title: Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.
abstract: The phylogenetic structure of the microbial community residing in a fermentation sample from a production-scale biogas plant fed with maize silage, green rye and liquid manure was analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. Sequencing of 109 clones from a bacterial and an archaeal 16S-rDNA amplicon library revealed that the obtained nucleotide sequences are similar but not identical to 16S-rDNA database sequences derived from different anaerobic environments including digestors and bioreactors. Most of the bacterial 16S-rDNA sequences could be assigned to the phylum Firmicutes with the most abundant class Clostridia and to the class Bacteroidetes, whereas most archaeal 16S-rDNA sequences cluster close to the methanogen Methanoculleus bourgensis. Further sequences of the archaeal library most probably represent so far non-characterised species within the genus Methanoculleus. A similar result derived from phylogenetic analysis of mcrA clone sequences. The mcrA gene product encodes the alpha-subunit of methyl-coenzyme-M reductase involved in the final step of methanogenesis. BLASTn analysis applying stringent settings resulted in assignment of 16S-rDNA metagenome sequence reads to 62 16S-rDNA amplicon sequences thus enabling frequency of abundance estimations for 16S-rDNA clone library sequences. Ribosomal Database Project (RDP) Classifier processing of metagenome 16S-rDNA reads revealed abundance of the phyla Firmicutes, Bacteroidetes and Euryarchaeota and the orders Clostridiales, Bacteroidales and Methanomicrobiales. Moreover, a large fraction of 16S-rDNA metagenome reads could not be assigned to lower taxonomic ranks, demonstrating that numerous microorganisms in the analysed fermentation sample of the biogas plant are still unclassified or unknown.
authors.affiliation: Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, D-33615 Bielefeld, Germany.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Kröber
authors.forename: Thomas
authors.initials: T
authors.lastname: Bekel
authors.forename: Naryttza N
authors.initials: NN
authors.lastname: Diaz
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Sebastian
authors.initials: S
authors.lastname: Jaenicke
authors.forename: Lutz
authors.initials: L
authors.lastname: Krause
authors.forename: Dimitri
authors.initials: D
authors.lastname: Miller
authors.forename: Kai J
authors.initials: KJ
authors.lastname: Runte
authors.forename: Prisca
authors.initials: P
authors.lastname: Viehöver
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlüter
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000378:metabolism; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001673:Biodegradation, Environmental; D018533:Biomass; D019149:Bioreactors; D004275:DNA, Ribosomal / Q000235:genetics*; D015723:Gene Library; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008697:Methane / Q000378:metabolism*; D019638:Methanomicrobiaceae / Q000235:genetics / Q000378:metabolism; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase; D008697:Methane