Research

Current activities

Major research topics

  • Diversity and oceanic distribution of marine phytoplankton, in particular green algae and Bolidophyceae.
  • Analysis of marine eukaryotic communities using metabarcoding (nuclear 18S rRNA, plastid 16S rRN), especially on populations sorted by flow cytometry.
  • Polar picoplankton communities and their adaptation to the long winter polar night.
  • Development of databases for the analysis of eukaryotic metabarcodes: PR2

Postdocs

  • Catherine Ribeiro-Gerikas, Post-doc. Bloom dynamics at the ice edge in the Arctic : culturing and metabarcoding approaches (ANR Green Edge + CG 29)
  • Valeria Jimenez, Post-doc. Survival of phytoplankton during the polar winter (ANR PhytoPol + Region Bretagne)

Collaborations

Projects

Phytopol

Phytoplankton survival in the polar night.

TaxMarc

Marine protists in a changing Arctic

Green Edge

The Arctic Spring Bloom.

Collaborations

International collaborative projects.

PR2

18S rRNA sequence database

RCC

Roscoff Culture Collection

Micro B3 (2012-2015)

Marine Microbial Biodiversity, Bioinformatics, Biotechnology

MaCuMBA (2012-2016)

Marine Microorganisms: Cultivation Methods for Improving their Biotechnological Applications

Malina (2008-2011)

The Beaufort Sea ecosystem.

Selected Publications

Bolidophyceae contains species with cells surrounded by 5 or 8 silica plates (Parmales) as well as naked flagellated species (formerly Bolidomonadales). Bolidophyceae share a common ancestor with diatoms. This review summarizes the current information on taxonomy, phylogeny, ecology, and physiology.
Frontiers in Marine Science, 5:370, 2018

A seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms.
The ISME journal, in press, 2018

The analysis of the 18S V4 region OSD metabarcoding dataset reveals that Chlorophyta are ubiquitous and can be locally dominant in coastal waters. Chlorophyta represented 29% of the global photosynthetic reads (Dinoflagellates excluded) and their contribution was especially high at oligotrophic stations (up to 94%) and along the European Atlantic coast. Mamiellophyceae dominated most coastal stations.
Scientific reports, 8:14020, 2018

We describe RCC1774, a strain isolated from the foreshore near Roscoff (France). It is phylogenetically related to members of the Acaryochloris genus but completely lacks Chl d. Instead, it possesses monovinyl-Chl a and b at a b/a molar ratio of 0.16, similar to that in Prochloron and Prochlorothrix. It differs from the latter by the presence of phycocyanin and a vestigial allophycocyanin energetically coupled to photosystems. Its very unusual pigment content compared to other Acaryochloris spp. is likely related to its specific lifestyle.
Scientific reports, 8: 9142, 2018

We compared the composition of eukaryotic communities using two genetic markers (18S rRNA V4 and V9 regions) at 27 sites sampled during Ocean Sampling Day 2014. Globally, the V4 and V9 regions of the 18S rRNA gene provided similar images of alpha diversity and ecological patterns.
Environmental Microbiology, (20), 2, pp. 506–520, https://doi.org/10.1111/1462-2920.13952, 2018

Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosystems. They play a major role as primary producers, but many species are mixotrophic or heterotrophic. Environmental metabarcoding based on high-throughput sequencing is increasingly applied to assess diversity and abundance of planktonic organisms, and reference databases are definitely needed to taxonomically assign the huge number of sequences. We provide an updated 18S rRNA reference database of dinoflagellates: DINOREF.
Molecular Ecology Resources, 18, 974-987, https://doi.org/10.1111/1755-0998.12781, 2018

Symbioses between eukaryotic algae and nitrogen-fixing cyanobacteria have been recognized in recent years as a key source of new nitrogen in the oceans. We investigated the composition of the small photosynthetic eukaryote communities associated with nitrogen-fixing cyanobacteria in the Brazilian South Atlantic Bight using a combination of flow cytometry sorting and high throughput sequencing of two genes: the V4 region of 18S rRNA and nifH.
The ISME Journal, (12), 5, pp. 1360–1374, https://doi.org/10.1038/s41396-018-0050-z, 2018

We obtained phenotypic and genetic data on a large set of prasinophyte clade VII culture strains that allowed us to clarify the taxonomy of this important marine group. We describe two novel classes, the Picocystophyceae and the Chloropicophyceae, the latter containing two novel genera, Chloropicon and Chloroparvula, and eight new species of marine picoplanktonic green algae.
Scientific Reports, (7), 1, pp. 14019, https://doi.org/10.1038/s41598-017-12412-5, 2017

Recent Publications

More Publications

Pdf files are available on Research Gate

. Can molecular tools enhance long-term monitoring of marine protists?. Journal of Plankton Research, in press, 2018.

PDF Source Document

. 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 and Phenotypic Characterization of Cultured Isolates. Protist, (168), 5, pp. 612–635, https://doi.org/10.1016/j.protis.2017.09.002, 2017.

PDF Project Project Source Document

. Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. The ISME Journal, (11), 2, pp. 512–528, https://doi.org/10.1038/ismej.2016.120, 2017.

PDF Project Project Project

. Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry. Journal of Phycology, (53), 2, pp. 271–282, https://doi.org/10.1111/jpy.12495, 2017.

Project Project

. Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex. Journal of Phycology, (53), 1, pp. 161–187, https://doi.org/10.1111/jpy.12489, 2017.

Project Project

. Short timescale dynamics of phytoplankton in Fildes Bay, Antarctica. Antarctic Science, (29), 3, pp. 217–228, https://doi.org/10.1017/S0954102016000699, 2017.

Project

. Benthic protists: the under-charted majority. FEMS Microbiology Ecology, (92), 8, pp. fiw120, https://doi.org/10.1093/femsec/fiw120, 2016.

. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms. The ISME Journal, (10), 10, pp. 2419–2434, https://doi.org/10.1038/ismej.2016.38, 2016.

Project Project Project Project

Submitted Publications

More Publications

. High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding. The ISME Journal, (submitted), 2018.

Project

. Pelagophyte assemblages of the global ocean display low intraspecific diversity. Environmental Microbiology, (submitted), 2018.

Project

Recent Talks

Slides available on Speaker Desk

Teaching

Recent teaching activity

Courses organized

  • 2017 - Co-organizer of ASIAME 2 (South Asia Workshop in Aquatic Microbial Ecology) in Andaman Islands, India - 15 days - November 2017
  • 2015-2017 - Metagenomics of marine microbes (6 h lecture, 4 h practical session) - Organizing Committee. Marine Ecological and Evolutionary Genomics, Roscoff, June 2015
  • 2014 - Organizer of International Phytoplankton course, Macaé, Brasil (2 weeks) - December 2014
  • 2013 - Co-organizer of ASIAME (First South East Asia Workshop in Aquatic Microbial Ecology) in Vietnam, Nha Trang- 10 days - October 2013
  • 2013 - Co-organizer of the UPMC Daniel-Jouvance School in Marine-Biology - Arraial do Cabo, Brasil - March 2013

Courses taught

  • 2018 Using phyloseq for metabarcode data analysis, Formation metabarcoding, Roscoff
  • 2017 R for microbial ecology, ASIAME 2, South Asia Workshop in Aquatic Microbial Ecology, India
  • 2012-2017 Metagenomics of marine microbes (6 h lecture, 4 h practical session), Marine Ecological and Evolutionary Genomics, Roscoff
  • 2018-2006 Eukaryotic picoplankton, Introduction to R and to metabarcode processing (10 days). ECODIM workshop (South America post graduate course), University of Concepcion, Chile (takes place every two years)
  • 2012 Introduction to flow cytometry (3 h lecture, 6 h practical session). Oceanography Institute, Universidade de Sao Paulo, May 2012

Tutorials available on line

R

Metabarcoding

Contact