%0 Journal Article %J Cell Reports Methods %D 2023 %T Tailoring confocal microscopy for real-time analysis of photosynthesis at single-cell resolution %A Storti, Mattia %A Hsine, Haythem %A Uwizeye, Clarisse %A Bastien, Olivier %A Yee, Daniel P. %A Chevalier, Fabien %A Decelle, Johan %A Giustini, Cécile %A Béal, Daniel %A Curien, Gilles %A Finazzi, Giovanni %A Tolleter, Dimitri %K rcc1383 %X Photoautotrophs’ environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single-cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells, or organs. Furthermore, cells within the same tissue may behave differently, being at different developmental/ physiological stages. Here, we describe an approach for single-cell and subcellular photophysiology based on the customization of confocal microscopy to assess chlorophyll fluorescence quenching by the saturation pulse method. We exploit this setup to (1) reassess the specialization of photosynthetic activities in developing tissues of non-vascular plants; (2) identify a specific subpopulation of phytoplankton cells in marine photosymbiosis, which consolidate energetic connections with their hosts; and (3) examine the link between light penetration and photoprotection responses inside the different tissues that constitute a plant leaf anatomy. %B Cell Reports Methods %P 100568 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S2667237523002126 %R 10.1016/j.crmeth.2023.100568 %0 Generic %D 2023 %T Taxonomic profling of microbes co-cultured with protists in the Roscoff Culture Collection %A Blocka, Zuzanna %X The ocean hosts an enormous diversity of microorganisms. However, most of these are notat present available for culture, which makes them difcult to study. We know that manymarine organisms rely on complex nutrient cycles which are difcult to unravel. Microalgaeproduces soluble carbon-, sulfur-, and nitrogen-containing compounds which are taken up byheterotrophic bacteria. The photosynthesizers, on the other hand, often rely on co-factors ofbacterial origin, such as vitamin B12. Since many ocean bacteria may rely on algal organicproducts to obtain essential nutrients, searching for microbes of interest in algal strain culturescan help pinpoint the method of cultivation. In this study, 16S meta-barcoding was performedon bacteria associated to sixty strains from the Roscoff Culture Collection. The bacterial taxonomic composition differed between the algal divisions. Hierarchical clustering revealed interand intra-division differences. The microbiota of the samples mostly belonged to Bacteroidota,Alpha- and Gammaproteobacteria. This is consistent with previous studies on the cycling ofnutrients in the ocean, as these groups are metabolically flexible and ubiquitous heterotrophs.Among the sequenced reads, there appear members of poorly described or undescribed prokaryotic lineages at high taxonomic levels, which could be subject to further study and cultivationefforts. Obtaining these organisms in pure culture could allow the description of new lineagesand their unique metabolisms, and potentially, the production of their bio-products of interest. %I ETH Zürich %G eng %9 Semester Project Report %0 Journal Article %J International Journal of Systematic and Evolutionary Microbiology %D 2023 %T \textit{Zobellia alginiliquefaciens sp. nov., a novel member of the flavobacteria isolated from the epibiota of the brown alga Ericaria zosteroides (C. Agardh) Molinari & Guiry 2020 %A Barbeyron, Tristan %A Le Duff, Nolwen %A Duchaud, Eric %A Thomas, François %K RCC7657 %X Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected from the Mediterranean Sea near Bastia in Corsica, France, was characterised using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30–33 °C, at pH 8–8.5 and with 4–5 % NaCl. LLG6346-3.1T used the seaweed polysaccharide alginic acid as a sole carbon source which was vigorously liquefied. The results of phylogenetic analyses indicated that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae , class Flavobacteriia ). LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.6 and 98.3 % to the type strains of Zobellia russellii and Zobellia roscoffensis , respectively, and of 97.4–98.5 % to members of other species of the genus Zobellia . The DNA G+C content of LLG6346-3.1T was determined to be 38.3 mol%. Digital DNA–DNA hybridisation predictions by the average nucleotide identity (ANI) and genome to genome distance calculator (GGDC) methods between LLG6346-3.1T and other members of the genus Zobellia showed values of 76–88 % and below 37 %, respectively. The results of phenotypic, phylogenetic and genomic analyses indicate that LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia , for which the name Zobellia alginiliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (= RCC7657T = LMG 32918T). %B International Journal of Systematic and Evolutionary Microbiology %V 73 %P 005924 %G eng %U https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005924 %R 10.1099/ijsem.0.005924 %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 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 Microorganisms %D 2022 %T Temperature Affects the Biological Control of Dinoflagellates by the Generalist Parasitoid Parvilucifera rostrata %A Schmitt, Matthew %A Telusma, Aaron %A Bigeard, Estelle %A Guillou, Laure %A Alves-de-Souza, Catharina %K dinoflagellate blooms %K functional response %K parasitic control %K RCC2800 %K RCC2823 %K RCC2982 %K RCC3018 %K RCC4398 %K temperature effect %X The increase in emerging harmful algal blooms in the last decades has led to an extensive concern in understanding the mechanisms behind these events. In this paper, we assessed the growth of two blooming dinoflagellates (Alexandrium minutum and Heterocapsa triquetra) and their susceptibility to infection by the generalist parasitoid Parvilucifera rostrata under a temperature gradient. The growth of the two dinoflagellates differed across a range of temperatures representative of the Penzé Estuary (13 to 22 °C) in early summer. A. minutum growth increased across this range and was the highest at 19 and 22 °C, whereas H. triquetra growth was maximal at intermediate temperatures (15–18 °C). Interestingly, the effect of temperature on the parasitoid infectivity changed depending on which host dinoflagellate was infected with the dinoflagellate responses to temperature following a positive trend in A. minutum (higher infections at 20–22 °C) and a unimodal trend in H. triquetra (higher infections at 18 °C). Low temperatures negatively affected parasitoid infections in both hosts (i.e., “thermal refuge”). These results demonstrate how temperature shifts may not only affect bloom development in microalgal species but also their control by parasitoids. %B Microorganisms %V 10 %P 385 %G eng %U https://www.mdpi.com/2076-2607/10/2/385 %R 10.3390/microorganisms10020385 %0 Journal Article %J Plant Science %D 2022 %T TOR signaling in the green picoalga Ostreococcus tauri %A Caló, Gonzalo %A De Marco, María Agustina %A Salerno, Graciela Lidia %A Martínez-Noël, Giselle María Astrid %K Carbon reserves %K Green algae %K Growth %K Nitrogen deprivation %K RCC745 %K TOR inhibitors %K TOR kinase %X Target of rapamycin (TOR) is a master regulator that controls growth and metabolism by integrating external and internal signals. Although there was a great progress in the study of TOR in plants and in the model alga Chlamydomonas, scarce data are available in other green algae. Thus, in this work we studied TOR signaling in Ostreococcus tauri, the smallest free-living eukaryote described to date. This picoalga is particularly important because it has a key site at the base of the green lineage and is part of the marine phytoplankton, contributing to global photosynthesis. We investigated OtTOR complex in silico and experimentally, by using first- and second-generation TOR inhibitors, such as rapamycin and PP242. We analyzed the effect of TOR down-regulation on cell growth and on the accumulation of carbon reserves. The results showed that O. tauri responds to TOR inhibitors more similarly to plants than to Chlamydomonas, being PP242 a valuable tool to study this pathway. Besides, Ottor expression analysis revealed that the kinase is dynamically regulated under nutritional stress. Our data indicate that TOR signaling is conserved in O. tauri and we propose this alga as a good and simple model for studying TOR kinase and its regulation. %B Plant Science %V 323 %P 111390 %8 oct %G eng %U https://www.sciencedirect.com/science/article/pii/S016894522200214X %R 10.1016/j.plantsci.2022.111390 %0 Journal Article %J Science of The Total Environment %D 2022 %T Trace metals exposure in three different coastal compartments show specific morphological and reproductive traits across generations in a sentinel copepod %A Das, Shagnika %A Souissi, Anissa %A Ouddane, Baghdad %A Hwang, Jiang-Shiou %A Souissi, Sami %K RCC1537 %X The effect of exposure from several compartments of the environment at the level of individuals were rarely investigated. This study reports the effect of contaminants from varied compartments like sediment resuspension, elutriation from resuspended sediment (extract) and seawater spiked trace metal mixtures (TM) on morphological and reproductive traits of the pelagic bioindicator copepod Eurytemora affinis. At the population level of E. affinis, lowest survival was observed in dissolved exposures (TM and extract) in the first generation (G1), showing some adaptation in the second generation (G2). An opposite trend for resuspended sediment showed higher sensitivity in survival at G2. At the individual level, prosome length and volume proved to be sensitive parameters for resuspended sediments, whereas clutch size and egg diameter were more sensitive to TM and extract. Although the generation of decontamination (G3, no exposure), showed a significant recovery at the population level (survival % along with clutch size) of E. affinis exposed to resuspended sediment, morphological characteristics like prosome length and volume showed no such recovery (lower than control, p <0.05). To the contrary, dissolved exposure showed no significant recovery from G1 to G3 on neither survival %, clutch size, egg diameter, prosome volume, but an increase of prosome length (p <0.05). Such tradeoffs in combatting the stress from varied sources of toxicity was observed in all exposures, from G1 to G3. The number of lipid droplets inside the body cavity of E. affinis showed a significant positive correlation with trace metal bioaccumulation (p <0.01) along with a negative correlation (p <0.05) with survival and clutch size in each treatment. This confirms the inability of copepods to utilize lipids under stressful conditions. Our study tenders certain morphological and reproductive markers that show specificity to different compartments of exposure, promising an advantage in risk assessment and fish feed studies. %B Science of The Total Environment %P 160378 %8 nov %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0048969722074800 %R 10.1016/j.scitotenv.2022.160378 %0 Journal Article %J Frontiers in Earth Science %D 2021 %T Temperature Induced Physiological Reaction Norms of the Coccolithophore Gephyrocapsa oceanica and Resulting Coccolith Sr/Ca and Mg/Ca Ratios %A Müller, Marius N. %A Blanco-Ameijeiras, Sonia %A Stoll, Heather M. %A Méndez-Vicente, Ana %A Lebrato, Mario %K rcc %K RCC1303 %X Coccolithophores are one of the major contributors to the pelagic production of calcium carbonate and their fossilized remains are a key component of the biogeochemical cycles of calcium (Ca), magnesium (Mg), and other divalent cations present in the intracellular precipitated calcitic structures (coccoliths). The geochemical signature of coccoliths (e.g., Sr/Ca and Mg/Ca ratios) is used as paleoproxy to reconstruct past environmental conditions and to understand the underlying physiological precipitation kinetics. Here, we present the elemental fractionation of Sr and Mg in calcite of the coccolithophore Gephyrocapsa oceanica from controlled laboratory experiments applying an extended temperature gradient (12 to 27°C). The physiological reaction norm of G. oceanica, in terms of growth rate, exhibited optimum behavior while the partition coefficient of Sr (DSr) was linearly correlated with temperature and DMg indicated no specific trend. Our results indicate: (1) a presumably secondary physiological control of DSr, and (2) the importance of calibrating coccolithophore-based proxies using experiments that include the full physiological reaction norms (i.e., a possible non-linear response) to environmental drivers (e.g., temperature, salinity, and pH, etc.). The presented results contribute to an improved understanding of the underlying physiological kinetics involved in regulating coccolith elemental fractionation and give additional implications for designing future laboratory experiments to calibrate and apply coccolithophore based paleoproxies on the fossil sediment record. %B Frontiers in Earth Science %V 9 %P 273 %G eng %U https://www.frontiersin.org/article/10.3389/feart.2021.582521 %R 10.3389/feart.2021.582521 %0 Journal Article %J Frontiers in Microbiology %D 2021 %T Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain %A Labban, Abbrar %A Palacio, Antonio S. %A García, Francisca C. %A Hadaidi, Ghaida %A Ansari, Mohd I. %A López-Urrutia, Ángel %A Alonso-Sáez, Laura %A Hong, Pei-Ying %A Morán, Xosé Anxelu G. %K rcc %K RCC546 %X Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24–34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94–1.38 d–1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38–24.4 d–1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules. %B Frontiers in Microbiology %V 12 %P 612732 %G eng %U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141594/ %R 10.3389/fmicb.2021.612732 %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 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 Thesis %D 2020 %T Thermal responses of marine phytoplankton : Implications to their biogeography in the present and future oceans %A Edullantes, Brisneve %K RCC2649 %K RCC291 %K RCC3404 %G eng %9 phd %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 Marine Pollution Bulletin %D 2020 %T Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure %A Bretherton, Laura %A Hillhouse, Jessica %A Kamalanathan, Manoj %A Finkel, Zoe V. %A Irwin, Andrew J. %A Quigg, Antonietta %K Chemical dispersants %K Chlorophyll %K crude oil %K Photosynthesis %K phytoplankton %K RCC1614 %K Trait-based analysis %X The Deepwater Horizon oil spill released millions of barrels of crude oil into the Gulf of Mexico, and saw widespread use of the chemical dispersant Corexit. We assessed the role of traits, such as cell size, cell wall, motility, and mixotrophy on the growth and photosynthetic response of 15 phytoplankton taxa to oil and Corexit. We collected growth and photosynthetic data on five algal cultures. These responses could be separated into resistant (Tetraselmis astigmatica, Ochromonas sp., Heterocapsa pygmaea) and sensitive (Micromonas pusilla, Prorocentrum minimum). We combined this data with 10 species previously studied and found that cell size is most important in determining the biomass response to oil, whereas motility/mixotrophy is more important in the dispersed oil. Our analysis accounted for a third of the variance observed, so further work is needed to identify other factors that contribute to oil resistance. %B Marine Pollution Bulletin %V 153 %P 110906 %G eng %U https://doi.org/10.1016/j.marpolbul.2020.110906 %R 10.1016/j.marpolbul.2020.110906 %0 Journal Article %J ChemRxiv %D 2020 %T A tunable 3D printed microfluidic resistive pulse sensor for the characterisation of algae and microplastics %A Pollard, M. %A Hunsicker, E. %A Platt, M. %K RCC5374 %K RCC893 %X Technologies that can detect and characterise particulates in liquids have applications in health, food and environmental monitoring. Here we present a low-cost and high-throughput multiuse counter that classifies a particle's size, concentration, porosity and shape. Using an additive manufacturing process, we have assembled a reusable flow resistive pulse sensor. The device remains stable for several days with repeat measurements. We demonstrate its use for characterising algae with spherical and rod structures as well as microplastics shed from teabags. We present a methodology that results in a specific signal for microplastics, namely a conductive pulse, in contrast to particles with smooth surfaces such as calibration particles or algae, allowing the presence of microplastics to be easily confirmed and quantified. In addition, the shape of the signal and particle are correlated, giving an extra physical property to characterise suspended particulates. The technology can rapidly screen volumes of liquid, 1 mL/ min, for the presence of microplastics and algae. %B ChemRxiv %G eng %R 10.26434/chemrxiv.12249833.v1 %0 Journal Article %J The ISME Journal %D 2019 %T Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth %A Kashiyama, Yuichiro %A Yokoyama, Akiko %A Shiratori, Takashi %A Hess, Sebastian %A Not, Fabrice %A Bachy, Charles %A Gutierrez-Rodriguez, Andres %A Kawahara, Jun %A Suzaki, Toshinobu %A Nakazawa, Masami %A Ishikawa, Takahiro %A Maruyama, Moe %A Wang, Mengyun %A Chen, Man %A Gong, Yingchun %A Seto, Kensuke %A Kagami, Maiko %A Hamamoto, Yoko %A Honda, Daiske %A Umetani, Takahiro %A Shihongi, Akira %A Kayama, Motoki %A Matsuda, Toshiki %A Taira, Junya %A Yabuki, Akinori %A Tsuchiya, Masashi %A Hirakawa, Yoshihisa %A Kawaguchi, Akane %A Nomura, Mami %A Nakamura, Atsushi %A Namba, Noriaki %A Matsumoto, Mitsufumi %A Tanaka, Tsuyoshi %A Yoshino, Tomoko %A Higuchi, Rina %A Yamamoto, Akihiro %A Maruyama, Tadanobu %A Yamaguchi, Aika %A Uzuka, Akihiro %A Miyagishima, Shinya %A Tanifuji, Goro %A Kawachi, Masanobu %A Kinoshita, Yusuke %A Tamiaki, Hitoshi %K Biochemistry %K Biogeochemistry %K Cellular microbiology %K microbial ecology %K RCC164 %K RCC22 %K RCC24 %K RCC375 %K RCC916 %X Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation. %B The ISME Journal %P 1 %8 feb %G eng %U http://www.nature.com/articles/s41396-019-0377-0 %R 10.1038/s41396-019-0377-0 %0 Journal Article %J Genome Biology and Evolution %D 2019 %T Tracing the evolution of the plastome and mitogenome in the chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code %A Turmel, Monique %A dos Santos, Adriana Lopes %A Otis, Christian %A Sergerie, Roxanne %A Lemieux, Claude %E Archibald, John %K RCC15 %K RCC1871 %K RCC2335 %K RCC2339 %K RCC287 %K RCC3374 %K RCC3402 %K RCC4434 %K RCC4572 %K RCC4656 %K RCC696 %K RCC856 %K RCC998 %K RCC999 %B Genome Biology and Evolution %V in press %8 apr %G eng %U https://www.biorxiv.org/content/10.1101/530998v1 https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evz074/5425330 %R 10.1093/gbe/evz074 %0 Journal Article %J Frontiers in Marine Science %D 2019 %T Transcriptome of thalassicolla nucleata holobiont reveals details of a radiolarian symbiotic relationship %A Liu, Zhenfeng %A Mesrop, Lisa Y. %A Hu, Sarah K. %A Caron, David A. %K Brandtodinium %K holobiont %K photosymbiosis %K radiolarian %K RCC3387 %K Transcriptome %B Frontiers in Marine Science %V 6 %P 1–11 %8 jun %G eng %U https://www.frontiersin.org/article/10.3389/fmars.2019.00284/full %R 10.3389/fmars.2019.00284 %0 Journal Article %D 2019 %T Transient transformation of ostreococcus species (OTTH595, RCC809 and RCC802) and bathycoccus %A Bouget, François Yves %K RCC802 %K RCC809 %G eng %U https://www.protocols.io/view/transient-transformation-of-ostreococcus-species-o-83uhynw %R 10.17504/protocols.io.83uhynw %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 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 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 Molecular ecology %D 2016 %T Transcriptomic profiling of Alexandrium fundyense during physical interaction with or exposure to chemical signals from the parasite Amoebophrya. %A Lu, Yameng %A Wohlrab, Sylke %A Groth, Marco %A Glöckner, Gernot %A Guillou, Laure %A John, Uwe %K 2016 %K Animals %K Dinoflagellida %K Dinoflagellida: genetics %K Dinoflagellida: parasitology %K Gene Expression Profiling %K Harmful Algal Bloom %K Host-Parasite Interactions %K Metabolic Networks and Pathways %K Microalgae %K Microalgae: genetics %K Microalgae: parasitology %K Parasites %K Parasites: chemistry %K RCC3037 %K RNA %K Sequence Analysis %K Signal Transduction %K Transcriptome %X Toxic microalgae have their own pathogens, and understanding the way in which these microalgae respond to antagonistic attacks may provide information about their capacity to persist during harmful algal bloom events. Here, we compared the effects of the physical presence of the parasite Amoebophrya sp. and exposure to waterborne cues from cultures infected with this parasite, on gene expression by the toxic dinoflagellates, Alexandrium fundyense. Compared with control samples, a total of 14,882 Alexandrium genes were differentially expressed over the whole-parasite infection cycle at three different time points (0, 6 and 96 h). RNA sequencing analyses indicated that exposure to the parasite and parasitic waterborne cues produced significant changes in the expression levels of Alexandrium genes associated with specific metabolic pathways. The observed upregulation of genes associated with glycolysis, the tricarboxylic acid cycle, fatty acid β-oxidation, oxidative phosphorylation and photosynthesis suggests that parasite infection increases the energy demand of the host. The observed upregulation of genes correlated with signal transduction indicates that Alexandrium could be sensitized by parasite attacks. This response might prime the defence of the host, as indicated by the increased expression of several genes associated with defence and stress. Our findings provide a molecular overview of the response of a dinoflagellate to parasite infection. %B Molecular ecology %V 25 %P 1294–307 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/26841307 %R 10.1111/mec.13566 %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 Ecology Progress Series %D 2012 %T Temperature-dependent growth and photophysiology of prokaryotic and eukaryotic oceanic picophytoplankton %A Kulk, Gemma %A De Vries, Pablo %A Van De Poll, Willem H. %A Visser, Ronald J W %A Buma, Anita G J %K Absorption %K Electron transport rate %K Eukaryotic picophytoplankton %K Growth %K Pigment %K Prochlorococcus %K rcc %K RCC407 %K rcc410 %K RCC879 %K temperature %X ABSTRACT: It is expected that climate change will expand the open oligotrophic oceans by enhanced thermal stratification. Because temperature defines the geographic distribution of picophytoplankton in open-ocean ecosystems and regulates photophysiological responses, it is important to understand how temperature affects picophytoplankton growth and photophysiology. Two prokaryotic and 2 eukaryotic picophytoplankton strains were acclimated to 3 different temperatures, ranging from 16 to 24°C. Temperature-dependent growth and photophysiology were assessed by measurements of specific growth rates, cell size, pigment composition, absorption and electron transport rates. Growth of Prochlorococcus marinus (eMED4), Prochlorococcus sp. (eMIT9313), Ostreococcus sp. (clade B) and Pelagomonas calceolata was positively related to temperature, especially in the prokaryotic strains. Changes in photophysiology included increased light harvesting, increased electron transport and reduced photoinhibition at elevated temperatures. However, the changes related to light harvesting and electron transport could not fully explain the observed difference in growth. This suggests that other processes, such as Calvin cycle activity, are likely to limit growth at sub-optimal temperatures in these picophytoplankton strains. The overall changes in photophysiology during temperature acclimation will possibly allow photosynthesis at higher irradiance intensities, but the genetically defined low temperature tolerances and photosynthetic characteristics of the different ecotypes will likely be more important in determining picophytoplankton (depth) distribution and community composition. %B Marine Ecology Progress Series %V 466 %P 43–55 %G eng %U http://www.int-res.com/abstracts/meps/v466/p43-55/ %R 10.3354/meps09898 %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 Molecular Biology and Evolution %D 2010 %T A timeline of the environmental genetics of the haptophytes %A Liu, Hui %A Aris-Brosou, Stephane %A Probert, Ian %A de Vargas, Colomban %K 2010 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X The use of genomic data and the rise of phylogenomics have radically changed our view of the eukaryotic tree of life at a high taxonomic level by identifying four to six "supergroups". Yet our understanding of the evolution of key innovations within each of these supergroups is limited because of poor species sampling relative to the massive diversity encompassed by each supergroup. Here we apply a multigene approach that incorporates a wide taxonomic diversity to infer the timeline of the emergence of strategic evolutionary transitions in the haptophytes, a group of ecologically and biogeochemically significant marine protists that belong to the Chromalveolata supergroup. Four genes (SSU, LSU, tufA and rbcL) were extensively analyzed under several Bayesian models to assess the robustness of the phylogeny, particularly with respect to (i) data partitioning, (ii) the origin of the genes (host vs. endosymbiont), (iii) across-site rate variation and (iv) across-lineage rate variation. We show with a relaxed clock analysis that the origin of haptophytes dates back to 824 MYA (95% highest probability density 1031-637 MYA). Our dating results show that the ability to calcify evolved earlier than previously thought, between 329-291 MYA, in the Carboniferous period, and that the transition from mixotrophy to autotrophy occurred during the same time period. Although these two transitions precede a habitat change of major diversities from coastal / neritic waters to the pelagic realm (291-243 MYA, around the P/Tr boundary event), the emergence of calcification, full autotrophy and oceanic lifestyle seem mutually independent. %B Molecular Biology and Evolution %V 27 %P 171–176 %G eng %U http://mbe.oxfordjournals.org/cgi/content/abstract/msp222v1 %R 10.1093/molbev/msp222 %0 Journal Article %J Genome Biology %D 2009 %T Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell %A von Dassow, Peter %A Ogata, Hiroyuki %A Probert, Ian %A Wincker, Patrick %A Da Silva, Corinne %A Audic, Stéphane %A Claverie, Jean-Michel %A de Vargas, Colomban %K 2009 %K rcc %K RCC1216 %K rcc1217 %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X BACKGROUND:Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38000 Expressed Sequence Tags (ESTs) from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism.RESULTS:The haploid and diploid transcriptomes showed a dramatic differentiation, with [almost equal to]20% greater transcriptome richness in diploid cells than in haploid cells and only [less than or equal to]50% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca2+, H+, and HCO3- pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog.CONCLUSIONS:This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined. %B Genome Biology %V 10 %P R114 %G eng %U http://genomebiology.com/2009/10/10/R114 %R 10.1186/gb-2009-10-10-r114 %0 Journal Article %J Biogeochemistry %D 2007 %T A taxonomic review of the genus Phaeocystis %A Medlin, Linda %A Zingone, Adriana %K Molecular clock %K P. cordata %K P. globosa %K P. jahnii %K P. pouchetii %K P. scrobiculata %K Phaeocystis antarctica %K rcc3541 %K rDNA analysis %X Phaeocystis is recognized both as a nuisance and as an ecologicallyphytoplankton species. Its polymorphic life cycle with bothand flagellated cells causes many taxonomic problems. Sequenceamong 22 isolates representing a global distribution of thehas been compared using three molecular markers. The-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) spacer is tooto resolve species. The most conserved 18S ribosomalacid (rDNA) analysis suggests that an undescribedPhaeocystis sp. (isolate PLY559) is a sister taxon to theunicellular Phaeocystis jahnii; this clade branched priorthe divergence of all other Phaeocystis species, including theones. The internal transcribed spacer (ITS) region showsvariation that some spatial population structure can be, at least in P. antarctica. P. globosa and P. pouchetii havedifferent ITS copies, suggestive of cryptic species that areable to hybridize. A molecular clock has been constructed thatthe divergence of the cold water colonial forms from the-water colonial forms to be about 30 Ma and the divergence of P.and P. pouchetii to be about 15 Ma. A short description ofcolonial stage and the flagellated stage for each formallyspecies is provided. Morphological information is alsoon a number of undescribed species. These include the strain559, consisting of non-colonial cells with peculiar tubular, a second non-colonial species from the north westernSea producing a lot of mucus, and a colonial species with-less flagellates found in Italian waters. In addition, threemorphotypes with scales different from those of P.were reported in the literature from Antarctic waters. Theemerging from both molecular and morphological data is that theof species in the genus is still underestimated and that crypticpseudocryptic diversity requires a sound assessment in futureof this genus. Based on all published observations, an emendedof the genus is provided. %B Biogeochemistry %V 83 %P 3–18 %G eng %R 10.1007/s10533-007-9087-1 %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 Journal of Bacteriology %D 2005 %T Two novel phycoerythrin-associated linker proteins in the marine cyanobacterium synechococcus sp. Strain WH8102 %A Six, Christophe %A Thomas, Jean-Claude %A Thion, Laurent %A Lemoine, Yves %A Zal, Frank %A Partensky, Frédéric %K 2005 %K rcc %K SBR$_\textrmP$hyto %K sbr?hyto %X The recent availability of the whole genome of Synechococcus sp. strain WH8102 allows us to have a global view of the complex structure of the phycobilisomes of this marine picocyanobacterium. Genomic analyses revealed several new characteristics of these phycobilisomes, consisting of an allophycocyanin core and rods made of one type of phycocyanin and two types of phycoerythrins (I and II). Although the allophycocyanin appears to be similar to that found commonly in freshwater cyanobacteria, the phycocyanin is simpler since it possesses only one complete set of alpha and beta subunits and two rod-core linkers (CpcG1 and CpcG2). It is therefore probably made of a single hexameric disk per rod. In contrast, we have found two novel putative phycoerythrin-associated linker polypeptides that appear to be specific for marine Synechococcus spp. The first one (SYNW2000) is unusually long (548 residues) and apparently results from the fusion of a paralog of MpeC, a phycoerythrin II linker, and of CpeD, a phycoerythrin-I linker. The second one (SYNW1989) has a more classical size (300 residues) and is also an MpeC paralog. A biochemical analysis revealed that, like MpeC, these two novel linkers were both chromophorylated with phycourobilin. Our data suggest that they are both associated (partly or totally) with phycoerythrin II, and we propose to name SYNW2000 and SYNW1989 MpeD and MpeE, respectively. We further show that acclimation of phycobilisomes to high light leads to a dramatic reduction of MpeC, whereas the two novel linkers are not significantly affected. Models for the organization of the rods are proposed. %B Journal of Bacteriology %V 187 %P 1685–1694 %G eng %U http://jb.asm.org/cgi/content/abstract/187/5/1685 %R 10.1128/JB.187.5.1685-1694.2005 %0 Journal Article %J Journal of Phycology %D 2003 %T A transient bloom of ¡i¿Ostreococcus¡/i¿ (chlorophyta, prasinophyceae) in west neck bay, long island, new york %A O'Kelly, C J %A Sieracki, M E %A Thier, E C %A Hobson, I C %K Aureococcus Anophagefferens Pelagophyceae %K bloom dynamics %K Gen %K Microalga %K Ostreococcus %K picoalgae %K picoplankton %K rcc %X The smallest known eukaryote, Ostreococcus tauri Courties et Chretiennot-Dinet, was first reported as the dominant picoplankter in a French lagoon known for its diverse phytoplankton community and high oyster productivity. Long-term seasonal blooms of this picoeukaryote were observed in association with stable plankton communities. On 5 June 2001, a distinctive monotypic picoplankton bloom was detected by flow cytometry as part of an ongoing study of "brown tide" (Aureococcus anophagefferens) bloom initiation in Long Island bays. The bloom reached a concentration of 5 x 10(5) cells.mL(-1) in West Neck Bay and lasted less than 2 weeks. Epifluorescence microscopy and TEM indicated that the bloom organism was an Ostreococcus-like picoalga, the first ever observed in a Long Island bay. Many cells of this alga contained numerous virus-like particles. The Ostreococcus-like picoalga, which resembles O. tauri, was rare in samples collected the following week. Instead, a substantial increase in the Synechococcus population was observed. Such rapid population changes have not previously been reported for Ostreococcus. Viral lysis and grazing by heterotrophic nanoflagellates may have contributed to the rapid decline of the Ostreococcus-like cells in West Neck Bay. %B Journal of Phycology %V 39 %P 850–854 %G eng %R 10.1046/j.1529-8817.2003.02201.x %0 Journal Article %J Archives of Microbiology %D 1992 %T \textit{Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b %A Chisholm, S W %A Frankel, S L %A Goericke, R %A Olson, R J %A Palenik, B %A Waterbury, J B %A West-Johnsrud, L %A Zettler, E R %K rcc %K systematics %K \#PROCHLOROPHYTE %B Archives of Microbiology %V 157 %P 297–300 %G eng %R 10.1007/BF00245165