publication . Article . 2015

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

Nelson, William C.; Stegen, James C.;
Open Access English
  • Published: 01 Jul 2015 Journal: Frontiers in Microbiology, volume 6 (issn: 1664-302X, eissn: 1664-302X, Copyright policy)
  • Publisher: Frontiers Media S.A.
Abstract
Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in 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. ‘Housekeepi...
Subjects
free text keywords: Parcubacteria, genome streamlining, streamlining, symbiosis, Microbiology, pan-genome, genomics, groundwater, QR1-502, Original Research, genome reconstruction, candidate phyla
74 references, page 1 of 5

Akopian D.Shen K.Zhang X.Shan S. O. (2013). Signal recognition particle: an essential protein-targeting machine. Annu. Rev. Biochem. 82, 693–721. 10.1146/annurev-biochem-072711-164732 23414305 [OpenAIRE] [PubMed] [DOI]

Alexeyenko A.Tamas I.Liu G.Sonnhammer E. (2006). Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22, E9–E15. 10.1093/bioinformatics/btl213 16873526 [PubMed] [DOI]

Aziz R. K.Bartels D.Best A. A.DeJongh M.Disz T.Edwards R. A.. (2008). The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. 10.1186/1471-2164-9-75 18261238 [OpenAIRE] [PubMed] [DOI]

Bacher A.Eberhardt S.Fischer M.Kis K.Richter G. (2000). Biosynthesis of vitamin b2 (riboflavin). Annu. Rev. Nutr. 20, 153–167. 10.1146/annurev.nutr.20.1.153 10940330 [PubMed] [DOI]

Bahar O.Goffer T.Burdman S. (2009). Type IV Pili are required for virulence, twitching motility, and biofilm formation of acidovorax avenae subsp. Citrulli. Mol. Plan t Microbe Interact. 22, 909–920. 10.1094/MPMI-22-8-0909 19589067 [PubMed] [DOI]

Bentley S. D.Maiwald M.Murphy L. D.Pallen M. J.Yeats C. A.Dover L. G.. (2003). Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet 361, 637–644. 10.1016/S0140-6736(03)12597-4 12606174 [PubMed] [DOI]

Bolger A. M.Lohse M.Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. 10.1093/bioinformatics/btu170 24695404 [OpenAIRE] [PubMed] [DOI]

Borisov V. B.Gennis R. B.Hemp J.Verkhovsky M. I. (2011). The cytochrome bd respiratory oxygen reductases. Biochim. Biophys. Acta 1807, 1398–1413. 10.1016/j.bbabio.2011.06.016 21756872 [OpenAIRE] [PubMed] [DOI]

Borrel G.Lehours A. C.Bardot C.Bailly X.Fonty G. (2010). Members of candidate divisions OP11, OD1 and SR1 are widespread along the water column of the meromictic Lake Pavin (France). Arch. Microbiol. 192, 559–567. 10.1007/s00203-010-0578-4 20495786 [OpenAIRE] [PubMed] [DOI]

Bostrom K. H.Simu K.Hagstrom A.Riemann L. (2004). Optimization of DNA extracti on for quantitative marine bacterioplankton community analysis. Limnol. Oceanogr. Methods 2, 365–373. 10.4319/lom.2004.2.365 [DOI]

Camacho C.Coulouris G.Avagyan V.Ma N.Papadopoulos J.Bealer K.. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421. 10.1186/1471-2105-10-421 20003500 [OpenAIRE] [PubMed] [DOI]

Carpousis A. J. (2007). The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu. Rev. Microbiol. 61, 71–87. 10.1146/annurev.micro.61.080706.093440 17447862 [PubMed] [DOI]

Chan P. P.Lowe T. M. (2009). GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37, D93–D97. 10.1093/nar/gkn787 18984615 [OpenAIRE] [PubMed] [DOI]

Chanyi R. M.Koval S. F. (2014). Role of type IV pili in predation by Bdellovibrio bacteriovorus. PLoS ONE 9:e113404. 10.1371/journal.pone.0113404 25409535 [OpenAIRE] [PubMed] [DOI]

Daub J.Eberhardt R. Y.Tate J. G.Burge S. W. (2015). Rfam: annotating families of non-coding RNA sequences. Methods Mol. Biol. 1269, 349–363. 10.1007/978-1-4939-2291-8_22 25577390 [PubMed] [DOI]

74 references, page 1 of 5
Abstract
Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in 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. ‘Housekeepi...
Subjects
free text keywords: Parcubacteria, genome streamlining, streamlining, symbiosis, Microbiology, pan-genome, genomics, groundwater, QR1-502, Original Research, genome reconstruction, candidate phyla
74 references, page 1 of 5

Akopian D.Shen K.Zhang X.Shan S. O. (2013). Signal recognition particle: an essential protein-targeting machine. Annu. Rev. Biochem. 82, 693–721. 10.1146/annurev-biochem-072711-164732 23414305 [OpenAIRE] [PubMed] [DOI]

Alexeyenko A.Tamas I.Liu G.Sonnhammer E. (2006). Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22, E9–E15. 10.1093/bioinformatics/btl213 16873526 [PubMed] [DOI]

Aziz R. K.Bartels D.Best A. A.DeJongh M.Disz T.Edwards R. A.. (2008). The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. 10.1186/1471-2164-9-75 18261238 [OpenAIRE] [PubMed] [DOI]

Bacher A.Eberhardt S.Fischer M.Kis K.Richter G. (2000). Biosynthesis of vitamin b2 (riboflavin). Annu. Rev. Nutr. 20, 153–167. 10.1146/annurev.nutr.20.1.153 10940330 [PubMed] [DOI]

Bahar O.Goffer T.Burdman S. (2009). Type IV Pili are required for virulence, twitching motility, and biofilm formation of acidovorax avenae subsp. Citrulli. Mol. Plan t Microbe Interact. 22, 909–920. 10.1094/MPMI-22-8-0909 19589067 [PubMed] [DOI]

Bentley S. D.Maiwald M.Murphy L. D.Pallen M. J.Yeats C. A.Dover L. G.. (2003). Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet 361, 637–644. 10.1016/S0140-6736(03)12597-4 12606174 [PubMed] [DOI]

Bolger A. M.Lohse M.Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. 10.1093/bioinformatics/btu170 24695404 [OpenAIRE] [PubMed] [DOI]

Borisov V. B.Gennis R. B.Hemp J.Verkhovsky M. I. (2011). The cytochrome bd respiratory oxygen reductases. Biochim. Biophys. Acta 1807, 1398–1413. 10.1016/j.bbabio.2011.06.016 21756872 [OpenAIRE] [PubMed] [DOI]

Borrel G.Lehours A. C.Bardot C.Bailly X.Fonty G. (2010). Members of candidate divisions OP11, OD1 and SR1 are widespread along the water column of the meromictic Lake Pavin (France). Arch. Microbiol. 192, 559–567. 10.1007/s00203-010-0578-4 20495786 [OpenAIRE] [PubMed] [DOI]

Bostrom K. H.Simu K.Hagstrom A.Riemann L. (2004). Optimization of DNA extracti on for quantitative marine bacterioplankton community analysis. Limnol. Oceanogr. Methods 2, 365–373. 10.4319/lom.2004.2.365 [DOI]

Camacho C.Coulouris G.Avagyan V.Ma N.Papadopoulos J.Bealer K.. (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421. 10.1186/1471-2105-10-421 20003500 [OpenAIRE] [PubMed] [DOI]

Carpousis A. J. (2007). The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E. Annu. Rev. Microbiol. 61, 71–87. 10.1146/annurev.micro.61.080706.093440 17447862 [PubMed] [DOI]

Chan P. P.Lowe T. M. (2009). GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37, D93–D97. 10.1093/nar/gkn787 18984615 [OpenAIRE] [PubMed] [DOI]

Chanyi R. M.Koval S. F. (2014). Role of type IV pili in predation by Bdellovibrio bacteriovorus. PLoS ONE 9:e113404. 10.1371/journal.pone.0113404 25409535 [OpenAIRE] [PubMed] [DOI]

Daub J.Eberhardt R. Y.Tate J. G.Burge S. W. (2015). Rfam: annotating families of non-coding RNA sequences. Methods Mol. Biol. 1269, 349–363. 10.1007/978-1-4939-2291-8_22 25577390 [PubMed] [DOI]

74 references, page 1 of 5
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publication . Article . 2015

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

Nelson, William C.; Stegen, James C.;