The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle
Abstract
Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. Themore »
- Authors:
-
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1211534
- Grant/Contract Number:
- AC06-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Parcubacteria; genomics; symbiosis; pan-genome; genome reconstruction; candidate phyla; groundwater; streamlining
Citation Formats
Nelson, William C., and Stegen, James C. The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. United States: N. p., 2015.
Web. doi:10.3389/fmicb.2015.00713.
Nelson, William C., & Stegen, James C. The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. United States. https://doi.org/10.3389/fmicb.2015.00713
Nelson, William C., and Stegen, James C. Tue .
"The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle". United States. https://doi.org/10.3389/fmicb.2015.00713. https://www.osti.gov/servlets/purl/1211534.
@article{osti_1211534,
title = {The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle},
author = {Nelson, William C. and Stegen, James C.},
abstractNote = {Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.},
doi = {10.3389/fmicb.2015.00713},
journal = {Frontiers in Microbiology},
number = ,
volume = 6,
place = {United States},
year = {Tue Jul 21 00:00:00 EDT 2015},
month = {Tue Jul 21 00:00:00 EDT 2015}
}
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- Gutiérrez-Preciado, Ana; Saghaï, Aurélien; Moreira, David
- Nature Ecology & Evolution, Vol. 2, Issue 11
Variation of the Bacterial Community in the Rhizoplane Iron Plaque of the Wetland Plant Typha latifolia
journal, November 2018
- Chi, Haochun; Yang, Lu; Yang, Wenjing
- International Journal of Environmental Research and Public Health, Vol. 15, Issue 12
The Geobacillus Pan-Genome: Implications for the Evolution of the Genus
journal, May 2016
- Bezuidt, Oliver K.; Pierneef, Rian; Gomri, Amin M.
- Frontiers in Microbiology, Vol. 7
Implications from distinct sulfate-reducing bacteria populations between cattle manure and digestate in the elucidation of H2S production during anaerobic digestion of animal slurry
journal, April 2017
- St-Pierre, Benoit; Wright, André-Denis G.
- Applied Microbiology and Biotechnology, Vol. 101, Issue 13
Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer
journal, May 2016
- Danczak, Robert E.; Yabusaki, Steven B.; Williams, Kenneth H.
- Frontiers in Earth Science, Vol. 4
Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea
journal, July 2017
- van de Water, Jeroen A. J. M.; Voolstra, Christian R.; Rottier, Cecile
- Microbial Ecology, Vol. 75, Issue 1
Microbial succession on decomposing root litter in a drought-prone Scots pine forest
journal, May 2019
- Herzog, Claude; Hartmann, Martin; Frey, Beat
- The ISME Journal, Vol. 13, Issue 9
Measurement of bacterial replication rates in microbial communities
journal, November 2016
- Brown, Christopher T.; Olm, Matthew R.; Thomas, Brian C.
- Nature Biotechnology, Vol. 34, Issue 12
Microbial diversity in European alpine permafrost and active layers
journal, January 2016
- Frey, Beat; Rime, Thomas; Phillips, Marcia
- FEMS Microbiology Ecology, Vol. 92, Issue 3
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”
journal, May 2016
- Ullrich, Sophie R.; González, Carolina; Poehlein, Anja
- Frontiers in Microbiology, Vol. 7
Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems
journal, February 2018
- Proctor, Caitlin R.; Besmer, Michael D.; Langenegger, Timon
- The ISME Journal, Vol. 12, Issue 5
Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland
journal, November 2018
- Miettinen, Hanna; Bomberg, Malin; Vikman, Minna
- Geosciences, Vol. 8, Issue 11