C. Meier and W. D. Bowman, Links between plant litter chemistry, species diversity, and below-ground ecosystem function, Proc Natl Acad Sci U S A, vol.105, pp.19780-19785, 2008.

W. K. Cornwell, J. H. Cornelissen, K. Amatangelo, E. Dorrepaal, and V. T. Eviner, Plant species traits are the predominant control on litter decomposition rates within biomes worldwide, Ecol Lett, vol.11, pp.1065-1071, 2008.

R. L. Sinsabaugh, C. L. Lauber, M. N. Weintraub, B. Ahmed, and S. D. Allison, Stoichiometry of soil enzyme activity at global scale, Ecol Lett, vol.11, pp.1252-1264, 2008.

D. Martinez, L. F. Larrondo, N. Putnam, M. D. Gelpke, and K. Huang, Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78, Nat Biotechnol, vol.22, pp.695-700, 2004.

D. Martinez, R. M. Berka, B. Henrissat, M. Saloheimo, and M. Arvas, Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina), Nat Biotechnol, vol.26, pp.553-560, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02669177

D. Martinez, J. Challacombe, I. Morgenstern, D. Hibbett, and M. Schmoll, Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion, Proc Natl Acad Sci U S A, vol.106, pp.1954-1959, 2009.

T. W. Jeffries, I. V. Grigoriev, J. Grimwood, J. M. Laplaza, and A. Aerts, Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis, Nat Biotechnol, vol.25, pp.319-345, 2007.

J. C. Frankland, Fungal succession -unravelling the unpredictable, Mycol Res, vol.102, pp.1-15, 1998.

U. N. Nielsen, G. Osler, C. D. Campbell, D. Burslem, and R. Van-der-wal, The influence of vegetation type, soil properties and precipitation on the composition of soil mite and microbial communities at the landscape scale, J Biogeogr, vol.37, pp.1317-1328, 2010.

L. Zinger, D. Lejon, F. Baptist, A. Bouasria, and S. Aubert, Contrasting diversity patterns of crenarchaeal, bacterial and fungal soil communities in an alpine landscape, PLoS ONE, vol.6, p.19950, 2011.
URL : https://hal.archives-ouvertes.fr/insu-00845128

J. M. Brulc, D. A. Antonopoulos, B. Miller, M. E. Wilson, M. K. Yannarell et al., Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases, Proc Natl Acad Sci U S A, vol.106, pp.1948-1953, 2009.

M. Hess, A. Sczyrba, R. Egan, T. W. Kim, and H. Chokhawala, Metagenomic discovery of biomass-degrading genes and genomes from cow rumen, Science, vol.331, pp.463-470, 2011.

M. Qi, P. Wang, N. O'toole, P. S. Barboza, and E. Ungerfeld, Snapshot of the Eukaryotic gene expression in Muskoxen rumen -A metatranscriptomic approach, PLoS ONE, vol.6, p.20521, 2011.

L. Tasse, J. Bercovici, S. Pizzut-serin, P. Robe, and J. Tap, Functional metagenomics to mine human gut microbiome for dietary fiber catabolic enzymes, Genome Res, vol.20, pp.1605-1612, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01204274

P. B. Pope, S. E. Denman, M. Jones, S. G. Tringe, and K. Barry, Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores, Proc Natl Acad Sci U S A, vol.107, pp.14793-798, 2009.

A. Tartar, M. Wheeler, X. Zhou, M. R. Coy, and D. G. Boucias, Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulotermes flavipes, Biotechnol Biofuels, vol.2, p.25, 2009.

F. Warnecke, P. Luginbühl, N. Ivanova, M. Ghassemian, and T. H. Richardson, Metagenomic and functional analysis of hindgut microbiota of a woodfeeding higher termite, Nature, vol.450, pp.560-565, 2007.

M. Allgaier, A. Reddy, J. I. Park, N. Ivanova, D. 'haeseleer et al., Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community, PLoS ONE, vol.5, p.8812, 2010.

S. Grant, W. D. Grant, D. A. Cowan, B. E. Jones, and Y. Ma, Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples, Appl Environ Microbiol, vol.72, pp.135-143, 2006.

J. Bailly, L. Fraissinet-tachet, M. Verner, J. Debaud, and M. Lemaire, Soil eukaryotic functional diversity, a metatranscriptomic approach, ISME J, vol.1, pp.632-642, 2007.
URL : https://hal.archives-ouvertes.fr/halsde-00180984

P. López-garcía and D. Moreira, Tracking microbial biodiversity through molecular and genomic ecology, Res Microbiol, vol.159, pp.67-73, 2008.

S. Jeon, J. Bunge, C. Leslin, T. Stoeck, and H. Sunhee, Environmental rRNA inventories miss over half of protistan diversity, BMC Microbiol, vol.8, p.222, 2008.

S. L. Stephenson, A. M. Fiore-donno, and M. Schnittler, Myxomycetes in soil, Soil Biol Biochem, vol.43, pp.2237-2242, 2011.

V. K. Sharma, N. Kumar, T. Prakash, and T. D. Taylor, MetaBioME: a database to explore commercially useful enzymes in metagenomics datasets, Nucl Ac Res, vol.38, pp.468-472, 2010.

M. Fischer, M. Knoll, D. Sirim, F. Wagner, and S. Funke, The cytochrome P450 engineering database: a navigation and prediction tool for the cytochrome P450 protein family, Bioinformatics, vol.23, pp.2015-2017, 2007.

M. H. Saier, C. V. Tran, and R. D. Barabote, TCDB: the transporter Classification Database for membrane transport protein analyses and information, Nucl Acids Res, vol.34, pp.181-186, 2006.

E. G. Danchin, M. N. Rosso, P. Vieira, J. De-almeida-engler, and P. M. Coutinho, Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes, Proc Natl Acad Sci U S A, vol.107, pp.17651-17656, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02669078

T. Y. James, F. Kauff, C. L. Schoch, P. B. Matheny, and V. Hofstetter, Reconstructing the early evolution of Fungi using a six-gene phylogeny, Nature, vol.443, pp.818-840, 2006.

R. J. Quinlan, M. D. Sweeney, L. L. Leggio, H. Otten, and J. Poulsen, Insight into oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components, Proc Natl Acad Sci U S A, vol.108, pp.15079-15084, 2011.

G. Liu, X. Wei, Y. Qin, and Y. Qu, Characterization of the endoglucanase and glucomannanase activities of a glycoside hydrolase family 45 protein from Penicillium decumbens 114-2, J Gen Appl Microbiol, vol.56, pp.223-229, 2010.

K. Sakamoto and H. Toyohara, Molecular cloning of glycoside hydrolase family 45 cellulase genes from brackish water clam Corbicula japonica, Comp Biochem Physiol B Biochem Mol Biol, vol.152, pp.390-396, 2009.

A. Saloheimo, B. Henrissat, A. M. Hoffrén, and M. Penttilä, A novel, small endoglucanase gene, egl5, from Trichoderma reesei isolated by expression in yeast, Mol Microbiol, vol.13, pp.219-228, 1994.
URL : https://hal.archives-ouvertes.fr/hal-00310648

B. Xu, U. Hellman, B. Ersson, and J. Janson, Purification, characterization and amino-acid sequence analysis of a thermostable, low molecular mass endoß-1,4-glucanase from blue mussel, Mytilus edulis, Eur J Biochem, vol.267, pp.4970-4977, 2000.

J. Frias-lopez, Y. Shi, G. W. Tyson, M. L. Coleman, and S. C. Schuster, Microbial community gene expression in ocean surface waters, Proc Natl Acad Sci U S A, vol.105, pp.3805-3810, 2008.

J. Gilbert, D. Field, Y. Huang, R. Edwards, and W. Li, Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities, PLoS ONE, vol.3, p.3042, 2008.

J. A. Gilbert, D. Field, P. Swift, S. Thomas, and D. Cummings, The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation, PLoS ONE, vol.5, p.15545, 2010.

P. M. Shrestha, M. Kube, R. Reinhardt, and W. Liesack, Transcriptional activity of paddy soil bacterial communities, Environ Microbiol, vol.11, pp.960-970, 2009.

T. Urich, A. Lanzen, J. Qi, D. H. Huson, and C. Schleper, Simultaneous assessment of soil microbial community structure and function through analysis of the metatranscriptome, PLoS ONE, vol.3, p.2527, 2008.

S. He, O. Wurtzel, K. Singh, J. L. Froula, and S. Yilmaz, Validation of two ribosomal RNA removal methods for microbial metatranscriptomics, Nature Met, vol.10, pp.807-812, 2010.

F. J. Stewart, E. A. Ottesen, and E. F. Delong, Development and quantitative analyses of a universal rRNA-substraction protocol for microbial metatranscriptomics, ISME J, vol.4, pp.896-907, 2010.

N. Sharkar, Polyadenylation of mRNA in prokaryotes, Ann Rev Biochem, vol.66, pp.173-197, 1997.

Q. Gao, J. K. Ying, S. Zhang, Y. Xiao, and G. , Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum, PLoS Genet, vol.7, p.1001264, 2011.

F. Martin, A. Kohler, C. Murat, R. Balestrini, and P. M. Coutinho, Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis, Nature, vol.464, pp.1033-1038, 2010.

E. F. Kirkness, B. J. Haas, W. Sun, H. R. Braig, and M. A. Perotti, Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle, Proc Natl Acad Sci U S A, vol.107, pp.12168-12173, 2010.

J. K. Colbourne, M. E. Pfrender, D. Gilbert, W. K. Thomas, and A. Tucker, The ecoresponsive genome of Daphnia pulex, Science, vol.331, pp.555-561, 2011.

C. Damon, V. Vallon, S. Zimmermann, M. Z. Haider, and V. Galeote, A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes, ISME J, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00647454

P. Sarkar, E. Bosneaga, and M. Auer, Plant cell walls throughout evolution: towards a molecular understanding of their design principles, J Exp Bot, vol.60, pp.3615-3635, 2009.

C. Schä-del, A. Blö-chl, A. Richter, and G. Hoch, Quantification of monosaccharide composition of hemicelluloses from different plant functional types, Plant Physiol Biochem, vol.48, pp.1-8, 2010.

J. Moukoumi, C. Munier-lamy, J. Berthelin, and J. Ranger, Effect of tree species substitution on organic matter biodegradability and mineral nutrient availability in a temperate topsoil, Ann For Sci, vol.63, pp.763-771, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00884027

A. J. King, S. M. Cragg, Y. Li, J. Dymond, and M. J. Guille, Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes, Proc Natl Acad Sci U S A, vol.107, pp.5345-5350, 2010.

Y. Pauchet, P. Wilkinson, R. Chauhan, and R. H. Ffrench-constant, Diversity of beetle genes encoding novel plant cell wall degrading enzymes, PLoS ONE, vol.5, p.15635, 2010.

H. Kellner, P. Luis, D. Portetelle, and M. Vandenbol, Screening of a soil metatranscriptomic library by functional complementation of Saccharomyces cerevisiae mutants, Microbiol Res, vol.166, pp.360-368, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02540430

S. D. Findley, M. R. Mormile, A. Sommer-hurley, X. Zhang, and P. Tipton, Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases, Appl Environ Microbiol, 2011.

C. Damon, G. Barroso, C. Férandon, J. Ranger, and L. Fraissinet-tachet, Performance of the COX1 gene as a marker for the study of metabolically active Pezizomycotina and Agaricomycetes fungal communities from the analysis of soil RNA, FEMS Microbiol Ecol, vol.74, pp.693-705, 2010.

B. Diez, C. Pedros-alio, and R. Massana, Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing, Appl Environ Microbiol, vol.67, pp.2932-2941, 2001.

W. Li and A. Godzik, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, vol.22, pp.1658-1659, 2006.

A. Conesa, S. Götz, J. M. García-gómez, J. Terol, and M. Talón, Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, pp.3674-367, 2005.

, Gene ontology: tool for the unification of biology, The Gene Ontology Consortium, vol.25, pp.25-29, 2000.

B. L. Cantarel, P. M. Coutinho, C. Rancurel, T. Bernard, and V. Lombard, The Carbohydrate-Active EnZyme database (CAZy): an expert resource for glycogenomics, Nucl Ac Res, vol.37, pp.233-238, 2009.

A. Levasseur, F. Piumi, P. M. Coutinho, C. Rancurel, and M. Asther, FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds, Fung Genet Biol, vol.45, pp.638-645, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02666159

D. Sirim, F. Wagner, A. Lisitsa, and J. Pleiss, The cytochrome P450 Engineering Database: integration of biochemical properties, BMC Biochem, vol.10, p.27, 2009.

M. Fischer and J. Pleiss, The lipase engineering database: a navigation and analysis tool for protein families, Nucl Ac Res, vol.31, pp.319-321, 2003.

N. D. Rawlings, A. J. Barrett, and A. Bateman, MEROPS: the peptidase database, Nucl Ac Res, vol.38, pp.227-233, 2009.

M. Gouy, S. Guindon, and O. Gascuel, SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building, Mol Biol Evol, vol.27, pp.221-224, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

D. H. Huson, D. C. Richter, S. Mitra, A. F. Auch, and S. C. Schuster, Methods for comparative metagenomics, BMC Bioinformatics, vol.10, issue.1, p.12, 2009.

A. Dereeper, V. Guignon, G. Blanc, S. Audic, and S. Buffet, Phylogeny.fr: a robust phylogenetic analysis for the non-specialist, Nucl Acids Res, vol.36, pp.465-469, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324099

P. M. Coutinho, M. R. Andersen, K. Kolenova, P. A. Vankuyk, and I. Benoit, Post-genomic insight into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae, Fung Genet Biol, vol.46, pp.161-169, 2009.