Ludwig Jardillier

Position: Professor
Detailed position: U-PSUD Professor

Team: Microbial diversity, ecology and evolution

Contact details:
Laboratoire Écologie, Systématique, Évolution
Bât. 360, rue du Doyen André Guinier
91405 Orsay Cedex

Tel: +33 (0)1 69 15 50 84


Email: ludwig.jardillier(at)

Laboratoire Ecologie, Systématique et Evolution

Research interests

At the global scale, aquatic ecosystems play major roles in climate regulation and carbon fluxes. Deciphering the processes involved in the functioning of these ecosystems and in the biogeochemical fluxes is essential to grasp their temporal dynamics and how they are affected by disturbances such as those produced by global changes.
Microbial communities are extremely complex in most environments, because of their diversity that is characterised by various metabolism, the numerous interactions they can sustain with other organisms in their environment, the life cycles composed of diverse development stages, the capacity of most microorganisms to enter into stages of low cellular activity when environmental conditions become unfavourable as well as their capacity to migrate and to colonise new environments. It is supposed that these features could allow microbial communities to be resilient when facing changing environmental conditions, either intra-annual variations (e.g. seasons) or inter-annual (e.g. global changes), and thus to maintain ecosystem functioning. It is usually assumed that the organisms at the top of trophic webs are more sensitive to changes in their environment. However, because microorganisms are at the bottom of trophic webs, any shift, even trifling, at the level of this community could impact and destabilise in cascade the functioning of the ecosystems.
The purpose of my research activities is to unravel the microbial diversity, to understand the processes that structure the microbial diversity and, in return, to identify the role played by the microorganisms in the functioning of aquatic ecosystems. This research takes place in a more general question in ecology which time at disclosing the links between diversity and stability of ecosystem functioning.

Current research projects

2018-2021    Collaborator of the Mobydick project: Marine Ecosystem Biodiversity and Dynamics of Carbon Around Kerguelen: An Integrated View, led by B. Quéguiner (MIO, University d’Aix-Marseille, Marseille), funded by ANR and LEFE-CYBER

2018-2019     Collaborator of the project Plankton-party: Planktonic Eukaryotic Parasites: the Particular Case of Phaeocystis Blooms, led by U. Christaki (ULCO, LOG, UMR CNRS 8187, Wimereux), funded by INSU-CNRS

2016-2020  Collaborator of the Ancestram project: Inferring the Characteristics of Ancestral Stramenopiles to Understand their Evolution and Ecological Success, led by D. Moreira (UPSud, ESE, UMR CNRS 8079, Orsay), funded by ANR

2016-2020  Collaborator of the project Floral Microbiology: Dynamics, Structure and Contribution to the Plant Microbiome, led by J. Vorholt and J. Massoni (Institute of Microbiology, Swiss Federal Institute of Technology -ETH-, Zurich, Suisse)

Main and current scientific administrative responsibilities

2018-present Assistant director of the laboratory Ecology, Systematic and Evolution

2018-present Member of the Scientific Council of the program CYBERLEFE of INSU-CNRS

2018-présent Co-manager of the UNICELL research facility

2017-présent Assistant scientist of the Research Centre in Experimental and Predictive Ecology (Saint-Pierre-les-Nemours)

2016-présent  Associate vice-president for Research of the Council of the Life Science department of the Paris-Sud University

2012-2018      Elected member of the University National Council, section Population Biology and Ecology

Laboratoire Ecologie, Systématique et Evolution


Current teaching activities

My teaching activities deal with ecology and, more particularly, on the ecology of aquatic ecosystems (both marine and freshwater). I develop especially the different fields in microbial ecology, from the diversity, the factors (biotic and abiotic) driving this diversity that determine its temporal dynamics and spatial distribution as well as the role of the microorganisms in ecosystem functioning.

I teach essentially in the undergraduate programs Organism Biology and Ecology and Urban  Ecolandscape and in the graduate programs  Biodiversity, Ecology, Evolution. My teachings are composed of  theoretical, practical and field classes.

Main and current teaching administrative responsibilities

2016-présent Co-head of the training Biodiversity and Ecosystem Functioning of the Biodiversity, Ecology and Evolution graduate degree

2015-présent Co-head of the teaching Stage Auvergne of the undergraduate Life Science degree

2010-présent Co-head of the teaching Quality and Management of Aquatic Ecosystems of the Biodiversity, Ecology and Evolution Graduate degree


2010-2011 Animator of the  workshop on Biodiversity in Aquatic Ecosystems as part of the event “Faites de la Science” at the University Paris-Sud

2011        Partner of the project “Chlorophylle”, lead by A. Kalos (independent artist), funded by the Région Ile-de-France, the “Conseil Général d’Essonne”, and the “synchrotron Soleil”, program “La Science de l’Art

2011        Public conference for the “Université Populaire des lacs d’Essonne” on small freshwater ecosystems

2015-2016 Partner of the project “Dendromité“, lead by C. Damesin (UPSud, ESE, UMR CNRS 8079, Orsay) and K. Bonneval (independent artist), funded by the “Diagonale Paris-Saclay”, call “Arts Science Diagonale”

2015-2016 Trainer for the “formation entreprises CNRS” “Atelier de Cytométrie” at the “Institut de Biologie Intégrative de la Cellule” (UMR 9198, Gif-sur-Yvette)

2016         Participant to the documentary “Dallol, aux Frontières de la Vie” made by O. Grunewald on a scientific field expedition lead by P. López-García

Laboratoire Ecologie, Systématique et Evolution


Current PhD and post-doctoral supervisions

2018-2019     Co-supervisor with U. Christaki of the post-doctoral project of I. Sassenhagen (LOG, ULCO, Wimereux), on Parasitism in Marine Environment during High Biomass Algal Blooms: the case-study Phaeocyctis

2017-2020   Co-supervisor with U. Christaki of the thesis project of S. Irion (LOG, ULCO, Wimereux) on The Biodiversity of the Marine Ecosystem and Carbon Fluxes around Kerguelen: The Role of the small Phytoplankton at the Cellular Scale, funded by ANR and Région des Hauts de France

2017-2020    Co-supervisor with P. López-García (UPSud, ESE, UMR CNRS 8079, Orsay), E. Thébault (iEES, SU, UMR CNRS 7618, Paris) and G. Restoux (AgroParisTech-INRA, GABI, Unité 1313, Jouy-en-Josas) of the PhD project of G. David  on The Ecology of Microbial Communities in Aquatic Ecosystems of the Regional Natural Park of the Haute Vallée de Chevreuse Revealed by Statistical and Modelling Approaches, funded by IDEX Paris-Saclay

Previous supervisions (since 2009)

2010-2014    Co-supervising with  P. López-García (UPSud, ESE, UMR 8079, Orsay) M. Simon’s PhD project on the Diversity, Spatial Distribution and Temporal Dynamics Temporelle of small eukaryotes in small freshwater systems

2013    Supervising M. Sorais‘s project, engineer (ANR PULSE), on the Occurence and Biomass of Haptophytes in Lakes of Various Environmental Conditions in Ile-de-France

2013   Co-supervising with  F. Hulot (UPSud, ESE, UMR 8079, Orsay) N. Chahine’s graduate project on the Microbial  Diversity in Ponds in Savanna under Various Environmental Constraints

2012   Co-supervising with G. Lacroix (UPMC, iEES, UMR 7618, Paris) B. Morisseau’s graduate project on the Prey-predator Interactions in Marine and Continental Aquatic Ecosystems: Consequences on the Trophic Web Topology

2012   Co-supervising with F. Guyot (MNHN, Institut de minéralogie, de physique des matériaux et de cosmochimie, UMR 7590, Paris) A. Saghaï’s graduate project on the Morphologic and Phylogenetic Characterisation of Magnetotactic bacteria in freshwater ecosystems in Ile-de-France

2011   Co-supervising with G. Lacroix (UPMC, iEES, UMR 7618, Paris) M. Sorais’s graduate project on the Influence of Predation Behaviour and Ecosystem Type (Marine or Freshwater d’Eau Douce) on Size Relationships between Predators and Preys

2010   Co-supervising with  P. López-García (UPSud, ESE, UMR 8079, Orsay) M. Simon’s graduate project on the Investigation of Haptophytes Molecular Diversity in Limnic Environments

Laboratoire Ecologie, Systématique et Evolution


C. Bernard: MNHN, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, Paris

U. Christaki: Université du Littoral, Laboratoire d’Océanologie et des Geosciences, UMR 8187, Wimereux

A. Cornille: CNRS, Unité Génétique Quantitative et Evolution,  INRA Le Moulon, Gif/Yvette

I. Domaizon: INRA, Centre Alpin de Recherches sur les Réseaux Trophiques et les Écosystèmes Lacustres, Thonon-les-Bains

E. Edeline: INRA, Unité Ecologie et santé des écosystèmes, Rennes

F. Guyot: MNHN, Institut de minéralogie, de physique des matériaux et de cosmochimie, UMR 7590, Paris

F. Hulot: Université Paris-Sud, Unité Ecologie Systématique et Evolution, UMR 8079, Orsay

B. Queguiner: Université Aix-Marseille, Mediterranean Institute of Oceanography, UMR 110, Marseille

G. Lacroix: CNRS, Institut d’Ecologie et des Sciences de l’Environnement de Paris, UMR 7618, Paris 

F. Lucas: Université Paris-Est-Créteil, Laboratoire Eau Environnement et Systèmes Urbains, MSE 308, Créteil

J. Massoni: Eidgenössische Technische Hochschule (ETH), The Vorholt Lab – Microbial Physiology, Zurich

I. Obernosterer: CNRS, Laboratoire d’Océanographie Microbienne, UMR 7621, Banyuls-sur-mer

E. Rochelle-Newall: IRD, Institut d’Ecologie et des Sciences de l’Environnement de Paris, UMR 7618, Paris

E. Thébault: CNRS, Institut d’Ecologie et des Sciences de l’Environnement de Paris, UMR 7618, Paris

M. Zubkov: The Scottish Association for Marine Science, Oban, Ecosse

Laboratoire Ecologie, Systématique et Evolution


  1. Lepère C, Domaizon I, Humbert J-F, Jardillier L, Hugoni M, Debroas D (2018) Diversity, spatial distribution and activity of fungi in freshwater ecosystems. Peer J in press
  2. Rochelle-Newall E, Niboyet A, Jardillier L, Fiorini S, Chollet S, Llavata M, de Santis E, Barot S, Lacroix G (2018) Impacts of elevated atmospheric CO2 concentration on terrestrial-aquatic carbon transfer and a downstream aquatic microbial community. Aquat Sci 80:27
  3. Longo WM, Huang Y, Yao Y, Zhao J, Giblin AE, Wang X, Zech R, Haberzetti T, Bradley R, Jardillier L, Toney J, Liu Z, Krivonogov S, Chu G, D’Andrea WJ, Harada N, Nagashima K, Sato M, Yonenobu H, Yamada K, Gotanda K, Shinozuka Y (2018) Widespread occurrence of distinct alkenones from Group I haptophytes in freshwater lakes: Implications for paleotemperature and paleo-environmental reconstructions. Earth Planet Sc Lett 492:239
  4. Debroas D, Domaizon I, Humbert JF, Jardillier L, Lepère C, Oudart A, Taib N (2017) Overview of freshwater microbial eukaryotes diversity: A first analysis of publicly available metabarcoding data. FEMS Microbiol Ecol 93:10.1093/femsec/fix023
  5. Simon M, López-García P, Deschamps P, Restoux 201G, Bertolino P, Moreira D, Jardillier L (2016) Resilience of freshwater microbial eukaryotic communities undergoing severe drought events. Frontiers Microbiol 7:812
  6. Roguet A, Laigle GS, Therial C, Bressy A, Soulignac F, Catherine A, Lacroix G, Jardillier L, Lerch TZ, Lucas FS (2015) Neutral community model explains the bacterial community assembly in freshwater lakes. FEMS Microbiol Ecol 91:fiv125
  7. Faure D, Bonin P, Duran R and the Microbial Ecology EC2CO-consortium (2015) Environmental microbiology as a mosaic of explored ecosystems and issues. Special Issue in Environ Sci Pollut R 22:13577-13598
  8. Grob C, Jardillier L, Hartman M, Ostrowski M, Zubkov M, Scanlan DJ (2015) Cell-Specific CO2 fixation rates of two distinct groups of plastidic protists in the Atlantic Ocean remain unchanged after nutrient addition. Environ Microbiol Rep 7:211-218
  9. Simon M, López-García P, Deschamps P, Moreira D, Restoux G, Bertolino P, Jardillier L (2015) Marked seasonality despite apparent hectic temporal dynamics of complex protist communities in shallow freshwater systems. ISME J 9:1941-1953
  10. Simon M, Jardillier L, Deschamps P, Moreira D, Restoux G, Bertolino P, López-García P (2014) Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems. Environ Microbiol 17:3610-3627
  11. Simon M, López-García P, Moreira D, Jardillier L (2013) New haptophyte lineages and multiple independent colonisations of freshwater ecosystems. Environ Microbiol Rep 5:322-332
  12. Kirkham A, Lepère C, Jardillier L, Not F, Bouman H, Mead A, Scanlan D (2013) A global perspective on marine photosynthetic picoeukaryote community structure. ISME J 7:922-936
  13. Kirkham A, Jardillier L, Tiganescu A, Pearman J, Zubkov M, Scanlan D (2011) Basin-scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional Transect. Environ Microbiol 13: 975-990
  14. Kirkham A, Jardillier L, Holland R, Zubkov M, Scanlan DJ (2011) Analysis of photosynthetic picoeukaryote community structure along an extended Ellett Line transect in the northern North Atlantic reveals a dominance of novel prymnesiophyte and prasinophyte phylotypes. Deep-Sea Res I 58: 733-744
  15. Jardillier L, Zubkov MV, Pearman J, Scanlan DJ (2010) Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. ISME J 4: 1180-1192
  16. Shi XL, Marie D, Jardillier L, Scanlan DJ, Vaulot D (2009) Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS ONE 4(10): e7657
  17. Zwirglmaier K, Jardillier L, Ostrowski M, Mazard S, Garzarek L, Vaulot D, Not F, Massana R, Ulloa O, Scanlan DJ (2008) Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ Microbiol 10:147-161
  18. Lepère C, Boucher D, Jardillier L, Domaizon I, Debroas D (2006) Succession and regulation factors of small eukaryote community composition in a lacustrine ecosystem (Lake Pavin). Appl Environ Microb 72: 2917-2981
  19. Lemarchand C, Jardillier L, Carrias J-F, Richardot M, Debroas D, Sime-Ngando T, Amblard C (2006) Community composition and activity of prokaryotes associated to detrital particles in two contrasting lake ecosystems. FEMS Microbiol Ecol 57: 442-451
  20. Boucher D, Jardillier L, Debroas D (2006) Succession of bacterial community composition over two consecutive years in two aquatic systems: a Natural Lake and a Lake-reservoir. FEMS Microbiol Ecol 55:79-97
  21. Jardillier L, Bettarel Y, Richardot M, Bardot C, Amblard C, Sime-Ngando T, Debroas D (2005) Effects of viruses and predators on prokaryotic community composition. Microbial Ecol 50: 557-569
  22. Jardillier L, Boucher D, Personnic S, Jacquet S, Thénot A, Sargos D, Amblard C, Debroas D (2005) Relative importance of nutrients and mortality factors on prokaryotic community composition in two lakes of different trophic status: microcosm experiments. FEMS Microbiol Ecol 53: 429-443
  23. Jardillier L, Basset M, Domaizon I, Belan A, Amblard C, Richardot M, Debroas D (2004) Bottom-up and top-down control of the bacterial community composition in the euphotic zone of a reservoir. Aquat Microb Ecol 35: 259-273