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Home > Research Teams > Adaptation des Microorganismes Eucaryotes à leur Environnement (AMEE)

En - Adaptation des Microorganismes Eucaryotes à leur Environnement (AMEE)

Team leader: MARMEISSE Roland

Co-Team leader:LUIS Patricia

Permanent members

DORE Jeanne Assistant Engineer (AI), UCB
HUGONI Mylène Lecturer (MCF), UCB
LUIS Patricia Lecturer (MCF), UCB
MARMEISSE Roland Senior Research Scientist (DR), CNRS
MELAYAH Delphine Lecturer (MCF), UCB
VALLON Laurent Technician (T), UCB

Non permanent members

BARBI Florian PhD Student (2012-2015)
BRAGALINI Claudia PhD Student (2012-2013 co-tutelle university of Turin, Italy)
ZILLER Antoine PhD Student (2013-2016)

Presentation :

Eukaryotic microorganisms (fungi, "protists") are major players in soil biology. They represent the main decomposers of plant organic matter (saprotrophic fungi), they regulate bacterial populations and biomass (phagotrophic protists) and many of them are either beneficial (eg. mycorrhizal symbiotic fungi) or on the contrary damaging (pathogenic) partners of macroorganisms, either plants or animals. Although their contributions to C and N terrestrial cycles are important, the level of functional diversity of the soil eukaryotic microflora remains under evaluated. Indeed, soil encompasses at different spatial scales a complex microflora whose taxonomic composition varies with time and for which only a small fraction is accessible to laboratory studies as numerous microbial species remain uncultivable.
Research activities of the AMEE team aim at better evaluating the roles of soil microbial eukaryotes. Two main programmes are developed.

Research programmes : 

Theme 1:Genomics and genetics of ectomycorrhizal symbiotic fungi

Most temperate forest trees (oak, beech, poplar, pine, fir…) and numerous fungal species (amanitas, boletes, truffles…) associate to each other to form the so-called ectomycorrhizal root symbiosis. This beneficial symbiosis leads to bidirectional fluxes of nutrients between the partners (plant sugars in exchange for soil-derived N, P and other minerals) and contributes to host plant fitness and optimal use of limiting and poorly accessible forest soil nutrients.
Although it is now well established that the capacity of forming ectomycorrhizas has appeared several times independently during fungal evolution, the fungal functions implicated in the establishment of a functional symbiotic association remain largely unknown.
Our research project aims at identifying experimentally these functions using the basidiomycete species Hebeloma cylindrosporum associated to Pinus pinaster (Fig. 1). We developed an insertional mutagenesis programme, which leads to the random insertion, within the fungal genome, of mutagenic T-DNA from the bacterium Agrobacterium tumefaciens. We thus obtained for the first time non symbiotic mutants of an ectomycorrhizal fungus.
Characterisation of the mutated genes will give us information on the fungal functions necessary for symbiosis establishment, as well as on the potential implication of homologous fungal genes in other plant/fungal interactions either symbiotic or pathogenic.
Since the public release of the full genomic sequence of H. cylindrosporum (, we also try to decipher globally, using transcriptomic and proteomic approaches, the genomic programs leading to a functional symbiosis. Targeted analysis of secreted proteins (i.e; the secretome) is also carried out to evaluate the controversial "saprotrophic potential" of symbiotic fungi and their capacity to mobilise nutrients from forest soils.

Figure 1. The basidiomycete fungus Hebeloma cylindrosporum associated with Pinus pinaster as a model to infer the genetic and molecular bases of differentiation and functioning of the ectomycorrhizal symbiosis. Its entire life cycle, from spore to spore, can be obtained under laboratory conditions (Debaud & Gay, 1987, New Phytol 105: 429-435); it can be easily transformed using Agrobacterium tumefaciens (Combier et al. 2003 FEMS Microbiol lett 220: 141-148) and a collection of mutant strains is available, including non mycorrhizal ones (Combier et al, 2004 Mol Plant Microbe Interact 17: 1029-1038). Its genome has been sequenced and annotated at the Joint Genome Institute ( in association with the AMEE team.

Theme 2: Adaptation of soil eukaryotic microbial communities to their environment

This research subject does not target a single species but aims at identifying the roles played by the different members of a soil microbial community. We aim at establishing what are the different functions really expressed in situ in the soils by the different eukaryotic organisms, cultivable or not. To reach this objective, we developed an environmental genomic approach called metatranscriptomics. A metatranscriptome represents the sum of the different genes expressed by the different soil eukaryotic organisms (i.e., the sum of their transcriptomes). From an experimental point of view, RNA synthesized by all organisms are directly extracted from soil samples and eukaryotic polyadenylated mRNA are specifically converted into cDNA which can be directly sequenced or cloned to constitute environmental cDNA libraries (Figure 2). The analysis of expressed genes reflects the activities performed in situ by microorganisms directly in soil. Genes of interest are selected by different approaches such as their expression in yeast or high-throughput systematic sequencing. This approach which goes from "soil RNA" to the expression of environmental functional gene in yeast has been validated in the laboratory. In parallel, an analysis of the taxonomic diversity of eukaryotes is also performed (Figure 2). In soils, some eukaryotic phyla are notoriously under-estimated and under-studied, this is the case for example of Foraminifera (Rhizaria) that we detected almost systematically in various soils and which were initially only known from the marine environment.

The metatranscriptomic approach is being developed in two different contexts:
-  In a context of ecotoxicology to understand the adaptive responses of eukaryotic microbial communities to heavy metal pollutions. This project led us to characterise novel gene families, from the soil metatranscriptomes, which confer a cadmium or zinc resistant phenotype to yeast metal-sensitive mutants.
-  In the context of global changes to understand how changes in land use or climate (change in the level of precipitations) affect the process of soil organic matter degradation, which is essential for nutrient cycling in soils. These projects involve high-throughput sequencing of total eukaryotic metatranscriptomes from different sites, as well as the specific study of selected families of genes coding lignocellulolytic enzymes and transporters of sugars and nitrogenous molecules.

Figure 2. The metatranscriptomic approach: from nucleic acids extracted from environmental samples to eukaryotic genes expressed in yeast. This experimental approach, validated in the laboratory, allows the analysis of all genes expressed by all eukaryotic microorganisms, cultivable or not, present in an environmental sample.

Experimental approaches and technical skills

Members of the AMEE team have developed, acquired and optimised a number of original techniques in the field of fungal genetics, molecular biology and environmental genomics. The main ones, which can be used for other projects are:
-  Agrotransformation and insertional mutagenesis in filamentous fungi.
-  Extraction and purification of intracellular and excreted fungal proteins for proteomic analyses
-  Extraction of soil RNA and from tree roots
-  Construction of environmental cDNA libraries enriched in full-length genes for phenotypic screening
-  Phenotypic screening of cDNA libraries in yeast (S. cerevisiae and others) and phenotyping of transformants (Omnilog and Bioscreen)
-  High-throughput sequencing (HiSeq & MiSeq technologies) of fungal or soil-extracted RNA and of PCR products.


Bibliography :


  • 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

  • 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

  • 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

  • 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

  • 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

  • Ziller, A., & Fraissinet-Tachet, L. (2018). Metallothionein diversity and distribution in the tree of life: a multifunctional protein. Metallomics. doi:10.1039/C8MT00165K


  • Adamo, M., Voyron, S., Girlanda, M., & Marmeisse, R. (2017). RNA extraction from decaying wood for (meta)transcriptomic analyses. Canadian Journal Of Microbiology, 63(10), 841-850. doi:10.1139/cjm-2017-0230

  • Doré, J., Kohler, A., Dubost, A., Lindquist, E., Kuo, A., Grigoriev, I. V., et al. (2017). The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation. Environmental Microbiology, 19(3), 1338–1354. doi:10.1111/1462-2920.13670

  • 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

  • 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(9), 824-835. doi:10.1016/j.tibtech.2017.02.003

  • Ziller, A., Yadav, R. K., Capdevila, M., Reddy, M. S., Vallon, L., Marmeisse, R., et al. (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. doi:10.1016/j.jinorgbio.2016.11.017


  • Barbi, F., Prudent, E., Vallon, L., Buée, M., Dubost, A., Legout, A., et al. (2016). Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes. Soil Biology And Biochemistry, 100, 149-159. doi:10.1016/j.soilbio.2016.06.008

  • Marmeisse, R., & Girlanda, M. (2016). 10 Mycorrhizal Fungi and the Soil Carbon and Nutrient Cycling. In I. S. Druzhinina & C. P. Kubicek (Eds.), Environmental And Microbial Relationships (p. 189-203). Cham: Springer International Publishing. Retrieved from

  • 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

  • Yadav, R. K., Bragalini, C., Fraissinet-Tachet, L., Marmeisse, R., & Luis, P. (2016). Metatranscriptomics of Soil Eukaryotic Communities. In F. Martin & S. Uroz (Eds.), Microbial Environmental Genomics (Meg) (Vol. 1399, p. 273-287). New York, NY: Springer New York. Retrieved from

  • Reddy, M. S., Kour, M., Aggarwal, S., Ahuja, S., Marmeisse, R., & Fraissinet-Tachet, L. (2016). Metal induction of a Pisolithus albus metallothionein and its potential involvement in heavy metal tolerance during mycorrhizal symbiosis. Environmental Microbiology, 18(8), 2446-2454. doi:10.1111/1462-2920.13149


  • Barbi, F. (2015). Impact de l’essence forestière sur les processus de dégradation et d’assimilation des polysaccharides végétaux par la communauté fongique des sols forestiers. Lyon 1. Retrieved from

  • 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

  • Doré, J., Perraud, M., Dieryckx, C., Kohler, A., Morin, E., Henrissat, B., et al. (2015). Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis. New Phytologist, 208(4), 1169-1187. doi:10.1111/nph.13546

  • 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

  • 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

  • Kohler, A., Kuo, A., Nagy, L. G., Morin, E., Barry, K. W., Buscot, F., et al. (2015). Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nature Genetics, advance online publication(4), 410. doi:10.1038/ng.3223