Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
复制标题
DOI：
10.1016/j.cub.2015.01.014
复制
发表时间：
2015-03-16
期刊：
影响因子：
9.2
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
--
作者：
Castelle, Cindy J.;Wrighton, Kelly C.;Banfield, Jillian F.
背景：古细菌代表了地球生物多样性的重要组成部分，但对它们的了解仍然远不如细菌。基因调查、一些宏基因组研究和一些单细胞测序项目揭示了许多很少研究的古菌门。某些谱系出现很深的分支，可能是一个主要的辐射门的一部分。这种辐射的结构和生物体的生理仍然几乎unknown.Results：我们使用基因组分辨宏基因组分析，调查的多样性，基因组大小，代谢能力，和潜在的作用，在陆地地下的生物地球化学循环的dichroea。我们对来自邻近科罗拉多河（美国）含水层的复杂沉积物和浮游生物群落的DNA进行了测序，并使用不依赖于培养的方法重建了第一个完整的基因组。为了提供分类背景，我们分析了另外151个新采样的古细菌序列。我们解决了两个新的门内的一个主要的，显然是深分支组的门（超门）。的生物体有小的基因组，代谢预测表明，他们的主要贡献，地球的地球化学循环涉及碳和氢的代谢，可能与共生和/或发酵为基础的lifestyles.Conclusions：结果大大扩大了基因组采样的域degreea和澄清分类命名内的一个主要超门。这项研究结合最近发表的关于缺乏培养代表的细菌门的工作，揭示了一个令人着迷的现象，即基因组小、蛋白质组组成新颖、两个领域相互依赖性强的生物体的重大辐射。
Background: Archaea represent a significant fraction of Earth's biodiversity, yet they remain much less well understood than Bacteria. Gene surveys, a few metagenomic studies, and some single-cell sequencing projects have revealed numerous little-studied archaeal phyla. Certain lineages appear to branch deeply and may be part of a major phylum radiation. The structure of this radiation and the physiology of the organisms remain almost unknown.Results: We used genome-resolved metagenomic analyses to investigate the diversity, genomes sizes, metabolic capacities, and potential roles of Archaea in terrestrial subsurface biogeochemical cycles. We sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River (USA) and reconstructed the first complete genomes for Archaea using cultivation-independent methods. To provide taxonomic context, we analyzed an additional 151 newly sampled archaeal sequences. We resolved two new phyla within a major, apparently deep-branching group of phyla (a superphylum). The organisms have small genomes, and metabolic predictions indicate that their primary contributions to Earth's biogeochemical cycles involve carbon and hydrogen metabolism, probably associated with symbiotic and/or fermentation-based lifestyles.Conclusions: The results dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum. This study, in combination with recently published work on bacterial phyla lacking cultivated representatives, reveals a fascinating phenomenon of major radiations of organisms with small genomes, novel proteome composition, and strong interdependence in both domains.