M. Albertsen, P. Hugenholtz, A. Skarshewski, K. L. Nielsen, G. W. Tyson et al., Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes, Nat. Biotechnol, vol.31, pp.533-538, 2013.

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

T. O. Delmont, A. M. Eren, L. Maccario, E. Prestat, Ö. C. Esen et al., Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics, Front. Microbiol, vol.6, p.358, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01589179

T. O. Delmont, E. Prestat, K. P. Keegan, M. Faubladier, P. Robe et al., Structure, fluctuation and magnitude of a natural grassland soil metagenome, ISME J, vol.6, pp.1677-1687, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00747243

T. O. Delmont, P. Simonet, and T. M. Vogel, Mastering methodological pitfalls for surviving the metagenomic jungle, Bioessays, vol.35, pp.744-754, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00846141

S. Demanèche, L. Philippot, M. M. David, E. Navarro, T. M. Vogel et al., Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach, Appl. Environ. Microbiol, vol.75, pp.534-537, 2009.

N. Fierer, J. Ladau, J. C. Clemente, J. W. Leff, S. M. Owens et al., Reconstructing the microbial diversity and function of preagricultural tallgrass prairie soils in the United States, Science, vol.342, pp.621-624, 2013.

J. A. Gilbert, J. K. Jansson, and R. Knight, The Earth Microbiome project: successes and aspirations, BMC Biol, vol.12, p.69, 2014.

J. A. Gilbert, F. Meyer, D. Antonopoulos, P. Balaji, C. T. Brown et al., Meeting report: the terabase metagenomics workshop and the vision of an earth microbiome project, Stand. Genomic Sci, vol.3, pp.243-248, 2010.

D. Hahn, R. I. Amann, W. Ludwig, A. D. Akkermans, and K. H. Schleifer, Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labelled oligonucleotides, J. Gen. Microbiol, vol.138, pp.879-887, 1992.

J. Handelsman, M. R. Rondon, S. F. Brady, J. Clardy, and R. M. Goodman, Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products, Chem. Biol, vol.5, pp.245-249, 1998.

A. C. Howe, J. K. Jansson, S. A. Malfatti, S. G. Tringe, J. M. Tiedje et al., Tackling soil diversity with the assembly of large, complex metagenomes, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.4904-4909, 2014.

J. Hultman, M. P. Waldrop, R. Mackelprang, M. M. David, J. Mcfarland et al., Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes, Nature, vol.521, pp.208-212, 2015.

S. Leininger, T. Urich, M. Schloter, L. Schwark, J. Qi et al., Archaea predominate among ammonia-oxidizing prokaryotes in soils, Nature, vol.442, pp.806-809, 2006.

M. D. Lynch and J. D. Neufeld, Ecology and exploration of the rare biosphere, Nat. Rev. Microbiol, vol.13, pp.217-229, 2015.

V. S. Pylro, L. Roesch, J. M. Ortega, and A. M. Amaral, Brazilian microbiome project: revealing the unexplored microbial diversitychallenges and prospects, Microb. Ecol, vol.67, pp.237-241, 2014.

C. Rinke, P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson et al., Insights into the phylogeny and coding potential of microbial dark matter, Nature, vol.499, pp.431-437, 2013.

V. Torsvik, J. Goksøyr, and F. L. Daae, High diversity in DNA of soil bacteria, Appl. Environ. Microbiol, vol.56, pp.782-787, 1990.

V. L. Torsvik, Isolation of bacterial DNA from soil, Soil Biol. Biochem, vol.12, pp.15-21, 1980.

S. G. Tringe, C. Mering-von, A. Kobayashi, A. A. Salamov, K. Chen et al., Comparative metagenomics of microbial communities, Science, vol.308, pp.554-557, 2005.

T. M. Vogel, P. Simonet, J. K. Jansson, P. R. Hirsch, J. M. Tiedje et al., TerraGenome: a consortium for the sequencing of a soil metagenome, Nat. Rev. Microbiol, vol.7, pp.252-252, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00391653

, Conflict of Interest Statement: The authors declare that the research was

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