The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle - PubMed (original) (raw)

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

William C Nelson et al. Front Microbiol. 2015.

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.

Keywords: Parcubacteria; candidate phyla; genome reconstruction; genomics; groundwater; pan-genome; streamlining; symbiosis.

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Figures

Figure 1

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.

Figure 2

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.

Figure 3

Figure 3

Distribution of gene conservation across the Parcubacteria genomes. Shaded subsections represent degree of conservation across all genomes, with the lowest black section representing genes conserved in 13–17 genomes, the gray section conserved in 2–12 genomes, etc. to the top white section representing genes unique to a single organism.

Figure 4

Figure 4

Coverage and %G+C of C7867-008 scaffold region containing CytO genes. %G+C was calculated across 120 nt windows with a step size of 30 nt. IGV (Thorvaldsdottir et al., 2013) was used to display the data.

Figure 5

Figure 5

Nucleotide usage and modification at positions 38, 39, and 40 of tRNAs. For each isotype, the three columns represent positions 38, 39, and 40 (in relation to E. coli standard). Color sections represent nucleotide and modification data. (A) Modomics nucleotide and modification data; (B) GtRNAdb nucleotide data; (C) OD1 nucleotide data.

Figure 6

Figure 6

YidC sequences from Parcubacteria have a unique region of charged residues. Positively charged residues at neutral pH are colored red; negatively charged residues are colored blue; histidine residues, which are positively charged below pH 6.0, are colored purple. The display was generated using UGENE (Okonechnikov et al., 2012).

Figure 7

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.

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