is widespread among strains isolated in different locations and moreover comparatively predictable, as indicated by the similar slopes of the linear regressions. Sinking velocity was positively correlated to temperature as well as individual cell PIC/POC over the sub-optimum to optimum temperature range in all strains. In the context of climate change our data point to an important influence of global warming on sinking velocities. It has recently been shown that seawater acidification has no effect on sinking velocity of a Mediterranean E. huxleyi strain, while nutrient limitation seems to have a small negative effect on sinking velocity. Given that warming, acidification, and lowered nutrient availability will occur simultaneously under climate change scenarios, the question is what the net effect of different influential factors will be. For example, will the effects of warming and nutrient limitation cancel? This question cannot be answered conclusively but analyses of field samples in addition to laboratory culture studies will improve predictions because in field samples multi-factor influences and even evolutionary changes are not excluded. As mentioned above, the approach of determining sinking rate followed here is applicable to field samples. Future studies could use it to analyse not only seasonal and geographic patterns but also changes in sinking velocity over geological time scales. %B PLOS ONE %V 13 %P e0194386 %G eng %U http://dx.plos.org/10.1371/journal.pone.0194386 %R 10.1371/journal.pone.0194386 %0 Journal Article %J eLife %D 2017 %T Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome %A Dorrell, Richard G %A Gile, Gillian %A McCallum, Giselle %A Méheust, Raphaël %A Bapteste, Eric P %A Klinger, Christen M %A Brillet-Guéguen, Loraine %A Freeman, Katalina D %A Richter, Daniel J %A Bowler, Chris %K 2017 %K RCC1486 %K RCC1523 %K RCC1537 %K RCC1587 %K SBR$_\textrmP$hyto$_\textrmE$PPO %X Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history. %B eLife %V 6 %P 1–45 %8 may %G eng %U http://elifesciences.org/lookup/doi/10.7554/eLife.23717 %R 10.7554/eLife.23717 %0 Journal Article %J Scientific Reports %D 2017 %T Chloropicophyceae, a new class of picophytoplanktonic prasinophytes %A Lopes dos Santos, Adriana %A Pollina, Thibaut %A Gourvil, Priscillia %A Corre, Erwan %A Marie, Dominique %A Garrido, José Luis %A Rodríguez, Francisco %A Noël, Mary-Hélène %A Vaulot, Daniel %A Eikrem, Wenche %K 2017 %K RCC1019 %K RCC1021 %K RCC1032 %K RCC1043 %K RCC1124 %K RCC138 %K RCC15 %K RCC1871 %K RCC19 %K RCC227 %K RCC2335 %K RCC2337 %K RCC2339 %K RCC287 %K RCC297 %K RCC3368 %K RCC3373 %K RCC3374 %K RCC3375 %K RCC3376 %K RCC3402 %K RCC4429 %K RCC4430 %K RCC4434 %K RCC4572 %K RCC4656 %K RCC696 %K RCC700 %K RCC701 %K RCC712 %K RCC713 %K RCC717 %K RCC719 %K RCC722 %K RCC726 %K RCC856 %K RCC857 %K RCC887 %K RCC917 %K RCC996 %K RCC997 %K RCC998 %K RCC999 %K sbr?hyto$_\textrmd$ipo %B Scientific Reports %V 7 %P 14019 %8 dec %G eng %U http://www.nature.com/articles/s41598-017-12412-5 %R 10.1038/s41598-017-12412-5 %0 Journal Article %J The ISME Journal %D 2017 %T Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters %A Lopes dos Santos, Adriana %A Gourvil, Priscillia %A Tragin, Margot %A Noël, Mary-Hélène %A Decelle, Johan %A Romac, Sarah %A Vaulot, Daniel %K 2016 %K MACUMBA %K MicroB3 %K RCC1019 %K RCC1021 %K RCC1032 %K RCC1043 %K RCC1124 %K RCC138 %K RCC15 %K RCC1871 %K RCC19 %K RCC227 %K RCC2335 %K RCC2337 %K RCC2339 %K RCC287 %K RCC297 %K RCC3368 %K RCC3373 %K RCC3374 %K RCC3375 %K RCC3376 %K RCC3402 %K RCC4429 %K RCC4430 %K RCC4434 %K RCC4656 %K RCC696 %K RCC700 %K RCC701 %K RCC712 %K RCC713 %K RCC717 %K RCC719 %K RCC722 %K RCC726 %K RCC856 %K RCC857 %K RCC917 %K RCC996 %K RCC997 %K RCC998 %K RCC999 %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B The ISME Journal %V 11 %P 512–528 %8 feb %G eng %U http://www.nature.com/doifinder/10.1038/ismej.2016.120 %R 10.1038/ismej.2016.120 %0 Journal Article %J Viruses %D 2017 %T Emerging interaction patterns in the emiliania huxleyi-EhV system %A Ruiz, Eliana %A Oosterhof, Monique %A Sandaa, Ruth-Anne %A Larsen, Aud %A Pagarete, António %K algae virus %K coccolithophore %K coccolithovirus %K cost of %K haptophyta %K infectivity trade-offs %K killing-the-winner %K marine viral ecology %K phycodnaviridae %K RCC1211 %K RCC1213 %K RCC1215 %K RCC1216 %K RCC1218 %K RCC1228 %K RCC1231 %K RCC1235 %K RCC1239 %K RCC1241 %K RCC1242 %K RCC1246 %K RCC1249 %K RCC1250 %K RCC1253 %K RCC1255 %K rcc1256 %K RCC1257 %K RCC1259 %K RCC1268 %K RCC1269 %K RCC1272 %K RCC1276 %K RCC1322 %K RCC1744 %K RCC1745 %K RCC1857 %K RCC3548 %K RCC3856 %K RCC3923 %K RCC3956 %K resistance %K viral-host interactions %X Viruses are thought to be fundamental in driving microbial diversity in the oceanic planktonic realm. That role and associated emerging infection patterns remain particularly elusive for eukaryotic phytoplankton and their viruses. Here we used a vast number of strains from the model system Emiliania huxleyi/Emiliania huxleyi Virus to quantify parameters such as growth rate (µ), resistance (R), and viral production (Vp) capacities. Algal and viral abundances were monitored by flow cytometry during 72-h incubation experiments. The results pointed out higher viral production capacity in generalist EhV strains, and the virus-host infection network showed a strong co-evolution pattern between E. huxleyi and EhV populations. The existence of a trade-off between resistance and growth capacities was not confirme %B Viruses %V 9 %P 61 %8 mar %G eng %U http://www.mdpi.com/1999-4915/9/3/61 %R 10.3390/v9030061 %0 Journal Article %J PLoS ONE %D 2017 %T Evolution of the scattering properties of phytoplankton cells from flow cytometry measurements %A Moutier, William %A Duforêt-Gaurier, Lucile %A Thyssen, Mélilotus %A Loisel, Hubert %A Mériaux, Xavier %A Courcot, Lucie %A Dessailly, David %A Rêve, Anne Hélène %A Grégori, Gerald %A Alvain, Séverine %A Barani, Aude %A Brutier, Laurent %A Dugenne, Mathilde %K RCC1 %K RCC950 %X Combining a modern, data-analytic perspective with a focus on applications in the social sciences, the Second Edition of Applied Regression Analysis and Generalized Linear Models provides in-depth coverage of regression analysis, generalized linear models, and closely related methods. Although the text is largely accessible to readers with a modest background in statistics and mathematics, author John Fox also presents more advanced material throughout the book. Key Updates to the Second Edition:Provides greatly enhanced coverage of generalized linear models, with an emphasis on models for categorical and count data Offers new chapters on missing data in regression models and on methods of model selection Includes expanded treatment of robust regression, time-series regression, nonlinear regression, and nonparametric regression Incorporates new examples using larger data sets Includes an extensive Web site at http://www.sagepub.com/fox that presents appendixes, data sets used in the book and for data-analytic exercises, and the data-analytic exercises themselves Intended Audience: This core text will be a valuable resource for graduate students and researchers in the social sciences (particularly sociology, political science, and psychology) and other disciplines that employ linear and related models for data analysis. High Praise for the First Edition: Even though the book is written with social scientists as the target audience, the depth of material and how it is conveyed give it far broader appeal. Indeed, I recommend it as a useful learning text and resource for researchers and students in any field that applies regression or linear models (that is, most everyone), including courses for undergraduate statistics majors.... The author is to be commended for giving us this book, which I trust will find a wide and enduring readership.-JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION [T]his wonderfully comprehensive book focuses on regression analysis and linear models.... We enthusiastically recommend this book — having used it in class, we know that it is thorough and well liked by students. -CHANCE %B PLoS ONE %V 12 %G eng %R 10.1371/journal.pone.0181180 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2017 %T Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton %A Monier, Adam %A Chambouvet, Aurelie %A Milner, David S. %A Attah, Victoria %A Terrado, Ramón %A Lovejoy, Connie %A Moreau, Hervé %A Santoro, Alyson E. %A Derelle, Evelyne %A Richards, Thomas A. %K rcc1107 %K RCC1621 %K RCC2573 %K RCC2593 %K RCC745 %K RCC809 %B Proceedings of the National Academy of Sciences %P 201708097 %G eng %U http://www.pnas.org/lookup/doi/10.1073/pnas.1708097114 %R 10.1073/pnas.1708097114 %0 Journal Article %J Biogeosciences %D 2017 %T Impact of trace metal concentrations on coccolithophore growth and morphology: laboratory simulations of Cretaceous stress %A Faucher, Giulia %A Hoffmann, Linn %A Bach, Lennart T. %A Bottini, Cinzia %A Erba, Elisabetta %A Riebesell, Ulf %K RCC1198 %K RCC1216 %K RCC1303 %X

Abstract. The Cretaceous ocean witnessed intervals of profound perturbations such as volcanic input of large amounts of CO$_\textrm2$, anoxia, eutrophication and introduction of biologically relevant metals. Some of these extreme events were characterized by size reduction and/or morphological changes of a few calcareous nannofossil species. The correspondence between intervals of high trace metal concentrations and coccolith dwarfism suggests a negative effect of these elements on nannoplankton biocalcification processes in past oceans. In order to test this hypothesis, we explored the potential effect of a mixture of trace metals on growth and morphology of four living coccolithophore species, namely \textitEmiliania huxleyi, Gephyrocapsa oceanica, Pleurochrysis carterae and \textitCoccolithus pelagicus. The phylogenetic history of coccolithophores shows that the selected living species are linked to Mesozoic species showing dwarfism under excess metal concentrations. The trace metals tested were chosen to simulate the environmental stress identified in the geological record and upon known trace metal interactions with living coccolithophore algae.

Our laboratory experiments demonstrated that elevated trace metal concentrations, similarly to the fossil record, affect coccolithophore algae size and/or weight. Smaller coccoliths were detected in \textitE. huxleyi and \textitC. pelagicus, while coccoliths of \textitG. oceanica showed a decrease in size only at the highest trace metal concentrations. \textitP. carterae coccolith size was unresponsive to changing trace metal concentrations. These differences among species allow discriminating the most- (\textitP. carterae), intermediate- (\textitE. huxleyi and \textitG. oceanica) and least-tolerant (\textitC. pelagicus) taxa. The fossil record and the experimental results converge on a selective response of coccolithophores to metal availability.

These species-specific differences must be considered before morphological features of coccoliths are used to reconstruct paleo-chemical conditions.

%B Biogeosciences %V 14 %P 3603–3613 %8 jul %G eng %U https://bg.copernicus.org/articles/14/3603/2017/ %R 10.5194/bg-14-3603-2017 %0 Journal Article %J Harmful Algae %D 2017 %T Mixotrophy in the marine red-tide cryptophyte Teleaulax amphioxeia and ingestion and grazing impact of cryptophytes on natural populations of bacteria in Korean coastal waters %A Yoo, Yeong Du %A Seong, Kyeong Ah %A Jeong, Hae Jin %A Yih, Wonho %A Rho, Jung Rae %A Nam, Seung Won %A Kim, Hyung Seop %K Bloom %K Flagellate %K Grazing impact %K Predator-prey relationship %K RCC1086 %K Red tide %X Cryptophytes are ubiquitous and one of the major phototrophic components in marine plankton communities. They often cause red tides in the waters of many countries. Understanding the bloom dynamics of cryptophytes is, therefore, of great importance. A critical step in this understanding is unveiling their trophic modes. Prior to this study, several freshwater cryptophyte species and marine Cryptomonas sp. and Geminifera cryophila were revealed to be mixotrophic. The trophic mode of the common marine cryptophyte species, Teleaulax amphioxeia has not been investigated yet. Thus, to explore the mixotrophic ability of T. amphioxeia by assessing the types of prey species that this species is able to feed on, the protoplasms of T. amphioxeia cells were carefully examined under an epifluorescence microscope and a transmission electron microscope after adding each of the diverse prey species. Furthermore, T. amphioxeia ingestion rates heterotrophic bacteria and the cyanobacterium Synechococcus sp. were measured as a function of prey concentration. Moreover, the feeding of natural populations of cryptophytes on natural populations of heterotrophic bacteria was assessed in Masan Bay in April 2006. This study reported for the first time, to our knowledge, that T. amphioxeia is a mixotrophic species. Among the prey organisms offered, T. amphioxeia fed only on heterotrophic bacteria and Synechococcus sp. The ingestion rates of T. amphioxeia on heterotrophic bacteria or Synechococcus sp. rapidly increased with increasing prey concentrations up to 8.6 × 106 cells ml-1, but slowly at higher prey concentrations. The maximum ingestion rates of T. amphioxeia on heterotrophic bacteria and Synechococcus sp. reached 0.7 and 0.3 cells predator-1 h-1, respectively. During the field experiments, the ingestion rates and grazing coefficients of cryptophytes on natural populations of heterotrophic bacteria were 0.3–8.3 cells predator-1 h-1 and 0.012–0.033 d-1, respectively. Marine cryptophytes, including T. amphioxeia, are known to be favorite prey species for many mixotrophic and heterotrophic dinoflagellates and ciliates. Cryptophytes, therefore, likely play important roles in marine food webs and may exert a considerable potential grazing impact on the populations of marine bacteria. %B Harmful Algae %V 68 %P 105–117 %G eng %U http://dx.doi.org/10.1016/j.hal.2017.07.012 %R 10.1016/j.hal.2017.07.012 %0 Journal Article %J American Journal of Botany %D 2017 %T Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta) %A Parks, Matthew %A Nakov, Teofil %A Ruck, Elizabeth %A Wickett, Norman J %A Alverson, Andrew J %A Rice, Ada L %A Conservation, Plant %A Botanic, Chicago %A Glencoe, Garden %K and %K b %K c %K citation %K diatoms %K e %K gene tree %K genome duplication %K j %K n %K nakov %K paleopolyploidy %K parks m %K polyploidy %K RCC205 %K RCC80 %K ruck %K synonymous divergence %K t %K these authors contributed equally %K to this work %K wickett %B American Journal of Botany %V 105 %P 1–18 %G eng %R 10.1101/181115 %0 Journal Article %J Science Advances %D 2017 %T Population genomics of picophytoplankton unveils novel chromosome hypervariability %A Blanc-Mathieu, Romain %A Krasovec, Marc %A Hebrard, Maxime %A Yau, Sheree %A Desgranges, Elodie %A Martin, Joel %A Schackwitz, Wendy %A Kuo, Alan %A Salin, Gerald %A Donnadieu, Cecile %A Desdevises, Yves %A Sanchez-Ferandin, Sophie %A Moreau, Hervé %A Rivals, Eric %A Grigoriev, Igor V. %A Grimsley, Nigel %A Eyre-Walker, Adam %A Piganeau, Gwenael %K RCC1105 %K RCC1108 %K RCC1110 %K RCC1112 %K RCC1114 %K RCC1115 %K RCC1116 %K RCC1117 %K RCC1118 %K RCC1123 %K RCC1558 %K RCC1559 %K RCC1561 %K RCC299 %K RCC4221 %K RCC809 %B Science Advances %V 3 %P e1700239 %8 jul %G eng %U http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700239 %R 10.1126/sciadv.1700239 %0 Journal Article %J Environmental Microbiology %D 2017 %T Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton %A Limardo, Alexander J. %A Sudek, Sebastian %A Choi, Chang Jae %A Poirier, Camille %A Rii, Yoshimi M. %A Blum, Marguerite %A Roth, Robyn %A Goodenough, Ursula %A Church, Matthew J. %A Worden, Alexandra Z. %K RCC1105 %K RCC715 %K RCC716 %K RCC809 %B Environmental Microbiology %8 jun %G eng %U http://doi.wiley.com/10.1111/1462-2920.13812 %R 10.1111/1462-2920.13812 %0 Journal Article %J Limnology and Oceanography: Methods %D 2017 %T Recommendations for obtaining unbiased chlorophyll estimates from in situ chlorophyll fluorometers: A global analysis of WET Labs ECO sensors %A Roesler, Collin %A Uitz, Julia %A Claustre, Hervé %A Boss, Emmanuel %A Xing, Xiaogang %A Organelli, Emanuele %A Briggs, Nathan %A Bricaud, Annick %A Schmechtig, Catherine %A Poteau, Antoine %A D'Ortenzio, Fabrizio %A Ras, Josephine %A Drapeau, Susan %A Haëntjens, Nils %A Barbieux, Marie %K RCC233 %K RCC42 %K RCC834 %X Chlorophyll fluorometers provide the largest in situ global data set for estimating phytoplankton biomass because of their ease of use, size, power consumption, and relatively low price. While in situ chlorophyll a (Chl) fluorescence is proxy for Chl a concentration, and hence phytoplankton biomass, there exist large natural variations in the relationship between in situ fluorescence and extracted Chl a concentration. Despite this large natural variability, we present here a global validation data set for the WET Labs Environmental Characterization Optics (ECO) series chlorophyll fluorometers that suggests a factor of 2 overestimation in the factory calibrated Chl a estimates for this specific manufacturer and series of sensors. We base these results on paired High Pressure Liquid Chromatography (HPLC) and in situ fluorescence match ups for which non-photochemically quenched fluorescence observations were removed. Additionally, we examined matchups between the factory-calibrated in situ fluorescence and estimates of chlorophyll concentration determined from in situ radiometry, absorption line height, NASA's standard ocean color algorithm as well as laboratory calibrations with phytoplankton monocultures spanning diverse species that support the factor of 2 bias. We therefore recommend the factor of 2 global bias correction be applied for the WET Labs ECO sensors, at the user level, to improve the global accuracy of chlorophyll concentration estimates and products derived from them. We recommend that other fluorometer makes and models should likewise undergo global analyses to identify potential bias in factory calibration. %B Limnology and Oceanography: Methods %V 15 %P 572–585 %G eng %R 10.1002/lom3.10185 %0 Journal Article %J Bulletin of Environmental Contamination and Toxicology %D 2017 %T Removal and biodegradation of phenanthrene, fluoranthene and pyrene by the marine algae rhodomonas baltica enriched from north atlantic coasts %A Arias, Andrés H %A Souissi, Anissa %A Glippa, Olivier %A Roussin, Marion %A Dumoulin, David %A Net, Sopheak %A Ouddane, Baghdad %A Souissi, Sami %K RCC350 %X This study is focused on the removal, accumulation and degradation of three environmental ubiquitous polycyclic aromatic hydrocarbons (PAHs), phenanthrene (PHE), fluoranthene (FLA) and pyrene (PYR), by the marine alga Rhodomonas baltica enriched from the English Channel. After separation, purification and culture in several phases, R. baltica was exposed to PAH concentrations that are frequently encountered in the field in several anthropized environments. The results showed that R. baltica can grow under PAH stress, efficiently remove up to 70% of these compounds from the medium by 216 h of culture and selectively bioaccumulate PAHs by their hydrophobicity. Between PHE, FLA and PYR, phenanthrene was the compound with higher degradation rates throughout incubation. The equilibrium partitioning theoretical approach showed that physico-chemical partitioning, rather than active bioconcentration, was the major factor governing the bioaccumulation, outlying a potential application in decontamination processes for this species. %B Bulletin of Environmental Contamination and Toxicology %V 98 %P 392–399 %G eng %U https://doi.org/10.1007/s00128-016-1967-4 %R 10.1007/s00128-016-1967-4 %0 Journal Article %J Frontiers in Microbiology %D 2017 %T Specificity re-evaluation of oligonucleotide probes for the detection of marine picoplankton by tyramide signal amplification-fluorescent in situ hybridization %A Riou, Virginie %A Périot, Marine %A Biegala, Isabelle C. %K CARD-FISH %K Eukaryota %K oligonucleotide %K PROBES %K Prokaryote %K RCC257 %K specificity %K TSA-FISH %X Oligonucleotide probes are increasingly being used to characterize natural microbial assemblages by Tyramide Signal Amplification-Fluorescent in situ Hybridization (TSA-FISH, or CAtalysed Reporter Deposition CARD-FISH). In view of the fast-growing rRNA databases, we re-evaluated the in silico specificity of eleven bacterial and eukaryotic probes and competitor frequently used for the quantification of marine picoplankton. We performed tests on cell cultures to decrease the risk for non-specific hybridization, before they are used on environmental samples. The probes were confronted to recent databases and hybridization conditions were tested against target strains matching perfectly with the probes, and against the closest non-target strains presenting one to four mismatches. We increased the hybridization stringency from 55% to 65% formamide for the Eub338+EubII+EubIII probe mix to be specific to the Eubacteria domain. In addition, we found that recent changes in the Gammaproteobacteria classification decreased the specificity of Gam42a probe, and that the Roseo536R and Ros537 probes were not specific to, and missed part of the Roseobacter clade. Changes in stringency conditions were important for bacterial probes; these induced respectively a significant increase, in Eubacteria and Roseobacter and no significant changes in Gammaproteobacteria concentrations from the investigated natural environment. We confirmed the eukaryotic probes original conditions, and propose the Euk1209+NChlo01+Chlo02 probe mix to target the largest picoeukaryotic diversity. Experiences acquired through these investigations leads us to propose the use of seven steps protocol for complete FISH probe specificity check-up to improve data quality in environmental studies. %B Frontiers in Microbiology %V 8 %P 854 %8 may %G eng %U http://journal.frontiersin.org/article/10.3389/fmicb.2017.00854/full %R 10.3389/fmicb.2017.00854 %0 Journal Article %J The ISME Journal %D 2017 %T Temperature is a key factor in Micromonas–virus interactions %A Demory, David %A Arsenieff, Laure %A Simon, Nathalie %A Six, Christophe %A Rigaut-jalabert, Fabienne %A Marie, Dominique %A Ge, Pei %A Bigeard, Estelle %A Jacquet, Stéphan %A Sciandra, Antoine %A Bernard, Olivier %A Rabouille, Sophie %A Baudoux, Anne-claire %K 2017 %K RCC4229 %K RCC4253 %K RCC4265 %K RCC451 %K RCC829 %K RCC834 %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?app %X The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4–32.5 °C. Similar growth temperature optima (Topt) were predicted for all three hosts but Mic-B exhibited a broader thermal tolerance than Mic-A and Mic-C, suggesting distinct thermoacclimation strategies. Similarly, the MicV-C virus displayed a remarkable thermal stability compared with MicV-A and MicV-B. Despite these divergences, infection dynamics showed that temperatures below Topt lengthened lytic cycle kinetics and reduced viral yield and, notably, that infection at temperatures above Topt did not usually result in cell lysis. Two mechanisms operated depending on the temperature and the biological system. Hosts either prevented the production of viral progeny or maintained their ability to produce virions with no apparent cell lysis, pointing to a possible switch in the viral life strategy. Hence, temperature changes critically affect the outcome of Micromonas infection and have implications for ocean biogeochemistry and evolution. %B The ISME Journal %V 11 %P 601–612 %8 mar %G eng %U http://dx.doi.org/10.1038/ismej.2016.160 http://www.nature.com/doifinder/10.1038/ismej.2016.160 %R 10.1038/ismej.2016.160 %0 Journal Article %J PloS one %D 2016 %T Identifying aspects of the post-transcriptional program governing the proteome of the green alga micromonas pusilla. %A Waltman, Peter H %A Guo, Jian %A Reistetter, Emily Nahas %A Purvine, Samuel %A Ansong, Charles K %A van Baren, Marijke J %A Wong, Chee-Hong %A Wei, Chia-Lin %A Smith, Richard D %A Callister, Stephen J %A Stuart, Joshua M %A Worden, Alexandra Z %K 2016 %K rcc %K RCC834 %X Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (¡2 ??m diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3' UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas. %B PloS one %V 11 %P e0155839 %8 jan %G eng %U http://dx.doi.org/10.1371/journal.pone.0155839 %R 10.1371/journal.pone.0155839 %0 Journal Article %J Frontiers in Marine Science %D 2016 %T P- and n-depletion trigger similar cellular responses to promote senescence in eukaryotic phytoplankton %A Rokitta, Sebastian D. %A von Dassow, Peter %A Rost, Björn %A John, Uwe %K 2016 %K rcc1217 %K RCC126 %B Frontiers in Marine Science %V 3 %8 jun %G eng %U http://journal.frontiersin.org/article/10.3389/fmars.2016.00109 http://journal.frontiersin.org/Article/10.3389/fmars.2016.00109/abstract %R 10.3389/fmars.2016.00109 %0 Journal Article %J Journal of Phycology %D 2016 %T Paradoxical effects of temperature and solar irradiance on the photodegradation state of killed phytoplankton %A Amiraux, Remi %A Jeanthon, Christian %A Vaultier, Frédéric %A Rontani, Jean-François %E Mock, T. %K 2016 %K rcc2022 %X The aim of this paper was to study the effects of temperature and irradiance on the photodegradation state of killed phytoplankton cells. For this purpose, killed cells of the diatom Chaetoceros neogracilis RCC2022 were irradiated (PAR radiations) at 36 and 446 J. s(-1.) m(-2) (for a same cumulative dose of irradiation energy) and at two temperatures (7 and 17°C). Analyses of specific lipid tracers (fatty acids and sterols) revealed that low temperatures and irradiances increased photooxidative damages of monounsaturated lipids (i.e. palmitoleic acid, cholesterol and campesterol). The high efficiency of type II photosensitized degradation processes was attributed to: (i) the relative preservation of the sensitizer (chlorophyll) at low irradiances allowing a longer production of singlet oxygen and (ii) the slow diffusion rate of singlet oxygen through membranes at low temperatures inducing more damages. Conversely, high temperatures and irradiances induced (i) a rapid degradation of the photosensitizer and a loss of singlet oxygen by diffusion outside the membranes (limiting type II photosensitized oxidation), and (ii) intense autoxidation processes degrading unsaturated cell lipids and oxidation products used as photodegradation tracers. Our results may likely explain the paradoxical relationship observed in situ between latitude and photodegradation state of phytoplankton cells. This article is protected by copyright. All rights reserved. %B Journal of Phycology %V 52 %P 475–485 %8 jun %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/26992328 http://doi.wiley.com/10.1111/jpy.12410 %R 10.1111/jpy.12410 %0 Journal Article %J Journal of Phycology %D 2016 %T Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII %A Lopes dos Santos, Adriana %A Gourvil, Priscillia %A Rodriguez-Hernandez, Francisco %A Garrido, José Luis %A Vaulot, Daniel %K 2016 %K MACUMBA %K rcc %K RCC1124 %K RCC15 %K RCC1871 %K RCC2337 %K RCC2339 %K RCC287 %K RCC3374 %K RCC3376 %K RCC3402 %K RCC719 %K RCC856 %K RCC857 %K RCC996 %K RCC998 %K RCC?o?dd %K SBR$_\textrmP$hyto$_\textrmD$IPO %K sbr?hyto$_\textrmd$ipo %X The ecological importance and diversity of pico/ nanoplanktonic algae remains poorly studied in marine waters, in part because many are tiny and without distinctive morphological features. Amongst green algae, Mamiellophyceae such as Micromonas or Bathycoccus are dominant in coastal waters while prasinophytes clade VII, yet not formerly described, appear to be major players in open oceanic waters. The pigment composition of 14 strains representative of different subclades of clade VII was analyzed using a method that improves the separation of loroxanthin and neoxanthin. All the prasinophytes clade VII analyzed here showed a pigment composition similar to that previously reported for RCC287 corresponding to pigment group prasino-2A. However, we detected in addition astaxanthin for which it is the first report in prasinophytes. Among the strains analyzed, the pigment signature is qualitatively similar within subclades A and B. By contrast, RCC3402 from subclade C (Picocystis) lacks loroxanthin, astaxanthin, and antheraxanthin but contains alloxanthin, diatoxanthin, and monadoxanthin that are usually found in diatoms or cryptophytes. For subclades A and B, loroxanthin was lowest at highest light irradiance suggesting a light-harvesting role of this pigment in clade VII as in Tetraselmis. %B Journal of Phycology %V 52 %P 148–155 %G eng %R 10.1111/jpy.12376 %0 Journal Article %J Environmental Microbiology %D 2016 %T Pigment variations in Emiliania huxleyi (CCMP370) as a response to changes in light intensity or quality %A Garrido, José L. %A Brunet, Christophe %A Rodríguez, Francisco %K 2016 %K RCC1255 %B Environmental Microbiology %V 18 %P 4412–4425 %8 dec %G eng %U http://doi.wiley.com/10.1111/1462-2920.13373 %R 10.1111/1462-2920.13373 %0 Journal Article %J Journal of Phycology %D 2016 %T Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex %A Percopo, Isabella %A Ruggiero, Maria Valeria %A Balzano, Sergio %A Gourvil, Priscillia %A Lundholm, Nina %A Siano, Raffaele %A Tammilehto, Anna %A Vaulot, Daniel %A Sarno, Diana %E Mock, T. %K RCC2002 %K RCC2004 %K RCC2005 %K RCC2517 %X A new nontoxic Pseudo-nitzschia species belonging to the P. pseudodelicatissima complex, P. arctica, was isolated from different areas of the Arctic. The erection of P. arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P. fryxelliana, and represents a new case of crypticity within the genus. Despite their morphological similarity, the two species are not closely related in phylogenies based on LSU, ITS and rbcL. Interestingly, P. arctica is phylogenetically most closely related to P. granii and P. subcurvata, from which the species is, however, morphologically different. P. granii and P. subcurvata lack the central larger interspace which is one of the defining features of the P. pseudodelicatissima complex. The close genetic relationship between P. arctica and the two species P. granii and P. subcurvata is demonstrated by analysis of the secondary structure of ITS2 which revealed no compensatory base changes, two hemi-compensatory base changes, and two deletions in P. arctica with respect to the other two species. These findings emphasize that rates of morphological differentiation, molecular evolution and speciation are often incongruent for Pseudo-nitzschia species, resulting in a restricted phylogenetic value for taxonomic characters used to discriminate species. The description of a new cryptic species, widely distributed in the Arctic and potentially representing an endemic component of the Arctic diatom flora, reinforces the idea of the existence of noncosmopolitan Pseudo-nitzschia species and highlights the need for combined morphological and molecular analyses to assess the distributional patterns of phytoplankton species. %B Journal of Phycology %V 52 %P 184–199 %8 apr %G eng %U http://doi.wiley.com/10.1111/jpy.12395 %R 10.1111/jpy.12395 %0 Journal Article %J Biogeosciences %D 2016 %T Temperature affects the morphology and calcification of Emiliania huxleyi strains %A Rosas-Navarro, Anaid %A Langer, Gerald %A Ziveri, Patrizia %K 2016 %K rcc1252 %K rcc1710 %X The global warming debate has sparked an unprecedented interest in temperature effects on coccolithophores. The calcification response to temperature changes reported in the literature, however, is ambiguous. The two main sources of this ambiguity are putatively differences in experimental setup and strain specificity. In this study we therefore compare three strains isolated in the North Pacific under identical experimental conditions. Three strains of Emiliania huxleyi type A were grown under non-limiting nutrient and light conditions, at 10, 15, 20 and 25 °C. All three strains displayed similar growth rate versus temperature relationships, with an optimum at 20–25 °C. Elemental production (particulate inorganic carbon (PIC), particulate organic carbon (POC), total particulate nitrogen (TPN)), coccolith mass, coccolith size, and width of the tube element cycle were positively correlated with temperature over the sub-optimum to optimum temperature range. The correlation between PIC production and coccolith mass/size supports the notion that coccolith mass can be used as a proxy for PIC production in sediment samples. Increasing PIC production was significantly positively correlated with the percentage of incomplete coccoliths in one strain only. Generally, coccoliths were heavier when PIC production was higher. This shows that incompleteness of coccoliths is not due to time shortage at high PIC production. Sub-optimal growth temperatures lead to an increase in the percentage of malformed coccoliths in a strain-specific fashion. Since in total only six strains have been tested thus far, it is presently difficult to say whether sub-optimal temperature is an important factor causing malformations in the field. The most important parameter in biogeochemical terms, the PIC : POC ratio, shows a minimum at optimum growth temperature in all investigated strains. This clarifies the ambiguous picture featuring in the literature, i.e. discrepancies between PIC : POC–temperature relationships reported in different studies using different strains and different experimental setups. In summary, global warming might cause a decline in coccolithophore's PIC contribution to the rain ratio, as well as improved fitness in some genotypes due to fewer coccolith malformations. %B Biogeosciences %V 13 %P 2913–2926 %8 may %G eng %U http://www.biogeosciences.net/13/2913/2016/ %R 10.5194/bg-13-2913-2016 %0 Journal Article %J The ISME Journal %D 2015 %T Environmental stability affects phenotypic evolution in a globally distributed marine picoplankton %A Schaum, C-Elisa %A Rost, Björn %A Collins, Sinéad %K oth95 %K rcc1107 %K RCC1108 %K RCC1114 %K RCC1558 %K rcc1645 %K rcc1662 %K rcc410 %K rcc422 %K RCC434 %K rcc501 %K rcc675 %K rcc747 %K RCC789 %K RCC809 %K rcc810 %X Marine phytoplankton can evolve rapidly when confronted with aspects of climate change because of their large population sizes and fast generation times. Despite this, the importance of environment fluctuations, a key feature of climate change, has received little attention—selection experiments with marine phytoplankton are usually carried out in stable environments and use single or few representatives of a species, genus or functional group. Here we investigate whether and by how much environmental fluctuations contribute to changes in ecologically important phytoplankton traits such as C:N ratios and cell size, and test the variability of changes in these traits within the globally distributed species Ostreococcus. We have evolved 16 physiologically distinct lineages of Ostreococcus at stable high CO2 (1031±87 ??atm CO2 , SH) and fluctuating high CO2 (1012±244 ??atm CO2 , FH) for 400 generations.We find that although both fluctuation and high CO2 drive evolution, FH- evolved lineages are smaller, have reduced C:N ratios and respond more strongly to further increases in CO2 than do SH-evolved lineages. This indicates that environmental fluctuations are an important factor to consider when predicting how the characteristics of future phytoplankton populations will have an impact on biogeochemical cycles and higher trophic levels in marine food webs. %B The ISME Journal %P 1–10 %G eng %U http://www.nature.com/doifinder/10.1038/ismej.2015.102 %R 10.1038/ismej.2015.102 %0 Journal Article %J The ISME Journal %D 2015 %T Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone %A Astorga-Eló, Marcia %A Ramírez-Flandes, Salvador %A DeLong, Edward F %A Ulloa, Osvaldo %K rcc %X Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus. %B The ISME Journal %V 9 %P 1264–1267 %G eng %U http://www.nature.com/doifinder/10.1038/ismej.2015.21 %R 10.1038/ismej.2015.21 %0 Journal Article %J Environmental microbiology reports %D 2015 %T Interplay between the genetic clades of ¡i¿Micromonas¡/i¿ and their viruses in the Western English Channel. %A Baudoux, A-C %A Lebredonchel, H %A Dehmer, H %A Latimier, M %A Edern, R %A Rigaut-Jalabert, F %A Ge, P %A Guillou, L %A Foulon, E %A Bozec, Y %A Cariou, T %A Desdevises, Y %A Derelle, E %A Grimsley, N %A Moreau, H %A Simon, N %K 2015 %K rcc %K RCC?o?dd %K sbr?hyto$_\textrmd$ipo %X The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regards to the genetic diversity of this host. During one year, we monitored the abundance of 3 clades of Micromonas and their viruses in the Western English Channel both in the environment, using clade-specific probes and flow cytometry, and in the laboratory, using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundances of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies, and genetic diversity. However, some viruses can also cross-infect different host clades suggesting a mechanism of horizontal gene transfer within Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas. %B Environmental microbiology reports %8 jun %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/26081716 %R 10.1111/1758-2229.12309 %0 Journal Article %J Frontiers in Microbiology %D 2015 %T Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains %A Stüken, Anke %A Riobó, Pilar %A Franco, José %A Jakobsen, Kjetill S. %A Guillou, Laure %A Figueroa, Rosa I. %K 2015 %K Alexandrium %K copy %K copy number variation %K Dinoflagellate %K gene dosage %K genome size %K number variation %K paralytic shellfish toxin %K paralytic shellfish toxin (PST) %K pst %K rcc %K RCC?o?dd %K saxitoxin %K saxitoxin (STX) %K sbr?hyto$_\textrmd$ipo %K stx %K sxtA %X Dinoflagellates are microscopic aquatic eukaryotes with huge genomes and an unusual cell regulation. For example, most genes are present in numerous copies and all copies seem to be obligatorily transcribed. The consequence of the gene copy number (CPN) for final protein synthesis is, however, not clear. One such gene is sxtA, the starting gene of paralytic shellfish toxin (PST) synthesis. PSTs are small neurotoxic compounds that can accumulate in the food chain and cause serious poisoning incidences when ingested. They are produced by dinoflagellates of the genera Alexandrium, Gymnodium, and Pyrodinium. Here we investigated if the genomic CPN of sxtA4 is related to PST content in Alexandrium minutum cells. SxtA4 is the 4th domain of the sxtA gene and its presence is essential for PST synthesis in dinoflagellates. We used PST and genome size measurements as well as quantitative PCR to analyze sxtA4 CPN and toxin content in 15 A. minutum strains. Our results show a strong positive correlation between the sxtA4 CPN and the total amount of PST produced in actively growing A. minutum cells. This correlation was independent of the toxin profile produced, as long as the strain contained the genomic domains sxtA1 and sxtA4. %B Frontiers in Microbiology %V 6 %P 1–10 %G eng %U http://journal.frontiersin.org/article/10.3389/fmicb.2015.00404 %R 10.3389/fmicb.2015.00404 %0 Journal Article %J Molecular Ecology Resources %D 2015 %T PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy %A Decelle, Johan %A Romac, Sarah %A Stern, Rowena F. %A Bendif, El Mahdi %A Zingone, Adriana %A Audic, Stéphane %A Guiry, Michael D. %A Guillou, Laure %A Tessier, Désiré %A Le Gall, Florence %A Gourvil, Priscillia %A dos Santos, Adriana Lopes %A Probert, Ian %A Vaulot, Daniel %A de Vargas, Colomban %A Christen, Richard %K 2015 %K MACUMBA %K rcc %K RCC?o?dd %K SBR$_\textrmP$hyto$_\textrmD$IPO %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %X Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF data- base that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classifica- tion were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing. %B Molecular Ecology Resources %V 15 %P 1435–1445 %G eng %U http://doi.wiley.com/10.1111/1755-0998.12401 %R 10.1111/1755-0998.12401 %0 Journal Article %J BMC Microbiology %D 2014 %T Diverse molecular signatures for ribosomally 'active' Perkinsea in marine sediments %A Chambouvet, Aurelie %A Berney, Cedric %A Romac, Sarah %A Audic, Stéphane %A Maguire, Finlay %A de Vargas, Colomban %A Richards, Thomas %K 2014 %K Biomarks %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X BACKGROUND:Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples. Only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity 'tag' sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations.RESULTS:We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97% sequence similarity as to suggest this diversity encompasses a range of biologically and ecologically distinct organisms.CONCLUSIONS:These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally 'active' and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the 'seed bank' microbial community. %B BMC Microbiology %V 14 %P 110 %G eng %U http://www.biomedcentral.com/1471-2180/14/110 %R 10.1186/1471-2180-14-110 %0 Journal Article %J Journal of Phycology %D 2014 %T Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta) %A Bendif, El Mahdi %A Probert, Ian %A Carmichael, Margaux %A Romac, Sarah %A Hagino, Kyoko %A de Vargas, Colomban %K 2014 %K cc3549 %K rcc %K rcc1210 %K RCC1213 %K rcc1220 %K rcc1227 %K rcc1229 %K RCC1242 %K rcc1252 %K RCC1253 %K rcc1258 %K RCC1259 %K rcc1260 %K rcc1271 %K RCC1281 %K rcc1288 %K RCC1292 %K rcc1297 %K RCC1300 %K RCC1303 %K RCC1305 %K RCC1316 %K RCC1562 %K rcc174 %K RCC1839 %K rcc3545 %K rrcc1247 %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %B Journal of Phycology %V 50 %P 140–148 %G eng %R 10.1111/jpy.12147 %0 Journal Article %J Scientific Data %D 2014 %T Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus %A Biller, Steven J. %A Berube, Paul M. %A Berta-Thompson, Jessie W. %A Kelly, Libusha %A Roggensack, Sara E. %A Awad, Lana %A Roache-Johnson, Kathryn H. %A Ding, Huiming %A Giovannoni, Stephen J. %A Rocap, Gabrielle %A Moore, Lisa R. %A Chisholm, Sallie W. %A H. %A Ding, Huiming %A Giovannoni, Stephen J. %A Moore, Lisa R. %A Chisholm, Sallie W. %K Environmental microbiology %K genomics %K rcc %K RCC?o?dd %X The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography. %B Scientific Data %V 1 %P 1–11 %8 sep %G eng %U http://www.nature.com/articles/sdata201434 %R 10.1038/sdata.2014.34 %0 Journal Article %J Cytometry %D 2014 %T An improved protocol for flow cytometry analysis of phytoplankton cultures and natural samples %A Marie, D %A Rigaut-Jalabert, F %A Vaulot, D %K ASSEMBLE %K MACUMBA %K RCC100 %K RCC1085 %K RCC114 %K RCC156 %K RCC168 %K rcc174 %K RCC180 %K RCC190 %K RCC263 %K RCC365 %K RCC400 %K RCC432 %K RCC446 %K RCC475 %K RCC480 %K RCC504 %K RCC745 %K RCC91 %K RCC?o?dd %K SBR$_\textrmP$hyto$_\textrmD$PO %X Preservation of cells, choice of fixative, storage, and thawing conditions are recurrent issues for the analysis of phytoplankton by flow cytometry. We examined the effects of addition of the surfactant Pluronic F68 to glutaraldehyde-fixed photosynthetic organisms in cultures and natural samples. In particular, we examined cell losses and modifications of side scatter (a proxy of cell size) and fluorescence of natural pigments. We found that different marine phytoplankton species react differently to the action of Pluronic F68. In particular, photosynthetic prokaryotes are less sensitive than eukaryotes. Observed cell losses may result from cell lysis or from cell adhesion to the walls of plastic tubes that are commonly used for flow cytometry analysis. The addition of the surfactant, Pluronic F68, has a positive effect on cells for long-term storage. We recommend to modify current protocols for preservation of natural marine planktonic samples, by fixing them with glutaraldehyde 0.25% (final concentration) and adding Pluronic F68 at a final concentration of 0.01% in the samples before preservation. Pluronic F68 also appears effective for preserving samples without fixation for subsequent sorting, e.g. for molecular biology analyses. (c) 2014 International Society for Advancement of Cytometry %B Cytometry %V 85 %P 962–968 %G eng %R 10.1002/cyto.a.22517 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2014 %T Marine algae and land plants share conserved phytochrome signaling systems %A Duanmu, Deqiang %A Bachy, Charles %A Sudek, Sebastian %A Wong, Chee-Hong %A Jimenez, Valeria %A Rockwell, Nathan C %A Martin, Shelley S %A Ngan, Chew Yee %A Reistetter, Emily N %A van Baren, Marijke J %A Price, Dana C %A Wei, Chia-Lin %A Reyes-Prieto, Adrian %A Lagarias, J Clark %A Worden, Alexandra Z %K Micromonas %K rcc %X Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte (¡2 µm cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae. %B Proceedings of the National Academy of Sciences of the United States of America %V 111 %P 15827–15832 %G eng %U http://www.pnas.org/content/111/44/15827.abstract %R 10.1073/pnas.1416751111 %0 Journal Article %J PLoS biology %D 2014 %T The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing %A Keeling, Patrick J %A Burki, Fabien %A Wilcox, Heather M %A Allam, Bassem %A Allen, Eric E %A Amaral-Zettler, Linda A %A Armbrust, E Virginia %A Archibald, John M %A Bharti, Arvind K %A Bell, Callum J %A Beszteri, Bank %A Bidle, Kay D %A Cameron, Connor T %A Campbell, Lisa %A Caron, David A %A Cattolico, Rose Ann %A Collier, Jackie L %A Coyne, Kathryn %A Davy, Simon K %A Deschamps, Phillipe %A Dyhrman, Sonya T %A Edvardsen, Bente %A Gates, Ruth D %A Gobler, Christopher J %A Greenwood, Spencer J %A Guida, Stephanie M %A Jacobi, Jennifer L %A Jakobsen, Kjetill S %A James, Erick R %A Jenkins, Bethany %A John, Uwe %A Johnson, Matthew D %A Juhl, Andrew R %A Kamp, Anja %A Katz, Laura A %A Kiene, Ronald %A Kudryavtsev, Alexander %A Leander, Brian S %A Lin, Senjie %A Lovejoy, Connie %A Lynn, Denis %A Marchetti, Adrian %A McManus, George %A Nedelcu, Aurora M %A Menden-Deuer, Susanne %A Miceli, Cristina %A Mock, Thomas %A Montresor, Marina %A Moran, Mary Ann %A Murray, Shauna %A Nadathur, Govind %A Nagai, Satoshi %A Ngam, Peter B %A Palenik, Brian %A Pawlowski, Jan %A Petroni, Giulio %A Piganeau, Gwenael %A Posewitz, Matthew C %A Rengefors, Karin %A Romano, Giovanna %A Rumpho, Mary E %A Rynearson, Tatiana %A Schilling, Kelly B %A Schroeder, Declan C %A Simpson, Alastair G B %A Slamovits, Claudio H %A Smith, David R %A Smith, G Jason %A Smith, Sarah R %A Sosik, Heidi M %A Stief, Peter %A Theriot, Edward %A Twary, Scott N %A Umale, Pooja E %A Vaulot, Daniel %A Wawrik, Boris %A Wheeler, Glen L %A Wilson, William H %A Xu, Yan %A Zingone, Adriana %A Worden, Alexandra Z %K 2014 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %X Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans %B PLoS biology %V 12 %P e1001889 %G eng %U http://dx.doi.org/10.1371%252Fjournal.pbio.1001889 %R 10.1371/journal.pbio.1001889 %0 Journal Article %J Trends in Ecology & Evolution %D 2014 %T The others: our biased perspective of eukaryotic genomes %A del Campo, Javier %A Sieracki, Michael E %A Molestina, Robert %A Keeling, Patrick %A Massana, Ramon %A Ruiz-Trillo, Iñaki %K rcc %X ?There is an important bias in eukaryotic knowledge, affecting cultures and genomes.?Eukaryotic genomics are biased towards multicellular organisms and their parasites.?A phylogeny-driven initiative is needed to overcome the eukaryotic genomic bias.?We propose to sequence neglected cultures and increase culturing efforts.?Single-cell genomics should be embraced as a tool to explore eukaryotic diversity. %B Trends in Ecology & Evolution %V 29 %P 252–259 %G eng %U http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(14)00064-0 %R 10.1016/j.tree.2014.03.006 %0 Journal Article %J Science %D 2014 %T Single-cell genomics reveals hundreds of coexisting subpopulations in wild prochlorococcus %A Kashtan, Nadav %A Roggensack, Sara E %A Rodrigue, Sébastien %A Thompson, Jessie W %A Biller, Steven J %A Coe, Allison %A Ding, Huiming %A Marttinen, Pekka %A Malmstrom, Rex R %A Stocker, Roman %A Follows, Michael J %A Stepanauskas, Ramunas %A Chisholm, Sallie W %K RCC278 %X Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct “genomic backbones,” each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats. %B Science %V 344 %P 416–420 %G eng %U http://www.sciencemag.org/content/344/6182/416.abstract %R 10.1126/science.1248575 %0 Journal Article %J Journal of Phycology %D 2014 %T Transcriptomic insights into the life history of bolidophytes , the sister lineage to diatoms %A Kessenich, Colton R %A Ruck, Elizabeth C %A Schurko, Andrew M %A Wickett, Norman J %A Alverson, Andrew J %K Bolidomonas %K CCMP1866 %K diatoms %K diplontic %K haplodiplontic %K life cycle %K Parmales %K RCC205 %K RCC?o?dd %K Transcriptome %X Diatoms are perhaps the most diverse lineage of eukaryotic algae, with their siliceous cell wall and diplontic life history often considered to have played important roles in their extraordinary diversification. The characteristic diminution of the diatom cell wall over the course of vegetative growth provides a reliable, intrinsic trigger for sexual reproduction, establishing a direct link between the evolution of their cell-wall and life- history features. It is unclear, however, whether the diplontic life cycle of diatoms represents an ancestral or derived trait. This uncertainty is based in part on our lack of understanding of the life cycle of the sister lineage to diatoms, which includes a mix of two free-living and separately classified forms: naked biflagellate unicells in the genus Bolidomonas and silicified forms in the order Parmales. These two forms might represent different life-history stages, although directly establishing such links can be difficult. We sequenced transcriptomes for Bolidomonas and two diatoms and found that \~0.1% of the coding regions in the two diploid diatoms are heterozygous, whereas Bolidomonas is virtually devoid of heterozygous alleles, consistent with expectations for a haploid genome. These results suggest that Bolidomonas is haploid and predict that parmaleans represent the diploid phase of a haplodiplontic life cycle. These data fill an important gap in our understanding of the origin of the diplontic life history of diatoms, which may represent an evolutionarily derived, adaptive feature. %B Journal of Phycology %V 983 %P 977–983 %G eng %U http://dx.doi.org/10.1111/jpy.12222 %R 10.1111/jpy.12222 %0 Journal Article %J Marine Drugs %D 2013 %T Bioprospecting marine plankton %A Abida, Heni %A Ruchaud, Sandrine %A Rios, Laurent %A Humeau, Anne %A Probert, Ian %A de Vargas, Colomban %A Bach, Stéphane %A Bowler, Chris %K 2013 %K MicroB3 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B Marine Drugs %V 11 %P 4594–4611 %G eng %U http://www.mdpi.com/1660-3397/11/11/4594 %R 10.3390/md11114594 %0 Journal Article %J Journal of Sea Research %D 2013 %T Characterization of ¡i¿Phaeocystis globosa¡/i¿ (haptophyceae), the blooming species in the southern north sea %A Rousseau, V %A Lantoine, F %A Rodriguez, F %A Le Gall, F %A Chrétiennot-Dinet, M.-J. %A Lancelot, C %K 2013 %K ASSEMBLE %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %K Souchotheque %B Journal of Sea Research %V 76 %P 105–113 %G eng %R 10.1016/j.seares.2012.07.011 %0 Journal Article %J PLoS ONE %D 2013 %T A gene island with two possible configurations is involved in chromatic acclimation in marine synechococcus %A Humily, Florian %A Partensky, Frédéric %A Six, Christophe %A Farrant, Gregory K %A Ratin, Morgane %A Marie, Dominique %A Garczarek, Laurence %K 2013 %K MACUMBA %K MicroB3 %K rcc %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto?app %X ¡p¿¡italic¿Synechococcus¡/italic¿, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine ¡italic¿Synechococcus¡/italic¿ radiation. A specific gene island was identified in all CA4-performing strains, containing two genes (¡italic¿fciA¡/italic¿/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the ¡italic¿mpeZ¡/italic¿ gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called ¡italic¿fciC¡/italic¿. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While ¡italic¿mpeZ¡/italic¿ is expressed more in blue light than green light, this is the reverse for ¡italic¿mpeW¡/italic¿, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process.¡/p¿ %B PLoS ONE %V 8 %P e84459 %G eng %U http://dx.doi.org/10.1371/journal.pone.0084459 %R 10.1371/journal.pone.0084459 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2013 %T Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida %A Collen, Jonas %A Porcel, Betina %A Carré, Wilfrid %A Ball, Steven G %A Chaparro, Cristian %A Tonon, Thierry %A Barbeyron, Tristan %A Michel, Gurvan %A Noel, Benjamin %A Valentin, Klaus %A Elias, Marek %A Artiguenave, François %A Arun, Alok %A Aury, Jean-Marc %A Barbosa-Neto, José F %A Bothwell, John H %A Bouget, François-Yves %A Brillet, Loraine %A Cabello-Hurtado, Francisco %A Capella-Gutiérrez, Salvador %A Charrier, Bénédicte %A Cladière, Lionel %A Cock, J Mark %A Coelho, Susana M %A Colleoni, Christophe %A Czjzek, Mirjam %A Da Silva, Corinne %A Delage, Ludovic %A Denoeud, France %A Deschamps, Philippe %A Dittami, Simon M %A Gabaldón, Toni %A Gachon, Claire M M %A Groisillier, Agnès %A Hervé, Cécile %A Jabbari, Kamel %A Katinka, Michael %A Kloareg, Bernard %A Kowalczyk, Nathalie %A Labadie, Karine %A Leblanc, Catherine %A Lopez, Pascal J %A McLachlan, Deirdre H %A Meslet-Cladiere, Laurence %A Moustafa, Ahmed %A Nehr, Zofia %A Nyvall Collén, Pi %A Panaud, Olivier %A Partensky, Frédéric %A Poulain, Julie %A Rensing, Stefan A %A Rousvoal, Sylvie %A Samson, Gaelle %A Symeonidi, Aikaterini %A Weissenbach, Jean %A Zambounis, Antonios %A Wincker, Patrick %A Boyen, Catherine %K RCC299 %X Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements. %B Proceedings of the National Academy of Sciences %V 110 %P 5247–5252 %G eng %U http://www.pnas.org/content/110/13/5247.abstract %R 10.1073/pnas.1221259110 %0 Journal Article %J Environmental Microbiology %D 2013 %T pico-PLAZA, a genome database of microbial photosynthetic eukaryotes %A Vandepoele, Klaas %A Van Bel, Michiel %A Richard, Guilhem %A Van Landeghem, Sofie %A Verhelst, Bram %A Moreau, Hervé %A Van de Peer, Yves %A Grimsley, Nigel %A Piganeau, Gwenael %K Micromonas %K rcc %X With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains. %B Environmental Microbiology %V 15 %P 2147–2153 %G eng %U http://dx.doi.org/10.1111/1462-2920.12174 %R 10.1111/1462-2920.12174 %0 Journal Article %J Marine Drugs %D 2011 %T Coccolithophores: Functional biodiversity, enzymes and bioprospecting %A Reid, Emma L %A Worthy, Charlotte A %A Probert, Ian %A Ali, Sohail T %A Love, John %A Napier, Johnathan %A Littlechild, Jenny A %A Somerfield, Paul J %A Allen, Michael J %K 2011 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %B Marine Drugs %V 9 %P 586–602 %G eng %U http://www.mdpi.com/1660-3397/9/4/586/ %R 10.3390/md9040586 %0 Journal Article %J Plant Physiology %D 2011 %T Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress %A Blot, N %A Mella-Flores, D %A Six, C %A Lecorguille, G %A Boutte, C %A Peyrat, A %A Monnier, A %A Ratin, M %A Gourvil, P %A Campbell, D A %A Garczarek, L %K 2011 %K rcc %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto?app %X Marine Synechococcus undergo a wide range of environmental stressors, especially high and variable irradiance, which may induce oxidative stress through the generation of reactive oxygen species (ROS). While light and ROS could act synergistically on the impairment of photosynthesis, inducing photodamage and inhibiting photosystem II repair, acclimation to high irradiance is also thought to confer resistance to other stressors. To identify the respective roles of light and ROS in the photoinhibition process and detect a possible light-driven tolerance to oxidative stress, we compared the photophysiological and transcriptomic responses of Synechococcus sp. WH7803 acclimated to low (LL) or high light (HL) to oxidative stress, induced by hydrogen peroxide (H2O2) or methylviologen. While photosynthetic activity was much more affected in HL than in LL cells, only HL cells were able to recover growth and photosynthesis after addition of 25 microM H2O2. Depending upon light conditions and H2O2 concentration, the latter oxidizing agent induced photosystem II inactivation through both direct damages to the reaction centres and inhibition of its repair cycle. Although the global transcriptome response appeared similar in LL and HL cells, some processes were specifically induced in HL cells that seemingly helped them withstand oxidative stress, including enhancement of photoprotection and ROS detoxification, repair of ROS-driven damages and regulation of redox state. Detection of putative LexA binding sites allowed the identification of the putative LexA regulon, which was down-regulated in HL compared to LL cells, but up-regulated by oxidative stress under both growth irradiances. %B Plant Physiology %V 156 %P 1934–1954 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21670225 %0 Journal Article %J Nature %D 2011 %T Sensitivity of coccolithophores to carbonate chemistry and ocean acidification %A Beaufort, L %A Probert, I %A de Garidel-Thoron, T %A Bendif, E M %A Ruiz-Pino, D %A Metzl, N %A Goyet, C %A Buchet, N %A Coupel, P %A Grelaud, M %A Rost, B %A Rickaby, R E M %A de Vargas, C %K 2011 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X Coccolithophores produce the major fraction of pelagic carbonate, a key component of the carbon cycle. The effect of elevated CO2 on their calcification is poorly understood. Culture experiments have yielded varied calcification responses to increased pCO2 between and within coccolithophore taxa. We used a novel automated method for pattern recognition and morphometric analysis to quantify the calcite mass of coccolithophores from ¿700 samples from present past (last 40-Kyr) oceans. Comparison of morphological data with ocean carbonate chemistry reconstructed in both space and time indicate decreasing calcification with increasing pCO2, and decreasing CO32. At pH ¡8.0, delicate Emiliania huxleyi are strongly affected by decalcification. However, highly calcified E. huxleyi morphotypes predominate in waters with lowest pH. This suggests that coccolithophore strains pre-adapted to future, more acidic oceans already populate regions of contemporary oceans. The future carbon feedback from coccolithophore calcification will depend on the genetic diversity and adaptability of coccolithophore populations. %B Nature %V 476 %P 80–83 %G eng %R 10.1038/nature10295 %0 Journal Article %J Journal of Phycology %D 2011 %T Transcriptome analyses reveal differential gene expression patterns between the life-cycle stages of Emiliania huxleyi (Haptophyta) and reflect specialization to different ecological niches %A Rokitta, Sebastian D %A de Nooijer, Lennart J %A Trimborn, Scarlett %A de Vargas, Colomban %A Rost, Björn %A John, Uwe %K 2011 %K endocytosis %K Life-cycle stages %K microarray %K quantitative RT-PCR %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %K transcriptome profiling %X Coccolithophores, especially the abundant, cosmopolitan species Emiliania huxleyi (Lohmann) W. W. Hay et H. P. Mohler, are one of the main driving forces of the oceanic carbonate pump and contribute significantly to global carbon cycling, due to their ability to calcify. A recent study indicates that termination of diploid blooms by viral infection induces life-cycle transition, and speculation has arisen about the role of the haploid, noncalcifying stage in coccolithophore ecology. To explore gene expression patterns in both life-cycle stages, haploid and diploid cells of E. huxleyi (RCC 1217 and RCC 1216) were acclimated to limiting and saturating photon flux densities. Transcriptome analyses were performed to assess differential genomic expression related to different ploidy levels and acclimation light intensities. Analyses indicated that life-cycle stages exhibit different properties of regulating genome expression (e.g., pronounced gene activation and gene silencing in the diploid stage), proteome maintenance (e.g., increased turnover of proteins in the haploid stage), as well as metabolic processing (e.g., pronounced primary metabolism and motility in the haploid stage and calcification in the diploid stage). Furthermore, higher abundances of transcripts related to endocytotic and digestive machinery were observed in the diploid stage. A qualitative feeding experiment indicated that both life-cycle stages are capable of particle uptake (0.5 ??m diameter) in late-stationary growth phase. Results showed that the two life-cycle stages represent functionally distinct entities that are evolutionarily shaped to thrive in the environment they typically inhabit. %B Journal of Phycology %V 47 %P 829–838 %G eng %U http://dx.doi.org/10.1111/j.1529-8817.2011.01014.x %R 10.1111/j.1529-8817.2011.01014.x %0 Journal Article %J FEMS Microbiology Ecology %D 2011 %T Whole Genome Amplification (WGA) of marine photosynthetic eukaryote populations %A Lepere, Cecile %A Demura, M %A Kawachi, M %A Romac, S %A Probert, I %A Vaulot, D %K 2011 %K PICOFUNPAC %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B FEMS Microbiology Ecology %V 76 %P 516–523 %G eng %R 10.1111/j.1574-6941.2011.01072.x %0 Journal Article %J Tetrahedron: Asymmetry %D 2009 %T Enantiocomplementary inverting sec-alkylsulfatase activity in cyano- and thio-bacteria Synechococcus and Paracoccus spp.: selectivity enhancement by medium engineering %A Gadler, Petra %A Reiter, Tamara C %A Hoelsch, Kathrin %A Weuster-Botz, Dirk %A Fabe, Kurt %K rcc %B Tetrahedron: Asymmetry %V 20 %P 115–118 %G eng %R 10.1016/j.tetasy.2009.01.007 %0 Journal Article %J Science %D 2009 %T Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas %A Worden, A Z %A Lee, J.- H %A Mock, T %A Rouzé, P %A Simmons, M P %A Aerts, A L %A Allen, A E %A Cuvelier, M L %A Derelle, E %A Everett, M V %A Foulon, E %A Grimwood, J %A Gundlach, H %A Henrissat, B %A Napoli, C %A McDonald, S M %A Parker, M S %A Rombauts, S %A Salamov, A %A Von Dassow, P %A Badger, J H %A Coutinho, P M %A Demir, E %A Dubchak, I %A Gentemann, C %A Eikrem, W %A Gready, J E %A John, U %A Lanier, W %A Lindquist, E A %A Lucas, S %A Mayer, K F X %A Moreau, H %A Not, F %A Otillar, R %A Panaud, O %A Pangilinan, J %A Paulsen, I %A Piegu, B %A Poliakov, A %A Robbens, S %A Schmutz, J %A Toulza, E %A Wyss, T %A Zelensky, A %A Zhou, K %A Armbrust, E V %A Bhattacharya, D %A Goodenough, U W %A Van de Peer, Y %A Grigoriev, I V %K rcc %K RCC299 %K RCC827 %K SBR$_\textrmP$hyto$_\textrmD$PO %K SBR$_\textrmP$hyto$_\textrmE$PPO %X The photosynthetic picoeukaryote Micromonas thrives from tropical to polar marine ecosystems and belongs to an anciently diverged sister clade to land plants. We sequenced genomes from two Micromonas isolates (22 Mb, CCMP1545; 21 Mb, RCC299) and the results improve understanding of their ecology and green-lineage evolution. Despite high 18S rDNA sequence identity, only 90% of their predicted genes were shared. Novel intronic repeat elements in CCMP1545, otherwise found only in metagenomic data, and unique riboswitch arrangements emphasized their independent evolutionary paths. Phylogenomic profiles revealed putative ancestral features, but also indicated selection/acquisition processes are actively shaping a ‘unique' gene pool in each differently than ‘core' genes. Current climate-change trajectories are predicted to produce conditions favoring picophytoplankton, making Micromonas potential indicators of biological change in ocean ecosystems. %B Science %V 324 %P 268–272 %G eng %R 10.1126/science.1167222 %0 Journal Article %J Genome Research %D 2009 %T Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus %A Monier, A %A Pagarete, A %A Allen, M J %A Read, B A %A de Vargas, C %A Claverie, J M %A Ogata, H %K 2009 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %B Genome Research %V 19 %P 1441–1449 %G eng %R 10.1101/gr.091686.109 %0 Journal Article %J Applied and Environmental Microbiology %D 2009 %T Light-dependent transcriptional regulation of genes of biogeochemical interest in the diploid and haploid life cycle stages of Emiliania huxleyi %A Richier, S %A Kerros, M E %A de Vargas, C %A Haramaty, L %A Falkowski, P G %A Gattuso, J P %K 2009 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore Emiliania huxleyi was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested. %B Applied and Environmental Microbiology %V 75 %P 3366–3369 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19304825 %R 10.1128/aem.02737-08 %0 Journal Article %J Nature %D 2009 %T Photosystem I gene cassettes are present in marine virus genomes %A Sharon, Itai %A Alperovitch, Ariella %A Rohwer, Forest %A Haynes, Matthew %A Glaser, Fabian %A Atamna-Ismaeel, Nof %A Pinter, Ron Y %A Partensky, Frédéric %A Koonin, Eugene V %A Wolf, Yuri I %A Nelson, Nathan %A Béjà, Oded %K RCC307 %K SBR$_\textrmP$hyto$_\textrmP$PM %B Nature %V 461 %P 258–262 %G eng %U http://dx.doi.org/10.1038/nature08284 http://www.nature.com/nature/journal/v461/n7261/suppinfo/nature08284_S1.html %R 10.1038/nature08284 %0 Journal Article %J Plant Physiology %D 2009 %T Photosystem II and pigment dynamics among ecotypes of the green alga Ostreococcus %A Six, C %A Sherrard, R %A Lionard, M %A Roy, S %A Campbell, D A %K rcc %K RCC809 %K SBR$_\textrmP$hyto$_\textrmP$PM %X We investigated the photophysiological response of three ecotypes of the picophytoplankter Ostreococcus and a larger prasinophyte Pyramimonas obovata to a sudden increase in light irradiance. The deepwater Ostreococcus sp. RCC809 showed very high susceptibility to primary photoinactivation, likely a consequence of high oxidative stress, which may relate to the recently noted plastid terminal oxidase activity in this strain. The three Ostreococcus ecotypes were all able of deploying modulation of photosystem II repair cycle in order to cope with the light increase, but the effective clearance of photoinactivated D1 protein appeared to be slower in the deep water Ostreococcus sp. RCC809, suggesting that this step is rate-limiting in the photosystem II repair cycle in this strain. The deepwater Ostreococcus moreover accumulated lutein and showed substantial use of the xanthophyll cycle under light stress, demonstrating its high sensitivity to light fluctuations. The sustained component of the non-photochemical quenching of fluorescence correlated well with the xanthophyll de-epoxidation activity. Comparisons with the larger prasinophyte Pyramimonas obovata suggest that the photophysiology of Ostreococcus ecotypes requires high photosystem II repair rates to counter a high susceptibility to photoinactivation, consistent with low pigment package effects in their minute-sized cells. %B Plant Physiology %V 151 %P 379–390 %G eng %R 10.1104/pp.109.140566 %0 Journal Article %J Limnology and Oceanography %D 2008 %T Contrasting photoacclimation strategies in ecotypes of the eukayotic picoplankter ¡i¿Ostreococcus¡/i¿ %A Six, C %A Finkel, Z V %A Rodriguez, F %A Marie, D %A Partensky, F %A Campbell, D A %K 2008 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?app %X Ostreococcus, the smallest known marine picoeukaryote, includes low- and high-light ecotypes. To determine the basis for niche partitioning between Ostreococcus sp. RCC809, isolated from the bottom of the tropical Atlantic euphotic zone, and the lagoon strain Ostreococcus tauri, we studied their photophysiologies under growth irradiances from 15 mmol photons m22 s21 to 800 mmol photons m22 s21 with a common nutrient replete regime. With increasing growth irradiance, both strains down-regulated cellular chlorophyll a and chlorophyll b (Chl a and Chl b) content, increased xanthophyll de-epoxidation correlated with nonphotochemical excitation quenching, and accumulated lutein. Ribulose-1,5-bisphosphate carboxylase/oxygenase content remained fairly stable. Under low-growth irradiances of 15–80 mmol photons m22 s21, O. sp. RCC809 had equivalent or slightly higher growth rates, lower Chl a, a higher Chl b : Chl a ratio, and a larger photosystem II (PSII) antenna than O. tauri. O. tauri was more phenotypically plastic in response to growth irradiance, with a larger dynamic range in growth rate, Chl a, photosystem cell content, and cellular absorption cross-section of PSII. Estimating the amino acid and nitrogen costs for photoacclimation showed that the deep-sea oceanic O. sp. RCC809 relies largely on lower nitrogen cost changes in PSII antenna size to achieve a limited range of s-type light acclimation. O. sp. RCC809, however, suffers photoinhibition under higher light. This limited capacity for photoacclimation is compatible with the stable low-light and nutrient conditions at the base of the euphotic layer of the tropical Atlantic Ocean. In the more variable, high-nutrient, lagoon environment, O. tauri can afford to use a higher cost n-type acclimation of photosystem contents to exploit a wider range of light. %B Limnology and Oceanography %V 53 %P 255–265 %G eng %R 10.4319/lo.2008.53.1.0255 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2008 %T An original adaptation of photosynthesis in the marine green alga Ostreococcus %A Cardol, Pierre %A Bailleul, Benjamin %A Rappaport, Fabrice %A Derelle, Evelyne %A Baal, Daniel %A Breyton, Cécile %A Bailey, Shaun %A Wollman, Francis André %A Grossman, Arthur %A Moreau, Hervé %A Finazzi, Giovanni %K rcc %K RCC745 %K RCC809 %X Adaptation of photosynthesis in marine environment has been examined in two strains of the green, picoeukaryote : OTH95, a surface/high-light strain, and RCC809, a deep-sea/low-light strain. Differences between the two strains include changes in the light-harvesting capacity, which is lower in OTH95, and in the photoprotection capacity, which is enhanced in OTH95. Furthermore, RCC809 has a reduced maximum rate of O evolution, which is limited by its decreased photosystem I (PSI) level, a possible adaptation to Fe limitation in the open oceans. This decrease is, however, accompanied by a substantial rerouting of the electron flow to establish an HO-to-HO cycle, involving PSII and a potential plastid plastoquinol terminal oxidase. This pathway bypasses electron transfer through the cytochrome complex and allows the pumping of “extra†protons into the thylakoid lumen. By promoting the generation of a large ΔpH, it facilitates ATP synthesis and nonphotochemical quenching when RCC809 cells are exposed to excess excitation energy. We propose that the diversion of electrons to oxygen downstream of PSII, but before PSI, reflects a common and compulsory strategy in marine phytoplankton to bypass the constraints imposed by light and/or nutrient limitation and allow successful colonization of the open-ocean marine environment. %B Proceedings of the National Academy of Sciences of the United States of America %V 105 %P 7881–7886 %G eng %U http://www.pnas.org/content/105/22/7881.abstract %R 10.1073/pnas.0802762105 %0 Journal Article %J Nature %D 2008 %T The Phaeodactylum genome reveals the evolutionary history of diatom genomes %A Bowler, Chris %A Allen, Andrew E %A Badger, Jonathan H %A Grimwood, Jane %A Jabbari, Kamel %A Kuo, Alan %A Maheswari, Uma %A Martens, Cindy %A Maumus, Florian %A Otillar, Robert P %A Rayko, Edda %A Salamov, Asaf %A Vandepoele, Klaas %A Beszteri, Bank %A Gruber, Ansgar %A Heijde, Marc %A Katinka, Michael %A Mock, Thomas %A Valentin, Klaus %A Verret, Frederic %A Berges, John A %A Brownlee, Colin %A Cadoret, Jean-Paul %A Chiovitti, Anthony %A Choi, Chang Jae %A Coesel, Sacha %A De Martino, Alessandra %A Detter, J Chris %A Durkin, Colleen %A Falciatore, Angela %A Fournet, Jerome %A Haruta, Miyoshi %A Huysman, Marie J J %A Jenkins, Bethany D %A Jiroutova, Katerina %A Jorgensen, Richard E %A Joubert, Yolaine %A Kaplan, Aaron %A Kroger, Nils %A Kroth, Peter G %A La Roche, Julie %A Lindquist, Erica %A Lommer, Markus %A Martin-Jezequel, Veronique %A Lopez, Pascal J %A Lucas, Susan %A Mangogna, Manuela %A McGinnis, Karen %A Medlin, Linda K %A Montsant, Anton %A Secq, Marie-Pierre Oudot-Le %A Napoli, Carolyn %A Obornik, Miroslav %A Parker, Micaela Schnitzler %A Petit, Jean-Louis %A Porcel, Betina M %A Poulsen, Nicole %A Robison, Matthew %A Rychlewski, Leszek %A Rynearson, Tatiana A %A Schmutz, Jeremy %A Shapiro, Harris %A Siaut, Magali %A Stanley, Michele %A Sussman, Michael R %A Taylor, Alison R %A Vardi, Assaf %A von Dassow, Peter %A Vyverman, Wim %A Willis, Anusuya %A Wyrwicz, Lucjan S %A Rokhsar, Daniel S %A Weissenbach, Jean %A Armbrust, E Virginia %A Green, Beverley R %A Van de Peer, Yves %A Grigoriev, Igor V %K 2008 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPOdipo %K sbr?hyto?ppo %B Nature %V 456 %P 239–244 %G eng %U http://dx.doi.org/10.1038/nature07410 http://www.nature.com/nature/journal/v456/n7219/suppinfo/nature07410_S1.html %R 10.1038/nature07410 %0 Journal Article %J Diseases of Aquatic Organisms %D 2008 %T Phylogenetic and morphological characterization of the green algae infesting blue mussel Mytilus edulis in the North and South Atlantic %A Rodriguez, F %A Feist, S W %A Guillou, L %A Harkestad, L S %A Bateman, K %A Renault, T %A Mortensen, S %K rcc %K RCC894 %K SBR$_\textrmP$hyto$_\textrmD$PO %B Diseases of Aquatic Organisms %V 81 %P 231–240 %G eng %R 10.3354/dao01956 %0 Journal Article %J Biogeosciences %D 2008 %T Picoplankton diversity in the south-east pacific ocean from cultures %A Le Gall, F %A Rigaut-Jalabert, F %A Marie, D %A Garczareck, L %A Viprey, M %A Godet, A %A Vaulot, D %K 2008 %K PICOFUNPAC %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?app %B Biogeosciences %V 5 %P 203–214 %G eng %R 10.5194/bg-5-203-2008 %0 Journal Article %J Molecular Biology and Evolution %D 2007 %T The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction %A Robbens, S %A Derelle, E %A Ferraz, C %A Wuyts, J %A Moreau, H %A Van de Peer, Y %K rcc %X The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most gene-dense mt genome of all Chlorophyta. Furthermore, it is characterized by a unique segmental duplication, encompassing 22 genes and covering 44% of the genome. Such a duplication has not been observed before in green algae, although it is also present in the mt genomes of higher plants. The quadripartite cp genome forms a circle of 71,666 bp, containing 86 genes divided over a larger and a smaller single-copy region, separated by 2 inverted repeat sequences. Based on genome size and number of genes, the Ostreococcus cp genome is the smallest known among the green algae. Phylogenetic analyses based on a concatenated alignment of cp, mt, and nuclear genes confirm the position of O. tauri within the Prasinophyceae, an early branch of the Chlorophyta. %B Molecular Biology and Evolution %V 24 %P 956–968 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17251180 %0 Journal Article %J Journal of Molecular Evolution %D 2007 %T Evolutionary analysis of the small heat shock proteins in five complete algal genomes %A Waters, E R %A Rioflorido, I %K *Evolution %K *Genome %K algae %K Algae/classification/*genetics %K Algal Proteins/*genetics %K Amino Acid Sequence %K Animals %K Chlamydomonas reinhardtii/genetics %K Diatoms/genetics %K Green/genetics %K Heat-Shock Proteins %K Molecular %K Molecular Sequence Data %K phylogeny %K Protein %K rcc %K Red/genetics %K Sequence Alignment %K Sequence Analysis %K Small/*genetics %K Species Specificity %X Small heat shock proteins (sHSPs) are chaperones that are crucial in the heat shock response but also have important nonstress roles within the cell. sHSPs are found in all three domains of life (Bacteria, Archaea, and Eukarya). These proteins are particularly diverse within land plants and the evolutionary origin of the land plant sHSP families is still an open question. Here we describe the identification of 17 small sHSPs from the complete genome sequences of five diverse algae: Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Ostreococcus lucimarinus, Ostreococcus tauri, and Thalassiosira pseudonana. Our analysis indicates that the number and diversity of algal sHSPs are not correlated with adaptation to extreme conditions. While all of the algal sHSPs identified are members of this large and important superfamily, none of these sHSPs are members of the diverse land plant sHSP families. The evolutionary relationships among the algal sHSPs and homologues from bacteria and other eukaryotes are consistent with the hypothesis that the land plant chloroplast and mitochondrion sHSPs did not originate from the endosymbionts of the chloroplast and mitochondria. In addition the evolutionary history of the sHSPs is very different from that of the HSP70s. Finally, our analysis of the algal sHSPs sequences in light of the known sHSP crystal structures and functional data suggests that the sHSPs possess considerable structural and functional diversity. %B Journal of Molecular Evolution %V 65 %P 162–174 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17684698 %0 Journal Article %J PLoS genetics %D 2007 %T Patterns and implications of gene gain and loss in the evolution of Prochlorococcus %A Kettler, G %A Martiny, A C %A Huang, K %A Zucker, J %A Coleman, M L %A Rodrigue, S %A Chen, F %A Lapidus, A %A Ferriera, S %A Johnson, J %A Steglich, C %A Church, G %A Richardson, P %A Chisholm, S W %K rcc %B PLoS genetics %V 3 %P e231 %G eng %R 10.1371/journal.pgen.0030231 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2007 %T The tiny eukaryote \textit{Ostreococcus provides genomic insights into the paradox of plankton speciation %A Palenik, B %A Grimwood, J %A Aerts, A %A Rouzé, P %A Salamov, A %A Putnam, N %A Dupont, C %A Jorgensen, R %A Derelle, E %A Rombauts, S %A Zhou, K %A Otillar, R %A Merchant, S S %A Podell, S %A Gaasterland, T %A Napoli, C %A Gendler, K %A Manuell, A %A Tai, V %A Vallon, O %A Piganeau, G %A Jancek, S %A Heijde, M %A Jabbari, K %A Bowler, C %A Lohr, M %A Robbens, S %A Werner, G %A Dubchak, I %A Pazour, G J %A Ren, Q %A Paulsen, I %A Delwiche, C %A Schmutz, J %A Rokhsar, D %A Van de Peer, Y %A Moreau, H %A Grigoriev, I V %K rcc %X The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size. %B Proceedings of the National Academy of Sciences of the United States of America %V 104 %P 7705–7710 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17460045 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2006 %T Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features %A Derelle, Evelyne %A Ferraz, Conchita %A Rombauts, Stephane %A Rouze, Pierre %A Worden, Alexandra Z %A Robbens, Steven %A Partensky, Frédéric %A Degroeve, Sven %A Echeynie, Sophie %A Cooke, Richard %A Saeys, Yvan %A Wuyts, Jan %A Jabbari, Kamel %A Bowler, Chris %A Panaud, Olivier %A Piegu, Benoit %A Ball, Steven G %A Ral, Jean-Philippe %A Bouget, François-Yves %A Piganeau, Gwenael %A De Baets, Bernard %A Picard, André %A Delseny, Michel %A Demaille, Jacques %A Van de Peer, Yves %A Moreau, Hervé %K rcc %K RCC745 %K SBR$_\textrmP$hyto %X The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry. %B Proceedings of the National Academy of Sciences of the United States of America %V 103 %P 11647–11652 %G eng %U http://www.pnas.org/cgi/content/abstract/103/31/11647 %R 10.1073/pnas.0604795103 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2006 %T Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment %A Palenik, Brian %A Ren, Qinghu %A Dupont, Chris L %A Myers, Garry S %A Heidelberg, John F %A Badger, Jonathan H %A Madupu, Ramana %A Nelson, William C %A Brinkac, Lauren M %A Dodson, Robert J %A Durkin, A Scott %A Daugherty, Sean C %A Sullivan, Stephen A %A Khouri, Hoda %A Mohamoud, Yasmin %A Halpin, Rebecca %A Paulsen, Ian T %K rcc %X Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments. %B Proceedings of the National Academy of Sciences of the United States of America %V 103 %P 13555–13559 %G eng %U http://www.pnas.org/cgi/content/abstract/103/36/13555 %R 10.1073/pnas.0602963103 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2006 %T Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment %A Palenik, Brian %A Ren, Qinghu %A Dupont, Chris L. %A Myers, Garry S. %A Heidelberg, John F. %A Badger, Jonathan H. %A Madupu, Ramana %A Nelson, William C. %A Brinkac, Lauren M. %A Dodson, Robert J. %A Durkin, A. Scott %A Daugherty, Sean C. %A Sullivan, Stephen A. %A Khouri, Hoda %A Mohamoud, Yasmin %A Halpin, Rebecca %A Paulsen, Ian T. %K cyanobacteria %K genomics %K Marine %K RCC1086 %X Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments. %B Proceedings of the National Academy of Sciences %V 103 %P 13555–13559 %G eng %U https://www.pnas.org/content/103/36/13555 %R 10.1073/pnas.0602963103 %0 Journal Article %J Environmental Microbiology %D 2005 %T Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae). %A Rodriguez, F %A Derelle, E %A Guillou, L %A Le Gall, F %A Vaulot, D %A Moreau, H %K rcc %K RCC113 %K Rcc141 %K RCC143 %K RCC343 %K RCC356 %K RCC371 %K RCC393 %K rcc410 %K RCC420 %K RCC434 %K rcc501 %K RCC658 %K RCC745 %K SBR$_\textrmP$hyto$_\textrmD$PO %B Environmental Microbiology %V 7 %P 853–859 %G eng %R 10.1111/j.1462-2920.2005.00758.x %0 Journal Article %J Molecular Biology and Evolution %D 2005 %T Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri %A Robbens, S %A Khadaroo, B %A Camasses, A %A Derelle, E %A Ferraz, C %A Inze, D %A Van, de Peer Y %A Moreau, H %K Anaphase Promoting Complex %K Arabidopsis Thaliana %K Cdk Activity %K cell division cycle %K Chlorophyta %K cyclin %K cyclin dependant kinase %K Green alga %K Kinase %K Ostreococcus tauri %K Plant %K Prasinophyceae %K rcc %K RCC745 %K Retinoblastoma Protein %K Saccharomyces Cerevisiae %K Yeast %X The cell cycle has been extensively studied in various organisms, and the recent access to an overwhelming amount of genomic data has given birth to a new integrated approach called comparative genomics. Comparing the cell cycle across species shows that its regulation is evolutionarily conserved; the best-known example is the pivotal role of cyclin-dependent kinases in all the eukaryotic lineages hitherto investigated. Interestingly, the molecular network associated with the activity of the CDK-cyclin complexes is also evolutionarily conserved, thus, defining a core cell cycle set of genes together with lineage-specific adaptations. In this paper, we describe the core cell cycle genes of Ostreococcus tauri, the smallest free-living eukaryotic cell having a minimal cellular organization with a nucleus, a single chloroplast, and only one mitochondrion. This unicellular marine green alga, which has diverged at the base of the green lineage, shows the minimal yet complete set of core cell cycle genes described to date. It has only one homolog of CDKA, CDKB, CDKD, cyclin A, cyclin B, cyclin D, cyclin H, Cks, Rb, E2F, DP, DEL, Cdc25, and Wee L We have also added the APC and SCF E3 ligases to the core cell cycle gene set. We discuss the potential of genome-wide analysis in the identification of divergent orthologs of cell cycle genes in different lineages by mining the genomes of evolutionarily important and strategic organisms. %B Molecular Biology and Evolution %V 22 %P 589–597 %G eng %R 10.1093/molbev/msi044 %0 Journal Article %J Molecular Biology and Evolution %D 2005 %T New insights into the nature and phylogeny of prasinophyte antenna proteins: Ostreococcus tauri, a case study %A Six, C %A Worden, A Z %A Rodriguez, F %A Moreau, H %A Partensky, F %K rcc %K RCC113 %K RCC114 %K RCC417 %K RCC745 %K SBR$_\textrmP$hyto$_\textrmD$PO %X The basal position of the Mamiellales (Prasinophyceae) within the green lineage makes these unicellular organisms key to elucidating early stages in the evolution of chlorophyll a/b–binding light-harvesting complexes (LHCs). Here, we unveil the complete and unexpected diversity of Lhc proteins in Ostreococcus tauri, a member of the Mamiellales order, based on results from complete genome sequencing. Like Mantoniella squamata, O. tauri possesses a number of genes encoding an unusual prasinophyte-specific Lhc protein type herein designated "Lhcp". Biochemical characterization of the complexes revealed that these polypeptides, which bind chlorophylls a, b, and a chlorophyll c–like pigment (Mg-2,4-divinyl-phaeoporphyrin a5 monomethyl ester) as well as a number of unusual carotenoids, are likely predominant. They are retrieved to some extent in both reaction center I (RCI)– and RCII-enriched fractions, suggesting a possible association to both photosystems. However, in sharp contrast to previous reports on LHCs of M. squamata, O. tauri also possesses other LHC subpopulations, including LHCI proteins (encoded by five distinct Lhca genes) and the minor LHCII polypeptides, CP26 and CP29. Using an antibody against plant Lhca2, we unambiguously show that LHCI proteins are present not only in O. tauri, in which they are likely associated to RCI, but also in other Mamiellales, including M. squamata. With the exception of Lhcp genes, all the identified Lhc genes are present in single copy only. Overall, the discovery of LHCI proteins in these prasinophytes, combined with the lack of the major LHCII polypeptides found in higher plants or other green algae, supports the hypothesis that the latter proteins appeared subsequent to LHCI proteins. The major LHC of prasinophytes might have arisen prior to the LHCII of other chlorophyll a/b–containing organisms, possibly by divergence of a LHCI gene precursor. However, the discovery in O. tauri of CP26-like proteins, phylogenetically placed at the base of the major LHCII protein clades, yields new insight to the origin of these antenna proteins, which have evolved separately in higher plants and green algae. Its diverse but numerically limited suite of Lhc genes renders O. tauri an exceptional model system for future research on the evolution and function of LHC components. %B Molecular Biology and Evolution %V 22 %P 2217–2230 %G eng %R 10.1093/molbev/msi220 %0 Journal Article %D 2004 %T Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences %A Romari, Khadidja %A Vaulot, Daniel %K Micromonas %K rcc %X Abstract We analyzed picoeukaryote assemblages at a French coastal site of the English Channel by sequencing cloned eukaryotic 18S rRNA genes in eight genetic libraries constructed from environmental samples (seven coastal , one estuarine) collected at different periods of the ... %V 49 %P 784–798 %G eng %R 10.4319/lo.2004.49.3.0784 %0 Journal Article %J Protist %D 2004 %T Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems %A Guillou, Laure %A Eikrem, W %A Chrétiennot-Dinet, M.-J. %A Le Gall, F %A Massana, R %A Romari, K %A Pedrós-Alió, C %A Vaulot, D %K 2004 %K PICODIV %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto %K SOMLIT %B Protist %V 155 %P 193–214 %G eng %R 10.1078/143446104774199592 %0 Journal Article %J Plant Physiology %D 2004 %T Starch division and partitioning. A mechanism for granule propagation and maintenance in the picophytoplanktonic green alga Ostreococcus tauri %A Ral, J P %A Derelle, E %A Ferraz, C %A Wattebled, F %A Farinas, B %A Corellou, F %A Buleon, A %A Slomianny, M C %A Delvalle, D %A D, Hulst C %A Rombauts, S %A Moreau, H %A Ball, S %K Adp Glucose Pyrophosphorylase %K Amylopectin %K Arabidopsis %K Bacterial Glycogen %K Biogenesis %K Biosynthesis %K Chlamydomonas Reinhardtii %K Enzyme %K Prasinophyceae %K rcc %K RCC745 %K Synthase %X Whereas Glc is stored in small-sized hydrosoluble glycogen particles in archaea, eubacteria, fungi, and animal cells, photosynthetic eukaryotes have resorted to building starch, which is composed of several distinct polysaccharide fractions packed into a highly organized semicrystalline granule. In plants, both the initiation of polysaccharide synthesis and the nucleation mechanism leading to formation of new starch granules are currently not understood. Ostreococcus tauri, a unicellular green alga of the Prasinophyceae family, defines the tiniest eukaryote with one of the smallest genomes. We show that it accumulates a single starch granule at the chloroplast center by using the same pathway as higher plants. At the time of plastid division, we observe elongation of the starch and division into two daughter structures that are partitioned in each newly formed chloroplast. These observations suggest that in this system the information required to initiate crystalline polysaccharide growth of a new granule is contained within the preexisting polysaccharide structure and the design of the plastid division machinery. %B Plant Physiology %V 136 %P 3333–3340 %G eng %R 10.1104/pp.104.044131 %0 Journal Article %J Nature %D 2003 %T The genome of a motile marine Synechococcus %A Palenik, B %A Brahamsha, B %A Larimer, F W %A Land, M %A Hauser, L %A Chain, P %A Lamerdin, J %A Regala, W %A Allen, E E %A McCarren, J %A Paulsen, I %A Dufresne, A %A Partensky, F %A Webb, E A %A Waterbury, J %K 2003 %K Cyanobacterium Synechococcus %K Degradation %K Ecology %K Gene %K IDENTIFICATION %K Polypeptide %K Prochlorococcus %K rcc %K SBR$_\textrmP$hyto %K sbr?hyto %K SEQUENCE %K Sp Pcc7942 %K Strains %X Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans(1). Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria(2). %B Nature %V 424 %P 1037–1042 %G eng %R 10.1038/nature01943 %0 Journal Article %J Journal of Phycology %D 2002 %T DNA libraries for sequencing the genome of Ostreococcus tauri (Chlorophyta, Prasinophyceae): The smallest free-living eukaryotic cell %A Derelle, E %A Ferraz, C %A Lagoda, P %A Eychenie, S %A Cooke, R %A Regad, F %A Sabau, X %A Courties, C %A Delseny, M %A Demaille, J %A Picard, A %A Moreau, H %K Pico$_\textrmR$eview %K rcc %K RCC745 %X Ostreococcus tauri is a marine photosynthetic picoeukaryote presenting a minimal cellular organization with one nucleus, one chloroplast, and one mitochondrion. It has the smallest genome described among free-living eukaryotic cells, and we showed by pulsed-field gel electrophoresis (PFGE) that it is divided between 15 bands ranging from 1.2 to 0.15 Mb, giving a total size of 9.7 Mb. A Bacterial Artificial Chromosome (BAC) library was prepared from genomic DNA extracted from a culture of O. tauri. A total of 2457 clones was obtained with an average insert size of around 70 kb, representing an 18-fold coverage of the genome. The library was spotted on high density filters, and several probes of coding sequences were hybridized to both the high density BAC library filters and directly to the dried PFGE gels of the O. tauri genomic DNA. These hybridizations allowed a preliminary organization of the library and the localization of several markers on the chromosomes. Randomly selected fragments were also sequenced, representing 12% of the O. tauri genome. Many sequences showed significant similarities in data banks, mainly with plant and algae sequences. About 1000 coding sequences could be identified. These data confirmed the position of O. tauri in the green lineage and the hypothesis of a very compact organization of its genome. %B Journal of Phycology %V 38 %P 1150–1156 %G eng %U c:%5CDV%5CPapers reprints%5CPhytoplankton Physiology%5CDerelle Ostreococcus DNA libraries JPhycol 02.pdf %R 10.1046/j.1529-8817.2002.02021.x %0 Journal Article %J Microbiology %D 2002 %T Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-'Synechococcus' clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon %A Laloui, W %A Palinska, K A %A Rippka, R %A Partensky, F %A de Marsac, N T %A Herdman, M %A Iteman, I %K 2002 %K Blue Green Alga %K Chlorophyll B %K community structure %K cyanobacteria %K Escherichia Coli %K Marine Prokaryote %K Multiple Evolutionary Origins %K North Atlantic Ocean %K Pacific Ocean %K rcc %K Rna Operon %K SBR$_\textrmP$hyto %K sbr?hyto %X PCR amplicons of the Internal Transcribed Spacer (ITS) of the rrn operon of three axenic OMF (oceanic, marine and freshwater) strains of 'Synechococcus' (wH7803, PCC 7001 and PCC 6307, respectively) differ greatly in length from that of the axenic Prochlorococcus marinus subsp. pastoris PCC 9511(T), although these four cyanobacteria cluster relatively closely in phylogenetic trees inferred from 165 rRNA gene sequences. The ITSs of three strains (PCC 9511(T), PCC 6307 and PCC 7001) were sequenced and compared with those available for strains Prochlorococcus MED4 (CCMP 1378) and MIT9313 from genome sequencing projects. In spite of large differences in length, sequence and mean DNA base composition, conserved domains important for transcriptional antitermination and folding of the rRNA transcripts were identified in all ITSs. A new group-specific primer permitted ITS amplification even with non-axenic isolates of Prochlorococcus and one OMF-'Synechococcus' strain. Prochlorococcus isolates of the high-light-adapted clade (HL) differed from representatives of the low-light-adapted Glade (LL) by the length of their ITS. Restriction fragment length polymorphism (RFLP) of the ITS amplicons revealed three subclusters among the HL strains. Size, sequence data and RFLP of the ITS amplicons will therefore be valuable markers for the identification of different Prochlorococcus genotypes and for their discrimination from other cyanobacterial relatives with which they often co-exist in oceanic ecosystems. %B Microbiology %V 148 %P 453–465 %G eng %R 10.1099/00221287-148-2-453 %0 Journal Article %J Applied and Environmental Microbiology %D 2002 %T Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences %A Rocap, G %A Distel, D L %A Waterbury, J B %A Chisholm, S W %K Divinyl Chlorophyll a %K genetic diversity %K Marine Cyanobacterium Synechococcus %K Multiple Evolutionary Origins %K North Atlantic %K Nucleotide Sequence %K rcc %K Region %K Rna Operon %K sargasso sea %K Water Column %X Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world's oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions. %B Applied and Environmental Microbiology %V 68 %P 1180–1191 %G eng %R 10.1128/AEM.68.3.1180-1191.2002 %0 Journal Article %J Microbiology - UK %D 2001 %T Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides %A West, N J %A Schonhuber, W A %A Fuller, N J %A Amann, R I %A Rippka, R %A Post, A F %A Scanlan, D J %K Escherichia Coli %K IDENTIFICATION %K Marine Cyanobacterium %K Nucleic Acid Probes %K Photosynthetic Prokaryote %K PICODIV %K Populations %K rcc %K Ribosomal Rna %K SEQUENCES %K Tyramide Signal Amplification %K Whole Cell Hybridization %X An in situ hybridization method was applied to the identification of marine cyanobacteria assignable to the genus Procholorococcus using harseradish-peroxidase-labelled 16S rRNA-targeted oligonucleotide probes in combination with tyramide signal amplification (TSA). With this method very bright signals were obtained, in contrast to hybridizations with oligonucleotides monolabelled with fluorochromes, which failed to give positive signals. Genotype-specific oligonucleotides for high light (HL)- and low light (LL)adapted members of this genus were identified by 16S rRNA sequence analyses and their specificities confirmed in whole-cell hybridizations with cultured strains of Prochlorococcus marinus Chisholm et al., 1992, Prochlorococcus sp. and Synechococcus sp. In situ hybridization of these genotype-specific probes to field samples from stratified water bodies collected in the North Atlantic Ocean and the Red Sea allowed a rapid assessment of the abundance and spatial distribution of HL- and LL-adapted Prochlorococcus. In both oceanic regions the LL-adapted Prochlorococcus populations were localized in deeper water whereas the HL-adapted Prochlorococcus populations were not only distinct in each region but also exhibited strikingly different depth distributions, HLI being confined to shallow wafer in the North Atlantic, in contrast to HLII, which was present throughout the water column in the Red Sea. %B Microbiology - UK %V 147 %P 1731–1744 %G eng %R 10.1099/00221287-147-7-1731 %0 Journal Article %J Marine Ecology - Progress Series %D 2000 %T Feeding rate of the oyster Crassostrea gigas in a natural planktonic community of the Mediterranean Thau Lagoon %A Dupuy, C %A Vaquer, A %A LamHoai, T %A Rougier, C %A Mazouni, N %A Lautier, J %A Collos, Y %A LeGall, S %K ABUNDANCE %K bivalve %K carbon %K COASTAL WATERS %K EPIFLUORESCENCE MICROSCOPY %K FILTRATION-RATE %K food source %K FOOD-CHAINS %K GEUKENSIA-DEMISSA %K heterotrophic protist %K microbial food web %K MYTILUS-EDULIS %K oyster %K PARTICLE SELECTION %K picophytoplankton %K rcc %K RETENTION %K Thau Lagoon %K trophic link %X The Mediterranean Thau Lagoon is an important oyster farming area in Europe. Oyster growth rates are among the highest in France, although chlorophyll a concentration is low. Previous studies have demonstrated that picophytoplankton, nano-microphytoplankton, dinoflagellates and loricate ciliates such as tintinnids are abundant. However, heterotrophic flagellates and aloricate ciliates have not been investigated. The aim of this study was to assess picophytoplankton, protist and zooplankton abundances in the Lagoon and to investigate the particular structure of the microbial food web, which may explain such paradoxical oyster growth. In oligotrophic waters in the Thau Lagoon, the picoeukaryote Ostreococcus tauri is the dominant autotrophic picoplankter, with an abundance maximum in summer. On 17 August 1998, following a rainfall event, pico- and nanophytoplankton abundances were not as high as expected and we observed a high abundance of large diatoms. At this time, the available carbon resources were produced by microphytoplankton (84.5%), and picoplank-tonic cells represented only 1.27 % in terms of carbon. Heterotrophic cells were low in abundance and constituted ¡14% of carbon resources. In order to evaluate the importance of the 'protozoan trophic link' for energy transfer from the microbial food web to large benthic suspension feeders, the oyster Crassostrea gigas was offered a planktonic community as potential prey. In the grazing experiment, all ¿5 mum flagellates, microphytoplankton, dinoflagellates, ciliates and large zooplankton were retained by the oyster gills. Only flagellates ¡5 pm and O. Tauri were not very well retained (45 and 2% respectively). The high clearance rates of C. Gigas found in this experiment can be explained by a low concentration of suspended particulate matter (0.65 mg l(-1)). The oysters adapted their retention mechanism when they Lived in oligotrophic waters. These results indicate that, under the given experimental conditions, picophytoplankton did not represent a valuable trophic resource for farmed oysters because (1) C. Gigas cannot retain picoparticles and (2) the picoplankton represented a poor carbon resource capable of being transferred via a weak heterotrophic protist community. In the oyster pens of the Thau Lagoon during this study, microphytoplanktonic primary producers, in particular diatoms, were the main food sources for bivalve suspension feeders. %B Marine Ecology - Progress Series %V 205 %P 171–184 %G eng %R 10.3354/meps205171 %0 Journal Article %J Transactions of the British Mycological Society %D 1988 %T Schizochytrium mangrovei sp. nov., a thraustochytrid from mangroves in India %A Raghu-Kumar, S. %K RCC893 %X Schizochytrium mangrovei sp. nov. on decaying mangrove leaves is described from Goa, India. In sea water/pine pollen cultures, the encysted zoospore divides by repeated binary divisions to form 4, 6, 8 or 12 cells. Instead of forming sporangia as in the other species of Schizochytrium, these cells directly become zoospores. In nutrient liquid media, the developmental stages resemble those of Ulkenia. A key to the species of Schizochytrium is given. %B Transactions of the British Mycological Society %V 90 %P 627–631 %8 jun %G eng %U http://linkinghub.elsevier.com/retrieve/pii/S0007153688800688 %R 10.1016/S0007-1536(88)80068-8