Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
PLoS One. 2011 Jan 26;6(1):e14519. doi: 10.1371/journal.pone.0014519.
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.
由于传统化石燃料的有限可用性，可再生资源的沼气生产作为替代能源正受到越来越多的关注。许多国家正在推广替代能源，以实现可持续的能源生产。在这项研究中，采用 Roche 的 GS FLX Titanium 技术对来自生产规模沼气发酵罐的宏基因组进行了分析，并与之前从同一社区 DNA 样本测序得到的数据集进行了比较，该样本之前是在 GS FLX 平台上进行测序的。基于 16S rRNA 特异性序列的分类学分析和使用 CARMA 的环境基因标签 (EGT) 分析表明，这两种方法都受益于 Titanium 平台获得的更长读长。结果证实梭菌是最普遍的分类类群，而产甲烷古菌中优势的是甲烷微菌目物种。然而，分析还确定了以前的研究中遗漏的其他分类群，包括链球菌属、醋菌属、Garciella 属、Tissierella 属和 Gelria 属的成员，它们也可能在导致甲烷形成的发酵过程中发挥作用。利用 CARMA 的功能将序列的分类信息与其分配的功能相关联，结果表明，厚壁菌门、拟杆菌门和变形菌门在多糖降解的功能背景下占主导地位，而甲烷微菌目代表了负责甲烷生产的最丰富的分类群。梭菌是参与还原辅酶 A 途径（Wood-Ljungdahl 途径）的最重要的类群，该途径是产乙酸作用的特征。根据分配给优势属 Methanoculleus 的 16S rRNA 特异性序列的分箱，表明该属由几个不同的种组成。对这些序列的系统发育分析将它们与氢营养型产甲烷菌 Methanoculleus bourgensis 放在了很近的位置。虽然稀疏分析仍表明覆盖不完全，但对 GS FLX Titanium 数据集的检查导致了更多属和功能元素的鉴定，为参与导致甲烷形成的厌氧发酵途径的群落提供了更完整的覆盖。
