G. C. Abell, J. Banks, D. J. Ross, J. P. Keane, S. S. Robert et al., Effects of estuarine sediment hypoxia on nitrogen fluxes and ammonia oxidizer gene transcription, FEMS Microbiology Ecology, vol.75, issue.1, pp.111-122, 2011.
DOI : 10.1111/j.1574-6941.2010.00988.x

F. Abram, Systems-based approaches to unravel multi-species microbial community functioning, Computational and Structural Biotechnology Journal, vol.13, pp.24-32, 2015.
DOI : 10.1016/j.csbj.2014.11.009
URL : http://doi.org/10.1016/j.csbj.2014.11.009

S. D. Allison and J. B. Martiny, Resistance, resilience, and redundancy in microbial communities, Proceedings of the National Academy of Sciences, vol.88, issue.6, pp.11512-11519, 2008.
DOI : 10.1890/05-1839
URL : http://www.pnas.org/content/105/Supplement_1/11512.full.pdf

J. Auguet, A. Barberan, and E. O. Casamayor, Global ecological patterns in uncultured Archaea, The ISME Journal, vol.82, issue.2, 2010.
DOI : 10.1126/science.1133420
URL : http://www.nature.com/ismej/journal/v4/n2/pdf/ismej2009109a.pdf

A. Barberán, S. T. Bates, E. O. Casamayor, and N. Fierer, Using network analysis to explore co-occurrence patterns in soil microbial communities, The ISME Journal, vol.3, issue.2, pp.343-351, 2012.
DOI : 10.1038/ismej.2008.106

R. D. Bardgett and W. H. Van-der-putten, Belowground biodiversity and ecosystem functioning, Nature, vol.47, issue.7528, pp.505-511, 2014.
DOI : 10.1016/j.ejsobi.2012.08.005

K. R. Barton, E. S. Bernhardt, C. M. Boot, E. B. Graham, E. K. Hall et al., MuMIn: Multi-Model Inference. R Package Version 1.0. 0. Vienna, Austria: R Foundation for Statistical Computing Available at: http://CRAN.R-project Linking microbial community structure and microbial processes: an empirical and conceptual overview, FEMS Microbiol. Ecol, 2011.

E. Blagodatskaya and Y. Kuzyakov, Active microorganisms in soil: Critical review of estimation criteria and approaches, Soil Biology and Biochemistry, vol.67, 2013.
DOI : 10.1016/j.soilbio.2013.08.024

N. J. Bouskill, J. Tang, W. J. Riley, and E. L. Brodie, Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition, Frontiers in Microbiology, vol.3, 2012.
DOI : 10.3389/fmicb.2012.00364

K. P. Burnham, A. , and D. R. , Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach, 2002.
DOI : 10.1007/b97636

K. P. Burnham, A. , and D. R. , Multimodel Inference, Sociological Methods & Research, vol.27, issue.1, pp.261-304, 2004.
DOI : 10.1017/CBO9781139164795

M. W. Cadotte, K. Carscadden, and N. Mirotchnick, Beyond species: functional diversity and the maintenance of ecological processes and services, Journal of Applied Ecology, vol.9, issue.5, 2011.
DOI : 10.1111/j.1461-0248.2005.00850.x

K. M. Carney and P. A. Matson, Plant Communities, Soil Microorganisms, and Soil Carbon Cycling: Does Altering the World Belowground Matter to Ecosystem Functioning?, Ecosystems, vol.84, issue.8, pp.928-940, 2005.
DOI : 10.1007/978-3-642-78966-3_17
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.462.2654

K. Chan and D. Heenan, The influence of crop rotation on soil structure and soil physical properties under conventional tillage, Soil and Tillage Research, vol.37, issue.2-3, pp.113-125, 1996.
DOI : 10.1016/0167-1987(96)01008-2

J. S. Clark, D. M. Bell, M. H. Hersh, M. C. Kwit, E. Moran et al., Individual-scale variation, species-scale differences: inference needed to understand diversity, Ecology Letters, vol.428, issue.12, pp.1273-1287, 2011.
DOI : 10.1038/nature02403

T. J. Dewitt, A. Sih, W. , and D. S. , Costs and limits of phenotypic plasticity, Trends in Ecology & Evolution, vol.13, issue.2, pp.77-81, 1998.
DOI : 10.1016/S0169-5347(97)01274-3

R. P. Dick, A review: long-term effects of agricultural systems on soil biochemical and microbial parameters, Agriculture, Ecosystems & Environment, vol.40, issue.1-4, pp.25-36, 1992.
DOI : 10.1016/0167-8809(92)90081-L

E. A. Dinsdale, R. A. Edwards, D. Hall, F. Angly, M. Breitbart et al., Functional metagenomic profiling of nine biomes Soil management to enhance bacterivore and fungivore nematode populations and their nitrogen mineralisation function, Nature Appl. Soil Ecol, vol.452, issue.25, pp.629-632, 2004.

N. Fierer, J. W. Leff, B. J. Adams, U. N. Nielsen, S. T. Bates et al., Cross-biome metagenomic analyses of soil microbial communities and their functional attributes, Proceedings of the National Academy of Sciences, vol.9, issue.5, pp.21390-21395, 2012.
DOI : 10.1186/1471-2105-9-386
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535587

T. Fukami, ASSEMBLY HISTORY INTERACTS WITH ECOSYSTEM SIZE TO INFLUENCE SPECIES DIVERSITY, Ecology, vol.85, issue.12, pp.3234-3242, 2004.
DOI : 10.1046/j.1365-2656.1998.00212.x

T. Fukami, I. A. Dickie, P. Wilkie, J. Paulus, B. C. Park et al., Assembly history dictates ecosystem functioning: evidence from wood decomposer communities, Ecology Letters, vol.72, issue.6, pp.675-684, 2010.
DOI : 10.1111/j.1461-0248.2010.01465.x

V. Gagic, I. Bartomeus, T. Jonsson, A. Taylor, C. Winqvist et al., Functional identity and diversity of animals predict ecosystem functioning better than species-based indices, Proceedings of the Royal Society B: Biological Sciences, vol.280, issue.52, 2015.
DOI : 10.1007/s10531-010-9850-9
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309003

E. B. Graham, W. R. Wieder, J. W. Leff, S. R. Weintraub, A. R. Townsend et al., Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes, Soil Biology and Biochemistry, vol.68, pp.279-282, 2014.
DOI : 10.1016/j.soilbio.2013.08.023

V. Gupta and J. Germida, Distribution of microbial biomass and its activity in different soil aggregate size classes as affected by cultivation, Soil Biology and Biochemistry, vol.20, issue.6, pp.777-786, 1988.
DOI : 10.1016/0038-0717(88)90082-X

S. B. Hagerty, K. J. Van-groenigen, S. D. Allison, B. A. Hungate, E. Schwartz et al., Accelerated microbial turnover but constant growth efficiency with warming in soil, Nature Climate Change, vol.43, issue.10, pp.903-906, 1038.
DOI : 10.1016/j.soilbio.2010.09.022

P. Hanson, N. Edwards, C. Garten, and J. Andrews, Separating root and soil microbial contributions to soil respiration: a review of methods and observations, Biogeochemistry, vol.48, issue.1, pp.115-146, 2000.
DOI : 10.1023/A:1006244819642

S. P. Hubbell, The Unified Neutral Theory of Biodiversity and Biogeography (MPB-32), 2001.

C. M. Jones, A. Spor, F. P. Brennan, M. Breuil, D. Bru et al., Recently identified microbial guild mediates soil N2O sink capacity, Nature Climate Change, vol.48, issue.9, pp.801-805, 1038.
DOI : 10.1186/1471-2105-9-307
URL : http://prodinra.inra.fr/ft/976B69C8-8EE2-49DD-9B1C-DF28F6E49158

S. E. Jones and J. T. Lennon, Dormancy contributes to the maintenance of microbial diversity, Proceedings of the National Academy of Sciences, vol.37, issue.suppl_1, pp.5881-5886, 2010.
DOI : 10.1093/nar/gkn879

C. Kaiser, O. Franklin, U. Dieckmann, and A. Richter, Microbial community dynamics alleviate stoichiometric constraints during litter decay, Ecology Letters, vol.3, issue.6, pp.680-690, 2014.
DOI : 10.1038/nclimate1951
URL : http://onlinelibrary.wiley.com/doi/10.1111/ele.12269/pdf

J. E. Knelman and D. R. Nemergut, Changes in community assembly may shift the relationship between biodiversity and ecosystem function, Frontiers in Microbiology, vol.7, 2014.
DOI : 10.1038/ismej.2013.11

C. L. Lauber, M. Hamady, R. Knight, and N. Fierer, Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale, Applied and Environmental Microbiology, vol.75, issue.15, pp.5111-5120, 2009.
DOI : 10.1128/AEM.00335-09

J. T. Lennon and S. E. Jones, Microbial seed banks: the ecological and evolutionary implications of dormancy, Nature Reviews Microbiology, vol.72, issue.2, pp.119-130, 1038.
DOI : 10.1073/pnas.72.6.2112

A. Lira-noriega, J. Soberón, and C. P. Miller, Process-based and correlative modeling of desert mistletoe distribution: a multiscalar approach, Ecosphere, vol.4, issue.8, 2013.
DOI : 10.1111/j.1467-9868.2010.00749.x

C. A. Lozupone and R. Knight, Global patterns in bacterial diversity, Proceedings of the National Academy of Sciences, vol.29, issue.1, pp.11436-11440, 2007.
DOI : 10.1093/nar/29.1.173

S. Manzoni, S. Schaeffer, G. Katul, A. Porporato, and J. Schimel, A theoretical analysis of microbial eco-physiological and diffusion limitations to carbon cycling in drying soils, Soil Biology and Biochemistry, vol.73, pp.69-83, 2014.
DOI : 10.1016/j.soilbio.2014.02.008

A. C. Martiny, K. Treseder, and G. Pusch, Phylogenetic conservatism of functional traits in microorganisms, The ISME Journal, vol.56, issue.4, pp.830-838, 2013.
DOI : 10.1126/science.1165340

J. B. Martiny, S. E. Jones, J. T. Lennon, A. C. Martiny, L. et al., Microbiomes in light of traits: a phylogenetic perspective Coastal hypoxia and sediment biogeochemistry, Science Biogeosciences, vol.350, issue.6, pp.3655-3706, 2009.

D. R. Nemergut, E. K. Costello, M. Hamady, C. Lozupone, L. Jiang et al., Global patterns in the biogeography of bacterial taxa Patterns and processes of microbial community assembly, Environ. Microbiol. Microbiol. Mol. Biol. Rev, vol.13, issue.77, pp.135-144, 1128.

D. R. Nemergut, A. Shade, and C. Violle, When, where and how does microbial community composition matter? Front, 2014.
DOI : 10.3389/fmicb.2014.00497
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176461

J. Oksanen, F. G. Blanchet, R. Kindt, P. Legendre, P. R. Minchin et al., Package 'Vegan'. Community Ecology Package, Version 2 Available at: http://CRAN.R-project.org Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska, Environ. Microbiol, vol.14, pp.993-1008, 2012.

J. R. Powell, A. Welsh, and S. Hallin, Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties, Ecology, vol.96, issue.7, pp.10-1890, 1985.
DOI : 10.1890/14-1127.1.sm

J. I. Prosser, B. J. Bohannan, T. P. Curtis, R. J. Ellis, M. K. Firestone et al., The role of ecological theory in microbial ecology, R Foundation for Statistical Computing, 2007.
DOI : 10.1038/nrmicro1643

D. C. Reed, C. K. Algar, J. A. Huber, D. , and G. J. , Gene-centric approach to integrating environmental genomics and biogeochemical models, Proc. Natl, 2014.
DOI : 10.1038/ismej.2012.94
URL : http://www.pnas.org/content/111/5/1879.full.pdf

J. D. Rocca, E. K. Hall, J. T. Lennon, S. E. Evans, M. P. Waldrop et al., Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed, The ISME Journal, vol.36, issue.8, pp.1693-1699, 2014.
DOI : 10.1073/pnas.1012681107
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511926

J. Rosindell, S. P. Hubbell, E. , and R. S. , The Unified Neutral Theory of Biodiversity and Biogeography at Age Ten, Trends in Ecology & Evolution, vol.26, issue.7, 2011.
DOI : 10.1016/j.tree.2011.03.024

J. Schimel, Ecosystem Consequences of Microbial Diversity and Community Structure, Arctic and Alpine Biodiversity: Patterns, Causes and Ecosystem Consequences, pp.239-254, 1995.
DOI : 10.1007/978-3-642-78966-3_17

J. P. Schimel and J. Gulledge, Microbial community structure and global trace gases, Global Change Biology, vol.62, issue.7, pp.745-758, 1998.
DOI : 10.1046/j.1365-2486.1998.00194.x

J. P. Schimel and M. N. Weintraub, The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model, Soil Biology and Biochemistry, vol.35, issue.4, pp.549-563, 2003.
DOI : 10.1016/S0038-0717(03)00015-4

R. L. Sinsabaugh, J. J. Shah, S. G. Findlay, K. A. Kuehn, and D. L. Moorhead, Scaling microbial biomass, metabolism and resource supply, Biogeochemistry, vol.46, issue.9, pp.175-190, 2015.
DOI : 10.3390/ijms14058841

J. C. Stegen, X. Lin, A. E. Konopka, and J. K. Fredrickson, Stochastic and deterministic assembly processes in subsurface microbial communities, The ISME Journal, vol.6, issue.9, pp.1653-1664, 2012.
DOI : 10.1371/journal.pone.0024570
URL : http://www.nature.com/ismej/journal/v6/n9/pdf/ismej201222a.pdf

J. Talbot, S. Allison, and K. Treseder, Decomposers in disguise: mycorrhizal fungi as regulators of soil C dynamics in ecosystems under global change, Functional Ecology, vol.86, issue.6, pp.955-963, 2008.
DOI : 10.1201/9781420027891.ch36

K. E. Todd-brown, F. M. Hopkins, S. N. Kivlin, J. M. Talbot, A. et al., A framework for representing microbial decomposition in coupled climate models, Biogeochemistry, vol.19, issue.12, pp.19-33, 2012.
DOI : 10.1029/2004GB002273

V. Torsvik and L. Øvreås, Microbial diversity and function in soil: from genes to ecosystems, Current Opinion in Microbiology, vol.5, issue.3, pp.240-245, 2002.
DOI : 10.1016/S1369-5274(02)00324-7

M. G. Van-der-heijden, R. D. Bardgett, N. M. Van-straalen, M. G. Heijden, J. N. Klironomos et al., The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity, Ecol. Lett. Nature, vol.11, issue.396, pp.69-72, 1038.

I. Verbaendert, S. Hoefman, P. Boeckx, N. Boon, D. Vos et al., genes of thermophilic Gram-positive denitrifiers, FEMS Microbiology Ecology, vol.89, issue.1, pp.162-180, 2014.
DOI : 10.1111/1574-6941.12346
URL : https://academic.oup.com/femsec/article-pdf/89/1/162/18104586/89-1-162.pdf

C. Wagg, S. F. Bender, F. Widmer, and M. G. Van-der-heijden, Soil biodiversity and soil community composition determine ecosystem multifunctionality, Proceedings of the National Academy of Sciences, vol.84, issue.4, pp.5266-5270, 2014.
DOI : 10.1890/0012-9658(2003)084[1539:TROPDA]2.0.CO;2
URL : http://www.pnas.org/content/111/14/5266.full.pdf

L. R. Walker and D. A. Wardle, Plant succession as an integrator of contrasting ecological time scales, Trends in Ecology & Evolution, vol.29, issue.9, 2014.
DOI : 10.1016/j.tree.2014.07.002

M. D. Wallenstein and E. K. Hall, A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning, Biogeochemistry, vol.61, issue.2, pp.35-47, 2012.
DOI : 10.2136/sssaj1997.03615995006100020015x

G. Wang, S. Jagadamma, M. A. Mayes, C. W. Schadt, J. M. Steinweg et al., Microbial dormancy improves development and experimental validation of ecosystem model, The ISME Journal, vol.2, issue.1, pp.226-237, 2015.
DOI : 10.1038/nclimate1331

W. R. Wieder, G. B. Bonan, A. , and S. D. , Global soil carbon projections are improved by modelling microbial processes, Nature Climate Change, vol.3, issue.10, pp.909-912, 2013.
DOI : 10.5194/gmd-5-1259-2012

©. Copyright, . Graham, . Knelman, . Schindlbacher, . Siciliano et al., This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited