The Rare Bacterial Biosphere, Annual Review of Marine Science, vol.4, issue.1, pp.449-466, 2012. ,
DOI : 10.1146/annurev-marine-120710-100948
Ecology and exploration of the rare biosphere, Nature Reviews Microbiology, vol.9, issue.4, pp.217-229, 2015. ,
DOI : 10.1038/ismej.2014.142
Microbial Ecology: Finding Structure in the Rare Biosphere, Current Biology, vol.24, issue.8, pp.315-317, 2014. ,
DOI : 10.1016/j.cub.2014.03.029
Patterns of Rare and Abundant Marine Microbial Eukaryotes, Current Biology, vol.24, issue.8, pp.813-821, 2014. ,
DOI : 10.1016/j.cub.2014.02.050
URL : https://hal.archives-ouvertes.fr/hal-01149637
Activity of abundant and rare bacteria in a coastal ocean, Proc. Natl. Acad. Sci. USA, pp.12776-12781, 2011. ,
DOI : 10.1093/nar/gkf450
Microbial diversity in the deep sea and the underexplored "rare biosphere", Proc. Natl. Acad. Sci. 103, pp.12115-12120, 2006. ,
DOI : 10.1093/bioinformatics/18.11.1546
Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters, Proc. Natl. Acad. Sci, pp.6004-6009, 2013. ,
DOI : 10.1093/nar/25.17.3389
URL : https://hal.archives-ouvertes.fr/hal-01354640
Ecology of the rare microbial biosphere of the Arctic Ocean, Proc. Natl. Acad. Sci. USA, pp.22427-22432, 2009. ,
DOI : 10.1371/journal.pbio.0060280
ABSTRACT, Applied and Environmental Microbiology, vol.83, issue.8, p.83, 2017. ,
DOI : 10.1128/AEM.03321-16
URL : https://hal.archives-ouvertes.fr/hal-01351448
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
Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands, The ISME Journal, vol.6, issue.7, pp.780-791, 2009. ,
DOI : 10.1007/BF00177045
Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study, Microbial Ecology, vol.72, issue.2, pp.248-265, 2017. ,
DOI : 10.1111/j.1574-6941.2010.00870.x
URL : https://hal.archives-ouvertes.fr/hal-01993653
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling, Current Biology, vol.25, issue.6, pp.690-701, 2015. ,
DOI : 10.1016/j.cub.2015.01.014
Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, vol.5, issue.7637, pp.353-358, 2017. ,
DOI : 10.3389/fmicb.2014.00354
Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses, The ISME Journal, vol.62, issue.3, pp.650-659, 2014. ,
DOI : 10.1093/bioinformatics/17.9.847
Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments, The ISME Journal, vol.65, issue.10, pp.1949-1965, 2012. ,
DOI : 10.1016/j.syapm.2010.08.001
Microbial Diversity and Biochemical Potential Encoded by Thermal Spring Metagenomes Derived from the Kamchatka Peninsula, Archaea, vol.63, issue.3, p.13, 2013. ,
DOI : 10.1016/j.mib.2011.04.007
in oxygen-depleted zones of two deep lakes, Environmental Microbiology Reports, vol.74, issue.2, pp.321-330, 2015. ,
DOI : 10.1128/MMBR.00034-09
URL : https://hal.archives-ouvertes.fr/hal-01354841
FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.5, issue.7, pp.2957-2963, 2011. ,
DOI : 10.1371/journal.pone.0011840
FROGS: Find, Rapidly, OTUs with Galaxy Solution, Bioinformatics, vol.73, issue.8, p.791, 2017. ,
DOI : 10.1093/bioinformatics/btx791
Table 2: Paired-end reads merging performance., PeerJ, vol.30, issue.5, p.2584, 2016. ,
DOI : 10.7717/peerj.2584/table-2
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing, Nature Methods, vol.7, issue.1, pp.57-59, 2013. ,
DOI : 10.1093/bioinformatics/btp636
URL : http://europepmc.org/articles/pmc3531572?pdf=render
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy, Applied and Environmental Microbiology, vol.73, issue.16, pp.5261-5267, 2007. ,
DOI : 10.1128/AEM.00062-07
BLAST+: architecture and applications, BMC Bioinformatics, vol.10, issue.1, p.421, 2009. ,
DOI : 10.1186/1471-2105-10-421
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-10-421?site=bmcbioinformatics.biomedcentral.com
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Research, vol.35, issue.21, pp.7188-7196, 2007. ,
DOI : 10.1093/nar/gkm864
URL : https://academic.oup.com/nar/article-pdf/35/21/7188/7041501/gkm864.pdf
ARB: a software environment for sequence data, Nucleic Acids Research, vol.32, issue.4, pp.1363-1371, 2004. ,
DOI : 10.1093/nar/gkh293
URL : https://academic.oup.com/nar/article-pdf/32/4/1363/6258500/gkh293.pdf
The SILVA and ???All-species Living Tree Project (LTP)??? taxonomic frameworks, Nucleic Acids Research, vol.6, issue.D1, pp.643-648, 2014. ,
DOI : 10.1093/nar/gkn879
URL : https://doi.org/10.1093/nar/gkt1209
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes, Bioinformatics, vol.1, issue.14, pp.1823-1829, 2012. ,
DOI : 10.1186/1748-7188-1-19
, Scientific REPORts |, vol.8, 2018.
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.57, issue.9, pp.1312-1313, 2014. ,
DOI : 10.1080/10635150802429642
Creating the CIPRES Science Gateway for inference of large phylogenetic trees, 2010 Gateway Computing Environments Workshop (GCE), pp.1-8, 2010. ,
DOI : 10.1109/GCE.2010.5676129
The growing tree of Archaea: new perspectives on their diversity, evolution and ecology, The ISME Journal, vol.12, issue.11, 2017. ,
DOI : 10.1038/nature21031
Predominant archaea in marine sediments degrade detrital proteins, Nature, vol.250, issue.7444, pp.215-218, 2013. ,
DOI : 10.1042/bj2500871
Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments, Nature Microbiology, vol.63, issue.6, p.16035, 2016. ,
DOI : 10.1371/journal.pone.0009490
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics, Science, vol.303, issue.2, pp.434-438, 2015. ,
DOI : 10.1006/jmbi.2000.4136
Methanogenesis and the Wood???Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association, Genome Biology and Evolution, vol.163, issue.6, pp.1706-1711, 2016. ,
DOI : 10.1128/JB.01424-07
Response of Archaeal Communities to Oil Spill in Bioturbated Mudflat Sediments, Microbial Ecology, vol.45, issue.13, pp.108-119, 2014. ,
DOI : 10.1021/es200649t
URL : https://hal.archives-ouvertes.fr/hal-01631847