T. Desantis, P. Hugenholtz, N. Larsen, M. Rojas, E. Brodie et al., Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB, Applied and Environmental Microbiology, vol.72, issue.7, pp.5069-5072, 1128.
DOI : 10.1128/AEM.03006-05

Z. Dong and D. Layzell, H 2 oxidation, O 2 uptake and CO 2 fixation in hydrogen treated soils, Plant and Soil, vol.229, issue.1, pp.1-12, 1023.
DOI : 10.1023/A:1004810017490

Z. Dong, L. Wu, B. Kettlewell, C. Caldwell, and D. Layzell, Hydrogen fertilization of soils - is this a benefit of legumes in rotation?, Plant, Cell and Environment, vol.22, issue.11, pp.1875-1879, 2003.
DOI : 10.1016/S0168-6496(96)00090-6

R. Edgar, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, vol.26, issue.19, pp.2460-2461, 2010.
DOI : 10.1093/bioinformatics/btq461

R. Edgar, B. Haas, J. Clemente, C. Quince, and R. Knight, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, issue.16, pp.2194-2200, 2011.
DOI : 10.1093/bioinformatics/btr381

D. Ehhalt and F. Rohrer, : a critical review, Tellus B: Chemical and Physical Meteorology, vol.104, issue.14347, pp.500-535, 2009.
DOI : 10.1029/2002GB001952

A. Golding, Y. Zou, X. Yang, B. Flynn, and Z. Dong, Plant growth promoting H<sub>2</sub>-oxidizing bacteria as seed inoculants for cereal crops, Agricultural Sciences, vol.03, issue.04, pp.510-516, 2012.
DOI : 10.4236/as.2012.34060

C. Greening, M. Berney, K. Hards, G. Cook, and C. R. , A soil actinobacterium scavenges atmospheric H2 using two membrane-associated, oxygen-dependent [NiFe] hydrogenases, Proceedings of the National Academy of Sciences, vol.111, issue.11, pp.4257-4261
DOI : 10.1073/pnas.1320586111

C. Greening, A. Biswas, C. Carere, C. Jackson, M. Taylor et al., Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival, The ISME Journal, vol.196, issue.3, pp.761-777, 2016.
DOI : 10.1038/ismej.2015.153

C. Greening, P. Constant, K. Hards, S. Morales, J. Oakeshott et al., Atmospheric Hydrogen Scavenging: from Enzymes to Ecosystems, Applied and Environmental Microbiology, vol.81, issue.4, pp.1190-1199, 1128.
DOI : 10.1128/AEM.03364-14

URL : https://hal.archives-ouvertes.fr/pasteur-01352155

C. Greening, S. Villas-boas, J. Robson, M. Berney, and G. Cook, The Growth and Survival of Mycobacterium smegmatis Is Enhanced by Co-Metabolism of Atmospheric H2, PLoS ONE, vol.9, issue.7, 2014.
DOI : 10.1371/journal.pone.0103034.s010

V. Häring and C. R. , Demonstration of two different H2-oxidizing activities in soil using an H2 consumption and a tritium exchange assay, Biology and Fertility of Soils, vol.12, issue.2, pp.125-128, 1994.
DOI : 10.1007/BF00337744

M. Hartmann, B. Frey, J. Mayer, P. Mader, and F. Widmer, Distinct soil microbial diversity under long-term organic and conventional farming, The ISME Journal, vol.46, issue.5, pp.1177-1194, 2015.
DOI : 10.1016/j.apsoil.2005.09.007

B. Hoffman, D. Dean, and L. Seefeldt, Climbing Nitrogenase: Toward a Mechanism of Enzymatic Nitrogen Fixation, Accounts of Chemical Research, vol.42, issue.5, pp.609-619, 1021.
DOI : 10.1021/ar8002128

S. Hunt and D. Layzell, Gas Exchange of Legume Nodules and the Regulation of Nitrogenase Activity, Annual Review of Plant Physiology and Plant Molecular Biology, vol.44, issue.1, 1993.
DOI : 10.1146/annurev.pp.44.060193.002411

M. Khdhiri, L. Hesse, M. Popa, L. Quiza, I. Lalonde et al., Soil carbon content and relative abundance of high affinity H2-oxidizing bacteria predict atmospheric H2 soil uptake activity better than soil microbial community composition, Soil Biology and Biochemistry, vol.85, pp.1-9, 2015.
DOI : 10.1016/j.soilbio.2015.02.030

URL : https://hal.archives-ouvertes.fr/pasteur-01352172

J. Kuczynski, J. Stombaugh, W. Walters, A. González, J. Caporaso et al., Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities, Current Protocols in Bioinformatics, vol.73, pp.10-17, 2011.
DOI : 10.1002/9780471729259.mc01e05s27

L. Favre, J. Focht, and D. , Conservation in soil of H 2 liberated from N 2 fixation by Hup ? nodules, Applied and Environmental Microbiology, vol.46, pp.304-311, 1983.

P. Langfelder and S. Horvath, WGCNA: an R package for weighted correlation network analysis, BMC Bioinformatics, vol.9, issue.1, pp.559-569, 2008.
DOI : 10.1186/1471-2105-9-559

M. Langille, J. Zaneveld, J. Caporaso, D. Mcdonald, D. Knights et al., Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nature Biotechnology, vol.51, issue.9, pp.814-821, 2013.
DOI : 10.1093/nar/gkr1178

P. Legendre and E. Gallagher, Ecologically meaningful transformations for ordination of species data, Oecologia, vol.129, issue.2, pp.271-280, 2001.
DOI : 10.1007/s004420100716

M. Li, A. Copeland, and J. Han, DUK-A Fast and efficient Kmer based sequence matching tool Available at https:// publications.lbl.gov/ islandora, pp.3-155200, 2011.

T. Magoc and S. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, issue.21, pp.2957-2963, 2011.
DOI : 10.1093/bioinformatics/btr507

D. Mccarthy, Y. Chen, and G. Smyth, Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation, Nucleic Acids Research, vol.40, issue.10, pp.4288-4297, 2012.
DOI : 10.1093/nar/gks042

L. Meredith, D. Rao, T. Bosak, V. Klepac-ceraj, K. Tada et al., Consumption of atmospheric hydrogen during the life cycle of soil-dwelling actinobacteria, Environmental Microbiology Reports, vol.52, issue.3, pp.226-238, 2014.
DOI : 10.1111/1758-2229.12116

C. Osborne, M. Peoples, and P. Janssen, Detection of a Reproducible, Single-Member Shift in Soil Bacterial Communities Exposed to Low Levels of Hydrogen, Applied and Environmental Microbiology, vol.76, issue.5, pp.1471-1479, 1128.
DOI : 10.1128/AEM.02072-09

M. Rasche and D. Arp, Hydrogen Inhibition of Nitrogen Reduction by Nitrogenase in Isolated Soybean Nodule Bacteroids, PLANT PHYSIOLOGY, vol.91, issue.2, pp.663-668, 1989.
DOI : 10.1104/pp.91.2.663

R. Development and C. Team, R: a language and environment for statistical computing, Vienna: R Foundation for Statistical Computing, 2008.

S. Rittenberg and N. Goodman, Mixotrophic growth of Hydrogenomonas eutropha, Journal of Bacteriology, vol.98, pp.617-622, 1969.

M. Robinson, D. Mccarthy, and G. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, issue.1, pp.139-140, 2010.
DOI : 10.1093/bioinformatics/btp616

C. Schäfer, B. Friedrich, and O. Lenza, Novel, Oxygen-Insensitive Group 5 [NiFe]-Hydrogenase in Ralstonia eutropha, Applied and Environmental Microbiology, vol.79, issue.17, pp.5137-5145, 2013.
DOI : 10.1128/AEM.01576-13

S. Schuler and C. R. , Soils contain two different activities for oxidation of hydrogen, FEMS Microbiology Letters, vol.73, issue.1, pp.77-83, 1990.
DOI : 10.1111/j.1574-6968.1990.tb03927.x

S. Stein, D. Selesi, R. Schilling, I. Pattis, M. Schmid et al., Microbial activity and bacterial composition of H 2 -treated soils with net CO 2 fixation, Soil Biology & Biochemistry, vol.37, 1938.

J. Tremblay, K. Singh, A. Fern, E. Kirton, S. He et al., Primer and platform effects on 16S rRNA tag sequencing, Frontiers in Microbiology, vol.74, pp.1-15, 2015.
DOI : 10.1073/pnas.74.11.5088

P. Vignais and B. Billoud, Occurrence, Classification, and Biological Function of Hydrogenases:?? An Overview, Chemical Reviews, vol.107, issue.10, pp.4206-4272, 2007.
DOI : 10.1021/cr050196r

Q. Wang, G. Garrity, J. Tiedje, and J. Cole, Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy, Applied and Environmental Microbiology, vol.73, issue.16, pp.5261-5267, 1128.
DOI : 10.1128/AEM.00062-07

J. Witty, Microelectrode Measurements of Hydrogen Concentrations and Gradients in Legume Nodules, Journal of Experimental Botany, vol.42, issue.6, pp.765-771, 1991.
DOI : 10.1093/jxb/42.6.765

Y. Zhang, X. He, and Z. Dong, Effect of hydrogen on soil bacterial community structure in two soils as determined by terminal restriction fragment length polymorphism, Plant and Soil, vol.37, issue.1-2, pp.295-305, 2009.
DOI : 10.1007/s11104-009-9894-3

J. Zhou, Y. Deng, F. Luo, Z. He, and Y. Yang, Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO 2, pp.122-00111, 2011.