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.; Brune, Andreas; Giovannoni, Stephen J.

doi:10.1128/mBio.00708-13

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

Journal Article · Tue Oct 22 00:00:00 EDT 2013 · mBio (Online)

DOI:https://doi.org/10.1128/mBio.00708-13· OSTI ID:1511374

Kantor, Rose S. ^[1]; Wrighton, Kelly C. ^[1]; Handley, Kim M. ^[1]; Sharon, Itai ^[1]; Hug, Laura A. ^[1]; Castelle, Cindy J. ^[1]; Thomas, Brian C. ^[1]; Banfield, Jillian F. ^[1]; Brune, Andreas ^[1]; Giovannoni, Stephen J. ^[1]

Univ. of California, Berkeley, CA (United States)

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.

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

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

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1511374

Journal Information:: mBio (Online), Vol. 4, Issue 5; ISSN 2150-7511

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 211 works

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Saccharibacteria (TM7) in the Human Oral Microbiome Bor, B.; Bedree, J. K.; Shi, W. Journal of Dental Research, Vol. 98, Issue 5 https://doi.org/10.1177/0022034519831671	journal	February 2019
Studying microbial functionality within the gut ecosystem by systems biology Hornung, Bastian; Martins dos Santos, Vitor A. P.; Smidt, Hauke Genes & Nutrition, Vol. 13, Issue 1 https://doi.org/10.1186/s12263-018-0594-6	journal	March 2018
Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation Xia, Yu; Wang, Yubo; Wang, Yi Biotechnology for Biofuels, Vol. 9, Issue 1 https://doi.org/10.1186/s13068-016-0524-z	journal	May 2016
Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities Danczak, R. E.; Johnston, M. D.; Kenah, C. Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0331-1	journal	September 2017
The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties Li, Peng; Xue, Yong; Shi, Jialiang Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0570-9	journal	October 2018
In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3) Youssef, Noha H.; Farag, Ibrahim F.; Rinke, Christian PLOS ONE, Vol. 10, Issue 6 https://doi.org/10.1371/journal.pone.0127499	journal	June 2015
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Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer Pan, Donald; Nolan, Jason; Williams, Kenneth H. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01199	journal	July 2017
New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes Kroeger, Marie E.; Delmont, Tom O.; Eren, A. M. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01635	journal	July 2018
Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function Ghuneim, Lydia-Ann J.; Jones, David L.; Golyshin, Peter N. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01971	journal	August 2018
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Gifted microbes for genome mining and natural product discovery Baltz, Richard H. Journal of Industrial Microbiology & Biotechnology, Vol. 44, Issue 4-5 https://doi.org/10.1007/s10295-016-1815-x	journal	August 2016
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A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization Dawson, Wayne; Hör, Jens; Egert, Markus Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00975	journal	May 2017
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