Site languages :




On this website

Home > Research Teams > Interactions Microeucaryotes-Bactéries-Archées (IMBA)

Interactions Microeukaryotes, Bacteria and Archaea (IMBA)

Team leader : FRAISSINET-TACHET Laurence
Coleader : HUGONI Mylène

Personnels permanents

CHAPULLIOT David Technician, INRAE
HUGONI Mylène Lecturer, UCB
MELAYAH Delphine Lecturer, UCB
VALLON Laurent Technician, UCB

Personnels non permanents

BONTEMPS Zélia PhD student (2020-2023)
MAUCOURT Flavien PhD student (2019-2022)

Microorganisms, their biodiversity, their functions and their interactions, are one of the major components of ecosystems. Indeed, they are the heart of a wide range of functions very important for ecosystems. At present, although it is suspected that the 3 microbial life domains interact with each other to carry out these functions, the knowledge to assess their interactions and key environmental factors impacting the structure of their communities and their activities are poorly documented. In particular, in presence of natural or anthropogenic disturbances, microorganisms are equipped with adaptive capacities to cope with these environmental constraints. Thus, understanding the distribution, dynamics and interactions of the whole microbes represents a critical point in order to understand the functional processes of ecosystems.

In this context, the IMBA team, created in 2020, is interested in identifying and understanding the distribution of microbial communities from the three life domains, its dynamics and its role in the functioning of ecosystems under strong environmental pressures of natural or anthropogenic origins. We focus our study on terrestrial or aquatic ecosystems presenting gradients of strong environmental pressures in which the recycling of organic matter plays a key role.

Our research is divided into two themes that aim to study, on the one hand, biodiversity and microbial interactions in the three life domains and, on the other hand, functions related to organic molecules.

PNG - 58 kb

Theme 1: Biodiversity and microeukaryotic-bacteria-archaea interactions

This first theme aims to assess the microbial biodiversity of the 3 life domains and the impact of environmental constraints on the structure of these communities. In addition, we are looking first for the identification of potential interactions carrying out in situ highlighted by co-occurrence networks, and second, by validation of potential coexistence of previously identified microbial partners. The exploration of microbial biodiversity is carried out without a priori. The existence of some microbial consortia are analysed in situ and reconstructed in laboratory by co-cultivation. The approaches used are based on the implementation of molecular ecology tools such as metabarcoding and metagenomics coupled with analyses of bioinformatics and biostatistics but also of classical microbial ecology tools (FISH (Fluorescent In Situ Hybridization) or MISH (Magnetic In Situ Hybridization)).

Theme 2: Functions related to the recycling of organic molecules during inter-domain microbial interactions

The theme 2 focuses on the functions essential to the survival of microorganisms in highly constrained environments, namely, their ability to jointly metabolise organic molecules. Thus, the functional diversity of microorganisms is analysed by targeted or not, approaches using a panel of tools of classical biochemistry to those of molecular ecology such as functional metabarcoding, metatranscriptomics or in perspective, metabolomics.

Bibliography :


  • Hugoni, M., Nunan, N., Thioulouse, J., Dubost, A., Abrouk, D., Martins, J.M.F., Goffner, D., Prigent-Combaret, C., Grundmann, G., 2021. Small-Scale Variability in Bacterial Community Structure in Different Soil Types. Microbial Ecology.

  • Sarazin, G., Jezequel, D., Leboulanger, C., Fouilland, E., Le Floc'h, E., Bouvy, M., Gérard, E., Agogué, H., Bernard, C., Hugoni, M., Grossi, V., Troussellier, M., Ader, M., 2021. Geochemistry of an endorheic thalassohaline ecosystem: the Dziani Dzaha crater lake (Mayotte Archipelago, Indian Ocean). Comptes Rendus Géoscience.


  • Bernard, C., Escalas, A., Villeriot, N., Agogué, H., Hugoni, M., Duval, C., Carré, C., Got, P., Sarazin, G., Jézéquel, D., Leboulanger, C., Grossi, V., Ader, M., Troussellier, M., 2019. Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). Microbial Ecology.

  • Lepère, C., Domaizon, I., Humbert, J.-F., Jardillier, L., Hugoni, M., Debroas, D., 2019. Diversity, spatial distribution and activity of fungi in freshwater ecosystems. PeerJ 7, e6247.

  • Luis, P., Saint‐Genis, G., Vallon, L., Bourgeois, C., Bruto, M., Marchand, C., Record, E., Hugoni, M., 2019. Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments. Environmental Microbiology 21, 1407-1424.

  • Luis, P., Vallon, L., Tran, F.H., Hugoni, M., Tran Van, V., Mavingui, P., Minard, G., Valiente Moro, C., 2019. Aedes albopictus mosquitoes host a locally structured mycobiota with evidence of reduced fungal diversity in invasive populations. Fungal Ecology 39, 257-266.

  • Mukherjee, A., Yadav, R., Marmeisse, R., Fraissinet-Tachet, L., Reddy, M.S., 2019. Heavy metal hypertolerant eukaryotic aldehyde dehydrogenase isolated from metal contaminated soil by metatranscriptomics approach. Biochimie 160, 183-192.

  • Thakur, B., Yadav, R., Vallon, L., Marmeisse, R., Fraissinet-Tachet, L., Sudhakara Reddy, M., 2019. Multi-metal tolerance of von Willebrand factor type D domain isolated from metal contaminated site by metatranscriptomics approach. Science of The Total Environment 661, 432-440.


  • Gérard, E., De Goeyse, S., Hugoni, M., Agogué, H., Richard, L., Milesi, V., Guyot, F., Lecourt, L., Borensztajn, S., Joseph, M.-B., Leclerc, T., Sarazin, G., Jézéquel, D., Leboulanger, C., Ader, M., 2018. Key Role of Alphaproteobacteria and Cyanobacteria in the Formation of Stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean). Frontiers in Microbiology 9, 796.

  • Hugoni, M., Escalas, A., Bernard, C., Nicolas, S., Jézéquel, D., Vazzoler, F., Sarazin, G., Leboulanger, C., Bouvy, M., Got, P., Ader, M., Troussellier, M., Agogué, H., 2018. Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island). Molecular Ecology.

  • Hugoni, M., Luis, P., Guyonnet, J., Haichar, F.Z., 2018. Plant host habitat and root exudates shape fungal diversity. Mycorrhiza 28, 451-463.

  • Lavergne, C., Hugoni, M., Hubas, C., Debroas, D., Dupuy, C., Agogué, H., 2018. Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study. Microbial Ecology 75, 364-374.

  • Lavergne, C., Hugoni, M., Dupuy, C., Agogué, H., 2018. First evidence of the presence and activity of archaeal C3 group members in an Atlantic intertidal mudflat. Scientific Reports 8, 11790.

  • Thakur, B., Yadav, R., Fraissinet-Tachet, L., Marmeisse, R., Sudhakara Reddy, M., 2018. Isolation of multi-metal tolerant ubiquitin fusion protein from metal polluted soil by metatranscriptomic approach. Journal of Microbiological Methods 152, 119-125.

  • Ziller, A., Fraissinet-Tachet, L., 2018. Metallothionein diversity and distribution in the tree of life: a multifunctional protein. Metallomics.


  • Hugoni, M., Vellet, A., Debroas, D., 2017. Unique and highly variable bacterial communities inhabiting the surface microlayer of an oligotrophic lake. Aquatic Microbial Ecology 79, 115-125.

  • Marmeisse, R., Kellner, H., Fraissinet-Tachet, L., Luis, P., 2017. Discovering Protein-Coding Genes from the Environment: Time for the Eukaryotes? Trends in Biotechnology 35, 824-835.

  • Ziller, A., Yadav, R.K., Capdevila, M., Reddy, M.S., Vallon, L., Marmeisse, R., Atrian, S., Palacios, Ò., Fraissinet-Tachet, L., 2017. Metagenomics analysis reveals a new metallothionein family: Sequence and metal-binding features of new environmental cysteine-rich proteins. Journal of Inorganic Biochemistry 167, 1–11.