title: Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis.
abstract: The microbial community structure of pig manure slurry (PMS) was determined with comparative analysis of 202 bacterial, 44 archaeal and 33 eukaryotic small subunit (SSU) rDNA partial sequences. Based on a criterion of 97% of sequence similarity, the phylogenetic analyses revealed a total of 108, eight and five phylotypes for the Bacteria, Archaea and Eukarya lineages, respectively. Only 36% of the bacterial phylotypes were closely related (>or=97% similarity) to any previously known sequence in databases. The bacterial groups most often represented in terms of phylotype and clone abundance were the Eubacterium (22% of total sequences), the Clostridium (15% of sequences), the Bacillus-Lactobacillus-Streptococcus subdivision (20% of sequences), theMycoplasma and relatives (10% of sequences) and the Flexibacter-Cytophaga-Bacteroides (20% of sequences). The global microbial community structure and phylotype diversity show a close relationship to the pig gastrointestinal tract ecosystem whereas phylotypes from the Acholeplasma-Anaeroplasma and the Clostridium purinolyticum groups appear to be better represented in manure. Archaeal diversity was dominated by three phylotypes clustering with a group of uncultured microorganisms of unknown activity and only distantly related to the Thermoplasmales and relatives. Other Archaea were methanogenic H2/CO2 utilisers. No known acetoclastic Archaea methanogen was found. Eukaryotic diversity was represented by a pluricellular nematode, two Alveolata, a Blastocystis and an Entamoebidae. Manure slurry physico-chemical characteristics were analysed. Possible inhibitory effects of acetate, sulphide and ammonia concentrations on the microbial anaerobic ecosystem are discussed.
authors.affiliation: Laboratoire de Biotechnologie de l'Environnement, Institut National de la Recherche Agronomique, Avenue des Etangs, 11100 Narbonne, France.
authors.forename: Raúl
authors.initials: R
authors.lastname: Snell-Castro
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Godon
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Delgenès
authors.forename: Patrick
authors.initials: P
authors.lastname: Dabert
mesh_terms: D000818:Animals; D001105:Archaea / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification*; D044822:Biodiversity; D004269:DNA, Bacterial / Q000032:analysis* / Q000235:genetics; D004275:DNA, Ribosomal / Q000032:analysis / Q000235:genetics*; D056890:Eukaryota / Q000235:genetics / Q000302:isolation & purification; D008372:Manure / Q000382:microbiology*; D017744:Medical Waste Disposal; D010802:Phylogeny; D013552:Swine / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D008372:Manure; D017744:Medical Waste Disposal