%0 Journal Article %J Organic Geochemistry %D 2023 %T Exploring the theoretical upper temperature limit of alkenone unsaturation indices: Implications for paleotemperature reconstructions %A Liao, Sian %A Novak, Joseph %A Huang, Yongsong %K Culture experiments %K RCC3483 %K RCC6484 %K Temperature calibrations %X The structural specificity, exceptional diagenetic stability, and linear response of unsaturation to temperature have made alkenones an indispensable tool for reconstructing past sea surface temperatures, with the well known U37K′ proxy widely applied in the past 40 years. However, U37K′ approaches unity at around 28 °C in cultures of Emiliania huxleyi (E. huxleyi), the most widely distributed alkenone producer in global oceans. Recent studies using surface sediments suggest U38MeK′ has ∼1.5 °C higher upper temperature limits than U37K′. However, E. huxleyi generally does not grow above 28 °C. Gephyrocapsa oceanica (G. oceanica), on the other hand, is the dominant alkenone producer when sea surface temperature is above 22 °C and thrives in ocean regions such as the Pacific Warm Pool. So far there have been no culture data for G. oceanica above 29 °C to evaluate the temperature response of alkenone distributions and the (theoretical) upper temperature limit of alkenone unsaturation indices. Here we performed the first culture experiments on two strains of G. oceanica isolated from warm ocean sites at up to 32 °C: RCC6484 from the Pacific Warm Pool and RCC3483 from the South China Sea. We show both strains display higher growth rates at higher temperature, with the highest growth rates at 32 °C (the highest temperature we tested), although alkenone production per cell decreases as temperature increases. Importantly, U37K′ and U38MeK′ values of RCC6484 and RCC3483 continue to respond to temperature changes beyond 28 °C, although temperature sensitivity decreases significantly above 28 °C. Above 30 °C, U37K′ and U38MeK′ responses to temperature further diminish, limiting their potential for paleo-SST applications using the currently available analytical technology. The ratio of C38:3 over C38:2 methyl ketone is on average 11 times higher than the ratio of C37:3 over C37:2 from 24 to 32 °C, suggesting a greater potential of using U38MeK′ for paleotemperature reconstruction in high temperature settings. %B Organic Geochemistry %V 180 %P 104606 %G eng %U https://www.sciencedirect.com/science/article/pii/S0146638023000529 %R 10.1016/j.orggeochem.2023.104606 %0 Journal Article %J Phycologia %D 2023 %T Morpho-molecular analysis of podolampadacean dinoflagellates (Dinophyceae), with the description of two new genera %A Mertens, Kenneth Neil %A Carbonell-Moore, M. Consuelo %A Chomérat, Nicolas %A Bilien, Gwenael %A Boulben, Sylviane %A Guillou, Laure %A Romac, Sarah %A Probert, Ian %A Ishikawa, Akira %A Nézan, Elisabeth %K Alatosphaera %K Blepharocysta %K desmoschisis %K Gaarderiella %K Lissodinium %K LSU rDNA %K Mysticella %K Podolampas %K Pseudalatosphaera %K SSU rDNA %X 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 ‘Blepharocysta’ hermosillae and ‘Blepharocysta’ denticulata. Most genera are well supported by concatenated LSU–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. %B Phycologia %P 1–19 %8 feb %G eng %U https://doi.org/10.1080/00318884.2022.2158281 %R 10.1080/00318884.2022.2158281 %0 Journal Article %J Journal of Experimental Botany %D 2023 %T A phospho-dawn of protein modification anticipates light onset in the picoeukaryote \textit{O. tauri %A Noordally, Zeenat B %A Hindle, Matthew M %A Martin, Sarah F %A Seaton, Daniel D %A Simpson, T Ian %A Le Bihan, Thierry %A Millar, Andrew J %K RCC745 %X Abstract Diel regulation of protein levels and protein modification had been less studied than transcript rhythms. Here, we compare transcriptome data under light-dark cycles to partial proteome and phosphoproteome data, assayed using shotgun mass-spectrometry, from the alga Ostreococcus tauri, the smallest free-living eukaryote. 10% of quantified proteins but two-thirds of phosphoproteins were rhythmic. Mathematical modelling showed that light-stimulated protein synthesis can account for the observed clustering of protein peaks in the daytime. Prompted by night-peaking and apparently dark-stable proteins, we also tested cultures under prolonged darkness, where the proteome changed less than under the diel cycle. Among the dark-stable proteins were prasinophyte-specific sequences that were also reported to accumulate when O. tauri formed lipid droplets. In the phosphoproteome, 39% of rhythmic phospho-sites reached peak levels just before dawn. This anticipatory phosphorylation suggests that a clock-regulated phospho-dawn prepares green cells for daytime functions. Acid-directed and proline-directed protein phosphorylation sites were regulated in antiphase, implicating the clock-related, casein kinases 1 and 2 in phase-specific regulation, alternating with the CMGC protein kinase family. Understanding the dynamic phosphoprotein network should be facilitated by the minimal kinome and proteome of O. tauri. The data are available from ProteomeXchange, with identifiers PXD001734, PXD001735 and PXD002909. %B Journal of Experimental Botany %P erad290 %8 jul %G eng %U https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erad290/7229478 %R 10.1093/jxb/erad290 %0 Journal Article %J Geophysical Research Letters %D 2023 %T Stable Carbon Isotope Signature of Methane Released from Phytoplankton %A Klintzsch, Thomas %A Geisinger, Hannah %A Wieland, Anna %A Langer, Gerald %A Nehrke, Gernot %A Bizic, Mina %A Greule, Markus %A Lenhart, Katharina %A Borsch, Christian %A Schroll, Moritz %A Keppler, Frank %K RCC1216 %K ⛔ No DOI found %X 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 ‘methane paradox’. 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. %B Geophysical Research Letters %8 feb %G eng %U https://essopenarchive.org/users/587513/articles/625160-stable-carbon-isotope-signature-of-methane-released-from-phytoplankton?commit=633a121ee07c48e6c59ffeca06fd5d5ebe1df4d4 %R 10.22541/essoar.167689993.32180072/v1 %0 Journal Article %J Communications Biology %D 2022 %T Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence %A Guérin, Nina %A Ciccarella, Marta %A Flamant, Elisa %A Frémont, Paul %A Mangenot, Sophie %A Istace, Benjamin %A Noel, Benjamin %A Belser, Caroline %A Bertrand, Laurie %A Labadie, Karine %A Cruaud, Corinne %A Romac, Sarah %A Bachy, Charles %A Gachenot, Martin %A Pelletier, Eric %A Alberti, Adriana %A Jaillon, Olivier %A Wincker, Patrick %A Aury, Jean-Marc %A Carradec, Quentin %K Biogeography %K comparative genomics %K metagenomics %K RCC100 %K Water microbiology %X The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata. %B Communications Biology %V 5 %P 1–14 %G eng %U https://www.nature.com/articles/s42003-022-03939-z %R 10.1038/s42003-022-03939-z %0 Journal Article %J Harmful Algae %D 2022 %T Intense blooms of Phaeocystis globosa in the South China Sea are caused by a unique “giant-colony” ecotype %A Zhang, Qing-Chun %A Liu, Chao %A Wang, Jin-Xiu %A Kong, Fan-Zhou %A Niu, Zhuang %A Xiang, Ling %A Yu, Ren-Cheng %K ecotype %K genetic diversity %K Giant colony %K Marker pigment %K RCC1736 %K RCC2055 %K RCC678 %K RCC736 %X 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'-hexanoyloxyfucoxanthin, hex-fuco, and 19'-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 “giant-colony” 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 “giant-colony” 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. %B Harmful Algae %V 114 %P 102227 %G eng %U https://www.sciencedirect.com/science/article/pii/S1568988322000555 %R 10.1016/j.hal.2022.102227 %0 Journal Article %J Journal of the Marine Biological Association of the United Kingdom %D 2022 %T Limpet larvae (Patella aspera Röding, 1798), obtained by gonad dissection and fecundation in vitro, settled and metamorphosed on crustose coralline algae %A Castejón, Diego %A Nogueira, Natacha %A Andrade, Carlos A. P. %K Early postlarvae %K lecithotrophy %K metamorphosis %K oocyte alkalinization %K pediveliger larvae %K RCC3458 %K settlement %X

The limpet Patella aspera Röding, 1798, is a native species from the Macaronesian region whose fishing is regulated. The early life of limpets, including the settlement process, is poorly known thus far. The current study evaluated different substrates to induce settlement in P. aspera, including microalgae strains (Halamphora coffeaeformis, Navicula incerta and Pavlova sp.) and crustose coralline algae (CCA) obtained from limpet shells. The results showed that gametes obtained by dissection and matured artificially using alkalinized seawater baths can produce viable larvae able to metamorphose to juveniles. Feeding was not required during larval development, suggesting lecithotrophy. Early postlarvae were identified by the shedding of the velum, and juveniles were identified by teleoconch and active grazing behaviour. The presence of CCA shortened the timing for settlement and increased the ratio of juveniles. The type and abundance of CCA can influence settlement success. Moreover, the results suggested that settlement and metamorphosis in true limpets (Patellogastropoda) might be triggered by a two-step mechanism, i.e. a first cue influencing the shift between swimming and crawling activity and a second cue determining settlement and metamorphosis to early postlarvae and juveniles.

%B Journal of the Marine Biological Association of the United Kingdom %P 1–12 %8 feb %G eng %R 10.1017/S0025315421000916 %0 Journal Article %J Phytochemistry %D 2022 %T Metabolic adaptation of diatoms to hypersalinity %A Nikitashina, Vera %A Stettin, Daniel %A Pohnert, Georg %K Diatomic algae %K Hypersalinity stress response %K Osmolytes %K Phaeodactylaceae %K Phaeodactylum tricornutum %K RCC75 %K Skeletonema marinoi %K Skeletonemataceae %K Thalassiosira pseudonana %K Thalassiosiraceae %K Untargeted metabolite profiling %X 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. %B Phytochemistry %P 113267 %G eng %U https://www.sciencedirect.com/science/article/pii/S0031942222001832 %R 10.1016/j.phytochem.2022.113267 %0 Journal Article %J mSphere %D 2021 %T Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality %A Pollara, Scott B. %A Becker, Jamie W. %A Nunn, Brook L. %A Boiteau, Rene %A Repeta, Daniel %A Mudge, Miranda C. %A Downing, Grayton %A Chase, Davis %A Harvey, Elizabeth L. %A Whalen, Kristen E. %E McMahon, Katherine %K rcc1731 %X Interactions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems by controlling primary production, structuring marine food webs, mediating carbon export, and influencing global climate. Phytoplankton-bacterium interactions are facilitated by secreted compounds; however, linking these chemical signals, their mechanisms of action, and their resultant ecological consequences remains a fundamental challenge. The bacterial quorumsensing signal 2-heptyl-4-quinolone (HHQ) induces immediate, yet reversible, cellular stasis (no cell division or mortality) in the coccolithophore Emiliania huxleyi; however, the mechanism responsible remains unknown. Using transcriptomic and proteomic approaches in combination with diagnostic biochemical and fluorescent cell-based assays, we show that HHQ exposure leads to prolonged S-phase arrest in phytoplankton coincident with the accumulation of DNA damage and a lack of repair despite the induction of the DNA damage response (DDR). While this effect is reversible, HHQ-exposed phytoplankton were also protected from viral mortality, ascribing a new role of quorum-sensing signals in regulating multitrophic interactions. Furthermore, our data demonstrate that in situ measurements of HHQ coincide with areas of enhanced micro- and nanoplankton biomass. Our results suggest bacterial communication signals as emerging players that may be one of the contributing factors that help structure complex microbial communities throughout the ocean. %B mSphere %V 6 %P e00009–21, /msphere/6/3/mSph.00009–21.atom %G eng %U https://msphere.asm.org/content/6/3/e00009-21 %R 10.1128/mSphere.00009-21 %0 Journal Article %J Ecological Modelling %D 2021 %T cyanoFilter: An R package to identify phytoplankton populations from flow cytometry data using cell pigmentation and granularity %A Olusoji, Oluwafemi D. %A Spaak, Jurg W. %A Holmes, Mark %A Neyens, Thomas %A Aerts, Marc %A De Laender, Frederik %K Ecology %K flow cytometry %K Gating %K phytoplankton %K RCC2375 %K rcc2380 %K RCC2434 %K RCC2555 %K Software %X Flow cytometry is often employed in ecology to measure traits and population size of bacteria and phytoplankton. This technique allows measuring millions of particles in a relatively small amount of time. However, distinguishing between different populations is not a straightforward task. Gating is a process in the identification of particles measured in flow cytometry. Gates can either be created manually using known characteristics of these particles, or by using automated clustering techniques. Available automated techniques implemented in statistical packages for flow cytometry are primarily developed for medicinal applications, while only two exist for phytoplankton. cyanoFilter is an R package built to identify phytoplankton populations from flow cytometry data. The package also integrates gating functions from two other automated algorithms. It also provides a gating accuracy test function that can be used to determine the accuracy of a desired gating function if monoculture flowcytometry data is available. The central algorithm in the package exploits observed pigmentation and granularity of phytoplankton cells. We demonstrate how its performance depends on strain similarity, using a model system of six cyanobacteria strains. Using the same system, we compare the performance of the central gating function in the package to similar functions in other packages. %B Ecological Modelling %V 460 %P 109743 %G eng %U https://www.sciencedirect.com/science/article/pii/S030438002100291X %R 10.1016/j.ecolmodel.2021.109743 %0 Journal Article %J Journal of Oceanology and Limnology %D 2021 %T Development of high-resolution chloroplast markers for intraspecific phylogeographic studies of Phaeocystis globosa %A Zhang, Qingchun %A Niu, Zhuang %A Wang, Jinxiu %A Liu, Chao %A Kong, Fanzhou %A Hu, Xiaokun %A Zhao, Jiayu %A Yu, Rencheng %K RCC2055 %K RCC736 %X 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–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–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–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–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. %B Journal of Oceanology and Limnology %V 39 %P 508–524 %8 mar %G eng %U https://link.springer.com/10.1007/s00343-020-9304-5 %R 10.1007/s00343-020-9304-5 %0 Journal Article %J Nature Communications %D 2021 %T Group 2i Isochrysidales produce characteristic alkenones reflecting sea ice distribution %A Wang, Karen Jiaxi %A Huang, Yongsong %A Majaneva, Markus %A Belt, Simon T. %A Liao, Sian %A Novak, Joseph %A Kartzinel, Tyler R. %A Herbert, Timothy D. %A Richter, Nora %A Cabedo-Sanz, Patricia %K RCC107 %K RCC1195 %K RCC1334 %K RCC5486 %X 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. %B Nature Communications %V 12 %P 15 %8 dec %G eng %U http://dx.doi.org/10.1038/s41467-020-20187-z http://www.nature.com/articles/s41467-020-20187-z %R 10.1038/s41467-020-20187-z %0 Journal Article %J Science of the Total Environment %D 2021 %T The influences of phytoplankton species, mineral particles and concentrations of dispersed oil on the formation and fate of marine oil-related aggregates %A Henry, Ingrid A. %A Netzer, Roman %A Davies, Emlyn %A Brakstad, Odd Gunnar %K Aggregation %K Dispersed oil %K Marine snow %K Mineral particles %K phytoplankton %K RCC1698 %K RCC1719 %K RCC290 %X The formation and fallout of oil-related marine snow have been associated with interactions between dispersed oil and small marine particles, like phytoplankton and mineral particles. In these studies, the influences of phytoplankton species, mineral particle concentration, and oil concentration on the aggregation of oil in seawater (SW) were investigated. The experiments were performed in a low-turbidity carousel incubation system, using natural SW at 13 °C. Aggregation was measured by silhouette camera analyses, and oil compound group distribution and depletion by gas chromatography (GC-FID or GC–MS). Aggregates with median sizes larger than 500 ??m in diameter were measured in the presence of dispersed oil and the phytoplankton species Thalassiosira rotula, Phaeocystis globosa, Skeletonema pseudocostatum, but not with the microalgae Micromonas pusilla. When mineral particles (diatomaceous earth) were incubated at different concentrations (5–30 mg/L) with dispersed oil and S. pseudocostatum, the largest aggregates were measured at the lower mineral particle concentration (5 mg/L). Since dispersed oil rapidly dilutes in the marine water column, experiments were performed with oil concentrations of from 10 mg/L to 0.01 mg/L in the presence of S. pseudocostatum and diatomaceous earth. Aggregates larger than 500 ??m was measured only at the highest oil concentrations (10 mg/L). However, oil attachment to the marine particles were also measured at low oil concentrations (<=1 mg/L). Depletion of oil compound groups (n-alkanes, naphthalenes, PAHs, decalins) were measured at all oil concentrations, both in aggregate and water phases, with biodegradation as the expected main depletion process. These results showed that oil concentration may be important for oil-related marine snow formation, but that even oil droplets at low concentrations may attach to the particles and be transported by prevailing currents. %B Science of the Total Environment %V 752 %P 141786 %8 jan %G eng %R 10.1016/j.scitotenv.2020.141786 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2021 %T Molecular bases of an alternative dual-enzyme system for light color acclimation of marine \textit{Synechococcus cyanobacteria %A Grébert, Théophile %A Nguyen, Adam A. %A Pokhrel, Suman %A Joseph, Kes Lynn %A Ratin, Morgane %A Dufour, Louison %A Chen, Bo %A Haney, Allissa M. %A Karty, Jonathan A. %A Trinidad, Jonathan C. %A Garczarek, Laurence %A Schluchter, Wendy M. %A Kehoe, David M. %A Partensky, Frédéric %K RCC2374 %K to add %X

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.

%B Proceedings of the National Academy of Sciences %V 118 %P e2019715118 %G eng %U http://www.pnas.org/lookup/doi/10.1073/pnas.2019715118 %R 10.1073/pnas.2019715118 %0 Journal Article %J Journal of Phycology %D 2021 %T No evidence of Phago-mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic %A Jimenez, Valeria %A Burns, John A. %A Le Gall, Florence %A Not, Fabrice %A Vaulot, Daniel %K Arctic %K Micromonas %K phago-mixotrophy %K phytoplankton %K rcc %K RCC21 %K RCC2288 %K RCC2306 %K RCC4298 %X In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phago-mixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity. %B Journal of Phycology %V 57 %P 435–446 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13125 %R 10.1111/jpy.13125 %0 Journal Article %J BMC Biology %D 2021 %T Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. %A Farhat, Sarah %A Le, Phuong %A Kayal, Ehsan %A Noel, Benjamin %A Bigeard, Estelle %A Corre, Erwan %A Maumus, Florian %A Florent, Isabelle %A Alberti, Adriana %A Aury, Jean-Marc %A Barbeyron, Tristan %A Cai, Ruibo %A Silva, Corinne Da %A Istace, Benjamin %A Labadie, Karine %A Marie, Dominique %A Mercier, Jonathan %A Rukwavu, Tsinda %A Szymczak, Jeremy %A Tonon, Thierry %A Alves-de-Souza, Catharina %A Rouze, Pierre %A de Peer, Yves Van %A Wincker, Patrick %A Rombauts, Stephane %A Porcel, Betina M %A Guillou, Laure %K Dinoflagellate %K genome %K Introner elements %K Non-canonical introns %K parasite %K RCC4383 %K RCC4398 %B BMC Biology %P 1–21 %G eng %R 10.1186/s12915-020-00927-9 %0 Journal Article %J Current Biology %D 2021 %T Rappemonads are haptophyte phytoplankton %A Kawachi, Masanobu %A Nakayama, Takuro %A Kayama, Motoki %A Nomura, Mami %A Miyashita, Hideaki %A Bojo, Othman %A Rhodes, Lesley %A Sym, Stuart %A Pienaar, Richard N. %A Probert, Ian %A Inouye, Isao %A Kamikawa, Ryoma %K environmental DNA sequences %K morphological evolution %K organellar phylogenomics %K phytoplankton diversity %K RCC3430 %K transmission electron microscopy %X 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. %B Current Biology %8 mar %G eng %U https://www.sciencedirect.com/science/article/pii/S0960982221003511 %R 10.1016/j.cub.2021.03.012 %0 Journal Article %J The ISME Journal %D 2021 %T Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts %A Bachy, Charles %A Yung, Charmaine C. M. %A Needham, David M. %A Gazitúa, Maria Consuelo %A Roux, Simon %A Limardo, Alexander J. %A Choi, Chang Jae %A Jorgens, Danielle M. %A Sullivan, Matthew B. %A Worden, Alexandra Z. %K RCC715 %K RCC716 %X The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (\textasciitilde210 kb) than BI-Viruses and BII-V1. BII-Vs share \textasciitilde90% of their proteins, and between 65% to 83% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters. %B The ISME Journal %P 1–19 %8 may %G eng %U https://www.nature.com/articles/s41396-021-00989-9 %R 10.1038/s41396-021-00989-9 %0 Journal Article %J Applied Phycology %D 2020 %T Aquatic virus culture collection: an absent (but necessary) safety net for environmental microbiologists %A Nissimov, Jozef I %A Campbell, Christine N %A Probert, Ian %A Wilson, William H %K algae %K Aquatic viruses %K bacteria %K biological preservation %K community resource %K culture collection %K genetic and metabolic diversity %B Applied Phycology %V 00 %P 1–15 %G eng %U https://doi.org/10.1080/26388081.2020.1770123 https://www.tandfonline.com/doi/full/10.1080/26388081.2020.1770123 %R 10.1080/26388081.2020.1770123 %0 Journal Article %J Symbiosis %D 2020 %T Better off alone? New insights in the symbiotic relationship between the flatworm Symsagittifera roscoffensis and the microalgae Tetraselmis convolutae %A Androuin, Thibault %A Six, Christophe %A Bordeyne, François %A de Bettignies, Florian %A Noisette, Fanny %A Davoult, Dominique %K Animal-plant %K Photobiology %K RCC1563 %K symbiosis %K Symsagittifera roscoffensis %K Tetraselmis convolutae %X The acoel flatworm Symsagittifera roscoffensis lives in obligatory symbiosis with the microalgal chlorophyte Tetraselmis convolutae. Although this interaction has been studied for more than a century, little is known on the potential reciprocal benefits of both partners, a subject that is still controversial. In order to provide new insights into this question, we have compared the photophysiology of the free-living microalgae to the symbiotic form in the flatworm, both acclimated at different light irradiances. Photosynthesis – Irradiance curves showed that the free-living T. convolutae had greater photosynthetic performance (i.e., oxygen production rates, ability to harvest light) than their symbiotic form, regardless of the light acclimation. However, they were affected by photoinhibition under high irradiances, which did not happen for the symbiotic form. The resistance of symbiotic microalgae to photoinhibition were corroborated by pigment analyses, which evidenced the induction of photoprotective mechanisms such as xanthophyll cycle as well as lutein and β-carotene accumulation. These processes were induced even under low light acclimation and exacerbated upon high light acclimation, suggesting a global stress situation for the symbiotic microalgae. We hypothesize that the internal conditions in the sub-epidermal zone of the flatworm (e.g., osmotic and pH), as well as the phototaxis toward high light imposed by the worm in its environment, would be major reasons for this chronic stress situation. Overall, our study suggests that the relationship between S. roscoffensis and T. convolutae may be a farming strategy in favor of the flatworm rather than a symbiosis with mutual benefits. %B Symbiosis %8 jun %G eng %U http://link.springer.com/10.1007/s13199-020-00691-y %R 10.1007/s13199-020-00691-y %0 Journal Article %J European Journal of Phycology %D 2020 %T Characterization of a lipid-producing thermotolerant marine photosynthetic pico-alga in the genus Picochlorum (Trebouxiophyceae) %A Mucko, Maja %A Padisák, Judit %A Gligora Udovič, Marija %A Pálmai, Tamás %A Novak, Tihana %A Medić, Nikola %A Gašparović, Blaženka %A Peharec Štefanić, Petra %A Orlić, Sandi %A Ljubešić, Zrinka %K morphology %K photosynthetic picoeukaryotes %K phylogeny %K physiology %K Picochlorum %K RCC1034 %K RCC13 %K RCC14 %K rcc289 %K RCC475 %K RCC6905 %K RCC846 %K RCC9 %K RCC945 %B European Journal of Phycology %V 00 %P 1–16 %8 aug %G eng %U https://doi.org/10.1080/09670262.2020.1757763 https://www.tandfonline.com/doi/full/10.1080/09670262.2020.1757763 %R 10.1080/09670262.2020.1757763 %0 Journal Article %J Frontiers in Microbiology %D 2020 %T Dinoflagellate host chloroplasts and mitochondria remain functional during amoebophrya infection %A Kayal, Ehsan %A Alves-de-Souza, Catharina %A Farhat, Sarah %A Velo-Suarez, Lourdes %A Monjol, Joanne %A Szymczak, Jeremy %A Bigeard, Estelle %A Marie, Dominique %A Noel, Benjamin %A Porcel, Betina M %A Corre, Erwan %A Six, Christophe %A Guillou, Laure %K amoebophrya %K chloroplast %K Dinoflagellate %K frontiers in microbiology %K frontiersin %K kleptoplast %K marine plankton %K org %K organelles %K parasitism %K RCC1627 %K RCC4398 %K www %X 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. %B Frontiers in Microbiology %V 11 %P 1–11 %8 dec %G eng %U https://www.frontiersin.org/articles/10.3389/fmicb.2020.600823/full %R 10.3389/fmicb.2020.600823 %0 Journal Article %J Microbiology Resource Announcements %D 2020 %T Draft whole-genome sequence of triparma laevis f. inornata (parmales, bolidophyceae), isolated from the oyashio region, western north pacific ocean %A Kuwata, Akira %A Saitoh, Kenji %A Nakamura, Yoji %A Ichinomiya, Mutsuo %A Sato, Naoki %E Stajich, Jason E. %K RCC4655 %X 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. %B Microbiology Resource Announcements %V 9 %P 13–14 %8 aug %G eng %U https://mra.asm.org/content/9/33/e00367-20 %R 10.1128/MRA.00367-20 %0 Journal Article %J Journal of Geophysical Research: Biogeosciences %D 2020 %T Effects of temperature and light on methane production of widespread marine phytoplankton %A Klintzsch, T. %A Langer, G. %A Wieland, A. %A Geisinger, H. %A Lenhart, K. %A Nehrke, G. %A Keppler, F. %K RCC1216 %B Journal of Geophysical Research: Biogeosciences %V 125 %8 sep %G eng %U 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 %R 10.1029/2020jg005793 %0 Journal Article %J Frontiers in Microbiology %D 2020 %T Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria %A Doré, Hugo %A Farrant, Gregory K. %A Guyet, Ulysse %A Haguait, Julie %A Humily, Florian %A Ratin, Morgane %A Pitt, Frances D. %A Ostrowski, Martin %A Six, Christophe %A Brillet-Guéguen, Loraine %A Hoebeke, Mark %A Bisch, Antoine %A Le Corguillé, Gildas %A Corre, Erwan %A Labadie, Karine %A Aury, Jean-Marc %A Wincker, Patrick %A Choi, Dong Han %A Noh, Jae Hoon %A Eveillard, Damien %A Scanlan, David J. %A Partensky, Frédéric %A Garczarek, Laurence %K amino-acid substitutions %K comparative genomics %K evolution %K genomic islands %K marine cyanobacteria %K niche adaptation %K Prochlorococcus %K rcc1084 %K RCC1085 %K RCC1086 %K RCC1087 %K RCC156 %K RCC158 %K rcc162 %K RCC2033 %K RCC2035 %K RCC2319 %K RCC2366 %K RCC2368 %K RCC2369 %K RCC2374 %K RCC2376 %K RCC2378 %K RCC2379 %K rcc2380 %K RCC2381 %K rcc2382 %K RCC2383 %K RCC2385 %K RCC2433 %K RCC2436 %K RCC2438 %K RCC2527 %K RCC2528 %K RCC2533 %K RCC2534 %K RCC2535 %K RCC2553 %K RCC2554 %K RCC2555 %K RCC2556 %K RCC2571 %K RCC2673 %K RCC278 %K rcc296 %K RCC307 %K RCC328 %K RCC3377 %K RCC407 %K RCC515 %K rcc539 %K rcc555 %K RCC556 %K rcc752 %K RCC753 %K rcc791 %K Synechococcus %B Frontiers in Microbiology %V 11 %P 1–23 %8 sep %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2020.567431/full %R 10.3389/fmicb.2020.567431 %0 Journal Article %J Marine Pollution Bulletin %D 2020 %T Formation and fate of oil-related aggregates (ORAs) in seawater at different temperatures %A Henry, Ingrid A. %A Netzer, Roman %A Davies, Emlyn J. %A Brakstad, Odd Gunnar %K Aggregation %K biodegradation %K Dispersed oil %K Marine snow %K Microbial communities %K RCC4289 %K Sinking %X In this study, the formation and fate of oil-related aggregates (ORAs) from chemically dispersed oil in seawater (SW) were investigated at different temperatures (5 °C, 13 °C, 20 °C). Experiments in natural SW alone, and in SW amended with typical marine snow constituents (phytoplankton and mineral particles), showed that the presence of algae stimulated the formation of large ORAs, while high SW temperature resulted in faster aggregate formation. The ORAs formed at 5 °C and 13 °C required mineral particles for sinking, while the aggregates also sank in the absence of mineral particles at 20°. Early in the experimental periods, oil compound accumulation in ORAs was faster than biodegradation, particularly in aggregates with algae, followed by rapid biodegradation. High abundances of bacteria associated with hydrocarbon biodegradation were determined in the ORAs, together with algae-associated bacteria, while clustering analyses showed separation between bacterial communities in experiments with oil alone and oil with algae/mineral particles. %B Marine Pollution Bulletin %V 159 %P 111483 %8 oct %G eng %U https://doi.org/10.1016/j.marpolbul.2020.111483 https://linkinghub.elsevier.com/retrieve/pii/S0025326X20306019 %R 10.1016/j.marpolbul.2020.111483 %0 Journal Article %J Geochemistry, Geophysics, Geosystems %D 2020 %T Li partitioning into coccoliths of Emiliania huxleyi : evaluating the general role of “vital effects” in explaining element partitioning in biogenic carbonates %A Langer, Gerald %A Sadekov, Aleksey %A Greaves, Mervyn %A Nehrke, Gernot %A Probert, Ian %A Misra, Sambuddha %A Thoms, Silke %K RCC3652 %X Abstract Emiliania huxleyi cells were grown in artificial seawater of different Li and Ca concentrations and coccolith Li/Ca ratios determined. Coccolith Li/Ca ratios were positively correlated to seawater Li/Ca ratios only if the seawater Li concentration was changed, not if the seawater Ca concentration was changed. This Li partitioning pattern of E. huxleyi was previously also observed in the benthic foraminifer Amphistegina lessonii and inorganically precipitated calcite. We argue that Li partitioning in both E. huxleyi and A. lessonii is dominated by a coupled transmembrane transport of Li and Ca from seawater to the site of calcification. We present a refined version of a recently proposed transmembrane transport model for Li and Ca. The model assumes that Li and Ca enter the cell via Ca channels, the Li flux being dependent on the Ca flux. While the original model features a linear function to describe the experimental data, our refined version uses a power function, changing the stoichiometry of Li and Ca. The version presented here accurately predicts the observed dependence of DLi on seawater Li/Ca ratios. Our data demonstrate that minor element partitioning in calcifying organisms is partly mediated by biological processes even if the partitioning behaviour of the calcifying organism is indistinguishable from that of inorganically precipitated calcium carbonate. %B Geochemistry, Geophysics, Geosystems %P 0–2 %8 jun %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1029/2020GC009129 %R 10.1029/2020GC009129 %0 Journal Article %J Biomolecules %D 2020 %T The polar lipidome of cultured emiliania huxleyi: A source of bioactive lipids with relevance for biotechnological applications %A Aveiro, Susana S. %A Melo, Tânia %A Figueiredo, Ana %A Domingues, Pedro %A Pereira, Hugo %A Maia, Inês B. %A Silva, Joana %A Domingues, M. Rosário %A Nunes, Cláudia %A Moreira, Ana S. P. %K Emiliania huxleyi %K haptophyta %K Lipidomics %K Mass spectrometry %K Microalgae %K RCC1250 %X Polar lipids from microalgae have aroused greater interest as a natural source of omega-3 (n-3) polyunsaturated fatty acids (PUFA), an alternative to fish, but also as bioactive compounds with multiple applications. The present study aims to characterize the polar lipid profile of cultured microalga Emiliania huxleyi using hydrophilic interaction liquid chromatography coupled with high-resolution mass spectrometry (HILIC–MS) and fatty acids (FA) analysis by gas chromatography (GC–MS). The lipidome of E. huxleyi revealed the presence of distinct n-3 PUFA (40% of total FA), namely docosahexaenoic acid (22:6n-3) and stearidonic acid (18:4n-3), which give this microalga an increased commercial value as a source of n-3 PUFA present in the form of polar lipids. A total of 134 species of polar lipids were identified and some of these species, particularly glycolipids, have already been reported for their bioactive properties. Among betaine lipids, the diacylglyceryl carboxyhydroxymethylcholine (DGCC) class is the least reported in microalgae. For the first time, monomethylphosphatidylethanolamine (MMPE) has been found in the lipidome of E. huxleyi. Overall, this study highlights the potential of E. huxleyi as a sustainable source of high-value polar lipids that can be exploited for different applications, namely human and animal nutrition, cosmetics, and pharmaceuticals. %B Biomolecules %V 10 %P 1434 %G eng %U https://www.mdpi.com/2218-273X/10/10/1434 %R 10.3390/biom10101434 %0 Journal Article %J Frontiers in Microbiology %D 2020 %T Synergic effects of temperature and irradiance on the physiology of the marine synechococcus strain WH7803 %A Guyet, Ulysse %A Nguyen, Ngoc A. %A Doré, Hugo %A Haguait, Julie %A Pittera, Justine %A Conan, Maël %A Ratin, Morgane %A Corre, Erwan %A Le Corguillé, Gildas %A Brillet-Guéguen, Loraine %A Hoebeke, Mark %A Six, Christophe %A Steglich, Claudia %A Siegel, Anne %A Eveillard, Damien %A Partensky, Frédéric %A Garczarek, Laurence %K light stress %K marine cyanobacteria %K rcc752 %K Synechococcus %K temperature stress %K transcriptomics %K UV radiations %X Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria. %B Frontiers in Microbiology %V 11 %P 1707 %8 jul %G eng %U www.frontiersin.org %R 10.3389/fmicb.2020.01707 %0 Journal Article %J Journal of Phycology %D 2019 %T Effects of elevated co 2 on growth, calcification and spectral dependence of photoinhibition in the coccolithophore Emiliania huxleyi (Prymnesiophyceae) %A Lorenzo, M. Rosario %A Neale, Patrick J. %A Sobrino, Cristina %A León, Pablo %A Vázquez, Víctor %A Bresnan, Eileen %A Segovia, María %K rcc1226 %B Journal of Phycology %P jpy.12885 %8 may %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12885 %R 10.1111/jpy.12885 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2019 %T Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus %A Sanfilippo, Joseph E. %A Nguyen, Adam A. %A Garczarek, Laurence %A Karty, Jonathan A. %A Pokhrel, Suman %A Strnat, Johann A. %A Partensky, Frédéric %A Schluchter, Wendy M. %A Kehoe, David M. %K RCC1086 %K RCC2035 %K rcc2380 %K rcc2382 %K RCC2385 %K RCC2433 %K RCC2437 %K RCC2528 %K RCC2533 %K RCC2534 %K RCC2535 %K RCC2571 %K RCC2673 %K RCC28 %K RCC307 %K RCC328 %K RCC515 %K rcc555 %K rcc791 %X 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–absorbing phycoerythrobilin (PEB) and blue-light–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. %B Proceedings of the National Academy of Sciences %V 116 %P 6457–6462 %8 mar %G eng %U http://www.pnas.org/lookup/doi/10.1073/pnas.1810491116 %R 10.1073/pnas.1810491116 %0 Journal Article %J Biogeosciences %D 2019 %T Methane production by three widespread marine phytoplankton species: release rates, precursor compounds, and potential relevance for the environment %A Klintzsch, Thomas %A Langer, Gerald %A Nehrke, Gernot %A Wieland, Anna %A Lenhart, Katharina %A Keppler, Frank %K RCC1216 %B Biogeosciences %V 16 %P 4129–4144 %8 oct %G eng %U https://www.biogeosciences.net/16/4129/2019/ %R 10.5194/bg-16-4129-2019 %0 Journal Article %J Genes %D 2019 %T Simplified transformation of ostreococcus tauri using polyethylene glycol %A Sanchez, Frédéric %A Geffroy, Solène %A Norest, Manon %A Yau, Sheree %A Moreau, Hervé %A Grimsley, Nigel %K bioluminescence %K Chlorophyta %K Ecosystem %K Gene Expression %K luciferase %K mamiellophyceae %K Ostreococcus %K picoeukaryote %K plankton %K Prasinophyte %K promoter %K RCC4221 %X Ostreococcustauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13–22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave ¿104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20–40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome. %B Genes %V 10 %P 399 %8 may %G eng %U https://www.mdpi.com/2073-4425/10/5/399 %R 10.3390/genes10050399 %0 Journal Article %J The ISME Journal %D 2019 %T Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth %A Kashiyama, Yuichiro %A Yokoyama, Akiko %A Shiratori, Takashi %A Hess, Sebastian %A Not, Fabrice %A Bachy, Charles %A Gutierrez-Rodriguez, Andres %A Kawahara, Jun %A Suzaki, Toshinobu %A Nakazawa, Masami %A Ishikawa, Takahiro %A Maruyama, Moe %A Wang, Mengyun %A Chen, Man %A Gong, Yingchun %A Seto, Kensuke %A Kagami, Maiko %A Hamamoto, Yoko %A Honda, Daiske %A Umetani, Takahiro %A Shihongi, Akira %A Kayama, Motoki %A Matsuda, Toshiki %A Taira, Junya %A Yabuki, Akinori %A Tsuchiya, Masashi %A Hirakawa, Yoshihisa %A Kawaguchi, Akane %A Nomura, Mami %A Nakamura, Atsushi %A Namba, Noriaki %A Matsumoto, Mitsufumi %A Tanaka, Tsuyoshi %A Yoshino, Tomoko %A Higuchi, Rina %A Yamamoto, Akihiro %A Maruyama, Tadanobu %A Yamaguchi, Aika %A Uzuka, Akihiro %A Miyagishima, Shinya %A Tanifuji, Goro %A Kawachi, Masanobu %A Kinoshita, Yusuke %A Tamiaki, Hitoshi %K Biochemistry %K Biogeochemistry %K Cellular microbiology %K microbial ecology %K RCC164 %K RCC22 %K RCC24 %K RCC375 %K RCC916 %X Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation. %B The ISME Journal %P 1 %8 feb %G eng %U http://www.nature.com/articles/s41396-019-0377-0 %R 10.1038/s41396-019-0377-0 %0 Journal Article %J New Phytologist %D 2019 %T Unveiling membrane thermoregulation strategies in marine picocyanobacteria %A Breton, Solène %A Jouhet, Juliette %A Guyet, Ulysse %A Gros, Valérie %A Pittera, Justine %A Demory, David %A Partensky, Frédéric %A Doré, Hugo %A Ratin, Morgane %A Maréchal, Éric %A Nguyen, Ngoc An %A Garczarek, Laurence %A Six, Christophe %K RCC2374 %K RCC2385 %K RCC515 %K rcc539 %B New Phytologist %P nph.16239 %8 oct %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16239 %R 10.1111/nph.16239 %0 Journal Article %J Molecular Ecology %D 2018 %T Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network %A Meng, Arnaud %A Corre, Erwan %A Probert, Ian %A Gutierrez-Rodriguez, Andres %A Siano, Raffaele %A Annamale, Anita %A Alberti, Adriana %A Da Silva, Corinne %A Wincker, Patrick %A Le Crom, Stéphane %A Not, Fabrice %A Bittner, Lucie %K Genomics/Proteomics %K Microbial Biology %K Molecular Evolution %K Protists %K rcc1491 %K RCC1516 %K RCC3387 %K rcc3468 %K rcc3507 %K transcriptomics %X Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g. sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization. This article is protected by copyright. All rights reserved. %B Molecular Ecology %P 0–2 %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/29624751%0Ahttp://doi.wiley.com/10.1111/mec.14579 %R 10.1111/mec.14579 %0 Journal Article %J Scientific Reports %D 2018 %T Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis %A Paerl, Ryan W. %A Bertrand, Erin M. %A Rowland, Elden %A Schatt, Phillippe %A Mehiri, Mohamed %A Niehaus, Thomas D. %A Hanson, Andrew D. %A Riemann, Lasse %A Yves-Bouget, Francois %K RCC4222 %K RCC745 %B Scientific Reports %V 8 %P 5940 %G eng %U http://www.nature.com/articles/s41598-018-24321-2 %R 10.1038/s41598-018-24321-2 %0 Journal Article %J Frontiers in Microbiology %D 2018 %T Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains %A Farhat, Sarah %A Florent, Isabelle %A Noel, Benjamin %A Kayal, Ehsan %A Da Silva, Corinne %A Bigeard, Estelle %A Alberti, Adriana %A Labadie, Karine %A Corre, Erwan %A Aury, Jean-Marc %A Rombauts, Stephane %A Wincker, Patrick %A Guillou, Laure %A Porcel, Betina M. %K amoebophrya %K Dinoflagellates %K Gene Expression %K infection %K oxidative stress response %K parasite %K plankton %K RCC1627 %K RCC3596 %K RCC4383 %K RCC4398 %K syndiniales %B Frontiers in Microbiology %V 9 %P 1–19 %8 oct %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full %R 10.3389/fmicb.2018.02251 %0 Journal Article %J bioRxiv %D 2018 %T Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri %A Smallwood, Authors Chuck R %A Chen, Jian-hua %A Kumar, Neeraj %A Chrisler, William %A Samuel, O %A Kyle, Jennifer E %A Nicora, Carrie D %A Boudreau, Rosanne %A Ekman, Axel %A Kim, K %A Moore, Ronald J %A Mcdermott, Gerry %A Cannon, William R %A Evans, James E %K ? No DOI found %K RCC745 %B bioRxiv %G eng %0 Journal Article %J Journal of Phycology %D 2018 %T Ontogenetic analysis of siliceous cell wall formation in Triparma laevis f. inornata (Parmales, Stramenopiles) %A Yamada, Kazumasa %A Katsura, Hirotaka %A Noël, Mary-Hélène %A Ichinomiya, Mutsuo %A Kuwata, Akira %A Sato, Shinya %A Yoshikawa, Shinya %K RCC4665 %B Journal of Phycology %P 0–2 %8 oct %G eng %U http://doi.wiley.com/10.1111/jpy.12800 %R 10.1111/jpy.12800 %0 Journal Article %J Genome Biology and Evolution %D 2018 %T Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends %A Klinger, Christen M %A Paoli, Lucas %A Newby, Robert J %A Wang, Matthew Yu-Wei %A Carroll, Hyrum D %A Leblond, Jeffrey D %A Howe, Christopher J %A Dacks, Joel B %A Bowler, Chris %A Cahoon, A Bruce %A Dorrell, Richard G %A Richardson, Elisabeth %K constructive neutral evolution %K Dinoflagellate %K plastid %K RCC1513 %K serial endosymbiosis %K transcript editing %X 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. %B Genome Biology and Evolution %V 10 %P 1019–1038 %G eng %U https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evy057/4935245 %R 10.1093/gbe/evy057 %0 Journal Article %J Environmental Microbiology Reports %D 2018 %T Relative stability of ploidy in a marine Synechococcus across various growth conditions %A Perez-Sepulveda, Blanca %A Pitt, Frances %A N'Guyen, An Ngoc %A Ratin, Morgane %A Garczarek, Laurence %A Millard, Andrew %A Scanlan, David J %K rcc752 %X Marine picocyanobacteria of the genus Synechococcus are ubiquitous phototrophs in oceanic systems. Consistent with these organisms occupying vast tracts of the nutrient impoverished ocean, most marine Synechococcus so far studied are monoploid i.e. contain a single chromosome copy. The exception is the oligoploid strain Synechococcus sp. WH7803, which on average possesses around 4 chromosome copies. Here, we set out to understand the role of resource availability (through nutrient deplete growth) and physical stressors (UV, exposure to low and high temperature) in regulating ploidy level in this strain. Using qPCR to assay ploidy status we demonstrate the relative stability of chromosome copy number in Synechococcus sp. WH7803. Such robustness in maintaining an oligoploid status even under nutrient and physical stress is indicative of a fundamental role, perhaps facilitating recombination of damaged DNA regions as a result of prolonged exposure to oxidative stress, or allowing added flexibility in gene expression via possessing multiple alleles. This article is protected by copyright. All rights reserved. %B Environmental Microbiology Reports %P in press %8 feb %G eng %U http://dx.doi.org/10.1111/1758-2229.12614 http://doi.wiley.com/10.1111/1758-2229.12614 %R 10.1111/1758-2229.12614 %0 Journal Article %J Frontiers in Microbiology %D 2017 %T Adaptation to blue light in marine synechococcus requires MpeU, an enzyme with similarity to phycoerythrobilin lyase isomerases %A Mahmoud, Rania M. %A Sanfilippo, Joseph E. %A Nguyen, Adam A. %A Strnat, Johann A. %A Partensky, Frédéric %A Garczarek, Laurence %A Abo El Kassem, Nabil %A Kehoe, David M. %A Schluchter, Wendy M. %K 2017 %K Blue light %K light harvesting complex %K Lyase isomerase %K marine cyanobacteria %K Marine Synechococcus %K phycobilin %K Phycobilisome %K Phycoerythrin %K Phycourobilin %K rcc555 %K sbr?hyto?app %X 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's oceans. %B Frontiers in Microbiology %V 8 %P 243 %8 feb %G eng %U http://journal.frontiersin.org/article/10.3389/fmicb.2017.00243/full %R 10.3389/fmicb.2017.00243 %0 Journal Article %J Photosynthesis Research %D 2017 %T Arctic Micromonas uses protein pools and non-photochemical quenching to cope with temperature restrictions on Photosystem II protein turnover %A Ni, Guangyan %A Zimbalatti, Gabrielle %A Murphy, Cole D. %A Barnett, Audrey B. %A Arsenault, Christopher M. %A Li, Gang %A Cockshutt, Amanda M. %A Campbell, Douglas A. %K 2016 %K á %K Photoinactivation %K photoinactivation á xanthophyll cycle %K Photosystem II %K Prasinophyte %K prasinophyte á photosystem ii %K RCC806 %K Xanthophyll cycle %B Photosynthesis Research %V 131 %P 203–220 %8 feb %G eng %U http://link.springer.com/10.1007/s11120-016-0310-6 %R 10.1007/s11120-016-0310-6 %0 Journal Article %J Scientific Reports %D 2017 %T Chloropicophyceae, a new class of picophytoplanktonic prasinophytes %A Lopes dos Santos, Adriana %A Pollina, Thibaut %A Gourvil, Priscillia %A Corre, Erwan %A Marie, Dominique %A Garrido, José Luis %A Rodríguez, Francisco %A Noël, Mary-Hélène %A Vaulot, Daniel %A Eikrem, Wenche %K 2017 %K RCC1019 %K RCC1021 %K RCC1032 %K RCC1043 %K RCC1124 %K RCC138 %K RCC15 %K RCC1871 %K RCC19 %K RCC227 %K RCC2335 %K RCC2337 %K RCC2339 %K RCC287 %K RCC297 %K RCC3368 %K RCC3373 %K RCC3374 %K RCC3375 %K RCC3376 %K RCC3402 %K RCC4429 %K RCC4430 %K RCC4434 %K RCC4572 %K RCC4656 %K RCC696 %K RCC700 %K RCC701 %K RCC712 %K RCC713 %K RCC717 %K RCC719 %K RCC722 %K RCC726 %K RCC856 %K RCC857 %K RCC887 %K RCC917 %K RCC996 %K RCC997 %K RCC998 %K RCC999 %K sbr?hyto$_\textrmd$ipo %B Scientific Reports %V 7 %P 14019 %8 dec %G eng %U http://www.nature.com/articles/s41598-017-12412-5 %R 10.1038/s41598-017-12412-5 %0 Journal Article %J Limnology and Oceanography %D 2017 %T Dimethylated sulfur compounds in symbiotic protists: A potentially significant source for marine DMS(P) %A Gutierrez-Rodriguez, Andres %A Pillet, Loic %A Biard, Tristan %A Said-Ahmad, Ward %A Amrani, Alon %A Simó, Rafel %A Not, Fabrice %K 2017 %K rcc1383 %K rcc1491 %K rcc3468 %K rcc3507 %K sbr?hyto$_\textrmd$ipo %B Limnology and Oceanography %8 feb %G eng %U http://doi.wiley.com/10.1002/lno.10491 %R 10.1002/lno.10491 %0 Journal Article %J Applied Optics %D 2017 %T On the discrimination of multiple phytoplankton groups from light absorption spectra of assemblages with mixed taxonomic composition and variable light conditions %A Organelli, Emanuele %A Nuccio, Caterina %A Lazzara, Luigi %A Uitz, Julia %A Bricaud, Annick %A Massi, Luca %K RCC151 %K RCC322 %K RCC904 %X According to recommendations of the international community of phytoplankton functional type algorithm devel- opers, a set of experiments on marine algal cultures was conducted to (1) investigate uncertainties and limits in phytoplankton group discrimination from hyperspectral light absorption properties of assemblages withmixed taxo- nomic composition, and (2) evaluate the extent to which modifications of the absorption spectral features due to variable light conditions affect the optical discrimination of phytoplankton. Results showed that spectral absorption signatures of multiple species can be extracted from mixed assemblages, even at low relative contributions. Errors in retrieved pigment abundances are, however, influenced by the co-occurrence of species with similar spectral features. Plasticity of absorption spectra due to changes in light conditions weakly affects interspecific differences, with errors ¡21% for retrievals of pigment concentrations from mixed assemblages. %B Applied Optics %V 56 %P 3952 %8 may %G eng %U https://www.osapublishing.org/abstract.cfm?URI=ao-56-14-3952 %R 10.1364/AO.56.003952 %0 Journal Article %J The ISME Journal %D 2017 %T Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters %A Lopes dos Santos, Adriana %A Gourvil, Priscillia %A Tragin, Margot %A Noël, Mary-Hélène %A Decelle, Johan %A Romac, Sarah %A Vaulot, Daniel %K 2016 %K MACUMBA %K MicroB3 %K RCC1019 %K RCC1021 %K RCC1032 %K RCC1043 %K RCC1124 %K RCC138 %K RCC15 %K RCC1871 %K RCC19 %K RCC227 %K RCC2335 %K RCC2337 %K RCC2339 %K RCC287 %K RCC297 %K RCC3368 %K RCC3373 %K RCC3374 %K RCC3375 %K RCC3376 %K RCC3402 %K RCC4429 %K RCC4430 %K RCC4434 %K RCC4656 %K RCC696 %K RCC700 %K RCC701 %K RCC712 %K RCC713 %K RCC717 %K RCC719 %K RCC722 %K RCC726 %K RCC856 %K RCC857 %K RCC917 %K RCC996 %K RCC997 %K RCC998 %K RCC999 %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B The ISME Journal %V 11 %P 512–528 %8 feb %G eng %U http://www.nature.com/doifinder/10.1038/ismej.2016.120 %R 10.1038/ismej.2016.120 %0 Journal Article %J Harmful Algae %D 2017 %T 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 %A Yoo, Yeong Du %A Seong, Kyeong Ah %A Jeong, Hae Jin %A Yih, Wonho %A Rho, Jung Rae %A Nam, Seung Won %A Kim, Hyung Seop %K Bloom %K Flagellate %K Grazing impact %K Predator-prey relationship %K RCC1086 %K Red tide %X 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 × 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 0.3–8.3 cells predator-1 h-1 and 0.012–0.033 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. %B Harmful Algae %V 68 %P 105–117 %G eng %U http://dx.doi.org/10.1016/j.hal.2017.07.012 %R 10.1016/j.hal.2017.07.012 %0 Journal Article %J American Journal of Botany %D 2017 %T Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta) %A Parks, Matthew %A Nakov, Teofil %A Ruck, Elizabeth %A Wickett, Norman J %A Alverson, Andrew J %A Rice, Ada L %A Conservation, Plant %A Botanic, Chicago %A Glencoe, Garden %K and %K b %K c %K citation %K diatoms %K e %K gene tree %K genome duplication %K j %K n %K nakov %K paleopolyploidy %K parks m %K polyploidy %K RCC205 %K RCC80 %K ruck %K synonymous divergence %K t %K these authors contributed equally %K to this work %K wickett %B American Journal of Botany %V 105 %P 1–18 %G eng %R 10.1101/181115 %0 Journal Article %J Bulletin of Environmental Contamination and Toxicology %D 2017 %T Removal and biodegradation of phenanthrene, fluoranthene and pyrene by the marine algae rhodomonas baltica enriched from north atlantic coasts %A Arias, Andrés H %A Souissi, Anissa %A Glippa, Olivier %A Roussin, Marion %A Dumoulin, David %A Net, Sopheak %A Ouddane, Baghdad %A Souissi, Sami %K RCC350 %X This study is focused on the removal, accumulation and degradation of three environmental ubiquitous polycyclic aromatic hydrocarbons (PAHs), phenanthrene (PHE), fluoranthene (FLA) and pyrene (PYR), by the marine alga Rhodomonas baltica enriched from the English Channel. After separation, purification and culture in several phases, R. baltica was exposed to PAH concentrations that are frequently encountered in the field in several anthropized environments. The results showed that R. baltica can grow under PAH stress, efficiently remove up to 70% of these compounds from the medium by 216 h of culture and selectively bioaccumulate PAHs by their hydrophobicity. Between PHE, FLA and PYR, phenanthrene was the compound with higher degradation rates throughout incubation. The equilibrium partitioning theoretical approach showed that physico-chemical partitioning, rather than active bioconcentration, was the major factor governing the bioaccumulation, outlying a potential application in decontamination processes for this species. %B Bulletin of Environmental Contamination and Toxicology %V 98 %P 392–399 %G eng %U https://doi.org/10.1007/s00128-016-1967-4 %R 10.1007/s00128-016-1967-4 %0 Journal Article %J Algae %D 2015 %T Morphology , molecular phylogeny , and pigment characterization of a novel phenotype of the dinoflagellate genus Pelagodinium from Korean waters %A Potvin, Éric %A Jeong, Hae Jin %A Kang, Nam Seon %A Noh, Jae Hoon %A Yang, Eun Jin %K foraminifera %K gymnodinium bei %K pelagic symbiont %K rcc %K suessiaceae %K suessiales %X 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. %B Algae %V 30 %P 183–195 %G eng %R 10.4490/algae.2015.30.3.183 %0 Journal Article %J Phycological Research %D 2015 %T Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae) %A Kamikawa, Ryoma %A Yubuki, Naoji %A Yoshida, Masaki %A Taira, Misaka %A Nakamura, Noriaki %A Ishida, Ken-ichiro %A Leander, Brian S. %A Miyashita, Hideaki %A Hashimoto, Tetsuo %A Mayama, Shigeki %A Inagaki, Yuji %K apochlorotic diatoms %K genetic diversity %K large subunit rrna %K molecular phylogenetic analysis %K nonphotosynthetic plastids %K plastid 16s rrna %K rcc %X 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 %B Phycological Research %V 63 %P 19–28 %G eng %U http://doi.wiley.com/10.1111/pre.12072 %R 10.1111/pre.12072 %0 Journal Article %J Journal of Phycology %D 2014 %T Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians %A Probert, Ian %A Siano, Raffaele %A Poirier, Camille %A Decelle, Johan %A Biard, Tristan %A Tuji, Akihiro %A Suzuki, Noritoshi %A Not, Fabrice %K Dinoflagellate %K MACUMBA %K Peridiniales %K polycystines %K Radiolaria %K rcc %K RCC3378 %K RCC3379 %K RCC3380 %K RCC3381 %K RCC3382 %K RCC3383 %K RCC3384 %K RCC3385 %K RCC3386 %K RCC3387 %K RCC3388 %K SBR$_\textrmP$hyto$_\textrmD$PO %K Scrippsiella %K symbiosis %K taxonomy %K Zooxanthella %X Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free-living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free-living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine-symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free-living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA-based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov. %B Journal of Phycology %V 50 %P 388–399 %G eng %U http://dx.doi.org/10.1111/jpy.12174 %R 10.1111/jpy.12174 %0 Journal Article %J Harmful Algae %D 2014 %T Genetic diversity of the harmful family Kareniaceae (Gymnodiniales, Dinophyceae) in France, with the description of ¡i¿Karlodinium gentienii¡/i¿ sp. nov.: A new potentially toxic dinoflagellate %A Nézan, Elisabeth %A Siano, Raffaele %A Boulben, Sylviane %A Six, Christophe %A Bilien, Gwenael %A Chèze, Karine %A Duval, Audrey %A Le Panse, Sophie %A Quéré, Julien %A Chomérat, Nicolas %K 2014 %K rcc %K sbr?hyto?app %X A B S T R A C T The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1–D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity. %B Harmful Algae %V 40 %P 75–91 %G eng %U http://linkinghub.elsevier.com/retrieve/pii/S1568988314001863 %R 10.1016/j.hal.2014.10.006 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2014 %T Marine algae and land plants share conserved phytochrome signaling systems %A Duanmu, Deqiang %A Bachy, Charles %A Sudek, Sebastian %A Wong, Chee-Hong %A Jimenez, Valeria %A Rockwell, Nathan C %A Martin, Shelley S %A Ngan, Chew Yee %A Reistetter, Emily N %A van Baren, Marijke J %A Price, Dana C %A Wei, Chia-Lin %A Reyes-Prieto, Adrian %A Lagarias, J Clark %A Worden, Alexandra Z %K Micromonas %K rcc %X 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 (¡2 µm 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. %B Proceedings of the National Academy of Sciences of the United States of America %V 111 %P 15827–15832 %G eng %U http://www.pnas.org/content/111/44/15827.abstract %R 10.1073/pnas.1416751111 %0 Journal Article %J PLoS biology %D 2014 %T The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing %A Keeling, Patrick J %A Burki, Fabien %A Wilcox, Heather M %A Allam, Bassem %A Allen, Eric E %A Amaral-Zettler, Linda A %A Armbrust, E Virginia %A Archibald, John M %A Bharti, Arvind K %A Bell, Callum J %A Beszteri, Bank %A Bidle, Kay D %A Cameron, Connor T %A Campbell, Lisa %A Caron, David A %A Cattolico, Rose Ann %A Collier, Jackie L %A Coyne, Kathryn %A Davy, Simon K %A Deschamps, Phillipe %A Dyhrman, Sonya T %A Edvardsen, Bente %A Gates, Ruth D %A Gobler, Christopher J %A Greenwood, Spencer J %A Guida, Stephanie M %A Jacobi, Jennifer L %A Jakobsen, Kjetill S %A James, Erick R %A Jenkins, Bethany %A John, Uwe %A Johnson, Matthew D %A Juhl, Andrew R %A Kamp, Anja %A Katz, Laura A %A Kiene, Ronald %A Kudryavtsev, Alexander %A Leander, Brian S %A Lin, Senjie %A Lovejoy, Connie %A Lynn, Denis %A Marchetti, Adrian %A McManus, George %A Nedelcu, Aurora M %A Menden-Deuer, Susanne %A Miceli, Cristina %A Mock, Thomas %A Montresor, Marina %A Moran, Mary Ann %A Murray, Shauna %A Nadathur, Govind %A Nagai, Satoshi %A Ngam, Peter B %A Palenik, Brian %A Pawlowski, Jan %A Petroni, Giulio %A Piganeau, Gwenael %A Posewitz, Matthew C %A Rengefors, Karin %A Romano, Giovanna %A Rumpho, Mary E %A Rynearson, Tatiana %A Schilling, Kelly B %A Schroeder, Declan C %A Simpson, Alastair G B %A Slamovits, Claudio H %A Smith, David R %A Smith, G Jason %A Smith, Sarah R %A Sosik, Heidi M %A Stief, Peter %A Theriot, Edward %A Twary, Scott N %A Umale, Pooja E %A Vaulot, Daniel %A Wawrik, Boris %A Wheeler, Glen L %A Wilson, William H %A Xu, Yan %A Zingone, Adriana %A Worden, Alexandra Z %K 2014 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %X 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's oceans %B PLoS biology %V 12 %P e1001889 %G eng %U http://dx.doi.org/10.1371%252Fjournal.pbio.1001889 %R 10.1371/journal.pbio.1001889 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2013 %T Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida %A Collen, Jonas %A Porcel, Betina %A Carré, Wilfrid %A Ball, Steven G %A Chaparro, Cristian %A Tonon, Thierry %A Barbeyron, Tristan %A Michel, Gurvan %A Noel, Benjamin %A Valentin, Klaus %A Elias, Marek %A Artiguenave, François %A Arun, Alok %A Aury, Jean-Marc %A Barbosa-Neto, José F %A Bothwell, John H %A Bouget, François-Yves %A Brillet, Loraine %A Cabello-Hurtado, Francisco %A Capella-Gutiérrez, Salvador %A Charrier, Bénédicte %A Cladière, Lionel %A Cock, J Mark %A Coelho, Susana M %A Colleoni, Christophe %A Czjzek, Mirjam %A Da Silva, Corinne %A Delage, Ludovic %A Denoeud, France %A Deschamps, Philippe %A Dittami, Simon M %A Gabaldón, Toni %A Gachon, Claire M M %A Groisillier, Agnès %A Hervé, Cécile %A Jabbari, Kamel %A Katinka, Michael %A Kloareg, Bernard %A Kowalczyk, Nathalie %A Labadie, Karine %A Leblanc, Catherine %A Lopez, Pascal J %A McLachlan, Deirdre H %A Meslet-Cladiere, Laurence %A Moustafa, Ahmed %A Nehr, Zofia %A Nyvall Collén, Pi %A Panaud, Olivier %A Partensky, Frédéric %A Poulain, Julie %A Rensing, Stefan A %A Rousvoal, Sylvie %A Samson, Gaelle %A Symeonidi, Aikaterini %A Weissenbach, Jean %A Zambounis, Antonios %A Wincker, Patrick %A Boyen, Catherine %K RCC299 %X 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. %B Proceedings of the National Academy of Sciences %V 110 %P 5247–5252 %G eng %U http://www.pnas.org/content/110/13/5247.abstract %R 10.1073/pnas.1221259110 %0 Journal Article %J Nucleic Acids Research %D 2013 %T The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy %A Guillou, Laure %A Bachar, Dipankar %A Audic, Stéphane %A Bass, David %A Berney, Cedric %A Bittner, Lucie %A Boutte, Christophe %A Burgaud, Gaetan %A de Vargas, Colomban %A Decelle, Johan %A del Campo, Javier %A Dolan, John %A Dunthorn, Micah %A Bente, Edvardsen %A Holzmann, Maria %A Kooistra, Wiebe H C F %A Lara, Enrique %A Lebescot, Noan %A Logares, Ramiro %A Mahé, Frédéric %A Massana, Ramon %A Montresor, Marina %A Morard, Raphael %A Not, Fabrice %A Pawlowski, Jan %A Probert, Ian %A Sauvadet, Anne-Laure %A Siano, Raffaele %A Stoeck, Thorsten %A Vaulot, Daniel %A Zimmermann, Pascal %A Christen, Richard %K 2013 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B Nucleic Acids Research %V 41 %P D597–D604 %G eng %R 10.1093/nar/gks1160 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2012 %T An original mode of symbiosis in open ocean plankton %A Decelle, J %A Probert, I %A Bittner, L %A Desdevises, Y %A Colin, S %A de Vargas, C %A Gali, M %A Simo, R %A Not, F %K 2012 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %B Proceedings of the National Academy of Sciences of the United States of America %V 109 %P 18000–18005 %G eng %R 10.1073/pnas.1212303109 %0 Journal Article %J Marine Drugs %D 2011 %T Coccolithophores: Functional biodiversity, enzymes and bioprospecting %A Reid, Emma L %A Worthy, Charlotte A %A Probert, Ian %A Ali, Sohail T %A Love, John %A Napier, Johnathan %A Littlechild, Jenny A %A Somerfield, Paul J %A Allen, Michael J %K 2011 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %B Marine Drugs %V 9 %P 586–602 %G eng %U http://www.mdpi.com/1660-3397/9/4/586/ %R 10.3390/md9040586 %0 Journal Article %J Marine Ecology Progress Series %D 2011 %T Relationships between pigment ratios and growth irradiance in 11 marine phytoplankton species %A Laviale, M %A Neveux, J %K cultures %K hplc %K irradiance %K of the publisher %K permitted without written consent %K phytoplankton %K pigment ratios %K rcc %K RCC?o?dd %K regression analysis %B Marine Ecology Progress Series %V 425 %P 63–77 %8 mar %G eng %U http://www.int-res.com/abstracts/meps/v425/p63-77/ %R 10.3354/meps09013 %0 Journal Article %J Journal of Nannoplankton Research %D 2010 %T A guide to extant coccolithophores (Calcihaptophycidae, Haptophyta) using light microscopy. %A Frada, Miguel %A Young, Jeremy %A Cachão, Mário %A Lino, Sílvia %A Martins, Ana %A Narciso, Áurea %A Probert, Ian %A de Vargas, Colomban %K 2010 %K ? No DOI found %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %B Journal of Nannoplankton Research %V 31 %P 58–112 %G eng %0 Journal Article %J Protist %D 2010 %T Pelagodinium gen. nov. and P. beii comb. nov., a dinoflagellate symbiont of planktonic foraminifera %A Siano, R %A Montresor, M %A Probert, I %A Not, F %A de Vargas, C %K 2010 %K ASSEMBLE %K rcc %K rcc1491 %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium béii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The presence of a single elongated apical vesicle (EAV) ornamented with a row of small knobs, absent in species of the genus Gymnodinium, calls into question the current taxonomic position of the symbiont. The presence of a type E extraplastidial eyespot, the arrangement of the amphiesmal vesicles in series and the absence of trichocysts confirm the affiliation with other symbiotic dinoflagellates and certain genetically related non-symbiotic genera, all belonging to the order Suessiales. The arrangement of the series of vesicles of the analyzed strain is unique within the Suessiales, and the ultrastructure of the pyrenoid is different from other symbiotic dinoflagellates. A large subunit (LSU) rDNA phylogenetic analysis confirmed that the analyzed pelagic symbiont clusters in an independent, well-supported clade within the Suessiales with other sequences of symbiotic dinoflagellates extracted from planktonic foraminifera. Hence a novel genus, Pelagodinium gen. nov., is erected for this pelagic, symbiotic dinoflagellate, and Gymnodinium béii is reclassified as Pelagodinium béii. %B Protist %V 161 %P 385–399 %G eng %R 10.1016/j.protis.2010.01.002 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2009 %T Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans %A Liu, H %A Probert, I %A Uitz, J %A Claustre, H %A Aris-Brossou, S %A Frada, M %A Not, F %A de Vargas, C %K 2009 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %B Proceedings of the National Academy of Sciences of the United States of America %V 106 %P 12803–12808 %G eng %R 10.1073/pnas.0905841106 %0 Journal Article %J Science %D 2009 %T Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas %A Worden, A Z %A Lee, J.- H %A Mock, T %A Rouzé, P %A Simmons, M P %A Aerts, A L %A Allen, A E %A Cuvelier, M L %A Derelle, E %A Everett, M V %A Foulon, E %A Grimwood, J %A Gundlach, H %A Henrissat, B %A Napoli, C %A McDonald, S M %A Parker, M S %A Rombauts, S %A Salamov, A %A Von Dassow, P %A Badger, J H %A Coutinho, P M %A Demir, E %A Dubchak, I %A Gentemann, C %A Eikrem, W %A Gready, J E %A John, U %A Lanier, W %A Lindquist, E A %A Lucas, S %A Mayer, K F X %A Moreau, H %A Not, F %A Otillar, R %A Panaud, O %A Pangilinan, J %A Paulsen, I %A Piegu, B %A Poliakov, A %A Robbens, S %A Schmutz, J %A Toulza, E %A Wyss, T %A Zelensky, A %A Zhou, K %A Armbrust, E V %A Bhattacharya, D %A Goodenough, U W %A Van de Peer, Y %A Grigoriev, I V %K rcc %K RCC299 %K RCC827 %K SBR$_\textrmP$hyto$_\textrmD$PO %K SBR$_\textrmP$hyto$_\textrmE$PPO %X The photosynthetic picoeukaryote Micromonas thrives from tropical to polar marine ecosystems and belongs to an anciently diverged sister clade to land plants. We sequenced genomes from two Micromonas isolates (22 Mb, CCMP1545; 21 Mb, RCC299) and the results improve understanding of their ecology and green-lineage evolution. Despite high 18S rDNA sequence identity, only 90% of their predicted genes were shared. Novel intronic repeat elements in CCMP1545, otherwise found only in metagenomic data, and unique riboswitch arrangements emphasized their independent evolutionary paths. Phylogenomic profiles revealed putative ancestral features, but also indicated selection/acquisition processes are actively shaping a ‘unique' gene pool in each differently than ‘core' genes. Current climate-change trajectories are predicted to produce conditions favoring picophytoplankton, making Micromonas potential indicators of biological change in ocean ecosystems. %B Science %V 324 %P 268–272 %G eng %R 10.1126/science.1167222 %0 Journal Article %J Nature %D 2009 %T Photosystem I gene cassettes are present in marine virus genomes %A Sharon, Itai %A Alperovitch, Ariella %A Rohwer, Forest %A Haynes, Matthew %A Glaser, Fabian %A Atamna-Ismaeel, Nof %A Pinter, Ron Y %A Partensky, Frédéric %A Koonin, Eugene V %A Wolf, Yuri I %A Nelson, Nathan %A Béjà, Oded %K RCC307 %K SBR$_\textrmP$hyto$_\textrmP$PM %B Nature %V 461 %P 258–262 %G eng %U http://dx.doi.org/10.1038/nature08284 http://www.nature.com/nature/journal/v461/n7261/suppinfo/nature08284_S1.html %R 10.1038/nature08284 %0 Journal Article %J Biogeosciences %D 2009 %T Strain-specific responses of Emiliania huxleyi to changing seawater carbonate chemistry %A Langer, G %A Nehrke, G %A Probert, I %A Ly, J %A Ziveri, P %K 2009 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %X Four strains of the coccolithophore E. huxleyi (RCC1212, RCC1216, RCC1238, RCC1256) were grown in dilute batch culture at four CO2 levels ranging from similar to 200 mu atm to similar to 1200 mu atm. Growth rate, particulate organic carbon content, and particulate inorganic carbon content were measured, and organic and inorganic carbon production calculated. The four strains did not show a uniform response to carbonate chemistry changes in any of the analysed parameters and none of the four strains displayed a response pattern previously described for this species. We conclude that the sensitivity of different strains of E. huxleyi to acidification differs substantially and that this likely has a genetic basis. We propose that this can explain apparently contradictory results reported in the literature. %B Biogeosciences %V 6 %P 2637–2646 %G eng %R 10.5194/bg-6-2637-2009 %0 Journal Article %J Environmental Microbiology %D 2008 %T Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probes %A Foulon, E %A Not, F %A Jalabert, F %A Cariou, T %A Massana, R %A Simon, N %K 2008 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %B Environmental Microbiology %V 10 %P 2433–2443 %G eng %R 10.1111/j.1462-2920.2008.01673.x %0 Journal Article %J Journal of Plant Research %D 2008 %T Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana %A Misumi, O %A Yoshida, Y %A Nishida, K %A Fujiwara, T %A Sakajiri, T %A Hirooka, S %A Nishimura, Y %A Kuroiwa, T %K rcc %X 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. %B Journal of Plant Research %V 121 %P 3–17 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18074102 %0 Journal Article %J Journal of Biological Chemistry %D 2008 %T Permeation properties of a P2X receptor in the green algae Ostreococcus tauri %A Fountain, S J %A Cao, L S %A Young, M T %A North, R A %K CELLS %K CHANNELS %K EXTRACELLULAR ATP %K FAMILY %K FUNCTIONAL-CHARACTERIZATION %K PERMEABILITY %K PHARMACOLOGY %K rcc %X We have cloned a P2X receptor (OtP2X) from the green algae Ostreococcus tauri. The 42-kDa receptor shares similar to 28% identity with human P2X receptors and 23% with the Dictyostelium P2X receptor. ATP application evoked flickery single channel openings in outside-out membrane patches from human embryonic kidney 293 cells expressing OtP2X. Whole-cell recordings showed concentration-dependent cation currents reversing close to zero mV; ATP gave a half-maximal current at 250 mu m. alpha beta-Methylene-ATP evoked only small currents in comparison to ATP (EC50 ¿ 5 mM). 2',3'-O-(4-Benzoylbenzoyl)-ATP, beta gamma-imido-ATP, ADP, and several other nucleotide triphosphates did not activate any current. The currents evoked by 300 mu m ATP were not inhibited by 100 mu m suramin, pyridoxal-phosphate-6-azophenyl-2',4'-disulfonic acid, 2',3'-O-(2,4,6-trinitrophenol)-ATP, or copper. Ion substitution experiments indicated permeabilities relative to sodium with the rank order calcium ¿ choline ¿ Tris ¿ tetraethylammonium ¿ N-methyl-D-glucosamine. However, OtP2X had a low relative calcium permeability (P-Ca/P-Na = 0.4) in comparison with other P2X receptors. This was due at least in part to the presence of an asparagine residue (Asn(353)) at a position in the second transmembrane domain in place of the aspartate that is completely conserved in all other P2X receptor subunits, because replacement of Asn(353) with aspartate increased calcium permeability by similar to 50%. The results indicate that the ability of ATP to gate cation permeation across membranes exists in cells that diverged in evolutionary terms from animals about I billion years ago. %B Journal of Biological Chemistry %V 283 %P 15122–15126 %G eng %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2397467 %R 10.1074/jbc.M801512200 %0 Journal Article %J Nature %D 2008 %T The Phaeodactylum genome reveals the evolutionary history of diatom genomes %A Bowler, Chris %A Allen, Andrew E %A Badger, Jonathan H %A Grimwood, Jane %A Jabbari, Kamel %A Kuo, Alan %A Maheswari, Uma %A Martens, Cindy %A Maumus, Florian %A Otillar, Robert P %A Rayko, Edda %A Salamov, Asaf %A Vandepoele, Klaas %A Beszteri, Bank %A Gruber, Ansgar %A Heijde, Marc %A Katinka, Michael %A Mock, Thomas %A Valentin, Klaus %A Verret, Frederic %A Berges, John A %A Brownlee, Colin %A Cadoret, Jean-Paul %A Chiovitti, Anthony %A Choi, Chang Jae %A Coesel, Sacha %A De Martino, Alessandra %A Detter, J Chris %A Durkin, Colleen %A Falciatore, Angela %A Fournet, Jerome %A Haruta, Miyoshi %A Huysman, Marie J J %A Jenkins, Bethany D %A Jiroutova, Katerina %A Jorgensen, Richard E %A Joubert, Yolaine %A Kaplan, Aaron %A Kroger, Nils %A Kroth, Peter G %A La Roche, Julie %A Lindquist, Erica %A Lommer, Markus %A Martin-Jezequel, Veronique %A Lopez, Pascal J %A Lucas, Susan %A Mangogna, Manuela %A McGinnis, Karen %A Medlin, Linda K %A Montsant, Anton %A Secq, Marie-Pierre Oudot-Le %A Napoli, Carolyn %A Obornik, Miroslav %A Parker, Micaela Schnitzler %A Petit, Jean-Louis %A Porcel, Betina M %A Poulsen, Nicole %A Robison, Matthew %A Rychlewski, Leszek %A Rynearson, Tatiana A %A Schmutz, Jeremy %A Shapiro, Harris %A Siaut, Magali %A Stanley, Michele %A Sussman, Michael R %A Taylor, Alison R %A Vardi, Assaf %A von Dassow, Peter %A Vyverman, Wim %A Willis, Anusuya %A Wyrwicz, Lucjan S %A Rokhsar, Daniel S %A Weissenbach, Jean %A Armbrust, E Virginia %A Green, Beverley R %A Van de Peer, Yves %A Grigoriev, Igor V %K 2008 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPOdipo %K sbr?hyto?ppo %B Nature %V 456 %P 239–244 %G eng %U http://dx.doi.org/10.1038/nature07410 http://www.nature.com/nature/journal/v456/n7219/suppinfo/nature07410_S1.html %R 10.1038/nature07410 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2007 %T The tiny eukaryote \textit{Ostreococcus provides genomic insights into the paradox of plankton speciation %A Palenik, B %A Grimwood, J %A Aerts, A %A Rouzé, P %A Salamov, A %A Putnam, N %A Dupont, C %A Jorgensen, R %A Derelle, E %A Rombauts, S %A Zhou, K %A Otillar, R %A Merchant, S S %A Podell, S %A Gaasterland, T %A Napoli, C %A Gendler, K %A Manuell, A %A Tai, V %A Vallon, O %A Piganeau, G %A Jancek, S %A Heijde, M %A Jabbari, K %A Bowler, C %A Lohr, M %A Robbens, S %A Werner, G %A Dubchak, I %A Pazour, G J %A Ren, Q %A Paulsen, I %A Delwiche, C %A Schmutz, J %A Rokhsar, D %A Van de Peer, Y %A Moreau, H %A Grigoriev, I V %K rcc %X The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size. %B Proceedings of the National Academy of Sciences of the United States of America %V 104 %P 7705–7710 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17460045 %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2006 %T Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment %A Palenik, Brian %A Ren, Qinghu %A Dupont, Chris L %A Myers, Garry S %A Heidelberg, John F %A Badger, Jonathan H %A Madupu, Ramana %A Nelson, William C %A Brinkac, Lauren M %A Dodson, Robert J %A Durkin, A Scott %A Daugherty, Sean C %A Sullivan, Stephen A %A Khouri, Hoda %A Mohamoud, Yasmin %A Halpin, Rebecca %A Paulsen, Ian T %K rcc %X 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. %B Proceedings of the National Academy of Sciences of the United States of America %V 103 %P 13555–13559 %G eng %U http://www.pnas.org/cgi/content/abstract/103/36/13555 %R 10.1073/pnas.0602963103 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2006 %T Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment %A Palenik, Brian %A Ren, Qinghu %A Dupont, Chris L. %A Myers, Garry S. %A Heidelberg, John F. %A Badger, Jonathan H. %A Madupu, Ramana %A Nelson, William C. %A Brinkac, Lauren M. %A Dodson, Robert J. %A Durkin, A. Scott %A Daugherty, Sean C. %A Sullivan, Stephen A. %A Khouri, Hoda %A Mohamoud, Yasmin %A Halpin, Rebecca %A Paulsen, Ian T. %K cyanobacteria %K genomics %K Marine %K RCC1086 %X 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. %B Proceedings of the National Academy of Sciences %V 103 %P 13555–13559 %G eng %U https://www.pnas.org/content/103/36/13555 %R 10.1073/pnas.0602963103 %0 Journal Article %J FEMS Microbiology Ecology %D 2005 %T Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene %A Zhu, Fei %A Massana, Ramon %A Not, Fabrice %A Marie, Dominique %A Vaulot, Daniel %K Coastal ecosystems %K Ecology %K Fluorescent in situ hybridization %K Micromonas %K picoplankton %K prasinophytes %K Quantitative PCR %K rcc %X 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. %B FEMS Microbiology Ecology %V 52 %P 79–92 %G eng %0 Journal Article %J Applied and Environmental Microbiology %D 2003 %T Quantitative assessment of picoeucaryotes in the natural environment using taxon specific oligonucleotide probes in association with TSA-FISH (Tyramide Signal Amplification - Fluorescent In Situ Hybridization) and flow cytometry %A Biegala, I C %A Not, F %A Vaulot, D %A Simon, N %K 2003 %K PICODIV %K rcc %K SBR$_\textrmP$hyto %K sbr?hyto %K SOMLIT %B Applied and Environmental Microbiology %V 69 %P 5519–5529 %G eng %R 10.1128/AEM.69.9.5519-5529.2003 %0 Journal Article %D 2002 %T Application of fluorescent in situ hybridization coupled with tyramide signal amplification (FISH-TSA) to assess eukaryotic picoplankton composition %A Not, F %A Simon, N %A Biegala, IC %A Vaulot, D %K rcc %X Photosynthetic picoeukaryotes (phytoplankton cells with a diameter smaller than 2 to 3 ??m) contribute significantly to both biomass and primary production in the oligotrophic open ocean and coastal waters, at certain times of the year. The identification of these organisms is difficult because of their small size and simple morphology, therefore hindering detailed ecological studies of their distribution and role. In this paper, we demonstrate the use of oligonucleotide probes specific to algal classes or to lower order taxa in combination with fluorescent in situ hybridization and tyramide signal amplification (FISH-TSA) to determine eukaryotic picophytoplankton diversity. Target cells were detected and enumerated using epifluorescence microscopy. The sensitivity of the technique and the specificity of the probes were tested on pure and mixed picoplanktonic strains, as well as on natural samples from the English Channel. In these samples, the community was dominated by cells belonging to the division Chlorophyta. Haptophyta, Bolidophyceae and Pelagophyceae were also detected at low abundance. The FISH-TSA method is readily applicable to the study of picoplankton diversity in natural communities. %V 28 %P 157–166 %G eng %R 10.3354/ame028157 %0 Journal Article %J European Journal of Phycology %D 1996 %T High degree of genetic variation in Prochlorococcus (Prochlorophyta) revealed by RFLP analysis %A Scanlan, D J %A Hess, W R %A Partensky, F %A Newman, J %A Vaulot, D %K DIVINYL CHLOROPHYLL-A %K FAMILY %K Marine Synechococcus %K Mediterranean Sea %K Multiple Evolutionary Origins %K north-atlantic %K NUCLEOTIDE-SEQUENCE %K picoplankton %K Prokaryote %K rcc %K RCC SBR$_\textrmP$hyto %K UNICELLULAR CYANOBACTERIUM %B European Journal of Phycology %V 31 %P 1–9 %G eng %R 10.1080/09670269600651131 %0 Journal Article %J Phycologia %D 1995 %T A new marine picoeucaryote: Ostreococcus tauri gen. et sp. nov. (Chlorophyta, Prasinophyceae) %A Chrétiennot-Dinet, M.-J. %A Courties, C %A Vaquer, A %A Neveux, J %A Claustre, H %A Lautier, J %A Machado, M C %K FRESH-WATER ECOSYSTEMS %K morphology %K picoplankton %K pigments %K PROCHLOROCOCCUS-MARINUS %K Prokaryote %K rcc %K RCC745 %K Size %B Phycologia %V 34 %P 285–292 %G eng %R 10.2216/i0031-8884-34-4-285.1