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

William C Nelson,James C Stegen

doi:10.3389/fmicb.2015.00713

William C Nelson, James C Stegen

Open Access

https://doi.org/10.3389/fmicb.2015.00713

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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.

Highlights

The Parcubacteria, known as Candidate Phylum OD1 bacteria (OD1), were originally identified by phylogenetic analysis of 16S rRNA genes amplified from a variety of environmental samples (Harris et al, 2004)
Members are non-respiring, lacking genes for the tricaboxylic acid cycle (TCA) and electron transport, leading to the proposal that Parcubacteria obligately ferment simple sugars to organic acids, some are apparently capable of degrading complex carbon sources such as cellulose and chitin
Reconstruction of OD1 Genomes from a Metagenomic Sample OD1 genomes were reconstructed from a metagenomic sample derived from groundwater communities sampled from a well adjacent to the Integrated Field Research Challenge (IFRC) (C7867) screened from 6-18 m

Summary

Introduction

The Parcubacteria, known as Candidate Phylum OD1 bacteria (OD1), were originally identified by phylogenetic analysis of 16S rRNA genes amplified from a variety of environmental samples (Harris et al, 2004). Members are non-respiring, lacking genes for the tricaboxylic acid cycle (TCA) and electron transport, leading to the proposal that Parcubacteria obligately ferment simple sugars to organic acids, some are apparently capable of degrading complex carbon sources such as cellulose and chitin. They have been implicated in hydrogen and sulfur cycles in anoxic sediments (Wrighton et al, 2012, 2014). We propose that OD1 organisms are ectosymbionts or parasites attached to the external surfaces of other microbial cells to facilitate access to nutrients and energy sources produced by the host

Materials and Methods

Results and Discussion

Defense