%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 Microbiology Spectrum %D 2023 %T Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus %A Moreno-Cabezuelo, José Ángel %A Gómez-Baena, Guadalupe %A Díez, Jesús %A García-Fernández, José Manuel %E Hom, Erik F. Y. %K RCC156 %K RCC407 %K RCC515 %K rcc539 %K rcc752 %X

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

%B Microbiology Spectrum %P e03275–22 %8 feb %G eng %U https://journals.asm.org/doi/10.1128/spectrum.03275-22 %R 10.1128/spectrum.03275-22 %0 Generic %D 2023 %T Novel dimethylsulfoniopropionate biosynthesis enzymes in diverse marine bacteria, cyanobacteria and abundant algae %A Wang, Jinyan %A Zhou, Shun %A Curson, Andrew %A Vieira, Ana %A Walsham, Keanu %A Monaco, Serena %A Li, Chun-Yang %A Rivera, Peter Paolo %A Wang, Xiao-Di %A Hanwell, Libby %A Zhu, Xiao-Yu %A Leão, Pedro %A Lea-Smith, David J. %A Zhang, Yuzhong %A Zhang, Xiaohua %A Todd, Jonathan %K RCC100 %K RCC2956 %K RCC4094 %K RCC4422 %K RCC6172 %X Abstract Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound[1] with roles in stress protection[2, 3], chemotaxis[4], nutrient and sulfur cycling[5] and, potentially, climate regulation[6, 7]. Marine algae and bacteria are considered significant DMSP producers, but many diverse representatives lack known DMSP synthesis genes/enzymes[8, 9]. Here, new DMSP biosynthesis enzymes were identified that considerably increase the number and diversity of potential DMSP-producing organisms, inferring new and significant global DMSP producers. A novel bifunctional DMSP biosynthesis enzyme, DsyGD, identified in the rhizobacterium Gynuella sunshinyii, produces DMSP at levels higher than any other bacterium from methylthiohydroxybutyrate (MTHB) via an N-terminal MTHB S-methyltransferase domain (termed DsyG) and a C-terminal dimethylsulfoniohydroxybutyrate (DMSHB) decarboxylase domain (termed DsyD, which is the first reported enzyme with this activity). DsyGD is also found in some filamentous cyanobacteria, not previously known to produce DMSP. Regulation of DMSP production and dsyGD transcription was consistent with their role in osmoprotection. Indeed, cloned dsyGD conferred osmotolerance to bacteria deficient in osmolyte production, something not previously demonstrated for any known DMSP synthesis gene, and which could be exploited for biotechnology e.g., engineering salt tolerance. DsyGD characterisation led to identification of phylogenetically distinct DsyG-like proteins, termed DSYE, with MTHB S-methyltransferase activity, in diverse and environmentally abundant Chlorophyta, Chlorachniophyta, Ochraphyta, Haptophyta and Bacillariophyta algae. These algae comprise a mix of low, high and previously unknown DMSP producers[10]. Algae containing DSYE, particularly bloom-forming Pelagophyceae species, which we showed to accumulate medium-high intracellular DMSP levels, were globally more abundant DMSP producers than Haptophyta, Dinophyta and Bacillariophyta with DSYB and/or TpMMT. This highlights the potential importance of Pelagophyceae and other DSYE containing algae in global DMSP production and sulfur cycling. %I In Review %8 mar %G eng %U https://www.researchsquare.com/article/rs-2678769/v1 %9 preprint %R 10.21203/rs.3.rs-2678769/v1 %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 New Phytologist %D 2023 %T Stimulating and toxic effect of chromium on growth and photosynthesis of a marine chlorophyte %A Zhang, Qiong %A Charles, Philip D. %A Bendif, El Mahdi %A Hester, Svenja S. %A Mohammad, Shabaz %A Rickaby, Rosalind E. M. %K chromium %K Photosynthesis %K phytoplankton %K proteomics %K RCC1 %K RCC1242 %K trace metal %X Marine phytoplankton can interchange trace metals in various biochemical functions, particularly under metal-limiting conditions. Here, we investigate the stimulating and toxicity effect of chromium (Cr) on a marine Chlorophyceae Osetreococcus tauri under Fe-replete and Fe-deficient conditions. We determined the growth, photosynthesis, and proteome expressions of Osetreococcus tauri cultured under different Cr and Fe concentrations. In Fe-replete conditions, the presence of Cr(VI) stimulated significantly the growth rate and the maximum yield of photochemistry of photosystem II (Fv/Fm) of the phytoplankton, while the functional absorption cross-section of photosystem II (σPSII) did not change. Minor additions of Cr(VI) partially rescued phytoplankton growth under Fe-limited conditions. Proteomic analysis of this alga grown in Fe-replete normal and Fe-replete with Cr addition media (10 μM Cr) showed that the presence of Cr significantly decreased the expression of phosphate-transporting proteins and photosynthetic proteins, while increasing the expression of proteins related to carbon assimilation. Cr can stimulate the growth and photosynthesis of O. tauri, but the effects are dependent on both the Cr(VI) concentration and the availability of Fe. The proteomic results further suggest that Cr(VI) addition might significantly increase starch production and carbon fixation. %B New Phytologist %V n/a %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19376 %R 10.1111/nph.19376 %0 Journal Article %J Cell Reports Methods %D 2023 %T Tailoring confocal microscopy for real-time analysis of photosynthesis at single-cell resolution %A Storti, Mattia %A Hsine, Haythem %A Uwizeye, Clarisse %A Bastien, Olivier %A Yee, Daniel P. %A Chevalier, Fabien %A Decelle, Johan %A Giustini, Cécile %A Béal, Daniel %A Curien, Gilles %A Finazzi, Giovanni %A Tolleter, Dimitri %K rcc1383 %X Photoautotrophs’ environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single-cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells, or organs. Furthermore, cells within the same tissue may behave differently, being at different developmental/ physiological stages. Here, we describe an approach for single-cell and subcellular photophysiology based on the customization of confocal microscopy to assess chlorophyll fluorescence quenching by the saturation pulse method. We exploit this setup to (1) reassess the specialization of photosynthetic activities in developing tissues of non-vascular plants; (2) identify a specific subpopulation of phytoplankton cells in marine photosymbiosis, which consolidate energetic connections with their hosts; and (3) examine the link between light penetration and photoprotection responses inside the different tissues that constitute a plant leaf anatomy. %B Cell Reports Methods %P 100568 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S2667237523002126 %R 10.1016/j.crmeth.2023.100568 %0 Journal Article %J Current Biology %D 2023 %T The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis %A Yee, Daniel P. %A Samo, Ty J. %A Abbriano, Raffaela M. %A Shimasaki, Bethany %A Vernet, Maria %A Mayali, Xavier %A Weber, Peter K. %A Mitchell, B. Greg %A Hildebrand, Mark %A Decelle, Johan %A Tresguerres, Martin %K RCC3387 %X Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.1 These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.2 However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA),3 proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.4,5 We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates6–8 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications. %B Current Biology %P S0960982223006152 %8 may %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0960982223006152 %R 10.1016/j.cub.2023.05.020 %0 Journal Article %J Frontiers in Microbiology %D 2022 %T Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas %A Ferrieux, Mathilde %A Dufour, Louison %A Doré, Hugo %A Ratin, Morgane %A Guéneuguès, Audrey %A Chasselin, Léo %A Marie, Dominique %A Rigaut-jalabert, Fabienne %A Le Gall, Florence %A Sciandra, Théo %A Monier, Garance %A Hoebeke, Mark %A Corre, Erwan %A Xia, Xiaomin %A Liu, Hongbin %A Scanlan, David J. %A Partensky, Frédéric %A Garczarek, Laurence %K RCC2374 %K RCC2385 %K RCC2533 %K RCC2534 %K RCC2571 %K RCC515 %K rcc539 %K rcc791 %X Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters. %B Frontiers in Microbiology %V 13 %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2022.893413 %R 10.3389/fmicb.2022.893413 %0 Journal Article %J Genome Biology and Evolution %D 2022 %T Diversity and evolution of pigment types in marine \textit{Synechococcus cyanobacteria %A Grébert, Théophile %A Garczarek, Laurence %A Daubin, Vincent %A Humily, Florian %A Marie, Dominique %A Ratin, Morgane %A Devailly, Alban %A Farrant, Gregory K. %A Mary, Isabelle %A Mella-Flores, Daniella %A Tanguy, Gwenn %A Labadie, Karine %A Wincker, Patrick %A Kehoe, David M. %A Partensky, Frédéric %E Angert, Esther %K RCC307 %K to add %X DNA integration and site-specific recombination, suggesting that their genomic variability relies D in part on a ‘tycheposon’-like mechanism. Comparison of the phylogenies obtained for PBS and E core genes revealed that the evolutionary history of PBS rod genes differs from the core T genome and is characterized by the co-existence of different alleles and frequent allelic P exchange. We propose a scenario for the evolution of the different pigment types and highlight E the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in C different Synechococcus lineages despite multiple speciation events. %B Genome Biology and Evolution %P evac035 %G eng %U https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac035/6547267 %R 10.1093/gbe/evac035 %0 Journal Article %J Limnology and Oceanography %D 2022 %T Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes %A Ebenezer, Vinitha %A Hu, Yingyu %A Carnicer, Olga %A Irwin, Andrew J. %A Follows, Michael J. %A Finkel, Zoe V. %K RCC138 %K RCC3374 %K RCC3375 %X Chloropicophyceae (Prasinophyte Clade VII) are small nonmotile coccoid cells with cell diameters ranging from 1 to 3 μm. Molecular surveys indicate they are relatively high in abundance in moderately oligotrophic oceanic waters and may substantively contribute to biogeochemical cycling in the sea. Here, we quantify the elemental and macromolecular composition of three subtropical Chloropicophyceae strains: Chloropicon mariensis, Chloropicon maureeniae, and Chloropicon roscoffensis under nutrient-sufficient exponential growth and nitrate starvation. Under nutrient-sufficient conditions the Chloropicophyceae are high in C : N and quite low in C : P and N : P relative to the canonical Redfield ratio, reflecting their relatively high nucleic acid composition compared to many other phytoplankton taxa. Nitrate starvation causes increases in C : N and C : P and decreases in N : P, primarily due to increases in carbohydrate and lipid and decreases in protein and RNA. There is genetic evidence that unlike most other green algae, Chloropicophyceae are diploid. The high nucleic acid content in the Chloropicon is consistent with the hypothesis that the nucleus, as a nonscalable component, takes up a larger and substantial proportion of cell mass in diploid picoeukaryotes. The elemental and macromolecular composition of these Chloropicophyceae, and relatively homeostatic response to N-starvation compared to diatoms, provides some insight into their success in the moderately oligotrophic ocean. %B Limnology and Oceanography %V n/a %G eng %U http://onlinelibrary.wiley.com/doi/abs/10.1002/lno.12013 %R 10.1002/lno.12013 %0 Journal Article %J mSystems %D 2022 %T Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts %A Doré, Hugo %A Leconte, Jade %A Guyet, Ulysse %A Breton, Solène %A Farrant, Gregory K. %A Demory, David %A Ratin, Morgane %A Hoebeke, Mark %A Corre, Erwan %A Pitt, Frances D. %A Ostrowski, Martin %A Scanlan, David J. %A Partensky, Frédéric %A Six, Christophe %A Garczarek, Laurence %K RCC1086 %K RCC1695 %K RCC2369 %K rcc2380 %K RCC2553 %K RCC2556 %K RCC2570 %K rcc791 %X Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of “who is where” by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades. %B mSystems %P e00656–22 %G eng %U https://journals.asm.org/doi/full/10.1128/msystems.00656-22 %R 10.1128/msystems.00656-22 %0 Journal Article %J Organic Geochemistry %D 2022 %T Group 2i Isochrysidales flourishes at exceedingly low growth temperatures (0 to 6 °C) %A Liao, Sian %A Huang, Yongsong %K RCC5486 %B Organic Geochemistry %P 104512 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0146638022001462 %R 10.1016/j.orggeochem.2022.104512 %0 Journal Article %J Microbiology Spectrum %D 2022 %T Marine \textit{Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate %A Domínguez-Martín, Maria Agustina %A López-Lozano, Antonio %A Melero-Rubio, Yesica %A Gómez-Baena, Guadalupe %A Jiménez-Estrada, Juan Andrés %A Kukil, Kateryna %A Díez, Jesús %A García-Fernández, José Manuel %E Hom, Erik F. Y. %K rcc752 %X Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment. %B Microbiology Spectrum %V 10 %P e00187–22 %8 aug %G eng %U https://journals.asm.org/doi/10.1128/spectrum.00187-22 %R 10.1128/spectrum.00187-22 %0 Journal Article %J Harmful Algae %D 2022 %T Mixotrophy in the bloom-forming genus Phaeocystis and other haptophytes %A Koppelle, Sebastiaan %A López-Escardó, David %A Brussaard, Corina P.D. %A Huisman, Jef %A Philippart, Catharina J.M. %A Massana, Ramon %A Wilken, Susanne %K RCC1130 %K RCC1303 %K rcc1383 %K RCC1455 %K RCC1486 %K RCC1523 %K RCC1537 %K RCC918 %X Phaeocystis is a globally widespread marine phytoplankton genus, best known for its colony-forming species that can form large blooms and odorous foam during bloom decline. In the North Sea, Phaeocystis globosa typically becomes abundant towards the end of the spring bloom, when nutrients are depleted and the share of mixo­ trophic protists increases. Although mixotrophy is widespread across the eukaryotic tree of life and is also found amongst haptophytes, a mixotrophic nutrition has not yet been demonstrated in Phaeocystis. Here, we sampled two consecutive Phaeocystis globosa spring blooms in the coastal North Sea. In both years, bacterial cells were observed inside 0.6 – 2% of P. globosa cells using double CARD-FISH hybridizations in combination with laser scanning confocal microscopy. Incubation experiments manipulating light and nutrient availability showed a trend towards higher occurrence of intracellular bacteria under P-deplete conditions. Based on counts of bacteria inside P. globosa cells in combination with theoretical values of prey digestion times, maximum ingestion rates of up to 0.08 bacteria cell− 1 h− 1 were estimated. In addition, a gene-based predictive model was applied to the transcriptome assemblies of seven Phaeocystis strains and 24 other haptophytes to assess their trophic mode. This model predicted a phago-mixotrophic feeding strategy in several (but not all) strains of P. globosa, P. antarctica and other haptophytes that were previously assumed to be autotrophic. The observation of bacterial cells inside P. globosa and the gene-based model predictions strongly suggest that the phago-mixotrophic feeding strategy is widespread among members of the Phaeocystis genus and other haptophytes, and might contribute to their remarkable success to form nuisance blooms under nutrient-limiting conditions. %B Harmful Algae %V 117 %P 102292 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S1568988322001202 %R 10.1016/j.hal.2022.102292 %0 Journal Article %J Journal of Phycology %D 2022 %T Molecular phylogeny of the spiny-surfaced species of the dinoflagellate Prorocentrum with the description of P. Thermophilum sp. nov. and P. criophilum sp. nov. (Prorocentrales, Dinophyceae) %A Gómez, Fernando %A Gourvil, Priscillia %A Li, Tangcheng %A Huang, Yulin %A Zhang, Huan %A Courcot, Lucie %A Artigas, Luis F. %A Soler Onís, Emilio %A Gutierrez-Rodriguez, Andres %A Lin, Senjie %K Dinophyta %K HABs %K harmful algae blooms %K molecular phylogenetics %K new species %K Prorocentraceae %K RCC6871 %K RCC6872 %K taxonomy %X Spiny-surfaced species of Prorocentrum forms harmful algal blooms, and its taxonomic identity is obscure due to the size and shape variability. Molecular phylogenies reveal two major clades: one for P. cordatum with sequences mainly retrieved as P. minimum, and other for P. shikokuense with sequences also retrieved as P. dentatum and P. donghaiense. Several closely related clades still need to be characterized. Here, we provide SSU- and LSU rRNA, and ITS gene sequences of the strain CCMP3122 isolated from Florida (initially named P. donghaiense) and strains Prorocentrum sp. RCC6871–2 from the Ross Sea, Antarctica. We describe Prorocentrum thermophilum sp. nov. based on the strain CCMP3122, a species also distributed in the open waters of Gulf of Mexico, New Zealand and the Arabian Gulf; and Prorocentrum criophilum sp. nov. based on the strain RCC6872, which is distributed in the Antarctic Ocean and the Arctic Sea. Prorocentrum thermophilum is roundish ( 14 μm long, 12 μm wide), with an inconspicuous anterior spine-like prolongation under light microscopy, valves with tiny, short knobs (5–7 per μm2), and several (<7) large trichocyst pores ( 0.3 μm) in the right valve, as well as smaller pores ( 0.15 μm). Prorocentrum criophilum is round in valve view ( 11 μm long, 10 μm wide) and asymmetrically roundish in lateral view, the periflagellar area was not discernible under light microscopy, valves with very tiny, short knobs (6–10 per μm2), and at least twelve large pores in the right valve. Other potentially undescribed species of spiny-surfaced Prorocentrum are discussed %B Journal of Phycology %V n/a %G eng %U http://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13298 %R 10.1111/jpy.13298 %0 Journal Article %J mBio %D 2022 %T Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation %A Haney, Allissa M. %A Sanfilippo, Joseph E. %A Garczarek, Laurence %A Partensky, Frédéric %A Kehoe, David M. %E Ruby, Edward %K rcc555 %X

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

%B mBio %V 13 %P e01511–22 %8 aug %G eng %U https://journals.asm.org/doi/10.1128/mbio.01511-22 %R 10.1128/mbio.01511-22 %0 Journal Article %J Molecular Phylogenetics and Evolution %D 2022 %T Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences %A Akita, Shingo %A Vieira, Christophe %A Hanyuda, Takeaki %A Rousseau, Florence %A Cruaud, Corinne %A Couloux, Arnaud %A Heesch, Svenja %A Cock, J. Mark %A Kawai, Hiroshi %K Ectocarpales %K genomics %K Heterokontophytes %K Phaeoexplorer %K Phaeophyceae %K RCC4962 %K RCC7086 %K RCC7088 %K RCC7090 %K RCC7092 %K RCC7094 %K RCC7096 %K RCC7098 %K RCC7101 %K RCC7104 %K RCC7107 %K RCC7108 %K RCC7109 %K RCC7112 %K RCC7115 %K RCC7116 %K RCC7117 %K RCC7120 %K RCC7123 %K RCC7124 %K RCC7125 %K RCC7127 %K RCC7129 %K RCC7131 %K RCC7134 %K RCC7137 %K RCC7138 %K RCC7139 %K stramenopiles %X In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling. %B Molecular Phylogenetics and Evolution %V 168 %P 107408 %8 mar %G eng %U https://www.sciencedirect.com/science/article/pii/S1055790322000215 %R 10.1016/j.ympev.2022.107408 %0 Journal Article %J Science of The Total Environment %D 2022 %T Trace metals exposure in three different coastal compartments show specific morphological and reproductive traits across generations in a sentinel copepod %A Das, Shagnika %A Souissi, Anissa %A Ouddane, Baghdad %A Hwang, Jiang-Shiou %A Souissi, Sami %K RCC1537 %X The effect of exposure from several compartments of the environment at the level of individuals were rarely investigated. This study reports the effect of contaminants from varied compartments like sediment resuspension, elutriation from resuspended sediment (extract) and seawater spiked trace metal mixtures (TM) on morphological and reproductive traits of the pelagic bioindicator copepod Eurytemora affinis. At the population level of E. affinis, lowest survival was observed in dissolved exposures (TM and extract) in the first generation (G1), showing some adaptation in the second generation (G2). An opposite trend for resuspended sediment showed higher sensitivity in survival at G2. At the individual level, prosome length and volume proved to be sensitive parameters for resuspended sediments, whereas clutch size and egg diameter were more sensitive to TM and extract. Although the generation of decontamination (G3, no exposure), showed a significant recovery at the population level (survival % along with clutch size) of E. affinis exposed to resuspended sediment, morphological characteristics like prosome length and volume showed no such recovery (lower than control, p <0.05). To the contrary, dissolved exposure showed no significant recovery from G1 to G3 on neither survival %, clutch size, egg diameter, prosome volume, but an increase of prosome length (p <0.05). Such tradeoffs in combatting the stress from varied sources of toxicity was observed in all exposures, from G1 to G3. The number of lipid droplets inside the body cavity of E. affinis showed a significant positive correlation with trace metal bioaccumulation (p <0.01) along with a negative correlation (p <0.05) with survival and clutch size in each treatment. This confirms the inability of copepods to utilize lipids under stressful conditions. Our study tenders certain morphological and reproductive markers that show specificity to different compartments of exposure, promising an advantage in risk assessment and fish feed studies. %B Science of The Total Environment %P 160378 %8 nov %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0048969722074800 %R 10.1016/j.scitotenv.2022.160378 %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 Geochemistry, Geophysics, Geosystems %D 2021 %T Carbon Isotope Fractionation in Noelaerhabdaceae Algae in Culture and a Critical Evaluation of the Alkenone Paleobarometer %A Phelps, Samuel R. %A Hennon, Gwenn M. M. %A Dyhrman, Sonya T. %A Hernández Limón, María D. %A Williamson, Olivia M. %A Polissar, Pratigya J. %K alkenone %K carbon dioxide %K carbon isotope %K coccolithophore %K irradiance %K paleobarometry %K rcc %K RCC1303 %X The carbon isotope fractionation in algal organic matter ($\varepsilon$p), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates $\varepsilon$p to changes in cellular carbon demand relative to diffusive CO2 supply, with larger $\varepsilon$p values occurring at lower carbon demand relative to supply (i.e., abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few million years, has not been studied closely. Here, we subject G. oceanica to various CO2 levels by increasing pCO2 in the culture headspace, as opposed to increasing dissolved inorganic carbon (DIC) and alkalinity concentrations at constant pH. We note no substantial change in physiology, but observe an increase in $\varepsilon$p as carbon demand relative to supply decreases, consistent with DIC manipulations. We compile existing Noelaerhabdaceae $\varepsilon$p data and show that the diffusive model poorly describes the data. A meta-analysis of individual treatments (unique combinations of lab, strain, and light conditions) shows that the slope of the $\varepsilon$p response depends on the light conditions and range of carbon demand relative to CO2 supply in the treatment, which is incompatible with the diffusive model. We model $\varepsilon$p as a multilinear function of key physiological and environmental variables and find that both photoperiod duration and light intensity are critical parameters, in addition to CO2 and cell size. While alkenone carbon isotope ratios indeed record CO2 information, irradiance and other factors are also necessary to properly describe alkenone $\varepsilon$p. %B Geochemistry, Geophysics, Geosystems %V 22 %P e2021GC009657 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1029/2021GC009657 %R 10.1029/2021GC009657 %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 Frontiers in Microbiology %D 2021 %T Disentangling the Effects of Ocean Carbonation and Acidification on Elemental Contents and Macromolecules of the Coccolithophore Emiliania huxleyi %A Xie, Emei %A Xu, Kui %A Li, Zhengke %A Li, Wei %A Yi, Xiangqi %A Li, Hongzhou %A Han, Yonghe %A Zhang, Hong %A Zhang, Yong %K rcc %K RCC1266 %X Elemental contents change with shifts in macromolecular composition of marine phytoplankton. Recent studies focus on the responses of elemental contents of coccolithophores, a major calcifying phytoplankton group, to changing carbonate chemistry, caused by the dissolution of anthropogenically derived CO2 into the surface ocean. However, the effects of changing carbonate chemistry on biomacromolecules, such as protein and carbohydrate of coccolithophores, are less documented. Here, we disentangled the effects of elevated dissolved inorganic carbon (DIC) concentration (900 to 4,930μmolkg-1) and reduced pH value (8.04 to 7.70) on physiological rates, elemental contents, and macromolecules of the coccolithophore Emiliania huxleyi. Compared to present DIC concentration and pH value, combinations of high DIC concentration and low pH value (ocean acidification) significantly increased pigments content, particulate organic carbon (POC), and carbohydrate content and had less impact on growth rate, maximal relative electron transport rate (rETRmax), particulate organic nitrogen (PON), and protein content. In high pH treatments, elevated DIC concentration significantly increased growth rate, pigments content, rETRmax, POC, particulate inorganic carbon (PIC), protein, and carbohydrate contents. In low pH treatments, the extents of the increase in growth rate, pigments and carbohydrate content were reduced. Compared to high pH value, under low DIC concentration, low pH value significantly increased POC and PON contents and showed less impact on protein and carbohydrate contents; however, under high DIC concentration, low pH value significantly reduced POC, PON, protein, and carbohydrate contents. These results showed that reduced pH counteracted the positive effects of elevated DIC concentration on growth rate, rETRmax, POC, PON, carbohydrate, and protein contents. Elevated DIC concentration and reduced pH acted synergistically to increase the contribution of carbohydrate–carbon to POC, and antagonistically to affect the contribution of protein–nitrogen to PON, which further shifted the carbon/nitrogen ratio of E. huxleyi. %B Frontiers in Microbiology %V 12 %P 3188 %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2021.737454 %R 10.3389/fmicb.2021.737454 %0 Journal Article %J Frontiers in Marine Science %D 2021 %T Effects of Epibiotic Diatoms on the Productivity of the Calanoid Copepod Acartia tonsa (Dana) in Intensive Aquaculture Systems %A Pan, Yen-Ju %A Wang, Wei-Lung %A Hwang, Jiang-Shiou %A Souissi, Sami %K rcc %K RCC350 %X We evaluated here the effects of the epibiotic diatom Tabularia sp. on the productivity of the calanoid copepod Acartia tonsa (Dana) for assessing their risk on copepod intensive aquaculture industry for the provision of live feed. In the first experiment, uninfested and intensively infested females were cultivated individually for the assessment of egg production. Intensively infested females appeared to have a significantly lower egg production (5.0–9.0 eggs/female/d) than uninfested females (22.0–26.0 eggs/female/d) during 5 consecutive days. In the second experiment, effects of culture densities on diatom epibiosis were investigated in 9 L cultures at three different densities (200, 400, and 600 ind. L–1). Another culture at higher volume (250 L) and lowest density (200 ind. L–1) was also carried out to test the effect of culture volume on diatom epibiosis. The infestation rate (%), infestation intensity (ratio of surface diatom coverage levels, classified as levels 0–3) and daily egg harvest rate (number of harvested eggs per day per liter) were evaluated among the four culture populations. The copepods had higher infestation rate (53.69–60.14%) and intensity rate (high ratios at level 2 and 3) when the densities were increased from 200 ind./L to 400 and 600 ind./L. Although egg harvest increased with increasing culture density, it seemed that the diatom-infested A. tonsa population reach a saturated egg production when the density was higher than 400 ind./L. Nevertheless, the differences of culture volumes (250 and 9 L) appeared to be not to have any effect when the copepods were cultivated at the same density (200 ind./L). This study reveals for the first time that the epibiosis of the diatom Tabularia sp. reduces the individual egg production, and egg harvest rate in high-density culture of the copepod A. tonsa. Our findings implicate that diatom epibiosis should be avoid in copepod intensive culture systems. %B Frontiers in Marine Science %V 8 %P 1386 %G eng %U https://www.frontiersin.org/article/10.3389/fmars.2021.728779 %R 10.3389/fmars.2021.728779 %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 Limnology and Oceanography %D 2021 %T Growth-dependent changes in elemental stoichiometry and macromolecular allocation in the coccolithophore Emiliania huxleyi under different environmental conditions %A Zhang, Yong %A Li, Zhengke %A Schulz, Kai G. %A Hu, Yingyu %A Irwin, Andrew J. %A Finkel, Zoe V. %K rcc %K RCC1266 %X The growth rate hypothesis (GRH) posits an increase in ribosomal ribonucleic acid (RNA) content, and therefore cellular phosphorus (P), with increasing growth rate. There is evidence that the GRH may not apply to phytoplankton under all conditions. Here, we experimentally controlled four conditions (light, temperature, pH, and CO2) to alter the growth rate of Emiliania huxleyi, a biogeochemically important coccolithophorid, and monitored changes in RNA, protein, and carbohydrate content. We show that an increase in growth rate caused by increasing light, pH, and CO2 resulted in increased RNA per unit of organic carbon (RNA : POC), but that increasing temperature, leading to increase of growth rate, resulted in a decrease in RNA : POC. Protein per unit of organic carbon (protein : POC) increased in our increased temperature, pH, and CO2 treatments that increased growth rate, but there was little change in protein : POC in our light treatment despite it inducing the same increase in growth rate. Carbohydrate per unit of organic carbon (Carbohydrate : POC) increased with growth rate under increased light and CO2 but did not vary significantly in the temperature or pH treatments. These results indicate that physiological acclimation to specific environmental conditions can lead to contrasting patterns in RNA, protein, and carbohydrate composition and therefore contrasting changes in carbon : nitrogen : phosphorus ratios with growth rate in E. huxleyi. %B Limnology and Oceanography %V 66 %P 2999–3009 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1002/lno.11854 %R 10.1002/lno.11854 %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 Geochimica et Cosmochimica Acta %D 2021 %T An isotope label method for empirical detection of carbonic anhydrase in the calcification pathway of the coccolithophore Emiliania huxleyi %A Zhang, Hongrui %A Blanco-Ameijeiras, Sonia %A Hopkinson, Brian M. %A Bernasconi, Stefano M. %A Mejia, Luz Maria %A Liu, Chuanlian %A Stoll, Heather %K Carbonic anhjydrase %K ccm %K coccolithophore %K Isotopic labelling %K rcc %K rcc1258 %X Coccolithophores are a group of phytoplankton widely distributed in the ocean, which secrete extracellular calcite plates termed coccoliths. Coccoliths have been increasingly employed as an archive for geochemical, ecological and paleoclimate studies in recent years. A robust application of coccolith-based geochemical proxies relies on understanding the carbon acquisition strategies and the pathways of carbon supply for calcification. Carbonic anhydrase (CA) plays important roles in the carbon concentrating mechanism s of aquatic algae and potentially also in calcification. However, it is difficult to independently assess the role of CA in carbon supply for photosynthesis versus calcification. To fill this gap, we explored a new method to detect the CA activity inside coccolithophore. To achieve this, coccolithophores were cultured with oxygen and carbon isotope labeled dissolved inorganic carbon (DIC). By exploiting the different behavior of oxygen and carbon isotopes with (sea)water, this double label method can elucidate the significance of CA activity in the calcification pathway. Application of this method to Emiliania huxleyi shows that CA is present in the calcification pathway, and that there is no significant difference in the CA activity between a high and low CO2 treatment. However, under low CO2 treatment E. huxleyi enhanced the bicarbonate pumping rate on both cell and chloroplast membranes. This novel method could be performed on other species of coccolithophores in the future and have a potential to extend our knowledge on coccolith oxygen isotope vital effects. %B Geochimica et Cosmochimica Acta %V 292 %P 78–93 %G eng %U https://www.sciencedirect.com/science/article/pii/S0016703720305597 %R 10.1016/j.gca.2020.09.008 %0 Journal Article %J Current Biology %D 2021 %T The mode of speciation during a recent radiation in open-ocean phytoplankton %A Filatov, Dmitry A. %A Bendif, El Mahdi %A Archontikis, Odysseas A. %A Hagino, Kyoko %A Rickaby, Rosalind E. M. %K phytoplankton %K population genetic modeling %K rcc1212 %K rcc1238 %K RCC1239 %K RCC1253 %K RCC1281 %K RCC1296 %K RCC1310 %K RCC1314 %K RCC1562 %K RCC1836 %K RCC3370 %K RCC3711 %K RCC3733 %K RCC3862 %K RCC3898 %K RCC4002 %K RCC4028 %K RCC4030 %K RCC4032 %K RCC4033 %K RCC4034 %K RCC4035 %K RCC4036 %K RCC5119 %K RCC5134 %K RCC5137 %K RCC5141 %K RCC6566 %K RCC6730 %K secondary contact %K sequence polymorphism %K speciation %X Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton. %B Current Biology %8 oct %G eng %U https://www.sciencedirect.com/science/article/pii/S0960982221013415 %R 10.1016/j.cub.2021.09.073 %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 Scientific Reports %D 2021 %T A novel characteristic of a phytoplankton as a potential source of straight-chain alkanes %A Harada, Naomi %A Hirose, Yuu %A Chihong, Song %A Kurita, Hirofumi %A Sato, Miyako %A Onodera, Jonaotaro %A Murata, Kazuyoshi %A Itoh, Fumihiro %K RCC3437 %K RCC4217 %K RCC4577 %K RCC4578 %K RCC5635 %K RCC5639 %X Biosynthesis of hydrocarbons is a promising approach for the production of alternative sources of energy because of the emerging need to reduce global consumption of fossil fuels. However, the suitability of biogenic hydrocarbons as fuels is limited because their range of the number of carbon atoms is small, and/or they contain unsaturated carbon bonds. Here, we report that a marine phytoplankton, Dicrateria rotunda, collected from the western Arctic Ocean, can synthesize a series of saturated hydrocarbons (n-alkanes) from C10H22 to C38H78, which are categorized as petrol (C10–C15), diesel oils (C16–C20), and fuel oils (C21–C38). The observation that these n-alkanes were also produced by ten other cultivated strains of Dicrateria collected from the Atlantic and Pacific oceans suggests that this capability is a common characteristic of Dicrateria. We also identified that the total contents of the n-alkanes in the Arctic D. rotunda strain increased under dark and nitrogen-deficient conditions. The unique characteristic of D. rotunda could contribute to the development of a new approach for the biosynthesis of n-alkanes. %B Scientific Reports %V 11 %P 14190 %G eng %U http://www.nature.com/articles/s41598-021-93204-w %R 10.1038/s41598-021-93204-w %0 Journal Article %J New Phytologist %D 2021 %T Role of silicon in the development of complex crystal shapes in coccolithophores %A Langer, Gerald %A Taylor, Alison R. %A Walker, Charlotte E. %A Meyer, Erin M. %A Ben Joseph, Oz %A Gal, Assaf %A Harper, Glenn M. %A Probert, Ian %A Brownlee, Colin %A Wheeler, Glen L. %K biomineralization %K Calcification %K coccolith %K coccolithophore %K evolution %K rcc %K RCC1178 %K RCC1181 %K RCC1456 %K RCC1460 %K RCC1461 %K RCC1477 %K RCC1800 %K RCC1801 %K RCC3777 %K RCC6506 %K silicon %X The development of calcification by the coccolithophores had a profound impact on ocean carbon cycling, but the evolutionary steps leading to the formation of these complex biomineralized structures are not clear. Heterococcoliths consisting of intricately shaped calcite crystals are formed intracellularly by the diploid life cycle phase. Holococcoliths consisting of simple rhombic crystals can be produced by the haploid life cycle stage but are thought to be formed extracellularly, representing an independent evolutionary origin of calcification. We use advanced microscopy techniques to determine the nature of coccolith formation and complex crystal formation in coccolithophore life cycle stages. We find that holococcoliths are formed in intracellular compartments in a similar manner to heterococcoliths. However, we show that silicon is not required for holococcolith formation and that the requirement for silicon in certain coccolithophore species relates specifically to the process of crystal morphogenesis in heterococcoliths. We therefore propose an evolutionary scheme in which the lower complexity holococcoliths represent an ancestral form of calcification in coccolithophores. The subsequent recruitment of a silicon-dependent mechanism for crystal morphogenesis in the diploid life cycle stage led to the emergence of the intricately shaped heterococcoliths, enabling the formation of the elaborate coccospheres that underpin the ecological success of coccolithophores. %B New Phytologist %V 231 %P 1845–1857 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17230 %R 10.1111/nph.17230 %0 Journal Article %J PLOS ONE %D 2021 %T Strain-specific morphological response of the dominant calcifying phytoplankton species Emiliania huxleyi to salinity change %A Gebühr, Christina %A Sheward, Rosie M. %A Herrle, Jens O. %A Bollmann, Jörg %K Calcification %K Carbonates %K Ecophysiology %K Marine ecology %K Marine geology %K Morphometry %K Paleoclimatology %K rcc1210 %K RCC1232 %K rcc1824 %K rcc868 %K RCC904 %K salinity %X The future physiology of marine phytoplankton will be impacted by a range of changes in global ocean conditions, including salinity regimes that vary spatially and on a range of short- to geological timescales. Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. Previous research has shown that the morphology of their exoskeletal calcified plates (coccoliths) responds to changing salinity in the most abundant coccolithophore species, Emiliania huxleyi. However, the extent to which these responses may be strain-specific is not well established. Here we investigated the growth response of six strains of E. huxleyi under low (ca. 25) and high (ca. 45) salinity batch culture conditions and found substantial variability in the magnitude and direction of response to salinity change across strains. Growth rates declined under low and high salinity conditions in four of the six strains but increased under both low and high salinity in strain RCC1232 and were higher under low salinity and lower under high salinity in strain PLYB11. When detailed changes in coccolith and coccosphere size were quantified in two of these strains that were isolated from contrasting salinity regimes (coastal Norwegian low salinity of ca. 30 and Mediterranean high salinity of ca. 37), the Norwegian strain showed an average 26% larger mean coccolith size at high salinities compared to low salinities. In contrast, coccolith size in the Mediterranean strain showed a smaller size trend (11% increase) but severely impeded coccolith formation in the low salinity treatment. Coccosphere size similarly increased with salinity in the Norwegian strain but this trend was not observed in the Mediterranean strain. Coccolith size changes with salinity compiled for other strains also show variability, strongly suggesting that the effect of salinity change on coccolithophore morphology is likely to be strain specific. We propose that physiological adaptation to local conditions, in particular strategies for plasticity under stress, has an important role in determining ecotype responses to salinity. %B PLOS ONE %V 16 %P e0246745 %8 feb %G eng %U https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0246745 %R 10.1371/journal.pone.0246745 %0 Journal Article %J Frontiers in Microbiology %D 2021 %T Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain %A Labban, Abbrar %A Palacio, Antonio S. %A García, Francisca C. %A Hadaidi, Ghaida %A Ansari, Mohd I. %A López-Urrutia, Ángel %A Alonso-Sáez, Laura %A Hong, Pei-Ying %A Morán, Xosé Anxelu G. %K rcc %K RCC546 %X Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24–34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94–1.38 d–1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38–24.4 d–1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules. %B Frontiers in Microbiology %V 12 %P 612732 %G eng %U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141594/ %R 10.3389/fmicb.2021.612732 %0 Journal Article %J Ecology Letters %D 2020 %T Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment %A Bestion, Elvire %A Barton, Samuel %A García, Francisca C. %A Warfield, Ruth %A Yvon-Durocher, Gabriel %E Hillebrand, Helmut %K biodiversity %K biodiversity loss %K climate change %K ecosystem functioning %K phytoplankton %K RCC1303 %K rcc1512 %K RCC4221 %K RCC623 %K RCC626 %K RCC652 %K RCC80 %K RCC834 %K thermal per- %X Rising sea surface temperatures are expected to lead to the loss of phytoplankton biodiversity. However, we currently understand very little about the interactions between warming, loss of phytoplankton diversity and its impact on the oceans' primary production. We experimentally manipulated the species richness of marine phytoplankton communities under a range of warming scenarios, and found that ecosystem production declined more abruptly with species loss in communities exposed to higher temperatures. Species contributing positively to ecosystem production in the warmed treatments were those that had the highest optimal temperatures for photosynthesis, implying that the synergistic impacts of warming and biodiversity loss on ecosystem functioning were mediated by thermal trait variability. As species were lost from the communities, the probability of taxa remaining that could tolerate warming diminished, resulting in abrupt declines in ecosystem production. Our results highlight the potential for synergistic effects of warming and biodiversity loss on marine primary production. %B Ecology Letters %V 23 %P 457–466 %8 mar %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13444 %R 10.1111/ele.13444 %0 Journal Article %J Aquaculture Research %D 2020 %T Assessments of first feeding protocols on the larviculture of California grunion Leuresthes tenuis (Osteichthyes: Atherinopsidae) %A Pan, Yen Ju %A Déposé, Emilien %A Souissi, Anissa %A Hénard, Stéphane %A Schaadt, Mike %A Mastro, Ed %A Souissi, Sami %K California grunion %K Copepod %K larval rearing %K live feed %K quiescent egg %K RCC350 %B Aquaculture Research %V 51 %P 3054–3058 %8 jul %G eng %U https://onlinelibrary.wiley.com/doi/10.1111/are.14637 %R 10.1111/are.14637 %0 Journal Article %J Organic Geochemistry %D 2020 %T C41 methyl and C42 ethyl alkenones are biomarkers for Group II Isochrysidales %A Liao, Sian %A Yao, Yuan %A Wang, Li %A Wang, Karen J. %A Amaral-Zettler, Linda %A Longo, William M. %A Huang, Yongsong %K 18S rDNA %K Biomarkers %K C41 and C42 alkenones %K culture %K evolution %K Isochrysidales %K RCC1207 %K RCC1346 %K RCC3483 %X Alkenones are polyunsaturated long-chain methyl or ethyl ketones produced by species in the Isochrysidales, an order of haptophyte algae. Based on phylogenetic data, members of the Isochrysidales have been classified into three groups with each group showing significant differences in alkenone profiles and preferred growth environments. Common carbon chain lengths of alkenones range from 37 to 40. Extended C41 methyl (C41Me) and C42 ethyl (C42Et) alkenones have been reported in hypersaline lakes in China (Lake Alahake and Lake Balikun), Canada (Lake Snakehole) and marine sediments (e.g., \~95 Ma in Blake-Bahama Basin). It is unclear, however, if these extended alkenones are produced by one or more groups of Isochrysidales. Here, we systematically examined alkenones from cultures of Group II (Isochrysis nuda, Isochrysis litoralis, Ruttnera lamellosa, Isochrysis galbana and Tisochrysis lutea) and Group III (Emiliania huxleyi and Gephyrocapsa oceanica) Isochrysidales and environmental samples of Group I Isochysidales. C41Me and C42Et alkenones were found in all Group II species with Isochrysis nuda producing the highest percentages, but not in alkenones produced by Group I nor Group III Isochrysidales. Our results indicate that extended C41Me and C42Et alkenones are specific biomarkers for Group II Isochrysidales. We also report the first temperature calibrations of alkenones for Isochrysis nuda and Isochrysis litoralis using culture experiments, and find temperatures inferred from extended alkenones in Balikun and Alahake surface sediments match warm-season temperatures based on Isochrysis nuda calibrations, which is further corroborated by genomic data indicating the dominance of Isochrysis nuda Isochrysidales. %B Organic Geochemistry %V 147 %P 104081 %8 sep %G eng %R 10.1016/j.orggeochem.2020.104081 %0 Journal Article %J Science Advances %D 2020 %T Dimorphism in cryptophytes—The case of Teleaulax amphioxeia / Plagioselmis prolonga and its ecological implications %A Altenburger, A %A Blossom, H E %A Garcia-Cuetos, L. %A Jakobsen, H H %A Carstensen, J %A Lundholm, N. %A Hansen, P. J. %A Moestrup, Ø. %A Haraguchi, L. %K RCC5152 %X Growing evidence suggests that sexual reproduction might be common in unicellular organisms, but observations are sparse. Limited knowledge of sexual reproduction constrains understanding of protist ecology. Although Teleaulax amphioxeia and Plagioselmis prolonga are common marine cryptophytes worldwide, and are also important plastid donors for some kleptoplastic ciliates and dinoflagellates, the ecology and development of these protists are poorly known. We demonstrate that P. prolonga is the haploid form of the diploid T. amphioxeia and describe the seasonal dynamics of these two life stages. The diploid T. amphioxeia dominates during periods of high dissolved inorganic nitrogen (DIN) and low irradiance, temperature, and grazing (winter and early spring), whereas the haploid P. prolonga becomes more abundant during the summer, when DIN is low and irradiance, temperature, and grazing are high. Dimorphic sexual life cycles might explain the success of this species by fostering high genetic diversity and enabling endurance in adverse conditions. %B Science Advances %V 6 %P eabb1611 %8 sep %G eng %U https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.abb1611 %R 10.1126/sciadv.abb1611 %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 Scientific Data %D 2020 %T Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis %A Hackl, Thomas %A Martin, Roman %A Barenhoff, Karina %A Duponchel, Sarah %A Heider, Dominik %A Fischer, Matthias G. %K RCC4623 %K RCC4624 %K RCC4625 %K RCC970 %B Scientific Data %V 7 %P 29 %8 dec %G eng %U http://www.nature.com/articles/s41597-020-0363-4 %R 10.1038/s41597-020-0363-4 %0 Journal Article %J Journal of Phycology %D 2020 %T Influence of temperature and CO 2 on Plasma-membrane permeability to CO 2 and HCO 3 - in the marine haptophytes emiliania huxleyi and calcidiscus leptoporus (prymnesiophyceae) %A Blanco-Ameijeiras, Sonia %A Stoll, Heather M. %A Zhang, Hongrui %A Hopkinson, Brian M. %E Raven, J. %K carbon concentrating mechanism %K CO2 %K haptophyte %K membrane %K PERMEABILITY %K RCC1130 %K rcc1258 %X Membrane permeabilities to CO2 and HCO3- constrain the function of CO2 concentrating mechanisms that algae use to supply inorganic carbon for photosynthesis. In diatoms and green algae, plasma membranes are moderately to highly permeable to CO2 but effectively impermeable to HCO3-. Here, CO2 and HCO3- membrane permeabilities were measured using an 18O-exchange technique on two species of haptophyte algae, Emiliania huxleyi and Calcidiscus leptoporus, which showed that the plasma membranes of these species are also highly permeable to CO2 (0.006–0.02 cm ? s-1) but minimally permeable to HCO3-. Increased temperature and CO2 generally increased CO2 membrane permeabilities in both species, possibly due to changes in lipid composition or CO2 channel proteins. Changes in CO2 membrane permeabilities showed no association with the density of calcium carbonate coccoliths surrounding the cell, which could potentially impede passage of compounds. Haptophyte plasma-membrane permeabilities to CO2 were somewhat lower than those of diatoms but generally higher than membrane permeabilities of green algae. One caveat of these measurements is that the model used to interpret 18O-exchange data assumes that carbonic anhydrase, which catalyzes 18O-exchange, is homogeneously distributed in the cell. The implications of this assumption were tested using a two-compartment model with an inhomogeneous distribution of carbonic anhydrase to simulate 18O-exchange data and then inferring plasma-membrane CO2 permeabilities from the simulated data. This analysis showed that the inferred plasma-membrane CO2 permeabilities are minimal estimates but should be quite accurate under most conditions. %B Journal of Phycology %P jpy.13017 %8 jun %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13017 %R 10.1111/jpy.13017 %0 Journal Article %J bioRxiv %D 2020 %T A novel single-domain Na +-selective voltage-gated channel in photosynthetic eukaryotes %A Helliwell, Katherine E %A Chrachri, Abdul %A Koester, Julie %A Wharam, Susan %A Wheeler, Glen L %A Brownlee, Colin %K RCC1456 %X The evolution of Na+-selective four-domain voltage-gated channels (4D-Navs) in animals allowed rapid Na+-dependent electrical excitability, and enabled the development of sophisticated systems for rapid and long-range signalling. Whilst bacteria encode single-domain Na+-selective voltage-gated channels (BacNav), they typically exhibit much slower kinetics than 4D-Navs, and are not thought to have crossed the prokaryote-eukaryote boundary. As such, the capacity for rapid Na+-selective signalling is considered to be confined to certain animal taxa, and absent from photosynthetic eukaryotes. Certainly, in land plants, such as the Venus Flytrap where fast electrical excitability has been described, this is most likely based on fast anion channels. Here, we report a unique class of eukaryotic Na+-selective single-domain channels (EukCatBs) that are present primarily in haptophyte algae, including the ecologically important calcifying coccolithophores. The EukCatB channels exhibit very rapid voltage-dependent activation and inactivation kinetics, and sensitivity to the highly selective 4D-Nav blocker tetrodotoxin. The results demonstrate that the capacity for rapid Na+-based signalling in eukaryotes is not restricted to animals or to the presence of 4D-Navs. The EukCatB channels therefore represent an independent evolution of fast Na+-based electrical signalling in eukaryotes that likely contribute to sophisticated cellular control mechanisms operating on very short time scales in unicellular algae. One Sentence Summary The capacity for rapid Na+-based signalling has evolved in ecologically important coccolithophore species via a novel class of voltage-gated Na+ channels, EukCatBs. %B bioRxiv %P 2020.04.29.068528 %8 apr %G eng %U https://doi.org/10.1101/2020.04.29.068528 %R 10.1101/2020.04.29.068528 %0 Journal Article %J Biogeosciences %D 2020 %T Senescence as the main driver of iodide release from a diverse range of marine phytoplankton %A Hepach, Helmke %A Hughes, Claire %A Hogg, Karen %A Collings, Susannah %A Chance, Rosie %K RCC1164 %K rcc1210 %K RCC1318 %K RCC1725 %K RCC2366 %K RCC4024 %K RCC4208 %K RCC4512 %K RCC4560 %B Biogeosciences %V 17 %P 2453–2471 %8 may %G eng %U https://www.biogeosciences.net/17/2453/2020/ %R 10.5194/bg-17-2453-2020 %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 Marine Pollution Bulletin %D 2020 %T Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure %A Bretherton, Laura %A Hillhouse, Jessica %A Kamalanathan, Manoj %A Finkel, Zoe V. %A Irwin, Andrew J. %A Quigg, Antonietta %K Chemical dispersants %K Chlorophyll %K crude oil %K Photosynthesis %K phytoplankton %K RCC1614 %K Trait-based analysis %X The Deepwater Horizon oil spill released millions of barrels of crude oil into the Gulf of Mexico, and saw widespread use of the chemical dispersant Corexit. We assessed the role of traits, such as cell size, cell wall, motility, and mixotrophy on the growth and photosynthetic response of 15 phytoplankton taxa to oil and Corexit. We collected growth and photosynthetic data on five algal cultures. These responses could be separated into resistant (Tetraselmis astigmatica, Ochromonas sp., Heterocapsa pygmaea) and sensitive (Micromonas pusilla, Prorocentrum minimum). We combined this data with 10 species previously studied and found that cell size is most important in determining the biomass response to oil, whereas motility/mixotrophy is more important in the dispersed oil. Our analysis accounted for a third of the variance observed, so further work is needed to identify other factors that contribute to oil resistance. %B Marine Pollution Bulletin %V 153 %P 110906 %G eng %U https://doi.org/10.1016/j.marpolbul.2020.110906 %R 10.1016/j.marpolbul.2020.110906 %0 Journal Article %J ChemRxiv %D 2020 %T A tunable 3D printed microfluidic resistive pulse sensor for the characterisation of algae and microplastics %A Pollard, M. %A Hunsicker, E. %A Platt, M. %K RCC5374 %K RCC893 %X Technologies that can detect and characterise particulates in liquids have applications in health, food and environmental monitoring. Here we present a low-cost and high-throughput multiuse counter that classifies a particle's size, concentration, porosity and shape. Using an additive manufacturing process, we have assembled a reusable flow resistive pulse sensor. The device remains stable for several days with repeat measurements. We demonstrate its use for characterising algae with spherical and rod structures as well as microplastics shed from teabags. We present a methodology that results in a specific signal for microplastics, namely a conductive pulse, in contrast to particles with smooth surfaces such as calibration particles or algae, allowing the presence of microplastics to be easily confirmed and quantified. In addition, the shape of the signal and particle are correlated, giving an extra physical property to characterise suspended particulates. The technology can rapidly screen volumes of liquid, 1 mL/ min, for the presence of microplastics and algae. %B ChemRxiv %G eng %R 10.26434/chemrxiv.12249833.v1 %0 Journal Article %J Current Biology %D 2019 %T Alternative mechanisms for fast na + /ca 2+ signaling in eukaryotes via a novel class of single-domain voltage-gated channels %A Helliwell, Katherine E. %A Chrachri, Abdul %A Koester, Julie A. %A Wharam, Susan %A Verret, Frederic %A Taylor, Alison R. %A Wheeler, Glen L. %A Brownlee, Colin %K action potentials %K BacNa v %K calcium channel %K diatoms %K EukCats %K gliding motility %K ion selectivity %K RCC299 %K signaling %K single-domain channel %K voltage-gated channel %X Rapid Na + /Ca 2+ -based action potentials govern essential cellular functions in eukaryotes, from the motile responses of unicellular protists, such as Paramecium [1, 2], to complex animal neuromuscular activity [3]. A key innovation underpinning this fundamental signaling process has been the evolution of four-domain voltage-gated Na + /Ca 2+ channels (4D-Ca v s/Na v s). These channels are widely distributed across eukaryote diversity [4], albeit several eukaryotes, including land plants and fungi, have lost voltage-sensitive 4D-Ca v /Na v s [5–7]. Because these lineages appear to lack rapid Na + /Ca 2+ -based action potentials, 4D-Ca v /Na v s are generally considered necessary for fast Na + /Ca 2+ -based signaling [7]. However, the cellular mechanisms underpinning the membrane physiology of many eukaryotes remain unexamined. Eukaryotic phytoplankton critically influence our climate as major primary producers. Several taxa, including the globally abundant diatoms, exhibit membrane excitability [8–10]. We previously demonstrated that certain diatom genomes encode 4D-Ca v /Na v s [4] but also proteins of unknown function, resembling prokaryote single-domain, voltage-gated Na + channels (BacNa v s) [4]. Here, we show that single-domain channels are actually broadly distributed across major eukaryote phytoplankton lineages and represent three novel classes of single-domain channels, which we refer collectively to as EukCats. Functional characterization of diatom EukCatAs indicates that they are voltage-gated Na + - and Ca 2+ -permeable channels, with rapid kinetics resembling metazoan 4D-Ca v s/Na v s. In Phaeodactylum tricornutum, which lacks 4D-Ca v /Na v s, EukCatAs underpin voltage-activated Ca 2+ signaling important for membrane excitability, and mutants exhibit impaired motility. EukCatAs therefore provide alternative mechanisms for rapid Na + /Ca 2+ signaling in eukaryotes and may functionally replace 4D-Ca v s/Na v s in pennate diatoms. Marine phytoplankton thus possess unique signaling mechanisms that may be key to environmental sensing in the oceans. Diatoms exhibit fast animal-like action potentials, but many species lack 4D-Ca v /Na v channels that underpin membrane excitability in animals. Diatoms do encode novel 1D voltage-gated channels (EukCatAs). Helliwell, Chrachri et al. show that EukCatAs are fast Na + and Ca 2+ channels that provide alternative mechanisms for rapid signaling in eukaryotes. %B Current Biology %V 29 %P 1503–1511.e6 %G eng %R 10.1016/j.cub.2019.03.041 %0 Journal Article %J SN Applied Sciences %D 2019 %T The influence of bio-optical properties of Emiliania huxleyi and Tetraselmis sp. on biomass and lipid production when exposed to different light spectra and intensities of an adjustable LED array and standard light sources %A Granata, Tim %A Habermacher, Patrick %A Härri, Vinzenz %A Egli, Marcel %K Bio-optical properties %K Biomass and lipid production %K jel classification q42 %K mathematics subject classification 92c99 %K rcc1210 %K RCC2604 %K Spectral irradiance %B SN Applied Sciences %V 1 %P 524 %8 jun %G eng %U http://link.springer.com/10.1007/s42452-019-0529-x %R 10.1007/s42452-019-0529-x %0 Journal Article %J PLOS ONE %D 2019 %T Relationship between coccolith length and thickness in the coccolithophore species Emiliania huxleyi and Gephyrocapsa oceanica %A Linge Johnsen, Simen Alexander %A Bollmann, Jörg %A Gebuehr, Christina %A Herrle, Jens O. %E Keller, David Peter %K rcc1210 %K RCC1223 %K RCC1232 %K rcc1824 %K rcc1843 %K rcc868 %B PLOS ONE %V 14 %P e0220725 %8 aug %G eng %U http://dx.plos.org/10.1371/journal.pone.0220725 %R 10.1371/journal.pone.0220725 %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 Frontiers in Marine Science %D 2019 %T Transcriptome of thalassicolla nucleata holobiont reveals details of a radiolarian symbiotic relationship %A Liu, Zhenfeng %A Mesrop, Lisa Y. %A Hu, Sarah K. %A Caron, David A. %K Brandtodinium %K holobiont %K photosymbiosis %K radiolarian %K RCC3387 %K Transcriptome %B Frontiers in Marine Science %V 6 %P 1–11 %8 jun %G eng %U https://www.frontiersin.org/article/10.3389/fmars.2019.00284/full %R 10.3389/fmars.2019.00284 %0 Journal Article %J bioRxiv %D 2018 %T A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum %A Annunziata, Rossella %A Ritter, Andrés %A Fortunato, Antonio Emidio %A Cheminant-Navarro, Soizic %A Agier, Nicolas %A Huysman, Marie J. J. %A Winge, Per %A Bones, Atle %A Bouget, François-Yves %A Lagomarsino, Marco Cosentino %A Bouly, Jean Pierre %A Falciatore, Angela %K RCC2967 %X Periodic light dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular bases controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we here unveil the key function of a Phaeodactylum tricornutum bHLH-PAS protein, named Pt bHLH1a, in the regulation of light-dependent rhythms. Peak expression of Pt bHLH1a mRNA occurs at the end of the light period and it is adjusted to photoperiod changes. Ectopic over-expression of Pt bHLH1a results in lines with altered cell division and gene expression and showing a phase shift in diurnal responses, compared to the wild-type cells. Reduced oscillations in gene expression are also observed in continuous darkness, showing that the regulation of rhythmicity by Pt bHLH1a is not directly dependent on light inputs and cell division. Pt bHLH1a orthologs are widespread in both pennate and centric diatom genomes, hinting at a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but still underinvestigated branch of the tree of life. %B bioRxiv %P 271445 %G eng %U https://www.biorxiv.org/content/early/2018/02/25/271445 %R 10.1101/271445 %0 Journal Article %J Nature %D 2018 %T Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms %A McQuaid, Jeffrey B. %A Kustka, Adam B. %A Obornik, Miroslav %A Horak, Ales %A McCrow, John P. %A Karas, Bogumil J. %A Zheng, Hong %A Kindeberg, Theodor %A Andersson, Andreas J. %A Barbeau, Katherine A. %A Allen, Andrew E. %K RCC2967 %X Iron is an essential nutrient for photosynthetic plankton (phytoplankton), but owing to its low solubility in vast areas of the ocean the concentration of this metal is low, limiting the growth of the phytoplankton. Andrew Allen and co-workers show that the phytoplankton Phaeodactylum tricornutum has developed a specific iron acquisition mechanism that relies on activity of the ISIP2A protein. ISIP2A represents a functional analogue of transferrin—a metazoan protein that binds iron with high affinity—as both proteins use similar iron binding, internalization and release mechanisms, suggesting their independent and convergent evolution. Both proteins bind iron through a synergistic interaction of ferric iron and CO32-, and because ocean acidification decreases CO32- concentration it may also decrease phytoplankton iron uptake and growth. %B Nature %V 555 %P 534–537 %8 mar %G eng %U http://dx.doi.org/10.1038/nature25982 http://www.nature.com/doifinder/10.1038/nature25982 %R 10.1038/nature25982 %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 Environmental Science %D 2018 %T Ostreococcus tauri luminescent reporter lines as biosensors for detecting pollution from copper-mine tailing effluents in coastal environments %A Henríquez-Castillo, Carlos %A Botebol, Hugo %A Mouton, Adelaide %A Ramírez-Flandes, Salvador %A Lozano, Jean-Claude %A Lelandais, Gaelle %A Andrade, Santiago %A Trefault, Nicole %A de la Iglesia, Rodrigo %A Bouget, François-Yves %K biosensors %K CDKA %K copper pollution %K ferritin %K frontiers in environmental science %K frontiersin %K luciferase reporter %K mine tailings %K org %K Ostreococcus %K RCC745 %K www %B Frontiers in Environmental Science %V 6 %P 1–11 %8 may %G eng %U https://www.frontiersin.org/article/10.3389/fenvs.2018.00022/full %R 10.3389/fenvs.2018.00022 %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 New Phytologist %D 2018 %T The requirement for calcification differs between ecologically important coccolithophore species %A Walker, Charlotte E. %A Taylor, Alison R. %A Langer, Gerald %A Durak, Grażyna M. %A Heath, Sarah %A Probert, Ian %A Tyrrell, Toby %A Brownlee, Colin %A Wheeler, Glen L. %K Calcification %K coccolithophore %K Coccolithus braarudii %K Emiliania huxleyi %K phytoplankton %K rcc1731 %B New Phytologist %V in press %8 jun %G eng %U http://doi.wiley.com/10.1111/nph.15272 %R 10.1111/nph.15272 %0 Journal Article %J Frontiers in Microbiology %D 2017 %T Diverse CO2-Induced responses in physiology and gene expression among eukaryotic phytoplankton %A Hennon, Gwenn M. M. %A Hernández Limón, María D. %A Haley, Sheean T. %A Juhl, Andrew R. %A Dyhrman, Sonya T. %K algae %K biophysical CCM %K C4 CCM %K carbon concentrating mechanism %K carbon concentrating mechanism (CCM) %K ccm %K photorespiration %K RCC1303 %K transcriptomics %X With rising atmospheric CO2, phytoplankton face shifts in ocean chemistry including increased dissolved CO2 and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. Here we compared the physiological and gene expression responses of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (\~400 ppm) and elevated (\~800 ppm) CO2. Dinoflagellates had significantly slower growth rates and higher, yet variable, chlorophyll a per cell under elevated CO2. The other phytoplankton tended to have increased growth rates and/or decreased chlorophyll a per cell. Carbon and nitrogen partitioning of cells shifted under elevated CO2 in some species, indicating potential changes in energy fluxes due to changes in carbon concentrating mechanisms (CCM) or photorespiration. Consistent with these phenotypic changes, gene set enrichment analyses revealed shifts in energy, carbon and nitrogen metabolic pathways, though with limited overlap between species in the genes and pathways involved. Similarly, gene expression responses across species revealed few conserved CO2-responsive genes within CCM and photorespiration categories, and a survey of available transcriptomes found high diversity in biophysical CCM and photorespiration expressed gene complements between and within the four phyla represented by these species. The few genes that displayed similar responses to CO2 across phyla were from understudied gene families, making them targets for further research to uncover the mechanisms of phytoplankton acclimation to elevated CO2. These results underscore that eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO2 perturbations and highlight the value of cross-phyla comparisons for identifying gene families that respond to environmental change. %B Frontiers in Microbiology %V 8 %P 1–14 %8 dec %G eng %U http://journal.frontiersin.org/article/10.3389/fmicb.2017.02547/full %R 10.3389/fmicb.2017.02547 %0 Journal Article %J Plant Physiology %D 2017 %T Glycerolipid characterization and nutrient deprivation-associated changes in the green picoalga ostreococcus tauri %A Degraeve-Guilbault, Charlotte %A Bréhélin, Claire %A Haslam, Richard %A Sayanova, Olga %A Marie-Luce, Glawdys %A Jouhet, Juliette %A Corellou, Florence %K rcc3401 %K RCC4222 %K RCC745 %K RCC788 %K RCC789 %K RCC802 %K RCC809 %K RCC834 %X The picoalga Ostreococcus tauri is a minimal photosynthetic eukaryote that has been used as a model system. O. tauri is known to efficiently produce docosahexaenoic acid (DHA). We provide a comprehensive study of the glycerolipidome of O. tauri and validate this species as model for related picoeukaryotes. O. tauri lipids displayed unique features that combined traits from the green and the chromalveolate lineages. The betaine lipid diacylglyceryl-hydroxymethyl-trimethyl-β-alanine and phosphatidyldimethylpropanethiol, both hallmarks of chromalveolates, were identified as presumed extraplastidial lipids. DHA was confined to these lipids, while plastidial lipids of prokaryotic type were characterized by the overwhelming presence of ω-3 C18 polyunsaturated fatty acids (FAs), 18:5 being restricted to galactolipids. C16:4, an FA typical of green microalgae galactolipids, also was a major component of O. tauri extraplastidial lipids, while the 16:4-coenzyme A (CoA) species was not detected. Triacylglycerols (TAGs) displayed the complete panel of FAs, and many species exhibited combinations of FAs diagnostic for plastidial and extraplastidial lipids. Importantly, under nutrient deprivation, 16:4 and ω-3 C18 polyunsaturated FAs accumulated into de novo synthesized TAGs while DHA-TAG species remained rather stable, indicating an increased contribution of FAs of plastidial origin to TAG synthesis. Nutrient deprivation further severely down-regulated the conversion of 18:3 to 18:4, resulting in obvious inversion of the 18:3/18:4 ratio in plastidial lipids, TAGs, as well as acyl-CoAs. The fine-tuned and dynamic regulation of the 18:3/18:4 ratio suggested an important physiological role of these FAs in photosynthetic membranes. Acyl position in structural and storage lipids together with acyl-CoA analysis further help to determine mechanisms possibly involved in glycerolipid synthesis. %B Plant Physiology %V 173 %P 2060–2080 %G eng %U http://www.plantphysiol.org/lookup/doi/10.1104/pp.16.01467 %R 10.1104/pp.16.01467 %0 Journal Article %J Marine Ecology Progress Series %D 2017 %T Identity of the limiting nutrient (N vs. P) affects the competitive success of mixotrophs %A Fischer, R %A HA, Giebel %A Ptacnik, R %K RCC744 %X ABSTRACT: Empirical and theoretical evidence predicts that mixotrophic bacterivores dominate over specialized heterotrophic bacterivores and specialist photoautotrophs under conditions of high light and low loss rates. Here we extend this concept towards nutrient limitation and ask whether the identity of the limiting nutrient affects the competition of mixotrophs with their specialist competitors. Due to their photosynthetic machinery, mixotrophs should have higher cellular N contents than heterotrophs and, following this assumption, a higher demand for N. Conversely, heterotrophs, with their potential high growth rates compared to mixotrophs, may have a higher demand for P (?growth rate hypothesis?). Simplified, mixotrophs should be more prone to N-limitation, while heterotrophs should be more prone to P-limitation. We tested these predictions in artificial food webs studying the competitive success of mixotrophic bacterivores under a range of light intensities and loss rates and under either P- or N-limitation. Under low-light conditions, mixotrophs were more successful than heterotrophs under P-limitation, whereas the heterotrophs were more successful under N-limitation. At higher light intensity, mixotrophs had an advantage over photoautotrophs, due to the acquisition of nutrients ingested with prey. Overall, the effects of the limiting nutrient on the competitive success of mixotrophs were stronger under conditions already unfavorable for mixotrophs (low light). Further, our results suggest that communities dominated by mixotrophs might have low and relatively stable seston C:nutrient ratios. The results presented here supplement existing data well and help to define the ecological niche of mixotrophic protists. %B Marine Ecology Progress Series %V 563 %P 51–63 %G eng %U https://www.int-res.com/abstracts/meps/v563/p51-63 %R 10.3354/meps11968 %0 Journal Article %J Biogeosciences %D 2017 %T Impact of trace metal concentrations on coccolithophore growth and morphology: laboratory simulations of Cretaceous stress %A Faucher, Giulia %A Hoffmann, Linn %A Bach, Lennart T. %A Bottini, Cinzia %A Erba, Elisabetta %A Riebesell, Ulf %K RCC1198 %K RCC1216 %K RCC1303 %X

Abstract. The Cretaceous ocean witnessed intervals of profound perturbations such as volcanic input of large amounts of CO$_\textrm2$, anoxia, eutrophication and introduction of biologically relevant metals. Some of these extreme events were characterized by size reduction and/or morphological changes of a few calcareous nannofossil species. The correspondence between intervals of high trace metal concentrations and coccolith dwarfism suggests a negative effect of these elements on nannoplankton biocalcification processes in past oceans. In order to test this hypothesis, we explored the potential effect of a mixture of trace metals on growth and morphology of four living coccolithophore species, namely \textitEmiliania huxleyi, Gephyrocapsa oceanica, Pleurochrysis carterae and \textitCoccolithus pelagicus. The phylogenetic history of coccolithophores shows that the selected living species are linked to Mesozoic species showing dwarfism under excess metal concentrations. The trace metals tested were chosen to simulate the environmental stress identified in the geological record and upon known trace metal interactions with living coccolithophore algae.

Our laboratory experiments demonstrated that elevated trace metal concentrations, similarly to the fossil record, affect coccolithophore algae size and/or weight. Smaller coccoliths were detected in \textitE. huxleyi and \textitC. pelagicus, while coccoliths of \textitG. oceanica showed a decrease in size only at the highest trace metal concentrations. \textitP. carterae coccolith size was unresponsive to changing trace metal concentrations. These differences among species allow discriminating the most- (\textitP. carterae), intermediate- (\textitE. huxleyi and \textitG. oceanica) and least-tolerant (\textitC. pelagicus) taxa. The fossil record and the experimental results converge on a selective response of coccolithophores to metal availability.

These species-specific differences must be considered before morphological features of coccoliths are used to reconstruct paleo-chemical conditions.

%B Biogeosciences %V 14 %P 3603–3613 %8 jul %G eng %U https://bg.copernicus.org/articles/14/3603/2017/ %R 10.5194/bg-14-3603-2017 %0 Journal Article %J Oikos %D 2017 %T Importance of mixotrophic bacterivory can be predicted by light and loss rates %A Fischer, Robert %A Giebel, Helge-Ansgar %A Hillebrand, Helmut %A Ptacnik, Robert %K RCC744 %X Recent observational studies form oligotrophic waters provide ample evidence that mixotrophic flagellates often account for the bulk of bacterivory. However, we lack a general framework that allows a mechanistic understanding of success of mixotrophs in the competition with heterotrophic bacterivores. This is especially needed for integrating mixotrophy in models of the microbial loop. Based on general tradeoffs linked to the combined resource use in mixotrophs (generalist versus specialist), we propose a concept where mixotrophs are favored by conditions of high light ? low losses, corresponding to the situation found in the surface waters of oligotrophic oceans. Under such conditions, they can achieve positive net growth at very low resource levels, allowing simultaneous competition with specialized protists. Conversely, heterotrophic bacterivores and photoautotrophs should be especially favored in more productive and low-light conditions. We show experimentally that the combined effect of light and loss rates (dilution) predicts the success of mixotrophic bacterivorous flagellates. Moreover, our results suggest that total bacterivory, contrary as seen in the traditional microbial loop concept, has a more intricate coupling to light. %B Oikos %V 126 %P 713–722 %8 may %G eng %U https://doi.org/10.1111/oik.03539 %R 10.1111/oik.03539 %0 Journal Article %J Physiologia Plantarum %D 2017 %T Photoinhibition in marine picocyanobacteria %A Soitamo, Arto %A Havurinne, Vesa %A Tyystjärvi, Esa %K RCC156 %K RCC2366 %K rcc296 %K RCC407 %X Marine Synechococcus and Prochlorococcus cyanobacteria have different antenna compositions although they are genetically near to each other, and different strains thrive in very different illumination conditions. We measured growth and photoinhibition of PSII in two low-light and one high-light Prochlorococcus strains and in one Synechococcus strain. All strains were found to be able to shortly utilize moderate or even high light, but the low-light strains bleached rapidly in moderate light. Measurements of photoinhibition in the presence of the antibiotic lincomycin showed that a low-light Prochlorococcus strain was more sensitive than a high-light strain and both were more sensitive than the marine Synechococcus. The action spectrum of photoinhibition showed an increase from blue to ultraviolet wavelengths in all strains, suggesting contribution of manganese absorption to photoinhibition, but blue light caused less photoinhibition in marine cyanobacteria than expected on the basis of earlier results from plants and cyanobacteria. The visible-light part of the action spectrum resembled the absorption spectrum of the organism, suggesting that photosynthetic antenna pigments, especially divinyl chlorophylls, have a more important role as photoreceptors of visible-light photoinhibition in marine cyanobacteria than in other photoautotrophs. %B Physiologia Plantarum %V 161 %P 97–108 %8 sep %G eng %U https://doi.org/10.1111/ppl.12571 %R 10.1111/ppl.12571 %0 Journal Article %J Science Advances %D 2017 %T Population genomics of picophytoplankton unveils novel chromosome hypervariability %A Blanc-Mathieu, Romain %A Krasovec, Marc %A Hebrard, Maxime %A Yau, Sheree %A Desgranges, Elodie %A Martin, Joel %A Schackwitz, Wendy %A Kuo, Alan %A Salin, Gerald %A Donnadieu, Cecile %A Desdevises, Yves %A Sanchez-Ferandin, Sophie %A Moreau, Hervé %A Rivals, Eric %A Grigoriev, Igor V. %A Grimsley, Nigel %A Eyre-Walker, Adam %A Piganeau, Gwenael %K RCC1105 %K RCC1108 %K RCC1110 %K RCC1112 %K RCC1114 %K RCC1115 %K RCC1116 %K RCC1117 %K RCC1118 %K RCC1123 %K RCC1558 %K RCC1559 %K RCC1561 %K RCC299 %K RCC4221 %K RCC809 %B Science Advances %V 3 %P e1700239 %8 jul %G eng %U http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700239 %R 10.1126/sciadv.1700239 %0 Journal Article %J mSystems %D 2017 %T Quantitative proteomics shows extensive remodeling induced by nitrogen limitation in prochlorococcus marinus SS120 %A Domínguez-Martín, Maria Agustina %A Gómez-Baena, Guadalupe %A Díez, Jesús %A López-Grueso, Maria José %A Beynon, Robert J. %A García-Fernández, José Manuel %E Huber, Julie A. %K RCC156 %X Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation. In total, 1,072 proteins, corresponding to 57% of the theoretical proteome, were identified—the maximum proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007 proteins. Statistically significant changes ( P value of ¡0.05) were observed for 408 proteins, with the majority of proteins (92.4%) downregulated after 8 h of treatment. There was a strong decrease in ribosomal proteins upon azaserine addition, while many transporters were increased. The regulatory proteins P II and PipX were decreased, and the global nitrogen regulator NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of proteins involved in nitrogen uptake and assimilation. %B mSystems %V 2 %P e00008–17 %8 jun %G eng %U http://msystems.asm.org/lookup/doi/10.1128/mSystems.00008-17 %R 10.1128/mSystems.00008-17 %0 Journal Article %J Limnology and Oceanography: Methods %D 2017 %T Recommendations for obtaining unbiased chlorophyll estimates from in situ chlorophyll fluorometers: A global analysis of WET Labs ECO sensors %A Roesler, Collin %A Uitz, Julia %A Claustre, Hervé %A Boss, Emmanuel %A Xing, Xiaogang %A Organelli, Emanuele %A Briggs, Nathan %A Bricaud, Annick %A Schmechtig, Catherine %A Poteau, Antoine %A D'Ortenzio, Fabrizio %A Ras, Josephine %A Drapeau, Susan %A Haëntjens, Nils %A Barbieux, Marie %K RCC233 %K RCC42 %K RCC834 %X Chlorophyll fluorometers provide the largest in situ global data set for estimating phytoplankton biomass because of their ease of use, size, power consumption, and relatively low price. While in situ chlorophyll a (Chl) fluorescence is proxy for Chl a concentration, and hence phytoplankton biomass, there exist large natural variations in the relationship between in situ fluorescence and extracted Chl a concentration. Despite this large natural variability, we present here a global validation data set for the WET Labs Environmental Characterization Optics (ECO) series chlorophyll fluorometers that suggests a factor of 2 overestimation in the factory calibrated Chl a estimates for this specific manufacturer and series of sensors. We base these results on paired High Pressure Liquid Chromatography (HPLC) and in situ fluorescence match ups for which non-photochemically quenched fluorescence observations were removed. Additionally, we examined matchups between the factory-calibrated in situ fluorescence and estimates of chlorophyll concentration determined from in situ radiometry, absorption line height, NASA's standard ocean color algorithm as well as laboratory calibrations with phytoplankton monocultures spanning diverse species that support the factor of 2 bias. We therefore recommend the factor of 2 global bias correction be applied for the WET Labs ECO sensors, at the user level, to improve the global accuracy of chlorophyll concentration estimates and products derived from them. We recommend that other fluorometer makes and models should likewise undergo global analyses to identify potential bias in factory calibration. %B Limnology and Oceanography: Methods %V 15 %P 572–585 %G eng %R 10.1002/lom3.10185 %0 Journal Article %J Protist %D 2017 %T Revision of the genus micromonas manton et parke (chlorophyta, mamiellophyceae), of the type species m. pusilla (butcher) manton & parke and of the species m. commoda van baren, bachy and worden and description of two new species based on the genetic %A Simon, Nathalie %A Foulon, Elodie %A Grulois, Daphne %A Six, Christophe %A Desdevises, Yves %A Latimier, Marie %A Le Gall, Florence %A Tragin, Margot %A Houdan, Aude %A Derelle, Evelyne %A Jouenne, Fabien %A Marie, Dominique %A Le Panse, Sophie %A Vaulot, Daniel %A Marin, Birger %K 2017 %K ASSEMBLE %K rcc %K RCC1109 %K RCC114 %K RCC2306 %K RCC2308 %K RCC299 %K RCC372 %K RCC373 %K RCC418 %K RCC434 %K RCC447 %K RCC448 %K RCC449 %K RCC450 %K RCC451 %K RCC461 %K RCC465 %K RCC472 %K RCC497 %K RCC498 %K RCC570 %K RCC629 %K RCC647 %K RCC658 %K RCC676 %K RCC692 %K RCC746 %K RCC803 %K RCC804 %K RCC805 %K RCC806 %K RCC807 %K RCC808 %K RCC828 %K RCC829 %K RCC830 %K RCC831 %K RCC833 %K RCC834 %K RCC835 %K RCC836 %K SBR$_\textrmP$hyto$_\textrmD$IPO %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto$_\textrmd$ipo %B Protist %V 168 %P 612–635 %8 nov %G eng %U http://linkinghub.elsevier.com/retrieve/pii/S1434461017300780 %R 10.1016/j.protis.2017.09.002 %0 Journal Article %J Nature Communications %D 2016 %T Decrease in coccolithophore calcification and CO2 since the middle Miocene %A Bolton, Clara T. %A Hernández-Sánchez, María T. %A Fuertes, Miguel-Ángel %A González-Lemos, Saúl %A Abrevaya, Lorena %A Méndez-Vicente, Ana %A Flores, José-Abel %A Probert, Ian %A Giosan, Liviu %A Johnson, Joel %A Stoll, Heather M. %K 2016 %K rcc %X Marine algae are instrumental in carbon cycling and atmospheric carbon dioxide (CO2) regulation. One group, coccolithophores, uses carbon to photosynthesize and to calcify, covering their cells with chalk platelets (coccoliths). How ocean acidification influences coccolithophore calcification is strongly debated, and the effects of carbonate chemistry changes in the geological past are poorly understood. This paper relates degree of coccolith calcification to cellular calcification, and presents the first records of size-normalized coccolith thickness spanning the last 14 Myr from tropical oceans. Degree of calcification was highest in the low-pH, high-CO2 Miocene ocean, but decreased significantly between 6 and 4 Myr ago. Based on this and concurrent trends in a new alkenone ep record, we propose that decreasing CO2 partly drove the observed trend via reduced cellular bicarbonate allocation to calcification. This trend reversed in the late Pleistocene despite low CO2, suggesting an additional regulator of calcification such as alkalinity. 1 %B Nature Communications %V 7 %P 10284 %G eng %U http://www.nature.com/doifinder/10.1038/ncomms10284 %R 10.1038/ncomms10284 %0 Journal Article %J FEMS Microbiology Ecology %D 2016 %T Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France) %A Klouch, Khadidja Z %A Schmidt, Sabine %A Andrieux-Loyer, Françoise %A Le Gac, Mickaël %A Hervio-Heath, Dominique %A Qui-Minet, Zujaila N %A Quéré, Julien %A Bigeard, Estelle %A Guillou, Laure %A Siano, Raffaele %E Laanbroek, Riks %K 2016 %K rcc %K sbr?hyto$_\textrmd$ipo %X The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces of the species presence in the study area dated back to 1873 ± 6. Specific aDNA could be quantified by a newly-developed real-time PCR assay in the upper core layers, in which the germination of the species (in up to 17-19 year-old sediments) was also obtained. In both cores studied, our quantitative paleogenetic data showed a statistically significant increasing trend in the abundance of A. minutum ITS1 rDNA copies over time, corroborating three decades of local plankton data that have documented an increasing trend in the species cell abundance. By comparison, paleogenetic data of the dinoflagellate Scrippsiella donghaienis did not show a coherent trend between the cores studied, supporting the hypothesis of the existence of a species-specific dynamic of A. minutum in the study area. This work contributes to the development of paleoecological research, further showing its potential for biogeographical, ecological and evolutionary studies on marine microbes. %B FEMS Microbiology Ecology %V 92 %P fiw101 %8 jul %G eng %U http://www.ncbi.nlm.nih.gov/pubmed/27162179 https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw101 %R 10.1093/femsec/fiw101 %0 Journal Article %J Phycologia %D 2016 %T New insights into the morphology and phylogeny of Heterosigma akashiwo (Raphidophyceae), with the description of Heterosigma minor sp. nov . %A Engesmo, Anette %A Eikrem, Wenche %A Seoane, Sergio %A Smith, Kirsty %A Edvardsen, Bente %A Hofgaard, Antje %A Tomas, Carmelo R. %K 2016 %K rcc1501 %K rcc1502 %B Phycologia %V 55 %P 279–294 %8 may %G eng %U http://www.phycologia.org/doi/10.2216/15-115.1 %R 10.2216/15-115.1 %0 Journal Article %J PLOS Pathogens %D 2016 %T A viral immunity chromosome in the marine picoeukaryote, ostreococcus tauri %A Yau, Sheree %A Hemon, Claire %A Derelle, Evelyne %A Moreau, Hervé %A Piganeau, Gwenael %A Grimsley, Nigel %E Ding, Shou-Wei %K 2016 %K RCC299 %K RCC4221 %K RCC809 %B PLOS Pathogens %V 12 %P e1005965 %8 oct %G eng %U http://dx.plos.org/10.1371/journal.ppat.1005965 %R 10.1371/journal.ppat.1005965 %0 Journal Article %J Scientific Reports %D 2015 %T Eco-physiological adaptation shapes the response of calcifying algae to nutrient limitation %A Šupraha, Luka %A Gerecht, Andrea C. %A Probert, Ian %A Henderiks, Jorijntje %K 2015 %K RCC1323 %K RCC1334 %B Scientific Reports %V 5 %P 16499 %G eng %U http://www.nature.com/articles/srep16499 %R 10.1038/srep16499 %0 Journal Article %J The ISME Journal %D 2015 %T Effects of low temperature on tropical and temperate isolates of marine Synechococcus %A Varkey, Deepa %A Mazard, Sophie %A Ostrowski, Martin %A Tetu, Sasha G %A Haynes, Paul %A Paulsen, Ian T %K rcc %B The ISME Journal %P 1–12 %G eng %U http://www.nature.com/doifinder/10.1038/ismej.2015.179 %R 10.1038/ismej.2015.179 %0 Journal Article %J PloS one %D 2015 %T Guanchochroma wildpretii gen. et spec. nov. (ochrophyta) provides new insights into the diversification and evolution of the algal class synchromophyceae. %A Schmidt, Maria %A Horn, Susanne %A Ehlers, Katrin %A Wilhelm, Christian %A Schnetter, Reinhard %K rcc %X A new relative of the chrysophyte genus Chrysopodocystis was found in Tenerife and termed Guanchochroma wildpretii. This unicellular alga was most noticeably discernible from Chrysopodocystis socialis (the only species of this genus) by the presence of a cyst-like stage with a multilayered lorica, which also functions as a dispersal unit and shows secondary wall growth. Secondary expansion of loricae (cell casings not involved in cell division, usually with a more or less pronounced opening) has never been observed previously and marks a unique feature of the new taxon. Plastids are non-randomly distributed within cells of G. wildpretii. 18S rRNA gene analyses identified the two species as sister lineages and placed them in a monophyletic group with the Synchromophyceae, a heterokont algal (Ochrophyta) class characterized by the presence of chloroplast complexes. Yet, neither Chrysopodocystis nor Guanchochroma showed this feature in ultrastructure analyses. Additionally, their 18S rRNA genes possessed distinct inserts, the highest GC-content known for Ochrophyta and exceptionally long branches on the Ochrophyta 18S rDNA phylogenetic tree, suggesting substantially increased substitution rates along their branch compared to Synchromophyceae. Plastid marker data (rbcL) recovered a monophyletic clade of Chrysopodocystis, Guanchochroma and Synchromophyceae as well, yet with lower supports for internal split order due to limited resolution of the marker. Evidence for the sequence of events leading to the formation of the plastid complex of Synchromophyceae still remains ambiguous because of the apparently short timeframe in which they occurred. %B PloS one %V 10 %P e0131821 %8 jan %G eng %U http://dx.doi.org/10.1371/journal.pone.0131821 %R 10.1371/journal.pone.0131821 %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 Experimental Marine Biology and Ecology %D 2015 %T Phosphorus availability modifies carbon production in Coccolithus pelagicus (Haptophyta) %A Gerecht, A.C. %A Šupraha, L. %A Edvardsen, B. %A Langer, G. %A Henderiks, J. %K Calcification %K Carbon production %K Coccolithus pelagicus %K Phosphorus limitation %K RCC1200 %K Semi-continuous culture %X The coccolithophore Coccolithus pelagicus (Wallich) Schiller fixes CO¡inf¿2¡/inf¿ into particulate organic carbon (POC) through photosynthesis and into particulate inorganic carbon (PIC) in the form of calcite. To examine the role of phosphorus (P) availability in the production of POC and PIC, C. pelagicus subsp. braarudii (Gaarder) Geisen et al. was grown in semi-continuous cultures at three initial phosphate concentrations (P-replete, 1, and 0.5??M [P]). Reduced P-availability (1 and 0.5??M [P]) decreased POC production, while PIC production only decreased when phosphate concentrations became growth limiting (0.5??M [P]). This decrease has not been observed previously in batch cultures, highlighting the inadequacy of the batch culture approach with regard to determining carbon production. The reduction in growth rate by 50% at 0.5??M [P] was accompanied by a doubling in cell volume (and POC). PIC production was halved, resulting in a lowered PIC to POC ratio. The average number of coccoliths per cell (and PIC content) remained the same among treatments, despite the significant change in cell size. Our data suggest that POC production in C. pelagicus is more sensitive towards a moderate reduction in phosphorus availability than PIC production. Once phosphorus availability limits cell division, however, phosphorus resources are invested into POC rather than PIC production. This reduces cell density and sinking rates, indicating that coccoliths do not act as ballast for reaching deeper nutrient-rich layers under nutrient limitation. %B Journal of Experimental Marine Biology and Ecology %V 472 %P 24–31 %8 nov %G eng %U http://linkinghub.elsevier.com/retrieve/pii/S0022098115001756 %R 10.1016/j.jembe.2015.06.019 %0 Journal Article %J The ISME Journal %D 2014 %T Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria %A Bombar, Deniz %A Heller, Philip %A Sanchez-Baracaldo, Patricia %A Carter, Brandon J %A Zehr, Jonathan P %K rcc %B The ISME Journal %V 8 %P 2530–2542 %G eng %U http://www.nature.com/doifinder/10.1038/ismej.2014.167 %R 10.1038/ismej.2014.167 %0 Journal Article %J The ISME journal %D 2014 %T Connecting thermal physiology and latitudinal niche partitioning in marine Synechococcus %A Pittera, Justine %A Humily, Florian %A Thorel, Maxine %A Grulois, Daphne %A Garczarek, Laurence %A Six, Christophe %K 2014 %K adaptation %K ecotype %K MACUMBA %K marine cyanobacteria %K MicroB3 %K rcc %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto?app %K Synechococcus %K temperature %X Marine Synechococcus cyanobacteria constitute a monophyletic group that displays a wide latitudinal distribution, ranging from the equator to the polar fronts. Whether these organisms are all physiologically adapted to stand a large temperature gradient or stenotherms with narrow growth temperature ranges has so far remained unexplored. We submitted a panel of six strains, isolated along a gradient of latitude in the North Atlantic Ocean, to long- and short-term variations of temperature. Upon a downward shift of temperature, the strains showed strikingly distinct resistance, seemingly related to their latitude of isolation, with tropical strains collapsing while northern strains were capable of growing. This behaviour was associated to differential photosynthetic performances. In the tropical strains, the rapid photosystem II inactivation and the decrease of the antioxydant [beta]-carotene relative to chl a suggested a strong induction of oxidative stress. These different responses were related to the thermal preferenda of the strains. The northern strains could grow at 10[thinsp][deg]C while the other strains preferred higher temperatures. In addition, we pointed out a correspondence between strain isolation temperature and phylogeny. In particular, clades I and IV laboratory strains were all collected in the coldest waters of the distribution area of marine Synechococus. We, however, show that clade I Synechococcus exhibit different levels of adaptation, which apparently reflect their location on the latitudinal temperature gradient. This study reveals the existence of lineages of marine Synechococcus physiologically specialised in different thermal niches, therefore suggesting the existence of temperature ecotypes within the marine Synechococcus radiation. %B The ISME journal %V 8 %P 1221–1236 %G eng %U http://dx.doi.org/10.1038/ismej.2013.228 10.1038/ismej.2013.228 %R 10.1038/ismej.2013.228 %0 Journal Article %J Conservation Physiology %D 2014 %T Exposure to bloom-like concentrations of two marine Synechococcus cyanobacteria (strains CC9311 and CC9902) differentially alters fish behaviour %A Hamilton, T. J. %A Paz-Yepes, J. %A Morrison, R. A. %A Palenik, B. %A Tresguerres, M. %K RCC1086 %X Coastal California experiences large-scale blooms of Synechococcus cyanobacteria, which are predicted to become more prevalent by the end of the 21st century as a result of global climate change. This study investigated whether exposure to bloom-like concentrations of two Synechococcus strains, CC9311 and CC9902, alters fish behaviour. Black perch (Embiotoca jacksoni) were exposed to Synechococcus strain CC9311 or CC9902 (1.5 × 106 cells ml-1) or to control seawater in experimental aquaria for 3 days. Fish movement inside a testing arena was then recorded and analysed using video camera-based motion-tracking software. Compared with control fish, fish exposed to CC9311 demonstrated a significant preference for the dark zone of the tank in the light–dark test, which is an indication of increased anxiety. Furthermore, fish exposed to CC9311 also had a statistically significant decrease in velocity and increase in immobility and they meandered more in comparison to control fish. There was a similar trend in velocity, immobility and meandering in fish exposed to CC9902, but there were no significant differences in behaviour or locomotion between this group and control fish. Identical results were obtained with a second batch of fish. Additionally, in this second trial we also investigated whether fish would recover after a 3 day period in seawater without cyanobacteria. Indeed, there were no longer any significant differences in behaviour among treatments, demonstrating that the sp. CC9311-induced alteration of behaviour is reversible. These results demonstrate that blooms of specific marine Synechococcus strains can induce differential sublethal effects in fish, namely alterations light–dark preference behaviour and motility. %B Conservation Physiology %V 2 %G eng %U https://doi.org/10.1093/conphys/cou020 %R 10.1093/conphys/cou020 %0 Journal Article %J Journal of Phycology %D 2014 %T Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta) %A Bendif, El Mahdi %A Probert, Ian %A Carmichael, Margaux %A Romac, Sarah %A Hagino, Kyoko %A de Vargas, Colomban %K 2014 %K cc3549 %K rcc %K rcc1210 %K RCC1213 %K rcc1220 %K rcc1227 %K rcc1229 %K RCC1242 %K rcc1252 %K RCC1253 %K rcc1258 %K RCC1259 %K rcc1260 %K rcc1271 %K RCC1281 %K rcc1288 %K RCC1292 %K rcc1297 %K RCC1300 %K RCC1303 %K RCC1305 %K RCC1316 %K RCC1562 %K rcc174 %K RCC1839 %K rcc3545 %K rrcc1247 %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %B Journal of Phycology %V 50 %P 140–148 %G eng %R 10.1111/jpy.12147 %0 Journal Article %J Applied and Environmental Microbiology %D 2014 %T Unveiling of the diversity of prasinoviruses (phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-Amplified DNA polymerase and major capsid protein genes %A Clerissi, Camille %A Grimsley, Nigel %A Ogata, Hiroyuki %A Hingamp, Pascal %A Poulain, Julie %A Desdevises, Yves %K Micromonas %K rcc %K TARA-Oceans %X Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale. %B Applied and Environmental Microbiology %V 80 %P 3150–3160 %G eng %U http://aem.asm.org/content/80/10/3150.abstract %R 10.1128/aem.00123-14 %0 Journal Article %J Marine Drugs %D 2013 %T Bioprospecting marine plankton %A Abida, Heni %A Ruchaud, Sandrine %A Rios, Laurent %A Humeau, Anne %A Probert, Ian %A de Vargas, Colomban %A Bach, Stéphane %A Bowler, Chris %K 2013 %K MicroB3 %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B Marine Drugs %V 11 %P 4594–4611 %G eng %U http://www.mdpi.com/1660-3397/11/11/4594 %R 10.3390/md11114594 %0 Journal Article %J PLoS ONE %D 2013 %T A gene island with two possible configurations is involved in chromatic acclimation in marine synechococcus %A Humily, Florian %A Partensky, Frédéric %A Six, Christophe %A Farrant, Gregory K %A Ratin, Morgane %A Marie, Dominique %A Garczarek, Laurence %K 2013 %K MACUMBA %K MicroB3 %K rcc %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto?app %X ¡p¿¡italic¿Synechococcus¡/italic¿, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine ¡italic¿Synechococcus¡/italic¿ radiation. A specific gene island was identified in all CA4-performing strains, containing two genes (¡italic¿fciA¡/italic¿/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the ¡italic¿mpeZ¡/italic¿ gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called ¡italic¿fciC¡/italic¿. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While ¡italic¿mpeZ¡/italic¿ is expressed more in blue light than green light, this is the reverse for ¡italic¿mpeW¡/italic¿, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process.¡/p¿ %B PLoS ONE %V 8 %P e84459 %G eng %U http://dx.doi.org/10.1371/journal.pone.0084459 %R 10.1371/journal.pone.0084459 %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 Proceedings of the National Academy of Sciences of the United States of America %D 2013 %T Phycoerythrin-specific bilin lyase–isomerase controls blue-green chromatic acclimation in marine Synechococcus %A Shukla, A %A Biswas, A %A Blot, N %A Partensky, F %A Karty, J A %A Hammad, L A %A Garczarek, L %A Gutu, A %A Schluchter, W M %A Kehoe, D M %K 2013 %K rcc %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto?app %B Proceedings of the National Academy of Sciences of the United States of America %V 109 %P 20136–20141 %G eng %R 10.1073/pnas.1211777109 %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 Protist %D 2011 %T Integrative taxonomy of the pavlovophyceae (haptophyta) : a reassessment %A Bendif, E M %A Probert, I %A Hervé, A %A Billard, C %A Goux, D %A Lelong, C %A Cadoret, J P %A Véron, B %K 2011 %K ASSEMBLE %K rcc %K RCC1523 %K rcc1524 %K rcc1525 %K RCC1526 %K RCC1527 %K RCC1528 %K RCC1529 %K RCC1530 %K RCC1531 %K RCC1532 %K RCC1533 %K RCC1534 %K RCC1535 %K RCC1536 %K RCC1537 %K RCC1538 %K RCC1539 %K RCC1540 %K RCC1541 %K RCC1542 %K RCC1543 %K RCC1544 %K RCC1545 %K RCC1546 %K RCC1548 %K RCC1549 %K RCC1551 %K RCC1552 %K RCC1553 %K RCC1554 %K RCC1557 %K SBR$_\textrmP$hyto$_\textrmE$PPO %X The Pavlovophyceae (Haptophyta) contains four genera (Pavlova, Diacronema, Exanthemachrysis and Rebecca) and only thirteen characterised species. Considering the importance of members of this class, we constructed molecular phylogenies inferred from sequencing of ribosomal gene markers with comprehensive coverage of the described diversity and using type strains when available add on culture strains. Moreover, the morphology and ultrastructure of 12 of the described species was re-examined and the pigment signatures of many culture strains were determined. The molecular analysis revealed that sequences of all described species differed, although those of Pavlova gyrans and P. pinguis were nearly identical, these potentially forming a single cryptic species complex. Four well-delineated genetic clades were identified, one of which included species of both Pavlova andDiacronema. Unique combinations of morphological/ultrastructural characters were identified foreach of these clades. The ancestral pigment signature of the Pavlovophyceae consisted of a basic set of pigments plus MV chl cPAV, the latter being entirely absent in the Pavlova + Diacronema clade and supplemented by DV chl cPAV in part of the Exanthemachrysis clade. Based on this combination of characters, we propose a taxonomic revision of the class, with transfer of several Pavlova species to an emended Diacronema genus. The evolution of the class is discussed in the context of the phylogenetic reconstruction presented. %B Protist %V 162 %P 738–761 %G eng %R 10.1016/j.protis.2011.05.001 %0 Journal Article %J Journal of Phycology %D 2011 %T New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliana huxleyi (prymnesiophyceae) from the cox1b-ATP4 genes %A Hagino, K %A Bendif, El Mahdi %A Young, J %A Kogame, K %A Takano, Y %A Probert, I %A Horiguchi, T %A de Vargas, C %A Okada, H %K 2011 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophore occurring from tropical to subpolar waters and exhibiting variations in morphology of coccoliths possibly related to environmental conditions. We examined morphological characters of coccoliths and partial mitochondrial sequences of the cytochrome oxidase 1b (cox1b) through adenosine triphosphate synthase 4 (atp4) genes of thirty-nine clonal E. huxleyi strains from the Atlantic and Pacific Oceans, Mediterranean Sea and their adjacent seas. Based on the morphological study of culture strains by SEM, Type O, a new morphotype characterized by coccoliths with an open central area, was separated from existing morphotypes A, B, B/C, C, R and var. corona, characterized by coccoliths with central area elements. Molecular phylogenetic studies revealed that E. huxleyi consists of at least two mitochondrial sequence groups with different temperature preferences/tolerances: a cool water group occurring in subarctic North Atlantic and Pacific and a warm water group occurring in the sub-tropical Atlantic and Pacific and in the Mediterranean Sea. %B Journal of Phycology %V 47 %P 1164–1176 %G eng %R 10.1111/j.1529-8817.2011.01053.x %0 Journal Article %J Proceedings of the National Academy of Sciences of the United States of America %D 2011 %T Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics %A Gobler, C J %A Berry, D L %A Dyhrman, S T %A Wilhelm, S W %A Salamov, A %A Lobanov, A V %A Zhang, Y %A Collier, J L %A Wurch, L L %A Kustka, A B %A Dill, B D %A Shah, M %A VerBerkmoes, N C %A Kuo, A %A Terry, A %A Pangilinan, J %A Lindquist, E A %A Lucas, S %A Paulsen, I T %A Hattenrath-Lehmann, T K %A Talmage, S C %A Walker, E A %A Koch, F %A Burson, A M %A Marcoval, M A %A Tang, Y Z %A LeCleir, G R %A Coyne, K J %A Berg, G M %A Bertrand, E M %A Saito, M A %A Gladyshev, V N %A Grigoriev, I V %K brown-tide blooms %K comparative genomics %K eutrophication %K evolution %K genome %K genomics %K long-island %K marine-phytoplankton %K multidrug %K proteins %K proteome %K rcc %K repeat %K responses %K san-francisco bay %K signal-transduction %K transporters %X Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium-and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs. %B Proceedings of the National Academy of Sciences of the United States of America %V 108 %P 4352–4357 %G eng %R 10.1073/pnas.1016106108 %0 Journal Article %J The ISME journal %D 2010 %T A new chlorophyll d -containing cyanobacterium : evidence for niche adaptation in the genus Acaryochloris %A Mohr, Remus %A Schliep, Martin %A Kurz, Thorsten %A Maldener, Iris %A Adams, David G %A Larkum, Anthony D W %A Chen, Min %A Hess, Wolfgang R %K acaryochloris %K chlorophyll d %K coral reef %K cyanobacteria %K microbial diversity %K overview %K rcc %K RCC1983 %X Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (231 260 31.200 S, 1511 540 50.400 E). The 16S ribosomal RNA is 2% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371965nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms. The %B The ISME journal %P 1456–1469 %G eng %R 10.1038/ismej.2010.67 %0 Conference Paper %B Third international barcode of life conference %D 2009 %T DNA barcoding of protists in culture collections %A Meusnier, Isabelle %A Andersen, Robert A %A Stern, Rowena %A Bertrand, C %A Kuepper, Frithjof %A Brand, Jerry %A Friedl, Thomas %A Blackburn, Susan %A Dinh, Donna %A Acreman, Judy %A Sedláček, Ivo %A Přibyl, Pavel %A Jutson, Maria %A Phang, Siew Moi %A Melkonian, M %A Karpov, S %A Hajibabaei, Mehrdad %K ? No DOI found %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %B Third international barcode of life conference %C Mexico City %G eng %0 Journal Article %J Microbiology and Molecular Biology Reviews %D 2009 %T Ecological genomics of marine picocyanobacteria %A Scanlan, D J %A Ostrowski, M %A Mazard, S %A Dufresne, A %A Garczarek, L %A Hess, W R %A Post, A F %A Hagemann, M %A Paulsen, I %A Partensky, F %K 2009 %K rcc %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto?app %B Microbiology and Molecular Biology Reviews %V 73 %P 249–299 %G eng %R 10.1128/MMBR.00035-08 %0 Journal Article %J Tetrahedron: Asymmetry %D 2009 %T Enantiocomplementary inverting sec-alkylsulfatase activity in cyano- and thio-bacteria Synechococcus and Paracoccus spp.: selectivity enhancement by medium engineering %A Gadler, Petra %A Reiter, Tamara C %A Hoelsch, Kathrin %A Weuster-Botz, Dirk %A Fabe, Kurt %K rcc %B Tetrahedron: Asymmetry %V 20 %P 115–118 %G eng %R 10.1016/j.tetasy.2009.01.007 %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 Applied and Environmental Microbiology %D 2009 %T Light-dependent transcriptional regulation of genes of biogeochemical interest in the diploid and haploid life cycle stages of Emiliania huxleyi %A Richier, S %A Kerros, M E %A de Vargas, C %A Haramaty, L %A Falkowski, P G %A Gattuso, J P %K 2009 %K rcc %K SBR$_\textrmP$hyto$_\textrmE$PPO %K sbr?hyto?ppo %X The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore Emiliania huxleyi was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested. %B Applied and Environmental Microbiology %V 75 %P 3366–3369 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19304825 %R 10.1128/aem.02737-08 %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 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 New Phytologist %D 2008 %T New tools for labeling silica in living diatoms %A Descles, J %A Vartanian, M %A El Harrak, A %A Quinet, M %A Bremond, N %A Sapriel, G %A Bibette, J %A Lopez, P J %K 3D-imaging %K BACILLARIOPHYCEAE %K BIOLOGY %K biomineralization %K DEPOSITION %K diatoms %K exocytosis %K FLUORESCENT %K nanopattern %K pH %K phaeodactylum-tricornutum %K PLANTS %K rcc %K THALASSIOSIRA-PSEUDONANA %K ultrastructure %K VESICLE %X Silicon biomineralization is a widespread mechanism found in several kingdoms that concerns both unicellular and multicellular organisms. As a result of genomic and molecular tools, diatoms have emerged as a good model for biomineralization studies and have provided most of the current knowledge on this process. However, the number of techniques available to study its dynamics at the cellular level is still rather limited. Here, new probes were developed specifically to label the pre-existing or the newly synthesized silica frustule of several diatoms species. It is shown that the LysoTracker Yellow HCK-123, which can be used to visualize silica frustules with common filter sets, presents an enhanced signal-to-noise ratio and allows details of the frustules to be imaged without of the use of ionophores. It is also demonstrated that methoxysilane derivatives can be coupled to fluorescein-5-isothiocyanate (FITC) to preferentially label the silica components of living cells. The coupling of labeling procedures might help to address the challenging question of the process of frustule exocytosis. %B New Phytologist %V 177 %P 822–829 %G eng %R 10.1111/j.1469-8137.2007.02303.x %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 Diseases of Aquatic Organisms %D 2008 %T Phylogenetic and morphological characterization of the green algae infesting blue mussel Mytilus edulis in the North and South Atlantic %A Rodriguez, F %A Feist, S W %A Guillou, L %A Harkestad, L S %A Bateman, K %A Renault, T %A Mortensen, S %K rcc %K RCC894 %K SBR$_\textrmP$hyto$_\textrmD$PO %B Diseases of Aquatic Organisms %V 81 %P 231–240 %G eng %R 10.3354/dao01956 %0 Journal Article %J Genome Biology %D 2007 %T Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life %A Lobanov, A V %A Fomenko, D E %A Zhang, Y %A Sengupta, A %A Hatfield, D L %A Gladyshev, V N %K rcc %X BACKGROUND: Selenocysteine (Sec) is a selenium-containing amino acid that is co-translationally inserted into nascent polypeptides by recoding UGA codons. Selenoproteins occur in both eukaryotes and prokaryotes, but the selenoprotein content of organisms (selenoproteome) is highly variable and some organisms do not utilize Sec at all. RESULTS: We analyzed the selenoproteomes of several model eukaryotes and detected 26 and 29 selenoprotein genes in the green algae Ostreococcus tauri and Ostreococcus lucimarinus, respectively, five in the social amoebae Dictyostelium discoideum, three in the fly Drosophila pseudoobscura, and 16 in the diatom Thalassiosira pseudonana, including several new selenoproteins. Distinct selenoprotein patterns were verified by metabolic labeling of O. tauri and D. discoideum with 75Se. More than half of the selenoprotein families were shared by unicellular eukaryotes and mammals, consistent with their ancient origin. Further analyses identified massive, independent selenoprotein losses in land plants, fungi, nematodes, insects and some protists. Comparative analyses of selenoprotein-rich and -deficient organisms revealed that aquatic organisms generally have large selenoproteomes, whereas several groups of terrestrial organisms reduced their selenoproteomes through loss of selenoprotein genes and replacement of Sec with cysteine. CONCLUSION: Our data suggest many selenoproteins originated at the base of the eukaryotic domain and show that the environment plays an important role in selenoproteome evolution. In particular, aquatic organisms apparently retained and sometimes expanded their selenoproteomes, whereas the selenoproteomes of some terrestrial organisms were reduced or completely lost. These findings suggest a hypothesis that, with the exception of vertebrates, aquatic life supports selenium utilization, whereas terrestrial habitats lead to reduced use of this trace element due to an unknown environmental factor. %B Genome Biology %V 8 %P R198 %G eng %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17880704 %0 Journal Article %J PLoS genetics %D 2007 %T Patterns and implications of gene gain and loss in the evolution of Prochlorococcus %A Kettler, G %A Martiny, A C %A Huang, K %A Zucker, J %A Coleman, M L %A Rodrigue, S %A Chen, F %A Lapidus, A %A Ferriera, S %A Johnson, J %A Steglich, C %A Church, G %A Richardson, P %A Chisholm, S W %K rcc %B PLoS genetics %V 3 %P e231 %G eng %R 10.1371/journal.pgen.0030231 %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 Journal of Bacteriology %D 2006 %T Biochemical bases of Type IV chromatic adaptation in marine Synechococcus spp. %A Everroad, C %A Six, C %A Partensky, F %A Thomas, J C %A Holtzendorff, J %A Wood, A M %K 2006 %K rcc %K SBR$_\textrmP$hyto %K sbr?hyto?app %B Journal of Bacteriology %V 188 %P 3345–3356 %G eng %R 10.1128/JB.188.9.3345-3356.2006 %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 Limnology and Oceanography %D 2005 %T Diel variations in the photosynthetic parameters of Prochlorococcus strain PCC 9511: combined effects of light and cell cycle %A Bruyant, F %A Babin, M %A Genty, B %A Prasil, O %A Behrenfeld, M J %A Claustre, H %A Bricaud, A %A Holtzendorff, J %A Koblizek, M %A Garczareck, L %A Partensky, F %K 2005 %K rcc %K SBR$_\textrmP$hyto %K sbr?hyto %B Limnology and Oceanography %V 50 %P 850–863 %G eng %R 10.4319/lo.2005.50.3.0850 %0 Journal Article %J Phycologia %D 2004 %T Phylogenetic analysis of the Nannochloris-like' algae and diagnoses of Picochlorum oklahomensis gen. et sp nov (Trebouxiophyceae, Chlorophyta) %A Henley, W J %A Hironaka, J L %A Guillou, L %A Buchheim, M A %A Buchheim, J A %A Fawley, M W %A Fawley, K P %K 18s- %K 2004 %K Aquatic-sciences %K cell-wall %K chlorella- %K green-alga %K life-cycle %K marvania-geminata %K morphology- %K Nanochlorum-eucaryotum %K position- %K rcc %K SBR$_\textrmP$hyto$_\textrmD$PO %K sbr?hyto %K SEQUENCES %X A broadly halotolerant new isolate of a small asexual coccoid chlorophyte and six new, related freshwater isolates provided the impetus for a phylogenetic analysis of the so-called 'Nannochloris-like' algae within the Trebouxiophyceae. Previous taxonomic disagreements concerning this group had not been rigorously tested with molecular phylogenetic analyses. We show with 18S ribosomal DNA (rDNA) sequence phylogeny that 19 of 22 isolates previously assigned to either Nannochloris or Nanochlorum fall within a diverse sister clade to a clade including the four 'true' Chlorella species sensu loto. In addition, Marvania geminata, Gloeotila contorta, Chlorella sp. Yanaqocha RA1, Koliella spiculiformis, 'Chlorella minutissima' C-1.1.9. and new Koliella, Gloeotila and Marvania isolates were included in the Nannochloris-like clade. Distinct freshwater and marine or saline lineages comprise at least three major subclades, generally corresponding to cell division pattern. Seven of 14 marine or saline isolates are known (and the others presumed) to divide by autosporulation. Eight freshwater isolates divide by binary fission, including two Koliella, two Gloeotila, N. bacillaris, Chlorella sp. Yanaqocha RA1, and two new unassigned isolates. Four freshwater isolates divide by budding or autosporulation (three Marvania, including CCAP 251/1b. previously assigned to N. coccoides). The autosporic taxa N. eucaryotum UTEX 2502 (marine) and C. minutissima C-1.1.9 (freshwater), which have nearly identical 18S rDNA sequences, are deeper-branching than the freshwater and marine or saline lineages. We propose including the 13 marine or saline, autosporic taxa (excluding N. eucaryotum UTEX 2502) in the new genus Picochlorum until distinctive morphological or biochemical characters are identified that would indicate multiple genera corresponding to subclades. Such characters exist in the freshwater lineages, supporting retention of Koliella, Gloeotila, Marvania and Nannochloris as distinct genera, although each is currently represented by few isolates. Nannochloris at this time may be restricted to N. bacillaris and Chlorella sp. Yanaqocha RA1. We also describe halotolerant P. oklahomensis Hironaka sp. nov. Based on 18S rDNA sequence and lack of chlorophyll b, Nannochloris sp. UTEX 2379 should be reassigned to the Eustigmatophyceae. %B Phycologia %V 43 %P 641–652 %G eng %R 10.2216/i0031-8884-43-6-641.1 %0 Journal Article %J Nature %D 2003 %T The genome of a motile marine Synechococcus %A Palenik, B %A Brahamsha, B %A Larimer, F W %A Land, M %A Hauser, L %A Chain, P %A Lamerdin, J %A Regala, W %A Allen, E E %A McCarren, J %A Paulsen, I %A Dufresne, A %A Partensky, F %A Webb, E A %A Waterbury, J %K 2003 %K Cyanobacterium Synechococcus %K Degradation %K Ecology %K Gene %K IDENTIFICATION %K Polypeptide %K Prochlorococcus %K rcc %K SBR$_\textrmP$hyto %K sbr?hyto %K SEQUENCE %K Sp Pcc7942 %K Strains %X Marine unicellular cyanobacteria are responsible for an estimated 20-40% of chlorophyll biomass and carbon fixation in the oceans(1). Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria(2). %B Nature %V 424 %P 1037–1042 %G eng %R 10.1038/nature01943 %0 Journal Article %J Journal of Phycology %D 2003 %T A transient bloom of ¡i¿Ostreococcus¡/i¿ (chlorophyta, prasinophyceae) in west neck bay, long island, new york %A O'Kelly, C J %A Sieracki, M E %A Thier, E C %A Hobson, I C %K Aureococcus Anophagefferens Pelagophyceae %K bloom dynamics %K Gen %K Microalga %K Ostreococcus %K picoalgae %K picoplankton %K rcc %X The smallest known eukaryote, Ostreococcus tauri Courties et Chretiennot-Dinet, was first reported as the dominant picoplankter in a French lagoon known for its diverse phytoplankton community and high oyster productivity. Long-term seasonal blooms of this picoeukaryote were observed in association with stable plankton communities. On 5 June 2001, a distinctive monotypic picoplankton bloom was detected by flow cytometry as part of an ongoing study of "brown tide" (Aureococcus anophagefferens) bloom initiation in Long Island bays. The bloom reached a concentration of 5 x 10(5) cells.mL(-1) in West Neck Bay and lasted less than 2 weeks. Epifluorescence microscopy and TEM indicated that the bloom organism was an Ostreococcus-like picoalga, the first ever observed in a Long Island bay. Many cells of this alga contained numerous virus-like particles. The Ostreococcus-like picoalga, which resembles O. tauri, was rare in samples collected the following week. Instead, a substantial increase in the Synechococcus population was observed. Such rapid population changes have not previously been reported for Ostreococcus. Viral lysis and grazing by heterotrophic nanoflagellates may have contributed to the rapid decline of the Ostreococcus-like cells in West Neck Bay. %B Journal of Phycology %V 39 %P 850–854 %G eng %R 10.1046/j.1529-8817.2003.02201.x %0 Journal Article %J Microbiology %D 2002 %T Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-'Synechococcus' clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon %A Laloui, W %A Palinska, K A %A Rippka, R %A Partensky, F %A de Marsac, N T %A Herdman, M %A Iteman, I %K 2002 %K Blue Green Alga %K Chlorophyll B %K community structure %K cyanobacteria %K Escherichia Coli %K Marine Prokaryote %K Multiple Evolutionary Origins %K North Atlantic Ocean %K Pacific Ocean %K rcc %K Rna Operon %K SBR$_\textrmP$hyto %K sbr?hyto %X PCR amplicons of the Internal Transcribed Spacer (ITS) of the rrn operon of three axenic OMF (oceanic, marine and freshwater) strains of 'Synechococcus' (wH7803, PCC 7001 and PCC 6307, respectively) differ greatly in length from that of the axenic Prochlorococcus marinus subsp. pastoris PCC 9511(T), although these four cyanobacteria cluster relatively closely in phylogenetic trees inferred from 165 rRNA gene sequences. The ITSs of three strains (PCC 9511(T), PCC 6307 and PCC 7001) were sequenced and compared with those available for strains Prochlorococcus MED4 (CCMP 1378) and MIT9313 from genome sequencing projects. In spite of large differences in length, sequence and mean DNA base composition, conserved domains important for transcriptional antitermination and folding of the rRNA transcripts were identified in all ITSs. A new group-specific primer permitted ITS amplification even with non-axenic isolates of Prochlorococcus and one OMF-'Synechococcus' strain. Prochlorococcus isolates of the high-light-adapted clade (HL) differed from representatives of the low-light-adapted Glade (LL) by the length of their ITS. Restriction fragment length polymorphism (RFLP) of the ITS amplicons revealed three subclusters among the HL strains. Size, sequence data and RFLP of the ITS amplicons will therefore be valuable markers for the identification of different Prochlorococcus genotypes and for their discrimination from other cyanobacterial relatives with which they often co-exist in oceanic ecosystems. %B Microbiology %V 148 %P 453–465 %G eng %R 10.1099/00221287-148-2-453 %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 Plant Physiology %D 1993 %T Photoacclimation of Prochlorococcus sp. (Prochlorophyta) strains isolated from the North Atlantic and the Mediterranean Sea %A Partensky, F %A Hoepffner, N %A Li, W K W %A Ulloa, O %A Vaulot, D %K hplc %K Photosynthesis %K Pigment %K rcc %K RCC SBR$_\textrmP$hyto %K sbr?hyto %K \#PROCHLOROPHYTE %B Plant Physiology %V 101 %P 295–296 %G eng %R 10.1104/pp.101.1.285