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

Nelson WC, Stegen JC - Front Microbiol (2015)

Bottom Line: 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.Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced.

View Article: PubMed Central - PubMed

Affiliation: Microbiology, Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA.

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. 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.

No MeSH data available.


Related in: MedlinePlus

Study site map. Map showing the location of the Hanford site within the state of Washington and the location of the four corner wells (blue markers) surrounding the IFRC within the 300 Area.
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Figure 1: Study site map. Map showing the location of the Hanford site within the state of Washington and the location of the four corner wells (blue markers) surrounding the IFRC within the 300 Area.

Mentions: The Hanford 300 Area is an unconfined aquifer containing an extensive and persistent uranium plume resulting from disposal of nuclear fuel fabrication wastes from 1943 to 1994 (Zachara et al., 2013). Similar to Rifle, CO, the 300A is the location of an IFRC site that has been investigating reactive mass transfer and biogeochemical processes controlling U(VI) concentrations in a linked vadose zone-groundwater-river system. The site is adjacent to the Columbia River (Figure 1) which experiences large variations in river stage associated with seasonal mountain snowpack dynamics. As a result of the large river stage variations the groundwater in the 300A is subject to changes in elevation level and even flow reversals that can alter chemical composition, flow velocity, and microbial community dynamics (Lin et al., 2012b). Previous investigations of community dynamics revealed the presence of Parcubacteria in the oxic portion of the Hanford 300 A aquifer (Lin et al., 2012a,b) that prompted this more detailed investigation into properties of these members of candidate phylum OD1.


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

Nelson WC, Stegen JC - Front Microbiol (2015)

Study site map. Map showing the location of the Hanford site within the state of Washington and the location of the four corner wells (blue markers) surrounding the IFRC within the 300 Area.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508563&req=5

Figure 1: Study site map. Map showing the location of the Hanford site within the state of Washington and the location of the four corner wells (blue markers) surrounding the IFRC within the 300 Area.
Mentions: The Hanford 300 Area is an unconfined aquifer containing an extensive and persistent uranium plume resulting from disposal of nuclear fuel fabrication wastes from 1943 to 1994 (Zachara et al., 2013). Similar to Rifle, CO, the 300A is the location of an IFRC site that has been investigating reactive mass transfer and biogeochemical processes controlling U(VI) concentrations in a linked vadose zone-groundwater-river system. The site is adjacent to the Columbia River (Figure 1) which experiences large variations in river stage associated with seasonal mountain snowpack dynamics. As a result of the large river stage variations the groundwater in the 300A is subject to changes in elevation level and even flow reversals that can alter chemical composition, flow velocity, and microbial community dynamics (Lin et al., 2012b). Previous investigations of community dynamics revealed the presence of Parcubacteria in the oxic portion of the Hanford 300 A aquifer (Lin et al., 2012a,b) that prompted this more detailed investigation into properties of these members of candidate phylum OD1.

Bottom Line: 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.Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced.

View Article: PubMed Central - PubMed

Affiliation: Microbiology, Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA.

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. 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.

No MeSH data available.


Related in: MedlinePlus