Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla

Frontiers in Microbiology

Eric D. Becraft¹  Ramunas Stepanauskas¹  Nicole Poulton¹  Julia M. Brown¹  Joseph Brown¹  Jonathan A. Eisen²  M. C. Y. Lau³  Tullis Onstott³  Filipa Godoy-Vitorino⁴  Duane Moser⁵  Jessica Jarett⁶  Tanja Woyke⁶  Natalia Ivanova⁶ 

[1] Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States;College of Biological Sciences, Genome Center, University of California, Davis, Davis, CA, United States;Department of Geosciences, Princeton University, Princeton, NJ, United States;Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, Puerto Rico;Desert Research Institute, Las Vegas, NV, United States;Joint Genome Institute, Walnut Creek, CA, United States;

关键词: microbial ecology;    microbial evolution;    uncultivated bacteria;    microbial dark matter;    microbial genomics;   

DOI  :  10.3389/fmicb.2017.02264

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown