Diversity, Ecology and Evolution of Microbes
Team
Purificación López-García
Research Director, CNRS

I am a biologist interested in very broad questions about the origin and early evolution of life on Earth, with a special focus on microbial lineages, which cover the vast majority of biological diversity.

puri.lopez@cnrs.fr

puri.lopez@universite-paris-saclay.fr

David Moreira
Research Director, CNRS

Many years ago, I had the chance to get an old microscope at home. It opened to me a new world full of wonderful organisms. Since then, I have always been interested in the diversity and evolution of microorganisms from the three domains of Life, trying to reconstruct their phylogeny and to understand how their genomes evolve. More recently, I also became interested in the evolutionary relationship between living (cells) and non-living (viruses) organisms.

david.moreira@universite-paris-saclay.fr

Ludwig Jardiller
Professor, Université Paris-Saclay

I am a microbial ecologist. The aim of my research activities is to better appreciate microbial diversity, to understand the processes that structure this diversity and to identify the role played by microorganisms in the functioning of aquatic ecosystems. more information...

Email: ludwig.jardillier@universite-paris-saclay.fr

Phone: 0033 169 157 989

Laura Eme
Research Director, CNRS

My primary research interests are in evolutionary microbiology. I am particularly interested in the origin and evolution of the eukaryotic cell. My investigations revolve broadly around three topics: (1) Understanding the relationships of eukaryotes with the other two domains of life (Archaea and Bacteria); (2) Characterizing the evolution of key features of the eukaryotic cell ; (3) Investigating the phylogenetic relationships within the Tree of eukaryotes as well as the horizontal exchange of genetic material that might have occurred between distantly related eukaryote lineages. To tackle those, I have mainly used comparative (meta)genomic and molecular phylogenetic approaches, and I have focused on understudied unicellular eukaryotes (protists).

laura.eme@cnrs.fr

laura.eme@universite-paris-saclay.fr

Yvan Zivanovic
Research scientist, CNRS

yvan.zivanovic@cnrs.fr yvan.zivanovic@universite-paris-saclay.fr

Philippe Deschamps
Research scientist, CNRS

philippe.deschamps@cnrs.fr

philippe.deschamps@universite-paris-saclay.fr

Miguel Iniesto
Associate professor, U. Paris-Saclay

My interest in research and teaching started during my Degree in Biology. After a Master Degree in Clinical Microbiology I joined the laboratory of Microbial Ecology (Department of Ecology) as a PhD student under the supervision of Professors María del Carmen Guerrero and Ana Isabel López-Archilla. My doctorate "Microbial Mats: the implication of these microbial communities in the early stages of fossilization", in collaboration with the group of Palaeontology headed by the Prof. Angela D. Buscalioni and Karim Benzerara (IMPMC, Sorbonne Université), allowed me to delve into a complex topic (microorganism-mediated fossil formation) with a highly multidisciplinary approach (merging ecology, microbiology, palaeontology, geology, mineralogy and statistics) and achieve results with a significant impact on the community.

Then I joined Arnaud Brayard's team as part of his project "After the end: the rebuilding marine communities during the Rediversification of the Lower Triassic "[AFTER]. During this first postdoc in the laboratory of Biogéosciences at the Université de Dijon, I studied the fossil formation of the exceptional deposit of "Paris Biota" (Triassic, USA).

After Dijon I moved to Paris and became member of the team Diversity, Ecology and Evolution of Microbes (DEEM) under the supervision of Purificación López-García to study the formation of microbialites. Bioinformatics, microbial ecology and mineralogy would help us to unveil the factors (abiotic and biological) that determine the generation of these organosedimentary structures. Microbialites are now in vogue because they have a direct link to two impact topics. First, they are the first evidences of life on Earth. Stromatolites (a type of microbialite) have been accepted as the first living communities in the Ancient Earth and there is a great debate about the biological origin or not of some structures aged 3,500 Ma. Knowing the mechanisms that explain the formation of these structures is capital to solve this debate and would have a direct impact on finding traces of life on Mars. In addition, these communities often mineralize in carbonate, and can therefore act as carbon reservoirs. Real understanding of mineralization processes within microbialites could help us to increase and stimulate CO2 uptake by these communities and try to minimize the impact of global change on a global scale. In addition to that, I also collaborate in the characterization of the microbial diversity of diverse unknown environments mainly by metabarcoding approaches, and I also collaborate as expert in statistics with the MDr Villar-Quiles, neurologist at the Pitié Salpetrière Hospital - Sorbonne Université.

Regarding my teaching activity, I participate in classes at all levels (undergraduate, professional undergraduate, and master's) in subjects related to ecology, molecular biology, and microbiology:

  • L2Pro - UE4 Bio-production - Microbiologie - Virologie (Responsible)
  • L3Pro - Formation en Apprentissage/en Stage
  • L3Pro - Exploration des Environnements Pro
  • L3Pro - Génie Génétique

  • L2BIO - Anglais scientifique

  • L2BIO - Milieux Aquatiques
  • L3BOE - Écologie : théorie et pratique

  • Master BEE - Mise à niveau en écologie aquatique

  • Master BEE - Milieux aquatiques : qualité et gestion
  • Master BEE - Méthodologie et Ecologie
  • Master BioSanté - Evolution et biodiversité des microorganismes
Maria Ciobanu
Research assistant, CNRS

maria-cristina.ciobanu-costache@cnrs.fr maria.ciobanu@universite-paris-saclay.fr

Phone +33 (0)1 69 16 63 42

Paola Bertolino
Technical assistant, CNRS

paola.bertolino@cnrs.fr

paola.bertolino@universite-paris-saclay.fr

Jelena Jaric
Technical assistant

jelena.jaric@universite-paris-saclay.fr

Julie Montagna
SYMBEK - assistant

julie.montagna@universite-paris-saclay.fr

Carmen Miravete
SYMBEK bioinformatics asisstant

carmen.miravete@universite-paris-saclay.fr

Ana Gutiérrez-Preciado
Postdoc

ana.gutierrez@universite-paris-saclay.fr

Kristina Prokina
Postdoc

kristina.prokina@universite-paris-saclay.fr

Bledina Dede
Postdoc

bledina.dede@universite-paris-saclay.fr

Jazmin Blaz
Postdoc (PhD student 2020-2023)

jazmin-itzel.blaz-sanchez@u-psud.fr

Paul Roginski
Postdoc

paul.roginski@universite-paris-saclay.fr

Lewen Liang
Postdoc

lewen.liang@universite-paris-saclay.fr

Romain Leroy
PhD student

romain.leroy@universite-paris-saclay.fr

Arthur Szylit
PhD student

arthur.szylit@univ-littoral.fr

Agathe Struillou
PhD student

agathe.struillou@universite-paris-saclay.fr

Luna Marin
PhD student

PhD student

Zoe Commander
PhD student

zoe.commander@inrae.fr

Pedro Romero
PhD student

pedro.romero@universite-paris-saclay.fr

Stagiaires
Visitors and interns

2023-2024 Zoé Commander (M2), Agathe Brédel (M2), Pénélope Degardin (M2), Zachary Galvani (M1)

2022-2023 Marina Grilo (M2), Agathe Struillo (M2)

2021-2022 Romain Leroy (M2), Juliette Thiébaut (M2)

2020-2021 Pierrick Lenormand (M2), Guillaume Peugnet (M1), Anouk Cohen-Solal (L1), Yannis Arab (L2), Alix Catry (M1 INSA), Chloé Barthalon (L3)

2019-2020 Jeanne Chaumont, David Boulesteix (M2), Dave Edison Rojas (M2 Erasmus), Iris Rizos (M1)


Former members
Pablo Aguilar
Invited professor 2024

pablo.aguilar@uantof.cl

Anabel López-Archilla
Invited professor 2023

Anabel is a collaborator from the Autonomus University of MAdrid (UAM).

Sergey Karpov
Invited prof., St Petersburg University

Sergey A. Karpov is a collaborator who has visited our lab in different occasions for several months in 2015-2018

sakarpov4@gmail.com

Carolina Cubillos
Postdoc 2021 - 2024

Postdoc

Electra Kotopoulou
Postdoc 2021-2023

Postdoc electra.kotopoulou@universite-paris-saclay

Guillaume Louvel
Postdoc 2021-2023

guillaume.louvel@universite-paris-saclay.fr

Lukas Novak
Postdoc 2021-2023

lukas.novak@u-psud.fr

Jolien van Hooff
Postdoc 2019-2022

jolien.van-hooff@u-psud.fr

Sergio Muñoz
Postdoc 2020-2022

My research interests are focused on understanding the nature of the mitochondrial ancestor, and the early evolution of mitochondria and eukaryotes. I am currently working on analyzing metagenomes from diverse and poorly sampled environments in search of novel alphaproteobacteria. I am also working on inferring robust and artefact-free phylogenies for the Alphaproteobacteria and mitochondria.

sergio.munoz@universite-paris-saclay.fr

Julien Massoni
Postdoc 2020-2022

julien.massoni@u-psud.fr

Luis J. Galindo
PhD student 2017-2020, postdoc 2020-2021

luis-javier.galindo-gonzalez@u-psud.fr

Guifré Torruella
Postdoc 2015-2020

guifré.torruella@u-psud.fr

Naoji Yubuki
Postdoc 2018-2021

My research has focused mainly on the biodiversity and evolution of protists living in aquatic and symbiotic environments. I have paid particular attention to the discovery of novel marine protists, characterization of the ultrastructure (e.g. microtubular cytoskeletons) and phylogenetic relationships and investigation of symbiotic relationships.

naoji.yubuki@u-psud.fr

Jeanne Caumartin
PhD student 2021-2024

Jeanne was a PhD student co-supervised with our collaborator Karim Benzerara (IMPMC, Sorbonne Université, Paris)

jeanne.caumartin@sorbonne-universite.fr

Brittany Baker
PhD student 2020-2024

brittany.baker@universite-paris-saclay.fr

Feriel Bouderka
PhD student 2020-2024

feriel.bouderka@universite-paris-saclay.fr

Fabian van Beveren
PhD student 2018-2022

fabian.van-beveren@u-psud.fr

Thomas Bacchetta
PhD student 2018-2022

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Gwendoline David
PhD student 2017-2020

gwendoline.david@u-psud.fr

Jodie Belilla
PhD student 2017-2020

jodie.belilla@u-psud.fr

Guillaume Reboul
PhD student 2017-2020

guillaume.reboul@u-psud.fr

Solenne Irion
PhD student 2017-2019

solene.irion@univ-littoral.fr

Other PhD students and postdocs
Former PhD students and postdocs

PhD students

Marie Ragon (2007-2011), Estelle Couradeau (2008-2012), Charles Bachy (2008-2012), Jonathan Lombard (2009-2012), Céline Petitjean (2009-2013), Marianne Simon (2010-2014), Aurélien Saghaï (2013-2016), Rafael Ponce-Toledo (2014-2018), Jodie Belilla (2017-2020), Guillaume Reboul (2017-2020), Gwendoline David (2017-2020), Luis Javier Galindo (2017-2020), Solène Irion (2017-2020)

Postdocs

Emmanuelle Gérard (2003-2005), Jan Slapeta (2003-2005), Enrique Lara (2007-2008), Ana Belén Martin-Cuadrado (2007), Achim Quaiser (2007-2008), William Marande (2008-2009), Philippe Deschamps (2009-2010), Marie Ragon (2011-2012), Giselle Walker (2014-2015), Kamil Szafranski (2015-2017), Romain Derelle (2015-2016), Magdalena Ruiz (2016-2017), Albert Reñé (2017), Hélène Timpano (2016-2018), Guifré Torruella (2016-2021)