S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

R. I. Amann, B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux et al., Combination of 16S Ribosomal-RNA-Targeted oligonucleotide probes with flow-cytometry for analyzing mixed microbial-populations, 1990.

B. W. Bestwick, I. J. Robbins, and L. M. Warren, Metabolic adaptations of the intertidal polychaete Cirriformia tentaculata to life in an oxygen-sink environment, Journal of Experimental Marine Biology and Ecology, vol.125, issue.3, 1989.
DOI : 10.1016/0022-0981(89)90096-8

F. Calendini and J. Martin, PaupUP v1.0.3.1 A free graphical frontend for Paup* Dos software, 2005.

C. Cépède, Recherches sur les Infusoires astomes, Arch. Zool. Exp. et Gén, vol.3, pp.341-609, 1910.

F. Chevenet, C. Brun, A. L. Banuls, B. Jacq, and R. Christen, TreeDyn: towards dynamic graphics and annotations for analyses of trees, BMC Bioinformatics, vol.7, issue.1, p.439, 2006.
DOI : 10.1186/1471-2105-7-439
URL : https://hal.archives-ouvertes.fr/hal-00321061

P. Chomczynski and N. Sacchi, Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction, Analytical Biochemistry, vol.162, issue.1, pp.156-159, 1987.
DOI : 10.1016/0003-2697(87)90021-2

P. Chomczynski and N. Sacchi, The single-step method of RNA isolation by acid guanidinium thiocyanate???phenol???chloroform extraction: twenty-something years on, Nature Protocols, vol.22, issue.2, pp.581-585, 2006.
DOI : 10.1006/abio.1987.9999

J. O. Corliss, The Ciliated Protozoa: Characterization, classification, and guide to the Literature, 1979.

D. Puytorac and P. , Contribution à l'étude cytologique et taxonomique des infusoires astomes, Ann. Sci. Nat. Zool, pp.85-270, 1954.

D. Puytorac, P. Schrével, and J. , Nouvelles espèces de ciliés astomes endoparasites d'annélides polychètes, Annales de la faculté des sciences de Clermont-Ferrand, vol.26, pp.85-99, 1965.

D. Puytorac, P. Grolière, C. A. Grain, and J. , Nouveaux arguments (Hysterophrya gen. nov, Raabellocineta gen. nov.) en faveur de liaisons phylétiques possibles entre ciliés Astomotida et Scuticociliatida. C. R. Acad. Sci, 1979.

M. S. Ewing and K. M. Kocan, Invasion and development strategies of lchthyophthirius multifiliis, a parasitic ciliate of fish, Parasitology Today, vol.8, issue.6, pp.204-208, 1992.
DOI : 10.1016/0169-4758(92)90265-4

P. Fauvel, Polychètes sédentaires. In: Fédération française des sociétés, 1927.

S. I. Fokin, Bacterial Endocytobionts of Ciliophora and Their Interactions with the Host Cell, Int. Rev. Cytol, vol.236, pp.181-249, 2004.
DOI : 10.1016/S0074-7696(04)36005-5

F. Gao, X. P. Fan, Z. Z. Yi, M. Struder-kypke, and W. B. Song, Phylogenetic consideration of two scuticociliate genera, Philasterides and Boveria (Protozoa, Ciliophora) based on 18 S rRNA gene sequences, Parasitology International, vol.59, issue.4, pp.549-555, 2010.
DOI : 10.1016/j.parint.2010.07.002

R. J. Gast, R. W. Sanders, and D. A. Caron, Ecological strategies of protists and their symbiotic relationships with prokaryotic microbes, Trends in Microbiology, vol.17, issue.12, pp.563-569, 2009.
DOI : 10.1016/j.tim.2009.09.001

J. D. George, The Life History of the Cirratulid Worm, Cirriformia Tentaculata, on an Intertidal Mudflat, Journal of the Marine Biological Association of the United Kingdom, vol.27, issue.01, pp.47-65, 1964.
DOI : 10.1038/199195a0

H. Görtz, Intracellular bacteria in ciliates, Int. Microbiol, vol.4, pp.143-150, 2001.

S. Guindon, F. Lethiec, P. Duroux, and O. Gascuel, PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference, Nucleic Acids Research, vol.33, issue.Web Server, pp.557-559, 2005.
DOI : 10.1093/nar/gki352
URL : https://hal.archives-ouvertes.fr/lirmm-00105317

T. A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95, NT. Nucl. Acid. S, vol.98, issue.41, pp.95-98, 1999.

R. Hovasse, Endosymbiose bactérienne et astomie chez les ciliés, C. R, 1945.

R. Hovasse, Endosymbiose bactérienne chez divers ciliés parasites intestinaux, C. R. Acad. Sci, vol.223, pp.560-562, 1946.

J. P. Huelsenbeck and F. Ronquist, MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, vol.17, issue.8, pp.754-755, 2001.
DOI : 10.1093/bioinformatics/17.8.754

A. Kouris, S. K. Juniper, G. Frebourg, and F. Gaill, Protozoan?bacterial symbiosis in a deep-sea hydrothermal vent folliculinid ciliate (Folliculinopsis sp.) from the Juan de Fuca Ridge, Marine Ecology, vol.98, issue.1, pp.63-71, 2007.
DOI : 10.1111/j.1439-0485.2004.00020.x

M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. Mcgettigan et al., Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, issue.21, pp.2947-2948, 2007.
DOI : 10.1093/bioinformatics/btm404
URL : https://hal.archives-ouvertes.fr/hal-00206210

L. Léger and O. Duboscq, Notes sur les infusoires endoparasites, Arch. Zool, 1904.

D. H. Lynn, The Ciliated Protozoa: characterization, classification, and guide to the literature, p.605, 2008.
DOI : 10.1007/978-1-4020-8239-9

D. H. Lynn, D. M. Suriano, and M. Beverleyburton, Chatton-Lwoff silver impregnation: an improved technique for the study of oncomiracidia (Platyhelminthes: Monogenea) chaetotaxy, Systematic Parasitology, vol.47, issue.1, pp.21-23, 1981.
DOI : 10.1007/BF00012235

O. F. Müller, Zoologia Danica, sen Animalium Daniae et Norvegiae rarium ac minus notorum, 1788.