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 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

A planktonic food web model reveals significant differences between the East and West side of Baffin Bay with eastern food webs more specialized pathways while the western ones are shorter causing higher carbon export.
Elementa: Science of the Anthropocene (in press), 2019

More than 1,000 cultures from the Arctic were obtained, characterized by 18S rRNA sequencing and optical microscopy and de-replicated.
Elementa (in press), 2019

Presentation of the data obtained during the 2015 and 2016 Ice Camps of the Green Edge project (Baffin Island).
Earth System Science Data (in press), 2019

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

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, in press, 2019

Recent Publications

More Publications

Pdf files are available on Research Gate

. Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations. The ISME journal 13:388-40, 2019.

PDF Project Source Document

. High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding. The ISME Journal, 13: 964–976, 2018.

PDF Dataset Project Source Document

. Bolidophyceae, a sister picoplanktonic group of diatoms - a review. Frontiers in Marine Science, 5:370, 2018.

PDF Dataset Project Project Source Document

. Can molecular tools enhance long-term monitoring of marine protists?. Journal of Plankton Research, 40:519–536, 2018.

PDF Source Document

. A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle. Scientific reports, 8: 9142, 2018.

PDF Project

. 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

. Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria. The ISME Journal, (12), 5, pp. 1360–1374, https://doi.org/10.1038/s41396-018-0050-z, 2018.

PDF Dataset Project Slides

Submitted Publications

More Publications

. 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

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

  • 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