@article {wang_meta-analysis_2024, title = {Meta-analysis reveals responses of coccolithophores and diatoms to warming}, journal = {Marine Environmental Research}, volume = {193}, year = {2024}, pages = {106275}, abstract = {A meta-analysis was conducted to explore the effects of warming on the physiological processes of coccolitho- phores and diatoms by synthesizing a large number of published literatures. A total of 154 studies consisting 301 experiments were synthesized in this study. Under a projected temperature increase of 3{\textendash}5 {\textopenbullet}C by IPCC AR6 at the end of this century, our results suggest that the growth and photosynthetic rate of coccolithophores were significantly enhanced by the rising temperature, while the calcification of coccolithophores was only slightly promoted. Warming also had significantly positive effects on the growth but not photosynthesis of diatoms. In comparison, the effect size of warming on the growth rate of coccolithophores was larger than that of diatoms. However, there was no significant effect of warming on either the ratio of particulate inorganic carbon to par- ticulate organic carbon (PIC:POC) of coccolithophores or the ratio of biogenic silica to carbon (BSi:C) of diatoms. Furthermore, the results reveal latitudinal and size-specific patterns of the effect sizes of warming. For diatoms, the effects of warming on growth were more prominent in high latitudes, specifically for the Southern Hemi- sphere species. In addition, the effect size of warming on the small-sized diatoms was larger than that of the large-sized diatoms. For coccolithophores, the growth of the Southern Hemisphere temperate strains was significantly promoted by warming. Overall, the results based on the meta-analysis indicate that the projected warming of the end of this century will be more favor to the growth of coccolithophores than that of diatoms, thus potentially affect the competitive advantages of coccolithophores over diatoms; while the mid-to high latitude species/strains of both coccolithophores and diatoms will benefit more than their counterparts in the lower latitudes. Therefore, this study offers novel insights into predicting both the inter- and intra-group competitive advantages of diatoms and coccolithophores under the future warming climate change scenario.}, keywords = {rcc1238}, issn = {01411136}, doi = {10.1016/j.marenvres.2023.106275}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0141113623004038}, author = {Wang, Jiawei and Zeng, Cong and Feng, Yuanyuan} } @booklet {hird_microalgal_2024, title = {Microalgal biofilm induces larval settlement in the model marine worm \textit{Platynereis dumerilii}, year = {2024}, publisher = {BioRxiv}, type = {preprint}, abstract = {A free-swimming larval stage features in many marine invertebrate life cycles. To transition to a seafloor-dwelling juvenile stage, larvae need to settle out of the plankton, guided by specific environmental cues that lead them to an ideal habitat for their future life on the seafloor. Although the marine annelid Platynereis dumerilii has been cultured in research labs since the 1950s and has a free-swimming larval stage, specific environmental cues that induce settlement in this nereid worm are yet to be identified. Here we demonstrate that microalgal biofilm is a key settlement cue for P. dumerilii larvae, inducing earlier onset of settlement, and enhancing subsequent juvenile growth as a primary food source. We tested the settlement response of P. dumerilii to 40 different strains of microalgae, predominantly diatom species, finding that P. dumerilii have species-specific preferences in their choice of settlement substrate. The most effective diatom species for inducing P. dumerilii larval settlement were benthic pennate species including Grammatophora marina, Achnanthes brevipes, and Nitzschia ovalis. The identification of specific environmental cues for P. dumerilii settlement enables a link between its ecology and the sensory and nervous system signalling that regulate larval behaviour and development. Incorporation of diatoms into P. dumerilii culture practices will improve the husbandry of this marine invertebrate model.}, keywords = {RCC7063}, doi = {10.1101/2024.01.23.576855}, url = {http://biorxiv.org/lookup/doi/10.1101/2024.01.23.576855}, author = {Hird, Cameron and Jekely, Gaspar and Williams, Elizabeth A} } @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 {groussman_marferret_2023, title = {MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes}, journal = {Scientific Data}, volume = {10}, number = {1}, year = {2023}, note = {Number: 1 Publisher: Nature Publishing Group}, pages = {926}, abstract = {Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.}, keywords = {Classification and taxonomy, Microbial genetics, transcriptomics}, issn = {2052-4463}, doi = {10.1038/s41597-023-02842-4}, url = {https://www.nature.com/articles/s41597-023-02842-4}, author = {Groussman, R. D. and Blaskowski, S. and Coesel, S. N. and Armbrust, E. V.} } @article {barbosa_microalga_2023, title = {The microalga \textit{Dunaliella and its applications: a review}, journal = {Applied Phycology}, volume = {4}, number = {1}, year = {2023}, pages = {99{\textendash}120}, keywords = {RCC3579, RCC5}, issn = {2638-8081}, doi = {10.1080/26388081.2023.2222318}, url = {https://www.tandfonline.com/doi/full/10.1080/26388081.2023.2222318}, author = {Barbosa, Miguel and In{\'a}cio, Leonardo Garcia and Afonso, Cl{\'e}lia and Maranh{\~a}o, Paulo} } @article {mertens_morpho-molecular_2023, title = {Morpho-molecular analysis of podolampadacean dinoflagellates (Dinophyceae), with the description of two new genera}, journal = {Phycologia}, year = {2023}, note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/00318884.2022.2158281}, month = {feb}, pages = {1{\textendash}19}, abstract = {Sequences were obtained for 58 podolampadacean single cells from France, Reunion Island (French territories) and Japan (6 SSU rDNA only, 40 SSU+LSU and 12 LSU only). The sequenced taxa belong to five of the eight described genera: Podolampas, Blepharocysta, Lissodinium, Gaarderiella and Mysticella. Two new genera, Alatosphaera and Pseudalatosphaera, were erected to accommodate {\textquoteleft}Blepharocysta{\textquoteright} hermosillae and {\textquoteleft}Blepharocysta{\textquoteright} denticulata. Most genera are well supported by concatenated LSU{\textendash}SSU rDNA phylogenies, with the least support for Lissodinium. Metabarcoding of podolampadaceans using the V4 region of SSU rDNA showed a resolution too low to discriminate genera or species. Roscoffia and Cabra are here considered podolampadaceans, whilst Lessardia is considered to belong in a separate family. The relationship of Rhinodinium to the Podolampadaceae needs further study. Desmoschisis was recorded for the first time in Alatosphaera and Pseudalatosphaera. Several ribotypes need further study to attribute a species name to them.}, keywords = {Alatosphaera, Blepharocysta, desmoschisis, Gaarderiella, Lissodinium, LSU rDNA, Mysticella, Podolampas, Pseudalatosphaera, SSU rDNA}, issn = {0031-8884}, doi = {10.1080/00318884.2022.2158281}, url = {https://doi.org/10.1080/00318884.2022.2158281}, author = {Mertens, Kenneth Neil and Carbonell-Moore, M. Consuelo and Chom{\'e}rat, Nicolas and Bilien, Gwenael and Boulben, Sylviane and Guillou, Laure and Romac, Sarah and Probert, Ian and Ishikawa, Akira and N{\'e}zan, Elisabeth} } @article {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 {nikitashina_metabolic_2022, title = {Metabolic adaptation of diatoms to hypersalinity}, journal = {Phytochemistry}, year = {2022}, pages = {113267}, abstract = {Microalgae are important primary producers and form the basis for the marine food web. As global climate changes, so do salinity levels that algae are exposed to. A metabolic response of algal cells partly alleviates the resulting osmotic stress. Some metabolites involved in the response are well studied, but the full metabolic implications of adaptation remain unclear. Improved analytical methodology provides an opportunity for additional insight. We can now follow responses to stress in major parts of the metabolome and derive comprehensive charts of the resulting metabolic re-wiring. In this study, we subjected three species of diatoms to high salinity conditions and compared their metabolome to controls in an untargeted manner. The three well-investigated species with sequenced genomes Phaeodactylum tricornutum, Thalassiosira pseudonana, and Skeletonema marinoi were selected for our survey. The microalgae react to salinity stress with common adaptations in the metabolome by amino acid up-regulation, production of saccharides, and inositols. But also species-specific dysregulation of metabolites is common. Several metabolites previously not connected with osmotic stress reactions are identified, including 4-hydroxyproline, pipecolinic acid, myo-inositol, threonic acid, and acylcarnitines. This expands our knowledge about osmoadaptation and calls for further functional characterization of metabolites and pathways in algal stress physiology.}, keywords = {Diatomic algae, Hypersalinity stress response, Osmolytes, Phaeodactylaceae, Phaeodactylum tricornutum, RCC75, Skeletonema marinoi, Skeletonemataceae, Thalassiosira pseudonana, Thalassiosiraceae, Untargeted metabolite profiling}, issn = {0031-9422}, doi = {10.1016/j.phytochem.2022.113267}, url = {https://www.sciencedirect.com/science/article/pii/S0031942222001832}, author = {Nikitashina, Vera and Stettin, Daniel and Pohnert, Georg} } @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 {gomez_molecular_2022, title = {Molecular phylogeny of the spiny-surfaced species of the dinoflagellate Prorocentrum with the description of P. Thermophilum sp. nov. and P. criophilum sp. nov. (Prorocentrales, Dinophyceae)}, journal = {Journal of Phycology}, volume = {n/a}, number = {n/a}, year = {2022}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13298}, abstract = {Spiny-surfaced species of Prorocentrum forms harmful algal blooms, and its taxonomic identity is obscure due to the size and shape variability. Molecular phylogenies reveal two major clades: one for P. cordatum with sequences mainly retrieved as P. minimum, and other for P. shikokuense with sequences also retrieved as P. dentatum and P. donghaiense. Several closely related clades still need to be characterized. Here, we provide SSU- and LSU rRNA, and ITS gene sequences of the strain CCMP3122 isolated from Florida (initially named P. donghaiense) and strains Prorocentrum sp. RCC6871{\textendash}2 from the Ross Sea, Antarctica. We describe Prorocentrum thermophilum sp. nov. based on the strain CCMP3122, a species also distributed in the open waters of Gulf of Mexico, New Zealand and the Arabian Gulf; and Prorocentrum criophilum sp. nov. based on the strain RCC6872, which is distributed in the Antarctic Ocean and the Arctic Sea. Prorocentrum thermophilum is roundish ( 14 μm long, 12 μm wide), with an inconspicuous anterior spine-like prolongation under light microscopy, valves with tiny, short knobs (5{\textendash}7 per μm2), and several (<7) large trichocyst pores ( 0.3 μm) in the right valve, as well as smaller pores ( 0.15 μm). Prorocentrum criophilum is round in valve view ( 11 μm long, 10 μm wide) and asymmetrically roundish in lateral view, the periflagellar area was not discernible under light microscopy, valves with very tiny, short knobs (6{\textendash}10 per μm2), and at least twelve large pores in the right valve. Other potentially undescribed species of spiny-surfaced Prorocentrum are discussed}, keywords = {Dinophyta, HABs, harmful algae blooms, molecular phylogenetics, new species, Prorocentraceae, RCC6871, RCC6872, taxonomy}, issn = {1529-8817}, doi = {10.1111/jpy.13298}, url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13298}, author = {G{\'o}mez, Fernando and Gourvil, Priscillia and Li, Tangcheng and Huang, Yulin and Zhang, Huan and Courcot, Lucie and Artigas, Luis F. and Soler On{\'\i}s, Emilio and Gutierrez-Rodriguez, Andres and Lin, Senjie} } @article {haney_multiple_2022, title = {Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation}, journal = {mBio}, volume = {13}, number = {4}, year = {2022}, month = {aug}, pages = {e01511{\textendash}22}, abstract = {

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

}, keywords = {rcc555}, issn = {2150-7511}, doi = {10.1128/mbio.01511-22}, url = {https://journals.asm.org/doi/10.1128/mbio.01511-22}, author = {Haney, Allissa M. and Sanfilippo, Joseph E. and Garczarek, Laurence and Partensky, Fr{\'e}d{\'e}ric and Kehoe, David M.}, editor = {Ruby, Edward} } @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 {six_marine_2021, title = {Marine Synechococcus picocyanobacteria: Light utilization across latitudes}, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, number = {38}, year = {2021}, note = {Publisher: National Academy of Sciences Section: Biological Sciences}, abstract = {

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

}, keywords = {?? Invalid DOI, RCC2035, rcc2382, RCC2385, RCC2421, RCC2527, RCC2535, RCC2553, RCC2570, RCC515, rcc539, rcc752, rcc791, to add}, issn = {0027-8424, 1091-6490}, doi = {10.1073/pnas.2111300118}, url = {http://www.pnas.org/content/118/38/e2111300118}, author = {Six, Christophe and Ratin, Morgane and Marie, Dominique and Corre, Erwan} } @article {dayras_microalgal_2021, title = {Microalgal Diet Influences the Nutritive Quality and Reproductive Investment of the Cyclopoid Copepod Paracyclopina nana}, journal = {Frontiers in Marine Science}, volume = {8}, year = {2021}, pages = {1147}, abstract = {Copepods represent an interesting alternative or a complement live food to brine shrimps and rotifers commonly used in aquaculture. They constitute the natural prey of many fish species and therefore do not require a potential nutritional enrichment. But an optimization of the microalgal diets used to feed copepods is essential to improve their mass culture. This study examined the effects of seven microalgal diets, namely single-species diets of Rhodomonas salina (R), Tisochrysis lutea (T), and Pavlova lutheri (=Diacronema lutheri) (P), two-species diets (R + T, T + P, and R + P), and a three-species diet (R + T + P), on the fatty acid and monosaccharide composition of the cyclopoid copepod Paracyclopina nana as well as its reproductive investment. Experiments were run during 15 days in 10-L beakers; starting with nauplii collected from a large 300-L batch culture. Copepods fatty acid contents were studied, particularly the relative amounts of docosahexaenoic acid (DHA) and eicosa-pentaenoic acid (EPA). The R + T, R, and T diets induced the highest total fatty acid amount in copepods. R + T and R also generated the lowest DHA/EPA ratios in copepods due to high EPA contents. The highest value of total monosaccharides was found in copepods fed with R + T + P. Diets R + T and R induced the greatest prosome volumes and clutch volumes in ovigerous females. Both prosome volume and clutch volume in P. nana ovigerous females were correlated to the individual EPA amount. The results demonstrated that all diets including R. salina enhanced the productivity of P. nana in mass culture, particularly when combined with T. lutea. R. salina, and T. lutea induced complementary fatty acid and monosaccharide profiles, confirming that R + T represents the best microalgae combination for productive culture of P. nana. Conversely, P. lutheri did not enhance the nutritional profile nor the fecundity of P. nana in the culture. This study is the first to demonstrate that R. salina is a suitable microalga for productive mass culture of P. nana for use as live food in aquaculture.}, keywords = {rcc, RCC1349, RCC1537, RCC20}, issn = {2296-7745}, doi = {10.3389/fmars.2021.697561}, url = {https://www.frontiersin.org/article/10.3389/fmars.2021.697561}, author = {Dayras, Paul and Bialais, Capucine and Sadovskaya, Irina and Lee, Min-Chul and Lee, Jae-Seong and Souissi, Sami} } @mastersthesis {busse_mixotrophy_2021, title = {Mixotrophy by Phytoflagellates in the Northern Gulf of Alaska: Impacts of Physico-Chemical Characteristics and Prey Concentration on Feeding by Photosynthetic Nano- and Dinoflagellates}, year = {2021}, school = {Western Washington University}, type = {masters}, keywords = {? No DOI found, RCC3010}, author = {Busse, Hana} } @article {filatov_mode_2021, title = {The mode of speciation during a recent radiation in open-ocean phytoplankton}, journal = {Current Biology}, year = {2021}, month = {oct}, abstract = {Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton.}, keywords = {phytoplankton, population genetic modeling, rcc1212, rcc1238, RCC1239, RCC1253, RCC1281, RCC1296, RCC1310, RCC1314, RCC1562, RCC1836, RCC3370, RCC3711, RCC3733, RCC3862, RCC3898, RCC4002, RCC4028, RCC4030, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, RCC5119, RCC5134, RCC5137, RCC5141, RCC6566, RCC6730, secondary contact, sequence polymorphism, speciation}, issn = {0960-9822}, doi = {10.1016/j.cub.2021.09.073}, url = {https://www.sciencedirect.com/science/article/pii/S0960982221013415}, author = {Filatov, Dmitry A. and Bendif, El Mahdi and Archontikis, Odysseas A. and Hagino, Kyoko and Rickaby, Rosalind E. M.} } @article {wang_moderating_2021, title = {The moderating role of population succession in the adaptive responses of Synechococcus assemblages: evidence from light intensity simulation experiment}, journal = {Photosynthetica}, volume = {59}, number = {4}, year = {2021}, pages = {587{\textendash}599}, abstract = {Synechococcus is one of the most abundant photoautotrophic picoplankton in the marine ecosystem. However, it is not clear how Synechococcus assemblages respond to light intensity variation in a genus group. Here, enriched Synechococcus assemblages from in situ coastal seawater were subjected to light intensity simulation experiments in a range of 9-243 μmol(photon) m{\textendash}2 s{\textendash}1. Characteristics concerning physiology, genomics, and metatranscriptomics were analyzed. Physiologically, the fitting model predicted photosynthesis indications and pigment contents increased with different trends following the light intensity. Genomic sequencing demonstrated that both the phylogenetic and phenotypic compositions of Synechococcus assemblage exhibited population succession. Especially, the proportion of Synechococcus pigment type 2 was changed significantly. In metatranscriptomics, most genes were downregulated in the high-light intensity group, while photosynthesis-related genes were entirely upregulated. The high upregulation of photosynthesis-related genes, such as psbO, psbA, apcB, and cpcB, corresponded to the succession of Synechococcus genotype and was responsible for the physiological shift in response to light intensity.}, issn = {03003604, 15739058}, doi = {10.32615/ps.2021.050}, url = {http://ps.ueb.cas.cz/doi/10.32615/ps.2021.050.html}, author = {Wang, T. and Chen, X. and Li, J.L. and Qin, S. and Cui, Y.L. and Xu, F.} } @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 {Stettin2020, title = {Metabolomics benefits from orbitrap GC{\textendash}MS{\textemdash}Comparison of low- and high-resolution GC{\textendash}MS}, journal = {Metabolites}, volume = {10}, number = {4}, year = {2020}, note = {tex.mendeley-tags: RCC75}, month = {apr}, pages = {143}, abstract = {The development of improved mass spectrometers and supporting computational tools is expected to enable the rapid annotation of whole metabolomes. Essential for the progress is the identification of strengths and weaknesses of novel instrumentation in direct comparison to previous instruments. Orbitrap liquid chromatography (LC){\textendash}mass spectrometry (MS) technology is now widely in use, while Orbitrap gas chromatography (GC){\textendash}MS introduced in 2015 has remained fairly unexplored in its potential for metabolomics research. This study aims to evaluate the additional knowledge gained in a metabolomics experiment when using the high-resolution Orbitrap GC{\textendash}MS in comparison to a commonly used unit-mass resolution single-quadrupole GC{\textendash}MS. Samples from an osmotic stress treatment of a non-model organism, the microalga Skeletonema costatum, were investigated using comparative metabolomics with low- and high-resolution methods. Resulting datasets were compared on a statistical level and on the level of individual compound annotation. Both MS approaches resulted in successful classification of stressed vs. non-stressed microalgae but did so using different sets of significantly dysregulated metabolites. High-resolution data only slightly improved conventional library matching but enabled the correct annotation of an unknown. While computational support that utilizes high-resolution GC{\textendash}MS data is still underdeveloped, clear benefits in terms of sensitivity, metabolic coverage, and support in structure elucidation of the Orbitrap GC{\textendash}MS technology for metabolomics studies are shown here.}, keywords = {Comparative metabolomics, Diatom, High-resolution mass spectrometry (HRMS), Instrument comparison, Mass Spectrometry (Orbitrap GC-MS), Metabolite identification, Orbitrap Gas Chromatography, Osmotic stress, RCC75}, issn = {2218-1989}, doi = {10.3390/metabo10040143}, url = {https://www.mdpi.com/2218-1989/10/4/143}, author = {Stettin, Daniel and Poulin, Remington X. and Pohnert, Georg} } @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 {Weynberg2017, title = {Marine prasinoviruses and their tiny plankton hosts : A review}, journal = {Viruses}, number = {March}, year = {2017}, note = {tex.mendeley-tags: 2017,RCC,rcc1105,rcc299,rcc809}, pages = {1{\textendash}20}, abstract = {Viruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism{\textendash}virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host{\textendash}virus system for examination of cellular and molecular processes in the marine environment.}, keywords = {2017, host interactions, marine virus ecology, rcc, RCC1105, RCC299, RCC809, virus, virus-driven evolution, virus{\textendash}host interactions}, issn = {1999-4915}, doi = {10.3390/v9030043}, author = {Weynberg, Karen D and Allen, Michael J and Wilson, William H} } @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 {Balzano2017c, title = {Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex}, journal = {Journal of Phycology}, volume = {53}, number = {1}, year = {2017}, note = {tex.mendeley-tags: RCC1984,RCC1985,RCC1986,RCC1988,RCC1989,RCC1990,RCC1991,RCC1992,RCC1993,RCC1995,RCC1997,RCC1999,RCC2000,RCC2002,RCC2003,RCC2004,RCC2005,RCC2006,RCC2008,RCC2010,RCC2011,RCC2012,RCC2014,RCC2016,RCC2017,RCC2021,RCC2037,RCC2038,RCC2039,RCC2042,RCC2043,RCC2261,RCC2262,RCC2263,RCC2264,RCC2265,RCC2266,RCC2267,RCC2268,RCC2269,RCC2270,RCC2272,RCC2273,RCC2274,RCC2275,RCC2276,RCC2277,RCC2278,RCC2279,RCC2280,RCC2281,RCC2282,RCC2318,RCC2506,RCC2517,RCC2520,RCC2521,RCC2522}, month = {feb}, pages = {161{\textendash}187}, abstract = {Seventy-five diatom strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM), as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, and Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. C. neogracilis generally occurred as single cells but also formed short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis, but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region.}, keywords = {RCC1984, RCC1985, RCC1986, RCC1988, RCC1989, RCC1990, RCC1991, RCC1992, RCC1993, RCC1995, RCC1997, RCC1999, RCC2000, RCC2002, RCC2003, RCC2004, RCC2005, RCC2006, RCC2008, RCC2010, RCC2011, RCC2012, RCC2014, RCC2016, RCC2017, RCC2021, RCC2037, RCC2038, RCC2039, RCC2042, RCC2043, RCC2261, RCC2262, RCC2263, RCC2264, RCC2265, RCC2266, RCC2267, RCC2268, RCC2269, RCC2270, RCC2272, RCC2273, RCC2274, RCC2275, RCC2276, RCC2277, RCC2278, RCC2279, RCC2280, RCC2281, RCC2282, RCC2318, RCC2506, RCC2517, RCC2520, RCC2521, RCC2522}, issn = {00223646}, doi = {10.1111/jpy.12489}, url = {http://doi.wiley.com/10.1111/jpy.12489}, author = {Balzano, Sergio and Percopo, Isabella and Siano, Raffaele and Gourvil, Priscillia and Chanoine, M{\'e}lanie and Marie, Dominique and Vaulot, Daniel and Sarno, Diana}, editor = {Wood, M.} } @article {Mincer2016, title = {Methanol production by a broad phylogenetic array of marine phytoplankton.}, journal = {PloS one}, volume = {11}, number = {3}, year = {2016}, note = {Publisher: Public Library of Science tex.mendeley-tags: 2016}, month = {jan}, pages = {e0150820}, abstract = {Methanol is a major volatile organic compound on Earth and serves as an important carbon and energy substrate for abundant methylotrophic microbes. Previous geochemical surveys coupled with predictive models suggest that the marine contributions are exceedingly large, rivaling terrestrial sources. Although well studied in terrestrial ecosystems, methanol sources are poorly understood in the marine environment and warrant further investigation. To this end, we adapted a Purge and Trap Gas Chromatography/Mass Spectrometry (P\&T-GC/MS) method which allowed reliable measurements of methanol in seawater and marine phytoplankton cultures with a method detection limit of 120 nanomolar. All phytoplankton tested (cyanobacteria: Synechococcus spp. 8102 and 8103, Trichodesmium erythraeum, and Prochlorococcus marinus), and Eukarya (heterokont diatom: Phaeodactylum tricornutum, coccolithophore: Emiliania huxleyi, cryptophyte: Rhodomonas salina, and non-diatom heterokont: Nannochloropsis oculata) produced methanol, ranging from 0.8-13.7 micromolar in culture and methanol per total cellular carbon were measured in the ranges of 0.09-0.3\%. Phytoplankton culture time-course measurements displayed a punctuated production pattern with maxima near early stationary phase. Stabile isotope labeled bicarbonate incorporation experiments confirmed that methanol was produced from phytoplankton biomass. Overall, our findings suggest that phytoplankton are a major source of methanol in the upper water column of the world{\textquoteright}s oceans.}, keywords = {2016}, issn = {1932-6203}, doi = {10.1371/journal.pone.0150820}, url = {http://dx.doi.org/10.1371/journal.pone.0150820}, author = {Mincer, Tracy J and Aicher, Athena C} } @article {Bendif2015, title = {Morphological and phylogenetic characterization of new gephyrocapsa isolates suggests introgressive hybridization in the Emiliania/Gephyrocapsa complex (haptophyta)}, journal = {Protist}, volume = {166}, number = {3}, year = {2015}, note = {tex.mendeley-tags: 2015,RCC1281,RCC1282,RCC1284,RCC1286,RCC1292,RCC1300,RCC1305,RCC1307,RCC1316,RCC1317,RCC1318,RCC1319,RCC1320,RCC1562,RCC1839,RCC3370,RCC3862,RCC3898,rcc}, pages = {323{\textendash}336}, abstract = {The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the No{\"e}laerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.}, keywords = {2015, coccolithophores, Emiliania huxleyi, Gephyrocapsa muellerae, Gephyrocapsa oceanica, hybridization, phylogeny., rcc, RCC1281, RCC1282, RCC1284, RCC1286, RCC1292, RCC1300, RCC1305, RCC1307, RCC1316, RCC1317, RCC1318, RCC1319, RCC1320, RCC1562, RCC1839, RCC3370, RCC3862, RCC3898, species concept}, issn = {14344610}, doi = {10.1016/j.protis.2015.05.003}, url = {http://www.sciencedirect.com/science/article/pii/S1434461015000243}, author = {Bendif, El Mahdi and Probert, Ian and Young, Jeremy R. and von Dassow, Peter} } @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 {Duanmu2014, title = {Marine algae and land plants share conserved phytochrome signaling systems}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {44}, year = {2014}, note = {tex.mendeley-tags: Micromonas,RCC,rcc}, pages = {15827{\textendash}15832}, abstract = {Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte ({\textexclamdown}2 {\textmu}m cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.}, keywords = {Micromonas, rcc}, doi = {10.1073/pnas.1416751111}, url = {http://www.pnas.org/content/111/44/15827.abstract}, author = {Duanmu, Deqiang and Bachy, Charles and Sudek, Sebastian and Wong, Chee-Hong and Jimenez, Valeria and Rockwell, Nathan C and Martin, Shelley S and Ngan, Chew Yee and Reistetter, Emily N and van Baren, Marijke J and Price, Dana C and Wei, Chia-Lin and Reyes-Prieto, Adrian and Lagarias, J Clark and Worden, Alexandra Z} } @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 {Subirana2013, title = {Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, o. mediterraneus sp. nov. (mamiellales, mamiellophyceae)}, journal = {Protist}, volume = {164}, number = {5}, year = {2013}, note = {tex.mendeley-tags: RCC1112,RCC1114,RCC1117,RCC143,RCC1620,RCC1621,RCC1623,RCC1624,RCC2572,RCC2573,RCC2574,RCC2575,RCC2577,RCC2578,RCC2579,RCC2582,RCC2583,RCC2584,RCC2585,RCC2587,RCC2590,RCC344,RCC356,RCC393,RCC501,RCC745,RCC809}, pages = {643{\textendash}659}, abstract = {Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 ??m diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species{\textquoteright} descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species{\textquoteright} divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus, we purified {\textquestiondown}30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov., previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades.}, keywords = {barcode, Chromosome, culture, ITS2, karyotype, picoeukaryote, rcc, RCC1112, RCC1114, RCC1117, RCC143, RCC1620, RCC1621, RCC1623, RCC1624, RCC2572, RCC2573, RCC2574, RCC2575, RCC2577, RCC2578, RCC2579, RCC2582, RCC2583, RCC2584, RCC2585, RCC2587, RCC2590, RCC344, RCC356, RCC393, rcc501, RCC745, RCC809, ribosomal gene}, doi = {10.1016/j.protis.2013.06.002}, url = {http://www.sciencedirect.com/science/article/pii/S1434461013000497}, author = {Subirana, Lucie and P{\'e}quin, B{\'e}rang{\`e}re and Michely, St{\'e}phanie and Escande, Marie-Line and Meilland, Julie and Derelle, Evelyne and Marin, Birger and Piganeau, Gwenael and Desdevises, Yves and Moreau, Herv{\'e} and Grimsley, Nigel H} } @article {Zeng2012, title = {Marine viruses exploit their host{\textquoteright}s two-component regulatory system in response to resource limitation}, journal = {Current Biology}, year = {2012}, note = {Publisher: Cell Press tex.mendeley-tags: rcc}, abstract = {Phosphorus (P) availability, which often limits productivity in marine ecosystems, shapes the P-acquisition gene content of the marine cyanobacteria Prochlorococcus [1 4] and its viruses (cyanophages) [5, 6]. As in other bacteria, in Prochlorococcus these genes are regulated by the PhoR/PhoB two-component regulatory system that is used to sense and respond to P availability and is typical of signal transduction systems found in diverse organisms [7]. Replication of cyanophage genomes requires a significant amount of P, and therefore these phages could gain a fitness advantage by influencing host P acquisition in P-limited environments. Here we show that the transcription of a phage-encoded high-affinity phosphate-binding protein gene (pstS) and alkaline phosphatase gene (phoA) both of which have host orthologs is elevated when the phages are infecting host cells that are P starved, relative to P-replete control cells. We further show that the phage versions of these genes are regulated by the host{\textquoteright}s PhoR/PhoB system. This not only extends this fundamental signaling mechanism to viruses but is also the first example of regulation of lytic phage genes by nutrient limitation in the host. As such, it reveals an important new dimension of the intimate coevolution of phage, host, and environment in the world{\textquoteright}s oceans. {\textordmasculine} Phage production, but not lytic cycle, is reduced in P-starved host cells {\textordmasculine} Transcription of phage P acquisition genes is upregulated in P-starved hosts {\textordmasculine} Phage P-acquisition genes are regulated by the host PhoR/PhoB two-component system {\textordmasculine} This is the first incidence of regulation of virus genes by a two-component system}, keywords = {NATL2A, rcc, RCC?o?dd}, doi = {10.1016/j.cub.2011.11.055}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982211013704}, author = {Zeng, Qinglu and Chisholm, Sallie W} } @article {Moreau2010, title = {Marine Prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer}, journal = {Journal of Virology}, volume = {84}, number = {24}, year = {2010}, note = {ISBN: 0022-538X tex.mendeley-tags: RCC1105,RCC745}, pages = {12555{\textendash}12563}, abstract = {Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.}, keywords = {RCC1105, RCC745}, doi = {10.1128/jvi.01123-10}, author = {Moreau, Herv{\'e} and Piganeau, Gwenael and Desdevises, Yves and Cooke, Richard and Derelle, Evelyne and Grimsley, Nigel} } @article {McDonald2010, title = {The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of Micromonas}, journal = {Molecular Biology and Evolution}, volume = {27}, number = {10}, year = {2010}, note = {tex.mendeley-tags: RCC299}, pages = {2268{\textendash}2283}, abstract = {The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (<=2 ??m diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer{\textendash}probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of {\textquotedblleft}mixed lineage gene affiliations{\textquotedblright} among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton.}, keywords = {rcc, RCC299}, doi = {10.1093/molbev/msq113}, url = {http://mbe.oxfordjournals.org/content/27/10/2268.abstract}, author = {McDonald, Sarah M and Plant, Joshua N and Worden, Alexandra Z} } @article {Marin2010, title = {Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons}, journal = {Protist}, volume = {161}, number = {2}, year = {2010}, note = {ISBN: 1618-0941 tex.mendeley-tags: Micromonas,rcc}, pages = {304{\textendash}336}, abstract = {Molecular phylogenetic analyses of the Mamiellophyceae classis nova, a ubiquitous group of largely picoplanktonic green algae comprising scaly and non-scaly prasinophyte unicells, were performed using single and concatenated gene sequence comparisons of the nuclear- and plastid-encoded rRNA operons. The study resolved all major clades within the class, identified molecular signature sequences for most clades through an exhaustive search for non-homoplasious synapomorphies [Marin et al. (2003): Protist 154: 99-145] and incorporated these signatures into the diagnoses of two novel orders, Monomastigales ord nov., Dolichomastigales ord. nov., and four novel families, Monomastigaceae fam. nov., Dolichomastigaceae fam. nov., Crustomastigaceae fam. nov., and Bathycoccaceae fam. nov., within a revised classification of the class. A database search for the presence of environmental rDNA sequences in the Monomastigales and Dolichomastigales identified an unexpectedly large genetic diversity of Monomastigales confined to freshwater, a novel clade (Dolicho$_\textrmB$) in the Dolichomastigaceae from deep sea sediments and a novel freshwater clade in the Crustomastigaceae. The Mamiellophyceae represent one of the ecologically most successful groups of eukaryotic, photosynthetic picoplankters in marine and likely also freshwater environments. Copyright 2009 Elsevier GmbH. All rights reserved.}, keywords = {Index Medicus, Micromonas, rcc}, doi = {10.1016/j.protis.2009.10.002}, author = {Marin, Birger and Melkonian, Michael} } @article {Zhu2005, title = {Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene}, journal = {FEMS Microbiology Ecology}, volume = {52}, number = {1}, year = {2005}, note = {tex.mendeley-tags: Micromonas,RCC,rcc}, pages = {79{\textendash}92}, abstract = {A quantitative PCR (QPCR) assay based on the use of SYBR Green I was developed to assess the abundance of specific groups of picoeukaryotes in marine waters. Six primer sets were designed targeting four different taxonomic levels: domain (Eukaryota), division (Chlorophyta), order (Mamiellales) and genus (Bathycoccus, Micromonas, and Ostreococcus). Reaction conditions were optimized for each primer set which was validated in silico, on agarose gels, and by QPCR against a variety of target and non-target cultures. The approach was tested by estimating gene copy numbers for Micromonas, Bathycoccus, and Ostreococcus in seawater samples to which cultured cells were added in various concentrations. QPCR was then used to determine that rRNA gene (rDNA) copy number varied from one to more than 12,000 in 18 strains of phytoplankton. Finally, QPCR was applied to environmental samples from a Mediterranean Sea coastal site and the results were compared to those obtained by Fluorescent in situ hybridization (FISH). The data obtained demonstrate that Chlorophyta and more specifically Mamiellales were important in these waters, especially during the winter picoplankton bloom. The timing of major abundance peaks of the targeted species was similar by QPCR and FISH. When used in conjunction with other techniques such as FISH or gene clone libraries, QPCR appears as very promising to quickly obtain data on the ecological distribution of important phytoplankton groups. Data interpretation must take into account primer specificity and the varying rRNA gene copy number among eukaryotes. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.}, keywords = {Coastal ecosystems, Ecology, Fluorescent in situ hybridization, Micromonas, picoplankton, prasinophytes, Quantitative PCR, rcc}, author = {Zhu, Fei and Massana, Ramon and Not, Fabrice and Marie, Dominique and Vaulot, Daniel} }