Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing

Kroeber, Magdalena, Bekel, Thomas, Diaz, Naryttza N., Goesmann, Alexander, Jaenicke, Sebastian, Krause, Lutz, Miller, Dimitri, Runte, Kai J., Viehoever, Prisca, Puehler, Alfred and Schlueter, Andreas (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. Journal of Biotechnology, 142 1: 38-49. doi:10.1016/j.jbiotec.2009.02.010


Author Kroeber, Magdalena
Bekel, Thomas
Diaz, Naryttza N.
Goesmann, Alexander
Jaenicke, Sebastian
Krause, Lutz
Miller, Dimitri
Runte, Kai J.
Viehoever, Prisca
Puehler, Alfred
Schlueter, Andreas
Title Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing
Journal name Journal of Biotechnology   Check publisher's open access policy
ISSN 0168-1656
1873-4863
Publication date 2009-06-01
Sub-type Article (original research)
DOI 10.1016/j.jbiotec.2009.02.010
Open Access Status Not Open Access
Volume 142
Issue 1
Start page 38
End page 49
Total pages 12
Place of publication Amsterdam, Netherlands
Publisher Elsevier
Language eng
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 α-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.
Keyword 454-pyrosequencing
Biogas fermentation
Metagenome
Methane production
Methanogenesis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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