The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology
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DOI：
10.1016/j.jbiotec.2008.05.008
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发表时间：
2008-08-31
影响因子：
4.1
通讯作者：
Goesmann, Alexander
中科院分区：
文献类型：
--
作者：
Schlueter, Andreas;Bekel, Thomas;Goesmann, Alexander
应用超快454焦磷酸测序技术，采用元基因组学方法分析了以可再生初级产品为饲料的规模化沼气厂产气微生物群落的组成和基因含量。在Genome Sequencer FLX系统上对分离的总群落DNA进行测序，获得了616,072个阅读片段，平均阅读长度为230个碱基，占141,664,289个碱基的序列信息。将获得的单次读数分配给COG(蛋白质的同源基团簇)类别，揭示了厌氧微生物联盟进行发酵代谢途径的遗传特征。单个读数的组装导致形成大小超过500个碱基的8752个重叠群。长于10kb的重叠群主要编码看家蛋白，如DNA聚合酶、重组酶、DNA连接酶、Sigma因子RpoD以及糖和氨基酸代谢相关基因。很大一部分重叠群被分配给古产甲烷菌甲烷杆菌MarisnigrijR1的基因组序列。对马里斯尼格里分枝杆菌JR1基因组的单次阅读图谱显示，包括产甲烷基因区域在内的参考基因组中约有%的区域被深度覆盖。这些结果表明，在所分析的发酵样品中，与甲烷菌属相关的物种在产甲烷方面起着主导作用。此外，将大量的重叠群序列分配给包括纤维分解功能基因区域的梭状芽孢杆菌基因组，表明在所研究的沼气发酵装置中，梭状芽孢杆菌对纤维素植物生物量的水解是重要的。来自沼气厂发酵罐中产气微生物群落的元基因组序列数据为改进沼气生产的生物技术过程提供了合理的方法基础。(C)2008爱思唯尔B.V.保留所有权利。
Composition and gene content of a biogas-producing microbial community from a production-scale biogas plant fed with renewable primary products was analysed by means of a metagenomic approach applying the ultrafast 454-pyrosequencing technology. Sequencing of isolated total community DNA on a Genome Sequencer FLX System resulted in 616,072 reads with an average read length of 230 bases accounting for 141,664,289 bases sequence information. Assignment of obtained single reads to COG (Clusters of Orthologous Groups of proteins) categories revealed a genetic profile characteristic for an anaerobic microbial consortium conducting fermentative metabolic pathways. Assembly of single reads resulted in the formation of 8752 contigs larger than 500 bases in size. Contigs longer than 10 kb mainly encode house-keeping proteins, e.g. DNA polymerase, recombinase, DNA ligase, sigma factor RpoD and genes involved in sugar and amino acid metabolism. A significant portion of contigs was allocated to the genome sequence of the archaeal methanogen Methanoculleus marisnigrijR1. Mapping of single reads to the M. marisnigri JR1 genome revealed that approximately 64% of the reference genome including methanogenesis gene regions are deeply covered. These results suggest that species related to those of the genus Methanoculleus play a dominant role in methanogenesis in the analysed fermentation sample. Moreover, assignment of numerous contig sequences to clostridial genomes including gene regions for cellulolytic functions indicates that clostridia are important for hydrolysis of cellulosic plant biomass in the biogas fermenter under study. Metagenome sequence data from a biogas-producing microbial community residing in a fermenter of a biogas plant provide the basis for a rational approach to improve the biotechnological process of biogas production. (C) 2008 Elsevier B.V. All rights reserved.