• [1]
    Eurostat. (1998) EU pig herd by member state, 1989 to 1998. Available from:
  • [2]
    Statistical Reference Centre, Canada (2001) Pigs, provinces. Available from:
  • [3]
    NASS (National Agricultural Statistics Service) (2002) Monthly hogs and pigs. Available from:
  • [4]
    Bernet, N., Delgenès, J.P., Moletta, R. (2000) Lisier de porc: la solution biologique. Biofutur 197, 4245.
  • [5]
    Martinez, J., Bozec, G. le (2000) Pig manure and environmental concerns in Europe. Cahiers Agric. 9 (3), 181190.
  • [6]
    Burton, C.H. and Turner, C. (2003) Manure Management, Treatment Strategies for Sustainable Agriculture, 2nd edn., Silsoe Research Institute, Wrest Park, Silsoe, Bedford, UK
  • [7]
    Bourque, D., Bisaillon, J.G., Beaudet, R., Sylvestre, M., Ishaque, M., Morin, A. (1987) Microbial degradation of malodorous substances of swine waste under aerobic conditions. Appl. Environ. Microbiol. 53, 137141.
  • [8]
    Mackie, R.I., Stroot, P.J., Varel, V.H. (1998) Biochemical identification and biological origin of key odor components in livestock waste. J. Anim. Sci. 76, 13311342.
  • [9]
    Zhu, J. (2000) A review of microbiology in swine manure odour control. Agric. Ecosyst. Environ. 78, 93106.
  • [10]
    Cho, J.C., Kim, S.J. (2000) Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. Appl. Environ. Microbiol. 66, 956965.
  • [11]
    Krapac, I.G., Dey, W.S., Roy, W.R., Smyth, C.A., Storment, E., Sargent, S.L., Steele, J.D. (2002) Impacts of swine manure pits on groundwater quality. Environ. Pollut. 120 (2), 475492.
  • [12]
    Zhu, J., Jacobson, L.N. (1999) Correlating microbes to major odorous compounds in swine manure. Environ. Qual. 28, 737744.
  • [13]
    Zhang, R.H., Day, D.L. (1996) Anaerobic decomposition of swine manure and ammonia generation in a deep pit. Trans. ASAE 39, 18111815.
  • [14]
    Rivière, J., Subtil, J.C., Catroux, G. (1974) Etude de l’évolution physico-chimique et microbiologique du lisier de porcs pendant le stockage anaérobie. Ann. Agron. 25, 383401.
  • [15]
    Bernard, C.R., Heduit, M. Evolution du lisier de porcs au cours du stockage. J. Rech. Porcine Fr. 1979, 177–184.
  • [16]
    Bernard, C.R., Heduit, M. Evolution du lisier de porcs au cours du stockage. J. Rech. Porcine Fr. 1979, 177–184.
  • [17]
    Whitehead, T.R., Cotta, M.A. (1999) Phylogenetic diversity of methanogenic archaea in swine waste storage pit. FEMS Microbiol. Lett. 179, 223226.
  • [18]
    Whitehead, T.R., Cotta, M.A. (2001) Characterisation and comparison of microbial populations in swine manure faeces and manure storage pits by 16S rDNA gene sequence analysis. Anaerobe 7, 181187.
  • [19]
    Leung, K., Topp, E. (2001) Bacterial community in liquide swine manure during storage: molecular analysis using DGGE/PCR of 16S rDNA. FEMS Microbiol. Ecol. 38, 169177.
  • [20]
    Amann, R.I., Ludwig, W., Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143169.
  • [21]
    Godon, J.J., Zumstein, E., Dabert, P., Habouzit, F., Moletta, R. (1997) Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 63, 28022813.
  • [22]
    Leser, T.D., Amenuvor, J.Z., Jensen, T.K., Lindecrona, R.H., Boye, M., Moller, K. (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbol. 68, 673690.
  • [23]
    APHA AWWA WPCF (1985) Standard methods for the examination of water and wastewater, 16th edn. American Public Health Association, Washington, DC
  • [24]
    Percheron, G., Bernet, N., Moletta, R. (1996) A new method for the determination of dissolved sulphide in strongly coloured anaerobically treated effluents. Bioprocess Eng. 15, 317322.
  • [25]
    Brosius, J., Dull, T.J., Sleeter, D.D., Noller, H.F. (1981) Gene organisation and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148, 107127.
  • [26]
    Edgcomb, V.P., Kysela, D.T., Teske, A., Gomez, A.V., Sogin, M.L. (2002) Benthic eukariotic diversity in the Guaymas Basin hydrothermal vent environment. Proc. Natl. Acad. Sci. USA 99, 76587662.
  • [27]
    J. Sambrook E.F. Fritsch T. Maniatis Molecular Cloning: A Laboratory Manual 1989 Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York.
  • [28]
    Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., Chandra, S., McGarrell, D.M., Schmidt, T.M., Garrity, G.M., Tiedje, J.M. (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31 (1), 442443.
  • [29]
    Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H. Yadhukumar Buchner A., Lai, T., Steppi, S., Jobb, G., Förster, W., Brettske, I., Gerber, S., Ginhart, A.W., Gross, O., Grumann, S., Hermann, S., Jost, R., König, A., Liss, T., Lüßmann, R., May, M., Nonhoff, B., Reichel, B., Strehlow, R., Stamatakis, A., Stuckmann, N., Vilbig, A., Lenke, M., Ludwig, T., Bode, A., Schleifer, K.H. (2004) ARB: a software environment for sequence data. Nucleic Acids Res. 32 (4), 13631371.
  • [30]
    T.H. Jukes C.R. Cantor Evolution of Protein Molecules H.N. Munro Mammalian Protein Metabolism 1969 Academic Press New York 21 132.
  • [31]
    Saitou, N., Nei, M. (1987) The neighbor-joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4, 406425.
  • [32]
    L.L. Speece Anaerobic Biotechnology 1996 Archaea Press Tennessee.
  • [33]
    Parkin, G.E., Speece, R.E., Yang, C.H.J., Kocher, W.M. (1983) Reponse of methane fermentation systems to industrial toxicants. J. WPCF 55, 4453.
  • [34]
    Karhadkar, P.P., Audic, J.M., Faup, G.M., Khanna, P. (1987) Sulphide and sulphate inhibition of methanogenesis. Wat. Res. 21, 10611066.
  • [35]
    Clancy, P.B., Venkataraman, N., Lynd, L.R. (1992) Biochemical inhibition of sulfate reduction in batch and continuous anaerobic digesters. Wat. Sci. Tech. 25, 5160.
  • [36]
    Koster, I.W., Koomen, E. (1988) Ammonia inhibition of the maximum growth rate (μm) of hydrogenotrophic methanogens at various pH-levels and temperatures. Appl. Microbiol. Biotechnol. 28, 500505.
  • [37]
    Weismann, U. (1994) Biological nitrogen removal from wastewater. Adv. Biochem. Eng. Biotech. 51, 113153.
  • [38]
    Levasseur, P. (2002) Compositions chimiques détaillées des aliments et des lisiers de porc. Techn. Porc. 25 (1), 1925.
  • [39]
    Good, I.J. (1953) The populations frequencies of species and the estimations of populations parameters. Biometrika 40, 237264.
  • [40]
    Leclerc, M., Moletta, R., Godon, J.J. (2004) Diversity of the archaeal community in 44 digester as determined by SSCP analysis and 16S rDNA sequencing. Environ. Microbol. 6, 809819.
  • [41]
    Dojka, M.A., Hugenholtz, P., Haack, S.K., Pace, N.R. (2001) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64, 38693877.
  • [42]
    Tajima, K., Nagamine, T., Matsui, H., Nakamura, M., Aminov, R.I. (2001) Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with know methanogens. FEMS Micrbiol. Lett. 200, 6772.
  • [43]
    Friedrich, M.W., Schmitt-Wagner, D., Lueders, T., Brune, A. (2001) Axial differences in community structure of Crenanchaeota and Euryarchaeota in the highly compartmentalised gut of the soil-feeding termite Cubitermes orthognathus. Appl. Environ. Microbiol. 67, 48804890.
  • [44]
    Quilez, J., Clavel, A., Sanchez-Acedo, C., Causape, A.C. (1995) Detection of Blastocystis sp. in pigs in Aragon (Spain). Vet. Parasitol. 56, 345348.
  • [45]
    Abe, N., Nagoshi, M., Takami, K., Sawano, Y., Yoshikawa, H. (2002) A survey of Blastocystis sp. in livestock, pets, and zoo animals in Japan. Vet. Parasitol. 106, 203212.
  • [46]
    Haque, R., Ali, I.K.M., Clark, C.G. W.A. Petri Jr. (1998) A case report of Entamoeba moshkouskii infection in a Bangladeshi child. Parasitol. Int. 47, 201202.
  • [47]
    Pryde, S.E., Richardson, A.J., Stewart, C.S., Flint, H.J. (1999) Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Appl. Environ. Microbiol. 65, 53725377.
  • [48]
    Cotta, M.A., Whitehead, T.R., Zeltwanger, R.L. (2003) Isolation, characterisation and comparison of bacteria from swine faeces and manure storage pits. Environ. Microbiol. 5 (9), 737745.
  • [49]
    Robinson, J.A., Smolenski, W.J., Ogilvie, M.L., Peters, J.P. (1989) In vitro total gas, CH4, H2, volatile fatty acids and lactate kinetics studies on luminal contents from the small intestine, cecum and colon of the pig. Appl. Environ. Microbiol. 55, 24602467.
  • [50]
    Garcia, J.L., Patel, B.K.C., Ollivier, B. (2000) Taxonomic, phylogenetic, and ecological diversity of mathanogenic archaea. Anaerobe 6, 205226.
  • [51]
    Shinzato, N., Matsumoto, T., Yamaoka, I., Oshima, T., Yamagishi, A. (1999) Phylogenetic diversity of symbiotic methanogens living in the hindgut of the lower termite Reticulitermes speratus analyzed by PCR and in situ hybridization. Appl. Environ. Microbiol. 65, 837840.
  • [52]
    Hongoh, Y., Ohkuma, M., Kudo, T. Molecular analysis on bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera; Rhinotermitidae). FEMS Microbiol. Ecol. 2003, 231–242.
  • [53]
    Tajima, K., Aminov, R.I., Nagamine, T., Ogata, K., Nakamura, M., Matsui, H., Benno, Y. (1999) Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29, 159169.
  • [54]
    Munson, M.A., Nedwell, D.B., Embley, T.M. (1997) Phylogenic diversity of Archaea in sediments samples from a costal salt marsh. Appl. Environ. Microbiol. 63, 47294733.
  • [55]
    Todorov, J.R., Chistoserdov, A.Y., Aller, J.Y. (2000) Molecular analysis of microbial communities in mobile deltaic muds of Southeastern Papua New Guinea. FEMS Microbiol. Ecol. 33, 147155.
  • [56]
    Grady, C.P.L., Daigger, G.T., Lim, H.C. Anaerobic Processes Biological Wastewater Treatment 1999, Marcel Dekker, New York599–672.
  • [57]
    Cummings, J.H., Pomare, E.W., Branch, W.J., Naylor, C.P., Macfarlane, G.T. (1987) Short chain fatty acids in human large intestine, portal, hepatic, and venous blood. Gut 28, 12211227.
  • [58]
    Aguilar, B., Casas, C., Lema, J.M. (1995) Degradation of volatile fatty acids by differently enriched methanogenic cultures: kinetics and inhibition. Wat. Res. 29, 505509.
  • [59]
    Warikoo, V., McInerney, M.J., Robinson, J.A., Suflita, J.M. (1996) Interspecies acetate transfer influences the extent of anaerobic benzoate degradation by syntrophic consortia. Appl. Environ. Microbiol. 62, 2632.
  • [60]
    Jackson, B.E., McInerney, M.J. (2002) Anaerobic microbial metabolism can proceed close to thermodynamic limits. Nature 415, 454456.
  • [61]
    Collins, M.D., Lawson, P.A., Willems, A., Cordoba, J.J., Fernandez-Garayzabal, J., Garcia, P., Cai, J., Hippe, H., Farrow, J.A.E. (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44, 812826.