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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)





  • Gérard, E., De Goeyse, S., Hugoni, M., Agogue, H., Richard, L., Milesi, V., et al. (2018). Key role of Alphaproteobacteria and Cyanobacteria in the formation of stromatolites of Lake Dziani Dzaha (Mayotte, Western Indian Ocean). Frontiers In Microbiology, 9. doi:10.3389/fmicb.2018.00796
    Résumé : Lake Dziani Dzaha is a thalassohaline tropical crater lake located on the “Petite Terre” Island of Mayotte (Comoros archipelago, Western Indian Ocean). Stromatolites are actively growing in the shallow waters of the lake shores. These stromatolites are mainly composed of aragonite with lesser proportions of hydromagnesite, calcite, dolomite and phyllosilicates. They are morphologically and texturally diverse ranging from tabular covered by a cauliflower-like crust to columnar ones with a smooth surface. High-throughput sequencing of bacterial and archaeal 16S rRNA genes combined with confocal laser scanning microscopy (CLSM) analysis revealed that the microbial composition of the mats associated with the stromatolites was clearly distinct from that of the Arthrospira-dominated lake water. Unicellular-colonial Cyanobacteria belonging to the Xenococcus genus of the Pleurocapsales order were detected in the cauliflower crust mats, whereas filamentous Cyanobacteria belonging to the Leptolyngbia genus were found in the smooth surface mats. Observations using CLSM, scanning electronic microscopy (SEM) and Raman spectroscopy indicated that the cauliflower texture consists of laminations of aragonite, magnesium-silicate phase and hydromagnesite. The associated microbial mat, as confirmed by laser microdissection and whole-genome amplification (WGA), is composed of Pleurocapsales coated by abundant filamentous and coccoid Alphaproteobacteria. These phototrophic Alphaproteobacteria promote the precipitation of aragonite in which they become incrusted. In contrast, the Pleurocapsales are not calcifying but instead accumulate silicon and magnesium in their sheaths, which may be responsible for the formation of the Mg-silicate phase found in the cauliflower crust. We therefore propose that Pleurocapsales and Alphaproteobacteria are involved in the formation of two distinct mineral phases present in the cauliflower texture: Mg-silicate and aragonite, respectively. These results point out the role of phototrophic Alphaproteobacteria in the formation of stromatolites, which may open new perspective for the analysis of the fossil record.
    Mots-clés : #2, alkaline lake, anoxygenic photrophic bacteria, aragonite, Hydromagnesite, Mg-silicate, Pleurocapsales, Stromatolites.

  • Hugoni, M., Escalas, A., Bernard, C., Nicolas, S., Jézéquel, D., Vazzoler, F., et al. (2018). Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island). Molecular Ecology. doi:10.1111/mec.14901
    Mots-clés : #2.

  • Hugoni, M., Luis, P., Guyonnet, J., & Haichar, F. Z. (2018). Plant host habitat and root exudates shape fungal diversity. Mycorrhiza. doi:10.1007/s00572-018-0857-5
    Mots-clés : #2, #4.

  • 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(2), 364-374. doi:10.1007/s00248-017-1048-1
    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.

  • 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(1). doi:10.1038/s41598-018-30222-1
    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(2), 115-125. doi:10.3354/ame01825
    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. doi:10.3389/fmicb.2016.00130
    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(6), 1236-1247. doi:10.1111/mec.13116
    Mots-clés : #2, #perso.

  • Hugoni, M., Agogué, H., Taib, N., Domaizon, I., Moné, A., Galand, P. E., et al. (2015). Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea. Microbial Ecology, 70(2), 473-483. doi:10.1007/s00248-015-0601-z
    Mots-clés : #2, #perso.

  • Hugoni, M., Domaizon, I., Taib, N., Biderre-Petit, C., Agogué, H., Galand, P. E., et al. (2015). Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes. Environmental Microbiology Reports, 7(2), 321–329. doi:10.1111/1758-2229.12251
    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., et al. (2013). Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems. Research In Microbiology, 164(4), 360-370. doi:10.1016/j.resmic.2013.01.004
    Mots-clés : #perso.

  • Hugoni, M., Taib, N., Debroas, D., Domaizon, I., Jouan Dufournel, I., Bronner, G., et al. (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(15), 6004-6009. doi:10.1073/pnas.1216863110
    Mots-clés : #perso.

Chapitre d’ouvrages


Communications Orales


  • Hugoni, M., Cantarel, A. A. M., Allard, V., Enjalbert, J., Gervaix, J., Saint Jean, S., et al. (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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