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 rRNA), 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 and metaPR2 (in progress)

Current Collaborations

Recent 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.

RCC

Roscoff Culture Collection

PR2

18S rRNA sequence database

metaPR2

18S rRNA metabarcode database

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

We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using three metabarcoding approaches.
Scientific Reports 11: 1368, 2021

We found no evidence of phago-mixotrophy in any M. polaris strain based on flow cytometric measurement of prey ingestion. In addition, in silico predictions reveal that members of the genus Micromonas lack a genetic signature of phagocytotic capacity..
Journal of Phycology 57, 435-446, 2021

Based on the phylogenetic placement and scale morphology of Pseudohaptolina sorokinii we propose the new combination Pseudohaptolina birgeri and emend the description of this species..
Phycologia, 56: 606-615, 2020

We describe two new species of Mantoniella, M. beaufortii and M. baffinensis that are most similar to the cosmopolitan M. squamata. Screening of global marine metabarcoding datasets indicates M. beaufortii has only been recorded in seawater and sea ice samples from the Arctic while no environmental barcode matches M. baffinensis suggesting that they are cold or ice-adapted Mantoniella species.
Journal of Phycology, 56: 37-51, 2020

More than 1,000 cultures from the Arctic were obtained, characterized by 18S rRNA sequencing and optical microscopy and de-replicated.
Elementa 8, p.6, 2020

We used metabarcoding to analyze the temporal dynamics of the three domains of life in Singapore waters.
Scientific Reports 9, 16390, 2019

Submitted Publications

More Publications

. An 18S V4 rDNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth.. Earth System Science Data (submitted) - deposited to BioRxiv, 2021.

Preprint PDF Dataset Project Project

. Transcriptomes from the Diatoms Thalassiosira and Minidiscus from the English Channel and Antarctica.. Scientific Data (submitted), 2021.

Preprint Project

. pr2-primer: an 18S rRNA primer database for protists. Methods in Ecology and Evolution (submitted), 2021.

Preprint Code Dataset Project

. A user guide to environmental protistology: primers, metabarcoding, sequencing, and analyses. Mol Ecol Res (submitted), 2019.

Preprint PDF Code Dataset Project

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

Project Project

Recent Talks

Slides available on Speaker Desk

More Talks

Teaching

Recent teaching activity

Courses organized

  • 2019 - Co-organizer of APC 12 (Advanced Phytoplankton Course) in Roscoff, France - 3 weeks - May-June 2019
  • 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

  • 2021 Scales in Plankton Ecology - ES3305/ES7022: Currents Issues in Ecology, coordinated by D. Wardle, ASE, Nanyang Technological University, Singapore - 3 h
  • 2021 Introduction to R / Data wrangling, plotting and mapping with R - ES7023 & ES0002: Fundamentals of Data Science for Earth and Environmental Systems Science , coordinated by D. Lallemant, ASE, Nanyang Technological University, Singapore - 9 h
  • 2020 Introduction to R / Scales in Marine Ecoystems - ES3307: Experimental Design and Analysis, coordinated by E. Slade, ASE, Nanyang Technological University, Singapore - 6 h
  • 2020 Introduction to R / Data wrangling, plotting and mapping with R - ES7023 & ES0002: Fundamentals of Data Science for Earth and Environmental Systems Science , coordinated by D. Lallemant, ASE, Nanyang Technological University, Singapore - 9 h
  • 2019 Introduction to R / Data wrangling, plotting and mapping with R - ES7023 & ES0002: Fundamentals of Data Science for Earth and Environmental Systems Science , coordinated by D. Lallemant, ASE, Nanyang Technological University, Singapore - 9 h
  • 2018 Using phyloseq for metabarcode data analysis, Formation metabarcoding, Roscoff - 3 h
  • 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

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