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首页> 美国卫生研究院文献>PLoS Clinical Trials >Going Deeper: Metagenome of a Hadopelagic Microbial Community
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Going Deeper: Metagenome of a Hadopelagic Microbial Community

机译：深入探讨：航海微生物群落的基因组学

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摘要

The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above.
机译：远洋深海微生物组合的序列数据很少，严重限制了地球上最大生物群落的分子探索。在这项研究中，对波多黎各海沟（PRT）深度6,000 m的重生环境中的大规模454焦磷酸测序宏基因组数据集进行了分析。总共产生了145 Mbp的组装序列数据，并与来自Sargasso海的两个远洋深海元基因组和两个代表性地表海水数据集进行了比较。在许多情况下，所有三个深层元基因组都显示出相似的趋势，但在PRT中得到了最大的放大，包括功能丰富的两组分信号转导机制和转录调控。 PRT元基因组中转运蛋白的代表性过高包括外膜孔蛋白，各种阳离子转运蛋白以及二羧酸和三羧酸盐转运蛋白，它们与普遍的分解代谢过程（例如丁酸，乙醛酸和二羧酸代谢）非常匹配。在PRT中还存在出乎意料的高含量的硫酸酯酶降解硫酸化多糖的现象。 PRT微生物最显着的适应性特征似乎是对重金属的抵抗力，这反映在目前存在的大量转运蛋白中，这些转运蛋白可以将其去除。作为元基因组方法的补充，单细胞基因组技术被用来从PRT，丙型杆菌，丙型细菌，拟杆菌和扁平菌中的优势门成员的四个未培养细胞生成部分全基因组序列数据。单细胞序列数据为从PRT元基因组中鉴定的许多高度丰富的功能属性提供了基因组背景，并且与172个可用参考海洋基因组相比，大量招募了PRT元基因组序列数据。通过这些多层面的序列方法，已经提供了新的见解，使人们能够了解存在于海洋深层的微生物中的独特功能属性，这些微生物远离上面生产力更高的阳光直射区域。

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