S. Dequiedt, Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management, Glob. Ecol. Biogeogr, vol.20, pp.641-652, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00698381

S. L. O'brien, Spatial scale drives patterns in soil bacterial diversity, Environ. Microbiol, vol.18, pp.2039-2051, 2016.

S. Terrat, Mapping and predictive variations of soil bacterial richness across France, PLoS One, vol.12, p.186766, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01843156

L. Ranjard, Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity, Nat. Commun, vol.4, p.1434, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00965686

Y. Deng, Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation, Environ. Microbiol, vol.18, pp.205-218, 2016.

M. Schleuning, J. Fründ, and D. García, Predicting ecosystem functions from biodiversity and mutualistic networks: An extension of trait-based concepts to plant-animal interactions, Ecography (Cop.), vol.38, pp.380-392, 2015.

L. A. Burkle, J. C. Marlin, and T. M. Knight, Plant-Pollinator Interactions over 120 Years: Loss of Species, Co-Occurrence and Function, Science, vol.339, pp.1611-1616, 2013.

M. G. Van-der-heijden, A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment, ISME J, vol.10, pp.389-399, 2016.

F. Massol and S. Petit, Interaction Networks in Agricultural Landscape Mosaics, Adv. Ecol. Res, vol.49, pp.291-338, 2013.

K. Faust and J. Raes, Microbial interactions: From networks to models, Nat. Rev. Microbiol, vol.10, pp.538-550, 2012.

B. Karimi, Microbial diversity and ecological networks as indicators of environmental quality, Environ. Chem. Lett, vol.15, pp.265-281, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01516976

J. A. Fuhrman, Microbial community structure and its functional implications, Nature, vol.459, pp.193-199, 2009.

M. Burmølle, D. Ren, T. Bjarnsholt, and S. J. Sørensen, Interactions in multispecies biofilms: Do they actually matter?, Trends Microbiol, vol.22, pp.84-91, 2014.

J. S. Madsen, S. J. Sørensen, and M. Burmølle, Bacterial social interactions and the emergence of community-intrinsic properties, Curr. Opin. Microbiol, vol.42, pp.104-109, 2018.

S. Shi, The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages, Ecol. Lett, vol.19, pp.926-936, 2016.

C. Zappelini, Diversity and complexity of microbial communities from a chlor-alkali tailings dump, Soil Biol. Biochem, vol.90, pp.101-110, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02372435

D. Mandakovic, Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience, Sci. Rep, vol.8, pp.1-12, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01774624

B. Ma, Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China, ISME J, vol.10, pp.1891-1901, 2016.

M. Lupatini, Network topology reveals high connectance levels and few key microbial genera within soils. Front, Environ. Sci, vol.2, pp.1-11, 2014.

E. Morriën, Soil networks become more connected and take up more carbon as nature restoration progresses, Nat. Commun, vol.8, 2017.

F. Constancias, Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape, vol.4, pp.518-531, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02633674

W. Horrigue, Predictive model of soil molecular microbial biomass, Ecol. Indic, vol.64, pp.203-211, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01844377

G. Lentendu, Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: A multiple barcoding approach, Mol. Ecol, vol.23, pp.3341-3355, 2014.

J. A. Steele, Marine bacterial, archaeal and protistan association networks reveal ecological linkages, ISME J, vol.5, pp.1414-1425, 2011.

B. Karimi, C. Meyer, D. Gilbert, and N. Bernard, Air pollution below WHO levels decreases by 40% the links of terrestrial microbial networks, Environ. Chem. Lett, vol.14, pp.467-475, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01516963

P. Lienhard, Pyrosequencing evidences the impact of cropping on soil bacterial and fungal diversity in Laos tropical grassland, Agron. Sustain. Dev, vol.34, pp.525-533, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00977920

O. X. Cordero and M. S. Datta, Microbial interactions and community assembly at microscales, Curr. Opin. Microbiol, vol.31, pp.227-234

M. Pagliai, N. Vignozzi, and S. Pellegrini, Soil structure and the effect of management practices, Soil Tillage Res, vol.79, pp.131-143, 2004.

R. Tecon and D. Or, Biophysical processes supporting the diversity of microbial life in soil, FEMS Microbiol. Rev, vol.41, pp.599-623, 2017.

M. A. Freilich, E. Wieters, B. R. Broitman, P. A. Marquet, and S. A. Navarrete, Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?, Ecology, vol.99, pp.690-699, 2018.

W. De-boer, L. B. Folman, R. C. Summerbell, and L. Boddy, Living in a fungal world: impact of fungi on soil bacterial niche development, FEMS Microbiol. Rev, vol.29, pp.795-811, 2005.

J. Meersmans, A high resolution map of French soil organic carbon, Agron. Sustain. Dev, vol.32, pp.841-851, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00930565

H. Stoyan, Spatial heterogeneity of soil respiration and related properties at the plant scale, Plant Soil, vol.222, pp.203-214, 2000.

M. Vos, A. B. Wolf, S. J. Jennings, and G. A. Kowalchuk, Micro-scale determinants of bacterial diversity in soil, FEMS Microbiol. Rev, vol.37, pp.936-954, 2013.

Z. S. Ma, The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome, Microb. Ecol, vol.75, pp.1063-1073, 2018.

S. Banerjee, Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil, Soil Biol. Biochem, vol.97, pp.188-198, 2016.

D. Berry and S. Widder, Deciphering microbial interactions and detecting keystone species with co-occurrence networks, Front. Microbiol, vol.5, pp.1-14, 2014.

A. Saito, H. Mitsui, R. Hattori, K. Minamisawa, and T. Hattori, Slow-growing and oligotrophic soil bacteria phylogenetically close to Bradyrhizobium japonicum, FEMS Microbiol. Ecol, vol.25, pp.277-286, 1998.

P. L. Siering, Microbial biogeochemistry of Boiling Springs Lake: A physically dynamic, oligotrophic, low-pH geothermal ecosystem, Geobiology, vol.11, pp.356-376, 2013.

S. J. Giovannoni, E. Schabtach, and R. W. Castenholz, Isosphaera pallida, gen. and comb. nov., a gliding, budding enbacterium from hot springs, Arch. Microbiol, vol.147, pp.276-284, 1987.

C. Masson-boivin and J. L. Sachs, Symbiotic nitrogen fixation by rhizobia -the roots of a success story, Curr. Opin. Plant Biol, vol.44, pp.7-15, 2018.

N. Fierer, M. A. Bradford, and R. B. Jackson, Toward an Ecological Classification of Soil Bacteria, Ecology, vol.88, pp.1354-1364, 2007.

B. Karimi, Biogeography of soil bacteria and archaea across France, Sci. Adv, vol.4, pp.1-14, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01843961

C. Lozupone and R. Knight, Global patterns in bacterial diversity, Proc. Natl. Acad. Sci. USA, vol.104, pp.11436-11440, 2007.

S. Terrat, Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition, Microb. Biotechnol, vol.8, pp.131-142, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01215318

R. D. Amore, A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling, BMC Genomics, vol.17, p.55, 2016.

J. Zhou, High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats, MBio, vol.6, pp.2288-2302, 2015.