title: Insights into the phylogeny and coding potential of microbial dark matter.
abstract: 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.
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Christian
authors.initials: C
authors.lastname: Rinke
authors.forename: Patrick
authors.initials: P
authors.lastname: Schwientek
authors.forename: Alexander
authors.initials: A
authors.lastname: Sczyrba
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.forename: Iain J
authors.initials: IJ
authors.lastname: Anderson
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.forename: Aaron
authors.initials: A
authors.lastname: Darling
authors.forename: Stephanie
authors.initials: S
authors.lastname: Malfatti
authors.forename: Brandon K
authors.initials: BK
authors.lastname: Swan
authors.forename: Esther A
authors.initials: EA
authors.lastname: Gies
authors.forename: Jeremy A
authors.initials: JA
authors.lastname: Dodsworth
authors.forename: Brian P
authors.initials: BP
authors.lastname: Hedlund
authors.forename: George
authors.initials: G
authors.lastname: Tsiamis
authors.forename: Stefan M
authors.initials: SM
authors.lastname: Sievert
authors.forename: Wen-Tso
authors.initials: WT
authors.lastname: Liu
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.forename: Ramunas
authors.initials: R
authors.lastname: Stepanauskas
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D001419:Bacteria / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D017753:Ecosystem; D020745:Genome, Archaeal / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis