RCC User committee - Dec 2018

The latest information on the Roscoff Culture Collection of algae, bacteria and viruses...

Transcript

1. Roscoff Culture Collection Collection de Cultures de Roscoff Station Biologique de Roscoff FR2424 et UMR7144 Director : Ian Probert, Curator: Priscillia Gourvil Scientific director: D. Vaulot
2. The Roscoff Culture Collection • Set up in 1998 from research collection • 4,632 strains (Dec 2018) • Large phylogenetic coverage • Large coverage of oceanic regions (arctic to tropics)
3. A few numbers for 2018 • 34, 190 transfers (660 strains per week) • 365 L of medium (7 L per week) • 6 Communications (posters, presentations..) • 50 visitors RCC • 49 people being trained • 167 orders (666 strains) slightly less than in 2017 (166 orders and 892 strains) • Strains sent to 20 countries The Roscoff Culture Collection
4. Personnel RCC Ian PROBERT IR UPMC Director Priscillia GOURVIL AI CNRS Curator Martin GACHENOT AI CDD UPMC Emilie GUILLOUD AI CDD UPMC Until 1/07/2018 Léna GOUHIER AI CDD UPMC Since 15/06/2018 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
5. Infrastructures • Culture space – 3 culture rooms – 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 – 2 -150°C freezer – Liquid nitrogen tanks
6. CRBM • Added in 2017 • Second -180°C • Liquid nitrogen tank • Shelves in all 3 rooms • Laminar flow hoods • Furniture for transfer room • Remains to be ordered • Light for shelves
7. 4,632 strains Backup cultures not taken into account Overview of RCC
8. Strains added per year Green Edge MACUMBA
9. New strains 2018 ASIAME2 Roscoff (Dynamo) LowPhox
10. New strains 2018
11. RCC sequences in GenBank
12. 36 papers related to strains available from RCC 1. Crenn, K., Duffieux, D. & Jeanthon, C. 2018. Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations. Front. Microbiol. 9:1–12. 2. Piedade, G.J., Wesdorp, E.M., Borbolla, E.M. & Maat, D.S. 2018. Influence of Irradiance and Temperature on the Virus MpoV ‐ 45T Infecting the Arctic Picophytoplankter Micromonas polaris. Viruses. 1–17. 3. Barak-Gavish, N., Frada, M.J., Ku, C., Lee, P.A., DiTullio, G.R., Malitsky, S., Aharoni, A. et al. 2018. Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP. Sci. Adv. 4:eaau5716. 4. 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. 5. Yamada, K., Katsura, H., Noël, M.-H., Ichinomiya, M., Kuwata, A., Sato, S. & Yoshikawa, S. 2018. Ontogenetic analysis of siliceous cell wall formation in Triparma laevis f. inornata (Parmales, Stramenopiles). J. Phycol. 0– 2. 6. Farhat, S., Florent, I., Noel, B., Kayal, E., Da Silva, C., Bigeard, E., Alberti, A. et al. 2018. Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains. Front. Microbiol. 9:1–19. 7. Krasovec, M., Sanchez-Brosseau, S., Grimsley, N. & Piganeau, G. 2018. Spontaneous mutation rate as a source of diversity for improving desirable traits in cultured microalgae. Algal Res. 35:85–90. 8. Demory, D., Baudoux, A.-C., Monier, A., Simon, N., Six, C., Ge, P., Rigaut-Jalabert, F. et al. 2018. Picoeukaryotes of the Micromonas genus: sentinels of a warming ocean. ISME J. 9. Trainic, M., Koren, I., Sharoni, S., Frada, M., Segev, L., Rudich, Y. & Vardi, A. 2018. Infection Dynamics of a Bloom-Forming Alga and Its Virus Determine Airborne Coccolith Emission from Seawater. iScience. 0. 10. Krasovec, M., Vancaester, E., Rombauts, S., Bucchini, F., Yau, S., Hemon, C., Lebredonchel, H. et al. 2018. Genome analyses of the microalga Picochlorum provide insights into the evolution of thermotolerance in the green lineage. Genome Biol. Evol. evy167. 11. Bachy, C., Charlesworth, C.J., Chan, A.M., Finke, J.F., Wong, C.-H., Wei, C.-L., Sudek, S. et al. 2018. Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environ. Microbiol. in press:1–23. 12. Zheng, Q., Chen, Q., Xu, Y., Suttle, C.A. & Jiao, N. 2018. A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses. Front. Microbiol. 9:1–7. 13. Walker, C.E., Taylor, A.R., Langer, G., Durak, G.M., Heath, S., Probert, I., Tyrrell, T. et al. 2018. The requirement for calcification differs between ecologically important coccolithophore species. New Phytol. in press. 14. Partensky, F., Six, C., Ratin, M., Garczarek, L., Vaulot, D., Probert, I., Calteau, A. et al. 2018. A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle. Sci. Rep. 8:9142. 15. Annunziata, R., Ritter, A., Fortunato, A.E., Cheminant-Navarro, S., Agier, N., Huysman, M.J.J., Winge, P. et al. 2018. A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum. bioRxiv. 271445. 16. Henríquez-Castillo, C., Botebol, H., Mouton, A., Ramírez-Flandes, S., Lozano, J.-C., Lelandais, G., Andrade, S. et al. 2018. Ostreococcus tauri Luminescent Reporter Lines as Biosensors for Detecting Pollution From Copper- Mine Tailing Effluents in Coastal Environments. Front. Environ. Sci. 6:1–11. 17. Kazamia, E., Sutak, R., Paz-Yepes, J., Dorrell, R.G., Vieira, F.R.J., Mach, J., Morrissey, J. et al. 2018. Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms. Sci. Adv. 4:eaar4536. 18. Mizrachi, A., Graff, S., Creveld, V., Shapiro, O.H. & Rosenwasser, S. 2018. Phenotypic variability in chloroplast redox state predicts cell fate in a marine diatom. bioRxiv. 19. Bachy, C., Charlesworth, C.J., Chan, A.M., Finke, J.F., Wong, C.-H., Wei, C.-L., Sudek, S. et al. 2018. Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environ. Microbiol. 1–23. 20. McQuaid, J.B., Kustka, A.B., Oborník, M., Horák, A., McCrow, J.P., Karas, B.J., Zheng, H. et al. 2018. Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms. Nature. 555:534–7. 21. Moniruzzaman, M., Gann, E.R. & Wilhelm, S.W. 2018. Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 – A Harmful Bloom Algae. Front. Microbiol. 9:1–16. 22. Liefer, J.D., Garg, A., Campbell, D.A., Irwin, A.J. & Finkel, Z. V 2018. Nitrogen starvation induces distinct photosynthetic responses and recovery dynamics in diatoms and prasinophytes. PLoS One. 13:e0195705. 23. Paerl, R.W., Bertrand, E.M., Rowland, E., Schatt, P., Mehiri, M., Niehaus, T.D., Hanson, A.D. et al. 2018. Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis. Sci. Rep. 8:5940. 24. Klinger, C.M., Paoli, L., Newby, R.J., Wang, M.Y.-W., Carroll, H.D., Leblond, J.D., Howe, C.J. et al. 2018. Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends. Genome Biol. Evol. 10:1019–38. 25. Garcia, N.S., Sexton, J., Riggins, T., Brown, J., Lomas, M.W. & Martiny, A.C. 2018. High Variability in Cellular Stoichiometry of Carbon, Nitrogen, and Phosphorus Within Classes of Marine Eukaryotic Phytoplankton Under Sufficient Nutrient Conditions. Front. Microbiol. 9:1–10. 26. Meng, A., Corre, E., Probert, I., Gutierrez-Rodriguez, A., Siano, R., Annamale, A., Alberti, A. et al. 2018. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Mol. Ecol. 0–2. 27. Smallwood, A.C.R., Chen, J., Kumar, N., Chrisler, W., Samuel, O., Kyle, J.E., Nicora, C.D. et al. 2018. Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri. bioRxiv. 28. Cheng, S., Melkonian, M., Smith, S.A., Brockington, S., Archibald, J.M., Delaux, P.-M., Li, F.-W. et al. 2018. 10KP: A phylodiverse genome sequencing plan. Gigascience. 7:1–9. 29. Perez-Sepulveda, B., Pitt, F., N’Guyen, A.N., Ratin, M., Garczarek, L., Millard, A. & Scanlan, D.J. 2018. Relative stability of ploidy in a marine Synechococcus across various growth conditions. Environ. Microbiol. Rep. in press. 30. Guyon, J., Schatt, P., Lozano, J., Liennard, M. & Bouget, F. 2018. Comparative Analysis of Culture Conditions for the Optimization of Carotenoid Production in Several Strains of the Picoeukaryote Ostreococcus. Mar. Drugs. 16:76. 31. Delmont, T.O. & Eren, A.M. 2018. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ. 6:e4320. 32. Moldovan, M.A. & Gelfand, M.S. 2018. Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. Front. Microbiol. 9:1–11. 33. Grébert, T., Doré, H., Partensky, F., Farrant, G.K., Boss, E.S., Picheral, M., Guidi, L. et al. 2018. Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria. Proc. Natl. Acad. Sci. in press:201717069. 34. Rastogi, A., Maheswari, U., Dorrell, R.G., Vieira, F.R.J., Maumus, F., Kustka, A., McCarthy, J. et al. 2018. Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms. Sci. Rep. 8:4834. 35. Rosas-Navarro, A., Langer, G. & Ziveri, P. 2018. Temperature effects on sinking velocity of different Emiliania huxleyi strains. PLoS One. 13:e0194386. 36. Carrillo, J.B., Gomez-Casati, D.F., Martín, M. & Busi, M. V. 2018. Identification and analysis of OsttaDSP, a phosphoglucan phosphatase from Ostreococcus tauri. PLoS One. 13:e0191621. Papers 2018
13. Papers 2018
14. Distribution 4,171 strains available (vs. 3 402 in 2017) 10 063 strains distributed
15. Distribution ~14 000 euros in 2018
16. Customer survey • Link sent with order and then sent again one month latter • Answer rate : 9.4% (30.5% in 2016) • Customers are globally satisfied • They would like to be able to order media Feed back through web site • Questions concerning culture shipment • Billing Customer feed back
17. Web site version 2.0
18. Twitter account
19. • Page dédiée au système de management de la qualité: • Documents relatifs au fonctionnement de la RCC • Protocoles, Procédure, doc informatifs… • Arborisation selon processus Gestion des Anomalies: 11 anomalies en 2018 • 8 concernant équipements/infrastructures Nécessité de maintenance/ jouvence des équipements • 2 concernant les envois de cultures Permis d’import à demander (et vérifier validité) pour certains pays Quality
20. ACOI Coimbra Collection of Algae Portugal Visiting other Culture Collections National Center for Marine Algae and Microbiota, USA Cawthron Institute Nouvelle-Zélande
21. • 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... Dissemination
22. RCC Outlook 2019 ▪ Organigramme ▪ Reorganisation within FR2424 (Station Biologique de Roscoff): ▪ RCC and RAS in CRBM will be part of "Access to Marine Ecosystems & Resources" (AMER) pole (with Service Mer and Service Observation) ▪ Moving to new building ▪ Cryo facility operational in Feb 2019 ▪ LEDs for 4°C, 15° and 22° C rooms in spring 2019 (hopefully!) ▪ Quality Management / Traceability ▪ NFS96-900 certification for joint EMBRC-France BRC by end 2019 (!!) ▪ Integration of ABS data in RCC database / web site ▪ Cryopreservation ▪ Participant in cryo WPs in ASSEMBLE+ and EBB projects ▪ Continue cryopreserving strains for which protocol is OK ▪ Test new protocols for cryo-recalcitrant strains (diatoms, dinoflagellates,…) Projects ▪ Moore Foundation (renewed) – Microalgal transformation, collaboration Banyuls ▪ Activities almost completed in NOMORFILM, EMBRIC, OCEANOMICS ▪ 12th Advanced Phytoplankton Course ▪ 3 week intensive taxonomy course hosted in Roscoff May/June 2019 ▪ 22 international students, 12 expert international teachers