Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities
Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities
复制标题
DOI：
10.1007/s12155-010-9089-z
复制
发表时间：
2010-06-01
影响因子：
3.6
通讯作者：
Hazen, Terry C.
中科院分区：
文献类型：
--
作者：
DeAngelis, Kristen M.;Gladden, John M.;Hazen, Terry C.
利用植物材料生产纤维素生物燃料已经重新开始，SSU rRNA基因扩增子焦解测序或系统发育微阵列分析表明，与它们起源的自然群落相比，适应群落显著简化。适应木质素和柳枝菊的联合体中的几个成员与以前被描述为生物质降解者的生物有关，而另一些成员则来自不太好描述的门。这些群落的复杂性的降低使它们成为元基因组测序的良好候选者，并可能使更多全长基因的重建成为可能，从而导致发现适应于原料和感兴趣的条件的新型木质纤维素降解酶。为了使这项技术在商业上具有大规模可行性，关键是要通过简化木质纤维生物质的分解和燃料生产来提高生产成本效益。许多自然生态系统有效地降解木质纤维生物质，并含有酶，一旦确定，可以用来提高商业生物质分解的效率。然而，最有可能产生相关酶的生态系统，如波多黎各的热带雨林土壤，往往过于复杂，无法使用当前的元基因组测序技术进行酶的发现。解决这一问题的一个潜在战略是在特定条件下有选择地在生物质上培养来自这些复杂生态系统的微生物群落，产生不那么复杂的生物质降解微生物种群。为了验证这一前提，我们在精确定义的条件下，从波多黎各土壤或绿色垃圾堆肥中培养微生物。或木质素分别作为唯一碳源。利用SSU rRNA基因扩增子焦磷酸测序或系统发育微阵列分析对两个适应于饲料的群落进行了系统发育分析，结果表明，与其衍生的自然群落相比，适应群落明显简化。适应木质素和柳枝菊的联合体中的几个成员与以前被描述为生物质降解者的生物有关，而另一些成员则来自不太好描述的门。这些群落复杂性的降低使它们成为元基因组测序的良好候选者，并可能使更多全长基因的重建成为可能，从而导致适应于原料和感兴趣的条件的新型木质纤维素降解酶的发现。
Producing cellulosic biofuels from plant material has recenSSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full-length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest.tly emerged as a key US Department of Energy goal. For this technology to be commercially viable on a large scale, it is critical to make production cost efficient by streamlining both the deconstruction of lignocellulosic biomass and fuel production. Many natural ecosystems efficiently degrade lignocellulosic biomass and harbor enzymes that, when identified, could be used to increase the efficiency of commercial biomass deconstruction. However, ecosystems most likely to yield relevant enzymes, such as tropical rain forest soil in Puerto Rico, are often too complex for enzyme discovery using current metagenomic sequencing technologies. One potential strategy to overcome this problem is to selectively cultivate the microbial communities from these complex ecosystems on biomass under defined conditions, generating less complex biomass-degrading microbial populations. To test this premise, we cultivated microbes from Puerto Rican soil or green waste compost under precisely defined conditions in the presence dried ground switchgrass (Panicum virgatum L.) or lignin, respectively, as the sole carbon source. Phylogenetic profiling of the two feedstock-adapted communities using SSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full-length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest.