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Equipe de Recherche Adaptation des Microorganismes Eucaryotes à leur Environnement (AMEE)

Mylène Hugoni

Maître de Conférences


  • Thèmes de recherches :
    1. Microorganismes eucaryotes dans l’environnement
    2. Diversité spécifique et fonctionnelle des Archaea en milieu aquatique

Parcours scientifique

  • Post-doctorat Laboratoire Ecologie Microbienne (UMR CNRS 5557, Université Lyon 1, Lyon)
  • Post-doctorat Laboratoire Microorganismes Génome et Environnement (UMR CNRS 6023, Université Blaise Pascal, Clermont)
  • Doctorat Laboratoire Microorganismes Génome et Environnement (UMR CNRS 6023, Université Blaise Pascal, Clermont)





  • 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.
    Résumé : In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10 cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers. A multiple factor analysis revealed that bacterial and archaeal 16S ribosomal RNA (rRNA) transcript diversity assessed by pyrosequencing was similar between day and night emersions. Potentially active benthic Bacteria were highly diverse and influenced by chlorophyll a and phosphate concentrations. While in oxic and suboxic sediments, Thaumarchaeota Marine Group I (MGI) was the most active archaeal phylum, suggesting the importance of the nitrogen cycle in muddy sediments, in anoxic sediments, the mysterious archaeal C3 group dominated the community. This work highlighted that active prokaryotes organize themselves vertically within sediments independently of diel fluctuations suggesting adaptation to physicochemical-specific conditions associated with sediment depth.
    Mots-clés : #2.


  • 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.
    Mots-clés : #2.


  • Lepère, C., Domaizon, I., Hugoni, M., Vellet, A., Debroas, D., 2016. Diversity and Dynamics of Active Small Microbial Eukaryotes in the Anoxic Zone of a Freshwater Meromictic Lake (Pavin, France). Frontiers in Microbiology 7.
    Résumé : Microbial eukaryotes play a crucial role in ecosystem functioning and oxygen is considered to be one of the strongest barriers against their local dispersal. However, diversity of microbial eukaryotes in freshwater habitats with oxygen gradients has previously received very little attention. We applied high-throughput sequencing (V4 region of the 18S rRNA gene) in conjunction with quantitative PCR (DNA and RNA) and fluorescent in situ hybridization analyses, to provide an unique spatio-temporal analysis of microbial eukaryotes diversity and potential activity in a meromictic freshwater lake (lake Pavin). This study revealed a high genetic diversity of unicellular eukaryotes in the permanent anoxic zone of lake Pavin and allowed the discrimination of active vs. inactive components. 42 % of the OTUs (Operational taxonomic Units) are exclusively present in the monimolimnion, where Alveolata (Ciliophora and Dinophyceae) and Fungi (Dikarya and Chytrids) are the most active phyla and are probably represented by species capable of anaerobic metabolism. Pigmented eukaryotes (Haptophyceae and Chlorophyceae) are also present and active in this zone, which opens up questions regarding their metabolism.
    Mots-clés : #2, 454 pyrosequencing, active biosphere, Anoxia, Lakes, Microbial Eukaryotes.


  • Debroas, D., Hugoni, M., Domaizon, I., 2015. Evidence for an active rare biosphere within freshwater protists community. Molecular Ecology 24, 1236-1247.
    Mots-clés : #2, #perso.

  • Hugoni, M., Agogué, H., Taib, N., Domaizon, I., Moné, A., Galand, P.E., Bronner, G., Debroas, D., Mary, I., 2015. Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea. Microbial Ecology 70, 473-483.
    Mots-clés : #2, #perso.

  • Hugoni, M., Domaizon, I., Taib, N., Biderre-Petit, C., Agogué, H., Galand, P.E., Debroas, D., Mary, I., 2015. Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes. Environmental microbiology reports 7, 321–329.
    Résumé : Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, Thaumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine Thaumarchaeota conduct the process of nitrification. A high number of 16S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes.
    Mots-clés : #2, #perso.


  • Hugoni, M., Etien, S., Bourges, A., Lepère, C., Domaizon, I., Mallet, C., Bronner, G., Debroas, D., Mary, I., 2013. Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems. Research in Microbiology 164, 360-370.
    Mots-clés : #perso.

  • Hugoni, M., Taib, N., Debroas, D., Domaizon, I., Jouan Dufournel, I., Bronner, G., Salter, I., Agogue, H., Mary, I., Galand, P.E., 2013. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proceedings of the National Academy of Sciences 110, 6004-6009.
    Mots-clés : #perso.

Chapitre d’ouvrages


Communications Orales


  • Hugoni, M., Cantarel, A.A.M., Allard, V., Enjalbert, J., Gervaix, J., Saint Jean, S., Pommier, T., Le Roux, X., 2016. Increasing wheat variety diversity within cropped fields can channel soil N dynamics in a favourable status for the sustainability of cropping systems, dans: .
    Mots-clés : #5, #AME, #colloque.


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