R. I. Adams, A. S. Amend, J. W. Taylor, and T. D. Bruns, A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: a Case Study of Fungi in Indoor Dust, Microbial Ecology, vol.14, issue.4, pp.735-741, 2013.
DOI : 10.1111/j.1600-0668.2004.00286.x

R. I. Adams, M. Miletto, J. W. Taylor, and T. D. Bruns, Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances, The ISME Journal, vol.15, issue.7, pp.1262-1273, 2013.
DOI : 10.1006/mcpr.2000.0324

S. M. Adl, A. G. Simpson, C. E. Lane, J. Luke?, D. Bass et al., The Revised Classification of Eukaryotes, Journal of Eukaryotic Microbiology, vol.56, issue.5, pp.429-93, 2012.
DOI : 10.1016/j.ympev.2010.04.020

R. Aurahs, M. Göker, G. W. Grimm, V. Hemleben, C. Hemleben et al., Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Lengthpolymorphic SSU rDNA Sequences, Bioinform. Biol. Insights, vol.3, pp.155-177, 2009.

W. H. Berger and F. L. Parker, Diversity of Planktonic Foraminifera in Deep-Sea Sediments, Science, vol.168, issue.3937, pp.1345-1347, 1970.
DOI : 10.1126/science.168.3937.1345

A. C. Boere, W. I. Rijpstra, G. J. De-lange, J. S. Sinninghe-damsté, and M. J. Coolen, Preservation potential of ancient plankton DNA in Pleistocene marine sediments, Geobiology, vol.172, issue.5, pp.377-393, 2011.
DOI : 10.1016/S0025-3227(00)00134-1

I. M. Bradley, A. J. Pinto, and J. S. Guest, ABSTRACT, Applied and Environmental Microbiology, vol.82, issue.19, pp.5878-5891, 2016.
DOI : 10.1128/AEM.01630-16

G. A. Brummer, C. Hemleben, M. , and S. , Planktonic foraminiferal ontogeny and new perspectives for micropalaeontology, Nature, vol.11, issue.6048, pp.50-52, 1986.
DOI : 10.1038/319050a0

E. Capo, D. Debroas, F. Arnaud, and I. Domaizon, Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity, Microbial Ecology, vol.39, issue.3, pp.865-875, 2015.
DOI : 10.1093/nar/gkr201
URL : https://hal.archives-ouvertes.fr/hal-01254671

M. T. Ceccherini, J. Ascher, A. Agnelli, F. Borgogni, O. L. Pantani et al., Experimental discrimination and molecular characterization of the extracellular soil DNA fraction, Antonie van Leeuwenhoek, vol.45, issue.4, pp.653-657, 2009.
DOI : 10.1007/s10482-009-9354-3

M. J. Coolen and J. Overmann, 217 000-year-old DNA sequences of green sulfur bacteria in Mediterranean sapropels and their implications for the reconstruction of the paleoenvironment, Environmental Microbiology, vol.62, issue.1, pp.238-249, 2007.
DOI : 10.1016/j.cub.2003.12.012

M. J. Coolen, J. P. Saenz, L. Giosan, N. Y. Trowbridge, P. Dimitrov et al., DNA and lipid molecular stratigraphic records of haptophyte succession in the Black Sea during the Holocene, Earth and Planetary Science Letters, vol.284, issue.3-4, pp.610-621, 2009.
DOI : 10.1016/j.epsl.2009.05.029

C. Corinaldesi, A. Dell-'anno, and R. Danovaro, Viral infection plays a key role in extracellular DNA dynamics in marine anoxic systems, Limnology and Oceanography, vol.52, issue.2, pp.508-516, 2007.
DOI : 10.4319/lo.2007.52.2.0508

C. Corinaldesi, M. Barucca, G. M. Luna, and A. Dell-'anno, Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments, Molecular Ecology, vol.230, issue.3, pp.642-54, 2011.
DOI : 10.3354/meps230011

C. Corinaldesi, M. Tangherlini, G. M. Luna, and A. D. Anno, Extracellular DNA can preserve the genetic signatures of present and past viral infection events in deep hypersaline anoxic basins, Proceedings of the Royal Society B: Biological Sciences, vol.36, issue.5577, pp.1-10, 2008.
DOI : 10.1016/j.soilbio.2004.02.004

A. Dell-'anno and R. Danovaro, Extracellular DNA Plays a Key Role in Deep-Sea Ecosystem Functioning, Science, vol.309, issue.5744, pp.2179-2179, 2005.
DOI : 10.1126/science.1117475

C. De-vargas, L. Zaninetti, H. Hilbrecht, and J. Pawlowski, Phylogeny and Rates of Molecular Evolution of Planktonic Foraminifera: SSU rDNA Sequences Compared to the Fossil Record, Journal of Molecular Evolution, vol.45, issue.3, pp.285-294, 1997.
DOI : 10.1007/PL00006232

C. De-vargas, S. Audic, N. Henry, J. Decelle, F. Mahe et al., Eukaryotic plankton diversity in the sunlit ocean, Eukaryotic plankton diversity in the sunlit ocean, pp.1261605-1261605, 2015.
DOI : 10.1111/j.1529-8817.2012.01150.x

A. Dutkiewicz, S. O-'callaghan, and R. D. Müller, Controls on the distribution of deep-sea sediments, Geochemistry, Geophysics, Geosystems, vol.40, issue.45, pp.3075-3098, 2016.
DOI : 10.1146/annurev-earth-042711-105521

P. Esling, F. Lejzerowicz, and J. Pawlowski, Accurate multiplexing and filtering for high-throughput amplicon-sequencing, Nucleic Acids Research, vol.43, issue.5, pp.2513-2524, 2015.
DOI : 10.1093/nar/gkv107
URL : https://hal.archives-ouvertes.fr/hal-01279130

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-225, 2010.
DOI : 10.1093/molbev/msp259
URL : https://hal.archives-ouvertes.fr/lirmm-00705187

L. Guillou, D. Bachar, S. Audic, D. Bass, C. Berney et al., The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy, pp.597-604, 1160.
DOI : 10.1093/nar/gks1160
URL : https://hal.archives-ouvertes.fr/hal-01253994

S. Guindon, J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

Ø. Hammer, D. A. Harper, R. , and P. D. , Paleontological statistics software package for education and data analysis, Palaeontol. Electron, vol.4, pp.9-18, 2001.

K. Katoh and D. M. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.30, issue.4, pp.772-780, 2013.
DOI : 10.1093/molbev/mst010
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603318

J. B. Kirkpatrick, E. A. Walsh, D. Hondt, and S. , Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales, Geology, vol.44, issue.8, pp.615-618, 2016.
DOI : 10.1130/G37933.1

M. Kucera, M. Weinelt, T. Kiefer, U. Pflaumann, A. Hayes et al., Reconstruction of sea-surface temperatures from assemblages of planktonic foraminifera: multi-technique approach based on geographically constrained calibration data sets and its application to glacial Atlantic and Pacific Oceans, Quaternary Science Reviews, vol.24, issue.7-9, pp.951-998, 2005.
DOI : 10.1016/j.quascirev.2004.07.014

B. Lecroq, F. Lejzerowicz, D. Bachar, R. Christen, P. Esling et al., Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments, Proceedings of the National Academy of Sciences, vol.22, issue.21, pp.13177-13182, 2011.
DOI : 10.1093/bioinformatics/btl446

F. Lejzerowicz, P. Esling, W. Majewski, W. Szczucinski, J. Decelle et al., Ancient DNA complements microfossil record in deep-sea subsurface sediments, Biology Letters, vol.104, issue.12, pp.20130283-20130283, 2013.
DOI : 10.1073/pnas.0700520104
URL : https://hal.archives-ouvertes.fr/hal-01258222

I. Letunic and P. Bork, Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Nucleic Acids Research, vol.39, issue.suppl, pp.475-478, 2011.
DOI : 10.1093/nar/gkr201

G. Lima-mendez, K. Faust, N. Henry, J. Decelle, S. Colin et al., Determinants of community structure in the global plankton interactome, and Raes, J.: Determinants of community structure in the global plankton interactome, pp.1262073-1262073, 2015.
DOI : 10.1103/PhysRevE.74.036104
URL : https://hal.archives-ouvertes.fr/hal-01234200

R. Morard, K. F. Darling, F. Mahé, S. Audic, Y. Ujiié et al., PFR 2 : a curated database of planktonic Foraminifera18S ribosomal DNA as a resource for studies of plankton ecology, biogeography, and evolution, Mol. Ecol. Resour, vol.49, pp.1-14, 2015.

R. Morard, Nomenclature for the Nameless: A Proposal for an Integrative Molecular Taxonomy of Cryptic Diversity Exemplified by Planktonic Foraminifera, Systematic Biology, vol.65, issue.5, pp.925-940, 2016.
DOI : 10.1093/sysbio/syw031
URL : https://hal.archives-ouvertes.fr/hal-01368819

J. N. Paulson, O. C. Stine, H. C. Bravo, and M. Pop, Differential abundance analysis for microbial marker-gene surveys, Nature Methods, vol.10, issue.12, pp.1200-1202, 2013.
DOI : 10.1186/1471-2105-12-449
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010126

S. B. Needleman and C. D. Wunsch, A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.48, issue.3, pp.443-453, 1970.
DOI : 10.1016/0022-2836(70)90057-4

J. Paw?owska, F. Lejzerowicz, P. Esling, W. Szczuci´nskiszczuci´nski, ?. Zaj et al., Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium, Geobiology, vol.31, issue.87, pp.277-88, 2014.
DOI : 10.2478/v10183-010-0010-4

J. Pawlowski and B. Lecroq, Short rDNA Barcodes for Species Identification in Foraminifera, Journal of Eukaryotic Microbiology, vol.57, issue.2, pp.197-205, 2010.
DOI : 10.1111/j.1550-7408.2009.00468.x

J. Pawlowski, S. Audic, S. Adl, D. Bass, L. Belbahri et al., CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms, CBOL Protist Working Group: Barcoding Eukaryotic richness beyond the Animal , Plant, and Fungal Kingdoms, p.1001419, 2012.
DOI : 10.1371/journal.pbio.1001419.s002
URL : https://hal.archives-ouvertes.fr/hal-01258240

J. Pawlowski, P. Esling, F. Lejzerowicz, T. Cedhagen, and T. A. Wilding, Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities, Molecular Ecology Resources, vol.30, issue.95, pp.1129-1140, 2014.
DOI : 10.1186/2047-217X-2-4

J. Pawlowski, F. Lejzerowicz, and P. Esling, Next-Generation Environmental Diversity Surveys of Foraminifera: Preparing the Future, The Biological Bulletin, vol.227, issue.2, pp.93-106, 2014.
DOI : 10.1086/BBLv227n2p93

J. N. Paulson, M. Pop, and H. C. Bravo, metagenomeSeq: Statistical analysis for sparse high-throughput sequencing, p.23, 2016.

M. W. Pedersen, A. Ginolhac, L. Orlando, J. Olsen, K. Andersen et al., A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa, Quaternary Science Reviews, vol.75, pp.161-168, 2013.
DOI : 10.1016/j.quascirev.2013.06.006

M. W. Pedersen, S. Overballe-petersen, L. Ermini, C. Sarkissian, . Der et al., Ancient and modern environmental DNA, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.5, issue.(Suppl. 2), pp.20130383-20130383, 2015.
DOI : 10.1126/science.1251156
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4275890

R. Development and C. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, p.23, 2014.

S. Rutherford, S. D-'hondt, and W. Prell, Environmental controls on the geographic distribution of zooplankton diversity, Nature, vol.400, issue.6746, pp.749-753, 1999.
DOI : 10.1038/23449

P. Taberlet, S. M. Prud-'homme, E. Campione, J. Roy, C. Miquel et al., Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies, Molecular Ecology, vol.3, issue.8, pp.1816-1820, 2012.
DOI : 10.1038/ismej.2009.20

A. Torti, M. A. Lever, and B. B. Jørgensen, Origin, dynamics, and implications of extracellular DNA pools in marine sediments, Marine Genomics, vol.24, pp.185-196, 2015.
DOI : 10.1016/j.margen.2015.08.007

A. A. Weber and J. Pawlowski, Can Abundance of Protists Be Inferred from Sequence Data: A Case Study of Foraminifera, PLoS ONE, vol.71, issue.12, pp.1-8, 2013.
DOI : 10.1371/journal.pone.0056739.s007

M. Yasuhara, D. P. Tittensor, H. Hillebrand, and B. Worm, Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model, Biological Reviews, vol.292, issue.89, pp.199-215, 2015.
DOI : 10.1126/science.1059412