Created 28/08/2019 Updated 18/03/2024
Share

2024

  1. Egge, Elianne, Daniel Vaulot, Aud Larsen, et Bente Edvardsen. 2024. « The Community of Marine Alveolate Parasites in the Atlantic Inflow to the Arctic Ocean Is Structured by Season, Depth and Water Mass ». bioRxiv. doi.org/10.1101/2024.03.01.582906..

  2. Ong, Denise Rui Ying, Andrés Gutiérrez-Rodríguez, Karl A. Safi, Dominique Marie, Karen E. Selph, Michael R. Stukel, Moira Décima, et Adriana Lopes Dos Santos. 2024. « Phago-Mixotrophy of Small Eukaryotic Phytoplankton Might Alleviate Iron Limitation in HNLC Southern Ocean ». Preprint. BioRxiv. doi.org/10.1101/2024.01.08.574519

  3. Itoïz, S., Mouronvalle, C., Smits, M., Le Goïc, N., Bidault, A., de Montaudouin, X., ... & Chambouvet, A. (2024). Co-infection of two eukaryotic pathogens within clam populations in Arcachon Bay. Frontiers in Microbiology, 14, 1250947. https://doi.org/10.3389/fmicb.2023.1250947

2023

  1. Alonso-Sáez L., Palacio A.S., Cabello A.M., Robaina-Estévez S., González J.M., Garczarek, L., López-Urrutia Á. 2023. Transcriptional mechanisms of thermal acclimation in Prochlorococcus. mBio e03425-22, doi: 10.1128/mbio.03425-22.

  2. Alves-de-Souza C., Guillou, L. 2023. Parvilucifera rostrata. Trends Parasitol., 39: 227-228, doi: 10.1016/j.pt.2022.12.009.

  3. Armstrong E.J., Lê-Hoang  J., Carradec  Q., Aury  J.-M., Noel  B., Hume  B.C.C., Voolstra  C.R., Poulain  J., Belser  C., Paz-García  D.A., Cruaud  C., Labadie  K., Da Silva  C., Moulin  C., Boissin  E., Bourdin  G., Iwankow  G., Romac  S., Agostini  S., Banaigs  B., Boss  E., Bowler  C., de Vargas  C., Douville  E., Flores  M., Forcioli  D., Furla  P., Galand  P.E., Gilson  E., Lombard  F., Pesant S., Reynaud S., Sullivan M.B., Sunagawa S., Thomas O.P., Troublé R., Thurber R.V., Zoccola D., Planes S., Allemand D., Wincker P. 2023. Host transcriptomic plasticity and photosymbiotic fidelity underpin Pocillopora acclimatization across thermal regimes in the Pacific Ocean. Nat. Commun. 14, 3056, doi: 10.1038/s41467-023-38610-6.

  4. Ban H., Endo H., The EukBank Team, Kuwata A., Ogata H. 2023. Global distribution and diversity of marine Parmales. bioRxiv doi:10.1101/2023.11.09.566328.

  5. Belser C., Poulain J., Labadie K., Gavory F., Alberti A., Guy J., Carradec Q., Cruaud C., Da Silva C., Engelen S., Mielle P., Perdereau A., Samson G., Gas S., Voolstra C.R., Galand P.E., Flores J.M., Hume B.C.C., Perna G., Ziegler M., Ruscheweyh H.-J., Boissin E., Romac S., Bourdin G., Iwankow G., Moulin C., Paz García D.A., Agostini S., Banaigs B., Boss E., Bowler C., de Vargas C., Douville, E., Forcioli, D., Furla, P., Gilson, E., Lombard, F., Pesant, S., Reynaud, S., Sunagawa, S., Thomas, O.P., Troublé, R., Thurber, R.V., Zoccola, D., Scarpelli, C., Jacoby, E.K., Oliveira, P.H., Aury J.-M., Allemand D., Planes S., Wincker P. 2023. Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition. Sci. Data 10, 326. doi: 10.1038/s41597-023-02204-0.

  6. Breton E, Savoye N, Rimmelin-Maury P, Sautour B, Goberville E, Lheureux A, Cariou T, Ferreira S, Agogué H, Alliouane S, Aubert F, Aubin S, Berthebaud E, Blayac H, Blondel L, Boulart C, Bozec Y, Bureau S, Caillo A, Cauvin A, Cazes J-B, Chasselin L, Claquin P, Conan P, Cordier M-A, Costes L, Crec’hriou R, Crispi O, Crouvoisier M, David V, Del Amo Y, De Lary H, Delebecq G, Devesa J, Domeau A, Durozier M, Emery C, Feunteun E, Fauchot J, Gentilhomme V, Geslin S, Giraud M, Grangeré K, Grégori G, Grossteffan E, Gueux A, Guillaudeau J, Guillou G, Harrewyn M, Jolly O, Jude-Lemeilleur F, Labatut P, Labourdette N, Lachaussée N, Lafont M, Lagadec V, Lambert C, Lamoureux J, Lanceleur L, Lebreton B, Lecuyer E, Lemeille D, Leredde Y, Leroux C, Leynaert A, L’Helguen S, Liénart C, Macé E, Maria E, Marie B, Marie D, Mas S, Mendes F, Mornet L, Mostajir B, Mousseau L, Nowaczyk A, Nunige S, Parra R, Paulin T, Pecqueur D, Petit F, Pineau P, Raimbault P, Rigaut-Jalabert F, Salmeron C, Salter I, Sauriau P-G, Seuront L, Sultan E, Valdès R, Vantrepotte V, Vidussi F, Voron F, Vuillemin R, Zudaire L. Garcia N. 2023. Data quality control considerations in multivariate environmental monitoring: experience of the French coastal network SOMLIT. Front. Mar. Sci. 10:1135446, doi: 10.3389/fmars.2023.1135446.

  7. Brunet M., Le Duff N., Rigaut-Jalabert F., Romac S., Barbeyron T., Thomas F. 2023. Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally mixed coastal temperate habitat. Environ. Microbiol., doi: 10.1111/1462-2920.16505.

  8. Canesi, M., Douville, E., Montagna, P. et al. 2023. Differences in carbonate chemistry up-regulation of long-lived reef-building corals. Sci. Rep. 13, 11589, doi: 10.1038/s41598-023-37598-9.

  9. Cerfonteyn M., Groben R., Vaulot D., Guðmundsson K., Vannier P., Pérez-Hernández M.D., Marteinsson V.Þ. 2023. The distribution and diversity of eukaryotic phytoplankton in the Icelandic marine environment. Sci. Rep. 13, 8519, doi: 10.1038/s41598-023-35537-2.

  10. D'Acapito A., Roret T., Zarkadas E., Mocaer P-Y., Lelchat F., Baudoux A-C., Schoehn G., Neumann E. 2023. Structural study of the Cobetia marina bacteriophage 1 (Carin-1) by cryo-EM. J. Virol., doi: 10.1128/jvi.00248-23.

  11. De La Cruz M.A.M., Hingpit B.W., Guillou L.,  Onda D.F.L. 2023. Effects of monsoons and storms on the structuring and diversity of picoeukaryotic microbial communities in a tropical coastal environment. Deep Sea Res. II, 209: 16, doi: 10.1016/j.dsr2.2023.105294.

  12. Dinasquet J., Zancker B., Nicosia A., Bigeard E., Baudoux A-C., Engel A., Guieu C., Sellegri K. 2023. Marine bacterial enrichment in the sea surface microlayer, and surface taxa aerosolization potential in the Western Mediterranean Sea. bioRxiv, doi: 10.1101/2023.04.26.538450.

  13. Doré H., Guyet U., Leconte J., Farrant GK., Alric B., Ratin M., Ostrowski M., Ferrieux M., Hoebeke M., Siltanen J., Le Corguillé G., Corre E., Wincker P., Scanlan DJ., Eveillard D., Partensky F., Garczarek L. 2023. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies. ISME J., doi: 10.1038/s41396-023-01386-0.

  14. Dufour, Louison, Laurence Garczarek, Bastian Gouriou, Julia Clairet, Morgane Ratin, et Frédéric Partensky. 2024. « Differential Acclimation Kinetics of the Two Forms of Type IV Chromatic Acclimaters Occurring in Marine Synechococcus Cyanobacteria ». Front. Microbiol. 15 (février): 1349322. https://doi.org/10.3389/fmicb.2024.1349322.

  15. Eckmann, Charlotte A., Jessica S. Eberle, Fabian Wittmers, Susanne Wilken, Kristin Bergauer, Camille Poirier, Marguerite Blum, et al. 2023. « Eukaryotic algal community composition in tropical environments from solar salterns to the open sea ». Front. Marine Science 10. https://doi.org/10.3389/fmars.2023.1131351.

  16. Hooper, Chantelle, Georgia M. Ward, Rachel Foster, Ilze Skujina, Joseph E. Ironside, Cédric Berney, et David Bass. 2023. « Long amplicons as a tool to identify variable regions of ribosomal RNA for improved taxonomic resolution and diagnostic assay design in microeukaryotes: using ascetosporea as a case study ». Front. Ecol Evol. 11. https://doi.org/10.3389/fevo.2023.1266151.

  17. Galand P.E., Ruscheweyh H.-J., Salazar G., Hochart C., Henry N., Hume B.C.C., Oliveira P.H., Perdereau A., Labadie K., Belser C., Boissin E., Romac S., Poulain J., Bourdin G., Iwankow G., Moulin C., Armstrong E.J., Paz-García D.A., Ziegler M., Agostini S., Banaigs B., Boss E., Bowler C., de Vargas C., Douville E., Flores M., Forcioli D., Furla P., Gilson E., Lombard F., Pesant S., Reynaud S., Thomas O.P., Troublé R., Zoccola D., Voolstra C.R., Thurber R.V., Sunagawa S., Wincker P., Allemand D., Planes S. 2023. Diversity of the Pacific Ocean coral reef microbiome. Nat. Commun. 14, 3039, doi: 10.1038/s41467-023-38500-x.

  18. Hochart C., Paoli L., Ruscheweyh H.-J., Salazar G., Boissin E., Romac S., Poulain J., Bourdin G., Iwankow G., Moulin C., Ziegler M., Porro B., Armstrong E.J., Hume B.C.C., Aury J.-M., Pogoreutz C., Paz-García D.A., Nugues M.M., Agostini S., Banaigs B., Boss E., Bowler C., de Vargas C., Douville E., Flores M., Forcioli D., Furla P., Gilson E., Lombard F., Pesant S., Reynaud S., Thomas O.P., Troublé R., Wincker P., Zoccola D., Allemand D., Planes S., Thurber R.V., Voolstra C.R., Sunagawa S., Galand P.E., 2023. Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean. Nat. Commun. 14, 3037, doi: 10.1038/s41467-023-38502-9.

  19. Itoïz, Sarah, Clara Mouronvalle, Morgan Perennou, Elisa Chailler, Morgan Smits, Evelyne Derelle, Sebastian Metz, et al. 2024. « Co-infection of two eukaryotic pathogens within clam populations in Arcachon Bay ». Frontiers in Microbiology 14. https://doi.org/10.3389/fmicb.2023.1250947.

  20. Kaneko H., Endo H., Henry N., Berney C.,  Mahé F., Poulain J.,..., de Vargas C. et al. 2023. Predicting global distributions of eukaryotic plankton communities from satellite data. Isme Commun. 3, 101, doi: 10.1038/s43705-023-00308-7.

  21. Jacquet S.,  Baudoux A-C., Desdevises Y., Le Guyader S.F. 2023. Les virus marins - Simples parasites ou acteurs majeurs des écosystèmes aquatiques ? Éditions Quae, 110 p.

  22. Lombard F., Bourdin G., Pesant S., Agostini S., Baudena A., Boissin E., Cassar N., Clampitt M., Conan P., Da Silva O., Dimier C., Douville E., Elineau A., Fin J., Flores J.M., Ghiglione J.-F., Hume B.C.C., Jalabert L., John S.G., Kelly R.L., Koren I., Lin Y., Marie D., McMinds R., Mériguet Z., Metzl N., Paz-García D.A., Pedrotti M.L., Poulain J., Pujo-Pay M., Ras J., Reverdin G., Romac S., Rouan A., Röttinger E., Vardi A., Voolstra C.R., Moulin C., Iwankow G., Banaigs B., Bowler C., de Vargas C., Forcioli D., Furla P., Galand P.E., Gilson E., Reynaud S., Sunagawa S., Sullivan M.B., Thomas O.P., Troublé R., Thurber R.V., Wincker P., Zoccola D., Allemand D., Planes S., Boss E., Gorsky G. 2023. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. Sci. Data 10, 324, doi: 10.1038/s41597-022-01757-w.

  23. Mertens K.N., Carbonell-Moore M.C., Chomerat N., Bilien G., Boulben S., Guillou L., Romac S., Probert I., Ishikawa A., Nezan E. 2023. Morpho-molecular analysis of podolampadacean dinoflagellates (Dinophyceae), with the description of two new genera. Phycologia, doi: 10.1080/00318884.2022.2158281.

  24. Metz S., Itoïz S., Obiol A., Derelle E., Massana R., Berney C., de Vargas C., Soudant P., Monier A., Chambouvet A. 2023. Global perspective of environmental distribution and diversity of Perkinsea (Alveolata) explored by a meta-analysis of eDNA surveys. Sci. Rep. 13, 20111, doi: 10.1038/s41598-023-47378-0.

  25. Mitra A., Caron D.A., Faure E., Flynn K.J., Gonçalves Leles S., Hansen P.J., McManus G.B., Not F., do Rosario Gomes H., Santoferrara L., Stoecker D.K., Tillmann U. 2023. The mixoplankton database – diversity of photo-phago-trophic plankton in form, function and distribution across the global ocean. J. Euk. Microbiol.,, e12972. doi: 10.1111/jeu.12972.

  26. Noel B., Denoeud F., Rouan A., Buitrago-López C., Capasso L., Poulain J., Boissin E., Pousse M., Da Silva C., Couloux A., Armstrong E., Carradec Q., Cruaud C., Labadie K., Lê-Hoang J., Tambutté S., Barbe V., Moulin C., Bourdin G., Iwankow G., Romac S., Agostini S., Banaigs B., Boss E., Bowler C., de Vargas C., Douville E., Flores J.M., Forcioli D., Furla P., Galand P.E., Lombard F., Pesant S., Reynaud S., Sullivan M.B., Sunagawa S., Thomas O.P., Troublé R., Thurber R.V., Allemand D., Planes S., Gilson E., Zoccola D., Wincker P., Voolstra C.R., Aury J.-M. 2023. Pervasive tandem duplications and convergent evolution shape coral genomes. Genome Biol., 24, 123, doi: 10.1186/s13059-023-02960-7.

  27. Ong D.R.Y., Gutiérrez-Rodríguez A., Garczarek L., Marie D., Lopes dos Santos A. 2023. Nested PCR Approach for petB Gene Metabarcoding of Marine Synechococcus Populations. Microbiol. Spectr., e04086-22, doi: 10.1128/spectrum.04086-22.

  28. Pascoal, F., Tomasino, M.P., Piredda, R. et al. 2023. Inter-comparison of marine microbiome sampling protocols. Isme Commun. 3, 84, doi: 10.1038/s43705-023-00278-w.

  29. Pierella Karlusich JJ., Pelletier E., Zinger E., Lombard F., Zingone A., Colin S., Gasol JM., Dorrell R., Henry N., Scalco E., Acinas SG., Wincker, P., de Vargas, C., Bowler C. 2023. A robust approach to estimate relative phytoplankton cell abundance from metagenomes. Mol. Ecol. Res., 23(1), 16-40, doi: 10.1111/1755-0998.13592.

  30. Porro B., Zamoum T., Forcioli D., ..., Romac S., ... de Vargas C. et al. 2023. Different environmental response strategies in sympatric corals from Pacific Islands. Commun. Earth Environ. 4, 311, doi: 10.1038/s43247-023-00946-8.

  31. Reddy, M.M., Goossens, C., Zhou, Y. et al. 2023. Multi-omics determination of metabolome diversity in natural coral populations in the Pacific Ocean. Commun. Earth Environ. 4, 281, doi: 10.1038/s43247-023-00942-y.

  32. Rigonato J., Budinich M., Murillo AA., Brandao MC., Pierella Karlusich JJ.,Soviadan YD. , Gregory AC., Endo H., Kokoszka F., Vik D., Henry N., Fremont P., Labadie L., Zayed AA., Dimier C., Picheral M., Searson S., Poulain J, Kandels S., Pesant S., Karsenti E., Bork P., Bowler C., de Vargas C., Eveillard D., Gehlen M., Iudicone D., Lombard F., Ogata H., Stemmann L., Sullivan MB., Sunagawa S., Wincker P., Chaffron S., Jaillon O. 2023. Ocean-wide comparisons of mesopelagic planktonic community structures.  Isme Commun. 3, 83, doi: 10.1038/s43705-023-00279-9.

  33. Rizos I., Debeljak P., Finet T., Klein D., Ayata S.-D., Not F., Bittner L. 2023. Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of Syndiniales marine parasites. Isme Commun. 3, 1–11. https://doi.org/10.1038/s43705-022-00203-7.

  34. Rouan A., Pousse M., Djerbi N., Porro B., Bourdin G., Carradec Q., Hume B.C., Poulain J., Lê-Hoang J., Armstrong E., Agostini S., Salazar G., Ruscheweyh H.-J., Aury J.-M., Paz-García D.A., McMinds R., Giraud-Panis M.-J., Deshuraud R., Ottaviani A., Morini L.D., Leone C., Wurzer L., Tran J., Zoccola D., Pey A., Moulin C., Boissin E., Iwankow G., Romac S., de Vargas C., Banaigs B., Boss E., Bowler C., Douville E., Flores M., Reynaud S., Thomas O.P., Troublé R., Thurber R.V., Planes S., Allemand D., Pesant S., Galand P.E., Wincker P., Sunagawa S., Röttinger E., Furla P., Voolstra C.R., Forcioli D., Lombard F., Gilson E., 2023. Telomere DNA length regulation is influenced by seasonal temperature differences in short-lived but not in long-lived reef-building corals. Nat. Commun. 14, 3038, doi: 10.1038/s41467-023-38499-1.

  35. Santi I., Beluche O., Beraud M., Buttigieg PL., Casotti R., Cox CJ., Cunliffe M., Davies N., de Cerio OD., Exter K., Kervella AE., Kotoulas G., Lagaisse R., Laroquette A., Louro B., Not F., Obst M., Pavloudi C., Poulain J., Præbel K., Vanaverbeke J., Pade N. 2023. European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation. Front. Mar. Sci., doi: 10.3389/fmars.2023.1118120.

  36. Sanz-Sáez I., Sánchez P., Salazar G., de Vargas C. et al. 2023. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. Isme Commun. 3, 92, doi: 10.1038/s43705-023-00290-0.

  37. Strauss, Jan, Chang Jae Choi, Jonathan Grone, Fabian Wittmers, Valeria Jimenez, Kriste Makareviciute-Fichtner, Charles Bachy, et al. 2023. « The Bay of Bengal Exposes Abundant Photosynthetic Picoplankton and Newfound Diversity along Salinity-Driven Gradients ». Environmental Microbiology, juin. https://doi.org/10.1111/1462-2920.16431.

  38. Strauss, Jan, Longji Deng, Shiqiang Gao, Andrew Toseland, Charles Bachy, Chong Zhang, Amy Kirkham, et al. 2023. « Plastid-Localized Xanthorhodopsin Increases Diatom Biomass and Ecosystem Productivity in Iron-Limited Surface Oceans ». Nature Microbiology, octobre, 1‑17. https://doi.org/10.1038/s41564-023-01498-5.

  39. Tilliette C., Gazeau F., Portlock G., Benavides M., Bonnet S., Guigue C., Leblond N., Lory C., Marie D., Montanes M., Pulido-Villena E., Sarthou G., Tedetti M., Vorrath M.-E., Whitby H., Guieu C. 2023. Influence of shallow hydrothermal fluid release on the functioning of phytoplankton communities. Front. Mar. Sci., 10, doi: 10.3389/fmars.2023.1082077.

  40. Vallet M., Kaftan F., Buaya A., Thines M., Guillou L., Svatoš A., Pohnert G. 2023. Single-cell metabolome profiling for phenotyping parasitic diseases in phytoplankton. Front. Anal. Sci. 2:1051955, doi: 10.3389/frans.2022.1051955.

  41. Vaulot, Daniel, Gust Bilcke, Peter Chaerle, Angela Falciatore, Priscillia Gourvil, Michael W Lomas, Ian Probert, et Wim Vyverman. 2023. « Culturing Diatoms ». HAL. https://hal.science/hal-04000031.

  42. Veglia A.J., Bistolas, K.S.I., Voolstra, C.R., Hume, B.C.C., Ruscheweyh, H.-J., Planes, S., Allemand, D., Boissin, E., Wincker, P., Poulain, J., Moulin, C., Bourdin, G., Iwankow, G., Romac, S., Agostini, S., Banaigs, B., Boss, E., Bowler, C., de Vargas, C., Douville, E., Flores, M., Forcioli, D., Furla, P., Galand, P.E., Gilson, E., Lombard, F., Pesant, S., Reynaud, S., Sunagawa, S., Thomas, O.P., Troublé, R., Zoccola, D., Correa, A.M.S., Vega Thurber, R.L., 2023. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun. Biol. 6, 1–13, doi: 10.1038/s42003-023-04917-9.

  43. Vergne A., Giraud E., Camuel A., Bardot C., Billard H., Bouquet C., Gully D., Mathonat F., Jeanthon C., Mary I., Caissard J-C., Lehours A-C. 2023. The Pharaoh’s snakes of the teasel: New insights into Francis Darwin’s observations. Ecology e4030, doi: 10.1002/ecy.4030.

  44. Voolstra, C.R., Hume, B.C.C., Armstrong, E.J. et al. 2023. Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation. npj biodivers 2, 15, doi:10.1038/s44185-023-00020-8.

  45. Walde M., Camplong C., de Vargas C., Baudoux A.-C., Simon N., 2023. Viral infection impacts the 3D subcellular structure of the abundant marine diatom Guinardia delicatula. Front.  Mar. Sci. 9, do: 10.3389/fmars.2022.1034235.

  46. Ying Ong DR., Gutiérrez-Rodríguez A., Garczarek L., Marie D., Lopes dos Santos A. 2023. Nested PCR approach for petB gene metabarcoding of marine Synechococcus populations. Microbiol. Spectr., doi: 10.1128/spectrum.04086-22.

  47. Zavadska D., Henry N., Auladell A., Berney C., Richter D.J. 2023. On the relationship between protist metabarcoding and protist metagenome-assembled genomes. bioRxiv, doi: 10.1101/2023.10.09.561583.Brunet M., Le Duff N., Rigaut-Jalabert F., Romac S., Barbeyron T. & Thomas F. 2023. Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally mixed coastal temperate habitat. Environ. Microbiol., online: 15.  10.1111/1462-2920.16505 

2022

  1. Abreu A., Bourgois E., Gristwood A., Troublé R., Acinas SG. , Bork P., Boss E., Bowler C., Budinich M., Chaffron S., de Vargas C., Delmont TO. , Eveillard D., Guidi L.,  Iudicone D., Kandels S., Morlon H., Lombard F., Pepperkok R., Pierella Karlusich JJ., Piganeau G., Régimbeau A., Sommeria-Klein G., Stemmann L., Sullivan WB., Sunagawa S., Wincker P., Zablocki O., Arendt D., Bilic J., Finn R., Heard E., Rouse B., Vamathevan J., Casotti R., Cancio I., Cunliffe M., Kervella AE., Kooistra WHCF., Obst M.,  Pade N., Power DM., Santi I., Tsagaraki TM., Vanaverbeke J. 2022. Priorities for ocean microbiome research. Nat. Microbiol. 7, 937–947 (2022). doi: 10.1038/s41564-022-01145-5.

  2. Alric B., Geffard O., Chaumot A. 2022. Metal bioavailable contamination engages richness decline, species turnover but unchanged functional diversity of stream macroinvertebrates at the scale of a French region. Environ. Pollut., 308: 11. doi: 10.1016/j.envpol.2022.119565.

  3. Arsenieff L., Kimura K., Kranzler CF., Baudoux AC., Thamatrakoln K. 2022. Diatom viruses. In: Falciatore, A., Mock, T. (eds) The Molecular Life of Diatoms, Springer, Cham. doi:10.1007/978-3-030-92499-7_24.

  4. Berney C., Ciaghi S., Romac S., Mahé F., de Vargas C., Jaillon O., Kirchmair M., Bass D., Neuhauser S. 2022. Unveiling hidden eukaryotes: diversity of Endomyxa (Rhizaria) in coastal marine habitats. bioRxiv,  doi: 10.1101/2022.07.18.500052.

  5. Berney C., Henry N., Mahé F., Richter DJ., de Vargas C. 2022. EukRibo: a manually curated eukaryotic 18S rDNA reference database to facilitate identification of new diversity. bioRxiv, doi: 10.1101/2022.11.03.515105.

  6. Boisard J., Duvernois-Berthet E., Duval L., Schrevel J., Guillou L. Labat A. Le Panse S., Prensier G., Ponger L., Florent I. 2022. . Marine gregarine genomes reveal the breadth of apicomplexan diversity with a partially conserved glideosome machinery. BMC Genomics 23, 485, doi: 10.1186/s12864-022-08700-8.

  7. Bonnet S., Benavides M., Le Moigne FAC., Camps M.,Torremocha A., Grosso O., Dimier C., Spungin D., Berman-Frank I., Garczarek L. Cornejo-Castillo FM. 2022. Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean. ISME J.,  doi: 10.1038/s41396-022-01319-3.

  8. Bruyant F., Amiraux R., Amyot, M.-P., Archambault, P., Artigue, L., Bardedo de Freitas, L., Bécu, G., Bélanger, S., Bourgain, P., Bricaud, A., Brouard, E., Brunet, C., Burgers, T., Caleb, D., Chalut, K., Claustre, H., Cornet-Barthaux, V., Coupel, P., Cusa, M., Cusset, F., Dadaglio, L., Davelaar, M., Deslongchamps, G., Dimier, C., Dinasquet, J., Dumont, D., Else, B., Eulaers, I., Ferland, J., Filteau, G., Forget, M.-H., Fort, J., Fortier, L., Galí, M., Gallinari, M., Garbus, S.-E., Garcia, N., Gérikas Ribeiro, C., Gombault, C., Gourvil, P., Goyens, C., Grant, C., Grondin, P.-L., Guillot, P., Hillion, S., Hussher, R., Joux, F., Joy-Warren, H., Joyal, G., Kieber, D., Lafond, A., Lagunas, J., Lajeunesse, P., Lalande, C., Larivière, J., Le Gall, F., Leblanc, K., Leblanc, M., Legras, J., Levesque, K., Lewis, K.-M., Leymarie, E., Leynaert, A., Linkowski, T., Lizotte, M., Lopes dos Santos, A., Marec, C., Marie, D., Massé, G., Massicotte, P., Matsuoka, A., Miller, L., Mirshak, S., Morata, N., Moriceau, B., Morin, P.-I., Morisset, S., Mosbech, A., Mucci, A., Nadaï, G., Nozais, C., Obernosterer, I., Paire, T., Panagiotopoulos, C., Parenteau, M., Pelletier, N., Picheral, M., Quéguiner, B., Raimbault, P., Ras, J., Rehm, E., Ribot Lacosta, L., Rontani, J.-F., Saint-Béat, B., Sansoulet, J., Sardet, N., Schmechtig, C., Sciandra, A., Sempéré, R., Sévigny, C., Toullec, J., Tragin, M., Tremblay, J.-E., Trottier, A.-P., Vaulot, D., Vladoiu, A., Xue, L., Yunda-Guarin, G., and Babin, M. 2022. The Green Edge cruise: investigating the marginal ice zone processes during late spring and early summer to understand the fate of the Arctic phytoplankton bloom. Earth Syst. Sci. Data Discuss. , doi: 10.5194/essd-14-4607-202210.5194/essd-2022-41.

  9. Câmara dos Reis M., Romac S., Le Gall F., Marie D., Frada MJ. , Koplovitz G., Cariou T., Henry N., de Vargas C., Jeanthon C. 2022. Exploring the phycosphere of Emiliania huxleyi: from bloom dynamics to microbiome assembly experiments. Mol. Ecol, doi: 10.1111/mec.16829.

  10. Caracciolo M., Rigaut-Jalabert F., Romac S., Mahé F., Forsans S., Gac J-P., Arsenieff L., Manno M., Chaffron S., Cariou T., Hoebeke M., Bozec Y., Goberville E., Le Gall F., Guilloux L., Baudoux A-C., de Vargas C., Not F., Thiébaut E., Henry N., Simon N. 2022. Seasonal temporal dynamics of marine protists communities in tidally mixed coastal waters. Mol. Ecol., doi: 10.1111/mec.16539.

  11. Caracciolo M., Berney. C, Alric B., Piredda R., Zingone A., Sarno D., Percopo I., Romac S., Le Gall F., Rigaut-Jalabert F., Baudoux A-C., Simon N., Henry N. 2022. Insight into diatoms diversity at two European coastal sites (LTER-MC in the Mediterranean Sea and SOMLIT-Astan in the Western English Channel) using a DNA metabarcoding approach. bioRxiv, doi:10.1101/2022.07.01.498404.

  12. Carrigee LA., Frick JP., Liu X., Karty JA., Trinidad JC., Tom IP., Yang X., Dufour L., Partensky F., Schluchter WM. 2022. The phycoerythrobilin isomerization activity of MpeV in Synechococcus sp. WH8020 is prevented by the presence of a histidine at position 141 within its phycoerythrin-I β-subunit substrate. Front. Microbiol., doi: 10.3389/fmicb.2022.1011189.

  13. Clerc T., Boscq S., Attia R., Kaminski Schierle GS., Charrier B., Läubli NF. 2022. Cultivation and imaging of S. latissima embryo monolayered cell sheets inside microfluidic devices. Bioengineering, 9: 718, doi: 10.3390/bioengineering9110718.

  14. Cordier T., Barrenechea AI., Henry N., Lejzerowicz F., Berney C., Morard R., Cambon-Bonavita M-A., Guidi L., Lombard F., Arbizu PM., Massana R., Orejas C., Poulain J., Smith CR., Wincker P., Arnaud-Haond S., Gooday AJ., de Vargas C., Pawlowski J. 2022. Patterns of eukaryotic diversity from the surface to the deep-ocean sediment. Sci. Adv., doi: 10.1126/sciadv.abj9309.

  15. Decelle J., Kayal E., Bigeard E., Gallet B., Bougoure J., Clode P., Schieber N., Templin R., Hehenberger E., Prensier G., Chevalier F., Schwab Y., Guillou L. 2022. Intracellular development and impact of a eukaryotic parasite on its zombified microalgal host in the marine plankton. ISME J., doi:10.1038/s41396-022-01274-z.

  16. Decelle J, Not F. 2022. Le plancton marin, un océan de symbioses. La Recherche 569, 28-33.

  17. Delmont TO., , Gaia M., Hinsinger DD., Frémont P., Vanni C., Fernandez-Guerra A., Murat Eren A., Kourlaiev A., d'Agata L., Clayssen Q., Villar E., Labadie K., Cruaud C., Poulain J., Da Silva C., Wessner M., Noel B., Aury J-M. Sunagawa S., Acinas SG., Bork P., Sardet C., Stemmann L., Lescot M., Babin M., Gorsky G., Grimsley N., Guidi L., Hingamp P., Kandels S., Iudicone D., Ogata H., Pesant S., Sullivan MB., Not F., Karp-Boss L., Emmanuel Boss E., Cochrane G., Follows M., Poulton N., Raes J., Sieracki M., Speich S., de Vargas C., Bowler C., Karsenti E.,  Pelletier E., Wincker P., Jaillon O. 2022. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genomics, doi: 10.1016/j.xgen.2022.100123.

  18. de Vargas C., Le Bescot N., Pollina T., Henry N., Romac S., Colin S., Haëntjens N., Carmichael M., Berger C., Le Guen D., Decelle J., Mahé F., Poulain J., Malpot E., Beaumont C., Hardy M., Guiffant D., Probert I., Gruber DF., Allen AE., Gorsky G., Follows MJ., Pochon X., Troublé R., Cael BB., Lombard F., Boss E., Prakash M., & the Plankton Planet core team. 2022. Plankton Planet: A frugal, cooperative measure of aquatic life at the planetary scale. Front. Mar. Sci. 9:936972. doi: 10.3389/fmars.2022.936972.

  19. Dinasquet J., Bigeard E., Gazeau F., Azam F., Guieu C., Marañón E., Ridame C., Van Wambeke F., Obernosterer I., Baudoux A-C. 2022. Impact of dust addition on the microbial food web under present and future conditions of pH and temperature. Biogeosciences, 19: 1303-1319, doi: 10.5194/bg-19-1303-2022.

  20. Dinasquet J., Landa M.,  Obernosterer I. 2022. SAR11 clade microdiversity and activity during the early spring blooms off Kerguelen Island, Southern Ocean. Environ. Microbiol. Rep., doi: 10.1111/1758-2229.13117.

  21. Doré H., Leconte J., Guyet U., Breton S., Farrant GK., Demory D., Ratin M., Hoebeke M., Corre E., Pitt FD., Ostrowski M., Scanlan DJ., Partensky F., Six C., Garczarek L. 2022. Global phylogeography of marine Synechococcus in coastal areas reveals strong community shifts. mSystems, doi: 10.1128/msystems.00656-22.

  22. Dorrell RG., Kuo A., Füssy Z., Richardson EH., Salamov A., Zarevski N., Freyria NJ., Ibarbalz FM., Jenkins J, Pierella Karlusich JJ., Stecca Steindorff A., Edgar RE, Handley L., Lail K., Lipzen A., Lombard V., McFarlane J., Nef C., Novák Vanclová AMG., Peng Y., Plott C., Potvin M., Rocha Jimenez Vieira F., Barry K., de Vargas C., Henrissat B., Pelletier E., Schmutz J., Wincker P., Dacks JB., Bowler C., Grigoriev IV., Lovejoy C. 2022. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Sci. Alliance, 6 (3) e202201833; doi: 10.26508/lsa.202201833.

  23. Ferrieux M., Dufour L., Doré H. , Ratin M., Gueneugues A., Chasselin L., Marie D., Rigaut-Jalabert F., Le Gall F., Sciandra T., Monier G., Hoebeke M., Corre E., Xia X., Liu H., Scanlan DJ., Partensky F., Garczarek L. 2022. Comparative thermophysiology of marine Synechococcus CRD1 strains isolated from different thermal niches in iron-depleted areas. Front. Microbiol. 13:893413. doi: 10.3389/fmicb.2022.893413.

  24. Geisen C., Ridame C., Journet E., Delmelle P., Marie D., Lo Monaco C., Metzl N., Ammar R., Kombo J. & Cardinal D. 2022. Phytoplanktonic response to simulated volcanic and desert dust deposition events in the South Indian and Southern Oceans. Limnol. Oceanogr., doi: 10.1002/lno.12100.

  25. Gérikas Ribeiro C., Lopes dos Santos A., Trefault N., Marie D., Lovejoy C., Vaulot D. 2022. Arctic phytoplankton spring bloom diversity across the marginal ice zone in Baffin Bay. bioRxiv, doi: 10.1101/2022.03.14.484350.

  26. González-Miguéns R., Soler-Zamora C., Useros F., Nogal-Prata S., Berney C., Blanco-Rotea A., Carrasco-Braganza MI., de Salvador-Velasco D., Guillén-Oterino A., Tenorio-Rodríguez D., Velázquez D., Heger, TJ., Sanmartín I., Lara E. 2022. Cyphoderia ampulla (Cyphoderiidae: Rhizaria), a tale of freshwater sailors: The causes and consequences of ecological transitions through the salinity barrier in a family of benthic protists. Mol. Ecol., doi: 10.1111/mec.16424.

  27. Grébert T., Garczarek L., Daubin V., Humily F., Marie D., Ratin M., Devailly A., Farrant GK., Mary I., Mella-Flores D., Tanguy G., Labadie K., Wincker P., Kehoe DM., Partensky F. 2022. Diversity and evolution of pigment types in marine Synechococcus cyanobacteria. Genome Biol. Evol., 14, 4, evac035, doi: 10.1093/gbe/evac035.

  28. Guérin N., Ciccarella M., Flamant E., Frémont P., Mangenot S., Istace B., Noel B., Romac S., Bachy C., Gachenot M., Pelletier E., Alberti A., Jaillon O., Cruaud C., Wincker P., Aury J-M., Carradec Q. 2022. Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence. Commun. Biol. 5, 983, doi: 10.1038/s42003-022-03939-z.

  29. Guillou L., Szymczak J., Alves-de-Souza C. 2022. Amoebophrya ceratii. Trends Parasitol., doi: 10.1016/j.pt.2022.11.009.

  30. Gutierrez-Rodriguez A., Dos Santos A.L., Safi K., Probert I., Not F., Fernandez D., Gourvil P., Bilewitch J., Hulston D., Pinkerton M., Nodder SD. 2022. Planktonic protist diversity across contrasting Subtropical and Subantarctic waters of the southwest Pacific. Prog. Oceanogr., 206: 23. doi: 10.1016/j.pocean.2022.102809.

  31. Haney AM., Sanfilippo JE., Garczarek L., Partensky F., Kehoe D.M. 2022. Multiple photolyases protect the marine cyanobacterium Synechococcus from ultraviolet radiation. mBio, doi: 10.1128/mbio.01511-22.

  32. Itoïz S., Metz S., Derelle E., Reñé A., Garcés E., Bass D., Soudant P., Chambouvet A. 2022. Emerging parasitic protists: The case of Perkinsea. Front. Microbiol. 12:735815. doi: 10.3389/fmicb.2021.735815.

  33. Jamy M., Biwer C., Vaulot D., Obiol A., Jing H., Peura S., Massana R., Burki F. 2022. Global patterns and rates of habitat transitions across the eukaryotic tree of life. Nat. Ecol. Evol.  doi: 10.1038/s41559-022-01838-4.

  34. Kumarapperuma I., Joseph KL., Wang C., Biju LM.,Tom IP., Weaver KD., Grébert T., Partensky F., Schluchter WM., Yang X. 2022. Crystal structure and molecular mechanism of an E/F type bilin lyase-isomerase. Structure, doi: 10.1016/j.str.2022.01.007.

  35. Llopis Monferrer N., Biard T., Sandin MM., Lombard F., Picheral M., Elineau A., Guidi L., Leynaert A., Treguer PJ., Not F. 2022. Siliceous Rhizaria abundances and diversity in the Mediterranean Sea assessed by combined imaging and metabarcoding approaches. Front. Mar. Sci, 9: 14, doi: 10.3389/fmars.2022.895995.

  36. Lopes dos Santos A., Gérikas Ribeiro C., Ong D., Garczarek L., Shi XL., Nodder SD., Vaulot D., Gutiérrez-Rodríguez A. 2022. Phytoplankton diversity and ecology through the lens of high throughput sequencing technologies. In Clementson L., Eriksen R., Willis A. (eds), Advances in Phytoplankton Ecology: Applications of Emerging Technologies, Elsevier, pp. 353-413, doi: 10.1016/B978-0-12-822861-6.00020-0.

  37. Lory C., Van Wambeke F., Fourquez M., Barani A., Guieu C., Tilliette C., Marie D., Nunige S., Berman-Frank I, Bonnet S.  2022. Assessing the contribution of diazotrophs to microbial Fe uptake using a group specific approach in the Western Tropical South Pacific Ocean. ISME Commun. 2, 41. doi: 10.1038/s43705-022-00122-7.

  38. Mahé F., Czech L., Stamatakis A., Quince C., de Vargas C., Dunthorn M., Rognes T. 2022. Swarm v3: towards tera-scale amplicon clustering, Bioinformatics, 38, 267–269, doi: 10.1093/bioinformatics/btab493.

  39. Mahwash J., Biwer C., Vaulot D., Obiol A., Jing H., Peura S., Massana R., Burki F. 2022. Global patterns and rates of habitat transitions across the eukaryotic tree of life. Nat. Ecol. Evol. 6, 1458–1470, doi: 10.1038/s41559-022-01838-4.

  40. Mansour JS., Hansen PJ., Leroux C., Not F. 2022. Carbon and nitrogen uptake through photosynthesis and feeding by photosymbiotic Acantharia. , Open Research Europe, doi: 10.12688/openreseurope.14983.1.

  41. Mériguet Z., Oddone A., Le Guen D., Pollina T., Bazile R., Moulin C., Troublé R., Prakash M, De Vargas C., Lombard F. 2022. Basin-scale underway quantitative survey of surface microplankton using affordable collection and imaging tools deployed from Tara. Front Mar Sci., 9: 12, doi: 10.3389/fmars.2022.916025.

  42. Metz S., Huber P., Accattatis V., Lopes dos Santos A., Bigeard E., Unrein F., Chambouvet A., Not F., Lara E., Devercelli M., 2022. Freshwater protists: unveiling the unexplored in a large floodplain system. Environ. Microbiol. 24, 1731–1745. doi: 10.1111/1462-2920.15838.

  43. Metz S., Huber P., Mateus-Barros E., Junger PC., de Melo M., Bagatini IL., Izaguirre I., Câmara dos Reis M., Llames ME., Accattatis V., Quiroga MV., Devercelli M., Schiaffino MR., Niño-García JP., Navarro MB., Modenutti B, Vieira H., SaracenoM. , Sabio y García CA., Pereira E., González-Revello A., Piccini C., Unrein F., Alonso C. Sarmento H. 2022. A georeferenced rRNA amplicon database of aquatic microbiomes from South America. Sci Data 9, 565. doi: 10.1038/s41597-022-01665-z.

  44. Meyer A, Alric B, Dézerald O, Billoir E, Coulaud R, Larras F, Mondy CP, Usseglio-Polatera P. 2022. Linking micropollutants to trait syndromes across freshwater diatom, macroinvertebrate, and fish assemblages. Water, 14(8):1184, doi: 10.3390/w14081184.

  45. Monferrer NL., Foulon V., Elies P. 2022. Enhanced scanning electron microscopy images using muscovite mica, an example with Rhizaria. Microsc. Res. Tech., doi: 10.1002/jemt.24095.

  46. Partensky F., Hess WR., Garczarek L. 2022. Marine Cyanobacteria. In Stal LJ., Cretoiu MS. (eds) The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, vol 3. Springer, Cham., pp. 103-157. doi: 10.1007/978-3-030-90383-1_3.

  47. Pollina T., Larson AG., Lombard F., Li H., Le Guen D., Colin S., de Vargas C., Prakash M. 2022. PlanktonScope : Affordable modular imaging platform for citizen oceanography. Front. Mar. Sci. doi: 10.3389/fmars.2022.949428.

  48. Richter DJ., Berney C., Strassert JFH., Jürgen FH., Poh YP., Herman EK., Muñoz-Gómez SA., Wideman JG., Burki F., de Vargas C. 2022. EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes. PCI Genomics, doi: 10.1101/2020.06.30.180687.

  49. Richter DJ., Watteaux R., Vannier T., Leconte J., Frémont P., Reygondeau G.,  Maillet N., Henry N., Benoit G., Da Silva O., Delmont TOFernndez-Guerra A., Suweis S., Narci R., Berney C., et al. 2022. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife 11: e78129, doi: 10.7554/eLife.78129.

  50. Ridame C., Dinasquet J., Hallstrøm S., Bigeard E., Riemann L., Van Wambeke F., Bressac M., Pulido-Villena E., Taillandier V., Gazeau F., Tovar-Sanchez A., Baudoux A.-C.,  Guieu C. 2022. N2 fixation in the Mediterranean Sea related to the composition of the diazotrophic community, and impact of dust under present and future environmental conditions. Biogeosciences, 19, 415–435, doi: 10.5194/bg-19-415-2022.

  51. Sandin MM., Romac S., Not F. 2022. Intra-genomic rDNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing. Environ. Microbiol.  doi: 10.1111/1462-2920.16081.

  52. Schmitt M., Telusma A., Bigeard E., Guillou L., Alves-De-Souza C. 2022. Temperature affects the biological control of dinoflagellates by the generalist parasitoid Parvilucifera rostrata. Microorganisms, 10, 385, doi: 10.3390/microorganisms10020385.

  53. Sehein TR., Gast RJ., Pachiadaki M., Guillou L., Edgcomb VP. 2022. Parasitic infections by Group II Syndiniales target selected dinoflagellate host populations within diverse protist assemblages in a model coastal pond. Environ. Microbiol. doi: 10.1111/1462-2920.15977.

  54. Supraha L., Klemm K., Gran-Stadniczeñko S., Hörstmann C., Vaulot D., Edvardsen B., John U. 2022. Diversity and biogeography of planktonic diatoms in Svalbard fjords: The role of dispersal and Arctic endemism in phytoplankton community structuring. Elementa: Science of the Anthropocene 10 (1): 00117, doi: 10.1525/elementa.2021.00117.

  55. Thyssen M., Grégori G., Créach V., Lahbib S., Dugenne M., Aardema HM., Artigas L-F., Huang B., Barani A., Beaugeard L., Bellaaj-Zouari A., Beran A., Casotti R., Del Amo Y., Denis M., Dubelaar GBJ., Endres S., Haraguchi L., Karlson B., Lambert C., Louchart A., Marie D., Moncoiffé G., Pecqueur D., Ribalet F., Rijkeboer M., Silovic T., Silva R., Marro S., Sosik HM., Sourisseau M., Tarran G., Van Oostende N., Zhao L., Zheng S. 2022. Interoperable vocabulary for marine microbial flow cytometry. Front. Mar. Sci. 9:975877. doi: 10.3389/fmars.2022.975877.

  56. Vaulot D., Wei Hung Sim C,  Ong D., Teo B., Biwer C., Jamy M., Lopes dos Santos A. 2022. metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Mol. Ecol. Res. doi: 10.1111/1755-0998.13674.

  57. Vernette C., Lecubin J., Sánchez P., Tara Oceans Coordinators, Sunagawa S., Delmont T.O., Acinas S.G., Pelletier E., Hingamp P., Lescot M. 2022. The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucl. Acids Res., 50, W1, W516–W526, doi: 10.1093/nar/gkac420.

  58. Waller R.F., Alves-de-Souza C., Cleves PA., Janouškovec J., Kayal E., Krueger T., Szymczak J., Yamada N., Guillou L. 2022. Comparative biology and ecology of apicomplexans and dinoflagellates: a unique meeting of minds and biology. Trends Parasitol., doi: 10.1016/j.pt.2022.09.010.

2021

  1. Bapteste E., Gérard P., Larose C., Blouin M., Not F., Campos L., Aïdan G., Selosse M-A., Adénis MS., Bouchard F., Dutreuil S., Corel E., Vigliotti C., Huneman P., Lapointe FJ., Lopez P. 2021. The epistemic revolution induced by microbiome studies: An interdisciplinary view. Biology 10(7):651. doi:10.3390/biology10070651.

  2. Berthelot H., Duhamel S., L'Helguen S., Maguer J-F. & Cassar N. 2021. Inorganic and organic carbon and nitrogen uptake strategies of picoplankton groups in the northwestern Atlantic Ocean. Limnol. Oceanogr., doi: 10.1002/lno.11909.

  3. Brandão, M.C., Benedetti, F., Martini, S. , ..., Henry N., De Vargas C., Sullivan MB., ...., Stemmann L. & Lombard F. 2021. Macroscale patterns of oceanic zooplankton composition and size structure. Sci. Rep. 11, 15714 (2021). doi:10.1038/s41598-021-94615-5. 

  4. Brandt M. I., Pradillon F., Trouche B., Henry N., Liautard-Haag C., Cambon-Bonavita M-A., Cueff-Gauchard V., Wincker P., Belser C., Poulain J., Arnaud-Haond S., Zeppilli D. 2021. Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA. Sci. Rep., 11(1), 7856. 10.1038/s41598-021-86396-8.

  5. Burot C., Amiraux R., Bonin P., Guasco S., Babin M., Joux F., Marie D., Vilgrain L., Heipieper H. J., Rontani J-F. 2021. Viability and stress state of bacteria associated with primary production or zooplankton-derived suspended particulate matter in summer along a transect in Baffin Bay (Arctic Ocean). Science of The Total Environment, 770, 145252. doi.org/10.1016/j.scitotenv.2021.145252.

  6. Caracciolo M., Beaugrand G., Hélaouët P., Gevaert F., Edwards M., Lizon F., Kléparski L., Goberville E. 2021. Annual phytoplankton succession results from niche-environment interaction, J. Plank. Res., 43: 85–102, doi.org/10.1093/plankt/fbaa060.

  7. Chaffron S., Delage E., Budinich M., Vintache D., Henry N., Nef C., Ardyna M., Zayed AA., Junger PC., Galand PE., Lovejoy C., Murray AE., Sarmento H., Tara Oceans coordinators, Acinas SG., Babin M., Iudicone D., Jaillon O., Karsenti E., Wincker P., Karp-Boss L., Sullivan MB., Bowler C., de Vargas C., Eveillard D. 2021. Environmental vulnerability o f the global ocean epipelagic plankton community interactome. Sci. Adv. 7, eabg1921. doi: 10.1126/sciadv.abg1921.

  8. Demory D., Weitz J., Baudoux A-C., Touzeau S., Simon N., Rabouille S., Sciandra A., Bernard O. 2021. A thermal trade-off between viral production and degradation drives phytoplankton-virus population dynamics. Ecol. Lett. doi.org/10.1111/ele.13722.

  9. Dittami S., Arboleda E., Auguet J., Bigalke A., Briand E., Cárdenas P., Cardini U., Decelle J., Engelen A., Eveillard D., Gachon C., Griffiths S., Harder T., Kayal E., Kazamia E., Lallier F.H., Media M., Marzinelli E., Morganti T., Núñez P., L, Prado S., Pintado J., Saha M., Selosse M., Skillings D., Stock W., Sunagawa S., Toulza E., Vorobev A., Leblanc C. & Not F. 2021. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 9:e10911. doi.org/10.7717/peerj.10911.

  10. Egge E., Elferink S., Vaulot D., John U., Bratbak G., Larsen A., Edvardsen B. 2021. An 18S V4 rDNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth. Earth Syst. Sci. Data, 13, 4913–4928, doi:10.5194/essd-13-4913-2021.

  11. Farhat S., Le P., Kayal E., Noel B., Bigeard E., Corre E., Maumus F., Florent I., Alberti A., Aury J-M., Barbeyron T., Cai R., Da Silva C., Istace B., Labadie K., Marie D., Mercier J., Rukwavu T., Szymczak J., Tonon T., Alves-de-Souza C., Rouzé P., Van de Peer Y., Wincker P., Rombauts S., Porcel BM., Guillou L. 2021. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol 19,1, doi: 10.1186/s12915-020-00927-9.

  12. Flores JM., Bourdin G., Kostinski, AB., Altaratz O., Dagan G., Lombard F., Haëntjens N., Boss E., Sullivan MB., Gorsky G., Lang-Yona N., Trainic M., Romac S., Voolstra CR., Rudich Y., Vardi A., Koren I. 2021. Diel cycle of sea spray aerosol concentration. Nat. Commun. 12, 5476. doi: 10.1038/s41467-021-25579-3.

  13. Garczarek L., Guyet U., Doré H., Farrant GK., Hoebeke M., Brillet-Guéguen L., Bisch A., Ferrieux M., Siltanen J., Corre E., Le Corguillé G., Ratin M., Pitt FD., Ostrowski M., Conan M., Siegel A., Labadie K., Aury JM., Wincker P.,  Scanlan DJ., Partensky F. 2021. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Res., doi.org/10.1093/nar/gkaa958.

  14. Geffroy S., Lechat M-M., Le Gac M., Rovillon G-A., Marie D., Bigeard E., Malo F., Amzil Z., Guillou L., Caruana AMN. 2021. From the sxtA4 gene to saxitoxin production: What controls the variability among Alexandrium minutum and Alexandrium pacificum strains? Front. Microbiol, 12. doi:10.3389/fmicb.2021.613199.

  15. Grébert T., Nguyen AA., Pokhrel S., Joseph KL., Ratin M., Dufour L., Chen B., Haney AM., Karty JA., Trinidad JC., Garczarek L., Schluchter WM., Kehoe DM., Partensky F. 2021. Molecular bases of an alternative dual-enzyme system for light color acclimation of marine Synechococcus cyanobacteria. Proc. Natl. Acad. Sci., 118 (9) e2019715118. doi: 10.1073/pnas.2019715118.

  16. Jiménez V., Burns JA.,  Le Gall F., Not F., Vaulot D. 2021. No evidence of phago-mixotropy in Micromonas polaris (Mamiellophyceae), the dominant picophytoplankton species in the Arctic. J. Phycol. doi.org/10.1111/jpy.13125.

  17. Kaneko H., Blanc-Mathieu R., Endo H., Chaffron S., Delmont TO., Gaia M., Henry N., Hernandez Velazquez R., Nguyen CH, Mamitsuka H., Forterre P.,  Jaillon O., de Vargas C., Sullivan MB., Suttle CA., Guidi L, Ogata H. 2021. Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. iScience 24, 102002. doi.org/10.1016/j.isci.2020.102002.

  18. Llopis Monferrer N., Leynaert A., Tréguer P., Gutiérrez‐Rodríguez A., Moriceau B., Gallinari M., Latasa M., L’Helguen S., Maguer J-F., Safi K., Pinkerton MH.,  Not, F. 2021. Role of small Rhizaria and diatoms in the pelagic silica production of the Southern Ocean. Limnol. Oceanogr. doi: 10.1002/lno.11743.

  19. Long M., Marie D., Szymczak J., Toullec J., Bigeard E., Sourisseau M., Le Gac M., Guillou L., Jauzein C. 2021. Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales). ISME Commun.,  doi:s43705-021-00035-x.

  20. Magalhães K., Lopes dos Santos A., Vaulot D.,  Cabral Oliveira M. 2021. Hemiselmis aquamarina sp. nov. (Cryptomonadales, Cryptophyceae), a cryptophyte with a novel phycobiliprotein type (Cr-PC 564). Protist, 125832, doi: 10.1016/j.protis.2021.125832.

  21. Mansour JS., Anestis K. 2021. Eco-evolutionary perspectives on mixoplankton. Front. Mar. Sci. 8:666160. doi: 10.3389/fmars.2021.666160.

  22. Mansour JS., Norlin A., Llopis Monferrer N., L'Helguen S., Not F. 2021. Carbon and nitrogen content to biovolume relationships for marine protist of the Rhizaria lineage (Radiolaria and Phaeodaria). Limnol. Oceanogr. doi.org/10.1002/lno.11714.

  23. Massicotte P., Rainer A., David A. , ... , Boeuf D. , ..., Jeanthon C., ...,Marie D., ...., Vaulot D., et al.. 2021. The Malina oceanographic expedition: How do changes in ice cover, permafrost and UV radiation impact on biodiversity and biogeochemical fluxes in the Arctic Ocean? Earth Syst. Sci. Data, 13, 1561–1592, doi:10.5194/essd-13-1561-2021.

  24. Metz S., Huber P., Accattatis V., Lopes dos Santos A., Bigeard E., Unrein F., Chambouvet A., Not F., Lara E.  Devercelli M. 2021. Freshwater protists: unveiling the unexplored in a large floodplain system. Environ Microbiol. https://doi.org/10.1111/1462-2920.15838.

  25. Pierella Karlusich JJ., Pelletier E., Lombard F., Carsique M., Dvorak E, Colin S., Picheral M., Cornejo-Castillo FM., Acinas SG., Pepperkok R., Karsenti E., de Vargas C., Wincker P., Bowler C., Foster RA. 2021. Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods. Nat. Commun. doi: 10.1038/s41467-021-24299-y.

  26. Qui-Minet ZN., Davoult D., Grall J., Delaunay C., Six C., Cariou T., Martin S. 2021. Physiology of maerl algae: Comparison of inter- and intraspecies variations. J. Phycol., 18.  10.1111/jpy.13119.

  27. Ramond P., Siano  R., Schmitt  S., de Vargas C., Marié L., Mémery L., Sourisseau M. 2021. Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front. Sci. Rep. 11, 2682, doi.org/10.1038/s41598-021-82071-0.

  28. Robla J., García-Hierrro J., Alguacil FJ., Dittami SM., Marie D., Villa E., Deragon E., Guillebault D., Mengs G., Medlin LK. 2021. Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters. Environ. Sci.: Water Res. Technol. doi: 10.1039/D0EW00927J.

  29. Sandin MM., Biard T., Romac S., O'Dogherty L., Suzuki N., Not F. 2021. A morpho-molecular perspective on the diversity and evolution of Spumellaria (Radiolaria). Protist, doi.org/10.1016/j.protis.2021.125806.

  30. Schoenle A., Hohlfeld M., Hermanns K., Mahé F., De Vargas C., Nitsche F., Arndt H. 2021. High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans. Commun. Biol., 4: 10. doi: 10.1038/s42003-021-02012-5.

  31. Singer D., Seppey CVW., Lentendu G., Dunthorn M., Bass D., Belbahri L., Blandenier G., Debroas D., de Groot GA., de Vargas C., Domaizon I., Duckert C.,  Izaguirre I., Koenig I., Mataloni G., Schiaffino MR., Mitchell EAD., Geisen S., Lara E. 2021. Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems. Environment International, 146, 106262, doi.org/10.1016/j.envint.2020.106262.

  32. Six C., Ratin M., Marie D., Corre E. 2021. Marine Synechococcus picocyanobacteria: Light utilization across latitudes. Proc. Natl. Acad. Sci., 118 (38) e2111300118. doi:10.1073/pnas.2111300118.

  33. Timsit Y., Lescot M., Valiadi M., Not F. 2021. Bioluminescence and photoreception in unicellular organisms: Light-signalling in a bio-communication perspective. Int. J. Mol. Sci. 22, 11311. doi: 10.3390/ijms222111311.

  34. Trefault N., De la Iglesia R., Moreno-Pino M., Lopes dos Santos A., Gérikas Ribeiro C, Parada-Pozo G., Cristi A., Marie D., Vaulot D. 2021. Annual phytoplankton dynamics in coastal waters from Fildes Bay, Western Antarctic Peninsula. Sci. Rep. 11, 1368, doi: 10.1038/s41598-020-80568-8.

  35. Vaulot D., Geisen S., Mahé F., Bass D. 2021. PR2-primers: an 18S rRNA primer database for protists. Mol. Ecol. Resour., doi:10.1101/2021.01.04.425170.

  36. Vergne A., Darbot V. , Bardot C. , Enault F. , Lejeune A-H. , Carrias J-F. , Corbara B. , Céréghino R. , Leroy C. , Jeanthon C. , Giraud E. , Mary I., Lehours A-C. 2021. Assemblages of anoxygenic bacteria in tank bromeliads exhibit a host-specific signature. J. Ecol. doi.org/10.1111/1365-2745.13657.

  37. Vernette C., Henry N., Lecubin J., de Vargas C., Hingamp P., Lescot M. 2021. The Ocean Barcode Atlas: A web service to explore the biodiversity and biogeography of marine organisms. Mol. Ecol. Resour., 00:1-12. doi.org/10.1111/1755-0998.13322.

2020

  1. Androuin T., Six C., Bordeyne F., de Bettignies F., Noisette F., Davoult D. 2020. Better off alone? New insights in the symbiotic relationship between the flatworm Symsagittifera roscoffensis and the microalgae Tetraselmis convolutae. Symbiosis. doi:10.1007/s13199-020-00691-y

  2. Arsenieff L., Le Gall F., Rigaut-Jalabert F., Mahé F., Sarno D., Gouhier L., Baudoux A.-C., Simon N. 2020. Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. The ISME Journal, doi: 10.1038/s41396-020-0659-6

  3. Baumeister T.U.H., Vallet M., Kaftan F., Guillou L., Svatoš A. & Pohnert G. 2020. Identification to species level of live single microalgal cells from plankton samples with matrix-free laser/desorption ionization mass spectrometry. Metabolomics, 16: 28.  doi: http://doi.org/10.1007/s11306-020-1646-7

  4. Bigeard E., Pillet L., Burns J., Not N. 2020. Collect of collodarian (Rhizaria, Radiolaria) nuclei for genomic analyses. dx.doi.org/10.17504/protocols.io.5kgg4tw

  5. Brandt M.I., Trouche B., Henry N., Liautard-Haag C., Maignien L., de Vargas C., Wincker P., Poulain J., Zeppilli D., Arnaud-Haond S. 2020. An assessment of environmental metabarcoding protocols aiming at favouring contemporary biodiversity in inventories of deep-sea communities. Frontiers in Marine Science, 7: 234.  doi: 10.3389/fmars.2020.00234.

  6. Busseni G., Caputi L., Piredda R., Fremont P., Hay Mele B., Campese L., Scalco E., Vargas C., Bowler C., D’Ovidio F., Zingone A., Ribera d’Alcalà M., Iudicone D. 2020. Large scale patterns of marine diatom richness: Drivers and trends in a changing ocean. Global Ecology and Biogeography. DOI: 10.1111/geb.13161.

  7. Cai R., Kayal E., Alves-de-Souza C., Bigeard E., Corre E., Jeanthon C., Marie D., Porcel BM., Siano R., Szymczak J., Wolf M., Guillou L. 2020. Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach. Scientific Reports 10:253 DOI: 10.1038/s41598-020-59524-z.

  8. Calmes B., Strittmatter M., Jacquemin B., Perrineau M-M., Rousseau C., Badis Y., Cock JM., Destombe C., Valero M., Gachon CMM. 2020. Parallelisable non-invasive biomass, fitness and growth measurement of macroalgae and other protists with nephelometry. Algal Research 46:10176 DOI: 10.1016/j.algal.2019.101762.

  9. Carrigee LA., Frick JP, Karty JA., Garczarek L. , Partensky F., Schluchter WM. 2020. MpeV is a lyase isomerase that ligates a doubly-linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus. J. Biol. Chem. doi: 10.1074/jbc.RA120.015289.

  10. Clerissi C., Guillou L., Escoubas J-M., Toulza E. 2020. Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers. BMC Microbiology 20:193. DOI: 10.1186/s12866-020-01860-1.

  11. Dittami SM., Corre E, Brillet-Guéguen L, Lipinska AP., Pontoizeau N., ..., Marie D., et al. 2020. The genome of Ectocarpus subulatus – a highly stress-tolerant brown alga. Marine Genomics doi:  10.1016/j.margen.2020.100740

  12. Doré H., Farrant G.K., Guyet U., Haguait J., Humily F., Ratin M.,..., Garczarek L. 2020. Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria. Front. Microbiol. 11:567431. https://doi.org/10.3389/fmicb.2020.567431

  13. Dupont S., Lokmer A., Corre E., ..., Guillou L., et al.. 2020. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses. Animal Microbiome, 2: 12.  doi: 10.1186/s42523-020-00032-w

  14. Elie J., Feizbakhsh O., Desban N., Josselin B., Baratte B., Bescond A., Duez J., Fant X., Bach S., Marie D., ... & Ruchaud S. 2020. Design of new disubstituted imidazo 1,2-b pyridazine derivatives as selective Haspin inhibitors. Synthesis, binding mode and anticancer biological evaluation. J. Enzym. Inhib. Med. Chem., 35: 1840-1853. doi.org/10.1080/14756366.2020.1825408

  15. Endo, H., Blanc-Mathieu, R., Li, Y. Salazar G, Henry N., ..., de Vargas C., et al. 2020. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nat. Ecol. Evol. . https://doi.org/10.1038/s41559-020-01288-w

  16. Flores J.M., Bourdin G., Altaratz O., Trainic M., Lang-Yona N., Dzimban E., Steinau S., Tettich F., Planes S., Allemand D., Agostini S., Banaigs B., Boissin E., Boss E., Douville E., Forcioli D., Furla P., Galand P.E., Sullivan M.B., Gilson É., Lombard F., Moulin C., Pesant S., Poulain J., Reynaud S., Romac S., Sunagawa S., Thomas O.P., Troublé R., de Vargas C., Thurber R.V., Voolstra C.R., Wincker P., Zoccola D., Bowler C., Gorsky G, Rudich Y., Vardi, A., Koren I. 2020. Tara Pacific expedition’s atmospheric measurements of marine aerosols across the Atlantic and Pacific oceans: Overview and preliminary results. Bull. Am. Meteorol., 101, E536–E554, doi: 10.1175/BAMS-D-18-0224.1.

  17. Gérikas Ribeiro C., Lopes Dos Santos A., Gourvil P., Le Gall F., Marie D., Tragin M., Probert I., Vaulot D. 2020. Culturable diversity of Arctic phytoplankton during pack ice melting. Elementa: Science of the Anthropocene, 8: 23.  doi: 10.1525/elementa.401

  18. Gérikas Ribeiro C., Lopes dos Santos A., Probert I., Vaulot D., Edvardsen B. 2020. Taxonomic reassignment of Pseudohaptolina birgeri comb. nov. (Haptophyta). Phycologia doi.org/10.1080/00318884.2020.1830255/bioRxiv. doi: 10.1101/2020.05.06.081489.

  19. Guyet U., Nguyen NA., Doré H., Haguait J., Pittera J., Conan M., Ratin M., Corre E., Le Corguillé G., Brillet-Guéguen L., Hoebeke M., Six C., Steglich C., Siegel A., Eveillard D., Partensky F., Garczarek L. 2020. Synergic effects of temperature and irradiance on the physiology of the marine Synechococcus strain WH7803. Front. Microbiol. 11:1707. doi: 10.3389/fmicb.2020.01707.

  20. Hallmann C., Nett..., Not F., ..., Kucera M. , Stuhr M. 2020. Reply to: Sources of C-30 steroid biomarkers in Neoproterozoic-Cambrian rocks and oils. Nat. Ecol. Evol., 4: 37-39.  10.1038/s41559-019-1049-1

  21. Holtrop T., Huisman J., Stomp M., Biersteker L., Aerts J., Grébert T., Partensky F., Garczarek L., van der Woerd HJ. 2020. Vibrational modes of water predict spectral niches for photosynthesis in lakes and oceans. Nat Ecol Evol.,  doi.org/10.1038/s41559-020-01330-x

  22. Jobard M., Wawrzyniak I., Bronner G., Marie D., Vellet A., Sime-Ngando T., Debroas D., Lepere C. 2020. Freshwater Perkinsea: diversity, ecology and genomic information. J. Plankton Res., 42: 3-17.  doi: 10.1093/plankt/fbz068

  23. Kayal E., Alves-de-Souza C., Farhat S., Velo-Suarez L., Monjol J., Szymczak J., Bigeard E., Marie D., Noel B., Porcel BM., Corre E., Six C., Guillou L. 2020. Dinoflagellate host chloroplasts and mitochondria remain functional during Amoebophrya infection. Front. Microbiol. 11:600823. doi: 10.3389/fmicb.2020.600823.

  24. Llopis Monferrer N., Boltovskoy D., Tréguer P., Sandin MM., Not F., Leynaert A. 2020. Estimating biogenic silica production of Rhizaria in the global ocean. Global Biogeochemical Cycles:0– DOI: 10.1029/2019GB006286.

  25. Logares R., Deutschmann IM., Junger PC., Giner CR., Krabberød AK., Schmidt TSB., Rubinat-Ripoll L., Mestre M., Salazar G., Ruiz-González C., Sebastián M., de Vargas C., Acinas SG., Duarte CM., Gasol JM., Massana R. 2020. Disentangling the mechanisms shaping the surface ocean microbiota. Microbiome 8:55. DOI: 10.1186/s40168-020-00827-8.

  26. Marie D., Rigaut-Jalabert, F. 2020. L'analyse des micro-organismes marins, pp 329-339. In La cytométrie en flux, 2nd edition, Grunwald D., Mayol J.-F. , Ronot X. (coordinators), Lavoisier, Paris.

  27. Massicotte P., Amiraux R., ..., Gérikas Ribeiro C., ..., Le Gall F., ..., Marie D., et al. 2020. Green Edge ice camp campaigns: understanding the processes controlling the under-ice Arctic phytoplankton spring bloom. Earth System Science Data 12:151–176. DOI: 10.5194/essd-12-151-2020.

  28. Metegnier G., Paulino S., Ramond P., Siano R, Sourisseau M., Destombe C, Le Gac M. 2020. Species specific gene expression dynamics during harmful algal blooms. Sci Rep 10, 6182. doi:10.1038/s41598-020-63326-8

  29. Nakamura Y., Sandin MM., Suzuki N., Tuji A., Not F. 2020. Phylogenetic Revision of the Order Entactinaria—Paleozoic Relict Radiolaria (Rhizaria, SAR). Protist 171:125712. DOI: 10.1016/j.protis.2019.125712.

  30. Palacio AS., Cabello AM., Garcia FC., Labban A., Moran XAG., Garczarek L., Alonso-Saez L. & Lopez-Urrutia A. 2020. Changes in population age-structure obscure the temperature-size rule in marine cyanobacteria. Front. Microb., 11: 2059. doi: 10.3389/fmicb.2020.02059

  31. Saint-Béat B., Fath BD., Aubry C., Colombet J., Dinasquet J., Fortier L., Galindo V., Grondin P-L., Joux F., Lalande C., LeBlanc M., Raimbault P., Sime-Ngando T., Tremblay J-E., Vaulot D., Maps F., Babin M., Deming JW., Bowman J. 2020. Contrasting pelagic ecosystem functioning in eastern and western Baffin Bay revealed by trophic network modeling. Elementa: Science of the Anthropocene 8. DOI: 10.1525/elementa.397.

  32. Schneider L., Anestis K., Mansour J., Anschütz A., Gypens N., Hansen P., John U., Klemm K., Martin J., Medic N., Not F., Stolte W. 2020. A dataset on trophic modes of aquatic protists. Biodiversity Data Journal 8. DOI: 10.3897/BDJ.8.e56648.

  33. Siano R., Chapelle A., Antoine V., Michel-Guillou E., Rigaut-Jalabert F., Guillou L., Hégaret H., Leynaert A., Curd A. 2020. Citizen participation in monitoring phytoplankton seawater discolorations. Mar. Policy, 117, doi: 10.1016/j.marpol.2018.01.022.

  34. Sunagawa S., Acinas SG., Bork P., Bowler C., Eveillard D., Gorsky G., Guidi L., Iudicone D., Karsenti E., Lombard F., Ogata H., Pesant S., Sullivan MB., Wincker P., de Vargas C. 2020. Tara Oceans: towards global ocean ecosystems biology. Nature Reviews Microbiology. DOI: 10.1038/s41579-020-0364-5.

  35. Thiroux S., Dupont S., Nesbo C.L., Bienvenu N., Krupovic M., L'Haridon S., Marie D., Forterre P., Godfroy A., Geslin C. 2020. The first head-tailed virus, MFTV1, produced by a hyperthermophilic mathanogenic dees-sea archaea. Environmental Microbiology. doi.org/10.1111/1462-2920.15271.

  36. Villar E., Cabrol L., Heimbürger-Boavida L-E. 2020. Widespread microbial mercury methylation genes in the global ocean. Environmental Microbiology Reports 00:1758-2229.12829. DOI: 10.1111/1758-2229.12829.

  37. Yamada Y., Guillemette R., Baudoux A.C., Patel N., Azam F. 2020. Viral attachment to biotic and abiotic surfaces in seawater. Appl. Environ. Microbiol., 86: 18.  doi: 10.1128/aem.01687-19

  38. Yau S., Lopes dos Santos A., Eikrem W., Gérikas Ribeiro C., Gourvil P., Balzano S., Escande M-L., Moreau H., Vaulot D. 2020. Mantoniella beaufortii and Mantoniella baffinensis sp. nov. (Mamiellales, Mamiellophyceae), two new green algal species from the high arctic 1. Journal of Phycology 56:37–51. DOI: 10.1111/jpy.12932.

2019

  1. Adl SM., Bass D., Lane CE., Lukeš J., Schoch CL., Smirnov A., Agatha S., Berney C., Brown MW., Burki F., Cárdenas P., Čepička I., Chistyakova L., del Campo J., Dunthorn M., Edvardsen B., Eglit Y., Guillou L., Hampl V., Heiss AA., Hoppenrath M., James TY., Karpov S., Kim E., Kolisko M., Kudryavtsev A., Lahr DJG., Lara E., Le Gall L., Lynn DH., Mann DG., Massana i Molera R., Mitchell EAD., Morrow C., Park JS., Pawlowski JW., Powell MJ., Richter DJ., Rueckert S., Shadwick L., Shimano S., Spiegel FW., Torruella i Cortes G., Youssef N., Zlatogursky V., Zhang Q. 2019. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. Journal of Eukaryotic Microbiology 66:4–119. DOI: 10.1111/jeu.12691.

  2. Alves-de-Souza C., Benevides TS., Menezes M., Jeanthon C., Guillou L. 2019. First report of vampyrellid predator–prey dynamics in a marine system. The ISME Journal 13:1110–1113. DOI: 10.1038/s41396-018-0329-0.

  3. Arsenieff L., Simon N., Rigaut-Jalabert F., Le Gall F., Chaffron S., Corre E., Com E., Bigeard E., Baudoux A-C. 2019. First Viruses Infecting the Marine Diatom Guinardia delicatula. Frontiers in Microbiology 9. DOI: 10.3389/fmicb.2018.03235.

  4. Breton S., Jouhet J., Guyet U., Gros V., Pittera J., Demory D., Partensky F., Doré H., Ratin M., Maréchal E., Nguyen NA., Garczarek L., Six C. 2019. Unveiling membrane thermoregulation strategies in marine picocyanobacteria. New Phytologist:nph.16239. DOI: 10.1111/nph.16239.

  5. Câmara dos Reis M., Lacativa Bagatini I., de Oliveira Vidal L., Bonnet M-P., da Motta Marques D., Sarmento H. 2019. Spatial heterogeneity and hydrological fluctuations drive bacterioplankton community composition in an Amazon floodplain system. PLoS ONE 14(8): e0220695. doi: 10.1371/journal.pone.0220695.

  6. Capotondi A., Jacox M., Bowler C., Kavanaugh M., Lehodey P., Barrie D., Brodie S., Chaffron S., Cheng W., Dias D.F., Eveillard D., Guidi L., Iudicone D., Lovenduski N.S., Nye J.A., Ortiz I., Pirhalla D., Pozo Buil M., Saba V., Sheridan S., Siedlecki S., Subramanian A., de Vargas C., Di Lorenzo E., Doney S.C., Hermann A.J., Joyce T., Merrifield M., Miller A.J., Not F. Pesant S. 2019. Observational needs supporting marine ecosystems modeling and forecasting: from the global ocean to regional and coastal systems. Front. Mar. Sci. 6:623. doi: 10.3389/fmars.2019.00623.

  7. Caputi L., Carradec Q., Eveillard D., Kirilovsky A., Pelletier E., Pierella Karlusich JJ., Rocha Jimenez Vieira F., Villar E., Chaffron S., Malviya S., Scalco E., Acinas SG., Alberti A., Aury J-M., Benoiston A-S., Bertrand A., Biard T., Bittner L., Boccara M., Brum JR., Brunet C., Busseni G., Carratalà A., Claustre H., Coelho LP., Colin S., D’Aniello S., Da Silva C., Del Core M., Doré H., Gasparini S., Kokoszka F., Jamet J-L., Lejeusne C., Lepoivre C., Lescot M., Lima-Mendez G., Lombard F., Lukeš J., Maillet N., Madoui M-A., Martinez E., Mazzocchi MG., Néou MB., Paz-Yepes J., Poulain J., Ramondenc S., Romagnan J-B., Roux S., Salvagio Manta D., Sanges R., Speich S., Sprovieri M., Sunagawa S., Taillander V., Tanaka A., Tirichine L., Trottier C., Uitz J., Veluchamy A., Veselá J., Vincent F., Yau S., Kandels-Lewis S., Searson S., Dimier C., Picheral M., Bork P., Boss E., de Vargas C., Follows MJ., Grimsley N., Guidi L., Hingamp P., Karsenti E., Sordino P., Stemmann L., Sullivan MB., Tagliabue A., Zingone A., Garczarek L., d’Ortenzio F., Testor P., Not F., Ribera d’Alcalà M., Wincker P., Bowler C., Iudicone D., Acinas SG., Bork P., Boss E., de Vargas C., Follows MJ., Gorsky G., Grimsley N., Hingamp P., Jaillon O., Kandels-Lewis S., Karp-Boss L., Karsenti E., Krzic U., Not F., Ogata H., Pesant S., Raes J., Reynaud EG., Sardet C., Sieracki M., Speich S., Stemmann L., Sullivan MB., Sunagawa S., Velayoudon D., Weissenbach J. 2019. Community-Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems. Global Biogeochemical Cycles. DOI: 10.1029/2018GB006022.

  8. Chénard C., Wijaya W., Vaulot D., Lopes dos Santos A., Martin P., Kaur A., Lauro FM. 2019. Temporal and spatial dynamics of Bacteria, Archaea and protists in equatorial coastal waters. Scientific Reports 9:16390. DOI: 10.1038/s41598-019-52648-x.

  9. Crenn K., Bunk B., Spröer C., Overmann J., Jeanthon C. 2019. Complete Genome Sequence of the Silicimonas algicola Type Strain, a Representative of the Marine Roseobacter Group Isolated from the Cell Surface of the Marine Diatom Thalassiosira delicatula. Microbiology Resource Announcements 8:8–9. DOI: 10.1128/MRA.00108-19.

  10. Faure E., Not F., Benoiston A-S., Labadie K., Bittner L., Ayata S-D. 2019. Mixotrophic protists display contrasted biogeographies in the global ocean. The ISME Journal. DOI: 10.1038/s41396-018-0340-5.

  11. Flynn KJ., Mitra A., Anestis K., Anschütz AA., Calbet A., Ferreira GD., Gypens N., Hansen PJ., John U., Martin JL., Mansour JS., Maselli M., Medić N., Norlin A., Not F., Pitta P., Romano F., Saiz E., Schneider LK., Stolte W., Traboni C. 2019. Mixotrophic protists and a new paradigm for marine ecology: Where does plankton research go now? Journal of Plankton Research 41:375–391. DOI: 10.1093/plankt/fbz026.

  12. Gérikas Ribeiro C., Lopes dos Santos A., Marie D., Le Gall F., Probert I., Tragin M., Gourvil P., Vaulot D. 2019. Culturable diversity of Arctic phytoplankton during pack ice melting. Elementa: Science of the Anthropocene in press. DOI: 10.1101/642264v1.

  13. Gleason FH., Nagarkar M., Chambouvet A., Guillou L. 2019. A review of the characteristics of the dinoflagellate parasite Ichthyodinium chabelardi and its potential effect on fin fish populations. Marine and Freshwater Research. DOI: 10.1071/MF18207.

  14. Gorsky G, Bourdin G, Lombard F, Pedrotti ML, Audrain S, Bin N, Boss E, Bowler C, Cassar N, Caudan L, Chabot G, Cohen NR, Conan P, Cron D, De Vargas C, Dolan JR, Douville E, Elineau A, Flores JM, Ghiglione JF, Haëntjens N, Hertau M, John SG, Kelly RL, Koren I, Lin Y, Marie D, Moulin C, Moucherie Y, Pesant S, Picheral M, Poulain J, Pujo-Pay M, Reverdin G, Romac S, Sullivan MB, Trainic M, Tressol M, Troublé R, Vardi A, Voolstra CR, Wincker P, Agostini S, Banaigs B, Boissin E, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Thomas OP, Vega Thurber RL, Zoccola D, Planes S, Allemand D and Karsenti E, 2019. Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018). Front. Mar. Sci. 6:750, doi: 10.3389/fmars.2019.00750.

  15. Gregory AC., Zayed AA., Conceição-Neto N., Temperton B., Bolduc B., Alberti A., Ardyna M., Arkhipova K., Carmichael M., Cruaud C., Dimier C., Domínguez-Huerta G., Ferland J., Kandels S., Liu Y., Marec C., Pesant S., Picheral M., Pisarev S., Poulain J., Tremblay J-É., Vik D., Babin M., Bork P., Boss E., Bowler C., Cochrane G., de Vargas C., Follows M., Gorsky G., Grimsley N., Guidi L., Hingamp P., Iudicone D., Jaillon O., Kandels-Lewis S., Karp-Boss L., Karsenti E., Not F., Ogata H., Pesant S., Poulton N., Raes J., Sardet C., Speich S., Stemmann L., Sullivan MB., Sunagawa S., Wincker P. 2019. Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell:1–15. DOI: 10.1016/j.cell.2019.03.040.

  16. Guillot L., Delage L., Viari A. Vandenbrouck Y., Com E., Ritter A., Lavigne R., Marie D., Peterlongo P., Potin P., Pineau P. 2019. Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes. BMC Genomics 20, 56, doi: 10.1186/s12864-019-5431-9.

  17. Gutierrez-Rodriguez A., Stukel MR., Lopes dos Santos A., Biard T., Scharek R., Vaulot D., Landry MR., Not F. 2019. High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding. The ISME Journal 13:964–976. DOI: 10.1038/s41396-018-0322-7.

  18. Ibarbalz FM., Henry N., Brandão MC., Martini S., Busseni G., Byrne H., Coelho LP., Endo H., Gasol JM., Gregory AC., Mahé F., Rigonato J., Royo-Llonch M., Salazar G., Sanz-Sáez I., Scalco E., Soviadan D., Zayed AA., Zingone A., Labadie K., Ferland J., Marec C., Kandels S., Picheral M., Dimier C., Poulain J., Pisarev S., Carmichael M., Pesant S., Babin M., Boss E., Iudicone D., Jaillon O., Acinas SG., Ogata H., Pelletier E., Stemmann L., Sullivan MB., Sunagawa S., Bopp L., de Vargas C., Karp-Boss L., Wincker P., Lombard F., Bowler C., Zinger L., Acinas SG., Babin M., Bork P., Boss E., Bowler C., Cochrane G., de Vargas C., Follows M., Gorsky G., Grimsley N., Guidi L., Hingamp P., Iudicone D., Jaillon O., Kandels S., Karp-Boss L., Karsenti E., Not F., Ogata H., Pesant S., Poulton N., Raes J., Sardet C., Speich S., Stemmann L., Sullivan MB., Sunagawa S., Wincker P. 2019. Global trends in marine plankton diversity across kingdoms of life. Cell 179:1084-1097.e21. DOI: 10.1016/j.cell.2019.10.008.

  19. John U., Lu Y., Wohlrab S., Groth M., Janouškovec J., Kohli GS., Mark FC., Bickmeyer U., Farhat S., Felder M., Frickenhaus S., Guillou L., Keeling PJ., Moustafa A., Porcel BM., Valentin K., Glöckner G. 2019. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. Science Advances 5:eaav1110. DOI: 10.1126/sciadv.aav1110.

  20. Kashiyama Y., Yokoyama A., Shiratori T., Hess S., Not F., Bachy C., Gutierrez-Rodriguez A., Kawahara J., Suzaki T., Nakazawa M., Ishikawa T., Maruyama M., Wang M., Chen M., Gong Y., Seto K., Kagami M., Hamamoto Y., Honda D., Umetani T., Shihongi A., Kayama M., Matsuda T., Taira J., Yabuki A., Tsuchiya M., Hirakawa Y., Kawaguchi A., Nomura M., Nakamura A., Namba N., Matsumoto M., Tanaka T., Yoshino T., Higuchi R., Yamamoto A., Maruyama T., Yamaguchi A., Uzuka A., Miyagishima S., Tanifuji G., Kawachi M., Kinoshita Y., Tamiaki H. 2019. Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth. The ISME Journal:1. DOI: 10.1038/s41396-019-0377-0.

  21. Lambert S., Tragin M., Lozano J-C., Ghiglione J-F., Vaulot D., Bouget F-Y., Galand PE. 2019. Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations. The ISME Journal 13:388–401. DOI: 10.1038/s41396-018-0281-z.

  22. Lelchat F., Mocaer PY., Ojima T., Michel G., Sarthou G., Bucciarelli E., Cérantola S., Colliec-Jouault S., Boisset C., Baudoux A-C. 2019. Viral degradation of marine bacterial exopolysaccharides. FEMS Microbiology Ecology. DOI: 10.1093/femsec/fiz079.

  23. Metz S., Lopes dos Santos A., Berman MC., Bigeard E., Licursi M., Not F., Lara E., Unrein F. 2019. Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing. FEMS Microbiology Ecology. DOI: 10.1093/femsec/fiz038.

  24. Morard R., Füllberg A., Brummer G-JA., Greco M., Jonkers L., Wizemann A., Weiner AKM., Darling K., Siccha M., Ledevin R., Kitazato H., de Garidel-Thoron T., de Vargas C., Kucera M. 2019. Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides. PLOS ONE 14:e0225246. DOI: 10.1371/journal.pone.0225246.

  25. Nettersheim BJ., Brocks JJ., Schwelm A., Hope JM., Not F., Lomas M., Schmidt C., Schiebel R., Nowack ECM., De Deckker P., Pawlowski J., Bowser SS., Bobrovskiy I., Zonneveld K., Kucera M., Stuhr M., Hallmann C. 2019. Putative sponge biomarkers in unicellular Rhizaria question an early rise of animals. Nature Ecology and Evolution 3. DOI: 10.1038/s41559-019-0806-5.

  26. Planes S., Allemand D., Agostini S., Banaigs B., Boissin E., Boss E., Bourdin G., Bowler C., Douville E., Flores JM., Forcioli D., Furla P., Galand PE., Ghiglione J-F., Gilson E., Lombard F., Moulin C., Pesant S., Poulain J., Reynaud S., Romac S., Sullivan MB., Sunagawa S., Thomas OP., Troublé R., de Vargas C., Vega Thurber R., Voolstra CR., Wincker P., Zoccola D. 2019. The Tara Pacific expedition—A pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean. PLOS Biology 17:e3000483. DOI: 10.1371/journal.pbio.3000483.

  27. Ramond P., Sourisseau M., Simon N., Romac S., Schmitt S., Rigaut-Jalabert F., Henry N., de Vargas C., Siano R. 2019. Coupling between taxonomic and functional diversity in protistan coastal communities. Environmental Microbiology 21:730–749. DOI: 10.1111/1462-2920.14537.

  28. Rombouts I., Simon N., Aubert A., Cariou T., Feunteun E., Guérin L., Hoebeke  M., McQuatters-Gollop, A., Rigaut-Jalabert F., Artigas L.F.  2019. Changes in marine phytoplankton diversity: assessment under the Marine Strategy Framework Directive. Ecological Indicators doi: 10.1016/j.ecolind.2019.02.009.

  29. Saha M., Berdalet E., Carotenuto Y., Fink P., Harder T., John U., Not F., Pohnert G., Potin P., Selander E., Vyverman W., Wichard T., Zupo V., Steinke M. 2019. Using chemical language to shape future marine health. Frontiers in Ecology and the Environment 17:530–537. DOI: 10.1002/fee.2113.

  30. Saint-Béat B., Fath BD., Aubry C., Colombet J., Dinasquet J., Fortier L., Galindo V., Grondin P-L., Joux F., Lalande C., LeBlanc M., Raimbault P., Sime-Ngando T., Tremblay J-E., Vaulot D., Maps F., Babin M. 2019. Contrasting pelagic ecosystem functioning in eastern and western Baffin Bay revealed by trophic network modeling. Elementa: Science of the Anthropocene. DOI: http://doi.org/10.1525/elementa.397

  31. Salazar G., Paoli L., Alberti A., Huerta-Cepas J., Ruscheweyh H-J., Cuenca M., Field CM., Coelho LP., Cruaud C., Engelen S., Gregory AC., Labadie K., Marec C., Pelletier E., Royo-Llonch M., Roux S., Sánchez P., Uehara H., Zayed AA., Zeller G., Carmichael M., Dimier C., Ferland J., Kandels S., Picheral M., Pisarev S., Poulain J., Acinas SG., Babin M., Bork P., Bowler C., de Vargas C., Guidi L., Hingamp P., Iudicone D., Karp-Boss L., Karsenti E., Ogata H., Pesant S., Speich S., Sullivan MB., Wincker P., Sunagawa S., Acinas SG., Babin M., Bork P., Boss E., Bowler C., Cochrane G., de Vargas C., Follows M., Gorsky G., Grimsley N., Guidi L., Hingamp P., Iudicone D., Jaillon O., Kandels-Lewis S., Karp-Boss L., Karsenti E., Not F., Ogata H., Pesant S., Poulton N., Raes J., Sardet C., Speich S., Stemmann L., Sullivan MB., Sunagawa S., Wincker P. 2019. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 179:1068-1083.e21. DOI: 10.1016/j.cell.2019.10.014.

  32. Sandin MM., Pillet L., Biard T., Poirier C., Bigeard E., Romac S., Suzuki N., Not F. 2019. Time Calibrated Morpho-molecular Classification of Nassellaria (Radiolaria). Protist 170:187–208. DOI: 10.1016/j.protis.2019.02.002.

  33. Sanfilippo JE., Garczarek L., Partensky F., Kehoe DM. 2019. Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis. Annual Review of Microbiology 73:407–433. DOI: 10.1146/annurev-micro-020518-115738.

  34. Sanfilippo JE., Nguyen AA., Garczarek L., Karty JA., Pokhrel S., Strnat JA., Partensky F., Schluchter WM., Kehoe DM. 2019. Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus. Proceedings of the National Academy of Sciences 116:6457–6462. DOI: 10.1073/pnas.1810491116.

  35. Sieracki ME., Poulton NJ., Jaillon O., Wincker P., de Vargas C., Rubinat-Ripoll L., Stepanauskas R., Logares R., Massana R. 2019. Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems. Scientific Reports 9:6025. DOI: 10.1038/s41598-019-42487-1.

  36. Tragin M., Vaulot D. 2019. Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding. Scientific Reports 9:5190. DOI: 10.1038/s41598-019-41680-6.

  37. Yamada Y., Guillemette R., Baudoux AC., Patel N., Azam F. 2019. Viral attachment to biotic and abiotic surfaces in seawater. Applied and Environmental Microbiology. DOI: 10.1128/AEM.01687-19.

2018

  1. Bass D., Czech L., Williams BAP., Berney C., Dunthorn M., Mahé F., Torruella G., Stentiford GD., Williams TA. 2018. Clarifying the Relationships between Microsporidia and Cryptomycota. Journal of Eukaryotic Microbiology 65:773–782. DOI: 10.1111/jeu.12519.

  2. Bass D., Tikhonenkov DV., Foster R., Dyala P., Janouskovec J., Keeling PJ., Gardner M., Neuhauser S., Hartikainen H., Mylnikov AP, Berney, C. 2018. Rhizarian ‘ Novel Clade 10 ’ Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates , including Aquavolon n . gen . Journal of Eukaryotic Microbiology:1–15. DOI: 10.1111/jeu.12524.

  3. Bulat S.A., Doronin M.V., Pavlov G.P., Karlov D.S., Marie D., Petit J-R. 2018. Unknown widespread iron- and sulfur-oxidizing bacteria beneath the East Antarctic ice sheet. Paleontol. J. 52, 1196–1203, doi: https://doi.org/10.1134/S003103011810007610.1134/S0031030118100076.

  4. Carradec Q., Pelletier E., Da Silva C., Alberti A., Seeleuthner Y., Blanc-Mathieu R., Lima-Mendez G., Rocha F., Tirichine L., Labadie K., Kirilovsky A., Bertrand A., Engelen S., Madoui M-A., Méheust R., Poulain J., Romac S., Richter DJ., Yoshikawa G., Dimier C., Kandels-Lewis S., Picheral M., Searson S., Jaillon O., Aury J-M., Karsenti E., Sullivan MB., Sunagawa S., Bork P., Not F., Hingamp P., Raes J., Guidi L., Ogata H., de Vargas C., Iudicone D., Bowler C., Wincker P. 2018. A global ocean atlas of eukaryotic genes. Nature Communications 9:373. DOI: 10.1038/s41467-017-02342-1.

  5. Clerissi C., Brunet S., Vidal-Dupiol J., Adjeroud M., Lepage P., Guillou L., Escoubas J-M., Toulza E. 2018. Protists Within Corals: The Hidden Diversity. Frontiers in Microbiology 9:2043. DOI: 10.3389/fmicb.2018.02043.

  6. Crenn K., Duffieux D., Jeanthon C. 2018. Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations. Frontiers in Microbiology 9:1–12. DOI: 10.3389/fmicb.2018.02879.

  7. Decelle J., Carradec Q., Pochon X., Henry N., Romac S., Dunthorn M., Kourlaiev A., Voolstra CR., Wincker P., de Vargas C. 2018. Worldwide occurrence and activity of the reef-building coral symbiont Symbiodinium in the open ocean. Current Biology:1–9. DOI: 10.1016/j.cub.2018.09.024.

  8. del Campo J., Kolisko M., Boscaro V., Santoferrara LF., Nenarokov S., Massana R., Guillou L., Simpson A., Berney C., de Vargas C., Brown MW., Keeling PJ., Wegener Parfrey L. 2018. EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology 16:e2005849. DOI: 10.1371/journal.pbio.2005849.

  9. Demory D., Baudoux A-C., Monier A., Simon N., Six C., Ge P., Rigaut-Jalabert F., Marie D., Sciandra A., Bernard O., Rabouille S. 2018. Picoeukaryotes of the Micromonas genus: sentinels of a warming ocean. The ISME Journal. DOI: 10.1038/s41396-018-0248-0.

  10. Farhat S., Florent I., Noel B., Kayal E., Da Silva C., Bigeard E., Alberti A., Labadie K., Corre E., Aury J-M., Rombauts S., Wincker P., Guillou L., Porcel B.M. 2018. Comparative time-scale gene expression analysis highlights the Infection processes of two Amoebophrya strains. Front Microbiol. 9:2251, doi: 10.3389/fmicb.2018.02251.

  11. Fernandez S., Sandin M.M., Beaulieu P.G., Clusa L., Martinez J.L., Ardura A., García-Vázquez E.. 2018. Environmental DNA for freshwater fish monitoring: insights for conservation within a protected area. PeerJ., 6:e4486. doi: 10.7717/peerj.4486.

  12. Flegontova O., Flegontov P., Malviya S., Poulain J., de Vargas C., Bowler C., Lukeš J., Horák A. 2018. Neobodonids are dominant kinetoplastids in the global ocean. Environmental Microbiology 20:878–889. DOI: 10.1111/1462-2920.14034.

  13. Gérikas Ribeiro C., Lopes dos Santos A., Marie D., Pereira Brandini F., Vaulot D. 2018. Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria. The ISME Journal 12:1360–1374. DOI: 10.1038/s41396-018-0050-z.

  14. Grébert T., Doré H., Partensky F., Farrant GK., Boss ES., Picheral M., Guidi L., Pesant S., Scanlan DJ., Wincker P., Acinas SG., Kehoe DM., Garczarek L. 2018. Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria. Proceedings of the National Academy of Sciences:201717069. DOI: 10.1073/pnas.1717069115.

  15. Hume B.C.C., Ziegler M., Poulain J., Pochon X., Romac S., Boissin E., de Vargas C., Planes S., Wincker P., Voolstra C.R. 2018. An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region. PeerJ., 6:e4816. doi: 10.7717/peerj.4816.

  16. Jacquemot L., Bettarel Y., Monjol J., Corre E., Halary S., Desnues C., Bouvier T., Ferrier-Pagès C., Baudoux A-C. 2018. Therapeutic Potential of a New Jumbo Phage That Infects Vibrio coralliilyticus, a Widespread Coral Pathogen. Frontiers in Microbiology 9:1–16. DOI: 10.3389/fmicb.2018.02501.

  17. Koenig I., Mulot M., and Mitchell E. A. D. 2018. Taxonomic and functional traits responses of Sphagnum peatland testate amoebae to experimentally manipulated water table. Ecol. Indicat. 85, 342–351, doi: 10.1016/j.ecolind.2017.10.017.

  18. Kuwata A., Yamada K., Ichinomiya M., Yoshikawa S., Tragin M., Vaulot D., Lopes dos Santos A. 2018. Bolidophyceae, a Sister Picoplanktonic Group of Diatoms – A Review. Front. Mar. Sci. 5:370. DOI: 10.3389/fmars.2018.00370.

  19. Leblanc K., Quéguiner B., Diaz, F., Cornet V., Michel-Rodriguez M., Durrieu de Madron X., Bowler C., Malviya S., Thyssen M., Grégori G., Rembauville M., Grosso O.,Poulain J., de Vargas C., Pujo-Pay M., Conan P. 2018. Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export. Nat. Commun. 9, 953, doi: 10.1038/s41467-018-03376-9.

  20. Lehours A-C., Enault F., Boeuf, D., Jeanthon C. 2018. Biogeographic patterns of aerobic anoxygenic phototrophic bacteria reveal an ecological consistency of phylogenetic clades in different oceanic biomes. Sci Rep 8, 4105. doi: 10.1038/s41598-018-22413-7.

  21. López-Escardó D., Paps J., de Vargas C., Massana R., Ruiz-Trillo I., del Campo J. 2018. Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. Scientific Reports 8:9106. DOI: 10.1038/s41598-018-27509-8.

  22. Meng A., Corre E., Probert I., Gutierrez-Rodriguez A., Siano R., Annamale A., Alberti A., Da Silva C., Wincker P., Le Crom S., Not F., Bittner L. 2018. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Mol. Ecol. doi: 10.1111/mec.14579.

  23. Meng A., Marchet C., Corre E., Peterlongo P., Alberti A., Da Silva C., Wincker P., Pelletier E., Probert I., Decelle J., Le Crom S., Not F., Bittner L. 2018. A de novo approach to disentangle partner identity and function in holobiont systems. Microbiome 6:105. DOI: 10.1186/s40168-018-0481-9.

  24. Mercier C., Lossouarn J., Nesbø CL., Haverkamp THA., Baudoux AC., Jebbar M., Bienvenu N., Thiroux S., Dupont S., Geslin C. 2018. Two viruses, MCV1 and MCV2, which infect Marinitoga bacteria isolated from deep-sea hydrothermal vents: functional and genomic analysis. Environ. Microbiol. 20:577–587. DOI: 10.1111/1462-2920.13967.

  25. Morard R., Garet-Delmas M-J., Mahé F., Romac S., Poulain J., Kucera M., de Vargas C. 2018. Surface ocean metabarcoding confirms limited diversity in planktonic foraminifera but reveals unknown hyper-abundant lineages. Scientific Reports 8:2539. DOI: 10.1038/s41598-018-20833-z.

  26. Mordret S., Piredda R., Vaulot D., Montresor M., Kooistra W.H.C.F., Sarno D. 2018. dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol Ecol Resour., doi: 10.1111/1755-0998.12781.

  27. Partensky F., Mella-Flores D., Six C., Garczarek L., Czjzek M., Marie D., Kotabová E., Felcmanová K., Prášil O. 2018. Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex. Photosynthesis Research 138:57–71. DOI: 10.1007/s11120-018-0539-3.

  28. Partensky F., Six C., Ratin M., Garczarek L., Vaulot D., Probert I., Calteau A., Gourvil P., Marie D., Grébert T., Bouchier C., Le Panse S., Gachenot M., Rodríguez F., Garrido JL. 2018. A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle. Scientific Reports 8:9142. DOI: 10.1038/s41598-018-27542-7.

  29. Partensky F., Vaulot D. 2018. Alain Sournia, phycologist and philosopher (1940-2018). Cahiers de Biologie Marine 59:403–407. DOI: 10.21411/CBM.A.EA424D0A.

  30. Paskerova GG., Miroliubova TS., Diakin A., Kováčiková M., Valigurová A., Guillou L., Aleoshin V V., Simdyanov TG. 2018. Fine structure and Molecular Phylogenetic Position of Two Marine Gregarines, Selenidium pygospionis sp. n. and S. pherusae sp. n., with Notes on the Phylogeny of Archigregarinida (Apicomplexa). Protist 169:826–852. DOI: 10.1016/j.protis.2018.06.004.

  31. Perez-Sepulveda B., Pitt F., N’Guyen AN., Ratin M., Garczarek L., Millard A., Scanlan DJ. 2018. Relative stability of ploidy in a marine Synechococcus across various growth conditions. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12614.

  32. Piredda R., Claverie J., Decelle J., de Vargas C., Dunthorn M., Edvardsen B., Eikrem W., Forster D., Kooistra WHCF., Logares R., Massana R., Montresor M., Not F., Ogata H., Pawlowski J., Romac S., Sarno D., Stoeck T., Zingone A. 2018. Diatom diversity through HTS-metabarcoding in coastal European seas. Scientific Reports 8:18059. DOI: 10.1038/s41598-018-36345-9.

  33. Pittera J., Jouhet J., Breton S., Garczarek L., Partensky F., Maréchal É., Nguyen NA., Doré H., Ratin M., Pitt FD., Scanlan DJ., Six C. 2018. Thermoacclimation and genome adaptation of the membrane lipidome in marine Synechococcus. Environmental Microbiology 20:612–631. DOI: 10.1111/1462-2920.13985.

  34. Qui-Minet Z.N., Delaunay C., Grall J.,  Six C., Cariou T., Bohner O., Legrand E., Davoult D., Martin S. 2018. The role of local environmental changes on maerl and its associated non-calcareous epiphytic flora in the Bay of Brest. Estuar Coast Shelf Sci., 208, doi: 10.1016/j.ecss.2018.04.032.

  35. Richter DJ., Fozouni P., Eisen MB., King N. 2018. Gene family innovation, conservation and loss on the animal stem lineage. eLife 7:1–43. DOI: 10.7554/eLife.34226.

  36. Seeleuthner Y., Mondy S., Lombard V., Carradec Q., Pelletier E., Wessner M., Leconte J., Mangot J-F., Poulain J., Labadie K., Logares R., Sunagawa S., de Berardinis V., Salanoubat M., Dimier C., Kandels-Lewis S., Picheral M., Searson S., Pesant S., Poulton N., Stepanauskas R., Bork P., Bowler C., Hingamp P., Sullivan MB., Iudicone D., Massana R., Aury J-M., Henrissat B., Karsenti E., Jaillon O., Sieracki M., de Vargas C., Wincker P. 2018. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans. Nature Communications 9:310. DOI: 10.1038/s41467-017-02235-3.

  37. Ser-Giacomi E., Zinger L., Malviya S., De Vargas C., Karsenti E., Bowler C., De Monte S. 2018. Ubiquitous abundance distribution of non-dominant plankton across the global ocean. Nature Ecology & Evolution. DOI: 10.1038/s41559-018-0587-2.

  38. Siano R., Chapelle A., Antoine V., Michel-Guillou E., Rigaut-Jalabert F., Guillou L., Hégaret H., Leynaert A., Curd A. 2018. Citizen participation in monitoring phytoplankton seawater discolorations. Marine Policy. DOI: 10.1016/j.marpol.2018.01.022.

  39. Simdyanov TG., Paskerova GG., Valigurová A., Diakin A., Kováčiková M., Schrével J., Guillou L., Dobrovolskij AA., Aleoshin V V. 2018. First Ultrastructural and Molecular Phylogenetic Evidence from the Blastogregarines, an Early Branching Lineage of Plesiomorphic Apicomplexa. Protist 169:697–726. DOI: 10.1016/j.protis.2018.04.006.

  40. Stern R., Kraberg A., Bresnan E., Kooistra WHCF., Lovejoy C., Montresor M., Morán XAG., Not F., Salas R., Siano R., Vaulot D., Amaral-Zettler L., Zingone A., Metfies K. 2018. Molecular analyses of protists in long-term observation programmes—current status and future perspectives. Journal of Plankton Research. DOI: 10.1093/plankt/fby035.

  41. Tragin M., Vaulot D. 2018. Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset. Scientific Reports 8:14020. DOI: 10.1038/s41598-018-32338-w.

  42. Tragin M., Zingone A., Vaulot D. 2018. Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of the 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta. Environmental Microbiology 20:506–520. DOI: 10.1111/1462-2920.13952.

  43. Villar E., Dani V., Bigeard E., Linhart T., Mendez-Sandin M., Bachy C., Six C., Lombard F., Sabourault C., Not F. 2018. Symbiont Chloroplasts Remain Active During Bleaching-Like Response Induced by Thermal Stress in Collozoum pelagicum (Collodaria, Retaria). Frontiers in Marine Science 5:1–11. DOI: 10.3389/fmars.2018.00387.

  44. Villar E., Vannier T., Vernette C., Lescot M., Cuenca M., Alexandre A., Bachelerie P., Rosnet T., Pelletier E., Sunagawa S., Hingamp P. 2018. The Ocean Gene Atlas: exploring the biogeography of plankton genes online. Nucleic Acids Research:1–7. DOI: 10.1093/nar/gky376.

  45. Vincent FJ., Colin S., Romac S., Scalco E., Bittner L., Garcia Y., Lopes RM., Dolan JR., Zingone A., de Vargas C., Bowler C. 2018. The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean. The ISME Journal. DOI: 10.1038/s41396-017-0029-1.

  46. Ward GM., Neuhauser S., Groben R., Ciaghi S., Berney C., Romac S., Bass D. 2018. Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae. Journal of Eukaryotic Microbiology:1–13. DOI: 10.1111/jeu.12501.

  47. Zhong KX., Suttle CA., Baudoux A., Derelle E., Colombet J., Cho A., Caleta J., Six C., Jacquet S., Millard AD. 2018. A New Freshwater Cyanosiphovirus Harboring Integrase. Frontiers in Microbiology 9:1–15. DOI: 10.3389/fmicb.2018.02204.

2017

  1. Alberti A., Poulain J., Engelen S., Labadie K., Romac S., Ferrera I., Albini G., Aury J-M., Belser C., Bertrand A., Cruaud C., Da Silva C., Dossat C., Gavory F., Gas S., Guy J., Haquelle M., Jacoby E., Jaillon O., Lemainque A., Pelletier E., Samson G., Wessner M., Bazire P., Beluche O., Bertrand L., Besnard-Gonnet M., Bordelais I., Boutard M., Dubois M., Dumont C., Ettedgui E., Fernandez P., Garcia E., Aiach NG., Guerin T., Hamon C., Brun E., Lebled S., Lenoble P., Louesse C., Mahieu E., Mairey B., Martins N., Megret C., Milani C., Muanga J., Orvain C., Payen E., Perroud P., Petit E., Robert D., Ronsin M., Vacherie B., Acinas SG., Royo-Llonch M., Cornejo-Castillo FM., Logares R., Fernández-Gómez B., Bowler C., Cochrane G., Amid C., Hoopen P Ten., De Vargas C., Grimsley N., Desgranges E., Kandels-Lewis S., Ogata H., Poulton N., Sieracki ME., Stepanauskas R., Sullivan MB., Brum JR., Duhaime MB., Poulos BT., Hurwitz BL., Acinas SG., Bork P., Boss E., Bowler C., De Vargas C., Follows M., Gorsky G., Grimsley N., Hingamp P., Iudicone D., Jaillon O., Kandels-Lewis S., Karp-Boss L., Karsenti E., Not F., Ogata H., Pesant S., Raes J., Sardet C., Sieracki ME., Speich S., Stemmann L., Sullivan MB., Sunagawa S., Wincker P., Pesant S., Karsenti E., Wincker P. 2017. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Scientific Data 4:170093. DOI: 10.1038/sdata.2017.93.

  2. Alves-de-Souza C., Benevides TS., Santos JBO., Von Dassow P., Guillou L., Menezes M. 2017. Does environmental heterogeneity explain temporal β diversity of small eukaryotic phytoplankton? Example from a tropical eutrophic coastal lagoon. Journal of Plankton Research:1–17. DOI: 10.1093/plankt/fbx026.

  3. Arrigoni R, Vacherie B, Benzoni F, Stefani F, Karsenti E, Jaillon O, Not F, Nunes F, Payri C, Wincker P, Barbe V. 2017. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications. Mol. Ecol. Resour., 17(5):1054-1071. doi: 10.1111/1755-0998.12640.

  4. Balzano S., Percopo I., Siano R., Gourvil P., Chanoine M., Marie D., Vaulot D., Sarno D. 2017. Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex. Journal of Phycology 53:161–187. DOI: 10.1111/jpy.12489.

  5. Berney C., Ciuprina A., Bender S., Brodie J., Edgcomb V., Kim E., Rajan J., Parfrey LW., Adl S., Audic S., Bass D., Caron DA., Cochrane G., Czech L., Dunthorn M., Geisen S., Glöckner FO., Mahé F., Quast C., Kaye JZ., Simpson AGB., Stamatakis A., del Campo J., Yilmaz P., de Vargas C. 2017. UniEuk : Time to Speak a Common Language in Protistology! Journal of Eukaryotic Microbiology 64:407–411. DOI: 10.1111/jeu.12414.

  6. Biard T., Bigeard E., Audic S., Poulain J., Gutierrez-Rodriguez A., Pesant S., Stemmann L., Not F. 2017. Biogeography and diversity of Collodaria (Radiolaria) in the global ocean. The ISME Journal 11:1331–1344. DOI: 10.1038/ismej.2017.12.

  7. Botebol H., Lelandais G., Six C., Lesuisse E., Meng A., Bittner L., Lecrom S., Sutak R., Lozano J-C., Schatt P., Vergé V., Blain S., Bouget F-Y. 2017. Acclimation of a low iron adapted Ostreococcus strain to iron limitation through cell biomass lowering. Scientific Reports 7:327. DOI: 10.1038/s41598-017-00216-6.

  8. Carr M., Richter D.J., Fozouni P., Smith T.J., Jeuck A., Leadbeater B.S.C., Nitsche F. 2017. A six-gene phylogeny provides new insights into choanoflagellate evolution. Mol. Phylogenet. Evol.,107:166-178, doi: 10.1016/j.ympev.2016.10.011.

  9. Chust G., Vogt M., Benedetti F., Nakov T., Villéger S., Aubert A., Vallina SM., Righetti D., Not F., Biard T., Bittner L., Benoiston A-S., Guidi L., Villarino E., Gaborit C., Cornils A., Buttay L., Irisson J-O., Chiarello M., Vallim AL., Blanco-Bercial L., Basconi L., Ayata S-D. 2017. Mare Incognitum: A Glimpse into Future Plankton Diversity and Ecology Research. Frontiers in Marine Science 4. DOI: 10.3389/fmars.2017.00068.

  10. Colin S., Coelho LP., Sunagawa S., Bowler C., Karsenti E., Bork P., Pepperkok R., de Vargas C. 2017. Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes. eLife 6:1–15. DOI: 10.7554/eLife.26066.

  11. Cuvelier ML., Guo J., Ortiz AC., van Baren MJ., Tariq MA., Partensky F., Worden AZ. 2017. Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress. PLOS ONE 12:e0172135. DOI: 10.1371/journal.pone.0172135.

  12. Dal Bello, M., Leclerc, J., Benedetti-Cecchi, L., Andrea De Lucia, G., Arvanitidis, C., Van Avesaath, P., . . . Hummel, H. 2017. Consistent patterns of spatial variability between NE Atlantic and Mediterranean rocky shores. J. Mar. Biol. Assoc. U. K., 97(3), 539-547. doi:10.1017/S0025315416001491.

  13. Demory D., Arsenieff L., Simon N., Six C., Rigaut-jalabert F., Marie D., Ge P., Bigeard E., Jacquet S., Sciandra A., Bernard O., Rabouille S., Baudoux A. 2017. Temperature is a key factor in Micromonas – virus interactions. The ISME Journal:1–12. DOI: 10.1038/ismej.2016.160.

  14. Dorrell RG., Gile G., McCallum G., Méheust R., Bapteste EP., Klinger CM., Brillet-Guéguen L., Freeman KD., Richter DJ., Bowler C. 2017. Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife 6:1–45. DOI: 10.7554/eLife.23717.

  15. Egas C., Henríquez-Castillo C., Delherbe N., Molina E., Dos Santos AL., Lavin P., De La Iglesia R., Vaulot D., Trefault N. 2017. Short timescale dynamics of phytoplankton in Fildes Bay, Antarctica. Antarctic Science 29:217–228. DOI: 10.1017/S0954102016000699.

  16. Ereskovsky A V., Richter DJ., Lavrov D V., Schippers KJ., Nichols SA. 2017. Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA. PLOS ONE 12:1–25. DOI: 10.1371/journal.pone.0183002.

  17. Fouilland E., Trottet A., Alves-de-Souza C., Bonnet D., Bouvier T., Bouvy M., Boyer S., Guillou L., Hatey E., Jing H., Leboulanger C., Le Floc'h E., Liu H., Mas S., Mostajir B., Nouguier J., Pecqueur D., Rochelle-Newall E., Roques C., Salles C., Tournoud M.G., Vasseur C., Vidussi F. 2017. Significant change in marine plankton structure and carbon production after the addition of river water in a mesocosm experiment. Microb Ecol., 74(2):289-301. doi: 10.1007/s00248-017-0962-6.

  18. Geisen S., Mitchell E.A.D., Wilkinson D.M. et al. 2017. Soil protistology rebooted : 30 fundamental questions to start with. Soil Biol.Biochem., 94–103. doi: 10.1016/j.soilbio.2017.04.001.

  19. Gérikas Ribeiro C., Marie D., Lopes dos Santos A.,  Pereira Brandini F., Vaulot D. 2017. Estimating microbial populations by flow cytometry: Comparison between instruments. Limnol.  Oceanogr. Methods, 14 (11), 750 - 758. doi: 10.1002/lom3.10135.

  20. Grzebyk D., Audic S., Lasserre B., Abadie E., de Vargas C., Bec B. 2017. Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene. Harmful Algae, 68:1-16, doi: 10.1016/j.hal.2017.06.003.

  21. Gutierrez-Rodriguez A., Pillet L., Biard T., Said-Ahmad W., Amrani A., Simó R., Not F. 2017. Dimethylated sulfur compounds in symbiotic protists: A potentially significant source for marine DMS(P). Limnology and Oceanography. DOI: 10.1002/lno.10491.

  22. Hubas C., Boeuf D., Jesus B., Thiney N., Bozec Y., Jeanthon C. 2017 A nanoscale study of carbon and nitrogen fluxes in mats of purple sulfur bacteria: implications for carbon cycling at the surface of coastal sediments. Frontiers in Microbiology 8:1995. DOI: 10.3389/fmicb.2017.01995.

  23. Hummel H., Van Avesaath P., Wijnhoven S., Kleine-Schaars L., Degraer S., Kerckhof F., . . . Rilov G. 2017. Geographic patterns of biodiversity in European coastal marine benthos. J. Mar. Biol. Assoc. U. K.,, 97(3), 507-523. doi:10.1017/S0025315416001119.

  24. Karlov D., Marie D., Sumbatyan D.A. , Chuvochina M., Kulichevskaya I.S., Alekhina I, Bulat S. 2017. Microbial communities within the water column of freshwater Lake Radok, East Antarctica: predominant 16S rDNA phylotypes and bacterial cultures.” Polar Biol. 40: 823-836. doi: 10.1007/s00300-016-2008-9.

  25. KleinJan H., Jeanthon C., Boyen C., Dittami SM. 2017. Exploring the cultivable Ectocarpus microbiome. Frontiers in Microbiology 8:2456. DOI: 10.3389/fmicb.2017.02456.

  26. Kotta, J., Orav-Kotta, H., Jänes, H., Hummel, H., Arvanitidis, C., Van Avesaath, P., . . . Weslawski, J. 2017. Essence of the patterns of cover and richness of intertidal hard bottom communities: A pan-European study. J. Mar. Biol. Assoc. U. K., 97(3), 525-538. doi:10.1017/S0025315416001351.

  27. Le Hérissé A., Vecoli M., Guidat C., Not F., Breuer P. et al. .2017 Middle Ordovician acritarchs and problematic organic-walled microfossils from the Saq-Hanadir transitional beds in the QSIM-801 well, Saudi Arabia. Rev. Micropaleontol., 2017, 60 (3), 289 - 318, doi:10.1016/j.revmic.2017.08.001.

  28. Leles SG., Mitra A., Flynn KJ., Stoecker DK., Hansen PJ., Calbet A., McManus GB., Sanders RW., Caron DA., Not F., Hallegraeff GM., Pitta P., Raven JA., Johnson MD., Glibert PM., Våge S. 2017. Oceanic protists with different forms of acquired phototrophy display contrasting biogeographies and abundance. Proceedings of the Royal Society B: Biological Sciences 284:20170664. DOI: 10.1098/rspb.2017.0664.

  29. Lopes dos Santos A., Gourvil P., Tragin M., Noël M-H., Decelle J., Romac S., Vaulot D. 2017. Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. The ISME Journal 11:512–528. DOI: 10.1038/ismej.2016.120.

  30. Lopes dos Santos A., Pollina T., Gourvil P., Corre E., Marie D., Garrido JL., Rodríguez F., Noël M-H., Vaulot D., Eikrem W. 2017. Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Scientific Reports 7:14019. DOI: 10.1038/s41598-017-12412-5.

  31. Mahé F., de Vargas C., Bass D., Czech L., Stamatakis A., Lara E., Singer D., Mayor J., Bunge J., Sernaker S., Siemensmeyer T., Trautmann I., Romac S., Berney C., Kozlov A., Mitchell EAD., Seppey CVW., Egge E., Lentendu G., Wirth R., Trueba G., Dunthorn M. 2017. Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nature Ecology & Evolution 1:0091. DOI: 10.1038/s41559-017-0091.

  32. Mahmoud RM., Sanfilippo JE., Nguyen AA., Strnat JA., Partensky F., Garczarek L., Abo El Kassem N., Kehoe DM., Schluchter WM. 2017. Adaptation to Blue Light in Marine Synechococcus Requires MpeU, an Enzyme with Similarity to Phycoerythrobilin Lyase Isomerases. Frontiers in Microbiology 8:243. DOI: 10.3389/fmicb.2017.00243.

  33. Mangot J., Logares R., Sánchez P., Latorre F., Seeleuthner Y., Mondy S., Sieracki ME., Jaillon O., Wincker P., Vargas C de., Massana R. 2017. Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells. Scientific Reports 7:41498. DOI: 10.1038/srep41498.

  34. Marie D., Le Gall F., Edern R., Gourvil P., Vaulot D. 2017. Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry. Journal of Phycology 53:271–282. DOI: 10.1111/jpy.12495.

  35. McQuatters-Gollop A., Johns D.G. , Bresnan E., Skinner J., Rombouts I,, Stern R., Aubert A., Johansen M., Bedford J., Knights A. 2017. From microscope to management: The critical value of plankton taxonomy to marine policy and biodiversity conservation. Mar. Policy, 83, 1-10, doi: 10.1016/j.marpol.2017.05.022.

  36. Ruiz E., Baudoux A., Nathalie S., Sandaa R., Thingstad TF. 2017. Micromonas vs Virus : new experimental insights challenge viral impact. Environmental Microbiology. DOI: 10.1111/462-2920.13733.

  37. Mocaër P-Y., Baudoux A. 2017. Les virus au service de l ’écologie marine. Virologie 21:160–172. DOI: 10.1684/vir.2017.0704.

  38. Morard R., Lejzerowicz F., Darling K.F., Lecroq-Bennet B., Winther Pedersen M., Orlando L., Pawlowski J., Mulitza S., de Vargas C., Kucera M. 2017. Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology, Biogeosciences, 14, 2741–2754, doi: 10.5194/bg-14-2741-2017, 2017.

  39. Puente A., Guinda X., Juanes J., Ramos E., Echavarri-Erasun B., De La Hoz C., . . . Van Avesaath, P. 2017. The role of physical variables in biodiversity patterns of intertidal macroalgae along European coasts. J. Mar. Biol. Assoc. U. K., 97(3), 549-560, doi:10.1017/S0025315416001673.

  40. Sauvadet AL., Lynn DH., Roussel EG., Le Panse S., Bigeard E., Schrével J., Guillou L. 2017. Redescription and phylogenetic analyses of Durchoniella spp. (Ciliophora, Astomatida) associated with the polychaete Cirriformia tentaculata (Montagu, 1808). European Journal of Protistology 61:265–277. DOI: 10.1016/j.ejop.2017.06.007.

  41. Selosse M-A., Charpin M., Not F. 2017. Mixotrophy everywhere on land and in water: the grand écart hypothesis. Ecology Letters 20:246–263. DOI: 10.1111/ele.12714.

  42. Simdyanov TG., Guillou L., Diakin AY., Mikhailov K V., Schrével J., Aleoshin V V. 2017. A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida). PeerJ 5:e3354. DOI: 10.7717/peerj.3354.

  43. Simion P., Philippe H., Baurain D., Jager M., Richter DJ., Di Franco A., Roure B., Satoh N., Quéinnec É., Ereskovsky A., Lapébie P., Corre E., Delsuc F., King N., Wörheide G., Manuel M. 2017. A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals. Current Biology:1–10. DOI: 10.1016/j.cub.2017.02.031.

  44. Simon N., Foulon E., Grulois D., Six C., Desdevises Y., Latimier M., Le Gall F., Tragin M., Houdan A., Derelle E., Jouenne F., Marie D., Le Panse S., Vaulot D., Marin B. 2017. 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. Protist 168:612–635. DOI: 10.1016/j.protis.2017.09.002.

  45. Xia X., Partensky F., Garczarek L., Suzuki K., Guo C., Yan Cheung S., Liu H. 2017. Phylogeography and pigment type diversity of Synechococcus cyanobacteria in surface waters of the northwestern pacific ocean. Environmental Microbiology 19:142–158. DOI: 10.1111/1462-2920.13541.

2016

  1. Amiraux R., Jeanthon C., Vaultier F., Rontani J-F. 2016. Paradoxical effects of temperature and solar irradiance on the photodegradation state of killed phytoplankton. Journal of Phycology. DOI: 10.1111/jpy.12410.

  2. Arroyo AS., López-Escardó D., de Vargas C., Ruiz-Trillo I. 2016. Hidden diversity of Acoelomorpha revealed through metabarcoding. Biology Letters 12:20160674. DOI: 10.1098/rsbl.2016.0674.Biard T., Stemmann L., Picheral M., Mayot N., Vandromme P., Hauss H., Gorsky G., Guidi L., Kiko R., Not F. 2016. In situ imaging reveals the biomass of giant protists in the global ocean. Nature 532:504–507. DOI: 10.1038/nature17652.

  3. Blanquart F., Valero M., Alves-de-Souza C., Dia A., Lepelletier F., Bigeard E., Jeanthon C., Destombe C., Guillou L. 2016. Evidence for parasite-mediated selection during short-lasting toxic algal blooms. Proceedings of the Royal Society B: Biological Sciences 283:20161870. DOI: 10.1098/rspb.2016.1870.

  4. Boeuf D., Lami R., Cunnington E., Jeanthon C. 2016. Summer Abundance and Distribution of Proteorhodopsin Genes in the Western Arctic Ocean. Frontiers in Microbiology 7:1–12. DOI: 10.3389/fmicb.2016.01584.

  5. Cabello AM., Cornejo-Castillo FM., Raho N., Blasco D., Vidal M., Audic S., de Vargas C., Latasa M., Acinas SG., Massana R. 2016. Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis. The ISME Journal 10:693–706. DOI: 10.1038/ismej.2015.147.

  6. Campo J del., Guillou L., Hehenberger E., Logares R., López-García P., Massana R. 2016. Ecological and evolutionary significance of novel protist lineages. European Journal of Protistology. DOI: http://dx.doi.org/10.1016/j.ejop.2016.02.002.

  7. Cornejo-Castillo FM., Cabello AM., Salazar G., Sa P., Lima-mendez G., Hingamp P., Alberti A., Sunagawa S., Bork P., Vargas C De., Raes J., Bowler C., Wincker P., Zehr JP. 2016. Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton. Nature Communications. DOI: 10.1038/ncomms11071.

  8. Crenn K., Serpin D., Lepleux C., Overmann J., Jeanthon C. 2016. Silicimonas algicola gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from the cell surface of the marine diatom Thalassiosira delicatula. International Journal of Systematic and Evolutionary Microbiology. DOI: 10.1099/ijsem.0.001394.

  9. Durak GM., Taylor AR., Probert I., de Vargas C., Audic S., Schroeder DC., Brownlee C., Wheeler GL. 2016. A role for diatom-like silicon transporters in calcifying coccolithophores. Nature Communications 7:10543. DOI: 10.1038/ncomms10543.

  10. Edvardsen B., Egge ES., Vaulot D. 2016. Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding – a review. Perspectives in Phycology 3:77–91. DOI: 10.1127/pip/2016/0052.

  11. Farrant GK., Doré H., Cornejo-Castillo FM., Partensky F., Ratin M., Ostrowski M., Pitt FD., Wincker P., Scanlan DJ., Iudicone D., Acinas SG., Garczarek L. 2016. Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria. Proceedings of the National Academy of Sciences 113:E3365–E3374. DOI: 10.1073/pnas.1524865113.

  12. Flegontova O., Flegontov P., Malviya S., Audic S., Wincker P., de Vargas C., Bowler C., Lukeš J., Horák A. 2016. Extreme Diversity of Diplonemid Eukaryotes in the Ocean. Current Biology 26:3060–3065. DOI: 10.1016/j.cub.2016.09.031.

  13. Forster D., Dunthorn M., Mahé F., Dolan JR., Audic S., Bass D., Bittner L., Boutte C., Christen R., Claverie J-M., Decelle J., Edvardsen B., Egge E., Eikrem W., Gobet A., Kooistra WHCF., Logares R., Massana R., Montresor M., Not F., Ogata H., Pawlowski J., Pernice MC., Romac S., Shalchian-Tabrizi K., Simon N., Richards TA., Santini S., Sarno D., Siano R., Vaulot D., Wincker P., Zingone A., de Vargas C., Stoeck T. 2016. Benthic protists: the under-charted majority. FEMS Microbiology Ecology 92:fiw120. DOI: 10.1093/femsec/fiw120.

  14. Gérikas Ribeiro C., Lopes dos Santos A., Marie D., Helena Pellizari V., Pereira Brandini F., Vaulot D. 2016. Pico and nanoplankton abundance and carbon stocks along the Brazilian Bight. PeerJ 4:e2587. DOI: 10.7717/peerj.2587.

  15. Gérikas Ribeiro C., Marie D., Lopes dos Santos A., Pereira Brandini F., Vaulot D. 2016. Estimating microbial populations by flow cytometry: Comparison between instruments. Limnology and Oceanography: Methods 14:750–758. DOI: 10.1002/lom3.10135.

  16. Gimmler A., Korn R., de Vargas C., Audic S., Stoeck T. 2016. The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates. Scientific Reports 6:33555. DOI: 10.1038/srep33555.

  17. Giner CR., Forn I., Romac S., Logares R., de Vargas C., Massana R. 2016. Environmental sequencing provides reasonable estimates of the relative abundance of specific picoeukaryotes. Applied and Environmental Microbiology. DOI: 10.1128/AEM.00560-16.

  18. Guidi L., Chaffron S., Bittner L., Eveillard D., Larhlimi A., Roux S., Darzi Y., Audic S., et al. 2016. Plankton networks driving carbon export in the oligotrophic ocean. Nature 532, 465–470. https://doi.org/10.1038/nature16942.

  19. Gutiérrez-Rodríguez A., Selph KE., Landry MR. 2016. Phytoplankton growth and microzooplankton grazing dynamics across vertical environmental gradients determined by transplant in situ dilution experiments. Journal of Plankton Research 38:271–289. DOI: 10.1093/plankt/fbv074.

  20. Hummel H., Van Avesaath P., Wijnhoven S., Kleine-Schaars L., Degraer S., Kerckhof F., Bojanic N., Skejic S., Vidjak O., Rousou M., Orav-Kotta H., Kotta J., Jourde J., Pedrotti ML., Leclerc J-C., Simon N., Rigaut-Jalabert F., Bachelet G., Lavesque N., Arvanitidis C., Pavloudi C., Faulwetter S., Crowe T., Coughlan J., Benedetti-Cecchi L., Dal Bello M., Magni P., Como S., Coppa S., Ikauniece A., Ruginis T., Jankowska E., Weslawski JM., Warzocha J., Gromisz S., Witalis B., Silva T., Ribeiro P., Fernandes De Matos VK., Sousa-Pinto I., Veiga P., Troncoso J., Guinda X., Juanes De La Pena JA., Puente A., Espinosa F., Pérez-Ruzafa A., Frost M., Mcneill CL., Peleg O., Rilov G. 2016. Geographic patterns of biodiversity in European coastal marine benthos. Journal of the Marine Biological Association of the United Kingdom. DOI: 10.1017/S0025315416001119.

  21. Ichinomiya M., dos Santos AL., Gourvil P., Yoshikawa S., Kamiya M., Ohki K., Audic S., de Vargas C., Noël M-H., Vaulot D., Kuwata A. 2016. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. The ISME Journal 10:2419–2434. DOI: 10.1038/ismej.2016.38.

  22. Jephcott TG., Alves-de-Souza C., Gleason FH., van Ogtrop FF., Sime-Ngando T., Karpov S a., Guillou L. 2016. Ecological impacts of parasitic chytrids, syndiniales and perkinsids on populations of marine photosynthetic dinoflagellates. Fungal Ecology 19:47–58. DOI: 10.1016/j.funeco.2015.03.007.

  23. Klouch ZK., Caradec F., Plus M., Hernández-Fariñas T., Pineau-Guillou L., Chapelle A., Schmitt S., Quéré J., Guillou L., Siano R. 2016. Heterogeneous distribution in sediments and dispersal in waters of Alexandrium minutum in a semi-enclosed coastal ecosystem. Harmful Algae 60:81–91. DOI: 10.1016/j.hal.2016.11.001.

  24. Klouch KZ., Schmidt S., Andrieux-Loyer F., Le Gac M., Hervio-Heath D., Qui-Minet ZN., Quéré J., Bigeard E., Guillou L., Siano R. 2016. Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France). FEMS Microbiology Ecology 92:fiw101. DOI: 10.1093/femsec/fiw101.

  25. Landry MR., Selph KE., Décima M., Gutiérrez-Rodríguez A., Stukel MR., Taylor AG., Pasulka AL. 2016. Phytoplankton production and grazing balances in the Costa Rica Dome. Journal of Plankton Research 38:366–379. DOI: 10.1093/plankt/fbv089.

  26. Le Bescot N., Mahé F., Audic S., Dimier C., Garet M-J., Poulain J., Wincker P., de Vargas C., Siano R. 2016. Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding. Environmental Microbiology 18:609–626. DOI: 10.1111/1462-2920.13039.

  27. Le Gac M., Metegnier G., Chomérat N., Pascale M., Quéré J., Bouchez O., Siano R., Destombe C., Guillou L., Chapelle A. 2016. Evolutionary processes and cellular functions underlying divergence in Alexandrium minutum. Molecular Ecology. DOI: 10.1111/mec.13815.

  28. Lehours A-C., Le Jeune A-H., Aguer J-P., Céréghino R., Corbara B., Kéraval B., Leroy C., Perrière F., Jeanthon C., Carrias J-F. 2016. Unexpectedly high bacteriochlorophyll α concentrations in Neotropical tank bromeliads. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12426.

  29. Lopes dos Santos A., Gourvil P., Rodriguez-Hernandez F., Garrido JL., Vaulot D. 2016. Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII. Journal of Phycology 52:148–155. DOI: 10.1111/jpy.12376.

  30. Lu Y., Wohlrab S., Groth M., Glöckner G., Guillou L., John U. 2016. Transcriptomic profiling of Alexandrium fundyense during physical interaction with or exposure to chemical signals from the parasite Amoebophrya. Molecular ecology 25:1294–307. DOI: 10.1111/mec.13566.

  31. Malviya S., Scalco E., Audic S., Vincent F., Veluchamy A., Bittner L., Poulain J., Wincker P., Iudicone D., de Vargas C., Zingone A., Bowler C. 2016. Insights into global diatom distribution and diversity in the world’s ocean. Proceedings of the National Academy of Sciences 348:1–10. DOI: 10.1073/pnas.1509523113.

  32. Marron AO., Ratcliffe S., Wheeler GL., Goldstein RE., King N., Not F., de Vargas C., Richter DJ. 2016. The Evolution of Silicon Transport in Eukaryotes. Molecular Biology and Evolution 33:3226–3248. DOI: 10.1093/molbev/msw209.

  33. Mitra A., Flynn KJ., Tillmann U., Raven JA., Caron D., Stoecker DK., Not F., Hansen PJ., Hallegraeff G., Sanders R., Wilken S., McManus G., Johnson M., Pitta P., Våge S., Berge T., Calbet A., Thingstad F., Jeong HJ., Burkholder J., Glibert PM., Granéli E., Lundgren V. 2016. Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition; Incorporation of Diverse Mixotrophic Strategies. Protist 167:106–120. DOI: 10.1016/j.protis.2016.01.003.

  34. Morard R., Escarguel G., Weiner AKM., André A., Douady CJ., Wade CM., Darling KF., Ujiié Y., Seears HA., Quillévéré F., de Garidel-Thoron T., de Vargas C., Kucera M. 2016. Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera. Systematic Biology. DOI: 10.1093/sysbio/syw031.

  35. Müller DG., Maier I., Marie D., Westermeier R. 2016. Nuclear DNA level and life cycle of kelps: Evidence for sex-specific polyteny in Macrocystis (Laminariales, Phaeophyceae). Journal of Phycology 52:157–160. DOI: 10.1111/jpy.12380.

  36. Nitsche F., Thomsen HA., Richter DJ. 2016. Bridging the gap between morphological species and molecular barcodes − exemplified by loricate choanoflagellates. European Journal of Protistology. DOI: 10.1016/j.ejop.2016.10.006.

  37. Paulsen ML., Doré H., Garczarek L., Seuthe L., Müller O., Sandaa R-A., Bratbak G., Larsen A. 2016. Synechococcus in the Atlantic Gateway to the Arctic Ocean. Frontiers in Marine Science. DOI: 10.3389/fmars.2016.00191.

  38. Percopo I., Ruggiero MV., Balzano S., Gourvil P., Lundholm N., Siano R., Tammilehto A., Vaulot D., Sarno D. 2016. Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex. Journal of Phycology 52:184–199. DOI: 10.1111/jpy.12395.

  39. Pittera J., Partensky F., Six C. 2016. Adaptive thermostability of light-harvesting complexes in marine picocyanobacteria. The ISME Journal.DOI: 10.1038/ismej.2016.102.

  40. Richter DJ., Nitsche F. 2016. Choanoflagellatea. In: Archibald JM, Simpson AGB, Slamovits CH, Margulis L, Melkonian M, Chapman DJ, Corliss JO eds. Handbook of the Protists. Cham: Springer International Publishing, 1–19. DOI: 10.1007/978-3-319-32669-6_5-1.

  41. Scholz B., Guillou L., Marano A V., Neuhauser S., Sullivan BK., Karsten U., Küpper FC., Gleason FH. 2016. Zoosporic parasites infecting marine diatoms – A black box that needs to be opened. Fungal Ecology 19:59–76. DOI: 10.1016/j.funeco.2015.09.002.

  42. Schrével J., Valigurová A., Prensier G., Chambouvet A., Florent I., Guillou L. 2016. Ultrastructure of Selenidium pendula, the Type Species of Archigregarines, and Phylogenetic Relations to Other Marine Apicomplexa. Protist 167:339–368. DOI: 10.1016/j.protis.2016.06.001.

  43. Schwelm A., Berney C., Dixelius C., Bassc D., Neuhauser S. 2016. The Large Subunit rDNA Sequence of Plasmodiophora brassicae Does not Contain Intra-species Polymorphism. Protist 167:544–554. DOI: 10.1016/j.protis.2016.08.008.

  44. Selph KE., Landry MR., Taylor AG., Gutiérrez-Rodríguez A., Stukel MR., Wokuluk J., Pasulka A. 2016. Phytoplankton production and taxon-specific growth rates in the Costa Rica Dome. Journal of Plankton Research 38:199–215. DOI: 10.1093/plankt/fbv063.

  45. Smirnov A., Nassonova E., Geisen S., Bonkowski M., Kudryavtsev A., Berney C., Glotova A., Bondarenko N., Dyková I., Mrva M., Fahrni J., Pawlowski J. 2016. Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida). Protist. DOI: 10.1016/j.protis.2016.10.006.

  46. Taylor AG., Landry MR., Freibott A., Selph KE., Gutiérrez-Rodríguez A. 2016. Patterns of microbial community biomass, composition and HPLC diagnostic pigments in the Costa Rica upwelling dome. Journal of Plankton Research 38:183–198. DOI: 10.1093/plankt/fbv086.

  47. Thomsen HA., Nitsche F., Richter DJ. 2016. Seasonal Occurrence of Loricate Choanoflagellates in Danish Inner Waters. Protist 167:622–638. DOI: 10.1016/j.protis.2016.09.002.

  48. Tragin M., Lopes dos Santos A., Christen R., Vaulot D. 2016. Diversity and ecology of green microalgae in marine systems: an overview based on 18S rRNA gene sequences. Perspectives in Phycology 3:141–154. DOI: 10.1127/pip/2016/0059.

  49. Vannier T., Leconte J., Seeleuthner Y., Mondy S., Pelletier E., Aury J-M., de Vargas C., Sieracki M., Iudicone D., Vaulot D., Wincker P., Jaillon O. 2016. Survey of the green picoalga Bathycoccus genomes in the global ocean. Scientific Reports 6:37900. DOI: 10.1038/srep37900.

  50. Ward GM., Bennett M., Bateman K., Stentiford GD., Kerr R., Feist SW., Williams ST., Berney C., Bass D. 2016. A new phylogeny and environmental DNA insight into paramyxids: an increasingly important but enigmatic clade of protistan parasites of marine invertebrates. International Journal for Parasitology 46:605–619. DOI: 10.1016/j.ijpara.2016.04.010.

  51. Weiner AKM., Morard R., Weinkauf MF., Darling KF., André A., Quillévéré F., Ujiie Y., Douady CJ., de Vargas C., Kucera M. 2016. Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution. Fontiers in Marine Science 3:1–15. DOI: 10.3389/fmars.2016.00255.

  52. Wichelen JVAN., Hondt SD., Claeys M., Vyverman W., Berney C., Bass D., Vanormelingen P. 2016. A Hotspot of Amoebae Diversity : 8 New Naked Amoebae Associated with. Acta Protozoologica 55:61–87. DOI: 10.4467/16890027AP.16.007.4942.

  53. Zheng Q., Liu Y., Jeanthon C., Zhang R., Lin W., Yao J., Jiao N. 2016. The geographic impact on genomic divergence as revealed by comparison of nine Citromicrobial genomes. Applied and Environmental Microbiology 82:AEM.02495-16. DOI: 10.1128/AEM.02495-16.

2015

  1. Alves-de-Souza C., Pecqueur D., Le Floc’h E., Mas S., Roques C., Mostajir B., Vidussi F., Velo-Suárez L., Sourisseau M., Fouilland E., Guillou L. 2015. Significance of Plankton Community Structure and Nutrient Availability for the Control of Dinoflagellate Blooms by Parasites: A Modeling Approach. PLOS ONE 10:e0127623. DOI: 10.1371/journal.pone.0127623.

  2. Balzano S., Corre E., Decelle J., Sierra R., Wincker P., Silva C Da., Poulain J., Evry C. 2015. Transcriptome analyses to investigate symbiotic relationships between marine protists . Frontiers in Microbiology 6. DOI: 10.3389/fmicb.2015.00098.

  3. Baudoux A-C., Lebredonchel H., Dehmer H., Latimier M., Edern R., Rigaut-Jalabert F., Ge P., Guillou L., Foulon E., Bozec Y., Cariou T., Desdevises Y., Derelle E., Grimsley N., Moreau H., Simon N. 2015. Interplay between the genetic clades of Micromonas and their viruses in the Western English Channel. Environmental Microbiology Reports. DOI: 10.1111/1758-2229.12309.

  4. Biard T., Pillet L., Decelle J., Poirier C., Suzuki N., Not F. 2015. Towards an Integrative Morpho-molecular Classification of the Collodaria (Polycystinea, Radiolaria). Protist 166:374–388. DOI: 10.1016/j.protis.2015.05.002.

  5. Boeuf D., Audic S., Brillet-Guéguen L., Caron C., Jeanthon C. 2015. MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution. Database 2015:bav080. DOI: 10.1093/database/bav080.

  6. Botebol H., Lesuisse E., Sutak R., Six C., Lozano J-C., Schatt P., Verge V., Kirilovsky A., Morrissey J., Leger T., Camadro J-M., Gueneugues A., Bowler C., Blain S., Bouget F-Y. 2015. Central role for ferritin in the day/night regulation of iron homeostasis in marine phytoplankton. Proceedings of the National Academy of Sciences:1–6. DOI: 10.1073/pnas.1506074112.

  7. Brum JR., Ignacio-Espinoza JC., Roux S., Doulcier G., Acinas SG., Alberti A., Chaffron S., Cruaud C., de Vargas C., Gasol JM., Gorsky G., Gregory AC., Guidi L., Hingamp P., Iudicone D., Not F., Ogata H., Pesant S., Poulos BT., Schwenck SM., Speich S., Dimier C., Kandels-Lewis S., Picheral M., Searson S., Bork P., Bowler C., Sunagawa S., Wincker P., Karsenti E., Sullivan MB. 2015. Patterns and ecological drivers of ocean viral communities. Science 348:1261498–1261498. DOI: 10.1126/science.1261498.

  8. Clerissi C., Desdevises Y., Romac S., Audic S., de Vargas C., Acinas SG., Casotti R., Poulain J., Wincker P., Hingamp P., Ogata H., Grimsley N. 2015. Deep sequencing of amplified P rasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes. Environmental Microbiology Reports 7:979–989. DOI: 10.1111/1758-2229.12345.

  9. Coupel P., Matsuoka A., Ruiz-Pino D., Gosselin M., Marie D., Tremblay J-É., Babin M. 2015. Pigment signatures of phytoplankton communities in the Beaufort Sea. Biogeosciences 12:991–1006. DOI: 10.5194/bg-12-991-2015.

  10. del Campo J., Mallo D., Massana R., de Vargas C., Richards T a., Ruiz-Trillo I. 2015. Diversity and distribution of unicellular opisthokonts along the European coast analysed using high-throughput sequencing. Environmental Microbiology. DOI: 10.1111/1462-2920.12759.

  11. de Vargas C., Audic S., Henry N., Decelle J., Mahe F., Logares R., Lara E., Berney C., Le Bescot N., Probert I., Carmichael M., Poulain J., Romac S., Colin S., Aury J-M., Bittner L., Chaffron S., Dunthorn M., Engelen S., Flegontova O., Guidi L., Horak A., Jaillon O., Lima-Mendez G., Luke J., Malviya S., Morard R., Mulot M., Scalco E., Siano R., Vincent F., Zingone A., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Acinas SG., Bork P., Bowler C., Gorsky G., Grimsley N., Hingamp P., Iudicone D., Not F., Ogata H., Pesant S., Raes J., Sieracki ME., Speich S., Stemmann L., Sunagawa S., Weissenbach J., Wincker P., Karsenti E., Boss E., Follows M., Karp-Boss L., Krzic U., Reynaud EG., Sardet C., Sullivan MB., Velayoudon D. 2015. Eukaryotic plankton diversity in the sunlit ocean. Science 348:1261605. DOI: 10.1126/science.1261605.

  12. Farrant GK., Hoebeke M., Partensky F., Andres G., Corre E., Garczarek L. 2015. WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data. BMC Bioinformatics 16:281. DOI: 10.1186/s12859-015-0705-y.

  13. Forster D., Bittner L., Karkar S., Dunthorn M., Romac S., Audic S., Lopez P., Stoeck T., Bapteste E. 2015. Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms. BMC Biology 13:16. DOI: 10.1186/s12915-015-0125-5.

  14. Decelle J., Colin S., Foster RA. 2015. Photosymbiosis in Marine Planktonic Protists. In: Marine protists: diversity and dynamics. Springer Japan, 465–500.

  15. Decelle J., Not F. 2015. Acantharia. In: eLS. 1–10. DOI: 10.1002/9780470015902.a0002102.pub2.

  16. Gleason FH., Jephcott TG., Küpper FC., Gerphagnon M., Sime-Ngando T., Karpov S a., Guillou L., van Ogtrop FF. 2015. Potential roles for recently discovered chytrid parasites in the dynamics of harmful algal blooms. Fungal Biology Reviews 29:20–33. DOI: 10.1016/j.fbr.2015.03.002.

  17. Kopf A., Bicak M., Kottmann R., Schnetzer J., Kostadinov I., Lehmann K., Fernandez-Guerra A., Jeanthon C., Rahav E., Ullrich M. et al. 2015. The ocean sampling day consortium. GigaScience 4:27. DOI: 10.1186/s13742-015-0066-5.

  18. Lavaud J., Six C., Campbell DA. 2015. Photosystem II repair in marine diatoms with contrasting photophysiologies. Photosynthesis Research. DOI: 10.1007/s11120-015-0172-3.

  19. Lehours A-C., Jeanthon C. 2015. The hydrological context determines the beta-diversity of aerobic anoxygenic phototrophic bacteria in European Arctic seas but does not favor endemism. Frontiers in Microbiology 6:1–9. DOI: 10.3389/fmicb.2015.00638.

  20. Lejzerowicz F., Esling P., Pillet L., Wilding TA., Black KD., Pawlowski J. 2015. High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems. Scientific Reports 5:13932. DOI: 10.1038/srep13932.

  21. Lelchat F., Cérantola S., Brandily C., Colliec-Jouault S., Baudoux A-C., Ojima T., Boisset C. 2015. The marine bacteria Cobetia marina DSMZ 4741 synthesizes an unexpected K-antigen-like exopolysaccharide. Carbohydrate Polymers 124:347–356. DOI: 10.1016/j.carbpol.2015.02.038.

  22. Lelchat F., Cozien J., Le Costaouec T., Brandilly C., Schmitt S., Baudoux A-C., Colliec-Jouault S., Boisset C. 2015. Exopolysaccharide biosynthesis and biodegradation by a marine hydrothermal Alteromonas sp. strain. Applied Microbiology and Biotechnology 99:2637–2647. DOI: 10.1007/s00253-014-6075-y.

  23. Lescot M., Hingamp P., Kojima KK., Villar E., Romac S., Veluchamy A., Boccara M., Jaillon O., Iudicone D., Bowler C., Wincker P., Claverie J-M., Ogata H. 2015. Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages. The ISME Journal:1–13. DOI: 10.1038/ismej.2015.192.

  24. Lima-Mendez G., Faust K., Henry N., Decelle J., Colin S., Carcillo F., Chaffron S., Ignacio-Espinosa JC., Roux S., Vincent F., Bittner L., Darzi Y., Wang J., Audic S., Berline L., Bontempi G., Cabello AM., Coppola L., Cornejo-Castillo FM., D’Ovidio F., De Meester L., Ferrera I., Garet-Delmas M-J., Guidi L., Lara E., Pesant S., Royo-Llonch M., Salazar G., Sanchez P., Sebastian M., Souffreau C., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Gorsky G., Not F., Ogata H., Speich S., Stemmann L., Weissenbach J., Wincker P., Acinas SG., Sunagawa S., Bork P., Sullivan MB., Karsenti E., Bowler C., de Vargas C., Raes J. 2015. Determinants of community structure in the global plankton interactome. Science 348:1262073–1262073. DOI: 10.1126/science.1262073.

  25. Lossouarn J., Nesbø CL., Mercier C., Zhaxybayeva O., Johnson MS., Charchuck R., Farasin J., Bienvenu N., Baudoux AC., Michoud G., Jebbar M., Geslin C. 2015. “Ménage à trois”: a selfish genetic element uses a virus to propagate within\n Thermotogales. Environmental Microbiology 17:3278–3288. DOI: 10.1111/1462-2920.12783.

  26. Mahé​ F., Rognes​ T., Quince C., de Vargas C., Dunthorn M. 2015. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ 3:e1420. DOI: 10.7717/peerj.1420.

  27. Massana R., Gobet A., Audic S., Bass D., Bittner L., Boutte C., Chambouvet A., Christen R., Claverie J-M., Decelle J., Dolan JR., Dunthorn M., Edvardsen B., Forn I., Forster D., Guillou L., Jaillon O., Kooistra WHCF., Logares R., Mahé F., Not F., Ogata H., Pawlowski J., Pernice MC., Probert I., Romac S., Richards T., Santini S., Shalchian-Tabrizi K., Siano R., Simon N., Stoeck T., Vaulot D., Zingone A., de Vargas C. 2015. Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing. Environmental Microbiology 17:4035–4049.

  28. Morard R., Darling KF., Mahé F., Audic S., Ujiié Y., Weiner AKM., André A., Seears HA., Wade CM., Quillévéré F., Douady CJ., Escarguel G., de Garidel-Thoron T., Siccha M., Kucera M., de Vargas C. 2015. PFR 2 : a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution. Molecular Ecology Resources 15:1472–1485. DOI: 10.1111/1755-0998.12410.

  29. Mordret S., Romac S., Henry N., Colin S., Carmichael M., Berney C., Audic S., Richter D., Pochon X., de Vargas C., Decelle J. 2015. The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.). The ISME Journal. DOI: 10.1038/ismej.2015.211.

  30. Nakamura Y., Imai I., Yamaguchi A., Tuji A., Not F., Suzuki N. 2015. Molecular Phylogeny of the Widely Distributed Marine Protists, Phaeodaria (Rhizaria, Cercozoa). Protist 166:363–373. DOI: 10.1016/j.protis.2015.05.004.

  31. Passarelli C., Meziane T., Thiney N., Boeuf D., Jesus B., Ruivo M., Jeanthon C., Hubas C. 2015. Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers. Estuarine, Coastal and Shelf Science 153:29–37. DOI: 10.1016/j.ecss.2014.11.013.

  32. Pesant S., Not F., Picheral M., Kandels-Lewis S., Le Bescot N., Gorsky G., Iudicone D., Karsenti E., Speich S., Troublé R., Dimier C., Searson S., Acinas SG., Bork P., Boss E., Bowler C., De Vargas C., Follows M., Grimsley N., Hingamp P., Jaillon O., Karp-Boss L., Krzic U., Ogata H., Raes J., Reynaud EG., Sardet C., Sieracki M., Stemmann L., Sullivan MB., Sunagawa S., Velayoudon D., Weissenbach J., Wincker P. 2015. Open science resources for the discovery and analysis of Tara Oceans data. Scientific Data 2:150023. DOI: 10.1038/sdata.2015.23.

  33. Richards TA., Leonard G., Mahe F., del Campo J., Romac S., Jones MDM., Maguire F., Dunthorn M., De Vargas C., Massana R., Chambouvet A. 2015. Molecular diversity and distribution of marine fungi across 130 European environmental samples. Proceedings of the Royal Society B: Biological Sciences 282:20152243–20152243. DOI: 10.1098/rspb.2015.2243.

  34. Stüken A., Riobó P., Franco J., Jakobsen KS., Guillou L., Figueroa RI. 2015. Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains. Frontiers in Microbiology 6:1–10. DOI: 10.3389/fmicb.2015.00404.

  35. Sunagawa S., Coelho LP., Chaffron S., Kultima JR., Labadie K., Salazar G., Djahanschiri B., Zeller G., Mende DR., Alberti A., Cornejo-Castillo FM., Costea PI., Cruaud C., D’Ovidio F., Engelen S., Ferrera I., Gasol JM., Guidi L., Hildebrand F., Kokoszka F., Lepoivre C., Lima-Mendez G., Poulain J., Poulos BT., Royo-Llonch M., Sarmento H., Vieira-Silva S., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Bowler C., de Vargas C., Gorsky G., Grimsley N., Hingamp P., Iudicone D., Jaillon O., Not F., Ogata H., Pesant S., Speich S., Stemmann L., Sullivan MB., Weissenbach J., Wincker P., Karsenti E., Raes J., Acinas SG., Bork P., Boss E., Bowler C., Follows M., Karp-Boss L., Krzic U., Reynaud EG., Sardet C., Sieracki M., Velayoudon D. 2015. Structure and function of the global ocean microbiome. Science 348:1261359–1261359. DOI: 10.1126/science.1261359.

  36. Suzuki N., Not F. 2015. Biology and Ecology of Radiolaria. In: Ohtsuka S, Suzaki T, Horiguchi T, Suzuki N, Not F eds. Marine Protists. Spinge Japan, 179–222. DOI: 10.1007/978-4-431-55130-0.

  37. Villar E., Farrant GK., Follows M., Garczarek L., Speich S., Audic S., Bittner L., Blanke B., Brum JR., Brunet C., Casotti R., Chase A., Dolan JR., D’Ortenzio F., Gattuso J-P., Grima N., Guidi L., Hill CN., Jahn O., Jamet J-L., Le Goff H., Lepoivre C., Malviya S., Pelletier E., Romagnan J-B., Roux S., Santini S., Scalco E., Schwenck SM., Tanaka A., Testor P., Vannier T., Vincent F., Zingone A., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Acinas SG., Bork P., Boss E., de Vargas C., Gorsky G., Ogata H., Pesant S., Sullivan MB., Sunagawa S., Wincker P., Karsenti E., Bowler C., Not F., Hingamp P., Iudicone D. 2015. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science 348:1261447–1261447. DOI: 10.1126/science.1261447.

  38. von Dassow P., John U., Ogata H., Probert I., Bendif EM., Kegel JU., Audic S., Wincker P., Da Silva C., Claverie J-M., Doney S., Glover DM., Flores DM., Herrera Y., Lescot M., Garet-Delmas M-J., de Vargas C. 2015. Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton. The ISME Journal 9:1365–1377. DOI: 10.1038/ismej.2014.221.