Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla
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 l...
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doaj-d025116ed0cf4241a30d6c8b0d8ad7672020-11-24T20:46:04ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-11-01810.3389/fmicb.2017.02264302970Rokubacteria: Genomic Giants among the Uncultured Bacterial PhylaEric D. Becraft0Tanja Woyke1Jessica Jarett2Natalia Ivanova3Filipa Godoy-Vitorino4Nicole Poulton5Julia M. Brown6Joseph Brown7M. C. Y. Lau8Tullis Onstott9Jonathan A. Eisen10Duane Moser11Ramunas Stepanauskas12Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesJoint Genome Institute, Walnut Creek, CA, United StatesJoint Genome Institute, Walnut Creek, CA, United StatesJoint Genome Institute, Walnut Creek, CA, United StatesDepartment of Natural Sciences, Inter American University of Puerto Rico, San Juan, Puerto RicoBigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesBigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesBigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesDepartment of Geosciences, Princeton University, Princeton, NJ, United StatesDepartment of Geosciences, Princeton University, Princeton, NJ, United StatesCollege of Biological Sciences, Genome Center, University of California, Davis, Davis, CA, United StatesDesert Research Institute, Las Vegas, NV, United StatesBigelow Laboratory for Ocean Sciences, East Boothbay, ME, United StatesRecent 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.http://journal.frontiersin.org/article/10.3389/fmicb.2017.02264/fullmicrobial ecologymicrobial evolutionuncultivated bacteriamicrobial dark mattermicrobial genomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Eric D. Becraft Tanja Woyke Jessica Jarett Natalia Ivanova Filipa Godoy-Vitorino Nicole Poulton Julia M. Brown Joseph Brown M. C. Y. Lau Tullis Onstott Jonathan A. Eisen Duane Moser Ramunas Stepanauskas |
spellingShingle |
Eric D. Becraft Tanja Woyke Jessica Jarett Natalia Ivanova Filipa Godoy-Vitorino Nicole Poulton Julia M. Brown Joseph Brown M. C. Y. Lau Tullis Onstott Jonathan A. Eisen Duane Moser Ramunas Stepanauskas Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla Frontiers in Microbiology microbial ecology microbial evolution uncultivated bacteria microbial dark matter microbial genomics |
author_facet |
Eric D. Becraft Tanja Woyke Jessica Jarett Natalia Ivanova Filipa Godoy-Vitorino Nicole Poulton Julia M. Brown Joseph Brown M. C. Y. Lau Tullis Onstott Jonathan A. Eisen Duane Moser Ramunas Stepanauskas |
author_sort |
Eric D. Becraft |
title |
Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla |
title_short |
Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla |
title_full |
Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla |
title_fullStr |
Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla |
title_full_unstemmed |
Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla |
title_sort |
rokubacteria: genomic giants among the uncultured bacterial phyla |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2017-11-01 |
description |
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. |
topic |
microbial ecology microbial evolution uncultivated bacteria microbial dark matter microbial genomics |
url |
http://journal.frontiersin.org/article/10.3389/fmicb.2017.02264/full |
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