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...

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Autores principales:	Rose S. Kantor, Kelly C. Wrighton, Kim M. Handley, Itai Sharon, Laura A. Hug, Cindy J. Castelle, Brian C. Thomas, Jillian F. Banfield
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Lenguaje:	EN
Publicado:	American Society for Microbiology 2013
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7163ac26fcd0496991822f010dbc5153
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spelling	oai:doaj.org-article:7163ac26fcd0496991822f010dbc51532021-11-15T15:42:47ZSmall Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla10.1128/mBio.00708-132150-7511https://doaj.org/article/7163ac26fcd0496991822f010dbc51532013-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00708-13https://doaj.org/toc/2150-7511ABSTRACT 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. IMPORTANCE 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.Rose S. KantorKelly C. WrightonKim M. HandleyItai SharonLaura A. HugCindy J. CastelleBrian C. ThomasJillian F. BanfieldAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 4, Iss 5 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Rose S. Kantor Kelly C. Wrighton Kim M. Handley Itai Sharon Laura A. Hug Cindy J. Castelle Brian C. Thomas Jillian F. Banfield Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
description	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 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. IMPORTANCE 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.
format	article
author	Rose S. Kantor Kelly C. Wrighton Kim M. Handley Itai Sharon Laura A. Hug Cindy J. Castelle Brian C. Thomas Jillian F. Banfield
author_facet	Rose S. Kantor Kelly C. Wrighton Kim M. Handley Itai Sharon Laura A. Hug Cindy J. Castelle Brian C. Thomas Jillian F. Banfield
author_sort	Rose S. Kantor
title	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_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_sort	small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla
publisher	American Society for Microbiology
publishDate	2013
url	https://doaj.org/article/7163ac26fcd0496991822f010dbc5153
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Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

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