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Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

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 s...

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Autores principales: Kantor, Rose S., Wrighton, Kelly C., Handley, Kim M., Sharon, Itai, Hug, Laura A., Castelle, Cindy J., Thomas, Brian C., Banfield, Jillian F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society of Microbiology 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812714/
https://www.ncbi.nlm.nih.gov/pubmed/24149512
http://dx.doi.org/10.1128/mBio.00708-13
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author Kantor, Rose S.
Wrighton, Kelly C.
Handley, Kim M.
Sharon, Itai
Hug, Laura A.
Castelle, Cindy J.
Thomas, Brian C.
Banfield, Jillian F.
author_facet Kantor, Rose S.
Wrighton, Kelly C.
Handley, Kim M.
Sharon, Itai
Hug, Laura A.
Castelle, Cindy J.
Thomas, Brian C.
Banfield, Jillian F.
author_sort Kantor, Rose S.
collection PubMed
description 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 phylum Tenericutes. 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.
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spelling pubmed-38127142013-10-31 Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla Kantor, Rose S. Wrighton, Kelly C. Handley, Kim M. Sharon, Itai Hug, Laura A. Castelle, Cindy J. Thomas, Brian C. Banfield, Jillian F. mBio Research Article 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 phylum Tenericutes. 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. American Society of Microbiology 2013-10-22 /pmc/articles/PMC3812714/ /pubmed/24149512 http://dx.doi.org/10.1128/mBio.00708-13 Text en Copyright © 2013 Kantor et al. http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license (http://creativecommons.org/licenses/by-nc-sa/3.0/) , which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kantor, Rose S.
Wrighton, Kelly C.
Handley, Kim M.
Sharon, Itai
Hug, Laura A.
Castelle, Cindy J.
Thomas, Brian C.
Banfield, Jillian F.
Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
title Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
title_full Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
title_fullStr Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
title_full_unstemmed Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
title_short Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
title_sort small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812714/
https://www.ncbi.nlm.nih.gov/pubmed/24149512
http://dx.doi.org/10.1128/mBio.00708-13
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