J. Bernoulli and O. ?ejnin, On the law of large numbers, 2005.

A. Blaud, T. Z. Lerch, T. Chevallier, N. Nunan, C. Chenu et al., Dynamics of bacterial communities in relation to soil aggregate formation during the decomposition of 13C-labelled rice straw, Applied Soil Ecology, vol.53, pp.1-9, 2012.
DOI : 10.1016/j.apsoil.2011.11.005
URL : https://hal.archives-ouvertes.fr/hal-00999935

R. Bryant, What If Ecological Communities Are Not Wholes?, pp.37-56, 2012.
DOI : 10.7551/mitpress/9780262017404.003.0003

J. W. Crawford, J. A. Harris, K. Ritz, and I. M. Young, Towards an evolutionary ecology of life in soil, Trends in Ecology & Evolution, vol.20, issue.2, pp.81-87, 2005.
DOI : 10.1016/j.tree.2004.11.014

A. Dechesne, D. Or, and B. F. Smets, Limited diffusive fluxes of substrate facilitate coexistence of two competing bacterial strains, FEMS Microbiology Ecology, vol.64, issue.1, pp.1-8, 2008.
DOI : 10.1111/j.1574-6941.2008.00446.x

T. Egli, The ecological and physiological significance of the growth of heterotrophic mi croorganisms with mixtures of substrates Advances in Microbial Ecology, pp.305-386, 1995.

D. S. Esser, J. H. Leveau, K. M. Meyer, and K. Wiegand, Spatial scales of interactions among bacteria and between bacteria and the leaf surface, FEMS Microbiology Ecology, vol.91, issue.3, pp.34-034, 2015.
DOI : 10.1093/femsec/fiu034

D. S. Feeney, J. W. Crawford, T. Daniell, P. D. Hallett, N. Nunan et al., Three-dimensional Microorganization of the Soil???Root???Microbe System, Microbial Ecology, vol.1, issue.1, pp.151-158, 2006.
DOI : 10.2136/sssaj2004.3520
URL : https://hal.archives-ouvertes.fr/bioemco-00136966

R. C. Foster, Microenvironments of soil microorganisms, Biology and Fertility of Soils, vol.6, issue.3, pp.189-203, 1988.
DOI : 10.1007/BF00260816

S. Gantner, M. Schmid, C. Durr, R. Schuhegger, A. Steidle et al., In situ quantitation of the spatial scale of calling distances and population density-independent N-acylhomoserine lactone-mediated communication by rhizobacteria colonized on plant roots, FEMS Microbiology Ecology, vol.56, issue.2, pp.188-194, 2006.
DOI : 10.1111/j.1574-6941.2005.00037.x

A. Hector, J. Joshi, S. P. Lawler, E. M. Spehn, and A. Wilby, Conservation implications of the link between biodiversity and ecosystem functioning, Oecologia, vol.129, issue.4, pp.624-628, 2001.
DOI : 10.1007/s004420100759

R. Horn and A. Smucker, Structure formation and its consequences for gas and water transport in unsaturated arable and forest soils, Soil and Tillage Research, vol.82, issue.1, pp.5-14, 2005.
DOI : 10.1016/j.still.2005.01.002

J. B. Hughes-martiny, B. J. Bohannan, J. H. Brown, R. K. Colwell, J. A. Fuhrman et al., Microbial biogeography: putting microorganisms on the map, Microbial biogeography: putting microorganisms on the map, pp.102-112, 2006.
DOI : 10.1007/978-1-4615-6968-8_3

B. Jaillard, A. Rapaport, J. Harmand, A. Brauman, and N. Nunan, Community assembly effects shape the biodiversity-ecosystem functioning relationships, Functional Ecology, vol.97, issue.6, pp.1523-1533, 2014.
DOI : 10.1111/j.1365-2745.2009.01535.x
URL : https://hal.archives-ouvertes.fr/hal-00937779

E. Jasinska, H. Wetzel, T. Baumgartl, and R. Horn, Heterogeneity of Physico-Chemical Properties in Structured Soils and Its Consequences, Pedosphere, vol.16, issue.3, pp.284-296, 2006.
DOI : 10.1016/S1002-0160(06)60054-4

S. Juarez, N. Nunan, A. Duday, V. Pouteau, S. Schmidt et al., Effects of different soil structures on the decomposition of native and??added organic carbon, European Journal of Soil Biology, vol.58, pp.81-90, 2013.
DOI : 10.1016/j.ejsobi.2013.06.005
URL : https://hal.archives-ouvertes.fr/hal-01567153

M. Keiluweit, J. J. Bougoure, P. S. Nico, J. Pett-ridge, P. K. Weber et al., Mineral protection of soil carbon counteracted by root exudates, Nature Climate Change, vol.59, issue.6, pp.588-595, 2015.
DOI : 10.1016/0048-9697(87)90127-6

G. Kilbertus, Etude des microhabitats contenus dans les aggrégats du sol, leur relation avec la biomasse bactérienne et la taille des procaryotes présents, Rev. Ecol. Biol. Sol, vol.17, pp.543-557, 1980.

A. J. King, K. R. Freeman, K. F. Mccormick, R. C. Lynch, C. Lozupone et al., Biogeography and habitat modelling of high-alpine bacteria, Nature Communications, vol.53, issue.5, pp.1-6, 2010.
DOI : 10.1093/comjnl/7.4.308

A. Konopka, What is microbial community ecology?, The ISME Journal, vol.100, issue.11, pp.1223-1230, 2009.
DOI : 10.1038/nature07840
URL : http://www.nature.com/ismej/journal/v3/n11/pdf/ismej200988a.pdf

Y. Kuzyakov, Review: Factors affecting rhizosphere priming effects, Journal of Plant Nutrition and Soil Science, vol.165, issue.4, pp.382-396, 2002.
DOI : 10.1002/1522-2624(200208)165:4<382::AID-JPLN382>3.0.CO;2-#

J. Lehmann, D. Solomon, J. Kinyangi, L. Dathe, S. Wirick et al., Spatial complexity of soil organic matter forms at nanometre scales, Nature Geoscience, vol.144, issue.4, pp.238-242, 2008.
DOI : 10.2136/sssaj2001.6541121x

T. Long and D. Or, Aquatic habitats and diffusion constraints affecting microbial coexistence in unsaturated porous media, Water Resources Research, vol.304, issue.5677, p.41, 2005.
DOI : 10.1126/science.1097394

P. Marschner, S. Marhan, and E. Kandeler, Microscale distribution and function of soil microorganisms in the interface between rhizosphere and detritusphere, Soil Biology and Biochemistry, vol.49, pp.174-183, 2012.
DOI : 10.1016/j.soilbio.2012.01.033

F. E. Moyano, N. Vasilyeva, L. Bouckaert, F. Cook, J. Craine et al., The moisture response of soil heterotrophic respiration: interaction with soil properties, Biogeosciences, vol.9, issue.3, pp.1173-1182, 2012.
DOI : 10.5194/bg-9-1173-2012-supplement
URL : https://hal.archives-ouvertes.fr/hal-01567157

C. W. Mueller, A. Kölbl, C. Hoeschen, F. Hillion, K. Heister et al., Submicron scale imaging of soil organic matter dynamics using NanoSIMS ??? From single particles to intact aggregates, Organic Geochemistry, vol.42, issue.12, pp.1476-1488, 2012.
DOI : 10.1016/j.orggeochem.2011.06.003

D. L. Mummey and P. D. Stahl, Analysis of Soil Whole- and Inner-Microaggregate Bacterial Communities, Microbial Ecology, vol.46, issue.1, pp.41-50, 2004.
DOI : 10.1007/s00248-003-1000-4

U. N. Nielsen, E. Ayres, D. H. Wall, and R. D. Bardgett, Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity-function relationships, European Journal of Soil Science, vol.41, issue.1, pp.105-116, 2011.
DOI : 10.1016/j.soilbio.2008.12.028

N. Nunan, K. Ritz, M. Rivers, D. S. Feeney, and I. M. Young, Investigating microbial micro-habitat structure using X-ray computed tomography, Geoderma, vol.133, issue.3-4, pp.398-407, 2006.
DOI : 10.1016/j.geoderma.2005.08.004
URL : https://hal.archives-ouvertes.fr/bioemco-00138740

S. A. Placella, E. L. Brodie, and M. K. Firestone, Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups, Proc. Natl. Acad. Sci, pp.10931-10936, 2012.
DOI : 10.1007/s00248-006-9103-3

C. Poll, T. Brune, D. Begerow, and E. Kandeler, Small-scale Diversity and Succession of Fungi in the Detritusphere of Rye Residues, Microbial Ecology, vol.39, issue.1, pp.130-140, 2010.
DOI : 10.1007/s00248-003-2018-3

L. Ranjard, S. Dequiedt, C. Prévost-bouré, N. Thioulouse, J. Saby et al., Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity, Nature Communications, vol.22, 1434.
DOI : 10.18637/jss.v022.i05
URL : https://hal.archives-ouvertes.fr/hal-00965686

B. G. Rawlins, J. Wragg, C. Reinhard, R. C. Atwood, A. Houston et al., Three-dimensional??soil??organic??matter??distribution, accessibility??and??microbial??respiration??in??macroaggregates??using??osmium??staining and??synchrotron??X-ray??computed tomography, SOIL, vol.2, issue.4, pp.659-671, 2016.
DOI : 10.5194/soil-2-659-2016

X. Raynaud and N. Nunan, Spatial Ecology of Bacteria at the Microscale in Soil, PLoS ONE, vol.90, issue.1, p.87217, 2014.
DOI : 10.1371/journal.pone.0087217.s002
URL : https://hal.archives-ouvertes.fr/hal-01252483

L. F. Roesch, R. R. Fulthorpe, A. Riva, G. Casella, A. K. Hadwin et al., Pyrosequencing enumerates and contrasts soil microbial diversity, The ISME Journal, vol.7, 2007.
DOI : 10.1038/ismej.2007.53

L. S. Ruamps, N. Nunan, and C. Chenu, Microbial biogeography at the soil pore scale, Soil Biology and Biochemistry, vol.43, issue.2, pp.280-286, 2011.
DOI : 10.1016/j.soilbio.2010.10.010
URL : https://hal.archives-ouvertes.fr/bioemco-00577735

C. Salome, N. Nunan, V. Pouteau, T. Z. Lerch, and C. Chenu, Carbon dynamics in topsoil and in subsoil may be controlled by different regulatory mechanisms, Global Change Biology, vol.40, issue.1, pp.416-426, 2010.
DOI : 10.1111/j.1365-2486.2009.01884.x
URL : https://hal.archives-ouvertes.fr/bioemco-00430863

J. Schimel, T. C. Balser, and M. Wallenstein, MICROBIAL STRESS-RESPONSE PHYSIOLOGY AND ITS IMPLICATIONS FOR ECOSYSTEM FUNCTION, Ecology, vol.88, issue.6, pp.1386-1394, 2007.
DOI : 10.1890/02-0433

J. Sierra and P. Renault, Respiratory Activity and Oxygen Distribution in Natural Aggregates in Relation to Anaerobiosis, Soil Science Society of America Journal, vol.60, issue.5, pp.1428-1438, 1996.
DOI : 10.2136/sssaj1996.03615995006000050020x

G. Stanford and S. J. Smith, Nitrogen Mineralization Potentials of Soils1, Soil Science Society of America Journal, vol.36, issue.3, p.465, 1972.
DOI : 10.2136/sssaj1972.03615995003600030029x

K. Sterelny, Local Ecological Communities*, Philosophy of Science, vol.73, issue.2, pp.215-231, 2006.
DOI : 10.1086/510819

D. T. Strong, H. De-wever, R. Merckx, and S. Recous, Spatial location of carbon decomposition in the soil pore system, European Journal of Soil Science, vol.61, issue.4, pp.739-750, 2004.
DOI : 10.1016/S0167-1987(99)00106-3

D. S. Treves, B. Xia, J. Zhou, and J. M. Tiedje, A Two-Species Test of the Hypothesis That Spatial Isolation Influences Microbial Diversity in Soil, Microbial Ecology, vol.45, issue.1, pp.20-28, 2003.
DOI : 10.1007/s00248-002-1044-x

S. Wertz, V. Degrange, J. I. Prosser, F. Poly, C. Commeaux et al., Maintenance of soil functioning following erosion of microbial diversity, Environmental Microbiology, vol.39, issue.12, pp.2162-2169, 2006.
DOI : 10.1641/0006-3568(2000)050[1089:EOGCOA]2.0.CO;2
URL : https://hal.archives-ouvertes.fr/hal-00127101

I. M. Young and J. W. Crawford, Interactions and Self-Organization in the Soil-Microbe Complex, Science, vol.304, issue.5677, pp.1634-1637, 2004.
DOI : 10.1126/science.1097394

I. M. Young and K. Ritz, Can there be a contemporary ecological dimension to soil biology without a habitat?, Soil Biology and Biochemistry, vol.30, issue.10-11, pp.1229-1232, 1998.
DOI : 10.1016/S0038-0717(97)00263-0