A. F. Brana, C. Mendez, L. A. Diaz, M. B. Manzanal, and C. Hardisson, Glycogen and trehalose accumulation during colony development in Streptomyces antibioticus, Microbiology, vol.132, pp.1319-1326, 1986.

S. Chakravorty, D. Helb, M. Burday, N. Connell, and D. Alland, A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria, Journal of Microbiological Methods, vol.69, issue.2, pp.330-339, 2007.
DOI : 10.1016/j.mimet.2007.02.005

R. Conrad, Soil microorganisms oxidizing atmospheric trace gases (CH 4, Indian. J. Microbiol, vol.2, issue.39, pp.193-203, 1999.

R. Conrad, M. Aragno, and W. Seiler, The inability of hydrogen bacteria to utilize atmospheric hydrogen is due to threshold and affinity for hydrogen, FEMS Microbiology Letters, vol.18, issue.3, pp.207-210, 1983.
DOI : 10.1111/j.1574-6968.1983.tb00479.x

P. Constant, L. Poissant, and R. Villemur, Isolation of Streptomyces sp. PCB7, the first microorganism demonstrating high-affinity uptake of tropospheric H2, The ISME Journal, vol.31, issue.10, pp.1066-1076, 2008.
DOI : 10.1038/ismej.2008.59

P. Constant, L. Poissant, and R. Villemur, Tropospheric H2 budget and the response of its soil uptake under the changing environment, Science of The Total Environment, vol.407, issue.6, pp.1809-1823, 2009.
DOI : 10.1016/j.scitotenv.2008.10.064
URL : https://hal.archives-ouvertes.fr/pasteur-00819952

P. Constant, S. P. Chowdhury, J. Pratscher, and R. Conrad, Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase, Environmental Microbiology, vol.26, issue.3, pp.821-829, 2010.
DOI : 10.1111/j.1462-2920.2009.02130.x

P. Constant, S. P. Chowdhury, L. Hesse, J. Pratscher, and R. Conrad, Genome Data Mining and Soil Survey for the Novel Group 5 [NiFe]-Hydrogenase To Explore the Diversity and Ecological Importance of Presumptive High-Affinity H2-Oxidizing Bacteria, Applied and Environmental Microbiology, vol.77, issue.17, pp.6027-6035, 2011.
DOI : 10.1128/AEM.00673-11

K. A. Datsenko and B. L. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc. Natl. Acad. Sci. USA, pp.6640-6645, 2000.
DOI : 10.1073/pnas.120163297

Z. Dong and D. B. , H 2 oxidation, O 2 uptake and CO 2 fixation in hydrogen treated soils, Plant and Soil, vol.229, issue.1, pp.1-12, 2001.
DOI : 10.1023/A:1004810017490

D. H. 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

J. A. Frank, C. I. Reich, S. Sharma, J. S. Weisbaum, B. A. Wilson et al., Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes, Applied and Environmental Microbiology, vol.74, issue.8, pp.2461-2470, 2008.
DOI : 10.1128/AEM.02272-07

C. G. Friedrich, Depression of hydrogenase during limitation of electron donors and depression of ribulosebisphosphate carboxylase during carbon limitation of Alcaligenes eutrophus, J. Bacteriol, vol.149, pp.203-210, 1982.

C. Greening and G. M. Cook, Integration of hydrogenase expression and hydrogen sensing in bacterial cell physiology, Current Opinion in Microbiology, vol.18, pp.30-38, 2014.
DOI : 10.1016/j.mib.2014.02.001

C. Greening, M. Berney, K. Hards, G. M. Cook, and R. Conrad, A soil actinobacterium scavenges atmospheric H 2 using two membrane-associated, oxygendependent [NiFe] hydrogenases, Proc. Natl. Acad. Sci. USA, pp.4257-4261, 2014.

C. Greening, S. G. Villas-bôas, J. R. Robson, M. Berney, and G. M. Cook, The Growth and Survival of Mycobacterium smegmatis Is Enhanced by Co-Metabolism of Atmospheric H2, PLoS ONE, vol.9, issue.7, p.103034, 2014.
DOI : 10.1371/journal.pone.0103034.s010

C. Greening, P. Constant, K. Hards, S. E. Morales, J. G. Oakeshott et al., Atmospheric Hydrogen Scavenging: from Enzymes to Ecosystems, Applied and Environmental Microbiology, vol.81, issue.4, pp.1190-1199, 2015.
DOI : 10.1128/AEM.03364-14
URL : https://hal.archives-ouvertes.fr/pasteur-01352155

B. Gust, G. L. Challis, K. Fowler, T. Kieser, and K. F. Chater, PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin, Proc. Natl. Acad. Sci. USA, pp.1541-1546, 2003.
DOI : 10.1073/pnas.0337542100

V. Häring and R. Conrad, 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

B. M. Hoffman, D. R. Dean, and L. C. Seefeldt, Climbing Nitrogenase: Toward a Mechanism of Enzymatic Nitrogen Fixation, Accounts of Chemical Research, vol.42, issue.5, pp.609-619, 2009.
DOI : 10.1021/ar8002128

M. Horch, L. Lauterbach, M. Saggu, P. Hildebrandt, F. Lendzian et al., Probing the Active Site of an O2-Tolerant NAD+-Reducing [NiFe]-Hydrogenase from Ralstonia eutropha H16 by In???Situ EPR and FTIR Spectroscopy, Angewandte Chemie International Edition, vol.126, issue.43, pp.8026-8029, 2010.
DOI : 10.1002/anie.201002197

S. Hoyt and G. H. Jones, RelA is required for actinomycin production in Streptomyces antibioticus, J. Bacteriol, vol.181, pp.3824-3829, 1999.

S. Hunt, S. Gaito, and D. Layzell, Model of gas exchange and diffusion in legume nodules, Planta, vol.3, issue.1, pp.128-141, 1988.
DOI : 10.1007/BF00394497

H. Ikeda, J. Ishikawa, A. Hanamoto, M. Shinose, H. Kikuchi et al., Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis, Nature Biotechnology, vol.21, issue.5, pp.526-531, 2003.
DOI : 10.1038/nbt820

S. G. Kang, W. Jin, M. Bibb, and K. J. Lee, A3(2) grown in continuous culture, FEMS Microbiology Letters, vol.168, issue.2, pp.221-226, 1998.
DOI : 10.1111/j.1574-6968.1998.tb13277.x

M. Khdhiri, L. Hesse, M. E. 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

S. B. Kim and M. Goodfellow, Streptomyces avermitilis sp. nov., nom. rev., a taxonomic home for the avermectin-producing streptomycetes, Int. J. Syst. Evol. Microbiol, vol.52, pp.2011-2014, 2002.

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

O. Lenz and B. Friedrich, A novel multicomponent regulatory system mediates H2 sensing in Alcaligenes eutrophus, Proc. Natl. Acad. Sci. USA 95, pp.12474-12479, 1998.
DOI : 10.1073/pnas.95.21.12474

O. Lenz, M. Bernhard, T. Buhrke, E. Schwartz, and B. Friedrich, The hydrogen-sensing apparatus in Ralstonia eutropha, J. Mol. Microbiol. Biotechnol, vol.4, pp.255-262, 2002.

L. K. Meredith, D. Rao, T. Bosak, V. Klepac-ceraj, K. R. 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, 2013.
DOI : 10.1111/1758-2229.12116

C. Mettel, Y. Kim, P. M. Shrestha, and W. Liesack, Extraction of mRNA from Soil, Applied and Environmental Microbiology, vol.76, issue.17, pp.5995-6000, 2010.
DOI : 10.1128/AEM.03047-09

A. Mortazavi, B. A. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nature Methods, vol.14, issue.7, pp.621-628, 2008.
DOI : 10.1038/nmeth.1226

P. C. Novelli, P. M. Lang, K. A. Masarie, D. F. Hurst, R. Myers et al., Molecular hydrogen in the troposphere: Global distribution and budget, Journal of Geophysical Research: Atmospheres, vol.5, issue.46, pp.30427-30444, 1999.
DOI : 10.1029/1999JD900788

O. ¯-mura, S. , H. Ikeda, J. Ishikawa, A. Hanamoto et al., Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites, Proc. Natl. Acad. Sci. USA, pp.12215-12220, 2001.

C. A. Osborne, M. B. Peoples, and P. H. 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, 2010.
DOI : 10.1128/AEM.02072-09

F. Popelier, J. Liessens, and W. Verstraete, Soil H2-uptake in relation to soil properties and rhizobial H2-production, Plant and Soil, vol.15, issue.4, pp.85-96, 1985.
DOI : 10.1007/BF02197803

R. Core and D. Team, R: A language and environment for statistical computing, In. Computing, R Foundation for Statistical Computing, 2008.

M. E. Rasche and D. J. 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

B. Rueda, E. M. Miguélez, C. Hardisson, and M. B. , hyphae during growth in liquid cultures under sporulating and non-sporulating conditions, FEMS Microbiology Letters, vol.194, issue.2, pp.181-185, 2001.
DOI : 10.1111/j.1574-6968.2001.tb09466.x

C. Schäfer, O. Friedrich, and . Lenz, 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 R. Conrad, Hydrogen oxidation in soil following rhizobial H2 production due to N2 fixation by a Vicia faba-Rhizobium leguminosarum symbiosis, Biology and Fertility of Soils, vol.52, issue.3, pp.190-195, 1991.
DOI : 10.1007/BF00335766

E. Schwartz, A. Henne, R. Cramm, T. Eitinger, B. Friedrich et al., Complete Nucleotide Sequence of pHG1: A Ralstonia eutropha H16 Megaplasmid Encoding Key Enzymes of H2-based Lithoautotrophy and Anaerobiosis, Journal of Molecular Biology, vol.332, issue.2, pp.369-383, 2003.
DOI : 10.1016/S0022-2836(03)00894-5

S. Stein, D. Selesi, R. Schilling, I. Pattis, M. Schmid et al., Microbial activity and bacterial composition of H2-treated soils with net CO2 fixation, Soil Biology and Biochemistry, vol.37, issue.10, pp.1938-1945, 2005.
DOI : 10.1016/j.soilbio.2005.02.035

S. Tarazona, F. García-alcalde, J. Dopazo, A. Ferrer, and A. Conesa, Differential expression in RNA-seq: A matter of depth, Genome Research, vol.21, issue.12, pp.2213-2223, 2011.
DOI : 10.1101/gr.124321.111

J. Tian, R. Bryk, M. Itoh, M. Suematsu, and C. Nathan, Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: Identification of ??-ketoglutarate decarboxylase, Proc. Natl. Acad. Sci. USA, pp.10670-10675, 2005.
DOI : 10.1073/pnas.0501605102

B. Tjaden, De novo assembly of bacterial transcriptomes from RNA-seq data, Genome Biology, vol.16, issue.1, 2015.
DOI : 10.1186/1471-2105-12-S14-S2

M. Ueki, R. Suzuki, S. Takamatsu, H. Takagi, M. Uramoto et al., Nocardamin Production by Streptomyces avermitilis, Actinomycetologica, vol.23, issue.2, pp.34-39, 2009.
DOI : 10.3209/saj.SAJ230203

P. M. 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

J. F. 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

G. Wu, D. E. Culley, and W. Zhang, Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism, Microbiology, vol.151, issue.7, pp.2175-2187, 2005.
DOI : 10.1099/mic.0.27833-0

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