@mastersthesis {mauro_influence_2024, title = {The influence of acclimation to density on organisms{\textquoteright} traits and population growth in \textit{Synechococcus sp. RS 9909}, year = {2024}, school = {Universit{\'e} catholique de Louvain}, type = {masters}, abstract = {In a constantly changing environment, it is essential to understand how different factors can affect the growth of populations, including its dependence on density, commonly referred to as density dependence. These factors can affect population growth directly, by inducing a higher mortality rate for example, but also indirectly by changing organisms{\textquoteright} traits, such as their size or their pigment content, enabling them to better cope with the changing environmental conditions in which they find themselves. This process, also known as acclimation, can have a strong influence on the density dependence of populations. It is therefore necessary, when studying population growth and density dependence, to take into account the initial conditions in which individuals have lived. Surprisingly, while many studies have looked at how acclimation to external conditions (light, temperature, pH) can affect density dependence, the impact of initial population density conditions on growth has never been studied. In this master{\textquoteright}s thesis, we studied how acclimation of a cyanobacterium of the genus Synechococcus to different population densities could impact organisms{\textquoteright} traits and population growth, including the density dependence. We found that populations acclimated to higher densities showed higher mean trait values for all but one trait, but less variability. Growth modelling showed the emergence of a non-linear density dependence from a certain initial acclimation density. In addition, comparison of these functions showed that populations acclimated to higher densities had higher growth rates and lower density dependence. This study is the first to show how initial population density conditions can affect individual characteristics and population growth, including density dependence, and demonstrates that it is important to take a more general interest in all the historical conditions experienced by populations in order to better predict their dynamics.}, keywords = {RCC2383, ⛔ No DOI found}, author = {Mauro, Nicola} } @booklet {krinos_intraspecific_2024, title = {Intraspecific diversity in thermal performance determines phytoplankton ecological niche}, year = {2024}, month = {feb}, publisher = {Ecology}, type = {preprint}, abstract = {Abstract Temperature has a primary influence on phytoplankton physiology and affects biodiversity and ecology. To examine how intraspecific diversity and temperature shape plankton populations, we grew 12 strains of the ecologically-important coccolithophore Gephyrocapsa huxleyi isolated from regions of different temperature for \~{}45 generations (2 months), each at 6-8 temperatures, and characterized the acclimated thermal response curve of each strain. Even with virtually identical temperature optima and overlapping cell size, strain growth rates varied between 0.45 and 1 day -1 . While some thermal curves were effectively symmetrical, others had more slowly declining growth rates above the {\textquotedblleft}thermal optimum,{\textquotedblright} and thermal niche widths varied between 16.7 and 24.8 {\textdegree}C. This suggests that different strains use distinct thermal response mechanisms. We investigated the ecological implications of such intraspecific diversity on thermal response using an ocean ecosystem simulation resolving distinct phytoplankton thermal phenotypes. Resolving model analogs of thermal {\textquotedblleft}generalists{\textquotedblright} and {\textquotedblleft}specialists{\textquotedblright} (similar to those observed in G. huxleyi) resulted in a distinctive global biogeography of preferred thermal niche widths with a nonlinear latitudinal pattern. We leveraged the model output to predict the ranges of the 12 strains we studied in the laboratory and demonstrated how this approach could refine predictions of phytoplankton thermal geographic range in situ . Our combination of observed thermal traits and modeled biogeography highlights the capacity of diverse groups to persist through temperature shifts. Significance Statement Intraspecific diversity in the phytoplankton may underpin their distribution. We show that within a single coccolithophore species, thermal response curves have diverse trait parameters. For example, many strains had a variable range of temperatures at which they could survive (thermal niche width). Adding this thermal niche width diversity to an ecosystem model simulation impacted phytoplankton coexistence and overall biomass. These observations show that thermal niche width is a gap in phytoplankton representation in ecosystem models that impacts modeled phytoplankton biogeography and concomitant carbon cycle dynamics. Including thermal tolerance is crucial to predictive modeling as ocean temperature dynamics change.}, keywords = {rcc1212, RCC3492, RCC3963, RCC4567, RCC6071, RCC874, RCC914}, doi = {10.1101/2024.02.14.580366}, url = {http://biorxiv.org/lookup/doi/10.1101/2024.02.14.580366}, author = {Krinos, Arianna I. and Shapiro, Sara K. and Li, Weixuan and Haley, Sheean T. and Dyhrman, Sonya T. and Dutkiewicz, Stephanie and Follows, Michael J. and Alexander, Harriet} } @article {harcourt_intraspecific_2024, title = {Intraspecific trait variation modulates the temperature effect on elemental quotas and stoichiometry in marine Synechococcus}, journal = {PLOS ONE}, volume = {19}, number = {3}, year = {2024}, note = {Publisher: Public Library of Science}, month = {mar}, pages = {e0292337}, abstract = {Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions, and we demonstrate contains extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in serially transferred cultures across a range of temperatures (16{\textendash}25{\textdegree}C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles.}, keywords = {Biogeochemistry, Cell enumeration techniques, Oceans, Particulates, Phylogenetics, phytoplankton, RCC1086, RCC2673, RCC515, Stoichiometry, Synechococcus}, issn = {1932-6203}, doi = {10.1371/journal.pone.0292337}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0292337}, author = {Harcourt, Renne and Garcia, Nathan S. and Martiny, Adam C.} } @booklet {devic_indel_2023, title = {An INDEL genomic approach to explore population diversity of phytoplankton : \textit{Bathycoccus , a case study}, year = {2023}, publisher = {Ecology}, type = {preprint}, abstract = {Abstract Although metabarcoding has generated large dataset on world-wide phytoplankton species diversity, little is known about the intraspecies diversity underlying adaptation to environmental niches. To gain insight into population diversity, a novel INDEL based method was developed on Bathycoccus prasinos . Oxford Nanopore Technology (ONT) sequencing was first used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December and January. When tested directly on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation and between years. This INDEL-based genotyping constitutes a new methodological approach that may be used to assess the population structure and diversity of other species.}, keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685}, doi = {10.1101/2023.02.09.527951}, url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951}, author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois} } @article {moreno-cabezuelo_integrated_2023, title = {Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus}, journal = {Microbiology Spectrum}, year = {2023}, month = {feb}, pages = {e03275{\textendash}22}, abstract = {

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

}, keywords = {RCC156, RCC407, RCC515, rcc539, rcc752}, issn = {2165-0497}, doi = {10.1128/spectrum.03275-22}, url = {https://journals.asm.org/doi/10.1128/spectrum.03275-22}, author = {Moreno-Cabezuelo, Jos{\'e} {\'A}ngel and G{\'o}mez-Baena, Guadalupe and D{\'\i}ez, Jes{\'u}s and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel}, editor = {Hom, Erik F. Y.} } @article {parsy_impact_2022, title = {Impact of salinities, metals and organic compounds found in saline oil \& gas produced water on microalgae and cyanobacteria}, journal = {Ecotoxicology and Environmental Safety}, volume = {234}, year = {2022}, pages = {113351}, abstract = {This work evaluates the impact of salinity and the toxicity of some metals and organic compounds commonly found in produced waters on the growth of model photosynthetic organisms. Five strains of marine microalgae and one cyanobacteria (i.e. Dunaliella salina, Nannochloropsis oceanica, Tetraselmis suecica, Picochlorum cos- tavermella, Coccomyxa simplex and Synechococcus rubescens) were tested in microplates as well as the freshwater Chlorella vulgaris selected as reference. Results revealed that D.salina was able to growth at high salinity (up to 135 g.L- 1). Copper was the most toxic metal for all strains (half maximal effective concentration between 0.1 and 10 mg.L- 1) except for D.salina and C.simplex. These two strains were the most resistant to all metals tested. All organic compounds presented half maximal effective concentration above 10 mg.L- 1, none of them being very toxic for the studied microorganisms. P.costavermella and C.simplex were the most resistant strains to organic compounds. Looking at tolerance to salinity, metals and organic compounds, D.salina appeared to be the best choice for biomass production in produced waters. In addition, growths in 80\% artificial produced water sup- plemented with f medium confirm the feasibility to use this medium to produce biomass.}, keywords = {RCC4223, RCC537, rcc752}, issn = {01476513}, doi = {10.1016/j.ecoenv.2022.113351}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0147651322001919}, author = {Parsy, Aur{\'e}lien and Guyoneaud, R{\'e}my and Lot, Marie-Claire and Baldoni-Andrey, Patrick and P{\'e}ri{\'e}, Fr{\'e}d{\'e}ric and Sambusiti, Cecilia} } @article {zhang_intense_2022, title = {Intense blooms of Phaeocystis globosa in the South China Sea are caused by a unique {\textquotedblleft}giant-colony{\textquotedblright} ecotype}, journal = {Harmful Algae}, volume = {114}, year = {2022}, pages = {102227}, abstract = {The haptophyte Phaeocystis globosa, an important causative agent of harmful algal blooms globally, exhibits varying morphological and physiological features and high genetic diversity, yet the relationship among these has never been elucidated. In this study, colony sizes and pigment profiles of 19 P. globosa isolates from the Pacific and Atlantic Oceans were determined. Genetic divergence of these strains was analyzed using the chloroplast rbcS-rpl27 intergenic spacer, a novel high-resolution molecular marker. Strains could be divided into four genetic clades based on these sequences, or two groups based on colony size and the identity of diagnostic pigments (19{\textquoteright}-hexanoyloxyfucoxanthin, hex-fuco, and 19{\textquoteright}-butanoyloxyfucoxanthin, but-fuco). Three strains from the South China Sea (SCS), all belonging to the same genetic clade, have unique biological features in forming giant colonies and possessing but-fuco as their diagnostic pigment. Based on these findings, we propose that these SCS strains should be a unique {\textquotedblleft}giant-colony{\textquotedblright} ecotype of P. globosa. During the period 2016-2021, more than 1000 rbcS-rpl27 sequences were obtained from 16 P. globosa colony samples and 18 phytoplankton samples containing solitary P. globosa cells in the SCS. Phylogenetic analysis indicated that >95\% of the sequences from P. globosa colonies in the SCS were comprised of the {\textquotedblleft}giant-colony{\textquotedblright} ecotype, whereas the genetic diversity of solitary cells was much higher. Results demonstrated that intense blooms of P. globosa featuring giant colonies in the SCS were mainly caused by this giant-colony P. globosa ecotype.}, keywords = {ecotype, genetic diversity, Giant colony, Marker pigment, RCC1736, RCC2055, RCC678, RCC736}, issn = {1568-9883}, doi = {10.1016/j.hal.2022.102227}, url = {https://www.sciencedirect.com/science/article/pii/S1568988322000555}, author = {Zhang, Qing-Chun and Liu, Chao and Wang, Jin-Xiu and Kong, Fan-Zhou and Niu, Zhuang and Xiang, Ling and Yu, Ren-Cheng} } @article {biller_isolation_2022, title = {Isolation and Characterization of Cyanobacterial Extracellular Vesicles}, journal = {Journal of Visualized Experiments}, year = {2022}, month = {feb}, abstract = {Cyanobacteria are a diverse group of photosynthetic, Gram-negative bacteria that play critical roles in global ecosystems and serve as essential biotechnology models. Recent work has demonstrated that both marine and freshwater cyanobacteria produce extracellular vesicles - small membrane-bound structures released from the outer surface of the microbes. While vesicles likely contribute to diverse biological processes, their specific functional roles in cyanobacterial biology remain largely unknown. To encourage and advance research in this area, a detailed protocol is presented for isolating, concentrating, and purifying cyanobacterial extracellular vesicles. The current work discusses methodologies that have successfully isolated vesicles from large cultures of Prochlorococcus, Synechococcus, and Synechocystis. Methods for quantifying and characterizing vesicle samples from these strains are presented. Approaches for isolating vesicles from aquatic field samples are also described. Finally, typical challenges encountered with cyanobacterial vesicle purification, methodological considerations for different downstream applications, and the trade-offs between approaches are also discussed.}, doi = {10.3791/63481}, author = {Biller, Steven and Mu{\~n}oz Marin, Maria and Lima, Steeve and Matinha-Cardoso, Jorge and Tamagnini, Paula and Oliveira, Paulo} } @article {tostevin_influence_2021, title = {The influence of elevated SiO2(aq) on intracellular silica uptake and microbial metabolism}, journal = {Geobiology}, volume = {n/a}, number = {n/a}, year = {2021}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gbi.12442}, abstract = {Microbes are known to accumulate intracellular SiO2(aq) up to 100s of mmol/l from modern seawater (SiO2(aq) <100 {\textmu}mol/l), despite having no known nutrient requirement for Si. Before the evolution of siliceous skeletons, marine silica concentrations were likely an order of magnitude higher than the modern ocean, raising the possibility that intracellular SiO2(aq) accumulation interfered with normal cellular function in non-silicifying algae. Yet, because few culturing studies have isolated the effects of SiO2(aq) at high concentration, the potential impact of elevated marine silica on early microbial evolution is unknown. Here, we test the influence of elevated SiO2(aq) on eukaryotic algae, as well as a prokaryote species. Our results demonstrate that under SiO2(aq) concentrations relevant to ancient seawater, intracellular Si accumulates to concentrations comparable to those found in siliceous algae such as diatoms. In addition, all eukaryotic algae showed a statistically significant response to the high-Si treatment, including reduced average cell sizes and/or a reduction in the maximum growth rate. In contrast, there was no consistent response to the high-Si treatment by the prokaryote species. Our results highlight the possibility that elevated marine SiO2(aq) may have been an environmental stressor during early eukaryotic evolution.}, keywords = {Archaean, culturing, microbial metabolism, Proterozoic, RCC1, RCC1216, rcc1512, RCC1547, rcc539, silica}, issn = {1472-4669}, doi = {10.1111/gbi.12442}, url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/gbi.12442}, author = {Tostevin, Rosalie and Snow, Joseph T. and Zhang, Qiong and Tosca, Nicholas J. and Rickaby, Rosalind E. M.} } @article {Henry2021, title = {The influences of phytoplankton species, mineral particles and concentrations of dispersed oil on the formation and fate of marine oil-related aggregates}, journal = {Science of the Total Environment}, volume = {752}, year = {2021}, note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC1698,RCC1719,RCC290}, month = {jan}, pages = {141786}, abstract = {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 {\textdegree}C. Aggregation was measured by silhouette camera analyses, and oil compound group distribution and depletion by gas chromatography (GC-FID or GC{\textendash}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{\textendash}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.}, keywords = {Aggregation, Dispersed oil, Marine snow, Mineral particles, phytoplankton, RCC1698, RCC1719, RCC290}, issn = {18791026}, doi = {10.1016/j.scitotenv.2020.141786}, author = {Henry, Ingrid A. and Netzer, Roman and Davies, Emlyn and Brakstad, Odd Gunnar} } @article {zhang_isotope_2021, title = {An isotope label method for empirical detection of carbonic anhydrase in the calcification pathway of the coccolithophore Emiliania huxleyi}, journal = {Geochimica et Cosmochimica Acta}, volume = {292}, year = {2021}, pages = {78{\textendash}93}, abstract = {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.}, keywords = {Carbonic anhjydrase, ccm, coccolithophore, Isotopic labelling, rcc, rcc1258}, issn = {0016-7037}, doi = {10.1016/j.gca.2020.09.008}, url = {https://www.sciencedirect.com/science/article/pii/S0016703720305597}, author = {Zhang, Hongrui and Blanco-Ameijeiras, Sonia and Hopkinson, Brian M. and Bernasconi, Stefano M. and Mejia, Luz Maria and Liu, Chuanlian and Stoll, Heather} } @article {Carrillo2020, title = {Identification and characterization of ChlreSEX4, a novel glucan phosphatase from Chlamydomonas reinhardtii green alga}, journal = {Archives of Biochemistry and Biophysics}, volume = {680}, year = {2020}, note = {Publisher: Academic Press Inc.}, month = {feb}, pages = {108235}, abstract = {Chlamydomonas reinhardtii is the best known unicellular green alga model which has long been used to investigate all kinds of cellular processes, including starch metabolism. Here we identified and characterized a novel enzyme, ChlreSEX4, orthologous to glucan phosphatase SEX4 from Arabidopsis thaliana, that is capable of binding and dephosphorylating amylopectin in vitro. We also reported that cysteine 224 and tryptophan 305 residues are critical for enzyme catalysis and substrate binding. Furthermore, we verified that ChlreSEX4 gene is expressed in vivo and that glucan phosphatase activity is measurable in Chlamydomonas protein extracts. In view of the results presented, we suggest ChlreSEX4 as a functional phosphoglucan phosphatase from C. reinhardtii. Our data obtained so far contribute to understanding the phosphoglucan phosphatases evolutionary process in the green lineage and their role in starch reversible phosphorylation. In addition, this allows to position Chlamydomonas as a potential tool to obtain starches with different degrees of phosphorylation for industrial or biotechnological purposes.}, keywords = {Chlamydomonas Reinhardtii, ChlreSEX4, Glucan phosphatase, SEX4, Starch phosphorylation}, issn = {10960384}, doi = {10.1016/j.abb.2019.108235}, author = {Carrillo, Julieta B. and Torresi, Florencia and Morales, Luisina L. and Ricordi, Micaela and Gomez-Casati, Diego F. and Busi, Maria V. and Mart{\'\i}n, Mariana} } @article {Baumeister2020, title = {Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry}, journal = {Metabolomics}, volume = {16}, number = {3}, year = {2020}, note = {ISBN: 0123456789 Publisher: Springer US tex.mendeley-tags: RCC 4667,RCC1717,RCC2561,RCC2562,RCC3008,RCC5791,RCC6807,RCC6808,RCC6809,RCC6810,RCC6811,RCC6812,RCC6813,RCC6814,RCC6815,RCC6816,RCC6817,RCC6818,RCC6819,RCC6820,RCC6821}, month = {mar}, pages = {28}, keywords = {ionization high-, Live single-cell mass spectrometry, matrix-free laser desorption, Matrix-free laser desorption/ionization high-resol, Metabolic fingerprinting, Microalgal identification, RCC1717, RCC2561, RCC2562, RCC3008, RCC4667, RCC5791, RCC6807, RCC6808, RCC6809, RCC6810, RCC6811, RCC6812, RCC6813, RCC6814, RCC6815, RCC6816, RCC6817, RCC6818, RCC6819, RCC6820, RCC6821, resolution mass spectrometry, Spectral pattern matching, Spectrum similarity}, issn = {1573-3882}, doi = {10.1007/s11306-020-1646-7}, url = {https://doi.org/10.1007/s11306-020-1646-7 http://link.springer.com/10.1007/s11306-020-1646-7}, author = {Baumeister, Tim U H and Vallet, Marine and Kaftan, Filip and Guillou, Laure and Svato{\v s}, Ale{\v s} and Pohnert, Georg} } @article {Uwizeye2020, title = {In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy}, journal = {bioRxiv}, year = {2020}, note = {tex.mendeley-tags: RCC100,RCC4014,RCC827,RCC909}, month = {jan}, pages = {2020.05.19.104166}, abstract = {Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.Competing Interest StatementThe authors have declared no competing interest.}, keywords = {RCC100, RCC4014, RCC827, RCC909}, doi = {10.1101/2020.05.19.104166}, url = {http://biorxiv.org/content/early/2020/05/20/2020.05.19.104166.abstract}, author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Gallet, Benoit and Keck, Jean-baptiste and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni and Moriscot, Christine and Chevalier, Fabien and Schieber, Nicole L and Templin, Rachel and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni} } @article {BlancoAmeijeiras2020, title = {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)}, journal = {Journal of Phycology}, year = {2020}, note = {tex.mendeley-tags: RCC1130,RCC1258}, month = {jun}, pages = {jpy.13017}, abstract = {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{\textendash}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.}, keywords = {carbon concentrating mechanism, CO2, haptophyte, membrane, PERMEABILITY, RCC1130, rcc1258}, issn = {0022-3646}, doi = {10.1111/jpy.13017}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13017}, author = {Blanco-Ameijeiras, Sonia and Stoll, Heather M. and Zhang, Hongrui and Hopkinson, Brian M.}, editor = {Raven, J.} } @article {Zhang2020, title = {Interactions of thallium with marine phytoplankton}, journal = {Geochimica et Cosmochimica Acta}, volume = {276}, year = {2020}, note = {Publisher: The Author(s) tex.mendeley-tags: RCC1,RCC1242,RCC1353,RCC1557,RCC174,RCC834,RCC950}, pages = {1{\textendash}13}, keywords = {bioaccumulation, biogeochemical cycle, metallome, phytoplankton, RCC1, RCC1242, RCC1353, RCC1557, rcc174, RCC834, RCC950, thallium}, issn = {00167037}, doi = {10.1016/j.gca.2020.02.024}, url = {https://doi.org/10.1016/j.gca.2020.02.024 https://linkinghub.elsevier.com/retrieve/pii/S0016703720301344}, author = {Zhang, Qiong and Rickaby, Rosalind E.M.} } @article {Vigor2020, title = {Isoprostanoid profiling of marine microalgae}, journal = {Biomolecules}, volume = {10}, number = {7}, year = {2020}, note = {Publisher: MDPI AG tex.mendeley-tags: RCC1349,RCC20,RCC69}, month = {jul}, pages = {1073}, abstract = {{\textexclamdown}p{\textquestiondown}Algae result from a complex evolutionary history that shapes their metabolic network. For example, these organisms can synthesize different polyunsaturated fatty acids, such as those found in land plants and oily fish. Due to the presence of numerous double-bonds, such molecules can be oxidized nonenzymatically, and this results in the biosynthesis of high-value bioactive metabolites named isoprostanoids. So far, there have been only a few studies reporting isoprostanoid productions in algae. To fill this gap, the current investigation aimed at profiling isoprostanoids by liquid chromatography -mass spectrometry/mass spectrometry (LC-MS/MS) in four marine microalgae. A good correlation was observed between the most abundant polyunsaturated fatty acids (PUFAs) produced by the investigated microalgal species and their isoprostanoid profiles. No significant variations in the content of oxidized derivatives were observed for Rhodomonas salina and Chaetoceros gracilis under copper stress, whereas increases in the production of C18-, C20- and C22-derived isoprostanoids were monitored in Tisochrysis lutea and Phaeodactylum tricornutum. In the presence of hydrogen peroxide, no significant changes were observed for C. gracilis and for T. lutea, while variations were monitored for the other two algae. This study paves the way to further studying the physiological roles of isoprostanoids in marine microalgae and exploring these organisms as bioresources for isoprostanoid production.{\textexclamdown}/p{\textquestiondown}}, keywords = {Isoprostanoids, Micro-LC-MS/MS, Microalgae, Oxidative stress, PUFAs, RCC1349, RCC20, RCC69}, issn = {2218-273X}, doi = {10.3390/biom10071073}, url = {https://www.mdpi.com/2218-273X/10/7/1073}, author = {Vigor, Claire and Oger, Camille and Reversat, Guillaume and Rocher, Amandine and Zhou, Bingqing and Linares-Maurizi, Amandyne and Guy, Alexandre and Bultel-Ponc{\'e}, Val{\'e}rie and Galano, Jean-Marie and Vercauteren, Joseph and Durand, Thierry and Potin, Philippe and Tonon, Thierry and Leblanc, Catherine} } @article {Lim2019, title = {In vitro enzymatic activity assays implicate the existence of the chlorophyll cycle in chlorophyll b-Containing cyanobacteria}, journal = {Plant and Cell Physiology}, number = {August}, year = {2019}, note = {tex.mendeley-tags: RCC1774}, month = {aug}, pages = {1{\textendash}12}, abstract = {In plants, chlorophyll (Chl) a and b are interconvertible by the action of three enzymes{\textemdash}chlorophyllide a oxygenase, Chl b reductase (CBR) and 7-hydroxymethyl chlorophyll a reductase (HCAR). These reactions are collectively referred to as the Chl cycle. In plants, this cyclic pathway ubiquitously exists and plays essential roles in acclimation to different light conditions at various developmental stages. By contrast, only a limited number of cyanobacteria species produce Chl b, and these include Prochlorococcus, Prochloron, Prochlorothrix and Acaryochloris. In this study, we investigated a possible existence of the Chl cycle in Chl b synthesizing cyanobacteria by testing in vitro enzymatic activities of CBR and HCAR homologs from Prochlorothrix hollandica and Acaryochloris RCC1774. All of these proteins show respective CBR and HCAR activity in vitro, indicating that both cyanobacteria possess the potential to complete the Chl cycle. It is also found that CBR and HCAR orthologs are distributed only in the Chl b-containing cyanobacteria that habitat shallow seas or freshwater, where light conditions change dynamically, whereas they are not found in Prochlorococcus species that usually habitat environments with fixed lighting. Taken together, our results implicate a possibility that the Chl cycle functions for light acclimation in Chl b-containing cyanobacteria.}, keywords = {chlorophyll cyanobacterium, evolution promiscuous activity, RCC1774}, issn = {0032-0781}, doi = {10.1093/pcp/pcz157}, url = {https://academic.oup.com/pcp/advance-article/doi/10.1093/pcp/pcz157/5544940}, author = {Lim, Hyunseok and Tanaka, Ayumi and Tanaka, Ryouichi and Ito, Hisashi} } @article {Granata2019, title = {The influence of bio-optical properties of Emiliania huxleyi and Tetraselmis sp. on biomass and lipid production when exposed to different light spectra and intensities of an adjustable LED array and standard light sources}, journal = {SN Applied Sciences}, volume = {1}, number = {6}, year = {2019}, note = {ISBN: 0123456789 Publisher: Springer International Publishing tex.mendeley-tags: RCC1210,RCC2604}, month = {jun}, pages = {524}, keywords = {Bio-optical properties, Biomass and lipid production, jel classification q42, mathematics subject classification 92c99, rcc1210, RCC2604, Spectral irradiance}, issn = {2523-3963}, doi = {10.1007/s42452-019-0529-x}, url = {http://link.springer.com/10.1007/s42452-019-0529-x}, author = {Granata, Tim and Habermacher, Patrick and H{\"a}rri, Vinzenz and Egli, Marcel} } @article {Sanfilippo2019, title = {Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus}, journal = {Proceedings of the National Academy of Sciences}, volume = {116}, number = {13}, year = {2019}, note = {tex.mendeley-tags: RCC1086,RCC2035,RCC2380,RCC2382,RCC2385,RCC2433,RCC2437,RCC2528,RCC2533,RCC2534,RCC2535,RCC2571,RCC2673,RCC28,RCC307,RCC328,RCC515,RCC555,RCC791}, month = {mar}, pages = {6457{\textendash}6462}, abstract = {Marine Synechococcus , a globally important group of cyanobacteria, thrives in various light niches in part due to its varied photosynthetic light-harvesting pigments. Many Synechococcus strains use a process known as chromatic acclimation to optimize the ratio of two chromophores, green-light{\textendash}absorbing phycoerythrobilin (PEB) and blue-light{\textendash}absorbing phycourobilin (PUB), within their light-harvesting complexes. A full mechanistic understanding of how Synechococcus cells tune their PEB to PUB ratio during chromatic acclimation has not yet been obtained. Here, we show that interplay between two enzymes named MpeY and MpeZ controls differential PEB and PUB covalent attachment to the same cysteine residue. MpeY attaches PEB to the light-harvesting protein MpeA in green light, while MpeZ attaches PUB to MpeA in blue light. We demonstrate that the ratio of mpeY to mpeZ mRNA determines if PEB or PUB is attached. Additionally, strains encoding only MpeY or MpeZ do not acclimate. Examination of strains of Synechococcus isolated from across the globe indicates that the interplay between MpeY and MpeZ uncovered here is a critical feature of chromatic acclimation for marine Synechococcus worldwide.}, keywords = {RCC1086, RCC2035, rcc2380, rcc2382, RCC2385, RCC2433, RCC2437, RCC2528, RCC2533, RCC2534, RCC2535, RCC2571, RCC2673, RCC28, RCC307, RCC328, RCC515, rcc555, rcc791}, issn = {0027-8424}, doi = {10.1073/pnas.1810491116}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1810491116}, author = {Sanfilippo, Joseph E. and Nguyen, Adam A. and Garczarek, Laurence and Karty, Jonathan A. and Pokhrel, Suman and Strnat, Johann A. and Partensky, Fr{\'e}d{\'e}ric and Schluchter, Wendy M. and Kehoe, David M.} } @article {Carrillo2018, title = {Identification and analysis of OsttaDSP, a phosphoglucan phosphatase from Ostreococcus tauri}, journal = {PLOS ONE}, volume = {13}, number = {1}, year = {2018}, note = {tex.mendeley-tags: RCC745}, month = {jan}, pages = {e0191621}, keywords = {RCC745}, issn = {1932-6203}, doi = {10.1371/journal.pone.0191621}, url = {http://dx.plos.org/10.1371/journal.pone.0191621}, author = {Carrillo, Julieta B and Gomez-Casati, Diego F. and Mart{\'\i}n, Mariana and Busi, Maria V.}, editor = {Permyakov, Eugene A.} } @article {Moniruzzaman2018, title = {Infection by a giant virus (AaV) induces widespread physiological reprogramming in aureococcus anophagefferens CCMP1984 {\textendash} a harmful bloom algae}, journal = {Frontiers in Microbiology}, volume = {9}, number = {April}, year = {2018}, note = {tex.mendeley-tags: RCC4094}, month = {apr}, pages = {1{\textendash}16}, abstract = {While viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, " giant " dsDNA viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of giant virus {\textendash} host interactions remain largely unknown. AaV, a giant virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens. To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host-virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional reprogramming of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2\%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal-expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides the insight into the Aureococcus {\textquoteright}virocell{\textquoteright}, and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.}, keywords = {Algal viruses, brown, Host-virus interaction, Mimiviridae, RCC4094, transcriptional profiles}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.00752}, url = {http://dx.doi.org/10.1101/256149 http://journal.frontiersin.org/article/10.3389/fmicb.2018.00752/full}, author = {Moniruzzaman, Mohammad and Gann, Eric R and Wilhelm, Steven W} } @article {Trainic, title = {Infection dynamics of a bloom-forming alga and its virus determine airborne coccolith emission from seawater}, journal = {iScience}, year = {2018}, note = {tex.mendeley-tags: RCC1216}, month = {aug}, abstract = {Summary Sea spray aerosols (SSA), have a profound effect on the climate; however, the contribution of oceanic microbial activity to SSA is not fully established. We assessed aerosolization of the calcite units (coccoliths) that compose the exoskeleton of the cosmopolitan bloom-forming coccolithophore, Emiliania huxleyi. Airborne coccolith emission occurs in steady-state conditions and increases by an order of magnitude during E. huxleyi infection by E. huxleyi virus (EhV). Airborne to seawater coccolith ratio is 1:108, providing estimation of airborne concentrations from seawater concentrations. The coccoliths{\textquoteright} unique aerodynamic structure yields a characteristic settling velocity of \~0.01 cm s-1, \~25 times slower than average sea salt particles, resulting in coccolith fraction enrichment in the air. The calculated enrichment was established experimentally, indicating that coccoliths may be key contributors to coarse mode SSA surface area, comparable with sea salt aerosols. This study suggests a coupling between key oceanic microbial interactions and fundamental atmospheric processes like SSA formation.}, keywords = {Atmospheric Science, Biogeoscience, Earth Sciences, Marine Organism, RCC1216}, issn = {25890042}, doi = {10.1016/j.isci.2018.07.017}, url = {https://www.cell.com/iscience/fulltext/S2589-0042(18)30105-6 https://linkinghub.elsevier.com/retrieve/pii/S2589004218301056}, author = {Trainic, Miri and Koren, Ilan and Sharoni, Shlomit and Frada, Miguel and Segev, Lior and Rudich, Yinon and Vardi, Assaf} } @article {Piedade2018, title = {Influence of irradiance and temperature on the virus MpoV - 45T infecting the arctic picophytoplankter micromonas polaris}, journal = {Viruses}, year = {2018}, note = {tex.mendeley-tags: RCC2257,RCC2258}, pages = {1{\textendash}17}, abstract = {Arctic marine ecosystems are currently undergoing rapid changes in temperature and light availability. Picophytoplankton, such as Micromonas polaris, are predicted to benefit from such changes. However, little is known about how these environmental changes affect the viruses that exert a strong mortality pressure on these small but omnipresent algae. Here we report on one-step infection experiments, combined with measurements of host physiology and viability, with 2 strains of M. polaris and the virus MpoV-45T under 3 light intensities (5, 60 and 160 ??mol quanta m-2 s-1), 2 light period regimes (16:8 and 24:0 h light:dark cycle) and 2 temperatures (3 and 7 {\textdegree}C). Our results show that low light intensity (16:8 h light:dark) delayed the decline in photosynthetic efficiency and cell lysis, while decreasing burst size by 46\%. In contrast, continuous light (24:0 h light:dark) shortened the latent period by 5 h for all light intensities, and even increased the maximum virus production rate and burst size under low light (by 157 and 69\%, respectively). Higher temperature (7 {\textdegree}C vs 3 {\textdegree}C) led to earlier cell lysis and increased burst size (by 19\%), except for the low light conditions. These findings demonstrate the ecological importance of light in combination with temperature as a controlling factor for Arctic phytoplankton host and virus dynamics seasonally, even more so in the light of global warming.}, keywords = {arctic algal viruses, global climate change, light intensity, light regime, RCC2257, RCC2258, virus growth}, issn = {1999-4915}, doi = {10.3390/v10120676}, author = {Piedade, Gon{\c c}alo J and Wesdorp, Ella M and Borbolla, Elena Montenegro and Maat, Douwe S} } @article {Smallwood2018, title = {Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri}, journal = {bioRxiv}, year = {2018}, note = {tex.mendeley-tags: RCC745}, keywords = {? No DOI found, RCC745}, author = {Smallwood, Authors Chuck R and Chen, Jian-hua and Kumar, Neeraj and Chrisler, William and Samuel, O and Kyle, Jennifer E and Nicora, Carrie D and Boudreau, Rosanne and Ekman, Axel and Kim, K and Moore, Ronald J and Mcdermott, Gerry and Cannon, William R and Evans, James E} } @article {Rastogi2017, title = {Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms}, journal = {Scientific Reports}, volume = {8}, number = {1}, year = {2018}, note = {ISBN: 4159801823106 Publisher: Springer US tex.mendeley-tags: RCC2967}, month = {dec}, pages = {4834}, abstract = {2 3 Diatoms are one of the most successful and ecologically important groups of eukaryotic 4 phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better 5 understanding of their biological innovations, evolutionary origins, and ecological 6 underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions 7 combined with published expressed sequence tags and protein sequences from multiple taxa 8 to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 9 novel genes. The new annotation additionally permitted the discovery for the first time of 10 extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping 11 which increases the diversity of transcripts to regulate gene expression in response to nutrient 12 limitations. In addition, we have used up-to-date reference sequence libraries to dissect the 13 taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete in 14 lineage-specific genes, with up to 47\% of the gene models present only possessing 15 orthologues in other stramenopile groups. Finally, we have performed a comprehensive de 16 novo annotation of repetitive elements showing novel classes of TEs such as SINE, MITE, LINE 17 and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene 18 function, evolution and ecology.}, keywords = {RCC2967}, issn = {2045-2322}, doi = {10.1038/s41598-018-23106-x}, url = {https://www.biorxiv.org/content/early/2017/08/14/176024\%0Ahttp://dx.doi.org/10.1101/176024 http://www.nature.com/articles/s41598-018-23106-x}, author = {Rastogi, Achal and Maheswari, Uma and Dorrell, Richard G. and Vieira, Fabio Rocha Jimenez and Maumus, Florian and Kustka, Adam and McCarthy, James and Allen, Andy E. and Kersey, Paul and Bowler, Chris and Tirichine, Leila} } @article {Fischer2017, title = {Identity of the limiting nutrient (N vs. P) affects the competitive success of mixotrophs}, journal = {Marine Ecology Progress Series}, volume = {563}, year = {2017}, note = {tex.mendeley-tags: RCC744}, pages = {51{\textendash}63}, abstract = {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.}, keywords = {RCC744}, doi = {10.3354/meps11968}, url = {https://www.int-res.com/abstracts/meps/v563/p51-63}, author = {Fischer, R and HA, Giebel and Ptacnik, R} } @article {faucher_impact_2017, title = {Impact of trace metal concentrations on coccolithophore growth and morphology: laboratory simulations of Cretaceous stress}, journal = {Biogeosciences}, volume = {14}, number = {14}, year = {2017}, note = {Publisher: Copernicus GmbH}, month = {jul}, pages = {3603{\textendash}3613}, abstract = {

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.

}, keywords = {RCC1198, RCC1216, RCC1303}, issn = {1726-4170}, doi = {10.5194/bg-14-3603-2017}, url = {https://bg.copernicus.org/articles/14/3603/2017/}, author = {Faucher, Giulia and Hoffmann, Linn and Bach, Lennart T. and Bottini, Cinzia and Erba, Elisabetta and Riebesell, Ulf} } @article {Fischer2017a, title = {Importance of mixotrophic bacterivory can be predicted by light and loss rates}, journal = {Oikos}, volume = {126}, number = {5}, year = {2017}, note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC744}, month = {may}, pages = {713{\textendash}722}, abstract = {Recent observational studies form oligotrophic waters provide ample evidence that mixotrophic flagellates often account for the bulk of bacterivory. However, we lack a general framework that allows a mechanistic understanding of success of mixotrophs in the competition with heterotrophic bacterivores. This is especially needed for integrating mixotrophy in models of the microbial loop. Based on general tradeoffs linked to the combined resource use in mixotrophs (generalist versus specialist), we propose a concept where mixotrophs are favored by conditions of high light ? low losses, corresponding to the situation found in the surface waters of oligotrophic oceans. Under such conditions, they can achieve positive net growth at very low resource levels, allowing simultaneous competition with specialized protists. Conversely, heterotrophic bacterivores and photoautotrophs should be especially favored in more productive and low-light conditions. We show experimentally that the combined effect of light and loss rates (dilution) predicts the success of mixotrophic bacterivorous flagellates. Moreover, our results suggest that total bacterivory, contrary as seen in the traditional microbial loop concept, has a more intricate coupling to light.}, keywords = {RCC744}, issn = {0030-1299}, doi = {10.1111/oik.03539}, url = {https://doi.org/10.1111/oik.03539}, author = {Fischer, Robert and Giebel, Helge-Ansgar and Hillebrand, Helmut and Ptacnik, Robert} } @article {Marie2017, title = {Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry}, journal = {Journal of Phycology}, volume = {53}, number = {2}, year = {2017}, note = {tex.mendeley-tags: 2016,RCC1008,RCC299,RCC350,RCC4108,RCC4548,RCC4549,RCC4550,RCC4551,RCC4552,RCC4553,RCC4554,RCC4555,RCC4556,RCC4557,RCC4558,RCC4559,RCC4560,RCC4561,RCC4562,RCC4563,RCC4564,RCC4565,RCC4566,RCC4567,RCC4568,RCC4569,RCC4570,RCC4571,RCC4572,RCC4573,RCC4574,RCC4575,RCC4576,RCC4577,RCC4578,RCC4579,RCC4657,RCC4658,RCC4659,RCC4660,RCC4661,RCC4662,RCC4663,RCC4664,RCC4665,RCC4666,RCC90}, month = {apr}, pages = {271{\textendash}282}, keywords = {2016, RCC1008, RCC299, RCC350, RCC4108, RCC4548, RCC4549, RCC4550, RCC4551, RCC4552, RCC4553, RCC4554, RCC4555, RCC4556, RCC4557, RCC4558, RCC4559, RCC4560, RCC4561, RCC4562, RCC4563, RCC4564, RCC4565, RCC4566, RCC4567, RCC4568, RCC4569, RCC4570, RCC4571, RCC4572, RCC4573, RCC4574, RCC4575, RCC4576, RCC4577, RCC4578, RCC4579, RCC4657, RCC4658, RCC4659, RCC4660, RCC4661, RCC4662, RCC4663, RCC4664, RCC4665, RCC4666, RCC90}, issn = {00223646}, doi = {10.1111/jpy.12495}, url = {http://doi.wiley.com/10.1111/jpy.12495}, author = {Marie, Dominique and Le Gall, Florence and Edern, Roseline and Gourvil, Priscillia and Vaulot, Daniel}, editor = {Valentin, K.} } @article {Waltman2016, title = {Identifying aspects of the post-transcriptional program governing the proteome of the green alga micromonas pusilla.}, journal = {PloS one}, volume = {11}, number = {7}, year = {2016}, note = {ISBN: 10.1371/journal.pone.0155839 Publisher: Public Library of Science tex.mendeley-tags: 2016,RCC,rcc834}, month = {jan}, pages = {e0155839}, abstract = {Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote ({\textexclamdown}2 ??m diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3{\textquoteright} UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.}, keywords = {2016, rcc, RCC834}, issn = {1932-6203}, doi = {10.1371/journal.pone.0155839}, url = {http://dx.doi.org/10.1371/journal.pone.0155839}, author = {Waltman, Peter H and Guo, Jian and Reistetter, Emily Nahas and Purvine, Samuel and Ansong, Charles K and van Baren, Marijke J and Wong, Chee-Hong and Wei, Chia-Lin and Smith, Richard D and Callister, Stephen J and Stuart, Joshua M and Worden, Alexandra Z} } @article {Baudoux2015, title = {Interplay between the genetic clades of {\textexclamdown}i{\textquestiondown}Micromonas{\textexclamdown}/i{\textquestiondown} and their viruses in the Western English Channel.}, journal = {Environmental microbiology reports}, year = {2015}, note = {tex.mendeley-tags: 2015,rcc,sbr?hyto$_\textrmd$ipo}, month = {jun}, abstract = {The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regards to the genetic diversity of this host. During one year, we monitored the abundance of 3 clades of Micromonas and their viruses in the Western English Channel both in the environment, using clade-specific probes and flow cytometry, and in the laboratory, using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundances of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies, and genetic diversity. However, some viruses can also cross-infect different host clades suggesting a mechanism of horizontal gene transfer within Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.}, keywords = {2015, rcc, RCC?o?dd, sbr?hyto$_\textrmd$ipo}, issn = {1758-2229}, doi = {10.1111/1758-2229.12309}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26081716}, author = {Baudoux, A-C and Lebredonchel, H and Dehmer, H and Latimier, M and Edern, R and Rigaut-Jalabert, F and Ge, P and Guillou, L and Foulon, E and Bozec, Y and Cariou, T and Desdevises, Y and Derelle, E and Grimsley, N and Moreau, H and Simon, N} } @article {Simmons2015, title = {Intron invasions trace algal speciation and reveal nearly identical Arctic and Antarctic Micromonas populations.}, journal = {Molecular biology and evolution}, year = {2015}, note = {tex.mendeley-tags: rcc}, month = {may}, abstract = {Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, recently new families of spliceosomal introns that are repeated hundreds of times in individual genomes have been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements (ILEs) in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence-absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where this alga is increasing in abundance due to climate change. The same two families were detected in metagenomic data from Antarctica - a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our work illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation and global distribution of this sentinel marine alga.}, keywords = {rcc}, issn = {1537-1719}, doi = {10.1093/molbev/msv122}, url = {http://mbe.oxfordjournals.org/cgi/content/long/msv122v1}, author = {Simmons, Melinda P and Bachy, Charles and Sudek, Sebastian and van Baren, Marijke J and Sudek, Lisa and Ares, Manuel and Worden, Alexandra Z} } @article {Marie2014, title = {An improved protocol for flow cytometry analysis of phytoplankton cultures and natural samples}, journal = {Cytometry}, volume = {85}, year = {2014}, note = {tex.mendeley-tags: RCC100,RCC1085,RCC114,RCC156,RCC168,RCC174,RCC180,RCC190,RCC263,RCC365,RCC400,RCC432,RCC446,RCC475,RCC480,RCC504,RCC745,RCC91}, pages = {962{\textendash}968}, abstract = {Preservation of cells, choice of fixative, storage, and thawing conditions are recurrent issues for the analysis of phytoplankton by flow cytometry. We examined the effects of addition of the surfactant Pluronic F68 to glutaraldehyde-fixed photosynthetic organisms in cultures and natural samples. In particular, we examined cell losses and modifications of side scatter (a proxy of cell size) and fluorescence of natural pigments. We found that different marine phytoplankton species react differently to the action of Pluronic F68. In particular, photosynthetic prokaryotes are less sensitive than eukaryotes. Observed cell losses may result from cell lysis or from cell adhesion to the walls of plastic tubes that are commonly used for flow cytometry analysis. The addition of the surfactant, Pluronic F68, has a positive effect on cells for long-term storage. We recommend to modify current protocols for preservation of natural marine planktonic samples, by fixing them with glutaraldehyde 0.25\% (final concentration) and adding Pluronic F68 at a final concentration of 0.01\% in the samples before preservation. Pluronic F68 also appears effective for preserving samples without fixation for subsequent sorting, e.g. for molecular biology analyses. (c) 2014 International Society for Advancement of Cytometry}, keywords = {ASSEMBLE, MACUMBA, RCC100, RCC1085, RCC114, RCC156, RCC168, rcc174, RCC180, RCC190, RCC263, RCC365, RCC400, RCC432, RCC446, RCC475, RCC480, RCC504, RCC745, RCC91, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$PO}, doi = {10.1002/cyto.a.22517}, author = {Marie, D and Rigaut-Jalabert, F and Vaulot, D} } @article {Frada2012, title = {In situ survey of life cycle phases of the coccolithophore Emiliania huxleyi (Haptophyta)}, journal = {Environmental Microbiology}, volume = {14}, number = {6}, year = {2012}, note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo}, pages = {1558{\textendash}1569}, abstract = {The cosmopolitan coccolithophore Emiliania huxleyi is characterized by a strongly differentiated haplodiplontic life cycle consisting of a diploid phase, generally bearing coccoliths (calcified) but that can be also non-calcified, and a non-calcified biflagellated haploid phase. Given most studies have focused on the bloom-producing calcified phase, there is little-to-no information about non-calcified cells in nature. Using field mesocoms as experimental platforms, we quantitatively surveyed calcified and non-calcified cells using the combined calcareous detection fluorescent in situ hybridization (COD-FISH) method and qualitatively screened for haploid specific transcripts using reverse transcription-PCR during E. huxleyi bloom successions. Diploid, calcified cells formed dense blooms that were followed by the massive proliferation of E. huxleyi viruses (EhVs), which caused bloom demise. Non-calcified cells were also detected throughout the experiment, accounting for a minor fraction of the population but becoming progressively more abundant during mid-late bloom periods concomitant with EhV burst. Non-calcified cell growth also paralleled a distinct window of haploid-specific transcripts and the appearance of autotrophic flagellates morphologically similar to haploid cells, both of which are suggestive of meiosis and sexual life cycling during natural blooms of this prominent marine phytoplankton species.}, keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo}, doi = {10.1111/j.1462-2920.2012.02745.x}, url = {http://dx.doi.org/10.1111/j.1462-2920.2012.02745.x}, author = {Frada, Miguel J and Bidle, Kay D and Probert, Ian and de Vargas, Colomban} } @article {Luo2011, title = {Individual genome assembly from complex community short-read metagenomic datasets}, journal = {The ISME journal}, volume = {6}, year = {2011}, note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: RCC307}, pages = {898{\textendash}901}, keywords = {RCC307}, doi = {10.1038/ismej.2011.147}, url = {http://dx.doi.org/10.1038/ismej.2011.147 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2011147s1.html}, author = {Luo, Chengwei and Tsementzi, Despina and Kyrpides, Nikos C and Konstantinidis, Konstantinos T} } @article {Bendif2011, title = {Integrative taxonomy of the pavlovophyceae (haptophyta) : a reassessment}, journal = {Protist}, volume = {162}, year = {2011}, note = {tex.mendeley-tags: 2011,RCC1526,RCC1527,RCC1528,RCC1529,RCC1530,RCC1531,RCC1532,RCC1533,RCC1534,RCC1535,RCC1536,RCC1537,RCC1538,RCC1539,RCC1540,RCC1541,RCC1542,RCC1543,RCC1544,RCC1545,RCC1546,RCC1548,RCC1549,RCC1551,RCC1552,RCC1553,RCC1554,RCC1557,rcc,rcc1523,rcc1524,rcc1525}, pages = {738{\textendash}761}, abstract = {The Pavlovophyceae (Haptophyta) contains four genera (Pavlova, Diacronema, Exanthemachrysis and Rebecca) and only thirteen characterised species. Considering the importance of members of this class, we constructed molecular phylogenies inferred from sequencing of ribosomal gene markers with comprehensive coverage of the described diversity and using type strains when available add on culture strains. Moreover, the morphology and ultrastructure of 12 of the described species was re-examined and the pigment signatures of many culture strains were determined. The molecular analysis revealed that sequences of all described species differed, although those of Pavlova gyrans and P. pinguis were nearly identical, these potentially forming a single cryptic species complex. Four well-delineated genetic clades were identified, one of which included species of both Pavlova andDiacronema. Unique combinations of morphological/ultrastructural characters were identified foreach of these clades. The ancestral pigment signature of the Pavlovophyceae consisted of a basic set of pigments plus MV chl cPAV, the latter being entirely absent in the Pavlova + Diacronema clade and supplemented by DV chl cPAV in part of the Exanthemachrysis clade. Based on this combination of characters, we propose a taxonomic revision of the class, with transfer of several Pavlova species to an emended Diacronema genus. The evolution of the class is discussed in the context of the phylogenetic reconstruction presented.}, keywords = {2011, ASSEMBLE, rcc, RCC1523, rcc1524, rcc1525, RCC1526, RCC1527, RCC1528, RCC1529, RCC1530, RCC1531, RCC1532, RCC1533, RCC1534, RCC1535, RCC1536, RCC1537, RCC1538, RCC1539, RCC1540, RCC1541, RCC1542, RCC1543, RCC1544, RCC1545, RCC1546, RCC1548, RCC1549, RCC1551, RCC1552, RCC1553, RCC1554, RCC1557, SBR$_\textrmP$hyto$_\textrmE$PPO}, doi = {10.1016/j.protis.2011.05.001}, author = {Bendif, E M and Probert, I and Herv{\'e}, A and Billard, C and Goux, D and Lelong, C and Cadoret, J P and V{\'e}ron, B} }