@article {dufour_differential_2024, title = {Differential acclimation kinetics of the two forms of type IV chromatic acclimaters occurring in marine Synechococcus cyanobacteria}, journal = {Frontiers in Microbiology}, volume = {15}, year = {2024}, pages = {1349322}, abstract = {Synechococcus , the second most abundant marine phytoplanktonic organism, displays the widest variety of pigment content of all marine oxyphototrophs, explaining its ability to colonize all spectral niches occurring in the upper lit layer of oceans. Seven Synechococcus pigment types (PTs) have been described so far based on the phycobiliprotein composition and chromophorylation of their light-harvesting complexes, called phycobilisomes. The most elaborate and abundant PT (3d) in the open ocean consists of cells capable of type IV chromatic acclimation (CA4), i.e., to reversibly modify the ratio of the blue light-absorbing phycourobilin (PUB) to the green light-absorbing phycoerythrobilin (PEB) in phycobilisome rods to match the ambient light color. Two genetically distinct types of chromatic acclimaters, so-called PTs 3dA and 3dB, occur at similar global abundance in the ocean, but the precise physiological differences between these two types and the reasons for their complementary niche partitioning in the field remain obscure. Here, photoacclimation experiments in different mixes of blue and green light of representatives of these two PTs demonstrated that they differ by the ratio of blue-to-green light required to trigger the CA4 process. Furthermore, shift experiments between 100\% blue and 100\% green light, and vice-versa , revealed significant discrepancies between the acclimation pace of the two types of chromatic acclimaters. This study provides novel insights into the finely tuned adaptation mechanisms used by Synechococcus cells to colonize the whole underwater light field.}, keywords = {RCC2319, RCC2369, RCC2374, RCC2533, RCC2553, RCC2571, RCC515, rcc555, RCC751}, issn = {1664-302X}, doi = {10.3389/fmicb.2024.1349322}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2024.1349322/full}, author = {Dufour, Louison and Garczarek, Laurence and Gouriou, Bastian and Clairet, Julia and Ratin, Morgane and Partensky, Fr{\'e}d{\'e}ric} } @article {roux_ecophysiological_2024, title = {Ecophysiological response of the cupped oyster Crassostrea gigas exposed to the green dinoflagellate Lepidodinium chlorophorum}, journal = {Aquaculture}, year = {2024}, month = {feb}, pages = {740644}, keywords = {RCC6911}, issn = {00448486}, doi = {10.1016/j.aquaculture.2024.740644}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0044848624001054}, author = {Roux, Pauline and Garc{\'\i}a-Corona, Jos{\'e} Luis and Ragueneau, Stacy and Schapira, Mathilde and Siano, Raffaele and Pernet, Fabrice and Queau, Isabelle and Malestroit, Pascale and Tallec, Kevin and Fleury, Elodie} } @article {dulong_exopolysaccharide_2024, title = {Exopolysaccharide from marine microalgae belonging to the \textit{Glossomastix genus: fragile gel behavior and suspension stability}, journal = {Bioengineered}, volume = {15}, number = {1}, year = {2024}, note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/21655979.2023.2296257}, month = {dec}, pages = {2296257}, abstract = {With the aim to find new polysaccharides of rheological interest with innovated properties, rhamnofucans produced as exopolysaccharides (EPS) in a photobioreactor (PBR) and an airlift bioreactor (ABR) by the marine microalgae Glossomastix sp. RCC3707 and RCC3688 were fully studied. Chemical characterizations have been conducted (UHPLC {\textendash} MS HR). Analyses by size-exclusion chromatography (SEC) coupled online with a multiangle light scattering detector (MALS) and a differential refractive index detector showed the presence of large structures with molar masses higher than 106 g.mol-1. The rheological studies of these EPS solutions, conducted at different concentrations and salinities, have evidenced interesting and rare behavior characteristic of weak and fragile hydrogels i.e. gel behavior with very low elastic moduli (between 10-2 and 10 Pa) and yield stresses (between 10-2 and 2 Pa) according to the EPS source, concentration, and salinity. These results were confirmed by diffusing wave spectroscopy. Finally, as one of potential application, solutions of EPS from Glossomastix sp. have evidenced very good properties as anti-settling stabilizers, using microcrystalline cellulose particles as model, studied by multiple light scattering (MLS) with utilization in cosmetic or food industry. Compared to alginate solution with same viscosity for which sedimentation is observed over few hours, microalgae EPS leads to a stable suspension over few days.}, keywords = {fragile gel, Glossomastix, Microalgae, Polysaccharide, RCC3688, RCC3707, stabilizer}, issn = {2165-5979}, doi = {10.1080/21655979.2023.2296257}, url = {https://doi.org/10.1080/21655979.2023.2296257}, author = {Dulong, Virginie and Rihouey, Christophe and Gaignard, Cl{\'e}ment and Bridiau, Nicolas and Gourvil, Priscilla and Laroche, C{\'e}line and Pierre, Guillaume and Varacavoudin, Tony and Probert, Ian and Maugard, Thierry and Michaud, Philippe and Picton, Luc and Le Cerf, Didier} } @article {harcourt_intraspecific_2024, title = {Intraspecific trait variation modulates the temperature effect on elemental quotas and stoichiometry in marine Synechococcus}, journal = {PLOS ONE}, volume = {19}, number = {3}, year = {2024}, note = {Publisher: Public Library of Science}, month = {mar}, pages = {e0292337}, abstract = {Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions, and we demonstrate contains extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in serially transferred cultures across a range of temperatures (16{\textendash}25{\textdegree}C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles.}, keywords = {Biogeochemistry, Cell enumeration techniques, Oceans, Particulates, Phylogenetics, phytoplankton, RCC1086, RCC2673, RCC515, Stoichiometry, Synechococcus}, issn = {1932-6203}, doi = {10.1371/journal.pone.0292337}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0292337}, author = {Harcourt, Renne and Garcia, Nathan S. and Martiny, Adam C.} } @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} } @booklet {sheward_short-term_2024, title = {Short-term response of Emiliania huxleyi growth and morphology to abrupt salinity stress}, year = {2024}, month = {feb}, publisher = {Biogeochemistry: Open Ocean}, type = {preprint}, abstract = {Abstract. The marine coccolithophore species Emiliania huxleyi tolerates a broad range of salinity conditions over its near-global distribution, including the relatively stable physiochemical conditions of open ocean environments and nearshore environments with dynamic and extreme short-term salinity fluctuations. Previous studies show that salinity impacts the physiology and morphology of E. huxleyi, suggesting that salinity stress influences the calcification of this globally important species. However, it remains unclear how rapidly E. huxleyi responds to salinity changes and therefore whether E. huxleyi morphology is sensitive to short-term, transient salinity events (such as occur on meteorological timescales) in addition longer duration salinity changes. Here, we investigate the real-time growth and calcification response of two E. huxleyi strains isolated from shelf-sea environments to the abrupt onset of hyposaline and hypersaline conditions over a time periods of 156 h (6.5 days). Morphological responses in the size of the cellular exoskeleton (coccosphere) and the calcium carbonate plates (coccoliths) that form the coccosphere occurred as rapidly as 24{\textendash}48 h following the abrupt onset of salinity 25 (hyposaline) and salinity 45 (hypersaline) conditions. Generally, cells tended towards smaller coccospheres (-24 \%) with smaller coccoliths (-7 to -11 \%) and reduced calcification under hyposaline conditions whereas cells growing under hypersaline conditions had either relatively stable coccosphere and coccolith sizes (Mediterranean strain RCC1232) or larger coccospheres (+35 \%) with larger coccoliths (+13 \%) and increased calcification (Norwegian strain PLYB11). This short-term response is consistent with reported coccolith size trends with salinity over longer durations of low and high salinity exposure in culture and under natural salinity gradients. The coccosphere size response of PLYB11 to salinity stress was greater in magnitude than observed in RCC1232 but occurred after a longer duration of exposure (ca. 96{\textendash}128 h) to the new salinity conditions compared to RCC1232. In both strains, coccosphere size changes were larger and occurred more rapidly than changes in coccolith size, which tended to occur more gradually over the course of the experiments. Variability in the magnitude and timing of rapid morphological responses to short-term salinity stress between these two strains supports previous suggestions that the response of E. huxleyi to salinity stress is strain specific. At the start of the experiments, the light condition was also switched from a light: dark cycle to continuous light with the aim of desynchronising cell division. As cell density and mean cell size data sampled every 4 h showed regular periodicity under all salinity conditions, the cell division cycle retained its entrainment to pre-experiment light: dark conditions for the entire experiment duration. Extended acclimation periods to continuous light are therefore advisable for E. huxleyi to ensure successful desynchronisation of the cell division cycle. When working with phased or synchronised populations, data should be compared between samples taken from the same phase of the cell division cycle to avoid artificially distorting the magnitude or even direction of physiological or (bio)geochemical response to the environmental stressor.}, keywords = {RCC1232}, doi = {10.5194/egusphere-2024-349}, url = {https://egusphere.copernicus.org/preprints/2024/egusphere-2024-349/}, author = {Sheward, Rosie M. and Geb{\"u}hr, Christina and Bollmann, J{\"o}rg and Herrle, Jens O.} } @article {das_assessing_2023, title = {Assessing indicators of arsenic toxicity using variable fluorescence in a commercially valuable microalgae: physiological and toxicological aspects}, journal = {Journal of Hazardous Materials}, year = {2023}, month = {mar}, pages = {131215}, abstract = {Indicators signaling Arsenic (As) stress through physiology of microalgae using non-destructive methods like variable fluorescence are rare but requisite. This study reports stress markers indicating arsenic (As) toxicity (in two concentrations 11.25{\textmu}g/L and 22.5{\textmu}g/L compared to a control) exposed to a microalga (Diacronema lutheri), using fast repetition rate fluorometry (FRRf). Growth and physiological parameters such as cell density, chl a and the maximum quantum yield Fv/Fm showed coherence and impeded after the exponential phase (day 9 - day 12) in As treatments compared to the control (p < 0.05). On contrary photo-physiological constants were elevated showing higher optical (aLHII) and functional [Sigma (σPSII)] absorption cross-section for the As treatments (p < 0.05) further implying the lack of biomass production yet an increase in light absorption. In addition, As exposure increased the energy dissipation by heat (NPQ-NSV) showing a strong relationship with the de-epoxidation ratio (DR) involving photoprotective pigments. Total As bioaccumulation by D. lutheri showed a strong affinity with Fe adsorption throughout the algal growth curve. This study suggests some prompt photo-physiological proxies signaling As contamination and endorsing its usefulness in risk assessments, given the high toxicity and ubiquitous presence of As in the ecosystem.}, keywords = {Arsenic bioaccumulation, de-epoxidation ratio (DR), Optical absorption cross section, pigment concentrations, RCC1537}, issn = {0304-3894}, doi = {10.1016/j.jhazmat.2023.131215}, url = {https://www.sciencedirect.com/science/article/pii/S0304389423004971}, author = {Das, Shagnika and Lizon, Fabrice and Gevaert, Fran{\c c}ois and Bialais, Capucine and Duong, Gwendoline and Ouddane, Baghdad and Souissi, Sami} } @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 {arnaldo_comparison_2023, title = {Comparison of different small-scale cultivation methods towards the valorization of a marine benthic diatom strain for lipid production}, journal = {Algal Research}, year = {2023}, pages = {103327}, keywords = {RCC5813}, issn = {22119264}, doi = {10.1016/j.algal.2023.103327}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926423003600}, author = {Arnaldo, Mary Dianne Grace and Gamage, Nadeeshani Dehel and Jaffrenou, Agathe and Rabesaotra, Vony and Mossion, Aur{\'e}lie and Wielgosz-Collin, Ga{\"e}tane and M{\'e}l{\'e}der, Vona} } @article {graeff_composition_2023, title = {Composition of galactolipids, betaine lipids and triglyceride-associated fatty acids of the symbiotic dinoflagellate Zooxanthella (Brandtodinium) nutricula: A glimpse into polyunsaturated fatty acids available to its polycystine radiolarian host}, journal = {Phycological Research}, volume = {n/a}, number = {n/a}, year = {2023}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pre.12530}, abstract = {

Zooxanthella nutricula is a photosynthetic dinoflagellate symbiont of polycystine radiolarians. As such, it is hypothesized to provide fixed organic carbon, including in the form of acylglycerolipids and sterols, to its non-photosynthetic host. We have previously characterized the sterols of Z. nutricula that may be transferred to its host and, in the present study, have turned our attention to three classes of fatty acid-containing lipids, chloroplast-associated galactolipids, betaine lipids, which are non-phosphorylated phospholipid analogs present in many eukaryotes, and triglycerides. Zooxanthella nutricula was observed using positive-ion electrospray/mass spectrometry (ESI/MS) and ESI/MS/MS to produce the galactolipids mono- and digalactosyldiacylglycerol (MGDG and DGDG, respectively) enriched in octadecapentaenoic (18:5(n-3)) and octadecatetraenoic (18:4(n-3)) acid to place it within a group of peridinin-containing dinoflagellates in a C18/C18 (sn-1/sn-2 fatty acid regiochemistry) cluster, as opposed to another cluster with C20/C18 MGDG and DGDG, where the C20 fatty acid is eicosapentaenoic acid (20:5(n-3)) and the C18 fatty acid is either 18:5(n-3) or 18:4(n-3). Zooxanthella nutricula was also observed to produce 38:10 (total number of fatty acid carbons:total number of double bonds), 38:6, and 44:7 diacylglycerylcarboxyhydroxymethylcholine (DGCC) as the sole type of betaine lipid. Although it is more difficult to determine which fatty acids are present in the sn-1 and sn-2 positions on the glycerol backbone of DGCC using ESI/MS/MS, gas chromatography/mass spectrometry (GC/MS)-based examination indicated the putatively DGCC-associated polyunsaturated fatty acid (PUFA) docosahexaenoic acid (22:6(n-3)). Coupled with the C18 PUFAs of MGDG and DGDG, and fatty acids associated with triglycerides (also examined via GC/MS), Z. nutricula could serve as a rich source of PUFAs for its radiolarian host. These data demonstrate that Z. nutricula produces a similar set of PUFA-containing lipids as Symbiodinium microadriaticum, a photosynthetic dinoflagellate symbiont of cnidarians, indicating a metabolic commonality in these phylogenetically discrete dinoflagellate symbionts with unrelated host organisms.

}, keywords = {Brandtodinium, chloroplast, Dinoflagellate, Dinophyceae, lipid, RCC3387, Zooxanthella}, issn = {1440-1835}, doi = {10.1111/pre.12530}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pre.12530}, author = {Graeff, Jori E. and Leblond, Jeffrey D.} } @article {ben-joseph_crystallization_2023, title = {Crystallization of Coccolith Calcite at Different Life-Cycle Phases Exhibits Distinct Degrees of Cellular Confinement}, journal = {Small Structures}, volume = {n/a}, number = {n/a}, year = {2023}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/sstr.202200353}, pages = {2200353}, abstract = {Coccolithophores are a group of unicellular marine algae that shape global geochemical cycles via the production of calcium carbonate crystals. Interestingly, different life-cycle phases of the same coccolithophore species produce very different calcitic scales, called coccoliths. In the widely studied diploid phase, the crystals have anisotropic and complex morphologies, while haploid cells produce coccoliths consisting solely of calcite crystals with simple rhombohedral morphology. Understanding how these two life-cycle phases control crystallization is a highly sought-after goal, yet, haploid phase crystallization has rarely been studied, and the process by which they form is unknown. Herein, advanced electron microscopy is employed to elucidate the cellular architecture of the calcification process in haploid cells. The results show that in contrast to diploid-phase calcification, the coccolith-forming vesicle of haploid-phase cells is voluminous. In this solution-like environment, the crystals nucleate and grow asynchronously in a process that resembles calcite growth in bulk solution, leading to the simple morphologies of the crystals. The two distinct mineralization regimes of coccolithophore life-cycle phases suggest that cellular architecture, and specifically confinement of the crystallization process, is a pivotal determinant of biomineral morphology and assembly.}, keywords = {biomineralization, calcites, Coccoliths, crystal growths, haploid{\textendash}diploid life cycles, RCC1181, RCC3777}, issn = {2688-4062}, doi = {10.1002/sstr.202200353}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/sstr.202200353}, author = {Ben-Joseph, Oz and de Haan, Diede and Rechav, Katya and Shimoni, Eyal and Levin-Zaidman, Smadar and Langer, Gerald and Probert, Ian and Wheeler, Glen L. and Gal, Assaf} } @article {lopez-pacheco_growth_2023, title = {Growth Behavior, Biomass Composition and Fatty Acid Methyl Esters (FAMEs) Production Potential of Chlamydomonas reinhardtii, and Chlorella vulgaris Cultures}, journal = {Marine Drugs}, volume = {21}, number = {8}, year = {2023}, month = {aug}, pages = {450}, abstract = {The production of biomolecules by microalgae has a wide range of applications in the development of various materials and products, such as biodiesel, food supplements, and cosmetics. Microalgae biomass can be produced using waste and in a smaller space than other types of crops (e.g., soja, corn), which shows microalgae{\textquoteright}s great potential as a source of biomass. Among the produced biomolecules of greatest interest are carbohydrates, proteins, lipids, and fatty acids. In this study, the production of these biomolecules was determined in two strains of microalgae (Chlamydomonas reinhardtii and Chlorella vulgaris) when exposed to different concentrations of nitrogen, phosphorus, and sulfur. Results show a significant microalgal growth (3.69 g L-1) and carbohydrates (163 mg g-1) increase in C. reinhardtii under low nitrogen concentration. Also, higher lipids content was produced under low sulfur concentration (246 mg g-1). It was observed that sulfur variation could affect in a negative way proteins production in C. reinhardtii culture. In the case of C. vulgaris, a higher biomass production was obtained in the standard culture medium (1.37 g L-1), and under a low-phosphorus condition, C. vulgaris produced a higher lipids concentration (248 mg g-1). It was observed that a low concentration of nitrogen had a better effect on the accumulation of fatty acid methyl esters (FAMEs) (C16-C18) in both microalgae. These results lead us to visualize the effects that the variation in macronutrients can have on the growth of microalgae and their possible utility for the production of microalgae-based subproducts.}, keywords = {RCC2488}, issn = {1660-3397}, doi = {10.3390/md21080450}, url = {https://www.mdpi.com/1660-3397/21/8/450}, author = {L{\'o}pez-Pacheco, Itzel Y. and Ayala-Moreno, Victoria Guadalupe and Mejia-Melara, Catherinne Arlette and Rodr{\'\i}guez-Rodr{\'\i}guez, Jos{\'e} and Cuellar-Bermudez, Sara P. and Gonz{\'a}lez-Gonz{\'a}lez, Reyna Berenice and Coronado-Apodaca, Karina G. and Farfan-Cabrera, Leonardo I. and Gonz{\'a}lez-Meza, Georgia Mar{\'\i}a and Iqbal, Hafiz M. N. and Parra-Sald{\'\i}var, Roberto} } @article {moreno-cabezuelo_integrated_2023, title = {Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus}, journal = {Microbiology Spectrum}, year = {2023}, month = {feb}, pages = {e03275{\textendash}22}, abstract = {

We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in Synechococcus sp. strains WH8102, WH7803, and BL107 and Prochlorococcus sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the EntnerDoudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in Prochlorococcus sp. strain SS120 and Synechococcus sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in Synechococcus sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria.

}, keywords = {RCC156, RCC407, RCC515, rcc539, rcc752}, issn = {2165-0497}, doi = {10.1128/spectrum.03275-22}, url = {https://journals.asm.org/doi/10.1128/spectrum.03275-22}, author = {Moreno-Cabezuelo, Jos{\'e} {\'A}ngel and G{\'o}mez-Baena, Guadalupe and D{\'\i}ez, Jes{\'u}s and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel}, editor = {Hom, Erik F. Y.} } @article {groussman_marferret_2023, title = {MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes}, journal = {Scientific Data}, volume = {10}, number = {1}, year = {2023}, note = {Number: 1 Publisher: Nature Publishing Group}, pages = {926}, abstract = {Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.}, keywords = {Classification and taxonomy, Microbial genetics, transcriptomics}, issn = {2052-4463}, doi = {10.1038/s41597-023-02842-4}, url = {https://www.nature.com/articles/s41597-023-02842-4}, author = {Groussman, R. D. and Blaskowski, S. and Coesel, S. N. and Armbrust, E. V.} } @article {mertens_morpho-molecular_2023, title = {Morpho-molecular analysis of podolampadacean dinoflagellates (Dinophyceae), with the description of two new genera}, journal = {Phycologia}, year = {2023}, note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/00318884.2022.2158281}, month = {feb}, pages = {1{\textendash}19}, abstract = {Sequences were obtained for 58 podolampadacean single cells from France, Reunion Island (French territories) and Japan (6 SSU rDNA only, 40 SSU+LSU and 12 LSU only). The sequenced taxa belong to five of the eight described genera: Podolampas, Blepharocysta, Lissodinium, Gaarderiella and Mysticella. Two new genera, Alatosphaera and Pseudalatosphaera, were erected to accommodate {\textquoteleft}Blepharocysta{\textquoteright} hermosillae and {\textquoteleft}Blepharocysta{\textquoteright} denticulata. Most genera are well supported by concatenated LSU{\textendash}SSU rDNA phylogenies, with the least support for Lissodinium. Metabarcoding of podolampadaceans using the V4 region of SSU rDNA showed a resolution too low to discriminate genera or species. Roscoffia and Cabra are here considered podolampadaceans, whilst Lessardia is considered to belong in a separate family. The relationship of Rhinodinium to the Podolampadaceae needs further study. Desmoschisis was recorded for the first time in Alatosphaera and Pseudalatosphaera. Several ribotypes need further study to attribute a species name to them.}, keywords = {Alatosphaera, Blepharocysta, desmoschisis, Gaarderiella, Lissodinium, LSU rDNA, Mysticella, Podolampas, Pseudalatosphaera, SSU rDNA}, issn = {0031-8884}, doi = {10.1080/00318884.2022.2158281}, url = {https://doi.org/10.1080/00318884.2022.2158281}, author = {Mertens, Kenneth Neil and Carbonell-Moore, M. Consuelo and Chom{\'e}rat, Nicolas and Bilien, Gwenael and Boulben, Sylviane and Guillou, Laure and Romac, Sarah and Probert, Ian and Ishikawa, Akira and N{\'e}zan, Elisabeth} } @article {veron_new_2023, title = {New species of Pavlovophyceae (Haptophyta) and revision of the genera Exanthemachrysis, Rebecca and Pavlova}, journal = {European Journal of Taxonomy}, volume = {861}, year = {2023}, month = {mar}, pages = {21{\textendash}47}, abstract = {The justification of the 4 genera that currently compose the class Pavlovophyceae is based on a low number of species and a relative paucity of available, traceable and referenced cultures. Previous integrative phylogeny work revealed strains that can refine and strengthen our knowledge of the genera in the class. The application of multiple light and electron microscopy techniques allowed us to prioritize the cytomorphological characters (pyrenoid, thylakoid, stigma, knob-scales, life stage / life cycle) used for the taxonomy of these algae and to describe two new species: Exanthemachrysis fresneliae V{\'e}ron sp.~nov. and Rebecca billardiae V{\'e}ron sp.~nov. Consequently, revisions of the two genera Exanthemachrysis Lepailleur emend. V{\'e}ron and Rebecca Green emend. V{\'e}ron were made. In addition, the genus Pavlova Butcher emend V{\'e}ron is revised in the light of these characters. Particular emphasis is placed on the life stages and habitat of the species.}, keywords = {habitats, haptophytes, new species, phytoplankton, pyrenoid, RCC1528, RCC1541}, issn = {2118-9773}, doi = {10.5852/ejt.2023.861.2063}, url = {https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/2063}, author = {Veron, Benoit and Rougier, Etienne and Taylor, Anthony and Goux, Didier} } @article {parsy_selection_2023, title = {Selection of photosynthetic microorganisms grown in artificial saline industrial effluents with liquid digestate: From screening to consortium cultures}, journal = {Algal Research}, year = {2023}, month = {mar}, pages = {103061}, abstract = {The objective of this study was to determine the feasibility of using saline industrial streams as a culture medium to grow microalgae and cyanobacteria. Experiments were performed to determine the extent of the growth in artificial saline produced water and aquifer water supplemented with liquid digestate. Tests were performed in 96-wells microplates. Media were composed with different proportion of saline artificial produced water or aquifer water supplemented with 5\% v/v liquid digestate (final concentrations: 149{\textendash}195 mgN{\textperiodcentered}L-1, 1.5{\textendash}2.7 mgP{\textperiodcentered}L-1). Media were completed to 100 \% with artificial seawater, corresponding to final salinities of 40, 70 and 100 g{\textperiodcentered}L-1. D. salina, N. oceanica and T. suecica showed the best growth rates. They were selected to perform mixed cultures in 80 mL tubes in the same culture media. Population evolutions were followed for 19 days. Depending on salinity and industrial effluent used, different species became predominant over the two others (N. oceanica, T. suecica and D. salina. at 40, 70 and 100 g{\textperiodcentered}L-1, respectively). It appears that mixed culture is a good solution to have a biomass production during a culture process where the culture media will evolve in terms of salinity and composition.}, keywords = {Aquifer water, cyanobacteria, Liquid digestate, Microalgae, Produced water, RCC4223, RCC537, rcc752}, issn = {2211-9264}, doi = {10.1016/j.algal.2023.103061}, url = {https://www.sciencedirect.com/science/article/pii/S2211926423000942}, author = {Parsy, Aur{\'e}lien and Sambusiti, Cecilia and Baldoni-Andrey, Patrick and P{\'e}ri{\'e}, Fr{\'e}d{\'e}ric and Guyoneaud, R{\'e}my} } @article {klintzsch_stable_2023, title = {Stable Carbon Isotope Signature of Methane Released from Phytoplankton}, journal = {Geophysical Research Letters}, year = {2023}, month = {feb}, abstract = {Aquatic ecosystems play an important role in global methane cycling and many field studies have reported methane supersaturation in the oxic surface mixed layer (SML) of the ocean and in the epilimnion of lakes. The origin of methane formed under oxic condition is hotly debated and several pathways have recently been offered to explain the {\textquoteleft}methane paradox{\textquoteright}. In this context, stable isotope measurements have been applied to constrain methane sources in supersaturated oxygenated waters. Here we present stable carbon isotope signatures for six widespread marine phytoplankton species, three haptophyte algae and three cyanobacteria, incubated under laboratory conditions. The observed isotopic patterns implicate that methane formed by phytoplankton might be clearly distinguished from methane produced by methanogenic archaea. Comparing results from phytoplankton experiments with isotopic data from field measurements, suggests that algal and cyanobacterial populations may contribute substantially to methane formation observed in the SML of oceans and lakes.}, keywords = {RCC1216, ⛔ No DOI found}, doi = {10.22541/essoar.167689993.32180072/v1}, url = {https://essopenarchive.org/users/587513/articles/625160-stable-carbon-isotope-signature-of-methane-released-from-phytoplankton?commit=633a121ee07c48e6c59ffeca06fd5d5ebe1df4d4}, author = {Klintzsch, Thomas and Geisinger, Hannah and Wieland, Anna and Langer, Gerald and Nehrke, Gernot and Bizic, Mina and Greule, Markus and Lenhart, Katharina and Borsch, Christian and Schroll, Moritz and Keppler, Frank} } @article {storti_tailoring_2023, title = {Tailoring confocal microscopy for real-time analysis of photosynthesis at single-cell resolution}, journal = {Cell Reports Methods}, year = {2023}, pages = {100568}, abstract = {Photoautotrophs{\textquoteright} environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single-cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells, or organs. Furthermore, cells within the same tissue may behave differently, being at different developmental/ physiological stages. Here, we describe an approach for single-cell and subcellular photophysiology based on the customization of confocal microscopy to assess chlorophyll fluorescence quenching by the saturation pulse method. We exploit this setup to (1) reassess the specialization of photosynthetic activities in developing tissues of non-vascular plants; (2) identify a specific subpopulation of phytoplankton cells in marine photosymbiosis, which consolidate energetic connections with their hosts; and (3) examine the link between light penetration and photoprotection responses inside the different tissues that constitute a plant leaf anatomy.}, keywords = {rcc1383}, issn = {26672375}, doi = {10.1016/j.crmeth.2023.100568}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2667237523002126}, author = {Storti, Mattia and Hsine, Haythem and Uwizeye, Clarisse and Bastien, Olivier and Yee, Daniel P. and Chevalier, Fabien and Decelle, Johan and Giustini, C{\'e}cile and B{\'e}al, Daniel and Curien, Gilles and Finazzi, Giovanni and Tolleter, Dimitri} } @article {alonso-saez_transcriptional_2023, title = {Transcriptional Mechanisms of Thermal Acclimation in \textit{Prochlorococcus}, journal = {mBio}, year = {2023}, pages = {e03425{\textendash}22}, abstract = {Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40{\textdegree}. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30{\textdegree}C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17{\textdegree}C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones.}, keywords = {RCC3377}, issn = {2150-7511}, doi = {10.1128/mbio.03425-22}, url = {https://journals.asm.org/doi/10.1128/mbio.03425-22}, author = {Alonso-S{\'a}ez, Laura and Palacio, Antonio S. and Cabello, Ana M. and Robaina-Est{\'e}vez, Semid{\'a}n and Gonz{\'a}lez, Jos{\'e} M. and Garczarek, Laurence and L{\'o}pez-Urrutia, {\'A}ngel}, editor = {Martiny, Jennifer B. H.} } @article {bordiga_unexpected_2023, title = {Unexpected silicon localization in calcium carbonate exoskeleton of cultured and fossil coccolithophores}, journal = {Scientific Reports}, volume = {13}, number = {1}, year = {2023}, note = {Number: 1 Publisher: Nature Publishing Group}, month = {may}, pages = {7417}, abstract = {Coccolithophores, marine calcifying phytoplankton, are important primary producers impacting the global carbon cycle at different timescales. Their biomineral structures, the calcite containing coccoliths, are among the most elaborate hard parts of any organism. Understanding the morphogenesis of coccoliths is not only relevant in the context of coccolithophore eco-physiology but will also inform biomineralization and crystal design research more generally. The recent discovery of a silicon (Si) requirement for crystal shaping in some coccolithophores has opened up a new avenue of biomineralization research. In order to develop a mechanistic understanding of the role of Si, the presence and localization of this chemical element in coccoliths needs to be known. Here, we document for the first time the uneven Si distribution in Helicosphaera carteri coccoliths through three synchrotron-based techniques employing X-ray Fluorescence and Infrared Spectromicroscopy. The enrichment of Si in specific areas of the coccoliths point to a targeted role of this element in the coccolith formation. Our findings mark a key step in biomineralization research because it opens the door for a detailed mechanistic understanding of the role Si plays in shaping coccolith crystals.}, keywords = {Biogeochemistry, Marine biology, Palaeontology, RCC1323}, issn = {2045-2322}, doi = {10.1038/s41598-023-34003-3}, url = {https://www.nature.com/articles/s41598-023-34003-3}, author = {Bordiga, M. and Lupi, C. and Langer, G. and Gianoncelli, A. and Birarda, G. and Pollastri, S. and Bonanni, V. and Bedolla, D. E. and Vaccari, L. and Gariani, G. and Cerino, F. and Cabrini, M. and Beran, A. and Zuccotti, M. and Fiorentino, G. and Zanoni, M. and Garagna, S. and Cobianchi, M. and Di Giulio, A.} } @article {ferrieux_comparative_2022, title = {Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas}, journal = {Frontiers in Microbiology}, volume = {13}, year = {2022}, abstract = {Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters.}, keywords = {RCC2374, RCC2385, RCC2533, RCC2534, RCC2571, RCC515, rcc539, rcc791}, issn = {1664-302X}, doi = {10.3389/fmicb.2022.893413}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2022.893413}, author = {Ferrieux, Mathilde and Dufour, Louison and Dor{\'e}, Hugo and Ratin, Morgane and Gu{\'e}neugu{\`e}s, Audrey and Chasselin, L{\'e}o and Marie, Dominique and Rigaut-jalabert, Fabienne and Le Gall, Florence and Sciandra, Th{\'e}o and Monier, Garance and Hoebeke, Mark and Corre, Erwan and Xia, Xiaomin and Liu, Hongbin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence} } @article {grebert_diversity_2022, title = {Diversity and evolution of pigment types in marine \textit{Synechococcus cyanobacteria}, journal = {Genome Biology and Evolution}, year = {2022}, pages = {evac035}, abstract = {DNA integration and site-specific recombination, suggesting that their genomic variability relies D in part on a {\textquoteleft}tycheposon{\textquoteright}-like mechanism. Comparison of the phylogenies obtained for PBS and E core genes revealed that the evolutionary history of PBS rod genes differs from the core T genome and is characterized by the co-existence of different alleles and frequent allelic P exchange. We propose a scenario for the evolution of the different pigment types and highlight E the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in C different Synechococcus lineages despite multiple speciation events.}, keywords = {RCC307, to add}, issn = {1759-6653}, doi = {10.1093/gbe/evac035}, url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac035/6547267}, author = {Gr{\'e}bert, Th{\'e}ophile and Garczarek, Laurence and Daubin, Vincent and Humily, Florian and Marie, Dominique and Ratin, Morgane and Devailly, Alban and Farrant, Gregory K. and Mary, Isabelle and Mella-Flores, Daniella and Tanguy, Gwenn and Labadie, Karine and Wincker, Patrick and Kehoe, David M. and Partensky, Fr{\'e}d{\'e}ric}, editor = {Angert, Esther} } @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 {guerin_genomic_2022, title = {Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence}, journal = {Communications Biology}, volume = {5}, number = {1}, year = {2022}, note = {Number: 1 Publisher: Nature Publishing Group}, pages = {1{\textendash}14}, abstract = {The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata.}, keywords = {Biogeography, comparative genomics, metagenomics, RCC100, Water microbiology}, issn = {2399-3642}, doi = {10.1038/s42003-022-03939-z}, url = {https://www.nature.com/articles/s42003-022-03939-z}, author = {Gu{\'e}rin, Nina and Ciccarella, Marta and Flamant, Elisa and Fr{\'e}mont, Paul and Mangenot, Sophie and Istace, Benjamin and Noel, Benjamin and Belser, Caroline and Bertrand, Laurie and Labadie, Karine and Cruaud, Corinne and Romac, Sarah and Bachy, Charles and Gachenot, Martin and Pelletier, Eric and Alberti, Adriana and Jaillon, Olivier and Wincker, Patrick and Aury, Jean-Marc and Carradec, Quentin} } @article {dore_global_2022, title = {Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts}, journal = {mSystems}, year = {2022}, note = {Publisher: American Society for Microbiology}, pages = {e00656{\textendash}22}, abstract = {Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of {\textquotedblleft}who is where{\textquotedblright} by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.}, keywords = {RCC1086, RCC1695, RCC2369, rcc2380, RCC2553, RCC2556, RCC2570, rcc791}, doi = {10.1128/msystems.00656-22}, url = {https://journals.asm.org/doi/full/10.1128/msystems.00656-22}, author = {Dor{\'e}, Hugo and Leconte, Jade and Guyet, Ulysse and Breton, Sol{\`e}ne and Farrant, Gregory K. and Demory, David and Ratin, Morgane and Hoebeke, Mark and Corre, Erwan and Pitt, Frances D. and Ostrowski, Martin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Garczarek, Laurence} } @article {vazquez_high-co2_2022, title = {High-CO2 Levels Rather than Acidification Restrict Emiliania huxleyi Growth and Performance}, journal = {Microbial Ecology}, year = {2022}, abstract = {The coccolithophore Emiliania huxleyi shows a variety of responses to ocean acidification (OA) and to high-CO2 concentrations, but there is still controversy on differentiating between these two factors when using different strains and culture methods. A heavily calcified type A strain isolated from the Norwegian Sea was selected and batch cultured in order to understand whether acclimation to OA was mediated mainly by CO2 or H+, and how it impacted cell growth performance, calcification, and physiological stress management. Emiliania huxleyi responded differently to each acidification method. CO2-enriched aeration (1200 {\textmu}atm, pH 7.62) induced a negative effect on the cells when compared to acidification caused by decreasing pH alone (pH 7.60). The growth rates of the coccolithophore were more negatively affected by high pCO2 than by low pH without CO2 enrichment with respect to the control (400 {\textmu}atm, pH 8.1). High CO2 also affected cell viability and promoted the accumulation of reactive oxygen species (ROS), which was not observed under low pH. This suggests a possible metabolic imbalance induced by high CO2 alone. In contrast, the affinity for carbon uptake was negatively affected by both low pH and high CO2. Photochemistry was only marginally affected by either acidification method when analysed by PAM fluorometry. The POC and PIC cellular quotas and the PIC:POC ratio shifted along the different phases of the cultures; consequently, calcification did not follow the same pattern observed in cell stress and growth performance. Specifically, acidification by HCl addition caused a higher proportion of severely deformed coccoliths, than CO2 enrichment. These results highlight the capacity of CO2 rather than acidification itself to generate metabolic stress, not reducing calcification.}, keywords = {Calcification, coccolithophores, Emiliania huxleyi, Ocean acidification, pCO2, Photochemistry, phytoplankton, rcc1226, Stress}, issn = {1432-184X}, doi = {10.1007/s00248-022-02035-3}, url = {https://doi.org/10.1007/s00248-022-02035-3}, author = {V{\'a}zquez, V{\'\i}ctor and Le{\'o}n, Pablo and Gordillo, Francisco J. L. and Jim{\'e}nez, Carlos and Concepci{\'o}n, I{\~n}iguez and Mackenzie, Kevin and Bresnan, Eileen and Segovia, Mar{\'\i}a} } @article {parsy_impact_2022, title = {Impact of salinities, metals and organic compounds found in saline oil \& gas produced water on microalgae and cyanobacteria}, journal = {Ecotoxicology and Environmental Safety}, volume = {234}, year = {2022}, pages = {113351}, abstract = {This work evaluates the impact of salinity and the toxicity of some metals and organic compounds commonly found in produced waters on the growth of model photosynthetic organisms. Five strains of marine microalgae and one cyanobacteria (i.e. Dunaliella salina, Nannochloropsis oceanica, Tetraselmis suecica, Picochlorum cos- tavermella, Coccomyxa simplex and Synechococcus rubescens) were tested in microplates as well as the freshwater Chlorella vulgaris selected as reference. Results revealed that D.salina was able to growth at high salinity (up to 135 g.L- 1). Copper was the most toxic metal for all strains (half maximal effective concentration between 0.1 and 10 mg.L- 1) except for D.salina and C.simplex. These two strains were the most resistant to all metals tested. All organic compounds presented half maximal effective concentration above 10 mg.L- 1, none of them being very toxic for the studied microorganisms. P.costavermella and C.simplex were the most resistant strains to organic compounds. Looking at tolerance to salinity, metals and organic compounds, D.salina appeared to be the best choice for biomass production in produced waters. In addition, growths in 80\% artificial produced water sup- plemented with f medium confirm the feasibility to use this medium to produce biomass.}, keywords = {RCC4223, RCC537, rcc752}, issn = {01476513}, doi = {10.1016/j.ecoenv.2022.113351}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0147651322001919}, author = {Parsy, Aur{\'e}lien and Guyoneaud, R{\'e}my and Lot, Marie-Claire and Baldoni-Andrey, Patrick and P{\'e}ri{\'e}, Fr{\'e}d{\'e}ric and Sambusiti, Cecilia} } @article {dominguez-martin_marine_2022, title = {Marine \textit{Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate}, journal = {Microbiology Spectrum}, volume = {10}, number = {4}, year = {2022}, month = {aug}, pages = {e00187{\textendash}22}, abstract = {Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment.}, keywords = {rcc752}, issn = {2165-0497}, doi = {10.1128/spectrum.00187-22}, url = {https://journals.asm.org/doi/10.1128/spectrum.00187-22}, author = {Dom{\'\i}nguez-Mart{\'\i}n, Maria Agustina and L{\'o}pez-Lozano, Antonio and Melero-Rubio, Yesica and G{\'o}mez-Baena, Guadalupe and Jim{\'e}nez-Estrada, Juan Andr{\'e}s and Kukil, Kateryna and D{\'\i}ez, Jes{\'u}s and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel}, editor = {Hom, Erik F. Y.} } @article {gomez_molecular_2022, title = {Molecular phylogeny of the spiny-surfaced species of the dinoflagellate Prorocentrum with the description of P. Thermophilum sp. nov. and P. criophilum sp. nov. (Prorocentrales, Dinophyceae)}, journal = {Journal of Phycology}, volume = {n/a}, number = {n/a}, year = {2022}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13298}, abstract = {Spiny-surfaced species of Prorocentrum forms harmful algal blooms, and its taxonomic identity is obscure due to the size and shape variability. Molecular phylogenies reveal two major clades: one for P. cordatum with sequences mainly retrieved as P. minimum, and other for P. shikokuense with sequences also retrieved as P. dentatum and P. donghaiense. Several closely related clades still need to be characterized. Here, we provide SSU- and LSU rRNA, and ITS gene sequences of the strain CCMP3122 isolated from Florida (initially named P. donghaiense) and strains Prorocentrum sp. RCC6871{\textendash}2 from the Ross Sea, Antarctica. We describe Prorocentrum thermophilum sp. nov. based on the strain CCMP3122, a species also distributed in the open waters of Gulf of Mexico, New Zealand and the Arabian Gulf; and Prorocentrum criophilum sp. nov. based on the strain RCC6872, which is distributed in the Antarctic Ocean and the Arctic Sea. Prorocentrum thermophilum is roundish ( 14 μm long, 12 μm wide), with an inconspicuous anterior spine-like prolongation under light microscopy, valves with tiny, short knobs (5{\textendash}7 per μm2), and several (<7) large trichocyst pores ( 0.3 μm) in the right valve, as well as smaller pores ( 0.15 μm). Prorocentrum criophilum is round in valve view ( 11 μm long, 10 μm wide) and asymmetrically roundish in lateral view, the periflagellar area was not discernible under light microscopy, valves with very tiny, short knobs (6{\textendash}10 per μm2), and at least twelve large pores in the right valve. Other potentially undescribed species of spiny-surfaced Prorocentrum are discussed}, keywords = {Dinophyta, HABs, harmful algae blooms, molecular phylogenetics, new species, Prorocentraceae, RCC6871, RCC6872, taxonomy}, issn = {1529-8817}, doi = {10.1111/jpy.13298}, url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13298}, author = {G{\'o}mez, Fernando and Gourvil, Priscillia and Li, Tangcheng and Huang, Yulin and Zhang, Huan and Courcot, Lucie and Artigas, Luis F. and Soler On{\'\i}s, Emilio and Gutierrez-Rodriguez, Andres and Lin, Senjie} } @article {haney_multiple_2022, title = {Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation}, journal = {mBio}, volume = {13}, number = {4}, year = {2022}, month = {aug}, pages = {e01511{\textendash}22}, abstract = {

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

}, keywords = {rcc555}, issn = {2150-7511}, doi = {10.1128/mbio.01511-22}, url = {https://journals.asm.org/doi/10.1128/mbio.01511-22}, author = {Haney, Allissa M. and Sanfilippo, Joseph E. and Garczarek, Laurence and Partensky, Fr{\'e}d{\'e}ric and Kehoe, David M.}, editor = {Ruby, Edward} } @article {lacour_photoacclimation_2022, title = {Photoacclimation of the polar diatom Chaetoceros neogracilis at low temperature}, journal = {PLOS ONE}, volume = {17}, number = {9}, year = {2022}, note = {Publisher: Public Library of Science}, month = {sep}, pages = {e0272822}, abstract = {Polar microalgae face two major challenges: 1- growing at temperatures (-1.7 to 5{\textdegree}C) that limit enzyme kinetics; and 2- surviving and exploiting a wide range of irradiance. The objective of this study is to understand the adaptation of an Arctic diatom to its environment by studying its ability to acclimate to changes in light and temperature. We acclimated the polar diatom Chaetoceros neogracilis to various light levels at two different temperatures and studied its growth and photosynthetic properties using semi-continuous cultures. Rubisco content was high, to compensate for low catalytic rates, but did not change detectably with growth temperature. Contrary to what is observed in temperate species, in C. neogracilis, carbon fixation rate (20 min 14C incorporation) equaled net growth rate (μ) suggesting very low or very rapid (<20 min) re-oxidation of the newly fixed carbon. The comparison of saturation irradiances for electron transport, oxygen net production and carbon fixation revealed alternative electron pathways that could provide energy and reducing power to the cell without consuming organic carbon which is a very limiting product at low temperatures. High protein contents, low re-oxidation of newly fixed carbon and the use of electron pathways alternative to carbon fixation may be important characteristics allowing efficient growth under those extreme environmental conditions.}, keywords = {5-bisphosphate carboxylase oxygenase, Carbon fixation, diatoms, Fluorescence, Light, Photons, Photosynthesis, pigments, RCC2278, Ribulose-1}, issn = {1932-6203}, doi = {10.1371/journal.pone.0272822}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0272822}, author = {Lacour, Thomas and Larivi{\`e}re, Jade and Ferland, Joannie and Morin, Philippe-Isra{\"e}l and Grondin, Pierre-Luc and Donaher, Natalie and Cockshutt, Amanda and Campbell, Douglas A. and Babin, Marcel} } @article {liu_phycosphere_2022, title = {Phycosphere pH of unicellular nano- and micro- phytoplankton cells and consequences for iron speciation}, journal = {The ISME Journal}, volume = {16}, number = {10}, year = {2022}, note = {Number: 10 Publisher: Nature Publishing Group}, month = {oct}, pages = {2329{\textendash}2336}, abstract = {Surface ocean pH is declining due to anthropogenic atmospheric CO2 uptake with a global decline of \textasciitilde0.3 possible by 2100. Extracellular pH influences a range of biological processes, including nutrient uptake, calcification and silicification. However, there are poor constraints on how pH levels in the extracellular microenvironment surrounding phytoplankton cells (the phycosphere) differ from bulk seawater. This adds uncertainty to biological impacts of environmental change. Furthermore, previous modelling work suggests that phycosphere pH of small cells is close to bulk seawater, and this has not been experimentally verified. Here we observe under 140 μmol photons{\textperiodcentered}m-2{\textperiodcentered}s-1 the phycosphere pH of Chlamydomonas concordia (5 {\textmu}m diameter), Emiliania huxleyi (5 {\textmu}m), Coscinodiscus radiatus (50 {\textmu}m) and C. wailesii (100 {\textmu}m) are 0.11 {\textpm} 0.07, 0.20 {\textpm} 0.09, 0.41 {\textpm} 0.04 and 0.15 {\textpm} 0.20 (mean {\textpm} SD) higher than bulk seawater (pH 8.00), respectively. Thickness of the pH boundary layer of C. wailesii increases from 18 {\textpm} 4 to 122 {\textpm} 17 {\textmu}m when bulk seawater pH decreases from 8.00 to 7.78. Phycosphere pH is regulated by photosynthesis and extracellular enzymatic transformation of bicarbonate, as well as being influenced by light intensity and seawater pH and buffering capacity. The pH change alters Fe speciation in the phycosphere, and hence Fe availability to phytoplankton is likely better predicted by the phycosphere, rather than bulk seawater. Overall, the precise quantification of chemical conditions in the phycosphere is crucial for assessing the sensitivity of marine phytoplankton to ongoing ocean acidification and Fe limitation in surface oceans.}, keywords = {Biogeochemistry, Microbial biooceanography, RCC1, rcc1731, Water microbiology}, issn = {1751-7370}, doi = {10.1038/s41396-022-01280-1}, url = {https://www.nature.com/articles/s41396-022-01280-1}, author = {Liu, Fengjie and Gledhill, Martha and Tan, Qiao-Guo and Zhu, Kechen and Zhang, Qiong and Sala{\"u}n, Pascal and Tagliabue, Alessandro and Zhang, Yanjun and Weiss, Dominik and Achterberg, Eric P. and Korchev, Yuri} } @mastersthesis {groussman_resolving_2022, title = {Resolving the molecular ecology of marine microbial eukaryotes with metatranscriptomes}, year = {2022}, school = {University of Washington}, type = {phd}, keywords = {RCC1007, ⛔ No DOI found}, url = {https://digital.lib.washington.edu/researchworks/bitstream/handle/1773/49735/Groussman_washington_0250E_25089.pdf}, author = {Groussman, Ryan D} } @article {de_la_broise_scale-up_2022, title = {Scale-Up to Pilot of a Non-Axenic Culture of Thraustochytrids Using Digestate from Methanization as Nitrogen Source}, journal = {Marine Drugs}, volume = {20}, number = {8}, year = {2022}, month = {aug}, pages = {499}, abstract = {The production of non-fish based docosahexaenoic acid (DHA) for feed and food has become a critical need in our global context of over-fishing. The industrial-scale production of DHA{\textendash}rich Thraustochytrids could be an alternative, if costs turned out to be competitive. In order to reduce production costs, this study addresses the feasibility of the non-axenic (non-sterile) cultivation of Aurantiochytrium mangrovei on industrial substrates (as nitrogen and mineral sources and glucose syrup as carbon and energy sources), and its scale-up from laboratory (250 mL) to 500 L cultures. Pilot-scale reactors were airlift cylinders. Batch and fed-batch cultures were tested. Cultures over 38 to 62 h achieved a dry cell weight productivity of 3.3 to 5.5 g.L-1.day-1, and a substrate to biomass yield of up to 0.3. DHA productivity ranged from 10 to 0.18 mg.L-1.day-1. Biomass productivity appears linearly related to oxygen transfer rate. Bacterial contamination of cultures was low enough to avoid impacts on fatty acid composition of the biomass. A specific work on microbial risks assessment (in supplementary files) showed that the biomass can be securely used as feed. However, to date, there is a law void in EU legislation regarding the recycling of nitrogen from digestate from animal waste for microalgae biomass and its usage in animal feed. Overall, the proposed process appears similar to the industrial yeast production process (non-axenic heterotrophic process, dissolved oxygen supply limiting growth, similar cell size). Such similarity could help in further industrial developments.}, keywords = {RCC893}, issn = {1660-3397}, doi = {10.3390/md20080499}, url = {https://www.mdpi.com/1660-3397/20/8/499}, author = {de la Broise, Denis and Ventura, Mariana and Chauchat, Luc and Guerreiro, Maurean and Michez, Teo and Vinet, Thibaud and Gautron, Nicolas and Le Grand, Fabienne and Bideau, Antoine and Go{\"\i}c, Nelly Le and Bidault, Adeline and Lambert, Christophe and Soudant, Philippe} } @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 {schmitt_temperature_2022, title = {Temperature Affects the Biological Control of Dinoflagellates by the Generalist Parasitoid Parvilucifera rostrata}, journal = {Microorganisms}, volume = {10}, number = {2}, year = {2022}, note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute}, pages = {385}, abstract = {The increase in emerging harmful algal blooms in the last decades has led to an extensive concern in understanding the mechanisms behind these events. In this paper, we assessed the growth of two blooming dinoflagellates (Alexandrium minutum and Heterocapsa triquetra) and their susceptibility to infection by the generalist parasitoid Parvilucifera rostrata under a temperature gradient. The growth of the two dinoflagellates differed across a range of temperatures representative of the Penz{\'e} Estuary (13 to 22 {\textdegree}C) in early summer. A. minutum growth increased across this range and was the highest at 19 and 22 {\textdegree}C, whereas H. triquetra growth was maximal at intermediate temperatures (15{\textendash}18 {\textdegree}C). Interestingly, the effect of temperature on the parasitoid infectivity changed depending on which host dinoflagellate was infected with the dinoflagellate responses to temperature following a positive trend in A. minutum (higher infections at 20{\textendash}22 {\textdegree}C) and a unimodal trend in H. triquetra (higher infections at 18 {\textdegree}C). Low temperatures negatively affected parasitoid infections in both hosts (i.e., {\textquotedblleft}thermal refuge{\textquotedblright}). These results demonstrate how temperature shifts may not only affect bloom development in microalgal species but also their control by parasitoids.}, keywords = {dinoflagellate blooms, functional response, parasitic control, RCC2800, RCC2823, RCC2982, RCC3018, RCC4398, temperature effect}, issn = {2076-2607}, doi = {10.3390/microorganisms10020385}, url = {https://www.mdpi.com/2076-2607/10/2/385}, author = {Schmitt, Matthew and Telusma, Aaron and Bigeard, Estelle and Guillou, Laure and Alves-de-Souza, Catharina} } @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 {stewart_altitudinal_2021, title = {Altitudinal Zonation of Green Algae Biodiversity in the French Alps}, journal = {Frontiers in Plant Science}, volume = {12}, year = {2021}, pages = {1066}, abstract = {Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes.}, keywords = {rcc, RCC1055, RCC130, RCC1563, RCC2501, RCC2960, RCC3402, RCC443, RCC4743, RCC537, RCC581, RCC6, RCC7, RCC891}, issn = {1664-462X}, doi = {10.3389/fpls.2021.679428}, url = {https://www.frontiersin.org/article/10.3389/fpls.2021.679428}, author = {Stewart, Adeline and Rioux, Delphine and Boyer, Fr{\'e}deric and Gielly, Ludovic and Pompanon, Fran{\c c}ois and Saillard, Am{\'e}lie and Thuiller, Wilfried and Valay, Jean-Gabriel and Mar{\'e}chal, {\'E}ric and Coissac, Eric} } @article {thomy_combining_2021, title = {Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri}, journal = {Cells}, volume = {10}, number = {3}, year = {2021}, pages = {664}, abstract = {Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration occurred randomly at a single locus in the genome and mainly as a single copy. Thus, we confirmed the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci. Furthermore, we often observed variations in the vector sequence itself. From these observations, we speculate that a nonhomologous end-joining-like mechanism is employed during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in this ecologically important marine alga.}, keywords = {RCC1115, RCC7079, RCC7080, RCC7081, RCC7082, RCC7083, RCC7084, RCC7085}, issn = {2073-4409}, doi = {10.3390/cells10030664}, url = {https://www.mdpi.com/2073-4409/10/3/664}, author = {Thomy, Julie and Sanchez, Fr{\'e}d{\'e}ric and Gut, Marta and Cruz, Fernando and Alioto, Tyler and Piganeau, Gwenael and Grimsley, Nigel and Yau, Sheree} } @booklet {thomy_combining_2021, title = {Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri}, year = {2021}, month = {feb}, publisher = {LIFE SCIENCES}, type = {preprint}, abstract = {Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration appears to be random, occurring mainly at a single locus, and thus confirming the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci, and often within the vector sequence itself. From these observations, we speculate that a non-homologous end joining-like mechanism is required during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in ecologically important marine algae.}, keywords = {RCC1115}, doi = {10.20944/preprints202102.0506.v1}, url = {https://www.preprints.org/manuscript/202102.0506/v1}, author = {Thomy, Julie and Sanchez, Fr{\'e}d{\'e}ric and Gut, Marta and Cruz, Fernando and Alioto, Tyler and Piganeau, Gwenael and Grimsley, Nigel and Yau, Sheree} } @article {croteau_contrasting_2021, title = {Contrasting nonphotochemical quenching patterns under high light and darkness aligns with light niche occupancy in Arctic diatoms}, journal = {Limnology and Oceanography}, volume = {66}, number = {S1}, year = {2021}, note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.11587}, pages = {S231{\textendash}S245}, abstract = {Over the seasons, Arctic diatom species occupy shifting habitats defined by contrasting light climates, constrained by snow and ice cover dynamics interacting with extreme photoperiod and solar angle variations. How Arctic diatom photoadaptation strategies differ across their heterogeneous light niches remains a poorly documented but crucial missing link to anticipate Arctic Ocean responses to shrinking sea-ice and increasing light. To address this question, we selected five Arctic diatom species with diverse life traits, representative of distinct light niches across the seasonal light environment continuum: from snow-covered dimly lit bottom ice to summer stratified waters. We studied their photoacclimation plasticity to two growth light levels and the subsequent responses of their nonphotochemical quenching (NPQ) and xanthophyll cycle to both dark incubations and light shifts. We deciphered NPQ and xanthophyll cycle tuning in darkness and their light-dependent induction kinetics, which aligned with species{\textquoteright} light niche occupancy. In ice-related species, NPQ was sustained in darkness and its induction was more reactive to moderate light shifts. Open-water species triggered strong NPQ induction in darkness and reached higher maximal NPQ under high light. Marginal ice zone species showed strong adaptation to light fluctuations with a dark response fine-tuned depending upon light history. We argue these traits are anchored in diverging photoadaption strategies fostering Arctic diatom success in their respective light niches.}, keywords = {RCC2046, RCC2278, RCC5318}, issn = {1939-5590}, doi = {10.1002/lno.11587}, url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11587}, author = {Croteau, Dany and Gu{\'e}rin, S{\'e}bastien and Bruyant, Flavienne and Ferland, Joannie and Campbell, Douglas A. and Babin, Marcel and Lavaud, Johann} } @inbook {Paredes2021, title = {Cryopreservation of algae}, booktitle = {Cryopreservation and freeze-drying protocols}, volume = {2180}, year = {2021}, pages = {607{\textendash}621}, publisher = {Springer Science+Business Media, LLC}, organization = {Springer Science+Business Media, LLC}, keywords = {cryopreservation, macroalgae, Microalgae}, isbn = {978-1-07-160783-1}, doi = {10.1007/978-1-0716-0783-1_32}, url = {http://link.springer.com/10.1007/978-1-0716-0783-1_32}, author = {Paredes, Estefania and Ward, Angela and Probert, Ian and Gouhier, L{\'e}na and Campbell, Christine N.}, editor = {Wolkers, Willem F. and Oldenhof, Harriette} } @article {uwizeye_cytoklepty_2021, title = {Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae}, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, number = {27}, year = {2021}, note = {Publisher: National Academy of Sciences Section: Biological Sciences}, month = {jul}, abstract = {Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts (Phaeocystis) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition.}, keywords = {3D electron microscopy, oceanic plankton, Photosynthesis, rcc, rcc1383, single-cell transcriptomics, symbiosis}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.2025252118}, url = {https://www.pnas.org/content/118/27/e2025252118}, author = {Uwizeye, Clarisse and Brisbin, Margaret Mars and Gallet, Benoit and Chevalier, Fabien and LeKieffre, Charlotte and Schieber, Nicole L. and Falconet, Denis and Wangpraseurt, Daniel and Schertel, Lukas and Stryhanyuk, Hryhoriy and Musat, Niculina and Mitarai, Satoshi and Schwab, Yannick and Finazzi, Giovanni and Decelle, Johan} } @article {morais_detection_2021, title = {Detection of Alexandrium minutum dinoflagellate in environ- mental samples using electrochemical genosensor}, journal = {Chemistry Proceedings}, year = {2021}, pages = {7}, abstract = {Dinoflagellates are aquatic microorganisms that inhabit both salt and fresh waters. These microorganisms are mostly harmless, however, under certain conditions, some species rapidly reproduce forming water blooms that not only discolor the waters but also compromise the health of every organism in the vicinity, as some dinoflagellates produce potent toxins deemed unsafe for human health (e.g. Alexandrium minutum). In this work, a disposable electrochemical genosensor for the detection of the toxic dinoflagellate Alexandrium minutum was developed. The analytical platform methodology consisted in a sandwich format heterogeneous hybridization of complementary DNA sequences assay. The 70 bp A. minutum-specific targeting probe, the 45 bp fluorescein isothiocyanate-labelled signaling DNA probe and the 25 bp thiolated-DNA-capture probe were designed, after analyzing public databases. To maximize the complementary DNA hybridization and to avoid the formation of strong secondary structures, a mixed mercaptohexanol (MCH) and self-assembled monolayer (SAM) A. minutum-specific DNA-capture probe was immobilized onto disposable screen-printed gold electrodes (SPGE). Using chronoamperometric measurements, the enzymatic amplification of the electrochemical signal was obtained with a concentration range from 0.12 to 1.0 nM, a LD of 24.78 pM with a RSD < 5.2 \%. This electrochemical genosensor was successfully applied to the selective analysis of the targeted A. minutum specific region of denatured genomic DNA, extracted from toxic dinoflagellates present in the Atlantic Ocean.}, keywords = {? No DOI found, RCC3029}, author = {Morais, Stephanie L and Barros, Piedade and Santos, Marlene and Delerue-Matos, Cristina and Gomes, Andreia C and Barroso, M F{\'a}tima} } @article {robla_determination_2021, title = {Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters}, journal = {Environmental Science: Water Research \& Technology}, volume = {7}, number = {7}, year = {2021}, note = {Publisher: The Royal Society of Chemistry}, month = {jul}, pages = {1230{\textendash}1239}, abstract = {The most important question in sampling is {\textquotedblleft}Is the sample representative of the target population?{\textquotedblright} This question is necessary to understand how valid the sample taken is to the original population and if generalizations can be made from the sample. Samples taken for water quality measurement range from 1 mL for bacterial contamination to 100 mL or up to 1000 L for protozoan parasites. With larger samples taken, the confidence in detecting rare events increases dramatically. Here we illustrate that hollow fiber filters as routinely used for kidney dialysis can be adapted for environmental use. The filters retain all organisms down to viral particles and organic matter above 70 kDA, the molecular cutoff for urea, one of the waste products removed in kidney dialysis. With these filters, 50 liters of water can be filtered in about 90 minutes. Backflush of the filters recovers viable cells with minimal cell lysis that can be processed downstream for molecular analysis. Recovery rates were as high as 89\% and 75\% for phytoplankton and bacteria, respectively.}, keywords = {rcc, RCC1507}, issn = {2053-1419}, doi = {10.1039/D0EW00927J}, url = {https://pubs.rsc.org/en/content/articlelanding/2021/ew/d0ew00927j}, author = {Robla, J. and Garc{\'\i}a-Hierrro, J. and Alguacil, F. J. and Dittami, S. M. and Marie, D. and Villa, E. and Deragon, E. and Guillebault, D. and Mengs, G. and Medlin, L. K.} } @article {long_dinophyceae_2021, title = {Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)}, journal = {ISME Communications}, volume = {1}, number = {1}, year = {2021}, note = {Bandiera_abtest: a Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Microbial ecology;Plant ecology;Water microbiology Subject_term_id: microbial-ecology;plant-ecology;water-microbiology}, pages = {1{\textendash}10}, abstract = {Parasites in the genus Amoebophrya sp. infest dinoflagellate hosts in marine ecosystems and can be determining factors in the demise of blooms, including toxic red tides. These parasitic protists, however, rarely cause the total collapse of Dinophyceae blooms. Experimental addition of parasite-resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or exudates into a well-established host-parasite coculture (Scrippsiella acuminata-Amoebophrya sp.) mitigated parasite success and increased the survival of the sensitive host. This effect was mediated by waterborne molecules without the need for a physical contact. The strength of the parasite defenses varied between dinoflagellate species, and strains of A. minutum and was enhanced with increasing resistant host cell concentrations. The addition of resistant strains or exudates never prevented the parasite transmission entirely. Survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. Parasite progeny drastically decreased with both species. Integrity of the dinospore membrane was altered by A. minutum, providing a first indication on the mode of action of anti-parasitic molecules. These results demonstrate that extracellular defenses can be an effective strategy against parasites that protects not only the resistant cells producing them, but also the surrounding community.}, keywords = {microbial ecology, Plant ecology, rcc, RCC1627, RCC4383, RCC4714, RCC749, Water microbiology}, issn = {2730-6151}, doi = {10.1038/s43705-021-00035-x}, url = {http://www.nature.com/articles/s43705-021-00035-x}, author = {Long, Marc and Marie, Dominique and Szymczak, Jeremy and Toullec, Jordan and Bigeard, Estelle and Sourisseau, Marc and Le Gac, Micka{\"e}l and Guillou, Laure and Jauzein, C{\'e}cile} } @article {benites_evolutionary_2021, title = {Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage}, journal = {Genome Biology and Evolution}, volume = {13}, number = {10}, year = {2021}, pages = {evab216}, abstract = {Although sex is now accepted as a ubiquitous and ancestral feature of eukaryotes, direct observation of sex is still lacking in most unicellular eukaryotic lineages. Evidence of sex is frequently indirect and inferred from the identification of genes involved in meiosis from whole genome data and/or the detection of recombination signatures from genetic diversity in natural populations. In haploid unicellular eukaryotes, sex-related chromosomes are named mating-type (MTs) chromosomes and generally carry large genomic regions where recombination is suppressed. These regions have been characterized in Fungi and Chlorophyta and determine gamete compatibility and fusion. Two candidate MT{\th} and MT{\`A} alleles, spanning 450{\textendash}650 kb, have recently been described in Ostreococcus tauri, a marine phytoplanktonic alga from the Mamiellophyceae class, an early diverging branch in the green lineage. Here, we investigate the architecture and evolution of these candidate MT{\th} and MT{\`A} alleles. We analyzed the phylogenetic profile and GC content of MT gene families in eight different genomes whose divergence has been previously estimated at up to 640 Myr, and found evidence that the divergence of the two MT alleles predates speciation in the Ostreococcus genus. Phylogenetic profiles of MT transspecific polymorphisms in gametologs disclosed candidate MTs in two additional species, and possibly a third. These Mamiellales MT candidates are likely to be the oldest mating-type loci described to date, which makes them fascinating models to investigate the evolutionary mechanisms of haploid sex determination in eukaryotes.}, keywords = {RCC1105, RCC1115, RCC2590, RCC299, rcc3401, RCC4221, RCC809, RCC834}, issn = {1759-6653}, doi = {10.1093/gbe/evab216}, url = {https://academic.oup.com/gbe/article/doi/10.1093/gbe/evab216/6380139}, author = {Benites, Luis Felipe and Bucchini, Fran{\c c}ois and Sanchez-Brosseau, Sophie and Grimsley, Nigel and Vandepoele, Klaas and Piganeau, Gwenael}, editor = {Wolfe, Kenneth} } @article {bock_experimental_2021, title = {Experimental identification and in silico prediction of bacterivory in green algae}, journal = {The ISME Journal}, year = {2021}, note = {Publisher: Nature Publishing Group}, month = {mar}, pages = {1{\textendash}14}, abstract = {While algal phago-mixotrophs play a major role in aquatic microbial food webs, their diversity remains poorly understood. Recent studies have indicated several species of prasinophytes, early diverging green algae, to be able to consume bacteria for nutrition. To further explore the occurrence of phago-mixotrophy in green algae, we conducted feeding experiments with live fluorescently labeled bacteria stained with CellTracker Green CMFDA, heat-killed bacteria stained with 5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF), and magnetic beads. Feeding was detected via microscopy and/or flow cytometry in five strains of prasinophytes when provided with live bacteria: Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, and Dolichomastix tenuilepis CCMP3274. No feeding was detected when heat-killed bacteria or magnetic beads were provided, suggesting a strong preference for live prey in the strains tested. In parallel to experimental assays, green algal bacterivory was investigated using a gene-based prediction model. The predictions agreed with the experimental results and suggested bacterivory potential in additional green algae. Our observations underline the likelihood of widespread occurrence of phago-mixotrophy among green algae, while additionally highlighting potential biases introduced when using prey proxy to evaluate bacterial ingestion by algal cells.}, keywords = {RCC180, RCC3375, RCC369, RCC618}, issn = {1751-7370}, doi = {10.1038/s41396-021-00899-w}, url = {http://www.nature.com/articles/s41396-021-00899-w}, author = {Bock, Nicholas A. and Charvet, Sophie and Burns, John and Gyaltshen, Yangtsho and Rozenberg, Andrey and Duhamel, Solange and Kim, Eunsoo} } @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 {geffroy_sxta4_2021, title = {From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?}, journal = {Frontiers in Microbiology}, volume = {12}, year = {2021}, pages = {613199}, abstract = {Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster (sxt). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene (sxtA4), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9{\textendash}187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum.}, keywords = {RCC2644, RCC2645, RCC3327, RCC4871, RCC4872, RCC4890, RCC7037, RCC7038, RCC7039}, issn = {1664-302X}, doi = {10.3389/fmicb.2021.613199}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.613199/full}, author = {Geffroy, Sol{\`e}ne and Lechat, Marc-Marie and Le Gac, Micka{\"e}l and Rovillon, Georges-Augustin and Marie, Dominique and Bigeard, Estelle and Malo, Florent and Amzil, Zouher and Guillou, Laure and Caruana, Amandine M. N.} } @article {schapira_les_2021, title = {Les Efflorescences de Lepidodinium chlorophorum au large de la Loire et de la Vilaine : D{\'e}terminisme et cons{\'e}quences sur la qualit{\'e} des masses d{\textquoteright}eau c{\^o}ti{\`e}res}, year = {2021}, abstract = {Ce projet, organis{\'e} en trois actions, avait pour objectif de mieux {\'e}valuer les risques d{\textquoteright}eaux color{\'e}es vertes se produisant sur le secteur c{\^o}tier situ{\'e} au large de la Loire et de la Vilaine, en termes (i) de fr{\'e}quence de ces {\'e}pisodes, (ii) d{\textquoteright}abondance et (iii) de localisation des zones {\`a} risque. Action 1 : Am{\'e}lioration du recensement des eaux vertes {\`a} L. chlorophorum Action 2 : Optimisation de l{\textquoteright}estimation des abondances de L. chlorophorum Action 3 : Identification des zones {\`a} risque au large de la Loire et de la Vilaine.}, keywords = {? No DOI found, rcc, RCC1489}, url = {https://archimer.ifremer.fr/doc/00724/83598/}, author = {Schapira, Mathilde and Roux, Pauline and Andre, Coralie and Mertens, Kenneth and Bilien, Gwenael and Terre Terrillon, Aouregan and Le Gac-Abernot, Chantal and Siano, Raffaele and Qu{\'e}r{\'e}, Julien and Bizzozero, Lucie and Bonneau, Francoise and Bouget, Jean-Francois and Cochennec-Laureau, Nathalie and Collin, Karine and Fortune, Mireille and Gabellec, Raoul and Le Merrer, Yoann and Manach, Soazig and Pierre-Duplessix, Olivier and Retho, Michael and Schmitt, Anne and Souchu, Philippe and Stachowski-Haberkorn, Sabine} } @inbook {reddy_marine_2021, title = {Marine Biodiscovery in a Changing World}, booktitle = {Progress in the Chemistry of Organic Natural Products 116}, series = {Progress in the Chemistry of Organic Natural Products}, year = {2021}, pages = {1{\textendash}36}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {The term {\textquotedblleft}marine biodiscovery{\textquotedblright} has been recently been adopted to describe the area of marine natural products dedicated to the search of new drugs. Several maritime countries such as Australia, New Zealand, South Korea, and Japan as well as some European countries have invested significantly in this area of research over the last 50 years. In the late 2000s, research in this field has received significant interest and support in Ireland for exploring new marine bioresources from the nutrient-rich waters of the Northeastern Atlantic Ocean. Despite undeniable success exemplified by the marketing of new drugs, especially in oncology, the integration of new technical but also environmental aspects should be considered. Indeed, global change, particularly in our oceans, such as climate change, biodiversity loss, and the emergence of microbial pathogens, not only affects the environment but ultimately contributes to social inequalities. In this contribution, new avenues and best practices are proposed, such as the development of biorepositories and shared data for the future of marine biodiscovery research. The extension of this type of scientific work will allow humanity to finally make the optimum use of marine bioresources.}, keywords = {Bioprospecting, Biorepositories, Data management system, Marine biodiscovery, Marine natural products, Screenings, taxonomy}, isbn = {978-3-030-80560-9}, doi = {10.1007/978-3-030-80560-9_1}, url = {https://doi.org/10.1007/978-3-030-80560-9_1}, author = {Reddy, Maggie M. and Jennings, Laurence and Thomas, Olivier P.}, editor = {Kinghorn, A. Douglas and Falk, Heinz and Gibbons, Simon and Asakawa, Yoshinori and Liu, Ji-Kai and Dirsch, Verena M.} } @article {grebert_molecular_2021, title = {Molecular bases of an alternative dual-enzyme system for light color acclimation of marine \textit{Synechococcus cyanobacteria}, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, number = {9}, year = {2021}, pages = {e2019715118}, abstract = {

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

}, keywords = {RCC2374, to add}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.2019715118}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2019715118}, author = {Gr{\'e}bert, Th{\'e}ophile and Nguyen, Adam A. and Pokhrel, Suman and Joseph, Kes Lynn and Ratin, Morgane and Dufour, Louison and Chen, Bo and Haney, Allissa M. and Karty, Jonathan A. and Trinidad, Jonathan C. and Garczarek, Laurence and Schluchter, Wendy M. and Kehoe, David M. and Partensky, Fr{\'e}d{\'e}ric} } @article {uwizeye_morphological_2021, title = {Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging}, journal = {Nature Communications}, volume = {12}, number = {1}, year = {2021}, note = {Number: 1 Publisher: Nature Publishing Group}, month = {feb}, pages = {1{\textendash}12}, abstract = {Phytoplankton account for a large proportion of global primary production and comprise a number of phylogenetically distinct lineages. Here, Uwizeye et al. use FIB-SEM to study ultrastructural plasticity of 7 distinct taxa and describe how subcellular organisation is linked to energy metabolism.}, keywords = {RCC100, RCC4014, RCC827, RCC909}, issn = {2041-1723}, doi = {10.1038/s41467-021-21314-0}, url = {http://www.nature.com/articles/s41467-021-21314-0}, author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Flori, Serena and Gallet, Benoit and Keck, Jean-baptiste and Bo, Davide Dal and Moriscot, Christine and Seydoux, Claire and Chevalier, Fabien and Schieber, Nicole L. and Templin, Rachel and Allorent, Guillaume and Courtois, Florence and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C. and Falconet, Denis and Finazzi, Giovanni} } @article {decamp_new_2021, title = {A New, Quick, and Simple Protocol to Evaluate Microalgae Polysaccharide Composition}, journal = {Marine Drugs}, volume = {19}, number = {2}, year = {2021}, pages = {101}, abstract = {In this work, a new methodological approach, relying on the high specificity of enzymes in a complex mixture, was developed to estimate the composition of bioactive polysaccharides produced by microalgae, directly in algal cultures. The objective was to set up a protocol to target oligomers commonly known to be associated with exopolysaccharides{\textquoteright} (EPS) nutraceutical and pharmaceutical activities (i.e., rhamnose, fucose, acidic sugars, etc.) without the constraints classically associated with chromatographic methods, while maintaining a resolution sufficiently high to enable their monitoring in the culture system. Determination of the monosaccharide content required the application of acid hydrolysis (2 M trifluoroacetic acid) followed by NaOH (2 M) neutralization. Quantification was then carried out directly on the fresh hydrolysate using enzyme kits corresponding to the main monosaccharides in a pre-determined composition of the polysaccharides under analysis. Initial results showed that the enzymes were not sensitive to the presence of TFA and NaOH, so the methodology could be carried out on fresh hydrolysate. The limits of quantification of the method were estimated as being in the order of the log of nanograms of monosaccharides per well, thus positioning it among the chromatographic methods in terms of analytical performance. A comparative analysis of the results obtained by the enzymatic method with a reference method (high-performance anion-exchange chromatography) confirmed good recovery rates, thus validating the closeness of the protocol. Finally, analyses of raw culture media were carried out and compared to the results obtained in miliQ water; no differences were observed. The new approach is a quick, functional analysis method allowing routine monitoring of the quality of bioactive polysaccharides in algal cultures grown in photobioreactors.}, keywords = {rcc2380, RCC3438}, issn = {1660-3397}, doi = {10.3390/md19020101}, url = {https://www.mdpi.com/1660-3397/19/2/101}, author = {Decamp, Antoine and Michelo, Orane and Rabbat, Christelle and Laroche, C{\'e}line and Grizeau, Dominique and Pruvost, J{\'e}r{\'e}my and Gon{\c c}alves, Olivier} } @article {Farhat2021, title = {Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.}, journal = {BMC Biology}, year = {2021}, note = {Publisher: BMC Biology tex.mendeley-tags: RCC4383,RCC4398}, pages = {1{\textendash}21}, keywords = {Dinoflagellate, genome, Introner elements, Non-canonical introns, parasite, RCC4383, RCC4398}, doi = {10.1186/s12915-020-00927-9}, author = {Farhat, Sarah and Le, Phuong and Kayal, Ehsan and Noel, Benjamin and Bigeard, Estelle and Corre, Erwan and Maumus, Florian and Florent, Isabelle and Alberti, Adriana and Aury, Jean-Marc and Barbeyron, Tristan and Cai, Ruibo and Silva, Corinne Da and Istace, Benjamin and Labadie, Karine and Marie, Dominique and Mercier, Jonathan and Rukwavu, Tsinda and Szymczak, Jeremy and Tonon, Thierry and Alves-de-Souza, Catharina and Rouze, Pierre and de Peer, Yves Van and Wincker, Patrick and Rombauts, Stephane and Porcel, Betina M and Guillou, Laure} } @article {royer_response_2021, title = {Response of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas to oxidative stress in three phytoplankton species}, journal = {Journal of Plankton Research}, volume = {43}, number = {5}, year = {2021}, month = {sep}, pages = {673{\textendash}690}, abstract = {Several phytoplankton species produce the metabolites dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) but their intracellular roles need to be better understood. To improve the understanding of the DMSP antioxidant function suggested by Sunda et al. (2002), we exposed the diatom Skeletonema costatum, the Prymnesiophyceae Phaeocystis globosa and the dinoflagellate Heterocapsa triquetra to experimental treatments known to cause potential oxidative stress (high light intensities (HL); HL with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU); menadione sodium bisulfite (MSB)). DMSP and DMSO concentrations decreased after 6 h in all treatments indicating an interaction with Reactive Oxygen Species (ROS) produced. DMSP and DMSO-to-cell ratios in control conditions were higher for H. triquetra, while being unable to grow under HL. DMSP and DMSO-to-cell carbon were the highest for P. globosa, while the other species had similar values. During long-term treatment, these ratios were not increased in high-light grown cells of P. globosa and S. costatum. Overall, this illustrates that (1) the DMSP- and DMSO-to-cell or carbon seems to be not indicative of the capability of the species to tolerate an oxidative stress, (2) these molecules could react with ROS and lower their cellular concentration, but no clues demonstrated that these molecules are part of the antioxidant response of the cell.}, keywords = {rcc, RCC1719, RCC4800}, issn = {0142-7873}, doi = {10.1093/plankt/fbab052}, url = {https://doi.org/10.1093/plankt/fbab052}, author = {Royer, C and Gypens, N and Cardol, P and Borges, A V and Roberty, S} } @article {langer_role_2021, title = {Role of silicon in the development of complex crystal shapes in coccolithophores}, journal = {New Phytologist}, volume = {231}, number = {5}, year = {2021}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.17230}, pages = {1845{\textendash}1857}, abstract = {The development of calcification by the coccolithophores had a profound impact on ocean carbon cycling, but the evolutionary steps leading to the formation of these complex biomineralized structures are not clear. Heterococcoliths consisting of intricately shaped calcite crystals are formed intracellularly by the diploid life cycle phase. Holococcoliths consisting of simple rhombic crystals can be produced by the haploid life cycle stage but are thought to be formed extracellularly, representing an independent evolutionary origin of calcification. We use advanced microscopy techniques to determine the nature of coccolith formation and complex crystal formation in coccolithophore life cycle stages. We find that holococcoliths are formed in intracellular compartments in a similar manner to heterococcoliths. However, we show that silicon is not required for holococcolith formation and that the requirement for silicon in certain coccolithophore species relates specifically to the process of crystal morphogenesis in heterococcoliths. We therefore propose an evolutionary scheme in which the lower complexity holococcoliths represent an ancestral form of calcification in coccolithophores. The subsequent recruitment of a silicon-dependent mechanism for crystal morphogenesis in the diploid life cycle stage led to the emergence of the intricately shaped heterococcoliths, enabling the formation of the elaborate coccospheres that underpin the ecological success of coccolithophores.}, keywords = {biomineralization, Calcification, coccolith, coccolithophore, evolution, rcc, RCC1178, RCC1181, RCC1456, RCC1460, RCC1461, RCC1477, RCC1800, RCC1801, RCC3777, RCC6506, silicon}, issn = {1469-8137}, doi = {10.1111/nph.17230}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17230}, author = {Langer, Gerald and Taylor, Alison R. and Walker, Charlotte E. and Meyer, Erin M. and Ben Joseph, Oz and Gal, Assaf and Harper, Glenn M. and Probert, Ian and Brownlee, Colin and Wheeler, Glen L.} } @article {das_single_2021, title = {Single toxicity of arsenic and combined trace metal exposure to a microalga of ecological and commercial interest: Diacronema lutheri}, journal = {Chemosphere}, year = {2021}, pages = {132949}, abstract = {Eco-toxicological assays with species of economic interest such as Diacronema lutheri are essential for industries that produce aquaculture feed, natural food additives and also in drug developing industries. Our study involved the exposure of a single and combined toxicity of arsenic (As V) to D. lutheri for the entire algal growth phase and highlighted that a combined exposure of As V with other essential (Copper, Cu; Nickel, Ni) and non-essential (Cadmium, Cd; Lead, Pb) trace metals reduced significantly the cell number, chlorophyll a content, and also significantly increased the de-epoxidation ratio (DR) as a stress response when compared to the single toxicity of As V. Arsenic, as one of the ubiquitous trace metal and an active industrial effluent is reported to have an increased bio-concentration factor when in mixture with other trace metals in this study. In the combined exposure, the concentration of total As bio-accumulated by D. lutheri was higher than in the single exposure. Hence, polluted areas with the prevalence of multiple contaminants along with the highly toxic trace metals like As can impose a greater risk to the exposed organisms that may get further bio-magnified in the food chain. Our study highlights the consequences and the response of D. lutheri in terms of contamination from single and multiple trace metals in order to obtain a safer biomass production for the growing need of natural derivatives.}, keywords = {Arsenic, bioaccumulation, Bioconcentration factor, Chlorophyll, de-epoxidation ratio, RCC1537, Trace metals mixture}, issn = {0045-6535}, doi = {10.1016/j.chemosphere.2021.132949}, url = {https://www.sciencedirect.com/science/article/pii/S0045653521034214}, author = {Das, Shagnika and Gevaert, Fran{\c c}ois and Ouddane, Baghdad and Duong, Gwendoline and Souissi, Sami} } @article {graeff_sterol_2021, title = {Sterol Composition of the Peridinioid Dinoflagellate Zooxanthella nutricula, A Symbiont of Polycystine Radiolarians}, journal = {Protist}, volume = {172}, number = {3}, year = {2021}, month = {jul}, pages = {125817}, abstract = {Some dinoflagellates, such as Symbiodinium, are able to form symbiotic relationships with larger marine organisms. An important aspect of dinoflagellate symbiosis involves the exchange of lipids, namely sterols, from the symbiont to the host. Much research has explored the lipid biochemistry of the symbiotic relationship between cnidarians and Symbiodinium dinoflagellates. However, no research has addressed the sterol biochemistry of the symbiosis between radiolarians and dinoflagellates such as Zooxanthella nutricula. To this end, we have provided the first sterol characterization of Z. nutricula isolated from a spumellarian polycystine radiolarian. Fifteen sterols and one steroidal ketone were observed where the major sterol identified was C27 22-dehydrocholesterol, which does not tend to be a dominant sterol among dinoflagellates, including closely related peridinioid species in the genus Heterocapsa. However, C30 dinosterol and dinostanol were major sterols in both Z. nutricula and Heterocapsa spp., thus indicating common sterols between closely related taxa. Major sterols of the distantly related genus Symbiodinium, a symbiont of foraminifera and cnidarians, have included C27 cholesterol and C30 gorgosterol, whereas in Z. nutricula these sterols were minor and absent, respectively. Our results indicate potentially different sterol pools available to cnidarian and radiolarian symbiont hosts during their respective relationships with symbiotic dinoflagellates.}, keywords = {Dinoflagellate, lipid, Peridiniales, Radiolaria, rcc, RCC3387, sterol}, issn = {1434-4610}, doi = {10.1016/j.protis.2021.125817}, url = {https://www.sciencedirect.com/science/article/pii/S1434461021000262}, author = {Graeff, Jori E. and Leblond, Jeffrey D.} } @article {gebuhr_strain-specific_2021, title = {Strain-specific morphological response of the dominant calcifying phytoplankton species Emiliania huxleyi to salinity change}, journal = {PLOS ONE}, volume = {16}, number = {2}, year = {2021}, note = {Publisher: Public Library of Science}, month = {feb}, pages = {e0246745}, abstract = {The future physiology of marine phytoplankton will be impacted by a range of changes in global ocean conditions, including salinity regimes that vary spatially and on a range of short- to geological timescales. Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. Previous research has shown that the morphology of their exoskeletal calcified plates (coccoliths) responds to changing salinity in the most abundant coccolithophore species, Emiliania huxleyi. However, the extent to which these responses may be strain-specific is not well established. Here we investigated the growth response of six strains of E. huxleyi under low (ca. 25) and high (ca. 45) salinity batch culture conditions and found substantial variability in the magnitude and direction of response to salinity change across strains. Growth rates declined under low and high salinity conditions in four of the six strains but increased under both low and high salinity in strain RCC1232 and were higher under low salinity and lower under high salinity in strain PLYB11. When detailed changes in coccolith and coccosphere size were quantified in two of these strains that were isolated from contrasting salinity regimes (coastal Norwegian low salinity of ca. 30 and Mediterranean high salinity of ca. 37), the Norwegian strain showed an average 26\% larger mean coccolith size at high salinities compared to low salinities. In contrast, coccolith size in the Mediterranean strain showed a smaller size trend (11\% increase) but severely impeded coccolith formation in the low salinity treatment. Coccosphere size similarly increased with salinity in the Norwegian strain but this trend was not observed in the Mediterranean strain. Coccolith size changes with salinity compiled for other strains also show variability, strongly suggesting that the effect of salinity change on coccolithophore morphology is likely to be strain specific. We propose that physiological adaptation to local conditions, in particular strategies for plasticity under stress, has an important role in determining ecotype responses to salinity.}, keywords = {Calcification, Carbonates, Ecophysiology, Marine ecology, Marine geology, Morphometry, Paleoclimatology, rcc1210, RCC1232, rcc1824, rcc868, RCC904, salinity}, issn = {1932-6203}, doi = {10.1371/journal.pone.0246745}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246745}, author = {Geb{\"u}hr, Christina and Sheward, Rosie M. and Herrle, Jens O. and Bollmann, J{\"o}rg} } @article {decelle_subcellular_2021, title = {Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae}, journal = {bioRxiv}, year = {2021}, note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article}, pages = {2021.03.13.435225}, abstract = {Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the {\textquotedblleft}greenhouse-like{\textquotedblright} colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low 13C and 15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged.}, doi = {10.1101/2021.03.13.435225}, url = {https://www.biorxiv.org/content/10.1101/2021.03.13.435225v1}, author = {Decelle, Johan and Veronesi, Giulia and LeKieffre, Charlotte and Gallet, Benoit and Chevalier, Fabien and Stryhanyuk, Hryhoriy and Marro, Sophie and Ravanel, St{\'e}phane and Tucoulou, R{\'e}mi and Schieber, Nicole and Finazzi, Giovanni and Schwab, Yannick and Musat, Niculina} } @article {labban_temperature_2021, title = {Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain}, journal = {Frontiers in Microbiology}, volume = {12}, year = {2021}, pages = {612732}, abstract = {Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24{\textendash}34{\textdegree}C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94{\textendash}1.38 d{\textendash}1, was very similar (0.34 {\textpm} 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38{\textendash}24.4 d{\textendash}1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.}, keywords = {rcc, RCC546}, issn = {1664-302X}, doi = {10.3389/fmicb.2021.612732}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141594/}, author = {Labban, Abbrar and Palacio, Antonio S. and Garc{\'\i}a, Francisca C. and Hadaidi, Ghaida and Ansari, Mohd I. and L{\'o}pez-Urrutia, {\'A}ngel and Alonso-S{\'a}ez, Laura and Hong, Pei-Ying and Mor{\'a}n, Xos{\'e} Anxelu G.} } @booklet {roquis_tropical_2021, title = {The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching}, number = {6:195}, year = {2021}, note = {Type: article}, month = {jul}, publisher = {Wellcome Open Research}, abstract = {

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

}, keywords = {chromatin structure, Histone H3 clipping, invertebrate epigenetics, Pocillopora acuta, Pocillopora damicornis, rcc, RCC4017}, doi = {10.12688/wellcomeopenres.17058.1}, url = {https://wellcomeopenresearch.org/articles/6-195}, author = {Roquis, David and Cosseau, C{\'e}line and Raffalli, Kelly Brener and Romans, Pascal and Masanet, Patrick and Mitta, Guillaume and Grunau, Christoph and Vidal-Dupiol, Jeremie} } @article {bachy_viruses_2021, title = {Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts}, journal = {The ISME Journal}, year = {2021}, note = {Publisher: Nature Publishing Group}, month = {may}, pages = {1{\textendash}19}, abstract = {The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (\textasciitilde210 kb) than BI-Viruses and BII-V1. BII-Vs share \textasciitilde90\% of their proteins, and between 65\% to 83\% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.}, keywords = {RCC715, RCC716}, issn = {1751-7370}, doi = {10.1038/s41396-021-00989-9}, url = {https://www.nature.com/articles/s41396-021-00989-9}, author = {Bachy, Charles and Yung, Charmaine C. M. and Needham, David M. and Gazit{\'u}a, Maria Consuelo and Roux, Simon and Limardo, Alexander J. and Choi, Chang Jae and Jorgens, Danielle M. and Sullivan, Matthew B. and Worden, Alexandra Z.} } @article {Bestion2020, title = {Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment}, journal = {Ecology Letters}, volume = {23}, number = {3}, year = {2020}, note = {tex.mendeley-tags: RCC1303,RCC1512,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834}, month = {mar}, pages = {457{\textendash}466}, abstract = {Rising sea surface temperatures are expected to lead to the loss of phytoplankton biodiversity. However, we currently understand very little about the interactions between warming, loss of phytoplankton diversity and its impact on the oceans{\textquoteright} primary production. We experimentally manipulated the species richness of marine phytoplankton communities under a range of warming scenarios, and found that ecosystem production declined more abruptly with species loss in communities exposed to higher temperatures. Species contributing positively to ecosystem production in the warmed treatments were those that had the highest optimal temperatures for photosynthesis, implying that the synergistic impacts of warming and biodiversity loss on ecosystem functioning were mediated by thermal trait variability. As species were lost from the communities, the probability of taxa remaining that could tolerate warming diminished, resulting in abrupt declines in ecosystem production. Our results highlight the potential for synergistic effects of warming and biodiversity loss on marine primary production.}, keywords = {biodiversity, biodiversity loss, climate change, ecosystem functioning, phytoplankton, RCC1303, rcc1512, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal per-}, issn = {1461-023X}, doi = {10.1111/ele.13444}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13444}, author = {Bestion, Elvire and Barton, Samuel and Garc{\'\i}a, Francisca C. and Warfield, Ruth and Yvon-Durocher, Gabriel}, editor = {Hillebrand, Helmut} } @article {Palacio2020, title = {Changes in population age-structure obscure the temperature-size rule in marine cyanobacteria}, journal = {Frontiers in Microbiology}, volume = {11}, year = {2020}, note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC2382,RCC3377}, month = {aug}, pages = {2059}, abstract = {The temperature-size Rule (TSR) states that there is a negative relationship between ambient temperature and body size. This rule has been independently evaluated for different phases of the life cycle in multicellular eukaryotes, but mostly for the average population in unicellular organisms. We acclimated two model marine cyanobacterial strains (Prochlorococcus marinus MIT9301 and Synechococcus sp. RS9907) to a gradient of temperatures and measured the changes in population age-structure and cell size along their division cycle. Both strains displayed temperature-dependent diel changes in cell size, and as a result, the relationship between temperature and average cell size varied along the day. We computed the mean cell size of new-born cells in order to test the prediction of the TSR on a single-growth stage. Our work reconciles previous inconsistent results when testing the TSR on unicellular organisms, and shows that when a single-growth stage is considered the predicted negative response to temperature is revealed.}, keywords = {cell cycle, Cell Division, cell size, Prochlorococcus, rcc2382, RCC3377, Synechococcus, temperature, temperature-size rule}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.02059}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.02059/full}, author = {Palacio, Antonio S. and Cabello, Ana Mar{\'\i}a and Garc{\'\i}a, Francisca C. and Labban, Abbrar and Mor{\'a}n, Xos{\'e} Anxelu G. and Garczarek, Laurence and Alonso-S{\'a}ez, Laura and L{\'o}pez-Urrutia, {\'A}ngel} } @article {Mucko2020, title = {Characterization of a lipid-producing thermotolerant marine photosynthetic pico-alga in the genus Picochlorum (Trebouxiophyceae)}, journal = {European Journal of Phycology}, volume = {00}, number = {00}, year = {2020}, note = {Publisher: Taylor \& Francis tex.mendeley-tags: RCC1034,RCC13,RCC14,RCC289,RCC475,RCC6905,RCC846,RCC9,RCC945}, month = {aug}, pages = {1{\textendash}16}, keywords = {morphology, photosynthetic picoeukaryotes, phylogeny, physiology, Picochlorum, RCC1034, RCC13, RCC14, rcc289, RCC475, RCC6905, RCC846, RCC9, RCC945}, issn = {0967-0262}, doi = {10.1080/09670262.2020.1757763}, url = {https://doi.org/10.1080/09670262.2020.1757763 https://www.tandfonline.com/doi/full/10.1080/09670262.2020.1757763}, author = {Mucko, Maja and Padis{\'a}k, Judit and Gligora Udovi{\v c}, Marija and P{\'a}lmai, Tam{\'a}s and Novak, Tihana and Medi{\'c}, Nikola and Ga{\v s}parovi{\'c}, Bla{\v z}enka and Peharec {\v S}tefani{\'c}, Petra and Orli{\'c}, Sandi and Ljube{\v s}i{\'c}, Zrinka} } @article {Cai2020, title = {Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach}, journal = {Scientific Reports}, volume = {10}, number = {1}, year = {2020}, note = {Publisher: Springer US tex.mendeley-tags: RCC1627,RCC1720,RCC3018,RCC3043,RCC3044,RCC3047,RCC3048,RCC3049,RCC3145,RCC3278,RCC3596,RCC4381,RCC4382,RCC4383,RCC4384,RCC4385,RCC4386,RCC4387,RCC4388,RCC4389,RCC4390,RCC4391,RCC4392,RCC4393,RCC4394,RCC4395,RCC4396,RCC4397,RCC4398,RCC4399,RCC4400,RCC4401,RCC4402,RCC4403,RCC4404,RCC4405,RCC4406,RCC4407,RCC4408,RCC4409,RCC4410,RCC4411,RCC4412,RCC4413,RCC4414,RCC4415,RCC4416,RCC4711,RCC4712,RCC4713,RCC4715,RCC4716,RCC4722,RCC4723,RCC4726,RCC4728,RCC4729,RCC4732,RCC4733,RCC4734,RCC5984,RCC5985,RCC5986,RCC5987,RCC5988,RCC5989,RCC5990,RCC5991,RCC5992,RCC5993,RCC5994,RCC5995,RCC5997,RCC5998,RCC5999,RCC6000,RCC6001,RCC6002,RCC6003,RCC6004,RCC6005,RCC6006,RCC6007,RCC6008,RCC6009,RCC6010,RCC6079,RCC6080,RCC6081,RCC6082,RCC6083,RCC6084,RCC6085,RCC6087,RCC6088,RCC6094,RCC6096,RCC6100,RCC6101,RCC6102,RCC6103,RCC6104,RCC6105,RCC6106,RCC6107,RCC6108,RCC6109,RCC6110,RCC6111,RCC6112,RCC6113,RCC6115,RCC6116,RCC6117,RCC6118,RCC6119,RCC6120,RCC6121}, month = {dec}, pages = {2531}, keywords = {RCC1627, RCC1720, RCC3018, RCC3043, RCC3044, RCC3047, RCC3048, RCC3049, RCC3145, RCC3278, RCC3596, RCC4381, RCC4382, RCC4383, RCC4384, RCC4385, RCC4386, RCC4387, RCC4388, RCC4389, RCC4390, RCC4391, RCC4392, RCC4393, RCC4394, RCC4395, RCC4396, RCC4397, RCC4398, RCC4399, RCC4400, RCC4401, RCC4402, RCC4403, RCC4404, RCC4405, RCC4406, RCC4407, RCC4408, RCC4409, RCC4410, RCC4411, RCC4412, RCC4413, RCC4414, RCC4415, RCC4416, RCC4711, RCC4712, RCC4713, RCC4715, RCC4716, RCC4722, RCC4723, RCC4726, RCC4728, RCC4729, RCC4732, RCC4733, RCC4734, RCC5984, RCC5985, RCC5986, RCC5987, RCC5988, RCC5989, RCC5990, RCC5991, RCC5992, RCC5993, RCC5994, RCC5995, RCC5997, RCC5998, RCC5999, RCC6000, RCC6001, RCC6002, RCC6003, RCC6004, RCC6005, RCC6006, RCC6007, RCC6008, RCC6009, RCC6010, RCC6079, RCC6080, RCC6081, RCC6082, RCC6083, RCC6084, RCC6085, RCC6087, RCC6088, RCC6094, RCC6096, RCC6100, RCC6101, RCC6102, RCC6103, RCC6104, RCC6105, RCC6106, RCC6107, RCC6108, RCC6109, RCC6110, RCC6111, RCC6112, RCC6113, RCC6115, RCC6116, RCC6117, RCC6118, RCC6119, RCC6120, RCC6121}, issn = {2045-2322}, doi = {10.1038/s41598-020-59524-z}, url = {http://dx.doi.org/10.1038/s41598-020-59524-z http://www.nature.com/articles/s41598-020-59524-z}, author = {Cai, Ruibo and Kayal, Ehsan and Alves-de-Souza, Catharina and Bigeard, Estelle and Corre, Erwan and Jeanthon, Christian and Marie, Dominique and Porcel, Betina M and Siano, Raffaele and Szymczak, Jeremy and Wolf, Matthias and Guillou, Laure} } @article {Ribeiro2020, title = {Culturable diversity of Arctic phytoplankton during pack ice melting}, journal = {Elementa: Science of the Anthropocene}, volume = {8}, number = {1}, year = {2020}, note = {tex.mendeley-tags: RCC5197,RCC5198,RCC5199,RCC5200,RCC5201,RCC5202,RCC5203,RCC5204,RCC5205,RCC5206,RCC5207,RCC5208,RCC5209,RCC5210,RCC5211,RCC5212,RCC5213,RCC5214,RCC5215,RCC5216,RCC5217,RCC5218,RCC5219,RCC5220,RCC5221,RCC5222,RCC5223,RCC5224,RCC5225,RCC5226,RCC5227,RCC5228,RCC5229,RCC5230,RCC5231,RCC5232,RCC5233,RCC5234,RCC5235,RCC5236,RCC5237,RCC5238,RCC5239,RCC5240,RCC5241,RCC5242,RCC5243,RCC5244,RCC5245,RCC5246,RCC5247,RCC5248,RCC5249,RCC5250,RCC5251,RCC5252,RCC5253,RCC5254,RCC5255,RCC5256,RCC5257,RCC5258,RCC5259,RCC5260,RCC5261,RCC5262,RCC5263,RCC5264,RCC5265,RCC5266,RCC5267,RCC5268,RCC5269,RCC5270,RCC5271,RCC5272,RCC5273,RCC5274,RCC5275,RCC5276,RCC5277,RCC5278,RCC5279,RCC5280,RCC5281,RCC5282,RCC5283,RCC5284,RCC5285,RCC5286,RCC5287,RCC5288,RCC5289,RCC5290,RCC5291,RCC5292,RCC5293,RCC5294,RCC5295,RCC5296,RCC5297,RCC5298,RCC5299,RCC5300,RCC5301,RCC5302,RCC5303,RCC5304,RCC5305,RCC5306,RCC5307,RCC5308,RCC5309,RCC5310,RCC5311,RCC5312,RCC5313,RCC5314,RCC5315,RCC5316,RCC5317,RCC5318,RCC5319,RCC5320,RCC5321,RCC5322,RCC5323,RCC5324,RCC5325,RCC5326,RCC5327,RCC5328,RCC5329,RCC5330,RCC5331,RCC5332,RCC5333,RCC5334,RCC5335,RCC5336,RCC5337,RCC5338,RCC5339,RCC5340,RCC5341,RCC5342,RCC5343,RCC5344,RCC5345,RCC5346,RCC5347,RCC5348,RCC5349,RCC5350,RCC5351,RCC5352,RCC5353,RCC5354,RCC5355,RCC5356,RCC5357,RCC5358,RCC5359,RCC5360,RCC5361,RCC5362,RCC5363,RCC5364,RCC5365,RCC5366,RCC5367,RCC5368,RCC5369,RCC5370,RCC5371,RCC5372,RCC5373,RCC5374,RCC5375,RCC5376,RCC5377,RCC5378,RCC5379,RCC5380,RCC5381,RCC5382,RCC5383,RCC5384,RCC5385,RCC5386,RCC5387,RCC5388,RCC5389,RCC5390,RCC5391,RCC5392,RCC5393,RCC5394,RCC5395,RCC5396,RCC5397,RCC5398,RCC5399,RCC5400,RCC5401,RCC5402,RCC5403,RCC5404,RCC5405,RCC5406,RCC5407,RCC5408,RCC5409,RCC5410,RCC5411,RCC5412,RCC5413,RCC5414,RCC5415,RCC5416,RCC5417,RCC5418,RCC5419,RCC5420,RCC5421,RCC5422,RCC5423,RCC5424,RCC5425,RCC5426,RCC5427,RCC5428,RCC5429,RCC5430,RCC5431,RCC5432,RCC5433,RCC5434,RCC5435,RCC5436,RCC5437,RCC5438,RCC5439,RCC5440,RCC5441,RCC5442,RCC5443,RCC5444,RCC5445,RCC5446,RCC5447,RCC5448,RCC5449,RCC5450,RCC5451,RCC5452,RCC5453,RCC5454,RCC5455,RCC5456,RCC5457,RCC5458,RCC5459,RCC5460,RCC5461,RCC5462,RCC5463,RCC5464,RCC5465,RCC5466,RCC5467,RCC5468,RCC5469,RCC5470,RCC5471,RCC5472,RCC5473,RCC5474,RCC5475,RCC5476,RCC5477,RCC5478,RCC5479,RCC5480,RCC5481,RCC5482,RCC5483,RCC5484,RCC5485,RCC5486,RCC5487,RCC5488,RCC5489,RCC5490,RCC5491,RCC5492,RCC5493,RCC5494,RCC5495,RCC5496,RCC5497,RCC5498,RCC5499,RCC5500,RCC5501,RCC5502,RCC5503,RCC5504,RCC5505,RCC5506,RCC5507,RCC5508,RCC5509,RCC5510,RCC5511,RCC5512,RCC5513,RCC5514,RCC5515,RCC5516,RCC5517,RCC5518,RCC5519,RCC5520,RCC5521,RCC5522,RCC5523,RCC5524,RCC5525,RCC5526,RCC5527,RCC5528,RCC5529,RCC5530,RCC5531,RCC5532,RCC5533,RCC5534,RCC5535,RCC5536,RCC5537,RCC5538,RCC5539,RCC5540,RCC5541,RCC5542,RCC5543,RCC5544,RCC5545,RCC5546,RCC5547,RCC5548,RCC5549,RCC5550,RCC5551,RCC5552,RCC5553,RCC5554,RCC5555,RCC5556,RCC5557,RCC5558,RCC5559,RCC5560,RCC5561,RCC5562,RCC5563,RCC5564,RCC5565,RCC5566,RCC5567,RCC5568,RCC5569,RCC5570,RCC5571,RCC5572,RCC5573,RCC5574,RCC5575,RCC5576,RCC5577,RCC5578,RCC5579,RCC5580,RCC5581,RCC5582,RCC5583,RCC5584,RCC5585,RCC5586,RCC5587,RCC5588,RCC5589,RCC5590,RCC5591,RCC5592,RCC5593,RCC5594,RCC5595,RCC5596,RCC5597,RCC5598,RCC5599,RCC5600,RCC5601,RCC5602,RCC5603,RCC5604,RCC5605,RCC5606,RCC5607,RCC5608,RCC5609,RCC5610,RCC5611,RCC5612}, month = {feb}, pages = {6}, abstract = {Massive phytoplankton blooms develop at the Arctic ice edge, sometimes extending far under the pack ice. An extensive culturing effort was conducted before and during a phytoplankton bloom in Baffin Bay between April and July 2016. Different isolation strategies were applied, including flow cytometry cell sorting, manual single cell pipetting and serial dilution. Although all three techniques yielded the most common organisms, each technique retrieved specific taxa, highlighting the importance of using several methods to maximize the number and diversity of isolated strains. More than 1,000 cultures were obtained, characterized by 18S rRNA sequencing and optical microscopy and de-replicated to a subset of 276 strains presented in this work. Strains grouped into 57 genotypes defined by 100\% 18S rRNA sequence similarity. These genotypes spread across five divisions: Heterokontophyta, Chlorophyta, Cryptophyta, Haptophyta and Dinophyta. Diatoms were the most abundant group (193 strains), mostly represented by the genera Chaetoceros and Attheya. The genera Rhodomonas and Pyramimonas were the most abundant non-diatom nanoplankton strains, while Micromonas polaris dominated the picoplankton. Diversity at the class level was higher during the peak of the bloom. Potentially new species were isolated, in particular within the genera Navicula, Nitzschia, Coscinodiscus, Thalassiosira, Pyramimonas, Mantoniella and Isochrysis.}, keywords = {RCC5197, RCC5198, RCC5199, RCC5200, RCC5201, RCC5202, RCC5203, RCC5204, RCC5205, RCC5206, RCC5207, RCC5208, RCC5209, RCC5210, RCC5211, RCC5212, RCC5213, RCC5214, RCC5215, RCC5216, RCC5217, RCC5218, RCC5219, RCC5220, RCC5221, RCC5222, RCC5223, RCC5224, RCC5225, RCC5226, RCC5227, RCC5228, RCC5229, RCC5230, RCC5231, RCC5232, RCC5233, RCC5234, RCC5235, RCC5236, RCC5237, RCC5238, RCC5239, RCC5240, RCC5241, RCC5242, RCC5243, RCC5244, RCC5245, RCC5246, RCC5247, RCC5248, RCC5249, RCC5250, RCC5251, RCC5252, RCC5253, RCC5254, RCC5255, RCC5256, RCC5257, RCC5258, RCC5259, RCC5260, RCC5261, RCC5262, RCC5263, RCC5264, RCC5265, RCC5266, RCC5267, RCC5268, RCC5269, RCC5270, RCC5271, RCC5272, RCC5273, RCC5274, RCC5275, RCC5276, RCC5277, RCC5278, RCC5279, RCC5280, RCC5281, RCC5282, RCC5283, RCC5284, RCC5285, RCC5286, RCC5287, RCC5288, RCC5289, RCC5290, RCC5291, RCC5292, RCC5293, RCC5294, RCC5295, RCC5296, RCC5297, RCC5298, RCC5299, RCC5300, RCC5301, RCC5302, RCC5303, RCC5304, RCC5305, RCC5306, RCC5307, RCC5308, RCC5309, RCC5310, RCC5311, RCC5312, RCC5313, RCC5314, RCC5315, RCC5316, RCC5317, RCC5318, RCC5319, RCC5320, RCC5321, RCC5322, RCC5323, RCC5324, RCC5325, RCC5326, RCC5327, RCC5328, RCC5329, RCC5330, RCC5331, RCC5332, RCC5333, RCC5334, RCC5335, RCC5336, RCC5337, RCC5338, RCC5339, RCC5340, RCC5341, RCC5342, RCC5343, RCC5344, RCC5345, RCC5346, RCC5347, RCC5348, RCC5349, RCC5350, RCC5351, RCC5352, RCC5353, RCC5354, RCC5355, RCC5356, RCC5357, RCC5358, RCC5359, RCC5360, RCC5361, RCC5362, RCC5363, RCC5364, RCC5365, RCC5366, RCC5367, RCC5368, RCC5369, RCC5370, RCC5371, RCC5372, RCC5373, RCC5374, RCC5375, RCC5376, RCC5377, RCC5378, RCC5379, RCC5380, RCC5381, RCC5382, RCC5383, RCC5384, RCC5385, RCC5386, RCC5387, RCC5388, RCC5389, RCC5390, RCC5391, RCC5392, RCC5393, RCC5394, RCC5395, RCC5396, RCC5397, RCC5398, RCC5399, RCC5400, RCC5401, RCC5402, RCC5403, RCC5404, RCC5405, RCC5406, RCC5407, RCC5408, RCC5409, RCC5410, RCC5411, RCC5412, RCC5413, RCC5414, RCC5415, RCC5416, RCC5417, RCC5418, RCC5419, RCC5420, RCC5421, RCC5422, RCC5423, RCC5424, RCC5425, RCC5426, RCC5427, RCC5428, RCC5429, RCC5430, RCC5431, RCC5432, RCC5433, RCC5434, RCC5435, RCC5436, RCC5437, RCC5438, RCC5439, RCC5440, RCC5441, RCC5442, RCC5443, RCC5444, RCC5445, RCC5446, RCC5447, RCC5448, RCC5449, RCC5450, RCC5451, RCC5452, RCC5453, RCC5454, RCC5455, RCC5456, RCC5457, RCC5458, RCC5459, RCC5460, RCC5461, RCC5462, RCC5463, RCC5464, RCC5465, RCC5466, RCC5467, RCC5468, RCC5469, RCC5470, RCC5471, RCC5472, RCC5473, RCC5474, RCC5475, RCC5476, RCC5477, RCC5478, RCC5479, RCC5480, RCC5481, RCC5482, RCC5483, RCC5484, RCC5485, RCC5486, RCC5487, RCC5488, RCC5489, RCC5490, RCC5491, RCC5492, RCC5493, RCC5494, RCC5495, RCC5496, RCC5497, RCC5498, RCC5499, RCC5500, RCC5501, RCC5502, RCC5503, RCC5504, RCC5505, RCC5506, RCC5507, RCC5508, RCC5509, RCC5510, RCC5511, RCC5512, RCC5513, RCC5514, RCC5515, RCC5516, RCC5517, RCC5518, RCC5519, RCC5520, RCC5521, RCC5522, RCC5523, RCC5524, RCC5525, RCC5526, RCC5527, RCC5528, RCC5529, RCC5530, RCC5531, RCC5532, RCC5533, RCC5534, RCC5535, RCC5536, RCC5537, RCC5538, RCC5539, RCC5540, RCC5541, RCC5542, RCC5543, RCC5544, RCC5545, RCC5546, RCC5547, RCC5548, RCC5549, RCC5550, RCC5551, RCC5552, RCC5553, RCC5554, RCC5555, RCC5556, RCC5557, RCC5558, RCC5559, RCC5560, RCC5561, RCC5562, RCC5563, RCC5564, RCC5565, RCC5566, RCC5567, RCC5568, RCC5569, RCC5570, RCC5571, RCC5572, RCC5573, RCC5574, RCC5575, RCC5576, RCC5577, RCC5578, RCC5579, RCC5580, RCC5581, RCC5582, RCC5583, RCC5584, RCC5585, RCC5586, RCC5587, RCC5588, RCC5589, RCC5590, RCC5591, RCC5592, RCC5593, RCC5594, RCC5595, RCC5596, RCC5597, RCC5598, RCC5599, RCC5600, RCC5601, RCC5602, RCC5603, RCC5604, RCC5605, RCC5606, RCC5607, RCC5608, RCC5609, RCC5610, RCC5611, RCC5612}, issn = {2325-1026}, doi = {10.1525/elementa.401}, url = {https://www.biorxiv.org/content/10.1101/642264v1 https://www.elementascience.org/article/10.1525/elementa.401/}, author = {Ribeiro, Catherine G{\'e}rikas and dos Santos, Adriana Lopes and Gourvil, Priscillia and Le Gall, Florence and Marie, Dominique and Tragin, Margot and Probert, Ian and Vaulot, Daniel} } @article {Wittek2020, title = {Dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas variations arising from sea ice shifts of salinity and temperature in the Prymnesiophyceae Phaeocystis antarctica}, journal = {Environmental Chemistry}, year = {2020}, note = {tex.mendeley-tags: RCC4023}, abstract = {Environmental context. Dimethylsulfoniopropionate and dimethylsulfoxide could have a climatic influence especially in the polar areas. We investigate the effect of sea ice salinity and temperature on the production of these two sulfur metabolites by a polar microalga, and suggest their potential roles of osmoregulator and cryoprotectant. These results bring new information about the sulfur cycle in sea ice that is useful for climate models.. The Southern Ocean, which includes the seasonal ice zone (SIZ), is a source of large sea-air fluxes of dimethylsulfide (DMS), a climate active gas involved in Earth cooling processes. In this area, the prymnesiophyte Phaeocystis antarctica (P. antarctica) is one of the main producers of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO), two metabolites that are precursors of DMS. These algae are also present in sea ice and contribute substantially to the high DMSP and DMSO concentrations observed in this habitat. DMSP and DMSO production in sea ice by P. antarctica is proposed to be promoted by its ability to live in extreme environmental conditions. We designed cell culture experiments to test that hypothesis, focusing on the impact of shifts of temperature and salinity on the DMSP and DMSO cell quotas. Our experiments show an increase in DMSP and DMSO cell quotas following shifts in salinity (34 to 75, at 4 {\textdegree}C), which suggests a potential osmoregulator function for both DMSP and DMSO. Stronger salinity shifts (up to 100) directly impact cell growth and induce a crash of the cultures. Combining the salinity (34 to 75) and temperature (4 {\textdegree}C to {\textendash}2.3 {\textdegree}C) shifts induces higher increases of DMSP and DMSO cell quotas that also suggests an implication of both metabolites in a cryoprotectant system. Experimental cell quotas (including diatom Fragilariopsis cylindrus quotas from a previous study) are then used to reconstruct DMSP and DMSO profiles in sea ice based on the biomass and taxonomy. Finally, the complexity of the transposition of rates obtained in the experimental domain to the real world is discussed.}, keywords = {RCC4023}, doi = {10.1071/EN19302}, url = {https://doi.org/10.1071/EN19302}, author = {Wittek, Boris and Carnat, Gauthier and Delille, Bruno and Tison, Jean-Louis and Gypens, Nathalie} } @article {Altenburger2020, title = {Dimorphism in cryptophytes{\textemdash}The case of Teleaulax amphioxeia / Plagioselmis prolonga and its ecological implications}, journal = {Science Advances}, volume = {6}, number = {37}, year = {2020}, note = {tex.mendeley-tags: RCC5152}, month = {sep}, pages = {eabb1611}, abstract = {Growing evidence suggests that sexual reproduction might be common in unicellular organisms, but observations are sparse. Limited knowledge of sexual reproduction constrains understanding of protist ecology. Although Teleaulax amphioxeia and Plagioselmis prolonga are common marine cryptophytes worldwide, and are also important plastid donors for some kleptoplastic ciliates and dinoflagellates, the ecology and development of these protists are poorly known. We demonstrate that P. prolonga is the haploid form of the diploid T. amphioxeia and describe the seasonal dynamics of these two life stages. The diploid T. amphioxeia dominates during periods of high dissolved inorganic nitrogen (DIN) and low irradiance, temperature, and grazing (winter and early spring), whereas the haploid P. prolonga becomes more abundant during the summer, when DIN is low and irradiance, temperature, and grazing are high. Dimorphic sexual life cycles might explain the success of this species by fostering high genetic diversity and enabling endurance in adverse conditions.}, keywords = {RCC5152}, issn = {2375-2548}, doi = {10.1126/sciadv.abb1611}, url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.abb1611}, author = {Altenburger, A and Blossom, H E and Garcia-Cuetos, L. and Jakobsen, H H and Carstensen, J and Lundholm, N. and Hansen, P. J. and Moestrup, {\O}. and Haraguchi, L.} } @article {Kayal2020, title = {Dinoflagellate host chloroplasts and mitochondria remain functional during amoebophrya infection}, journal = {Frontiers in Microbiology}, volume = {11}, number = {December}, year = {2020}, note = {tex.mendeley-tags: RCC1627,RCC4398}, month = {dec}, pages = {1{\textendash}11}, abstract = {Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya . We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.}, keywords = {amoebophrya, chloroplast, Dinoflagellate, frontiers in microbiology, frontiersin, kleptoplast, marine plankton, org, organelles, parasitism, RCC1627, RCC4398, www}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.600823}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.600823/full}, author = {Kayal, Ehsan and Alves-de-Souza, Catharina and Farhat, Sarah and Velo-Suarez, Lourdes and Monjol, Joanne and Szymczak, Jeremy and Bigeard, Estelle and Marie, Dominique and Noel, Benjamin and Porcel, Betina M and Corre, Erwan and Six, Christophe and Guillou, Laure} } @article {Fitzsimons2020, title = {Dissolved organic phosphorus uptake by marine phytoplankton is enhanced by the presence of dissolved organic nitrogen}, journal = {Journal of Experimental Marine Biology and Ecology}, volume = {530-531}, number = {July}, year = {2020}, note = {Publisher: Elsevier tex.mendeley-tags: RC2563,RCC2565}, month = {sep}, pages = {151434}, abstract = {Organic nutrients can constitute the major fractions (up to 70\%) of aquatic nitrogen (N) and phosphorus (P), but their cycling is poorly understood relative to the inorganic pools. Some phytoplankton species access P from the dissolved organic phosphorus (DOP) pool through expression of alkaline phosphatase (AP), which hydrolyses orthophosphate from organic molecules, and is thought to occur either at low concentrations of dissolved inorganic P (DIP), or elevated ratios of dissolved inorganic N (DIN) to DIP. Three algal strains native to the North-East Atlantic Ocean (coccolithophore, dinoflagellate and diatom species) were grown under representative, temperate conditions, and the dissolved N and P components amended to include dissolved organic N (DON) and DOP. The activity of AP was measured to determine the rate of DOP uptake by each algal species. The addition of DON and DOP enhanced the growth of the algal species, regardless of DIN and DIP concentrations. In cultures where the total concentrations and absolute N: P ratio was unchanged but the N pool included both DON and DIN, an increase in alkaline phosphatase activity (APA) was measured. This suggested that the presence of DON triggered the selective uptake of DOP. The uptake of organic P was confirmed by detection of adenosine in DOP-amended culture media, indicating that P had been cleaved from ADP and ATP added to the media as DOP, and cellular P concentration in these cultures exceeded the calculated concentration based on uptake of DIP only. Our data demonstrates that organic nutrients can enhance and sustain marine algal productivity. The findings have implications for marine ecosystem function and health, since climate change scenarios predict variable riverine inputs to coastal areas, altered N: P ratios, and changes in the inorganic to organic balance of the nutrient pools.}, keywords = {Alkaline phosphatase, COASTAL WATERS, Dissolved organic nitrogen, Dissolved organic phosphorus, Marine algae, P-limitation, RCC2563, RCC2565}, issn = {00220981}, doi = {10.1016/j.jembe.2020.151434}, url = {https://doi.org/10.1016/j.jembe.2020.151434 https://linkinghub.elsevier.com/retrieve/pii/S0022098119304666}, author = {Fitzsimons, Mark F. and Probert, Ian and Gaillard, Fanny and Rees, Andrew P.} } @article {Arsenieff2020, title = {Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel}, journal = {The ISME Journal}, year = {2020}, note = {Publisher: Springer US tex.mendeley-tags: RCC4657,RCC4658,RCC4659,RCC4660,RCC4661,RCC4662,RCC4663,RCC4664,RCC4665,RCC4666,RCC5154,RCC5839,RCC5840,RCC5841,RCC5842,RCC5843,RCC5844,RCC5845,RCC5846,RCC5847,RCC5848,RCC5849,RCC5850,RCC5851,RCC5852,RCC5853,RCC5854,RCC5855,RCC5856,RCC5857,RCC5859,RCC5860,RCC5861,RCC5862,RCC5863,RCC5864,RCC5865,RCC5866,RCC5867,RCC5868,RCC5869,RCC5870,RCC5871,RCC5872,RCC5873,RCC5875,RCC5876,RCC5877,RCC5878,RCC5879,RCC5880,RCC5881,RCC5882,RCC5883,RCC5884,RCC5885,RCC5886,RCC5887,RCC5921}, month = {apr}, keywords = {RCC4657, RCC4658, RCC4659, RCC4660, RCC4661, RCC4662, RCC4663, RCC4664, RCC4665, RCC4666, RCC5154, RCC5839, RCC5840, RCC5841, RCC5842, RCC5843, RCC5844, RCC5845, RCC5846, RCC5847, RCC5848, RCC5849, RCC5850, RCC5851, RCC5852, RCC5853, RCC5854, RCC5855, RCC5856, RCC5857, RCC5859, RCC5860, RCC5861, RCC5862, RCC5863, RCC5864, RCC5865, RCC5866, RCC5867, RCC5868, RCC5869, RCC5870, RCC5871, RCC5872, RCC5873, RCC5875, RCC5876, RCC5877, RCC5878, RCC5879, RCC5880, RCC5881, RCC5882, RCC5883, RCC5884, RCC5885, RCC5886, RCC5887, RCC5921}, issn = {1751-7362}, doi = {10.1038/s41396-020-0659-6}, url = {http://dx.doi.org/10.1038/s41396-020-0659-6 http://www.nature.com/articles/s41396-020-0659-6}, author = {Arsenieff, Laure and Le Gall, Florence and Rigaut-jalabert, Fabienne and Mah{\'e}, Fr{\'e}d{\'e}ric and Sarno, Diana and Gouhier, L{\'e}na and Baudoux, Anne-claire and Simon, Nathalie} } @article {Klintzsch2020, title = {Effects of temperature and light on methane production of widespread marine phytoplankton}, journal = {Journal of Geophysical Research: Biogeosciences}, volume = {125}, number = {9}, year = {2020}, note = {Publisher: American Geophysical Union (AGU) tex.mendeley-tags: RCC1216}, month = {sep}, keywords = {RCC1216}, issn = {2169-8953}, doi = {10.1029/2020jg005793}, url = {https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2020JG005793 https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020JG005793 https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020JG005793}, author = {Klintzsch, T. and Langer, G. and Wieland, A. and Geisinger, H. and Lenhart, K. and Nehrke, G. and Keppler, F.} } @article {Morais2020, title = {Electrochemical genosensor for the detection of Alexandrium minutum dinoflagellates}, journal = {Talanta}, year = {2020}, note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC3029}, pages = {121416}, keywords = {RCC3029}, issn = {00399140}, doi = {10.1016/j.talanta.2020.121416}, url = {https://doi.org/10.1016/j.talanta.2020.121416 https://linkinghub.elsevier.com/retrieve/pii/S0039914020307074}, author = {Morais, Stephanie L. and Barros, Piedade and Santos, Marlene and Delerue-Matos, Cristina and Gomes, Andreia C. and F{\'a}tima Barroso, M.} } @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 {Carrillo2020, title = {Identification and characterization of ChlreSEX4, a novel glucan phosphatase from Chlamydomonas reinhardtii green alga}, journal = {Archives of Biochemistry and Biophysics}, volume = {680}, year = {2020}, note = {Publisher: Academic Press Inc.}, month = {feb}, pages = {108235}, abstract = {Chlamydomonas reinhardtii is the best known unicellular green alga model which has long been used to investigate all kinds of cellular processes, including starch metabolism. Here we identified and characterized a novel enzyme, ChlreSEX4, orthologous to glucan phosphatase SEX4 from Arabidopsis thaliana, that is capable of binding and dephosphorylating amylopectin in vitro. We also reported that cysteine 224 and tryptophan 305 residues are critical for enzyme catalysis and substrate binding. Furthermore, we verified that ChlreSEX4 gene is expressed in vivo and that glucan phosphatase activity is measurable in Chlamydomonas protein extracts. In view of the results presented, we suggest ChlreSEX4 as a functional phosphoglucan phosphatase from C. reinhardtii. Our data obtained so far contribute to understanding the phosphoglucan phosphatases evolutionary process in the green lineage and their role in starch reversible phosphorylation. In addition, this allows to position Chlamydomonas as a potential tool to obtain starches with different degrees of phosphorylation for industrial or biotechnological purposes.}, keywords = {Chlamydomonas Reinhardtii, ChlreSEX4, Glucan phosphatase, SEX4, Starch phosphorylation}, issn = {10960384}, doi = {10.1016/j.abb.2019.108235}, author = {Carrillo, Julieta B. and Torresi, Florencia and Morales, Luisina L. and Ricordi, Micaela and Gomez-Casati, Diego F. and Busi, Maria V. and Mart{\'\i}n, Mariana} } @article {Baumeister2020, title = {Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry}, journal = {Metabolomics}, volume = {16}, number = {3}, year = {2020}, note = {ISBN: 0123456789 Publisher: Springer US tex.mendeley-tags: RCC 4667,RCC1717,RCC2561,RCC2562,RCC3008,RCC5791,RCC6807,RCC6808,RCC6809,RCC6810,RCC6811,RCC6812,RCC6813,RCC6814,RCC6815,RCC6816,RCC6817,RCC6818,RCC6819,RCC6820,RCC6821}, month = {mar}, pages = {28}, keywords = {ionization high-, Live single-cell mass spectrometry, matrix-free laser desorption, Matrix-free laser desorption/ionization high-resol, Metabolic fingerprinting, Microalgal identification, RCC1717, RCC2561, RCC2562, RCC3008, RCC4667, RCC5791, RCC6807, RCC6808, RCC6809, RCC6810, RCC6811, RCC6812, RCC6813, RCC6814, RCC6815, RCC6816, RCC6817, RCC6818, RCC6819, RCC6820, RCC6821, resolution mass spectrometry, Spectral pattern matching, Spectrum similarity}, issn = {1573-3882}, doi = {10.1007/s11306-020-1646-7}, url = {https://doi.org/10.1007/s11306-020-1646-7 http://link.springer.com/10.1007/s11306-020-1646-7}, author = {Baumeister, Tim U H and Vallet, Marine and Kaftan, Filip and Guillou, Laure and Svato{\v s}, Ale{\v s} and Pohnert, Georg} } @article {Uwizeye2020, title = {In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy}, journal = {bioRxiv}, year = {2020}, note = {tex.mendeley-tags: RCC100,RCC4014,RCC827,RCC909}, month = {jan}, pages = {2020.05.19.104166}, abstract = {Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.Competing Interest StatementThe authors have declared no competing interest.}, keywords = {RCC100, RCC4014, RCC827, RCC909}, doi = {10.1101/2020.05.19.104166}, url = {http://biorxiv.org/content/early/2020/05/20/2020.05.19.104166.abstract}, author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Gallet, Benoit and Keck, Jean-baptiste and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni and Moriscot, Christine and Chevalier, Fabien and Schieber, Nicole L and Templin, Rachel and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni} } @article {Vigor2020, title = {Isoprostanoid profiling of marine microalgae}, journal = {Biomolecules}, volume = {10}, number = {7}, year = {2020}, note = {Publisher: MDPI AG tex.mendeley-tags: RCC1349,RCC20,RCC69}, month = {jul}, pages = {1073}, abstract = {{\textexclamdown}p{\textquestiondown}Algae result from a complex evolutionary history that shapes their metabolic network. For example, these organisms can synthesize different polyunsaturated fatty acids, such as those found in land plants and oily fish. Due to the presence of numerous double-bonds, such molecules can be oxidized nonenzymatically, and this results in the biosynthesis of high-value bioactive metabolites named isoprostanoids. So far, there have been only a few studies reporting isoprostanoid productions in algae. To fill this gap, the current investigation aimed at profiling isoprostanoids by liquid chromatography -mass spectrometry/mass spectrometry (LC-MS/MS) in four marine microalgae. A good correlation was observed between the most abundant polyunsaturated fatty acids (PUFAs) produced by the investigated microalgal species and their isoprostanoid profiles. No significant variations in the content of oxidized derivatives were observed for Rhodomonas salina and Chaetoceros gracilis under copper stress, whereas increases in the production of C18-, C20- and C22-derived isoprostanoids were monitored in Tisochrysis lutea and Phaeodactylum tricornutum. In the presence of hydrogen peroxide, no significant changes were observed for C. gracilis and for T. lutea, while variations were monitored for the other two algae. This study paves the way to further studying the physiological roles of isoprostanoids in marine microalgae and exploring these organisms as bioresources for isoprostanoid production.{\textexclamdown}/p{\textquestiondown}}, keywords = {Isoprostanoids, Micro-LC-MS/MS, Microalgae, Oxidative stress, PUFAs, RCC1349, RCC20, RCC69}, issn = {2218-273X}, doi = {10.3390/biom10071073}, url = {https://www.mdpi.com/2218-273X/10/7/1073}, author = {Vigor, Claire and Oger, Camille and Reversat, Guillaume and Rocher, Amandine and Zhou, Bingqing and Linares-Maurizi, Amandyne and Guy, Alexandre and Bultel-Ponc{\'e}, Val{\'e}rie and Galano, Jean-Marie and Vercauteren, Joseph and Durand, Thierry and Potin, Philippe and Tonon, Thierry and Leblanc, Catherine} } @article {Langer2020, title = {Li partitioning into coccoliths of Emiliania huxleyi : evaluating the general role of {\textquotedblleft}vital effects{\textquotedblright} in explaining element partitioning in biogenic carbonates}, journal = {Geochemistry, Geophysics, Geosystems}, year = {2020}, note = {ISBN: 0000000272 tex.mendeley-tags: RCC3652}, month = {jun}, pages = {0{\textendash}2}, abstract = {Abstract Emiliania huxleyi cells were grown in artificial seawater of different Li and Ca concentrations and coccolith Li/Ca ratios determined. Coccolith Li/Ca ratios were positively correlated to seawater Li/Ca ratios only if the seawater Li concentration was changed, not if the seawater Ca concentration was changed. This Li partitioning pattern of E. huxleyi was previously also observed in the benthic foraminifer Amphistegina lessonii and inorganically precipitated calcite. We argue that Li partitioning in both E. huxleyi and A. lessonii is dominated by a coupled transmembrane transport of Li and Ca from seawater to the site of calcification. We present a refined version of a recently proposed transmembrane transport model for Li and Ca. The model assumes that Li and Ca enter the cell via Ca channels, the Li flux being dependent on the Ca flux. While the original model features a linear function to describe the experimental data, our refined version uses a power function, changing the stoichiometry of Li and Ca. The version presented here accurately predicts the observed dependence of DLi on seawater Li/Ca ratios. Our data demonstrate that minor element partitioning in calcifying organisms is partly mediated by biological processes even if the partitioning behaviour of the calcifying organism is indistinguishable from that of inorganically precipitated calcium carbonate.}, keywords = {RCC3652}, issn = {1525-2027}, doi = {10.1029/2020GC009129}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2020GC009129}, author = {Langer, Gerald and Sadekov, Aleksey and Greaves, Mervyn and Nehrke, Gernot and Probert, Ian and Misra, Sambuddha and Thoms, Silke} } @article {Calmes2020, title = {Parallelisable non-invasive biomass, fitness and growth measurement of macroalgae and other protists with nephelometry}, journal = {Algal Research}, volume = {46}, number = {November 2019}, year = {2020}, note = {Publisher: Elsevier tex.mendeley-tags: RCC149,RCC3088,RCC3510,RCC3553}, pages = {101762}, abstract = {With the exponential development of algal aquaculture and blue biotechnology, there is a strong demand for simple, inexpensive, high-throughput, quantitative phenotyping assays to measure the biomass, growth and fertility of algae and other marine protists. Here, we validate nephelometry, a method that relies on measuring the scattering of light by particles in suspension, as a non-invasive tool to measure in real-time the biomass of aquatic micro-organisms, such as microalgae, filamentous algae, as well as non-photosynthetic protists. Nephelometry is equally applicable to optic density and chlorophyll fluorescence measurements for the quantification of some microalgae, but outperforms other spectroscopy methods to quantify the biomass of biofilm-forming and filamentous algae, highly pigmented species and non-photosynthetic eukaryotes. Thanks to its insensitivity to the sample{\textquoteright}s pigmentation, nephelometry is also the method of choice when chlorophyll content varies between samples or time points, for example due to abiotic stress or pathogen infection. As examples, we illustrate how nephelometry can be combined with fluorometry or image analysis to monitor the quantity and time-course of spore release in fertile kelps or the progression of symptoms in diseased algal cultures.}, keywords = {Algal cultivation, Biomass, Biotechnology, Nephelometry, Phenotyping, RCC149, RCC3088, RCC3510, rcc3553}, issn = {22119264}, doi = {10.1016/j.algal.2019.101762}, url = {https://doi.org/10.1016/j.algal.2019.101762}, author = {Calmes, Beno{\^\i}t and Strittmatter, Martina and Jacquemin, Bertrand and Perrineau, Marie Mathilde and Rousseau, C{\'e}line and Badis, Yacine and Cock, J. Mark and Destombe, Christophe and Valero, Myriam and Gachon, Claire M.M.} } @article {Gebser2020, title = {Phytoplankton-derived zwitterionic gonyol and dimethylsulfonioacetate interfere with microbial dimethylsulfoniopropionate sulfur cycling}, journal = {MicrobiologyOpen}, number = {February}, year = {2020}, note = {tex.mendeley-tags: RCC1731,RCC75,RCC76RCC1217,RCC841}, month = {feb}, pages = {e1014}, keywords = {rcc1217, rcc1731, RCC75, RCC76, RCC841, school of life sciences, university of essex}, issn = {20458827}, doi = {10.1002/mbo3.1014}, url = {http://doi.wiley.com/10.1002/mbo3.1014}, author = {Gebser, Bj{\"o}rn and Thume, Kathleen and Steinke, Michael and Pohnert, Georg} } @article {Avilan2020, title = {ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum}, journal = {bioRxiv}, year = {2020}, note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC2967}, month = {mar}, pages = {2020.03.05.978130}, abstract = {{\textbullet} Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta-and tetraphosphate, or (p)ppGpp. In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes. {\textbullet} Here, we studied the function of ppGpp in the diatom P. tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression. {\textbullet} We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using non-targeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments. {\textbullet} Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.}, keywords = {chloroplast, diatoms, lipid droplets, Phaeodactylum tricornutum, Photosynthesis, ppGpp, proteome, RCC2967}, doi = {10.1101/2020.03.05.978130}, url = {https://doi.org/10.1101/2020.03.05.978130}, author = {Avilan, Luisana and Lebrun, Regine and Puppo, Carine and Citerne, Sylvie and Cuin{\'e}, Stephane and Li-Beisson, Yonghua and Menand, Benoit and Field, Ben and Gontero, Brigitte} } @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 {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 {Castillo2020, title = {Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using virus fluorescence in situ hybridization}, journal = {Frontiers in Microbiology}, volume = {11}, year = {2020}, note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC4221}, month = {jul}, pages = {1559}, abstract = {One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.}, keywords = {culture system, marine picoeukaryote, Ostreococcus tauri, Ostreococcus tauri virus 5, RCC4221, virus fluorescence in situ hybridization, virus-host interactions}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.01559}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.01559/full}, author = {Castillo, Yaiza M. and Sebasti{\'a}n, Marta and Forn, Irene and Grimsley, Nigel and Yau, Sheree and Moraru, Cristina and Vaqu{\'e}, Dolors} } @article {Decelle2019, title = {Algal remodeling in a ubiquitous planktonic photosymbiosis}, journal = {Current Biology}, volume = {29}, number = {6}, year = {2019}, note = {Publisher: Cell Press tex.mendeley-tags: RCC1719}, month = {mar}, pages = {968{\textendash}978.e4}, abstract = {Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae.}, keywords = {RCC1719}, issn = {0960-9822}, doi = {10.1016/J.CUB.2019.01.073}, url = {https://www.sciencedirect.com/science/article/abs/pii/S0960982219301320$\#$undfig1}, author = {Decelle, Johan and Stryhanyuk, Hryhoriy and Gallet, Benoit and Veronesi, Giulia and Schmidt, Matthias and Balzano, Sergio and Marro, Sophie and Uwizeye, Clarisse and Jouneau, Pierre-Henri and Lupette, Josselin and Jouhet, Juliette and Mar{\'e}chal, {\'E}ric and Schwab, Yannick and Schieber, Nicole L. and Tucoulou, R{\'e}mi and Richnow, Hans and Finazzi, Giovanni and Musat, Niculina} } @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 {Sanfilippo2019, title = {Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus}, journal = {Proceedings of the National Academy of Sciences}, volume = {116}, number = {13}, year = {2019}, note = {tex.mendeley-tags: RCC1086,RCC2035,RCC2380,RCC2382,RCC2385,RCC2433,RCC2437,RCC2528,RCC2533,RCC2534,RCC2535,RCC2571,RCC2673,RCC28,RCC307,RCC328,RCC515,RCC555,RCC791}, month = {mar}, pages = {6457{\textendash}6462}, abstract = {Marine Synechococcus , a globally important group of cyanobacteria, thrives in various light niches in part due to its varied photosynthetic light-harvesting pigments. Many Synechococcus strains use a process known as chromatic acclimation to optimize the ratio of two chromophores, green-light{\textendash}absorbing phycoerythrobilin (PEB) and blue-light{\textendash}absorbing phycourobilin (PUB), within their light-harvesting complexes. A full mechanistic understanding of how Synechococcus cells tune their PEB to PUB ratio during chromatic acclimation has not yet been obtained. Here, we show that interplay between two enzymes named MpeY and MpeZ controls differential PEB and PUB covalent attachment to the same cysteine residue. MpeY attaches PEB to the light-harvesting protein MpeA in green light, while MpeZ attaches PUB to MpeA in blue light. We demonstrate that the ratio of mpeY to mpeZ mRNA determines if PEB or PUB is attached. Additionally, strains encoding only MpeY or MpeZ do not acclimate. Examination of strains of Synechococcus isolated from across the globe indicates that the interplay between MpeY and MpeZ uncovered here is a critical feature of chromatic acclimation for marine Synechococcus worldwide.}, keywords = {RCC1086, RCC2035, rcc2380, rcc2382, RCC2385, RCC2433, RCC2437, RCC2528, RCC2533, RCC2534, RCC2535, RCC2571, RCC2673, RCC28, RCC307, RCC328, RCC515, rcc555, rcc791}, issn = {0027-8424}, doi = {10.1073/pnas.1810491116}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1810491116}, author = {Sanfilippo, Joseph E. and Nguyen, Adam A. and Garczarek, Laurence and Karty, Jonathan A. and Pokhrel, Suman and Strnat, Johann A. and Partensky, Fr{\'e}d{\'e}ric and Schluchter, Wendy M. and Kehoe, David M.} } @article {Iglesias2019, title = {NMR characterization and evaluation of antibacterial and antiobiofilm activity of organic extracts from stationary phase batch cultures of five marine microalgae (Dunaliella sp., D. salina, Chaetoceros calcitrans, C. gracilis and Tisochrysis lutea)}, journal = {Phytochemistry}, volume = {164}, number = {April}, year = {2019}, note = {Publisher: Elsevier tex.mendeley-tags: RCC1349,RCC1811,RCC3579,RCC5,RCC5953}, month = {aug}, pages = {192{\textendash}205}, keywords = {Antibacterial, Antibiofilm, Chaetoceros, Dunaliella, Metabolite identification, NMR, RCC1349, RCC1811, RCC3579, RCC5, RCC5953, Tisochrysis}, issn = {00319422}, doi = {10.1016/j.phytochem.2019.05.001}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0031942219300184}, author = {Iglesias, Ma Jos{\'e} and Soengas, Raquel and Probert, Ian and Guilloud, Emilie and Gourvil, Priscillia and Mehiri, Mohamed and L{\'o}pez, Yuly and Cepas, Virginio and Guti{\'e}rrez-del-R{\'\i}o, Ignacio and Redondo-Blanco, Sa{\'u}l and Villar, Claudio J. and Lomb{\'o}, Felipe and Soto, Sara and Ortiz, Fernando L{\'o}pez} } @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 {Demory2019, title = {Picoeukaryotes of the Micromonas genus: sentinels of a warming ocean}, journal = {The ISME Journal}, volume = {13}, number = {1}, year = {2019}, note = {tex.ids= Demory2018 tex.mendeley-tags: RCC114,RCC1697,RCC1862,RCC2257,RCC2306,RCC299,RCC451,RCC497,RCC746,RCC829,RCC834 publisher: Nature Publishing Group}, month = {jan}, pages = {132{\textendash}146}, abstract = {Photosynthetic picoeukaryotesx in the genus Micromonas show among the widest latitudinal distributions on Earth, experiencing large thermal gradients from poles to tropics. Micromonas comprises at least four different species often found in sympatry. While such ubiquity might suggest a wide thermal niche, the temperature response of the different strains is still unexplored, leaving many questions as for their ecological success over such diverse ecosystems. Using combined experiments and theory, we characterize the thermal response of eleven Micromonas strains belonging to four species. We demonstrate that the variety of specific responses to temperature in the Micromonas genus makes this environmental factor an ideal marker to describe its global distribution and diversity. We then propose a diversity model for the genus Micromonas, which proves to be representative of the whole phytoplankton diversity. This prominent primary producer is therefore a sentinel organism of phytoplankton diversity at the global scale. We use the diversity within Micromonas to anticipate the potential impact of global warming on oceanic phytoplankton. We develop a dynamic, adaptive model and run forecast simulations, exploring a range of adaptation time scales, to probe the likely responses to climate change. Results stress how biodiversity erosion depends on the ability of organisms to adapt rapidly to temperature increase.}, keywords = {Biogeography, change ecology, Climate, microbial ecology, RCC114, RCC1697, RCC1862, RCC2257, RCC2306, RCC299, RCC451, RCC497, RCC746, RCC829, RCC834}, issn = {1751-7362}, doi = {10.1038/s41396-018-0248-0}, url = {http://www.nature.com/articles/s41396-018-0248-0}, author = {Demory, David and Baudoux, Anne-claire and Monier, Adam and Simon, Nathalie and Six, Christophe and Ge, Pei and Rigaut-jalabert, Fabienne and Marie, Dominique and Sciandra, Antoine and Bernard, Olivier and Rabouille, Sophie} } @article {LingeJohnsen2019, title = {Relationship between coccolith length and thickness in the coccolithophore species Emiliania huxleyi and Gephyrocapsa oceanica}, journal = {PLOS ONE}, volume = {14}, number = {8}, year = {2019}, note = {tex.mendeley-tags: RCC1210,RCC1223,RCC1232,RCC1824,RCC1843,RCC868}, month = {aug}, pages = {e0220725}, keywords = {rcc1210, RCC1223, RCC1232, rcc1824, rcc1843, rcc868}, issn = {1932-6203}, doi = {10.1371/journal.pone.0220725}, url = {http://dx.plos.org/10.1371/journal.pone.0220725}, author = {Linge Johnsen, Simen Alexander and Bollmann, J{\"o}rg and Gebuehr, Christina and Herrle, Jens O.}, editor = {Keller, David Peter} } @article {Gaignard2019, title = {Screening of marine microalgae: Investigation of new exopolysaccharide producers}, journal = {Algal Research}, volume = {44}, year = {2019}, note = {tex.ids= Gaignard2019a tex.mendeley-tags: RCC1084,RCC1196,RCC1504,RCC1714,RCC1774,RCC1786,RCC1863,RCC1978,RCC1983,RCC2035,RCC232,RCC2350,RCC2352,RCC2368,RCC2380,RCC2381,RCC2383,RCC2436,RCC2558,RCC2598,RCC2608,RCC2614,RCC2624,RCC2638,RCC269,RCC2696,RCC2703,RCC2932,RCC3069,RCC3072,RCC3092,RCC3093,RCC3436,RCC3649,RCC377,RCC4094,RCC4438,RCC4555,RCC4621,RCC4631,RCC4657,RCC76,RCC775,RCC821,RCC97 publisher: Elsevier}, month = {dec}, pages = {101711}, abstract = {Biopolymers, such as exopolysaccharides are widely exploited by industry as hydrocolloids (gelling, thickening agents) and biological agents (anti-inflammatory, anti-parasitic, antioxidant, etc.). In this study, 166 marine microalgae and cyanobacteria species have been screened in order to identify strains producing original exopolysaccharides. This screening allowed the highlighting of 45 positive strains. In a second time, the monosaccharide compositions from 20 EPS of them were determined by GC/MS and HPAEC-PAD. The results led to a discovery of 8 new genera of microalgae producing EPS, including polymers with a very original composition like richness in GlcA. Finally, a phylogenic tree has been contructed in order to assess the link between the phylogeny of microalgae and the global composition of their exopolymers, based on data obtained in this study and from the literature.}, keywords = {rcc1084, RCC1196, RCC1504, RCC1714, RCC1774, RCC1786, RCC1863, RCC1978, RCC1983, RCC2035, RCC232, RCC2350, RCC2352, RCC2368, rcc2380, RCC2381, RCC2383, RCC2436, RCC2558, RCC2598, RCC2608, RCC2614, RCC2624, RCC2638, RCC269, RCC2696, RCC2703, RCC2932, RCC3069, RCC3072, RCC3092, RCC3093, RCC3436, RCC3649, RCC377, RCC4094, RCC4438, RCC4555, RCC4621, RCC4631, RCC4657, RCC76, RCC775, RCC821, RCC97}, issn = {22119264}, doi = {10.1016/j.algal.2019.101711}, url = {https://www.sciencedirect.com/science/article/pii/S2211926419303261 https://linkinghub.elsevier.com/retrieve/pii/S2211926419303261}, author = {Gaignard, C. and Laroche, C. and Pierre, G. and Dubessay, P. and Delattre, C. and Gardarin, C. and Gourvil, P. and Probert, I. and Dubuffet, A. and Michaud, P.} } @article {Sanchez2019, title = {Simplified transformation of ostreococcus tauri using polyethylene glycol}, journal = {Genes}, volume = {10}, number = {5}, year = {2019}, note = {tex.mendeley-tags: RCC4221}, month = {may}, pages = {399}, abstract = {Ostreococcustauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13{\textendash}22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave {\textquestiondown}104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20{\textendash}40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome.}, keywords = {bioluminescence, Chlorophyta, Ecosystem, Gene Expression, luciferase, mamiellophyceae, Ostreococcus, picoeukaryote, plankton, Prasinophyte, promoter, RCC4221}, issn = {2073-4425}, doi = {10.3390/genes10050399}, url = {https://www.mdpi.com/2073-4425/10/5/399}, author = {Sanchez, Fr{\'e}d{\'e}ric and Geffroy, Sol{\`e}ne and Norest, Manon and Yau, Sheree and Moreau, Herv{\'e} and Grimsley, Nigel} } @article {Kashiyama2019, title = {Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth}, journal = {The ISME Journal}, year = {2019}, note = {Publisher: Springer US tex.mendeley-tags: RCC164,RCC22,RCC24,RCC375,RCC916}, month = {feb}, pages = {1}, abstract = {Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation.}, keywords = {Biochemistry, Biogeochemistry, Cellular microbiology, microbial ecology, RCC164, RCC22, RCC24, RCC375, RCC916}, issn = {1751-7362}, doi = {10.1038/s41396-019-0377-0}, url = {http://www.nature.com/articles/s41396-019-0377-0}, author = {Kashiyama, Yuichiro and Yokoyama, Akiko and Shiratori, Takashi and Hess, Sebastian and Not, Fabrice and Bachy, Charles and Gutierrez-Rodriguez, Andres and Kawahara, Jun and Suzaki, Toshinobu and Nakazawa, Masami and Ishikawa, Takahiro and Maruyama, Moe and Wang, Mengyun and Chen, Man and Gong, Yingchun and Seto, Kensuke and Kagami, Maiko and Hamamoto, Yoko and Honda, Daiske and Umetani, Takahiro and Shihongi, Akira and Kayama, Motoki and Matsuda, Toshiki and Taira, Junya and Yabuki, Akinori and Tsuchiya, Masashi and Hirakawa, Yoshihisa and Kawaguchi, Akane and Nomura, Mami and Nakamura, Atsushi and Namba, Noriaki and Matsumoto, Mitsufumi and Tanaka, Tsuyoshi and Yoshino, Tomoko and Higuchi, Rina and Yamamoto, Akihiro and Maruyama, Tadanobu and Yamaguchi, Aika and Uzuka, Akihiro and Miyagishima, Shinya and Tanifuji, Goro and Kawachi, Masanobu and Kinoshita, Yusuke and Tamiaki, Hitoshi} } @article {Breton2019, title = {Unveiling membrane thermoregulation strategies in marine picocyanobacteria}, journal = {New Phytologist}, number = {July}, year = {2019}, note = {ISBN: 0000000244022 tex.mendeley-tags: RCC2374,RCC2385,RCC515,RCC539}, month = {oct}, pages = {nph.16239}, keywords = {RCC2374, RCC2385, RCC515, rcc539}, issn = {0028-646X}, doi = {10.1111/nph.16239}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16239}, author = {Breton, Sol{\`e}ne and Jouhet, Juliette and Guyet, Ulysse and Gros, Val{\'e}rie and Pittera, Justine and Demory, David and Partensky, Fr{\'e}d{\'e}ric and Dor{\'e}, Hugo and Ratin, Morgane and Mar{\'e}chal, {\'E}ric and Nguyen, Ngoc An and Garczarek, Laurence and Six, Christophe} } @article {Beuvier2019, title = {X-ray nanotomography of coccolithophores reveals that coccolith mass and segment number correlate with grid size}, journal = {Nature Communications}, volume = {10}, number = {1}, year = {2019}, note = {Publisher: Springer US tex.mendeley-tags: RCC1212,RCC1216,RCC1314,RCC3370,RCC4032,RCC4036}, month = {dec}, pages = {751}, abstract = {Coccolithophores of the No{\"e}laerhabdaceae family are covered by imbricated coccoliths, each composed of multiple calcite crystals radially distributed around the periphery of a grid. The factors that determine coccolith size remain obscure. Here, we used synchrotron-based three-dimensional Coherent X-ray Diffraction Imaging to study coccoliths of 7 species of Gephyrocapsa, Emiliania and Reticulofenestra with a resolution close to 30 nm. Segmentation of 45 coccoliths revealed remarkable size, mass and segment number variations, even within single coccospheres. In particular, we observed that coccolith mass correlates with grid perimeter which scales linearly with crystal number. Our results indirectly support the idea that coccolith mass is determined in the coccolith vesicle by the size of the organic base plate scale (OBPS) around which R-unit nucleation occurs every 110{\textendash}120 nm. The curvation of coccoliths allows inference of a positive correlation between cell nucleus, OBPS and coccolith sizes.}, keywords = {Biomaterials, Marine biology, rcc1212, RCC1216, RCC1314, RCC3370, RCC4032, RCC4036}, issn = {2041-1723}, doi = {10.1038/s41467-019-08635-x}, url = {http://www.nature.com/articles/s41467-019-08635-x}, author = {Beuvier, T. and Probert, I. and Beaufort, L. and Such{\'e}ras-Marx, B. and Chushkin, Y. and Zontone, F. and Gibaud, A.} } @article {Cheng2018, title = {10KP: A phylodiverse genome sequencing plan}, journal = {GigaScience}, volume = {7}, number = {3}, year = {2018}, pages = {1{\textendash}9}, keywords = {10kp, 12 february 2018, 2018, 4, accepted, access article distributed under, and reproduction in any, attribution license, biodiversity, by, c the author, creative commons, creativecommons, Distribution, genome sequencing, genomics, http, licenses, medium, mgiseq, open community, org, phylogenomics, PLANTS, press, published by oxford university, received, s, samples, the terms of the, this is an open, which permits unrestricted reuse}, issn = {2047-217X}, doi = {10.1093/gigascience/giy013}, url = {https://academic.oup.com/gigascience/article/7/3/1/4880447}, author = {Cheng, Shifeng and Melkonian, Michael and Smith, Stephen A and Brockington, Samuel and Archibald, John M and Delaux, Pierre-Marc and Li, Fay-Wei and Melkonian, Barbara and Mavrodiev, Evgeny V and Sun, Wenjing and Fu, Yuan and Yang, Huanming and Soltis, Douglas E and Graham, Sean W and Soltis, Pamela S and Liu, Xin and Xu, Xun and Wong, Gane Ka-Shu} } @article {Meng2018, title = {Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network}, journal = {Molecular Ecology}, year = {2018}, note = {tex.mendeley-tags: RCC1491,RCC1516,RCC3387,RCC3468,RCC3507}, pages = {0{\textendash}2}, abstract = {Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g. sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56\% and 57\% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization. This article is protected by copyright. All rights reserved.}, keywords = {Genomics/Proteomics, Microbial Biology, Molecular Evolution, Protists, rcc1491, RCC1516, RCC3387, rcc3468, rcc3507, transcriptomics}, issn = {09621083}, doi = {10.1111/mec.14579}, url = {http://www.ncbi.nlm.nih.gov/pubmed/29624751\%0Ahttp://doi.wiley.com/10.1111/mec.14579}, author = {Meng, Arnaud and Corre, Erwan and Probert, Ian and Gutierrez-Rodriguez, Andres and Siano, Raffaele and Annamale, Anita and Alberti, Adriana and Da Silva, Corinne and Wincker, Patrick and Le Crom, St{\'e}phane and Not, Fabrice and Bittner, Lucie} } @article {Guyon2018, title = {Comparative analysis of culture conditions for the optimization of carotenoid production in several strains of the picoeukaryote ostreococcus}, journal = {Marine Drugs}, volume = {16}, number = {3}, year = {2018}, note = {tex.mendeley-tags: 2018,RCC745,RCC802,RCC809,rcc}, pages = {76}, abstract = {Microalgae are promising sources for the sustainable production of compounds of interest for biotechnologies. Compared to higher plants, microalgae have a faster growth rate and can be grown in industrial photobioreactors. The microalgae biomass contains specific metabolites of high added value for biotechnology such as lipids, polysaccharides or carotenoid pigments. Studying carotenogenesis is important for deciphering the mechanisms of adaptation to stress tolerance as well as for biotechnological production. In recent years, the picoeukaryote Ostreococcus tauri has emerged as a model organism thanks to the development of powerful genetic tools. Several strains of Ostreococcus isolated from different environments have been characterized with respect to light response or iron requirement. We have compared the carotenoid contents and growth rates of strains of Ostreococcus (OTTH595, RCC802 and RCC809) under a wide range of light, salinity and temperature conditions. Carotenoid profiles and productivities varied in a strain-specific and stress-dependent manner. Our results also illustrate that phylogenetically related microalgal strains originating from different ecological niches present specific interests for the production of specific molecules under controlled culture conditions.}, keywords = {2018, carotenoids, GROWTH RATE, Light, Ostreococcus, rcc, RCC745, RCC802, RCC809, salinity, temperature}, issn = {1660-3397}, doi = {10.3390/md16030076}, url = {http://www.mdpi.com/1660-3397/16/3/76}, author = {Guyon, Jean-baptiste and Schatt, Philippe and Lozano, Jean-Claude and Liennard, Marion and Bouget, Fran{\c c}ois-Yves} } @article {Farhat2018, title = {Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains}, journal = {Frontiers in Microbiology}, volume = {9}, number = {October}, year = {2018}, note = {tex.mendeley-tags: RCC1627,RCC3596,RCC4383,RCC4398}, month = {oct}, pages = {1{\textendash}19}, keywords = {amoebophrya, Dinoflagellates, Gene Expression, infection, oxidative stress response, parasite, plankton, RCC1627, RCC3596, RCC4383, RCC4398, syndiniales}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.02251}, url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full}, author = {Farhat, Sarah and Florent, Isabelle and Noel, Benjamin and Kayal, Ehsan and Da Silva, Corinne and Bigeard, Estelle and Alberti, Adriana and Labadie, Karine and Corre, Erwan and Aury, Jean-Marc and Rombauts, Stephane and Wincker, Patrick and Guillou, Laure and Porcel, Betina M.} } @article {Partensky2018, title = {Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex}, journal = {Photosynthesis Research}, volume = {138}, number = {1}, year = {2018}, note = {tex.mendeley-tags: RCC752}, pages = {57{\textendash}71}, abstract = {The extrinsic PsbU and PsbV proteins are known to play a critical role in stabilizing the Mn4CaO5 cluster of the PSII oxygen-evolving complex (OEC). However, most isolates of the marine cyanobacterium Prochlorococcus naturally miss these proteins, even though they have kept the main OEC protein, PsbO. A structural homology model of the PSII of such a natural deletion mutant strain (P. marinus MED4) did not reveal any obvious compensation mechanism for this lack. To assess the physiological consequences of this unusual OEC, we compared oxygen evolution between Prochlorococcus strains missing psbU and psbV (PCC 9511 and SS120) and two marine strains possessing these genes (Prochlorococcus sp. MIT9313 and Synechococcus sp. WH7803). While the low light-adapted strain SS120 exhibited the lowest maximal O2 evolution rates (Pmax per divinyl-chlorophyll a, per cell or per photosystem II) of all four strains, the high light-adapted strain PCC 9511 displayed even higher PChlmax and PPSIImax at high irradiance than Synechococcus sp. WH7803. Furthermore, thermoluminescence glow curves did not show any alteration in the B-band shape or peak position that could be related to the lack of these extrinsic proteins. This suggests an efficient functional adaptation of the OEC in these natural deletion mutants, in which PsbO alone is seemingly sufficient to ensure proper oxygen evolution. Our study also showed that Prochlorococcus strains exhibit negative net O2 evolution rates at the low irradiances encountered in minimum oxygen zones, possibly explaining the very low O2 concentrations measured in these environments, where Prochlorococcus is the dominant oxyphototroph.}, keywords = {rcc752}, issn = {1573-5079}, doi = {10.1007/s11120-018-0539-3}, url = {https://doi.org/10.1007/s11120-018-0539-3}, author = {Partensky, Fr{\'e}d{\'e}ric and Mella-Flores, Daniella and Six, Christophe and Garczarek, Laurence and Czjzek, Mirjam and Marie, Dominique and Kotabov{\'a}, Eva and Felcmanov{\'a}, Kristina and Pr{\'a}{\v s}il, Ond{\v r}ej} } @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 {Garcia2018, title = {High variability in cellular stoichiometry of carbon, nitrogen, and phosphorus within classes of marine eukaryotic phytoplankton under sufficient nutrient conditions}, journal = {Frontiers in Microbiology}, volume = {9}, number = {March}, year = {2018}, note = {tex.mendeley-tags: RCC103,RCC1242,RCC1562,RCC4023,RCC449,RCC931}, pages = {1{\textendash}10}, abstract = {Current hypotheses suggest that cellular elemental stoichiometry of marine eukaryotic phytoplankton such as the ratios of cellular carbon:nitrogen:phosphorus (C:N:P) vary between phylogenetic groups based traits like evolutionary history and cell size. To investigate how phylogenetic structure, cell volume, growth rate and temperature interact to affect the cellular elemental stoichiometry of marine eukaryotic phytoplankton, we examined the C:N:P composition in 30 isolates across 7 classes of marine phytoplankton that were grown with a sufficient supply of nutrients with nitrate as the nitrogen source. The isolates covered a wide range in cell volume (5 orders of magnitude), growth rate ({\textexclamdown}0.01-0.9 d-1), and habitat temperature (2-24{\textdegree}C). Our analysis indicates that C:N:P is highly variable, with statistical model residuals accounting for over half of the total variance with no relationship between phylogeny and elemental stoichiometry. Furthermore, our data indicated that variability in C:P, N:P and C:N within Bacillariophyceae (diatoms) was as high as that among all of the isolates that we examined. In addition, a linear statistical model identified a positive relationship between diatom cell volume and C:P and N:P. Among all of the isolates that we examined, the statistical model identified temperature as a significant factor, consistent with the temperature-dependent translation efficiency model, but temperature only explained 5\% of the total statistical model variance. While some of our results support data from previous field studies, the high variability of elemental ratios within Bacillariophyceae contradicts previous work that suggests that this cosmopolitan group of microalgae has consistently low C:P and N:P ratios in comparison with other groups.}, keywords = {cell size, Diatom, Dinoflagellate, eukaryote, frontiers in microbiology, frontiersin, Growth, org, protist, prymnesiophyte, RCC103, RCC1242, RCC1562, RCC4023, RCC449, RCC931, temperature, www}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.00543}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2018.00543/full}, author = {Garcia, Nathan S. and Sexton, Julie and Riggins, Tracey and Brown, Jeff and Lomas, Michael W. and Martiny, Adam C.} } @article {Carrillo2018, title = {Identification and analysis of OsttaDSP, a phosphoglucan phosphatase from Ostreococcus tauri}, journal = {PLOS ONE}, volume = {13}, number = {1}, year = {2018}, note = {tex.mendeley-tags: RCC745}, month = {jan}, pages = {e0191621}, keywords = {RCC745}, issn = {1932-6203}, doi = {10.1371/journal.pone.0191621}, url = {http://dx.plos.org/10.1371/journal.pone.0191621}, author = {Carrillo, Julieta B and Gomez-Casati, Diego F. and Mart{\'\i}n, Mariana and Busi, Maria V.}, editor = {Permyakov, Eugene A.} } @article {Moniruzzaman2018, title = {Infection by a giant virus (AaV) induces widespread physiological reprogramming in aureococcus anophagefferens CCMP1984 {\textendash} a harmful bloom algae}, journal = {Frontiers in Microbiology}, volume = {9}, number = {April}, year = {2018}, note = {tex.mendeley-tags: RCC4094}, month = {apr}, pages = {1{\textendash}16}, abstract = {While viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, " giant " dsDNA viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of giant virus {\textendash} host interactions remain largely unknown. AaV, a giant virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens. To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host-virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional reprogramming of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2\%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal-expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides the insight into the Aureococcus {\textquoteright}virocell{\textquoteright}, and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.}, keywords = {Algal viruses, brown, Host-virus interaction, Mimiviridae, RCC4094, transcriptional profiles}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.00752}, url = {http://dx.doi.org/10.1101/256149 http://journal.frontiersin.org/article/10.3389/fmicb.2018.00752/full}, author = {Moniruzzaman, Mohammad and Gann, Eric R and Wilhelm, Steven W} } @article {Grebert2018, title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria}, journal = {Proceedings of the National Academy of Sciences}, volume = {in press}, year = {2018}, note = {tex.mendeley-tags: 2018,RCC1016,RCC1017,RCC1018,RCC1020,RCC1023,RCC1027,RCC1030,RCC1031,RCC1084,RCC1085,RCC1086,RCC1087,RCC1096,RCC1097,RCC1649,RCC1661,RCC1688,RCC2032,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2370,RCC2372,RCC2373,RCC2374,RCC2375,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2384,RCC2385,RCC2415,RCC2432,RCC2433,RCC2434,RCC2435,RCC2436,RCC2437,RCC2438,RCC2457,RCC2525,RCC2526,RCC2527,RCC2528,RCC2529,RCC2530,RCC2532,RCC2533,RCC2534,RCC2536,RCC2553,RCC2554,RCC2555,RCC2556,RCC2567,RCC2568,RCC2569,RCC2570,RCC2571,RCC2673,RCC30,RCC3010,RCC3012,RCC3014,RCC307,RCC316,RCC318,RCC325,RCC326,RCC328,RCC37,RCC44,RCC46,RCC47,RCC515,RCC539,RCC542,RCC543,RCC550,RCC552,RCC553,RCC555,RCC556,RCC557,RCC558,RCC559,RCC62,RCC650,RCC66,RCC752,RCC753,RCC790,RCC791,RCC792,RCC793,RCC794,sbr?hyto?app}, month = {feb}, pages = {201717069}, abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined so far due to the lack of a single-genetic marker resolving all pigment types (PT). Here, we developed a novel and robust method based on three distinct marker genes to estimate the relative abundance of all Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to unveil for the first time the global distribution of Synechococcus PTs and to decipher their realized environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified local populations in which CA4 might be inactive due to the lack of specific CA4 genes, notably in warm high nutrient low chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study brings unprecedented insights into the ecology of Synechococcus PTs and highlights the complex interactions between vertical phylogeny, pigmentation and environmental parameters that shape Synechococcus populations and evolution.}, keywords = {2018, RCC1016, RCC1017, RCC1018, RCC1020, RCC1023, RCC1027, RCC1030, RCC1031, rcc1084, RCC1085, RCC1086, RCC1087, RCC1096, RCC1097, RCC1649, RCC1661, RCC1688, RCC2032, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2370, RCC2372, RCC2373, RCC2374, RCC2375, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2384, RCC2385, RCC2415, RCC2432, RCC2433, RCC2434, RCC2435, RCC2436, RCC2437, RCC2438, RCC2457, RCC2525, RCC2526, RCC2527, RCC2528, RCC2529, RCC2530, RCC2532, RCC2533, RCC2534, RCC2536, RCC2553, RCC2554, RCC2555, RCC2556, RCC2567, RCC2568, RCC2569, RCC2570, RCC2571, RCC2673, rcc30, RCC3010, RCC3012, RCC3014, RCC307, RCC316, RCC318, RCC325, RCC326, RCC328, RCC37, RCC44, RCC46, RCC47, RCC515, rcc539, RCC542, RCC543, RCC550, RCC552, RCC553, rcc555, RCC556, RCC557, RCC558, RCC559, RCC62, RCC650, RCC66, rcc752, RCC753, RCC790, rcc791, RCC792, RCC793, RCC794, sbr?hyto?app}, issn = {0027-8424}, doi = {10.1073/pnas.1717069115}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1717069115}, author = {Gr{\'e}bert, Th{\'e}ophile and Dor{\'e}, Hugo and Partensky, Fr{\'e}d{\'e}ric and Farrant, Gregory K. and Boss, Emmanuel S. and Picheral, Marc and Guidi, Lionel and Pesant, St{\'e}phane and Scanlan, David J. and Wincker, Patrick and Acinas, Silvia G. and Kehoe, David M. and Garczarek, Laurence} } @article {Liefer2018, title = {Nitrogen starvation induces distinct photosynthetic responses and recovery dynamics in diatoms and prasinophytes}, journal = {PLOS ONE}, volume = {13}, number = {4}, year = {2018}, note = {ISBN: 1111111111 tex.mendeley-tags: RCC745}, month = {apr}, pages = {e0195705}, abstract = {Nitrogen stress is an important control on the growth of phytoplankton and varying responses to this common condition among taxa may affect their relative success within phytoplankton communities.We analyzed photosynthetic responses to nitrogen (N) stress in two classes of phytoplankton that often dominate their respective size ranges, diatoms and prasinophytes, selecting species of distinct niches within each class. Changes in photosynthetic structures appeared similar within each class during N stress, but photophysiological and growth responses were more species -or niche-specific. In the coastal diatom Thalassiosira pseudonana and the oceanic diatom T. weissflogii, N starvation induced large declines in photosynthetic pigments and Photosystem II (PSII) quantity and activity as well as increases in the effective absorption cross-section of PSII photochemistry (σ{\textquoteright}PSII). These diatoms also increased photoprotection through energy-dependent non-photochemical quenching (NPQ) during N starvation. Resupply of N in diatoms caused rapid recovery of growth and relaxation of NPQ, while recovery of PSII photochemistry was slower. In contrast, the prasinophytes Micromonas sp., an Arctic Ocean species, and Ostreococcus tauri, a temperate coastal eutrophile, showed little change in photosynthetic pigments and structures and a decline or no change, respectively, inσ{\textquoteright}PSII with N starvation. Growth and PSII function recovered quickly in Micromonas sp. after resupply of N while O. tauri failed to recover N-replete levels of electron transfer from PSII and growth, possibly due to their distinct photoprotective strategies. O. tauri induced energy-dependent NPQ for photoprotection that may suit its variable and nutrient-rich habitat. Micromonas sp. relies upon both energy-dependent NPQ and a sustained, energy-independent NPQ mechanism. A strategy in Micromonas sp. that permits photoprotection with little change in photosynthetic structures is consistent with its Arctic niche, where low temperatures and thus low biosynthetic rates create higher opportunity costs to rebuild photosynthetic structures.}, keywords = {RCC745}, issn = {1932-6203}, doi = {10.1371/journal.pone.0195705}, url = {http://dx.plos.org/10.1371/journal.pone.0195705}, author = {Liefer, Justin D and Garg, Aneri and Campbell, Douglas A and Irwin, Andrew J and Finkel, Zoe V}, editor = {Ianora, Adrianna} } @article {Partensky2018, title = {A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle}, journal = {Scientific Reports}, volume = {8}, number = {1}, year = {2018}, note = {tex.mendeley-tags: RCC1774}, month = {dec}, pages = {9142}, keywords = {RCC1774}, issn = {2045-2322}, doi = {10.1038/s41598-018-27542-7}, url = {http://www.nature.com/articles/s41598-018-27542-7}, author = {Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Ratin, Morgane and Garczarek, Laurence and Vaulot, Daniel and Probert, Ian and Calteau, Alexandra and Gourvil, Priscillia and Marie, Dominique and Gr{\'e}bert, Th{\'e}ophile and Bouchier, Christiane and Le Panse, Sophie and Gachenot, Martin and Rodr{\'\i}guez, Francisco and Garrido, Jos{\'e} L.} } @article {Moldovan2018, title = {Pangenomic definition of prokaryotic species and the phylogenetic structure of prochlorococcus spp.}, journal = {Frontiers in Microbiology}, volume = {9}, number = {March}, year = {2018}, note = {tex.mendeley-tags: RCC158,RCC162,RCC269,RCC278,RCC3307,RCC407}, pages = {1{\textendash}11}, keywords = {monophyly, pangenome, paraphyly, prokaryotic species, RCC158, rcc162, RCC269, RCC278, RCC3307, RCC407, species definition, taxonomy}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.00428}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2018.00428/full}, author = {Moldovan, Mikhail A. and Gelfand, Mikhail S.} } @article {Mizrachi2018, title = {Phenotypic variability in chloroplast redox state predicts cell fate in a marine diatom}, journal = {bioRxiv}, year = {2018}, note = {arXiv: 319517 tex.arxivid: 319517 tex.mendeley-tags: RCC2967}, keywords = {RCC2967}, doi = {10.1101/319517}, author = {Mizrachi, Avia and Graff, Shiri and Creveld, Van and Shapiro, Orr H and Rosenwasser, Shilo} } @article {yau_rapidity_2018, title = {Rapidity of Genomic Adaptations to Prasinovirus Infection in a Marine Microalga}, journal = {Viruses}, volume = {10}, number = {8}, year = {2018}, note = {Number: 8 Publisher: Multidisciplinary Digital Publishing Institute}, pages = {441}, abstract = {Prasinoviruses are large dsDNA viruses commonly found in aquatic systems worldwide, where they can infect and lyse unicellular prasinophyte algae such as Ostreococcus. Host susceptibility is virus strain-specific, but resistance of susceptible Ostreococcus tauri strains to a virulent virus arises frequently. In clonal resistant lines that re-grow, viruses are usually present for many generations, and genes clustered on chromosome 19 show physical rearrangements and differential expression. Here, we investigated changes occurring during the first two weeks after inoculation of the prasinovirus OtV5. By serial dilutions of cultures at the time of inoculation, we estimated the frequency of resistant cells arising in virus-challenged O. tauri cultures to be 10\−3\–10\−4 of the inoculated population. Re-growing resistant cells were detectable by flow cytometry 3 days post-inoculation (dpi), visible re-greening of cultures occurred by 6 dpi, and karyotypic changes were visually detectable at 8 dpi. Resistant cell lines showed a modified spectrum of host-virus specificities and much lower levels of OtV5 adsorption.}, keywords = {adsorption, Chromosome, host range, karyotype, mamiellophyceae, phycodnaviridae, RCC1105, RCC4221, RCC4223, rearrangement, resistance, specificity, \textitOstreococcus tauri}, doi = {10.3390/v10080441}, url = {https://www.mdpi.com/1999-4915/10/8/441}, author = {Yau, Sheree and Caravello, Ga{\"e}tan and Fonvieille, Nad{\`e}ge and Desgranges, Elodie and Moreau, Herv{\'e} and Grimsley, Nigel} } @article {EMI4:EMI412614, title = {Relative stability of ploidy in a marine Synechococcus across various growth conditions}, journal = {Environmental Microbiology Reports}, year = {2018}, note = {tex.mendeley-tags: RCC752}, month = {feb}, pages = {in press}, abstract = {Marine picocyanobacteria of the genus Synechococcus are ubiquitous phototrophs in oceanic systems. Consistent with these organisms occupying vast tracts of the nutrient impoverished ocean, most marine Synechococcus so far studied are monoploid i.e. contain a single chromosome copy. The exception is the oligoploid strain Synechococcus sp. WH7803, which on average possesses around 4 chromosome copies. Here, we set out to understand the role of resource availability (through nutrient deplete growth) and physical stressors (UV, exposure to low and high temperature) in regulating ploidy level in this strain. Using qPCR to assay ploidy status we demonstrate the relative stability of chromosome copy number in Synechococcus sp. WH7803. Such robustness in maintaining an oligoploid status even under nutrient and physical stress is indicative of a fundamental role, perhaps facilitating recombination of damaged DNA regions as a result of prolonged exposure to oxidative stress, or allowing added flexibility in gene expression via possessing multiple alleles. This article is protected by copyright. All rights reserved.}, keywords = {rcc752}, issn = {17582229}, doi = {10.1111/1758-2229.12614}, url = {http://dx.doi.org/10.1111/1758-2229.12614 http://doi.wiley.com/10.1111/1758-2229.12614}, author = {Perez-Sepulveda, Blanca and Pitt, Frances and N{\textquoteright}Guyen, An Ngoc and Ratin, Morgane and Garczarek, Laurence and Millard, Andrew and Scanlan, David J} } @article {Mahmoud2017, title = {Adaptation to blue light in marine synechococcus requires MpeU, an enzyme with similarity to phycoerythrobilin lyase isomerases}, journal = {Frontiers in Microbiology}, volume = {8}, number = {February}, year = {2017}, note = {tex.mendeley-tags: 2017,rcc555,sbr?hyto?app}, month = {feb}, pages = {243}, abstract = {Marine Synechococcus cyanobacteria have successfully adapted to environments with different light colors, which likely contributes to this genus being the second most abundant photosynthetic microorganism worldwide. Populations of Synechococcus that grow in deep, blue ocean waters contain large amounts of the blue-light absorbing chromophore phycourobilin (PUB) in their light harvesting complexes (phycobilisomes). Here we show that all Synechococcus strains adapted to blue light possess a gene called mpeU. MpeU is structurally similar to phycobilin lyases, enzymes that ligate chromophores to phycobiliproteins. Interruption of mpeU caused a reduction in PUB content, produced impaired phycobilisomes and reduced growth rate more strongly in blue than green light. When mpeU was reintroduced in the mpeU mutant background, the mpeU-less phenotype was complemented in terms of PUB content and phycobilisome content. Fluorescence spectra of mpeU mutant cells and purified phycobilisomes revealed red-shifted phycoerythrin emission peaks, likely indicating a defect in chromophore ligation to phycoerythrin-I (PE-I) or phycoerythrin-II (PE-II). Our results suggest that MpeU is a lyase-isomerase that attaches a phycoerythrobilin to a PEI or PEII subunit and isomerizes it to PUB. MpeU is therefore an important determinant in adaptation of Synechococcus spp. to capture photons in blue light environments throughout the world{\textquoteright}s oceans.}, keywords = {2017, Blue light, light harvesting complex, Lyase isomerase, marine cyanobacteria, Marine Synechococcus, phycobilin, Phycobilisome, Phycoerythrin, Phycourobilin, rcc555, sbr?hyto?app}, issn = {1664-302X}, doi = {10.3389/fmicb.2017.00243}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.00243/full}, author = {Mahmoud, Rania M. and Sanfilippo, Joseph E. and Nguyen, Adam A. and Strnat, Johann A. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence and Abo El Kassem, Nabil and Kehoe, David M. and Schluchter, Wendy M.} } @article {Gu2017, title = {Adenoides sinensis , a new sand-dwelling dinoflagellate species from China and reexamination of A. eludens from an Atlantic strain}, journal = {Phycologia}, volume = {57}, number = {October}, year = {2017}, note = {tex.mendeley-tags: 2017,RCC1982,rcc,sbr?hyto$_\textrmd$ipo}, pages = {1{\textendash}13}, abstract = {The sand-dwelling?1dinoflagellate generaAdenoidesandPseudadenoidesare morphologically very close butdistinct in their molecular phylogeny. We established three cultures by isolating single cells from sand samples collected inintertidal zones of Qingdao (Yellow Sea), Dongshan (South China Sea) and Brittany (English Channel, North Atlantic,France). Strain morphology was examined with light and scanning electron microscopy, and both large subunitribosomal DNA (LSU rDNA) and small subunit ribosomal DNA (SSU rDNA) sequences were amplified. Molecularphylogeny, corroborated by morphological examination showing the existence of a ventral pore, confirmed theidentification of the French strain (RCC1982) asAdenoides eludens. The Chinese strains differed fromAdenoides eludensin two additional posterior intercalary plates and differed fromPseudadenoidesin one additional apical plate having theplate formula of Po, Cp, X, 50,600, 4S, 5000, 5p, 10000or alternatively Po, Cp, X, 50,600, 5S, 5000, 3p, 20000. Maximumlikelihood and Bayesian inference carried out with concatenated LSU and SSU sequences demonstrated that the Chinesestrains were closely related but different fromA. eludensand, in corroboration with morphological evidence, supportedtheir classification as a distinct species,Adenoides sinensis sp. nov. Morphological and molecular results confirmed theclose relationship between the two generaAdenoidesandPseudadenoides.}, keywords = {2017, rcc, RCC1982, sbr?hyto$_\textrmd$ipo}, doi = {10.2216/17-76.1}, author = {Gu, Haifeng and Li, Xintian and Chom{\'e}rat, Nicolas and Luo, Zhaohe and Sarno, Diana and Gourvil, Priscillia and Balzano, Sergio and Siano, Raffaele} } @article {Gnouma2017, title = {Changes in fatty acids profile, monosaccharide profile and protein content during batch growth of Isochrysis galbana (T.iso)}, journal = {Aquaculture Research}, volume = {48}, number = {9}, year = {2017}, note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC1349}, month = {sep}, pages = {4982{\textendash}4990}, abstract = {Abstract To investigate the nutritional value of the marine micro-alga Isochrysis galbana Tahitian Isochrysis strain (T.iso) as an alternative feed for aquaculture during culture age, its biochemical composition was studied under autotrophic and controlled culture conditions at different growth stages: exponential phase, early and late stationary phases and decay phase. Analysis showed that C14:0, C16:0, C16:1, C18:4 (n-3) and C22:6 (n-3) were the most abundant fatty acids in this alga at different growth stages. The highest values of monounsaturated fatty acids were recorded at the late stationary and the decay phases. However, the highest levels of polyunsaturated fatty acids were observed at the early stationary phase. At all growth stages, I. galbana (T.iso) contained arabinose, xylose, mannose, galactose and glucose. Glucose represented the main sugar, and its content per dry alga biomass weight increased with increasing age of the culture and reached about fourfold in the decay phase. The maximum protein content was also observed during this last phase.}, keywords = {fatty acids, growth phases, Isochrysis galbana (T.iso), monosaccharides, proteins, RCC1349}, issn = {1355-557X}, doi = {10.1111/are.13316}, url = {https://doi.org/10.1111/are.13316}, author = {Gnouma, Asma and Sadovskaya, Irina and Souissi, Anissa and Sebai, Khaled and Medhioub, Amel and Grard, Thierry and Souissi, Sami} } @article {Dorrell2017, title = {Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome}, journal = {eLife}, volume = {6}, year = {2017}, month = {may}, pages = {1{\textendash}45}, abstract = {Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25\% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history.}, keywords = {2017, RCC1486, RCC1523, RCC1537, RCC1587, SBR$_\textrmP$hyto$_\textrmE$PPO}, issn = {2050-084X}, doi = {10.7554/eLife.23717}, url = {http://elifesciences.org/lookup/doi/10.7554/eLife.23717}, author = {Dorrell, Richard G and Gile, Gillian and McCallum, Giselle and M{\'e}heust, Rapha{\"e}l and Bapteste, Eric P and Klinger, Christen M and Brillet-Gu{\'e}guen, Loraine and Freeman, Katalina D and Richter, Daniel J and Bowler, Chris} } @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 {Satjarak2017, title = {Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes}, journal = {Journal of Phycology}, volume = {53}, number = {2}, year = {2017}, note = {tex.mendeley-tags: RCC1987,RCC2009,RCC2015,RCC2500,RCC2501,RCC2502,RCC619}, month = {apr}, pages = {415{\textendash}424}, keywords = {RCC1987, RCC2009, RCC2015, RCC2500, RCC2501, RCC2502, RCC619}, issn = {00223646}, doi = {10.1111/jpy.12515}, url = {http://doi.wiley.com/10.1111/jpy.12515}, author = {Satjarak, Anchittha and Graham, Linda E.}, editor = {Wood, M.} } @article {Stuart2016, title = {Copper toxicity response influences mesotrophic S ynechococcus community structure}, journal = {Environmental Microbiology}, volume = {19}, number = {2}, year = {2017}, note = {ISBN: 3907122046 tex.mendeley-tags: 2016,RCC1086,RCC2673}, month = {feb}, pages = {756{\textendash}769}, abstract = {Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, {\textquotedblleft}species{\textquotedblright} also known as clades. We compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co-occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe-limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbor stress-tolerant subgroups, and thus fitness tradeoffs may govern Cu-tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations. This}, keywords = {2016, alkylsuccinate, methanogenic, n -alkane, paraffin, RCC1086, RCC2673, smithella, syntrophy}, issn = {14622912}, doi = {10.1111/1462-2920.13630}, url = {http://doi.wiley.com/10.1111/1462-2920.13630}, author = {Stuart, Rhona K. and Bundy, Randelle and Buck, Kristen and Ghassemain, Majid and Barbeau, Kathy and Palenik, Brian} } @article {Gutierrez-Rodriguez2017, title = {Dimethylated sulfur compounds in symbiotic protists: A potentially significant source for marine DMS(P)}, journal = {Limnology and Oceanography}, number = {February}, year = {2017}, note = {tex.mendeley-tags: 2017,rcc1383,rcc1491,rcc3468,rcc3507,sbr?hyto$_\textrmd$ipo}, month = {feb}, keywords = {2017, rcc1383, rcc1491, rcc3468, rcc3507, sbr?hyto$_\textrmd$ipo}, issn = {00243590}, doi = {10.1002/lno.10491}, url = {http://doi.wiley.com/10.1002/lno.10491}, author = {Gutierrez-Rodriguez, Andres and Pillet, Loic and Biard, Tristan and Said-Ahmad, Ward and Amrani, Alon and Sim{\'o}, Rafel and Not, Fabrice} } @article {LopesdosSantos2016, title = {Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters}, journal = {The ISME Journal}, volume = {11}, number = {2}, year = {2017}, note = {tex.mendeley-tags: 2016,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, month = {feb}, pages = {512{\textendash}528}, keywords = {2016, MACUMBA, MicroB3, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, issn = {1751-7362}, doi = {10.1038/ismej.2016.120}, url = {http://www.nature.com/doifinder/10.1038/ismej.2016.120}, author = {Lopes dos Santos, Adriana and Gourvil, Priscillia and Tragin, Margot and No{\"e}l, Mary-H{\'e}l{\`e}ne and Decelle, Johan and Romac, Sarah and Vaulot, Daniel} } @article {Moutier2017, title = {Evolution of the scattering properties of phytoplankton cells from flow cytometry measurements}, journal = {PLoS ONE}, volume = {12}, number = {7}, year = {2017}, note = {ISBN: 1111111111 tex.mendeley-tags: RCC1,RCC950}, abstract = {Combining a modern, data-analytic perspective with a focus on applications in the social sciences, the Second Edition of Applied Regression Analysis and Generalized Linear Models provides in-depth coverage of regression analysis, generalized linear models, and closely related methods. Although the text is largely accessible to readers with a modest background in statistics and mathematics, author John Fox also presents more advanced material throughout the book. Key Updates to the Second Edition:Provides greatly enhanced coverage of generalized linear models, with an emphasis on models for categorical and count data Offers new chapters on missing data in regression models and on methods of model selection Includes expanded treatment of robust regression, time-series regression, nonlinear regression, and nonparametric regression Incorporates new examples using larger data sets Includes an extensive Web site at http://www.sagepub.com/fox that presents appendixes, data sets used in the book and for data-analytic exercises, and the data-analytic exercises themselves Intended Audience: This core text will be a valuable resource for graduate students and researchers in the social sciences (particularly sociology, political science, and psychology) and other disciplines that employ linear and related models for data analysis. High Praise for the First Edition: Even though the book is written with social scientists as the target audience, the depth of material and how it is conveyed give it far broader appeal. Indeed, I recommend it as a useful learning text and resource for researchers and students in any field that applies regression or linear models (that is, most everyone), including courses for undergraduate statistics majors.... The author is to be commended for giving us this book, which I trust will find a wide and enduring readership.-JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION [T]his wonderfully comprehensive book focuses on regression analysis and linear models.... We enthusiastically recommend this book {\textemdash} having used it in class, we know that it is thorough and well liked by students. -CHANCE}, keywords = {RCC1, RCC950}, issn = {19326203}, doi = {10.1371/journal.pone.0181180}, author = {Moutier, William and Dufor{\^e}t-Gaurier, Lucile and Thyssen, M{\'e}lilotus and Loisel, Hubert and M{\'e}riaux, Xavier and Courcot, Lucie and Dessailly, David and R{\^e}ve, Anne H{\'e}l{\`e}ne and Gr{\'e}gori, Gerald and Alvain, S{\'e}verine and Barani, Aude and Brutier, Laurent and Dugenne, Mathilde} } @article {Fischer2017a, title = {Importance of mixotrophic bacterivory can be predicted by light and loss rates}, journal = {Oikos}, volume = {126}, number = {5}, year = {2017}, note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC744}, month = {may}, pages = {713{\textendash}722}, abstract = {Recent observational studies form oligotrophic waters provide ample evidence that mixotrophic flagellates often account for the bulk of bacterivory. However, we lack a general framework that allows a mechanistic understanding of success of mixotrophs in the competition with heterotrophic bacterivores. This is especially needed for integrating mixotrophy in models of the microbial loop. Based on general tradeoffs linked to the combined resource use in mixotrophs (generalist versus specialist), we propose a concept where mixotrophs are favored by conditions of high light ? low losses, corresponding to the situation found in the surface waters of oligotrophic oceans. Under such conditions, they can achieve positive net growth at very low resource levels, allowing simultaneous competition with specialized protists. Conversely, heterotrophic bacterivores and photoautotrophs should be especially favored in more productive and low-light conditions. We show experimentally that the combined effect of light and loss rates (dilution) predicts the success of mixotrophic bacterivorous flagellates. Moreover, our results suggest that total bacterivory, contrary as seen in the traditional microbial loop concept, has a more intricate coupling to light.}, keywords = {RCC744}, issn = {0030-1299}, doi = {10.1111/oik.03539}, url = {https://doi.org/10.1111/oik.03539}, author = {Fischer, Robert and Giebel, Helge-Ansgar and Hillebrand, Helmut and Ptacnik, Robert} } @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 {Balzano2017c, title = {Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex}, journal = {Journal of Phycology}, volume = {53}, number = {1}, year = {2017}, note = {tex.mendeley-tags: RCC1984,RCC1985,RCC1986,RCC1988,RCC1989,RCC1990,RCC1991,RCC1992,RCC1993,RCC1995,RCC1997,RCC1999,RCC2000,RCC2002,RCC2003,RCC2004,RCC2005,RCC2006,RCC2008,RCC2010,RCC2011,RCC2012,RCC2014,RCC2016,RCC2017,RCC2021,RCC2037,RCC2038,RCC2039,RCC2042,RCC2043,RCC2261,RCC2262,RCC2263,RCC2264,RCC2265,RCC2266,RCC2267,RCC2268,RCC2269,RCC2270,RCC2272,RCC2273,RCC2274,RCC2275,RCC2276,RCC2277,RCC2278,RCC2279,RCC2280,RCC2281,RCC2282,RCC2318,RCC2506,RCC2517,RCC2520,RCC2521,RCC2522}, month = {feb}, pages = {161{\textendash}187}, abstract = {Seventy-five diatom strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM), as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, and Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. C. neogracilis generally occurred as single cells but also formed short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis, but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region.}, keywords = {RCC1984, RCC1985, RCC1986, RCC1988, RCC1989, RCC1990, RCC1991, RCC1992, RCC1993, RCC1995, RCC1997, RCC1999, RCC2000, RCC2002, RCC2003, RCC2004, RCC2005, RCC2006, RCC2008, RCC2010, RCC2011, RCC2012, RCC2014, RCC2016, RCC2017, RCC2021, RCC2037, RCC2038, RCC2039, RCC2042, RCC2043, RCC2261, RCC2262, RCC2263, RCC2264, RCC2265, RCC2266, RCC2267, RCC2268, RCC2269, RCC2270, RCC2272, RCC2273, RCC2274, RCC2275, RCC2276, RCC2277, RCC2278, RCC2279, RCC2280, RCC2281, RCC2282, RCC2318, RCC2506, RCC2517, RCC2520, RCC2521, RCC2522}, issn = {00223646}, doi = {10.1111/jpy.12489}, url = {http://doi.wiley.com/10.1111/jpy.12489}, author = {Balzano, Sergio and Percopo, Isabella and Siano, Raffaele and Gourvil, Priscillia and Chanoine, M{\'e}lanie and Marie, Dominique and Vaulot, Daniel and Sarno, Diana}, editor = {Wood, M.} } @article {Parks2017, title = {Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)}, journal = {American Journal of Botany}, volume = {105}, number = {3}, year = {2017}, note = {tex.mendeley-tags: RCC205,RCC80}, pages = {1{\textendash}18}, keywords = {and, b, c, citation, diatoms, e, gene tree, genome duplication, j, n, nakov, paleopolyploidy, parks m, polyploidy, RCC205, RCC80, ruck, synonymous divergence, t, these authors contributed equally, to this work, wickett}, doi = {10.1101/181115}, author = {Parks, Matthew and Nakov, Teofil and Ruck, Elizabeth and Wickett, Norman J and Alverson, Andrew J and Rice, Ada L and Conservation, Plant and Botanic, Chicago and Glencoe, Garden} } @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 {Derelle2017, title = {Prasinovirus attack of ostreococcus is furtive by day but savage by night}, journal = {Journal of Virology}, volume = {92}, number = {4}, year = {2017}, note = {tex.mendeley-tags: RCC4221}, month = {nov}, pages = {JVI.01703{\textendash}17}, abstract = {Prasinoviruses are large DNA viruses that infect diverse genera of green microalgae worldwide in aquatic ecosystems, but molecular knowledge of their life-cycles is lacking. Several complete genomes of both these viruses and their marine algal hosts are now available and have been used to show the pervasive presence of these species in microbial metagenomes. We have analysed the life-cycle of OtV5, a lytic virus, using RNA-Seq from 12 time points of healthy or infected Ostreococcus tauri cells over a day/night cycle in culture. In the day, viral gene transcription remained low while host nitrogen metabolism gene transcription was initially strongly repressed for two successive time points before being induced for 8 hours, but in the night viral transcription increased steeply while host nitrogen metabolism genes were repressed and many host functions that are normally reduced in the night appeared to be compensated either by genes expressed from the virus or by increased expression of a subset of 4.4 \% of the host{\textquoteright}s genes. Some host cells lysed progressively during the night, but a larger proportion lysed the following morning. Our data suggest that the life-cycles of algal viruses mirror the diurnal rhythms of their hosts.}, keywords = {accepted 9, mamiellophyceae, ncldv, Ostreococcus, phycodnaviridae, prasinophytes, RCC4221, received 28 september 2017}, issn = {0022-538X}, doi = {10.1128/JVI.01703-17}, url = {http://jvi.asm.org/lookup/doi/10.1128/JVI.01703-17}, author = {Derelle, Evelyne and Yau, Sheree and Moreau, Herv{\'e} and Grimsley, Nigel H.} } @article {Limardo2017, title = {Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton}, journal = {Environmental Microbiology}, year = {2017}, note = {tex.mendeley-tags: RCC1105,RCC715,RCC716,RCC809}, month = {jun}, keywords = {RCC1105, RCC715, RCC716, RCC809}, issn = {14622912}, doi = {10.1111/1462-2920.13812}, url = {http://doi.wiley.com/10.1111/1462-2920.13812}, author = {Limardo, Alexander J. and Sudek, Sebastian and Choi, Chang Jae and Poirier, Camille and Rii, Yoshimi M. and Blum, Marguerite and Roth, Robyn and Goodenough, Ursula and Church, Matthew J. and Worden, Alexandra Z.} } @article {Dominguez-Martin2017, title = {Quantitative proteomics shows extensive remodeling induced by nitrogen limitation in prochlorococcus marinus SS120}, journal = {mSystems}, volume = {2}, number = {3}, year = {2017}, note = {tex.mendeley-tags: RCC156}, month = {jun}, pages = {e00008{\textendash}17}, abstract = {Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation. In total, 1,072 proteins, corresponding to 57\% of the theoretical proteome, were identified{\textemdash}the maximum proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007 proteins. Statistically significant changes ( P value of {\textexclamdown}0.05) were observed for 408 proteins, with the majority of proteins (92.4\%) downregulated after 8 h of treatment. There was a strong decrease in ribosomal proteins upon azaserine addition, while many transporters were increased. The regulatory proteins P II and PipX were decreased, and the global nitrogen regulator NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of proteins involved in nitrogen uptake and assimilation.}, keywords = {RCC156}, issn = {2379-5077}, doi = {10.1128/mSystems.00008-17}, url = {http://msystems.asm.org/lookup/doi/10.1128/mSystems.00008-17}, author = {Dom{\'\i}nguez-Mart{\'\i}n, Maria Agustina and G{\'o}mez-Baena, Guadalupe and D{\'\i}ez, Jes{\'u}s and L{\'o}pez-Grueso, Maria Jos{\'e} and Beynon, Robert J. and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel}, editor = {Huber, Julie A.} } @article {Andersen2017, title = {Rediscovery of the Ochromonas type species Ochromonas triangulata (Chrysophyceae) from its type locality (Lake Veysove, Donetsk region, Ukraine)}, journal = {Phycologia}, volume = {56}, number = {6}, year = {2017}, note = {tex.ids= Andersen2017a tex.mendeley-tags: 2017,RCC21}, pages = {591{\textendash}604}, abstract = {Ochromonas triangulata, the type species for a genus with over 125 taxa, was collected for only the second time, again from the type locality. Cell morphology, cell division, palmelloid stage and cyst structure generally agreed with the original description. Molecular phylogenetic analysis based on the 18S rRNA gene revealed 13 clades of Ochromonas-like flagellates as well as the clade represented by our O. triangulata strain and the nearly identical strain RCC-21/AC025. We also conducted a concatenated analysis using the 18S rRNA and the rbcL genes, and we recovered the same 14 clades. One clade, containing strains CCAP 933/27 and CCMP1861, previously named Ochromonas tuberculata, was re-identified as Chrysastrella paradoxa and Chrysastrella breviappendiculata, respectively. One clade included the Poterioochromonas strains but we were unable to convincingly connect species names to the strains because authentic strains were unknown or not examined. Organisms in the clade that included the well-known Ochromonas danica were assigned to Chlorochromonas. The generic name Melkoniania gen. nov. was proposed for one distinct clade of marine flagellates. These changes addressed some of the issues associated with the polyphyletic Ochromonas sensu lato but many problems remained.}, keywords = {2017, RCC21}, issn = {0031-8884}, doi = {10.2216/17-15.1}, url = {http://www.phycologia.org/doi/10.2216/17-15.1}, author = {Andersen, Robert A. and Graf, Louis and Malakhov, Yuriy and Yoon, Hwan Su} } @article {Arias2017, title = {Removal and biodegradation of phenanthrene, fluoranthene and pyrene by the marine algae rhodomonas baltica enriched from north atlantic coasts}, journal = {Bulletin of Environmental Contamination and Toxicology}, volume = {98}, number = {3}, year = {2017}, note = {tex.mendeley-tags: RCC350}, pages = {392{\textendash}399}, abstract = {This study is focused on the removal, accumulation and degradation of three environmental ubiquitous polycyclic aromatic hydrocarbons (PAHs), phenanthrene (PHE), fluoranthene (FLA) and pyrene (PYR), by the marine alga Rhodomonas baltica enriched from the English Channel. After separation, purification and culture in several phases, R. baltica was exposed to PAH concentrations that are frequently encountered in the field in several anthropized environments. The results showed that R. baltica can grow under PAH stress, efficiently remove up to 70\% of these compounds from the medium by 216 h of culture and selectively bioaccumulate PAHs by their hydrophobicity. Between PHE, FLA and PYR, phenanthrene was the compound with higher degradation rates throughout incubation. The equilibrium partitioning theoretical approach showed that physico-chemical partitioning, rather than active bioconcentration, was the major factor governing the bioaccumulation, outlying a potential application in decontamination processes for this species.}, keywords = {RCC350}, issn = {1432-0800}, doi = {10.1007/s00128-016-1967-4}, url = {https://doi.org/10.1007/s00128-016-1967-4}, author = {Arias, Andr{\'e}s H and Souissi, Anissa and Glippa, Olivier and Roussin, Marion and Dumoulin, David and Net, Sopheak and Ouddane, Baghdad and Souissi, Sami} } @article {Cuvelier2017, title = {Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress}, journal = {PLOS ONE}, volume = {12}, number = {3}, year = {2017}, note = {ISBN: 1111111111 tex.mendeley-tags: RCC299}, month = {mar}, pages = {e0172135}, keywords = {RCC299}, issn = {1932-6203}, doi = {10.1371/journal.pone.0172135}, url = {http://dx.plos.org/10.1371/journal.pone.0172135}, author = {Cuvelier, Marie L and Guo, Jian and Ortiz, Alejandra C. and van Baren, Marijke J. and Tariq, Muhammad Akram and Partensky, Fr{\'e}d{\'e}ric and Worden, Alexandra Z}, editor = {Cockshutt, Amanda M.} } @article {Simon2017, title = {Revision of the genus micromonas manton et parke (chlorophyta, mamiellophyceae), of the type species m. pusilla (butcher) manton \& parke and of the species m. commoda van baren, bachy and worden and description of two new species based on the genetic}, journal = {Protist}, volume = {168}, number = {5}, year = {2017}, note = {tex.mendeley-tags: 2017,RCC1109,RCC114,RCC2306,RCC2308,RCC299,RCC372,RCC373,RCC418,RCC434,RCC447,RCC448,RCC449,RCC450,RCC451,RCC461,RCC465,RCC472,RCC497,RCC498,RCC570,RCC629,RCC647,RCC658,RCC676,RCC692,RCC746,RCC803,RCC804,RCC805,RCC806,RCC807,RCC808,RCC828,RCC829,RCC830,RCC831,RCC833,RCC834,RCC835,RCC836,sbr?hyto$_\textrmd$ipo}, month = {nov}, pages = {612{\textendash}635}, keywords = {2017, ASSEMBLE, rcc, RCC1109, RCC114, RCC2306, RCC2308, RCC299, RCC372, RCC373, RCC418, RCC434, RCC447, RCC448, RCC449, RCC450, RCC451, RCC461, RCC465, RCC472, RCC497, RCC498, RCC570, RCC629, RCC647, RCC658, RCC676, RCC692, RCC746, RCC803, RCC804, RCC805, RCC806, RCC807, RCC808, RCC828, RCC829, RCC830, RCC831, RCC833, RCC834, RCC835, RCC836, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo}, issn = {14344610}, doi = {10.1016/j.protis.2017.09.002}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1434461017300780}, author = {Simon, Nathalie and Foulon, Elodie and Grulois, Daphne and Six, Christophe and Desdevises, Yves and Latimier, Marie and Le Gall, Florence and Tragin, Margot and Houdan, Aude and Derelle, Evelyne and Jouenne, Fabien and Marie, Dominique and Le Panse, Sophie and Vaulot, Daniel and Marin, Birger} } @article {Demory2017, title = {Temperature is a key factor in Micromonas{\textendash}virus interactions}, journal = {The ISME Journal}, volume = {11}, number = {3}, year = {2017}, note = {Publisher: Nature Publishing Group tex.mendeley-tags: 2017,RCC4229,RCC4253,RCC4265,RCC451,RCC829,RCC834,sbr?hyto$_\textrmd$ipo,sbr?hyto?app}, month = {mar}, pages = {601{\textendash}612}, abstract = {The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4{\textendash}32.5 {\textdegree}C. Similar growth temperature optima (Topt) were predicted for all three hosts but Mic-B exhibited a broader thermal tolerance than Mic-A and Mic-C, suggesting distinct thermoacclimation strategies. Similarly, the MicV-C virus displayed a remarkable thermal stability compared with MicV-A and MicV-B. Despite these divergences, infection dynamics showed that temperatures below Topt lengthened lytic cycle kinetics and reduced viral yield and, notably, that infection at temperatures above Topt did not usually result in cell lysis. Two mechanisms operated depending on the temperature and the biological system. Hosts either prevented the production of viral progeny or maintained their ability to produce virions with no apparent cell lysis, pointing to a possible switch in the viral life strategy. Hence, temperature changes critically affect the outcome of Micromonas infection and have implications for ocean biogeochemistry and evolution.}, keywords = {2017, RCC4229, RCC4253, RCC4265, RCC451, RCC829, RCC834, sbr?hyto$_\textrmd$ipo, sbr?hyto?app}, issn = {1751-7362}, doi = {10.1038/ismej.2016.160}, url = {http://dx.doi.org/10.1038/ismej.2016.160 http://www.nature.com/doifinder/10.1038/ismej.2016.160}, author = {Demory, David and Arsenieff, Laure and Simon, Nathalie and Six, Christophe and Rigaut-jalabert, Fabienne and Marie, Dominique and Ge, Pei and Bigeard, Estelle and Jacquet, St{\'e}phan and Sciandra, Antoine and Bernard, Olivier and Rabouille, Sophie and Baudoux, Anne-claire} } @article {Bolton2016, title = {Decrease in coccolithophore calcification and CO2 since the middle Miocene}, journal = {Nature Communications}, volume = {7}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc}, pages = {10284}, abstract = {Marine algae are instrumental in carbon cycling and atmospheric carbon dioxide (CO2) regulation. One group, coccolithophores, uses carbon to photosynthesize and to calcify, covering their cells with chalk platelets (coccoliths). How ocean acidification influences coccolithophore calcification is strongly debated, and the effects of carbonate chemistry changes in the geological past are poorly understood. This paper relates degree of coccolith calcification to cellular calcification, and presents the first records of size-normalized coccolith thickness spanning the last 14 Myr from tropical oceans. Degree of calcification was highest in the low-pH, high-CO2 Miocene ocean, but decreased significantly between 6 and 4 Myr ago. Based on this and concurrent trends in a new alkenone ep record, we propose that decreasing CO2 partly drove the observed trend via reduced cellular bicarbonate allocation to calcification. This trend reversed in the late Pleistocene despite low CO2, suggesting an additional regulator of calcification such as alkalinity. 1}, keywords = {2016, rcc}, issn = {2041-1723}, doi = {10.1038/ncomms10284}, url = {http://www.nature.com/doifinder/10.1038/ncomms10284}, author = {Bolton, Clara T. and Hern{\'a}ndez-S{\'a}nchez, Mar{\'\i}a T. and Fuertes, Miguel-{\'A}ngel and Gonz{\'a}lez-Lemos, Sa{\'u}l and Abrevaya, Lorena and M{\'e}ndez-Vicente, Ana and Flores, Jos{\'e}-Abel and Probert, Ian and Giosan, Liviu and Johnson, Joel and Stoll, Heather M.} } @article {Ichinomiya2016, title = {Diversity and oceanic distribution of Parmales (Bolidophyceae), a picoplankton group closely related to diatoms}, journal = {The ISME Journal}, volume = {in press}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, keywords = {2016, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, doi = {10.1038/ismej.2016.38}, author = {Ichinomiya, Mutsuo and Lopes dos Santos, A and Gourvil, Priscillia and Yoshikawa, Shinya and Kamiya, Mitsunobu and Ohki, Kaori and Audic, S and de Vargas, Colomban and Vaulot, Daniel and Kuwata, Akira} } @article {Klouch2016, title = {Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France)}, journal = {FEMS Microbiology Ecology}, volume = {92}, number = {7}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo}, month = {jul}, pages = {fiw101}, abstract = {The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces of the species presence in the study area dated back to 1873 {\textpm} 6. Specific aDNA could be quantified by a newly-developed real-time PCR assay in the upper core layers, in which the germination of the species (in up to 17-19 year-old sediments) was also obtained. In both cores studied, our quantitative paleogenetic data showed a statistically significant increasing trend in the abundance of A. minutum ITS1 rDNA copies over time, corroborating three decades of local plankton data that have documented an increasing trend in the species cell abundance. By comparison, paleogenetic data of the dinoflagellate Scrippsiella donghaienis did not show a coherent trend between the cores studied, supporting the hypothesis of the existence of a species-specific dynamic of A. minutum in the study area. This work contributes to the development of paleoecological research, further showing its potential for biogeographical, ecological and evolutionary studies on marine microbes.}, keywords = {2016, rcc, sbr?hyto$_\textrmd$ipo}, issn = {1574-6941}, doi = {10.1093/femsec/fiw101}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27162179 https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw101}, author = {Klouch, Khadidja Z and Schmidt, Sabine and Andrieux-Loyer, Fran{\c c}oise and Le Gac, Micka{\"e}l and Hervio-Heath, Dominique and Qui-Minet, Zujaila N and Qu{\'e}r{\'e}, Julien and Bigeard, Estelle and Guillou, Laure and Siano, Raffaele}, editor = {Laanbroek, Riks} } @article {Waltman2016, title = {Identifying aspects of the post-transcriptional program governing the proteome of the green alga micromonas pusilla.}, journal = {PloS one}, volume = {11}, number = {7}, year = {2016}, note = {ISBN: 10.1371/journal.pone.0155839 Publisher: Public Library of Science tex.mendeley-tags: 2016,RCC,rcc834}, month = {jan}, pages = {e0155839}, abstract = {Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote ({\textexclamdown}2 ??m diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3{\textquoteright} UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.}, keywords = {2016, rcc, RCC834}, issn = {1932-6203}, doi = {10.1371/journal.pone.0155839}, url = {http://dx.doi.org/10.1371/journal.pone.0155839}, author = {Waltman, Peter H and Guo, Jian and Reistetter, Emily Nahas and Purvine, Samuel and Ansong, Charles K and van Baren, Marijke J and Wong, Chee-Hong and Wei, Chia-Lin and Smith, Richard D and Callister, Stephen J and Stuart, Joshua M and Worden, Alexandra Z} } @article {LopesdosSantos2016a, title = {Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII}, journal = {Journal of Phycology}, volume = {52}, number = {1}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc,rcc1124,rcc15,rcc1871,rcc2337,rcc2339,rcc287,rcc3374,rcc3376,rcc3402,rcc719,rcc856,rcc857,rcc996,rcc998,sbr?hyto$_\textrmd$ipo}, pages = {148{\textendash}155}, abstract = {The ecological importance and diversity of pico/ nanoplanktonic algae remains poorly studied in marine waters, in part because many are tiny and without distinctive morphological features. Amongst green algae, Mamiellophyceae such as Micromonas or Bathycoccus are dominant in coastal waters while prasinophytes clade VII, yet not formerly described, appear to be major players in open oceanic waters. The pigment composition of 14 strains representative of different subclades of clade VII was analyzed using a method that improves the separation of loroxanthin and neoxanthin. All the prasinophytes clade VII analyzed here showed a pigment composition similar to that previously reported for RCC287 corresponding to pigment group prasino-2A. However, we detected in addition astaxanthin for which it is the first report in prasinophytes. Among the strains analyzed, the pigment signature is qualitatively similar within subclades A and B. By contrast, RCC3402 from subclade C (Picocystis) lacks loroxanthin, astaxanthin, and antheraxanthin but contains alloxanthin, diatoxanthin, and monadoxanthin that are usually found in diatoms or cryptophytes. For subclades A and B, loroxanthin was lowest at highest light irradiance suggesting a light-harvesting role of this pigment in clade VII as in Tetraselmis.}, keywords = {2016, MACUMBA, rcc, RCC1124, RCC15, RCC1871, RCC2337, RCC2339, RCC287, RCC3374, RCC3376, RCC3402, RCC719, RCC856, RCC857, RCC996, RCC998, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, sbr?hyto$_\textrmd$ipo}, doi = {10.1111/jpy.12376}, author = {Lopes dos Santos, Adriana and Gourvil, Priscillia and Rodriguez-Hernandez, Francisco and Garrido, Jos{\'e} Luis and Vaulot, Daniel} } @article {Garrido2016, title = {Pigment variations in Emiliania huxleyi (CCMP370) as a response to changes in light intensity or quality}, journal = {Environmental Microbiology}, volume = {18}, number = {12}, year = {2016}, note = {tex.mendeley-tags: 2016,rcc1255}, month = {dec}, pages = {4412{\textendash}4425}, keywords = {2016, RCC1255}, issn = {14622912}, doi = {10.1111/1462-2920.13373}, url = {http://doi.wiley.com/10.1111/1462-2920.13373}, author = {Garrido, Jos{\'e} L. and Brunet, Christophe and Rodr{\'\i}guez, Francisco} } @article {Percopo2016b, title = {Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex}, journal = {Journal of Phycology}, volume = {52}, number = {2}, year = {2016}, note = {tex.mendeley-tags: RCC2002,RCC2004,RCC2005,RCC2517}, month = {apr}, pages = {184{\textendash}199}, abstract = {A new nontoxic Pseudo-nitzschia species belonging to the P. pseudodelicatissima complex, P. arctica, was isolated from different areas of the Arctic. The erection of P. arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P. fryxelliana, and represents a new case of crypticity within the genus. Despite their morphological similarity, the two species are not closely related in phylogenies based on LSU, ITS and rbcL. Interestingly, P. arctica is phylogenetically most closely related to P. granii and P. subcurvata, from which the species is, however, morphologically different. P. granii and P. subcurvata lack the central larger interspace which is one of the defining features of the P. pseudodelicatissima complex. The close genetic relationship between P. arctica and the two species P. granii and P. subcurvata is demonstrated by analysis of the secondary structure of ITS2 which revealed no compensatory base changes, two hemi-compensatory base changes, and two deletions in P. arctica with respect to the other two species. These findings emphasize that rates of morphological differentiation, molecular evolution and speciation are often incongruent for Pseudo-nitzschia species, resulting in a restricted phylogenetic value for taxonomic characters used to discriminate species. The description of a new cryptic species, widely distributed in the Arctic and potentially representing an endemic component of the Arctic diatom flora, reinforces the idea of the existence of noncosmopolitan Pseudo-nitzschia species and highlights the need for combined morphological and molecular analyses to assess the distributional patterns of phytoplankton species.}, keywords = {RCC2002, RCC2004, RCC2005, RCC2517}, issn = {00223646}, doi = {10.1111/jpy.12395}, url = {http://doi.wiley.com/10.1111/jpy.12395}, author = {Percopo, Isabella and Ruggiero, Maria Valeria and Balzano, Sergio and Gourvil, Priscillia and Lundholm, Nina and Siano, Raffaele and Tammilehto, Anna and Vaulot, Daniel and Sarno, Diana}, editor = {Mock, T.} } @article {Lu2016, title = {Transcriptomic profiling of Alexandrium fundyense during physical interaction with or exposure to chemical signals from the parasite Amoebophrya.}, journal = {Molecular ecology}, volume = {25}, number = {6}, year = {2016}, note = {tex.mendeley-tags: 2016,RCC3037}, pages = {1294{\textendash}307}, abstract = {Toxic microalgae have their own pathogens, and understanding the way in which these microalgae respond to antagonistic attacks may provide information about their capacity to persist during harmful algal bloom events. Here, we compared the effects of the physical presence of the parasite Amoebophrya sp. and exposure to waterborne cues from cultures infected with this parasite, on gene expression by the toxic dinoflagellates, Alexandrium fundyense. Compared with control samples, a total of 14,882 Alexandrium genes were differentially expressed over the whole-parasite infection cycle at three different time points (0, 6 and 96 h). RNA sequencing analyses indicated that exposure to the parasite and parasitic waterborne cues produced significant changes in the expression levels of Alexandrium genes associated with specific metabolic pathways. The observed upregulation of genes associated with glycolysis, the tricarboxylic acid cycle, fatty acid β-oxidation, oxidative phosphorylation and photosynthesis suggests that parasite infection increases the energy demand of the host. The observed upregulation of genes correlated with signal transduction indicates that Alexandrium could be sensitized by parasite attacks. This response might prime the defence of the host, as indicated by the increased expression of several genes associated with defence and stress. Our findings provide a molecular overview of the response of a dinoflagellate to parasite infection.}, keywords = {2016, Animals, Dinoflagellida, Dinoflagellida: genetics, Dinoflagellida: parasitology, Gene Expression Profiling, Harmful Algal Bloom, Host-Parasite Interactions, Metabolic Networks and Pathways, Microalgae, Microalgae: genetics, Microalgae: parasitology, Parasites, Parasites: chemistry, RCC3037, RNA, Sequence Analysis, Signal Transduction, Transcriptome}, issn = {1365-294X}, doi = {10.1111/mec.13566}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26841307}, author = {Lu, Yameng and Wohlrab, Sylke and Groth, Marco and Gl{\"o}ckner, Gernot and Guillou, Laure and John, Uwe} } @article {Yau2016, title = {A viral immunity chromosome in the marine picoeukaryote, ostreococcus tauri}, journal = {PLOS Pathogens}, volume = {12}, number = {10}, year = {2016}, note = {tex.mendeley-tags: 2016,RCC299,RCC4221,RCC809}, month = {oct}, pages = {e1005965}, keywords = {2016, RCC299, RCC4221, RCC809}, issn = {1553-7374}, doi = {10.1371/journal.ppat.1005965}, url = {http://dx.plos.org/10.1371/journal.ppat.1005965}, author = {Yau, Sheree and Hemon, Claire and Derelle, Evelyne and Moreau, Herv{\'e} and Piganeau, Gwenael and Grimsley, Nigel}, editor = {Ding, Shou-Wei} } @article {Supraha2015, title = {Eco-physiological adaptation shapes the response of calcifying algae to nutrient limitation}, journal = {Scientific Reports}, volume = {5}, number = {November}, year = {2015}, note = {Publisher: Nature Publishing Group tex.mendeley-tags: 2015,RCC1323,RCC1334}, pages = {16499}, keywords = {2015, RCC1323, RCC1334}, issn = {2045-2322}, doi = {10.1038/srep16499}, url = {http://www.nature.com/articles/srep16499}, author = {{\v S}upraha, Luka and Gerecht, Andrea C. and Probert, Ian and Henderiks, Jorijntje} } @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 {MartinezMartinez2015, title = {New lipid envelope-containing dsDNA virus isolates infecting Micromonas pusilla reveal a separate phylogenetic group}, journal = {Aquatic Microbial Ecology}, volume = {74}, year = {2015}, note = {tex.mendeley-tags: rcc}, pages = {17{\textendash}28}, abstract = {Viral infection of phytoplankton has major implications for biochemical and energy cycles, community dynamics, and microbial evolution in the marine environment. The non-bloom forming picoplankter Micromonas pusilla, a significant component of the plankton community worldwide, is known to be susceptible to infection by both dsDNA and dsRNA viruses. Logically, comprehensive knowledge of the ecology of M. pusilla requires a better understanding of the div - ersity and infection mechanisms of their viruses. Here, we investigated 19 new M. pusilla-specific viruses (MpVs) isolated from different locations and years. We performed partial characterization of those MpVs including structural characteristics, genome size, phylogenetic analysis based on partial DNA polymerase gene sequences, host range, and stability at different temperatures and upon exposure to chloroform. Combined, these characteristics allowed classification of the MpVs into 2 groups. Exposure to chloroform led to loss of infectivity by all MpVs in one group, which sug- gests the presence of an outer lipid envelope. In addition, all except one of the members in that group formed a monophylogenetic clade that was distinct from all other MpV isolates. The distinc- tive characteristics of the 2 MpV groups suggest different infection strategies, which may have im- portant implications for the ecology of both host and virus populations in the environment. Knowl- edge gained from our study adds value to the MpV isolates as a scientific resource as it will aid in developing and testing in the laboratory new hypotheses about the ecological and biogeochemical implications of M. pusilla viral infection in the environment}, keywords = {characterization, micromonas pusilla, ncldv, phycodnaviridae, rcc, RCC?o?dd, virus diversity}, issn = {0948-3055}, doi = {10.3354/ame01723}, url = {http://www.int-res.com/abstracts/ame/v74/n1/p17-28/}, author = {Mart{\'\i}nez Mart{\'\i}nez, J and Boere, A and Gilg, I and van Lent, Jwm and Witte, Hj and van Bleijswijk, Jdl and Brussaard, Cpd} } @article {Stuken2015, title = {Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains}, journal = {Frontiers in Microbiology}, volume = {6}, number = {May}, year = {2015}, note = {tex.mendeley-tags: 2015,rcc,sbr?hyto$_\textrmd$ipo}, pages = {1{\textendash}10}, abstract = {Dinoflagellates are microscopic aquatic eukaryotes with huge genomes and an unusual cell regulation. For example, most genes are present in numerous copies and all copies seem to be obligatorily transcribed. The consequence of the gene copy number (CPN) for final protein synthesis is, however, not clear. One such gene is sxtA, the starting gene of paralytic shellfish toxin (PST) synthesis. PSTs are small neurotoxic compounds that can accumulate in the food chain and cause serious poisoning incidences when ingested. They are produced by dinoflagellates of the genera Alexandrium, Gymnodium, and Pyrodinium. Here we investigated if the genomic CPN of sxtA4 is related to PST content in Alexandrium minutum cells. SxtA4 is the 4th domain of the sxtA gene and its presence is essential for PST synthesis in dinoflagellates. We used PST and genome size measurements as well as quantitative PCR to analyze sxtA4 CPN and toxin content in 15 A. minutum strains. Our results show a strong positive correlation between the sxtA4 CPN and the total amount of PST produced in actively growing A. minutum cells. This correlation was independent of the toxin profile produced, as long as the strain contained the genomic domains sxtA1 and sxtA4.}, keywords = {2015, Alexandrium, copy, copy number variation, Dinoflagellate, gene dosage, genome size, number variation, paralytic shellfish toxin, paralytic shellfish toxin (PST), pst, rcc, RCC?o?dd, saxitoxin, saxitoxin (STX), sbr?hyto$_\textrmd$ipo, stx, sxtA}, issn = {1664-302X}, doi = {10.3389/fmicb.2015.00404}, url = {http://journal.frontiersin.org/article/10.3389/fmicb.2015.00404}, author = {St{\"u}ken, Anke and Riob{\'o}, Pilar and Franco, Jos{\'e} and Jakobsen, Kjetill S. and Guillou, Laure and Figueroa, Rosa I.} } @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 {Decelle2015, title = {PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy}, journal = {Molecular Ecology Resources}, volume = {15}, number = {6}, year = {2015}, note = {tex.mendeley-tags: 2015,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {1435{\textendash}1445}, abstract = {Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF data- base that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classifica- tion were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.}, keywords = {2015, MACUMBA, rcc, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, issn = {1755098X}, doi = {10.1111/1755-0998.12401}, url = {http://doi.wiley.com/10.1111/1755-0998.12401}, author = {Decelle, Johan and Romac, Sarah and Stern, Rowena F. and Bendif, El Mahdi and Zingone, Adriana and Audic, St{\'e}phane and Guiry, Michael D. and Guillou, Laure and Tessier, D{\'e}sir{\'e} and Le Gall, Florence and Gourvil, Priscillia and dos Santos, Adriana Lopes and Probert, Ian and Vaulot, Daniel and de Vargas, Colomban and Christen, Richard} } @article {Abby2014, title = {Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers?}, journal = {Frontiers in microbiology}, volume = {5}, year = {2014}, note = {Publisher: Frontiers tex.mendeley-tags: rcc}, month = {jan}, pages = {505}, abstract = {Marine phytoplankton produce half of the oxygen we breathe and their astounding diversity is just starting to be unraveled. Many microbial phytoplankton are thought to be phototrophic, depending solely on inorganic sources of carbon and minerals for growth rather than preying on other planktonic cells. However, there is increasing evidence that symbiotic associations, to a large extent with bacteria, are required for vitamin or nutrient uptake for many eukaryotic microalgae. Here, we use in silico approaches to look for putative symbiotic interactions by analysing the gene content of microbial communities associated with 13 different Ostreococcus tauri (Chlorophyta, Mamilleophyceae) cultures sampled from the Mediterranean Sea. While we find evidence for bacteria in all cultures, there is no ubiquitous bacterial group, and the most prevalent group, Flavobacteria, is present in 10 out of 13 cultures. Among seven of the microbiomes, we detected genes predicted to encode type 3 secretion systems (T3SS, in 6/7 microbiomes) and/or putative type 6 secretion systems (T6SS, in 4/7 microbiomes). Phylogenetic analyses show that the corresponding genes are closely related to genes of systems identified in bacterial-plant interactions, suggesting that these T3SS might be involved in cell-to-cell interactions with O. tauri.}, keywords = {bacterial diversity, Bacterial symbiosis, Illumina sequencing, microbiome, Ostreococcus, phycosphere, phytoplankton, picoeukaryote, rcc, RCC?o?dd, secretion system}, issn = {1664-302X}, doi = {10.3389/fmicb.2014.00505}, url = {http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00505/abstract}, author = {Abby, Sophie S and Touchon, Marie and De Jode, Aurelien and Grimsley, Nigel and Piganeau, Gwenael} } @article {Pittera2014, title = {Connecting thermal physiology and latitudinal niche partitioning in marine Synechococcus}, journal = {The ISME journal}, volume = {8}, number = {6}, year = {2014}, note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: 2014,macumba,microb3,rcc,sbr?hyto?app}, pages = {1221{\textendash}1236}, abstract = {Marine Synechococcus cyanobacteria constitute a monophyletic group that displays a wide latitudinal distribution, ranging from the equator to the polar fronts. Whether these organisms are all physiologically adapted to stand a large temperature gradient or stenotherms with narrow growth temperature ranges has so far remained unexplored. We submitted a panel of six strains, isolated along a gradient of latitude in the North Atlantic Ocean, to long- and short-term variations of temperature. Upon a downward shift of temperature, the strains showed strikingly distinct resistance, seemingly related to their latitude of isolation, with tropical strains collapsing while northern strains were capable of growing. This behaviour was associated to differential photosynthetic performances. In the tropical strains, the rapid photosystem II inactivation and the decrease of the antioxydant [beta]-carotene relative to chl a suggested a strong induction of oxidative stress. These different responses were related to the thermal preferenda of the strains. The northern strains could grow at 10[thinsp][deg]C while the other strains preferred higher temperatures. In addition, we pointed out a correspondence between strain isolation temperature and phylogeny. In particular, clades I and IV laboratory strains were all collected in the coldest waters of the distribution area of marine Synechococus. We, however, show that clade I Synechococcus exhibit different levels of adaptation, which apparently reflect their location on the latitudinal temperature gradient. This study reveals the existence of lineages of marine Synechococcus physiologically specialised in different thermal niches, therefore suggesting the existence of temperature ecotypes within the marine Synechococcus radiation.}, keywords = {2014, adaptation, ecotype, MACUMBA, marine cyanobacteria, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app, Synechococcus, temperature}, doi = {10.1038/ismej.2013.228}, url = {http://dx.doi.org/10.1038/ismej.2013.228 10.1038/ismej.2013.228}, author = {Pittera, Justine and Humily, Florian and Thorel, Maxine and Grulois, Daphne and Garczarek, Laurence and Six, Christophe} } @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 {Lepelletier2014a, title = {Dinomyces arenysensis gen. et sp. nov. (rhizophydiales, dinomycetaceae fam. nov.), a chytrid infecting marine dinoflagellates}, journal = {Protist}, volume = {165}, number = {2}, year = {2014}, note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app}, pages = {230{\textendash}244}, abstract = {Environmental 18S rRNA gene surveys of microbial eukaryotes have recently revealed the diversity of major parasitic agents in pelagic freshwater systems, consisting primarily of chytrid fungi. To date, only a few studies have reported the presence of chydrids in the marine environment and a limited number of marine chytrids have been properly identified and characterized. Here, we report the isolation and cultivation of a marine chytrid from samples taken during a bloom of the toxic dinoflagellate Alexandrium minutum in the Arenys de Mar harbour (Mediterranean Sea, Spain). Cross-infections using cultures and natural phytoplankton communities revealed that this chytrid is only able to infect certain species of dinoflagellates, with a rather wide host range but with a relative preference for Alexandrium species. Phylogenetic analyses showed that it belongs to the order Rhizophydiales, but cannot be included in any of the existing families within this order. Several ultrastructural characters confirmed the placement of this taxon within the Rhizophydiales as well its novelty notably in terms of zoospore structure. This marine chytridial parasitoid is described as a new genus and species, Dinomyces arenysensis, within the Dinomycetaceae fam. nov.}, keywords = {2014, chytrid, Dinoflagellates, Dinomyces arenysensis, Fungi, MACUMBA, microbial parasitoids, rcc, RCC?o?dd, Rhizophydiales., SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app}, doi = {10.1016/j.protis.2014.02.004}, url = {http://www.sciencedirect.com/science/article/pii/S1434461014000170}, author = {Lepelletier, Fr{\'e}d{\'e}ric and Karpov, Sergey A and Alacid, Elisabet and Le Panse, Sophie and Bigeard, Estelle and Garc{\'e}s, Esther and Jeanthon, Christian and Guillou, Laure} } @article {Biller2014, title = {Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus}, journal = {Scientific Data}, volume = {1}, year = {2014}, note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc}, month = {sep}, pages = {1{\textendash}11}, abstract = {The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity{\textemdash}both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.}, keywords = {Environmental microbiology, genomics, rcc, RCC?o?dd}, issn = {2052-4463}, doi = {10.1038/sdata.2014.34}, url = {http://www.nature.com/articles/sdata201434}, author = {Biller, Steven J. and Berube, Paul M. and Berta-Thompson, Jessie W. and Kelly, Libusha and Roggensack, Sara E. and Awad, Lana and Roache-Johnson, Kathryn H. and Ding, Huiming and Giovannoni, Stephen J. and Rocap, Gabrielle and Moore, Lisa R. and Chisholm, Sallie W. and H. and Ding, Huiming and Giovannoni, Stephen J. and Moore, Lisa R. and Chisholm, Sallie W.} } @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 {Lepelletier2014, title = {Parvilucifera rostrata sp. nov., a novel parasite in the phylum Perkinsozoa that infects the toxic dinoflagellate Alexandrium minutum (Dinophyceae)}, journal = {Protist}, volume = {165}, year = {2014}, note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app}, pages = {31{\textendash}49}, keywords = {2014, MACUMBA, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo, sbr?hyto?app}, doi = {10.1016/j.protis.2013.09.005}, author = {Lepelletier, F and Karpov, S A and Le Panse, S and Bigeard, E and Skovgaard, A and Jeanthon, C and Guillou, L} } @article {Dia2014, title = {Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum}, journal = {Molecular Ecology}, volume = {23}, number = {3}, year = {2014}, note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo}, pages = {549{\textendash}560}, abstract = {Organisms with sexual and asexual reproductive systems benefit from both types of reproduction. Sexual recombination generates new combinations of alleles, whereas clonality favours the spread of the fittest genotype through the entire population. Therefore, the rate of sexual vs. clonal reproduction has a major influence on the demography and genetic structure of natural populations. We addressed the effect of reproductive system on populations of the dinoflagellate Alexandrium minutum. More specifically, we monitored the spatiotemporal genetic diversity during and between bloom events in two estuaries separated by 150 km for two consecutive years. An analysis of population genetic patterns using microsatellite markers revealed surprisingly high genotypic and genetic diversity. Moreover, there was significant spatial and temporal genetic differentiation during and between bloom events. Our results demonstrate that (i) interannual genetic differentiation can be very high, (ii) estuaries are partially isolated during bloom events and (iii) genetic diversity can change rapidly during a bloom event. This rapid genetic change may reflect selective effects that are nevertheless not strong enough to reduce allelic diversity. Thus, sexual reproduction and/or migration may regularly erase any genetic structure produced within estuaries during a bloom event.}, keywords = {2014, bloom dynamics, clonality, linkage disequilibrium, MACUMBA, population genetics, rcc, RCC?o?dd, resting cyst, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sexual reproduction}, doi = {10.1111/mec.12617}, url = {http://dx.doi.org/10.1111/mec.12617}, author = {Dia, A and Guillou, L and Mauger, S and Bigeard, E and Marie, D and Valero, M and Destombe, C} } @article {Clerissi2014, title = {Unveiling of the diversity of prasinoviruses (phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-Amplified DNA polymerase and major capsid protein genes}, journal = {Applied and Environmental Microbiology}, volume = {80}, number = {10}, year = {2014}, note = {tex.mendeley-tags: Micromonas,rcc}, pages = {3150{\textendash}3160}, abstract = {Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.}, keywords = {Micromonas, rcc, TARA-Oceans}, doi = {10.1128/aem.00123-14}, url = {http://aem.asm.org/content/80/10/3150.abstract}, author = {Clerissi, Camille and Grimsley, Nigel and Ogata, Hiroyuki and Hingamp, Pascal and Poulain, Julie and Desdevises, Yves} } @article {Humily2013, title = {A gene island with two possible configurations is involved in chromatic acclimation in marine synechococcus}, journal = {PLoS ONE}, volume = {8}, number = {12}, year = {2013}, note = {Publisher: Public Library of Science tex.mendeley-tags: 2013,macumba,rcc,sbr?hyto?app}, pages = {e84459}, abstract = {{\textexclamdown}p{\textquestiondown}{\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown}, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine {\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown} radiation. A specific gene island was identified in all CA4-performing strains, containing two genes ({\textexclamdown}italic{\textquestiondown}fciA{\textexclamdown}/italic{\textquestiondown}/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called {\textexclamdown}italic{\textquestiondown}fciC{\textexclamdown}/italic{\textquestiondown}. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} is expressed more in blue light than green light, this is the reverse for {\textexclamdown}italic{\textquestiondown}mpeW{\textexclamdown}/italic{\textquestiondown}, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process.{\textexclamdown}/p{\textquestiondown}}, keywords = {2013, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app}, doi = {10.1371/journal.pone.0084459}, url = {http://dx.doi.org/10.1371/journal.pone.0084459}, author = {Humily, Florian and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Farrant, Gregory K and Ratin, Morgane and Marie, Dominique and Garczarek, Laurence} } @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 {Shukla2013, title = {Phycoerythrin-specific bilin lyase{\textendash}isomerase controls blue-green chromatic acclimation in marine Synechococcus}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2013}, note = {tex.mendeley-tags: 2013,rcc,sbr?hyto?app}, pages = {20136{\textendash}20141}, keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app}, doi = {10.1073/pnas.1211777109}, author = {Shukla, A and Biswas, A and Blot, N and Partensky, F and Karty, J A and Hammad, L A and Garczarek, L and Gutu, A and Schluchter, W M and Kehoe, D M} } @article {Vandepoele2013, title = {pico-PLAZA, a genome database of microbial photosynthetic eukaryotes}, journal = {Environmental Microbiology}, volume = {15}, number = {8}, year = {2013}, note = {tex.mendeley-tags: Micromonas,rcc}, pages = {2147{\textendash}2153}, abstract = {With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.}, keywords = {Micromonas, rcc}, doi = {10.1111/1462-2920.12174}, url = {http://dx.doi.org/10.1111/1462-2920.12174}, author = {Vandepoele, Klaas and Van Bel, Michiel and Richard, Guilhem and Van Landeghem, Sofie and Verhelst, Bram and Moreau, Herv{\'e} and Van de Peer, Yves and Grimsley, Nigel and Piganeau, Gwenael} } @article {Guillou2013, title = {The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy}, journal = {Nucleic Acids Research}, volume = {41}, year = {2013}, note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {D597{\textendash}D604}, keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, doi = {10.1093/nar/gks1160}, author = {Guillou, Laure and Bachar, Dipankar and Audic, St{\'e}phane and Bass, David and Berney, Cedric and Bittner, Lucie and Boutte, Christophe and Burgaud, Gaetan and de Vargas, Colomban and Decelle, Johan and del Campo, Javier and Dolan, John and Dunthorn, Micah and Bente, Edvardsen and Holzmann, Maria and Kooistra, Wiebe H C F and Lara, Enrique and Lebescot, Noan and Logares, Ramiro and Mah{\'e}, Fr{\'e}d{\'e}ric and Massana, Ramon and Montresor, Marina and Morard, Raphael and Not, Fabrice and Pawlowski, Jan and Probert, Ian and Sauvadet, Anne-Laure and Siano, Raffaele and Stoeck, Thorsten and Vaulot, Daniel and Zimmermann, Pascal and Christen, Richard} } @article {Balzano2012, title = {Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples}, journal = {The ISME journal}, volume = {6}, number = {8}, year = {2012}, note = {ISBN: 1751-7362 tex.mendeley-tags: 2012,rcc,sbr?hyto$_\textrmd$ipo}, pages = {1480{\textendash}1498}, abstract = {The composition of photosynthetic pico and nanoeukaryotes was investigated in the North East Pacific and the Arctic Ocean with special emphasis on the Beaufort Sea during the MALINA cruise in summer 2009. Photosynthetic populations were sorted using flow cytometry based on their size and pigment fluorescence. Diversity of the sorted photosynthetic eukaryotes was determined using terminal-restriction fragment length polymorphism analysis and cloning/sequencing of the 18S ribosomal RNA gene. Picoplankton was dominated by Mamiellophyceae, a class of small green algae previously included in the prasinophytes: in the North East Pacific, the contribution of an Arctic Micromonas ecotype increased steadily northward becoming the only taxon occurring at most stations throughout the Beaufort Sea. In contrast, nanoplankton was more diverse: North Pacific stations were dominated by Pseudo-nitzschia sp. whereas those in the Beaufort Sea were dominated by two distinct Chaetoceros species as well as by Chrysophyceae, Pelagophyceae and Chrysochromulina spp.. This study confirms the importance of Arctic Micromonas within picoplankton throughout the Beaufort Sea and demonstrates that the photosynthetic picoeukaryote community in the Arctic is much less diverse than at lower latitudes. Moreover, in contrast to what occurs in warmer waters, most of the key pico- and nanoplankton species found in the Beaufort Sea could be successfully established in culture.}, keywords = {2012, ASSEMBLE, Chaetoceros, MALINA, Pyramimonas, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, Souchotheque}, issn = {1751-7362}, doi = {10.1038/ismej.2011.213}, author = {Balzano, Sergio and Marie, Dominique and Gourvil, Priscillia and Vaulot, Daniel} } @article {Balzano2012a, title = {Diversity of cultured photosynthetic flagellates in the North East Pacific and Arctic Oceans in summer}, journal = {Biogeosciences}, volume = {9}, year = {2012}, note = {tex.mendeley-tags: 2012,macumba,rcc,sbr?hyto$_\textrmd$ipo}, pages = {4553{\textendash}4571}, keywords = {2012, ASSEMBLE, MACUMBA, MALINA, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo}, doi = {10.5194/bg-9-4553-2012}, author = {Balzano, Sergio and Gourvil, Priscillia and Siano, Raffaele and Chanoine, M{\'e}lanie and Marie, Dominique and Lessard, Sylvie and Sarno, Diana and Vaulot, Daniel} } @article {Giovagnetti2012, title = {Growth and photophysiological responses of two picoplanktonic {\textexclamdown}i{\textquestiondown}Minutocellus species{\textexclamdown}/i{\textquestiondown}, strains RCC967 and RCC703 (Bacillariophyceae)}, journal = {European Journal of Phycology}, volume = {47}, number = {4}, year = {2012}, note = {ISBN: 0967-0262 tex.mendeley-tags: rcc703,rcc967}, pages = {408{\textendash}420}, abstract = {Reaching up to 50\% of the total biomass in oligotrophic waters and armed with a set of ecological and biological properties related to their small size, picophytoplankton ({\textexclamdown}3.0 mm) are a good model to address ecophysiological questions regarding phytoplankton biodiversity. Two picoplanktonic diatoms, one isolated from an upwelling ecosystem in the Pacific Ocean (Minutocellus sp., strain RCC967), and another from oceanic waters in the Indian Ocean (Minutocellus sp., strain RCC703) were used to test hypotheses on the functional relation between ecological niche adaptation and photosynthetic regulation capacity and efficiency. Cultures were subjected to five sine light climates, each one set to peak at a different photon flux density, respectively 10, 50, 100, 250 and 500 mmol photons m(-2) s(-1). Growth rate, photosynthesis, non-photochemical fluorescence quenching, pigment composition, and particulate organic carbon and nitrogen content were followed daily for 5 days. Growth rate and physiological response curves were different in the two species, in agreement with their distinct habitats of origin. Such differences could be related to the diverse photoacclimative strategies displayed by the two species, revealing a clear adaptive divergence despite their close taxonomic relationship. Photoacclimative strategies of the two picoplanktonic diatoms are discussed in the light of functional diversity and ecosystem adaptation.}, keywords = {carbon, diatoms, elemental stoichiometry, fluctuating light, marine-phytoplankton, non-photochemical fluorescence quenching, phaeodactylum-tricornutum, photoacclimation, photoprotection, photoregulation, Photosynthesis, picoeukaryotes, planktonic diatoms, rcc703, rcc967, RCC?o?dd, violaxanthin cycle, Xanthophyll cycle, xanthophyll-cycle activity}, doi = {10.1080/09670262.2012.733030}, author = {Giovagnetti, V and Cataldo, M L and Conversano, F and Brunet, C} } @article {Decelle2012, title = {An original mode of symbiosis in open ocean plankton}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, note = {tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo}, pages = {18000{\textendash}18005}, keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1073/pnas.1212303109}, author = {Decelle, J and Probert, I and Bittner, L and Desdevises, Y and Colin, S and de Vargas, C and Gali, M and Simo, R and Not, F} } @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 {Treusch2012, title = {Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids}, journal = {The ISME journal}, volume = {6}, year = {2012}, note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,RCC,rcc}, pages = {481{\textendash}492}, keywords = {Bathycoccus, CHRYSOPHYCEAE, key?aper, Micromonas, Ostreococcus, pelagophyceae, Prasinophyceae, Prymnesiophyceae, QPCR, rcc, TRFLP}, doi = {10.1038/ismej.2011.117}, url = {http://dx.doi.org/10.1038/ismej.2011.117 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2011117s1.html}, author = {Treusch, Alexander H and Demir-Hilton, Elif and Vergin, Kevin L and Worden, Alexandra Z and Carlson, Craig A and Donatz, Michael G and Burton, Robert M and Giovannoni, Stephen J} } @article {Clerissi2012, title = {Prasinoviruses of the marine green alga Ostreococcus tauri are mainly species specific}, journal = {Journal of Virology}, volume = {86}, number = {8}, year = {2012}, note = {tex.mendeley-tags: RCC1110,RCC1114,RCC1115,RCC1116,RCC1117,RCC1123,RCC1558,RCC1561,RCC745}, pages = {4611{\textendash}4619}, abstract = {Prasinoviruses infecting unicellular green algae in the order Mamiellales (class Mamiellophyceae) are commonly found in coastal marine waters where their host species frequently abound. We tested 40 Ostreococcus tauri viruses on 13 independently isolated wild-type O. tauri strains, 4 wild-type O. lucimarinus strains, 1 Ostreococcus sp. ({\textquotedblleft}Ostreococcus mediterraneus{\textquotedblright}) clade D strain, and 1 representative species of each of two other related species of Mamiellales, Bathycoccus prasinos and Micromonas pusilla. Thirty-four out of 40 viruses infected only O. tauri, 5 could infect one other species of the Ostreococcus genus, and 1 infected two other Ostreococcus spp., but none of them infected the other genera. We observed that the overall susceptibility pattern of Ostreococcus strains to viruses was related to the size of two host chromosomes known to show intraspecific size variations, that genetically related viruses tended to infect the same host strains, and that viruses carrying inteins were strictly strain specific. Comparison of two complete O. tauri virus proteomes revealed at least three predicted proteins to be candidate viral specificity determinants.}, keywords = {rcc, RCC1110, RCC1114, RCC1115, RCC1116, RCC1117, RCC1123, RCC1558, RCC1561, RCC745}, issn = {0022-538X}, doi = {10.1128/jvi.07221-11}, url = {http://jvi.asm.org/content/86/8/4611.abstract}, author = {Clerissi, Camille and Desdevises, Yves and Grimsley, Nigel} } @article {Guillou2011, title = {Characterization of the Parmales: much more than the resolution of a taxonomic enigma}, journal = {Journal of Phycology}, volume = {47}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo}, pages = {2{\textendash}4}, keywords = {2011, rcc, SBR$_\textrmP$hyto, sbr?hyto$_\textrmd$ipo}, doi = {10.1111/j.1529-8817.2010.00951.x}, author = {Guillou, L} } @article {Jeanthon2011, title = {Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea}, journal = {Biogeosciences}, volume = {8}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app}, pages = {1955{\textendash}1970}, keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo, sbr?hyto?app}, doi = {10.5194/bg-8-1955-2011}, author = {Jeanthon, Christian and Boeuf, Dominique and Dahan, Oc{\'e}ane and Le Gall, F and Garczarek, Laurence and Bendif, El Mahdi and Lehours, Anne-Catherine} } @article {Demir-Hilton2011, title = {Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus}, journal = {The ISME journal}, volume = {5}, year = {2011}, note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: RCC745}, pages = {1095{\textendash}1107}, keywords = {rcc, RCC745}, doi = {10.1038/ismej.2010.209}, url = {http://dx.doi.org/10.1038/ismej.2010.209 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2010209s1.html http://www.nature.com/ismej/journal/v5/n7/full/ismej2010209a.html}, author = {Demir-Hilton, Elif and Sudek, Sebastian and Cuvelier, Marie L and Gentemann, Chelle L and Zehr, Jonathan P and Worden, Alexandra Z} } @article {Karpowicz2011, title = {The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage}, journal = {Journal of Biological Chemistry}, volume = {286}, number = {24}, year = {2011}, note = {ISBN: 1083-351X (Electronic)0?021-9258 (Linking) tex.mendeley-tags: rcc745,rcc809}, month = {jun}, pages = {21427{\textendash}21439}, abstract = {The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52\% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18\% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32\% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30\% are eukaryote-specific. Finally, 8\% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.}, keywords = {RCC745, RCC809}, issn = {0021-9258}, doi = {10.1074/jbc.M111.233734}, url = {http://www.jbc.org/cgi/doi/10.1074/jbc.M111.233734}, author = {Karpowicz, Steven J. and Prochnik, Simon E. and Grossman, Arthur R. and Merchant, Sabeeha S.} } @article {Bendif2011, title = {Integrative taxonomy of the pavlovophyceae (haptophyta) : a reassessment}, journal = {Protist}, volume = {162}, year = {2011}, note = {tex.mendeley-tags: 2011,RCC1526,RCC1527,RCC1528,RCC1529,RCC1530,RCC1531,RCC1532,RCC1533,RCC1534,RCC1535,RCC1536,RCC1537,RCC1538,RCC1539,RCC1540,RCC1541,RCC1542,RCC1543,RCC1544,RCC1545,RCC1546,RCC1548,RCC1549,RCC1551,RCC1552,RCC1553,RCC1554,RCC1557,rcc,rcc1523,rcc1524,rcc1525}, pages = {738{\textendash}761}, abstract = {The Pavlovophyceae (Haptophyta) contains four genera (Pavlova, Diacronema, Exanthemachrysis and Rebecca) and only thirteen characterised species. Considering the importance of members of this class, we constructed molecular phylogenies inferred from sequencing of ribosomal gene markers with comprehensive coverage of the described diversity and using type strains when available add on culture strains. Moreover, the morphology and ultrastructure of 12 of the described species was re-examined and the pigment signatures of many culture strains were determined. The molecular analysis revealed that sequences of all described species differed, although those of Pavlova gyrans and P. pinguis were nearly identical, these potentially forming a single cryptic species complex. Four well-delineated genetic clades were identified, one of which included species of both Pavlova andDiacronema. Unique combinations of morphological/ultrastructural characters were identified foreach of these clades. The ancestral pigment signature of the Pavlovophyceae consisted of a basic set of pigments plus MV chl cPAV, the latter being entirely absent in the Pavlova + Diacronema clade and supplemented by DV chl cPAV in part of the Exanthemachrysis clade. Based on this combination of characters, we propose a taxonomic revision of the class, with transfer of several Pavlova species to an emended Diacronema genus. The evolution of the class is discussed in the context of the phylogenetic reconstruction presented.}, keywords = {2011, ASSEMBLE, rcc, RCC1523, rcc1524, rcc1525, RCC1526, RCC1527, RCC1528, RCC1529, RCC1530, RCC1531, RCC1532, RCC1533, RCC1534, RCC1535, RCC1536, RCC1537, RCC1538, RCC1539, RCC1540, RCC1541, RCC1542, RCC1543, RCC1544, RCC1545, RCC1546, RCC1548, RCC1549, RCC1551, RCC1552, RCC1553, RCC1554, RCC1557, SBR$_\textrmP$hyto$_\textrmE$PPO}, doi = {10.1016/j.protis.2011.05.001}, author = {Bendif, E M and Probert, I and Herv{\'e}, A and Billard, C and Goux, D and Lelong, C and Cadoret, J P and V{\'e}ron, B} } @article {Blot2011, title = {Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress}, journal = {Plant Physiology}, volume = {156}, year = {2011}, note = {ISBN: 1532-2548 (Electronic) 0032-0889 (Linking) tex.mendeley-tags: 2011,rcc,sbr?hyto?app}, pages = {1934{\textendash}1954}, abstract = {Marine Synechococcus undergo a wide range of environmental stressors, especially high and variable irradiance, which may induce oxidative stress through the generation of reactive oxygen species (ROS). While light and ROS could act synergistically on the impairment of photosynthesis, inducing photodamage and inhibiting photosystem II repair, acclimation to high irradiance is also thought to confer resistance to other stressors. To identify the respective roles of light and ROS in the photoinhibition process and detect a possible light-driven tolerance to oxidative stress, we compared the photophysiological and transcriptomic responses of Synechococcus sp. WH7803 acclimated to low (LL) or high light (HL) to oxidative stress, induced by hydrogen peroxide (H2O2) or methylviologen. While photosynthetic activity was much more affected in HL than in LL cells, only HL cells were able to recover growth and photosynthesis after addition of 25 microM H2O2. Depending upon light conditions and H2O2 concentration, the latter oxidizing agent induced photosystem II inactivation through both direct damages to the reaction centres and inhibition of its repair cycle. Although the global transcriptome response appeared similar in LL and HL cells, some processes were specifically induced in HL cells that seemingly helped them withstand oxidative stress, including enhancement of photoprotection and ROS detoxification, repair of ROS-driven damages and regulation of redox state. Detection of putative LexA binding sites allowed the identification of the putative LexA regulon, which was down-regulated in HL compared to LL cells, but up-regulated by oxidative stress under both growth irradiances.}, keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=21670225}, author = {Blot, N and Mella-Flores, D and Six, C and Lecorguille, G and Boutte, C and Peyrat, A and Monnier, A and Ratin, M and Gourvil, P and Campbell, D A and Garczarek, L} } @article {Gobler2011, title = {Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {11}, year = {2011}, note = {ISBN: 0027-8424 tex.mendeley-tags: RCC,rcc}, pages = {4352{\textendash}4357}, abstract = {Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium-and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.}, keywords = {brown-tide blooms, comparative genomics, eutrophication, evolution, genome, genomics, long-island, marine-phytoplankton, multidrug, proteins, proteome, rcc, repeat, responses, san-francisco bay, signal-transduction, transporters}, doi = {10.1073/pnas.1016106108}, author = {Gobler, C J and Berry, D L and Dyhrman, S T and Wilhelm, S W and Salamov, A and Lobanov, A V and Zhang, Y and Collier, J L and Wurch, L L and Kustka, A B and Dill, B D and Shah, M and VerBerkmoes, N C and Kuo, A and Terry, A and Pangilinan, J and Lindquist, E A and Lucas, S and Paulsen, I T and Hattenrath-Lehmann, T K and Talmage, S C and Walker, E A and Koch, F and Burson, A M and Marcoval, M A and Tang, Y Z and LeCleir, G R and Coyne, K J and Berg, G M and Bertrand, E M and Saito, M A and Gladyshev, V N and Grigoriev, I V} } @article {Beaufort2011, title = {Sensitivity of coccolithophores to carbonate chemistry and ocean acidification}, journal = {Nature}, volume = {476}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo}, pages = {80{\textendash}83}, abstract = {Coccolithophores produce the major fraction of pelagic carbonate, a key component of the carbon cycle. The effect of elevated CO2 on their calcification is poorly understood. Culture experiments have yielded varied calcification responses to increased pCO2 between and within coccolithophore taxa. We used a novel automated method for pattern recognition and morphometric analysis to quantify the calcite mass of coccolithophores from {\textquestiondown}700 samples from present past (last 40-Kyr) oceans. Comparison of morphological data with ocean carbonate chemistry reconstructed in both space and time indicate decreasing calcification with increasing pCO2, and decreasing CO32. At pH {\textexclamdown}8.0, delicate Emiliania huxleyi are strongly affected by decalcification. However, highly calcified E. huxleyi morphotypes predominate in waters with lowest pH. This suggests that coccolithophore strains pre-adapted to future, more acidic oceans already populate regions of contemporary oceans. The future carbon feedback from coccolithophore calcification will depend on the genetic diversity and adaptability of coccolithophore populations.}, keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1038/nature10295}, author = {Beaufort, L and Probert, I and de Garidel-Thoron, T and Bendif, E M and Ruiz-Pino, D and Metzl, N and Goyet, C and Buchet, N and Coupel, P and Grelaud, M and Rost, B and Rickaby, R E M and de Vargas, C} } @article {gile_dna_2010, title = {Dna Barcoding of Chlorarachniophytes Using Nucleomorph Its Sequences1}, journal = {Journal of Phycology}, volume = {46}, number = {4}, year = {2010}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1529-8817.2010.00851.x}, pages = {743{\textendash}750}, abstract = {Chlorarachniophytes are a small group of marine photosynthetic protists. They are best known as examples of an intermediate stage of secondary endosymbiosis: their plastids are derived from green algae and retain a highly reduced nucleus, called a nucleomorph, between the inner and outer pairs of membranes. Chlorarachniophytes can be challenging to identify to the species level, due to their small size, complex life cycles, and the fact that even genus-level diagnostic morphological characters are observable only by EM. Few species have been formally described, and many available culture collection strains remain unnamed. To alleviate this difficulty, we have developed a barcoding system for rapid and accurate identification of chlorarachniophyte species in culture, based on the internal transcribed spacer (ITS) region of the nucleomorph rRNA cistron. Although this is a multicopy locus, encoded in both subtelomeric regions of each chromosome, interlocus variability is low due to gene conversion by homologous recombination in this region. Here, we present barcode sequences for 39 cultured strains of chlorarachniophytes (>80\% of currently available strains). Based on barcode data, other published molecular data, and information from culture records, we were able to recommend names for 21 out of the 24 unidentified, partially identified, or misidentified chlorarachniophyte strains in culture. Most strains could be assigned to previously described species, but at least two to as many as five new species may be present among cultured strains.}, keywords = {Bigelowiella, Chlorarachnion, culture collections, Gymnochlora, internal transcribed spacer, Lotharella, Norrisiella, Partenskyella, RCC337, RCC375, RCC376, RCC435, RCC530, RCC531, RCC623, RCC626}, issn = {1529-8817}, doi = {10.1111/j.1529-8817.2010.00851.x}, url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.2010.00851.x}, author = {Gile, Gillian H. and Stern, Rowena F. and James, Erick R. and Keeling, Patrick J.} } @article {Moreau2010, title = {Marine Prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer}, journal = {Journal of Virology}, volume = {84}, number = {24}, year = {2010}, note = {ISBN: 0022-538X tex.mendeley-tags: RCC1105,RCC745}, pages = {12555{\textendash}12563}, abstract = {Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.}, keywords = {RCC1105, RCC745}, doi = {10.1128/jvi.01123-10}, author = {Moreau, Herv{\'e} and Piganeau, Gwenael and Desdevises, Yves and Cooke, Richard and Derelle, Evelyne and Grimsley, Nigel} } @article {Scanlan2009, title = {Ecological genomics of marine picocyanobacteria}, journal = {Microbiology and Molecular Biology Reviews}, volume = {73}, year = {2009}, note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?app}, pages = {249{\textendash}299}, keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app}, doi = {10.1128/MMBR.00035-08}, author = {Scanlan, D J and Ostrowski, M and Mazard, S and Dufresne, A and Garczarek, L and Hess, W R and Post, A F and Hagemann, M and Paulsen, I and Partensky, F} } @article {Gadler2009, title = {Enantiocomplementary inverting sec-alkylsulfatase activity in cyano- and thio-bacteria Synechococcus and Paracoccus spp.: selectivity enhancement by medium engineering}, journal = {Tetrahedron: Asymmetry}, volume = {20}, year = {2009}, note = {tex.mendeley-tags: rcc}, pages = {115{\textendash}118}, keywords = {rcc}, doi = {10.1016/j.tetasy.2009.01.007}, author = {Gadler, Petra and Reiter, Tamara C and Hoelsch, Kathrin and Weuster-Botz, Dirk and Fabe, Kurt} } @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 {Richier2009, title = {Light-dependent transcriptional regulation of genes of biogeochemical interest in the diploid and haploid life cycle stages of Emiliania huxleyi}, journal = {Applied and Environmental Microbiology}, volume = {75}, year = {2009}, note = {Edition: 2009/03/24 ISBN: 1098-5336 (Electronic) tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo}, pages = {3366{\textendash}3369}, abstract = {The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore Emiliania huxleyi was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested.}, keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1128/aem.02737-08}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=19304825}, author = {Richier, S and Kerros, M E and de Vargas, C and Haramaty, L and Falkowski, P G and Gattuso, J P} } @article {Sharon2009, title = {Photosystem I gene cassettes are present in marine virus genomes}, journal = {Nature}, volume = {461}, number = {7261}, year = {2009}, note = {Publisher: Macmillan Publishers Limited. All rights reserved tex.mendeley-tags: RCC307}, pages = {258{\textendash}262}, keywords = {RCC307, SBR$_\textrmP$hyto$_\textrmP$PM}, doi = {10.1038/nature08284}, url = {http://dx.doi.org/10.1038/nature08284 http://www.nature.com/nature/journal/v461/n7261/suppinfo/nature08284_S1.html}, author = {Sharon, Itai and Alperovitch, Ariella and Rohwer, Forest and Haynes, Matthew and Glaser, Fabian and Atamna-Ismaeel, Nof and Pinter, Ron Y and Partensky, Fr{\'e}d{\'e}ric and Koonin, Eugene V and Wolf, Yuri I and Nelson, Nathan and B{\'e}j{\`a}, Oded} } @article {Jancek2008, title = {Clues about the genetic basis of adaptation emerge from comparing the proteomes of two Ostreococcus ecotypes (Chlorophyta, Prasinophyceae)}, journal = {Molecular Biology and Evolution}, volume = {25}, number = {11}, year = {2008}, note = {Edition: 2008/08/06 ISBN: 1537-1719 (Electronic) 0737-4038 (Linking) tex.mendeley-tags: RCC,rcc}, pages = {2293{\textendash}2300}, abstract = {We compared the proteomes of two picoplanktonic Ostreococcus unicellular green algal ecotypes to analyze the genetic basis of their adaptation with their ecological niches. We first investigated the function of the species-specific genes using Gene Ontology databases and similarity searches. Although most species-specific genes had no known function, we identified several species-specific functions involved in various cellular processes, which could be critical for environmental adaptations. Additionally, we investigated the rate of evolution of orthologous genes and its distribution across chromosomes. We show that faster evolving genes encode significantly more membrane or excreted proteins, consistent with the notion that selection acts on cell surface modifications that is driven by selection for resistance to viruses and grazers, keystone actors of phytoplankton evolution. The relationship between GC content and chromosome length also suggests that both strains have experienced recombination since their divergence and that lack of recombination on the two outlier chromosomes could explain part of their peculiar genomic features, including higher rates of evolution.}, keywords = {adaptation, Base Composition, Chlorophyta/*genetics, Ecosystem, Physiological/*genetics, Phytoplankton/genetics, Proteome/*genetics, rcc, Species Specificity}, doi = {10.1093/molbev/msn168}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18678753}, author = {Jancek, S and Gourbiere, S and Moreau, H and Piganeau, G} } @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 {Cardol2008, title = {An original adaptation of photosynthesis in the marine green alga Ostreococcus}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {22}, year = {2008}, note = {tex.mendeley-tags: RCC745,RCC809}, pages = {7881{\textendash}7886}, abstract = {Adaptation of photosynthesis in marine environment has been examined in two strains of the green, picoeukaryote : OTH95, a surface/high-light strain, and RCC809, a deep-sea/low-light strain. Differences between the two strains include changes in the light-harvesting capacity, which is lower in OTH95, and in the photoprotection capacity, which is enhanced in OTH95. Furthermore, RCC809 has a reduced maximum rate of O evolution, which is limited by its decreased photosystem I (PSI) level, a possible adaptation to Fe limitation in the open oceans. This decrease is, however, accompanied by a substantial rerouting of the electron flow to establish an HO-to-HO cycle, involving PSII and a potential plastid plastoquinol terminal oxidase. This pathway bypasses electron transfer through the cytochrome complex and allows the pumping of {\^a}{\texteuro}{\oe}extra{\^a}{\texteuro} protons into the thylakoid lumen. By promoting the generation of a large {\^I}{\textquotedblright}pH, it facilitates ATP synthesis and nonphotochemical quenching when RCC809 cells are exposed to excess excitation energy. We propose that the diversion of electrons to oxygen downstream of PSII, but before PSI, reflects a common and compulsory strategy in marine phytoplankton to bypass the constraints imposed by light and/or nutrient limitation and allow successful colonization of the open-ocean marine environment.}, keywords = {rcc, RCC745, RCC809}, doi = {10.1073/pnas.0802762105}, url = {http://www.pnas.org/content/105/22/7881.abstract}, author = {Cardol, Pierre and Bailleul, Benjamin and Rappaport, Fabrice and Derelle, Evelyne and Baal, Daniel and Breyton, C{\'e}cile and Bailey, Shaun and Wollman, Francis Andr{\'e} and Grossman, Arthur and Moreau, Herv{\'e} and Finazzi, Giovanni} } @article {Bowler2008, title = {The Phaeodactylum genome reveals the evolutionary history of diatom genomes}, journal = {Nature}, volume = {456}, number = {7219}, year = {2008}, note = {Publisher: Macmillan Publishers Limited. All rights reserved tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo}, pages = {239{\textendash}244}, keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPOdipo, sbr?hyto?ppo}, doi = {10.1038/nature07410}, url = {http://dx.doi.org/10.1038/nature07410 http://www.nature.com/nature/journal/v456/n7219/suppinfo/nature07410_S1.html}, author = {Bowler, Chris and Allen, Andrew E and Badger, Jonathan H and Grimwood, Jane and Jabbari, Kamel and Kuo, Alan and Maheswari, Uma and Martens, Cindy and Maumus, Florian and Otillar, Robert P and Rayko, Edda and Salamov, Asaf and Vandepoele, Klaas and Beszteri, Bank and Gruber, Ansgar and Heijde, Marc and Katinka, Michael and Mock, Thomas and Valentin, Klaus and Verret, Frederic and Berges, John A and Brownlee, Colin and Cadoret, Jean-Paul and Chiovitti, Anthony and Choi, Chang Jae and Coesel, Sacha and De Martino, Alessandra and Detter, J Chris and Durkin, Colleen and Falciatore, Angela and Fournet, Jerome and Haruta, Miyoshi and Huysman, Marie J J and Jenkins, Bethany D and Jiroutova, Katerina and Jorgensen, Richard E and Joubert, Yolaine and Kaplan, Aaron and Kroger, Nils and Kroth, Peter G and La Roche, Julie and Lindquist, Erica and Lommer, Markus and Martin-Jezequel, Veronique and Lopez, Pascal J and Lucas, Susan and Mangogna, Manuela and McGinnis, Karen and Medlin, Linda K and Montsant, Anton and Secq, Marie-Pierre Oudot-Le and Napoli, Carolyn and Obornik, Miroslav and Parker, Micaela Schnitzler and Petit, Jean-Louis and Porcel, Betina M and Poulsen, Nicole and Robison, Matthew and Rychlewski, Leszek and Rynearson, Tatiana A and Schmutz, Jeremy and Shapiro, Harris and Siaut, Magali and Stanley, Michele and Sussman, Michael R and Taylor, Alison R and Vardi, Assaf and von Dassow, Peter and Vyverman, Wim and Willis, Anusuya and Wyrwicz, Lucjan S and Rokhsar, Daniel S and Weissenbach, Jean and Armbrust, E Virginia and Green, Beverley R and Van de Peer, Yves and Grigoriev, Igor V} } @article {Rodriguez2008, title = {Phylogenetic and morphological characterization of the green algae infesting blue mussel Mytilus edulis in the North and South Atlantic}, journal = {Diseases of Aquatic Organisms}, volume = {81}, year = {2008}, note = {tex.mendeley-tags: RCC894}, pages = {231{\textendash}240}, keywords = {rcc, RCC894, SBR$_\textrmP$hyto$_\textrmD$PO}, doi = {10.3354/dao01956}, author = {Rodriguez, F and Feist, S W and Guillou, L and Harkestad, L S and Bateman, K and Renault, T and Mortensen, S} } @article {LeGall2008, title = {Picoplankton diversity in the south-east pacific ocean from cultures}, journal = {Biogeosciences}, volume = {5}, year = {2008}, note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app}, pages = {203{\textendash}214}, keywords = {2008, PICOFUNPAC, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app}, doi = {10.5194/bg-5-203-2008}, author = {Le Gall, F and Rigaut-Jalabert, F and Marie, D and Garczareck, L and Viprey, M and Godet, A and Vaulot, D} } @article {Viprey2008, title = {Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach}, journal = {Environmental Microbiology}, volume = {10}, number = {7}, year = {2008}, note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo}, pages = {1804{\textendash}1822}, abstract = {The genetic diversity of picoplanktonic (i.e. cells that can pass through a 3 mum pore-size filter) green algae was investigated in the Mediterranean Sea in late summer by a culture-independent approach. Genetic libraries of the 18S rRNA gene were constructed using two different primer sets. The first set is commonly used to amplify the majority of eukaryotic lineages, while the second was composed of a general eukaryotic forward primer and a reverse primer biased towards the phylum Chloroplastida. A total of 3980 partial environmental sequences were obtained: 1668 using the general eukaryotic primer set and 2312 using the Chloroplastida-biased primer set. Of these sequences, 65 (4\%) and 594 (26\%) belonged to the Chloroplastida respectively. A 99.5\% sequence similarity cut-off value allowed classification of these 659 Chloroplastida sequences into 74 different operational taxonomic units. A majority of the Chloroplastida sequences (99\%) belonged to the prasinophytes. In addition to the seven independent prasinophyte lineages previously described, we discovered two new clades (clades VIII and IX), as well as a significant genetic diversity at the species and subspecies levels, notably among the genera Crustomastix, Dolichomastix and Mamiella (Mamiellales), but also within Pyramimonas and Halosphaera (Pyramimonadales). Such diversity within prasinophytes has not previously been observed by cloning approaches, illustrating the power of using targeted primers for clone library construction. Prasinophyte assemblages differed especially in relation to nutrient levels. Micromonas and Ostreococcus were mainly recovered from mesotrophic areas, whereas Mamiella, Crustomastix and Dolichomastix were mostly detected in oligotrophic surface waters. Within genera such as Ostreococcus or Crustomastix for which several clades were observed, depth seemed to be the main factor controlling differential distribution of genotypes.}, keywords = {2008, rcc, sbr?hyto$_\textrmd$ipo}, author = {Viprey, Manon and Guillou, Laure and Ferr{\'e}ol, Martial and Vaulot, Daniel} } @article {Six2007, title = {Diversity and evolution of phycobilisomes in marine Synechococcus spp. - a comparative genomics study}, journal = {Genome Biology}, volume = {8}, year = {2007}, note = {tex.mendeley-tags: 2007,rcc,sbr?hyto?app}, pages = {R259}, keywords = {2007, rcc, SBR$_\textrmP$hyto, sbr?hyto?app}, doi = {10.1186/gb-2007-8-12-r259}, author = {Six, C and Thomas, J.-C. and Garczarek, L and Ostrowski, M and Dufresne, A and Blot, N and Scanlan, D J and Partensky, F} } @article {Lobanov2007, title = {Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life}, journal = {Genome Biology}, volume = {8}, number = {9}, year = {2007}, note = {tex.mendeley-tags: RCC,rcc}, pages = {R198}, abstract = {BACKGROUND: Selenocysteine (Sec) is a selenium-containing amino acid that is co-translationally inserted into nascent polypeptides by recoding UGA codons. Selenoproteins occur in both eukaryotes and prokaryotes, but the selenoprotein content of organisms (selenoproteome) is highly variable and some organisms do not utilize Sec at all. RESULTS: We analyzed the selenoproteomes of several model eukaryotes and detected 26 and 29 selenoprotein genes in the green algae Ostreococcus tauri and Ostreococcus lucimarinus, respectively, five in the social amoebae Dictyostelium discoideum, three in the fly Drosophila pseudoobscura, and 16 in the diatom Thalassiosira pseudonana, including several new selenoproteins. Distinct selenoprotein patterns were verified by metabolic labeling of O. tauri and D. discoideum with 75Se. More than half of the selenoprotein families were shared by unicellular eukaryotes and mammals, consistent with their ancient origin. Further analyses identified massive, independent selenoprotein losses in land plants, fungi, nematodes, insects and some protists. Comparative analyses of selenoprotein-rich and -deficient organisms revealed that aquatic organisms generally have large selenoproteomes, whereas several groups of terrestrial organisms reduced their selenoproteomes through loss of selenoprotein genes and replacement of Sec with cysteine. CONCLUSION: Our data suggest many selenoproteins originated at the base of the eukaryotic domain and show that the environment plays an important role in selenoproteome evolution. In particular, aquatic organisms apparently retained and sometimes expanded their selenoproteomes, whereas the selenoproteomes of some terrestrial organisms were reduced or completely lost. These findings suggest a hypothesis that, with the exception of vertebrates, aquatic life supports selenium utilization, whereas terrestrial habitats lead to reduced use of this trace element due to an unknown environmental factor.}, keywords = {rcc}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17880704}, author = {Lobanov, A V and Fomenko, D E and Zhang, Y and Sengupta, A and Hatfield, D L and Gladyshev, V N} } @article {Probert2007a, title = {Light and electron microscope observations of Algirosphaera robusta (Prymnesiophyceae)}, journal = {Journal of Phycology}, volume = {43}, year = {2007}, note = {tex.mendeley-tags: 2007,rcc}, pages = {319{\textendash}332}, keywords = {2007, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO}, doi = {10.1111/j.1529-8817.2007.00324.x}, author = {Probert, I and Fresnel, J and Billard, C and Geisen, Markus and Young, J R} } @article {Palenik2007, title = {The tiny eukaryote \textit{Ostreococcus provides genomic insights into the paradox of plankton speciation}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {18}, year = {2007}, note = {tex.mendeley-tags: RCC,rcc}, pages = {7705{\textendash}7710}, abstract = {The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.}, keywords = {rcc}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17460045}, author = {Palenik, B and Grimwood, J and Aerts, A and Rouz{\'e}, P and Salamov, A and Putnam, N and Dupont, C and Jorgensen, R and Derelle, E and Rombauts, S and Zhou, K and Otillar, R and Merchant, S S and Podell, S and Gaasterland, T and Napoli, C and Gendler, K and Manuell, A and Tai, V and Vallon, O and Piganeau, G and Jancek, S and Heijde, M and Jabbari, K and Bowler, C and Lohr, M and Robbens, S and Werner, G and Dubchak, I and Pazour, G J and Ren, Q and Paulsen, I and Delwiche, C and Schmutz, J and Rokhsar, D and Van de Peer, Y and Moreau, H and Grigoriev, I V} } @article {Bruyant2005, title = {Diel variations in the photosynthetic parameters of Prochlorococcus strain PCC 9511: combined effects of light and cell cycle}, journal = {Limnology and Oceanography}, volume = {50}, year = {2005}, note = {tex.mendeley-tags: 2005,rcc,sbr?hyto}, pages = {850{\textendash}863}, keywords = {2005, rcc, SBR$_\textrmP$hyto, sbr?hyto}, doi = {10.4319/lo.2005.50.3.0850}, author = {Bruyant, F and Babin, M and Genty, B and Prasil, O and Behrenfeld, M J and Claustre, H and Bricaud, A and Holtzendorff, J and Koblizek, M and Garczareck, L and Partensky, F} } @article {Rodriguez2005h, title = {Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae).}, journal = {Environmental Microbiology}, volume = {7}, year = {2005}, note = {tex.mendeley-tags: RCC113,RCC143,RCC343,RCC356,RCC371,RCC393,RCC410,RCC420,RCC434,RCC501,RCC658,RCC745,Rcc141}, pages = {853{\textendash}859}, keywords = {rcc, RCC113, Rcc141, RCC143, RCC343, RCC356, RCC371, RCC393, rcc410, RCC420, RCC434, rcc501, RCC658, RCC745, SBR$_\textrmP$hyto$_\textrmD$PO}, doi = {10.1111/j.1462-2920.2005.00758.x}, author = {Rodriguez, F and Derelle, E and Guillou, L and Le Gall, F and Vaulot, D and Moreau, H} } @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 {Henley2004, title = {Phylogenetic analysis of the Nannochloris-like{\textquoteright} algae and diagnoses of Picochlorum oklahomensis gen. et sp nov (Trebouxiophyceae, Chlorophyta)}, journal = {Phycologia}, volume = {43}, number = {6}, year = {2004}, note = {tex.mendeley-tags: 2004,rcc,sbr?hyto}, pages = {641{\textendash}652}, abstract = {A broadly halotolerant new isolate of a small asexual coccoid chlorophyte and six new, related freshwater isolates provided the impetus for a phylogenetic analysis of the so-called {\textquoteright}Nannochloris-like{\textquoteright} algae within the Trebouxiophyceae. Previous taxonomic disagreements concerning this group had not been rigorously tested with molecular phylogenetic analyses. We show with 18S ribosomal DNA (rDNA) sequence phylogeny that 19 of 22 isolates previously assigned to either Nannochloris or Nanochlorum fall within a diverse sister clade to a clade including the four {\textquoteright}true{\textquoteright} Chlorella species sensu loto. In addition, Marvania geminata, Gloeotila contorta, Chlorella sp. Yanaqocha RA1, Koliella spiculiformis, {\textquoteright}Chlorella minutissima{\textquoteright} C-1.1.9. and new Koliella, Gloeotila and Marvania isolates were included in the Nannochloris-like clade. Distinct freshwater and marine or saline lineages comprise at least three major subclades, generally corresponding to cell division pattern. Seven of 14 marine or saline isolates are known (and the others presumed) to divide by autosporulation. Eight freshwater isolates divide by binary fission, including two Koliella, two Gloeotila, N. bacillaris, Chlorella sp. Yanaqocha RA1, and two new unassigned isolates. Four freshwater isolates divide by budding or autosporulation (three Marvania, including CCAP 251/1b. previously assigned to N. coccoides). The autosporic taxa N. eucaryotum UTEX 2502 (marine) and C. minutissima C-1.1.9 (freshwater), which have nearly identical 18S rDNA sequences, are deeper-branching than the freshwater and marine or saline lineages. We propose including the 13 marine or saline, autosporic taxa (excluding N. eucaryotum UTEX 2502) in the new genus Picochlorum until distinctive morphological or biochemical characters are identified that would indicate multiple genera corresponding to subclades. Such characters exist in the freshwater lineages, supporting retention of Koliella, Gloeotila, Marvania and Nannochloris as distinct genera, although each is currently represented by few isolates. Nannochloris at this time may be restricted to N. bacillaris and Chlorella sp. Yanaqocha RA1. We also describe halotolerant P. oklahomensis Hironaka sp. nov. Based on 18S rDNA sequence and lack of chlorophyll b, Nannochloris sp. UTEX 2379 should be reassigned to the Eustigmatophyceae.}, keywords = {18s-, 2004, Aquatic-sciences, cell-wall, chlorella-, green-alga, life-cycle, marvania-geminata, morphology-, Nanochlorum-eucaryotum, position-, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SEQUENCES}, doi = {10.2216/i0031-8884-43-6-641.1}, author = {Henley, W J and Hironaka, J L and Guillou, L and Buchheim, M A and Buchheim, J A and Fawley, M W and Fawley, K P} } @article {Latasa2004, title = {Pigment suites and taxonomic groups in Prasinophyceae}, journal = {Journal of Phycology}, volume = {40}, number = {6}, year = {2004}, note = {tex.mendeley-tags: 2004,rcc,sbr?hyto}, month = {dec}, pages = {1149{\textendash}1155}, keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto}, issn = {00223646}, doi = {10.1111/j.1529-8817.2004.03136.x}, url = {http://doi.wiley.com/10.1111/j.1529-8817.2004.03136.x}, author = {Latasa, Mikel and Scharek, Renate and Gall, Florence Le and Guillou, Laure and Le Gall, F} } @article {Vaulot2004, title = {The roscoff culture collection (RCC): a collection dedicated to marine picoplankton}, journal = {Nova Hedwigia}, volume = {79}, number = {1/2}, year = {2004}, note = {tex.mendeley-tags: 2004,rcc,sbr?hyto}, pages = {49{\textendash}70}, keywords = {10$_\textrmb$est, 2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto}, doi = {10.1127/0029-5035/2004/0079-0049}, author = {Vaulot, D and Le Gall, F and Marie, D and Guillou, L and Partensky, F} } @article {Guillou2001, title = {Grazing impact of two small heterotrophic flagellates on Prochlorococcus and Synechococcus}, journal = {Aquatic Microbial Ecology}, volume = {26}, number = {2}, year = {2001}, note = {tex.mendeley-tags: 2001,rcc,sbr?hyto}, pages = {201{\textendash}207}, abstract = {In open oceanic waters, phytoplankton biomass is dominated by organisms below 2 to 3 mum in size (pico- and small nanophytoplankton). The cell concentration of these populations is very stable in time and space as a consequence of nutrient limitation and strong grazing pressure, Although the identity of the organisms that directly graze on picoplankton is largely unknown, they are thought to be very small, i.e. {\textexclamdown}3 to 5 {\textexclamdown}mu{\textquestiondown}m, Here, we analyze the grazing impact of 2 small flagellates, Symbiomonas scintillans and Picophagus flagellatus, upon 2 oceanic cyanobacteria, Prochlorococcus and Synechococcus. S. scintillans does not feed on the 2 cyanobacteria. In contrast, P. flagellatus appears as an active predator capable of drastically reducing prey concentrations. The flagellate displays a substantial division rate of the order of 2 doublings d(-1) when fed on Prochlorococcus cells, but no significant growth is recorded when Synechococcus is used as prey. As the majority ({\textquestiondown} 80\%) of P. flagellatus cells can pass throughout a 2 mum filter, the impact of such tiny predators should be taken into consideration during field experiments that rely on size fractionation to separate grazers from prey.}, keywords = {2001, Algal Class, Equatorial Pacific, Growth Rates, Laboratory Cultures, Marine, Nanoplankton, PICODIV, picoplankton, Prey, rcc, SBR$_\textrmP$hyto, sbr?hyto, Size, Sp Nov}, doi = {10.3354/ame026201}, author = {Guillou, L and Jacquet, S and Chr{\'e}tiennot-Dinet, M.-J. and Vaulot, D} } @article {Guillou1999, title = {Bolidomonas: a new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta)}, journal = {Journal of Phycology}, volume = {35}, year = {1999}, note = {tex.mendeley-tags: 1999,rcc,sbr?hyto}, pages = {368{\textendash}381}, abstract = {A new algal class, the Bolidophyceae (Heterokonta), is described from one genus, Bolidomonas, gen, nov., and two species, Bolidomonas pacifica, sp, nov and Bolidomonas mediterranea, sp, nov., isolated from the equatorial Pacific Ocean and the Mediterranean Sea, respectively. Both species are approximately 1.2 mu m in diameter and have two unequal flagella; the longer flagellum bears tubular hairs, whereas the shorter is smooth. The flagellar basal apparatus is restricted to two basal bodies, and there is no transitional helix. Cells are naked, devoid of walls or siliceous structures. The internal cellular organization is simple with a single plastid containing a ring genophore and a girdle lamella, one mitochondrion with tubular cristae, and one Golgi apparatus close to the basal bodies. The Mediterranean and the Pacific species differ in the insertion angle between their flagella and their pattern of swimming, these differences possibly being linked to each other. Analyses of the SSU rDNA gene place the two strains as a sister group to the diatoms, Moreover, pigment analyses confirm this position, as fucoxanthin is found as the major carotenoid in both lineages. These data strongly suggest that the ancestral heterokont that gave rise to the diatom lineage was probably a biflagellated unicell.}, keywords = {10$_\textrmb$est, 1999, Bolidophyceae, CELL-CYCLE, CHRYSOPHYCEAE, diatoms, DIVINYL-CHLOROPHYLL, FINE-STRUCTURE, FLAGELLAR APPARATUS, Heterokonta, Marine, marine picoeukaryotes, oligotrophic ocean, rcc, RNA, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCE, sp-nov, stramenopiles, ultrastructure}, doi = {10.1046/j.1529-8817.1999.3520368.x}, author = {Guillou, L and Chr{\'e}tiennot-Dinet, M.-J. and Medlin, L K and Claustre, H and Loiseaux-de Go{\"e}r, S and Vaulot, D} } @article {Guillou1999a, title = {Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions}, journal = {Applied and Environmental Microbiology}, volume = {65}, number = {10}, year = {1999}, note = {ISBN: 0099-2240 Publisher: Amer Soc Microbiology tex.address: 1325 Massachusetts Avenue, NW, Washington, DC 20005-4171, USA tex.mendeley-tags: 1999,rcc,sbr?hyto}, pages = {4528{\textendash}4536}, abstract = {The diversity and abundance of the Bolidophyceae (Heterokonta), a newly described picoplanktonic algal class which is a sister group to the diatoms, was assessed in the equatorial Pacific Ocean and in the Mediterranean Sea by culture isolation, molecular biology techniques, and pigment analyses. Eight strains of Bolidophyceae were isolated in culture from different mesotrophic and oligotrophic areas. The corresponding small subunit (SSU) rRNA gene sequences allowed us to design two probes specific for the Bolidophyceae. These probes have been used in natural samples (i) to selectively amplify and detect Bolidophyceae sequences and (ii) to quantify the relative abundance of Bolidophyceae within the picoeukaryote community. Sequences available to date indicate that the class Bolidophyceae comprises at least three different clades, two corresponding to the previously described species Bolidomonas pacifica and Bolidomonas mediterranea and the third one corresponding to a subspecies of B. Pacifica. Amplification of the SSU rRNA gene from natural samples with universal primers and hybridization using a Bolidomonas-specific probe followed by a eukaryote-specific probe allowed us to estimate the contribution of the Bolidophyceae to the eukaryotic DNA in both Pacific and Mediterranean waters to be lower than 1\%. Similarly, high-performance liquid chromatography analyses of fucoxanthin, the major carotenoid present in Bolidophyceae, indicated that less than 4\% of the total chlorophyll a in the picoplanktonic fraction in the equatorial Pacific was due to Bolidophyceae. Consequently, although strains of Bolidophyceae have been isolated from samples collected at several stations, this new class seems to have been a minor component of the natural picoeukaryotic populations in the ecosystems investigated, at least during the periods sampled.}, keywords = {1999, ATLANTIC, BACTERIOPLANKTON, community structure, flow-cytometry, MOLECULAR PHYLOGENY, PACIFIC, phytoplankton, PIGMENT SIGNATURES, rcc, RNA GENE SEQUENCE, SBR$_\textrmP$hyto, sbr?hyto, ULTRAPHYTOPLANKTON}, doi = {10.1128/AEM.65.10.4528-4536.1999}, author = {Guillou, L and Moon-van der Staay, S Y and Claustre, H and Partensky, F and Vaulot, D} } @article {Guillou1999b, title = {Symbiomonas scintillans gen. et sp nov and Picophagus flagellatus gen. et sp nov (Heterokonta): Two new heterotrophic flagellates of picoplanktonic size}, journal = {Protist}, volume = {150}, number = {4}, year = {1999}, note = {ISBN: 1434-4610 Publisher: Urban \& Fischer Verlag tex.address: Branch Office Jena, P O Box No.100 537, D-07705 Jena, Germany tex.mendeley-tags: 1999,rcc,sbr?hyto}, pages = {383{\textendash}398}, abstract = {Two new oceanic free-living heterotrophic Heterokonta species with picoplanktonic size ({\textexclamdown} 2 mu m) are described, Symbiomonas scintillans Guillou et Chretiennot-Dinet gen. Ef sp. Nov, was isolated from samples collected both in the equatorial Pacific Ocean and the Mediterranean Sea. This new species possesses ultrastructural features of the bicosoecids, such as the absence of a helix in the flagellar transitional region (found in Cafeteria roenbergensis and in a few bicosoecids), and a flagellar root system very similar to that of C. Roenbergensis, Acronema sippewissettensis, and Bicosoeca maris. This new species is characterized by a single flagellum with mastigonemes, the presence of endosymbiotic bacteria located close to the nucleus, the absence of a lorica and a R3 root composed of a 6+3+x microtubular structure. Phylogenetical analyses of nuclear-encoded SSU rDNA gene sequences indicate that this species is close to the bicosoecids C. Roenbergensis and Siluania monomastiga. Picophagus flagellatus Guillou et Chretiennot-Dinet gen. Et sp. Nov. Was collected in the equatorial Pacific Ocean, Cells are naked and possess two flagella, This species is characterized by the lack of a transitional helix and lateral filaments on the flagellar tubular hairs, the absence of siliceous scales, two unequal flagella, R1 + R3 roots, and the absence of a rhizoplast. SSU rDNA analyses place this strain at the base of the Chrysophyceae/Synurophyceae lineages.}, keywords = {1999, APPARATUS, DEVELOPAYELLA-ELEGANS, EMPHASIS, MOLECULAR PHYLOGENY, picophytoplankton, PLASTIDS, rcc, RDNA, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCES}, doi = {10.1016/S1434-4610(99)70040-4}, author = {Guillou, L and Chr{\'e}tiennot-Dinet, M.-J. and Boulben, S and Moon-van der Staay, S Y and Vaulot, D} } @article {Courties1998, title = {Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta, Prasinophyceae)}, journal = {Journal of Phycology}, volume = {34}, number = {5}, year = {1998}, note = {tex.mendeley-tags: RCC745}, pages = {844{\textendash}849}, abstract = {Ostreococcus tauri Courties et Chretiennot-Dinet is the smallest described autotrophic eukaryote dominating the phytoplanktonic assemblage of the marine Mediterranean Thau lagoon (France). Its taxonomic position was partly elucidated from ultrastructure and high-pressure liquid chromatography (HLPC) pigment analysis. The sequence analysis of the 18S rDNA gene of O. Tauri measured here is available in EMBL Nucleotide Sequence Database (accession number: Y15814) and allowed to clarify its phylogenetic position. O. Tauri belongs to the Prasinophyceae and appears very close to Mantoniella, a typical scaly Prasinophyceae, morphologically very different from the naked and coccoid Ostreococcus. An electrophoretic analysis of O. Tauri shows that the nucleus contains 10.20 mbp. This small genome fragmented into 14 chromosomes ranging in size from 300 to 1500 kbp, confirms the minimalist characteristics of Ostreococcus tauri.}, keywords = {rcc, RCC745, SBR$_\textrmP$hyto}, doi = {10.1046/j.1529-8817.1998.340844.x}, author = {Courties, C and Perasso, R and Chr{\'e}tiennot-Dinet, M.-J. and Gouy, M and Guillou, L and Troussellier, M} } @article {Moore1995, title = {Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties}, journal = {Marine Ecology - Progress Series}, volume = {116}, year = {1995}, note = {tex.mendeley-tags: RCC,rcc}, pages = {259{\textendash}275}, keywords = {GROWTH RATE, Light, MARINE OPTICS, rcc, Synechococcus, temperature, \#PROCHLOROPHYTE}, doi = {10.3354/meps116259}, author = {Moore, L R and Goericke, R and Chisholm, S W} } @article {Chisholm1992, title = {\textit{Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b}, journal = {Archives of Microbiology}, volume = {157}, year = {1992}, note = {tex.mendeley-tags: RCC,rcc}, pages = {297{\textendash}300}, keywords = {rcc, systematics, \#PROCHLOROPHYTE}, doi = {10.1007/BF00245165}, author = {Chisholm, S W and Frankel, S L and Goericke, R and Olson, R J and Palenik, B and Waterbury, J B and West-Johnsrud, L and Zettler, E R} } @article {ISI:A1984AAU2400012, title = {Purification and properties of ι-carrageenase from a marine bacterium}, journal = {Canadian Journal of Microbiology}, volume = {30}, number = {12}, year = {1984}, note = {tex.mendeley-tags: RCC5933}, month = {dec}, pages = {1500{\textendash}1506}, keywords = {RCC5933}, issn = {0008-4166}, doi = {10.1139/m84-239}, url = {http://www.nrcresearchpress.com/doi/10.1139/m84-239}, author = {Greer, C. W. and Yaphe, W.} }