DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
Nature. 2013 Jul 25;499(7459):431-7. doi: 10.1038/nature12352. Epub 2013 Jul 14.
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
基因组测序通过为塑造生物圈的进化和功能多样性提供蓝图，增强了我们对生物世界的理解。然而，由于我们历史上无法在实验室中培养大多数微生物，目前可用的微生物基因组在系统发育上的广度有限。我们应用单细胞基因组学来靶向和测序来自 9 个不同生境的 201 个未培养古菌和细菌细胞，这些生境属于生命之树的 29 个主要未被发现的分支，即所谓的“微生物暗物质”。通过这些额外的基因组信息，我们能够解决许多门内和门间的关系，并提出两个新的超门。我们揭示了意想不到的代谢特征，扩展了我们对生物学的理解，并挑战了生命三个域之间的既定界限。其中包括一种新型的氨基酸用于opal 终止密码子，细菌中的古菌型嘌呤合成以及与细菌相似的古菌中的完整 sigma 因子。单细胞基因组还可以在某些生境中将高达 20%的宏基因组读数在系统发育上锚定，从而促进对生态系统功能的生物体水平解释。这项研究极大地扩展了生命之树的基因组代表性，并为更好地理解我们星球上的生物进化提供了一个系统的步骤。
