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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

Pan-omics analysis. (A) New genes identified as a function of number of genomes analyzed. A power regression curve is fitted to the data. (B) Total pan-genome gene count as a function of genomes analyzed. Power regression curves are fitted to the data. Blue, all Parcubacterial genomes; red, C7867 subgroup genomes; green, subgroup OD1-i genomes.
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Figure 7: Pan-omics analysis. (A) New genes identified as a function of number of genomes analyzed. A power regression curve is fitted to the data. (B) Total pan-genome gene count as a function of genomes analyzed. Power regression curves are fitted to the data. Blue, all Parcubacterial genomes; red, C7867 subgroup genomes; green, subgroup OD1-i genomes.

Mentions: The large number of unique genes per genome suggests a large and open pan genome. We assessed new gene and total gene accumulation as a function of genomes analyzed (Figure 7). The number of new genes identified per genome added approaches 20% of the median gene complement (Figure 7A). This level of novelty between genomes drives a near linear increase in pan-genome size as a function of genome count (Figure 7B). While this type of analysis has typically been performed on intraspecies datasets (Tettelin et al., 2005; Grote et al., 2012), its use is being expanded to higher phylogenetic levels to examine evolutionary signals (Zhang and Sievert, 2014). Potential evolutionary histories that would result in this gene distribution include: (1) an ancestral genome that was significantly larger with a broad diversity of genes and over time, descendent lineages lost different sets of genes depending on local selective forces; and (2) the ancestral genome was not significantly larger and descendent lineages acquired various genes that provided selective advantage under local conditions. There is not strong evidence for either of these options. With the apparent size of the pan genome approaching 10,000 genes, it seems unlikely that any ancestral genome contained all genes in the described pan-genome; on the other hand, newly acquired genes frequently (but not always) have a detectably different nucleotide usage signature than the rest of the genome. Over time that signature will decay to become consistent with the rest of the genome. Nucleotide skew analysis did not indicate newly acquired genes within the OD1 genomes (data not shown), and thus any acquisition of adaptive genes either occurred long ago (relative to the mutation rate) or the adaptive genes came from a donor with a similar nucleotide usage.


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

Nelson WC, Stegen JC - Front Microbiol (2015)

Pan-omics analysis. (A) New genes identified as a function of number of genomes analyzed. A power regression curve is fitted to the data. (B) Total pan-genome gene count as a function of genomes analyzed. Power regression curves are fitted to the data. Blue, all Parcubacterial genomes; red, C7867 subgroup genomes; green, subgroup OD1-i genomes.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 7: Pan-omics analysis. (A) New genes identified as a function of number of genomes analyzed. A power regression curve is fitted to the data. (B) Total pan-genome gene count as a function of genomes analyzed. Power regression curves are fitted to the data. Blue, all Parcubacterial genomes; red, C7867 subgroup genomes; green, subgroup OD1-i genomes.
Mentions: The large number of unique genes per genome suggests a large and open pan genome. We assessed new gene and total gene accumulation as a function of genomes analyzed (Figure 7). The number of new genes identified per genome added approaches 20% of the median gene complement (Figure 7A). This level of novelty between genomes drives a near linear increase in pan-genome size as a function of genome count (Figure 7B). While this type of analysis has typically been performed on intraspecies datasets (Tettelin et al., 2005; Grote et al., 2012), its use is being expanded to higher phylogenetic levels to examine evolutionary signals (Zhang and Sievert, 2014). Potential evolutionary histories that would result in this gene distribution include: (1) an ancestral genome that was significantly larger with a broad diversity of genes and over time, descendent lineages lost different sets of genes depending on local selective forces; and (2) the ancestral genome was not significantly larger and descendent lineages acquired various genes that provided selective advantage under local conditions. There is not strong evidence for either of these options. With the apparent size of the pan genome approaching 10,000 genes, it seems unlikely that any ancestral genome contained all genes in the described pan-genome; on the other hand, newly acquired genes frequently (but not always) have a detectably different nucleotide usage signature than the rest of the genome. Over time that signature will decay to become consistent with the rest of the genome. Nucleotide skew analysis did not indicate newly acquired genes within the OD1 genomes (data not shown), and thus any acquisition of adaptive genes either occurred long ago (relative to the mutation rate) or the adaptive genes came from a donor with a similar nucleotide usage.

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