@article {varga_cytotoxicity_2024, title = {Cytotoxicity of Prymnesium parvum extracts and prymnesin analogs on epithelial fish gill cells RTgill-W1 and the human colon cell line HCEC-1CT}, journal = {Archives of Toxicology}, year = {2024}, month = {jan}, abstract = {Harmful algal blooms kill fish populations worldwide, as exemplified by the haptophyte microalga Prymnesium~parvum. The suspected causative agents are prymnesins, categorized as A-, B-, and C-types based on backbone carbon atoms. Impacts of P.~parvum extracts and purified prymnesins were tested on the epithelial rainbow trout fish gill cell line RTgill-W1 and on the human colon epithelial cells HCEC-1CT. Cytotoxic potencies ranked A > C > B-type with concentrations spanning from low (A- and C-type) to middle (B-type) nM ranges. Although RTgill-W1 cells were about twofold more sensitive than HCEC-1CT, the cytotoxicity of prymnesins is not limited to fish gills. Both cell lines responded rapidly to prymnesins; with EC50 values for B-types in RTgill-W1 cells of 110 {\textpm} 11~nM and 41.5 {\textpm} 0.6~nM after incubations times of 3 and 24~h. Results of fluorescence imaging and measured lytic effects suggest plasma membrane interactions. Postulating an osmotic imbalance as mechanisms of toxicity, incubations with prymnesins in media lacking either Cl-, Na+, or Ca2+ were performed. Cl- removal reduced morphometric rearrangements observed in RTgill-W1 and cytotoxicity in HCEC-1CT cells. Ca2+-free medium in RTgill-W1 cells exacerbated effects on the cell nuclei. Prymnesin composition of different P.~parvum strains showed that analog composition within one type scarcely influenced the cytotoxic potential, while analog type potentially dictate potency. Overall, A-type prymnesins were the most potent ones in both cell lines followed by the C-types, and lastly B-types. Disturbance of Ca2+ and Cl- ionoregulation may be integral to prymnesin toxicity.}, keywords = {Fluorescence microscopy, Ichthyotoxin, Ionoregulation, Microalgae, MS, RCC1436, RCC191, UHPLC}, issn = {1432-0738}, doi = {10.1007/s00204-023-03663-5}, url = {https://doi.org/10.1007/s00204-023-03663-5}, author = {Varga, Elisabeth and Prause, H{\'e}l{\`e}ne-Christine and Riepl, Matthias and Hochmayr, Nadine and Berk, Deniz and Attakpah, Eva and Kiss, Endre and Medi{\'c}, Nikola and Del Favero, Giorgia and Larsen, Thomas Ostenfeld and Hansen, Per Juel and Marko, Doris} } @article {koslova_endogenous_2024, title = {Endogenous virophages are active and mitigate giant virus infection in the marine protist Cafeteria burkhardae}, journal = {Proceedings of the National Academy of Sciences}, volume = {121}, number = {11}, year = {2024}, note = {Publisher: Proceedings of the National Academy of Sciences}, month = {mar}, pages = {e2314606121}, abstract = {Endogenous viral elements (EVEs) are common genetic passengers in various protists. Some EVEs represent viral fossils, whereas others are still active. The marine heterotrophic flagellate Cafeteria burkhardae contains several EVE types related to the virophage mavirus, a small DNA virus that parasitizes the lytic giant virus CroV. We hypothesized that endogenous virophages may act as an antiviral defense system in protists, but no protective effect of virophages in wild host populations has been shown so far. Here, we tested the activity of virophage EVEs and studied their impact on giant virus replication. We found that endogenous mavirus-like elements (EMALEs) from globally distributed Cafeteria populations produced infectious virus particles specifically in response to CroV infection. However, reactivation was stochastic, often inefficient, and poorly reproducible. Interestingly, only one of eight EMALE types responded to CroV infection, implying that other EMALEs may be linked to different giant viruses. We isolated and cloned several reactivated virophages and characterized their particles, genomes, and infection dynamics. All tested virophages inhibited the production of CroV during coinfection, thereby preventing lysis of the host cultures in a dose-dependent manner. Comparative genomics of different C. burkhardae strains revealed that inducible EMALEs are common and are not linked to specific geographic locations. We demonstrate that naturally occurring virophage EVEs reactivate upon giant virus infection, thus providing a striking example that eukaryotic EVEs can become active under specific conditions. Moreover, our results support the hypothesis that virophages can act as an adaptive antiviral defense system in protists.}, keywords = {RCC970}, doi = {10.1073/pnas.2314606121}, url = {https://www.pnas.org/doi/full/10.1073/pnas.2314606121}, author = {Koslov{\'a}, Anna and Hackl, Thomas and Bade, Felix and Sanchez Kasikovic, Alexander and Barenhoff, Karina and Schimm, Fiona and Mersdorf, Ulrike and Fischer, Matthias G.} } @article {cho_genomic_2024, title = {Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses}, journal = {PLOS Genetics}, volume = {20}, number = {4}, year = {2024}, note = {Publisher: Public Library of Science}, pages = {e1011218}, abstract = {Symbiomonas scintillans Guillou et Chr{\'e}tiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC247, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.}, keywords = {Eukaryota, Gene prediction, genomics, metagenomics, RCC24, RCC257, Shotgun sequencing, Transcriptome analysis, Viral genomics, Whole genome amplification}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1011218}, url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011218}, author = {Cho, Anna and Lax, Gordon and Livingston, Samuel J. and Masukagami, Yumiko and Naumova, Mariia and Millar, Olivia and Husnik, Filip and Keeling, Patrick J.} } @booklet {krinos_intraspecific_2024, title = {Intraspecific diversity in thermal performance determines phytoplankton ecological niche}, year = {2024}, month = {feb}, publisher = {Ecology}, type = {preprint}, abstract = {Abstract Temperature has a primary influence on phytoplankton physiology and affects biodiversity and ecology. To examine how intraspecific diversity and temperature shape plankton populations, we grew 12 strains of the ecologically-important coccolithophore Gephyrocapsa huxleyi isolated from regions of different temperature for \~{}45 generations (2 months), each at 6-8 temperatures, and characterized the acclimated thermal response curve of each strain. Even with virtually identical temperature optima and overlapping cell size, strain growth rates varied between 0.45 and 1 day -1 . While some thermal curves were effectively symmetrical, others had more slowly declining growth rates above the {\textquotedblleft}thermal optimum,{\textquotedblright} and thermal niche widths varied between 16.7 and 24.8 {\textdegree}C. This suggests that different strains use distinct thermal response mechanisms. We investigated the ecological implications of such intraspecific diversity on thermal response using an ocean ecosystem simulation resolving distinct phytoplankton thermal phenotypes. Resolving model analogs of thermal {\textquotedblleft}generalists{\textquotedblright} and {\textquotedblleft}specialists{\textquotedblright} (similar to those observed in G. huxleyi) resulted in a distinctive global biogeography of preferred thermal niche widths with a nonlinear latitudinal pattern. We leveraged the model output to predict the ranges of the 12 strains we studied in the laboratory and demonstrated how this approach could refine predictions of phytoplankton thermal geographic range in situ . Our combination of observed thermal traits and modeled biogeography highlights the capacity of diverse groups to persist through temperature shifts. Significance Statement Intraspecific diversity in the phytoplankton may underpin their distribution. We show that within a single coccolithophore species, thermal response curves have diverse trait parameters. For example, many strains had a variable range of temperatures at which they could survive (thermal niche width). Adding this thermal niche width diversity to an ecosystem model simulation impacted phytoplankton coexistence and overall biomass. These observations show that thermal niche width is a gap in phytoplankton representation in ecosystem models that impacts modeled phytoplankton biogeography and concomitant carbon cycle dynamics. Including thermal tolerance is crucial to predictive modeling as ocean temperature dynamics change.}, keywords = {rcc1212, RCC3492, RCC3963, RCC4567, RCC6071, RCC874, RCC914}, doi = {10.1101/2024.02.14.580366}, url = {http://biorxiv.org/lookup/doi/10.1101/2024.02.14.580366}, author = {Krinos, Arianna I. and Shapiro, Sara K. and Li, Weixuan and Haley, Sheean T. and Dyhrman, Sonya T. and Dutkiewicz, Stephanie and Follows, Michael J. and Alexander, Harriet} } @article {granata_microbial_2024, title = {Microbial Factories and Exploiting Synergies of Bioreactor Technologies to Produce Bioproducts}, journal = {Fermentation}, volume = {10}, number = {3}, year = {2024}, note = {Number: 3 Publisher: Multidisciplinary Digital Publishing Institute}, month = {mar}, pages = {135}, abstract = {Microbial factories, including microalgae biofactories, have the enormous potential to produce biochemicals for manufacturing diverse bioproducts. A strategic approach to biofactories is maintaining cultures in bioreactors with sufficient resource inputs to optimize biochemical precursors for manufacturing bioproducts. Exploiting synergies that use the waste output from a bioreactor containing one microbial culture as a resource input to another bioreactor with a different microbe can lead to overall efficiencies in biofactories. In this paper, two synergies are evaluated. The first is between yeast and algae bioreactors, where data are presented on oxygen (O2) uptake by aerobic yeast cultures and their production of carbon dioxide (CO2) and the uptake of CO2 by algae and their production of O2. The second focuses on a carbon capture reactor, which is utilized to increase CO2 levels to promote higher algal production. This approach of waste as a resource for bioreactor cultures is a novel synergy that can be important to bioreactor designs and, ultimately, to the production of bioproducts.}, keywords = {bioproducts, bioreactors, carbon capture, RCC2604, synergies}, issn = {2311-5637}, doi = {10.3390/fermentation10030135}, url = {https://www.mdpi.com/2311-5637/10/3/135}, author = {Granata, Tim and Rattenbacher, Bernd and Kehl, Florian and Egli, Marcel} } @article {kamakura_transcriptional_2024, title = {Transcriptional responses to salinity-induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis}, journal = {Journal of Phycology}, volume = {n/a}, number = {n/a}, year = {2024}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13437}, abstract = {Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up-regulation of mechanosensitive ion channels and down-regulation of Ca2+-ATPases in cells with flat valves suggested that cytosolic Ca2+ levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up-regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up-regulation of genes encoding frustule-related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity-induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca2+ levels, and downstream responses, such as Ca2+-dependent regulation of actin dynamics and frustule-related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures.}, keywords = {cytoskeletal element, morphological plasticity, osmotic pressure, polymorphism, RNA-Seq, transporter, valve morphogenesis}, issn = {1529-8817}, doi = {10.1111/jpy.13437}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13437}, author = {Kamakura, Shiho and Bilcke, Gust and Sato, Shinya} } @article {cho_phylogenomic_2023, title = {Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean}, journal = {Molecular Phylogenetics and Evolution}, year = {2023}, month = {nov}, pages = {107964}, abstract = {Unlike morphologically conspicuous ochrophytes, many flagellates belonging to basally branching stramenopiles are small and often overlooked. As a result, many of these lineages are known only through molecular surveys and identified as MArine STramenopiles (MAST), and remain largely uncharacterized at the cellular or genomic level. These likely phagotrophic flagellates are not only phylogenetically diverse, but also extremely abundant in some environments, making their characterization all the more important. MAST-6 is one example of a phylogenetically distinct group that has been known to be associated with sediments, but little else is known about it. Indeed, until the present study, only a single species from this group, Pseudophyllomitus vesiculosus (Pseudophyllomitidae), has been both formally described and associated with genomic information. Here, we describe four new species including two new genera of sediment-dwelling MAST-6, Vomastramonas tehuelche gen. et sp. nov., Mastreximonas tlaamin gen. et sp. nov., one undescribed Pseudophyllomitus sp., BSC2, and a new species belonging to Placididea, the potentially halotolerant Haloplacidia sinai sp. nov. We also provide two additional bikosian transcriptomes from a public culture collection, to allow for better phylogenetic reconstructions of deep-branching stramenopiles. With the SSU rRNA sequences of the new MAST-6 species, we investigate the phylogenetic diversity of the MAST-6 group and show a high relative abundance of MAST-6 related to M. tlaamin in samples across various depths and geographical locations. Using the new MAST-6 species, we also update the phylogenomic tree of stramenopiles, particularly focusing on the paraphyly of Bigyra.}, keywords = {benthic protists, Bigyra, MAST-6, phylogenomics, Placididea, RCC1078, RCC257, Stramenopile}, issn = {1055-7903}, doi = {10.1016/j.ympev.2023.107964}, url = {https://www.sciencedirect.com/science/article/pii/S1055790323002646}, author = {Cho, Anna and Tikhonenkov, Denis V. and Lax, Gordon and Prokina, Kristina I. and Keeling, Patrick J.} } @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 {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 {sorokina_draft_2022, title = {Draft genome assembly and sequencing dataset of the marine diatom Skeletonema costatum RCC75}, journal = {Data in Brief}, year = {2022}, month = {feb}, pages = {107931}, abstract = {Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. Skeletonema costatum is a cosmopolitan marine diatom, principally occurring in coastal regions, and is one of the most abundant members of the Skeletonema genus. Here we present a draft assembly of the Skeletonema costatum RCC75 genome, obtained from PacBio and Illumina NovaSeq data. This dataset will expand the knowledge of the Bacillariophyceae genetics and contribute to the global understanding of phytoplankton{\textquoteright}s physiological, ecological, and environmental functioning.}, keywords = {Algal genome, BACILLARIOPHYCEAE, diatoms, genome sequencing, Illumina sequencing, PacBio sequencing, RCC75}, issn = {2352-3409}, doi = {10.1016/j.dib.2022.107931}, url = {https://www.sciencedirect.com/science/article/pii/S2352340922001433}, author = {Sorokina, Maria and Barth, Emanuel and Zulfiqar, Mahnoor and Kwantes, Michiel and Pohnert, Georg and Steinbeck, Christoph} } @article {zhang_intense_2022, title = {Intense blooms of Phaeocystis globosa in the South China Sea are caused by a unique {\textquotedblleft}giant-colony{\textquotedblright} ecotype}, journal = {Harmful Algae}, volume = {114}, year = {2022}, pages = {102227}, abstract = {The haptophyte Phaeocystis globosa, an important causative agent of harmful algal blooms globally, exhibits varying morphological and physiological features and high genetic diversity, yet the relationship among these has never been elucidated. In this study, colony sizes and pigment profiles of 19 P. globosa isolates from the Pacific and Atlantic Oceans were determined. Genetic divergence of these strains was analyzed using the chloroplast rbcS-rpl27 intergenic spacer, a novel high-resolution molecular marker. Strains could be divided into four genetic clades based on these sequences, or two groups based on colony size and the identity of diagnostic pigments (19{\textquoteright}-hexanoyloxyfucoxanthin, hex-fuco, and 19{\textquoteright}-butanoyloxyfucoxanthin, but-fuco). Three strains from the South China Sea (SCS), all belonging to the same genetic clade, have unique biological features in forming giant colonies and possessing but-fuco as their diagnostic pigment. Based on these findings, we propose that these SCS strains should be a unique {\textquotedblleft}giant-colony{\textquotedblright} ecotype of P. globosa. During the period 2016-2021, more than 1000 rbcS-rpl27 sequences were obtained from 16 P. globosa colony samples and 18 phytoplankton samples containing solitary P. globosa cells in the SCS. Phylogenetic analysis indicated that >95\% of the sequences from P. globosa colonies in the SCS were comprised of the {\textquotedblleft}giant-colony{\textquotedblright} ecotype, whereas the genetic diversity of solitary cells was much higher. Results demonstrated that intense blooms of P. globosa featuring giant colonies in the SCS were mainly caused by this giant-colony P. globosa ecotype.}, keywords = {ecotype, genetic diversity, Giant colony, Marker pigment, RCC1736, RCC2055, RCC678, RCC736}, issn = {1568-9883}, doi = {10.1016/j.hal.2022.102227}, url = {https://www.sciencedirect.com/science/article/pii/S1568988322000555}, author = {Zhang, Qing-Chun and Liu, Chao and Wang, Jin-Xiu and Kong, Fan-Zhou and Niu, Zhuang and Xiang, Ling and Yu, Ren-Cheng} } @article {falciatore_light-driven_2022, title = {Light-driven processes: key players of the functional biodiversity in microalgae}, journal = {Comptes Rendus. Biologies}, volume = {345}, number = {2}, year = {2022}, pages = {1{\textendash}24}, doi = {10.5802/crbiol.80}, url = {https://comptes-rendus.academie-sciences.fr/biologies/articles/10.5802/crbiol.80/}, author = {Falciatore, Angela and Bailleul, Benjamin and Boulouis, Alix and Bouly, Jean-Pierre and Bujaldon, Sandrine and Cheminant-Navarro, Soizic and Choquet, Yves and Vitry, Catherine de and Eberhard, Stephan and Jaubert, Marianne and Kuras, Richard and Lafontaine, Ingrid and Landier, Sophie and Selles, Julien and Vallon, Olivier and Wostrikoff, Katia} } @article {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 {koppelle_mixotrophy_2022, title = {Mixotrophy in the bloom-forming genus Phaeocystis and other haptophytes}, journal = {Harmful Algae}, volume = {117}, year = {2022}, pages = {102292}, abstract = {Phaeocystis is a globally widespread marine phytoplankton genus, best known for its colony-forming species that can form large blooms and odorous foam during bloom decline. In the North Sea, Phaeocystis globosa typically becomes abundant towards the end of the spring bloom, when nutrients are depleted and the share of mixo- trophic protists increases. Although mixotrophy is widespread across the eukaryotic tree of life and is also found amongst haptophytes, a mixotrophic nutrition has not yet been demonstrated in Phaeocystis. Here, we sampled two consecutive Phaeocystis globosa spring blooms in the coastal North Sea. In both years, bacterial cells were observed inside 0.6 {\textendash} 2\% of P. globosa cells using double CARD-FISH hybridizations in combination with laser scanning confocal microscopy. Incubation experiments manipulating light and nutrient availability showed a trend towards higher occurrence of intracellular bacteria under P-deplete conditions. Based on counts of bacteria inside P. globosa cells in combination with theoretical values of prey digestion times, maximum ingestion rates of up to 0.08 bacteria cell- 1 h- 1 were estimated. In addition, a gene-based predictive model was applied to the transcriptome assemblies of seven Phaeocystis strains and 24 other haptophytes to assess their trophic mode. This model predicted a phago-mixotrophic feeding strategy in several (but not all) strains of P. globosa, P. antarctica and other haptophytes that were previously assumed to be autotrophic. The observation of bacterial cells inside P. globosa and the gene-based model predictions strongly suggest that the phago-mixotrophic feeding strategy is widespread among members of the Phaeocystis genus and other haptophytes, and might contribute to their remarkable success to form nuisance blooms under nutrient-limiting conditions.}, keywords = {RCC1130, RCC1303, rcc1383, RCC1455, RCC1486, RCC1523, RCC1537, RCC918}, issn = {15689883}, doi = {10.1016/j.hal.2022.102292}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1568988322001202}, author = {Koppelle, Sebastiaan and L{\'o}pez-Escard{\'o}, David and Brussaard, Corina P.D. and Huisman, Jef and Philippart, Catharina J.M. and Massana, Ramon and Wilken, Susanne} } @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 {carrigee_phycoerythrobilin_2022, title = {The phycoerythrobilin isomerization activity of MpeV in Synechococcus sp. WH8020 is prevented by the presence of a histidine at position 141 within its phycoerythrin-I β-subunit substrate}, journal = {Frontiers in Microbiology}, volume = {13}, year = {2022}, pages = {1011189}, abstract = {Marine Synechococcus efficiently harvest available light for photosynthesis using complex antenna systems, called phycobilisomes, composed of an allophycocyanin core surrounded by rods, which in the open ocean are always constituted of phycocyanin and two phycoerythrin (PE) types: PEI and PEII. These cyanobacteria display a wide pigment diversity primarily resulting from differences in the ratio of the two chromophores bound to PEs, the green-light absorbing phycoerythrobilin and the blue-light absorbing phycourobilin. Prior to phycobiliprotein assembly, bilin lyases post-translationally catalyze the ligation of phycoerythrobilin to conserved cysteine residues on α- or β-subunits, whereas the closely related lyase-isomerases isomerize phycoerythrobilin to phycourobilin during the attachment reaction. MpeV was recently shown in Synechococcus sp. RS9916 to be a lyase-isomerase which doubly links phycourobilin to two cysteine residues (C50 and C61; hereafter C50, 61) on the β-subunit of both PEI and PEII. Here we show that Synechococcus sp. WH8020, which belongs to the same pigment type as RS9916, contains MpeV that demonstrates lyase-isomerase activity on the PEII β-subunit but only lyase activity on the PEI β-subunit. We also demonstrate that occurrence of a histidine at position 141 of the PEI β-subunit from WH8020, instead of a leucine in its counterpart from RS9916, prevents the isomerization activity by WH8020 MpeV, showing for the first time that both the substrate and the enzyme play a role in the isomerization reaction. We propose a structural-based mechanism for the role of H141 in blocking isomerization. More generally, the knowledge of the amino acid present at position 141 of the β-subunits may be used to predict which phycobilin is bound at C50, 61 of both PEI and PEII from marine Synechococcus strains.}, keywords = {RCC2437, RCC307, RCC751}, issn = {1664-302X}, doi = {10.3389/fmicb.2022.1011189}, url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1011189/full}, author = {Carrigee, Lyndsay A. and Frick, Jacob P. and Liu, Xindi and Karty, Jonathan A. and Trinidad, Jonathan C. and Tom, Irin P. and Yang, Xiaojing and Dufour, Louison and Partensky, Fr{\'e}d{\'e}ric and Schluchter, Wendy M.} } @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} } @article {akita_providing_2022, title = {Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences}, journal = {Molecular Phylogenetics and Evolution}, volume = {168}, year = {2022}, month = {mar}, pages = {107408}, abstract = {In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.}, keywords = {Ectocarpales, genomics, Heterokontophytes, Phaeoexplorer, Phaeophyceae, RCC4962, RCC7086, RCC7088, RCC7090, RCC7092, RCC7094, RCC7096, RCC7098, RCC7101, RCC7104, RCC7107, RCC7108, RCC7109, RCC7112, RCC7115, RCC7116, RCC7117, RCC7120, RCC7123, RCC7124, RCC7125, RCC7127, RCC7129, RCC7131, RCC7134, RCC7137, RCC7138, RCC7139, stramenopiles}, issn = {1055-7903}, doi = {10.1016/j.ympev.2022.107408}, url = {https://www.sciencedirect.com/science/article/pii/S1055790322000215}, author = {Akita, Shingo and Vieira, Christophe and Hanyuda, Takeaki and Rousseau, Florence and Cruaud, Corinne and Couloux, Arnaud and Heesch, Svenja and Cock, J. Mark and Kawai, Hiroshi} } @article {eyal_variability_2022, title = {The variability in the structural and functional properties of coccolith base plates}, journal = {Acta Biomaterialia}, volume = {148}, year = {2022}, pages = {336{\textendash}344}, abstract = {Biomineralization processes exert varying levels of control over crystallization, ranging from poorly ordered polycrystalline arrays to intricately shaped single crystals. Coccoliths, calcified scales formed by unicellular algae, are a model for a highly controlled crystallization process. The coccolith crystals nucleate next to an organic oval structure that was termed the base plate, leading to the assumption that it is responsible for the oriented nucleation of the crystals via stereochemical interactions. In recent years, several works focusing on a well-characterized model species demonstrated a fundamental role for indirect interactions that facilitate coccolith crystallization. Here, we developed the tools to extract the base plates from five different species, giving the opportunity to systematically explore the relations between base plate and coccolith properties. We used multiple imaging techniques to evaluate the structural and chemical features of the base plates under native hydrated conditions. The results show a wide range of properties, overlaid on a common rudimentary scaffold that lacks any detectable structural or chemical motifs that can explain direct nucleation control. This work emphasizes that it is the combination between the base plate and the chemical environment inside the cell that cooperatively facilitate the exquisite control over the crystallization process. Statement of significance Biological organic scaffolds can serve as functional surfaces that guide the formation of inorganic materials. However, in many cases the specific interactions that facilitate such tight regulation are complex and not fully understood. In this work, we elucidate the architecture of such amodel biological template, an organic scale that directs the assembly of exquisite crystalline arrays of marine microalgae. By using cryo electron microscopy, we reveal the native state organization of these scales from several species. The observed similarities and differences allow us to propose that the chemical microenvironment, rather than stereochemical matching, is the pivotal regulator of the process.}, keywords = {biomineralization, Calcite, Coccoliths, Cryo electron tomography, Crystallization, RCC1130, RCC1181, RCC190, RCC3777}, issn = {1742-7061}, doi = {10.1016/j.actbio.2022.06.027}, url = {https://www.sciencedirect.com/science/article/pii/S174270612200366X}, author = {Eyal, Zohar and Krounbi, Leilah and Ben Joseph, Oz and Avrahami, Emanuel M. and Pinkas, Iddo and Peled-Zehavi, Hadas and Gal, Assaf} } @article {park_bioluminescence_2021, title = {Bioluminescence capability and intensity in the dinoflagellate Alexandrium species}, journal = {ALGAE}, volume = {36}, year = {2021}, abstract = {Some species in the dinoflagellate genus Alexandrium are bioluminescent. Of the 33 formally described Alexandrium species, the bioluminescence capability of only nine species have been tested, and eight have been reported to be bioluminescent. The present study investigated the bioluminescence capability of seven Alexandrium species that had not been tested. Alexandrium mediterraneum, A. pohangense, and A. tamutum were bioluminescent, but A. andersonii, A. hiranoi, A. insuetum, and A. pseudogonyaulax were not. We also measured the bioluminescent intensity of A. affine, A. fraterculus, A. mediterraneum, A. ostenfeldii, A. pacificum, A. pohangense, A. tamarense, and A. tamutum. The mean 200-second-integrated bioluminescence intensity per cell ranged from 0.02 to 32.2 {\texttimes} 104 relative luminescence unit per cell (RLU cell-1), and the mean maximum bioluminescence intensity per cell per second (BLMax) ranged from 0.01 to 10.3 {\texttimes} 104 RLU cell-1 s-1. BLMax was significantly correlated with the maximum growth rates of Alexandrium species, except for A. tamarense. A phylogenetic tree based on large subunit ribosomal DNA (LSU rDNA), showed that the bioluminescent species A. affine, A. catenella, A. fraterculus, A. mediterraneum, A. pacificum, and A. tamarense formed a large clade. However, the toxicity or mixotrophic capability of these species was split. Thus, their bioluminescence capability in this clade was more consistent than their toxicity or mixotrophic capability. Phylogenetic trees based on LSU rDNA and the luciferase gene of Alexandrium were consistent except for A. pohangense. The results of the present study can provide a basis for understanding the interspecific diversity in bioluminescence of Alexandrium.}, keywords = {RCC4104}, doi = {10.4490/algae.2021.36.12.6}, author = {Park, Sang Ah and Jeong, Hae Jin and Ok, Jin and Kang, Heechang and You, Jihyun and Eom, Se and Yoo, Yeong and Lee, Moo Joon} } @article {zhang_development_2021, title = {Development of high-resolution chloroplast markers for intraspecific phylogeographic studies of Phaeocystis globosa}, journal = {Journal of Oceanology and Limnology}, volume = {39}, number = {2}, year = {2021}, month = {mar}, pages = {508{\textendash}524}, abstract = {Phaeocystis globosa is an important harmful algal bloom causative species distributing widely in temperate and tropical coastal waters in the world. The morphological, physiological, and biochemical characteristics are different among geographic strains, which can not be distinguished with nuclear ribosomal DNA markers at present. Therefore, the genetic distance and phylogeographic relationships of nuclear 28S rDNA D1{\textendash}D2 and ITS regions, and three chloroplast intergenic spacers (petN-trnS1, trnM1-psbA, and rbcS-rpl27) were analyzed and compared among 13 strains of P. globosa isolated from the Pacific Ocean and Atlantic Ocean in this study. In addition, the nucleotide polymorphisms of 28S rDNA D1{\textendash}D2, ITS, and rbcS-rpl27 regions were evaluated in two P. globosa strains. The various levels of nucleotide polymorphism were in the nuclear 28S rDNA D1{\textendash}D2 region and ITS region, but no polymorphism was in the chloroplast rbcS-rpl27 intergenic spacer. A reasonable intraspecific phylogeographic relationship was presented by rbcS-rpl27 intergenic spacer, which had the strongest distinction to geographic strains compared to those of 28S rDNA D1{\textendash}D2 and ITS regions. In the phylogenetic tree of rbcS-rpl27 intergenic spacer, the two strains from the North Sea of the Atlantic Ocean were divided firstly from the species of P. globosa, and then formed an independent clade, while the other Atlantic strains and all of Pacific strains joined up to build the other clade. It was implied that at least two genetically distant populations of P. globosa existed in the Atlantic coastal regions. This study provided a high-resolution chloroplast marker to analyze intraspecific phylogeographic populations of P. globosa, and preliminarily clarified the genetic relationships of the Pacific and Atlantic strains of P. globosa.}, keywords = {RCC2055, RCC736}, issn = {2096-5508, 2523-3521}, doi = {10.1007/s00343-020-9304-5}, url = {https://link.springer.com/10.1007/s00343-020-9304-5}, author = {Zhang, Qingchun and Niu, Zhuang and Wang, Jinxiu and Liu, Chao and Kong, Fanzhou and Hu, Xiaokun and Zhao, Jiayu and Yu, Rencheng} } @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 {Wang2021, title = {Group 2i Isochrysidales produce characteristic alkenones reflecting sea ice distribution}, journal = {Nature Communications}, volume = {12}, number = {1}, year = {2021}, note = {Publisher: Springer US tex.mendeley-tags: RCC107,RCC1195,RCC1334,RCC5486}, month = {dec}, pages = {15}, abstract = {Alkenones are biomarkers produced solely by algae in the order Isochrysidales that have been used to reconstruct sea surface temperature (SST) since the 1980s. However, alkenone-based SST reconstructions in the northern high latitude oceans show significant bias towards warmer temperatures in core-tops, diverge from other SST proxies in down core records, and are often accompanied by anomalously high relative abundance of the C 37 tetra-unsaturated methyl alkenone (\%C 37:4 ). Elevated \%C 37:4 is widely interpreted as an indicator of low sea surface salinity from polar water masses, but its biological source has thus far remained elusive. Here we identify a lineage of Isochrysidales that is responsible for elevated C 37:4 methyl alkenone in the northern high latitude oceans through next-generation sequencing and lab-culture experiments. This Isochrysidales lineage co-occurs widely with sea ice in marine environments and is distinct from other known marine alkenone-producers, namely Emiliania huxleyi and Gephyrocapsa oceanica . More importantly, the \%C 37:4 in seawater filtered particulate organic matter and surface sediments is significantly correlated with annual mean sea ice concentrations. In sediment cores from the Svalbard region, the \%C 37:4 concentration aligns with the Greenland temperature record and other qualitative regional sea ice records spanning the past 14 kyrs, reflecting sea ice concentrations quantitatively. Our findings imply that \%C 37:4 is a powerful proxy for reconstructing sea ice conditions in the high latitude oceans on thousand- and, potentially, on million-year timescales.}, keywords = {RCC107, RCC1195, RCC1334, RCC5486}, issn = {2041-1723}, doi = {10.1038/s41467-020-20187-z}, url = {http://dx.doi.org/10.1038/s41467-020-20187-z http://www.nature.com/articles/s41467-020-20187-z}, author = {Wang, Karen Jiaxi and Huang, Yongsong and Majaneva, Markus and Belt, Simon T. and Liao, Sian and Novak, Joseph and Kartzinel, Tyler R. and Herbert, Timothy D. and Richter, Nora and Cabedo-Sanz, Patricia} } @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 {harada_novel_2021, title = {A novel characteristic of a phytoplankton as a potential source of straight-chain alkanes}, journal = {Scientific Reports}, volume = {11}, number = {1}, year = {2021}, note = {Bandiera_abtest: a Cc_license_type: cc_by Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Biofuels;Biological techniques Subject_term_id: biofuels;biological-techniques}, pages = {14190}, abstract = {Biosynthesis of hydrocarbons is a promising approach for the production of alternative sources of energy because of the emerging need to reduce global consumption of fossil fuels. However, the suitability of biogenic hydrocarbons as fuels is limited because their range of the number of carbon atoms is small, and/or they contain unsaturated carbon bonds. Here, we report that a marine phytoplankton, Dicrateria rotunda, collected from the western Arctic Ocean, can synthesize a series of saturated hydrocarbons (n-alkanes) from C10H22 to C38H78, which are categorized as petrol (C10{\textendash}C15), diesel oils (C16{\textendash}C20), and fuel oils (C21{\textendash}C38). The observation that these n-alkanes were also produced by ten other cultivated strains of Dicrateria collected from the Atlantic and Pacific oceans suggests that this capability is a common characteristic of Dicrateria. We also identified that the total contents of the n-alkanes in the Arctic D. rotunda strain increased under dark and nitrogen-deficient conditions. The unique characteristic of D. rotunda could contribute to the development of a new approach for the biosynthesis of n-alkanes.}, keywords = {RCC3437, RCC4217, RCC4577, RCC4578, RCC5635, RCC5639}, issn = {2045-2322}, doi = {10.1038/s41598-021-93204-w}, url = {http://www.nature.com/articles/s41598-021-93204-w}, author = {Harada, Naomi and Hirose, Yuu and Chihong, Song and Kurita, Hirofumi and Sato, Miyako and Onodera, Jonaotaro and Murata, Kazuyoshi and Itoh, Fumihiro} } @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 {kawachi_rappemonads_2021, title = {Rappemonads are haptophyte phytoplankton}, journal = {Current Biology}, year = {2021}, month = {mar}, abstract = {Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 which is responsible for around 50\% of global net primary production.12,13 However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.14, 15, 16, 17 The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions,15 has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities.}, keywords = {environmental DNA sequences, morphological evolution, organellar phylogenomics, phytoplankton diversity, RCC3430, transmission electron microscopy}, issn = {0960-9822}, doi = {10.1016/j.cub.2021.03.012}, url = {https://www.sciencedirect.com/science/article/pii/S0960982221003511}, author = {Kawachi, Masanobu and Nakayama, Takuro and Kayama, Motoki and Nomura, Mami and Miyashita, Hideaki and Bojo, Othman and Rhodes, Lesley and Sym, Stuart and Pienaar, Richard N. and Probert, Ian and Inouye, Isao and Kamikawa, Ryoma} } @article {Carrigee2020, title = {CpeY is a phycoerythrobilin lyase for cysteine 82 of the phycoerythrin I α-subunit in marine Synechococcus}, journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics}, year = {2020}, note = {Publisher: Elsevier B.V tex.mendeley-tags: RCC555}, month = {apr}, pages = {148215}, keywords = {rcc555}, issn = {00052728}, doi = {10.1016/j.bbabio.2020.148215}, url = {https://doi.org/10.1016/j.bbamem.2019.183135 https://linkinghub.elsevier.com/retrieve/pii/S0005272820300657}, author = {Carrigee, Lyndsay A. and Mahmoud, Rania M. and Sanfilippo, Joseph E. and Frick, Jacob P. and Strnat, Johann A. and Karty, Jonathan A. and Chen, Bo and Kehoe, David M. and Schluchter, Wendy M.} } @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 {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 {Kuwata2020, title = {Draft whole-genome sequence of triparma laevis f. inornata (parmales, bolidophyceae), isolated from the oyashio region, western north pacific ocean}, journal = {Microbiology Resource Announcements}, volume = {9}, number = {33}, year = {2020}, note = {ISBN: 9781493991730 tex.mendeley-tags: RCC4655}, month = {aug}, pages = {13{\textendash}14}, abstract = {We present the first draft whole-genome sequence for the Parmales (Bolidophyceae, Heterokonta), a picoplanktonic sister group of diatoms, using a Triparma laevis f. inornata strain that was isolated from the Oyashio region in the western North Pacific Ocean.}, keywords = {RCC4655}, issn = {2576-098X}, doi = {10.1128/MRA.00367-20}, url = {https://mra.asm.org/content/9/33/e00367-20}, author = {Kuwata, Akira and Saitoh, Kenji and Nakamura, Yoji and Ichinomiya, Mutsuo and Sato, Naoki}, editor = {Stajich, Jason E.} } @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 {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 {Helliwell2020, title = {A novel single-domain Na +-selective voltage-gated channel in photosynthetic eukaryotes}, journal = {bioRxiv}, year = {2020}, note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC1456}, month = {apr}, pages = {2020.04.29.068528}, abstract = {The evolution of Na+-selective four-domain voltage-gated channels (4D-Navs) in animals allowed rapid Na+-dependent electrical excitability, and enabled the development of sophisticated systems for rapid and long-range signalling. Whilst bacteria encode single-domain Na+-selective voltage-gated channels (BacNav), they typically exhibit much slower kinetics than 4D-Navs, and are not thought to have crossed the prokaryote-eukaryote boundary. As such, the capacity for rapid Na+-selective signalling is considered to be confined to certain animal taxa, and absent from photosynthetic eukaryotes. Certainly, in land plants, such as the Venus Flytrap where fast electrical excitability has been described, this is most likely based on fast anion channels. Here, we report a unique class of eukaryotic Na+-selective single-domain channels (EukCatBs) that are present primarily in haptophyte algae, including the ecologically important calcifying coccolithophores. The EukCatB channels exhibit very rapid voltage-dependent activation and inactivation kinetics, and sensitivity to the highly selective 4D-Nav blocker tetrodotoxin. The results demonstrate that the capacity for rapid Na+-based signalling in eukaryotes is not restricted to animals or to the presence of 4D-Navs. The EukCatB channels therefore represent an independent evolution of fast Na+-based electrical signalling in eukaryotes that likely contribute to sophisticated cellular control mechanisms operating on very short time scales in unicellular algae. One Sentence Summary The capacity for rapid Na+-based signalling has evolved in ecologically important coccolithophore species via a novel class of voltage-gated Na+ channels, EukCatBs.}, keywords = {RCC1456}, doi = {10.1101/2020.04.29.068528}, url = {https://doi.org/10.1101/2020.04.29.068528}, author = {Helliwell, Katherine E and Chrachri, Abdul and Koester, Julie and Wharam, Susan and Wheeler, Glen L and Brownlee, Colin} } @article {Morales-Sanchez2020, title = {Production of carbohydrates, lipids and polyunsaturated fatty acids (PUFA) by the polar marine microalga Chlamydomonas malina RCC2488}, journal = {Algal Research}, volume = {50}, number = {July}, year = {2020}, note = {tex.mendeley-tags: RCC2488}, month = {sep}, pages = {102016}, keywords = {RCC2488}, issn = {22119264}, doi = {10.1016/j.algal.2020.102016}, url = {https://linkinghub.elsevier.com/retrieve/pii/S2211926420303477}, author = {Morales-S{\'a}nchez, Daniela and Schulze, Peter S.C. and Kiron, Viswanath and Wijffels, Ren{\'e} H.} } @article {Bretherton2020, title = {Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure}, journal = {Marine Pollution Bulletin}, volume = {153}, number = {January}, year = {2020}, note = {Publisher: Elsevier tex.mendeley-tags: RCC1614}, pages = {110906}, abstract = {The Deepwater Horizon oil spill released millions of barrels of crude oil into the Gulf of Mexico, and saw widespread use of the chemical dispersant Corexit. We assessed the role of traits, such as cell size, cell wall, motility, and mixotrophy on the growth and photosynthetic response of 15 phytoplankton taxa to oil and Corexit. We collected growth and photosynthetic data on five algal cultures. These responses could be separated into resistant (Tetraselmis astigmatica, Ochromonas sp., Heterocapsa pygmaea) and sensitive (Micromonas pusilla, Prorocentrum minimum). We combined this data with 10 species previously studied and found that cell size is most important in determining the biomass response to oil, whereas motility/mixotrophy is more important in the dispersed oil. Our analysis accounted for a third of the variance observed, so further work is needed to identify other factors that contribute to oil resistance.}, keywords = {Chemical dispersants, Chlorophyll, crude oil, Photosynthesis, phytoplankton, RCC1614, Trait-based analysis}, issn = {18793363}, doi = {10.1016/j.marpolbul.2020.110906}, url = {https://doi.org/10.1016/j.marpolbul.2020.110906}, author = {Bretherton, Laura and Hillhouse, Jessica and Kamalanathan, Manoj and Finkel, Zoe V. and Irwin, Andrew J. and Quigg, Antonietta} } @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 {Helliwell2019, title = {Alternative mechanisms for fast na + /ca 2+ signaling in eukaryotes via a novel class of single-domain voltage-gated channels}, journal = {Current Biology}, volume = {29}, number = {9}, year = {2019}, note = {tex.mendeley-tags: RCC299}, pages = {1503{\textendash}1511.e6}, abstract = {Rapid Na + /Ca 2+ -based action potentials govern essential cellular functions in eukaryotes, from the motile responses of unicellular protists, such as Paramecium [1, 2], to complex animal neuromuscular activity [3]. A key innovation underpinning this fundamental signaling process has been the evolution of four-domain voltage-gated Na + /Ca 2+ channels (4D-Ca v s/Na v s). These channels are widely distributed across eukaryote diversity [4], albeit several eukaryotes, including land plants and fungi, have lost voltage-sensitive 4D-Ca v /Na v s [5{\textendash}7]. Because these lineages appear to lack rapid Na + /Ca 2+ -based action potentials, 4D-Ca v /Na v s are generally considered necessary for fast Na + /Ca 2+ -based signaling [7]. However, the cellular mechanisms underpinning the membrane physiology of many eukaryotes remain unexamined. Eukaryotic phytoplankton critically influence our climate as major primary producers. Several taxa, including the globally abundant diatoms, exhibit membrane excitability [8{\textendash}10]. We previously demonstrated that certain diatom genomes encode 4D-Ca v /Na v s [4] but also proteins of unknown function, resembling prokaryote single-domain, voltage-gated Na + channels (BacNa v s) [4]. Here, we show that single-domain channels are actually broadly distributed across major eukaryote phytoplankton lineages and represent three novel classes of single-domain channels, which we refer collectively to as EukCats. Functional characterization of diatom EukCatAs indicates that they are voltage-gated Na + - and Ca 2+ -permeable channels, with rapid kinetics resembling metazoan 4D-Ca v s/Na v s. In Phaeodactylum tricornutum, which lacks 4D-Ca v /Na v s, EukCatAs underpin voltage-activated Ca 2+ signaling important for membrane excitability, and mutants exhibit impaired motility. EukCatAs therefore provide alternative mechanisms for rapid Na + /Ca 2+ signaling in eukaryotes and may functionally replace 4D-Ca v s/Na v s in pennate diatoms. Marine phytoplankton thus possess unique signaling mechanisms that may be key to environmental sensing in the oceans. Diatoms exhibit fast animal-like action potentials, but many species lack 4D-Ca v /Na v channels that underpin membrane excitability in animals. Diatoms do encode novel 1D voltage-gated channels (EukCatAs). Helliwell, Chrachri et al. show that EukCatAs are fast Na + and Ca 2+ channels that provide alternative mechanisms for rapid signaling in eukaryotes.}, keywords = {action potentials, BacNa v, calcium channel, diatoms, EukCats, gliding motility, ion selectivity, RCC299, signaling, single-domain channel, voltage-gated channel}, issn = {09609822}, doi = {10.1016/j.cub.2019.03.041}, author = {Helliwell, Katherine E. and Chrachri, Abdul and Koester, Julie A. and Wharam, Susan and Verret, Frederic and Taylor, Alison R. and Wheeler, Glen L. and Brownlee, Colin} } @article {kusch_dead_2019, title = {Dead in the Water: The Vicious Cycle of Blanks During Natural Level 14 C Manipulation of Marine Algal Cultures}, journal = {Frontiers in Marine Science}, volume = {6}, year = {2019}, note = {Publisher: Frontiers}, abstract = {Authentic biomarker standards were obtained from algal cultures in an attempt to accurately determine blank C added during sample processing for compound-specific radiocarbon analysis. Emiliania huxleyi and Thalassiosira pseudonana were grown under manipulated Δ14C dissolved inorganic carbon (DIC) levels and chlorophyll a and either alkenones (E. huxleyi) or low molecular weight (LMW) alkanoic acids (T. pseudonana) were isolated from the respective biomass using preparative liquid chromatography (LC), wet chemical techniques or preparative gas chromatography, respectively. DI14C in the seawater medium was determined pre- and post-growth. Biomarker Δ14C values mostly agree within 1-2? analytical uncertainties. In those cases where biomarker Δ14C values differ significantly, chlorophyll a is up to 104{\textperthousand} more 14C-depleted than alkenones or LMW alkanoic acids, consistent with a larger LC blank compared to the other purification methods. However, in the majority of experimental setups pre- and post-growth DIC Δ14C values seem to be compromised by an unknown and variable blank C contribution. DIC Δ14C values deviate strongly from the anticipated Δ14C values (by up to ca. 560{\textperthousand}), pre- and post-growth Δ14C values differ significantly (by up to ca. 460{\textperthousand}), and changes are not unidirectional. Accordingly, since the substrate Δ14C value cannot unequivocally be constrained, blank C contributions for the different biomarker purification methods cannot be accurately calculated. This study illustrates the challenges and problems of producing authentic standards that are not readily commercially available and exemplifies how a laborious and time-consuming culturing approach may enter a vicious cycle of blank C contamination hampering accurate blank C determination.}, keywords = {Algal cultures, Alkanoic acids, alkenones, Authentic standards, Blank, chlorophyll a, Compound-specific radiocarbon analysis, natural level 14 C manipulation, rcc1238}, issn = {2296-7745}, doi = {10.3389/fmars.2019.00780}, url = {https://www.frontiersin.org/articles/10.3389/fmars.2019.00780/full}, author = {Kusch, Stephanie and Benthien, Albert and Richter, Klaus-Uwe and Rost, Bj{\"o}rn and Mollenhauer, Gesine} } @article {Krasovec2019, title = {First estimation of the spontaneous mutation rate in Diatoms}, journal = {Genome Biology and Evolution}, volume = {1}, year = {2019}, note = {tex.mendeley-tags: RCC2967}, pages = {1{\textendash}23}, keywords = {diatoms, Mutation accumulation, mutation rate in phaeodactylum, mutation spectrum, phaeodactylum, RCC2967, running title, spontaneous mutation rate, tricornutum}, issn = {1759-6653}, doi = {10.1093/gbe/evz130}, url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evz130/5520952}, author = {Krasovec, Marc and Sanchez-Brosseau, Sophie and Piganeau, Gwenael}, editor = {Baer, Charles} } @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 {LevyKarin2019, title = {MetaEuk {\textendash} sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics}, journal = {bioRxiv}, year = {2019}, month = {jan}, pages = {851964}, abstract = {Background: Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics. Results: MetaEuk is a toolkit for high-throughput, reference-based discovery and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk\&\#039;s power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted \>12,000,000 protein-coding genes in eight days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups. Conclusion: The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation.}, doi = {10.1101/851964}, url = {http://biorxiv.org/content/early/2019/11/25/851964.abstract}, author = {Levy Karin, Eli and Mirdita, Milot and Soeding, Johannes} } @article {Klintzsch2019, title = {Methane production by three widespread marine phytoplankton species: release rates, precursor compounds, and potential relevance for the environment}, journal = {Biogeosciences}, volume = {16}, number = {20}, year = {2019}, note = {tex.mendeley-tags: RCC1216}, month = {oct}, pages = {4129{\textendash}4144}, keywords = {RCC1216}, issn = {1726-4189}, doi = {10.5194/bg-16-4129-2019}, url = {https://www.biogeosciences.net/16/4129/2019/}, author = {Klintzsch, Thomas and Langer, Gerald and Nehrke, Gernot and Wieland, Anna and Lenhart, Katharina and Keppler, Frank} } @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 {Tsuboi2019, title = {Short-term changes in marine prokaryotic and eukaryotic microalgal communities exposed to the leachate of a seafloor hydrothermal sulfide}, journal = {Water, Air, \& Soil Pollution}, volume = {230}, year = {2019}, note = {tex.mendeley-tags: RCC,RCC1089,RCC262}, pages = {175}, abstract = {The effects of increased mining of seafloor massive sulfide deposits on marine ecosystems have not been characterized. In this study, the impact of leaching metals from a hydrothermal sulfide on photosynthetic protist and cyanobacterial communities in marine environments was investigated by amplicon analyses of small subunit rDNA (SSU rDNA) and rRNA (SSU rRNA). Seawater samples collected from the Iheya North region and Suruga Bay, Japan, were incubated with or without a leachate containing zinc, copper, cadmium, and manganese, of the actual seafloor hydrothermal sulfide from the Hakurei site in the Izena Hole region. The relative abundances of prasinophytes, diatom protists, and the cyanobacteria Synechococcus decreased substantially during incubation with leachate, indicating the vulnerability of these lineages to the leachate. Phylogenetic analysis based on the cyanobacterial phycocyanin cpcBA/rpcBA operon obtained from samples incubated with or without leachate indicated that the individual lineages of Synechococcus can determine sensitivity to heavy metals in different marine regions as well as particular clades and ecotypes.}, keywords = {rcc, RCC1089, RCC262}, doi = {10.1007/s11270-019-4224-8}, author = {Tsuboi, Shun and Yamaguchi, Haruyo and Fuchida, Shigeshi and Koshikawa, Hiroshi and Kawachi, Masanobu} } @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 {Kuwata2018, title = {Bolidophyceae, a sister picoplanktonic group of diatoms {\textendash} a review}, journal = {Frontiers in Marine Science}, volume = {5}, year = {2018}, note = {tex.mendeley-tags: RCC1657,RCC201,RCC205,RCC206,RCC212,RCC239}, month = {oct}, pages = {370}, keywords = {RCC1657, RCC201, RCC205, RCC206, rcc212, RCC239}, issn = {2296-7745}, doi = {10.3389/fmars.2018.00370}, url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00370/full}, author = {Kuwata, Akira and Yamada, Kazumasa and Ichinomiya, Mutsuo and Yoshikawa, Shinya and Tragin, Margot and Vaulot, Daniel and Lopes dos Santos, Adriana} } @article {McQuaid2018, title = {Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms}, journal = {Nature}, volume = {555}, number = {7697}, year = {2018}, note = {Publisher: Nature Publishing Group tex.mendeley-tags: RCC2967}, month = {mar}, pages = {534{\textendash}537}, abstract = {Iron is an essential nutrient for photosynthetic plankton (phytoplankton), but owing to its low solubility in vast areas of the ocean the concentration of this metal is low, limiting the growth of the phytoplankton. Andrew Allen and co-workers show that the phytoplankton Phaeodactylum tricornutum has developed a specific iron acquisition mechanism that relies on activity of the ISIP2A protein. ISIP2A represents a functional analogue of transferrin{\textemdash}a metazoan protein that binds iron with high affinity{\textemdash}as both proteins use similar iron binding, internalization and release mechanisms, suggesting their independent and convergent evolution. Both proteins bind iron through a synergistic interaction of ferric iron and CO32-, and because ocean acidification decreases CO32- concentration it may also decrease phytoplankton iron uptake and growth.}, keywords = {RCC2967}, issn = {0028-0836}, doi = {10.1038/nature25982}, url = {http://dx.doi.org/10.1038/nature25982 http://www.nature.com/doifinder/10.1038/nature25982}, author = {McQuaid, Jeffrey B. and Kustka, Adam B. and Obornik, Miroslav and Horak, Ales and McCrow, John P. and Karas, Bogumil J. and Zheng, Hong and Kindeberg, Theodor and Andersson, Andreas J. and Barbeau, Katherine A. and Allen, Andrew E.} } @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 {Kenworthy2018, title = {Compared stress tolerance to short-term exposure in native and invasive tunicates from the NE Atlantic: when the invader performs better}, journal = {Marine Biology}, volume = {165}, number = {10}, year = {2018}, note = {tex.mendeley-tags: RCC179}, pages = {164}, abstract = {{The combined impact of invasive species and climate change threatens natural systems worldwide, often facilitating the expansion of harmful invasive species. It is imperative to understand the mechanisms behind why species become invasive and widespread. Traditionally, it is thought that invasive species have greater tolerances to a wider array of environmental conditions than natives. We, therefore, tested the hypothesis that invasive species are more tolerant to the effects of short-term exposure to temperature and salinity stress. Using unifactorial experiments, we compared the tolerances of two common fouling NE Atlantic ascidians, the native Ciona intestinalis and the invasive Styela clava, to increased temperature and decreased salinity. We measured lethal and behavioural responses affecting 50\% of populations to give an indication of the tolerance limits for temperature (LT50) and salinity (EC50), and respiration rate to give an indication of the change in metabolic response. The invasive S. clava was more tolerant to increased stress (LT50 = 29.5 {\textdegree}C}, keywords = {RCC179}, issn = {1432-1793}, doi = {10.1007/s00227-018-3420-1}, url = {https://doi.org/10.1007/s00227-018-3420-1}, author = {Kenworthy, Joseph M and Davoult, Dominique and Lejeusne, Christophe} } @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 {Kazamia2018, title = {Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms}, journal = {Science Advances}, volume = {4}, number = {5}, year = {2018}, note = {tex.mendeley-tags: RCC2967}, month = {may}, pages = {eaar4536}, keywords = {RCC2967}, issn = {2375-2548}, doi = {10.1126/sciadv.aar4536}, url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aar4536}, author = {Kazamia, Elena and Sutak, Robert and Paz-Yepes, Javier and Dorrell, Richard G and Vieira, Fabio Rocha Jimenez and Mach, Jan and Morrissey, Joe and Leon, S{\'e}bastien and Lam, France and Pelletier, Eric and Camadro, Jean-michel and Bowler, Chris and Lesuisse, Emmanuel} } @article {Trainic, title = {Infection dynamics of a bloom-forming alga and its virus determine airborne coccolith emission from seawater}, journal = {iScience}, year = {2018}, note = {tex.mendeley-tags: RCC1216}, month = {aug}, abstract = {Summary Sea spray aerosols (SSA), have a profound effect on the climate; however, the contribution of oceanic microbial activity to SSA is not fully established. We assessed aerosolization of the calcite units (coccoliths) that compose the exoskeleton of the cosmopolitan bloom-forming coccolithophore, Emiliania huxleyi. Airborne coccolith emission occurs in steady-state conditions and increases by an order of magnitude during E. huxleyi infection by E. huxleyi virus (EhV). Airborne to seawater coccolith ratio is 1:108, providing estimation of airborne concentrations from seawater concentrations. The coccoliths{\textquoteright} unique aerodynamic structure yields a characteristic settling velocity of \~0.01 cm s-1, \~25 times slower than average sea salt particles, resulting in coccolith fraction enrichment in the air. The calculated enrichment was established experimentally, indicating that coccoliths may be key contributors to coarse mode SSA surface area, comparable with sea salt aerosols. This study suggests a coupling between key oceanic microbial interactions and fundamental atmospheric processes like SSA formation.}, keywords = {Atmospheric Science, Biogeoscience, Earth Sciences, Marine Organism, RCC1216}, issn = {25890042}, doi = {10.1016/j.isci.2018.07.017}, url = {https://www.cell.com/iscience/fulltext/S2589-0042(18)30105-6 https://linkinghub.elsevier.com/retrieve/pii/S2589004218301056}, author = {Trainic, Miri and Koren, Ilan and Sharoni, Shlomit and Frada, Miguel and Segev, Lior and Rudich, Yinon and Vardi, Assaf} } @article {Smallwood2018, title = {Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri}, journal = {bioRxiv}, year = {2018}, note = {tex.mendeley-tags: RCC745}, keywords = {? No DOI found, RCC745}, author = {Smallwood, Authors Chuck R and Chen, Jian-hua and Kumar, Neeraj and Chrisler, William and Samuel, O and Kyle, Jennifer E and Nicora, Carrie D and Boudreau, Rosanne and Ekman, Axel and Kim, K and Moore, Ronald J and Mcdermott, Gerry and Cannon, William R and Evans, James E} } @article {Rastogi2017, title = {Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms}, journal = {Scientific Reports}, volume = {8}, number = {1}, year = {2018}, note = {ISBN: 4159801823106 Publisher: Springer US tex.mendeley-tags: RCC2967}, month = {dec}, pages = {4834}, abstract = {2 3 Diatoms are one of the most successful and ecologically important groups of eukaryotic 4 phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better 5 understanding of their biological innovations, evolutionary origins, and ecological 6 underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions 7 combined with published expressed sequence tags and protein sequences from multiple taxa 8 to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 9 novel genes. The new annotation additionally permitted the discovery for the first time of 10 extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping 11 which increases the diversity of transcripts to regulate gene expression in response to nutrient 12 limitations. In addition, we have used up-to-date reference sequence libraries to dissect the 13 taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete in 14 lineage-specific genes, with up to 47\% of the gene models present only possessing 15 orthologues in other stramenopile groups. Finally, we have performed a comprehensive de 16 novo annotation of repetitive elements showing novel classes of TEs such as SINE, MITE, LINE 17 and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene 18 function, evolution and ecology.}, keywords = {RCC2967}, issn = {2045-2322}, doi = {10.1038/s41598-018-23106-x}, url = {https://www.biorxiv.org/content/early/2017/08/14/176024\%0Ahttp://dx.doi.org/10.1101/176024 http://www.nature.com/articles/s41598-018-23106-x}, author = {Rastogi, Achal and Maheswari, Uma and Dorrell, Richard G. and Vieira, Fabio Rocha Jimenez and Maumus, Florian and Kustka, Adam and McCarthy, James and Allen, Andy E. and Kersey, Paul and Bowler, Chris and Tirichine, Leila} } @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 {Yamada2018, title = {Ontogenetic analysis of siliceous cell wall formation in Triparma laevis f. inornata (Parmales, Stramenopiles)}, journal = {Journal of Phycology}, year = {2018}, note = {ISBN: 0000000266291 tex.mendeley-tags: RCC4665}, month = {oct}, pages = {0{\textendash}2}, keywords = {RCC4665}, issn = {00223646}, doi = {10.1111/jpy.12800}, url = {http://doi.wiley.com/10.1111/jpy.12800}, author = {Yamada, Kazumasa and Katsura, Hirotaka and No{\"e}l, Mary-H{\'e}l{\`e}ne and Ichinomiya, Mutsuo and Kuwata, Akira and Sato, Shinya and Yoshikawa, Shinya} } @article {Fiore2018, title = {A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae}, journal = {bioRxiv}, year = {2018}, note = {tex.mendeley-tags: RCC299,RCC834}, keywords = {? No DOI found, RCC299, RCC834}, url = {http://dx.doi.org/10.1101/484824}, author = {Fiore, Cara L. and Alexander, Harriet and Soule, Melissa C. Kido and Kujawinski, Elizabeth B.} } @article {Klinger2018, title = {Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends}, journal = {Genome Biology and Evolution}, volume = {10}, number = {April}, year = {2018}, note = {tex.mendeley-tags: RCC1513}, pages = {1019{\textendash}1038}, abstract = {Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes. Because reports of this process have been limited to manual assessment of individual lineages, global trends concerning this RNA editing and its effect on the biological function of the plastid are largely unknown. Using novel bioinformatic methods, we examine the dynamics and evolution of RNA editing over a large multispecies data set of dinoflagellates, including novel sequence data from the peridinin dinoflagellate Pyrocystis lunula and the fucoxanthin dinoflagellate Karenia mikimotoi. We demonstrate that while most individual RNA editing events in dinoflagellate plastids are restricted to single species, global patterns, and functional consequences of editing are broadly conserved. We find that editing is biased toward specific codon positions and regions of genes, and generally corrects otherwise deleterious changes in the genome prior to translation, though this effect is more prevalent in peridinin than fucoxanthin lineages. Our results support a model for promiscuous editing application subsequently shaped by purifying selection, and suggest the presence of an underlying editing mechanism transferred from the peridinin-containing ancestor into fucoxanthin plastids postendosymbiosis, with remarkably conserved functional consequences in the new lineage.}, keywords = {constructive neutral evolution, Dinoflagellate, plastid, RCC1513, serial endosymbiosis, transcript editing}, issn = {1759-6653}, doi = {10.1093/gbe/evy057}, url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evy057/4935245}, author = {Klinger, Christen M and Paoli, Lucas and Newby, Robert J and Wang, Matthew Yu-Wei and Carroll, Hyrum D and Leblond, Jeffrey D and Howe, Christopher J and Dacks, Joel B and Bowler, Chris and Cahoon, A Bruce and Dorrell, Richard G and Richardson, Elisabeth} } @article {Muller2018, title = {Stable isotope fractionation of strontium in coccolithophore calcite: Influence of temperature and carbonate chemistry}, journal = {Geobiology}, volume = {16}, number = {3}, year = {2018}, note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC1200}, month = {may}, pages = {297{\textendash}306}, abstract = {Abstract Marine calcifying eukaryotic phytoplankton (coccolithophores) is a major contributor to the pelagic production of CaCO3 and plays an important role in the biogeochemical cycles of C, Ca and other divalent cations present in the crystal structure of calcite. The geochemical signature of coccolithophore calcite is used as palaeoproxy to reconstruct past environmental conditions and to understand the underlying physiological mechanisms (vital effects) and precipitation kinetics. Here, we present the stable Sr isotope fractionation between seawater and calcite (?88/86Sr) of laboratory cultured coccolithophores in individual dependence of temperature and seawater carbonate chemistry. Coccolithophores were cultured within a temperature and a pCO2 range from 10 to 25{\textdegree}C and from 175 to 1,240 ?atm, respectively. Both environmental drivers induced a significant linear increase in coccolith stable Sr isotope fractionation. The temperature correlation at constant pCO2 for Emiliania huxleyi and Coccolithus braarudii is expressed as ?88/86Sr = ?7.611 ? 10?3 T + 0.0061. The relation of ?88/86Sr to pCO2 was tested in Emiliania huxleyi at 10 and 20{\textdegree}C and resulted in ?88/86Sr = ?5.394 ? 10?5 pCO2 ? 0.0920 and ?88/86Sr = ?5.742 ? 10?5 pCO2 ? 0.1351, respectively. No consistent relationship was found between coccolith ?88/86Sr and cellular physiology impeding a direct application of fossil coccolith ?88/86Sr as coccolithophore productivity proxy. An overall significant correlation was detected between the elemental distribution coefficient (DSr) and ?88/86Sr similar to inorganic calcite with a physiologically induced offset. Our observations indicate (i) that temperature and pCO2 induce specific effects on coccolith ?88/86Sr values and (ii) that strontium elemental ratios and stable isotope fractionation are mainly controlled by precipitation kinetics when embedded into the crystal lattice and subject to vital effects during the transmembrane transport from seawater to the site of calcification. These results provide an important step to develop a coccolith ?88/86Sr palaeoproxy complementing the existing toolbox of palaeoceanography.}, keywords = {coccolithophores, paleoproxy calibration, phytoplankton, RCC1200, stable Sr isotope fractionation}, issn = {1472-4677}, doi = {10.1111/gbi.12276}, url = {https://doi.org/10.1111/gbi.12276}, author = {M{\"u}ller, M N and Krabbenh{\"o}ft, A and Vollstaedt, H and Brandini, F P and Eisenhauer, A} } @article {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 {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 {Kuhlisch2017, title = {A fast and direct liquid chromatography-mass spectrometry method to detect and quantify polyunsaturated aldehydes and polar oxylipins in diatoms}, journal = {Limnology and Oceanography: Methods}, volume = {15}, number = {1}, year = {2017}, note = {Publisher: John Wiley \& Sons, Ltd tex.mendeley-tags: RCC75,RCC776}, month = {jan}, pages = {70{\textendash}79}, abstract = {Abstract Polyunsaturated aldehydes (PUAs) are a group of microalgal metabolites that have attracted a lot of attention due to their biological activity. Determination of PUAs has become an important routine procedure in plankton and biofilm investigations, especially those that deal with chemically mediated interactions. Here we introduce a fast and direct derivatization free method that allows quantifying PUAs in the nanomolar range, sufficient to undertake the analysis from cultures and field samples. The sample preparation requires one simple filtration step and the initiation of PUA formation by cell disruption. After centrifugation the samples are ready for measurement without any further handling. Within one chromatographic run this method additionally allows us to monitor the formation of the polar oxylipins arising from the cleavage of precursor fatty acids. The robust method is based on analyte separation and detection using ultra high performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (UHPLC-APCI MS) and enables high throughput investigations by employing an analysis time of only 5 min. Our protocol thus provides an alternative and extension to existing PUA determinations based on gas chromatography-mass spectrometry (GC-MS) with shorter run times and without any chemical derivatization. It also enables researchers with widely available LC-MS analytical platforms to monitor PUAs. Additionally, non-volatile oxylipins such as ?-oxo-acids and related compounds can be elucidated and monitored.}, keywords = {RCC75, RCC776}, issn = {1541-5856}, doi = {10.1002/lom3.10143}, url = {https://doi.org/10.1002/lom3.10143}, author = {Kuhlisch, Constanze and Deicke, Michael and Ueberschaar, Nico and Wichard, Thomas and Pohnert, Georg} } @article {Yoo2017a, title = {Mixotrophy in the marine red-tide cryptophyte Teleaulax amphioxeia and ingestion and grazing impact of cryptophytes on natural populations of bacteria in Korean coastal waters}, journal = {Harmful Algae}, volume = {68}, number = {May 2005}, year = {2017}, note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC1086}, pages = {105{\textendash}117}, abstract = {Cryptophytes are ubiquitous and one of the major phototrophic components in marine plankton communities. They often cause red tides in the waters of many countries. Understanding the bloom dynamics of cryptophytes is, therefore, of great importance. A critical step in this understanding is unveiling their trophic modes. Prior to this study, several freshwater cryptophyte species and marine Cryptomonas sp. and Geminifera cryophila were revealed to be mixotrophic. The trophic mode of the common marine cryptophyte species, Teleaulax amphioxeia has not been investigated yet. Thus, to explore the mixotrophic ability of T. amphioxeia by assessing the types of prey species that this species is able to feed on, the protoplasms of T. amphioxeia cells were carefully examined under an epifluorescence microscope and a transmission electron microscope after adding each of the diverse prey species. Furthermore, T. amphioxeia ingestion rates heterotrophic bacteria and the cyanobacterium Synechococcus sp. were measured as a function of prey concentration. Moreover, the feeding of natural populations of cryptophytes on natural populations of heterotrophic bacteria was assessed in Masan Bay in April 2006. This study reported for the first time, to our knowledge, that T. amphioxeia is a mixotrophic species. Among the prey organisms offered, T. amphioxeia fed only on heterotrophic bacteria and Synechococcus sp. The ingestion rates of T. amphioxeia on heterotrophic bacteria or Synechococcus sp. rapidly increased with increasing prey concentrations up to 8.6 {\texttimes} 106 cells ml-1, but slowly at higher prey concentrations. The maximum ingestion rates of T. amphioxeia on heterotrophic bacteria and Synechococcus sp. reached 0.7 and 0.3 cells predator-1 h-1, respectively. During the field experiments, the ingestion rates and grazing coefficients of cryptophytes on natural populations of heterotrophic bacteria were 0.3{\textendash}8.3 cells predator-1 h-1 and 0.012{\textendash}0.033 d-1, respectively. Marine cryptophytes, including T. amphioxeia, are known to be favorite prey species for many mixotrophic and heterotrophic dinoflagellates and ciliates. Cryptophytes, therefore, likely play important roles in marine food webs and may exert a considerable potential grazing impact on the populations of marine bacteria.}, keywords = {Bloom, Flagellate, Grazing impact, Predator-prey relationship, RCC1086, Red tide}, issn = {18781470}, doi = {10.1016/j.hal.2017.07.012}, url = {http://dx.doi.org/10.1016/j.hal.2017.07.012}, author = {Yoo, Yeong Du and Seong, Kyeong Ah and Jeong, Hae Jin and Yih, Wonho and Rho, Jung Rae and Nam, Seung Won and Kim, Hyung Seop} } @article {Steele2017, title = {Occurrence of chlorophyll allomers during virus-induced mortality and population decline in the ubiquitous picoeukaryote Ostreococcus tauri}, journal = {Environmental Microbiology}, volume = {in press}, year = {2017}, note = {ISBN: 3907122046 tex.mendeley-tags: RCC745}, month = {nov}, pages = {1{\textendash}41}, abstract = {Phytoplankton have been shown to harbour a diversity of hydrocarbonoclastic bacteria (HCB), yet it is not understood how these phytoplankton-associated HCB would respond in the event of an oil spill at sea. Here, we assess the diversity and dynamics of the bacterial community associated with a natural population of marine phytoplankton under oil spill-simulated conditions, and compare it to that of the free-living (non phytoplankton-associated) bacterial community. Whilst the crude oil severely impacted the phytoplankton population and was likely conducive to marine oil snow (MOS) formation, analysis of the MiSeq-derived 16S rRNA data revealed dramatic and differential shifts in the oil-amended communities that included blooms of recognised HCB (e.g. Thalassospira, Cycloclasticus), including putative novel phyla, as well as other groups with previously unqualified oil-degrading potential (Olleya, Winogradskyella, and members of the inconspicuous BD7-3 phylum). Notably, the oil biodegradation potential of the phytoplankton-associated community exceeded that of the free-living community, and it showed a preference to degrade substituted and non-substituted polycyclic aromatic hydrocarbons. Our study provides evidence of compartmentalisation of hydrocarbon-degrading capacity in the marine water column, wherein HCB associated with phytoplankton are better tuned to degrading crude oil hydrocarbons than that by the community of planktonic free-living bacteria.}, keywords = {biodegradation, crude oil, eukaryotic phytoplankton, hydrocarbon-degrading bacteria (HCB), marine environment, micro- algae, RCC745}, issn = {14622912}, doi = {10.1111/1462-2920.13980}, url = {http://doi.wiley.com/10.1111/1462-2920.13980}, author = {Steele, Deborah J. and Kimmance, Susan A. and Franklin, Daniel J. and Airs, Ruth L.} } @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 {Leliaert2016, title = {Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.}, journal = {Scientific Reports}, volume = {6}, year = {2016}, note = {tex.mendeley-tags: 2016,RCC15,RCC299}, month = {may}, pages = {25367}, keywords = {2016, RCC15, RCC299}, issn = {2045-2322}, doi = {10.1038/srep25367}, url = {http://www.nature.com/articles/srep25367}, author = {Leliaert, Frederik and Tronholm, Ana and Lemieux, Claude and Turmel, Monique and DePriest, Michael S. and Bhattacharya, Debashish and Karol, Kenneth G. and Fredericq, Suzanne and Zechman, Frederick W. and Lopez-Bautista, Juan 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 {Potvin2015, title = {Morphology , molecular phylogeny , and pigment characterization of a novel phenotype of the dinoflagellate genus Pelagodinium from Korean waters}, journal = {Algae}, volume = {30}, number = {3}, year = {2015}, note = {tex.mendeley-tags: rcc}, pages = {183{\textendash}195}, abstract = {The dinoflagellate genus Pelagodinium is genetically classified in distinct sub-clades and subgroups. However, it is dif- ficult to determine whether this genetic diversity represents intra- or interspecific divergence within the genus since only the morphology of the type strain of the genus Pelagodinium, Pelagodinium bei, is available. An isolate associated with the genus Pelagodinium from Shiwha Bay, Korea, was recently cultured. This isolate formed a subgroup with 3 to 4 strains from the Atlantic Ocean, Mediterranean Sea, and Indian Ocean. This subgroup was distinct from the subgroup contain- ing P. bei. The morphology of the isolate was analyzed using optical and scanning electron microscopy and was almost identical to that of P. bei except that this isolate had two series of amphiesmal vesicles (AVs) in the cingulum, unlike P. bei that has one series. When the pigment compositions of the isolate and P. bei were analyzed using high-performance liquid chromatography, these two strains had peridinin as a major accessory pigment and their pigment compositions were almost identical. In addition, the swimming behaviors of these two strains were very similar. The re-examination of the type culture of P. bei revealed two series in the cingulum as for the isolate. The new findings on the number of series of AVs in the cingulum, the pigment composition, and the swimming behaviors suggest that P. bei and the isolate may be conspecific despite their association to genetically different subgroups. This study provides a basis to further understand the molecular classification within Pelagodinium combining genetic, morphological, pigment, and behavioral data.}, keywords = {foraminifera, gymnodinium bei, pelagic symbiont, rcc, suessiaceae, suessiales}, doi = {10.4490/algae.2015.30.3.183}, author = {Potvin, {\'E}ric and Jeong, Hae Jin and Kang, Nam Seon and Noh, Jae Hoon and Yang, Eun Jin} } @article {Kamikawa2015, title = {Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)}, journal = {Phycological Research}, volume = {63}, year = {2015}, note = {tex.mendeley-tags: rcc}, pages = {19{\textendash}28}, abstract = {In order to obtain insights into the evolution of colorless (apochlorotic) diatoms, we investigated newly established apochlorotic strains of Nitzschia spp. using light and electron microscopy and molecular phylogenetic analyses. Fluores- cence microscopic observations demonstrated that the apochlorotic diatoms lack chlorophylls. Transmission electron microscopy of two apochlorotic strains also demonstrated that their plastids lacked thylakoids; instead, having four- membrane-bound organelles without thylakoids, similar to nonphotosynthetic plastid remnants. From the apochlorotic strains, we also found plastid small subunit rRNA genes that were unusually long branched in phylogenetic analyses, as observed in other nonphotosynthetic plastids. Molecular phylogenetic analysis of the nucleus-encoded large subunit rRNA genes showed eight distinct lineages for apochlo- rotic diatoms. The eight apochlorotic lineages were not monophyletic, suggesting that the loss of photosynthesis took place multiple times independently within Nitzschia. Several diatoms, including Nitzschia spp., are mixotrophic, which is an expected mode of nutrition that would help explain the evolutionary switch from a photosynthetic lifestyle to a heterotrophic lifestyle. Key}, keywords = {apochlorotic diatoms, genetic diversity, large subunit rrna, molecular phylogenetic analysis, nonphotosynthetic plastids, plastid 16s rrna, rcc}, issn = {13220829}, doi = {10.1111/pre.12072}, url = {http://doi.wiley.com/10.1111/pre.12072}, author = {Kamikawa, Ryoma and Yubuki, Naoji and Yoshida, Masaki and Taira, Misaka and Nakamura, Noriaki and Ishida, Ken-ichiro and Leander, Brian S. and Miyashita, Hideaki and Hashimoto, Tetsuo and Mayama, Shigeki and Inagaki, Yuji} } @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 {DelCampo2014, title = {The others: our biased perspective of eukaryotic genomes}, journal = {Trends in Ecology \& Evolution}, volume = {29}, number = {5}, year = {2014}, note = {Publisher: Elsevier tex.mendeley-tags: RCC,rcc}, pages = {252{\textendash}259}, abstract = {?There is an important bias in eukaryotic knowledge, affecting cultures and genomes.?Eukaryotic genomics are biased towards multicellular organisms and their parasites.?A phylogeny-driven initiative is needed to overcome the eukaryotic genomic bias.?We propose to sequence neglected cultures and increase culturing efforts.?Single-cell genomics should be embraced as a tool to explore eukaryotic diversity.}, keywords = {rcc}, doi = {10.1016/j.tree.2014.03.006}, url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(14)00064-0}, author = {del Campo, Javier and Sieracki, Michael E and Molestina, Robert and Keeling, Patrick and Massana, Ramon and Ruiz-Trillo, I{\~n}aki} } @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 {Kashtan2014, title = {Single-cell genomics reveals hundreds of coexisting subpopulations in wild prochlorococcus}, journal = {Science}, volume = {344}, number = {6182}, year = {2014}, note = {tex.mendeley-tags: RCC278}, pages = {416{\textendash}420}, abstract = {Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct {\textquotedblleft}genomic backbones,{\textquotedblright} each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.}, keywords = {RCC278}, doi = {10.1126/science.1248575}, url = {http://www.sciencemag.org/content/344/6182/416.abstract}, author = {Kashtan, Nadav and Roggensack, Sara E and Rodrigue, S{\'e}bastien and Thompson, Jessie W and Biller, Steven J and Coe, Allison and Ding, Huiming and Marttinen, Pekka and Malmstrom, Rex R and Stocker, Roman and Follows, Michael J and Stepanauskas, Ramunas and Chisholm, Sallie W} } @article {Kessenich2014, title = {Transcriptomic insights into the life history of bolidophytes , the sister lineage to diatoms}, journal = {Journal of Phycology}, volume = {983}, year = {2014}, note = {tex.mendeley-tags: RCC205}, pages = {977{\textendash}983}, abstract = {Diatoms are perhaps the most diverse lineage of eukaryotic algae, with their siliceous cell wall and diplontic life history often considered to have played important roles in their extraordinary diversification. The characteristic diminution of the diatom cell wall over the course of vegetative growth provides a reliable, intrinsic trigger for sexual reproduction, establishing a direct link between the evolution of their cell-wall and life- history features. It is unclear, however, whether the diplontic life cycle of diatoms represents an ancestral or derived trait. This uncertainty is based in part on our lack of understanding of the life cycle of the sister lineage to diatoms, which includes a mix of two free-living and separately classified forms: naked biflagellate unicells in the genus Bolidomonas and silicified forms in the order Parmales. These two forms might represent different life-history stages, although directly establishing such links can be difficult. We sequenced transcriptomes for Bolidomonas and two diatoms and found that \~0.1\% of the coding regions in the two diploid diatoms are heterozygous, whereas Bolidomonas is virtually devoid of heterozygous alleles, consistent with expectations for a haploid genome. These results suggest that Bolidomonas is haploid and predict that parmaleans represent the diploid phase of a haplodiplontic life cycle. These data fill an important gap in our understanding of the origin of the diplontic life history of diatoms, which may represent an evolutionarily derived, adaptive feature.}, keywords = {Bolidomonas, CCMP1866, diatoms, diplontic, haplodiplontic, life cycle, Parmales, RCC205, RCC?o?dd, Transcriptome}, doi = {10.1111/jpy.12222}, url = {http://dx.doi.org/10.1111/jpy.12222}, author = {Kessenich, Colton R and Ruck, Elizabeth C and Schurko, Andrew M and Wickett, Norman J and Alverson, Andrew J} } @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 {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 {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 {Stern2012, title = {Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker}, journal = {PLoS ONE}, volume = {7}, year = {2012}, note = {tex.mendeley-tags: 2012,rcc,sbr?hyto$_\textrmd$ipo}, pages = {e42780}, keywords = {2012, ASSEMBLE, Barcoding, ITS, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo}, doi = {10.1371/journal.pone.0042780}, url = {http://www.plosone.org/article/info\%253Adoi\%252F10.1371\%252Fjournal.pone.0042780}, author = {Stern, Rowena F and Andersen, Robert A and Jameson, Ian and K{\"u}pper, Frithjof C and Coffroth, Mary-Alice and Vaulot, Daniel and Gall, Florence Le and Veron, Benoit and Brand, Jerry J and Skelton, Hayley and Kasai, Fumai and Lilly, Emily L and Keeling, Patrick J} } @article {Baines2012, title = {Significant silicon accumulation by marine picocyanobacteria}, journal = {Nature Geoscience}, volume = {5}, number = {12}, year = {2012}, note = {arXiv: 9605103 [cs] ISBN: 1752-08941?752-0908 Publisher: Nature Publishing Group tex.arxivid: cs/9605103 tex.mendeley-tags: rcc1084,rcc1086,rcc752}, pages = {886{\textendash}891}, abstract = {The marine silicon cycle is thought to be intimately tied to the carbon cycle through its effect on the growth of diatoms. These unicellular algae form substantial blooms in cold, nutrient-rich waters. Their dense, siliceous cell walls promote the sinking of particulate matter, and all the carbon and nutrients contained therein1. As such, diatoms are thought to be the primary organisms responsible for the low levels of dissolved silicon observed in the surface ocean and the export of mineral silica to depth. Here, we use synchrotron X-ray fluorescence microscopy to determine the elemental composition of individual diatoms and cyanobacterial cells from the eastern equatorial Pacific and the Sargasso Sea.We show that cells of Synechococcus, a small unicellular marine cyanobacterium that dominates in nutrient-depleted waters2, can exhibit cellular ratios of silicon to sulphur, and silicon to phosphorus, approaching those detected in diatoms in the same location. Silicon accumulation was also observed in cultured Synechococcus strains. We estimate that the water column inventory of silicon in Synechococcus can exceed that of diatomsinsomecases.We suggest that picocyanobacteriamay exert a previously unrecognized influence on the oceanic silicon cycle, especially in nutrient-poorwaters.}, keywords = {rcc1084, RCC1086, rcc752}, issn = {1752-0894}, doi = {10.1038/ngeo1641}, url = {http://www.nature.com/doifinder/10.1038/ngeo1641}, author = {Baines, Stephen B. and Twining, Benjamin S. and Brzezinski, Mark a. and Krause, Jeffrey W. and Vogt, Stefan and Assael, Dylan and McDaniel, Hannah} } @article {Kulk2012, title = {Temperature-dependent growth and photophysiology of prokaryotic and eukaryotic oceanic picophytoplankton}, journal = {Marine Ecology Progress Series}, volume = {466}, year = {2012}, note = {tex.mendeley-tags: RCC407,RCC410,RCC879}, pages = {43{\textendash}55}, abstract = {ABSTRACT: It is expected that climate change will expand the open oligotrophic oceans by enhanced thermal stratification. Because temperature defines the geographic distribution of picophytoplankton in open-ocean ecosystems and regulates photophysiological responses, it is important to understand how temperature affects picophytoplankton growth and photophysiology. Two prokaryotic and 2 eukaryotic picophytoplankton strains were acclimated to 3 different temperatures, ranging from 16 to 24{\textdegree}C. Temperature-dependent growth and photophysiology were assessed by measurements of specific growth rates, cell size, pigment composition, absorption and electron transport rates. Growth of Prochlorococcus marinus (eMED4), Prochlorococcus sp. (eMIT9313), Ostreococcus sp. (clade B) and Pelagomonas calceolata was positively related to temperature, especially in the prokaryotic strains. Changes in photophysiology included increased light harvesting, increased electron transport and reduced photoinhibition at elevated temperatures. However, the changes related to light harvesting and electron transport could not fully explain the observed difference in growth. This suggests that other processes, such as Calvin cycle activity, are likely to limit growth at sub-optimal temperatures in these picophytoplankton strains. The overall changes in photophysiology during temperature acclimation will possibly allow photosynthesis at higher irradiance intensities, but the genetically defined low temperature tolerances and photosynthetic characteristics of the different ecotypes will likely be more important in determining picophytoplankton (depth) distribution and community composition.}, keywords = {Absorption, Electron transport rate, Eukaryotic picophytoplankton, Growth, Pigment, Prochlorococcus, rcc, RCC407, rcc410, RCC879, temperature}, issn = {01718630}, doi = {10.3354/meps09898}, url = {http://www.int-res.com/abstracts/meps/v466/p43-55/}, author = {Kulk, Gemma and De Vries, Pablo and Van De Poll, Willem H. and Visser, Ronald J W and Buma, Anita G J} } @article {Thompson2012, title = {Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga}, journal = {Science}, volume = {337}, number = {6101}, year = {2012}, note = {tex.mendeley-tags: 2012,microb3,rcc,sbr?hyto$_\textrmd$ipo}, pages = {1546{\textendash}1550}, abstract = {Symbioses between nitrogen (N)2{\textendash}fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N2 fixation.}, keywords = {2012, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo}, doi = {10.1126/science.1222700}, url = {http://www.sciencemag.org/content/337/6101/1546.abstract}, author = {Thompson, Anne W and Foster, Rachel A and Krupke, Andreas and Carter, Brandon J and Musat, Niculina and Vaulot, Daniel and Kuypers, Marcel M M and Zehr, Jonathan P} } @article {Kirkham2011, title = {Basin-scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional Transect}, journal = {Environmental Microbiology}, volume = {13}, number = {4}, year = {2011}, note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: Micromonas,RCC,rcc}, pages = {975{\textendash}990}, abstract = {Summary Photosynthetic picoeukaryotes (PPEs) of a size {\textexclamdown} 3 {\textmu}m play a crucial role in oceanic primary production. However, little is known of the structure of the PPE community over large spatial scales. Here, we investigated the distribution of various PPE classes along an Atlantic Meridional Transect sampled in boreal autumn 2004 that encompasses a range of ocean provinces (gyres, upwelling, temperate regions), using dot blot hybridization technology targeting plastid 16S rRNA gene amplicons. Two algal classes, Prymnesiophyceae and Chrysophyceae, dominated the PPE community throughout the Atlantic Ocean, over a range of water masses presenting different trophic profiles. However, these classes showed strongly complementary distributions with Chrysophyceae dominating northern temperate waters, the southern gyre and equatorial regions, while prymnesiophytes dominated the northern gyre. Phylogenetic analyses using both plastid and nuclear rRNA genes revealed a high diversity among members of both classes, including sequences contained in lineages with no close cultured counterpart. Other PPE classes were less prevalent along the transect, with members of the Cryptophyceae, Pelagophyceae and Eustigmatophyceae essentially restricted to specific regions. Multivariate statistical analyses revealed strong relationships between the distribution patterns of some of these latter PPE classes and temperature, light intensity and nutrient concentrations. Cryptophyceae, for example, were mostly found in the upwelling region and associated with higher nutrient concentrations. However, the key classes of Prymnesiophyceae and Chrysophyceae were not strongly influenced by the variables measured. Although there appeared to be a positive relationship between Chrysophyceae distribution and light intensity, the complementary distributions of these classes could not be explained by the variables recorded and this requires further explanation.}, keywords = {Micromonas, rcc}, doi = {10.1111/j.1462-2920.2010.02403.x}, url = {http://dx.doi.org/10.1111/j.1462-2920.2010.02403.x}, author = {Kirkham, Amy R and Jardillier, Ludwig E and Tiganescu, Ana and Pearman, John and Zubkov, Mikhail V and Scanlan, David J} } @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 {Ota2011, title = {Gymnochlora dimorpha sp. nov., a chlorarachniophyte with unique daughter cell behaviour.}, journal = {Phycologia}, volume = {50}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo}, pages = {317{\textendash}326}, keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo}, doi = {10.2216/09-102.1}, author = {Ota, S and Kudo, A and Ishida, K} } @article {Luo2011, title = {Individual genome assembly from complex community short-read metagenomic datasets}, journal = {The ISME journal}, volume = {6}, year = {2011}, note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: RCC307}, pages = {898{\textendash}901}, keywords = {RCC307}, doi = {10.1038/ismej.2011.147}, url = {http://dx.doi.org/10.1038/ismej.2011.147 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2011147s1.html}, author = {Luo, Chengwei and Tsementzi, Despina and Kyrpides, Nikos C and Konstantinidis, Konstantinos T} } @article {Hagino2011, title = {New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliana huxleyi (prymnesiophyceae) from the cox1b-ATP4 genes}, journal = {Journal of Phycology}, volume = {47}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo}, pages = {1164{\textendash}1176}, abstract = {Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophore occurring from tropical to subpolar waters and exhibiting variations in morphology of coccoliths possibly related to environmental conditions. We examined morphological characters of coccoliths and partial mitochondrial sequences of the cytochrome oxidase 1b (cox1b) through adenosine triphosphate synthase 4 (atp4) genes of thirty-nine clonal E. huxleyi strains from the Atlantic and Pacific Oceans, Mediterranean Sea and their adjacent seas. Based on the morphological study of culture strains by SEM, Type O, a new morphotype characterized by coccoliths with an open central area, was separated from existing morphotypes A, B, B/C, C, R and var. corona, characterized by coccoliths with central area elements. Molecular phylogenetic studies revealed that E. huxleyi consists of at least two mitochondrial sequence groups with different temperature preferences/tolerances: a cool water group occurring in subarctic North Atlantic and Pacific and a warm water group occurring in the sub-tropical Atlantic and Pacific and in the Mediterranean Sea.}, keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1111/j.1529-8817.2011.01053.x}, author = {Hagino, K and Bendif, El Mahdi and Young, J and Kogame, K and Takano, Y and Probert, I and Horiguchi, T and de Vargas, C and Okada, H} } @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 {Ishida2011, title = {Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximately 1 Mbp}, journal = {Phycological Research}, volume = {59}, number = {2}, year = {2011}, note = {Publisher: Blackwell Publishing Asia tex.mendeley-tags: RCC,rcc}, pages = {120{\textendash}122}, abstract = {SUMMARY The nucleomorph genome size of the recently described chlorarachniophyte Partenskyella glossopodia, which forms an independent lineage in the phylogeny of chlorarachniophytes, was analyzed by pulse-field gel electrophoresis and Southern hybridization. These analyses showed that the nucleomorph genome of P. glossopodia is composed of three linear chromosomes that are about 445 kbp, 313 kbp, and 275 kbp in size. Thus, the total genome size is approximately 1033 kbp, which is significantly larger than the known size of chlorarachniophyte nucleomorph genomes, i.e. 330{\textendash}610 kbp. This is the first study to report a nucleomorph genome that reaches approximately 1 Mbp in size.}, keywords = {Chlorarachniophytes, genome reduction, genome size, nucleomorph, Partenskyella glossopodia, rcc}, doi = {10.1111/j.1440-1835.2011.00608.x}, url = {http://dx.doi.org/10.1111/j.1440-1835.2011.00608.x}, author = {Ishida, Ken-ichiro and Endo, Hiroko and Koike, Sayaka} } @article {Lepere2011, title = {Whole Genome Amplification (WGA) of marine photosynthetic eukaryote populations}, journal = {FEMS Microbiology Ecology}, volume = {76}, year = {2011}, note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo}, pages = {516{\textendash}523}, keywords = {2011, PICOFUNPAC, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo}, doi = {10.1111/j.1574-6941.2011.01072.x}, author = {Lepere, Cecile and Demura, M and Kawachi, M and Romac, S and Probert, I and Vaulot, D} } @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 {Mohr2010, title = {A new chlorophyll d -containing cyanobacterium : evidence for niche adaptation in the genus Acaryochloris}, journal = {The ISME journal}, year = {2010}, note = {tex.mendeley-tags: RCC,RCC1983,rcc}, pages = {1456{\textendash}1469}, abstract = {Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (231 260 31.200 S, 1511 540 50.400 E). The 16S ribosomal RNA is 2\% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371965nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms. The}, keywords = {acaryochloris, chlorophyll d, coral reef, cyanobacteria, microbial diversity, overview, rcc, RCC1983}, doi = {10.1038/ismej.2010.67}, author = {Mohr, Remus and Schliep, Martin and Kurz, Thorsten and Maldener, Iris and Adams, David G and Larkum, Anthony D W and Chen, Min and Hess, Wolfgang R} } @article {Minge2010, title = {A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum}, journal = {BMC Evolutionary Biology}, volume = {10}, year = {2010}, note = {ISBN: 1471-2148 tex.mendeley-tags: 2010,rcc}, pages = {191}, abstract = {Background: Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates. Results: We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae. Conclusions: L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum.}, keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO}, doi = {10.1186/1471-2148-10-191}, author = {Minge, M A and Shalchian-Tabrizi, K and Torresen, O K and Takishita, K and Probert, I and Inagaki, Y and Klaveness, D and Jakobsen, K S} } @conference {Meusnier2009, title = {DNA barcoding of protists in culture collections}, booktitle = {Third international barcode of life conference}, year = {2009}, note = {tex.mendeley-tags: RCC,rcc}, address = {Mexico City}, keywords = {? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmD$PO}, author = {Meusnier, Isabelle and Andersen, Robert A and Stern, Rowena and Bertrand, C and Kuepper, Frithjof and Brand, Jerry and Friedl, Thomas and Blackburn, Susan and Dinh, Donna and Acreman, Judy and Sedl{\'a}{\v c}ek, Ivo and P{\v r}ibyl, Pavel and Jutson, Maria and Phang, Siew Moi and Melkonian, M and Karpov, S and Hajibabaei, Mehrdad} } @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 {Misumi2008, title = {Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana}, journal = {Journal of Plant Research}, volume = {121}, number = {1}, year = {2008}, note = {tex.mendeley-tags: RCC,rcc}, pages = {3{\textendash}17}, abstract = {Algae play a more important role than land plants in the maintenance of the global environment and productivity. Progress in genome analyses of these organisms means that we can now obtain information on algal genomes, global annotation and gene expression. The full genome information for several algae has already been analyzed. Whole genomes of the red alga Cyanidioshyzon merolae, the green algae Ostreococcus tauri and Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana have been sequenced. Genome composition and the features of cells among the four algae were compared. Each alga maintains basic genes as photosynthetic eukaryotes and possesses additional gene groups to represent their particular characteristics. This review discusses and introduces the latest research that makes the best use of the particular features of each organism and the significance of genome analysis to study biological phenomena. In particular, examples of post-genome studies of organelle multiplication in C. merolae based on analyzed genome information are presented.}, keywords = {rcc}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18074102}, author = {Misumi, O and Yoshida, Y and Nishida, K and Fujiwara, T and Sakajiri, T and Hirooka, S and Nishimura, Y and Kuroiwa, T} } @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 {Kettler2007, title = {Patterns and implications of gene gain and loss in the evolution of Prochlorococcus}, journal = {PLoS genetics}, volume = {3}, year = {2007}, note = {tex.mendeley-tags: RCC,rcc}, pages = {e231}, keywords = {rcc}, doi = {10.1371/journal.pgen.0030231}, author = {Kettler, G and Martiny, A C and Huang, K and Zucker, J and Coleman, M L and Rodrigue, S and Chen, F and Lapidus, A and Ferriera, S and Johnson, J and Steglich, C and Church, G and Richardson, P and Chisholm, S W} } @article {Khan2007, title = {Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny}, journal = {Molecular Biology and Evolution}, volume = {24}, number = {8}, year = {2007}, note = {tex.mendeley-tags: RCC,rcc}, pages = {1832{\textendash}1842}, abstract = {Cryptophytes are a group of unicellular algae with chlorophyll c-containing plastids derived from the uptake of a secondary (i.e., eukaryotic) endosymbiont. Biochemical and molecular data indicate that cryptophyte plastids are derived from red algae, yet the question of whether or not cryptophytes acquired their red algal plastids independent of those in heterokont, haptophyte, and dinoflagellate algae is of long-standing debate. To better understand the origin and evolution of the cryptophyte plastid, we have sequenced the plastid genome of Rhodomonas salina CCMP1319: at 135,854 bp, it is the largest secondary plastid genome characterized thus far. It also possesses interesting features not seen in the distantly related cryptophyte Guillardia theta or in other red secondary plastids, including pseudogenes, introns, and a bacterial-derived gene for the tau/gamma subunit of DNA polymerase III (dnaX), the first time putative DNA replication machinery has been found encoded in any plastid genome. Phylogenetic analyses indicate that dnaX was acquired by lateral gene transfer (LGT) in an ancestor of Rhodomonas, most likely from a firmicute bacterium. A phylogenomic survey revealed no additional cases of LGT, beyond a noncyanobacterial type rpl36 gene similar to that recently characterized in other cryptophytes and haptophytes. Rigorous concatenated analysis of 45 proteins encoded in 15 complete plastid genomes produced trees in which the heterokont, haptophyte, and cryptophyte (i.e., chromist) plastids were monophyletic, and heterokonts and haptophytes were each other{\textquoteright}s closest relatives. However, statistical support for chromist monophyly disappears when amino acids are recoded according to their chemical properties in order to minimize the impact of composition bias, and a significant fraction of the concatenate appears consistent with a sister-group relationship between cryptophyte and haptophyte plastids.}, keywords = {*DNA Replication, *Gene Transfer, *Genome, Bacteria/*genetics, Cryptophyta/*genetics, DNA, evolution, genes, Horizontal, Molecular, phylogeny, Plant, Plastids/*genetics, rcc, Sequence Analysis, symbiosis}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17522086}, author = {Khan, H and Parks, N and Kozera, C and Curtis, B A and Parsons, B J and Bowman, S and Archibald, J M} } @article {Palenik2006, title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {36}, year = {2006}, note = {tex.mendeley-tags: RCC,rcc}, pages = {13555{\textendash}13559}, abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.}, keywords = {rcc}, doi = {10.1073/pnas.0602963103}, url = {http://www.pnas.org/cgi/content/abstract/103/36/13555}, author = {Palenik, Brian and Ren, Qinghu and Dupont, Chris L and Myers, Garry S and Heidelberg, John F and Badger, Jonathan H and Madupu, Ramana and Nelson, William C and Brinkac, Lauren M and Dodson, Robert J and Durkin, A Scott and Daugherty, Sean C and Sullivan, Stephen A and Khouri, Hoda and Mohamoud, Yasmin and Halpin, Rebecca and Paulsen, Ian T} } @article {palenik_genome_2006, title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment}, journal = {Proceedings of the National Academy of Sciences}, volume = {103}, number = {36}, year = {2006}, note = {Publisher: National Academy of Sciences Section: Biological Sciences}, pages = {13555{\textendash}13559}, abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.}, keywords = {cyanobacteria, genomics, Marine, RCC1086}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.0602963103}, url = {https://www.pnas.org/content/103/36/13555}, author = {Palenik, Brian and Ren, Qinghu and Dupont, Chris L. and Myers, Garry S. and Heidelberg, John F. and Badger, Jonathan H. and Madupu, Ramana and Nelson, William C. and Brinkac, Lauren M. and Dodson, Robert J. and Durkin, A. Scott and Daugherty, Sean C. and Sullivan, Stephen A. and Khouri, Hoda and Mohamoud, Yasmin and Halpin, Rebecca and Paulsen, Ian T.} } @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 {Robbens2005, title = {Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri}, journal = {Molecular Biology and Evolution}, volume = {22}, number = {3}, year = {2005}, note = {tex.mendeley-tags: RCC745}, pages = {589{\textendash}597}, abstract = {The cell cycle has been extensively studied in various organisms, and the recent access to an overwhelming amount of genomic data has given birth to a new integrated approach called comparative genomics. Comparing the cell cycle across species shows that its regulation is evolutionarily conserved; the best-known example is the pivotal role of cyclin-dependent kinases in all the eukaryotic lineages hitherto investigated. Interestingly, the molecular network associated with the activity of the CDK-cyclin complexes is also evolutionarily conserved, thus, defining a core cell cycle set of genes together with lineage-specific adaptations. In this paper, we describe the core cell cycle genes of Ostreococcus tauri, the smallest free-living eukaryotic cell having a minimal cellular organization with a nucleus, a single chloroplast, and only one mitochondrion. This unicellular marine green alga, which has diverged at the base of the green lineage, shows the minimal yet complete set of core cell cycle genes described to date. It has only one homolog of CDKA, CDKB, CDKD, cyclin A, cyclin B, cyclin D, cyclin H, Cks, Rb, E2F, DP, DEL, Cdc25, and Wee L We have also added the APC and SCF E3 ligases to the core cell cycle gene set. We discuss the potential of genome-wide analysis in the identification of divergent orthologs of cell cycle genes in different lineages by mining the genomes of evolutionarily important and strategic organisms.}, keywords = {Anaphase Promoting Complex, Arabidopsis Thaliana, Cdk Activity, cell division cycle, Chlorophyta, cyclin, cyclin dependant kinase, Green alga, Kinase, Ostreococcus tauri, Plant, Prasinophyceae, rcc, RCC745, Retinoblastoma Protein, Saccharomyces Cerevisiae, Yeast}, doi = {10.1093/molbev/msi044}, author = {Robbens, S and Khadaroo, B and Camasses, A and Derelle, E and Ferraz, C and Inze, D and Van, de Peer Y and Moreau, H} } @article {Vaulot1994, title = {Phaeocystis spp.: morphology, ploidy, pigment composition and genome size of cultured strains}, journal = {Journal of Phycology}, volume = {30}, year = {1994}, note = {tex.mendeley-tags: RCC,rcc}, pages = {1022{\textendash}1035}, keywords = {rcc, RCC SBR$_\textrmP$hyto}, doi = {10.1111/j.0022-3646.1994.01022.x}, author = {Vaulot, D and Birrien, J.-L. and Marie, D and Casotti, R and Veldhuis, M J W and Kraay, G W and Chr{\'e}tiennot-Dinet, M.-J.} }