title: The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis.
abstract: OBJECTIVE
  To identify the bacterial and archaeal composition in a mesophilic biogas digester treating pig manure and to compare the consistency of two 16S rDNA-based methods to investigate the microbial structure.
  
  
  RESULTS
  Sixty-nine bacterial operational taxonomic units (OTU) and 25 archaeal OTU were identified by sequencing two 16S rDNA clone libraries. Most bacterial OTU were identified as phyla of Firmicutes (47.2% of total clones), Bacteroides (35.4%) and Spirochaetes (13.2%). Methanoculleus bourgensis (29.0%), Methanosarcina barkeri (27.4%) and Methanospirillum hungatei (10.8%) were the dominant methanogens. Only 9% of bacterial and 20% of archaeal OTU matched cultured isolates at a similarity index of >or=97%. About 78% of the dominant bacterial (with abundance >3%) and 83% of archaeal OTU were recovered from the denaturing gradient gel electrophoresis (DGGE) bands of V3 regions in 16S rDNAs.
  
  
  CONCLUSIONS
  In the digester, most bacterial and archaeal species were uncultured; bacteria belonging to Firmicutes, Bacteroides and Spirochaetes seem to take charge of cellulolysis, proteolysis, acidogenesis, sulfur-reducing and homoacetogenesis; the most methanogens were typical hydrogenotrophic or hydrogenotrophic/aceticlastic; DGGE profiles reflected the dominant microbiota.
  
  
  CONCLUSIONS
  This study gave a first insight of the overall microbial structure in a rural biogas digester and also indicated DGGE was useful in displaying its dominant microbiota.
authors.affiliation: Key Laboratory of Synthetic Biology, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: F H
authors.initials: FH
authors.lastname: Liu
authors.forename: S B
authors.initials: SB
authors.lastname: Wang
authors.forename: J S
authors.initials: JS
authors.lastname: Zhang
authors.forename: J
authors.initials: J
authors.lastname: Zhang
authors.forename: X
authors.initials: X
authors.lastname: Yan
authors.forename: H K
authors.initials: HK
authors.lastname: Zhou
authors.forename: G P
authors.initials: GP
authors.lastname: Zhao
authors.forename: Z H
authors.initials: ZH
authors.lastname: Zhou
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001673:Biodegradation, Environmental; D019149:Bioreactors; D004275:DNA, Ribosomal / Q000235:genetics*; D004586:Electrophoresis / Q000379:methods; D015723:Gene Library; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008372:Manure / Q000382:microbiology*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013552:Swine
chemical_list: D004275:DNA, Ribosomal; D008372:Manure; D012336:RNA, Ribosomal, 16S