Daniel Vaulot on Daniel Vaulot

PhenoMap (2020-2023)

Tue, 27 Apr 2021 00:00:00 +0000

Aim

Rapidly accumulating environmental sequencing data have revealed that eukaryotic microbes are far more diverse and complex than previously thought. However, meta-barcoding and meta-genomics surveys are severely limited by the fact that the majority of environmental sequences do not match a sequence with associated phenotypic/taxonomic information in reference databases. Phytoplankton, a polyphyletic group of single-celled photosynthetic organisms that play key roles in aquatic food webs and global biogeochemical cycles, comprise an important part of this undescribed diversity. PHENOMAP will address this major “phenotype gap” for marine phytoplankton by undertaking targeted phenotypic description of key cryptic lineages. The work plan integrates a suite of state of the art methods that will be applied to two outstanding existing resources: the Roscoff Culture Collection, which is the largest and most diverse service collection of living microalgal strains in the world, and the Tara protist sample collection that contains over 15,000 fixed plankton samples from the worldwide Tara Oceans expeditions (2009-2018). Additional targeted sampling at 3 French marine stations will complement these resources. Phenotypic analyses will include light, fluorescence and electron microscopy for both live and fixed samples, as well as photosynthetic pigment analysis for cultures. For fixed samples, fluorescent in-situ hybridisation will be used to target cells belonging to the most abundant cryptic environmental lineages. Genetic barcoding of morphologically identified single cells isolated from fixed and live samples will complete the experimental strategy. We aim to formally describe at least 100 new taxa (including many high taxonomic rank lineages) and link genotypic to phenotypic information for hundreds of additional existing species, adding significant value to integrated community databases (PR2, PhytoRef, UniEuk, Ecotaxa) that are increasingly central to studies on phytoplankton biology, ecology and evolution. Widespread dissemination of scientific outputs and development of innovative educational and outreach resources is integral to the PHENOMAP approach.

Partners

Station Biologique de Roscoff RCC (Ian Probert, Pris Gourvil, Daniel Vaulot)
Station Biologique de Roscoff UMR7144 (C. de Vargas, S. Romac)
LERBO, IFREMER, Concarneau (Nicolas Chomerat, K. Mertens)

Funding

ANR France

Phytopol (2015-2021)

Wed, 27 Apr 2016 00:00:00 +0000

Phytoplankton survival in the polar night

Goals

Phytoplankton is responsible for nearly half of the photosynthesis on the planet. In polar regions, phototrophic organisms need to survive during long periods of darkness occurring in winter. However survival mechanisms remain mysterious and elucidating them would provide a key to understanding how primary production is sustained in polar ecosystems which are among the highest productive areas on the planet. Until now, studies have been hampered by the difficulty to access these environments, especially in winter. The Norwegian project MicroPolar to which the two French PIs are associated has offered a unique opportunity to sample polar waters every two months for one year, including during winter (January, March, May, August and November 2014). PhytoPol was taking advantage of this to address the question of the survival of phytoplankton during long darkness. The project is structured in three tasks: i) characterize dominant Arctic photosynthetic pico- and nano-phytoplankton strains, ii) determine the physiological mechanism(s) used to survive long periods in the dark, and iii) elucidate the molecular mechanisms of these adaptations.

Period

2015-2021

Partners

Station Biologique de Roscoff DIPO team (Daniel Vaulot, Fabrice Not, Valeria Jimenez, Catherine Ribeiro)
Observatoire Océanographique de Banyuls (Hervé Moreau (deceased), Sheree Yau).

Funding

ANR France
Région Bretagne

TaxMarc (2018-2021)

Wed, 27 Apr 2016 00:00:00 +0000

Green Edge (2015-2016)

Wed, 27 Apr 2016 00:00:00 +0000

Aim

Climate change has triggered fundamental modifications of marine biotopes in the Arctic Ocean (AO). The decrease in the extent of the ice pack during summer has led to a 20% increase in pan-Arctic primary production (PP) over the last decade. Phytoplankton blooms now occur earlier in several parts of the AO. In other parts, the structure of the phytoplankton community is shifting toward smaller species, typical of more oligotrophic conditions and some species found in warmer waters now migrate into the Arctic Ocean.

Phytoplankton grow in the top tens of meters of both ice-free and ice-covered waters. The phytoplankton spring bloom (PSB) that develops at the ice-edge accounts for >50% of annual primary production in the AO and is generally associated with both large energy transfer to higher trophic levels and export of carbon to the bottom. In turn, the culture, health and economic capacity building of Northerners are closely associated with marine resources supported by the PSB. The Arctic PSB develops in the seasonally-covered ice zone (SIZ), the extent of which is expected to increase significantly during the next years, possibly over the whole AO as early as in 2030. How the PSB will evolve in this context is currently unknown.

Partners

Université Laval and UMI CNRS Takuvik, Québec, Canada: Connie Lovejoy, Marcel Babin
Station Biologique de Roscoff : Daniel Vaulot, Adriana Lopes dos Santos, Priscilla Gourvil, Florence Le Gall, Catherine Gérikas-Ribeiro, Ian Probert, Margot Tragin, Dominique Marie

Field network

Ice Camp, Baffin Island : May-July 2016
Cruise Amundsen, Baffin Bay, June-July 2016

Funding

ANR France
Fondation Total
Département du Finistère

Collaborations (2017-2019)

Wed, 27 Apr 2016 00:00:00 +0000

2017-2019 - Catalyst (New Zealand)

Objectives

The objective of this research is to develop and implement the use of high-throughput sequencing techniques to assess the diversity and community structure of planktonic systems. This objective will be achieved merging the French team world class expertise in high-throughput sequencing and genomic approaches with the NZ teams chemical and biological oceanographic expertise and field-sampling capacities. In addition to filling a fundamental knowledge gap, joint-field research project will provide a reference baseline against which detect/evaluate changes in the pelagic ecosystem structure and function in response to environmental changes associated to human-derived activities (e.g. climate change, ocean acidification).

Partners

New Zealand - NIWA (Andres Gutierrez, Linn Hoffmann, and Moira Decima)
France - Station Biologique de Roscoff (Fabrice Not, Ian Probert, Daniel Vaulot, Adriana Lopes dos Santos)

Cruises

Campbell Plateau - May 2017
Ross Sea - Feb 2018
Salp - Oct - Nov 2018

2017-2019 - MicrAntar (ECOS-Chili)

Inter-annual variation of Microbial Eukaryotic Communities in Antarctica

Objectives

Size-fractionated samples of microbial eukaryotes collected at a fixed station at Fildes Bay, King George Island, Western Antarctic Peninsula, will be analyzed in terms of taxonomic diversity. Diversity of microbial eukaryotes will be accessed during five consecutive summers, in order to analyze the central patterns of summer inter-annual variation in microbial eukaryote communities, and the differences between size fractions. The integrated use of high throughput amplicon sequencing, multivariate statistical analysis and network analysis will allow us to link the taxonomic information with the environmental information and determine the amount of variability explained by environmental variables measured.

Funding

ECOS-Sud grant number C16B02

Partners

Chili - Universidad Mayor (Nicole Trefault) / Pontifical Universidad de Chile (Rodrigo de la Iglesia)
France - Station Biologique de Roscoff (Daniel Vaulot, Adriana Lopes dos Santos)

2015-2018 - PicoBras (COFECUB, CAPES France- Brasil)

Picophytoplankton in the tropical South West Atlantic off Brazil

Objectives

The PicoBras project focuses on the taxonomic diversity of small picoplanktonic algae, their control by viruses, and their potential contribution to carbon biomass and nitrogen fixation in Brazilian South West Atlantic waters. The pico-phytoplankton off Brazil has received much less attention that the larger cells such as diatoms, dinoflagellates or coccolithophorids that produce short-lived blooms. However pico-phytoplankton contributes to the back bone of oceanic production in off-shore waters. The project associates one team from France (D. Vaulot, Roscoff) with an internationally recognized expertise in studies on plankton diversity and ecology and one team from Brazil (F. Brandini, São Paulo) with a very good knowledge of environmental conditions and phytoplankton production in the South West Atlantic Ocean. The project was developed within the framework of the Brazilian CNPq-INCT project “Caracterização Ambiental e Avaliação dos Recursos Biogênicos e Oceânicos na Margem Continental Brasileira - CARBOM”, taking advantage of seasonal cross-shelf transects sampled during CARBOM cruises. The project combines several approaches: applying the latest advances in gene analysis to characterize natural populations, in particular meta-barcoding, assessing the role of picophytoplankton in open-ocean symbioses, determining its susceptibility to viral infection. The data obtained will bring a better understanding of the role of this important group of phytoplankton in tropical waters of the Southwestern Atlantic and will be crucial for predictions of shifts in communities in response to global change and better ecosystem-based fishery management, which are among the main targets of CARBOM.

Funding

CAPES-COFECUB grant number Te871-15

Partners

Brazil - Universidad de São Paulo (Frederico Brandini, Catherine Gerikas-Ribeiro)
France - Station Biologique de Roscoff (Daniel Vaulot, Adriana Lopes dos Santos)

RCC

Wed, 27 Apr 2016 00:00:00 +0000

PR2

Wed, 27 Apr 2016 00:00:00 +0000

metaPR2

Wed, 27 Apr 2016 00:00:00 +0000

The aim of this project is to make publicly available a database of curated metabarcodes processed with dada2 and for which taxonomy is assigned with PR2.

We have developed an interactive web site (https://shiny.metapr2.org) which allows to visualize, analyze and download the processed data. This includes treemaps of taxonomy, barplots as a function of environmental variables, abundance maps as well as alpha and beta diversity analyses.

Please cite: Vaulot, D., Sim, C.W.H., 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. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13674

The latest version of the database (1.1) has been released in Spring 2022 and contains 41 public data sets including:

Biomarks
Blanes Time Series - 2004-2013
Malaspina - 2010-2011
Ocean Sampling Day - 2014 and 2015
Tara Oceans - V4 and V9 - 2009-2012 - The Tara V4 data have been reprocessed with dada2
Tara Arctic - V4
Many Arctic datasets

The database contains also other non-public data sets from our own work, in particular in the Arctic (Green Edge, MicroPolar). If you are interested please contact me.

Ocean Barcode Atlas

Micro B3 (2012-2015)

Wed, 27 Apr 2016 00:00:00 +0000

MaCuMBA (2012-2016)

Wed, 27 Apr 2016 00:00:00 +0000

Marine microorganisms: Cultivation methods for improving their biotechnological applications.

Macumba was a European FP7 collaborative project (FP7-KBBE 311975)

Period: August 2012 – July 2016 (48 months)
Consortium: 22 partners from 11 countries
Coordinator: Stichting Koninklijk Netherlands Instituut voor Zeeonderzoek (NIOZ), The Netherlands

Marine microorganisms form an almost untapped resource of biotechnological potential. However, its use is hindered by the low success rate of isolation of novel microorganisms and often by poor growth efficiency. Hence, the vast majority of marine microorganisms has not been cultivated and is often considered as unculturable. MaCuMBA aims at improving the isolation rate and growth efficiency of marine microorganisms from conventional and extreme habitats, by applying innovative methods, and the use of automated high throughput procedures.

The approaches include the co-cultivation of interdependent microorganisms, as well as gradient cultures and other methods mimicking the natural environment, and the exploitation of cell-to-cell communication. Signalling molecules produced by microorganisms may be necessary for stimulating growth of the same or other species, or may prevent their growth. Signalling molecules also represent an interesting and marketable product.

MACUMBA web site

Malina (2008-2011)

Wed, 27 Apr 2016 00:00:00 +0000

Aim

How do changes in ice cover, permafrost and UV radiation impact on biodiversity and biogeochemical fluxes in the Arctic Ocean?

Understanding how biodiversity and biogeochemical fluxes are controlled by light penetration of the ocean and how they are affected by ongoing changes of the climate in the Arctic is the overall goal of the Malina project. The focus is set on three processes - primary production, bacterial activity and organic matter photo-oxidation - that play a major role in the organic ⇔ inorganic carbon fluxes. Thus the general objective is to determine the impact of climate change on the fate of terrestrial carbon exported to the Arctic Ocean, on photosynthetic production of organic carbon, and on microbial diversity.

Duration

The Malina project was launched in fall 2008 and lasted four years studying the southern Beaufort Sea and the shelf adjacent to Mackenzie river outlet. The field component of Malina was a cruise on baord the Amundsen ice breaker during the summer 2009.

Funding

ANR France

Supervision

Wed, 16 May 2018 00:00:00 +0000

Post docs

2018 Margot Tragin - now post-doc at IFREMER
2016-2019 Catherine Ribeiro-Gerikas - now post-doc at U. Mayor (Santiago, Chile)
2016-2019 Valeria Jimenez - now post-doc in Roscoff
2012-2017 Adriana Lopes dos Santos - now Assistant Professor at Nanyang Technological University in Singapore
2009-2012 Sergio Balzano - now Researcher at Stazione Zoologica in Naples
2008-2009 Shuhei Ota
2008-2009 Cécile Lepère - now Professor at the Université of Clermont Ferrand (France)
2006-2008 Xiaoli Shi - now Researcher at Chinese Academy of Science in Nanjing.
2006-2008 Fabien Jouenne - now at SCROL (web development)
2005 Aude Houdan (co-direction with N. Simon)
2002-2004 Francisco Rodriguez (co-direction with L. Guillou)
2002-2003 Fei Zhu
2002-2003 Agnès Groisillier
2000-2002 Khadidja Romari
1997-1999 [Michael Rappé][https://rappelab.wordpress.com]
1996-1997 Seung-Yeo Moon, University of Seoul
1991 Raffaella Casotti, visiting researcher
1987 Ning Xiu Ren, visiting scientist from China.

PhD Students

2014-2017 Margot Tragin, Université de Pierre et Marie Curie (Paris-06), PhD - now Post-doc, IFREMER
2014-2015 Catherine Ribeiro-Gerikas, Universidade de São Paulo, PhD co-supervision - now Post-doc, U. Mayor, Santiago, Chile
2005-2009 Sylvie Masquelier, Université de Paris 6 PhD - now R&D director, InoculumPlus
2004-2007 Manon Viprey, Université de Paris 6 PhD - now Primary School Teacher
2000-2004 Fabrice Not, Université de Paris 6 PhD (co-direction with N. Simon) - now Directeur de Recherche (Senior Scientist), CNRS
1999-2003 Isabelle Mary, Université de Rennes PhD - now Associate Professor, Clermond-Ferrand Université
1996-1999 Stéphan Jacquet, Université de Paris 6, PhD - now Directeur de Recherche (Senior Scientist), INRA
1995-1998 Laure Guillou, Université de Paris 6, PhD - now Directeur de Recherche (Senior Scientist) - CNRS
1991-1995 Nathalie Simon, Université de Paris 6, PhD - now Associate Professor, Sorbonne Université
1986-1988 Fréderic Partensky, Université de Paris 6, PhD - now Directeur de Recherche (Senior Scientist), CNRS

PhD Committee or Jury

2023 & Javier Florenza Garcia, Uppsala University, Sweden, PhD examiner
2023-2025 & Margaux Crédeville, Université Paris-Saclay, PhD committee
2021-2024 Clarence Sim, NTU ASE, Singapore, PhD committee
2021 Ina Jungersen Andresen, University of Oslo, PhD jury
2015 Shruti Malviya, Université de Paris 11 - PhD Jury
2014-2018 Solenn Mordret, Statione Zoologica di Napoli & Open University - PhD committee
2013-2017 Thomas Vannier, Genoscope - PhD committee

Master Students

2014 Christian Castro Romero, Université de Bretagne Occidentale, Master 2
2014 Thibaut Pollina, Ecole Pratique des Hautes Etudes, Master 1
2011 Frédéric Gaboyer, Université de Paris-Sud, Master 2
2004 Manon Viprey, Université de Paris 6 DEA
2002 Bastien Simonnet, Université de Marseille DEA
2001 Alexis Dufresne, Université de Rennes DEA (co-direction with F. Partensky)
2000 Héloïse Felman, Université de Paris 6 DEA
1999 Isabelle Mary, Université de Rennes DEA
1996 Stéphan Jacquet, Université de Paris 6 DEA
1995 Laure Guillou, Université de Paris 6 DEA
1994 Mario Acquarone, University of Milano Master
1994 Julie Parpais, Université de Paris 6 DEA
1991 Valérie Cariou, Université de Paris 6 DEA
1989 Nicolas Boucher, Université de Paris 6 DEA

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses

Mon, 01 Dec 2025 00:00:00 +0000

Pelagophyte assemblages of the global ocean display low intraspecific diversity

Mon, 01 Dec 2025 00:00:00 +0000

Transcriptomes from the Diatoms Thalassiosira and Minidiscus from the English Channel and Antarctica.

Mon, 01 Dec 2025 00:00:00 +0000

Daniel Vaulot on Daniel Vaulot

PhenoMap (2020-2023)

Aim

Partners

Funding

Phytopol (2015-2021)

Phytoplankton survival in the polar night

Goals

Period

Partners

Funding

TaxMarc (2018-2021)

Green Edge (2015-2016)

Aim

Partners

Field network

Funding

Collaborations (2017-2019)

2017-2019 - Catalyst (New Zealand)

Objectives

Partners

Cruises

2017-2019 - MicrAntar (ECOS-Chili)

Objectives

Funding

Partners

2015-2018 - PicoBras (COFECUB, CAPES France- Brasil)

Objectives

Funding

Partners

RCC

PR2

metaPR2

Related projects

Micro B3 (2012-2015)

MaCuMBA (2012-2016)

Malina (2008-2011)

Aim

Duration

Funding

Supervision

Post docs

PhD Students

PhD Committee or Jury

Master Students

A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses

Pelagophyte assemblages of the global ocean display low intraspecific diversity

Transcriptomes from the Diatoms Thalassiosira and Minidiscus from the English Channel and Antarctica.