The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle.
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 seque...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-07-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00713/full |
| _version_ | 1819059504090710016 |
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| author | William C Nelson James C. Stegen |
| author_facet | William C Nelson James C. Stegen |
| author_sort | William C Nelson |
| collection | DOAJ |
| description | 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. ‘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 and DNA repair 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 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. |
| first_indexed | 2024-12-21T14:12:09Z |
| format | Article |
| id | doaj.art-ff2b663ed42e4e5daf50a768df0f81a8 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-21T14:12:09Z |
| publishDate | 2015-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-ff2b663ed42e4e5daf50a768df0f81a82022-12-21T19:01:01ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2015-07-01610.3389/fmicb.2015.00713144940The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle.William C Nelson0James C. Stegen1Pacific Northwest National LaboratoryPacific Northwest National LaboratoryCandidate 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. ‘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 and DNA repair 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 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.http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00713/fullGenomicsSymbiosispan-genomeGenome reconstructiongenome streamliningParcubacteria |
| spellingShingle | William C Nelson James C. Stegen The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. Frontiers in Microbiology Genomics Symbiosis pan-genome Genome reconstruction genome streamlining Parcubacteria |
| title | The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. |
| title_full | The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. |
| title_fullStr | The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. |
| title_full_unstemmed | The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. |
| title_short | The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. |
| title_sort | reduced genomes of parcubacteria od1 contain signatures of a symbiotic lifestyle |
| topic | Genomics Symbiosis pan-genome Genome reconstruction genome streamlining Parcubacteria |
| url | http://journal.frontiersin.org/Journal/10.3389/fmicb.2015.00713/full |
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