Monotonic or unimodal diversity-productivity gradients: what does competition theory predict?, Ecology, vol.76, pp.2019-2027, 1995. ,
A trait-based approach for modelling microbial litter decomposition, Ecol. Lett, vol.15, pp.1058-1070, 2012. ,
Shifts between Nitrospira-and Nitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices, Environ. Microbiol, vol.12, pp.315-326, 2010. ,
Quantifying the evidence for biodiversity effects on ecosystem functioning and services, Ecol. Lett, vol.9, pp.1146-1156, 2006. ,
Exploration of community traits as ecological markers in microbial metagenomes, Mol. Ecol, vol.21, 1909. ,
PhenoLink-a web-tool for linking phenotype to ?omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains, BMC Genomics, vol.13, p.170, 2012. ,
ECOLOGY: From Individuals to Ecosystems, 2006. ,
Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM), Environ. Microbiol, vol.14, pp.2851-2869, 2012. ,
The contribution of species richness and composition to bacterial services, Nature, vol.436, pp.1157-1160, 2005. ,
Active microorganisms in soil: critical review of estimation criteria and approaches, Soil Biol. Biochem, vol.67, pp.192-211, 2013. ,
Microbial minorities modulate methane consumption through niche partitioning, ISME J, vol.7, pp.2214-2228, 2013. ,
Trait-based representation of biological nitrification: model development, testing, and predicted community composition, Front. Microbiol, vol.3, p.364, 2012. ,
Plant-driven variation in decomposition rates improves projections of global litter stock distribution, Biogeosciences, vol.9, pp.565-576, 2012. ,
Inclusion of facilitation into ecological theory, Trends Ecol. Evol, vol.18, pp.45-54, 2003. ,
Evolutionary history and the effect of biodiversity on plant productivity, Proc. Natl. Acad. Sci. U.S.A, vol.105, pp.17012-17017, 2008. ,
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample, Proc. Natl. Acad. Sci, vol.108, pp.4516-4522, 2011. ,
Biodiversity loss and its impact on humanity, Nature, vol.486, pp.59-67, 2012. ,
Prochlorococcus contributes to new production in the Sargasso Sea deep chlorophyll maximum, Geophys. Res. Lett, vol.34, p.10604, 2007. ,
Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands, Environ. Microbiol, vol.10, pp.2609-2622, 2008. ,
Effects of fungal inocula on the decomposition of lignin and structural polysaccharides in Pinus sylvestris litter, Biol. Fert. Soils, vol.33, pp.246-251, 2001. ,
Incorporating plant functional diversity effects in ecosystem service assessments, Proc. Natl. Acad. Sci. U.S.A, vol.104, pp.20684-20689, 2007. ,
Evidence for a threeway trade-off between nitrogen and phosphorus competitive abilities and cell size in phytoplankton, Ecology, vol.92, pp.2085-2095, 2011. ,
The deep, dark energy biosphere: intraterrestrial life on earth, Annu. Rev. Earth Planet. Sci, vol.40, pp.551-568, 2012. ,
Toward an ecological classification of soil bacteria, Ecology, vol.88, pp.1354-1364, 2007. ,
Functional and phylogenetic diversity as predictors of biodiversity-ecosystemfunction relationships, Ecology, vol.92, pp.1573-1581, 2011. ,
Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton, ISME J, vol.7, pp.137-147, 2013. ,
Analytical approaches to the characterization of samples of microbial communities using patterns of potential C source utilization, Soil Biol. Biochem, vol.28, pp.213-221, 1996. ,
Pole-to-pole biogeography of surface and deep marine bacterial communities, Proc. Natl. Acad. Sci. U.S.A, vol.109, pp.17633-17638, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-02531848
Microbial biogeography: from taxonomy to traits, Science, vol.320, pp.1039-1043, 2008. ,
The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil, Microb. Ecol, vol.47, pp.104-113, 2004. ,
Ecosystem response of pasture soil communities to fumigationinduced microbial diversity reductions: an examination of the biodiversityecosystem function relationship, Oikos, vol.90, pp.279-294, 2000. ,
URL : https://hal.archives-ouvertes.fr/hal-01862695
Evidence for the existence of three primary strategies in plants and its relevance to ecological and evolutionary theory, Am. Nat, vol.111, pp.1169-1194, 1977. ,
Advanced microscopy of microbial cells, Adv. Biochem. Eng. Biotechnol, vol.124, pp.21-54, 2011. ,
Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild, PLoS ONE, vol.7, p.51962, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-02644162
Competition for light causes plant biodiversity loss after eutrophication, Science, vol.324, pp.636-638, 2009. ,
A functional trait approach to fen restoration analysis, Appl. Veg. Sci, vol.16, pp.658-666, 2013. ,
Conceptualizing functional traits and ecological characteristics of methaneoxidizing bacteria as life strategies, Environ. Microbiol. Rep, vol.5, pp.335-345, 2013. ,
Microbial life under extreme energy limitation, Nat. Rev. Microbiol, vol.11, pp.83-94, 2013. ,
Effects of biodiversity on ecosystem functioning: a consensus of current knowledge, Ecol. Monogr, vol.75, pp.3-35, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00188090
Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function, Environ. Microbiol, vol.9, pp.1878-1889, 2007. ,
Microbial biogeography: putting microorganisms on the map, Nat. Rev. Microbiol, vol.4, pp.102-112, 2006. ,
Untangling genomes from metagenomes: revealing an uncultured class of marine euryarchaeota, Science, vol.335, pp.587-590, 2012. ,
A community-level concept of controls on decomposition processes: decomposition of barley straw by Phanerochaete chrysosporium or Phlebia radiata in pure or mixed culture, Soil Biol. Biochem, vol.27, pp.173-179, 1995. ,
Phenotypic and genotypic heterogeneity among closely related soilborne N 2? and N 2 O-producing Bacillus isolates harboring the nosZ gene, FEMS Microbiol. Ecol, vol.76, pp.541-552, 2011. ,
Dormancy contributes to the maintenance of microbial diversity, Proc. Natl. Acad. Sci. U.S.A, vol.107, pp.5881-5886, 2010. ,
Context dependent effects of ectomycorrhizal species richness on tree seedling productivity, Oikos, vol.93, pp.353-364, 2001. ,
Genotypic richness and dissimilarity opposingly affect ecosystem functioning, Ecol. Lett, vol.14, pp.537-545, 2011. ,
TRY-a global database of plant traits, Glob. Change Biol, vol.17, pp.2905-2935, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00639535
Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics, Proc. Natl. Acad. Sci. U.S.A, vol.105, pp.2504-2509, 2008. ,
Predicting changes in community composition and ecosystem functioning from plant traits: revisiting the Holy Grail, Funct. Ecol, vol.16, pp.545-556, 2002. ,
A novel framework for linking functional diversity of plants with other trophic levels for the quantification of ecosystem services, J. Veg. Sci, vol.24, pp.942-948, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02522208
Mapping the niche space of soil microorganisms using taxonomy and traits, Ecology, vol.93, pp.1867-1879, 2012. ,
Microbial seed banks: the ecological and evolutionary implications of dormancy, Nat. Rev. Microbiol, vol.119, pp.119-130, 2011. ,
Soil microbial diversity in grasslands and its importance for grassland functioning and services, Grassland Productivity and Ecosystem Services, pp.158-165, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01631829
Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands, PLoS ONE, vol.8, p.61069, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02522205
The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level, Ecol. Lett, vol.10, pp.1170-1181, 2007. ,
Biodiversity and ecosystem functioning: recent theoretical advances, Oikos, vol.91, pp.3-17, 2000. ,
Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species, Ecol. Lett, vol.11, pp.995-1003, 2008. ,
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw, Nature, vol.480, pp.368-371, 2011. ,
Phylogenetic conservatism of functional traits in microorganisms, ISME J, vol.7, pp.830-838, 2012. ,
High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use, ISME J, vol.6, pp.1210-1221, 2012. ,
Rebuilding community ecology from functional traits, Trends Ecol. Evol, vol.21, pp.178-185, 2006. ,
Global patterns in the biogeography of bacterial taxa, Environ. Microbiol, vol.13, pp.135-144, 2011. ,
A guide to the natural history of freshwater lake bacteria. Microbiol, Mol. Biol. Rev, vol.75, pp.14-49, 2011. ,
Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization, Proc. Natl. Acad. Sci. U.S.A, vol.5, pp.11376-11381, 2001. ,
Effects of grazing on microbial functional groups involved in soil N dynamics, Ecol. Monogr, vol.75, pp.65-80, 2005. ,
URL : https://hal.archives-ouvertes.fr/bioemco-00171793
Function-specific response to depletion of microbial diversity, ISME J, vol.5, pp.351-361, 2011. ,
Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree, Environ. Microbiol, vol.11, pp.3096-3104, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-02668737
Loss in microbial diversity affects nitrogen cycling in soil, ISME J, vol.7, pp.1609-1619, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-02651652
Horizontal gene transfer and the evolution of bacterial and archaeal population structure, Trends Genet, vol.29, pp.170-175, 2013. ,
Cell size distributions of soil bacterial and archaeal taxa, Appl. Environ. Microbiol, vol.79, pp.7610-7617, 2013. ,
The role of ecological theory in microbial ecology, Nat. Rev. Microbiol, vol.5, pp.384-392, 2007. ,
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data, Mol. Syst. Biol, vol.7, p.473, 2011. ,
Using plant functional traits to explain diversity-productivity relationships, PLoS ONE, vol.7, p.36760, 2012. ,
Characterization of Prochlorococcus clades from iron-depleted oceanic regions, Proc. Natl. Acad. Sci. U.S.A, vol.107, pp.16184-16189, 2010. ,
Relating phylogenetic and functional diversity among denitrifiers and quantifying their capacity to predict community functioning, Front. Microbiol, vol.3, p.209, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-02532817
Community niche predicts the functioning of denitrifying bacterial assemblages, Ecology, vol.90, pp.3324-3332, 2009. ,
URL : https://hal.archives-ouvertes.fr/halsde-00525103
Classification of bacteria and archaea: past, present and future, Syst. Appl. Microbiol, vol.32, pp.533-542, 2009. ,
The species richness productivity controversy, Trends Ecol. Evol, vol.17, pp.113-114, 2002. ,
Ecosystem effects of biodiversity manipulations in European grasslands, Ecol. Monogr, vol.75, pp.37-63, 2005. ,
The bacterial species dilemma and the genomic-phylogenetic species concept, Philos. Trans. R. Soc. Lond. B. Biol. Sci, vol.361, pp.1899-1909, 2006. ,
Single cell genomics: an individual look at microbes, Curr.Opin. Microbiol, vol.15, pp.613-620, 2012. ,
Interactive effects of drought and N fertilization on the spatial distribution of methane assimilation in grassland soils, Glob. Change Biol, vol.17, pp.1300-1302, 1997. ,
Prokaryotic diversity-Magnitude, dynamics, and controlling factors, Science, vol.296, pp.1064-1066, 2002. ,
Evolutionary trade-offs among decomposers determine responses to nitrogen enrichment, Ecol. Lett, vol.14, pp.933-938, 2011. ,
The power of species sorting: local factors drive bacterial community composition over a wide range of spatial scales, Proc. Natl. Acad. Sci. U.S.A, vol.104, pp.20404-20409, 2007. ,
Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity, Nature, vol.396, pp.69-72, 1998. ,
Let the concept of trait be functional! Oikos, vol.116, pp.882-892, 2007. ,
Quantitative phylogenetic assessment of microbial communities in diverse environments, Science, vol.315, pp.1126-1130, 2007. ,
A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning, Biogeochemistry, vol.109, pp.35-47, 2012. ,
Microbial metabolic exchange in 3D, ISME J, vol.7, pp.770-780, 2013. ,
Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils, Environ. Microbiol, vol.7, pp.676-684, 2005. ,
Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance, Environ. Microbiol, vol.9, pp.2211-2219, 2007. ,
URL : https://hal.archives-ouvertes.fr/halsde-00155947
Initial community evenness favours functionality under selective stress, Nature, vol.458, pp.623-626, 2009. ,
Functional redundancy supports biodiversity and ecosystem function in a closed and constant environment, Ecology, vol.85, pp.1534-1540, 2004. ,
Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla, Science, vol.337, pp.1661-1665, 2012. ,
Genetic diversity and disease control in rice, Nature, vol.406, pp.718-722, 2000. ,
, Conflict of Interest Statement: The authors declare that the research was con