Unusual biology across a group comprising more than 15% of domain Bacteria

Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C.; Sharon, Itai; Castelle, Cindy J.; Singh, Andrea; Wilkins, Michael J.; Wrighton, Kelly C.; Williams, Kenneth H.; Banfield, Jillian F.

doi:10.1038/nature14486

Unusual biology across a group comprising more than 15% of domain Bacteria

Journal Article · Mon Jun 15 00:00:00 EDT 2015 · Nature (London)

DOI:https://doi.org/10.1038/nature14486· OSTI ID:1512215

Brown, Christopher T. ^[1]; Hug, Laura A. ^[1]; Thomas, Brian C. ^[1]; Sharon, Itai ^[1]; Castelle, Cindy J. ^[1]; Singh, Andrea ^[1]; Wilkins, Michael J. ^[2]; Wrighton, Kelly C. ^[2]; Williams, Kenneth H. ^[3]; Banfield, Jillian F. ^[4]

Univ. of California, Berkeley, CA (United States)
The Ohio State Univ., Columbus, OH (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

All rights reserved. A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1512215

Journal Information:: Nature (London), Journal Name: Nature (London) Journal Issue: 7559 Vol. 523; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Small genomes and the difficulty to define minimal translation and metabolic machineries Gil, Rosario; Peretó, Juli Frontiers in Ecology and Evolution, Vol. 3 https://doi.org/10.3389/fevo.2015.00123	journal	October 2015
Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths Ben Maamar, Sarah; Aquilina, Luc; Quaiser, Achim Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01457	journal	December 2015
Protist-Bacteria Associations: Gammaproteobacteria and Alphaproteobacteria Are Prevalent as Digestion-Resistant Bacteria in Ciliated Protozoa Gong, Jun; Qing, Yao; Zou, Songbao Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00498	journal	April 2016
Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria Hamilton, Trinity L.; Bovee, Roderick J.; Sattin, Sarah R. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00598	journal	April 2016
Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity Flood, Beverly E.; Fliss, Palmer; Jones, Daniel S. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00603	journal	May 2016
Bacterial Active Community Cycling in Response to Solar Radiation and Their Influence on Nutrient Changes in a High-Altitude Wetland Molina, Verónica; Hernández, Klaudia; Dorador, Cristina Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01823	journal	November 2016
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Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities Gravuer, Kelly; Eskelinen, Anu Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01271	journal	July 2017
Editorial: Virus Discovery by Metagenomics: The (Im)possibilities Dutilh, Bas E.; Reyes, Alejandro; Hall, Richard J. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01710	journal	September 2017
Changes in the Drinking Water Microbiome: Effects of Water Treatments Along the Flow of Two Drinking Water Treatment Plants in a Urbanized Area, Milan (Italy) Bruno, Antonia; Sandionigi, Anna; Bernasconi, Marzia Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02557	journal	October 2018
Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community Savio, Domenico; Stadler, Philipp; Reischer, Georg H. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00028	journal	February 2019
Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems Chen, Lin-Xing; Al-Shayeb, Basem; Méheust, Raphaël Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00928	journal	May 2019
Aedes spp. and Their Microbiota: A Review Scolari, Francesca; Casiraghi, Maurizio; Bonizzoni, Mariangela Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02036	journal	September 2019
Discovery of High Abundances of Aster-Like Nanoparticles in Pelagic Environments: Characterization and Dynamics Colombet, Jonathan; Billard, Hermine; Viguès, Bernard Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02376	journal	October 2019
Erratum: The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse No authors listed Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02636	journal	November 2019
A Bioinformatics Guide to Plant Microbiome Analysis Lucaciu, Rares; Pelikan, Claus; Gerner, Samuel M. Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01313	journal	October 2019
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Additional file 10 of Expanding magnetic organelle biogenesis in the domain Bacteria Lin, Wei; Zhang, Wensi; Paterson, Greig A. figshare https://doi.org/10.6084/m9.figshare.13173105.v1	image	January 2020
Additional file 5 of Expanding magnetic organelle biogenesis in the domain Bacteria Lin, Wei; Zhang, Wensi; Paterson, Greig A. figshare https://doi.org/10.6084/m9.figshare.13173120	image	January 2020
Additional file 6 of Expanding magnetic organelle biogenesis in the domain Bacteria Lin, Wei; Zhang, Wensi; Paterson, Greig A. figshare https://doi.org/10.6084/m9.figshare.13173123.v1	image	January 2020
Additional file 7 of Expanding magnetic organelle biogenesis in the domain Bacteria Lin, Wei; Zhang, Wensi; Paterson, Greig A. figshare https://doi.org/10.6084/m9.figshare.13173126	image	January 2020
Additional file 8 of Expanding magnetic organelle biogenesis in the domain Bacteria Lin, Wei; Zhang, Wensi; Paterson, Greig A. figshare https://doi.org/10.6084/m9.figshare.13173129.v1	image	January 2020
Additional file 9 of Expanding magnetic organelle biogenesis in the domain Bacteria Lin, Wei; Zhang, Wensi; Paterson, Greig A. figshare https://doi.org/10.6084/m9.figshare.13173132	image	January 2020
Additional file 2 of Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge Pan, Jie; Xu, Wei; Zhou, Zhichao figshare https://doi.org/10.6084/m9.figshare.18739327.v1	dataset	January 2022
Additional file 1 of PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes Zeng, Jiaxiong; Tu, Qichao; Yu, Xiaoli figshare https://doi.org/10.6084/m9.figshare.20227033	dataset	January 2022
Additional file 2 of PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes Zeng, Jiaxiong; Tu, Qichao; Yu, Xiaoli figshare https://doi.org/10.6084/m9.figshare.20227036	dataset	January 2022
Additional file 3 of PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes Zeng, Jiaxiong; Tu, Qichao; Yu, Xiaoli figshare https://doi.org/10.6084/m9.figshare.20227039.v1	dataset	January 2022
Additional file 2 of Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin Jaffe, Alexander L.; Bardot, Corinne; Le Jeune, Anne-Hélène figshare https://doi.org/10.6084/m9.figshare.22615967.v1	dataset	January 2023
Additional file 1 of Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system Wang, Yulin; Zhang, Yulin; Hu, Yu figshare https://doi.org/10.6084/m9.figshare.22619041	dataset	January 2023
Additional file 2 of A glimpse of the paleome in endolithic microbial communities Wegner, Carl-Eric; Stahl, Raphaela; Velsko, Irina figshare https://doi.org/10.6084/m9.figshare.24196829	dataset	January 2023
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