Insights into the phylogeny and coding potential of microbial dark matter

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…

• NS
  National Science Foundation

  Awards: 1232982, 1136727, DE-AC02-05CH11231, OCE-1136727, 1136488, 0452333
• UD
  U.S. Department of Energy

  Awards: -AC02-05CH11231, Contract No. DE-AC02-05CH11231, 05CH11231, No. DE-AC02-05CH11231, AC02-05CH11231, DE-AC02, DE-AC02-05CH11231, DE-AC02-
• NA
  National Aeronautics and Space Administration

  Awards: DE-AC02-05CH11231, NNX11AR78G, EXO-NNX11AR78G
• AP
  Alfred P. Sloan Foundation

  Award: DE-AC02-05CH11231
• WH
  Woods Hole Oceanographic Institution
• UO
  University of Nevada, Las Vegas
• CI
  Canadian Institute for Advanced Research
• TF
  Tula Foundation
• JG
  Joint Genome Institute

  Awards: DE-AC02-05CH11231, AC02-05CH11231
• BF
  Bundesministerium für Bildung und Forschung
• OO
  Office of Science

  Awards: AC02-05CH11231, -AC02-05CH11231, DE-AC02, No. DE-AC02-05CH11231, Contract No. DE-AC02-05CH11231
• NS
  Natural Sciences and Engineering Research Council of Canada

  Award: DE-AC02-05CH11231
• AR
  Australian Research Council

  Award: DP120103498
• BC
  British Columbia Knowledge Development Fund
• OO
  Office of International Science and Engineering