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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

Phylogeny of RplB sequences discovered on C7867 scaffolds. A single deeply-branching Thaumaracheal sequence is not displayed. Edge colors denote estimated taxonomy, indicated by phylum names to the right. Node label colors indicate the source of the sampled DNA, black; Hanford IFRC, green; Rifle IFRC, blue; Lake Sakinaw, red; Homestake Mine drainage. Boldface indicates sequences from reconstructed genomes used in the comparison.
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Figure 2: Phylogeny of RplB sequences discovered on C7867 scaffolds. A single deeply-branching Thaumaracheal sequence is not displayed. Edge colors denote estimated taxonomy, indicated by phylum names to the right. Node label colors indicate the source of the sampled DNA, black; Hanford IFRC, green; Rifle IFRC, blue; Lake Sakinaw, red; Homestake Mine drainage. Boldface indicates sequences from reconstructed genomes used in the comparison.

Mentions: OD1 genomes were reconstructed from a metagenomic sample derived from groundwater communities sampled from a well adjacent to the IFRC (C7867) screened from 6-18 m. Approximately 35% of the paired-end reads assembled into 253,569 scaffolds with an N50 of 1245. Scaffolds longer than 2 kb (N = 17,044) were screened for phylogenetic marker genes using AMPHORA2 (Wu and Scott, 2012). The markers were used to derive an estimated taxonomy for the scaffolds containing marker genes. Phylogenetic analysis of RplB sequences identified shows that 40% of all RplB sequences identified within the assembly set are from OD1 bacteria (Figure 2). Previous community surveys performed within the IFRC have shown that Parcubacteria are usually in low abundance, with the summed relative abundance of all Parcubacterial OTUs being under 2% of the total population, however, sporadic blooms have been observed bringing relative abundance of individual OTUs to >14% (Lin et al., 2012b). The current result likely reflects both the serendipitous capture of a Parcubacterial bloom at the sample site and bias in the assembly process favorable to assembly of OD1 genomic sequence, perhaps due to its phylogenetic distance from other organisms present in the data set. Scaffolds containing marker genes assigned to OD1 were used to probe emergent self-organizing maps based on tetranucleotide content to generate putative genome-specific bins. Bins were both checked for specificity and scored for completeness of genomic information by assessing their complement of conserved single-copy genes (CSCG) (as in Rinke et al., 2013). Previous work on Parcubacteria has reported that they have very small genomes that must either lack certain genes conserved in most other bacteria, or contain instead divergent orthologs that are not easily recognizable (Kantor et al., 2013). As such, the gene complement of the complete OD1 RAAC4 genome was used as the standard for completeness. From the C7867 metagenome, 8 partial OD1 genomes (C7867-001 to C7867-008) were obtained with estimated completeness ranging from 69% to 97% (Table 1). The genomes have average read coverage ranging from 8- to 42-fold. Despite this moderate coverage, the genomes assembled well, ranging from 3 to 29 scaffolds in each bin. Genome sizes are small, with estimates for complete genome length ranging from ~600 to 900 kb, and G+C content ranging from 36% to 56%.


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

Nelson WC, Stegen JC - Front Microbiol (2015)

Phylogeny of RplB sequences discovered on C7867 scaffolds. A single deeply-branching Thaumaracheal sequence is not displayed. Edge colors denote estimated taxonomy, indicated by phylum names to the right. Node label colors indicate the source of the sampled DNA, black; Hanford IFRC, green; Rifle IFRC, blue; Lake Sakinaw, red; Homestake Mine drainage. Boldface indicates sequences from reconstructed genomes used in the comparison.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Phylogeny of RplB sequences discovered on C7867 scaffolds. A single deeply-branching Thaumaracheal sequence is not displayed. Edge colors denote estimated taxonomy, indicated by phylum names to the right. Node label colors indicate the source of the sampled DNA, black; Hanford IFRC, green; Rifle IFRC, blue; Lake Sakinaw, red; Homestake Mine drainage. Boldface indicates sequences from reconstructed genomes used in the comparison.
Mentions: OD1 genomes were reconstructed from a metagenomic sample derived from groundwater communities sampled from a well adjacent to the IFRC (C7867) screened from 6-18 m. Approximately 35% of the paired-end reads assembled into 253,569 scaffolds with an N50 of 1245. Scaffolds longer than 2 kb (N = 17,044) were screened for phylogenetic marker genes using AMPHORA2 (Wu and Scott, 2012). The markers were used to derive an estimated taxonomy for the scaffolds containing marker genes. Phylogenetic analysis of RplB sequences identified shows that 40% of all RplB sequences identified within the assembly set are from OD1 bacteria (Figure 2). Previous community surveys performed within the IFRC have shown that Parcubacteria are usually in low abundance, with the summed relative abundance of all Parcubacterial OTUs being under 2% of the total population, however, sporadic blooms have been observed bringing relative abundance of individual OTUs to >14% (Lin et al., 2012b). The current result likely reflects both the serendipitous capture of a Parcubacterial bloom at the sample site and bias in the assembly process favorable to assembly of OD1 genomic sequence, perhaps due to its phylogenetic distance from other organisms present in the data set. Scaffolds containing marker genes assigned to OD1 were used to probe emergent self-organizing maps based on tetranucleotide content to generate putative genome-specific bins. Bins were both checked for specificity and scored for completeness of genomic information by assessing their complement of conserved single-copy genes (CSCG) (as in Rinke et al., 2013). Previous work on Parcubacteria has reported that they have very small genomes that must either lack certain genes conserved in most other bacteria, or contain instead divergent orthologs that are not easily recognizable (Kantor et al., 2013). As such, the gene complement of the complete OD1 RAAC4 genome was used as the standard for completeness. From the C7867 metagenome, 8 partial OD1 genomes (C7867-001 to C7867-008) were obtained with estimated completeness ranging from 69% to 97% (Table 1). The genomes have average read coverage ranging from 8- to 42-fold. Despite this moderate coverage, the genomes assembled well, ranging from 3 to 29 scaffolds in each bin. Genome sizes are small, with estimates for complete genome length ranging from ~600 to 900 kb, and G+C content ranging from 36% to 56%.

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