@article {granata_microbial_2024, title = {Microbial Factories and Exploiting Synergies of Bioreactor Technologies to Produce Bioproducts}, journal = {Fermentation}, volume = {10}, number = {3}, year = {2024}, note = {Number: 3 Publisher: Multidisciplinary Digital Publishing Institute}, month = {mar}, pages = {135}, abstract = {Microbial factories, including microalgae biofactories, have the enormous potential to produce biochemicals for manufacturing diverse bioproducts. A strategic approach to biofactories is maintaining cultures in bioreactors with sufficient resource inputs to optimize biochemical precursors for manufacturing bioproducts. Exploiting synergies that use the waste output from a bioreactor containing one microbial culture as a resource input to another bioreactor with a different microbe can lead to overall efficiencies in biofactories. In this paper, two synergies are evaluated. The first is between yeast and algae bioreactors, where data are presented on oxygen (O2) uptake by aerobic yeast cultures and their production of carbon dioxide (CO2) and the uptake of CO2 by algae and their production of O2. The second focuses on a carbon capture reactor, which is utilized to increase CO2 levels to promote higher algal production. This approach of waste as a resource for bioreactor cultures is a novel synergy that can be important to bioreactor designs and, ultimately, to the production of bioproducts.}, keywords = {bioproducts, bioreactors, carbon capture, RCC2604, synergies}, issn = {2311-5637}, doi = {10.3390/fermentation10030135}, url = {https://www.mdpi.com/2311-5637/10/3/135}, author = {Granata, Tim and Rattenbacher, Bernd and Kehl, Florian and Egli, Marcel} } @article {strauss_bay_2023, title = {The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients}, journal = {Environmental Microbiology}, year = {2023}, abstract = {The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29{\textdegree}C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 {\textpm} 4.4 {\texttimes} 104 cells ml-1 , predominantly HLII, whereas LLII and {\textquoteright}rare{\textquoteright} ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 {\textpm} 2.3 {\texttimes} 104 cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 {\texttimes} 104 cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto {\textquoteright}rare{\textquoteright} picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.}, keywords = {RCC393, RCC809}, issn = {1462-2920}, doi = {10.1111/1462-2920.16431}, author = {Strauss, Jan and Choi, Chang Jae and Grone, Jonathan and Wittmers, Fabian and Jimenez, Valeria and Makareviciute-Fichtner, Kriste and Bachy, Charles and Jaeger, Gualtiero Spiro and Poirier, Camille and Eckmann, Charlotte and Spezzano, Rachele and L{\"o}scher, Carolin R. and Sarma, V. V. S. S. and Mahadevan, Amala and Worden, Alexandra Z.} } @article {cruz_bioprospecting_2023, title = {Bioprospecting for industrially relevant exopolysaccharide-producing cyanobacteria under Portuguese simulated climate}, journal = {Scientific Reports}, volume = {13}, number = {1}, year = {2023}, note = {Number: 1 Publisher: Nature Publishing Group}, pages = {13561}, abstract = {Cyanobacterial exopolysaccharides (EPS) are potential candidates for the production of sustainable biopolymers. Although the bioactive and physicochemical properties of cyanobacterial-based EPS are attractive, their commercial exploitation is limited by the high production costs. Bioprospecting and characterizing novel EPS-producing strains for industrially relevant conditions is key to facilitate their implementation in various biotechnological applications and fields. In the present work, we selected twenty-five Portuguese cyanobacterial strains from a diverse taxonomic range (including some genera studied for the first time) to be grown in diel light and temperature, simulating the Portuguese climate conditions, and evaluated their growth performance and proximal composition of macronutrients. Synechocystis and Cyanobium genera, from marine and freshwater origin, were highlighted as fast-growing (0.1{\textendash}0.2~g~L-1~day-1) with distinct biomass composition. Synechocystis sp. LEGE 07367 and Chroococcales cyanobacterium LEGE 19970, showed a production of 0.3 and 0.4~g~L-1 of released polysaccharides (RPS). These were found to be glucan-based polymers with high molecular weight and a low number of monosaccharides than usually reported for cyanobacterial EPS. In addition, the absence of known cyanotoxins in these two RPS producers was also confirmed. This work provides the initial steps for the development of cyanobacterial EPS bioprocesses under the Portuguese climate.}, keywords = {Biochemistry, Biotechnology, Microbiology, rcc2380}, issn = {2045-2322}, doi = {10.1038/s41598-023-40542-6}, url = {https://www.nature.com/articles/s41598-023-40542-6}, author = {Cruz, Jos{\'e} Diogo and Delattre, C{\'e}dric and Felpeto, Aldo Barreiro and Pereira, Hugo and Pierre, Guillaume and Morais, Jo{\~a}o and Petit, Emmanuel and Silva, Joana and Azevedo, Joana and Elboutachfaiti, Redouan and Maia, In{\^e}s B. and Dubessay, Pascal and Michaud, Philippe and Vasconcelos, Vitor} } @article {edullantes_comparison_2023, title = {Comparison of thermal traits between non-toxic and potentially toxic marine phytoplankton: Implications to their responses to ocean warming}, journal = {Journal of Experimental Marine Biology and Ecology}, volume = {562}, year = {2023}, pages = {151883}, abstract = {Understanding the effect of temperature on growth in marine phytoplankton is crucial in predicting the biogeography and phenology of algal blooms in the warming ocean. Here, we investigated the temperature dependence of the growth of non-toxic and potentially toxic marine phytoplankton. Using non-toxic strains (Prorocentrum sp. NRR 188, Prorocentrum micans CCAP 1136/15, and Alexandrium tamutum PARALEX 242) and potentially toxic strains (Prorocentrum minimum Poulet, Prorocentrum lima CCAP 1136/11, and Alexandrium minutum PARALEX 246) of dinoflagellates as test organisms, we measured their growth rates along a wide temperature gradient and estimated their maximum growth rates, thermal traits (e.g. thermal optima (Topt), critical thermal minima (CTmin), critical thermal maximum (CTmax), fundamental thermal niche (FTN), and skewness), thermal sensitivity, and warming vulnerability. To allow a comparison of these traits with an adequate number of observations, we independently analyzed datasets compiled from published laboratory experiments. Our experiments revealed that the temperature traits were independent of the toxicity of phytoplankton, except for Topt and CTmax. Also, the results of the analysis of the published datasets showed that maximum growth rates and thermal traits were comparable between non-toxic and potentially toxic phytoplankton. Our findings suggest that non-toxic and potentially toxic phytoplankton have generally comparable temperature traits that they can use to respond to climate change. However, depending on the climate scenario, non-toxic phytoplankton may be more vulnerable to warming than potentially toxic phytoplankton. Further studies are needed to improve our understanding of the response of marine phytoplankton to temperature, which can advance our ability to predict algal blooms in response to ongoing climate change.}, keywords = {Growth experiment, Growth models, Microalgal ecophysiology, RCC2649, RCC291, RCC3034, Thermal performance, Thermal physiology, Toxic microalgae}, issn = {0022-0981}, doi = {10.1016/j.jembe.2023.151883}, url = {https://www.sciencedirect.com/science/article/pii/S0022098123000151}, author = {Edullantes, Brisneve and Low-Decarie, Etienne and Steinke, Michael and Cameron, Tom} } @article {ebenezer_elemental_2022, title = {Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes}, journal = {Limnology and Oceanography}, volume = {n/a}, number = {n/a}, year = {2022}, note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.12013}, abstract = {Chloropicophyceae (Prasinophyte Clade VII) are small nonmotile coccoid cells with cell diameters ranging from 1 to 3 μm. Molecular surveys indicate they are relatively high in abundance in moderately oligotrophic oceanic waters and may substantively contribute to biogeochemical cycling in the sea. Here, we quantify the elemental and macromolecular composition of three subtropical Chloropicophyceae strains: Chloropicon mariensis, Chloropicon maureeniae, and Chloropicon roscoffensis under nutrient-sufficient exponential growth and nitrate starvation. Under nutrient-sufficient conditions the Chloropicophyceae are high in C : N and quite low in C : P and N : P relative to the canonical Redfield ratio, reflecting their relatively high nucleic acid composition compared to many other phytoplankton taxa. Nitrate starvation causes increases in C : N and C : P and decreases in N : P, primarily due to increases in carbohydrate and lipid and decreases in protein and RNA. There is genetic evidence that unlike most other green algae, Chloropicophyceae are diploid. The high nucleic acid content in the Chloropicon is consistent with the hypothesis that the nucleus, as a nonscalable component, takes up a larger and substantial proportion of cell mass in diploid picoeukaryotes. The elemental and macromolecular composition of these Chloropicophyceae, and relatively homeostatic response to N-starvation compared to diatoms, provides some insight into their success in the moderately oligotrophic ocean.}, keywords = {RCC138, RCC3374, RCC3375}, issn = {1939-5590}, doi = {10.1002/lno.12013}, url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/lno.12013}, author = {Ebenezer, Vinitha and Hu, Yingyu and Carnicer, Olga and Irwin, Andrew J. and Follows, Michael J. and Finkel, Zoe V.} } @article {leblond_galactolipids_2022, title = {Galactolipids of the genus Amphidinium (Dinophyceae): an hypothesis that they are basal to those of other peridinin-containing dinoflagellates}, journal = {European Journal of Phycology}, year = {2022}, note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/09670262.2022.2092215}, pages = {1{\textendash}10}, abstract = {The genus Amphidinium is shown in many phylogenies to be basal to other peridinin-containing, photosynthetic dinoflagellates as one of the first photosynthetic genera to arise after the evolution of heterotrophic genera. As part of our continuing examination of the plastid-associated galactolipids, namely mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively), in dinoflagellates, we here examine the galactolipid composition of members of the genus Amphidinium. We show that this genus is characterized by an abundance of 20:5(n-3)/18:5(n-3) and 20:5(n-3)/18:4(n-3) forms of MGDG and DGDG (with sn-1/sn-2 regiochemical specificity of fatty acids), but also sometimes with generally lesser amounts of some polyunsaturated C18/C18 forms, thus placing the examined species within a previously identified cluster of C20/C18 MGDG- and DGDG-containing, peridinin-containing dinoflagellates. We also show that Testudodinium testudo, previously known as Amphidinium testudo, conversely falls within a previously identified C18/C18 cluster, indicating a distinct difference in galactolipid biosynthesis capability. While it is likely that further revision of the genus may occur in the future and/or more basal peridinin-containing, photosynthetic genera may be discovered, at the current time Amphidinium is the currently agreed-upon most basal dinoflagellate genus for which isolates are available for biochemical characterization such as what we describe in this paper. Thus, because of the presumed basal position of the genus Amphidinium, we present a hypothesis that its galactolipids currently represent those that are ancestral to other genera of peridinin-containing dinoflagellates, including those within the C18/C18 cluster.}, keywords = {Amphidinium, chloroplast, Dinoflagellate, Dinophyceae, lipid, RCC1981, Testudodinium}, issn = {0967-0262}, doi = {10.1080/09670262.2022.2092215}, url = {https://doi.org/10.1080/09670262.2022.2092215}, author = {Leblond, Jeffrey D. and Elkins, Lindsey C. and Graeff, Jori E. and Sabir, Kyra} } @article {falciatore_light-driven_2022, title = {Light-driven processes: key players of the functional biodiversity in microalgae}, journal = {Comptes Rendus. Biologies}, volume = {345}, number = {2}, year = {2022}, pages = {1{\textendash}24}, doi = {10.5802/crbiol.80}, url = {https://comptes-rendus.academie-sciences.fr/biologies/articles/10.5802/crbiol.80/}, author = {Falciatore, Angela and Bailleul, Benjamin and Boulouis, Alix and Bouly, Jean-Pierre and Bujaldon, Sandrine and Cheminant-Navarro, Soizic and Choquet, Yves and Vitry, Catherine de and Eberhard, Stephan and Jaubert, Marianne and Kuras, Richard and Lafontaine, Ingrid and Landier, Sophie and Selles, Julien and Vallon, Olivier and Wostrikoff, Katia} } @article {leblond_sterols_2022, title = {Sterols of Testudodinium testudo (formerly Amphidinium testudo): Production of the Δ8(14) sterol gymnodinosterol and chemotaxonomic relationship to the Kareniaceae}, journal = {Journal of Eukaryotic Microbiology}, volume = {n/a}, number = {n/a}, year = {2022}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jeu.12929}, pages = {e12929}, abstract = {Testudodinium testudo is a peridinin-containing dinoflagellate recently renamed from Amphidinium testudo. While T. testudo has been shown via phylogenetic analysis of small subunit ribosomal RNA genes to reside in a clade separate from the genus Amphidinium, it does possess morphological features similar to Amphidinium sensu stricto. Previous studies of Amphidinium carterae and Amphidinium corpulentum have found the sterols to be enriched in Δ8(14) sterols, such as 4α-methyl-5α-ergosta-8(14),24(28)-dien-3β-ol (amphisterol), uncommon to most other dinoflagellate taxa and thus considered possible biomarkers for the genus Amphidinium. Here, we provide an examination of the sterols of T. testudo and show they are dominated not by amphisterol, but rather by a different Δ8(14) sterol, (24R)-4α-methyl-5α-ergosta-8(14),22-dien-3β-ol (gymnodinosterol), previously thought to be a major sterol only within the Kareniaceae genera Karenia, Karlodinium, and Takayama. Also found to be present at low levels were 4α-methyl-5α-ergosta-8,14,22-trien-3β-ol, a sterol previously observed in Karenia brevis to be an intermediate in the production of gymnodinosterol, and cholesterol, a sterol common to many other dinoflagellates. The presence of gymnodinosterol in T. testudo is the first report of this sterol as the sole major sterol in a dinoflagellate outside of the Kareniaceae. The implication of this chemotaxonomic relationship to the Kareniaceae is discussed.}, keywords = {Amphidinium, Dinoflagellate, Dinophyceae, lipid, RCC1981, sterol, Testudodinium}, issn = {1550-7408}, doi = {10.1111/jeu.12929}, url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/jeu.12929}, author = {Leblond, Jeffrey D. and Elkins, Lindsey C. and Sabir, Kyra and Graeff, Jori E.} } @article {arin_taxonomic_2022, title = {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)}, journal = {European Journal of Phycology}, volume = {57}, number = {3}, year = {2022}, pages = {277{\textendash}296}, abstract = {

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{\textendash}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.

}, keywords = {RCC3007, RCC3008, RCC5795}, issn = {0967-0262, 1469-4433}, doi = {10.1080/09670262.2021.1966838}, url = {https://www.tandfonline.com/doi/full/10.1080/09670262.2021.1966838}, author = {Arin, Laura and Re{\~n}{\'e}, Albert and Gallisai, Rachele and Sarno, Diana and Garc{\'e}s, Esther and Estrada, Marta} } @article {eyal_variability_2022, title = {The variability in the structural and functional properties of coccolith base plates}, journal = {Acta Biomaterialia}, volume = {148}, year = {2022}, pages = {336{\textendash}344}, abstract = {Biomineralization processes exert varying levels of control over crystallization, ranging from poorly ordered polycrystalline arrays to intricately shaped single crystals. Coccoliths, calcified scales formed by unicellular algae, are a model for a highly controlled crystallization process. The coccolith crystals nucleate next to an organic oval structure that was termed the base plate, leading to the assumption that it is responsible for the oriented nucleation of the crystals via stereochemical interactions. In recent years, several works focusing on a well-characterized model species demonstrated a fundamental role for indirect interactions that facilitate coccolith crystallization. Here, we developed the tools to extract the base plates from five different species, giving the opportunity to systematically explore the relations between base plate and coccolith properties. We used multiple imaging techniques to evaluate the structural and chemical features of the base plates under native hydrated conditions. The results show a wide range of properties, overlaid on a common rudimentary scaffold that lacks any detectable structural or chemical motifs that can explain direct nucleation control. This work emphasizes that it is the combination between the base plate and the chemical environment inside the cell that cooperatively facilitate the exquisite control over the crystallization process. Statement of significance Biological organic scaffolds can serve as functional surfaces that guide the formation of inorganic materials. However, in many cases the specific interactions that facilitate such tight regulation are complex and not fully understood. In this work, we elucidate the architecture of such amodel biological template, an organic scale that directs the assembly of exquisite crystalline arrays of marine microalgae. By using cryo electron microscopy, we reveal the native state organization of these scales from several species. The observed similarities and differences allow us to propose that the chemical microenvironment, rather than stereochemical matching, is the pivotal regulator of the process.}, keywords = {biomineralization, Calcite, Coccoliths, Cryo electron tomography, Crystallization, RCC1130, RCC1181, RCC190, RCC3777}, issn = {1742-7061}, doi = {10.1016/j.actbio.2022.06.027}, url = {https://www.sciencedirect.com/science/article/pii/S174270612200366X}, author = {Eyal, Zohar and Krounbi, Leilah and Ben Joseph, Oz and Avrahami, Emanuel M. and Pinkas, Iddo and Peled-Zehavi, Hadas and Gal, Assaf} } @article {park_bioluminescence_2021, title = {Bioluminescence capability and intensity in the dinoflagellate Alexandrium species}, journal = {ALGAE}, volume = {36}, year = {2021}, abstract = {Some species in the dinoflagellate genus Alexandrium are bioluminescent. Of the 33 formally described Alexandrium species, the bioluminescence capability of only nine species have been tested, and eight have been reported to be bioluminescent. The present study investigated the bioluminescence capability of seven Alexandrium species that had not been tested. Alexandrium mediterraneum, A. pohangense, and A. tamutum were bioluminescent, but A. andersonii, A. hiranoi, A. insuetum, and A. pseudogonyaulax were not. We also measured the bioluminescent intensity of A. affine, A. fraterculus, A. mediterraneum, A. ostenfeldii, A. pacificum, A. pohangense, A. tamarense, and A. tamutum. The mean 200-second-integrated bioluminescence intensity per cell ranged from 0.02 to 32.2 {\texttimes} 104 relative luminescence unit per cell (RLU cell-1), and the mean maximum bioluminescence intensity per cell per second (BLMax) ranged from 0.01 to 10.3 {\texttimes} 104 RLU cell-1 s-1. BLMax was significantly correlated with the maximum growth rates of Alexandrium species, except for A. tamarense. A phylogenetic tree based on large subunit ribosomal DNA (LSU rDNA), showed that the bioluminescent species A. affine, A. catenella, A. fraterculus, A. mediterraneum, A. pacificum, and A. tamarense formed a large clade. However, the toxicity or mixotrophic capability of these species was split. Thus, their bioluminescence capability in this clade was more consistent than their toxicity or mixotrophic capability. Phylogenetic trees based on LSU rDNA and the luciferase gene of Alexandrium were consistent except for A. pohangense. The results of the present study can provide a basis for understanding the interspecific diversity in bioluminescence of Alexandrium.}, keywords = {RCC4104}, doi = {10.4490/algae.2021.36.12.6}, author = {Park, Sang Ah and Jeong, Hae Jin and Ok, Jin and Kang, Heechang and You, Jihyun and Eom, Se and Yoo, Yeong and Lee, Moo Joon} } @booklet {marc_dinophyceae_2021, title = {Dinophyceae use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)}, year = {2021}, note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article}, month = {jan}, pages = {2021.01.05.425281}, abstract = {Parasites of the genus Amoebophrya sp. are important contributors to marine ecosystems and can be determining factors in the demise of blooms of Dinophyceae, including microalgae commonly responsible for toxic red tides. Yet they rarely lead to the total collapse of Dinophyceae blooms. The addition of resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or their exudate into a well-established host-parasite culture (Scrippsiella acuminata-Amoebophrya sp.) mitigated the success of the parasite and increased the survival of the sensitive host. Effect were mediated via water-borne molecules without the need of a physical contact. Severity of the anti-parasitic defenses fluctuated depending on the species, the strain and its concentration, but never totally prevented the parasite transmission. The survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. The progeny drastically decreased with both species. Integrity of the membrane of dinospores was altered by A. minutum which provided a first indication on the mode of action of these anti-parasitic molecules. These results demonstrate that extracellular defenses are an effective strategy against parasites that does not only protect the resistant cells but also have the potential to affect the whole surrounding community.}, keywords = {rcc, RCC1627, RCC4383, RCC4714, RCC749}, doi = {10.1101/2021.01.05.425281}, url = {https://www.biorxiv.org/content/10.1101/2021.01.05.425281v1}, author = {Marc, Long and Dominique, Marie and Jeremy, Szymczak and Jordan, Toullec and Estelle, Bigeard and Marc, Sourisseau and Mickael, Le Gac and Laure, Guillou and C{\'e}cile, Jauzein} } @article {eich_effects_2021, title = {Effects of UV Radiation on the Chlorophyte Micromonas polaris Host{\textendash}Virus Interactions and MpoV-45T Virus Infectivity}, journal = {Microorganisms}, volume = {9}, year = {2021}, pages = {2429}, abstract = {Polar seas are under threat of enhanced UV-radiation as well as increasing shipping activities. Considering the ecological importance of marine viruses, it is timely to study the impact of UV-AB on Arctic phytoplankton host{\textendash}virus interactions and also test the efficacy of ballast water (BW) UV-C treatment on virus infectivity. This study examined the effects of: (i) ecologically relevant doses of UV-AB radiation on Micromonas polaris RCC2258 and its virus MpoV-45T, and (ii) UV-C radiation (doses 25{\textendash}800 mJ cm-2) on MpoV-45T and other temperate algal viruses. Total UV-AB exposure was 6, 12, 28 and 48 h (during the light periods, over 72 h total). Strongest reduction in algal growth and photosynthetic efficiency occurred for 28 and 48 h UV-AB treatments, and consequently the virus production rates and burst sizes were reduced by more than half (compared with PAR-only controls). For the shorter UV-AB exposed cultures, negative effects by UV (especially Fv/Fm) were overcome without impacting virus proliferation. To obtain the BW desired log-4 reduction in virus infectivity, a UV-C dose of at least 400 mJ cm-2 was needed for MpoV-45T and the temperate algal viruses. This is higher than the commonly used dose of 300 mJ cm-2 in BW treatment.}, keywords = {RCC2258}, doi = {10.3390/microorganisms9122429}, author = {Eich, Charlotte} } @article {pinto_features_2021, title = {Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere}, journal = {Microorganisms}, volume = {9}, year = {2021}, pages = {1777}, abstract = {Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phyco-spheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B12 while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the {\textquoteright}opportunistic{\textquoteright} behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions.}, keywords = {RCC4221}, doi = {10.3390/microorganisms9081777}, author = {Pinto, Jordan and Lami, Rapha{\"e}l and Krasovec, Marc and Grimaud, R{\'e}gis and Urios, Laurent and Lupette, Josselin and Escande, Marie-Line and Sanchez, Fr{\'e}d{\'e}ric and Intertaglia, Laurent and Grimsley, Nigel and Piganeau, Gwenael and Sanchez, Sophie} } @article {Dore2020, title = {Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria}, journal = {Frontiers in Microbiology}, volume = {11}, number = {September}, year = {2020}, note = {tex.mendeley-tags: RCC1084,RCC1085,RCC1086,RCC1087,RCC156,RCC158,RCC162,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2374,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2385,RCC2433,RCC2436,RCC2438,RCC2527,RCC2528,RCC2533,RCC2534,RCC2535,RCC2553,RCC2554,RCC2555,RCC2556,RCC2571,RCC2673,RCC278,RCC296,RCC307,RCC328,RCC3377,RCC407,RCC515,RCC539,RCC555,RCC556,RCC752,RCC753,RCC791}, month = {sep}, pages = {1{\textendash}23}, keywords = {amino-acid substitutions, comparative genomics, evolution, genomic islands, marine cyanobacteria, niche adaptation, Prochlorococcus, rcc1084, RCC1085, RCC1086, RCC1087, RCC156, RCC158, rcc162, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2374, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2385, RCC2433, RCC2436, RCC2438, RCC2527, RCC2528, RCC2533, RCC2534, RCC2535, RCC2553, RCC2554, RCC2555, RCC2556, RCC2571, RCC2673, RCC278, rcc296, RCC307, RCC328, RCC3377, RCC407, RCC515, rcc539, rcc555, RCC556, rcc752, RCC753, rcc791, Synechococcus}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.567431}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.567431/full}, author = {Dor{\'e}, Hugo and Farrant, Gregory K. and Guyet, Ulysse and Haguait, Julie and Humily, Florian and Ratin, Morgane and Pitt, Frances D. and Ostrowski, Martin and Six, Christophe and Brillet-Gu{\'e}guen, Loraine and Hoebeke, Mark and Bisch, Antoine and Le Corguill{\'e}, Gildas and Corre, Erwan and Labadie, Karine and Aury, Jean-Marc and Wincker, Patrick and Choi, Dong Han and Noh, Jae Hoon and Eveillard, Damien and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence} } @article {Barton2020, title = {Evolutionary temperature compensation of carbon fixation in marine phytoplankton}, journal = {Ecology Letters}, year = {2020}, note = {tex.mendeley-tags: RCC1303,RCC1512,RCC1773,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834}, month = {feb}, pages = {ele.13469}, abstract = {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.}, keywords = {climate change, evolutionary ecology, metabolism, phytoplankton physiology, RCC1303, rcc1512, RCC1773, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal performance curves}, issn = {1461-023X}, doi = {10.1111/ele.13469}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13469}, author = {Barton, Samuel and Jenkins, James and Buckling, Angus and Schaum, C.-Elisa and Smirnoff, Nicholas and Raven, John A. and Yvon-Durocher, Gabriel}, editor = {Ezenwa, Vanessa} } @article {bottini_high_2020, title = {High resolution spatial analyses of trace elements in coccoliths reveal new insights into element incorporation in coccolithophore calcite}, journal = {Scientific Reports}, volume = {10}, number = {1}, year = {2020}, note = {Number: 1 Publisher: Nature Publishing Group}, pages = {9825}, abstract = {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 {\texttimes} 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.}, keywords = {Environmental chemistry, Environmental impact, Marine chemistry, Pollution remediation, RCC1198, RCC1303}, issn = {2045-2322}, doi = {10.1038/s41598-020-66503-x}, url = {http://www.nature.com/articles/s41598-020-66503-x}, author = {Bottini, Cinzia and Dapiaggi, Monica and Erba, Elisabetta and Faucher, Giulia and Rotiroti, Nicola} } @article {Guyet2020, title = {Synergic effects of temperature and irradiance on the physiology of the marine synechococcus strain WH7803}, journal = {Frontiers in Microbiology}, volume = {11}, year = {2020}, note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC752}, month = {jul}, pages = {1707}, abstract = {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.}, keywords = {light stress, marine cyanobacteria, rcc752, Synechococcus, temperature stress, transcriptomics, UV radiations}, issn = {1664302X}, doi = {10.3389/fmicb.2020.01707}, url = {www.frontiersin.org}, author = {Guyet, Ulysse and Nguyen, Ngoc A. and Dor{\'e}, Hugo and Haguait, Julie and Pittera, Justine and Conan, Ma{\"e}l and Ratin, Morgane and Corre, Erwan and Le Corguill{\'e}, Gildas and Brillet-Gu{\'e}guen, Loraine and Hoebeke, Mark and Six, Christophe and Steglich, Claudia and Siegel, Anne and Eveillard, Damien and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence} } @article {GerikasRibeiro2020, title = {Taxonomic reassignment of \textit{Pseudohaptolina birgeri comb. nov . (Haptophyta)}, journal = {Phycologia}, volume = {in press}, year = {2020}, note = {tex.mendeley-tags: RCC5268,RCC5270}, month = {oct}, pages = {1{\textendash}10}, keywords = {RCC5268, RCC5270}, issn = {0031-8884}, doi = {10.1080/00318884.2020.1830255}, url = {https://www.biorxiv.org/content/10.1101/2020.05.06.081489v1 https://www.tandfonline.com/doi/full/10.1080/00318884.2020.1830255}, author = {G{\'e}rikas Ribeiro, Catherine and Lopes dos Santos, Adriana and Probert, Ian and Vaulot, Daniel and Edvardsen, Bente} } @mastersthesis {Edullantes2020, title = {Thermal responses of marine phytoplankton : Implications to their biogeography in the present and future oceans}, year = {2020}, note = {Number: September tex.mendeley-tags: RCC2649,RCC291,RCC3404}, type = {phd}, keywords = {RCC2649, RCC291, RCC3404}, author = {Edullantes, Brisneve} } @article {Yau2020, title = {Virus-host coexistence in phytoplankton through the genomic lens}, journal = {Science Advances}, volume = {6}, number = {14}, year = {2020}, note = {tex.mendeley-tags: RCC2590,RCC2596}, month = {apr}, pages = {eaay2587}, abstract = {Virus-microbe interactions in the ocean are commonly described by {\textquotedblleft}boom and bust{\textquotedblright} 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 {\textquotedblleft}accordion{\textquotedblright} 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.}, keywords = {RCC2590, RCC2596}, issn = {2375-2548}, doi = {10.1126/sciadv.aay2587}, url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aay2587}, author = {Yau, Sheree and Krasovec, Marc and Benites, L. Felipe and Rombauts, Stephane and Groussin, Mathieu and Vancaester, Emmelien and Aury, Jean-Marc and Derelle, Evelyne and Desdevises, Yves and Escande, Marie-Line and Grimsley, Nigel and Guy, Julie and Moreau, Herv{\'e} and Sanchez-Brosseau, Sophie and Van de Peer, Yves and Vandepoele, Klaas and Gourbi{\`e}re, S{\'e}bastien and Piganeau, Gwenael} } @article {Granata2019, title = {The influence of bio-optical properties of Emiliania huxleyi and Tetraselmis sp. on biomass and lipid production when exposed to different light spectra and intensities of an adjustable LED array and standard light sources}, journal = {SN Applied Sciences}, volume = {1}, number = {6}, year = {2019}, note = {ISBN: 0123456789 Publisher: Springer International Publishing tex.mendeley-tags: RCC1210,RCC2604}, month = {jun}, pages = {524}, keywords = {Bio-optical properties, Biomass and lipid production, jel classification q42, mathematics subject classification 92c99, rcc1210, RCC2604, Spectral irradiance}, issn = {2523-3963}, doi = {10.1007/s42452-019-0529-x}, url = {http://link.springer.com/10.1007/s42452-019-0529-x}, author = {Granata, Tim and Habermacher, Patrick and H{\"a}rri, Vinzenz and Egli, Marcel} } @article {Gafar2019, title = {Particulate inorganic to organic carbon production as a predictor for coccolithophorid sensitivity to ongoing ocean acidification}, journal = {Limnology and Oceanography Letters}, volume = {4}, number = {3}, year = {2019}, note = {Publisher: John Wiley \& Sons, Ltd tex.mendeley-tags: RCC1130,RCC1141,RCC1168,RCC1198,RCC1200,RCC1323,RCC1334}, month = {jun}, pages = {62{\textendash}70}, abstract = {Ocean acidification (OA) can induce shifts in plankton community composition, with coccolithophores being mostly negatively impacted. This is likely to change particulate inorganic and organic carbon (PIC and POC, respectively) production, with impacts on the biological carbon pump. Hence, assessing and, most importantly, understanding species-specific sensitivities of coccolithophores is paramount. In a multispecies comparison, spanning more than two orders of magnitude in terms of POC and PIC production rates, among Calcidiscus leptoporus, Coccolithus pelagicus subsp. braarudii, Emiliania huxleyi, Gephyrocapsa oceanica, and Scyphosphaera apsteinii, we found that cellular PIC : POC was a good predictor for a species{\textquoteright} OA sensitivity. This is likely related to the need for cellular pH homeostasis, which is challenged by the process of calcification producing protons internally, especially when seawater pH decreases in an OA scenario. With higher PIC : POC, species and strains being more sensitive to OA coccolithophores may shift toward less calcified varieties in the future.}, keywords = {RCC1130, RCC1141, RCC1168, RCC1198, RCC1200, RCC1323, RCC1334}, issn = {2378-2242}, doi = {10.1002/lol2.10105}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10105}, author = {Gafar, N. A. and Eyre, B. D. and Schulz, K. G.} } @article {Engesmo2018, title = {Development of a qPCR assay to detect and quantify ichthyotoxic flagellates along the Norwegian coast, and the first Norwegian record of Fibrocapsa japonica (Raphidophyceae)}, journal = {Harmful Algae}, volume = {75}, year = {2018}, note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC1501,RCC1502}, pages = {105{\textendash}117}, abstract = {Blooms of ichthyotoxic microalgae pose a great challenge to the aquaculture industry world-wide, and there is a need for fast and specific methods for their detection and quantification in monitoring programs. In this study, quantitative real-time PCR (qPCR) assays for the detection and enumeration of three ichthyotoxic flagellates: the dinoflagellate Karenia mikimotoi (Miyake \& Kominami ex Oda) Hansen \& Moestrup and the two raphidophytes Heterosigma akashiwo (Hada) Hada ex Hara \& Chihara and Fibrocapsa japonica Toriumi \& Takano were developed. Further, a previously published qPCR assay for the dinoflagellate Karlodinium veneficum (Ballantine) Larsen was used. Monthly samples collected for three years (Aug 2009{\textendash}Jun 2012) in outer Oslofjorden, Norway were analysed, and the results compared with light microscopy cell counts. The results indicate a higher sensitivity and a lower detection limit (down to 1 cell L-1) for both qPCR assays. Qualitative and semi-quantitative results were further compared with those obtained by environmental 454 high throughput sequencing (HTS, metabarcoding) and scanning electron microscopy (SEM) examination from the same samplings. All four species were detected by qPCR and HTS and/or SEM in outer Oslofjorden (Aug 2009{\textendash}Jun 2012); Karlodinium veneficum was present year-round, whereas Karenia mikimotoi, Heterosigma akashiwo and Fibrocapsa japonica appeared mainly during the autumn in all three years. This is the first observation of Fibrocapsa japonica in Norwegian coastal waters. This species has previously been recorded off the Swedish west coast and German Bight, which may suggest a northward dispersal.}, keywords = {454 high throughput environmental sequencing, Heterosigma akashiwo, Karenia mikimotoi, Karlodinium veneficum, Molecular monitoring, rcc1501, rcc1502, RDNA, SEM}, issn = {15689883}, doi = {10.1016/j.hal.2018.04.007}, url = {https://doi.org/10.1016/j.hal.2018.04.007}, author = {Engesmo, Anette and Strand, David and Gran-Stadnicze{\~n}ko, Sandra and Edvardsen, Bente and Medlin, Linda K. and Eikrem, Wenche} } @article {Smallwood2018, title = {Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri}, journal = {bioRxiv}, year = {2018}, note = {tex.mendeley-tags: RCC745}, keywords = {? No DOI found, RCC745}, author = {Smallwood, Authors Chuck R and Chen, Jian-hua and Kumar, Neeraj and Chrisler, William and Samuel, O and Kyle, Jennifer E and Nicora, Carrie D and Boudreau, Rosanne and Ekman, Axel and Kim, K and Moore, Ronald J and Mcdermott, Gerry and Cannon, William R and Evans, James E} } @article {Delmont2018, title = {Linking pangenomes and metagenomes: the Prochlorococcus metapangenome}, journal = {PeerJ}, volume = {6}, year = {2018}, note = {ISBN: 2167-8359 tex.mendeley-tags: RCC156,RCC158,RCC162,RCC269,RCC278,RCC296,RCC3377,RCC407}, pages = {e4320}, abstract = {Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.}, keywords = {RCC156, RCC158, rcc162, RCC269, RCC278, rcc296, RCC3377, RCC407}, issn = {2167-8359}, doi = {10.7717/peerj.4320}, url = {https://peerj.com/articles/4320}, author = {Delmont, Tom O. and Eren, A. Murat} } @article {Muller2018, title = {Stable isotope fractionation of strontium in coccolithophore calcite: Influence of temperature and carbonate chemistry}, journal = {Geobiology}, volume = {16}, number = {3}, year = {2018}, note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC1200}, month = {may}, pages = {297{\textendash}306}, abstract = {Abstract Marine calcifying eukaryotic phytoplankton (coccolithophores) is a major contributor to the pelagic production of CaCO3 and plays an important role in the biogeochemical cycles of C, Ca and other divalent cations present in the crystal structure of calcite. The geochemical signature of coccolithophore calcite is used as palaeoproxy to reconstruct past environmental conditions and to understand the underlying physiological mechanisms (vital effects) and precipitation kinetics. Here, we present the stable Sr isotope fractionation between seawater and calcite (?88/86Sr) of laboratory cultured coccolithophores in individual dependence of temperature and seawater carbonate chemistry. Coccolithophores were cultured within a temperature and a pCO2 range from 10 to 25{\textdegree}C and from 175 to 1,240 ?atm, respectively. Both environmental drivers induced a significant linear increase in coccolith stable Sr isotope fractionation. The temperature correlation at constant pCO2 for Emiliania huxleyi and Coccolithus braarudii is expressed as ?88/86Sr = ?7.611 ? 10?3 T + 0.0061. The relation of ?88/86Sr to pCO2 was tested in Emiliania huxleyi at 10 and 20{\textdegree}C and resulted in ?88/86Sr = ?5.394 ? 10?5 pCO2 ? 0.0920 and ?88/86Sr = ?5.742 ? 10?5 pCO2 ? 0.1351, respectively. No consistent relationship was found between coccolith ?88/86Sr and cellular physiology impeding a direct application of fossil coccolith ?88/86Sr as coccolithophore productivity proxy. An overall significant correlation was detected between the elemental distribution coefficient (DSr) and ?88/86Sr similar to inorganic calcite with a physiologically induced offset. Our observations indicate (i) that temperature and pCO2 induce specific effects on coccolith ?88/86Sr values and (ii) that strontium elemental ratios and stable isotope fractionation are mainly controlled by precipitation kinetics when embedded into the crystal lattice and subject to vital effects during the transmembrane transport from seawater to the site of calcification. These results provide an important step to develop a coccolith ?88/86Sr palaeoproxy complementing the existing toolbox of palaeoceanography.}, keywords = {coccolithophores, paleoproxy calibration, phytoplankton, RCC1200, stable Sr isotope fractionation}, issn = {1472-4677}, doi = {10.1111/gbi.12276}, url = {https://doi.org/10.1111/gbi.12276}, author = {M{\"u}ller, M N and Krabbenh{\"o}ft, A and Vollstaedt, H and Brandini, F P and Eisenhauer, A} } @article {LopesdosSantos2017, title = {Chloropicophyceae, a new class of picophytoplanktonic prasinophytes}, journal = {Scientific Reports}, volume = {7}, number = {1}, year = {2017}, note = {tex.mendeley-tags: 2017,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4572,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC887,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo}, month = {dec}, pages = {14019}, keywords = {2017, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4572, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC887, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo}, issn = {2045-2322}, doi = {10.1038/s41598-017-12412-5}, url = {http://www.nature.com/articles/s41598-017-12412-5}, author = {Lopes dos Santos, Adriana and Pollina, Thibaut and Gourvil, Priscillia and Corre, Erwan and Marie, Dominique and Garrido, Jos{\'e} Luis and Rodr{\'\i}guez, Francisco and No{\"e}l, Mary-H{\'e}l{\`e}ne and Vaulot, Daniel and Eikrem, Wenche} } @article {faucher_impact_2017, title = {Impact of trace metal concentrations on coccolithophore growth and morphology: laboratory simulations of Cretaceous stress}, journal = {Biogeosciences}, volume = {14}, number = {14}, year = {2017}, note = {Publisher: Copernicus GmbH}, month = {jul}, pages = {3603{\textendash}3613}, abstract = {

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.

}, keywords = {RCC1198, RCC1216, RCC1303}, issn = {1726-4170}, doi = {10.5194/bg-14-3603-2017}, url = {https://bg.copernicus.org/articles/14/3603/2017/}, author = {Faucher, Giulia and Hoffmann, Linn and Bach, Lennart T. and Bottini, Cinzia and Erba, Elisabetta and Riebesell, Ulf} } @article {Marie2017, title = {Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry}, journal = {Journal of Phycology}, volume = {53}, number = {2}, year = {2017}, note = {tex.mendeley-tags: 2016,RCC1008,RCC299,RCC350,RCC4108,RCC4548,RCC4549,RCC4550,RCC4551,RCC4552,RCC4553,RCC4554,RCC4555,RCC4556,RCC4557,RCC4558,RCC4559,RCC4560,RCC4561,RCC4562,RCC4563,RCC4564,RCC4565,RCC4566,RCC4567,RCC4568,RCC4569,RCC4570,RCC4571,RCC4572,RCC4573,RCC4574,RCC4575,RCC4576,RCC4577,RCC4578,RCC4579,RCC4657,RCC4658,RCC4659,RCC4660,RCC4661,RCC4662,RCC4663,RCC4664,RCC4665,RCC4666,RCC90}, month = {apr}, pages = {271{\textendash}282}, keywords = {2016, RCC1008, RCC299, RCC350, RCC4108, RCC4548, RCC4549, RCC4550, RCC4551, RCC4552, RCC4553, RCC4554, RCC4555, RCC4556, RCC4557, RCC4558, RCC4559, RCC4560, RCC4561, RCC4562, RCC4563, RCC4564, RCC4565, RCC4566, RCC4567, RCC4568, RCC4569, RCC4570, RCC4571, RCC4572, RCC4573, RCC4574, RCC4575, RCC4576, RCC4577, RCC4578, RCC4579, RCC4657, RCC4658, RCC4659, RCC4660, RCC4661, RCC4662, RCC4663, RCC4664, RCC4665, RCC4666, RCC90}, issn = {00223646}, doi = {10.1111/jpy.12495}, url = {http://doi.wiley.com/10.1111/jpy.12495}, author = {Marie, Dominique and Le Gall, Florence and Edern, Roseline and Gourvil, Priscillia and Vaulot, Daniel}, editor = {Valentin, K.} } @article {Blanc-Mathieu2017, title = {Population genomics of picophytoplankton unveils novel chromosome hypervariability}, journal = {Science Advances}, volume = {3}, number = {7}, year = {2017}, note = {tex.mendeley-tags: RCC1105,RCC1108,RCC1110,RCC1112,RCC1114,RCC1115,RCC1116,RCC1117,RCC1118,RCC1123,RCC1558,RCC1559,RCC1561,RCC299,RCC4221,RCC809}, month = {jul}, pages = {e1700239}, keywords = {RCC1105, RCC1108, RCC1110, RCC1112, RCC1114, RCC1115, RCC1116, RCC1117, RCC1118, RCC1123, RCC1558, RCC1559, RCC1561, RCC299, RCC4221, RCC809}, issn = {2375-2548}, doi = {10.1126/sciadv.1700239}, url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700239}, author = {Blanc-Mathieu, Romain and Krasovec, Marc and Hebrard, Maxime and Yau, Sheree and Desgranges, Elodie and Martin, Joel and Schackwitz, Wendy and Kuo, Alan and Salin, Gerald and Donnadieu, Cecile and Desdevises, Yves and Sanchez-Ferandin, Sophie and Moreau, Herv{\'e} and Rivals, Eric and Grigoriev, Igor V. and Grimsley, Nigel and Eyre-Walker, Adam and Piganeau, Gwenael} } @article {Simmons2016, title = {Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the eastern north pacific ocean}, journal = {Applied and Environmental Microbiology}, volume = {82}, number = {6}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc}, month = {mar}, pages = {1693{\textendash}1705}, abstract = {Eukaryotic algae within the picoplankton size class (<=2 ??m in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus , during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 {\texttimes} 10 5 and 3.37 {\texttimes} 10 5 cells ? ml -1 , respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 {\texttimes} 10 5 cells ? ml -1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 {\textpm} 327 18S rRNA gene copies ? ml -1 . Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos ) and BII. These share 82\% {\textpm} 6\% nucleotide identity across homologs, while the Ostreococcus spp. share 75\% {\textpm} 8\%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO 3 - and low-affinity NH 4 + transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography.}, keywords = {2016, rcc}, issn = {0099-2240}, doi = {10.1128/AEM.02730-15}, url = {http://aem.asm.org/lookup/doi/10.1128/AEM.02730-15}, author = {Simmons, Melinda P. and Sudek, Sebastian and Monier, Adam and Limardo, Alexander J. and Jimenez, Valeria and Perle, Christopher R. and Elrod, Virginia A. and Pennington, J. Timothy and Worden, Alexandra Z.}, editor = {Schloss, P. D.} } @article {Edvardsen2016, title = {Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding {\textendash} a review}, journal = {Perspectives in Phycology}, volume = {3}, number = {2}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo}, month = {apr}, pages = {77{\textendash}91}, keywords = {2016, rcc, sbr?hyto$_\textrmd$ipo}, issn = {2198-011X}, doi = {10.1127/pip/2016/0052}, url = {https://dx.doi.org/10.6084/m9.figshare.2759983.v1 http://www.schweizerbart.de/papers/pip/detail/3/85671/Diversity_and_distribution_of_haptophytes_revealed?af=crossref}, author = {Edvardsen, Bente and Egge, Elianne Sirnaes and Vaulot, Daniel} } @article {Engesmo2016, title = {New insights into the morphology and phylogeny of Heterosigma akashiwo (Raphidophyceae), with the description of Heterosigma minor sp. nov .}, journal = {Phycologia}, volume = {55}, number = {3}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc1501,rcc1502}, month = {may}, pages = {279{\textendash}294}, keywords = {2016, rcc1501, rcc1502}, issn = {0031-8884}, doi = {10.2216/15-115.1}, url = {http://www.phycologia.org/doi/10.2216/15-115.1}, author = {Engesmo, Anette and Eikrem, Wenche and Seoane, Sergio and Smith, Kirsty and Edvardsen, Bente and Hofgaard, Antje and Tomas, Carmelo R.} } @article {Schmidt2015, title = {Guanchochroma wildpretii gen. et spec. nov. (ochrophyta) provides new insights into the diversification and evolution of the algal class synchromophyceae.}, journal = {PloS one}, volume = {10}, number = {7}, year = {2015}, note = {Publisher: Public Library of Science tex.mendeley-tags: rcc}, month = {jan}, pages = {e0131821}, abstract = {A new relative of the chrysophyte genus Chrysopodocystis was found in Tenerife and termed Guanchochroma wildpretii. This unicellular alga was most noticeably discernible from Chrysopodocystis socialis (the only species of this genus) by the presence of a cyst-like stage with a multilayered lorica, which also functions as a dispersal unit and shows secondary wall growth. Secondary expansion of loricae (cell casings not involved in cell division, usually with a more or less pronounced opening) has never been observed previously and marks a unique feature of the new taxon. Plastids are non-randomly distributed within cells of G. wildpretii. 18S rRNA gene analyses identified the two species as sister lineages and placed them in a monophyletic group with the Synchromophyceae, a heterokont algal (Ochrophyta) class characterized by the presence of chloroplast complexes. Yet, neither Chrysopodocystis nor Guanchochroma showed this feature in ultrastructure analyses. Additionally, their 18S rRNA genes possessed distinct inserts, the highest GC-content known for Ochrophyta and exceptionally long branches on the Ochrophyta 18S rDNA phylogenetic tree, suggesting substantially increased substitution rates along their branch compared to Synchromophyceae. Plastid marker data (rbcL) recovered a monophyletic clade of Chrysopodocystis, Guanchochroma and Synchromophyceae as well, yet with lower supports for internal split order due to limited resolution of the marker. Evidence for the sequence of events leading to the formation of the plastid complex of Synchromophyceae still remains ambiguous because of the apparently short timeframe in which they occurred.}, keywords = {rcc}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131821}, url = {http://dx.doi.org/10.1371/journal.pone.0131821}, author = {Schmidt, Maria and Horn, Susanne and Ehlers, Katrin and Wilhelm, Christian and Schnetter, Reinhard} } @article {Baudoux2015, title = {Interplay between the genetic clades of {\textexclamdown}i{\textquestiondown}Micromonas{\textexclamdown}/i{\textquestiondown} and their viruses in the Western English Channel.}, journal = {Environmental microbiology reports}, year = {2015}, note = {tex.mendeley-tags: 2015,rcc,sbr?hyto$_\textrmd$ipo}, month = {jun}, abstract = {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.}, keywords = {2015, rcc, RCC?o?dd, sbr?hyto$_\textrmd$ipo}, issn = {1758-2229}, doi = {10.1111/1758-2229.12309}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26081716}, author = {Baudoux, A-C and Lebredonchel, H and Dehmer, H and Latimier, M and Edern, R and Rigaut-Jalabert, F and Ge, P and Guillou, L and Foulon, E and Bozec, Y and Cariou, T and Desdevises, Y and Derelle, E and Grimsley, N and Moreau, H and Simon, N} } @article {Gerecht2015, title = {Phosphorus availability modifies carbon production in Coccolithus pelagicus (Haptophyta)}, journal = {Journal of Experimental Marine Biology and Ecology}, volume = {472}, year = {2015}, note = {tex.mendeley-tags: RCC1200}, month = {nov}, pages = {24{\textendash}31}, abstract = {The coccolithophore Coccolithus pelagicus (Wallich) Schiller fixes CO{\textexclamdown}inf{\textquestiondown}2{\textexclamdown}/inf{\textquestiondown} into particulate organic carbon (POC) through photosynthesis and into particulate inorganic carbon (PIC) in the form of calcite. To examine the role of phosphorus (P) availability in the production of POC and PIC, C. pelagicus subsp. braarudii (Gaarder) Geisen et al. was grown in semi-continuous cultures at three initial phosphate concentrations (P-replete, 1, and 0.5??M [P]). Reduced P-availability (1 and 0.5??M [P]) decreased POC production, while PIC production only decreased when phosphate concentrations became growth limiting (0.5??M [P]). This decrease has not been observed previously in batch cultures, highlighting the inadequacy of the batch culture approach with regard to determining carbon production. The reduction in growth rate by 50\% at 0.5??M [P] was accompanied by a doubling in cell volume (and POC). PIC production was halved, resulting in a lowered PIC to POC ratio. The average number of coccoliths per cell (and PIC content) remained the same among treatments, despite the significant change in cell size. Our data suggest that POC production in C. pelagicus is more sensitive towards a moderate reduction in phosphorus availability than PIC production. Once phosphorus availability limits cell division, however, phosphorus resources are invested into POC rather than PIC production. This reduces cell density and sinking rates, indicating that coccoliths do not act as ballast for reaching deeper nutrient-rich layers under nutrient limitation.}, keywords = {Calcification, Carbon production, Coccolithus pelagicus, Phosphorus limitation, RCC1200, Semi-continuous culture}, issn = {00220981}, doi = {10.1016/j.jembe.2015.06.019}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022098115001756}, author = {Gerecht, A.C. and {\v S}upraha, L. and Edvardsen, B. and Langer, G. and Henderiks, J.} } @article {Bellec2014, title = {Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton}, journal = {BMC Evolutionary Biology}, volume = {14}, number = {1}, year = {2014}, note = {tex.mendeley-tags: RCC1105,RCC1107,RCC1108,RCC1109,RCC114,RCC2482,RCC2483,RCC2484,RCC2485,RCC344,RCC356,RCC373,RCC418,RCC461,RCC464,RCC465,RCC629,RCC658,RCC745,RCC789,RCC834}, pages = {59}, abstract = {BACKGROUND:Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny, to complete absence of correspondence between trees. The degree of cospeciation is generally linked to the level of host specificity in the symbiont species and the opportunity they have to switch hosts. In this study, we investigated cophylogeny for the first time in a microalgae-virus association in the open sea, where symbionts are believed to be highly host-specific but have wide opportunities to switch hosts. We studied prasinovirus-Mamiellales associations using 51 different viral strains infecting 22 host strains, selected from the characterisation and experimental testing of the specificities of 313 virus strains on 26 host strains.RESULTS:All virus strains were restricted to their host genus, and most were species-specific, but some of them were able to infect different host species within a genus. Phylogenetic trees were reconstructed for viruses and their hosts, and their congruence was assessed based on these trees and the specificity data using different cophylogenetic methods, a topology-based approach, Jane, and a global congruence method, ParaFit. We found significant congruence between virus and host trees, but with a putatively complex evolutionary history.CONCLUSIONS:Mechanisms other than true cospeciation, such as host-switching, might explain a part of the data. It has been observed in a previous study on the same taxa that the genomic divergence between host pairs is larger than between their viruses. It implies that if cospeciation predominates in this algae-virus system, this would support the hypothesis that prasinoviruses evolve more slowly than their microalgal hosts, whereas host switching would imply that these viruses speciated more recently than the divergence of their host genera.}, keywords = {rcc, RCC1105, rcc1107, RCC1108, RCC1109, RCC114, RCC2482, RCC2483, RCC2484, RCC2485, RCC344, RCC356, RCC373, RCC418, RCC461, RCC464, RCC465, RCC629, RCC658, RCC745, RCC789, RCC834, SBR$_\textrmP$hyto$_\textrmD$PO}, doi = {10.1186/1471-2148-14-59}, url = {http://www.biomedcentral.com/1471-2148/14/59}, author = {Bellec, Laure and Clerissi, Camille and Edern, Roseline and Foulon, Elodie and Simon, Nathalie and Grimsley, Nigel and Desdevises, Yves} } @article {Keeling2014, title = {The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing}, journal = {PLoS biology}, volume = {12}, number = {6}, year = {2014}, note = {Publisher: Public Library of Science tex.mendeley-tags: 2014,rcc,sbr?hyto$_\textrmd$ipo}, pages = {e1001889}, abstract = {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{\textquoteright}s oceans}, keywords = {2014, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo}, doi = {10.1371/journal.pbio.1001889}, url = {http://dx.doi.org/10.1371\%252Fjournal.pbio.1001889}, author = {Keeling, Patrick J and Burki, Fabien and Wilcox, Heather M and Allam, Bassem and Allen, Eric E and Amaral-Zettler, Linda A and Armbrust, E Virginia and Archibald, John M and Bharti, Arvind K and Bell, Callum J and Beszteri, Bank and Bidle, Kay D and Cameron, Connor T and Campbell, Lisa and Caron, David A and Cattolico, Rose Ann and Collier, Jackie L and Coyne, Kathryn and Davy, Simon K and Deschamps, Phillipe and Dyhrman, Sonya T and Edvardsen, Bente and Gates, Ruth D and Gobler, Christopher J and Greenwood, Spencer J and Guida, Stephanie M and Jacobi, Jennifer L and Jakobsen, Kjetill S and James, Erick R and Jenkins, Bethany and John, Uwe and Johnson, Matthew D and Juhl, Andrew R and Kamp, Anja and Katz, Laura A and Kiene, Ronald and Kudryavtsev, Alexander and Leander, Brian S and Lin, Senjie and Lovejoy, Connie and Lynn, Denis and Marchetti, Adrian and McManus, George and Nedelcu, Aurora M and Menden-Deuer, Susanne and Miceli, Cristina and Mock, Thomas and Montresor, Marina and Moran, Mary Ann and Murray, Shauna and Nadathur, Govind and Nagai, Satoshi and Ngam, Peter B and Palenik, Brian and Pawlowski, Jan and Petroni, Giulio and Piganeau, Gwenael and Posewitz, Matthew C and Rengefors, Karin and Romano, Giovanna and Rumpho, Mary E and Rynearson, Tatiana and Schilling, Kelly B and Schroeder, Declan C and Simpson, Alastair G B and Slamovits, Claudio H and Smith, David R and Smith, G Jason and Smith, Sarah R and Sosik, Heidi M and Stief, Peter and Theriot, Edward and Twary, Scott N and Umale, Pooja E and Vaulot, Daniel and Wawrik, Boris and Wheeler, Glen L and Wilson, William H and Xu, Yan and Zingone, Adriana and Worden, Alexandra Z} } @article {Collen2013, title = {Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida}, journal = {Proceedings of the National Academy of Sciences}, volume = {110}, number = {13}, year = {2013}, note = {tex.mendeley-tags: RCC299}, pages = {5247{\textendash}5252}, abstract = {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.}, keywords = {RCC299}, doi = {10.1073/pnas.1221259110}, url = {http://www.pnas.org/content/110/13/5247.abstract}, author = {Collen, Jonas and Porcel, Betina and Carr{\'e}, Wilfrid and Ball, Steven G and Chaparro, Cristian and Tonon, Thierry and Barbeyron, Tristan and Michel, Gurvan and Noel, Benjamin and Valentin, Klaus and Elias, Marek and Artiguenave, Fran{\c c}ois and Arun, Alok and Aury, Jean-Marc and Barbosa-Neto, Jos{\'e} F and Bothwell, John H and Bouget, Fran{\c c}ois-Yves and Brillet, Loraine and Cabello-Hurtado, Francisco and Capella-Guti{\'e}rrez, Salvador and Charrier, B{\'e}n{\'e}dicte and Cladi{\`e}re, Lionel and Cock, J Mark and Coelho, Susana M and Colleoni, Christophe and Czjzek, Mirjam and Da Silva, Corinne and Delage, Ludovic and Denoeud, France and Deschamps, Philippe and Dittami, Simon M and Gabald{\'o}n, Toni and Gachon, Claire M M and Groisillier, Agn{\`e}s and Herv{\'e}, C{\'e}cile and Jabbari, Kamel and Katinka, Michael and Kloareg, Bernard and Kowalczyk, Nathalie and Labadie, Karine and Leblanc, Catherine and Lopez, Pascal J and McLachlan, Deirdre H and Meslet-Cladiere, Laurence and Moustafa, Ahmed and Nehr, Zofia and Nyvall Coll{\'e}n, Pi and Panaud, Olivier and Partensky, Fr{\'e}d{\'e}ric and Poulain, Julie and Rensing, Stefan A and Rousvoal, Sylvie and Samson, Gaelle and Symeonidi, Aikaterini and Weissenbach, Jean and Zambounis, Antonios and Wincker, Patrick and Boyen, Catherine} } @article {Subirana2013, title = {Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, o. mediterraneus sp. nov. (mamiellales, mamiellophyceae)}, journal = {Protist}, volume = {164}, number = {5}, year = {2013}, note = {tex.mendeley-tags: RCC1112,RCC1114,RCC1117,RCC143,RCC1620,RCC1621,RCC1623,RCC1624,RCC2572,RCC2573,RCC2574,RCC2575,RCC2577,RCC2578,RCC2579,RCC2582,RCC2583,RCC2584,RCC2585,RCC2587,RCC2590,RCC344,RCC356,RCC393,RCC501,RCC745,RCC809}, pages = {643{\textendash}659}, abstract = {Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 ??m diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species{\textquoteright} descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species{\textquoteright} divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus, we purified {\textquestiondown}30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov., previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades.}, keywords = {barcode, Chromosome, culture, ITS2, karyotype, picoeukaryote, rcc, RCC1112, RCC1114, RCC1117, RCC143, RCC1620, RCC1621, RCC1623, RCC1624, RCC2572, RCC2573, RCC2574, RCC2575, RCC2577, RCC2578, RCC2579, RCC2582, RCC2583, RCC2584, RCC2585, RCC2587, RCC2590, RCC344, RCC356, RCC393, rcc501, RCC745, RCC809, ribosomal gene}, doi = {10.1016/j.protis.2013.06.002}, url = {http://www.sciencedirect.com/science/article/pii/S1434461013000497}, author = {Subirana, Lucie and P{\'e}quin, B{\'e}rang{\`e}re and Michely, St{\'e}phanie and Escande, Marie-Line and Meilland, Julie and Derelle, Evelyne and Marin, Birger and Piganeau, Gwenael and Desdevises, Yves and Moreau, Herv{\'e} and Grimsley, Nigel H} } @article {Blanc-Mathieu2013, title = {Organellar inheritance in the green lineage: Insights from ostreococcus tauri}, journal = {Genome Biology and Evolution}, volume = {5}, number = {8}, year = {2013}, note = {tex.mendeley-tags: RCC1108,RCC1110,RCC1112,RCC1114,RCC1115,RCC1116,RCC1117,RCC1118,RCC1123,RCC1558,RCC1559,RCC1561,RCC745}, pages = {1503{\textendash}1511}, abstract = {Along the green lineage (Chlorophyta and Streptophyta), mitochondria and chloroplast are mainly uniparentally transmitted and their evolution is thus clonal. The mode of organellar inheritance in their ancestor is less certain. The inability to make clear phylogenetic inference is partly due to a lack of information for deep branching organisms in this lineage. Here, we investigate organellar evolution in the early branching green alga Ostreococcus tauri using population genomics data from the complete mitochondrial and chloroplast genomes. The haplotype structure is consistent with clonal evolution in mitochondria, while we find evidence for recombination in the chloroplast genome. The number of recombination events in the genealogy of the chloroplast suggests that recombination, and thus biparental inheritance, is not rare. Consistent with the evidence of recombination, we find that the ratio of the number of nonsynonymous to the synonymous polymorphisms per site is lower in chloroplast than in the mitochondria genome. We also find evidence for the segregation of two selfish genetic elements in the chloroplast. These results shed light on the role of recombination and the evolutionary history of organellar inheritance in the green lineage.}, keywords = {rcc, RCC1108, RCC1110, RCC1112, RCC1114, RCC1115, RCC1116, RCC1117, RCC1118, RCC1123, RCC1558, RCC1559, RCC1561, RCC745}, doi = {10.1093/gbe/evt106}, url = {http://gbe.oxfordjournals.org/content/5/8/1503.abstract}, author = {Blanc-Mathieu, Romain and Sanchez-Ferandin, Sophie and Eyre-Walker, Adam and Piganeau, Gwenael} } @article {Monier2012, title = {Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges}, journal = {Environmental Microbiology}, volume = {14}, number = {1}, year = {2012}, note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: Micromonas,RCC,rcc}, pages = {162{\textendash}176}, abstract = {Phosphate (PO4) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO4 using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO4 transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO4 uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO4-availability may not serve as a simple bottom-up control of marine phytoplankton.}, keywords = {Micromonas, rcc}, doi = {10.1111/j.1462-2920.2011.02576.x}, url = {http://dx.doi.org/10.1111/j.1462-2920.2011.02576.x}, author = {Monier, Adam and Welsh, Rory M and Gentemann, Chelle and Weinstock, George and Sodergren, Erica and Armbrust, E Virginia and Eisen, Jonathan A and Worden, Alexandra Z} } @article {Ishida2011, title = {Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximately 1 Mbp}, journal = {Phycological Research}, volume = {59}, number = {2}, year = {2011}, note = {Publisher: Blackwell Publishing Asia tex.mendeley-tags: RCC,rcc}, pages = {120{\textendash}122}, abstract = {SUMMARY The nucleomorph genome size of the recently described chlorarachniophyte Partenskyella glossopodia, which forms an independent lineage in the phylogeny of chlorarachniophytes, was analyzed by pulse-field gel electrophoresis and Southern hybridization. These analyses showed that the nucleomorph genome of P. glossopodia is composed of three linear chromosomes that are about 445 kbp, 313 kbp, and 275 kbp in size. Thus, the total genome size is approximately 1033 kbp, which is significantly larger than the known size of chlorarachniophyte nucleomorph genomes, i.e. 330{\textendash}610 kbp. This is the first study to report a nucleomorph genome that reaches approximately 1 Mbp in size.}, keywords = {Chlorarachniophytes, genome reduction, genome size, nucleomorph, Partenskyella glossopodia, rcc}, doi = {10.1111/j.1440-1835.2011.00608.x}, url = {http://dx.doi.org/10.1111/j.1440-1835.2011.00608.x}, author = {Ishida, Ken-ichiro and Endo, Hiroko and Koike, Sayaka} } @article {Edvardsen2011, title = {Ribosomal DNA phylogenies and a morphological revision privide the basis for a new taxonomy of Prymnesiales (Haptophyta)}, journal = {European Journal of Phycology}, volume = {46}, year = {2011}, note = {tex.mendeley-tags: 2011,RCC1185,RCC1187,RCC1189,RCC1385,RCC1387,RCC1388,RCC1390,RCC1432,RCC1438,RCC1440,RCC1441,RCC1448,RCC1453,RCC2056,RCC2057,RCC2059,RCC2060,RCC2061,RCC2063,RCC2064,RCC305,RCC339,RCC3417,RCC3421,RCC3422,RCC3424,RCC3425,RCC3429,RCC406,rcc}, pages = {202{\textendash}228}, keywords = {2011, ASSEMBLE, rcc, RCC1185, RCC1187, RCC1189, RCC1385, RCC1387, RCC1388, RCC1390, RCC1432, RCC1438, RCC1440, RCC1441, RCC1448, RCC1453, RCC2056, RCC2057, RCC2059, RCC2060, RCC2061, RCC2063, RCC2064, RCC305, RCC339, RCC3417, RCC3421, RCC3422, RCC3424, RCC3425, RCC3429, RCC406, SBR$_\textrmP$hyto$_\textrmE$PPO}, doi = {10.1080/09670262.2011.594095}, author = {Edvardsen, B and Eikrem, W and Throndsen, J and A., Saez and Probert, I and Medlin, L} } @article {Worden2009, title = {Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas}, journal = {Science}, volume = {324}, year = {2009}, note = {tex.mendeley-tags: RCC299,RCC827}, pages = {268{\textendash}272}, abstract = {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 {\textquoteleft}unique{\textquoteright} gene pool in each differently than {\textquoteleft}core{\textquoteright} genes. Current climate-change trajectories are predicted to produce conditions favoring picophytoplankton, making Micromonas potential indicators of biological change in ocean ecosystems.}, keywords = {rcc, RCC299, RCC827, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO}, doi = {10.1126/science.1167222}, author = {Worden, A Z and Lee, J.- H and Mock, T and Rouz{\'e}, P and Simmons, M P and Aerts, A L and Allen, A E and Cuvelier, M L and Derelle, E and Everett, M V and Foulon, E and Grimwood, J and Gundlach, H and Henrissat, B and Napoli, C and McDonald, S M and Parker, M S and Rombauts, S and Salamov, A and Von Dassow, P and Badger, J H and Coutinho, P M and Demir, E and Dubchak, I and Gentemann, C and Eikrem, W and Gready, J E and John, U and Lanier, W and Lindquist, E A and Lucas, S and Mayer, K F X and Moreau, H and Not, F and Otillar, R and Panaud, O and Pangilinan, J and Paulsen, I and Piegu, B and Poliakov, A and Robbens, S and Schmutz, J and Toulza, E and Wyss, T and Zelensky, A and Zhou, K and Armbrust, E V and Bhattacharya, D and Goodenough, U W and Van de Peer, Y and Grigoriev, I V} } @article {Vaulot2008, title = {The diversity of small eukaryotic phytoplankton ({\textexclamdown}3 {\textmu}m) in marine ecosystems}, volume = {32}, number = {5}, year = {2008}, note = {Publication Title: FEMS microbiology reviews tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo}, pages = {795{\textendash}820}, abstract = {Small cells dominate photosynthetic biomass and primary production in many marine ecosystems. Traditionally, picoplankton refers to cells {\textexclamdown} or =2 microm. Here we extend the size range of the organisms considered to 3 microm, a threshold often used operationally in field studies. While the prokaryotic component of picophytoplankton is dominated by two genera, Prochlorococcus and Synechococcus, the eukaryotic fraction is much more diverse. Since the discovery of the ubiquitous Micromonas pusilla in the early 1950s, just over 70 species that can be {\textexclamdown}3 microm have been described. In fact, most algal classes contain such species. Less than a decade ago, culture-independent approaches (in particular, cloning and sequencing, denaturing gradient gel electrophoresis, FISH) have demonstrated that the diversity of eukaryotic picoplankton is much more extensive than could be assumed from described taxa alone. These approaches revealed the importance of certain classes such as the Prasinophyceae but also unearthed novel divisions such as the recently described picobiliphytes. In the last couple of years, the first genomes of photosynthetic picoplankton have become available, providing key information on their physiological capabilities. In this paper, we discuss the range of methods that can be used to assess small phytoplankton diversity, present the species described to date, review the existing molecular data obtained on field populations, and end up by looking at the promises offered by genomics.}, keywords = {2008, diversity, genomics, Marine ecosystems, Micro-algae, picoplankton, rcc, sbr?hyto$_\textrmd$ipo, taxonomy}, author = {Vaulot, Daniel and Eikrem, Wenche and Viprey, Manon and Moreau, Herv{\'e}} } @article {Derelle2008, title = {Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga {\textexclamdown}i{\textquestiondown}Ostreococcus tauri{\textexclamdown}/i{\textquestiondown}}, journal = {PLoS ONE}, volume = {3}, number = {5}, year = {2008}, note = {Publisher: Public Library of Science tex.mendeley-tags: RCC,rcc}, pages = {e2250}, abstract = {Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon.}, keywords = {rcc}, doi = {10.1371/journal.pone.0002250}, url = {http://dx.doi.org/10.1371/journal.pone.0002250}, author = {Derelle, Evelyne and Ferraz, Conchita and Escande, Marie-Line and Eycheni{\'e}, Sophie and Cooke, Richard and Piganeau, Gwenael and Desdevises, Yves and Bellec, Laure and Moreau, Herv{\'e} and Grimsley, Nigel} } @article {Everroad2006, title = {Biochemical bases of Type IV chromatic adaptation in marine Synechococcus spp.}, journal = {Journal of Bacteriology}, volume = {188}, year = {2006}, note = {tex.mendeley-tags: 2006,rcc,sbr?hyto?app}, pages = {3345{\textendash}3356}, keywords = {2006, rcc, SBR$_\textrmP$hyto, sbr?hyto?app}, doi = {10.1128/JB.188.9.3345-3356.2006}, author = {Everroad, C and Six, C and Partensky, F and Thomas, J C and Holtzendorff, J and Wood, A M} } @article {Derelle2006, title = {Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {31}, year = {2006}, note = {tex.mendeley-tags: RCC745}, pages = {11647{\textendash}11652}, abstract = {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{\textquoteright}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.}, keywords = {rcc, RCC745, SBR$_\textrmP$hyto}, doi = {10.1073/pnas.0604795103}, url = {http://www.pnas.org/cgi/content/abstract/103/31/11647}, author = {Derelle, Evelyne and Ferraz, Conchita and Rombauts, Stephane and Rouze, Pierre and Worden, Alexandra Z and Robbens, Steven and Partensky, Fr{\'e}d{\'e}ric and Degroeve, Sven and Echeynie, Sophie and Cooke, Richard and Saeys, Yvan and Wuyts, Jan and Jabbari, Kamel and Bowler, Chris and Panaud, Olivier and Piegu, Benoit and Ball, Steven G and Ral, Jean-Philippe and Bouget, Fran{\c c}ois-Yves and Piganeau, Gwenael and De Baets, Bernard and Picard, Andr{\'e} and Delseny, Michel and Demaille, Jacques and Van de Peer, Yves and Moreau, Herv{\'e}} } @article {Guillou2004, title = {Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems}, journal = {Protist}, volume = {155}, year = {2004}, note = {tex.mendeley-tags: 2004,rcc,sbr?hyto}, pages = {193{\textendash}214}, keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SOMLIT}, doi = {10.1078/143446104774199592}, author = {Guillou, Laure and Eikrem, W and Chr{\'e}tiennot-Dinet, M.-J. and Le Gall, F and Massana, R and Romari, K and Pedr{\'o}s-Ali{\'o}, C and Vaulot, D} } @article {Derelle2002, title = {DNA libraries for sequencing the genome of Ostreococcus tauri (Chlorophyta, Prasinophyceae): The smallest free-living eukaryotic cell}, journal = {Journal of Phycology}, volume = {38}, number = {6}, year = {2002}, note = {tex.mendeley-tags: RCC745}, pages = {1150{\textendash}1156}, abstract = {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.}, keywords = {Pico$_\textrmR$eview, rcc, RCC745}, doi = {10.1046/j.1529-8817.2002.02021.x}, url = {c:\%5CDV\%5CPapers reprints\%5CPhytoplankton Physiology\%5CDerelle Ostreococcus DNA libraries JPhycol 02.pdf}, author = {Derelle, E and Ferraz, C and Lagoda, P and Eychenie, S and Cooke, R and Regad, F and Sabau, X and Courties, C and Delseny, M and Demaille, J and Picard, A and Moreau, H} }