Biodegradation of isoprene in the terrestrial and marine environment. Bacteria

Although isoprene is emitted from the biosphere in amounts similar to methane, we know very little of its biodegradation. This project aims to investigate bacteria responsible for isoprene biodegradation using both cultivation-dependent and cultivation-independent methods. We are sequencing the genomes of isoprene-utilizing isolates and carrying out comparative genomics in order to advance our understanding of their physiology, biochemistry and molecular biology. In parallel, we are using cultivation-independent methods, including DNA-stable isotope probing (DNA-SIP), using labelled isoprene, to retrieve sequence data of active organisms that may be resistant to laboratory cultivation. Labelled DNA from DNA-SIP experiments is used for amplicon sequencing of 16S rRNA and metabolically functional genes, which provides phylogenetic information on active isoprene degraders. In addition, metagenome sequencing of labelled DNA and genome assembly and reconstruction allows us to identify novel genes or pathways used by isoprene degraders.

尽管异戊二烯（isoprene）从生物圈的释放量与甲烷（methane）相当，但我们对其生物降解过程的认知却极为匮乏。本项目拟通过依赖培养与非依赖培养两种研究手段，探究负责异戊二烯生物降解的细菌类群。我们将对利用异戊二烯的分离菌株进行基因组测序，并开展比较基因组学（comparative genomics）分析，以深化对其生理学、生物化学及分子生物学的理解。与此同时，我们将采用非依赖培养的方法，包括使用标记异戊二烯的DNA稳定同位素探针（DNA-stable isotope probing, DNA-SIP）技术，获取那些难以在实验室培养的活性生物的序列数据。DNA-SIP实验所得的标记DNA，将用于16S核糖体RNA（16S rRNA）及代谢功能基因的扩增子测序（amplicon sequencing），以此为活性异戊二烯降解菌提供系统发育信息。此外，对标记DNA进行宏基因组测序（metagenome sequencing）并开展基因组组装与重建，可帮助我们识别异戊二烯降解菌所使用的新型基因或代谢通路。