Skip to main content
Reports and publications: Publication

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.


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