Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.
Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21297863/pdf/?tool=EBI |
| _version_ | 1818405246918983680 |
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| author | Sebastian Jaenicke Christina Ander Thomas Bekel Regina Bisdorf Marcus Dröge Karl-Heinz Gartemann Sebastian Jünemann Olaf Kaiser Lutz Krause Felix Tille Martha Zakrzewski Alfred Pühler Andreas Schlüter Alexander Goesmann |
| author_facet | Sebastian Jaenicke Christina Ander Thomas Bekel Regina Bisdorf Marcus Dröge Karl-Heinz Gartemann Sebastian Jünemann Olaf Kaiser Lutz Krause Felix Tille Martha Zakrzewski Alfred Pühler Andreas Schlüter Alexander Goesmann |
| author_sort | Sebastian Jaenicke |
| collection | DOAJ |
| description | Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation. |
| first_indexed | 2024-12-14T08:53:00Z |
| format | Article |
| id | doaj.art-42388a19288249b899da046596d37146 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T08:53:00Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-42388a19288249b899da046596d371462022-12-21T23:08:59ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-0161e1451910.1371/journal.pone.0014519Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.Sebastian JaenickeChristina AnderThomas BekelRegina BisdorfMarcus DrögeKarl-Heinz GartemannSebastian JünemannOlaf KaiserLutz KrauseFelix TilleMartha ZakrzewskiAlfred PühlerAndreas SchlüterAlexander GoesmannBiogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21297863/pdf/?tool=EBI |
| spellingShingle | Sebastian Jaenicke Christina Ander Thomas Bekel Regina Bisdorf Marcus Dröge Karl-Heinz Gartemann Sebastian Jünemann Olaf Kaiser Lutz Krause Felix Tille Martha Zakrzewski Alfred Pühler Andreas Schlüter Alexander Goesmann Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS ONE |
| title | Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. |
| title_full | Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. |
| title_fullStr | Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. |
| title_full_unstemmed | Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. |
| title_short | Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. |
| title_sort | comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454 pyrosequencing |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21297863/pdf/?tool=EBI |
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