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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)





  • 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.
    Résumé : Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.
    Mots-clés : #3, #ibio, #imba.

  • 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.
    Mots-clés : #imba.


  • Mani, K., Taib, N., Hugoni, M., Bronner, G., Bragança, J.M., Debroas, D., 2020. Transient Dynamics of Archaea and Bacteria in Sediments and Brine Across a Salinity Gradient in a Solar Saltern of Goa, India. Frontiers in Microbiology 11.
    Résumé : The microbial fluctuations along an increasing salinity gradient during two different salt production phases - initial salt harvesting (ISH) phase and peak salt harvesting (PSH) phase of Siridao solar salterns in Goa, India were examined through high-throughput sequencing of 16S rRNA genes. Elemental analysis of the brine samples showed the abundance of sodium (Na+) and chloride (Cl-) ions thereby indicating its thalassohaline nature. Comparison of relative abundance of sequences revealed that Archaea (34% to 91%) transited from sediment to brine while Bacteria (17% to 51%) transited from brine to sediment with increasing salinity. Incidence of Archaea was found to be significantly enriched even in low salinity and moderate salinity sediments with their relative sequence abundance reaching as high as 85%. Euryarchaeota was found to be the dominant archaeal phylum containing 19 and 17 genera in sediments and brine, respectively. Phylotypes belonging to Halorubrum, Haloarcula, Halorhabdus, and Haloplanus were common in both sediments and brine. Occurence of Halobacterium and Natronomonas were exclusive to sediments while Halonotius was exclusive to brine. Among sediments, relative sequence incidence of Halorubrum, and Halorhabdus decreased while Haloarcula, Haloplanus, and Natronomonas increased with increasing salinity. Similarly, the relative abundance of Haloarcula and Halorubrum increased with increasing salinity in brine. Sediments and brine samples harbored about 20 and 17 bacterial phyla, respectively. Bacteroidetes, Proteobacteria, and Chloroflexi were the common bacterial phyla in both sediments and brine while Firmicutes were dominant albeit in sediments alone. Further, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were observed to be the abundant class within the Proteobacteria. Among the bacterial genera, phylotypes belonging to Rubricoccus and Halomonas were widely detected in both brine and sediment while Thioalkalispira, Desulfovermiculus, and Marinobacter were selectively present in sediments alone. This study suggests that Bacteria are more susceptible to salinity fluctuations than Archaea, with many bacterial genera being compartment and phase-specific. Our study further indicated that Archaea rather than Bacteria could withstand the wide salinity fluctuation and attain a stable community structure within a short time-frame.
    Mots-clés : #2, Archaea, Bacteria, Hypersaline environments, Illumina sequencing, metabarcoding, Solar saltern.


  • 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.
    Résumé : Lake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean2014–2015 = 652 ± 179 μg chlorophyll a L−1). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha.
    Mots-clés : #2, #imba, Cyanobacteria, Diversity, Extreme environment, Phytoplankton, Picoeukaryote, Thalassohaline lake.

  • 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.
    Résumé : High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.
    Mots-clés : #2, #imba.

  • 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.
    Résumé : Mangroves are forest ecosystems located at the interface between land and sea where sediments presented a variety of contrasted environmental conditions (i.e. oxic/anoxic, non-sulfidic/sulfidic, organic matter content) providing an ideal ecosystem to study microbial communities with niche differentiation and distinct community structures. In this work, prokaryotic and fungal compositions were investigated during both wet and dry seasons in New Caledonian mangrove sediments, from the surface to deeper horizons under the two most common tree species in this region (Avicennia marina and Rhizophora stylosa), using high-throughput sequencing. Our results showed that Bacteria and Archaea communities were mainly shaped by sediment depth while the fungal community was almost evenly distributed according to sediment depth, vegetation cover and season. A detailed analysis of prokaryotic and fungal phyla showed a dominance of Ascomycota over Basidiomycota whatever the compartment, while there was a clear shift in prokaryotic composition. Some prokaryotic phyla were enriched in surface layers such as Proteobacteria, Euryarchaeota while others were mostly associated with deeper layers as Chloroflexi, Bathyarchaeota, Aminicenantes. Our results highlight the importance of considering fungal and prokaryotic counterparts for a better understanding of the microbial succession involved in plant organic matter decomposition in tropical coastal sediments.
    Mots-clés : #2, #imba.

  • 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.
    Résumé : The Asian tiger mosquito Aedes albopictus, native to Southeast Asia, has invaded a wide range of tropical and temperate areas worldwide. Recent studies pointed out that invasive populations from Europe harbored reduced bacterial microbiota compared to the native populations. Beside bacteria, mosquitoes also contain fungal communities that have so far been largely ignored. To investigate whether the mosquito invasion process displays a similar impact on fungal diversity, we compared the mycobiota structure of three autochthonous mosquito populations in Vietnam and six populations recently introduced in France and Madagascar. All mosquito populations host a locally structured fungal community and carry a “core mycobiota” dominated by yeasts. However, invasive populations from France and Madagascar harbor a lower fungal diversity compared to Vietnamese populations. These results suggest that similar factors shape the overall composition of the mosquito-associated microbiota during the invasion process as bacterial and fungal communities demonstrate a loss of diversity.
    Mots-clés : #2, #7, #imba, Asian tiger mosquito, Biogeography, Fungal ecology, Metataxogenomic, Mycobiota.


  • 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.
    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, #imba, alkaline lake, anoxygenic photrophic bacteria, aragonite, Hydromagnesite, Mg-silicate, Pleurocapsales, Stromatolites.

  • 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.
    Mots-clés : #2, #imba.

  • Hugoni, M., Luis, P., Guyonnet, J., Haichar, F.Z., 2018. Plant host habitat and root exudates shape fungal diversity. Mycorrhiza 28, 451-463.
    Mots-clés : #2, #4, #imba.

  • 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, #imba.

  • 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.
    Mots-clés : #2, #imba.


  • 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, #imba.


  • 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, #imba, 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, #imba, #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, #imba, #perso.

  • Hugoni, M., Domaizon, I., Taib, N., Biderre-Petit, C., Agogué, H., Galand, P.E., Debroas, D., Mary, I., 2015. Temporal dynamics of active <i>A</i> <i>rchaea</i> in oxygen-depleted zones of two deep lakes: Active archaeal communities in lacustrine ecosystems. 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, #imba, #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 : #imba, #perso.

Chapitre d’ouvrages


  • Bronner, G., Debroas, D., Enault, F., Hugoni, M., Jouan-Dufournel, I., Mary, I., Ravet, V., Roux, S., Taïb, N., 2016. Study of Prokaryotes and Viruses in Aquatic Ecosystems by Metagenetic and Metagenomic Approaches, dans: Sime-Ngando, T., Boivin, P., Chapron, E., Jezequel, D., Meybeck, M. (Éd.), Lake Pavin. Springer International Publishing, Cham, p. 245-254.
    Mots-clés : #imba.


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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