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

The Ocean Sampling Day (OSD) project provided metabarcoding data for the V4 hyper-variable regions of the 18S rRNA gene from 157 samples collected at 143 mostly coastal stations. In this paper we focus on the class Mamiellophyceae, which was found at nearly all OSD stations and represented 55 % of the green microalgae (Chlorophyta) reads in the 2014 OSD dataset. We performed phylogenetic analyses of unique OSD metabarcodes (ASV, amplicon single variants) and reference GenBank sequences from cultures and from the environment, focusing on the four most represented genera: Ostreococcus (45 % of the Mamiellophyceae reads), Micromonas (34 %), Bathycoccus (10 %) and Mantoniella (8.7 %). These analyses uncovered novel diversity within each genus except Bathycoccus. In Ostreococcus, a new clade (E) with 2 very clear base pair differences compared to the oceanic clade B in the V4 region was the second most represented clade after the coastal Ostreococcus “lucimarinus”. Within Micromonas, ten clades were found exceeding the 4 species and 2 candidate species already described. Finally, we found 2 new environmental clades of Mantoniella. Each Mamiellophyceae clade had a specific distribution in the OSD dataset suggesting that they are adapted to different ecological niches.
Scientific Reports 9: 5190, 2019

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 13:388-40, 2019

We used DNA metabarcoding of the 18S rRNA gene and particle interceptor traps (PITs) to characterize the taxonomic composition of particles sinking out of the photic layer in the California Current Ecosystem (CCE), a productive system with high export potential. Sequences affiliated with Radiolaria dominated the eukaryotic assemblage in fixed traps (90%), with Dinophyta and Metazoa making minor contributions. The prominence of Radiolaria decreased drastically in live traps, possibly due to selective consumption by copepods, heterotrophic nanoflagellates, and phaeodarians that were heavily enriched in these traps. Our findings identify Radiolaria as major actors in export fluxes in the CCE.
The ISME Journal, 13: 964–976, 2018

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

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

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

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

. DINOREF : A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Molecular Ecology Resources, 18, 974-987, https://doi.org/10.1111/1755-0998.12781, 2018.

PDF Dataset Project

. 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

. Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Scientific Reports, (7), 1, pp. 14019, https://doi.org/10.1038/s41598-017-12412-5, 2017.

PDF Dataset Project Project

. 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

Submitted Publications

More Publications

. Culturable diversity of Arctic phytoplankton during pack ice melting. Elementa, Science of the Anthropocene (submitted), 2019.

Preprint Dataset Project Project Project Project

. Mantoniella beaufortii and Mantoniella baffinensis sp. nov. (Mamiellales, Mamiellophyceae), two new green algal species from the high Arctic. Journal of Phycology (submitted), 2018.

Preprint PDF Dataset Project Project 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

  • 2019 R course - part of ES7023 & ES0002: Fundamentals of Data Science for Earth and Environmental Systems Science ASE, Nanyang Technological University, Singapore
  • 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