TY - JOUR
T1 - Rokubacteria
T2 - Genomic giants among the uncultured bacterial phyla
AU - Becraft, Eric D.
AU - Woyke, Tanja
AU - Jarett, Jessica
AU - Ivanova, Natalia
AU - Godoy-Vitorino, Filipa
AU - Poulton, Nicole
AU - Brown, Julia M.
AU - Brown, Joseph
AU - Lau, M. C.Y.
AU - Onstott, Tullis
AU - Eisen, Jonathan A.
AU - Moser, Duane
AU - Stepanauskas, Ramunas
N1 - Funding Information:
We thank the staff of the Bigelow Laboratory Single-Cell Genomics Center and the Joint Genome Institute for the generation of single-cell and metagenomic data. We are grateful to Olukayode Kuloyo, Borja Linage, Sarah Hendrickson, Cara Magnabosco, Melody Lindsay, Petra Diamonds and the management and staff for Finsch diamond mine, South Africa for their help obtaining the samples. We are also grateful to Laura Vann for her help obtaining Nevada field samples. Thanks also to Darrell Lacy, Levi Kryder, and John Klenke of the Nevada Nuclear Waste Repository Program Office (NWRPO) and the Nature Conservancy for access to and sampling assistance with well OV-2. We are grateful to Refuge Manager, Annji Bagozzi, and the U.S. Fish and Wildlife service for permitting and guidance related to the sampling of Crystal Spring at Ash Meadows National Wildlife Refuge. We are also grateful to Jaret Heise, Tom Regan, Kathy Hart, and many others at the Sanford Underground Research Facility for safe underground access and sampling assistance. Special thanks to Brittany Kruger, Joshua Sackett, and Scott Hamilton-Brehm of the Moser Lab for sample and metadata collection. This work was supported by the U.S. National Science Foundation grants DEB-1441717 and OCE-1335810. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
Publisher Copyright:
© 2017 Becraft, Woyke, Jarett, Ivanova, Godoy-Vitorino, Poulton, Brown, Brown, Lau, Onstott, Eisen, Moser and Stepanauskas.
PY - 2017/11/28
Y1 - 2017/11/28
N2 - Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.
AB - Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.
KW - Microbial dark matter
KW - Microbial ecology
KW - Microbial evolution
KW - Microbial genomics
KW - Uncultivated bacteria
UR - http://www.scopus.com/inward/record.url?scp=85035810369&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85035810369&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2017.02264
DO - 10.3389/fmicb.2017.02264
M3 - Article
C2 - 29234309
AN - SCOPUS:85035810369
SN - 1664-302X
VL - 8
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
IS - NOV
M1 - 2264
ER -