现有基因组序列只能让我们对微生物引人注目的多样性有一个很有限的认识，因为它们中绝大部分从未被培养出纯培养物。在这项研究中，Tanja Woyke及其同事利用单细胞基因组学方法来研究和测序来自九个多样化生境的201种未培养的古生菌和细菌细胞。该信息显示了无数的“门”内和“门”间关系以及若干出乎意料的代谢特征。在这些新数据的基础上，作者提出了对古生菌域和细菌域的分类修正，包括提议将古生菌重新归入三个“超级门”（superphyla）中。（生物谷 Bioon.com）
生物谷推荐的英文摘要
Nature doi:10.1038/nature12352
Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke, Patrick Schwientek, Alexander Sczyrba, Natalia N. Ivanova, Iain J. Anderson, Jan-Fang Cheng, Aaron Darling, Stephanie Malfatti, Brandon K. Swan, Esther A. Gies, Jeremy A. Dodsworth, Brian P. Hedlund, George Tsiamis, Stefan M. Sievert, Wen-Tso Liu, Jonathan A. Eisen, Steven J. Hallam, Nikos C. Kyrpides, Ramunas Stepanauskas, Edward M. Rubin, Philip Hugenholtz & Tanja Woyke
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.
