Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage
Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage
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DOI：
10.1038/ismej.2015.158
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发表时间：
2016-04-01
期刊：
影响因子：
11
通讯作者：
Singer, Steven W.
中科院分区：
文献类型：
--
作者：
Hiras, Jennifer;Wu, Yu-Wei;Singer, Steven W.
最近的研究已经扩展了绿细菌门，表明绿色硫细菌（GSB），该门的原始培养代表，是更广泛谱系的一部分，其成员具有与拟杆菌门成员重叠的更多样化的代谢能力。未培养的克隆OPB 56的16 S rRNA基因是从黄石国家公园的黑曜石池中发现的，它与绿藻门和拟杆菌门有较远的亲缘关系;然而，OPB 56和相关克隆的详细发育和功能仍然未知。培养的嗜热菌财团从堆肥适应生长的离子液体预处理柳枝稷提供了一个财团，其中最丰富的成员之一，NICIL-2，与OPB 56相关的克隆集群。利用NICIL-2的全长16 S rRNA基因进行的系统发育分析表明，它是一个单系分支的一部分，称为OPB 56，与拟杆菌和绿杆菌不同。使用自动分箱算法从来自适于在离子液体预处理的柳枝稷上生长的培养物的宏基因组数据中回收接近完整的基因组草图（>95%完整），并且将该基因组用于基于标记基因的系统发育分析和代谢重建。从黄石国家公园和内华达州大沸泉的温泉中获得的宏基因组数据集重建了另外六个与NICIL-2相关的基因组。与16 S rRNA基因系统发育分析相反，蛋白质系统发育分析与Chlorobea，Ignavibacteria和OPB 56聚类成一个单一的门水平分支最一致。NICIL-2的代谢重建表现出与Ignavibacteria类和Rhodothermaceae家族（一种分支很深的拟杆菌属谱系）的密切联系。NICIL-2基因组的系统发育和功能分析的结合细化了门的成员Chlorobi，并强调门Chlorobi和拟杆菌之间的密切进化和代谢关系。
Recent studies have expanded the phylum Chlorobi, demonstrating that the green sulfur bacteria (GSB), the original cultured representatives of the phylum, are a part of a broader lineage whose members have more diverse metabolic capabilities that overlap with members of the phylum Bacteroidetes. The 16S rRNA gene of an uncultivated clone, OPB56, distantly related to the phyla Chlorobi and Bacteroidetes, was recovered from Obsidian Pool in Yellowstone National Park; however, the detailed phylogeny and function of OPB56 and related clones have remained unknown. Culturing of thermophilic bacterial consortia from compost by adaptation to grow on ionic-liquid pretreated switchgrass provided a consortium in which one of the most abundant members, NICIL-2, clustered with OPB56-related clones. Phylogenetic analysis using the full-length 16S rRNA gene from NICIL-2 demonstrated that it was part of a monophyletic clade, referred to as OPB56, distinct from the Bacteroidetes and Chlorobi. A near complete draft genome (>95% complete) was recovered from metagenomic data from the culture adapted to grow on ionic-liquid pretreated switchgrass using an automated binning algorithm, and this genome was used for marker gene-based phylogenetic analysis and metabolic reconstruction. Six additional genomes related to NICIL-2 were reconstructed from metagenomic data sets obtained from thermal springs at Yellowstone National Park and Nevada Great Boiling Spring. In contrast to the 16S rRNA gene phylogenetic analysis, protein phylogenetic analysis was most consistent with the clustering of the Chlorobea, Ignavibacteria and OPB56 into a single phylum level clade. Metabolic reconstruction of NICIL-2 demonstrated a close linkage with the class Ignavibacteria and the family Rhodothermaceae, a deeply branching Bacteroidetes lineage. The combined phylogenetic and functional analysis of the NICIL-2 genome has refined the membership in the phylum Chlorobi and emphasized the close evolutionary and metabolic relationship between the phyla Chlorobi and the Bacteroidetes.