Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA.
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Appl Environ Microbiol. 2018 Apr 16;84(9). doi: 10.1128/AEM.02694-17. Print 2018 May 1.
Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, sp. strain Rt8.B8 (renamed here ), strain NA10 (renamed here ), and sp. strain Wai35.B1 (renamed here ), degraded Avicel and lignocellulose (switchgrass). was more efficient than in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity. Enrichments yielded genomic signatures closely related to that of , but there was also evidence for other thermophilic fermentative anaerobes (, , , and ). One enrichment, containing 89.8% and 9.7% , had a capacity for switchgrass solubilization comparable to that of These results refine the known biodiversity of and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes. The genus contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.
使用 Obsidian Pool（美国黄石国家公园）的宏基因组数据和 13 个基因组序列，重新评估了极度嗜热属的全属生物多样性。更新后的核心基因组包含 1401 个直系同源群（13 个物种的平均基因组大小=2516 个基因）。泛基因组仍然是开放的，共有 3493 个直系同源群，编码多种多结构域糖苷水解酶（GHs）。其中包括三个具有 GH48 结构域的纤维素酶，它们位于葡聚糖降解基因座（GDL）中，是微晶纤维素利用的特异性决定因素。最近测序的三个物种，命名为 sp. strain Rt8.B8（更名为）、strain NA10（更名为）和 sp. strain Wai35.B1（更名为），可降解纤维素和木质纤维素（柳枝稷）。在这方面，比其他 12 种被研究的物种更有效率，这不仅基于基因组的内容和组织，还基于保守 GH 的特定结构域特征。对 Obsidian Pool 中富含木质纤维素的样本进行宏基因组分析，揭示了属生物多样性的有限新信息。富集物产生的基因组特征与密切相关，但也有其他嗜热发酵厌氧菌（、、、和）的证据。一个含有 89.8%和 9.7%的富集物，具有与相当的柳枝稷溶解能力。这些结果细化了已知的生物多样性，并表明基于当前信息，在 70°C 以上温度下的微晶纤维素降解仅限于该属中产生含有 GH48 结构域的酶的某些成员。属包含最耐热的能够木质纤维素解构的细菌，它们是用于生产生物燃料和生物基化学品的综合生物加工的有前途的候选物。这里的重点是该属对植物生物质降解的现存能力，以及根据 13 个物种的分析和环境样本的宏基因组序列信息，从核心和泛基因组推断出这种能力的程度。微晶水解的关键是葡聚糖降解基因座（GDL）的含量，该基因座一组编码糖苷水解酶（GHs）的基因，其中几个具有 GH48 和家族 3 碳水化合物结合模块结构域，作为主要的纤维素酶。解决 GDL 与木质纤维素降解之间的关系将有助于努力识别该属中更丰产的成员，并开发代谢工程策略来改善这一特性。
