Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.
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.
Kröber
Magdalena
M
Institut für Genomforschung und Systembiologie, Centrum für Biotechnology (CeBiTec), Universität Bielefeld, D-33615 Bielefeld, Germany.
Bekel
Thomas
T
Diaz
Naryttza N
NN
Goesmann
Alexander
A
Jaenicke
Sebastian
S
Krause
Lutz
L
Miller
Dimitri
D
Runte
Kai J
KJ
Viehöver
Prisca
P
Pühler
Alfred
A
Schlüter
Andreas
A
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
D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C021572:methyl coenzyme M reductase; D008697:Methane