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Equipe de Recherche "Adaptation des Microorganismes Eucaryotes à leur Environnement"

Patricia Luis

Maître de Conférences


  • Thèmes de recherches :
    - Écologie des champignons du sol
    - Impact des perturbations environnementales sur la diversité fonctionnelle des communautés fongiques

Parcours scientifique

  • Doctorat en Biologie végétale et forestière (2004) à l’Université de Lorraine (Nancy-1)
  • Post-doctorat (2004-2006) à l’Université de Leipzig (Allemagne)
  • Post-doctorat (2006-2008) à Gembloux Agro-Bio Tech (Belgique)

- Encadrement :

  • Directrice de la thèse de Florian Barbi (2012-2015) Impact de l’essence forestière sur les processus de dégradation et d’absorption des polysaccharides végétaux par les microorganismes eucaryotes des sols forestiers
  • Co-encadrante de la thèse de Claudia Bragalini (2011-2014)
  • Co-encadrante de la thèse de Martino Adamo (2014-2017)

- Enseignement :

  • Biologie végétale
  • Microbiologie
  • Ecologie microbienne



  • Barbi F, 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.
    Résumé : Fungi are the main organisms responsible for plant biomass degradation in soils. While many studies have evaluated the impact of tree species on the taxonomic diversity of soil fungi, very few of them have addressed their functional gene diversity. In the present study, we assessed the impact of tree species, differing with respect to litter quality, and sampling dates on the diversity of four expressed fungal gene-families: one housekeeping gene used as taxonomic marker and three others encoding key enzymes implicated in lignocellulose degradation selected as functional markers. This was performed by the high-throughput sequencing of gene-fragments amplified from forest soil mRNA using fungal specific primers. Messenger RNAs were extracted from 10 soil samples collected over two seasons in plots planted with either the conifer Picea abies or the angiosperm Fagus sylvatica in a common garden experiment. Independently of the gene-family, less than 20% of the fungal transcripts were identified in both forest types. For all four fungal gene-families, variance partitioning identified the tree species and its interaction with the sampling plot as the factors that contributed most to global gene diversity (between 29% and 32%), while the sampling dates accounted for less than 9%. Further analysis of the contribution of soil proprieties revealed that the tree species-generated C/N ratio is the most important factor driving functional gene distribution (between 6% and 29% of the variation explained). Similarly, for each fungal gene family, statistical analyses identified tree species as the main factor responsible for variations in similarity between samples (as estimated by the Bray-Curtis β diversity index). These results highlight that tree species, differing with respect to litter quality, selected different soil fungal communities expressing different set of genes involved in plant organic matter degradation.
    Mots-clés : #2, #ibio, Diversity, Forest soil, Fungal transcripts, High-throughput sequencing, Lignocellulolytic enzymes, Soil organic matter.


  • Barbi F, et al. 2014. PCR Primers to Study the Diversity of Expressed Fungal Genes Encoding Lignocellulolytic Enzymes in Soils Using High-Throughput Sequencing. PLoS ONE. 9:e116264. doi: 10.1371/journal.pone.0116264.
    Résumé : Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes. This can be tackled by environmental genomic approaches involving the systematic sequencing of key enzyme-coding gene families using soil-extracted RNA as material. Such an approach necessitates the design and evaluation of gene family-specific PCR primers producing sequence fragments compatible with high-throughput sequencing approaches. In the present study, we developed and evaluated PCR primers for the specific amplification of fungal CAZy Glycoside Hydrolase gene families GH5 (subfamily 5) and GH11 encoding endo-β-1,4-glucanases and endo-β-1,4-xylanases respectively as well as Basidiomycota class II peroxidases, corresponding to the CAZy Auxiliary Activity family 2 (AA2), active on lignin. These primers were experimentally validated using DNA extracted from a wide range of Ascomycota and Basidiomycota species including 27 with sequenced genomes. Along with the published primers for Glycoside Hydrolase GH7 encoding enzymes active on cellulose, the newly design primers were shown to be compatible with the Illumina MiSeq sequencing technology. Sequences obtained from RNA extracted from beech or spruce forest soils showed a high diversity and were uniformly distributed in gene trees featuring the global diversity of these gene families. This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the discovery of complex patterns in gene expression of soil fungal communities.
    Mots-clés : #2, #ibio.

  • Bragalini C, et al. 2014. Solution Hybrid Selection Capture for the Recovery of Functional Full-Length Eukaryotic cDNAs From Complex Environmental Samples. DNA Research. doi: 10.1093/dnares/dsu030.
    Mots-clés : #2, #ibio.

  • Bruto M, Prigent-Combaret C, Luis P, Moënne-Loccoz Y, Muller D. 2014. Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes. Proceedings of the Royal Society B: Biological Sciences. 281:20140848. doi: 10.1098/rspb.2014.0848.
    Résumé : Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.
    Mots-clés : #2, #3, #ibio, adaptive horizontal transfer, inter-domain transfer, lateral gene transfer.

  • Kellner H, et al. 2014. Widespread Occurrence of Expressed Fungal Secretory Peroxidases in Forest Soils. PLoS ONE. 9:e95557. doi: 10.1371/journal.pone.0095557.
    Résumé : Fungal secretory peroxidases mediate fundamental ecological functions in the conversion and degradation of plant biomass. Many of these enzymes have strong oxidizing activities towards aromatic compounds and are involved in the degradation of plant cell wall (lignin) and humus. They comprise three major groups: class II peroxidases (including lignin peroxidase, manganese peroxidase, versatile peroxidase and generic peroxidase), dye-decolorizing peroxidases, and heme-thiolate peroxidases (e.g. unspecific/aromatic peroxygenase, chloroperoxidase). Here, we have repeatedly observed a widespread expression of all major peroxidase groups in leaf and needle litter across a range of forest ecosystems (e.g. Fagus, Picea, Acer, Quercus, and Populus spp.), which are widespread in Europe and North America. Manganese peroxidases and unspecific peroxygenases were found expressed in all nine investigated forest sites, and dye-decolorizing peroxidases were observed in five of the nine sites, thereby indicating biological significance of these enzymes for fungal physiology and ecosystem processes. Transcripts of selected secretory peroxidase genes were also analyzed in pure cultures of several litter-decomposing species and other fungi. Using this information, we were able to match, in environmental litter samples, two manganese peroxidase sequences to Mycena galopus and Mycena epipterygia and one unspecific peroxygenase transcript to Mycena galopus, suggesting an important role of this litter- and coarse woody debris-dwelling genus in the disintegration and transformation of litter aromatics and organic matter formation.
    Mots-clés : #2.

  • Yadav RK, et al. 2014. Construction of sized eukaryotic cDNA libraries using low input of total environmental metatranscriptomic RNA. BMC Biotechnology. 14:80. doi: 10.1186/1472-6750-14-80.
    Résumé : PMID: 25183040
    Mots-clés : #2.


  • Luis P, Gauthier A, Trouvelot S, Poinssot B, Frettinger P. 2013. The identification of Plasmopara viticola genes potentially involved in pathogenesis on grapevine suggests new similarities between oomycetes and true fungi. Phytopathology. 130501115210007. doi: 10.1094/PHYTO-06-12-0121-R.
    Mots-clés : #2.


  • Damon C, et al. 2012. Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PloS one. 7:e28967.
    Mots-clés : #2.


  • Damon C, et al. 2011. A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. The ISME Journal. 5:1871–1880.
    Mots-clés : #2.

  • Kellner H, Luis P, Portetelle D, Vandenbol M. 2011. Screening of a soil metatranscriptomic library by functional complementation of Saccharomyces cerevisiae mutants. Microbiological Research. 166:360-368. doi: 10.1016/j.micres.2010.07.006.
    Résumé : Metatranscriptomics applied to environmental transcripts provides unique opportunities to reveal microbial activity in the environment and to discover novel enzymes of potential use in biotechnological applications. Here, by functional complementation of a pho5− mutation (affecting a repressible acid phosphatase) and a his3− mutation in Saccharomyces cerevisiae, we identified fungal genes encoding an acid phosphatase and an imidazoleglycerol-phosphate dehydratase in a metatranscriptomic library, which was obtained by reverse-transcribed polyA fraction of total RNA extracted from the organic layer of a sugar maple forest soil, constructed in the modified yeast secretion vector pTEF-MF-SfiI A/B. Yeast transformants exhibiting phosphatase activity were identified in a colony-staining assay and transformants with his3−-complementing genes were detected by plating on histidine-deficient medium. In each screen one DNA insert was found and sequenced. The sequenced his3−-complementing gene showed strong similarity to a basidiomycete imidazoleglycerol-phosphate dehydratase (76% identity to a Phaffia rhodozyma enzyme). The candidate showing phosphatase activity was found to produce phosphatase extracellularly, the enzyme showing highest activity at pH 4 and between 40 and 50 °C when 4-nitrophenyl phosphate was used as substrate. The sequenced insert showed strong similarity to a basidiomycete acid phosphatase (60% identity to Postia placenta).
    Mots-clés : #2, Fungal genes, HIS3, PHO5, Phytase, yeast.


  • Kellner H, Luis P, Schlitt B, Buscot F. 2009. Temporal changes in diversity and expression patterns of fungal laccase genes within the organic horizon of a brown forest soil. Soil Biology and Biochemistry. 41:1380–1389.
    Mots-clés : #2.

Chapitre d’ouvrages


  • Yadav RK, Bragalini C, Fraissinet-Tachet L, Marmeisse R, Luis P. 2016. Metatranscriptomics of Soil Eukaryotic Communities. In: Microbial Environmental Genomics (MEG). Martin, F & Uroz, S. Vol. 1399 Springer New York: New York, NY p. 273-287.
    Mots-clés : #2.


  • Bruto M, et al. 2013. Horizontal Acquisition of Prokaryotic Genes for Eukaryote Functioning and Niche Adaptation. In: Evolutionary Biology: Exobiology and Evolutionary Mechanisms. Pontarotti, P. Springer Berlin Heidelberg p. 165-179.
    Résumé : Horizontal gene transfer (HGT) is a major mechanism of evolution, in that it is pervasive and can dramatically affect lifestyle by allowing adaptation to specialized niches. Although research has mostly focused on HGT within prokaryotes, examples of inter-domain transfers from prokaryotes to eukaryotes are increasing, and such inter-domain HGT is emerging as a very significant component in ecological and evolutionary terms. Here, different cases of intra- and inter-domain HGT conferring an adaptive advantage to eukaryotes are reviewed to examine novel trends and HGT paradigms. Thus, HGT appears to play an important role in eukaryotic adaptation to specific environmental conditions, including in the ecological evolution toward parasitic lifestyles and pathogenesis. The diversity of prokaryotes and their genetic potential are emerging as a vast reservoir to foster rapid eukaryote evolution.
    Mots-clés : #2, #3, Animal Genetics and Genomics, Animal Systematics/Taxonomy/Biogeography, Biodiversity, evolutionary biology, HGT dynamic, Interdomain gene transfer, Lateral gene transfer (LGT), Plant Genetics & Genomics, Plant Systematics/Taxonomy/Biogeography.

  • Fraissinet-Tachet L, Marmeisse R, Zinger L, Luis P. 2013. Metatranscriptomics of Soil Eukaryotic Communities. In: The Ecological Genomics of Fungi. Francisrtin,. John Wiley & Sons, Inc p. 305–323.
    Résumé : Environmental RNA-based metatranscriptomics is assumed to better reflect ongoing biological activities. This type of metatranscriptomics has been developed for environments as diverse as freshwater and seawater or soils. The eukaryotic 3’ polyadenylated messenger RNAs can be isolated from ribosomal, noncoding RNAs and bacterial mRNAs that dominate environmental metatranscriptomes. Proofs of concept for this protocol have now been established for various ecosystems such as soils or bovine and termite digesters. However, eukaryotic metratranscriptomics is still in its infancy. Researchers who engage in this field have therefore to face methodological and conceptual issues that are addressed in this chapter. One of the most challenging aspects in environmental transcriptomics remains RNA extraction from environmental samples. Metagenomes or metatranscriptomes systematic sequencing approaches are limited when it comes to unknown or undescribed proteins.
    Mots-clés : #2, environmental metatranscriptomes, metatranscriptomes systematic sequencing, Metatranscriptomics, soil eukaryotic communities.


Communications Orales