RCC User committee - Nov 2017

Our report for 2017 on the progress of the RCC and future perspectives.

Transcript

1. Roscoff Culture Collection Collection de Cultures de Roscoff Station Biologique de Roscoff FR2424 et UMR7144 Director : Ian Probert, Scientific director: D. Vaulot Curators Priscillia Gourvil, Florence Le Gall,
2. The Roscoff Collection • Set up in 1998 from research collection • 4,524 strains (Nov 2017) • Large phylogenetic coverage • Large coverage of oceanic regions (arctic to tropics)
3. Personnel RCC Ian PROBERT IR UPMC Director Priscillia GOURVIL AI CNRS Curator Martin GACHENOT T CDD UPMC Emilie GUILLOUD AI CDD UPMC Support Daniel VAULOT DR CNRS Scientific director Florence LE GALL IE CNRS Isolation Fabienne JALABERT IR CNRS Microscopie Dominique MARIE IR CNRS Flow cytometry sorting Christian JEANTHON DR CNRS Bacteria Anne-Claire BAUDOUX CR CNRS Viruses
4. Infrastructures • Culture space – 2 culture rooms – 1 experiment room – 14 culture cabinets – 1 transfer laboratory • 4 flow cytometers – FACSAria – high speed sorter (2003) – FACSCanto – analysis (2008) – Beckmann Coulter Quanta – analysis (2009) – Accuri C6 – analysis (2011) – Guava - analysis (2016) • 4 microscopes equiped for digital imaging • Cryopreservation equipment – Progressive freezer – -150°C freezer – Liquid nitrogen tanks
5. CRBM • Commandes faites pour : • étagères (13 et 22°C) • second -180°C • alimentation azote • photobioreacteurs
6. Major groups • Cyanobacteria • Picoeukaryotes (prasinophytes, pelagophytes etc…) • Haptophytes (Coccolithophrids, Emiliania, Phaeocystis) • Diatoms • Macroalgues • Phototrophic bacteria • Bacteria associated to phytoplankton • Eukaryotic parasites • Symbionts • Viruses of prasinophytes
7. 4,524 strains Backup cultures not taken into account Overview of RCC Dec 2016
8. Strains added per year
9. New strains 2017 New Zealand Philippines Phenomer Green Edge Brazil Chile D. Caron
10. New strains 2017
11. 35 papers related to strains available from RCC 1. Ruiz, E., Baudoux, A., Nathalie, S., Sandaa, R., and Thingstad, T. F. (2017). Micromonas vs Virus : new experimental insights challenge viral impact. Environ. Microbiol. in press. doi:10.1111/462-2920.13733. 2. Domínguez-Martín, M. A., Gómez-Baena, G., Díez, J., López-Grueso, M. J., Beynon, R. J., and García-Fernández, J. M. (2017). Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcus marinus SS120. mSystems 2, e00008-17. doi:10.1128/mSystems.00008-17. 3. Paerl, R. W., Bouget, F.-Y., Lozano, J.-C., Vergé, V., Schatt, P., Allen, E. E., et al. (2017). Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. ISME J. 11, 753–765. doi:10.1038/ismej.2016.145. 4. Lopes dos Santos, A., Gourvil, P., Tragin, M., Noël, M.-H., Decelle, J., Romac, S., et al. (2017). Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. ISME J. 11, 512–528. doi:10.1038/ismej.2016.120. 5. Dorrell, R. G., Gile, G., McCallum, G., Méheust, R., Bapteste, E. P., Klinger, C. M., et al. (2017). Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. Elife 6, 1–45. doi:10.7554/eLife.23717. 6. Monier, A., Chambouvet, A., Milner, D. S., Attah, V., Terrado, R., Lovejoy, C., et al. (2017). Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton. Proc. Natl. Acad. Sci., 201708097. doi:10.1073/pnas.1708097114. 7. Balzano, S., Percopo, I., Siano, R., Gourvil, P., Chanoine, M., Marie, D., et al. (2017). Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex. J. Phycol. 53, 161–187. doi:10.1111/jpy.12489. 8. Botebol, H., Lelandais, G., Six, C., Lesuisse, E., Meng, A., Bittner, L., et al. (2017). Acclimation of a low iron adapted Ostreococcus strain to iron limitation through cell biomass lowering. Sci. Rep. 7, 327. doi:10.1038/s41598-017-00216-6. 9. van Tol, H. M., Amin, S. A., and Armbrust, E. V. (2017). Ubiquitous marine bacterium inhibits diatom cell division. ISME J. 11, 31–42. doi:10.1038/ismej.2016.112. 10. Gu, H., Li, X., Chomerat, N., Luo, Z., Sarno, D., Gourvil, P., et al. (2017). Adenoides sinensis , a new sand-dwelling dinoflagellate species from China and reexamination of A. eludens from an Atlantic strain. Phycologia 57, 1–13. doi:10.2216/17-76.1. 11. Dittami, S. M., Heesch, S., Olsen, J. L., and Collen, J. (2017). Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae. J. Phycol. in press. doi:10.1111/jpy.12547-16-147. 12. Pittera, J., Partensky, F., and Six, C. (2017). Adaptive thermostability of light-harvesting complexes in marine picocyanobacteria. ISME J. 11, 112–124. doi:10.1038/ismej.2016.102. 13. Stuart, R. K., Bundy, R., Buck, K., Ghassemain, M., Barbeau, K., and Palenik, B. (2017). Copper toxicity response influences mesotrophic S ynechococcus community structure. Environ. Microbiol. 19, 756–769. doi:10.1111/1462-2920.13630. 14. Riou, V., Périot, M., and Biegala, I. C. (2017). Specificity Re-evaluation of Oligonucleotide Probes for the Detection of Marine Picoplankton by Tyramide Signal Amplification-Fluorescent In Situ Hybridization. Front. Microbiol. 8, 854. doi:10.3389/fmicb.2017.00854. 15. Andersen, R. A., Graf, L., Malakhov, Y., and Yoon, H. S. (2017). Rediscovery of the Ochromonas type species Ochromonas triangulata (Chrysophyceae) from its type locality (Lake Veysove, Donetsk region, Ukraine). Phycologia 56, 591–604. doi:10.2216/17-15.1. 16. Katz, A., Bonifacie, M., Hermoso, M., Cartigny, P., and Calmels, D. (2017). Laboratory-grown coccoliths exhibit novital effect in clumped isotope (Δ47) composition on a range of geologically relevant temperatures. Geochim. Cosmochim. Acta 208, 335–353. doi:10.1016/j.gca.2017.02.025. 17. Limardo, A. J., Sudek, S., Choi, C. J., Poirier, C., Rii, Y. M., Blum, M., et al. (2017). Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton. Environ. Microbiol. doi:10.1111/1462-2920.13812. 18. Weynberg, K. D., Allen, M. J., and Wilson, W. H. (2017). Marine Prasinoviruses and Their Tiny Plankton Hosts : A Review. Viruses, 1–20. doi:10.3390/v9030043. 19. Demory, D., Arsenieff, L., Simon, N., Six, C., Rigaut-Jalabert, F., Marie, D., et al. (2017). Temperature is a key factor in Micromonas–virus interactions. ISME J. 11, 601–612. doi:10.1038/ismej.2016.160. 20. Organelli, E., Nuccio, C., Lazzara, L., Uitz, J., Bricaud, A., and Massi, L. (2017). On the discrimination of multiple phytoplankton groups from light absorption spectra of assemblages with mixed taxonomic composition and variable light conditions. Appl. Opt. 56, 3952. doi:10.1364/AO.56.003952. 21. Mackey, K. R. M., Post, A. F., McIlvin, M. R., and Saito, M. A. (2017). Physiological and proteomic characterization of light adaptations in marine Synechococcus. Environ. Microbiol. 19, 2348–2365. doi:10.1111/1462- 2920.13744. 22. Pittera, J., Jouhet, J., Breton, S., Garczarek, L., Partensky, F., Maréchal, É., et al. (2017). Thermoacclimation and genome adaptation of the membrane lipidome in marine Synechococcus. Environ. Microbiol., in press. doi:10.1111/1462-2920.13985. 23. Blanc-Mathieu, R., Krasovec, M., Hebrard, M., Yau, S., Desgranges, E., Martin, J., et al. (2017). Population genomics of picophytoplankton unveils novel chromosome hypervariability. Sci. Adv. 3, e1700239. doi:10.1126/sciadv.1700239. 24. Cuvelier, M. L., Guo, J., Ortiz, A. C., van Baren, M. J., Tariq, M. A., Partensky, F., et al. (2017). Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress. PLoS One 12, e0172135. doi:10.1371/journal.pone.0172135. 25. Simon, N., Foulon, E., Grulois, D., Six, C., Desdevises, Y., Latimier, M., et al. (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 Based on the Genetic. Protist 168, 612–635. doi:10.1016/j.protis.2017.09.002. 26. Maat, D., Biggs, T., Evans, C., van Bleijswijk, J., van der Wel, N., Dutilh, B., et al. (2017). Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses. Viruses 9, 134. doi:10.3390/v9060134. 27. Gutierrez-Rodriguez, A., Pillet, L., Biard, T., Said-Ahmad, W., Amrani, A., Simó, R., et al. (2017). Dimethylated sulfur compounds in symbiotic protists: A potentially significant source for marine DMS(P). Limnol. Oceanogr. doi:10.1002/lno.10491. 28. Mahmoud, R. M., Sanfilippo, J. E., Nguyen, A. A., Strnat, J. A., Partensky, F., Garczarek, L., et al. (2017). Adaptation to Blue Light in Marine Synechococcus Requires MpeU, an Enzyme with Similarity to Phycoerythrobilin Lyase Isomerases. Front. Microbiol. 8, 243. doi:10.3389/fmicb.2017.00243. 29. Ruiz, E., Oosterhof, M., Sandaa, R.-A., Larsen, A., and Pagarete, A. (2017). Emerging Interaction Patterns in the Emiliania huxleyi-EhV System. Viruses 9, 61. doi:10.3390/v9030061. 30. McClelland, H., Bruggeman, J., Hermoso, M., and Rickaby, R. (2017). The origin of carbon isotope vital effects in coccolith calcite. Nat. Commun. 8, 1–16. doi:10.1038/ncomms14511. 31. Satjarak, A., and Graham, L. E. (2017). Comparative DNA sequence analyses of Pyramimonas parkeae (Prasinophyceae) chloroplast genomes. J. Phycol. 53, 415–424. doi:10.1111/jpy.12515. 32. Lopes dos Santos, A., Pollina, T., Gourvil, P., Corre, E., Marie, D., Garrido, J. L., et al. (2017). Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Sci. Rep. 7, 14019. doi:10.1038/s41598-017-12412-5. 33. Marie, D., Le Gall, F., Edern, R., Gourvil, P., and Vaulot, D. (2017). Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry. J. Phycol. 53, 271–282. doi:10.1111/jpy.12495. 34. Walter, J. M., Coutinho, F. H., Dutilh, B. E., Swings, J., Thompson, F. L., and Thompson, C. C. (2017). Ecogenomics and Taxonomy of Cyanobacteria Phylum. Front. Microbiol. 8. doi:10.3389/fmicb.2017.02132. 35. Ni, G., Zimbalatti, G., Murphy, C. D., Barnett, A. B., Arsenault, C. M., Li, G., et al. (2017). Arctic Micromonas uses protein pools and non-photochemical quenching to cope with temperature restrictions on Photosystem II protein turnover. Photosynth. Res. 131, 203–220. doi:10.1007/s11120-016-0310-6. Papers 2017
12. Papers 2017
13. Papers 2017
14. Distribution 3 402 strains available 9 242 strains distributed ~18 000 euros in 2017
15. Youtube RCC
16. Dissemination • Organisation d’un concours poster scientifique avec des élèves 16-18 ans ∟ Collaboration avec le lycée Le Gros Chêne à Pontivy • E-learning : Cours disponibles sur Moodle : RCC, protocole de Nagoya etc...
17. RCC Outlook 2018 ▪ New cultures to integrate ▪ Roscoff (diatoms and parasites - Florence pour thèse Laure Arsenieff) : 150 souches ▪ Macroalgae (Myriam Valero and Marl Cock teams) ▪ Cryopreservation ▪ New groups cryopreserved (diatoms) ▪ Continue cryo-preserving strains for which protocole is OK : Emilie in 2018 ▪ Taxonomic characterization ▪ Acaryochloris tomasii : chlorophyll b cyanobacteria ▪ Mamiellophyceae : new oceanic Bathycoccus, Malina arctica, RCC391 ▪ Cryptophyceae : collaboration with Brazil (Karoline) ▪ Pelagophyceae from the Arctic (Catherine) ▪ Antarctic diatoms (Flo, Adriana, Daniel) : collaboration with Brazil (Luciano Fernandés) ▪ Projects ▪ Nomorfilm EU- 250 strains - Antibacterial substances ▪ PolysAlg ANR - 80 souches. - Polysaccharides ▪ Oceanomics. GreenSea et Soliance - 80 strains. Inhibiteurs de CDK-Kinase, Lipids ▪ EMBRIC. 5 strains. ▪ Moore Foundation (renewed) - 13 strains - Microalgal transformation ▪ EMBRC - France ▪ Web site version 2.0 : early 2018 ▪ Moving to new building ▪ 15° and 22° C rooms ▪ Cryopreservation