P. Audet, B. D. Pinno, and E. Thiffault, Reclamation of boreal forest after oil sands mining: anticipating novel challenges in novel environments, Canadian Journal of Forest Research, vol.117, issue.3, pp.364-371, 2015.
DOI : 10.1890/070037

E. A. Johnson and K. Miyanishi, Creating New Landscapes and Ecosystems, Annals of the New York Academy of Sciences, vol.7, issue.1, pp.120-145, 2008.
DOI : 10.1111/j.1752-1688.1995.tb04026.x

A. Energy and R. , ST98: 2017, Alberta's Energy Reserves & Supply, 2017.

A. Energy, Alberta's Oil Sands Leased Area, 2017.

K. Prach and A. Tolvanen, How can we restore biodiversity and ecosystem services in mining and industrial sites?, Environmental Science and Pollution Research, vol.17, issue.14, pp.13587-13590, 2016.
DOI : 10.1017/CBO9780511612565

A. T. Lima, K. Mitchell, D. W. O-'connell, J. Verhoeven, and P. Van-cappellen, The legacy of surface mining: Remediation, restoration, reclamation and rehabilitation, Environmental Science & Policy, vol.66, 2016.
DOI : 10.1016/j.envsci.2016.07.011

A. Province, Conservation and Reclamation Regulation (Alberta Queen's Printer, 2016.

B. D. Pinno and R. C. Errington, Maximizing Natural Trembling Aspen Seedling Establishment on a Reclaimed Boreal Oil Sands Site, Ecological Restoration, vol.33, issue.1, pp.43-50, 2015.
DOI : 10.3368/er.33.1.43

URL : http://er.uwpress.org/content/33/1/43.full.pdf

S. Uroz, M. Buée, A. Deveau, S. Mieszkin, and F. Martin, Ecology of the forest microbiome: Highlights of temperate and boreal??ecosystems, Soil Biology and Biochemistry, vol.103, pp.471-488, 2016.
DOI : 10.1016/j.soilbio.2016.09.006

URL : https://hal.archives-ouvertes.fr/hal-01490075

S. E. Smith and D. Read, J. Mycorrhizal Symbiosis, 2008.

D. J. Read, J. R. Leake, and J. Perez-moreno, Mycorrhizal fungi as drivers of ecosystem processes in heathland and boreal forest biomes, Canadian Journal of Botany, vol.56, issue.8, pp.1243-1263, 2004.
DOI : 10.1007/s005720050299

R. L. Peterson, C. Wagg, and M. Pautler, Associations between microfungal endophytes and roots: do structural features indicate function?, Botany, vol.43, issue.5, pp.445-456, 2008.
DOI : 10.1139/cjm-47-8-741

T. R. Horton, E. Cázares, and T. D. Bruns, Ectomycorrhizal, vesicular-arbuscular and dark septate fungal colonization of bishop pine ( Pinus muricata ) seedlings in the first 5 months of growth after wildfire, Mycorrhiza, vol.8, issue.1, pp.11-18, 1998.
DOI : 10.1007/s005720050205

S. Uroz, P. Oger, E. Morin, and P. Frey-klett, ABSTRACT, Applied and Environmental Microbiology, vol.78, issue.8, pp.3020-3024, 2012.
DOI : 10.1128/AEM.06742-11

U. Vik, Different bacterial communities in ectomycorrhizae and surrounding soil, Scientific Reports, vol.29, issue.1, p.3471, 2013.
DOI : 10.1007/BF00044631

S. Marupakula, S. Mahmood, and R. D. Finlay, roots colonized by different ectomycorrhizal fungi, Environmental Microbiology, vol.43, issue.D1, pp.1470-1483, 2016.
DOI : 10.1016/j.soilbio.2010.12.009

M. G. Van-der-heijden, R. D. Bardgett, and N. M. Van-straalen, The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems, Ecology Letters, vol.80, issue.3, pp.296-310, 2008.
DOI : 10.1890/0012-9658(2000)081[1858:MIATRO]2.0.CO;2

S. M. Rowland, C. E. Prescott, S. J. Grayston, S. A. Quideau, and G. Bradfield, Recreating a Functioning Forest Soil in Reclaimed Oil Sands in Northern Alberta: An Approach for Measuring Success in Ecological Restoration, Journal of Environment Quality, vol.38, issue.4, pp.1580-1590, 2009.
DOI : 10.2134/jeq2008.0317

R. Mcmillan, S. A. Quideau, M. D. Mackenzie, and O. Biryukova, Nitrogen Mineralization and Microbial Activity in Oil Sands Reclaimed Boreal Forest Soils, Journal of Environment Quality, vol.36, issue.5, pp.1470-1478, 2007.
DOI : 10.2134/jeq2006.0530

P. A. Dimitriu, C. E. Prescott, S. A. Quideau, and S. J. Grayston, Impact of reclamation of surface-mined boreal forest soils on microbial community composition and function, Soil Biology and Biochemistry, vol.42, issue.12, pp.2289-2297, 2010.
DOI : 10.1016/j.soilbio.2010.09.001

M. D. Mackenzie and S. A. Quideau, Microbial community structure and nutrient availability in oil sands reclaimed boreal soils, Applied Soil Ecology, vol.44, issue.1, pp.32-41, 2010.
DOI : 10.1016/j.apsoil.2009.09.002

M. L. Béasse, S. A. Quideau, and S. W. Oh, Soil microbial communities identify organic amendments for use during oil sands reclamation, Ecological Engineering, vol.75, pp.199-207, 2015.
DOI : 10.1016/j.ecoleng.2014.11.042

B. Barnes, The Clonal Growth Habit of American Aspens, Ecology, vol.47, issue.3, pp.439-447, 1966.
DOI : 10.2307/1932983

D. A. Perala and A. A. Alm, Reproductive ecology of birch: A review, Forest Ecology and Management, vol.32, issue.1, pp.1-38, 1990.
DOI : 10.1016/0378-1127(90)90104-J

D. Ally, K. Ritland, and S. P. Otto, Molecular Ecology, vol.109, issue.22, pp.4897-4911, 2008.
DOI : 10.1093/oxfordjournals.molbev.a004186

R. S. Gardner, Clonal diversity of quaking aspen (Populus tremuloides): how multiple clones may add to the resilience and persistence of this forest type, 2013.

M. C. Namroud, A. Park, F. Tremblay, and . Bergeron, Clonal and spatial genetic structures of aspen

, Mol. Ecol, vol.14, pp.2969-2980, 2005.

K. E. Mock, C. A. Rowe, M. B. Hooten, J. Dewoody, and V. D. Hipkins, ), Molecular Ecology, vol.10, issue.22, pp.4827-4844, 2008.
DOI : 10.1648/0273-8570-71.2.187

D. E. Jelinski and W. M. Cheliak, GENETIC DIVERSITY AND SPATIAL SUBDIVISION OF POPULUS TREMULOIDES (SALICACEAE) IN A HETEROGENEOUS LANDSCAPE, American Journal of Botany, vol.13, issue.7, p.728, 1992.
DOI : 10.1139/g79-054

J. J. Worrall, Recent declines of Populus tremuloides in North America linked to climate, Forest Ecology and Management, vol.299, pp.35-51, 2013.
DOI : 10.1016/j.foreco.2012.12.033

D. Kulakowski, C. Matthews, D. Jarvis, and T. Veblen, ), Journal of Vegetation Science, vol.255, issue.1, pp.168-176, 2013.
DOI : 10.1111/j.1654-1103.2012.01437.x

K. D. Krasnow and S. L. Stephens, Evolving paradigms of aspen ecology and management: impacts of stand condition and fire severity on vegetation dynamics, Ecosphere, vol.6, issue.1, pp.1-16, 2015.
DOI : 10.1016/j.foreco.2010.05.020

P. A. Dimitriu and S. J. Grayston, Relationship Between Soil Properties and Patterns of Bacterial ??-diversity Across Reclaimed and Natural Boreal Forest Soils, Microbial Ecology, vol.66, issue.3, pp.563-573, 2010.
DOI : 10.1007/s00248-009-9590-0

M. D. Mackenzie and S. A. Quideau, Laboratory-based nitrogen mineralization and biogeochemistry of two soils used in oil sands reclamation. Can, J. Soil. Sci, vol.92, pp.131-142, 2012.

A. S. Hahn and S. A. Quideau, Long-term effects of organic amendments on the recovery of plant and soil microbial communities following disturbance in the Canadian boreal forest, Plant and Soil, vol.61, issue.1-2, pp.331-344, 2012.
DOI : 10.2136/sssaj1997.03615995006100020015x

D. L. Mummey, P. D. Stahl, and J. S. Buyer, Soil microbiological properties 20 years after surface mine reclamation: spatial analysis of reclaimed and undisturbed sites, Soil Biology and Biochemistry, vol.34, issue.11, pp.1717-1725, 2002.
DOI : 10.1016/S0038-0717(02)00158-X

J. Masse, C. E. Prescott, S. Renaut, Y. Terrat, and S. J. Grayston, Plant community and nitrogen deposition as drivers of ?-and ?-prokaryotic diversity in reconstructed oil-sands soils and natural boreal forest soils, Appl. Environ. Microb, vol.83, pp.3319-3335, 2017.

E. K. Mitter, J. R. De-freitas, and J. J. Germida, Bacterial Root Microbiome of Plants Growing in Oil Sands Reclamation Covers, Frontiers in Microbiology, vol.6, p.70, 2017.
DOI : 10.1128/mBio.02527-14

M. Hungria, P. Menna, J. R. Delamuta, and . Bradyrhizobium, the ancestor of all rhizobia: phylogeny of housekeeping and nitrogen-fixation genes in Biological nitrogen fixation, pp.191-202, 2015.

D. Vaninsberghe, K. R. Maas, and E. Cardenas, Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils, The ISME Journal, vol.63, issue.11, pp.2435-2441, 2015.
DOI : 10.1016/j.soilbio.2012.08.023

T. D. Bugg, M. Ahmad, E. M. Hardiman, and R. Rahmanpour, Pathways for degradation of lignin in bacteria and fungi, Natural Product Reports, vol.19, issue.12, pp.1883-1896, 2011.
DOI : 10.1016/j.cub.2008.12.031

H. Nacke, C. Fischer, A. Thürmer, P. Meinicke, and R. Daniel, Land Use Type Significantly Affects Microbial Gene Transcription in Soil, Microbial Ecology, vol.31, issue.4, pp.919-930, 2014.
DOI : 10.1021/ar9701777

N. R. Gottel, ABSTRACT, Applied and Environmental Microbiology, vol.77, issue.17, pp.5934-5944, 2011.
DOI : 10.1128/AEM.05255-11

S. L. Doty, Variable Nitrogen Fixation in Wild Populus, PLOS ONE, vol.356, issue.5, p.155979, 2016.
DOI : 10.1371/journal.pone.0155979.s002

S. D. Brown, Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoides, Journal of Bacteriology, vol.194, issue.9, pp.2383-2387, 2012.
DOI : 10.1128/JB.00198-12

A. Willems, The taxonomy of rhizobia: an overview, Plant and Soil, vol.56, issue.1-2, pp.3-14, 2006.
DOI : 10.1099/00207713-51-3-945

R. Rivas, A New Species of Devosia That Forms a Unique Nitrogen-Fixing Root-Nodule Symbiosis with the Aquatic Legume Neptunia natans (L.f.) Druce, Applied and Environmental Microbiology, vol.68, issue.11, pp.5217-5222, 2002.
DOI : 10.1128/AEM.68.11.5217-5222.2002

R. Rivas, Description of Devosia neptuniae sp. nov. that Nodulates and Fixes Nitrogen in Symbiosis with Neptunia natans, an Aquatic Legume from India, Systematic and Applied Microbiology, vol.26, issue.1, pp.47-53, 2003.
DOI : 10.1078/072320203322337308

, SCiENtiFiC RePoRTS |, vol.8, 2018.

R. C. Rooney, S. E. Bayley, and D. W. Schindler, Oil sands mining and reclamation cause massive loss of peatland and stored carbon, Proc. Natl. Acad. Sci. USA, pp.4933-4937, 2012.
DOI : 10.1016/j.foreco.2005.08.015

I. K. Kravchenko, A. K. Kizilova, S. A. Bykova, E. V. Men-'ko, and V. Gal-'chenko, Molecular analysis of high-affinity methane-oxidizing enrichment cultures isolated from a forest biocenosis and agrocenoses, Microbiology, vol.69, issue.9, pp.106-114, 2010.
DOI : 10.1016/S0168-6496(03)00205-8

F. Rodríguez and O. , Hydrocarbon-degrading potential of microbial communities from Arctic plants, Journal of Applied Microbiology, vol.7, issue.1, pp.71-83, 2013.
DOI : 10.1089/10665270050081478

X. Liu, Using community analysis to explore bacterial indicators for disease suppression of tobacco bacterial wilt, Scientific Reports, vol.73, issue.1, p.36773, 2016.
DOI : 10.1128/AEM.01996-06

B. D. Pinno, S. M. Landhäusser, P. S. Chow, S. A. Quideau, and M. D. Mackenzie, ) on reclamation soils, Canadian Journal of Forest Research, vol.11, issue.1, pp.1-7, 2014.
DOI : 10.4141/cjss2011-004

G. M. Jamro, S. X. Chang, and M. A. Naeth, Organic capping type affected nitrogen availability and associated enzyme activities in reconstructed oil sands soils in Alberta, Canada, Ecological Engineering, vol.73, pp.92-101, 2014.
DOI : 10.1016/j.ecoleng.2014.09.005

S. W. Simard, M. D. Jones, and D. M. Durall, Carbon and Nutrient Fluxes Within and Between Mycorrhizal Plants, pp.33-74, 2003.
DOI : 10.1007/978-3-540-38364-2_2

J. E. Hobbie and E. A. Hobbie, N IN SYMBIOTIC FUNGI AND PLANTS ESTIMATES NITROGEN AND CARBON FLUX RATES IN ARCTIC TUNDRA, Ecology, vol.87, issue.4, pp.816-822, 2006.
DOI : 10.1016/S0031-9422(02)00204-2

N. H. Nguyen and T. Bruns, The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses, Microbial Ecology, vol.75, issue.4, pp.914-921, 2015.
DOI : 10.1128/AEM.02110-08

R. M. Miller, B. A. Carnes, and T. B. Moorman, Factors Influencing Survival of Vesicular-Arbuscular Mycorrhiza Propagules During Topsoil Storage, The Journal of Applied Ecology, vol.22, issue.1, p.259, 1985.
DOI : 10.2307/2403343

J. A. Harris, P. Birch, and K. C. Short, Changes in the microbial community and physico-chemical characteristics of topsoils stockpiled during opencast mining. Soil Use Manag, pp.161-168, 1989.

M. Hartmann, Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests, The ISME Journal, vol.61, issue.12, pp.2199-2218, 2012.
DOI : 10.1046/j.1462-2920.2003.00451.x

URL : https://hal.archives-ouvertes.fr/hal-01546179

M. Hartmann, Resistance and resilience of the forest soil microbiome to logging-associated compaction, The ISME Journal, vol.61, issue.1, pp.226-244, 2014.
DOI : 10.1016/S0167-1987(99)00106-3

T. R. Horton and T. D. Bruns, Multiple-host fungi are the most frequent and abundant ectomycorrhizal types in a mixed stand of Douglas fir (Pseudotsuga menziesii) and bishop pine (Pinus muricata), New Phytologist, vol.139, issue.2, pp.331-339, 1998.
DOI : 10.1046/j.1469-8137.1998.00185.x

T. R. Horton and T. Bruns, The molecular revolution in ectomycorrhizal ecology: peeking into the black-box, Molecular Ecology, vol.144, issue.8, pp.1855-1871, 2001.
DOI : 10.1046/j.1469-8137.1999.00504.x

C. Phosri, Diversity and community composition of ectomycorrhizal fungi in a dry deciduous dipterocarp forest in Thailand, Biodiversity and Conservation, vol.6, issue.9, pp.2287-2298, 2012.
DOI : 10.3923/jbs.2006.1059.1064

E. A. Lilleskov and T. D. Bruns, via soil food webs, Mycologia, vol.97, issue.4, pp.762-769, 2005.
DOI : 10.2307/3807824

J. Gaster, J. Karst, and S. M. Landhäusser, The role of seedling nutrient status on development of ectomycorrhizal fungal communities in two soil types following surface mining disturbance, Pedobiologia, vol.58, issue.4, pp.129-135, 2015.
DOI : 10.1016/j.pedobi.2015.07.001

S. L. Hankin, J. Karst, and S. M. Landhäusser, Influence of tree species and salvaged soils on the recovery of ectomycorrhizal fungi in upland boreal forest restoration after surface mining, Botany, vol.75, issue.6, pp.267-277, 2015.
DOI : 10.1007/s00442-013-2713-9

G. Bois, Y. Piché, M. Fung, and D. Khasa, Mycorrhizal inoculum potentials of pure reclamation materials and revegetated tailing sands from the Canadian oil sand industry, Mycorrhiza, vol.74, issue.3, pp.149-158, 2005.
DOI : 10.2307/3792865

T. Vralstad, E. Myhre, and T. Schumacher, Molecular diversity and phylogenetic affinities of symbiotic root-associated ascomycetes of the Helotiales in burnt and metal polluted habitats, New Phytologist, vol.17, issue.1, pp.131-148, 2002.
DOI : 10.1007/s005720100110

M. Op-de-beeck, J. Ruytinx, and M. M. Smits, Belowground fungal communities in pioneer Scots pine stands growing on heavy metal polluted and non-polluted soils, Soil Biology and Biochemistry, vol.86, pp.58-66, 2015.
DOI : 10.1016/j.soilbio.2015.03.007

M. Likar and M. Regvar, Application of temporal temperature gradient gel electrophoresis for characterisation of fungal endophyte communities of Salix caprea L. in a heavy metal polluted soil, Science of The Total Environment, vol.407, issue.24, pp.6179-6187, 2009.
DOI : 10.1016/j.scitotenv.2009.08.045

H. Addy, M. Piercey, and R. Currah, Microfungal endophytes in roots, Canadian Journal of Botany, vol.78, issue.1, pp.1-13, 2005.
DOI : 10.1127/0029-5035/2004/0078-0475

O. 'hanlon and R. , Below-ground ectomycorrhizal communities: the effect of small scale spatial and short term temporal variation, Symbiosis, vol.57, pp.57-71, 2012.

G. Palfner, M. A. Casanova-katny, and D. J. Read, The mycorrhizal community in a forest chronosequence of Sitka spruce [Picea sitchensis (Bong.) Carr.] in Northern England, Mycorrhiza, vol.145, issue.1, pp.571-579, 2005.
DOI : 10.1046/j.1469-8137.2000.00605.x

B. Twieg, D. Durall, and S. Simard, Ectomycorrhizal fungal succession in mixed temperate forests, New Phytologist, vol.5, issue.2, pp.437-447, 2007.
DOI : 10.1111/j.1469-8137.1995.tb04309.x

URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02173.x/pdf

K. G. Peay, P. G. Kennedy, and T. D. Bruns, Rethinking ectomycorrhizal succession: are root density and hyphal exploration types drivers of spatial and temporal zonation?, Fungal Ecology, vol.4, issue.3, pp.233-240, 2011.
DOI : 10.1016/j.funeco.2010.09.010

E. Canada, Canadian climate normals, 1971.

R. C. Errington and B. D. Pinno, Early successional plant community dynamics on a reclaimed oil sands mine in comparison with natural boreal forest communities, ??coscience, vol.76, issue.2-4, pp.133-144, 2016.
DOI : 10.1007/978-0-387-87458-6

URL : http://www.energy.gov.ab.ca/LandAccess/pdfs/OSAagreeStats.pdf

, Soil Classification Working Group The Canadian System of Soil Classification, Research Branch Agriculture and Agri-Food Publication 1646, 1998.

J. A. Poland, P. J. Brown, M. E. Sorrells, and J. Jannink, Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach, PLoS ONE, vol.19, issue.2, p.32253, 2012.
DOI : 10.1371/journal.pone.0032253.s007

G. A. Tuskan, The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray), Science, vol.313, issue.5793, pp.1596-1604, 2006.
DOI : 10.1126/science.1128691

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.9, issue.11, pp.1754-1760, 2009.
DOI : 10.1186/1471-2105-9-128

H. Li, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.9, issue.11, pp.2078-2079, 2009.
DOI : 10.1146/annurev.genom.9.081307.164359

A. Rimmer, Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications, Nature Genetics, vol.46, issue.8, pp.912-918, 2014.
DOI : 10.1093/bioinformatics/btm091

URL : http://europepmc.org/articles/pmc4753679?pdf=render

T. Gosselin and L. Bernatchez, stackr: GBS/RAD Data Exploration, Manipulation and Visualization Using R. https, p.154432, 2016.

J. C. Gower, A General Coefficient of Similarity and Some of Its Properties, Biometrics, vol.27, issue.4, p.857, 1971.
DOI : 10.2307/2528823

A. Mastretta-yanes, assembly optimization for population genetic inference, Molecular Ecology Resources, vol.108, issue.1, pp.28-41, 2015.
DOI : 10.1038/hdy.2011.132

M. E. Dorken and C. G. Eckert, Severely reduced sexual reproduction in northern populations of a clonal plant, Decodonverticillatus (Lythraceae), Journal of Ecology, vol.85, issue.3, pp.339-350, 2001.
DOI : 10.2307/2960610

T. Jombart, adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics, vol.3, issue.11, pp.1403-1405, 2008.
DOI : 10.1093/oxfordjournals.jhered.a111573

URL : https://hal.archives-ouvertes.fr/hal-00428105

R. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2014.

M. Nei, Analysis of Gene Diversity in Subdivided Populations, Proc. Natl. Acad. Sci. USA, pp.3321-3323, 1973.
DOI : 10.1073/pnas.70.12.3321

URL : http://www.pnas.org/content/70/12/3321.full.pdf

J. Goudet, hierfstat, a package for r to compute and test hierarchical F-statistics, Molecular Ecology Notes, vol.52, issue.3, pp.184-186, 2005.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

K. Kennedy, M. W. Hall, M. D. Lynch, G. Moreno-hagelsieb, and J. Neufeld, ABSTRACT, Applied and Environmental Microbiology, vol.80, issue.18, pp.5717-5722, 2014.
DOI : 10.1128/AEM.01451-14

, SCiENtiFiC RePoRTS |, vol.8, 2018.

P. Schmidt, Illumina metabarcoding of a soil fungal community, Soil Biology and Biochemistry, vol.65, pp.128-132, 2013.
DOI : 10.1016/j.soilbio.2013.05.014

D. P. Herlemann, Transitions in bacterial communities along the 2000???km salinity gradient of the Baltic Sea, The ISME Journal, vol.60, issue.10, pp.1571-1579, 2011.
DOI : 10.3354/ame043233

H. Toju, A. S. Tanabe, S. Yamamoto, and H. Sato, High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples, PLoS ONE, vol.4, issue.7, p.40863, 2012.
DOI : 10.1371/journal.pone.0040863.t004

T. White, T. Bruns, S. Lee, and J. Taylor, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics in PCR protocols: a guide to methods and applications, pp.315-322, 1990.

R. C. Edgar and H. Flyvbjerg, Error filtering, pair assembly and error correction for next-generation sequencing reads, Bioinformatics, vol.3, issue.21, pp.3476-3482, 2015.
DOI : 10.1093/bioinformatics/btt593

R. C. Edgar, UPARSE: highly accurate OTU sequences from microbial amplicon reads, Nature Methods, vol.486, issue.10, pp.996-998, 2013.
DOI : 10.1093/nar/gkr1184

J. G. Caporaso, QIIME allows analysis of high-throughput community sequencing data, Nature Methods, vol.8, issue.5, pp.335-336, 2010.
DOI : 10.1038/nmeth.f.303

V. S. Pylro, L. Roesch, J. M. Ortega, and A. M. Do-amaral, Brazilian Microbiome Project: Revealing the Unexplored Microbial Diversity???Challenges and Prospects, Microbial Ecology, vol.12, issue.7, pp.237-241, 2014.
DOI : 10.1111/j.1462-2920.2010.02201.x

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-3066, 2002.
DOI : 10.1093/nar/gkf436

M. N. Price, P. S. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, p.9490, 2010.
DOI : 10.1371/journal.pone.0009490.s003

URL : http://doi.org/10.1371/journal.pone.0009490

U. Koljalg, Towards a unified paradigm for sequence-based identification of fungi, Molecular Ecology, vol.6, issue.21, pp.5271-5277, 2013.
DOI : 10.1016/j.funeco.2013.03.004

A. Chao, Nonparametric estimation of the number of classes in a population. Scand, J. Stat, vol.11, pp.265-270, 1984.

J. Pinheiro, D. Bates, S. Debroy, D. Sarkar, and . Team, nlme: Linear and Nonlinear Mixed Effects Models. R package 3, pp.1-131, 2017.

J. Oksanen, Community Ecology Package. CRAN.R-project.org, 2017.

D. H. Parks, G. W. Tyson, P. Hugenholtz, and R. G. Beiko, STAMP: statistical analysis of taxonomic and functional profiles, Bioinformatics, vol.5, issue.21, pp.3123-3124, 2014.
DOI : 10.1371/journal.pcbi.1000352

H. Wickham, Elegant Graphics for Data Analysis, 2009.

K. R. Clarke, R. N. Gorley, and . Primerv7, , 2015.

J. D. Storey, A direct approach to false discovery rates, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol.82, issue.3, pp.479-498, 2002.
DOI : 10.1016/S0378-3758(99)00041-5