R. I. Amann, L. Krumholz, and D. A. Stahl, Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology, J. Bacteriol, vol.172, pp.762-770, 1990.

R. I. Amann, W. Ludwig, and K. H. Schleifer, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiological Rev, vol.59, pp.143-169, 1995.

. Anonyme, V08-056. Microbiologie alimentaire -Dénombrement des Clostridium perfringens par comptage des colonies à 37 degrés Celsius -Méthode de routine. 14 pages, 1999.

. Anonyme, XP X33-018. Caractérisation des boues -Dénombrement des Salmonella -Méthode de dénombrement en milieu liquide (méthode du Nombre le Plus Probable -NPP). 20 pages, 2004.

K. M. Arrus, R. A. Holley, K. H. Ominski, M. Tenuta, and G. Blank, Influence of temperature on Salmonella survival in hog manure slurry and seasonal temperature profiles in farm manure storage reservoirs, Livestock Science, vol.102, issue.3, pp.226-236, 2006.

P. A. Beloeil, P. Fravalo, C. Chauvin, C. Fablet, G. Salvat et al., Listeria spp. contamination in piggeries: comparison of three sites of environmental swabbing for detection and risk factor hypothesis. 1: Journal of Veterinay Medecine. B, Infectious Diseases and Veterinary Public Health, vol.50, pp.155-60, 2003.

J. G. Bisaillon, R. Beaudet, M. Sylvestre, M. Ishaque, A. Morin et al., Aspects microbiologiques du lisier de porc, Sciences et Techniques de l'Eau, vol.17, pp.397-400, 1984.

M. Bohnert, F. Dilasser, C. Dalet, J. Mengaud, and P. Cossart, Use of Specific Oligonucleotides for Direct Enumeration of Listeria monocytogenes in Food Samples by Colony Hybridization and Rapid Detection by PCR, Research in Microbiology, vol.143, pp.271-280, 1992.

F. J. Bornay-llinares, L. Navarro-i-martinez, F. Garcia-orenes, H. Araez, and M. D. Pérez-murcia, Detection of intestinal parasites in pig slurry : a preliminary study from five farms in spain", Livestock Sciences, vol.102, pp.237-242, 2006.

M. Chachkhiani, P. Dabert, T. Abzianidze, G. Partskhaladze, L. Tsiklauri et al., 16S rDNA characterisation of bacterial and archaeal communities during start-up of anaerobic thermophilic digestion of cattle manure, Bioresource Technol, vol.93, pp.227-232, 2004.

H. N. Chinivasagam, R. J. Thomas, K. Casey, E. Mcgahan, E. A. Gardner et al., Microbiological status of piggery effluent from 13 piggeries in the south east Queensland region of Australia, Journal of Applied Microbiology, vol.97, pp.883-891, 2004.

I. Corrégé, K. Proux, P. Fravalo, C. 1. Cornou, and J. Y. Flého, Les salmonelles en élevage porcin : caractérisation et rôle épidémiologique du statut des cochettes, Journées Rech. Porcine, vol.34, pp.309-315, 2002.

C. Coté, A. Villeneuve, L. Lessard, and S. Quessy, Fate of pathogenic and nonpathogenic microorganisms during storage of liquid hog manure in Quebec, Livestock Science, vol.102, issue.3, pp.204-225, 2006.

C. Côté, D. I. Massé, and S. Quessy, Reduction of indicator and pathogenic microorganisms by psychrophilic anaerobic digestion in swine slurries, Bioresource Technology, vol.97, issue.4, pp.686-691, 2006.

M. A. Cotta, T. R. Whitehead, and R. L. Zeltwanger, Isolation, characterisation and comparison of bacteria from swine faeces and manure storage pits, Environ. Microbiol, vol.5, issue.9, pp.737-782, 2003.

P. Dabert, J. Delgenès, R. Moletta, and J. Godon, Contribution of molecular microbiology to the study in water pollution removal of microbial community dynamics, Reviews in Environmental Science and Biotechnology, vol.1, pp.39-42, 2002.

C. Delbès, R. Moletta, and J. J. Godon, Bacterial and archaeal 16S rDNA and 16S rRNA dynamics during an acetate crisis in an anaerobic digestor ecosystem, FEMS Microbiology Ecology, vol.35, pp.19-26, 2001.

S. L. Dollhopf, S. A. Hashsham, and J. M. Tiedje, Interpreting 16S rDNA T-RFLP data: Application of self-organizing maps and principal components analysis to describe community dynamics and convergence, Microb Ecol, vol.42, pp.495-505, 2001.

J. Dunbar, L. O. Ticknor, and C. R. Kuske, Phylogenetic specificity 466 and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities, Appl Environ Microbiol, vol.67, pp.190-197, 2001.

C. Fablet, C. Robinault, J. P. Jolly, M. Collet, M. ,. Chemaly et al., , 2006.

, Salmonella Enterica level in French pig farms effluents: Experimental and field data Livestock Science, vol.102, pp.216-225

J. M. Farber and P. I. Peterkin, Listeria monocytogenes, a Food-Borne Pathogen, Microbiol. Reviews, vol.55, pp.476-511, 1991.

G. Peter, D. , H. Neil, C. Sagar, M. Johnston-lee et al., Persistence of zoonitic pathogens in surface soil treated with différent rates of liquid pig manure, Applied soil Ecology, vol.25, issue.3, pp.181-276, 2004.

J. J. Godon, E. Zumstein, P. Dabert, F. Habouzit, and R. Moletta, Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis, Applied and Environmental Microbiology, vol.63, issue.7, pp.2802-2815, 1997.

S. Grewal, S. Sreevatsan, and F. C. Michel, Persistence of Listeria and Salmonella during swine manure treatment, Compost Science and Utilization, vol.15, issue.1, pp.53-62, 2007.

G. Tiffany, T. Y. Richard, and A. Holley, Pathogen Survival in Swine Manure Environments and Transmission of Human Enteric Illness-A review." ; In Hog Manure Management and Human Health, pp.51-71, 2003.

H. G. Heilig, E. G. Zoetendal, E. E. Vaughan, P. Marteau, A. D. Akkermans et al., Molecular diversity of Lactobacillus spp and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA, Applied and Environmental Microbiology, vol.68, issue.1, pp.114-123, 2002.

V. R. Hill and M. D. Sobsey, Microbial indicator reductions in alternative treatment systems for awine wastewater, Water Science and Technology, vol.38, pp.119-122, 1998.

V. R. Hill and M. D. Sobsey, Performance of swine waste lagoons for removing Salmonella and enteric microbial indicators, Transactions of the Asae, vol.46, pp.781-788, 2003.

C. Hölzel and J. Bauer, Salmonella spp. in Bavarian liquid pig manure: Occurrence and relevance for the distribution of antibiotic resistance, Zoonoses and Public Health, vol.55, issue.3, pp.133-138, 2008.

M. L. Hutchison, L. D. Walters, M. A. Avery, and S. M. , Declines of zoonotic agents in liquid livestock wastes stored in batches on-farm, Journal of Applied Microbiology, vol.99, issue.1, pp.58-65, 2005.

M. L. Hutchison, L. D. Walters, S. M. Avery, and M. A. , Decline of zoonotic agents in livestock waste and bedding heaps, Journal of Applied Microbiology, vol.99, issue.2, pp.354-362, 2005.

M. L. Hutchison, L. D. Walters, S. M. Avery, B. A. Synge, and A. Moore, Levels of zoonotic agents in British livestock manures, Letters in Applied Microbiology, vol.39, issue.2, pp.207-214, 2004.

M. L. Hutchison, L. D. Walters, A. Moore, K. M. Crookes, and S. M. Avery, Effect of length of time before incorporation on survival of pathogenic bacteria present in livestock wastes applied to agricultural soil, Applied and Environmental Microbiology, vol.70, issue.9, pp.5111-5118, 2004.

P. Juteau, D. Tremblay, C. B. Ould-moulaye, and J. G. Bisaillon, Swine waste treatement by self heating aerobic thermophilic bioreactors, Water Research, vol.38, pp.539-546, 2004.

K. Leung and E. Topp, Bacterial community dynamics in liquid swine manure during storage: molecular analysis using DGGE/PCR of 16S rDNA, Fems Microbiol. Ecol, vol.38, pp.169-177, 2001.

L. Pascal, Mieux connaître les lisiers de porc. Compositions, volumes et analyses. Edité par l'Institut Technique du Porc, 1998.

P. Levasseur and N. Lemaire, Etat des lieux du traitement des lisiers de porcs en France, vol.26, pp.41-42, 2003.

P. Loisel, J. Harmand, O. Zemb, E. Latrille, C. Lobry et al., Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity, Environmental Microbiology, vol.8, issue.4, pp.720-751, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01000437

L. Loyon, F. Béline, F. Guiziou, and H. Boursier, Bilan environnemental des procédés de traitement biologique des lisiers de porcs, 2003.

C. Mannion, P. B. Lynch, J. Egan, and F. C. Leonard, Seasonal effects on the survival characteristics of Salmonella Typhimurium and Salmonella Derby in pig slurry during storage, Journal of Applied Microbiology, vol.103, issue.5, pp.1386-1392, 2007.

M. Gildas, , 2000.

, Déjection porcines et problème environnementaux en, Europe, vol.9, pp.181-190, 2000.

N. Fiona, A. Groves-simon, and J. , Pathogen survival during livestock manure storage and following land application, Chambers Brian J, 2005.

, Bioressource Technology, vol.96, pp.135-143

I. Placha, J. Venglovsky, N. Sasakova, and I. F. Svoboda, The effect of summer and winter seasons on the survival of Salmonella Typhimurium and indicator micro-organisms during the storage of solid fraction of pig slurry, J. of Appl. Microbiol, vol.91, issue.6, pp.1036-1043, 2001.

P. Payment and P. Hartemann, Les contaminants de l'eau et leurs effets sur la santé, Rev. des Sciences de l'Eau, vol.11, pp.199-210, 1998.

P. Peu, F. Beline, and J. Martinez, Volatile fatty acids analysis from pig slurry using highperformance liquid chromatography, Intern. J. Environ. Anal. Chem, vol.84, pp.1017-1022, 2004.

P. Peu, H. Brugere, A. M. Pourcher, M. Kerouredan, J. J. Godon et al., Dynamics of a pig slurry microbial community during anaerobic storage and management, Appl Environ Microbiol, vol.72, issue.5, pp.3578-85, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02588187

A. M. Pourcher, P. Morand, F. Picard-bonnaud, S. Billaudel, S. Montpoeho et al., Decrease of enteric micro-organisms from rural sewage sludge during their composting in mixture with straw, Journal of Applied Microbiology, vol.99, issue.3, pp.528-539, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00015499

A. M. Pourcher, F. Picard-bonnaud, V. Ferré, A. Gosinska, V. Stan et al., Survival of faecal indicators and enteroviruses in soil after land-spreading of municipal sewage sludge, Applied Soil Ecology, vol.35, pp.473-479, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02588424

E. W. Rice, K. R. Fox, R. J. Miltner, D. A. Lytle, and C. H. Johnson, Evaluating Plant Performance With Endospores, J. Amer. Water Works Ass, vol.88, pp.122-130, 1996.

A. Ramette, Multivariate analyses in microbial ecology, FEMS Microbiol Ecol, vol.62, pp.142-160, 2007.

B. Rufete, M. D. Perez-murcia, A. Perez-espinosa, R. Moral, J. Moreno-caselles et al., , 2006.

, Total and faecal coliform bacteria persistence in a pig slurry amended soil, Livestock Science, vol.102, issue.3, pp.211-215

R. Snell-castro, Caractérisation de la communauté microbienne de lisier et de fumiers de porcs par des méthodes moléculaires, vol.254, 2004.

R. Snell-castro, J. Delgenès, and J. Godon, Characterization of the microbial small rDNA diversity in pig manure storage pit, FEMS Microbiology Ecology, vol.52, pp.229-242, 2005.

G. Talbot, E. Topp, M. F. Palin, and D. I. Massé, Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors, Water Res, vol.42, pp.513-537, 2008.

G. A. Toranzos, G. A. Mcfeters, and J. J. Burrego, Detection of indicator microorganisms in environmental freshwaters and drinking waters, pp.184-194, 1997.

. C. Turner, 2202) The thermal inactivation of E. coli in straw and pig manure, Bioresource Technology, vol.84, issue.1, pp.57-61

M. I. Van-dyke and A. J. Mccarthy, Molecular biological detection and characterization of Clostridium populations in municipal landfill sites, Appl. Environ. Microbiol, vol.68, pp.2049-2053, 2002.

M. B. Vanotti, P. D. Millner, and P. G. Hunt, Removal of pathogen and indicator microoganisms from liquid swine manure in multi-step biological and chemical treatment, Bioresource Technology, vol.96, pp.209-214, 2005.

M. Watabe, J. R. Rao, T. A. Stewart, J. Xu, B. C. Millar et al., Prevalence of bacterial faecal pathogens in separated and unseparated stored pig slurry, Letters in Appl. Microbiol, vol.36, pp.208-212, 2003.

W. G. Weisburg, S. M. Barns, D. A. Pelletier, and D. J. Lane, 16s Ribosomal DNA Amplification for Phylogenetic Study, J. Bacteriol, vol.173, pp.697-703, 1991.

T. R. Whitehead and M. A. Cotta, Characterisation and comparison of microbial populations in swine faeces and manure storage pits by 16S rDNA gene sequence analyses, Anaerobe, vol.7, pp.181-187, 2001.

J. Wood, K. P. Scott, G. Avgustin, C. J. Newbold, and H. J. Flint, Estimation of the relative abundance of different Bacteroides and Prevotella ribotypes in gut samples by restriction enzyme profiling of PCR-amplified 16S rRNA gene sequences, Appl. Environ. Microbiol, vol.64, pp.3683-3689, 1998.

O. Zemb, B. Haegeman, J. P. Delgenes, P. Lebaron, and J. J. Godon, safum: statistical analysis of SSCP fingerprints using PCA projections, dendrograms and diversity estimators, Molecular Ecology Notes, vol.7, pp.717-898, 2007.

C. J. Ziemer, M. A. Cotta, and T. R. Whitehead, Application of group specific amplified rDNA restriction analysis to characterize swine fecal and manure storage pit samples, Anaerobe, vol.10, pp.217-227, 2004.

. Publications, . Rapports, . Aux, and . Effectues,

J. Martinez, P. Dabert, S. Barrington, M. L. Daumer, L. Loyon et al., Livestock waste treatment systems of the future: A challenge to environmental quality, food safety, and sustainability. Accepté, révisions mineures dans Bioresource Technology Béline, Water Science and Technology, vol.57, pp.1909-1914

P. Dabert, A. M. Pourcher, P. Peu, H. Brugère, and J. Godon, Évaluation de la survie de la flore fécale porcine au travers des filières de gestion des lisiers. accepté pour publication dans l'ouvrage Maladies émergentes

P. M. Fravalo and P. Dabert, Impact du traitement biologique du lisier de porcs sur les germes d'intérêt sanitaire : exemple de 17 élevages bretons. 5 et 6 février 2008. 40 èmes Journées de la Recherche Porcine Paris. Vol40, pp.19-24, 2008.

A. M. Pourcher, R. Marti, A. Thorigné, B. Jegou, and P. Dabert, effect of anaerobic storage and aerobic digestion on the micro-organisms of in pig manure: cultural and molecular approaches. xiii congrès international de l'international society for animal hygiene, pp.926-932, 2007.

F. Béline, M. L. Daumer, L. Loyon, A. M. Pourcher, P. Dabert et al., The efficiency of biological aerobic treatment of piggery wastewater to control nitrogen, phosphorus, pathogen and gas emissions, 8th Specialised Conference on Small Water and Wastewater Systems, vol.7, pp.6-9, 2008.

A. Dabert, P. Pourcher, A. M. Marti, R. Jégou, B. Thorigné et al., Analyse statistique de profils microbiens : Développement du logiciel SAFUS -Étude des filières de traitement biologique du lisier. Stage d'Ingénieur en Informatique (4ème année) de l'INSA de Rennes Cousin F. (2007) Suivi moléculaire des micro-organismes du lisier de porc au travers des filières de traitement, 1p. Mémoires de stages Bocquel M, 2007.

E. Besson, Développement d'un logiciel d'analyse des profils de communautés microbiennes obtenus par électrophorèse capillaire SSCP. Stage d'Ingénieur en Informatique (4ème année) de l'INSA de Rennes Thorigné, A. -2006. Impact sanitaire des traitements des lisiers de porcs : suivi des germes indicateurs de contamination fécale et de deux germes pathogènes, 2007.

B. L. Jégou, Etude de l'impact sanitaire des traitements biologiques des lisiers de porcs par des méthodes culturales et moléculaires, Master MUM, Agrocampus Rennes, vol.88, 2006.