U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


A New View of the Tree of Life
Published: April 11, 2016
Posted: November 01, 2016

Access to a wealth of environments and the ability to reconstruct genomes for previously unknown and uncultured lineages has greatly expanded understanding of the diversity of life on earth.

The Science
A comprehensive three domain tree of life was constructed from all lineages for which sequenced genomes are available. The tree highlights the diversity contained in candidate phyla: lineages with no cultivated representatives for which genome sequences are derived from environmental surveys.

The Impact
The tree of life is one of the most important organizing principles in biology. The new depiction will be useful not only to biologists who study microbial ecology, but also to biochemists searching for novel genes and researchers studying evolution and earth history. This updated view highlights the weight of diversity found within the bacteria and within lineages with no cultured representatives.

Summary
This tree presents a new view of the diversity of life from a genome perspective. Exploration of new environments and deeper sequencing of well-studied systems continue to uncover new organisms and lineages on the tree. To construct a comprehensive tree of life, researchers gathered 3,085 genomes representing all genera for which genomes are available and including over 1,000 newly reconstructed genomes targeting candidate phyla representatives. Sample sites for new genomes included extreme environments like Chile’s Atacama Desert salt flats and Yellowstone National Park hot springs, but also more common environments such as groundwater, estuarine sediment, meadow soil, and dolphin oral microbiomes. The tree inferred from this genomic perspective shows the predominance of bacterial diversity compared to the divergence seen in the Archaea and Eukarya.  Collapsing the tree based on sequence divergence rather than taxonomy highlighted the amount of diversity found within candidate phyla, emphasizing the importance of environmental surveys for discovery of organisms not tractable in laboratory experiments.

Contacts (BER PM)
Todd Anderson
Todd.Anderson@science.doe.gov

David Lesmes
David.Lesmes@science.doi.gov

(PI Contact)
Jillian Banfield
University of California Berkeley
jbanfield@berkeley.edu

Funding
This research was largely supported by Lawrence Berkeley National Laboratory’s (LBNL) Genomes to Watershed Scientific Focus Area funded by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research (BER) under contract DE-AC02-05CH11231. Additional support was provided by LBNL EFRC award DE-AC02-05CH11231; National Aeronautics and Space Administration NESSF grant 12 PLANET12R-0025 and National Science Foundation DEB grant 1406956; DOE BER grant DOE-SC10010566; Office of Naval Research grants N00014-07-1-0287, N00014-10-1-0233, and N00014-11-1-0918; and the Thomas C. and Joan M. Merigan Endowment at Stanford University. In addition, funding was provided by the Ministry of Economy, Trade, and Industry of Japan, and metagenome sequence was generated by DOE’s Joint Genome Institute via the Community Science Program.

Publication
Hug, L. A., B. J. Baker, K. Anantharaman, C. T. Brown, A. J. Probst, C. J. Castelle, C. N. Butterfield, A. W. Hernsdorf, Y. Amano, K. Ise, Y. Suzuki, N. Dudek, D. A. Relman, K. M. Finstad, R. Amundson, B. C. Thomas, and J. F. Banfield. 2016. “A New View of the Tree of Life,” Nature Microbiology 1(16048), DOI: 10.1038/nmicrobiol.2016.48. (Reference link)

Topic Areas:

  • Research Area: Subsurface Biogeochemical Research
  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: DOE Joint Genome Institute (JGI)

Division: SC-23.1 Climate and Environmental Sciences Division, BER

 

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