Insights into the phylogeny and coding potential of microbial dark matter

Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip and Woyke, Tanja (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499 7459: 431-437. doi:10.1038/nature12352


Author Rinke, Christian
Schwientek, Patrick
Sczyrba, Alexander
Ivanova, Natalia N.
Anderson, Iain J.
Cheng, Jan-Fang
Darling, Aaron
Malfatti, Stephanie
Swan, Brandon K.
Gies, Esther A.
Dodsworth, Jeremy A.
Hedlund, Brian P.
Tsiamis, George
Sievert, Stefan M.
Liu, Wen-Tso
Eisen, Jonathan A.
Hallam, Steven J.
Kyrpides, Nikos C.
Stepanauskas, Ramunas
Rubin, Edward M.
Hugenholtz, Philip
Woyke, Tanja
Title Insights into the phylogeny and coding potential of microbial dark matter
Journal name Nature   Check publisher's open access policy
ISSN 0028-0836
1476-4687
Publication date 2013-07-25
Year available 2013
Sub-type Article (original research)
DOI 10.1038/nature12352
Open Access Status Not yet assessed
Volume 499
Issue 7459
Start page 431
End page 437
Total pages 7
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Language eng
Subject 1000 General
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.
Formatted 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.
Keyword Lateral gene-transfer
Hydrothermal vent
Sp-nov
Diversity
Bacteria
Archaea
Division
Eukaryotes
Genome
Metagenomics
Species-nova
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID DE-AC02-05CH11231
031A190
EXO-NNX11AR78G
OISE 096842
DP120103498
Institutional Status UQ

 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 632 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 662 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Sun, 01 Sep 2013, 10:06:06 EST by System User on behalf of School of Chemistry & Molecular Biosciences