Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
Abstract
Cultivation-independent surveys of microbial diversity have revealed many bacterial phyla that lack cultured representatives. These lineages, referred to as candidate phyla, have been detected across many environments. Here, we deeply sequenced microbial communities from acetate-stimulated aquifer sediment to recover the complete and essentially complete genomes of single representatives of the candidate phyla SR1, WWE3, TM7, and OD1. All four of these genomes are very small, 0.7 to 1.2 Mbp, and have large inventories of novel proteins. Additionally, all lack identifiable biosynthetic pathways for several key metabolites. The SR1 genome uses the UGA codon to encode glycine, and the same codon is very rare in the OD1 genome, suggesting that the OD1 organism could also transition to alternate coding. Interestingly, the relative abundance of the members of SR1 increased with the appearance of sulfide in groundwater, a pattern mirrored by a member of the phylumTenericutes. All four genomes encode type IV pili, which may be involved in interorganism interaction. On the basis of these results and other recently published research, metabolic dependence on other organisms may be widely distributed across multiple bacterial candidate phyla. Few or no genomic sequences exist for members of the numerous bacterial phyla lacking cultivated representatives, making itmore »
- Authors:
-
- Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1511374
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mBio (Online)
- Additional Journal Information:
- Journal Name: mBio (Online); Journal Volume: 4; Journal Issue: 5; Journal ID: ISSN 2150-7511
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Kantor, Rose S., Wrighton, Kelly C., Handley, Kim M., Sharon, Itai, Hug, Laura A., Castelle, Cindy J., Thomas, Brian C., Banfield, Jillian F., Brune, Andreas, and Giovannoni, Stephen J. Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla. United States: N. p., 2013.
Web. doi:10.1128/mBio.00708-13.
Kantor, Rose S., Wrighton, Kelly C., Handley, Kim M., Sharon, Itai, Hug, Laura A., Castelle, Cindy J., Thomas, Brian C., Banfield, Jillian F., Brune, Andreas, & Giovannoni, Stephen J. Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla. United States. https://doi.org/10.1128/mBio.00708-13
Kantor, Rose S., Wrighton, Kelly C., Handley, Kim M., Sharon, Itai, Hug, Laura A., Castelle, Cindy J., Thomas, Brian C., Banfield, Jillian F., Brune, Andreas, and Giovannoni, Stephen J. Tue .
"Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla". United States. https://doi.org/10.1128/mBio.00708-13. https://www.osti.gov/servlets/purl/1511374.
@article{osti_1511374,
title = {Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla},
author = {Kantor, Rose S. and Wrighton, Kelly C. and Handley, Kim M. and Sharon, Itai and Hug, Laura A. and Castelle, Cindy J. and Thomas, Brian C. and Banfield, Jillian F. and Brune, Andreas and Giovannoni, Stephen J.},
abstractNote = {Cultivation-independent surveys of microbial diversity have revealed many bacterial phyla that lack cultured representatives. These lineages, referred to as candidate phyla, have been detected across many environments. Here, we deeply sequenced microbial communities from acetate-stimulated aquifer sediment to recover the complete and essentially complete genomes of single representatives of the candidate phyla SR1, WWE3, TM7, and OD1. All four of these genomes are very small, 0.7 to 1.2 Mbp, and have large inventories of novel proteins. Additionally, all lack identifiable biosynthetic pathways for several key metabolites. The SR1 genome uses the UGA codon to encode glycine, and the same codon is very rare in the OD1 genome, suggesting that the OD1 organism could also transition to alternate coding. Interestingly, the relative abundance of the members of SR1 increased with the appearance of sulfide in groundwater, a pattern mirrored by a member of the phylumTenericutes. All four genomes encode type IV pili, which may be involved in interorganism interaction. On the basis of these results and other recently published research, metabolic dependence on other organisms may be widely distributed across multiple bacterial candidate phyla. Few or no genomic sequences exist for members of the numerous bacterial phyla lacking cultivated representatives, making it difficult to assess their roles in the environment. This paper presents three complete and one essentially complete genomes of members of four candidate phyla, documents consistently small genome size, and predicts metabolic capabilities on the basis of gene content. These metagenomic analyses expand our view of a lifestyle apparently common across these candidate phyla.},
doi = {10.1128/mBio.00708-13},
journal = {mBio (Online)},
number = 5,
volume = 4,
place = {United States},
year = {Tue Oct 22 00:00:00 EDT 2013},
month = {Tue Oct 22 00:00:00 EDT 2013}
}
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Figures / Tables:
FIG 1: Complete and nearly complete genomes from four CP (RAAC1 to RAAC4) were reconstructed. (Left) Phylogeny of selected CP based on 16S rRNA genes. The maximum-likelihood tree shown was constructed from an alignment containing 111 taxa and 1,565 unambiguously aligned positions. Bootstrap values of >80% are displayed as filledmore »
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